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Name the five senses.
Hearing, sight, taste, touch, and smell. But how do we hear, see, taste, touch and smell? It all has to do, obviously, with the nervous system.
The Senses
The sensory division of the peripheral nervous system (PNS) includes several sense organs—the eyes, ears, mouth, nose, and skin. Each sense organ has special cells, called sensory receptors, that respond to a particular type of stimulus. For example, the nose has sensory receptors that respond to chemicals, which we perceive as odors. Sensory receptors send nerve impulses to sensory nerves, which carry the nerve impulses to the central nervous system. The brain then interprets the nerve impulses to form a response.
Sight
Sight is the ability to sense light, and the eye is the organ that senses light. Light first passes through the cornea of the eye, which is a clear outer layer that protects the eye (see Figure below). Light enters the eye through an opening called the pupil. The light then passes through the lens, which focuses it on the retina at the back of the eye. The retina contains light receptor cells. These cells send nerve impulses to the optic nerve, which carries the impulses to the brain. The brain interprets the impulses and “tells” us what we are seeing.
The eye is the organ that senses light and allows us to see.
Hearing
Hearing is the ability to sense sound waves, and the ear is the organ that senses sound. Sound waves enter the auditory canal and travel to the eardrum (see Figure below). They strike the eardrum and make it vibrate. The vibrations then travel through several other structures inside the ear and reach the cochlea. The cochlea is a coiled tube filled with liquid. The liquid moves in response to the vibrations, causing tiny hair cells lining the cochlea to bend. In response, the hair cells send nerve impulses to the auditory nerve, which carries the impulses to the brain. The brain interprets the impulses and “tells” us what we are hearing.
The ear is the organ that senses sound waves and allows us to hear. It also senses body position so we can keep our balance.
Balance
The ears are also responsible for the sense of balance. Balance is the ability to sense and maintain body position. The semicircular canals inside the ear (see Figure above) contain fluid that moves when the head changes position. Tiny hairs lining the semicircular canals sense movement of the fluid. In response, they send nerve impulses to the vestibular nerve, which carries the impulses to the brain. The brain interprets the impulses and sends messages to the peripheral nervous system. This system maintains the body’s balance by triggering contractions of skeletal muscles as needed.
Taste and Smell
Taste and smell are both abilities to sense chemicals. Like other sense receptors, both taste receptors and odor receptors send nerve impulses to the brain, and the brain “tells” use what we are tasting or smelling.
Taste receptors are found in tiny bumps on the tongue called taste buds (see Figure below). There are separate taste receptors for sweet, salty, sour, bitter, and meaty tastes. The meaty taste is called umami.
Taste buds on the tongue contain taste receptor cells.
Odor receptors line the passages of the nose (see Figure below). They sense chemicals in the air. In fact, odor receptors can sense hundreds of different chemicals. Did you ever notice that food seems to have less taste when you have a stuffy nose? This occurs because the sense of smell contributes to the sense of taste, and a stuffy nose interferes with the ability to smell.
Odor receptors. Odor receptors and their associated nerves (in yellow) line the top of the nasal passages.
Touch
Touch is the ability to sense pressure. Pressure receptors are found mainly in the skin. They are especially concentrated on the tongue, lips, face, palms of the hands, and soles of the feet. Some touch receptors sense differences in temperature or pain. How do pain receptors help maintain homeostasis? (Hint: What might happen if we couldn’t feel pain?)
Why I do Science
If your kids don't like broccoli, it may not be their fault, it may just be their genes talking. Dr. Danielle Reed is a geneticist working to understand the genetics of taste. Can all people detect the same tastes? No. Why not? It has to do with a person's genes. People may actually taste foods differently.
Summary
• Human senses include sight, hearing, balance, taste, smell, and touch.
• Sensory organs such as the eyes contain cells called sensory receptors that respond to particular sensory stimuli.
• Sensory nerves carry nerve impulses from sensory receptors to the central nervous system.
• The brain interprets the nerve impulses to form a response.
Review
1. List the five human senses.
2. Describe how we see.
3. Describe how we hear.
4. Why does food taste different when you have a stuffy nose?
5. What might happen if we couldn’t feel pain? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.22%3A_Senses.txt |
Is coffee a drug?
Maybe. But that doesn't necessarily mean it is bad for you. Looks tasty, though. Other than taste, why do many people have a cup of coffee in the morning? Does it help them wake up? For many people, it does. Why? The caffeine in the coffee stimulates the central nervous system. This drug is one of the milder drugs affecting the nervous system.
Drugs and the Nervous System
A drug is any chemical that affects the body’s structure or function. Many drugs, including both legal and illegal drugs, are psychoactive drugs. This means that they affect the central nervous system, generally by influencing the transmission of nerve impulses. For example, some psychoactive drugs mimic neurotransmitters. At the link below, you can watch an animation showing how psychoactive drugs affect the brain.
Examples of Psychoactive Drugs
Caffeine is an example of a psychoactive drug. It is found in coffee and many other products (see Table below). Caffeine is a central nervous system stimulant. Like other stimulant drugs, it makes you feel more awake and alert. Other psychoactive drugs include alcohol, nicotine, and marijuana. Each has a different effect on the central nervous system. Alcohol, for example, is a depressant. It has the opposite effects of a stimulant like caffeine.
Product Caffeine Content (mg)
Coffee (8 oz) 130
Tea (8 oz) 55
Cola (8 oz) 25
Coffee ice cream (8 oz) 60
Hot cocoa (8 oz) 10
Dark chocolate candy (1.5 oz) 30
Drug Abuse and Addiction
Psychoactive drugs may bring about changes in mood that users find desirable, so the drugs may be abused. Drug abuse is use of a drug without the advice of a medical professional and for reasons not originally intended. Continued use of a psychoactive drug may lead to drug addiction, in which the drug user is unable to stop using the drug. Over time, a drug user may need more of the drug to get the desired effect. This can lead to drug overdose and death.
Summary
• Drugs are chemicals that affect the body’s structure or function.
• Psychoactive drugs, such as caffeine and alcohol, affect the central nervous system by influencing the transmission of nerve impulses in the brain.
• Psychoactive drugs may be abused and lead to drug addiction.
Review
1. What is a psychoactive drug? Give two examples.
2. Define drug abuse. When does drug addiction occur?
13.24: Nervous System Disorders
Ever had a headache that just won't go away?
We all get headaches. Headaches are a relatively minor problem associated with the nervous system. But what about more serious issues of the nervous system? As you can probably imagine, these can be extremely serious.
Disorders of the Nervous System
There are several different types of problems that can affect the nervous system.
• Vascular disorders involve problems with blood flow. For example, a stroke occurs when a blood clot blocks blood flow to part of the brain. Brain cells die quickly if their oxygen supply is cut off. This may cause paralysis and loss of other normal functions, depending on the part of the brain that is damaged.
• Nervous tissue may become infected by microorganisms. Meningitis, for example, is caused by a viral or bacterial infection of the tissues covering the brain. This may cause the brain to swell and lead to brain damage and death.
• Encephalitis is a brain infection most often caused by viruses. The immune system tries to fight off a brain infection, just as it tries to fight off other infections. But sometimes this can do more harm than good. The immune system’s response may cause swelling in the brain. With no room to expand, the brain pushes against the skull. This may injure the brain and even cause death. Medicines can help fight some viral infections of the brain, but not all infections.
• Brain or spinal cord injuries may cause paralysis and other disabilities. Injuries to peripheral nerves can cause localized pain or numbness.
• Abnormal brain functions can occur for a variety of reasons. Examples include headaches, such as migraine headaches, and epilepsy, in which seizures occur.
• Nervous tissue may degenerate, or break down. Alzheimer’s disease is an example of this type of disorder, as is Amyotrophic Lateral Sclerosis, or ALS. ALS is also known as Lou Gehrig's disease. It leads to a gradual loss of higher brain functions.
• In addition to ALS and Alzheimer's disease, other serious nervous system diseases include multiple sclerosis, Huntington’s disease, and Parkinson’s disease. These diseases rarely, if ever, occur in young people. Their causes and symptoms are listed below (Table below). The diseases have no known cure, but medicines may help control their symptoms.
Disease Cause Symptoms
Multiple Sclerosis The immune system attacks and damages the central nervous system so neurons cannot function properly. muscle weakness, difficulty moving, problems with coordination, difficulty maintaining balance
Huntington's Disease An inherited gene codes for an abnormal protein that causes the death of neurons. uncontrolled jerky movements, loss of muscle control, issues with memory and learning
Parkinson's Disease An abnormally low level of a neurotransmitter affects the part of the brain that controls movement. uncontrolled shaking, slowed movements, issues associated with speaking
Alzheimer's Disease Abnormal changes in the brain cause the gradual loss of most normal brain activity. memory loss, confusion, mood swings, gradual loss of control over mental and physical abilities
Alzheimer's Disease: Is the Cure in the Genes?
By 2050, as the U.S. population ages, 15 million Americans will suffer from Alzheimer's disease — triple today's number. But genetic studies may provide information leading to a cure.
In April 2011, an international analysis of the genes of more than 50,000 people led to the discovery of five new genes that make Alzheimer's disease more likely in the elderly and provide clues about what might start the Alzheimer's disease process and fuel its progress in a person’s brain.
Summary
• Disorders of the nervous system include blood flow problems such as stroke, infections such as meningitis, brain injuries, and degeneration of nervous tissue, as in Alzheimer’s disease.
Review
1. Identify three nervous system disorders.
2. Multiple sclerosis is a disease in which the myelin sheaths of neurons in the central nervous system break down. What symptoms might this cause? Why? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.23%3A_Drugs_and_the_Nervous_System.txt |
What's a hormone?
This messenger pigeon is delivering a letter, making sure it gets to where it needs to go. It could be said that hormones are biological messengers, and they originate from the endocrine system. The nervous system isn’t the only message-relaying system of the human body. The endocrine system also carries messages. The endocrine system is a system of glands that release chemical messenger molecules into the bloodstream. The messenger molecules are hormones. Hormones act slowly compared with the rapid transmission of electrical messages by the nervous system. They must travel through the bloodstream to the cells they affect, and this takes time. On the other hand, because endocrine hormones are released into the bloodstream, they travel throughout the body. As a result, endocrine hormones can affect many cells and have body-wide effects.
Glands of the Endocrine System
The major glands of the endocrine system are shown in Figure below. You can access a similar, animated endocrine system chart at the link below.
The glands of the endocrine system are the same in males and females except for the testes, which are found only in males, and ovaries, which are found only in females.
Hypothalamus
The hypothalamus is actually part of the brain (see Figure below), but it also secretes hormones. Some of its hormones “tell” the pituitary gland either to secrete or to stop secreting its hormones. In this way, the hypothalamus provides a link between the nervous and endocrine systems. The hypothalamus also produces hormones that directly regulate body processes. These hormones travel to the pituitary gland, which stores them until they are needed. The hormones include antidiuretic hormone and oxytocin.
• Antidiuretic hormone stimulates the kidneys to conserve water by producing more concentrated urine.
• Oxytocin stimulates the contractions of childbirth, among other functions.
The hypothalamus and pituitary gland are located close together at the base of the brain.
Pituitary Gland
The pea-sized pituitary gland is attached to the hypothalamus by a thin stalk (see Figure above). It consists of two bulb-like lobes. The posterior (back) lobe stores hormones from the hypothalamus. The anterior (front) lobe secretes pituitary hormones. Several pituitary hormones and their effects are listed in Table below. Most pituitary hormones control other endocrine glands. That’s why the pituitary is often called the “master gland” of the endocrine system.
Hormone Target Effect(s)
Adrenocorticotropic hormone (ACTH) Adrenal glands Stimulates the cortex of each adrenal gland to secrete its hormones.
Thyroid-stimulating hormone (TSH) Thyroid gland Stimulates the thyroid gland to secrete thyroid hormone.
Growth hormone (GH) Body cells Stimulates body cells to synthesize proteins and grow.
Follicle-stimulating hormone (FSH) Ovaries, testes Stimulates the ovaries to develop mature eggs; stimulates the testes to produce sperm.
Luteinizing hormone (LH) Ovaries, testes Stimulates the ovaries and testes to secrete sex hormones; stimulates the ovaries to release eggs.
Prolactin (PRL) Mammary glands Stimulates the mammary glands to produce milk.
Other Endocrine Glands
Other glands of the endocrine system are described below. You can refer to Figure above to see where they are located.
• The thyroid gland is a large gland in the neck. Thyroid hormones increase the rate of metabolism in cells throughout the body. They control how quickly cells use energy and make proteins.
• The two parathyroid glands are located behind the thyroid gland. Parathyroid hormone helps keep the level of calcium in the blood within a narrow range. It stimulates bone cells to dissolve calcium in bone matrix and release it into the blood.
• The pineal gland is a tiny gland located at the base of the brain. It secretes the hormone melatonin. This hormone controls sleep-wake cycles and several other processes.
• The pancreas is located near the stomach. Its hormones include insulin and glucagon. These two hormones work together to control the level of glucose in the blood. Insulin causes excess blood glucose to be taken up by the liver, which stores the glucose as glycogen. Glucagon stimulates the liver to break down glycogen into glucose and release it back into the blood. The pancreas also secretes digestive enzymes into the digestive tract.
• The two adrenal glands are located above the kidneys. Each gland has an inner and outer part. The outer part, called the cortex, secretes hormones such as cortisol, which helps the body deal with stress, and aldosterone, which helps regulate the balance of minerals in the body. The inner part of each adrenal gland, called the medulla, secretes fight-or-flight hormones such as adrenaline, which prepare the body to respond to emergencies. For example, adrenaline increases the amount of oxygen and glucose going to the muscles.
• The gonads secrete sex hormones. The male gonads are called testes. They secrete the male sex hormone testosterone. The female gonads are called ovaries. They secrete the female sex hormone estrogen. Sex hormones are involved in the changes of puberty. They also control the production of gametes by the gonads.
Summary
• The endocrine system consists of glands that secrete hormones into the bloodstream.
• The endocrine system is regulated by a part of the brain called the hypothalamus, which also secretes hormones.
• The hypothalamus controls the pituitary gland, which is called the “master gland” of the endocrine system because its hormones regulate other endocrine glands.
• Other endocrine glands include the thyroid gland and pancreas.
Review
1. Explain how the nervous system is linked with the endocrine system.
2. List five of the major glands of the endocrine system.
3. Name three pituitary hormones, and state how they affect their targets. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.25%3A_Glands.txt |
Steroid hormones. How do they work?
As hormones, they are the messengers of the endocrine system. Obviously they must change something in the cell.
How Hormones Work
Hormones are the messenger molecules of the endocrine system. Endocrine hormones travel throughout the body in the blood. However, each hormone affects only certain cells, called target cells. A target cell is the type of cell on which a hormone has an effect. A target cell is affected by a particular hormone because it has receptor proteins that are specific to that hormone. A hormone travels through the bloodstream until it finds a target cell with a matching receptor it can bind to. When the hormone binds to a receptor, it causes a change within the cell. Exactly how this works depends on whether the hormone is a steroid hormone or a non-steroid hormone.
Steroid Hormones
Steroid hormones are made of lipids, such as phospholipids and cholesterol. They are fat soluble, so they can diffuse across the plasma membrane of target cells and bind with receptors in the cytoplasm of the cell (see Figure below). The steroid hormone and receptor form a complex that moves into the nucleus and influences the expression of genes, essentially acting as a transcription factor. Examples of steroid hormones include cortisol and sex hormones.
A steroid hormone crosses the plasma membrane of a target cell and binds with a receptor inside the cell.
Non-Steroid Hormones
Non-steroid hormones are made of amino acids. They are not fat soluble, so they cannot diffuse across the plasma membrane of target cells. Instead, a non-steroid hormone binds to a receptor on the cell membrane (see Figure below). The binding of the hormone triggers an enzyme inside the cell membrane. The enzyme activates another molecule, called the second messenger, which influences processes inside the cell. Most endocrine hormones are non-steroid hormones, including insulin and thyroid hormones.
A non-steroid hormone binds with a receptor on the plasma membrane of a target cell. Then, a secondary messenger affects cell processes.
Summary
• Hormones work by binding to protein receptors either inside target cells or on their plasma membranes.
• The binding of a steroid hormone forms a hormone-receptor complex that affects gene expression in the nucleus of the target cell.
• The binding of a non-steroid hormone activates a second messenger that affects processes within the target cell.
Review
1. Define hormone.
2. Compare and contrast how steroid and non-steroid hormones affect target cells.
13.27: Hormone Regulation
On or off?
Hormones alter conditions inside the cell, usually in response to a stimulus. That means they are activated at specific times. So they must be turned on and then turned back off. What turns these hormones and their responses on or off?
Hormone Regulation: Feedback Mechanisms
Hormones control many cell activities, so they are very important for homeostasis. But what controls the hormones themselves? Most hormones are regulated by feedback mechanisms. A feedback mechanism is a loop in which a product feeds back to control its own production. Most hormone feedback mechanisms involve negative feedback loops. Negative feedback keeps the concentration of a hormone within a narrow range.
Negative Feedback
Negative feedback occurs when a product feeds back to decrease its own production. This type of feedback brings things back to normal whenever they start to become too extreme. The thyroid gland is a good example of this type of regulation. It is controlled by the negative feedback loop shown in Figure below.
The thyroid gland is regulated by a negative feedback loop. The loop includes the hypothalamus and pituitary gland in addition to the thyroid.
Here’s how thyroid regulation works. The hypothalamus secretes thyrotropin-releasing hormone, or TRH. TRH stimulates the pituitary gland to produce thyroid-stimulating hormone, or TSH. TSH, in turn, stimulates the thyroid gland to secrete its hormones. When the level of thyroid hormones is high enough, the hormones feedback to stop the hypothalamus from secreting TRH and the pituitary from secreting TSH. Without the stimulation of TSH, the thyroid gland stops secreting its hormones. Soon, the level of thyroid hormone starts to fall too low. What do you think happens next?
Negative feedback also controls insulin secretion by the pancreas.
Positive feedback
Positive feedback occurs when a product feeds back to increase its own production. This causes conditions to become increasingly extreme. An example of positive feedback is milk production by a mother for her baby. As the baby suckles, nerve messages from the nipple cause the pituitary gland to secrete prolactin. Prolactin, in turn, stimulates the mammary glands to produce milk, so the baby suckles more. This causes more prolactin to be secreted and more milk to be produced. This example is one of the few positive feedback mechanisms in the human body. What do you think would happen if milk production by the mammary glands was controlled by negative feedback instead?
Summary
• Most hormones are controlled by negative feedback, in which the hormone feeds back to decrease its own production. This type of feedback brings things back to normal whenever they start to become too extreme.
• Positive feedback is much less common because it causes conditions to become increasingly extreme.
Review
1. What is negative feedback?
2. Why are negative feedback mechanisms more common than positive feedback mechanisms in the human body?
3. What might happen if an endocrine hormone such as thyroid hormone was controlled by positive instead of negative feedback?
4. Tasha had a thyroid test. Her doctor gave her an injection of TSH and 15 minutes later measured the level of thyroid hormone in her blood. What is TSH? Why do you think Tasha’s doctor gave her an injection of TSH? How would this affect the level of thyroid hormones in her blood if her thyroid is normal? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.26%3A_Hormones.txt |
How tall can a person become?
This may be an exaggeration, but the world's tallest person, Robert Pershing Wadlow, stood almost nine feet tall when he died at the age of 22. Is growing that tall due to a problem with the endocrine system?
Endocrine System Disorders
Diseases of the endocrine system are relatively common. An endocrine disease usually involves the secretion of too much or not enough hormone. When too much hormone is secreted, it is called hypersecretion. When not enough hormone is secreted, it is calledhyposecretion.
Hypersecretion
Hypersecretion by an endocrine gland is often caused by a tumor. For example, a tumor of the pituitary gland can cause hypersecretion of growth hormone. If this occurs in childhood, it results in very long arms and legs and abnormally tall stature by adulthood. The condition is commonly known as gigantism (see Figure below).
Hypersecretion of growth hormone leads to abnormal growth, often called gigantism.
Hyposecretion
Destruction of hormone-secreting cells of a gland may result in not enough of a hormone being secreted. This occurs in type 1 diabetes. In this case, the body’s own immune system attacks and destroys cells of the pancreas that secrete insulin, making type 1 diabetes an autoimmune disease. A person with type 1 diabetes must frequently monitor the level of glucose in the blood (see Figure below). If the level of blood glucose is too high, insulin is injected to bring it under control. If it is too low, a small amount of sugar is consumed.
To measure the level of glucose in the blood, a drop of blood is placed on a test strip, which is read by a meter.
Hormone Resistance
In some cases, an endocrine gland secretes a normal amount of hormone, but target cells do not respond to the hormone. Often, this is because target cells have become resistant to the hormone. Type 2 diabetes is an example of this type of endocrine disorder. In type 2 diabetes, body cells do not respond to normal amounts of insulin. As a result, cells do not take up glucose and the amount of glucose in the blood becomes too high. This type of diabetes is usually treated with medication and diet. The addition of extra insulin to the treatment can help some patients.
Summary
• Endocrine system disorders usually involve the secretion of too much or not enough hormone. For example, a tumor of the adrenal gland may lead to excessive secretion of growth hormone, which causes gigantism.
• In Type 1 diabetes, the pancreas does not secrete enough insulin, which causes high levels of glucose in the blood.
Review
1. Define hypersecretion. Give an example of an endocrine disorder that involves hypersecretion.
2. Explain why a person with type 2 diabetes is not affected by normal amounts of insulin. Will providing extra insulin help this person?
13.29: Heart
What's the most active muscle in the body?
The human heart. An absolutely remarkable organ. Obviously, its main function is to pump blood throughout the body. And it does this extremely well. On average, this muscular organ will beat about 100,000 times in one day and about 35 million times in a year. During an average lifetime, the human heart will beat more than 2.5 billion times.
The Circulatory System
The circulatory system can be compared to a system of interconnected, one-way roads that range from superhighways to back alleys. Like a network of roads, the job of the circulatory system is to allow the transport of materials from one place to another. As described in Figure below, the materials carried by the circulatory system include hormones, oxygen, cellular wastes, and nutrients from digested food. Transport of all these materials is necessary to maintain homeostasis of the body. The main components of the circulatory system are theheart, blood vessels, and blood.
The function of the circulatory system is to move materials around the body.
The Heart
The heart is a muscular organ in the chest. It consists mainly of cardiac muscle tissue and pumps blood through blood vessels by repeated, rhythmic contractions. The heart has four chambers, as shown in Figure below: two upper atria (singular, atrium) and two lowerventricles. Valves between chambers keep blood flowing through the heart in just one direction.
The chambers of the heart and the valves between them are shown here.
Blood Flow Through the Heart
Blood flows through the heart in two separate loops, which are indicated by the arrows in Figure above. You can think of them as a "left side loop" and a "right side loop." The right side of the heart collects oxygen-poor blood from the body and pumps the blood to the lungs. In the lungs, carbon dioxide is released and oxygen obtained by the blood. The left side of the heart carries the oxygen-rich blood back from the lungs and pumps it to the rest of the body. The blood delivers oxygen to the body's cells, returning the oxygen-poor blood back to the heart.
1. Blood from the body enters the right atrium of the heart. The right atrium pumps the blood to the right ventricle, which pumps it to the lungs.
2. Blood from the lungs enters the left atrium of the heart. The left atrium pumps the blood to the left ventricle, which pumps it to the body.
Heartbeat
Unlike skeletal muscle, cardiac muscle contracts without stimulation by the nervous system. Instead, specialized cardiac muscle cells send out electrical impulses that stimulate the contractions. As a result, the atria and ventricles normally contract with just the right timing to keep blood pumping efficiently through the heart.
Summary
• The heart contracts rhythmically to pump blood to the lungs and the rest of the body.
• Specialized cardiac muscle cells trigger the contractions.
Review
1. What are the main components of the circulatory system?
2. Describe how blood flows through the heart.
3. What controls heartbeat? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.28%3A_Endocrine_System_Disorders.txt |
How does blood travel around the body?
Through blood vessels, of course. This image of veins is from William Harvey's (1578-1657)Exercitatio Anatomica de Motu Cordis et Sanguinis in Animalibus. Harvey was the first to describe in detail the systemic circulation and properties of blood being pumped to the brain and body by the heart.
Blood Vessels
Blood vessels form a network throughout the body to transport blood to all the body cells. There are three major types of blood vessels: arteries, veins, and capillaries. All three are shown in Figure below and described below.
Blood vessels include arteries, veins, and capillaries.
• Arteries are muscular blood vessels that carry blood away from the heart. They have thick walls that can withstand the pressure of blood being pumped by the heart. Arteries generally carry oxygen-rich blood. The largest artery is the aorta, which receives blood directly from the heart.
• Veins are blood vessels that carry blood toward the heart. This blood is no longer under much pressure, so many veins have valves that prevent backflow of blood. Veins generally carry deoxygenated blood. The largest vein is the inferior vena cava, which carries blood from the lower body to the heart. The superior vena cava brings blood back to the heart from the upper body.
• Capillaries are the smallest type of blood vessels. They connect very small arteries and veins. The exchange of gases and other substances between cells and the blood takes place across the extremely thin walls of capillaries.
Blood Vessels and Homeostasis
Blood vessels help regulate body processes by either constricting (becoming narrower) or dilating (becoming wider). These actions occur in response to signals from the autonomic nervous system or the endocrine system. Constriction occurs when the muscular walls of blood vessels contract. This reduces the amount of blood that can flow through the vessels (see Figure below). Dilation occurs when the walls relax. This increases blood flows through the vessels.
When a blood vessel constricts, less blood can flow through it.
Constriction and dilation allow the circulatory system to change the amount of blood flowing to different organs. For example, during a fight-or-flight response, dilation and constriction of blood vessels allow more blood to flow to skeletal muscles and less to flow to digestive organs. Dilation of blood vessels in the skin allows more blood to flow to the body surface so the body can lose heat. Constriction of these blood vessels has the opposite effect and helps conserve body heat.
Blood Vessels and Blood Pressure
The force exerted by circulating blood on the walls of blood vessels is called blood pressure. Blood pressure is highest in arteries and lowest in veins. When you have your blood pressure checked, it is the blood pressure in arteries that is measured. High blood pressure, or hypertension, is a serious health risk but can often be controlled with lifestyle changes or medication.
Summary
• Arteries carry blood away from the heart, veins carry blood toward the heart, and capillaries connect arteries and veins.
Review
1. How do arteries differ from veins?
2. What is blood pressure? What is hypertension?
3. To take your pulse, you press your fingers against an artery near the surface of the body. What are you feeling and measuring when you take your pulse? Why can’t you take your pulse by pressing your fingers against a vein?
13.31: Circulatory System
How does oxygen get into the blood?
The main function of the circulatory system is to pump blood carrying oxygen around the body. But how does that oxygen get into the blood in the first place? You may already know that this occurs in the lungs. So the blood must also be pumped to the lungs, and this happens separately from the rest of the body.
Pulmonary and Systemic Circulations
The circulatory system actually consists of two separate systems: pulmonary circulation and systemic circulation.
Pulmonary Circulation
Pulmonary circulation is the part of the circulatory system that carries blood between the heart and lungs (the term “pulmonary” means “of the lungs”). It is illustrated in Figure below. Deoxygenated blood leaves the right ventricle through pulmonary arteries, which transport it to the lungs. In the lungs, the blood gives up carbon dioxide and picks up oxygen. The oxygenated blood then returns to the left atrium of the heart through pulmonary veins.
The pulmonary circulation carries blood between the heart and lungs.
Systemic Circulation
Systemic circulation is the part of the circulatory system that carries blood between the heart and body. It is illustrated in Figure below. Oxygenated blood leaves the left ventricle through the aorta. The aorta and other arteries transport the blood throughout the body, where it gives up oxygen and picks up carbon dioxide. The deoxygenated blood then returns to the right atrium through veins.
The systemic circulation carries blood between the heart and body.
Summary
• The pulmonary circulation carries blood between the heart and lungs.
• The systemic circulation carries blood between the heart and body.
Review
1. Compare and contrast pulmonary and systemic circulations. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.30%3A_Blood_Vessels.txt |
Eat healthy, exercise, and don't smoke. Why?
Normally blood needs to flow freely through our arteries. Plaque in an artery can restrict the flow of blood. As you can probably imagine, this is not an ideal situation. And eating right, exercising, and not smoking can help keep your arteries healthy.
Cardiovascular Disease
Diseases of the heart and blood vessels, called cardiovascular diseases (CVD), are very common. The leading cause of CVD is atherosclerosis.
Atherosclerosis
Atherosclerosis is the buildup of plaque inside arteries (see Figure below). Plaque consists of cell debris, cholesterol, and other substances. Factors that contribute to plaque buildup include a high-fat diet and smoking. As plaque builds up, it narrows the arteries and reduces blood flow.
The fatty material inside the artery on the right is plaque. Notice how much narrower the artery has become. Less blood can flow through it than the normal artery.
Atherosclerosis normally begins in late childhood and is typically found in most major arteries. It does not usually have any early symptoms. Causes of atherosclerosis include a high-fat diet, high cholesterol, smoking, obesity, and diabetes. Atherosclerosis becomes a threat to health when the plaque buildup prevents blood circulation in the heart or the brain. A blocked blood vessel in the heart can cause a heart attack. Blockage of the circulation in the brain can cause a stroke.
Ways to prevent atherosclerosis include eating healthy foods, getting plenty of exercise and not smoking. A diet high in saturated fat and cholesterol can raise your body's cholesterol levels, which can lead to increased plaque in your arteries. Cholesterol and saturated fat are found mostly in animal products, such as meat, eggs, milk and other dairy products.
Coronary Heart Disease
Atherosclerosis of arteries that supply the heart muscle is called coronary heart disease. This disease may or may not have symptoms, such as chest pain. As the disease progresses, there is an increased risk of heart attack. A heart attack occurs when the blood supply to part of the heart muscle is blocked and cardiac muscle fibers die. Coronary heart disease is the leading cause of death of adults in the United States.
The image below shows the way in which a blocked coronary artery can cause a heart attack. The loss of oxygen to the heart muscle cause that part of the tissue to die. Maybe one day, stem cell therapy will allow for the replacement of the dead cells with new cardiac muscle cells.
A blockage in a coronary artery stops oxygen from getting to part of the heart muscle, so areas of the heart that depend on the blood flow from the blocked artery are starved of oxygen.
Stroke
Atherosclerosis in the arteries of the brain can also lead to a stroke. A stroke is a loss of brain function due to a blockage of the blood supply to the brain. Risk factors for stroke include old age, high blood pressure, having a previous stroke, diabetes, high cholesterol, and smoking. The best way to reduce the risk of stroke is to have low blood pressure.
Preventing Cardiovascular Disease
Many factors may increase the risk of developing coronary heart disease and other CVDs. The risk of CVDs increases with age and is greater in males than females at most ages. Having a close relative with CVD also increases the risk. These factors cannot be controlled, but other risk factors can, including smoking, lack of exercise, and high-fat diet. By making healthy lifestyle choices, you can reduce your risk of developing CVD.
Summary
• A disease that affects the heart or blood vessels is called a cardiovascular disease (CVD).
• The leading cause of CVD is atherosclerosis, or the buildup of plaque inside arteries.
• Healthy lifestyle choices can reduce the risk of developing CVD.
Review
1. What is atherosclerosis? What is the result of atherosclerosis?
2. List controllable factors that increase the risk of cardiovascular disease.
3. What is the leading cause of death of adults in the United States?
4. How can you reduce your risk of developing CVD? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.32%3A_Circulatory_System_Diseases.txt |
What exactly is blood?
All your cells need oxygen, as oxygen is the final electron acceptor during cellular respiration. How do they get this oxygen? From blood. Blood cells flow through the vessels of the human circulatory system. But what exactly is blood? It does transport oxygen, but also has other functions.
Blood
Blood is a fluid connective tissue. It circulates throughout the body through blood vessels by the pumping action of the heart. Blood in arteries carries oxygen and nutrients to all the body’s cells. Blood in veins carries carbon dioxide and other wastes away from the cells to be excreted. Blood also defends the body against infection, repairs body tissues, transportshormones, and controls the body’s pH.
Composition of Blood
The fluid part of blood is called plasma. It is a watery golden-yellow liquid that contains many dissolved substances and blood cells. Types of blood cells in plasma include red blood cells, white blood cells, and platelets (see Figure below).
Cells in blood include red blood cells, white blood cells, and platelets.
• The trillions of red blood cells in blood plasma carry oxygen. Red blood cells containhemoglobin, a protein with iron that binds with oxygen. Red blood cells are made in the marrow of long bones, rib bones, the skull, and the vertebrae. These cells survive for about 120 days, and then they are destroyed. Mature red blood cells lack a nucleus and other organelles, allowing for more hemoglobin, and therefore more oxygen to be carried by each cell.
• White blood cells are generally larger than red blood cells but far fewer in number. They defend the body against foreign bacteria, viruses and other pathogens. For example, white blood cells called phagocytes swallow and destroy microorganisms and debris in the blood, neutrophils engulf bacteria and other parasites, and lymphocytes fight infections caused by bacteria and viruses.
• Platelets are cell fragments involved in blood clotting. They stick to tears in blood vesselsand to each other, forming a plug at the site of injury. They also release chemicals that are needed for clotting to occur.
Blood type is a genetic characteristic associated with the presence or absence of certain molecules, called antigens, on the surface of red blood cells. The most commonly known blood types are the ABO and Rhesus blood types.
• ABO blood type is determined by two common antigens, often referred to simply as antigens A and B. A person may have blood type A (only antigen A), B (only antigen B), AB (both antigens), or O (no antigens).
• Rhesus blood type is determined by one common antigen. A person may either have the antigen (Rh+) or lack the antigen (Rh-).
Blood type is important for medical reasons. A person who needs a blood transfusion must receive blood that is the same type as his or her own. Otherwise, the transfused blood may cause a potentially life-threatening reaction in the patient’s bloodstream.
Summary
• Blood is a fluid connective tissue that contains a liquid component called plasma.
• Blood also contains dissolved substances and blood cells.
• Red blood cells carry oxygen, white blood cells defend the body, and platelets help blood clot.
Review
1. What type of tissue is blood?
2. Identify three types of blood cells and their functions.
3. People with type O blood are called “universal donors” because they can donate blood to anyone else, regardless of their ABO blood type. Explain why. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.33%3A_Blood.txt |
Where does oxygen get into blood?
Red blood cells are like trucks that transport cargo on a highway system. Their cargo is oxygen, and the highways are blood vessels. Where do red blood cells pick up their cargo of oxygen? The answer is the lungs. The lungs are organs of the respiratory system. The respiratory system is the body system that brings air containing oxygen into the body and releases carbon dioxide into the atmosphere.
Respiration
The job of the respiratory system is the exchange of gases between the body and the outside air. This process, called respiration, actually consists of two parts. In the first part, oxygen in the air is drawn into the body and carbon dioxide is released from the body through the respiratory tract. In the second part, the circulatory system delivers the oxygen to body cells and picks up carbon dioxide from the cells in return. The lungs are organs of the respiratory system. It is in the lungs where oxygen is transferred from the respiratory system to the circulatory system.
The use of the word “respiration” in relation to gas exchange is different from its use in the term cellular respiration. Recall that cellular respiration is the metabolic process by which cells obtain energy by “burning” glucose. Cellular respiration uses oxygen and releases carbon dioxide. Respiration by the respiratory system supplies the oxygen and takes away the carbon dioxide.
• Respiration is the process in which gases are exchanged between the body and the outside air.
• The lungs and other organs of the respiratory system bring oxygen into the body and release carbon dioxide into the atmosphere.
Review
1. What is respiration?
2. Describe the two parts of respiration.
3. How is respiration different from cellular respiration?
13.35: Respiratory System Organs
Are all noses alike?
It all starts with the nose. OK, in humans maybe not the nose pictured above, but one similar to the nose below. Though the passage of air is probably similar in cows and humans. Air comes in and then where does it go?
Organs of the Respiratory System
The organs of the respiratory system that bring air into the body are divided among the upperrespiratory tract and lower respiratory tract. These organs are shown in Figure below. In addition to the lungs, these organs include the pharynx, larynx, trachea and bronchi. Thenasal cavity is also part of the respiratory system. The nose and nasal cavity filter, warm, and moisten the air we inhale. Hairs and mucus produced in the nose trap particles in the air and prevent them from reaching the lungs.
The organs of the respiratory system move air into and out of the body.
• The pharynx is a long tube that is shared with the digestive system. Both food and air travel through the pharynx.
• The larynx, or voice box, contains vocal cords, which allow us to produce vocal sounds. Air passes through thin tissues in the larynx, producing sound.
• The trachea, or wind pipe, is a long tube that leads down to the chest.
• The trachea divides as it enters the lungs to form the right and left bronchi, which branch into smaller bronchioles within each lung. The bronchioles lead to alveoli, the sites of gas exchange.
Summary
• The organs of the respiratory system include the lungs, pharynx, larynx, trachea, and bronchi.
Review
1. Describe the main organs of the respiratory system. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.34%3A_Respiration.txt |
Grapes. Why? What do these have in common with a breath of air?
Below are the parts of the lungs where oxygen moves from the lungs into the blood. If the alveoli below were purple, they could resemble a bunch of grapes. Of course, as the alveoli are in the lungs, they must be very small to provide enough area for the exchange of gases. In fact, there are about 300 million alveoli in the adult lung.
Journey of a Breath of Air
Take in a big breath of air through your nose. As you inhale, you may feel the air pass down your throat and notice your chest expand. Now exhale and observe the opposite events occurring. Inhaling and exhaling may seem like simple actions, but they are just part of the complex process of respiration, which includes these four steps:
1. Ventilation
2. Pulmonary gas exchange
3. Gas transport
4. Peripheral gas exchange
Ventilation
Respiration begins with ventilation. This is the process of moving air in and out of the lungs. The lungs are the organs in which gas exchange takes place between blood and air.
• Air enters the respiratory system through the nose. As the air passes through the nasal cavity, mucus and hairs trap any particles in the air. The air is also warmed and moistened so it won’t harm delicate tissues of the lungs.
• Next, the air passes through the pharynx, a long tube that is shared with the digestive system. A flap of connective tissue called the epiglottis closes when food is swallowed to prevent choking.
• From the pharynx, air next passes through the larynx, or voice box. The larynx contains vocal cords, which allow us to produce vocal sounds.
• After the larynx, air moves into the trachea, or wind pipe. This is a long tube that leads down to the chest.
• In the chest, the trachea divides as it enters the lungs to form the right and left bronchi. The bronchi contain cartilage, which prevents them from collapsing. Mucus in the bronchi traps any remaining particles in air. Tiny, hair-like structures called cilia line the bronchi and sweep the particles and mucus toward the throat so they can be expelled from the body.
• Finally, air passes from the bronchi into smaller passages called bronchioles. The bronchioles end in tiny air sacs called alveoli.
Pulmonary Gas Exchange
Pulmonary gas exchange is the exchange of gases between inhaled air and the blood. It occurs in the alveoli of the lungs. Alveoli (singular, alveolus) are grape-like clusters surrounded by networks of thin-walled pulmonary capillaries. After you inhale, there is a greater concentration of oxygen in the alveoli than in the blood of the pulmonary capillaries, so oxygen diffuses from the alveoli into the blood across the capillaries (see Figure below). Carbon dioxide, in contrast, is more concentrated in the blood of the pulmonary capillaries than in the alveoli, so it diffuses in the opposite direction.
Alveoli are tiny sacs in the lungs where gas exchange takes place.
Gas Transport
After the blood in the pulmonary capillaries becomes saturated with oxygen, it leaves the lungs and travels to the heart. The heart pumps the oxygen-rich blood into arteries, which carry it throughout the body. Eventually, the blood travels into capillaries that supply body tissues. These capillaries are called peripheral capillaries.
Peripheral Gas Exchange
The cells of the body have a much lower concentration of oxygen than does the oxygenated blood in the peripheral capillaries. Therefore, oxygen diffuses from the peripheral capillaries into body cells. Carbon dioxide is produced by cells as a byproduct of cellular respiration, so it is more concentrated in the cells than in the blood of the peripheral capillaries. As a result, carbon dioxide diffuses in the opposite direction.
Back to the Lungs
The carbon dioxide from body cells travels in the blood from the peripheral capillaries to veins and then to the heart. The heart pumps the blood to the lungs, where the carbon dioxide diffuses into the alveoli. Then, the carbon dioxide passes out of the body through the other structures of the respiratory system, bringing the process of respiration full circle.
Gas Exchange and Homeostasis
Gas exchange is needed to provide cells with the oxygen they need for cellular respiration. Cells cannot survive for long without oxygen. Gas exchange is also needed to carry away carbon dioxide waste. Some of the carbon dioxide in the blood dissolves to form carbonic acid, which keeps blood pH within a normal range.
Blood pH may become unbalanced if the rate of breathing is too fast or too slow. When breathing is too fast, blood contains too little carbon dioxide and becomes too basic. When breathing is too slow, blood contains too much carbon dioxide and becomes too acidic. Clearly, to maintain proper blood pH, the rate of breathing must be regulated.
Summary
• Respiration begins with ventilation, the process of moving air into and out of the lungs.
• Gas exchange in the lungs takes place across the thin walls of pulmonary arteries in tiny air sacs called alveoli.
• Oxygenated blood is transported by the circulatory system from lungs to tissues throughout the body.
• Gas exchange between blood and body cells occurs across the walls of peripheral capillaries.
• Gas exchange helps maintain homeostasis by supplying cells with oxygen, carrying away carbon dioxide waste, and maintaining proper pH of the blood.
Review
1. Outline the pathway of a breath of air from the nose to the alveoli.
2. Describe how pulmonary gas exchange occurs.
3. What is peripheral gas exchange.
4. Sometimes people who are feeling anxious breathe too fast and become lightheaded. This is called hyperventilation. Hyperventilation can upset the pH balance of the blood, resulting in blood that is too basic. Explain why. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.36%3A_Processes_of_Breathing.txt |
What allows you to take a deep breath?
Deep breath in…now blow out those candles. We've all done that. Taking that deep breath in is an active process. You can usually feel your chest move. Why? Obviously, muscles in your chest are doing the work.
Regulation of Breathing
To understand how breathing is regulated, you first need to understand how breathing occurs.
How Breathing Occurs
Inhaling is an active movement that results from the contraction of a muscle called the diaphragm. The diaphragm is large, sheet-like muscle below the lungs (see Figure below). When the diaphragm contracts, the ribcage expands and the contents of the abdomen move downward. This results in a larger chest volume, which decreases air pressure inside the lungs. With lower air pressure inside than outside the lungs, air rushes into the lungs. When the diaphragm relaxes, the opposite events occur. The volume of the chest cavity decreases, air pressure inside the lungs increases, and air flows out of the lungs, like air rushing out of a balloon.
Breathing depends on contractions of the diaphragm.
Control of Breathing
The regular, rhythmic contractions of the diaphragm are controlled by the brain stem. It sends nerve impulses to the diaphragm through the autonomic nervous system. The brain stem monitors the level of carbon dioxide in the blood. If the level becomes too high, it “tells” the diaphragm to contract more often. Breathing speeds up, and the excess carbon dioxide is released into the air. The opposite events occur when the level of carbon dioxide in the blood becomes too low. In this way, breathing keeps blood pH within a narrow range.
Summary
• Breathing occurs due to repeated contractions of a large muscle called the diaphragm.
• The rate of breathing is regulated by the brain stem. It monitors the level of carbon dioxide in the blood and triggers faster or slower breathing as needed to keep the level within a narrow range.
Review
1. Explain why contraction of the diaphragm causes the lungs to fill with air.
2. Explain how the rate of breathing is controlled.
13.38: Respiratory System Diseases
Does making ATP start with the lungs?
The importance of a nice pair of healthy lungs is obvious. We all need oxygen to get into our lungs, so the oxygen can be transferred to the blood, so it can be transported around our body, so each cell can receive its fair share of oxygen, allowing oxygen to serve as the final electron acceptor during the electron transport chain of cellular respiration, allowing the cell to produce lots of ATP. And it all starts with the lungs.
Diseases of the Respiratory System
When you have a cold, your nasal passages may become so congested that it’s hard to breathe through your nose. Many other diseases also affect the respiratory system, most of them more serious than the common cold. Some lung diseases, such as lung cancer, can be especially dangerous. The following list includes just a sample of respiratory system diseases.
• Asthma is a disease in which the air passages of the lungs periodically become too narrow, often with excessive mucus production. This causes difficulty breathing, coughing, and chest tightness. An asthma attack may be triggered by allergens, strenuous exercise, stress, or other factors.
• Pneumonia is a disease in which some of the alveoli of the lungs fill with fluid so gas exchange cannot occur. Symptoms usually include coughing, chest pain, and difficulty breathing. Pneumonia may be caused by an infection or injury of the lungs.
• Emphysema is a lung disease in which walls of the alveoli break down so less gas can be exchanged in the lungs (see Figure below). This causes shortness of breath. The damage to the alveoli is usually caused by smoking and is irreversible.
• Pneumonia and emphysema are caused by damage to the alveoli of the lungs.
Causes of Respiratory Diseases
Many respiratory diseases are caused by pathogens. Certain bacteria, viruses, and fungi are pathogens of the respiratory system. The common cold and flu are caused by viruses. Tuberculosis, whooping cough, and acute bronchitis are caused by bacteria. The pathogens that cause colds, flu, and TB can be passed from person to person by coughing and sneezing.
Air pollution is another significant cause of respiratory disease. The quality of the air you breathe can affect the health of your lungs. Asthma, heart and lung diseases, allergies, and several types of cancers are all linked to air quality. Air pollution is not just found outdoors; indoor air pollution can also be responsible for health problems.
Smoking is the most significant cause of respiratory disease as well as cardiovascular disease and cancer. Exposure to tobacco smoke by smoking or by breathing air that contains tobacco smoke is the leading cause of preventable death in the United States. Regular smokers die about 10 years earlier than nonsmokers. The Centers for Disease Control and Prevention (CDC) describes tobacco use as "the single most important preventable risk to human health in developed countries and an important cause of [early] death worldwide."
Summary
• Diseases of the respiratory system include asthma, pneumonia, and emphysema.
• Review
• Identify and describe three diseases of the respiratory system, and state what triggers or causes each disease. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.37%3A_Respiratory_System_Regulation.txt |
Specifically, our energy comes from what?
The respiratory and circulatory systems work together to provide cells with the oxygen they need for cellular respiration. Cells also need glucose for cellular respiration. Glucose is a simple sugar that comes from the food we eat. To get glucose from food, digestion must occur. This process is carried out by the digestive system.
Overview of the Digestive System
The digestive system consists of organs that break down food and absorb nutrients such as glucose. Organs of the digestive system are shown in Figure below. Most of the organs make up the gastrointestinal tract. The rest of the organs are called accessory organs.
The digestive system includes organs from the mouth to the anus.
The Gastrointestinal Tract
The gastrointestinal (GI) tract is a long tube that connects the mouth with the anus. It is more than 9 meters (30 feet) long in adults and includes the esophagus, stomach, and small and large intestines. Food enters the mouth, passes through the other organs of the GI tract, and then leaves the body through the anus.
The organs of the GI tract are lined with mucous membranes that secrete digestive enzymes and absorb nutrients. The organs are also covered by layers of muscle that enable peristalsis.Peristalsis is an involuntary muscle contraction that moves rapidly along an organ like a wave (see Figure below).
Peristalsis pushes food through the GI tract.
Accessory Organs of Digestion
Other organs involved in digestion include the liver, gall bladder, and pancreas. They are called accessory organs because food does not pass through them. Instead, they secrete or store substances needed for digestion.
Functions of the Digestive System
The digestive system has three main functions: digestion of food, absorption of nutrients, and elimination of solid food waste. Digestion is the process of breaking down food into components the body can absorb. It consists of two types of processes: mechanical digestion and chemical digestion.
• Mechanical digestion is the physical breakdown of chunks of food into smaller pieces. This type of digestion takes place mainly in the mouth and stomach.
• Chemical digestion is the chemical breakdown of large, complex food molecules into smaller, simpler nutrient molecules that can be absorbed by the blood. This type of digestion begins in the mouth and stomach but occurs mainly in the small intestine.
After food is digested, the resulting nutrients are absorbed. Absorption is the process in which substances pass into the bloodstream, where they can circulate throughout the body. Absorption of nutrients occurs mainly in the small intestine. Any remaining matter from food that cannot be digested and absorbed passes into the large intestine as waste. The waste later passes out of the body through the anus in the process of elimination.
Summary
• The digestive system consists of organs that break down food, absorb nutrients, and eliminate waste.
• The breakdown of food occurs in the process of digestion.
Review
1. What organs make up the gastrointestinal tract? What are the accessory organs of digestion?
2. Describe peristalsis and its role in digestion.
3. Define mechanical and chemical digestion. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.39%3A_Digestive_System_Organs.txt |
What's the first step in the digestion process?
It all starts with the mouth. Food goes in, you chew it up, swallow it, then what happens? The process of turning that food into energy and proteins and other things necessary for life begins. But it all starts with the mouth.
The Start of Digestion: Mouth to Stomach
Does the sight or aroma of your favorite food make your mouth water? When this happens, you are getting ready for digestion.
Mouth
The mouth is the first digestive organ that food enters. The sight, smell, or taste of food stimulates the release of digestive enzymes by salivary glands inside the mouth. The major salivary enzyme is amylase. It begins the chemical digestion of carbohydrates by breaking down starch into sugar.
The mouth also begins the process of mechanical digestion. Sharp teeth in the front of the mouth cut or tear food when you bite into it (see Figure below). Broad teeth in the back of the mouth grind food when you chew. Food is easier to chew because it is moistened by saliva from the salivary glands. The tongue helps mix the food with saliva and also helps you swallow. After you swallow, the chewed food passes into the pharynx.
Teeth are important for mechanical digestion.
Esophagus
From the pharynx, the food moves into the esophagus. The esophagus is a long, narrow tube that passes food from the pharynx to the stomach by peristalsis. The esophagus has no other digestive functions. At the end of the esophagus, a muscle called a sphincter controls the entrance to the stomach. The sphincter opens to let food into the stomach and then closes again to prevent food from passing back into the esophagus.
Stomach
The stomach is a sac-like organ in which food is further digested both mechanically and chemically. (To see an animation of how the stomach digests food, go to the link below.) Churning movements of the stomach’s thick, muscular walls complete the mechanical breakdown of food. The churning movements also mix food with digestive fluids secreted by the stomach. One of these fluids is hydrochloric acid. It kills bacteria in food and gives the stomach the low (acidic) pH needed by digestive enzymes that work in the stomach. The main enzyme is pepsin, which chemically digests protein.
The stomach stores the partly digested food until the small intestine is ready to receive it. When the small intestine is empty, a sphincter opens to allow the partially digested food to enter the small intestine.
Summary
• Digestion consists of mechanical and chemical digestion.
• Mechanical digestion occurs in the mouth and stomach.
• Chemical digestion occurs mainly in the small intestine.
• The pancreas and liver secrete fluids that aid in digestion.
Review
1. What is amylase and what is its role?
2. Describe functions of the stomach.
3. What is pepsin?
13.41: Digestive System Diseases
What's worse than an upset stomach?
You've probably had an upset stomach. Most likely it was due to something you ate. But imagine bleeding from your stomach. That's a little different than your stomach just being upset. Stomach ulcers can be very serious.
Diseases of the Digestive System
Many diseases can affect the digestive system. Three of the most common diseases that affect the digestive system are food allergies, ulcers, and heartburn. Foodborne illnesses and food intolerance are also serious issues associated with the digestive system.
• Food allergies occur when the immune system reacts to substances in food as though they were harmful “foreign invaders.” Foods that are most likely to cause allergies are pictured in Figure below, and include nuts, eggs, grains and milk. Symptoms of food allergies often include vomiting and diarrhea. Symptoms of food allergies include itching and swelling of the lips and mouth. More serious symptoms include trouble breathing. In some instances, a food allergy can trigger anaphylaxis, which is an extremely severe reaction. Emergency medical treatment is critical for this condition, which left untreated, can lead to death.
These foods are the most common causes of food allergies.
• Ulcers are sores in the lining of the stomach or duodenum that are usually caused by bacterial infections. They may also be caused by the acidic environment of the stomach. Stomach acids may damage the lining of the stomach. Symptoms typically include abdominal pain and bleeding.
• Heartburn is a painful burning sensation in the chest caused by stomach acid backing up into the esophagus. The stomach acid may eventually cause serious damage to the esophagus unless the problem is corrected.
Summary
• Digestive system diseases include food allergies, ulcers, and heartburn.
Review
1. Describe two diseases of the digestive system.
2. List three foods that cause common food allergies. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.40%3A_Digestion.txt |
Are these really good for you?
Fresh fruit and vegetables. Every child's favorite. Especially those vegetables. When your mother tells you to "eat your vegetables," there is a reason for that. Yes, they are actually good for you.
Food and Nutrients
Did you ever hear the saying, “You are what you eat”? It’s not just a saying. It’s actually true. What you eat plays an important role in your health. Eating a variety of the right types of foods promotes good health and provides energy for growth and activity. This is because healthful foods are rich in nutrients. Nutrients are substances the body needs for energy, building materials, and control of body processes. There are six main classes of nutrients:carbohydrates, proteins, lipids, water, vitamins, and minerals. These six classes are categorized as macronutrients or micronutrients depending on how much of them the body needs.
Macronutrients
Nutrients the body needs in relatively large amounts are called macronutrients. They include carbohydrates, proteins, lipids, and water. All macronutrients except water can be used by the body for energy. (The energy in food is measured in a unit called a Calorie.) The exact amount of each macronutrient that an individual needs depends on many factors, including gender and age. Recommended daily intakes by teens of three macronutrients are shown in Table below. Based on your gender and age, how many grams of proteins should you eat each day?
Gender/Age Carbohydrates (g/day) Proteins (g/day) Water (L/day) (includes water in food)
Males 9–13 years 130 34 2.4
Males 14-18 years 130 52 3.3
Females 9-13 years 130 34 2.1
Females 14-18 years 130 46 2.3
• Carbohydrates include sugars, starches, and fiber. Sugars and starches are used by the body for energy. One gram of carbohydrates provides 4 Calories of energy. Fiber, which is found in plant foods, cannot be digested but is needed for good health. Simple carbohydrates are small carbohydrates found in foods such as fruits and milk. These carbohydrates include lactose, fructose and glucose. Complex carbohydrates are much larger molecules. Starch, which is a complex carbohydrate found in vegetables and grains, is made of thousands of glucose units bonded together.
• Dietary proteins are broken down during digestion to provide the amino acids needed for protein synthesis. Any extra proteins in the diet not needed for this purpose are used for energy or stored as fat. One gram of proteins provides 4 Calories of energy. Eating protein provides the amino acids for your cells to produce your own antibodies, muscle fibers and enzymes (as well as many other types of proteins).
• Lipids provide the body with energy and serve other vital functions, such as protecting neurons and providing the membranes that surround all cells. One gram of lipids provides 9 Calories of energy. You need to eat small amounts of lipids for good health. However, large amounts can be harmful, especially if they contain saturated fatty acids from animal foods.
• Water is essential to life because biochemical reactions take place in water. Most people can survive only a few days without water.
Micronutrients
Nutrients the body needs in relatively small amounts are called micronutrients. They include vitamins and minerals. Vitamins are organic compounds that are needed by the body to function properly. Several vitamins are described in Table below. Vitamins play many roles in good health, ranging from maintaining good vision to helping blood clot. Vitamin B12 is produced by bacteria in the large intestine. Vitamin D is synthesized by the skin when it is exposed to UV light. Most other vitamins must be obtained from foods like those listed inTable below.
Vitamin Function Good Food Sources
A good vision carrots, spinach
B12 normal nerve function meat, milk
C making connective tissue oranges, red peppers
D healthy bones and teeth salmon, eggs
E normal cell membranes vegetable oils, nuts
K blood clotting spinach, soybeans
Minerals are chemical elements that are essential for body processes. They include calcium, which helps form strong bones and teeth, and potassium, which is needed for normal nerve and muscle function. Good sources of minerals include leafy, green vegetables, whole grains, milk, and meats.
Vitamins and minerals do not provide energy, but they are still essential for good health. The necessary amounts can usually be met with balanced eating. However, people who do not eat enough of the right foods may need vitamin or mineral supplements.
Summary
• Nutrients are substances that the body needs for energy, building materials, and control of body processes.
• Carbohydrates, proteins, lipids, and water are nutrients needed in relatively large amounts.
• Vitamins and minerals are nutrients needed in much smaller amounts.
Review
1. Based on your gender and age, how many grams of proteins should you eat each day?
2. Compare and contrast macronutrients and micronutrients. Give examples of each.
3. What are minerals? Give two examples.
4. What is a good source of vitamin A?
5. Why do you need vitamin | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.42%3A_Food_and_Nutrients.txt |
What do you do with your waste?
Toxic waste must be disposed of properly or there can be serious consequences. Now, your waste should not be as colorful or toxic as shown here (if it is, get yourself to a doctor as soon as possible), but it still needs to be removed from you. And that is the role of the excretory system. The excretory system gets rid of waste and excess water.
Excretion
If you exercise on a hot day, you are likely to lose a lot of water in sweat. Then, for the next several hours, you may notice that you do not pass urine as often as normal and that your urine is darker than usual. Do you know why this happens? Your body is low on water and trying to reduce the amount of water lost in urine. The amount of water lost in urine is controlled by the kidneys, the main organs of the excretory system.
Excretion is the process of removing wastes and excess water from the body. It is one of the major ways the body maintains homeostasis. Although the kidneys are the main organs of excretion, several other organs also excrete wastes. They include the large intestine, liver, skin, and lungs. All of these organs of excretion, along with the kidneys, make up the excretory system. The roles of the excretory organs other than the kidney are summarized below:
• The large intestine eliminates solid wastes that remain after the digestion of food.
• The liver breaks down excess amino acids and toxins in the blood.
• The skin eliminates excess water and salts in sweat.
• The lungs exhale water vapor and carbon dioxide.
Summary
• Excretion is the process of removing wastes and excess water from the body. It is one of the major ways the body maintains homeostasis.
• Organs of excretion make up the excretory system. They include the kidneys, large intestine, liver, skin, and lungs.
• Review
• What is excretion?
• List organs of the excretory system and their functions.
13.44: Urinary System
How is it determined what's waste and what's not?
Shown above is a major process of maintaining homeostasis. Getting rid of waste and excess water. Such a basic process is actually very complex. It involves an intricate exchange of material through the kidney.
Urinary System
The kidneys are part of the urinary system, which is shown in Figure below. The main function of the urinary system is to filter waste products and excess water from the blood and excrete them from the body.
The kidneys are the chief organs of the urinary system.
Kidneys and Nephrons
The kidneys are a pair of bean-shaped organs just above the waist. A cross-section of a kidney is shown in Figure below. The function of the kidney is to filter blood and form urine.Urine is the liquid waste product of the body that is excreted by the urinary system. Nephronsare the structural and functional units of the kidneys. A single kidney may have more than a million nephrons!
Each kidney is supplied by a renal artery and renal vein.
As shown in Figure below, each nephron acts as a tiny filtering plant. It filters blood and forms urine in the following steps:
1. Blood enters the kidney through the renal artery, which branches into capillaries. When blood passes through capillaries of the glomerulus of a nephron, blood pressure forces some of the water and dissolved substances in the blood to cross the capillary walls intoBowman’s capsule.
2. The filtered substances pass to the renal tubule of the nephron. In the renal tubule, some of the filtered substances are reabsorbed and returned to the bloodstream. Other substances are secreted into the fluid.
3. The fluid passes to a collecting duct, which reabsorbs some of the water and returns it to the bloodstream. The fluid that remains in the collecting duct is urine.
The parts of a nephron and their functions are shown in this diagram.
Excretion of Urine
From the collecting ducts of the kidneys, urine enters the ureters, two muscular tubes that move the urine by peristalsis to the bladder (see Figure above). The bladder is a hollow, sac-like organ that stores urine. When the bladder is about half full, it sends a nerve impulse to a sphincter to relax and let urine flow out of the bladder and into the urethra. The urethra is a muscular tube that carries urine out of the body. Urine leaves the body through another sphincter in the process of urination. This sphincter and the process of urination are normally under conscious control.
Summary
• The kidneys filter blood and form urine. They are part of the urinary system, which also includes the ureters, bladder, and urethra.
• Each kidney has more than a million nephrons, which are the structural and functional units of the kidney.
• Each nephron is like a tiny filtering plant.
Review
1. Describe how nephrons filter blood and form urine.
2. State the functions of the ureters, bladder, and urethra. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.43%3A_Excretion.txt |
Why is a bean-shaped organ so important?
Shown above are the isolated kidneys from many little mice. OK, they're really just kidney beans. But this is what the important kidney looks like. Why is it so important? Your kidneys filter and remove wastes from your blood.
The Kidneys
The kidneys are a pair of bean-shaped organs just above the waist. They are important organs with many functions in the body, including producing hormones, absorbing minerals, and filtering blood and producing urine.
A cross-section of a kidney is shown in Figure below. The function of the kidney is to filter blood and form urine. Urine is the liquid waste product of the body that is excreted by the urinary system. Wastes in the blood come from the normal breakdown of tissues, such as muscles, and from food. The body uses food for energy. After the body has taken the nutrients it needs from food, some of the wastes are absorbed into the blood. If the kidneys did not remove them, these wastes would build up in the blood and damage the body.
Kidneys and Nephrons
The actual removal of wastes from the blood occurs in tiny units inside the kidneys called nephrons. Nephrons are the structural and functional units of the kidneys. A single kidney may have more than a million nephrons! This is further discussed in the Urinary Systemconcept.
Each kidney is supplied by a renal artery and renal vein.
Kidneys and Homeostasis
The kidneys play many vital roles in homeostasis. They work with many other organ systems to do this. For example, they work with the circulatory system to filter blood, and with the urinary system to remove wastes.
The kidneys filter all the blood in the body many times each day and produce a total of about 1.5 liters of urine. The kidneys control the amount of water, ions, and other substances in the blood by excreting more or less of them in urine. The kidneys also secrete hormones that help maintain homeostasis. Erythropoietin, for example, is a kidney hormone that stimulates bone marrow to produce red blood cells when more are needed. They also secrete renin, which regulates blood pressure, and calcitriol, the active form of vitamin D, which helps maintain calcium for bones. The kidneys themselves are also regulated by hormones. For example, antidiuretic hormone from the hypothalamus stimulates the kidneys to produce more concentrated urine when the body is low on water.
Other Functions
In addition to filtering blood and producing urine, the kidneys are also involved in maintaining the water level in the body, and regulating red blood cell levels and blood pressure.
• As the kidneys are mainly involved in the production of urine, they react to changes in the body’s water level throughout the day. As water intake decreases, the kidneys adjust accordingly and leave water in the body instead of helping remove it through the urine, maintaining the water level in the body.
• The kidneys also need constant pressure to filter the blood. When the blood pressure drops too low, the kidneys increase the pressure. One way is by producing angiotensin, a blood vessel-constricting protein. This protein also signals the body to retain sodium and water. Together, the constriction of blood vessels and retention of sodium and water help restore normal blood pressure.
• When the kidneys don’t get enough oxygen, they send out a signal in the form of the hormone erythropoietin, which stimulates the bone marrow to produce more oxygen-carrying red blood cells.
Summary
• The kidneys maintain homeostasis by controlling the amount of water, ions, and other substances in the blood.
• Kidneys also secrete hormones that have other homeostatic functions.
• Review
• What is the nephron? How many nephrons are in each kidney?
• Explain how the kidneys maintain homeostasis.
• What is the role of antidiuretic hormone? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.45%3A_Kidneys.txt |
How do you block the flow of urine?
Kidney stones. Imagine having that travel through your excretory system. OK, that's not a kidney stone, but you get the idea. Kidney stones can be more than a few millimeters in diameter. Painful? Sometimes extremely uncomfortable. And how does a stone leave the kidney? The same way urine does.
Kidney Disease and Dialysis
A person can live a normal, healthy life with just one kidney. However, at least one kidney must function properly to maintain life. Diseases that threaten the health and functioning of the kidneys include kidney stones, infections, and diabetes.
• Kidney stones are mineral crystals that form in urine inside the kidney. Kidney stones can form when substances in the urine, such as calcium, oxalate, and phosphorus, become highly concentrated. They may be extremely painful. If they block a ureter, they must be removed so urine can leave the kidney and be excreted. A kidney stone may not cause symptoms until it moves around within your kidney or passes into your ureter. A stone may stay in the kidney or travel down the urinary tract. Kidney stones vary in size. A small stone may pass on its own, causing little or no pain. A larger stone may get stuck along the urinary tract and can block the flow of urine, causing severe pain or bleeding.
• Bacterial infections of the urinary tract, especially the bladder, are very common. Bladder infections can be treated with antibiotics prescribed by a doctor. If untreated, they may lead to kidney damage.
• Uncontrolled diabetes may damage capillaries of nephrons. As a result, the kidneys lose much of their ability to filter blood. This is called kidney failure. The only cure for kidney failure is a kidney transplant, but it can be treated with dialysis. Dialysis is a medical procedure in which blood is filtered through a machine (see Figure below).
A dialysis machine filters a patient’s blood.
Summary
• Kidney diseases include kidney stones, infections, and kidney failure due to diabetes.
• Kidney failure may be treated with dialysis.
Review
1. Tom was seriously injured in a car crash. As a result, he had to have one of his kidneys removed. Does Tom need dialysis? Why or why not?
2. What are kidney stones? How do they form?
13.47: Barriers to Pathogens
How does your body keep most enemies out?
Many would consider the moat around this castle, together with the thick stone castle walls, as the first line of defense. Their role is to keep the enemy out, and protect what's inside.
The First Line of Defense
Does this organism look like a space alien? A scary creature from a nightmare? In fact, it’s a 1-cm long worm that lives in the human body and causes serious harm. It enters the body through a hair follicle of the skin when it’s in a much smaller stage of its life cycle. Like this worm, many other organisms can make us sick if they manage to enter our body. Fortunately for us, our immune system is able to keep out most such invaders.
The immune system protects the body from worms, germs, and other agents of harm. The immune system is like a medieval castle. The outside of the castle was protected by a moat and high stone walls. Inside the castle, soldiers were ready to fight off any invaders that managed to get through the outer defenses. Like a medieval castle, the immune system has a series of defenses. In fact, it has three lines of defense. Only pathogens that are able to get through all three lines of defense can harm the body.
The body’s first line of defense consists of different types of barriers that keep most pathogens out of the body. Pathogens are disease-causing agents, such as bacteria and viruses. These and other types of pathogens are described in Figure below. Regardless of the type of pathogen, however, the first line of defense is always the same.
Types of pathogens that commonly cause human diseases include bacteria, viruses, fungi, and protozoa. Which type of pathogen causes the common cold? Which type causes athlete’s foot?
Mechanical Barriers
Mechanical barriers physically block pathogens from entering the body. The skin is the most important mechanical barrier. In fact, it is the single most important defense the body has. The outer layer of the skin is tough and very difficult for pathogens to penetrate.
Mucous membranes provide a mechanical barrier at body openings. They also line the respiratory, GI, urinary, and reproductive tracts. Mucous membranes secrete mucus, a slimy substance that traps pathogens. The membranes also have hair-like cilia. The cilia sweep mucus and pathogens toward body openings where they can be removed from the body. When you sneeze or cough, pathogens are removed from the nose and throat (see Figure below). Tears wash pathogens from the eyes, and urine flushes pathogens out of the urinary tract.
A sneeze can expel many pathogens from the respiratory tract. That’s why you should always cover your mouth and nose and when you sneeze.
Chemical Barriers
Chemical barriers destroy pathogens on the outer body surface, at body openings, and on inner body linings. Sweat, mucus, tears, and saliva all contain enzymes that kill pathogens. Urine is too acidic for many pathogens, and semen contains zinc, which most pathogens cannot tolerate. In addition, stomach acid kills pathogens that enter the GI tract in food or water.
Biological Barriers
Biological barriers are living organisms that help protect the body. Millions of harmless bacteria live on the human skin. Many more live in the GI tract. The harmless bacteria use up food and space so harmful bacteria cannot grow.
Summary
• Barriers that keep out pathogens are the body’s first line of defense.
• The first line of defense includes mechanical, chemical, and biological barriers.
Review
1. What is the role of the body’s first line of defense?
2. Identify three types of barriers in the body’s first line of defense. Give an example of each type of barrier.
3. Which type of pathogen causes the common cold? Which type causes athlete’s foot? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.46%3A_Excretory_System_Diseases.txt |
What happens when an enemy gets past the first line of defense?
For this running back to make it past the first line of defense, there usually has to be a hole or break in the line. He then runs into the secondary, or the second line of defense. Whenever the skin is broken, it is possible for pathogens to easily enter your body. They get past the first line of defense, and run into the second line of defense.
The Second Line of Defense
If you have a cut on your hand, the break in the skin provides a way for pathogens to enter your body. Assume bacteria enter through the cut and infect the wound. These bacteria would then encounter the body’s second line of defense.
Inflammatory Response
The cut on your hand may become red, warm, and swollen. These are signs of aninflammatory response. This is the first reaction of the body to tissue damage or infection. As explained in Figure below, the response is triggered by chemicals called cytokines andhistamines, which are released when tissue is injured or infected. The chemicals communicate with other cells and coordinate the inflammatory response. You can see an animation of the inflammatory response at this link:http://www.sumanasinc.com/webcontent/animations/content/inflammatory.html.
This drawing shows what happens during the inflammatory response. Why are changes in capillaries important for this response?
Leukocytes
The chemicals that trigger an inflammatory response attract leukocytes to the site of injury or infection. Leukocytes are white blood cells. Their role is to fight infections and get rid of debris. Leukocytes may respond with either a nonspecific or a specific defense.
• A nonspecific defense is the same no matter what type of pathogen is involved. An example of a nonspecific defense is phagocytosis. This is the process in which leukocytes engulf and break down pathogens and debris. It is illustrated in Figure below. The immune system's first line of defense is also a nonspecific defense.
• A specific defense is tailored to a particular pathogen. Leukocytes involved in this type of defense are part of the immune response and are described in other concepts.
In this image, leukocytes (white) are attacking pathogens (star-shaped).
Summary
• The second line of defense attacks pathogens that manage to enter the body.
• The second line of defense includes the inflammatory response and phagocytosis by nonspecific leukocytes.
Review
1. What is a nonspecific defense?
2. What is the body’s second life of defense? When does it take effect?
3. Identify the roles of nonspecific leukocytes in the body’s second line of defense.
4. Jera cut her finger. The next day, the skin around the cut became red and warm. Why are these signs of infection?
13.49: Lymphatic System
What happens when your tonsils cause more problems than they solve?
Almost all of us have had a sore throat at some time. Maybe you had your tonsils out when you were younger? Why? Your tonsils are two lumps of tissue that work as germ fighters for your body. But sometimes germs like to hang out there, where they cause infections. In other words, your tonsils can cause more problems than they solve. So, you have them taken out.
Lymphatic System
Like the immune systems of other vertebrates, the human immune system is adaptive. If pathogens manage to get through the body’s first two lines of defense, the third line of defense takes over. The third line of defense is referred to as the immune response. This defense is specific to a particular pathogen, and it allows the immune system to “remember” the pathogen after the infection is over. If the pathogen tries to invade the body again, the immune response against that pathogen will be much faster and stronger.
The immune response mainly involves the lymphatic system. The lymphatic system is a major part of the immune system. It produces leukocytes called lymphocytes. Lymphocytes are the key cells involved in the immune response. They recognize and help destroy particular pathogens in body fluids and cells. They also destroy certain cancer cells.
Structures of the Lymphatic System
Figure below shows the structures of the lymphatic system. They include organs, lymph vessels, lymph, and lymph nodes. Organs of the lymphatic system are the bone marrow, thymus, spleen, and tonsils.
• Bone marrow is found inside many bones. It produces lymphocytes.
• The thymus is located in the upper chest behind the breast bone. It stores and matures lymphocytes.
• The spleen is in the upper abdomen. It filters pathogens and worn out red blood cells from the blood, and then lymphocytes in the spleen destroy them.
• The tonsils are located on either side of the pharynx in the throat. They trap pathogens, which are destroyed by lymphocytes in the tonsils.
The lymphatic system consists of organs, vessels, and lymph.
Lymphatic Vessels and Lymph
Lymphatic vessels make up a body-wide circulatory system. The fluid they circulate is lymph.Lymph is a fluid that leaks out of capillaries into spaces between cells. As the lymph accumulates between cells, it diffuses into tiny lymphatic vessels. The lymph then moves through the lymphatic system from smaller to larger vessels. It finally drains back into the bloodstream in the chest. As lymph passes through the lymphatic vessels, pathogens are filtered out at small structures called lymph nodes (see Figure above). The filtered pathogens are destroyed by lymphocytes.
Lymphocytes
The human body has as many as two trillion lymphocytes, and lymphocytes make up about 25% of all leukocytes. The majority of lymphocytes are found in the lymphatic system, where they are most likely to encounter pathogens. The rest are found in the blood. There are two major types of lymphocytes, called B cells and T cells. These cells get their names from the organs in which they mature. B cells mature in bone marrow, and T cells mature in the thymus. Both B and T cells recognize and respond to particular pathogens.
Antigen Recognition
B cells and T cells actually recognize and respond to antigens on pathogens. Antigens are molecules that the immune system recognizes as foreign to the body. Antigens are also found on cancer cells and the cells of transplanted organs. They trigger the immune system to react against the cells that carry them. This is why a transplanted organ may be rejected by the recipient’s immune system.
How do B and T cells recognize specific antigens? They have receptor molecules on their surface that bind only with particular antigens.
As shown in Figure below, the fit between an antigen and a matching receptor molecule is like a key in a lock.
An antigen fits the matching receptor molecule like a key in a lock.
Summary
• The body’s third line of defense is the immune response. This involves the lymphatic system. This system filters pathogens from lymph and produces lymphocytes.
• Lymphocytes are the key cells in the immune response. They are leukocytes that become activated by a particular antigen. There are two major type of lymphocytes: B cells and T cells.
Review
1. What is the lymphatic system?
2. List three organs of the lymphatic system and their functions.
3. What are lymph nodes? What is their function?
4. What are the two major types of lymphocytes?
5. What are antigens, and how do lymphocytes “recognize” them? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.48%3A_Inflammatory_Response_and_Leukocytes.txt |
What are those Y-shaped things floating around the cell?
They are antibodies, which are large proteins. And they signal specific antigens for destruction. It does help that the antigens are usually attached to pathogens.
Humoral Immune Response
There are actually two types of immune responses: humoral and cell-mediated. The humoral immune response involves mainly B cells and takes place in blood and lymph.
B Cell Activation
B cells must be activated by an antigen before they can fight pathogens. This happens in the sequence of events shown in Figure below. First, a B cell encounters its matching antigen and engulfs it. The B cell then displays fragments of the antigen on its surface. This attracts a helper T cell. The helper T cell binds to the B cell at the antigen site and releases cytokines that “tell” or signal the B cell to develop into a plasma cell.
Activation of a B cell must occur before it can respond to pathogens. What role do T cells play in the activation process?
Plasma Cells and Antibody Production
Plasma cells are activated B cells that secrete antibodies. Antibodies are large, Y-shaped proteins that recognize and bind to antigens. Plasma cells are like antibody factories, producing many copies of a single type of antibody. The antibodies travel throughout the body in blood and lymph. Each antibody binds to just one kind of antigen. When it does, it forms an antigen-antibody complex (see Figure below). The complex flags the antigen-bearing cell for destruction by phagocytosis.
An antibody matches only one type of antigen.
Memory Cells
Most plasma cells live for just a few days, but some of them live much longer. They may even survive for the lifetime of the individual. Long-living plasma cells are called memory cells.They retain a “memory” of a specific pathogen long after an infection is over. They help launch a rapid response against the pathogen if it invades the body again in the future.
Summary
• Activated B cells produce antibodies to a particular antigen.
• Memory B cells remain in the body after the immune response is over and provide immunity to pathogens bearing the antigen.
Review
1. How do plasma cells help fight pathogens? Include the role of antibodies in your response.
2. If a disease destroyed a person’s helper T cells, how might this affect the ability to launch an immune response?
3. What are memory cells? What is their role?
13.51: Cell-Mediated Immune Response
Do cells really attack other cells?
They sure do. Depicted here is a group of T cells attacking a cancer cell. When they can, the T cells search out and destroy “bad” cells.
Cell-Mediated Immune Response
In addition to the humoral response, the other type of immune response is the cell-mediated immune response, which involves mainly T cells. It leads to the destruction of cells that are infected with viruses. Some cancer cells are also destroyed in this way. There are several different types of T cells involved in a cell-mediated immune response, including helper, cytotoxic, and regulatory T cells.
T Cell Activation
All three types of T cells must be activated by an antigen before they can fight an infection or cancer. T cell activation is illustrated in Figure below. It begins when a B cell or nonspecific leukocyte engulfs a virus and displays its antigens. When the T cell encounters the matching antigen on a leukocyte, it becomes activated. What happens next depends on which type of T cell it is.
T cell activation requires another leukocyte to engulf a virus and display its antigen.
Helper T Cells
Helper T cells are like the “managers” of the immune response. They secrete cytokines, which activate or control the activities of other lymphocytes. Most helper T cells die out once a pathogen has been cleared from the body, but a few remain as memory cells. These memory cells are ready to produce large numbers of antigen-specific helper T cells like themselves if they are exposed to the same antigen in the future.
Cytotoxic T Cells
Cytotoxic T cells destroy virus-infected cells and some cancer cells. Once activated, a cytotoxic T cell divides rapidly and produces an “army” of cells identical to itself. These cells travel throughout the body “searching” for more cells to destroy. Figure below shows how a cytotoxic T cell destroys a body cell infected with viruses. This T cell releases toxins that form pores in the membrane of the infected cell. This causes the cell to burst, destroying both the cell and the viruses inside it.
A cytotoxic T cell releases toxins that destroy an infected body cell and the viruses it contains.
After an infection has been brought under control, most cytotoxic T cells die off. However, a few remain as memory cells. If the same pathogen enters the body again, the memory cells mount a rapid immune response. They quickly produce many copies of cytotoxic T cells specific to the antigen of that pathogen.
Regulatory T Cells
Regulatory T cells are responsible for ending the cell-mediated immune response after an infection has been curbed. They also suppress T cells that mistakenly react against self antigens. What might happen if these T cells were not suppressed?
Summary
• Activated T cells destroy certain cancer cells and cells infected by viruses.
• Memory T cells remain in the body after the immune response and provide antigen-specific immunity to the virus.
Review
1. Describe one way that cytotoxic T cells destroy cells infected with viruses.
2. What are regulatory T cells?
13.52: Immunity
Is giving shots to young children a good thing?
Many, if not most, children hated going to the doctor, as it often meant getting a shot. Why? The shot actually contained a weakened or dead pathogen. And putting some of that dead pathogen into you was a good thing.
Immunity
Memory B and T cells help protect the body from re-infection by pathogens that infected the body in the past. Being able to resist a pathogen in this way is called immunity. Immunity can be active or passive.
Active Immunity
Active immunity results when an immune response to a pathogen produces memory cells. As long as the memory cells survive, the pathogen will be unable to cause a serious infection in the body. Some memory cells last for a lifetime and confer permanent immunity.
Active immunity can also result from immunization. Immunization is the deliberate exposure of a person to a pathogen in order to provoke an immune response and the formation of memory cells specific to that pathogen. The pathogen is often injected. However, only part of a pathogen, a weakened form of the pathogen, or a dead pathogen is typically used. This causes an immune response without making the immunized person sick. This is how you most likely became immune to measles, mumps, and chicken pox.
Passive Immunity
Passive immunity results when antibodies are transferred to a person who has never been exposed to the pathogen. Passive immunity lasts only as long as the antibodies survive in body fluids. This is usually between a few days and a few months. Passive immunity may be acquired by a fetus through its mother’s blood. It may also be acquired by an infant though the mother’s breast milk. Older children and adults can acquire passive immunity through the injection of antibodies.
Summary
• Immunity is the ability to resist infection by a pathogen.
• Active immunity results from an immune response to a pathogen and the formation of memory cells.
• Passive immunity results from the transfer of antibodies to a person who has not been exposed to the pathogen.
Review
1. What is immunity? What role do memory cells play in immunity?
2. How is active immunity different from passive immunity? Why does active immunity last longer?
3. Explain how immunization prevents a disease such as measles, which is caused by a virus. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.50%3A_Humoral_Immune_Response.txt |
Have you ever started to sneeze and not known why?
A beautiful sea of flowers. A nice sight, unless you have an allergic reaction. It is not uncommon to have reactions to pollen.
Allergies
Your immune system usually protects you from pathogens and keeps you well. However, like any other body system, the immune system itself can develop problems. Sometimes it responds to harmless foreign substances as though they were pathogens. Sometimes it attacks the body’s own cells. Certain diseases can also attack and damage the immune system and interfere with its ability to defend the body.
An allergy is a disease in which the immune system makes an inflammatory response to a harmless antigen. Any antigen that causes an allergy is called an allergen. Allergens may be inhaled or ingested, or they may come into contact with the skin. Two common causes of allergies are shown in Figure below. Inhaling ragweed pollen may cause coughing and sneezing. Skin contact with oils in poison ivy may cause an itchy rash. Other common causes of allergies include dust mites, mold, animal dander, insect stings, latex, and certain food and medications. Symptoms of a common allergy such as pollen can include sneezing, a runny nose, nasal congestion and itchy, watery eyes.
Ragweed and poison ivy are common causes of allergies. Are you allergic to these plants?
The symptoms of allergies can range from mild to severe. Mild allergy symptoms are often treated with antihistamines. These are drugs that reduce or eliminate the effects of the histamines that cause allergy symptoms. Recall that histamines trigger the inflammatory response. The most severe allergic reaction is called anaphylaxis. This is a life-threatening response caused by a massive release of histamines. It requires emergency medical treatment.
Summary
• Allergies occur when the immune system makes an inflammatory response to a harmless antigen.
• An antigen that causes an allergy is called an allergen.
Review
1. What is an allergen? Give two examples.
2. Define anaphylaxis. What causes the symptoms of anaphylaxis?
3. Sometimes people with an allergy get allergy shots. They are injected with tiny amounts of the allergen that triggers the allergic reaction. The shots are repeated at regular intervals, and the amount of allergen that is injected each time gradually increases. How do you think this might help an allergy? Do you think this approach just treats allergy symptoms or might it cure the allergy?
13.54: Autoimmune Diseases
Joint pain. Not an uncommon problem as you grow older. Is it due to normal wear and tear on the joints? Possibly. But rheumatoid arthritis is an autoimmune disease, which means the body's immune system mistakenly attacks healthy tissue.
Autoimmune Diseases
Autoimmune diseases occur when the immune system fails to recognize the body’s own molecules as “self,” or belonging to the person. Instead, it attacks body cells as though they were dangerous pathogens. There are more than 80 known autoimmune diseases. Recall that regulatory T cells help regulate the immune system. When autoimmune disorders occur, these regulatory T cells fail in their function. This results in damage to various organs and tissues. The type of autoimmune disorder depends on the type of body tissue that is affected.
Some relatively common autoimmune diseases are listed in Table below. These diseases cannot be cured, although they can be treated to relieve symptoms and prevent some of the long-term damage they cause.
Name of Disease Tissues Attacked by Immune System Results of Immune System Attack
Rheumatoid arthritis tissues inside joints joint damage and pain
Type 1 diabetes insulin-producing cells of the pancreas inability to produce insulin, highblood sugar
Multiple sclerosis myelin sheaths of central nervous system neurons muscle weakness, pain, fatigue
Systemic lupus erythematosus joints, heart, other organs joint and organ damage and pain
Why does the immune system attack body cells? In some cases, it’s because of exposure to pathogens that have antigens similar to the body’s own molecules. When this happens, the immune system not only attacks the pathogens, it also attacks body cells with the similar molecules.
Summary
• Autoimmune diseases occur when the immune system fails to distinguish self from non-self. As a result, the immune system attacks the body’s own cells.
Review
1. What is an autoimmune disease? Name an example.
2. Rheumatic fever is caused by a virus that has antigens similar to molecules in human heart tissues. When the immune system attacks the virus, it may also attack the heart. What type of immune system disease is rheumatic fever? Explain your answer.
3. Can autoimmune disease be cured?
13.55: Immunodeficiency
Which is stronger?
You or little tiny pathogens? Usually you are. Normally your body can put up a strong defense against enemy pathogens. But what if it can't? What happens if your immune system is "sick"?
Immunodeficiency
Immunodeficiency occurs when the immune system is not working properly. As a result, it cannot fight off pathogens that a normal immune system would be able to resist. Most commonly, immunodeficiency diseases occur when T or B cells (or both) do not work as well as they should, or when your body doesn't produce enough antibodies.
Rarely, the problem is caused by a defective gene. Inherited immunodeficiency disorders that affect B cells include hypogammaglobulinemia, which usually leads to respiratory and gastrointestinal infections, and agammaglobulinemia, which results in severe infections early in life, and is often deadly.
More often, immunodeficiency is acquired during a person’s lifetime. Immunodeficiency may occur for a variety of reasons:
• The immune system naturally becomes less effective as people get older. This is why older people are generally more susceptible to disease.
• The immune system may be damaged by other disorders, such as obesity or drug abuse.
• Certain medications can suppress the immune system. This is an intended effect of drugs given to people with transplanted organs. In many cases, however, it is an unwanted side effect of drugs used to treat other diseases.
• Some pathogens attack and destroy cells of the immune system. An example is the virus known as HIV. It is the most common cause of immunodeficiency in the world today.
Summary
• In an immunodeficiency disease, the immune system does not work normally. As a consequence, it cannot defend the body.
• Review
• What is immunodeficiency?
• List three possible reasons for acquired immunodeficiency. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.53%3A_Allergies.txt |
How long can a person live with HIV?
Years ago, a diagnosis of an HIV infection was a death sentence. Not today. With the proper medical treatment, an individual can live well over 10 or 20 or more productive years with an AIDS diagnosis. One of the most famous individuals with HIV is Earvin “Magic” Johnson, a retired professional basketball player. He was diagnosed in 1991. Over 20 years later, he is still doing well.
HIV and AIDS
Human immunodeficiency virus (HIV) is a virus that attacks the immune system. An example of HIV is shown in Figure below. Many people infected with HIV eventually develop acquired immune deficiency syndrome (AIDS). This may not occur until many years after the virus first enters the body.
HIV is a virus that attacks cells of the immune system.
HIV Transmission
HIV is transmitted, or spread, through direct contact of mucous membranes or body fluids such as blood, semen, or breast milk. As shown in Figure below, transmission of the virus can occur through sexual contact or the use of contaminated hypodermic needles. It can also be transmitted through an infected mother’s blood to her baby during late pregnancy or birth or through breast milk after birth. In the past, HIV was also transmitted through blood transfusions. Because donated blood is now screened for HIV, the virus is no longer transmitted this way. HIV is not spread through saliva, touching or in swimming pools.
HIV may be transmitted in all of the ways shown here. Based on how HIV is transmitted, what can people do to protect themselves from becoming infected? What choices can they make to prevent infection?
HIV and the Immune System
HIV infects and destroys helper T cells. As shown in Figure below, the virus injects its own DNA into a helper T cell and uses the T cell’s “machinery” to make copies of itself. In the process the T cell is destroyed, and the virus copies go on to infect other helper T cells.
This diagram shows how HIV infects and destroys T cells.
HIV is able to evade the immune system and keep destroying T cells. This occurs in two ways:
• The virus frequently mutates and changes its surface antigens. This prevents antigen-specific lymphocytes from developing that could destroy cells infected with the virus.
• The virus uses the plasma membranes of host cells to hide its own antigens. This prevents the host’s immune system from detecting the antigens and destroying infected cells.
As time passes, the number of HIV copies keeps increasing, while the number of helper T cells keeps decreasing. The graph in Figure below shows how the number of T cells typically declines over a period of many years following the initial HIV infection. As the number of T cells decreases, so does the ability of the immune system to defend the body. As a result, an HIV-infected person develops frequent infections. Medicines can slow down the virus but not get rid of it, so there is no cure at present for HIV infections or AIDS. There also is no vaccine to immunize people against HIV infection, but scientists are working to develop one.
It typically takes several years after infection with HIV for the drop in T cells to cripple the immune system. What do you think explains the brief spike in T cells that occurs early in the HIV infection shown here?
AIDS
AIDS is not a single disease but a set of diseases. It results from years of damage to the immune system by HIV. It occurs when helper T cells fall to a very low level and opportunistic diseases occur (see Figure above). Opportunistic diseases are infections and tumors that are rare except in people with immunodeficiency. The diseases take advantage of the opportunity presented by people whose immune systems can’t fight back. Opportunistic diseases are usually the direct cause of death of people with AIDS.
AIDS and HIV were first identified in 1981. Scientists think that the virus originally infected monkeys but then jumped to human populations, probably sometime during the early to mid-1900s. This most likely occurred in West Africa, but the virus soon spread around the world (see Figure below). Since then, HIV has killed more than 25 million people worldwide. The hardest hit countries are in Africa, where medicines to slow down the virus are least available. The worldwide economic toll of HIV and AIDS has also been enormous.
This map shows the number of people in different countries with HIV infections and AIDS in 2008. The rate of spread of the infection is higher Africa than in the U.S., yet the U.S. has a relatively large number of people with HIV infections and AIDS. Why might there be more survivors with HIV infections and AIDS in the U.S. than in Africa?
HIV Research: Beyond the Vaccine
Over the past 15 years, the number of people who die of AIDS each year in the United States has dropped by 70 percent. But AIDS remains a serious public health crisis among low-income African-Americans, particularly women. And in sub-Saharan Africa, the virus killed more than 1.6 million people in 2007 alone. Innovative research approaches could lead to new treatments and possibly a cure for AIDS. HIV/AIDS has been described as a disease of poverty. Individuals with poor access to health care are less likely to see a doctor early on in their HIV infection, and thus they may be more likely to transmit the infection. HIV is now the leading cause of death for African American women between 24 and 35 years old.
For patients who have access to drugs, infection with the virus has ceased to be a death sentence. In 1995, combinations of drugs called highly active anti-retroviral therapy (HAART) were developed. For some patients, drugs can reduce the amount of virus to undetectable levels. But some amount of virus always hides in the body's immune cells and attacks again if the patient stops taking his or her medication. Researchers are working on developing a drug to wipe out this hidden virus, which could mean the end of AIDS.
Summary
• HIV is a virus that attacks cells of the immune system and eventually causes AIDS.
• AIDS is the chief cause of immunodeficiency in the world today.
Review
1. What is the relationship between HIV and AIDS?
2. Identify two ways that HIV can be transmitted.
3. What cells are affected by HIV?
4. What happens to the number of HIV copies and the helper T cells over time in an infected individual?
5. Draw a graph to show the progression of an untreated HIV infection. Include a line that shows how the number of HIV copies changes over time. Include another line that shows how the number of helper T cells changes over time.
6. What are opportunistic diseases? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.56%3A_HIV_and_AIDS.txt |
Would you believe the male reproductive structures are over 100 feet long?
The male reproductive system has two goals: to produce and deliver sperm and to secrete testosterone. Might seem simple. But there are a number of complicated processes and structures - including over 100 feet of tubules - that go into these simple goals.
The male reproductive system has two main functions: (1) to produce sperm, the male gamete, and (2) to release the male sex hormone, testosterone, into the body.
Male Reproductive Structures
The reproductive system in both males and females consists of structures that produce reproductive cells, or gametes, and secrete sex hormones. A gamete is a haploid cell that combines with another haploid gamete during fertilization. Recall that haploid cells have one complete set of chromosomes; in humans that would be 22 autosomes and one sex chromosome.
Sex hormones are chemical messengers that control sexual development and reproduction. The male reproductive system consists of structures that produce male gametes called sperm and secrete the male sex hormone testosterone.
The main structures of the male reproductive system are shown in Figure below. Locate them in the figure as you read about them below.
Male Reproductive Structures. Organs of the male reproductive system include the penis, testes, and epididymis. Several ducts and glands are also part of the system. Do you know the reproductive functions of any of these structures?
Penis
The penis is an external genital organ with a long shaft and enlarged tip called the glans penis. The shaft of the penis contains erectile tissues that can fill with blood and cause an erection. When this occurs, the penis gets bigger and stiffer. The urethra passes through the penis. Sperm pass out of the body through the urethra. (During urination, the urethra carries urine from the bladder.)
Testes
The two testes (singular, testis) are located below the penis. They hang between the thighs in a sac of skin called the scrotum. Each testis contains more than 30 meters (over 90 feet) of tiny, tightly packed tubules called seminiferous tubules. These tubules are the functional units of the testes. They produce sperm and secrete testosterone.
Epididymis
The seminiferous tubules within each testis join to form the epididymis. The epididymis(plural, epididymis) is a coiled tube about 6 meters (20 feet) long lying atop the testis inside the scrotum. The functions of the epididymis are to mature and store sperm until they leave the body.
Ducts and Glands
In addition to these organs, the male reproductive system consists of a series of ducts and glands. Ducts include the vas deferens and ejaculatory ducts. They transport sperm from the epididymis to the urethra in the penis. Glands include the seminal vesicles and prostate gland. They secrete substances that become part of semen.
Semen
Semen is the fluid that carries sperm through the urethra and out of the body. In addition to sperm, it contains secretions from the glands. The secretions control pH and provide sperm with nutrients for energy.
Summary
• The male reproductive system consists of structures that produce sperm and secrete testosterone.
• Male reproductive structures include the penis, testes, and epididymis.
Review
1. What is a gamete?
2. What are sex hormones?
3. What are the two major roles of the male reproductive system?
4. Name two male reproductive organs and identify their functions. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.57%3A_Male_Reproductive_Structures.txt |
What changes happen during puberty?
A lot changes during this time. A boy has to start shaving, his voice deepens, he gets taller, as well as a few other changes.
Sexual Development in Males
The only obvious difference between boys and girls at birth is their reproductive organs. However, even the reproductive organs start out the same in both sexes.
Development Before Birth
In the first several weeks after fertilization, males and females are essentially the same except for their chromosomes. Females have two X chromosomes (XX), and males have an X and aY chromosome (XY). Then, during the second month after fertilization, genes on the Y chromosome of males cause the secretion of testosterone. Testosterone stimulates the reproductive organs to develop into male organs. (Without testosterone, the reproductive organs always develop into female organs.) Although boys have male reproductive organs at birth, the organs are immature and not yet able to produce sperm or secrete testosterone.
Puberty and Its Changes
The reproductive organs grow very slowly during childhood and do not mature until puberty. Puberty is the period during which humans become sexually mature. In the U.S., boys generally begin puberty at about age 12 and complete it at about age 18.
What causes puberty to begin? The hypothalamus in the brain “tells” the pituitary gland to secrete hormones that target the testes. The main pituitary hormone involved is luteinizing hormone (LH). It stimulates the testes to secrete testosterone. Testosterone, in turn, promotes protein synthesis and growth. It brings about most of the physical changes of puberty, some of which are shown in Figure below. In addition to the changes shown below, during puberty male facial hair begins to grow, the shoulders broaden, and the male voice deepens.
Some of the changes that occur in boys during puberty are shown in this figure. Pubic hair grows, and the penis and testes both become larger.
Adolescent Growth Spurt
Another obvious change that occurs during puberty is rapid growth. This is called the adolescent growth spurt. In boys, it is controlled by testosterone. The rate of growth usually starts to increase relatively early in puberty. At its peak rate, growth in height is about 10 centimeters (almost 4 inches) per year in the average male. Growth generally remains rapid for several years. Growth and development of muscles occur toward the end of the growth spurt in height. Muscles may continue to develop and gain strength after growth in height is finished.
Summary
• The male reproductive system forms before birth but does not become capable of reproduction until it matures during puberty.
• Puberty lasts from about ages 12 to 18 years and is controlled by hormones.
Review
1. What happens to a developing baby that lacks testosterone?
2. List three physical changes that occur in males during puberty.
3. Explain how and why boys change so much during puberty.
13.59: Human Sperm
How many sperm does it take to fertilize an egg?
85 million sperm per day are produced...per testicle. That's 170,000,000 every day. This means that a single male may produce more than a quadrillion (1,000,000,000,000) sperm cells in his lifetime! But it only takes one to fertilize an egg.
Production and Delivery of Sperm
A sexually mature male produces an astounding number of sperm—typically, hundreds of millions each day! Sperm production usually continues uninterrupted until death, although the number and quality of sperm decline during later adulthood.
Spermatogenesis
The process of producing mature sperm is called spermatogenesis. Sperm are produced in the seminiferous tubules of the testes and become mature in the epididymis. The entire process takes about 9 to 10 weeks.
If you look inside the seminiferous tubule shown in Figure below, you can see cells in various stages of spermatogenesis. The tubule is lined with spermatogonia, which are diploid, sperm-producing cells. Surrounding the spermatogonia are other cells. Some of these other cells secrete substances to nourish sperm, and some secrete testosterone, which is needed for sperm production.
Seminiferous Tubule. Cross section of a testis and seminiferous tubules.
Spermatogonia lining the seminiferous tubule undergo mitosis to form primary spermatocytes, which are also diploid. The primary spermatocytes undergo the first meiotic division to form secondary spermatocytes, which are haploid. Spermatocytes make up the next layer of cells inside the seminiferous tubule. Finally, the secondary spermatocytes complete meiosis to form spermatids. Spermatids make up a third layer of cells in the tubule.
Sperm Maturation
After spermatids form, they move into the epididymis to mature into sperm, like the one shown in Figure below. The spermatids grow a tail and lose excess cytoplasm from the head. When a sperm is mature, the tail can rotate like a propeller, so the sperm can propel itself forward. Mitochondria in the connecting piece produce the energy (ATP) needed for movement. The head of the mature sperm consists mainly of the nucleus, which carries copies of the father’s chromosomes. The part of the head called the acrosome produces enzymes that help the sperm head penetrate an egg.
Mature Sperm Cell. A mature sperm cell has several structures that help it reach and penetrate an egg. These structures include the tail, mitochondria, and acrosome. How does each structure contribute to the sperm’s function?
Ejaculation
Sperm are released from the body during ejaculation. Ejaculation occurs when muscle contractions propel sperm from the epididymis. The sperm are forced through the ducts and out of the body through the urethra. As sperm travel through the ducts, they mix with fluids from the glands to form semen. Hundreds of millions of sperm are released with each ejaculation.
Summary
• Sperm are produced in the testes in the process of spermatogenesis.
• Sperm mature in the epididymis before being ejaculated from the body through the penis.
Review
1. Outline the process of spermatogenesis. Name the cells involved in the process?
2. Where do sperm mature and how do they leave the body?
3. If a man did not have functioning epididymis, predict how his sperm would be affected. How would this influence his ability to reproduce?
4. How does each mature sperm structure contribute to the sperm’s function? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.58%3A_Male_Reproductive_Development.txt |
Think producing millions of sperm each day is complicated?
If producing millions of sperm each day, as in the male reproductive system, is complicated, that is nothing compared to what must occur in the female reproductive system. This system is controlled by an intricate dance of hormones, cycles, and events.
Female Reproductive Structures
The female reproductive system consists of structures that produce female gametes called eggs and secrete the female sex hormone estrogen. The female reproductive system has several other functions as well:
1. It receives sperm during sexual intercourse.
2. It supports the development of a fetus.
3. It delivers a baby during birth.
4. It breast feeds a baby after birth.
The main structures of the female reproductive system are shown in Figure below. Most of the structures are inside the pelvic region of the body. Locate the structures in the figure as you read about them below.
Female Reproductive Structures. Organs of the female reproductive system include the vagina, uterus, ovaries, and fallopian tubes.
External Structures
The external female reproductive structures are referred to collectively as the vulva. They include the labia (singular, labium), which are the “lips” of the vulva. The labia protect the vagina and urethra, both of which have openings in the vulva.
Vagina
The vagina is a tube-like structure about 9 centimeters (3.5 inches) long. It begins at the vulva and extends upward to the uterus. It has muscular walls lined with mucous membranes. The vagina has two major reproductive functions. It receives sperm during sexual intercourse, and it provides a passageway for a baby to leave the mother’s body during birth.
Uterus
The uterus is a muscular organ shaped like an upside-down pear. It has a thick lining of tissues called the endometrium. The lower, narrower end of the uterus is known as the cervix. The uterus is where a fetus grows and develops until birth. During pregnancy, the uterus can expand greatly to make room for the baby as it grows. During birth, contractions of the muscular walls of the uterus push the baby through the cervix and out of the body.
Ovaries
The two ovaries are small, egg-shaped organs that lie on either side of the uterus. They produce eggs and secrete estrogen. Each egg is located inside a structure called a follicle.Cells in the follicle protect the egg and help it mature.
Fallopian Tubes
Extending from the upper corners of the uterus are the two fallopian tubes. Each tube reaches (but is not attached to) one of the ovaries. The ovary end of the tube has a fringelike structure that moves in waves. The motion sweeps eggs from the ovary into the tube.
Breasts
The breasts are not directly involved in reproduction, but they nourish a baby after birth. Each breast contains mammary glands, which secrete milk. The milk drains into ducts leading to the nipple. A suckling baby squeezes the milk out of the ducts and through the nipple.
Summary
• The female reproductive system consists of structures that produce eggs and secrete female sex hormones. They also provide a site for fertilization and enable the development and birth of a fetus.
• Female reproductive structures include the vagina, uterus, ovaries, and fallopian tubes.
Review
1. List three general functions of the female reproductive system.
2. Describe the uterus, and state its role in reproduction.
3. What are the roles of the ovaries and the follicles?
4. What are the fallopian tubes? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.60%3A_Female_Reproductive_Structures.txt |
What changes happen during puberty?
A lot changes during this time. Girls may become interested in many new things, including the art of makeup.
Sexual Development in Females
Female reproductive organs form before birth. However, as in males, the organs do not mature until puberty.
Development Before Birth
Unlike males, females are not influenced by the male sex hormone testosterone during embryonic development. This is because they lack a Y chromosome. As a result, females do not develop male reproductive organs. By the third month of fetal development, most of the internal female organs have formed. Immature eggs also form in the ovary before birth. Whereas a mature male produces sperm throughout his life, a female produces all the eggs she will ever make before birth.
Changes of Puberty
Like baby boys, baby girls are born with all their reproductive organs present but immature and unable to function. Female reproductive organs also grow very little until puberty. Girls begin puberty a year or two earlier than boys, at an average age of 10 years. Girls also complete puberty sooner than boys, in about 4 years instead of 6.
Puberty in girls starts when the hypothalamus “tells” the pituitary gland to secrete hormones that target the ovaries. Two pituitary hormones are involved: luteinizing hormone (LH) and follicle-stimulating hormone (FSH). These hormones stimulate the ovary to produce estrogen. Estrogen, in turn, promotes growth and other physical changes of puberty. It stimulates growth and development of the internal reproductive organs, breasts, and pubic hair (see Figure below).
Changes in Females During Puberty. Two obvious changes of puberty in girls are growth and development of the breasts and pubic hair. The stages begin around age 10 and are completed by about age 14.
Adolescent Growth Spurt
Like boys, girls also go through an adolescent growth spurt. However, girls typically start their growth spurt a year or two earlier than boys (and therefore a couple of centimeters shorter, on average). Girls also have a shorter growth spurt. For example, they typically reach their adult height by about age 15. In addition, girls generally do not grow as fast as boys do during the growth spurt, even at their peak rate of growth. As a result, females are about 10 centimeters (about 4 inches) shorter, on average, than males by the time they reach their final height.
Menarche
One of the most significant changes in females during puberty is menarche. Menarche is the beginning of menstruation, or monthly periods as the ovaries begin the cyclic release of an egg. In U.S. girls, the average age of menarche is 12.5 years, although there is a lot of variation in this age. The variation may be due to a combination of genetic factors and environmental factors, such as diet.
Summary
• Female reproductive organs form before birth. However, they do not mature until puberty.
Review
1. State two ways that puberty differs in girls and boys.
2. Define menstruation. What is the first menstrual period called?
3. Males and females are quite similar in height when they begin the adolescent growth spurt. Why are females about 10 centimeters shorter than males by adulthood? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.61%3A_Female_Reproductive_Development.txt |
What's amazing about these cells?
Many things. A human egg cell. Just add sperm and you have the necessary ingredients for a new baby. What's amazing about these cells is that they are all produced before the girl is even born. Before the girl is even born, plans for the next generation have begun. And that is the start of an amazing process.
Egg Production
At birth, a female’s ovaries contain all the eggs she will ever produce. However, the eggs do not start to mature until she enters puberty. After menarche, one egg typically matures each month until a woman reaches middle adulthood.
Oogenesis
The process of producing eggs in the ovary is called oogenesis. Eggs, like sperm, are haploid cells, and their production occurs in several steps that involve different types of cells, as shown in Figure below. You can follow the process of oogenesis in the figure as you read about it below.
Oogenesis. Oogenesis begins before birth but is not finished until after puberty. A mature egg forms only if a secondary oocyte is fertilized by a sperm.
Oogenesis begins long before birth when an oogonium with the diploid number of chromosomes undergoes mitosis. It produces a diploid daughter cell called a primary oocyte. The primary oocyte, in turn, starts to go through the first cell division of meiosis (meiosis I). However, it does not complete meiosis until much later. The primary oocyte remains in a resting state, nestled in a tiny, immature follicle until puberty.
Maturation of a Follicle
Beginning in puberty, each month one of the follicles and its primary oocyte starts to mature (also see Figure below). The primary oocyte resumes meiosis and divides to form asecondary oocyte and a smaller cell, called a polar body. Both the secondary oocyte and polar body are haploid cells. The secondary oocyte has most of the cytoplasm from the original cell and is much larger than the polar body.
Maturation of a Follicle and Ovulation. A follicle matures and its primary oocyte (follicle) resumes meiosis to form a secondary oocyte in the secondary follicle. The follicle ruptures and the oocyte leaves the ovary during ovulation. What happens to the ruptured follicle then?
Ovulation and Fertilization
After 12–14 days, when the follicle is mature, it bursts open, releasing the secondary oocyte from the ovary. This event is called ovulation (see Figure above). The follicle, now called acorpus luteum, starts to degenerate, or break down. After the secondary oocyte leaves the ovary, it is swept into the nearby fallopian tube by the waving, fringelike end (see Figure below).
Egg Entering Fallopian Tube. After ovulation, the fringelike end of the fallopian tube sweeps the oocyte inside of the tube, where it begins its journey to the uterus.
If the secondary oocyte is fertilized by a sperm as it is passing through the fallopian tube, it completes meiosis and forms a mature egg and another polar body. (The polar bodies break down and disappear.) If the secondary oocyte is not fertilized, it passes into the uterus as an immature egg and soon disintegrates.
Summary
• Immature eggs form in the ovaries before birth.
• Each month, starting in puberty, one egg matures and is released from the ovary.
• Release of an egg is called ovulation.
Review
1. When does a female begin to produce her eggs?
2. What is a polar body?
3. Describe ovulation.
4. Predict how blockage of both fallopian tubes would affect a woman’s ability to reproduce naturally. Explain your answer.
5. Create a flow chart showing the steps in which an oogonium develops into a mature egg. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.62%3A_Human_Egg_Cells.txt |
What's the most important part of the female menstrual cycle?
A menstrual cycle calendar. A lot of things to keep track of. And for a few very important reasons, it is important to know when a woman is ovulating. But what's the most important part of the female menstrual cycle? That depends on who you ask.
Menstrual Cycle
Ovulation, the release of an egg from an ovary, is part of the menstrual cycle, which typically occurs each month in a sexually mature female unless she is pregnant. Another part of the cycle is the monthly period, or menstruation. Menstruation is the process in which theendometrium of the uterus is shed from the body. The menstrual cycle is controlled by hormones from the hypothalamus, pituitary gland, and ovaries.
Phases of the Menstrual Cycle
As shown in Figure below, the menstrual cycle occurs in several phases. The cycle begins with menstruation. During menstruation, arteries that supply the endometrium of the uterus constrict. As a result, the endometrium breaks down and detaches from the uterus. It passes out of the body through the vagina over a period of several days.
Phases of the Menstrual Cycle. The menstrual cycle occurs in the phases shown here.
After menstruation, the endometrium begins to build up again. At the same time, a follicle starts maturing in an ovary. Ovulation occurs around day 14 of the cycle. After it occurs, the endometrium continues to build up in preparation for a fertilized egg. What happens next depends on whether the egg is fertilized.
If the egg is fertilized, the endometrium will be maintained and help nourish the egg. The ruptured follicle, now called the corpus luteum, will secrete the hormone progesterone. This hormone keeps the endometrium from breaking down. If the egg is not fertilized, the corpus luteum will break down and disappear. Without progesterone, the endometrium will also break down and be shed. A new menstrual cycle thus begins.
Menopause
For most women, menstrual cycles continue until their mid- or late- forties. Then women go through menopause, a period during which their menstrual cycles slow down and eventually stop, generally by their early fifties. After menopause, women can no longer reproduce naturally because their ovaries no longer produce eggs.
Summary
• The menstrual cycle includes events that take place in the ovary, such as ovulation.
• The menstrual cycle also includes changes in the uterus, including menstruation.
• Menopause occurs when menstruation stops occurring, usually in middle adulthood.
Review
1. Define menstruation.
2. What is menopause? When does it occur?
3. What is the corpus luteum?
4. Compare and contrast what happens in the menstrual cycle when the egg is fertilized with what happens when the egg is not fertilized.
5. Make a cycle diagram to represent the main events of the menstrual cycle in both the ovaries and the uterus, including the days when they occur.
13.64: Fertilization
How far does a sperm have to swim?
Sperm swimming to an egg. If fertilization occurs, the egg will have all the "instructions" to grow into a new organism. That one cell will become two, then four, then eight, then sixteen, and on and on and on. And after about 9 months, that one cell will have become a new baby. But it all starts with the sperm swimming to the egg. A sperm cell is about two thousandths of an inch long. And although they are small, they can swim roughly 8 inches in an hour. To reach an egg, they will ultimately they have to swim around 192,000 times their own length.
Cleavage and Implantation
A day or two after an ovary releases an egg, the egg may unite with a sperm. Sperm are deposited in the vagina during sexual intercourse. They propel themselves through the uterus and enter a fallopian tube. This is where fertilization usually takes place.
When a sperm penetrates the egg, it triggers the egg to complete meiosis. The sperm also undergoes changes. Its tail falls off, and its nucleus fuses with the nucleus of the egg. The resulting cell, called a zygote, contains all the chromosomes needed for a new human organism. Half the chromosomes come from the egg and half from the sperm.
Morula and Blastocyst Stages
The zygote spends the next few days traveling down the fallopian tube toward the uterus, where it will take up residence. As it travels, it divides by mitosis several times to form a ball of cells called a morula. The cell divisions are called cleavage. They increase the number of cells but not the overall size of the new organism. As more cell divisions occur, a fluid-filled cavity forms inside the ball of cells. At this stage, the ball of cells is called a blastocyst.
The cells of the blastocyst form an inner cell mass and an outer cell layer, as shown in Figure below. The inner cell mass is called the embryoblast. These cells will soon develop into an embryo. The outer cell layer is called the trophoblast. These cells will develop into other structures needed to support and nourish the embryo.
Blastocyst. The blastocyst consists of an outer layer of cells called the trophoblast and an inner cell mass called the embryoblast. The blastocyst fluid-filled cavity is also known as the blastocoel or blastocoele.
Implantation
The blastocyst continues down the fallopian tube and reaches the uterus about 4 or 5 days after fertilization. When the outer cells of the blastocyst contact cells of the endometrium lining the uterus, the blastocyst embeds in the endometrium. The process of embedding is called implantation. It generally occurs about a week after fertilization.
Summary
• Fertilization is the union of a sperm and egg, resulting in the formation of a zygote.
• The zygote undergoes many cell divisions before it implants in the lining of the uterus.
Review
1. What happens during fertilization? Where does it usually take place?
2. What is implantation? When does it occur?
3. Describe a morula and blastocyst. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.63%3A_Menstrual_Cycle.txt |
At one time, did we really all look alike?
We all start as a single cell and soon grow into an embryo. Notice the remarkable details beginning to form. The eyes, backbone, and limb buds are obvious. Think about the amazing complexity that must be going on inside the embryo, and the tremendous amount of growth and development still to come. So, yes, at one time we all looked similar.
Growth and Development of the Embryo
After implantation occurs, the blastocyst is called an embryo. The embryonic stage lasts through the eighth week following fertilization. During this time, the embryo grows in size and becomes more complex. It develops specialized cells and tissues and starts to form most organs.
Formation of Cell Layers
During the second week after fertilization, cells in the embryo migrate to form three distinct cell layers, called the ectoderm, mesoderm, and endoderm. Each layer will soon develop into different types of cells and tissues, as shown in Figure below.
Cell Layers of the Embryo. The migration of cells into three layers occurs in the 2-week-old embryo. What organs eventually develop from the ectoderm cell layer? Which cell layer develops into muscle tissues?
Differentiation of Cells
A zygote is a single cell. How does a single cell develop into many different types of cells? During the third week after fertilization, the embryo begins to undergo cellular differentiation. Differentiation is the process by which unspecialized cells become specialized. As illustrated in Figure below, differentiation occurs as certain genes are expressed ("switched on") while other genes are switched off. Because of this process, cells develop unique structures and abilities that suit them for their specialized functions.
Cellular differentiation occurs in the 3-week-old embryo.
Organ Formation
After cells differentiate, all the major organs begin to form during the remaining weeks of embryonic development. A few of the developments that occur in the embryo during weeks 4 through 8 are listed in Figure below. As the embryo develops, it also grows in size. By the eighth week of development, the embryo is about 30 millimeters (just over 1 inch) in length. It may also have begun to move.
Embryonic Development (Weeks 4–8). Most organs develop in the embryo during weeks 4 through 8. If the embryo is exposed to toxins during this period, the effects are likely to be very damaging. Can you explain why? (Note: the drawings of the embryos are not to scale.)
Summary
• The embryonic stage begins with implantation.
• An embryo forms three distinct cell layers, and each layer develops into different types of cells and organs.
Review
1. Explain how the embryo forms specialized cells.
2. What organs eventually develop from the ectoderm cell layer?
3. Which cell layer develops into muscle tissues?
4. If the embryo is exposed to toxins during weeks 4 through 8, the effects are likely to be very damaging. Can you explain why?
13.66: Fetus Growth and Development
What characterizes this fetus as human?
The human fetus. Notice the details in the face and hands. Compare this to the human embryo, and the amount of growth and development is truly remarkable.
Growth and Development of the Fetus
From the end of the eighth week until birth, the developing human organism is referred to as a fetus. Birth typically occurs at about 38 weeks after fertilization, so the fetal period generally lasts about 30 weeks. During this time, as outlined in Figure below, the organs complete their development. The fetus also grows rapidly in length and weight.
Fetal Development (Weeks 9–38). Organ development is completed and body size increases dramatically during weeks 9–38.
By the 38th week, the fetus is fully developed and ready to be born (see Figure below). A 38-week fetus normally ranges from 36 to 51 centimeters (14–20 inches) in length and weighs between 2.7 and 4.6 kilograms (about 6–10 pounds).
A 38-week-old fetus has completed development and will soon be born.
Summary
• The fetal stage begins about two months after fertilization and continues until birth.
• During this stage, organs continue to develop, and the fetus grows in size.
Review
1. Make a flow chart of embryonic and fetal development.
2. Why would an embryo be more susceptible than a fetus to damage by toxins? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.65%3A_Embryo_Growth_and_Development.txt |
How does a developing baby breathe?
Or eat? From mom, of course. Shown is a detailed representation of the placenta. And this is where all these interactions occur.
Placenta and Related Structures
The fetus could not grow and develop without oxygen and nutrients from the mother. Wastes from the fetus must also be removed in order for it to survive. The exchange of these substances between the mother and fetus occurs through the placenta.
Placenta
The placenta is a temporary organ that begins to form from the trophoblast layer of cells shortly after implantation. The placenta continues to develop and grow to meet the needs of the growing fetus. A fully developed placenta is made up of a large mass of blood vessels from both the mother and fetus. The maternal and fetal vessels are close together but separated by tiny spaces. This allows the mother’s and fetus’s blood to exchange substances across their capillary walls without the blood actually mixing.
The fetus is connected to the placenta through the umbilical cord, a tube that contains two arteries and a vein. Blood from the fetus enters the placenta through the umbilical arteries, exchanges gases and other substances with the mother’s blood, and travels back to the fetus through the umbilical vein.
The fetus and the placenta. Notice the fetus is attached to the placenta by the umbilical cord, made of two arteries and one vein.
Amniotic Sac and Fluid
Attached to the placenta is the amniotic sac, an enclosed membrane that surrounds and protects the fetus. It contains amniotic fluid, which consists of water and dissolved substances. The fluid allows the fetus to move freely until it grows to fill most of the available space. The fluid also cushions the fetus and helps protect it from injury.
Summary
• The placenta allows nutrients and wastes to be exchanged between the mother and fetus.
• The fetus is connected to the placenta through the umbilical cord.
Review
1. What makes up a placenta?
2. Describe the role of the placenta in fetal development.
3. What is the umbilical cord? What occurs in the umbilical cord?
13.68: Pregnancy and Childbirth
Why is it called labor?
So…the mother carries the developing baby for nine months. We know about the tremendous growth and development of the embryo and fetus. Then comes labor.
Pregnancy and Childbirth
Pregnancy is the carrying of one or more offspring from fertilization until birth. It is the development of an embryo and fetus from the expectant mother’s point of view.
The Mother’s Role
The pregnant mother plays a critical role in the development of the embryo and fetus. She must avoid toxic substances such as alcohol, which can damage the developing offspring. She must also provide all the nutrients and other substances needed for normal growth and development. Most nutrients are needed in greater amounts by a pregnant woman, but some are especially important, including folic acid (vitamin B9), calcium, iron, and omega-3 fatty acids.
Childbirth
Near the time of birth, the amniotic sac breaks in a gush of fluid. Often when this occurs, women say that their "water broke." Labor usually begins within a day of this event. Labor involves contractions of the muscular walls of the uterus, which cause the cervix to dilate. With the mother’s help, the contractions eventually push the fetus out of the uterus and through the vagina. Within seconds of birth, the umbilical cord is cut. Without this connection to the placenta, the baby cannot exchange gases, so carbon dioxide quickly builds up in the baby’s blood. This stimulates the brain to trigger breathing, and the newborn takes its first breath.
Immediately after birth.
Summary
• A pregnant woman should avoid toxins and take in adequate nutrients for normal fetal growth and development.
• During childbirth, contractions of the uterus push the child out of the body.
Review
1. What causes the fetus to be pushed out of the uterus during birth?
2. Why is the umbilical cord cut before a newborn has started to breathe on its own? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.67%3A_Fetal_Development_and_the_Placenta.txt |
What's the main difference between an adorable little baby and a teenager?
This quiet little baby will soon grow into someone who talks and expresses feelings and attitudes. What's the main difference between an adorable little baby and a teenager? Plenty.
From Birth to Adulthood
For the first year after birth, a baby is called an infant. Childhood begins at age two and continues until adolescence. Adolescence is the last stage of life before adulthood.
Infancy
Infancy is the first year of life after birth. Infants are born with a surprising range of abilities. For example, they have well-developed senses of touch, hearing, and smell. They can also communicate their needs by crying. During their first year, they develop many other abilities, including those described below.
By 6 weeks after birth, infants typically start smiling (see Figure below) and making vocal sounds. By 6 months, infants are babbling. They have also learned to sit and are starting to crawl. The deciduous teeth (baby teeth) have started to come in. By 12 months, infants may be saying their first words. They usually can stand with help and may even have started to walk.
A baby’s first smile is an early milestone in infant development.
Infancy is the period of most rapid growth after birth. Growth is even faster during infancy that it is during puberty. By the end of the first year, the average baby is twice as long as it was at birth and three times as heavy.
Childhood
A toddler is a child aged 1 to 3 years. Children of this age are learning to walk, or “toddle.” Growth is still relatively rapid during the toddler years but it has begun to slow down. During the next three years, children achieve many more milestones.
• By age 4, most children can run, climb stairs, and scribble with a crayon. They know many words and use simple sentences. The majority are also toilet trained.
• By age five, children are able to carry on conversations, recognize letters and words, and use a pencil to trace letters. They can usually tie their own shoelaces and may be learning to ride a bicycle, swing a bat, kick a ball and play other games (Figure below).
• By age 6, most children begin losing their deciduous teeth, and their permanent teeth start coming in. They speak fluently and are learning to read and write. They spend more time with peers and develop friendships.
Five year olds can usually play various games.
Older children continue to grow slowly until they start the adolescent growth spurt during puberty. They also continue to develop mentally, emotionally, and socially. Think about all the ways you have changed since you were as young as the child in Figure above. What milestones of development did you achieve during these childhood years?
Puberty
Puberty is the stage of life when a child becomes sexually mature. Puberty begins when the pituitary gland tells the testes to secrete testosterone in boys, and in girls the pituitary gland signals the ovaries to secrete estrogen. Changes that occur during puberty are discussed in the Male Reproductive Development and Female Reproductive Development concepts.
Adolescence
Adolescence is the period of transition between the beginning of puberty and adulthood. Adolescence is also a time of significant mental, emotional, and social changes. For example:
• Adolescents generally develop the ability to think abstractly.
• Adolescents may have mood swings because of surging hormones.
• Adolescents usually try to be more independent from their parents.
• Adolescents typically spend much of their time with peers.
• Adolescents may start to develop intimate relationships.
Summary
• Growth and development are most rapid during infancy and slower throughout the rest of childhood until adolescence.
• Adolescence involves mental, emotional, and social changes in addition to the physical changes of puberty.
• Review
• Distinguish infancy from childhood.
• What is a toddler?
• List two abilities of an infant.
• Describe three changes associated with adolescence.
• Think about all the ways you have changed since you were a five year old child. List milestones of development you have achieved since then. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.69%3A_Development_from_Birth_to_Adulthood.txt |
Does getting older have to be a bad thing?
Being older doesn't necessarily mean being unable to do things and not enjoy life. These seniors look as if they thoroughly enjoy life. And some would say that life begins after all the children have moved out of the house.
Adulthood and Aging
Adulthood does not have a definite starting point. A person may be physically mature by age 16 or 17 but not defined as an adult by law until older ages. In the U.S., you can’t join the armed forces or vote until age 18. You can’t buy or use alcohol or take on many legal and financial responsibilities until age 21.
The video below, 21 Years, is a daily video pictorial of the aging process, from birth to 21 years. Over 7,500 images of the same person have been condensed in a little over 6 minutes.
Early Adulthood
Early adulthood coincides with the 20s and early 30s. During early adulthood, people generally form intimate relationships, both in friendship and love. Many people become engaged or marry during this time. Often they are completing their education and becoming established in a career. Health problems in young adults tend to be minor. The most common causes of death are homicides, car crashes, and suicides.
Middle Adulthood
Middle adulthood lasts from the mid-30s to the mid-60s. During this stage of life, many people raise a family and strive to attain career goals. They start showing physical signs of aging, such as wrinkles and gray hair. Typically, vision, strength and reaction time start declining. Diseases such as type 2 diabetes, cardiovascular or heart disease, and cancer are often diagnosed during this stage of life. These diseases are also the chief causes of death in middle adulthood.
Heart Disease
Heart disease is the number one killer of Americans, and one of the main killers of people the world over. A common cause of heart disease is arteriosclerosis. This is the stiffening or hardening of the arteries that happens, in part, because of growing older. Atherosclerosis, which is the buildup of fatty deposits in the arteries, is another cause of cardiovascular disease. When fat accumulates along the walls of arteries, there is less space for blood to flow. This makes it harder for blood to get to all the parts of the body that need it, including the heart itself. The accumulation of fatty deposits, or plaque, can eventually lead to a heart attack or stroke.
Other changes to the heart occur during middle adulthood. For example, to help the heart pump blood through stiffer blood vessels, some parts of the heart wall thicken. The size of the four chambers of the heart also change, as do the valves between the chambers. The resting heart rate does not change as you age, but the heart cannot beat as fast when you are physically active or stressed, as it did when you were younger.
Both genetic and lifestyle choices lead to heart disease. Though you cannot change your genetic background, there are things you can do to slow or prevent the onset of heart disease, especially as you grow older.
• try to be more physically active,
• if you smoke, quit,
• follow a heart healthy diet,
• keep a healthy weight.
Old Age
Old age begins in the mid-60s and lasts until the end of life. Many people over 65 have retired from work, freeing up their time for hobbies, grandchildren, and other interests. Stamina, strength, reflex time, and the senses all decline during old age, and the number of brain cells decreases as well. The immune system becomes less efficient, increasing the risk of serious illnesses such as cancer and pneumonia. Diseases such as Alzheimer’s disease that cause loss of mental function also become more common.
Causes of Aging
Why do we decline in all these ways as we age? Generally, it’s because cells stop dividing and die. There are at least two reasons why cells stop dividing:
1. Cells are programmed to divide only a set number of times.
2. Mutations accumulate in DNA, and cells with damaged DNA may not divide.
Summary
• During early adulthood, people form intimate relationships and start careers.
• Serious health problems start showing up in middle adulthood and old age.
• Aging occurs as cells lose their ability to divide.
Review
1. When does adulthood begin?
2. What are the most common causes of death associated with early adulthood?
3. What diseases are often diagnosed during middle adulthood?
4. Aging is associated with the death of cells. Give two reasons why cells die.
5. List three ways to help prevent heart disease as a person ages. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.70%3A_Adulthood_and_Aging.txt |
What does “safe sex” truly mean?
“Safe Sex.” The thought of a sexually transmitted infection should be enough to make you think about and believe in this saying.
Understanding Sexually Transmitted Infections
A shocking statistic made headlines in 2008. A recent study had found that one in four teen girls in the U.S. had a sexually transmitted infection. A sexually transmitted infection (STI)(also known as a sexually transmitted disease, or STD) is an infection caused by a pathogen that spreads mainly through sexual contact. Worldwide, a million people a day become infected with STIs. The majority of them are under the age of 25.
To be considered an STI, an infection must have only a small chance of spreading naturally in ways other than sexual contact. Some infections that can spread through sexual contact, such as the common cold, spread more commonly by other means. These infections are not considered STIs.
Pathogens that Cause STIs
STIs may be caused by several different types of pathogens, including protozoa, insects, bacteria, and viruses. For example:
• Protozoa cause an STI called trichomoniasis. The pathogen infects the vagina in females and the urethra in males, causing symptoms such as burning and itching. Trichomoniasis is common in young people.
• Pubic lice, like the one in Figure below, are insect parasites that are transmitted sexually. They suck the blood of their host and irritate the skin in the pubic area.
Pubic lice like this one are only about as big as the head of a pin.
Most STIs are caused by bacteria or viruses. Bacterial STIs can be cured with antibiotics. Viral STIs cannot be cured. Once you are infected with a viral STI, you are likely to be infected for life.
How STIs Spread
Most of the pathogens that cause STIs enter the body through mucous membranes of the reproductive organs. All sexual behaviors that involve contact between mucous membranes put a person at risk for infection. This includes vaginal, anal, and oral sexual behaviors. Many STIs can also be transmitted through body fluids such as blood, semen, and breast milk. Therefore, behaviors such as sharing injection or tattoo needles is another way these STIs can spread.
Why are STIs common in young people? One reason is that young people often take risks. They may think, “It can’t happen to me.” They also may not know how STIs are spread, so they don’t know how to protect themselves. In addition, young people may have multiple sexual partners.
Preventing STIs
The only completely effective way to prevent infection with STIs is to avoid sexual contact and other risky behaviors. Using condoms can lower the risk of becoming infected with STIs during some types of sexual activity. However, condoms are not foolproof. Pathogens may be present on areas of the body not covered by condoms. Condoms can also break or be used incorrectly.
Summary
• STIs are diseases caused by pathogens that spread through sexual contact.
• Abstinence from sexual activity and other risk behaviors is the only completely effective way to prevent the spread of STIs.
Review
1. Describe how STIs spread.
2. What causes most STIs?
3. Can bacterial STIs be cured? If so, how? What about viral STIs?
4. What is the only completely effective way to prevent a sexually transmitted infection?
5. Assume you are preparing a public service announcement (PSA) to explain to teens how and why to avoid STIs. List three facts you think it would be important to include for an informative and persuasive PSA.
Explore More
Use this resource to answer the questions that follow.
1. List five facts about STDs.
2. List five myths about STDs. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.71%3A_Sexually_Transmitted_Infections.txt |
Single-celled organisms. Can they be dangerous?
These are chlamydia. Innocent-looking single-celled organisms. But these bacteria can lead to painful and devastating consequences.
Chlamydia trachomatis inclusion bodies (brown) in a McCoy cell culture. (public domain; CDC-PHIL)
Bacterial STIs
Many STIs are caused by bacteria. Some of the most common bacterial STIs are chlamydia, gonorrhea, and syphilis. Bacterial STIs can be cured with antibiotics.
Chlamydia
Chlamydia is the most common STI in the United States. As shown in the graph in Figure below, females are much more likely than males to develop chlamydia. Like most STIs, rates of chlamydia are highest in teens and young adults.
This graph shows the number of cases of chlamydia per 100,000 people in the U.S. in 2004. Which age group had the highest rates? How much higher were the rates for females aged 15–19 than for males in the same age group?
Symptoms of chlamydia may include a burning sensation during urination and a discharge from the vagina or penis. Chlamydia can be cured with antibiotics, but often there are no symptoms, so people do not seek treatment. Untreated chlamydia can lead to more serious problems, such as pelvic inflammatory disease (PID). This is an infection of the uterus, fallopian tubes, and/or ovaries. It can scar a woman’s reproductive organs and make it difficult for her to become pregnant.
Gonorrhea
Gonorrhea is another common STI. Symptoms of gonorrhea may include painful urination and discharge from the vagina or penis. Gonorrhea usually can be cured with antibiotics, although the bacteria have developed resistance to many of the drugs. Gonorrhea infections may not cause symptoms, especially in females, so they often go untreated. Untreated gonorrhea can lead to PID in females. It can lead to inflammation of the reproductive organs in males as well.
Syphilis
Syphilis is less common than chlamydia or gonorrhea but more serious if untreated. Early symptoms of syphilis infection include a small sore on or near the genitals. The sore is painless and heals on its own, so it may go unnoticed. If treated early, most cases of syphilis can be cured with antibiotics. Untreated syphilis can cause serious damage to the heart, brain, and other organs. It may eventually lead to death.
Summary
• Bacterial STIs include chlamydia, gonorrhea, and syphilis.
• Bacterial STIs usually can be cured with antibiotics.
Review
1. Identify three common STIs that are caused by bacteria.
2. Often, STIs do not cause symptoms. Why is it important to detect and treat STIs even when they do not cause symptoms? Give an example of the consequences of an untreated STI.
3. Which age group had the highest rates of chlamydia? How much higher were the rates for females aged 15–19 than for males in the same age group?
4. Explain how a lack of symptoms might contribute to the spread of STIs.
13.73: Viral Sexually Transmitted Infections
How long does a viral STI last?
This is the Human Papilloma Virus, which causes a viral STI. Viral STIs can be especially dangerous, as they cannot be cured. Once you get one, it's yours for life. And also, it's the person's you give it to.
Viral STIs
STIs caused by viruses include genital herpes, hepatitis B, genital warts, and HIV/AIDS. Whereas bacterial STIs can usually be cured with antibiotics, viral STIs cannot be cured.
Genital Herpes
Genital herpes is an STI caused by a herpes virus. In the United States, as many as one in four people are infected with the virus. Symptoms of genital herpes include painful blisters on the genitals (see Figure below). The blisters usually go away on their own, but the virus remains in the body, causing periodic outbreaks of blisters throughout life. Outbreaks may be triggered by stress, illness, or other factors. A person with genital herpes is most likely to transmit the virus during an outbreak.
Blisters like these on the genitals are a sign of genital herpes.
Hepatitis B
Hepatitis B is inflammation of the liver caused by infection with the hepatitis B virus. In many people, the immune system quickly eliminates the virus from the body. However, in a small percentage of people, the virus remains in the body and continues to cause illness. It may eventually damage the liver and increase the risk of liver cancer, which is usually fatal.
Genital Warts and Cervical Cancer
Infections with the human papillomavirus (HPV) are very common. HPV may cause genital warts, which are small, rough growths on the genitals. It may also cause cancer of the cervix in females. A simple test, called a Pap test, can detect cervical cancer. If the cancer is detected early, it usually can be cured with surgery. There is also a vaccine , GARDASIL, to prevent infection with HPV. The vaccine is recommended for females aged 11 to 26 years.
Summary
• Viral STIs include genital herpes, hepatitis B, genital warts, and cervical cancer.
• Viral STIs cannot be cured, but some of them can be prevented with vaccines.
Review
1. Name and describe an STI caused by a virus.
2. Discuss treatment for the human papillomavirus.
3. Compare and contrast bacterial and viral STIs with regard to their treatment, cure, and prevention. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.72%3A_Bacterial_Sexually_Transmitted.txt |
What is integumentary?
Because the organs of the integumentary system are external to the body, you may think of them as little more than “accessories,” like clothing or jewelry. But the organs of the integumentary system serve important biological functions. They provide a protective covering for the body and help the body maintain homeostasis.
The Skin
The skin is the major organ of the integumentary system, which also includes the nails and hair. In fact, the skin is the body’s largest organ, and a remarkable one at that. Consider these skin facts. The average square inch (6.5 cm2) of skin has 20 blood vessels, 650 sweat glands, and more than a thousand nerve endings. It also has an incredible 60,000 pigment-producingcells. All of these structures are packed into a stack of cells that is just 2 mm thick, or about as thick as the cover of a book.
Although the skin is thin, it consists of two distinct layers, called the epidermis and the dermis. These layers are shown in Figure below.
Layers of Human Skin. The outer layer of the skin is the epidermis, and the inner layer is the dermis. Most skin structures originate in the dermis.
Epidermis
The epidermis is the outer layer of skin, consisting of epithelial cells and little else (see Figure below). For example, there are no nerve endings or blood vessels in the epidermis. The innermost cells of the epidermis are continuously dividing through mitosis to form new cells. The newly formed cells move up through the epidermis toward the skin surface, while producing a tough, fibrous protein called keratin. The cells become filled with keratin and die by the time they reach the surface, where they form a protective, waterproof layer called thestratum corneum. The dead cells are gradually shed from the surface of the skin and replaced by other cells.
Cell Layers of the Epidermis. The epidermis consists mainly of epithelial cells.
The epidermis also contains melanocytes, which are cells that produce melanin. Melanin is the brownish pigment that gives skin much of its color. Everyone has about the same number of melanocytes, but the melanocytes of people with darker skin produce more melanin. The amount of melanin produced is determined by heredity and exposure to UV light, which increases melanin output. Exposure to UV light also stimulates the skin to produce vitamin D. Because melanin blocks UV light from penetrating the skin, people with darker skin may be at greater risk of vitamin D deficiency.
Dermis
The dermis is the lower layer of the skin, located directly beneath the epidermis (see Figure below). It is made of tough connective tissue and attached to the epidermis by collagen fibers. The dermis contains blood vessels and nerve endings. Because of the nerve endings, skin can feel touch, pressure, heat, cold, and pain. The dermis also contains hair follicles and two types of glands.
• Hair follicles are the structures where hairs originate. Hairs grow out of follicles, pass through the epidermis, and exit at the surface of the skin.
• Sebaceous glands produce an oily substance called sebum. Sebum is secreted into hair follicles and makes its way to the skin surface. It waterproofs the hair and skin and helps prevent them from drying out. Sebum also has antibacterial properties, so it inhibits the growth of microorganisms on the skin.
• Sweat glands produce the salty fluid called sweat, which contains excess water, salts, and other waste products. The glands have ducts that pass through the epidermis and open to the surface through pores in the skin.
Structures of the Dermis. The dermis contains most of the structures found in skin.
Functions of the Skin
The skin has multiple roles in the body. Many of these roles are related to homeostasis. The skin’s main functions are preventing water loss from the body and serving as a barrier to the entry of microorganisms. In addition, melanin in the skin blocks UV light and protects deeper layers from its damaging effects.
The skin also helps regulate body temperature. When the body is too warm, sweat is released by the sweat glands and spreads over the skin surface. As the sweat evaporates, it cools the body. Blood vessels in the skin also dilate, or widen, when the body is too warm. This allows more blood to flow through the skin, bringing body heat to the surface, where it radiates into the environment. When the body is too cool, sweat glands stop producing sweat, and blood vessels in the skin constrict, or narrow, thus conserving body heat.
Skin Problems
In part because it is exposed to the environment, the skin is prone to injury and other problems. Two common problems of the skin are acne and skin cancer (see Figure below).
• Acne is a condition in which red bumps called pimples form on the skin due to a bacterial infection. It affects more than 85 percent of teens and may continue into adulthood. The underlying cause of acne is excessive secretion of sebum, which plugs hair follicles and makes them good breeding grounds for bacteria.
• Skin cancer is a disease in which skin cells grow out of control. It is caused mainly by excessive exposure to UV light. People with lighter skin are at greater risk of developing skin cancer because they have less melanin to block harmful UV radiation. The best way to prevent skin cancer is to avoid UV exposure by using sunscreen and wearing protective clothing.
ABCDs of Skin Cancer. A brown spot on the skin is likely to be a harmless mole, but it could be a sign of skin cancer. Unlike moles, skin cancers are generally asymmetrical, have irregular borders, may be very dark in color, and may have a relatively great diameter.
Summary
• The skin consists of two layers: the epidermis, which contains mainly epithelial cells, and the dermis, which contains most of skin’s other structures, including blood vessels, nerve endings, hair follicles, and glands.
• Skin protects the body from injury, water loss, and microorganisms. It also plays a major role in maintaining a stable body temperature.
• Common skin problems include acne and skin cancer.
Review
1. What organs make up the integumentary system?
2. Describe how new epidermal cells form, develop, and are shed from the body.
3. What is keratin?
4. What is the function of the stratum corneum?
5. What is acne? What causes acne?
6. Assume that you get a paper cut, but it doesn’t bleed. How deep is the cut? How do you know?
7. Skin cancer has been increasing over recent decades. What could explain this? (Hint: What is the main cause of skin cancer?)
8. Explain how melanin is related to skin color, vitamin D production, and skin cancer.
9. Explain how the skin helps the body maintain a stable temperature. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/13%3A_Human_Biology/13.74%3A_Skin.txt |
• 1.1: The Science of Life
Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized following a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere.
• 1.2: The Nature of Science
Biology is the science that studies living organisms and their interactions with one another and their environments. Science attempts to describe and understand the nature of the universe in whole or in part. Science has many fields; those fields related to the physical world and its phenomena are considered natural sciences. A hypothesis is a tentative explanation for an observation.
• 1.3: An Example of Scientific Inquiry- Darwin and Evolution
• 1.4: Core Concepts in Biology
01: The Science of Biology
Biology is the science that studies life. What exactly is life? This may sound like a silly question with an obvious answer, but it is not easy to define life. For example, a branch of biology called virology studies viruses, which exhibit some of the characteristics of living entities but lack others. It turns out that although viruses can attack living organisms, cause diseases, and even reproduce, they do not meet the criteria that biologists use to define life.
From its earliest beginnings, biology has wrestled with four questions: What are the shared properties that make something “alive”? How do those various living things function? When faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? And, finally—what biologists ultimately seek to understand—how did this diversity arise and how is it continuing? As new organisms are discovered every day, biologists continue to seek answers to these and other questions.
Properties of Life
All groups of living organisms share several key characteristics or functions: order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing. When viewed together, these eight characteristics serve to define life.
Order
Organisms are highly organized structures that consist of one or more cells. Even very simple, single-celled organisms are remarkably complex. Inside each cell, atoms make up molecules. These in turn make up cell components or organelles. Multicellular organisms, which may consist of millions of individual cells, have an advantage over single-celled organisms in that their cells can be specialized to perform specific functions, and even sacrificed in certain situations for the good of the organism as a whole. How these specialized cells come together to form organs such as the heart, lung, or skin in organisms like the toad shown in Figure \(1\) will be discussed later.
Sensitivity or Response to Stimuli
Organisms respond to diverse stimuli. For example, plants can bend toward a source of light or respond to touch (Figure \(2\)). Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phototaxis). Movement toward a stimulus is considered a positive response, while movement away from a stimulus is considered a negative response.
CONCEPT IN ACTION
Watch this video to see how the sensitive plant responds to a touch stimulus.
Reproduction
Single-celled organisms reproduce by first duplicating their DNA, which is the genetic material, and then dividing it equally as the cell prepares to divide to form two new cells. Many multicellular organisms (those made up of more than one cell) produce specialized reproductive cells that will form new individuals. When reproduction occurs, DNA containing genes is passed along to an organism’s offspring. These genes are the reason that the offspring will belong to the same species and will have characteristics similar to the parent, such as fur color and blood type.
Adaptation
All living organisms exhibit a “fit” to their environment. Biologists refer to this fit as adaptation and it is a consequence of evolution by natural selection, which operates in every lineage of reproducing organisms. Examples of adaptations are diverse and unique, from heat-resistant Archaea that live in boiling hot springs to the tongue length of a nectar-feeding moth that matches the size of the flower from which it feeds. All adaptations enhance the reproductive potential of the individual exhibiting them, including their ability to survive to reproduce. Adaptations are not constant. As an environment changes, natural selection causes the characteristics of the individuals in a population to track those changes.
Growth and Development
Organisms grow and develop according to specific instructions coded for by their genes. These genes provide instructions that will direct cellular growth and development, ensuring that a species’ young (Figure \(3\)) will grow up to exhibit many of the same characteristics as its parents.
Regulation
Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, such as the transport of nutrients, response to stimuli, and coping with environmental stresses. For example, organ systems such as the digestive or circulatory systems perform specific functions like carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body.
Homeostasis
To function properly, cells require appropriate conditions such as proper temperature, pH, and concentrations of diverse chemicals. These conditions may, however, change from one moment to the next. Organisms are able to maintain internal conditions within a narrow range almost constantly, despite environmental changes, through a process called homeostasis or “steady state”—the ability of an organism to maintain constant internal conditions. For example, many organisms regulate their body temperature in a process known as thermoregulation. Organisms that live in cold climates, such as the polar bear (Figure \(4\)), have body structures that help them withstand low temperatures and conserve body heat. In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat.
Energy Processing
All organisms (such as the California condor shown in Figure \(5\)) use a source of energy for their metabolic activities. Some organisms capture energy from the Sun and convert it into chemical energy in food; others use chemical energy from molecules they take in.
Levels of Organization of Living Things
Living things are highly organized and structured, following a hierarchy on a scale from small to large. The atom is the smallest and most fundamental unit of matter. It consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical structure consisting of at least two atoms held together by a chemical bond. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by combining smaller units called monomers. An example of a macromolecule is deoxyribonucleic acid (DNA) (Figure \(6\)), which contains the instructions for the functioning of the organism that contains it.
CONCEPT IN ACTION
To see an animation of this DNA molecule, click here.
Some cells contain aggregates of macromolecules surrounded by membranes; these are called organelles. Organelles are small structures that exist within cells and perform specialized functions. All living things are made of cells; the cellitself is the smallest fundamental unit of structure and function in living organisms. (This requirement is why viruses are not considered living: they are not made of cells. To make new viruses, they have to invade and hijack a living cell; only then can they obtain the materials they need to reproduce.) Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic. Prokaryotes are single-celled organisms that lack organelles surrounded by a membrane and do not have nuclei surrounded by nuclear membranes; in contrast, the cells of eukaryotes do have membrane-bound organelles and nuclei.
In most multicellular organisms, cells combine to make tissues, which are groups of similar cells carrying out the same function. Organs are collections of tissues grouped together based on a common function. Organs are present not only in animals but also in plants. An organ system is a higher level of organization that consists of functionally related organs. For example vertebrate animals have many organ systems, such as the circulatory system that transports blood throughout the body and to and from the lungs; it includes organs such as the heart and blood vessels. Organisms are individual living entities. For example, each tree in a forest is an organism. Single-celled prokaryotes and single-celled eukaryotes are also considered organisms and are typically referred to as microorganisms.
ART CONNECTION
Which of the following statements is false?
1. Tissues exist within organs which exist within organ systems.
2. Communities exist within populations which exist within ecosystems.
3. Organelles exist within cells which exist within tissues.
4. Communities exist within ecosystems which exist in the biosphere.
Answer
B
All the individuals of a species living within a specific area are collectively called a population. For example, a forest may include many white pine trees. All of these pine trees represent the population of white pine trees in this forest. Different populations may live in the same specific area. For example, the forest with the pine trees includes populations of flowering plants and also insects and microbial populations. A community is the set of populations inhabiting a particular area. For instance, all of the trees, flowers, insects, and other populations in a forest form the forest’s community. The forest itself is an ecosystem. An ecosystem consists of all the living things in a particular area together with the abiotic, or non-living, parts of that environment such as nitrogen in the soil or rainwater. At the highest level of organization (Figure \(7\)), the biosphere is the collection of all ecosystems, and it represents the zones of life on Earth. It includes land, water, and portions of the atmosphere.
The Diversity of Life
The science of biology is very broad in scope because there is a tremendous diversity of life on Earth. The source of this diversity is evolution, the process of gradual change during which new species arise from older species. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems.
In the 18th century, a scientist named Carl Linnaeus first proposed organizing the known species of organisms into a hierarchical taxonomy. In this system, species that are most similar to each other are put together within a grouping known as a genus. Furthermore, similar genera (the plural of genus) are put together within a family. This grouping continues until all organisms are collected together into groups at the highest level. The current taxonomic system now has eight levels in its hierarchy, from lowest to highest, they are: species, genus, family, order, class, phylum, kingdom, domain. Thus species are grouped within genera, genera are grouped within families, families are grouped within orders, and so on (Figure \(8\)).
The highest level, domain, is a relatively new addition to the system since the 1990s. Scientists now recognize three domains of life, the Eukarya, the Archaea, and the Bacteria. The domain Eukarya contains organisms that have cells with nuclei. It includes the kingdoms of fungi, plants, animals, and several kingdoms of protists. The Archaea, are single-celled organisms without nuclei and include many extremophiles that live in harsh environments like hot springs. The Bacteria are another quite different group of single-celled organisms without nuclei (Figure \(9\)). Both the Archaea and the Bacteria are prokaryotes, an informal name for cells without nuclei. The recognition in the 1990s that certain “bacteria,” now known as the Archaea, were as different genetically and biochemically from other bacterial cells as they were from eukaryotes, motivated the recommendation to divide life into three domains. This dramatic change in our knowledge of the tree of life demonstrates that classifications are not permanent and will change when new information becomes available.
In addition to the hierarchical taxonomic system, Linnaeus was the first to name organisms using two unique names, now called the binomial naming system. Before Linnaeus, the use of common names to refer to organisms caused confusion because there were regional differences in these common names. Binomial names consist of the genus name (which is capitalized) and the species name (all lower-case). Both names are set in italics when they are printed. Every species is given a unique binomial which is recognized the world over, so that a scientist in any location can know which organism is being referred to. For example, the North American blue jay is known uniquely as Cyanocitta cristata. Our own species is Homo sapiens.
EVOLUTION IN ACTION: Carl Woese and the Phylogenetic Tree
The evolutionary relationships of various life forms on Earth can be summarized in a phylogenetic tree. A phylogenetic tree is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. A phylogenetic tree is composed of branch points, or nodes, and branches. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length of each branch can be considered as estimates of relative time.
In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. Woese proposed the domain as a new taxonomic level and Archaea as a new domain, to reflect the new phylogenetic tree (Figure \(10\)). Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape). Various genes were used in phylogenetic studies. Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, found in some slightly altered form in every organism, conserved (meaning that these genes have remained only slightly changed throughout evolution), and of an appropriate length.
Branches of Biological Study
The scope of biology is broad and therefore contains many branches and sub disciplines. Biologists may pursue one of those sub disciplines and work in a more focused field. For instance, molecular biology studies biological processes at the molecular level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. Microbiology is the study of the structure and function of microorganisms. It is quite a broad branch itself, and depending on the subject of study, there are also microbial physiologists, ecologists, and geneticists, among others.
Another field of biological study, neurobiology, studies the biology of the nervous system, and although it is considered a branch of biology, it is also recognized as an interdisciplinary field of study known as neuroscience. Because of its interdisciplinary nature, this sub discipline studies different functions of the nervous system using molecular, cellular, developmental, medical, and computational approaches.
Paleontology, another branch of biology, uses fossils to study life’s history (Figure \(11\)). Zoology and botany are the study of animals and plants, respectively. Biologists can also specialize as biotechnologists, ecologists, or physiologists, to name just a few areas. Biotechnologists apply the knowledge of biology to create useful products. Ecologists study the interactions of organisms in their environments. Physiologists study the workings of cells, tissues and organs. This is just a small sample of the many fields that biologists can pursue. From our own bodies to the world we live in, discoveries in biology can affect us in very direct and important ways. We depend on these discoveries for our health, our food sources, and the benefits provided by our ecosystem. Because of this, knowledge of biology can benefit us in making decisions in our day-to-day lives.
The development of technology in the twentieth century that continues today, particularly the technology to describe and manipulate the genetic material, DNA, has transformed biology. This transformation will allow biologists to continue to understand the history of life in greater detail, how the human body works, our human origins, and how humans can survive as a species on this planet despite the stresses caused by our increasing numbers. Biologists continue to decipher huge mysteries about life suggesting that we have only begun to understand life on the planet, its history, and our relationship to it. For this and other reasons, the knowledge of biology gained through this textbook and other printed and electronic media should be a benefit in whichever field you enter.
CAREERS IN ACTION: Forensic Scientist
Forensic science is the application of science to answer questions related to the law. Biologists as well as chemists and biochemists can be forensic scientists. Forensic scientists provide scientific evidence for use in courts, and their job involves examining trace material associated with crimes. Interest in forensic science has increased in the last few years, possibly because of popular television shows that feature forensic scientists on the job. Also, the development of molecular techniques and the establishment of DNA databases have updated the types of work that forensic scientists can do. Their job activities are primarily related to crimes against people such as murder, rape, and assault. Their work involves analyzing samples such as hair, blood, and other body fluids and also processing DNA (Figure \(12\)) found in many different environments and materials. Forensic scientists also analyze other biological evidence left at crime scenes, such as insect parts or pollen grains. Students who want to pursue careers in forensic science will most likely be required to take chemistry and biology courses as well as some intensive math courses.
Summary
Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized following a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere. Evolution is the source of the tremendous biological diversity on Earth today. A diagram called a phylogenetic tree can be used to show evolutionary relationships among organisms. Biology is very broad and includes many branches and sub disciplines. Examples include molecular biology, microbiology, neurobiology, zoology, and botany, among others.
Glossary
atom
a basic unit of matter that cannot be broken down by normal chemical reactions
biology
the study of living organisms and their interactions with one another and their environments
biosphere
a collection of all ecosystems on Earth
cell
the smallest fundamental unit of structure and function in living things
community
a set of populations inhabiting a particular area
ecosystem
all living things in a particular area together with the abiotic, nonliving parts of that environment
eukaryote
an organism with cells that have nuclei and membrane-bound organelles
evolution
the process of gradual change in a population that can also lead to new species arising from older species
homeostasis
the ability of an organism to maintain constant internal conditions
macromolecule
a large molecule typically formed by the joining of smaller molecules
molecule
a chemical structure consisting of at least two atoms held together by a chemical bond
organ
a structure formed of tissues operating together to perform a common function
organ system
the higher level of organization that consists of functionally related organs
organelle
a membrane-bound compartment or sac within a cell
organism
an individual living entity
phylogenetic tree
a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both
population
all individuals within a species living within a specific area
prokaryote
a unicellular organism that lacks a nucleus or any other membrane-bound organelle
tissue
a group of similar cells carrying out the same function | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/01%3A_The_Science_of_Biology/1.01%3A_The_Science_of_Life.txt |
Like geology, physics, and chemistry, biology is a science that gathers knowledge about the natural world. Specifically, biology is the study of life. The discoveries of biology are made by a community of researchers who work individually and together using agreed-on methods. In this sense, biology, like all sciences is a social enterprise like politics or the arts.
The methods of science include careful observation, record keeping, logical and mathematical reasoning, experimentation, and submitting conclusions to the scrutiny of others. Science also requires considerable imagination and creativity; a well-designed experiment is commonly described as elegant, or beautiful. Like politics, science has considerable practical implications and some science is dedicated to practical applications, such as the prevention of disease (Figure \(2\)). Other science proceeds largely motivated by curiosity. Whatever its goal, there is no doubt that science, including biology, has transformed human existence and will continue to do so.
The Nature of Science
Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? Science (from the Latin scientia, meaning "knowledge") can be defined as knowledge about the natural world.
Science is a very specific way of learning, or knowing, about the world. The history of the past 500 years demonstrates that science is a very powerful way of knowing about the world; it is largely responsible for the technological revolutions that have taken place during this time. There are however, areas of knowledge and human experience that the methods of science cannot be applied to. These include such things as answering purely moral questions, aesthetic questions, or what can be generally categorized as spiritual questions. Science has cannot investigate these areas because they are outside the realm of material phenomena, the phenomena of matter and energy, and cannot be observed and measured.
The scientific method is a method of research with defined steps that include experiments and careful observation. The steps of the scientific method will be examined in detail later, but one of the most important aspects of this method is the testing of hypotheses. A hypothesis is a suggested explanation for an event, which can be tested. Hypotheses, or tentative explanations, are generally produced within the context of a scientific theory. A scientific theory is a generally accepted, thoroughly tested and confirmed explanation for a set of observations or phenomena. Scientific theory is the foundation of scientific knowledge. In addition, in many scientific disciplines (less so in biology) there are scientific laws, often expressed in mathematical formulas, which describe how elements of nature will behave under certain specific conditions. There is not an evolution of hypotheses through theories to laws as if they represented some increase in certainty about the world. Hypotheses are the day-to-day material that scientists work with and they are developed within the context of theories. Laws are concise descriptions of parts of the world that are amenable to formulaic or mathematical description.
Natural Sciences
What would you expect to see in a museum of natural sciences? Frogs? Plants? Dinosaur skeletons? Exhibits about how the brain functions? A planetarium? Gems and minerals? Or maybe all of the above? Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics (Figure \(3\)). However, those fields of science related to the physical world and its phenomena and processes are considered natural sciences. Thus, a museum of natural sciences might contain any of the items listed above.
There is no complete agreement when it comes to defining what the natural sciences include. For some experts, the natural sciences are astronomy, biology, chemistry, earth science, and physics. Other scholars choose to divide natural sciences into life sciences, which study living things and include biology, and physical sciences, which study nonliving matter and include astronomy, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on two sciences and are interdisciplinary.
Scientific Inquiry
One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. Two methods of logical thinking are used: inductive reasoning and deductive reasoning.
Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data can be qualitative (descriptive) or quantitative (consisting of numbers), and the raw data can be supplemented with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data. Brain studies often work this way. Many brains are observed while people are doing a task. The part of the brain that lights up, indicating activity, is then demonstrated to be the part controlling the response to that task.
Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reasoning, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a general principle or law to forecast specific results. From those general principles, a scientist can extrapolate and predict the specific results that would be valid as long as the general principles are valid. For example, a prediction would be that if the climate is becoming warmer in a region, the distribution of plants and animals should change. Comparisons have been made between distributions in the past and the present, and the many changes that have been found are consistent with a warming climate. Finding the change in distribution is evidence that the climate change conclusion is a valid one.
Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis-based science. Descriptive (or discovery) science aims to observe, explore, and discover, while hypothesis-based science begins with a specific question or problem and a potential answer or solution that can be tested. The boundary between these two forms of study is often blurred, because most scientific endeavors combine both approaches. Observations lead to questions, questions lead to forming a hypothesis as a possible answer to those questions, and then the hypothesis is tested. Thus, descriptive science and hypothesis-based science are in continuous dialogue.
Hypothesis Testing
Biologists study the living world by posing questions about it and seeking science-based responses. This approach is common to other sciences as well and is often referred to as the scientific method. The scientific method was used even in ancient times, but it was first documented by England’s Sir Francis Bacon (1561–1626) (Figure \(4\)), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost anything as a logical problem-solving method.
The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: “Why is the classroom so warm?”
Recall that a hypothesis is a suggested explanation that can be tested. To solve a problem, several hypotheses may be proposed. For example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.” But there could be other responses to the question, and therefore other hypotheses may be proposed. A second hypothesis might be, “The classroom is warm because there is a power failure, and so the air conditioning doesn’t work.”
Once a hypothesis has been selected, a prediction may be made. A prediction is similar to a hypothesis but it typically has the format “If . . . then . . . .” For example, the prediction for the first hypothesis might be, “If the student turns on the air conditioning, then the classroom will no longer be too warm.”
A hypothesis must be testable to ensure that it is valid. For example, a hypothesis that depends on what a bear thinks is not testable, because it can never be known what a bear thinks. It should also be falsifiable, meaning that it can be disproven by experimental results. An example of an unfalsifiable hypothesis is “Botticelli’s Birth of Venus is beautiful.” There is no experiment that might show this statement to be false. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. This is important. A hypothesis can be disproven, or eliminated, but it can never be proven. Science does not deal in proofs like mathematics. If an experiment fails to disprove a hypothesis, then we find support for that explanation, but this is not to say that down the road a better explanation will not be found, or a more carefully designed experiment will be found to falsify the hypothesis.
Each experiment will have one or more variables and one or more controls. A variable is any part of the experiment that can vary or change during the experiment. A control is a part of the experiment that does not change. Look for the variables and controls in the example that follows. As a simple example, an experiment might be conducted to test the hypothesis that phosphate limits the growth of algae in freshwater ponds. A series of artificial ponds are filled with water and half of them are treated by adding phosphate each week, while the other half are treated by adding a salt that is known not to be used by algae. The variable here is the phosphate (or lack of phosphate), the experimental or treatment cases are the ponds with added phosphate and the control ponds are those with something inert added, such as the salt. Just adding something is also a control against the possibility that adding extra matter to the pond has an effect. If the treated ponds show lesser growth of algae, then we have found support for our hypothesis. If they do not, then we reject our hypothesis. Be aware that rejecting one hypothesis does not determine whether or not the other hypotheses can be accepted; it simply eliminates one hypothesis that is not valid (Figure \(5\)). Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected.
Example \(1\)
In the example below, the scientific method is used to solve an everyday problem. Which part in the example below is the hypothesis? Which is the prediction? Based on the results of the experiment, is the hypothesis supported? If it is not supported, propose some alternative hypotheses.
1. My toaster doesn’t toast my bread.
2. Why doesn’t my toaster work?
3. There is something wrong with the electrical outlet.
4. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
5. I plug my coffeemaker into the outlet.
6. My coffeemaker works.
Solution
The hypothesis is #3 (there is something wrong with the electrical outlet), and the prediction is #4 (if something is wrong with the outlet, then the coffeemaker also won’t work when plugged into the outlet). The original hypothesis is not supported, as the coffee maker works when plugged into the outlet. Alternative hypotheses may include (1) the toaster might be broken or (2) the toaster wasn’t turned on.
In practice, the scientific method is not as rigid and structured as it might at first appear. Sometimes an experiment leads to conclusions that favor a change in approach; often, an experiment brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion; instead, scientists continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests.
Basic and Applied Science
The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or bettering our lives? This question focuses on the differences between two types of science: basic science and applied science.
Basic science or “pure” science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not focused on developing a product or a service of immediate public or commercial value. The immediate goal of basic science is knowledge for knowledge’s sake, though this does not mean that in the end it may not result in an application.
In contrast, applied science or “technology,” aims to use science to solve real-world problems, making it possible, for example, to improve a crop yield, find a cure for a particular disease, or save animals threatened by a natural disaster. In applied science, the problem is usually defined for the researcher.
Some individuals may perceive applied science as “useful” and basic science as “useless.” A question these people might pose to a scientist advocating knowledge acquisition would be, “What for?” A careful look at the history of science, however, reveals that basic knowledge has resulted in many remarkable applications of great value. Many scientists think that a basic understanding of science is necessary before an application is developed; therefore, applied science relies on the results generated through basic science. Other scientists think that it is time to move on from basic science and instead to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention; however, few solutions would be found without the help of the knowledge generated through basic science.
One example of how basic and applied science can work together to solve practical problems occurred after the discovery of DNA structure led to an understanding of the molecular mechanisms governing DNA replication. Strands of DNA, unique in every human, are found in our cells, where they provide the instructions necessary for life. During DNA replication, new copies of DNA are made, shortly before a cell divides to form new cells. Understanding the mechanisms of DNA replication enabled scientists to develop laboratory techniques that are now used to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine paternity. Without basic science, it is unlikely that applied science would exist.
Another example of the link between basic and applied research is the Human Genome Project, a study in which each human chromosome was analyzed and mapped to determine the precise sequence of DNA subunits and the exact location of each gene. (The gene is the basic unit of heredity; an individual’s complete collection of genes is his or her genome.) Other organisms have also been studied as part of this project to gain a better understanding of human chromosomes. The Human Genome Project (Figure \(6\)) relied on basic research carried out with non-human organisms and, later, with the human genome. An important end goal eventually became using the data for applied research seeking cures for genetically related diseases.
While research efforts in both basic science and applied science are usually carefully planned, it is important to note that some discoveries are made by serendipity, that is, by means of a fortunate accident or a lucky surprise. Penicillin was discovered when biologist Alexander Fleming accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew, killing the bacteria. The mold turned out to be Penicillium, and a new antibiotic was discovered. Even in the highly organized world of science, luck—when combined with an observant, curious mind—can lead to unexpected breakthroughs.
Reporting Scientific Work
Whether scientific research is basic science or applied science, scientists must share their findings for other researchers to expand and build upon their discoveries. Communication and collaboration within and between sub disciplines of science are key to the advancement of knowledge in science. For this reason, an important aspect of a scientist’s work is disseminating results and communicating with peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the limited few who are present. Instead, most scientists present their results in peer-reviewed articles that are published in scientific journals. Peer-reviewed articles are scientific papers that are reviewed, usually anonymously by a scientist’s colleagues, or peers. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research described in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings. The experimental results must be consistent with the findings of other scientists.
There are many journals and the popular press that do not use a peer-review system. A large number of online open-access journals, journals with articles available without cost, are now available many of which use rigorous peer-review systems, but some of which do not. Results of any studies published in these forums without peer review are not reliable and should not form the basis for other scientific work. In one exception, journals may allow a researcher to cite a personal communication from another researcher about unpublished results with the cited author’s permission.
Summary
Biology is the science that studies living organisms and their interactions with one another and their environments. Science attempts to describe and understand the nature of the universe in whole or in part. Science has many fields; those fields related to the physical world and its phenomena are considered natural sciences.
A hypothesis is a tentative explanation for an observation. A scientific theory is a well-tested and consistently verified explanation for a set of observations or phenomena. A scientific law is a description, often in the form of a mathematical formula, of the behavior of an aspect of nature under certain circumstances. Two types of logical reasoning are used in science. Inductive reasoning uses results to produce general scientific principles. Deductive reasoning is a form of logical thinking that predicts results by applying general principles. The common thread throughout scientific research is the use of the scientific method. Scientists present their results in peer-reviewed scientific papers published in scientific journals.
Science can be basic or applied. The main goal of basic science is to expand knowledge without any expectation of short-term practical application of that knowledge. The primary goal of applied research, however, is to solve practical problems.
Glossary
applied science
a form of science that solves real-world problems
basic science
science that seeks to expand knowledge regardless of the short-term application of that knowledge
control
a part of an experiment that does not change during the experiment
deductive reasoning
a form of logical thinking that uses a general statement to forecast specific results
descriptive science
a form of science that aims to observe, explore, and find things out
falsifiable
able to be disproven by experimental results
hypothesis
a suggested explanation for an event, which can be tested
hypothesis-based science
a form of science that begins with a specific explanation that is then tested
inductive reasoning
a form of logical thinking that uses related observations to arrive at a general conclusion
life science
a field of science, such as biology, that studies living things
natural science
a field of science that studies the physical world, its phenomena, and processes
peer-reviewed article
a scientific report that is reviewed by a scientist’s colleagues before publication
physical science
a field of science, such as astronomy, physics, and chemistry, that studies nonliving matter
science
knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method
scientific law
a description, often in the form of a mathematical formula, for the behavior of some aspect of nature under certain specific conditions
scientific method
a method of research with defined steps that include experiments and careful observation
scientific theory
a thoroughly tested and confirmed explanation for observations or phenomena
variable
a part of an experiment that can vary or change | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/01%3A_The_Science_of_Biology/1.02%3A_The_Nature_of_Science.txt |
Are dinosaurs evidence of past life forms?
Evolution can be described as a change in species over time. Dinosaur fossils are significant evidence of evolution and of past life on Earth.
Evolution of Life
The diversity of life on Earth today is the result of evolution. Life began on Earth at least 3.5 to 4 billion years ago, and it has been evolving ever since. At first, all living things on Earth were simple, single-celled organisms. Much later, the first multicellular organisms evolved, and after that, Earth’s biodiversity greatly increased. Figure below shows a timeline of the history of life on Earth. You can also find an interactive timeline of the history of life at the link below.http://www.johnkyrk.com/evolution.html
This timeline shows the history of life on Earth. In the entire span of the time, humans are a relatively new addition.
Today, the most accepted theory of life on Earth is evolution, and there is a vast amount of evidence supporting this theory. However, this wasn’t always the case.
An introduction to evolution and natural selection can be viewed at http://www.youtube.com/watch?v=GcjgWov7mTM.
As you view Introduction to Evolution and Natural Selection,focus on these concepts:
1. the relationship between evolution and natural selection,
2. the relationship between natural selection and variation,
3. the evolution of the peppered moth.
Darwin and the Theory of Evolution
The idea of evolution has been around for centuries. In fact, it goes all the way back to the ancient Greek philosopher Aristotle. However, evolution is most often associated with Charles Darwin. Darwin published a book on evolution in 1859 titled On the Origin of Species. In the book, Darwin stated the theory of evolution by natural selection. He also presented a great deal of evidence that evolution occurs.
Evolution is a change in the characteristics of living things over time. As described by Darwin, evolution occurs by a process called natural selection. In natural selection, some members of a species, being better adapted or suited to their environment, produce more offspring than others, so they pass "advantageous traits" to their offspring. Over many generations, this can lead to major changes in the characteristics of the species. Evolution explains how living things are changing today and how modern living things have descended from ancient life forms that no longer exist on Earth. As living things evolve, they generally become better suited for their environment. This is because they evolve adaptations. An adaptation is a trait that helps an organism survive and reproduce in a given environment.
Despite all the evidence Darwin presented, his theory was not well-received at first. Many people found it hard to accept the idea that humans had evolved from an ape-like ancestor, and they saw evolution as a challenge to their religious beliefs. Look at the cartoon in Figure below. Drawn in 1871, it depicts Darwin himself as an ape. The cartoon reflects how many people felt about Darwin and his theory during his own time. Darwin had actually expected this type of reaction to his theory and had waited a long time before publishing his book for this reason. It was only when another scientist, named Alfred Russel Wallace, developed essentially the same theory of evolution that Darwin put his book into print.
Charles Darwin’s name is linked with the theory of evolution. This cartoon from the 1870s makes fun of both Darwin and his theory.
Although Darwin presented a great deal of evidence for evolution in his book, he was unable to explain how evolution occurs. That’s because he knew nothing about genes. As a result, he didn’t know how characteristics are passed from parents to offspring, let alone how they could change over time.
Evolutionary Theory After Darwin
Since Darwin’s time, scientists have gathered even more evidence to support the theory of evolution. Some of the evidence comes from fossils, and some comes from studies that show how similar living things are to one another. By the 1930s, scientists had also learned about genes. As a result, they could finally explain how characteristics of organisms could pass from one generation to the next and change over time.
Using modern technology, scientists can now directly compare the genes of living species. The more genes different species share in common, the more closely related the species are presumed to be. Consider humans and chimpanzees. They share about 98% of their genes. This means that they shared a common ancestor in the not-too-distant past. This is just one of many pieces of evidence that show we are part of the evolution of life on Earth.
Misconceptions About Evolution
Today, evolution is still questioned by some people. Often, people who disagree with the theory of evolution do not really understand it. For example, some people think that the theory of evolution explains how life on Earth first began. In fact, the theory explains only how life changed after it first appeared. Some people think the theory of evolution means that humans evolved from modern apes. In fact, the theory suggests humans and modern apes have a common ancestor that lived several million years ago. These and other misconceptions about evolution contribute to the controversy that still surrounds this fundamental principle of biology.
Summary
• Life began on Earth at least 3.5 to 4 billion years ago, and it has been evolving ever since.
• Darwin stated the theory of evolution by natural selection, presenting a great deal of evidence to support his theory.
• Evolution is a change in the characteristics of living things over time. Evolution occurs by natural selection.
• Characteristics of organisms are passed from one generation to the next through their genes.
Explore More
Use this resource to answer the questions that follow.
• Natural Selection at evolution.berkeley.edu/evosit...election.shtml.
1. What is meant by differential reproduction?
2. What is the end result of this process?
3. What three things are necessary for evolution by natural selection?
Review
1. What is evolution?
2. What is natural selection?
3. Briefly, explain the theory of evolution. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/01%3A_The_Science_of_Biology/1.03%3A_An_Example_of_Scientific_Inquiry-_Darwin_and_Evolution/1.3.01%3A_Evolution_of_Life.txt |
Theory vs. theory. Is a scientific theory different from the everyday use of the word theory?
A scientific theory is accepted as a scientific truth, supported by evidence collected by many scientists. The theory of evolution by natural selection is a classic scientific theory.
Scientific Theories
With repeated testing, some hypotheses may eventually become scientific theories. Keep in mind, a hypothesis is a possible answer to a scientific question. A scientific theory is a broad explanation for events that is widely accepted as true. To become a theory, a hypothesis must be tested over and over again, and it must be supported by a great deal of evidence.
People commonly use the word theory to describe a guess about how or why something happens. For example, you might say, “I think a woodchuck dug this hole in the ground, but it’s just a theory.” Using the word theory in this way is different from the way it is used in science. A scientific theory is more like a fact than a guess because it is so well-supported. There are several well-known theories in biology, including the theory of evolution, cell theory, and germ theory.
Two videos explaining scientific theories can be seen at http://www.youtube.com/watch?v=S5YGhprR6KE and http://www.youtube.com/watch?v=jdWMcMW54fA.
As you view Know the Difference (Between Hypothesis and Theory), focus on these concepts:
1. the controversy surrounding the words ‘‘hypothesis’’ and ‘‘theory’’,
2. the scientific use of the words ‘‘hypothesis’’ and ‘‘theory’’,
3. the criteria for a ‘‘hypothesis,’’
4. the National Academy of Sciences definition of ‘‘theory’’,
5. the meaning of the statement, ‘‘theories are the bedrock of our understanding of nature’’.
The Theory of Evolution
The theory of evolution by natural selection is a scientific theory. Evolution is a change in the characteristics of living things over time. Evolution occurs by a process called natural selection. In natural selection, some living things produce more offspring than others, so they pass more genes to the next generation than others do. Over many generations, this can lead to major changes in the characteristics of living things. The theory of evolution by natural selection explains how living things are changing today and how modern living things have descended from ancient life forms that no longer exist on Earth. No evidence has been identified that proves this theory is incorrect. More on the theory of evolution will be presented in additional concepts.
The Cell Theory
The cell theory is another important scientific theory of biology. According to the cell theory, the cell is the smallest unit of structure and function of all living organisms, all living organisms are made up of at least one cell, and living cells always come from other living cells. Once again, no evidence has been identified that proves this theory is incorrect. More on the cell theory will be presented in additional concepts.
The Germ Theory
The germ theory of disease, also called the pathogenic theory of medicine, is a scientific theory that proposes that microorganisms are the cause of many diseases. Like the other scientific theories, lots of evidence has been identified that supports this theory, and no evidence has been identified that proves the theory is incorrect.
Summary
• With repeated testing, some hypotheses may eventually become scientific theories. A scientific theory is a broad explanation for events that is widely accepted as true.
• Evolution is a change species over time. Evolution occurs by natural selection.
• The cell theory states that all living things are made up of cells, and living cells always come from other living cells.
• The germ theory proposes that microorganisms are the cause of many diseases.
Explore More
Use these resources to answer the questions that follow.
Explore More I
1. How is the word ‘‘theory’’ used in common language?
2. How is the word ‘‘theory’’ used in science?
3. Provide a detailed definition for a ‘‘scientific theory’’.
Explore More II
1. What is a scientific law?
2. What is a scientific theory?
3. Give two examples of scientific theories.
4. Can a scientific theory become a law? Why or why not?
Review
1. Contrast how the term theory is used in science and in everyday language.
2. Explain how a hypothesis could become a theory.
3. Describe the evidence that proves the cell theory is incorrect. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/01%3A_The_Science_of_Biology/1.03%3A_An_Example_of_Scientific_Inquiry-_Darwin_and_Evolution/1.3.02%3A_Scientific_Theories.txt |
Skills to Develop
• Identify and describe the properties of life
• Describe the levels of organization among living things
• Recognize and interpret a phylogenetic tree
• List examples of different sub disciplines in biology
Biology is the science that studies life, but what exactly is life? This may sound like a silly question with an obvious response, but it is not always easy to define life. For example, a branch of biology called virology studies viruses, which exhibit some of the characteristics of living entities but lack others. It turns out that although viruses can attack living organisms, cause diseases, and even reproduce, they do not meet the criteria that biologists use to define life. Consequently, virologists are not biologists, strictly speaking. Similarly, some biologists study the early molecular evolution that gave rise to life; since the events that preceded life are not biological events, these scientists are also excluded from biology in the strict sense of the term.
From its earliest beginnings, biology has wrestled with three questions: What are the shared properties that make something “alive”? And once we know something is alive, how do we find meaningful levels of organization in its structure? And, finally, when faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? As new organisms are discovered every day, biologists continue to seek answers to these and other questions.
Properties of Life
All living organisms share several key characteristics or functions: order, sensitivity or response to the environment, reproduction, adaptation, growth and development, regulation, homeostasis, energy processing, and evolution. When viewed together, these nine characteristics serve to define life.
Order
Organisms are highly organized, coordinated structures that consist of one or more cells. Even very simple, single-celled organisms are remarkably complex: inside each cell, atoms make up molecules; these in turn make up cell organelles and other cellular inclusions. In multicellular organisms (Figure \(1\)), similar cells form tissues. Tissues, in turn, collaborate to create organs (body structures with a distinct function). Organs work together to form organ systems.
Sensitivity or Response to Stimuli
Organisms respond to diverse stimuli. For example, plants can bend toward a source of light, climb on fences and walls, or respond to touch (Figure \(2\)). Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phototaxis). Movement toward a stimulus is considered a positive response, while movement away from a stimulus is considered a negative response.
Link to Learning
Video: Watch this video to see how plants respond to a stimulus—from opening to light, to wrapping a tendril around a branch, to capturing prey.
Reproduction
Single-celled organisms reproduce by first duplicating their DNA, and then dividing it equally as the cell prepares to divide to form two new cells. Multicellular organisms often produce specialized reproductive germline cells that will form new individuals. When reproduction occurs, genes containing DNA are passed along to an organism’s offspring. These genes ensure that the offspring will belong to the same species and will have similar characteristics, such as size and shape.
Growth and Development
Organisms grow and develop following specific instructions coded for by their genes. These genes provide instructions that will direct cellular growth and development, ensuring that a species’ young (Figure \(3\)) will grow up to exhibit many of the same characteristics as its parents.
Regulation
Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, respond to stimuli, and cope with environmental stresses. Two examples of internal functions regulated in an organism are nutrient transport and blood flow. Organs (groups of tissues working together) perform specific functions, such as carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body.
Homeostasis
In order to function properly, cells need to have appropriate conditions such as proper temperature, pH, and appropriate concentration of diverse chemicals. These conditions may, however, change from one moment to the next. Organisms are able to maintain internal conditions within a narrow range almost constantly, despite environmental changes, through homeostasis (literally, “steady state”)—the ability of an organism to maintain constant internal conditions. For example, an organism needs to regulate body temperature through a process known as thermoregulation. Organisms that live in cold climates, such as the polar bear (Figure \(4\)), have body structures that help them withstand low temperatures and conserve body heat. Structures that aid in this type of insulation include fur, feathers, blubber, and fat. In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat.
Energy Processing
All organisms use a source of energy for their metabolic activities. Some organisms capture energy from the sun and convert it into chemical energy in food; others use chemical energy in molecules they take in as food (Figure \(5\)).
Levels of Organization of Living Things
Living things are highly organized and structured, following a hierarchy that can be examined on a scale from small to large. The atom is the smallest and most fundamental unit of matter. It consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical structure consisting of at least two atoms held together by one or more chemical bonds. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by polymerization (a polymer is a large molecule that is made by combining smaller units called monomers, which are simpler than macromolecules). An example of a macromolecule is deoxyribonucleic acid (DNA) (Figure \(6\)), which contains the instructions for the structure and functioning of all living organisms.
Link to Learning
Video: Watch this video that animates the three-dimensional structure of the DNA molecule shown in Figure \(6\).
Some cells contain aggregates of macromolecules surrounded by membranes; these are called organelles. Organelles are small structures that exist within cells. Examples of organelles include mitochondria and chloroplasts, which carry out indispensable functions: mitochondria produce energy to power the cell, while chloroplasts enable green plants to utilize the energy in sunlight to make sugars. All living things are made of cells; the cell itself is the smallest fundamental unit of structure and function in living organisms. (This requirement is why viruses are not considered living: they are not made of cells. To make new viruses, they have to invade and hijack the reproductive mechanism of a living cell; only then can they obtain the materials they need to reproduce.) Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic. Prokaryotes are single-celled or colonial organisms that do not have membrane-bound nuclei; in contrast, the cells of eukaryotes do have membrane-bound organelles and a membrane-bound nucleus.
In larger organisms, cells combine to make tissues, which are groups of similar cells carrying out similar or related functions. Organs are collections of tissues grouped together performing a common function. Organs are present not only in animals but also in plants. An organ system is a higher level of organization that consists of functionally related organs. Mammals have many organ systems. For instance, the circulatory system transports blood through the body and to and from the lungs; it includes organs such as the heart and blood vessels. Organisms are individual living entities. For example, each tree in a forest is an organism. Single-celled prokaryotes and single-celled eukaryotes are also considered organisms and are typically referred to as microorganisms.
All the individuals of a species living within a specific area are collectively called a population. For example, a forest may include many pine trees. All of these pine trees represent the population of pine trees in this forest. Different populations may live in the same specific area. For example, the forest with the pine trees includes populations of flowering plants and also insects and microbial populations. A community is the sum of populations inhabiting a particular area. For instance, all of the trees, flowers, insects, and other populations in a forest form the forest’s community. The forest itself is an ecosystem. An ecosystem consists of all the living things in a particular area together with the abiotic, non-living parts of that environment such as nitrogen in the soil or rain water. At the highest level of organization (Figure \(7\)), the biosphere is the collection of all ecosystems, and it represents the zones of life on earth. It includes land, water, and even the atmosphere to a certain extent.
Art Connection
Which of the following statements is false?
1. Tissues exist within organs which exist within organ systems.
2. Communities exist within populations which exist within ecosystems.
3. Organelles exist within cells which exist within tissues.
4. Communities exist within ecosystems which exist in the biosphere.
The Diversity of Life
The fact that biology, as a science, has such a broad scope has to do with the tremendous diversity of life on earth. The source of this diversity is evolution, the process of gradual change during which new species arise from older species. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems.
The evolution of various life forms on Earth can be summarized in a phylogenetic tree (Figure \(8\)). A phylogenetic tree is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. A phylogenetic tree is composed of nodes and branches. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length of each branch is proportional to the time elapsed since the split.
Evolution Connection: Carl Woese and the Phylogenetic Tree
In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The organizational scheme was based mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which are used by modern systematics. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. The first two are prokaryotic cells with microbes that lack membrane-enclosed nuclei and organelles. The third domain contains the eukaryotes and includes unicellular microorganisms together with the four original kingdoms (excluding bacteria). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree (Figure \(8\)). Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape).
Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, present in every organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese’s approach was revolutionary because comparisons of physical features are insufficient to differentiate between the prokaryotes that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability (Figure \(9\)). The comparison of homologous DNA and RNA sequences provided Woese with a sensitive device that revealed the extensive variability of prokaryotes, and which justified the separation of the prokaryotes into two domains: bacteria and archaea.
Branches of Biological Study
The scope of biology is broad and therefore contains many branches and subdisciplines. Biologists may pursue one of those subdisciplines and work in a more focused field. For instance, molecular biology and biochemistry study biological processes at the molecular and chemical level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. Microbiology, the study of microorganisms, is the study of the structure and function of single-celled organisms. It is quite a broad branch itself, and depending on the subject of study, there are also microbial physiologists, ecologists, and geneticists, among others.
Career Connection: Forensic Scientist
Forensic science is the application of science to answer questions related to the law. Biologists as well as chemists and biochemists can be forensic scientists. Forensic scientists provide scientific evidence for use in courts, and their job involves examining trace materials associated with crimes. Interest in forensic science has increased in the last few years, possibly because of popular television shows that feature forensic scientists on the job. Also, the development of molecular techniques and the establishment of DNA databases have expanded the types of work that forensic scientists can do. Their job activities are primarily related to crimes against people such as murder, rape, and assault. Their work involves analyzing samples such as hair, blood, and other body fluids and also processing DNA (Figure \(10\)) found in many different environments and materials. Forensic scientists also analyze other biological evidence left at crime scenes, such as insect larvae or pollen grains. Students who want to pursue careers in forensic science will most likely be required to take chemistry and biology courses as well as some intensive math courses.
Another field of biological study, neurobiology, studies the biology of the nervous system, and although it is considered a branch of biology, it is also recognized as an interdisciplinary field of study known as neuroscience. Because of its interdisciplinary nature, this subdiscipline studies different functions of the nervous system using molecular, cellular, developmental, medical, and computational approaches.
Paleontology, another branch of biology, uses fossils to study life’s history (Figure \(11\)). Zoology and botany are the study of animals and plants, respectively. Biologists can also specialize as biotechnologists, ecologists, or physiologists, to name just a few areas. This is just a small sample of the many fields that biologists can pursue.
Biology is the culmination of the achievements of the natural sciences from their inception to today. Excitingly, it is the cradle of emerging sciences, such as the biology of brain activity, genetic engineering of custom organisms, and the biology of evolution that uses the laboratory tools of molecular biology to retrace the earliest stages of life on earth. A scan of news headlines—whether reporting on immunizations, a newly discovered species, sports doping, or a genetically-modified food—demonstrates the way biology is active in and important to our everyday world.
Summary
Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized parts of a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere. The great diversity of life today evolved from less-diverse ancestral organisms over billions of years. A diagram called a phylogenetic tree can be used to show evolutionary relationships among organisms.
Biology is very broad and includes many branches and subdisciplines. Examples include molecular biology, microbiology, neurobiology, zoology, and botany, among others.
Art Connections
Figure \(7\): Which of the following statements is false?
1. Tissues exist within organs which exist within organ systems.
2. Communities exist within populations which exist within ecosystems.
3. Organelles exist within cells which exist within tissues.
4. Communities exist within ecosystems which exist in the biosphere.
Answer
Communities exist within populations which exist within ecosystems.
Glossary
atom
smallest and most fundamental unit of matter
biochemistry
study of the chemistry of biological organisms
biosphere
collection of all the ecosystems on Earth
botany
study of plants
cell
smallest fundamental unit of structure and function in living things
community
set of populations inhabiting a particular area
ecosystem
all the living things in a particular area together with the abiotic, nonliving parts of that environment
eukaryote
organism with cells that have nuclei and membrane-bound organelles
evolution
process of gradual change during which new species arise from older species and some species become extinct
homeostasis
ability of an organism to maintain constant internal conditions
macromolecule
large molecule, typically formed by the joining of smaller molecules
microbiology
study of the structure and function of microorganisms
molecule
chemical structure consisting of at least two atoms held together by one or more chemical bonds
molecular biology
study of biological processes and their regulation at the molecular level, including interactions among molecules such as DNA, RNA, and proteins
neurobiology
study of the biology of the nervous system
organ
collection of related tissues grouped together performing a common function
organ system
level of organization that consists of functionally related interacting organs
organelle
small structures that exist within cells and carry out cellular functions
organism
individual living entity
paleontology
study of life’s history by means of fossils
phylogenetic tree
diagram showing the evolutionary relationships among various biological species based on similarities and differences in genetic or physical traits or both; in essence, a hypothesis concerning evolutionary connections
population
all of the individuals of a species living within a specific area
prokaryote
single-celled organism that lacks organelles and does not have nuclei surrounded by a nuclear membrane
tissue
group of similar cells carrying out related functions
zoology
study of animals | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/01%3A_The_Science_of_Biology/1.04%3A__Core_Concepts_in_Biology.txt |
• 2.1: The Nature of Atoms
At its most fundamental level, life is made up of matter. Matter occupies space and has mass. All matter is composed of elements, substances that cannot be broken down or transformed chemically into other substances. Each element is made of atoms, each with a constant number of protons and unique properties. Each element is designated by its chemical symbol and possesses unique properties. These unique properties allow elements to combine and to bond with each other in specific ways.
• 2.2: Elements Found in Living Systems
• 2.3: The Nature of Chemical Bonds
At its most fundamental level, life is made up of matter. Matter occupies space and has mass. All matter is composed of elements, substances that cannot be broken down or transformed chemically into other substances. Each element is made of atoms, each with a constant number of protons and unique properties. Each element is designated by its chemical symbol and possesses unique properties. These unique properties allow elements to combine and to bond with each other in specific ways.
• 2.4: Water- A Vital Compound
Do you ever wonder why scientists spend time looking for water on other planets? It is because water is essential to life; even minute traces of it on another planet can indicate that life could or did exist on that planet. Water is one of the more abundant molecules in living cells and the one most critical to life as we know it. Approximately 60–70 percent of your body is made up of water. Without it, life simply would not exist.
• 2.5: Properties of Water
The polarity of the water molecule and its resulting hydrogen bonding make water a unique substance with special properties that are intimately tied to the processes of life. Life originally evolved in a watery environment, and most of an organism’s cellular chemistry and metabolism occur inside the watery contents of the cell’s cytoplasm. Understanding the characteristics of water helps to elucidate its importance in maintaining life.
• 2.6: Acids and Bases
02: The Nature of Molecules and the Properties of Water
At its most fundamental level, life is made up of matter. Matter occupies space and has mass. All matter is composed of elements, substances that cannot be broken down or transformed chemically into other substances. Each element is made of atoms, each with a constant number of protons and unique properties. A total of 118 elements have been defined; however, only 92 occur naturally, and fewer than 30 are found in living cells. The remaining 26 elements are unstable and, therefore, do not exist for very long or are theoretical and have yet to be detected.
Each element is designated by its chemical symbol (such as H, N, O, C, and Na), and possesses unique properties. These unique properties allow elements to combine and to bond with each other in specific ways.
Atoms
An atom is the smallest component of an element that retains all of the chemical properties of that element. For example, one hydrogen atom has all of the properties of the element hydrogen, such as it exists as a gas at room temperature, and it bonds with oxygen to create a water molecule. Hydrogen atoms cannot be broken down into anything smaller while still retaining the properties of hydrogen. If a hydrogen atom were broken down into subatomic particles, it would no longer have the properties of hydrogen.
At the most basic level, all organisms are made of a combination of elements. They contain atoms that combine together to form molecules. In multicellular organisms, such as animals, molecules can interact to form cells that combine to form tissues, which make up organs. These combinations continue until entire multicellular organisms are formed.
All atoms contain protons, electrons, and neutrons (Figure \(1\)). The only exception is hydrogen (H), which is made of one proton and one electron. A proton is a positively charged particle that resides in the nucleus (the core of the atom) of an atom and has a mass of 1 and a charge of +1. An electron is a negatively charged particle that travels in the space around the nucleus. In other words, it resides outside of the nucleus. It has a negligible mass and has a charge of –1.
Neutrons, like protons, reside in the nucleus of an atom. They have a mass of 1 and no charge. The positive (protons) and negative (electrons) charges balance each other in a neutral atom, which has a net zero charge.
Because protons and neutrons each have a mass of 1, the mass of an atom is equal to the number of protons and neutrons of that atom. The number of electrons does not factor into the overall mass, because their mass is so small.
As stated earlier, each element has its own unique properties. Each contains a different number of protons and neutrons, giving it its own atomic number and mass number. The atomic number of an element is equal to the number of protons that element contains. The mass number, or atomic mass, is the number of protons plus the number of neutrons of that element. Therefore, it is possible to determine the number of neutrons by subtracting the atomic number from the mass number.
These numbers provide information about the elements and how they will react when combined. Different elements have different melting and boiling points, and are in different states (liquid, solid, or gas) at room temperature. They also combine in different ways. Some form specific types of bonds, whereas others do not. How they combine is based on the number of electrons present. Because of these characteristics, the elements are arranged into the periodic table of elements, a chart of the elements that includes the atomic number and relative atomic mass of each element. The periodic table also provides key information about the properties of elements (Figure \(2\))—often indicated by color-coding. The arrangement of the table also shows how the electrons in each element are organized and provides important details about how atoms will react with each other to form molecules.
Isotopes are different forms of the same element that have the same number of protons, but a different number of neutrons. Some elements, such as carbon, potassium, and uranium, have naturally occurring isotopes. Carbon-12, the most common isotope of carbon, contains six protons and six neutrons. Therefore, it has a mass number of 12 (six protons and six neutrons) and an atomic number of 6 (which makes it carbon). Carbon-14 contains six protons and eight neutrons. Therefore, it has a mass number of 14 (six protons and eight neutrons) and an atomic number of 6, meaning it is still the element carbon. These two alternate forms of carbon are isotopes. Some isotopes are unstable and will lose protons, other subatomic particles, or energy to form more stable elements. These are called radioactive isotopes or radioisotopes.
ART CONNECTION
How many neutrons do (K) potassium-39 and potassium-40 have, respectively?
EVOLUTION IN ACTION: Carbon Dating
Carbon-14 (14C) is a naturally occurring radioisotope that is created in the atmosphere by cosmic rays. This is a continuous process, so more 14C is always being created. As a living organism develops, the relative level of 14C in its body is equal to the concentration of 14C in the atmosphere. When an organism dies, it is no longer ingesting 14C, so the ratio will decline. 14C decays to 14N by a process called beta decay; it gives off energy in this slow process.
After approximately 5,730 years, only one-half of the starting concentration of 14C will have been converted to 14N. The time it takes for half of the original concentration of an isotope to decay to its more stable form is called its half-life. Because the half-life of 14C is long, it is used to age formerly living objects, such as fossils. Using the ratio of the 14C concentration found in an object to the amount of 14C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined. Based on this amount, the age of the fossil can be calculated to about 50,000 years (Figure \(3\)). Isotopes with longer half-lives, such as potassium-40, are used to calculate the ages of older fossils. Through the use of carbon dating, scientists can reconstruct the ecology and biogeography of organisms living within the past 50,000 years.
CONCEPT IN ACTION
To learn more about atoms and isotopes, and how you can tell one isotope from another, visit this site and run the simulation.
Chemical Bonds
How elements interact with one another depends on how their electrons are arranged and how many openings for electrons exist at the outermost region where electrons are present in an atom. Electrons exist at energy levels that form shells around the nucleus. The closest shell can hold up to two electrons. The closest shell to the nucleus is always filled first, before any other shell can be filled. Hydrogen has one electron; therefore, it has only one spot occupied within the lowest shell. Helium has two electrons; therefore, it can completely fill the lowest shell with its two electrons. If you look at the periodic table, you will see that hydrogen and helium are the only two elements in the first row. This is because they only have electrons in their first shell. Hydrogen and helium are the only two elements that have the lowest shell and no other shells.
The second and third energy levels can hold up to eight electrons. The eight electrons are arranged in four pairs and one position in each pair is filled with an electron before any pairs are completed.
Looking at the periodic table again (Figure \(2\)), you will notice that there are seven rows. These rows correspond to the number of shells that the elements within that row have. The elements within a particular row have increasing numbers of electrons as the columns proceed from left to right. Although each element has the same number of shells, not all of the shells are completely filled with electrons. If you look at the second row of the periodic table, you will find lithium (Li), beryllium (Be), boron (B), carbon (C), nitrogen (N), oxygen (O), fluorine (F), and neon (Ne). These all have electrons that occupy only the first and second shells. Lithium has only one electron in its outermost shell, beryllium has two electrons, boron has three, and so on, until the entire shell is filled with eight electrons, as is the case with neon.
Not all elements have enough electrons to fill their outermost shells, but an atom is at its most stable when all of the electron positions in the outermost shell are filled. Because of these vacancies in the outermost shells, we see the formation of chemical bonds, or interactions between two or more of the same or different elements that result in the formation of molecules. To achieve greater stability, atoms will tend to completely fill their outer shells and will bond with other elements to accomplish this goal by sharing electrons, accepting electrons from another atom, or donating electrons to another atom. Because the outermost shells of the elements with low atomic numbers (up to calcium, with atomic number 20) can hold eight electrons, this is referred to as the octet rule. An element can donate, accept, or share electrons with other elements to fill its outer shell and satisfy the octet rule.
When an atom does not contain equal numbers of protons and electrons, it is called an ion. Because the number of electrons does not equal the number of protons, each ion has a net charge. Positive ions are formed by losing electrons and are called cations. Negative ions are formed by gaining electrons and are called anions.
For example, sodium only has one electron in its outermost shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons and only 10 electrons, leaving it with an overall charge of +1. It is now called a sodium ion.
The chlorine atom has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons and 18 electrons, giving it a net negative (–1) charge. It is now called a chloride ion. This movement of electrons from one element to another is referred to as electron transfer. As Figure \(4\) illustrates, a sodium atom (Na) only has one electron in its outermost shell, whereas a chlorine atom (Cl) has seven electrons in its outermost shell. A sodium atom will donate its one electron to empty its shell, and a chlorine atom will accept that electron to fill its shell, becoming chloride. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium) or –1 (chloride) charge.
Ionic Bonds
There are four types of bonds or interactions: ionic, covalent, hydrogen bonds, and van der Waals interactions. Ionic and covalent bonds are strong interactions that require a larger energy input to break apart. When an element donates an electron from its outer shell, as in the sodium atom example above, a positive ion is formed. The element accepting the electron is now negatively charged. Because positive and negative charges attract, these ions stay together and form an ionic bond, or a bond between ions. The elements bond together with the electron from one element staying predominantly with the other element. When Na+ and Cl ions combine to produce NaCl, an electron from a sodium atom stays with the other seven from the chlorine atom, and the sodium and chloride ions attract each other in a lattice of ions with a net zero charge.
Covalent Bonds
Another type of strong chemical bond between two or more atoms is a covalent bond. These bonds form when an electron is shared between two elements and are the strongest and most common form of chemical bond in living organisms. Covalent bonds form between the elements that make up the biological molecules in our cells. Unlike ionic bonds, covalent bonds do not dissociate in water.
The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds. The electron from the hydrogen atom divides its time between the outer shell of the hydrogen atom and the incomplete outer shell of the oxygen atom. To completely fill the outer shell of an oxygen atom, two electrons from two hydrogen atoms are needed, hence the subscript “2” in H2O. The electrons are shared between the atoms, dividing their time between them to “fill” the outer shell of each. This sharing is a lower energy state for all of the atoms involved than if they existed without their outer shells filled.
There are two types of covalent bonds: polar and nonpolar. Nonpolar covalent bonds form between two atoms of the same element or between different elements that share the electrons equally. For example, an oxygen atom can bond with another oxygen atom to fill their outer shells. This association is nonpolar because the electrons will be equally distributed between each oxygen atom. Two covalent bonds form between the two oxygen atoms because oxygen requires two shared electrons to fill its outermost shell. Nitrogen atoms will form three covalent bonds (also called triple covalent) between two atoms of nitrogen because each nitrogen atom needs three electrons to fill its outermost shell. Another example of a nonpolar covalent bond is found in the methane (CH4) molecule. The carbon atom has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one. These elements all share the electrons equally, creating four nonpolar covalent bonds (Figure \(5\)).
In a polar covalent bond, the electrons shared by the atoms spend more time closer to one nucleus than to the other nucleus. Because of the unequal distribution of electrons between the different nuclei, a slightly positive (δ+) or slightly negative (δ–) charge develops. The covalent bonds between hydrogen and oxygen atoms in water are polar covalent bonds. The shared electrons spend more time near the oxygen nucleus, giving it a small negative charge, than they spend near the hydrogen nuclei, giving these molecules a small positive charge.
Hydrogen Bonds
Ionic and covalent bonds are strong bonds that require considerable energy to break. However, not all bonds between elements are ionic or covalent bonds. Weaker bonds can also form. These are attractions that occur between positive and negative charges that do not require much energy to break. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. These bonds give rise to the unique properties of water and the unique structures of DNA and proteins.
When polar covalent bonds containing a hydrogen atom form, the hydrogen atom in that bond has a slightly positive charge. This is because the shared electron is pulled more strongly toward the other element and away from the hydrogen nucleus. Because the hydrogen atom is slightly positive (δ+), it will be attracted to neighboring negative partial charges (δ–). When this happens, a weak interaction occurs between the δ+ charge of the hydrogen atom of one molecule and the δ– charge of the other molecule. This interaction is called a hydrogen bond. This type of bond is common; for example, the liquid nature of water is caused by the hydrogen bonds between water molecules (Figure \(6\)). Hydrogen bonds give water the unique properties that sustain life. If it were not for hydrogen bonding, water would be a gas rather than a liquid at room temperature.
Hydrogen bonds can form between different molecules and they do not always have to include a water molecule. Hydrogen atoms in polar bonds within any molecule can form bonds with other adjacent molecules. For example, hydrogen bonds hold together two long strands of DNA to give the DNA molecule its characteristic double-stranded structure. Hydrogen bonds are also responsible for some of the three-dimensional structure of proteins.
van der Waals Interactions
Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. They occur between polar, covalently bound, atoms in different molecules. Some of these weak attractions are caused by temporary partial charges formed when electrons move around a nucleus. These weak interactions between molecules are important in biological systems.
CAREERS IN ACTION: Radiography Technician
Have you or anyone you know ever had a magnetic resonance imaging (MRI) scan, a mammogram, or an X-ray? These tests produce images of your soft tissues and organs (as with an MRI or mammogram) or your bones (as happens in an X-ray) by using either radiowaves or special isotopes (radiolabeled or fluorescently labeled) that are ingested or injected into the body. These tests provide data for disease diagnoses by creating images of your organs or skeletal system.
MRI imaging works by subjecting hydrogen nuclei, which are abundant in the water in soft tissues, to fluctuating magnetic fields, which cause them to emit their own magnetic field. This signal is then read by sensors in the machine and interpreted by a computer to form a detailed image.
Some radiography technologists and technicians specialize in computed tomography, MRI, and mammography. They produce films or images of the body that help medical professionals examine and diagnose. Radiologists work directly with patients, explaining machinery, preparing them for exams, and ensuring that their body or body parts are positioned correctly to produce the needed images. Physicians or radiologists then analyze the test results.
Radiography technicians can work in hospitals, doctors’ offices, or specialized imaging centers. Training to become a radiography technician happens at hospitals, colleges, and universities that offer certificates, associate’s degrees, or bachelor’s degrees in radiography.
Summary
Matter is anything that occupies space and has mass. It is made up of atoms of different elements. All of the 92 elements that occur naturally have unique qualities that allow them to combine in various ways to create compounds or molecules. Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can be donated or shared between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.
Art Connections
Figure \(2\): How many neutrons do (K) potassium-39 and potassium-40 have, respectively?
Answer
Potassium-39 has twenty neutrons. Potassium-40 has twenty one neutrons.
Glossary
anion
a negative ion formed by gaining electrons
atomic number
the number of protons in an atom
cation
a positive ion formed by losing electrons
chemical bond
an interaction between two or more of the same or different elements that results in the formation of molecules
covalent bond
a type of strong bond between two or more of the same or different elements; forms when electrons are shared between elements
electron
a negatively charged particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a charge of –1
electron transfer
the movement of electrons from one element to another
element
one of 118 unique substances that cannot be broken down into smaller substances and retain the characteristic of that substance; each element has a specified number of protons and unique properties
hydrogen bond
a weak bond between partially positively charged hydrogen atoms and partially negatively charged elements or molecules
ion
an atom or compound that does not contain equal numbers of protons and electrons, and therefore has a net charge
ionic bond
a chemical bond that forms between ions of opposite charges
isotope
one or more forms of an element that have different numbers of neutrons
mass number
the number of protons plus neutrons in an atom
matter
anything that has mass and occupies space
neutron
a particle with no charge that resides in the nucleus of an atom; has a mass of 1
nonpolar covalent bond
a type of covalent bond that forms between atoms when electrons are shared equally between atoms, resulting in no regions with partial charges as in polar covalent bonds
nucleus
(chemistry) the dense center of an atom made up of protons and (except in the case of a hydrogen atom) neutrons
octet rule
states that the outermost shell of an element with a low atomic number can hold eight electrons
periodic table of elements
an organizational chart of elements, indicating the atomic number and mass number of each element; also provides key information about the properties of elements
polar covalent bond
a type of covalent bond in which electrons are pulled toward one atom and away from another, resulting in slightly positive and slightly negative charged regions of the molecule
proton
a positively charged particle that resides in the nucleus of an atom; has a mass of 1 and a charge of +1
radioactive isotope
an isotope that spontaneously emits particles or energy to form a more stable element
van der Waals interaction
a weak attraction or interaction between molecules caused by slightly positively charged or slightly negatively charged atoms | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/02%3A_The_Nature_of_Molecules_and_the_Properties_of_Water/2.01%3A_The_Nature_of_Atoms.txt |
Elements
Elements consist of only one kind of atom and cannot be decomposed into simpler substances. Our planet is made up of some 90 elements. (Tiny amounts — sometimes only a few atoms — of additional elements have been made in nuclear physics laboratories, but they play no role in our story). Of these 90, only 25 or so are used to build living things. The table shows the 11 most prevalent elements in the lithosphere (the earth's crust) and in the human body.
Living matter
• uses only a fraction of the elements available to it
• but, as the table shows, the relative proportions of those it does acquire from its surroundings are quite different from the proportions in the environment
So,
• the composition of living things is not simply a reflection of the elements available to them
• For example, hydrogen, carbon, and nitrogen together represent less than 1% of the atoms found in the earth's crust but some 74% of the atoms in living matter.
• one of the properties of life is to take up certain elements that are scarce in the nonliving world and concentrate them within living cells.
Some sea animals accumulate elements like vanadium and iodine within their cells to concentrations a thousand or more times as great as in the surrounding sea water. It has even been proposed that uranium be "mined" from the sea by extracting it from certain algae that can take up uranium from sea water and concentrate it within their cells.
There is still some uncertainty about the exact number of elements required by living things. Some elements, e.g., aluminum, are found in tiny amounts in living tissue, but whether they are playing an essential role or are simply an accidental acquisition (aluminum probably is) is sometimes difficult to determine.
Atoms
Each element is made up of one kind of atom. We can define an atom as the smallest part of an element that can enter into combination with other elements.
Structure of the atom
Each atom consists of a small, dense, positively-charged nucleus surrounded by much lighter, negatively-charged electrons. The nucleus of the simplest atom, the hydrogen atom (H), consists of a single positively-charged proton. Because of its single proton, the atom of hydrogen is assigned an atomic number of 1 and a single electron. The charge of the electron is the same magnitude as that of the proton, so the atom as a whole is electrically neutral. Its proton accounts for almost all the weight of the atom.
The nucleus of the atom of the element helium (He) has two protons (hence helium has an atomic number of 2) and two neutrons. Neutrons have the same weight as protons but no electrical charge. The helium atom has two electrons so that, once again, the atom as a whole is neutral.
The structure of each of the other kinds of atoms follows the same plan. From Lithium (At. No. = 3) to uranium (At. No. = 92), the atoms of each element can be listed in order of increasing atomic number. There are no gaps in the list. Each element has a unique atomic number and its atoms have one more proton and one more electron than the atoms of the element that precedes it in the list.
Electrons
Atomic Number Element Energy Levels or "shells"
K L M N O
1 Hydrogen (H) 1
2 Helium (He) 2
3 Lithium (Li) 2 1
4 Beryllium (Be) 2 2
5 Boron (B) 2 3
6 Carbon (C) 2 4
7 Nitrogen (N) 2 5
8 Oxygen (O) 2 6
9 Fluorine (F) 2 7
10 Neon (Ne) 2 8
11 Sodium (Na) 2 8 1
12 Magnesium (Mg) 2 8 2
13 Aluminum (Al) 2 8 3
14 Silicon (Si) 2 8 4
15 Phosphorus (P) 2 8 5
16 Sulfur (S) 2 8 6
17 Chlorine (Cl) 2 8 7
18 Argon (Ar) 2 8 8
19 Potassium (K) 2 8 8 1
20 Calcium (Ca) 2 8 8 2
21 Scandium (Sc) 2 8 9 2
22 Titanium (Ti) 2 8 10 2
23 Vanadium (V) 2 8 11 2
24 Chromium (Cr) 2 8 13 1
25 Manganese (Mn) 2 8 13 2
26 Iron (Fe) 2 8 14 2
27 Cobalt (Co) 2 8 15 2
28 Nickel (Ni) 2 8 16 2
29 Copper (Cu) 2 8 18 1
30 Zinc (Zn) 2 8 18 2
31 Gallium (Ga) 2 8 18 3
32 Germanium (Ge) 2 8 18 4
33 Arsenic (As) 2 8 18 5
34 Selenium (Se) 2 8 18 6
35 Bromine (Br) 2 8 18 7
36 Krypton (Kr) 2 8 18 8
42 Molybdenum (Mo) 2 8 18 13 1
48 Cadmium (Cd) 2 8 18 18 2
50 Tin (Sn) 2 8 18 18 4
53 Iodine (I) 2 8 18 18 7
Electrons are confined to relatively discrete regions around the nucleus. The two electrons of helium, for example, are confined to a spherical zone surrounding the nucleus called the K shell or K energy level.
Lithium (At. No. = 3) has three electrons, two in the K shell and one located farther from the nucleus in the L shell. Being farther away from the opposite (+) charges of the nucleus, this third electron is held less tightly.
Each of the following elements, in order of increasing atomic number, adds one more electron to the L shell until we reach neon (At. No. = 10) which has eight electrons in the L shell.
Sodium places its eleventh electron in a still higher energy level, the M shell.
From sodium to argon, this shell is gradually filled with electrons until, once again, a maximum of eight is reached.
Note that after the K shell with its maximum of two electrons, the maximum number of electrons in any other outermost shell is eight.
As we shall see, the chemical properties of each element are strongly influenced by the number of electrons in its outermost energy level (shell).
This table shows the electronic structure of the atoms of elements 1 – 36 with those that have been demonstrated to be used by living things shown in red. Four elements of still higher atomic numbers that have been shown to be used by living things are also included.
The electronic structure of an atom plays the major role in its chemistry.
The pattern of electrons in an atom — especially those in the outermost shell — determines
• the valence of the atom; that is, the ratios with which it interacts with other atoms, and to a large degree,
• the electronegativity of the atom; that is, the strength with which it attracts other electrons.
Elements with the same number of electrons in their outermost shell show similar chemical properties.
Example 1: Fluorine, chlorine, bromine, and iodine each have 7 electrons in their outermost shell. These so-called halogens are also quite similar in their chemical behavior. When dissolved in water, for example, they all produce germicidal solutions.
Example 2: Those elements with 1, 2, or 3 electrons in their outermost shell are the metals.
Example 3: Those elements with 4, 5, 6, or 7 in their outermost shell are the nonmetals.
Example 4: Helium (with its 2), neon, argon, and krypton (each with 8) have "filled" their outermost shells. They are the so-called inert or "noble" gases. They have no chemistry at all. Under normal conditions they do not interact with other atoms. So, it is the number and arrangement of the electrons in the atoms of an element that establish the chemical behavior of that element.
This is how it works:
The atoms of an element interact with other atoms in such ways and ratios that they can "fill" their outermost shell with 8 electrons (2 for hydrogen). They may do this by
• acquiring more electrons from another atom
• losing electrons to another atom
• sharing electrons with another atom
The number of electrons that an atom must acquire, or lose, or share to reach a stable configuration of 8 (2 for hydrogen) is called its valence.
Hydrogen, lithium, sodium, and potassium atoms all have a single electron in their outermost shell. Fluorine, chlorine, bromine, and iodine atoms all have 7. Any atom of the first group will interact with a single atom of any of the second group forming, HCl, NaCl, KI, etc. The result of all of these interactions is a pair of atoms each with an outermost shell like that of one of the inert gases: 2 for hydrogen, 8 for the others.
The elements with 2 electrons in their outermost shell interact with chlorine and the other halogens to form, e.g., BeCl2, MgCl2, CaCl2. Again, the result is a pair of atoms each with a stable octet of electrons in its outermost shell.
The elements with 3 electrons in their outermost shell will interact with chlorine in a ratio of 1:3, forming BCl3, AlCl3.
Carbon atoms, with their 4 electrons in the L shell interact with chlorine to form CCl4.
Nitrogen, with its 5 outermost electrons, interacts with hydrogen atoms in a ratio of 1:3, forming ammonia (NH3).
Oxygen and sulfur, with their 6 outermost electrons react with hydrogen to form water (H2O) and hydrogen sulfide (H2S).
What determines whether a pair of atoms swap or share electrons?
The answer is their relative electronegativities. If two atoms differ greatly in their affinity for electrons; that is, in their electronegativity, then the strongly electronegative atom will take the electron away from the weakly electronegative one.
Example: Na (weakly electronegative) gives up its single electron to an atom of chlorine (strongly electronegative) to form NaCl. The sodium atom now has only 10 electrons but still 11 protons so there is a net positive charge of one on the atom. Similarly, chlorine now has one more electron than proton so its now has a net negative charge of 1. Electrically charged atoms are called ions. The mutual attraction of opposite electrical charges holds the ions together by ionic bonds.
Example: Carbon and hydrogen are both only weakly electronegative so neither can remove electrons from the other. Instead they achieve a stable configuration by sharing their outermost electrons forming covalent bonds of CH4.
Isotopes
The number of protons in the nucleus of its atoms, which is its atomic number, defines each element. However, the nuclei of a given element may have varying numbers of neutrons. Because neutrons have weight (about the same as that of protons), such atoms differ in the atomic weight.
Atoms of the same element that differ in their atomic weight are called isotopes.
Atomic weights are expressed in terms of a standard atom: the isotope of carbon that has 6 protons and 6 neutrons in its nucleus. This atom is designated carbon-12 or 12C. It is arbitrarily assigned an atomic weight of 12 daltons (named after John Dalton, the pioneer in the study of atomic weights). Thus a dalton is 1/12 the weight of an atom of 12C. Both protons and neutrons have weights very close to 1 dalton each. Carbon-12 is the most common isotope of carbon. Carbon-13 (13C) with 6 protons and 7 neutrons, and carbon-14 (14C) with 6 protons and 8 neutrons are found in much smaller quantities.
Isotopes as "tracers"
One can prepare, for example, a carbon compound used by living things that has many of its normal 12C atoms replaced by 14C atoms. Carbon-14 happens to be radioactive. By tracing the fate of radioactivity within the organism, one can learn the normal pathway of this carbon compound in that organism. Thus 14C serves as an isotopic "label" or "tracer".
The basis of this technique is that the weight of the nucleus of an atom has little or no effect on the chemical properties of that atom. The chemistry of an element and the atoms of which it is made — whatever their atomic weight — is a function of the atomic number of that element. As long as the atom had 6 protons, it is an atom of carbon irrespective of the number of neutrons. Thus while 6 protons and 8 neutrons produce an isotope of carbon, 14C, 7 protons and 7 neutrons produce a totally-different element, nitrogen-14. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/02%3A_The_Nature_of_Molecules_and_the_Properties_of_Water/2.02%3A_Elements_Found_in_Living_Systems.txt |
At its most fundamental level, life is made up of matter. Matter occupies space and has mass. All matter is composed of elements, substances that cannot be broken down or transformed chemically into other substances. Each element is made of atoms, each with a constant number of protons and unique properties. A total of 118 elements have been defined; however, only 92 occur naturally, and fewer than 30 are found in living cells. The remaining 26 elements are unstable and, therefore, do not exist for very long or are theoretical and have yet to be detected.
Each element is designated by its chemical symbol (such as H, N, O, C, and Na), and possesses unique properties. These unique properties allow elements to combine and to bond with each other in specific ways.
Atoms
An atom is the smallest component of an element that retains all of the chemical properties of that element. For example, one hydrogen atom has all of the properties of the element hydrogen, such as it exists as a gas at room temperature, and it bonds with oxygen to create a water molecule. Hydrogen atoms cannot be broken down into anything smaller while still retaining the properties of hydrogen. If a hydrogen atom were broken down into subatomic particles, it would no longer have the properties of hydrogen.
At the most basic level, all organisms are made of a combination of elements. They contain atoms that combine together to form molecules. In multicellular organisms, such as animals, molecules can interact to form cells that combine to form tissues, which make up organs. These combinations continue until entire multicellular organisms are formed.
All atoms contain protons, electrons, and neutrons (Figure \(1\)). The only exception is hydrogen (H), which is made of one proton and one electron. A proton is a positively charged particle that resides in the nucleus (the core of the atom) of an atom and has a mass of 1 and a charge of +1. An electron is a negatively charged particle that travels in the space around the nucleus. In other words, it resides outside of the nucleus. It has a negligible mass and has a charge of –1.
Neutrons, like protons, reside in the nucleus of an atom. They have a mass of 1 and no charge. The positive (protons) and negative (electrons) charges balance each other in a neutral atom, which has a net zero charge.
Because protons and neutrons each have a mass of 1, the mass of an atom is equal to the number of protons and neutrons of that atom. The number of electrons does not factor into the overall mass, because their mass is so small.
As stated earlier, each element has its own unique properties. Each contains a different number of protons and neutrons, giving it its own atomic number and mass number. The atomic number of an element is equal to the number of protons that element contains. The mass number, or atomic mass, is the number of protons plus the number of neutrons of that element. Therefore, it is possible to determine the number of neutrons by subtracting the atomic number from the mass number.
These numbers provide information about the elements and how they will react when combined. Different elements have different melting and boiling points, and are in different states (liquid, solid, or gas) at room temperature. They also combine in different ways. Some form specific types of bonds, whereas others do not. How they combine is based on the number of electrons present. Because of these characteristics, the elements are arranged into the periodic table of elements, a chart of the elements that includes the atomic number and relative atomic mass of each element. The periodic table also provides key information about the properties of elements (Figure \(2\))—often indicated by color-coding. The arrangement of the table also shows how the electrons in each element are organized and provides important details about how atoms will react with each other to form molecules.
Isotopes are different forms of the same element that have the same number of protons, but a different number of neutrons. Some elements, such as carbon, potassium, and uranium, have naturally occurring isotopes. Carbon-12, the most common isotope of carbon, contains six protons and six neutrons. Therefore, it has a mass number of 12 (six protons and six neutrons) and an atomic number of 6 (which makes it carbon). Carbon-14 contains six protons and eight neutrons. Therefore, it has a mass number of 14 (six protons and eight neutrons) and an atomic number of 6, meaning it is still the element carbon. These two alternate forms of carbon are isotopes. Some isotopes are unstable and will lose protons, other subatomic particles, or energy to form more stable elements. These are called radioactive isotopes or radioisotopes.
ART CONNECTION
How many neutrons do (K) potassium-39 and potassium-40 have, respectively?
EVOLUTION IN ACTION: Carbon Dating
Carbon-14 (14C) is a naturally occurring radioisotope that is created in the atmosphere by cosmic rays. This is a continuous process, so more 14C is always being created. As a living organism develops, the relative level of 14C in its body is equal to the concentration of 14C in the atmosphere. When an organism dies, it is no longer ingesting 14C, so the ratio will decline. 14C decays to 14N by a process called beta decay; it gives off energy in this slow process.
After approximately 5,730 years, only one-half of the starting concentration of 14C will have been converted to 14N. The time it takes for half of the original concentration of an isotope to decay to its more stable form is called its half-life. Because the half-life of 14C is long, it is used to age formerly living objects, such as fossils. Using the ratio of the 14C concentration found in an object to the amount of 14C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined. Based on this amount, the age of the fossil can be calculated to about 50,000 years (Figure \(3\)). Isotopes with longer half-lives, such as potassium-40, are used to calculate the ages of older fossils. Through the use of carbon dating, scientists can reconstruct the ecology and biogeography of organisms living within the past 50,000 years.
CONCEPT IN ACTION
To learn more about atoms and isotopes, and how you can tell one isotope from another, visit this site and run the simulation.
Chemical Bonds
How elements interact with one another depends on how their electrons are arranged and how many openings for electrons exist at the outermost region where electrons are present in an atom. Electrons exist at energy levels that form shells around the nucleus. The closest shell can hold up to two electrons. The closest shell to the nucleus is always filled first, before any other shell can be filled. Hydrogen has one electron; therefore, it has only one spot occupied within the lowest shell. Helium has two electrons; therefore, it can completely fill the lowest shell with its two electrons. If you look at the periodic table, you will see that hydrogen and helium are the only two elements in the first row. This is because they only have electrons in their first shell. Hydrogen and helium are the only two elements that have the lowest shell and no other shells.
The second and third energy levels can hold up to eight electrons. The eight electrons are arranged in four pairs and one position in each pair is filled with an electron before any pairs are completed.
Looking at the periodic table again (Figure \(2\)), you will notice that there are seven rows. These rows correspond to the number of shells that the elements within that row have. The elements within a particular row have increasing numbers of electrons as the columns proceed from left to right. Although each element has the same number of shells, not all of the shells are completely filled with electrons. If you look at the second row of the periodic table, you will find lithium (Li), beryllium (Be), boron (B), carbon (C), nitrogen (N), oxygen (O), fluorine (F), and neon (Ne). These all have electrons that occupy only the first and second shells. Lithium has only one electron in its outermost shell, beryllium has two electrons, boron has three, and so on, until the entire shell is filled with eight electrons, as is the case with neon.
Not all elements have enough electrons to fill their outermost shells, but an atom is at its most stable when all of the electron positions in the outermost shell are filled. Because of these vacancies in the outermost shells, we see the formation of chemical bonds, or interactions between two or more of the same or different elements that result in the formation of molecules. To achieve greater stability, atoms will tend to completely fill their outer shells and will bond with other elements to accomplish this goal by sharing electrons, accepting electrons from another atom, or donating electrons to another atom. Because the outermost shells of the elements with low atomic numbers (up to calcium, with atomic number 20) can hold eight electrons, this is referred to as the octet rule. An element can donate, accept, or share electrons with other elements to fill its outer shell and satisfy the octet rule.
When an atom does not contain equal numbers of protons and electrons, it is called an ion. Because the number of electrons does not equal the number of protons, each ion has a net charge. Positive ions are formed by losing electrons and are called cations. Negative ions are formed by gaining electrons and are called anions.
For example, sodium only has one electron in its outermost shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons and only 10 electrons, leaving it with an overall charge of +1. It is now called a sodium ion.
The chlorine atom has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons and 18 electrons, giving it a net negative (–1) charge. It is now called a chloride ion. This movement of electrons from one element to another is referred to as electron transfer. As Figure \(4\) illustrates, a sodium atom (Na) only has one electron in its outermost shell, whereas a chlorine atom (Cl) has seven electrons in its outermost shell. A sodium atom will donate its one electron to empty its shell, and a chlorine atom will accept that electron to fill its shell, becoming chloride. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium) or –1 (chloride) charge.
Ionic Bonds
There are four types of bonds or interactions: ionic, covalent, hydrogen bonds, and van der Waals interactions. Ionic and covalent bonds are strong interactions that require a larger energy input to break apart. When an element donates an electron from its outer shell, as in the sodium atom example above, a positive ion is formed. The element accepting the electron is now negatively charged. Because positive and negative charges attract, these ions stay together and form an ionic bond, or a bond between ions. The elements bond together with the electron from one element staying predominantly with the other element. When Na+ and Cl ions combine to produce NaCl, an electron from a sodium atom stays with the other seven from the chlorine atom, and the sodium and chloride ions attract each other in a lattice of ions with a net zero charge.
Covalent Bonds
Another type of strong chemical bond between two or more atoms is a covalent bond. These bonds form when an electron is shared between two elements and are the strongest and most common form of chemical bond in living organisms. Covalent bonds form between the elements that make up the biological molecules in our cells. Unlike ionic bonds, covalent bonds do not dissociate in water.
The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds. The electron from the hydrogen atom divides its time between the outer shell of the hydrogen atom and the incomplete outer shell of the oxygen atom. To completely fill the outer shell of an oxygen atom, two electrons from two hydrogen atoms are needed, hence the subscript “2” in H2O. The electrons are shared between the atoms, dividing their time between them to “fill” the outer shell of each. This sharing is a lower energy state for all of the atoms involved than if they existed without their outer shells filled.
There are two types of covalent bonds: polar and nonpolar. Nonpolar covalent bonds form between two atoms of the same element or between different elements that share the electrons equally. For example, an oxygen atom can bond with another oxygen atom to fill their outer shells. This association is nonpolar because the electrons will be equally distributed between each oxygen atom. Two covalent bonds form between the two oxygen atoms because oxygen requires two shared electrons to fill its outermost shell. Nitrogen atoms will form three covalent bonds (also called triple covalent) between two atoms of nitrogen because each nitrogen atom needs three electrons to fill its outermost shell. Another example of a nonpolar covalent bond is found in the methane (CH4) molecule. The carbon atom has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one. These elements all share the electrons equally, creating four nonpolar covalent bonds (Figure \(5\)).
In a polar covalent bond, the electrons shared by the atoms spend more time closer to one nucleus than to the other nucleus. Because of the unequal distribution of electrons between the different nuclei, a slightly positive (δ+) or slightly negative (δ–) charge develops. The covalent bonds between hydrogen and oxygen atoms in water are polar covalent bonds. The shared electrons spend more time near the oxygen nucleus, giving it a small negative charge, than they spend near the hydrogen nuclei, giving these molecules a small positive charge.
Hydrogen Bonds
Ionic and covalent bonds are strong bonds that require considerable energy to break. However, not all bonds between elements are ionic or covalent bonds. Weaker bonds can also form. These are attractions that occur between positive and negative charges that do not require much energy to break. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. These bonds give rise to the unique properties of water and the unique structures of DNA and proteins.
When polar covalent bonds containing a hydrogen atom form, the hydrogen atom in that bond has a slightly positive charge. This is because the shared electron is pulled more strongly toward the other element and away from the hydrogen nucleus. Because the hydrogen atom is slightly positive (δ+), it will be attracted to neighboring negative partial charges (δ–). When this happens, a weak interaction occurs between the δ+ charge of the hydrogen atom of one molecule and the δ– charge of the other molecule. This interaction is called a hydrogen bond. This type of bond is common; for example, the liquid nature of water is caused by the hydrogen bonds between water molecules (Figure \(6\)). Hydrogen bonds give water the unique properties that sustain life. If it were not for hydrogen bonding, water would be a gas rather than a liquid at room temperature.
Hydrogen bonds can form between different molecules and they do not always have to include a water molecule. Hydrogen atoms in polar bonds within any molecule can form bonds with other adjacent molecules. For example, hydrogen bonds hold together two long strands of DNA to give the DNA molecule its characteristic double-stranded structure. Hydrogen bonds are also responsible for some of the three-dimensional structure of proteins.
van der Waals Interactions
Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. They occur between polar, covalently bound, atoms in different molecules. Some of these weak attractions are caused by temporary partial charges formed when electrons move around a nucleus. These weak interactions between molecules are important in biological systems.
CAREERS IN ACTION: Radiography Technician
Have you or anyone you know ever had a magnetic resonance imaging (MRI) scan, a mammogram, or an X-ray? These tests produce images of your soft tissues and organs (as with an MRI or mammogram) or your bones (as happens in an X-ray) by using either radiowaves or special isotopes (radiolabeled or fluorescently labeled) that are ingested or injected into the body. These tests provide data for disease diagnoses by creating images of your organs or skeletal system.
MRI imaging works by subjecting hydrogen nuclei, which are abundant in the water in soft tissues, to fluctuating magnetic fields, which cause them to emit their own magnetic field. This signal is then read by sensors in the machine and interpreted by a computer to form a detailed image.
Some radiography technologists and technicians specialize in computed tomography, MRI, and mammography. They produce films or images of the body that help medical professionals examine and diagnose. Radiologists work directly with patients, explaining machinery, preparing them for exams, and ensuring that their body or body parts are positioned correctly to produce the needed images. Physicians or radiologists then analyze the test results.
Radiography technicians can work in hospitals, doctors’ offices, or specialized imaging centers. Training to become a radiography technician happens at hospitals, colleges, and universities that offer certificates, associate’s degrees, or bachelor’s degrees in radiography.
Summary
Matter is anything that occupies space and has mass. It is made up of atoms of different elements. All of the 92 elements that occur naturally have unique qualities that allow them to combine in various ways to create compounds or molecules. Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can be donated or shared between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.
Art Connections
Figure \(2\): How many neutrons do (K) potassium-39 and potassium-40 have, respectively?
Answer
Potassium-39 has twenty neutrons. Potassium-40 has twenty one neutrons.
Glossary
anion
a negative ion formed by gaining electrons
atomic number
the number of protons in an atom
cation
a positive ion formed by losing electrons
chemical bond
an interaction between two or more of the same or different elements that results in the formation of molecules
covalent bond
a type of strong bond between two or more of the same or different elements; forms when electrons are shared between elements
electron
a negatively charged particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a charge of –1
electron transfer
the movement of electrons from one element to another
element
one of 118 unique substances that cannot be broken down into smaller substances and retain the characteristic of that substance; each element has a specified number of protons and unique properties
hydrogen bond
a weak bond between partially positively charged hydrogen atoms and partially negatively charged elements or molecules
ion
an atom or compound that does not contain equal numbers of protons and electrons, and therefore has a net charge
ionic bond
a chemical bond that forms between ions of opposite charges
isotope
one or more forms of an element that have different numbers of neutrons
mass number
the number of protons plus neutrons in an atom
matter
anything that has mass and occupies space
neutron
a particle with no charge that resides in the nucleus of an atom; has a mass of 1
nonpolar covalent bond
a type of covalent bond that forms between atoms when electrons are shared equally between atoms, resulting in no regions with partial charges as in polar covalent bonds
nucleus
(chemistry) the dense center of an atom made up of protons and (except in the case of a hydrogen atom) neutrons
octet rule
states that the outermost shell of an element with a low atomic number can hold eight electrons
periodic table of elements
an organizational chart of elements, indicating the atomic number and mass number of each element; also provides key information about the properties of elements
polar covalent bond
a type of covalent bond in which electrons are pulled toward one atom and away from another, resulting in slightly positive and slightly negative charged regions of the molecule
proton
a positively charged particle that resides in the nucleus of an atom; has a mass of 1 and a charge of +1
radioactive isotope
an isotope that spontaneously emits particles or energy to form a more stable element
van der Waals interaction
a weak attraction or interaction between molecules caused by slightly positively charged or slightly negatively charged atoms
2.03: The Nature of Chemical Bonds
Electronegativity
The electronegativity of an atom is a measure of its affinity for electrons. The atoms of the various elements differ in their affinity for electrons.
This image distorts the conventional periodic table of the elements so that the greater the electronegativity of an atom, the higher its position in the table. Although fluorine (F) is the most electronegative element, it is the electronegativity of runner-up oxygen (O) that is exploited by life. The shuttling of electrons between carbon (C) and oxygen (O) atoms powers life.
1. Moving electrons against the gradient (O to C) — as occurs in photosynthesis — requires energy (and stores it).
2. Moving electrons down the gradient (C to O) — as occurs in cellular respiration — releases energy.
The relative electronegativity of two interacting atoms also plays a major part in determining what kind of chemical bond forms between them.
Chemical Bonds
Three main types of chemical bonds:Ionic Bond, Covalent Bond, Polar Covalent Bond.
Ionic Bond
Example of an ionic bond is : Sodium (Na) and Chlorine (Cl) = Ionic Bond. There is a large difference in electronegativity between Na and Cl atoms, so
• the chlorine atom takes an electron from the sodium atom
• converting the atoms into ions (Na+) and (Cl)
• These are held together by their opposite electrical charge forming ionic bonds
• Each sodium ion is held by 6 chloride ions while each chloride ion is, in turn, held by 6 sodium ions
• Result: a crystal lattice (not molecules) of common table salt (NaCl)
Covalent Bond
Example of a covalent bond is: Carbon (C) and Hydrogen (H) = Covalent Bond. There is only a small difference in electronegativity between the C and H atoms, so
• the two atoms share the electrons
• Result: a covalent bond (depicted as C:H or C-H)
• The atoms are held together by their mutual affinity for their shared electrons
• An array of atoms held together by covalent bonds forms a true molecule
Polar Covalent Bond
Example of a polar covalent bond is: Hydrogen (H) and Oxygen (O) = Polar Covalent Bond. There is a moderate difference in electronegativity, causing the oxygen atom to pull the electron of the hydrogen atom closer to itself. This results in a polar covalent bond. Oxygen does this with 2 hydrogen atoms to form a molecule of water
Molecules, like water, with polar covalent bonds are themselves polar; that is, have partial electrical charges across the molecule and may be attracted to each other (as occurs with water molecules). These species are good solvents for polar and/or hydrophilic compounds may form hydrogen bonds. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/02%3A_The_Nature_of_Molecules_and_the_Properties_of_Water/2.03%3A_The_Nature_of_Chemical_Bonds/2.3.01%3A_Electronegativity_and_types_of_Chemical_Bonds.txt |
Do you ever wonder why scientists spend time looking for water on other planets? It is because water is essential to life; even minute traces of it on another planet can indicate that life could or did exist on that planet. Water is one of the more abundant molecules in living cells and the one most critical to life as we know it. Approximately 60–70 percent of your body is made up of water. Without it, life simply would not exist.
Water Is Polar
The hydrogen and oxygen atoms within water molecules form polar covalent bonds. The shared electrons spend more time associated with the oxygen atom than they do with hydrogen atoms. There is no overall charge to a water molecule, but there is a slight positive charge on each hydrogen atom and a slight negative charge on the oxygen atom. Because of these charges, the slightly positive hydrogen atoms repel each other and form the unique shape seen in Figure 2.1.6. Each water molecule attracts other water molecules because of the positive and negative charges in the different parts of the molecule. Water also attracts other polar molecules (such as sugars), forming hydrogen bonds. When a substance readily forms hydrogen bonds with water, it can dissolve in water and is referred to as hydrophilic (“water-loving”). Hydrogen bonds are not readily formed with nonpolar substances like oils and fats (Figure \(1\)). These nonpolar compounds are hydrophobic (“water-fearing”) and will not dissolve in water.
Water Stabilizes Temperature
The hydrogen bonds in water allow it to absorb and release heat energy more slowly than many other substances. Temperature is a measure of the motion (kinetic energy) of molecules. As the motion increases, energy is higher and thus temperature is higher. Water absorbs a great deal of energy before its temperature rises. Increased energy disrupts the hydrogen bonds between water molecules. Because these bonds can be created and disrupted rapidly, water absorbs an increase in energy and temperature changes only minimally. This means that water moderates temperature changes within organisms and in their environments. As energy input continues, the balance between hydrogen-bond formation and destruction swings toward the destruction side. More bonds are broken than are formed. This process results in the release of individual water molecules at the surface of the liquid (such as a body of water, the leaves of a plant, or the skin of an organism) in a process called evaporation. Evaporation of sweat, which is 90 percent water, allows for cooling of an organism, because breaking hydrogen bonds requires an input of energy and takes heat away from the body.
Conversely, as molecular motion decreases and temperatures drop, less energy is present to break the hydrogen bonds between water molecules. These bonds remain intact and begin to form a rigid, lattice-like structure (e.g., ice) (Figure \(2\)a). When frozen, ice is less dense than liquid water (the molecules are farther apart). This means that ice floats on the surface of a body of water (Figure \(2\)b). In lakes, ponds, and oceans, ice will form on the surface of the water, creating an insulating barrier to protect the animal and plant life beneath from freezing in the water. If this did not happen, plants and animals living in water would freeze in a block of ice and could not move freely, making life in cold temperatures difficult or impossible.
CONCEPTS IN ACTION
Click here to see a 3-D animation of the structure of an ice lattice. (credit: image created by Jane Whitney using Visual Molecular Dynamics (VMD) software1)
Water Is an Excellent Solvent
Because water is polar, with slight positive and negative charges, ionic compounds and polar molecules can readily dissolve in it. Water is, therefore, what is referred to as a solvent—a substance capable of dissolving another substance. The charged particles will form hydrogen bonds with a surrounding layer of water molecules. This is referred to as a sphere of hydration and serves to keep the particles separated or dispersed in the water. In the case of table salt (NaCl) mixed in water (Figure \(3\)), the sodium and chloride ions separate, or dissociate, in the water, and spheres of hydration are formed around the ions. A positively charged sodium ion is surrounded by the partially negative charges of oxygen atoms in water molecules. A negatively charged chloride ion is surrounded by the partially positive charges of hydrogen atoms in water molecules. These spheres of hydration are also referred to as hydration shells. The polarity of the water molecule makes it an effective solvent and is important in its many roles in living systems.
Water Is Cohesive
Have you ever filled up a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water actually forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the liquid-air (gas) interface, although there is no more room in the glass. Cohesion gives rise to surface tension, the capacity of a substance to withstand rupture when placed under tension or stress. When you drop a small scrap of paper onto a droplet of water, the paper floats on top of the water droplet, although the object is denser (heavier) than the water. This occurs because of the surface tension that is created by the water molecules. Cohesion and surface tension keep the water molecules intact and the item floating on the top. It is even possible to “float” a steel needle on top of a glass of water if you place it gently, without breaking the surface tension (Figure \(4\)).
These cohesive forces are also related to the water’s property of adhesion, or the attraction between water molecules and other molecules. This is observed when water “climbs” up a straw placed in a glass of water. You will notice that the water appears to be higher on the sides of the straw than in the middle. This is because the water molecules are attracted to the straw and therefore adhere to it.
Cohesive and adhesive forces are important for sustaining life. For example, because of these forces, water can flow up from the roots to the tops of plants to feed the plant.
CONCEPT IN ACTION
To learn more about water, visit the U.S. Geological Survey Water Science for Schools: All About Water! website.
Buffers, pH, Acids, and Bases
The pH of a solution is a measure of its acidity or alkalinity. You have probably used litmus paper, paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator, to test how much acid or base (alkalinity) exists in a solution. You might have even used some to make sure the water in an outdoor swimming pool is properly treated. In both cases, this pH test measures the amount of hydrogen ions that exists in a given solution. High concentrations of hydrogen ions yield a low pH, whereas low levels of hydrogen ions result in a high pH. The overall concentration of hydrogen ions is inversely related to its pH and can be measured on the pH scale (Figure \(5\)). Therefore, the more hydrogen ions present, the lower the pH; conversely, the fewer hydrogen ions, the higher the pH.
The pH scale ranges from 0 to 14. A change of one unit on the pH scale represents a change in the concentration of hydrogen ions by a factor of 10, a change in two units represents a change in the concentration of hydrogen ions by a factor of 100. Thus, small changes in pH represent large changes in the concentrations of hydrogen ions. Pure water is neutral. It is neither acidic nor basic, and has a pH of 7.0. Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. The blood in your veins is slightly alkaline (pH = 7.4). The environment in your stomach is highly acidic (pH = 1 to 2). Orange juice is mildly acidic (pH = approximately 3.5), whereas baking soda is basic (pH = 9.0).
Acids are substances that provide hydrogen ions (H+) and lower pH, whereas bases provide hydroxide ions (OH) and raise pH. The stronger the acid, the more readily it donates H+. For example, hydrochloric acid and lemon juice are very acidic and readily give up H+ when added to water. Conversely, bases are those substances that readily donate OH. The OH ions combine with H+ to produce water, which raises a substance’s pH. Sodium hydroxide and many household cleaners are very alkaline and give up OH rapidly when placed in water, thereby raising the pH.
Most cells in our bodies operate within a very narrow window of the pH scale, typically ranging only from 7.2 to 7.6. If the pH of the body is outside of this range, the respiratory system malfunctions, as do other organs in the body. Cells no longer function properly, and proteins will break down. Deviation outside of the pH range can induce coma or even cause death.
So how is it that we can ingest or inhale acidic or basic substances and not die? Buffers are the key. Buffersreadily absorb excess H+ or OH, keeping the pH of the body carefully maintained in the aforementioned narrow range. Carbon dioxide is part of a prominent buffer system in the human body; it keeps the pH within the proper range. This buffer system involves carbonic acid (H2CO3) and bicarbonate (HCO3) anion. If too much H+ enters the body, bicarbonate will combine with the H+ to create carbonic acid and limit the decrease in pH. Likewise, if too much OH is introduced into the system, carbonic acid will rapidly dissociate into bicarbonate and H+ ions. The H+ ions can combine with the OH ions, limiting the increase in pH. While carbonic acid is an important product in this reaction, its presence is fleeting because the carbonic acid is released from the body as carbon dioxide gas each time we breathe. Without this buffer system, the pH in our bodies would fluctuate too much and we would fail to survive.
Summary
Water has many properties that are critical to maintaining life. It is polar, allowing for the formation of hydrogen bonds, which allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent. The hydrogen bonds between water molecules give water the ability to hold heat better than many other substances. As the temperature rises, the hydrogen bonds between water continually break and reform, allowing for the overall temperature to remain stable, although increased energy is added to the system. Water’s cohesive forces allow for the property of surface tension. All of these unique properties of water are important in the chemistry of living organisms.
The pH of a solution is a measure of the concentration of hydrogen ions in the solution. A solution with a high number of hydrogen ions is acidic and has a low pH value. A solution with a high number of hydroxide ions is basic and has a high pH value. The pH scale ranges from 0 to 14, with a pH of 7 being neutral. Buffers are solutions that moderate pH changes when an acid or base is added to the buffer system. Buffers are important in biological systems because of their ability to maintain constant pH conditions.
Footnotes
1. 1 Humphrey, W., Dalke, A. and Schulten, K., "VMD—Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. http://www.ks.uiuc.edu/Research/vmd/
Glossary
acid
a substance that donates hydrogen ions and therefore lowers pH
adhesion
the attraction between water molecules and molecules of a different substance
base
a substance that absorbs hydrogen ions and therefore raises pH
buffer
a solution that resists a change in pH by absorbing or releasing hydrogen or hydroxide ions
cohesion
the intermolecular forces between water molecules caused by the polar nature of water; creates surface tension
evaporation
the release of water molecules from liquid water to form water vapor
hydrophilic
describes a substance that dissolves in water; water-loving
hydrophobic
describes a substance that does not dissolve in water; water-fearing
litmus paper
filter paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator
pH scale
a scale ranging from 0 to 14 that measures the approximate concentration of hydrogen ions of a substance
solvent
a substance capable of dissolving another substance
surface tension
the cohesive force at the surface of a body of liquid that prevents the molecules from separating
temperature
a measure of molecular motion | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/02%3A_The_Nature_of_Molecules_and_the_Properties_of_Water/2.04%3A_Water-_A_Vital_Compound.txt |
Skills to Develop
• Describe the properties of water that are critical to maintaining life
• Explain why water is an excellent solvent
• Provide examples of water’s cohesive and adhesive properties
• Discuss the role of acids, bases, and buffers in homeostasis
Why do scientists spend time looking for water on other planets? Why is water so important? It is because water is essential to life as we know it. Water is one of the more abundant molecules and the one most critical to life on Earth. Approximately 60–70 percent of the human body is made up of water. Without it, life as we know it simply would not exist.
The polarity of the water molecule and its resulting hydrogen bonding make water a unique substance with special properties that are intimately tied to the processes of life. Life originally evolved in a watery environment, and most of an organism’s cellular chemistry and metabolism occur inside the watery contents of the cell’s cytoplasm. Special properties of water are its high heat capacity and heat of vaporization, its ability to dissolve polar molecules, its cohesive and adhesive properties, and its dissociation into ions that leads to the generation of pH. Understanding these characteristics of water helps to elucidate its importance in maintaining life.
Water’s Polarity
One of water’s important properties is that it is composed of polar molecules: the hydrogen and oxygen within water molecules (H2O) form polar covalent bonds. While there is no net charge to a water molecule, the polarity of water creates a slightly positive charge on hydrogen and a slightly negative charge on oxygen, contributing to water’s properties of attraction. Water’s charges are generated because oxygen is more electronegative than hydrogen, making it more likely that a shared electron would be found near the oxygen nucleus than the hydrogen nucleus, thus generating the partial negative charge near the oxygen.
As a result of water’s polarity, each water molecule attracts other water molecules because of the opposite charges between water molecules, forming hydrogen bonds. Water also attracts or is attracted to other polar molecules and ions. A polar substance that interacts readily with or dissolves in water is referred to as hydrophilic (hydro- = “water”; -philic = “loving”). In contrast, non-polar molecules such as oils and fats do not interact well with water, as shown in Figure $1$ and separate from it rather than dissolve in it, as we see in salad dressings containing oil and vinegar (an acidic water solution). These nonpolar compounds are called hydrophobic (hydro- = “water”; -phobic = “fearing”).
Water’s States: Gas, Liquid, and Solid
The formation of hydrogen bonds is an important quality of the liquid water that is crucial to life as we know it. As water molecules make hydrogen bonds with each other, water takes on some unique chemical characteristics compared to other liquids and, since living things have a high water content, understanding these chemical features is key to understanding life. In liquid water, hydrogen bonds are constantly formed and broken as the water molecules slide past each other. The breaking of these bonds is caused by the motion (kinetic energy) of the water molecules due to the heat contained in the system. When the heat is raised as water is boiled, the higher kinetic energy of the water molecules causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas (steam or water vapor). On the other hand, when the temperature of water is reduced and water freezes, the water molecules form a crystalline structure maintained by hydrogen bonding (there is not enough energy to break the hydrogen bonds) that makes ice less dense than liquid water, a phenomenon not seen in the solidification of other liquids.
Water’s lower density in its solid form is due to the way hydrogen bonds are oriented as it freezes: the water molecules are pushed farther apart compared to liquid water. With most other liquids, solidification when the temperature drops includes the lowering of kinetic energy between molecules, allowing them to pack even more tightly than in liquid form and giving the solid a greater density than the liquid.
The lower density of ice, illustrated and pictured in Figure $2$, an anomaly, causes it to float at the surface of liquid water, such as in an iceberg or in the ice cubes in a glass of ice water. In lakes and ponds, ice will form on the surface of the water creating an insulating barrier that protects the animals and plant life in the pond from freezing. Without this layer of insulating ice, plants and animals living in the pond would freeze in the solid block of ice and could not survive. The detrimental effect of freezing on living organisms is caused by the expansion of ice relative to liquid water. The ice crystals that form upon freezing rupture the delicate membranes essential for the function of living cells, irreversibly damaging them. Cells can only survive freezing if the water in them is temporarily replaced by another liquid like glycerol.
Link to Learning
Video: Click here to see a 3-D animation of the structure of an ice lattice. (Image credit: Jane Whitney. Image created using Visual Molecular Dynamics VMD software.2)
Water’s High Heat Capacity
Water’s high heat capacity is a property caused by hydrogen bonding among water molecules. Water has the highest specific heat capacity of any liquids. Specific heat is defined as the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius. For water, this amount is one calorie. It therefore takes water a long time to heat and long time to cool. In fact, the specific heat capacity of water is about five times more than that of sand. This explains why the land cools faster than the sea. Due to its high heat capacity, water is used by warm blooded animals to more evenly disperse heat in their bodies: it acts in a similar manner to a car’s cooling system, transporting heat from warm places to cool places, causing the body to maintain a more even temperature.
Water’s Heat of Vaporization
Water also has a high heat of vaporization, the amount of energy required to change one gram of a liquid substance to a gas. A considerable amount of heat energy (586 cal) is required to accomplish this change in water. This process occurs on the surface of water. As liquid water heats up, hydrogen bonding makes it difficult to separate the liquid water molecules from each other, which is required for it to enter its gaseous phase (steam). As a result, water acts as a heat sink or heat reservoir and requires much more heat to boil than does a liquid such as ethanol (grain alcohol), whose hydrogen bonding with other ethanol molecules is weaker than water’s hydrogen bonding. Eventually, as water reaches its boiling point of 100° Celsius (212° Fahrenheit), the heat is able to break the hydrogen bonds between the water molecules, and the kinetic energy (motion) between the water molecules allows them to escape from the liquid as a gas. Even when below its boiling point, water’s individual molecules acquire enough energy from other water molecules such that some surface water molecules can escape and vaporize: this process is known as evaporation.
The fact that hydrogen bonds need to be broken for water to evaporate means that a substantial amount of energy is used in the process. As the water evaporates, energy is taken up by the process, cooling the environment where the evaporation is taking place. In many living organisms, including in humans, the evaporation of sweat, which is 90 percent water, allows the organism to cool so that homeostasis of body temperature can be maintained.
Water’s Solvent Properties
Since water is a polar molecule with slightly positive and slightly negative charges, ions and polar molecules can readily dissolve in it. Therefore, water is referred to as a solvent, a substance capable of dissolving other polar molecules and ionic compounds. The charges associated with these molecules will form hydrogen bonds with water, surrounding the particle with water molecules. This is referred to as a sphere of hydration, or a hydration shell, as illustrated in Figure $3$ and serves to keep the particles separated or dispersed in the water.
When ionic compounds are added to water, the individual ions react with the polar regions of the water molecules and their ionic bonds are disrupted in the process of dissociation. Dissociation occurs when atoms or groups of atoms break off from molecules and form ions. Consider table salt (NaCl, or sodium chloride): when NaCl crystals are added to water, the molecules of NaCl dissociate into Na+ and Cl ions, and spheres of hydration form around the ions, illustrated in Figure $3$. The positively charged sodium ion is surrounded by the partially negative charge of the water molecule’s oxygen. The negatively charged chloride ion is surrounded by the partially positive charge of the hydrogen on the water molecule.
Water’s Cohesive and Adhesive Properties
Have you ever filled a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the liquid-gas (water-air) interface, although there is no more room in the glass.
Cohesion allows for the development of surface tension, the capacity of a substance to withstand being ruptured when placed under tension or stress. This is also why water forms droplets when placed on a dry surface rather than being flattened out by gravity. When a small scrap of paper is placed onto the droplet of water, the paper floats on top of the water droplet even though paper is denser (heavier) than the water. Cohesion and surface tension keep the hydrogen bonds of water molecules intact and support the item floating on the top. It’s even possible to “float” a needle on top of a glass of water if it is placed gently without breaking the surface tension, as shown in Figure $4$.
These cohesive forces are related to water’s property of adhesion, or the attraction between water molecules and other molecules. This attraction is sometimes stronger than water’s cohesive forces, especially when the water is exposed to charged surfaces such as those found on the inside of thin glass tubes known as capillary tubes. Adhesion is observed when water “climbs” up the tube placed in a glass of water: notice that the water appears to be higher on the sides of the tube than in the middle. This is because the water molecules are attracted to the charged glass walls of the capillary more than they are to each other and therefore adhere to it. This type of adhesion is called capillary action, and is illustrated in Figure $5$.
Why are cohesive and adhesive forces important for life? Cohesive and adhesive forces are important for the transport of water from the roots to the leaves in plants. These forces create a “pull” on the water column. This pull results from the tendency of water molecules being evaporated on the surface of the plant to stay connected to water molecules below them, and so they are pulled along. Plants use this natural phenomenon to help transport water from their roots to their leaves. Without these properties of water, plants would be unable to receive the water and the dissolved minerals they require. In another example, insects such as the water strider, shown in Figure $6$, use the surface tension of water to stay afloat on the surface layer of water and even mate there.
pH, Buffers, Acids, and Bases
The pH of a solution indicates its acidity or alkalinity.
$\ce{H_2O(I) \leftrightharpoons H^+ (aq) + O^- (aq)} \nonumber$
litmus or pH paper, filter paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator, to test how much acid (acidity) or base (alkalinity) exists in a solution. You might have even used some to test whether the water in a swimming pool is properly treated. In both cases, the pH test measures the concentration of hydrogen ions in a given solution.
Hydrogen ions are spontaneously generated in pure water by the dissociation (ionization) of a small percentage of water molecules into equal numbers of hydrogen (H+) ions and hydroxide (OH-) ions. While the hydroxide ions are kept in solution by their hydrogen bonding with other water molecules, the hydrogen ions, consisting of naked protons, are immediately attracted to un-ionized water molecules, forming hydronium ions (H30+). Still, by convention, scientists refer to hydrogen ions and their concentration as if they were free in this state in liquid water.
The concentration of hydrogen ions dissociating from pure water is 1 × 10-7 moles H+ ions per liter of water. Moles (mol) are a way to express the amount of a substance (which can be atoms, molecules, ions, etc), with one mole being equal to 6.02 x 1023 particles of the substance. Therefore, 1 mole of water is equal to 6.02 x 1023 water molecules. The pH is calculated as the negative of the base 10 logarithm of this concentration. The log10 of 1 × 10-7 is -7.0, and the negative of this number (indicated by the “p” of “pH”) yields a pH of 7.0, which is also known as neutral pH. The pH inside of human cells and blood are examples of two areas of the body where near-neutral pH is maintained.
Non-neutral pH readings result from dissolving acids or bases in water. Using the negative logarithm to generate positive integers, high concentrations of hydrogen ions yield a low pH number, whereas low levels of hydrogen ions result in a high pH. An acid is a substance that increases the concentration of hydrogen ions (H+) in a solution, usually by having one of its hydrogen atoms dissociate. A base provides either hydroxide ions (OH) or other negatively charged ions that combine with hydrogen ions, reducing their concentration in the solution and thereby raising the pH. In cases where the base releases hydroxide ions, these ions bind to free hydrogen ions, generating new water molecules.
The stronger the acid, the more readily it donates H+. For example, hydrochloric acid (HCl) completely dissociates into hydrogen and chloride ions and is highly acidic, whereas the acids in tomato juice or vinegar do not completely dissociate and are considered weak acids. Conversely, strong bases are those substances that readily donate OHor take up hydrogen ions. Sodium hydroxide (NaOH) and many household cleaners are highly alkaline and give up OH rapidly when placed in water, thereby raising the pH. An example of a weak basic solution is seawater, which has a pH near 8.0, close enough to neutral pH that marine organisms adapted to this saline environment are able to thrive in it.
The pH scale is, as previously mentioned, an inverse logarithm and ranges from 0 to 14 (Figure $7$). Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. Extremes in pH in either direction from 7.0 are usually considered inhospitable to life. The pH inside cells (6.8) and the pH in the blood (7.4) are both very close to neutral. However, the environment in the stomach is highly acidic, with a pH of 1 to 2. So how do the cells of the stomach survive in such an acidic environment? How do they homeostatically maintain the near neutral pH inside them? The answer is that they cannot do it and are constantly dying. New stomach cells are constantly produced to replace dead ones, which are digested by the stomach acids. It is estimated that the lining of the human stomach is completely replaced every seven to ten days.
Link to Learning
Watch this video for a straightforward explanation of pH and its logarithmic scale.
So how can organisms whose bodies require a near-neutral pH ingest acidic and basic substances (a human drinking orange juice, for example) and survive? Buffers are the key. Buffers readily absorb excess H+ or OH, keeping the pH of the body carefully maintained in the narrow range required for survival. Maintaining a constant blood pH is critical to a person’s well-being. The buffer maintaining the pH of human blood involves carbonic acid (H2CO3), bicarbonate ion (HCO3), and carbon dioxide (CO2). When bicarbonate ions combine with free hydrogen ions and become carbonic acid, hydrogen ions are removed, moderating pH changes. Similarly, as shown in Figure $8$, excess carbonic acid can be converted to carbon dioxide gas and exhaled through the lungs. This prevents too many free hydrogen ions from building up in the blood and dangerously reducing the blood’s pH. Likewise, if too much OH is introduced into the system, carbonic acid will combine with it to create bicarbonate, lowering the pH. Without this buffer system, the body’s pH would fluctuate enough to put survival in jeopardy.
Other examples of buffers are antacids used to combat excess stomach acid. Many of these over-the-counter medications work in the same way as blood buffers, usually with at least one ion capable of absorbing hydrogen and moderating pH, bringing relief to those that suffer “heartburn” after eating. The unique properties of water that contribute to this capacity to balance pH—as well as water’s other characteristics—are essential to sustaining life on Earth.
Link to Learning
To learn more about water. Visit the U.S. Geological Survey Water Science for Schools All About Water! website.
Summary
Water has many properties that are critical to maintaining life. It is a polar molecule, allowing for the formation of hydrogen bonds. Hydrogen bonds allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent. The hydrogen bonds between water molecules cause the water to have a high heat capacity, meaning it takes a lot of added heat to raise its temperature. As the temperature rises, the hydrogen bonds between water continually break and form anew. This allows for the overall temperature to remain stable, although energy is added to the system. Water also exhibits a high heat of vaporization, which is key to how organisms cool themselves by the evaporation of sweat. Water’s cohesive forces allow for the property of surface tension, whereas its adhesive properties are seen as water rises inside capillary tubes. The pH value is a measure of hydrogen ion concentration in a solution and is one of many chemical characteristics that is highly regulated in living organisms through homeostasis. Acids and bases can change pH values, but buffers tend to moderate the changes they cause. These properties of water are intimately connected to the biochemical and physical processes performed by living organisms, and life would be very different if these properties were altered, if it could exist at all.
Footnotes
1. 1 W. Humphrey W., A. Dalke, and K. Schulten, “VMD—Visual Molecular Dynamics,” Journal of Molecular Graphics 14 (1996): 33-38.
2. 2 W. Humphrey W., A. Dalke, and K. Schulten, “VMD—Visual Molecular Dynamics,” Journal of Molecular Graphics 14 (1996): 33-38.
Glossary
acid
molecule that donates hydrogen ions and increases the concentration of hydrogen ions in a solution
adhesion
attraction between water molecules and other molecules
base
molecule that donates hydroxide ions or otherwise binds excess hydrogen ions and decreases the concentration of hydrogen ions in a solution
buffer
substance that prevents a change in pH by absorbing or releasing hydrogen or hydroxide ions
calorie
amount of heat required to change the temperature of one gram of water by one degree Celsius
capillary action
occurs because water molecules are attracted to charges on the inner surfaces of narrow tubular structures such as glass tubes, drawing the water molecules to the sides of the tubes
cohesion
intermolecular forces between water molecules caused by the polar nature of water; responsible for surface tension
dissociation
release of an ion from a molecule such that the original molecule now consists of an ion and the charged remains of the original, such as when water dissociates into H+ and OH-
evaporation
separation of individual molecules from the surface of a body of water, leaves of a plant, or the skin of an organism
heat of vaporization of water
high amount of energy required for liquid water to turn into water vapor
hydrophilic
describes ions or polar molecules that interact well with other polar molecules such as water
hydrophobic
describes uncharged non-polar molecules that do not interact well with polar molecules such as water
litmus paper
(also, pH paper) filter paper that has been treated with a natural water-soluble dye that changes its color as the pH of the environment changes so it can be used as a pH indicator
pH paper
see litmus paper
pH scale
scale ranging from zero to 14 that is inversely proportional to the concentration of hydrogen ions in a solution
solvent
substance capable of dissolving another substance
specific heat capacity
the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius
sphere of hydration
when a polar water molecule surrounds charged or polar molecules thus keeping them dissolved and in solution
surface tension
tension at the surface of a body of liquid that prevents the molecules from separating; created by the attractive cohesive forces between the molecules of the liquid | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/02%3A_The_Nature_of_Molecules_and_the_Properties_of_Water/2.05%3A_Properties_of_Water.txt |
Acids and bases. Why are these important in biology?
It comes back to a number of biological processes. For example, enzymes work best at specific levels of acids or bases. Take your stomach, a very acidic environment. The enzymes that work in that environment could not work in your mouth. What would your food taste like if your mouth was also a very acidic environment?
Acids and Bases
Water is the main ingredient of many solutions. A solution is a mixture of two or moresubstances that has the same composition throughout. Some solutions are acids and some are bases. To understand acids and bases, you need to know more about pure water. In pure water (such as distilled water), a tiny fraction of water molecules naturally breaks down to form ions. An ion is an electrically charged atom or molecule. The breakdown of water is represented by the chemical equation
2 H2O → H3O+ + OH-
The products of this reaction are a hydronium ion (H3O+) and a hydroxide ion (OH-). The hydroxide ion, which has a negative charge, forms when a water molecule gives up a positively charged hydrogen ion (H+). The hydronium ion, which has positive charge, forms when another water molecule accepts the hydrogen ion.
Acidity and pH
The concentration of hydronium ions in a solution is known as acidity. In pure water, the concentration of hydronium ions is very low; only about 1 in 10 million water molecules naturally breaks down to form a hydronium ion. As a result, pure water is essentially neutral. Acidity is measured on a scale called pH, as shown in Figure below. Pure water has a pH of 7, so the point of neutrality on the pH scale is 7.
Acidity and the pH Scale Water has a pH of 7, so this is the point of neutrality on the pH scale. Acids have a pH less than 7, and bases have a pH greater than 7. Approximate pHs of examples are shown.
Acids
If a solution has a higher concentration of hydronium ions than pure water, it has a pH lower than 7. A solution with a pH lower than 7 is called an acid. As the hydronium ion concentration increases, the pH value decreases. Therefore, the more acidic a solution is, the lower its pH value is. Did you ever taste vinegar? Like other acids, it tastes sour. Stronger acids can be harmful to organisms. For example, stomach acid would eat through the stomach if it were not lined with a layer of mucus. Strong acids can also damage materials, even hard materials such as glass.
Bases
If a solution has a lower concentration of hydronium ions than pure water, it has a pH higher than 7. A solution with a pH higher than 7 is called a base. Bases, such as baking soda, have a bitter taste. Like strong acids, strong bases can harm organisms and damage materials. For example, lye can burn the skin, and bleach can remove the color from clothing.
Acids and Bases in Organisms
Acids and bases are important in living things because most enzymes can do their job only at a certain level of acidity. Cells secrete acids and bases to maintain the proper pH for enzymes to work. For example, every time you digest food, acids and bases are at work in your digestive system. Consider the acidic environment of the stomach. The acidic environment helps with the digestion of food. The enzyme pepsin, which helps break down proteins in the stomach can only function optimally in the low pH environment. The stomach secretes a strong acid that allows pepsin to work, and the stomach to do its job. However, when stomach contents enter the small intestine, the acid must be neutralized. This is because enzymes in the small intestine need a basic environment in order to work. An organ called the pancreas secretes a strong base into the small intestine, and this base neutralizes the acid.
Summary
• A solution is a mixture of two or more substances that has the same composition throughout. Some solutions are acids, some are bases.
• Pure water has a pH of 7, so the point of neutrality on the pH scale is 7.
• Acids have a higher concentration of hydronium ions than pure water, and a pH lower than 7.
• Bases have a lower concentration of hydronium ions than pure water, and a pH higher than 7.
• Acids and bases are important in living organisms because most enzymes function best at a specific pH.
Explore More
Use these resources to answer the questions that follow.
Explore More I
1. What is the definition of pH?
2. What is a strong acid?
3. What is the pH scale?
4. What is the pH range of most cellular processes?
5. Use the pH slider to find the pH of
1. digestive juices.
2. Windex.
3. soapy water.
4. sea water.
5. beer.
6. vinegar.
Review
1. What is the pH of a neutral solution?
2. Distinguish between an acid and a base.
3. Describe an example of an acid or a base that is involved in human digestion.
4. Assume that you test an unknown solution and find that it has a pH of 7.2. What type of solution is it? How do you know?
5. Are the following acids or bases?
1. milk
2. coffee
3. soap | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/02%3A_The_Nature_of_Molecules_and_the_Properties_of_Water/2.06%3A_Acids_and_Bases.txt |
Learning Objectives
• Explain the properties of carbon that allow it to serve as a building block for biomolecules
Carbon is the fourth most abundant element in the universe and is the building block of life on earth. On earth, carbon circulates through the land, ocean, and atmosphere, creating what is known as the Carbon Cycle. This global carbon cycle can be divided further into two separate cycles: the geological carbon cycles takes place over millions of years, whereas the biological or physical carbon cycle takes place from days to thousands of years. In a nonliving environment, carbon can exist as carbon dioxide (CO2), carbonate rocks, coal, petroleum, natural gas, and dead organic matter. Plants and algae convert carbon dioxide to organic matter through the process of photosynthesis, the energy of light.
Carbon is Important to Life
In its metabolism of food and respiration, an animal consumes glucose (C6H12O6), which combines with oxygen (O2) to produce carbon dioxide (CO2), water (H2O), and energy, which is given off as heat. The animal has no need for the carbon dioxide and releases it into the atmosphere. A plant, on the other hand, uses the opposite reaction of an animal through photosynthesis. It intakes carbon dioxide, water, and energy from sunlight to make its own glucose and oxygen gas. The glucose is used for chemical energy, which the plant metabolizes in a similar way to an animal. The plant then emits the remaining oxygen into the environment.
Cells are made of many complex molecules called macromolecules, which include proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon. The carbon atom has unique properties that allow it to form covalent bonds to as many as four different atoms, making this versatile element ideal to serve as the basic structural component, or “backbone,” of the macromolecules.
Structure of Carbon
Individual carbon atoms have an incomplete outermost electron shell. With an atomic number of 6 (six electrons and six protons), the first two electrons fill the inner shell, leaving four in the second shell. Therefore, carbon atoms can form four covalent bonds with other atoms to satisfy the octet rule. The methane molecule provides an example: it has the chemical formula CH4. Each of its four hydrogen atoms forms a single covalent bond with the carbon atom by sharing a pair of electrons. This results in a filled outermost shell.
Key Points
• All living things contain carbon in some form.
• Carbon is the primary component of macromolecules, including proteins, lipids, nucleic acids, and carbohydrates.
• Carbon’s molecular structure allows it to bond in many different ways and with many different elements.
• The carbon cycle shows how carbon moves through the living and non-living parts of the environment.
Key Terms
• octet rule: A rule stating that atoms lose, gain, or share electrons in order to have a full valence shell of 8 electrons (has some exceptions).
• carbon cycle: the physical cycle of carbon through the earth’s biosphere, geosphere, hydrosphere, and atmosphere; includes such processes as photosynthesis, decomposition, respiration and carbonification
• macromolecule: a very large molecule, especially used in reference to large biological polymers (e.g., nucleic acids and proteins) | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.01%3A_Carbon-_The_Framework_of_Biological_Molecules/3.1.01%3A_Carbon/3.1.1A%3A_The_Chemical_Basis_for_Life.txt |
Learning Objectives
• Discuss the role of hydrocarbons in biomacromolecules
Hydrocarbons
Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH4). Hydrocarbons are often used as fuels: the propane in a gas grill or the butane in a lighter. The many covalent bonds between the atoms in hydrocarbons store a great amount of energy, which is released when these molecules are burned (oxidized). Methane, an excellent fuel, is the simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen atoms. The geometry of the methane molecule, where the atoms reside in three dimensions, is determined by the shape of its electron orbitals. The carbon and the four hydrogen atoms form a shape known as a tetrahedron, with four triangular faces; for this reason, methane is described as having tetrahedral geometry.
As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both. Furthermore, individual carbon-to-carbon bonds may be single, double, or triple covalent bonds; each type of bond affects the geometry of the molecule in a specific way. This three-dimensional shape or conformation of the large molecules of life (macromolecules) is critical to how they function.
Hydrocarbon Chains
Hydrocarbon chains are formed by successive bonds between carbon atoms and may be branched or unbranched. The overall geometry of the molecule is altered by the different geometries of single, double, and triple covalent bonds. The hydrocarbons ethane, ethene, and ethyne serve as examples of how different carbon-to-carbon bonds affect the geometry of the molecule. The names of all three molecules start with the prefix “eth-,” which is the prefix for two carbon hydrocarbons. The suffixes “-ane,” “-ene,” and “-yne” refer to the presence of single, double, or triple carbon-carbon bonds, respectively. Thus, propane, propene, and propyne follow the same pattern with three carbon molecules, butane, butene, and butyne for four carbon molecules, and so on. Double and triple bonds change the geometry of the molecule: single bonds allow rotation along the axis of the bond, whereas double bonds lead to a planar configuration and triple bonds to a linear one. These geometries have a significant impact on the shape a particular molecule can assume.
Hydrocarbon Rings
The hydrocarbons discussed so far have been aliphatic hydrocarbons, which consist of linear chains of carbon atoms. Another type of hydrocarbon, aromatic hydrocarbons, consists of closed rings of carbon atoms. Ring structures are found in hydrocarbons, sometimes with the presence of double bonds, which can be seen by comparing the structure of cyclohexane to benzene. The benzene ring is present in many biological molecules including some amino acids and most steroids, which includes cholesterol and the hormones estrogen and testosterone. The benzene ring is also found in the herbicide 2,4-D. Benzene is a natural component of crude oil and has been classified as a carcinogen. Some hydrocarbons have both aliphatic and aromatic portions; beta-carotene is an example of such a hydrocarbon.
Key Points
• Hydrocarbons are molecules that contain only carbon and hydrogen.
• Due to carbon’s unique bonding patterns, hydrocarbons can have single, double, or triple bonds between the carbon atoms.
• The names of hydrocarbons with single bonds end in “-ane,” those with double bonds end in “-ene,” and those with triple bonds end in “-yne”.
• The bonding of hydrocarbons allows them to form rings or chains.
Key Terms
• covalent bond: A type of chemical bond where two atoms are connected to each other by the sharing of two or more electrons.
• aliphatic: Of a class of organic compounds in which the carbon atoms are arranged in an open chain.
• aromatic: Having a closed ring of alternate single and double bonds with delocalized electrons. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.01%3A_Carbon-_The_Framework_of_Biological_Molecules/3.1.01%3A_Carbon/3.1.1B%3A_Hydrocarbons.txt |
Learning Objectives
• Give examples of isomers
The three-dimensional placement of atoms and chemical bonds within organic molecules is central to understanding their chemistry. Molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds are known as isomers.
Structural Isomers
Structural isomers (such as butane and isobutane ) differ in the placement of their covalent bonds. Both molecules have four carbons and ten hydrogens (C4H10), but the different arrangement of the atoms within the molecules leads to differences in their chemical properties. For example, due to their different chemical properties, butane is suited for use as a fuel for cigarette lighters and torches, whereas isobutane is suited for use as a refrigerant and a propellant in spray cans.
Geometric Isomers
Geometric isomers, on the other hand, have similar placements of their covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds. In the simple molecule butene (C4H8), the two methyl groups (CH3) can be on either side of the double covalent bond central to the molecule. When the carbons are bound on the same side of the double bond, this is the cis configuration; if they are on opposite sides of the double bond, it is a trans configuration. In the trans configuration, the carbons form a more or less linear structure, whereas the carbons in the cis configuration make a bend (change in direction) of the carbon backbone.
Cis or Trans Configurations
In triglycerides (fats and oils), long carbon chains known as fatty acids may contain double bonds, which can be in either the cis or trans configuration. Fats with at least one double bond between carbon atoms are unsaturated fats. When some of these bonds are in the cis configuration, the resulting bend in the carbon backbone of the chain means that triglyceride molecules cannot pack tightly, so they remain liquid (oil) at room temperature. On the other hand, triglycerides with trans double bonds (popularly called trans fats), have relatively linear fatty acids that are able to pack tightly together at room temperature and form solid fats.
In the human diet, trans fats are linked to an increased risk of cardiovascular disease, so many food manufacturers have reduced or eliminated their use in recent years. In contrast to unsaturated fats, triglycerides without double bonds between carbon atoms are called saturated fats, meaning that they contain all the hydrogen atoms available. Saturated fats are a solid at room temperature and usually of animal origin.
Key Points
• Isomers are molecules with the same chemical formula but have different structures.
• Isomers differ in how their bonds are positioned to surrounding atoms.
• When the carbons are bound on the same side of the double bond, this is the cis configuration; if they are on opposite sides of the double bond, it is a trans configuration.
• Triglycerides, which show both cis and trans configurations, can occur as either saturated or unsaturated, depending upon how many hydrogen atoms they have attached to them.
Key Terms
• fatty acid: Any of a class of aliphatic carboxylic acids, of general formula CnH2n+1COOH, that occur combined with glycerol as animal or vegetable oils and fats.
• isomer: Any of two or more compounds with the same molecular formula but with different structure. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.01%3A_Carbon-_The_Framework_of_Biological_Molecules/3.1.01%3A_Carbon/3.1.1C%3A_Organic_Isomers.txt |
Learning Objectives
• Give examples of enantiomers
Stereoisomers are a type of isomer where the order of the atoms in the two molecules is the same but their arrangement in space is different. The two main types of stereoisomerism are diastereomerism (including ‘cis-trans isomerism’) and optical isomerism (also known as ‘enantiomerism’ and ‘chirality’). Optical isomers are stereoisomers formed when asymmetric centers are present; for example, a carbon with four different groups bonded to it. Enantiomers are two optical isomers (i.e. isomers that are reflections of each other). Every stereocenter in one isomer has the opposite configuration in the other. They share the same chemical structure and chemical bonds, but differ in the three-dimensional placement of atoms so that they are mirror images, much as a person’s left and right hands are. Compounds that are enantiomers of each other have the same physical properties except for the direction in which they rotate polarized light and how they interact with different optical isomers of other compounds.
The amino acid alanine is example of an entantiomer. The two structures, D-alanine and L-alanine, are non-superimposable. In nature, only the L-forms of amino acids are used to make proteins. Some D forms of amino acids are seen in the cell walls of bacteria, but never in their proteins. Similarly, the D-form of glucose is the main product of photosynthesis and the L-form of the molecule is rarely seen in nature.
Organic compounds that contain a chiral carbon usually have two non-superposable structures. These two structures are mirror images of each other and are, thus, commonly called enantiomorphs; hence, this structural property is now commonly referred to as enantiomerism. Enantiopure compounds refer to samples having, within the limits of detection, molecules of only one chirality.
Enantiomers of each other often show different chemical reactions with other substances that are also enantiomers. Since many molecules in the bodies of living beings are enantiomers themselves, there is sometimes a marked difference in the effects of two enantiomers on living beings. In drugs, for example, often only one of a drug’s enantiomers is responsible for the desired physiologic effects, while the other enantiomer is less active, inactive, or sometimes even responsible for adverse effects. Owing to this discovery, drugs composed of only one enantiomer (“enantiopure”) can be developed to enhance the pharmacological efficacy and sometimes do away with some side effects.
Key Points
• Enantiomers are stereoisomers, a type of isomer where the order of the atoms in the two molecules is the same but their arrangement in space is different.
• Many molecules in the bodies of living beings are enantiomers; there is sometimes a large difference in the effects of two enantiomers on organisms.
• Enantiopure compounds refer to samples having, within the limits of detection, molecules of only one chirality.
• Compounds that are enantiomers of each other have the same physical properties except for the direction in which they rotate polarized light and how they interact with different optical isomers of other compounds.
Key Terms
• enantiomer: One of a pair of stereoisomers that is the mirror image of the other, but may not be superimposed on this other stereoisomer.
• chirality: The phenomenon in chemistry, physics, and mathematics in which objects are mirror images of each other, but are not identical.
• stereoisomer: one of a set of the isomers of a compound in which atoms are arranged differently about a chiral center; they exhibit optical activity
3.1.1E: Organic Molecules and Functional
Learning Objectives
• Describe the importance of functional groups to organic molecules
Location of Functional Groups
Functional groups are groups of atoms that occur within organic molecules and confer specific chemical properties to those molecules. When functional groups are shown, the organic molecule is sometimes denoted as “R.” Functional groups are found along the “carbon backbone” of macromolecules which is formed by chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen. Molecules with other elements in their carbon backbone are substituted hydrocarbons. Each of the four types of macromolecules—proteins, lipids, carbohydrates, and nucleic acids—has its own characteristic set of functional groups that contributes greatly to its differing chemical properties and its function in living organisms.
Properties of Functional Groups
A functional group can participate in specific chemical reactions. Some of the important functional groups in biological molecules include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl groups. These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids.
Classifying Functional Groups
Functional groups are usually classified as hydrophobic or hydrophilic depending on their charge or polarity. An example of a hydrophobic group is the non-polar methane molecule. Among the hydrophilic functional groups is the carboxyl group found in amino acids, some amino acid side chains, and the fatty acid heads that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H+) from the COOH group resulting in the negatively charged COOgroup; this contributes to the hydrophilic nature of whatever molecule it is found on. Other functional groups, such as the carbonyl group, have a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules, again making the molecule more hydrophilic.
Hydrogen Bonds between Functional Groups
Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly and maintain the appropriate shape needed to function correctly. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate.
Key Points
• Functional groups are collections of atoms that attach the carbon skeleton of an organic molecule and confer specific properties.
• Each type of organic molecule has its own specific type of functional group.
• Functional groups in biological molecules play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids.
• Functional groups include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl.
Key Terms
• hydrophobic: lacking an affinity for water; unable to absorb, or be wetted by water
• hydrophilic: having an affinity for water; able to absorb, or be wetted by water | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.01%3A_Carbon-_The_Framework_of_Biological_Molecules/3.1.01%3A_Carbon/3.1.1D%3A_Organic_Enantiomers.txt |
Learning Objectives
• Identify the four major classes of biological macromolecules
Nutrients are the molecules that living organisms require for survival and growth but that animals and plants cannot synthesize themselves. Animals obtain nutrients by consuming food, while plants pull nutrients from soil.
Many critical nutrients are biological macromolecules. The term “macromolecule” was first coined in the 1920s by Nobel laureate Hermann Staudinger. Staudinger was the first to propose that many large biological molecules are built by covalently linking smaller biological molecules together.
Monomers and Polymers
Biological macromolecules play a critical role in cell structure and function. Most (but not all) biological macromolecules are polymers, which are any molecules constructed by linking together many smaller molecules, called monomers. Typically all the monomers in a polymer tend to be the same, or at least very similar to each other, linked over and over again to build up the larger macromolecule. These simple monomers can be linked in many different combinations to produce complex biological polymers, just as a few types of Lego blocks can build anything from a house to a car.
Examples of these monomers and polymers can be found in the sugar you might put in your coffee or tea. Regular table sugar is the disaccharide sucrose (a polymer), which is composed of the monosaccharides fructose and glucose (which are monomers). If we were to string many carbohydrate monomers together we could make a polysaccharide like starch. The prefixes “mono-” (one), “di-” (two),and “poly-” (many) will tell you how many of the monomers have been joined together in a molecule.
Biological macromolecules all contain carbon in ring or chain form, which means they are classified as organic molecules. They usually also contain hydrogen and oxygen, as well as nitrogen and additional minor elements.
Four Classes of Biological Macromolecules
There are four major classes of biological macromolecules:
1. carbohydrates
2. lipids
3. proteins
4. nucleic acids
Each of these types of macromolecules performs a wide array of important functions within the cell; a cell cannot perform its role within the body without many different types of these crucial molecules. In combination, these biological macromolecules make up the majority of a cell’s dry mass. (Water molecules make up the majority of a cell’s total mass.) All the molecules both inside and outside of cells are situated in a water-based (i.e., aqueous) environment, and all the reactions of biological systems are occurring in that same environment.
Interactive: Monomers and Polymers
Carbohydrates, proteins, and nucleic acids are built from small molecular units that are connected to each other by strong covalent bonds. The small molecular units are called monomers (mono means one, or single), and they are linked together into long chains called polymers (poly means many, or multiple). Each different type of macromolecule, except lipids, is built from a different set of monomers that resemble each other in composition and size. Lipids are not polymers, because they are not built from monomers (units with similar composition).
Key Points
• Biological macromolecules are important cellular components and perform a wide array of functions necessary for the survival and growth of living organisms.
• The four major classes of biological macromolecules are carbohydrates, lipids, proteins, and nucleic acids.
Key Terms
• polymer: A relatively large molecule consisting of a chain or network of many identical or similar monomers chemically bonded to each other.
• monomer: A relatively small molecule that can form covalent bonds with other molecules of this type to form a polymer. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.01%3A_Carbon-_The_Framework_of_Biological_Molecules/3.1.02%3A_Synthesis_of_Biological_Macromolecules/3.1.2A%3A_.txt |
Learning Objectives
• Explain dehydration (or condensation) reactions
Dehydration Synthesis
Most macromolecules are made from single subunits, or building blocks, called monomers. The monomers combine with each other via covalent bonds to form larger molecules known as polymers. In doing so, monomers release water molecules as byproducts. This type of reaction is known as dehydration synthesis, which means “to put together while losing water. ” It is also considered to be a condensation reaction since two molecules are condensed into one larger molecule with the loss of a smaller molecule (the water.)
In a dehydration synthesis reaction between two un-ionized monomers, such as monosaccharide sugars, the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water in the process. The removal of a hydrogen from one monomer and the removal of a hydroxyl group from the other monomer allows the monomers to share electrons and form a covalent bond. Thus, the monomers that are joined together are being dehydrated to allow for synthesis of a larger molecule.
When the monomers are ionized, such as is the case with amino acids in an aqueous environment like cytoplasm, two hydrogens from the positively-charged end of one monomer are combined with an oxygen from the negatively-charged end of another monomer, again forming water, which is released as a side-product, and again joining the two monomers with a covalent bond.
As additional monomers join via multiple dehydration synthesis reactions, the chain of repeating monomers begins to form a polymer. Different types of monomers can combine in many configurations, giving rise to a diverse group of macromolecules. Three of the four major classes of biological macromolecules (complex carbohydrates, nucleic acids, and proteins), are composed of monomers that join together via dehydration synthesis reactions. Complex carbohydrates are formed from monosaccharides, nucleic acids are formed from mononucleotides, and proteins are formed from amino acids.
There is great diversity in the manner by which monomers can combine to form polymers. For example, glucose monomers are the constituents of starch, glycogen, and cellulose. These three are polysaccharides, classified as carbohydrates, that have formed as a result of multiple dehydration synthesis reactions between glucose monomers. However, the manner by which glucose monomers join together, specifically locations of the covalent bonds between connected monomers and the orientation (stereochemistry) of the covalent bonds, results in these three different polysaccharides with varying properties and functions. In nucleic acids and proteins, the location and stereochemistry of the covalent linkages connecting the monomers do not vary from molecule to molecule, but instead the multiple kinds of monomers (five different monomers in nucleic acids, A, G, C, T, and U mononucleotides; 21 different amino acids monomers in proteins) are combined in a huge variety of sequences. Each protein or nucleic acid with a different sequence is a different molecule with different properties.
Key Points
• During dehydration synthesis, either the hydrogen of one monomer combines with the hydroxyl group of another monomer releasing a molecule of water, or two hydrogens from one monomer combine with one oxygen from the other monomer releasing a molecule of water.
• The monomers that are joined via dehydration synthesis reactions share electrons and form covalent bonds with each other.
• As additional monomers join via multiple dehydration synthesis reactions, this chain of repeating monomers begins to form a polymer.
• Complex carbohydrates, nucleic acids, and proteins are all examples of polymers that are formed by dehydration synthesis.
• Monomers like glucose can join together in different ways and produce a variety of polymers. Monomers like mononucleotides and amino acids join together in different sequences to produce a variety of polymers.
Key Terms
• covalent bond: A type of chemical bond where two atoms are connected to each other by the sharing of two or more electrons.
• monomer: A relatively small molecule which can be covalently bonded to other monomers to form a polymer. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.01%3A_Carbon-_The_Framework_of_Biological_Molecules/3.1.02%3A_Synthesis_of_Biological_Macromolecules/3.1.2B%3A_.txt |
Learning Objectives
• Explain hydrolysis reactions
Polymers are broken down into monomers in a process known as hydrolysis, which means “to split water,” a reaction in which a water molecule is used during the breakdown. During these reactions, the polymer is broken into two components. If the components are un-ionized, one part gains a hydrogen atom (H-) and the other gains a hydroxyl group (OH–) from a split water molecule. This is what happens when monosaccharides are released from complex carbohydrates via hydrolysis.
If the components are ionized after the split, one part gains two hydrogen atoms and a positive charge, the other part gains an oxygen atom and a negative charge. This is what happens when amino acids are released from protein chains via hydrolysis.
These reactions are in contrast to dehydration synthesis (also known as condensation) reactions. In dehydration synthesis reactions, a water molecule is formed as a result of generating a covalent bond between two monomeric components in a larger polymer. In hydrolysis reactions, a water molecule is consumed as a result of breaking the covalent bond holding together two components of a polymer.
Dehydration and hydrolysis reactions are chemical reactions that are catalyzed, or “sped up,” by specific enzymes; dehydration reactions involve the formation of new bonds, requiring energy, while hydrolysis reactions break bonds and release energy.
In our bodies, food is first hydrolyzed, or broken down, into smaller molecules by catalytic enzymes in the digestive tract. This allows for easy absorption of nutrients by cells in the intestine. Each macromolecule is broken down by a specific enzyme. For instance, carbohydrates are broken down by amylase, sucrase, lactase, or maltase. Proteins are broken down by the enzymes trypsin, pepsin, peptidase and others. Lipids are broken down by lipases. Once the smaller metabolites that result from these hydrolytic enzymezes are absorbed by cells in the body, they are further broken down by other enzymes. The breakdown of these macromolecules is an overall energy-releasing process and provides energy for cellular activities.
Key Points
• Hydrolysis reactions use water to breakdown polymers into monomers and is the opposite of dehydration synthesis, which forms water when synthesizing a polymer from monomers.
• Hydrolysis reactions break bonds and release energy.
• Biological macromolecules are ingested and hydrolyzed in the digestive tract to form smaller molecules that can be absorbed by cells and then further broken down to release energy.
Key Terms
• enzyme: a globular protein that catalyses a biological chemical reaction
• hydrolysis: A chemical process of decomposition involving the splitting of a bond by the addition of water.
Exercise \(1\)
1. What are biological macromolecules? Name the four major classes.
2. Biological macromolecules are organic. What does that mean?
3. What are monomers? What are polymer?
4. Explain the process “dehydration synthesis.” Is there another name for this process? Explain.
5. Explain Figure 1 in your own words.
6. Give an example of how condensation can form different carbohydrates.
7. Explain the process of Hydrolysis.
8. Explain Figure 2 in your own words.
9. What role do enzymes play in hydrolysis and condensation? Explain.
10. In our bodies, food is hydrolyzed, or broken down into smaller molecules. Explain why.
11. The breakdown of macromolecules provides...
12. Create a comparison chart to indicate the enzymes that break down carbohydrates, proteins, and lipids. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.01%3A_Carbon-_The_Framework_of_Biological_Molecules/3.1.02%3A_Synthesis_of_Biological_Macromolecules/3.1.2C%3A_.txt |
Learning Objectives
• Describe the structure of mono-, di-, and poly-saccharides
Carbohydrates can be represented by the stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule. Therefore, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. The origin of the term “carbohydrate” is based on its components: carbon (“carbo”) and water (“hydrate”). Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.
Monosaccharides
Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars. In monosaccharides, the number of carbons usually ranges from three to seven. If the sugar has an aldehyde group (the functional group with the structure R-CHO), it is known as an aldose, and if it has a ketone group (the functional group with the structure RC(=O)R’), it is known as a ketose. Depending on the number of carbons in the sugar, they also may be known as trioses (three carbons), pentoses (five carbons), and or hexoses (six carbons). Monosaccharides can exist as a linear chain or as ring-shaped molecules; in aqueous solutions they are usually found in ring forms.
Common Monosaccharides
Glucose (C6H12O6) is a common monosaccharide and an important source of energy. During cellular respiration, energy is released from glucose and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water, and glucose, in turn, is used for energy requirements for the plant.
Galactose (a milk sugar) and fructose (found in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C6H12O6), they differ structurally and stereochemically. This makes them different molecules despite sharing the same atoms in the same proportions, and they are all isomers of one another, or isomeric monosaccharides. Glucose and galactose are aldoses, and fructose is a ketose.
Disaccharides
Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (also known as a condensation reaction or dehydration synthesis). During this process, the hydroxyl group of one monosaccharide combines with the hydrogen of another monosaccharide, releasing a molecule of water and forming a covalent bond. A covalent bond formed between a carbohydrate molecule and another molecule (in this case, between two monosaccharides) is known as a glycosidic bond. Glycosidic bonds (also called glycosidic linkages) can be of the alpha or the beta type.
Common Disaccharides
Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt sugar, is a disaccharide formed by a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.
Polysaccharides
A long chain of monosaccharides linked by glycosidic bonds is known as a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may contain different types of monosaccharides. Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides.
Plants are able to synthesize glucose, and the excess glucose is stored as starch in different plant parts, including roots and seeds. Starch is the stored form of sugars in plants and is made up of glucose monomers that are joined by α1-4 or 1-6 glycosidic bonds. The starch in the seeds provides food for the embryo as it germinates while the starch that is consumed by humans is broken down by enzymes into smaller molecules, such as maltose and glucose. The cells can then absorb the glucose.
Common Polysaccharides
Glycogen is the storage form of glucose in humans and other vertebrates. It is made up of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever blood glucose levels decrease, glycogen is broken down to release glucose in a process known as glycogenolysis.
Cellulose is the most abundant natural biopolymer. The cell wall of plants is mostly made of cellulose and provides structural support to the cell. Cellulose is made up of glucose monomers that are linked by β 1-4 glycosidic bonds. Every other glucose monomer in cellulose is flipped over, and the monomers are packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells.
Carbohydrate Function
Carbohydrates serve various functions in different animals. Arthropods have an outer skeleton, the exoskeleton, which protects their internal body parts. This exoskeleton is made of chitin, which is a polysaccharide-containing nitrogen. It is made of repeating units of N-acetyl-β-d-glucosamine, a modified sugar. Chitin is also a major component of fungal cell walls.
Key Points
• Monosaccharides are simple sugars made up of three to seven carbons, and they can exist as a linear chain or as ring-shaped molecules.
• Glucose, galactose, and fructose are monosaccharide isomers, which means they all have the same chemical formula but differ structurally and chemically.
• Disaccharides form when two monosaccharides undergo a dehydration reaction (a condensation reaction); they are held together by a covalent bond.
• Sucrose (table sugar) is the most common disaccharide, which is composed of the monomers glucose and fructose.
• A polysaccharide is a long chain of monosaccharides linked by glycosidic bonds; the chain may be branched or unbranched and can contain many types of monosaccharides.
Key Terms
• isomer: Any of two or more compounds with the same molecular formula but with different structure.
• dehydration reaction: A chemical reaction in which two molecules are covalently linked in a reaction that generates H2O as a second product.
• biopolymer: Any macromolecule of a living organism that is formed from the polymerization of smaller entities; a polymer that occurs in a living organism or results from life. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.02%3A_Carbohydrates-_Energy_Storage_and_Structural_Molecules/3.2.1A%3A_Carbohydrate_Mol.txt |
Learning Objectives
• Describe the benefits provided to organisms by carbohydrates
Benefits of Carbohydrates
Biological macromolecules are large molecules that are necessary for life and are built from smaller organic molecules. One major class of biological macromolecules are carbohydrates, which are further divided into three subtypes: monosaccharides, disaccharides, and polysaccharides. Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Importantly, carbohydrates provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many basic foods.
Carbohydrates in Nutrition
Carbohydrates have been a controversial topic within the diet world. People trying to lose weight often avoid carbs, and some diets completely forbid carbohydrate consumption, claiming that a low-carb diet helps people to lose weight faster. However, carbohydrates have been an important part of the human diet for thousands of years; artifacts from ancient civilizations show the presence of wheat, rice, and corn in our ancestors’ storage areas.
Carbohydrates should be supplemented with proteins, vitamins, and fats to be parts of a well-balanced diet. Calorie-wise, a gram of carbohydrate provides 4.3 Kcal. In comparison, fats provide 9 Kcal/g, a less desirable ratio. Carbohydrates contain soluble and insoluble elements; the insoluble part is known as fiber, which is mostly cellulose. Fiber has many uses; it promotes regular bowel movement by adding bulk, and it regulates the rate of consumption of blood glucose. Fiber also helps to remove excess cholesterol from the body. Fiber binds and attaches to the cholesterol in the small intestine and prevents the cholesterol particles from entering the bloodstream. Then cholesterol exits the body via the feces. Fiber-rich diets also have a protective role in reducing the occurrence of colon cancer. In addition, a meal containing whole grains and vegetables gives a feeling of fullness. As an immediate source of energy, glucose is broken down during the process of cellular respiration, which produces adenosine triphosphate (ATP), the energy currency of the cell. Without the consumption of carbohydrates, the availability of “instant energy” would be reduced. Eliminating carbohydrates from the diet is not the best way to lose weight. A low-calorie diet that is rich in whole grains, fruits, vegetables, and lean meat, together with plenty of exercise and plenty of water, is the more sensible way to lose weight.
Key Points
• Carbohydrates provide energy to the body, particularly through glucose, a simple sugar that is found in many basic foods.
• Carbohydrates contain soluble and insoluble elements; the insoluble part is known as fiber, which promotes regular bowel movement, regulates the rate of consumption of blood glucose, and also helps to remove excess cholesterol from the body.
• As an immediate source of energy, glucose is broken down during the process of cellular respiration, which produces ATP, the energy currency of the cell.
• Since carbohydrates are an important part of the human nutrition, eliminating them from the diet is not the best way to lose weight.
Key Terms
• carbohydrate: A sugar, starch, or cellulose that is a food source of energy for an animal or plant; a saccharide.
• glucose: a simple monosaccharide (sugar) with a molecular formula of C6H12O6; it is a principal source of energy for cellular metabolism
• ATP: A nucleotide that occurs in muscle tissue, and is used as a source of energy in cellular reactions, and in the synthesis of nucleic acids. ATP is the abbreviation for adenosine triphosphate. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.02%3A_Carbohydrates-_Energy_Storage_and_Structural_Molecules/3.2.1B%3A_Importance_of_Ca.txt |
You may have heard that something is "encoded in your DNA." What does that mean?
Nucleic acids. Essentially the "instructions" or "blueprints" of life. Deoxyribonucleic acid, or DNA, is the unique blueprints to make the proteins that give you your traits. Half of these blueprints come from your mother, and half from your father. Therefore, every person that has ever lived - except for identical twins - has his or her own unique set of blueprints - or instructions - or DNA.
Nucleic Acids
A nucleic acid is an organic compound, such as DNA or RNA, that is built of small units callednucleotides. Many nucleotides bind together to form a chain called a polynucleotide. The nucleic acid DNA (deoxyribonucleic acid) consists of two polynucleotide chains. The nucleic acid RNA (ribonucleic acid) consists of just one polynucleotide chain.
An overview of DNA can be seen at http://www.youtube.com/watch?v=_-vZ_g7K6P0 (28:05).
As you view DNA, focus on the following concept:
1. the structure and role of DNA.
Structure of Nucleic Acids
Each nucleotide consists of three smaller molecules:
1. sugar
2. phosphate group
3. nitrogen base
If you look at Figure below, you will see that the sugar of one nucleotide binds to the phosphate group of the next nucleotide. These two molecules alternate to form the backbone of the nucleotide chain. This backbone is known as the sugar-phosphate backbone.
The nitrogen bases in a nucleic acid stick out from the backbone. There are four different types of bases: cytosine (C), adenine (A), guanine (G), and either thymine (T) in DNA, or uracil (U) in RNA. In DNA, bonds form between bases on the two nucleotide chains and hold the chains together. Each type of base binds with just one other type of base: cytosine always binds with guanine, and adenine always binds with thymine. These pairs of bases are calledcomplementary base pairs.
Nucleic Acid. Sugars and phosphate groups form the backbone of a polynucleotide chain. Hydrogen bonds between complementary bases hold two polynucleotide chains together.
The binding of complementary bases allows DNA molecules to take their well-known shape, called a double helix, which is shown in Figure below. A double helix is like a spiral staircase. The double helix shape forms naturally and is very strong, making the two polynucleotide chains difficult to break apart.
DNA Molecule. Bonds between complementary bases help form the double helix of a DNA molecule. The letters A, T, G, and C stand for the bases adenine, thymine, guanine, and cytosine. The sequence of these four bases in DNA is a code that carries instructions for making proteins. Shown is how the DNA winds into a chromosome.
An animation of DNA structure can be viewed at http://www.youtube.com/watch?v=qy8dk5iS1f0.
Roles of Nucleic Acids
DNA is also known as the hereditary material or genetic information. It is found in genes, and its sequence of bases makes up a code. Between "starts" and "stops," the code carries instructions for the correct sequence of amino acids in a protein (see Figure below). DNA and RNA have different functions relating to the genetic code and proteins. Like a set of blueprints, DNA contains the genetic instructions for the correct sequence of amino acids in proteins. RNA uses the information in DNA to assemble the correct amino acids and help make the protein. The information in DNA is passed from parent cells to daughter cells whenever cells divide. The information in DNA is also passed from parents to offspring when organisms reproduce. This is how inherited characteristics are passed from one generation to the next.
The letters G, U, C, and A stand for the bases in RNA. Each group of three bases makes up a code word, and each code word represents one amino acid (represented here by a single letter, such as V, H, or L). A string of code words specifies the sequence of amino acids in a protein.
Summary
• DNA and RNA are nucleic acids. Nucleic acids are built of small units called nucleotides.
• The bases of DNA are adenine, guanine, cytosine and thymine. In RNA, thymine is replaced by uracil.
• In DNA, A always binds to T, and G always binds to C.
• The shape of the DNA molecule is known as a double helix.
• DNA contains the genetic instructions for the correct sequence of amino acids in proteins. RNA uses the information in DNA to assemble the correct amino acids and help make the protein.
Explore More
Use this resource to answer the questions that follow.
• What is DNA? at learn.genetics.utah.edu/content/begin/dna/.
1. Why is DNA referred to as the "instructions"?
2. Where is DNA located in the cell?
3. What do A, C, G and T refer to? How can only four letters tell the cell what to do?
4. What is a gene?
Review
1. Identify the three parts of a nucleotide.
2. What is DNA?
3. What are complementary base pairs? Give an example.
4. Describe the shape of DNA.
5. How are DNA and RNA related to proteins?
3.03: Nucleic Acids- Information Molecules
Learning Objectives
• Describe the structure of nucleic acids and the types of molecules that contain them
Types of Nucleic Acids
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is found in the nucleus of eukaryotes and in the chloroplasts and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope, but rather free-floating within the cytoplasm.
The entire genetic content of a cell is known as its genome and the study of genomes is genomics. In eukaryotic cells, but not in prokaryotes, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes. A chromosome may contain tens of thousands of genes. Many genes contain the information to make protein products; other genes code for RNA products. DNA controls all of the cellular activities by turning the genes “on” or “off. ”
The other type of nucleic acid, RNA, is mostly involved in protein synthesis. In eukaryotes, the DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA (mRNA). Other types of RNA—like rRNA, tRNA, and microRNA—are involved in protein synthesis and its regulation.
Nucleotides
DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide: DNA or RNA. Each nucleotide is made up of three components:
1. a nitrogenous base
2. a pentose (five-carbon) sugar
3. a phosphate group
Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.
Nitrogenous Base
The nitrogenous bases are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus, decreasing the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).
Adenine and guanine are classified as purines. The primary structure of a purine consists of two carbon-nitrogen rings. Cytosine, thymine, and uracil are classified as pyrimidines which have a single carbon-nitrogen ring as their primary structure. Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, the nitrogenous bases are simply known by their symbols A, T, G, C, and U. DNA contains A, T, G, and C whereas RNA contains A, U, G, and C.
Five-Carbon Sugar
The pentose sugar in DNA is deoxyribose and in RNA it is ribose. The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”).
Phosphate Group
The phosphate residue is attached to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′3′ phosphodiester linkage. The phosphodiester linkage is not formed by simple dehydration reaction like the other linkages connecting monomers in macromolecules: its formation involves the removal of two phosphate groups. A polynucleotide may have thousands of such phosphodiester linkages.
Key Points
• The two main types of nucleic acids are DNA and RNA.
• Both DNA and RNA are made from nucleotides, each containing a five-carbon sugar backbone, a phosphate group, and a nitrogen base.
• DNA provides the code for the cell ‘s activities, while RNA converts that code into proteins to carry out cellular functions.
• The sequence of nitrogen bases (A, T, C, G) in DNA is what forms an organism’s traits.
• The nitrogen bases A and T (or U in RNA) always go together and C and G always go together, forming the 5′-3′ phosphodiester linkage found in the nucleic acid molecules.
Key Terms
• nucleotide: the monomer comprising DNA or RNA molecules; consists of a nitrogenous heterocyclic base that can be a purine or pyrimidine, a five-carbon pentose sugar, and a phosphate group
• genome: the cell’s complete genetic information packaged as a double-stranded DNA molecule
• monomer: A relatively small molecule which can be covalently bonded to other monomers to form a polymer. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.03%3A_Nucleic_Acids-_Information_Molecules/3.3A%3A_DNA_and_RNA.txt |
Learning Objectives
• Differentiate among the types and functions of proteins
Types and Functions of Proteins
Proteins perform essential functions throughout the systems of the human body. These long chains of amino acids are critically important for:
• catalyzing chemical reactions
• synthesizing and repairing DNA
• transporting materials across the cell
• receiving and sending chemical signals
• responding to stimuli
• providing structural support
Proteins (a polymer) are macromolecules composed of amino acid subunits (the monomers ). These amino acids are covalently attached to one another to form long linear chains called polypeptides, which then fold into a specific three-dimensional shape. Sometimes these folded polypeptide chains are functional by themselves. Other times they combine with additional polypeptide chains to form the final protein structure. Sometimes non-polypeptide groups are also required in the final protein. For instance, the blood protein hemogobin is made up of four polypeptide chains, each of which also contains a heme molecule, which is ring structure with an iron atom in its center.
Proteins have different shapes and molecular weights, depending on the amino acid sequence. For example, hemoglobin is a globular protein, which means it folds into a compact globe-like structure, but collagen, found in our skin, is a fibrous protein, which means it folds into a long extended fiber-like chain. You probably look similar to your family members because you share similar proteins, but you look different from strangers because the proteins in your eyes, hair, and the rest of your body are different.
Because form determines function, any slight change to a protein’s shape may cause the protein to become dysfunctional. Small changes in the amino acid sequence of a protein can cause devastating genetic diseases such as Huntington’s disease or sickle cell anemia.
Enzymes
Enzymes are proteins that catalyze biochemical reactions, which otherwise would not take place. These enzymes are essential for chemical processes like digestion and cellular metabolism. Without enzymes, most physiological processes would proceed so slowly (or not at all) that life could not exist.
Because form determines function, each enzyme is specific to its substrates. The substrates are the reactants that undergo the chemical reaction catalyzed by the enzyme. The location where substrates bind to or interact with the enzyme is known as the active site, because that is the site where the chemistry occurs. When the substrate binds to its active site at the enzyme, the enzyme may help in its breakdown, rearrangement, or synthesis. By placing the substrate into a specific shape and microenvironment in the active site, the enzyme encourages the chemical reaction to occur. There are two basic classes of enzymes:
• Catabolic enzymes: enzymes that break down their substrate
• Anabolic enzymes: enzymes that build more complex molecules from their substrates
Enzymes are essential for digestion: the process of breaking larger food molecules down into subunits small enough to diffuse through a cell membrane and to be used by the cell. These enzymes include amylase, which catalyzes the digestion carbohydrates in the mouth and small intestine; pepsin, which catalyzes the digestion of proteins in the stomach; lipase, which catalyzes reactions need to emulsify fats in the small intestine; and trypsin, which catalyzes the further digestion of proteins in the small intestine.
Enzymes are also essential for biosynthesis: the process of making new, complex molecules from the smaller subunits that are provided to or generated by the cell. These biosynthetic enzymes include DNA Polymerase, which catalyzes the synthesis of new strands of the genetic material before cell division; fatty acid synthetase, which the synthesis of new fatty acids for fat or membrane lipid formation; and components of the ribosome, which catalyzes the formation of new polypeptides from amino acid monomers.
Hormones
Some proteins function as chemical-signaling molecules called hormones. These proteins are secreted by endocrine cells that act to control or regulate specific physiological processes, which include growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps to regulate blood glucose levels. Other proteins act as receptors to detect the concentrations of chemicals and send signals to respond. Some types of hormones, such as estrogen and testosterone, are lipid steroids, not proteins.
Other Protein Functions
Proteins perform essential functions throughout the systems of the human body. In the respiratory system, hemoglobin (composed of four protein subunits) transports oxygen for use in cellular metabolism. Additional proteins in the blood plasma and lymph carry nutrients and metabolic waste products throughout the body. The proteins actin and tubulin form cellular structures, while keratin forms the structural support for the dead cells that become fingernails and hair. Antibodies, also called immunoglobins, help recognize and destroy foreign pathogens in the immune system. Actin and myosin allow muscles to contract, while albumin nourishes the early development of an embryo or a seedling.
Key Points
• Proteins are essential for the main physiological processes of life and perform functions in every system of the human body.
• A protein’s shape determines its function.
• Proteins are composed of amino acid subunits that form polypeptide chains.
• Enzymes catalyze biochemical reactions by speeding up chemical reactions, and can either break down their substrate or build larger molecules from their substrate.
• The shape of an enzyme’s active site matches the shape of the substrate.
• Hormones are a type of protein used for cell signaling and communication.
Key Terms
• amino acid: Any of 20 naturally occurring α-amino acids (having the amino, and carboxylic acid groups on the same carbon atom), and a variety of side chains, that combine, via peptide bonds, to form proteins.
• polypeptide: Any polymer of (same or different) amino acids joined via peptide bonds.
• catalyze: To accelerate a process. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.04%3A_Proteins-_Molecules_with_Diverse_Structures_and_Functions/3.4A%3A_Types_and_Functions_of_Proteins.txt |
Learning Objectives
• Describe the structure of an amino acid and the features that confer its specific properties
Structure of an Amino Acid
Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. In the aqueous environment of the cell, the both the amino group and the carboxyl group are ionized under physiological conditions, and so have the structures -NH3+ and -COO, respectively. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. This R group, or side chain, gives each amino acid proteins specific characteristics, including size, polarity, and pH.
Types of Amino Acids
The name “amino acid” is derived from the amino group and carboxyl-acid-group in their basic structure. There are 21 amino acids present in proteins, each with a specific R group or side chain. Ten of these are considered essential amino acids in humans because the human body cannot produce them and they must be obtained from the diet. All organisms have different essential amino acids based on their physiology.
Characteristics of Amino Acids
Which categories of amino acid would you expect to find on the surface of a soluble protein, and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?
The chemical composition of the side chain determines the characteristics of the amino acid. Amino acids such as valine, methionine, and alanine are nonpolar (hydrophobic), while amino acids such as serine, threonine, and cysteine are polar (hydrophilic). The side chains of lysine and arginine are positively charged so these amino acids are also known as basic (high pH) amino acids. Proline is an exception to the standard structure of an amino acid because its R group is linked to the amino group, forming a ring-like structure.
Amino acids are represented by a single upper case letter or a three-letter abbreviation. For example, valine is known by the letter V or the three-letter symbol val.
Peptide Bonds
The sequence and the number of amino acids ultimately determine the protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond. When two amino acids are covalently attached by a peptide bond, the carboxyl group of one amino acid and the amino group of the incoming amino acid combine and release a molecule of water. Any reaction that combines two monomers in a reaction that generates H2O as one of the products is known as a dehydration reaction, so peptide bond formation is an example of a dehydration reaction.
Polypeptide Chains
The resulting chain of amino acids is called a polypeptide chain. Each polypeptide has a free amino group at one end. This end is called the N terminal, or the amino terminal, and the other end has a free carboxyl group, also known as the C or carboxyl terminal. When reading or reporting the amino acid sequence of a protein or polypeptide, the convention is to use the N-to-C direction. That is, the first amino acid in the sequence is assumed to the be one at the N terminal and the last amino acid is assumed to be the one at the C terminal.
Although the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically any polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have folded properly, combined with any additional components needed for proper functioning, and is now functional.
Key Points
• Each amino acid contains a central C atom, an amino group (NH2), a carboxyl group (COOH), and a specific R group.
• The R group determines the characteristics (size, polarity, and pH) for each type of amino acid.
• Peptide bonds form between the carboxyl group of one amino acid and the amino group of another through dehydration synthesis.
• A chain of amino acids is a polypeptide.
Key Terms
• amino acid: Any of 20 naturally occurring α-amino acids (having the amino, and carboxylic acid groups on the same carbon atom), and a variety of side chains, that combine, via peptide bonds, to form proteins.
• R group: The R group is a side chain specific to each amino acid that confers particular chemical properties to that amino acid.
• polypeptide: Any polymer of (same or different) amino acids joined via peptide bonds. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.04%3A_Proteins-_Molecules_with_Diverse_Structures_and_Functions/3.4B%3A_Amino_Acids.txt |
Learning Objectives
• Summarize the four levels of protein structure
The shape of a protein is critical to its function because it determines whether the protein can interact with other molecules. Protein structures are very complex, and researchers have only very recently been able to easily and quickly determine the structure of complete proteins down to the atomic level. (The techniques used date back to the 1950s, but until recently they were very slow and laborious to use, so complete protein structures were very slow to be solved.) Early structural biochemists conceptually divided protein structures into four “levels” to make it easier to get a handle on the complexity of the overall structures. To determine how the protein gets its final shape or conformation, we need to understand these four levels of protein structure: primary, secondary, tertiary, and quaternary.
Primary Structure
A protein’s primary structure is the unique sequence of amino acids in each polypeptide chain that makes up the protein. Really, this is just a list of which amino acids appear in which order in a polypeptide chain, not really a structure. But, because the final protein structure ultimately depends on this sequence, this was called the primary structure of the polypeptide chain. For example, the pancreatic hormone insulin has two polypeptide chains, A and B.
The gene, or sequence of DNA, ultimately determines the unique sequence of amino acids in each peptide chain. A change in nucleotide sequence of the gene’s coding region may lead to a different amino acid being added to the growing polypeptide chain, causing a change in protein structure and therefore function.
The oxygen-transport protein hemoglobin consists of four polypeptide chains, two identical α chains and two identical β chains. In sickle cell anemia, a single amino substitution in the hemoglobin β chain causes a change the structure of the entire protein. When the amino acid glutamic acid is replaced by valine in the β chain, the polypeptide folds into an slightly-different shape that creates a dysfunctional hemoglobin protein. So, just one amino acid substitution can cause dramatic changes. These dysfunctional hemoglobin proteins, under low-oxygen conditions, start associating with one another, forming long fibers made from millions of aggregated hemoglobins that distort the red blood cells into crescent or “sickle” shapes, which clog arteries. People affected by the disease often experience breathlessness, dizziness, headaches, and abdominal pain.
Secondary Structure
A protein’s secondary structure is whatever regular structures arise from interactions between neighboring or near-by amino acids as the polypeptide starts to fold into its functional three-dimensional form. Secondary structures arise as H bonds form between local groups of amino acids in a region of the polypeptide chain. Rarely does a single secondary structure extend throughout the polypeptide chain. It is usually just in a section of the chain. The most common forms of secondary structure are the α-helix and β-pleated sheet structures and they play an important structural role in most globular and fibrous proteins.
In the α-helix chain, the hydrogen bond forms between the oxygen atom in the polypeptide backbone carbonyl group in one amino acid and the hydrogen atom in the polypeptide backbone amino group of another amino acid that is four amino acids farther along the chain. This holds the stretch of amino acids in a right-handed coil. Every helical turn in an alpha helix has 3.6 amino acid residues. The R groups (the side chains) of the polypeptide protrude out from the α-helix chain and are not involved in the H bonds that maintain the α-helix structure.
In β-pleated sheets, stretches of amino acids are held in an almost fully-extended conformation that “pleats” or zig-zags due to the non-linear nature of single C-C and C-N covalent bonds. β-pleated sheets never occur alone. They have to held in place by other β-pleated sheets. The stretches of amino acids in β-pleated sheets are held in their pleated sheet structure because hydrogen bonds form between the oxygen atom in a polypeptide backbone carbonyl group of one β-pleated sheet and the hydrogen atom in a polypeptide backbone amino group of another β-pleated sheet. The β-pleated sheets which hold each other together align parallel or antiparallel to each other. The R groups of the amino acids in a β-pleated sheet point out perpendicular to the hydrogen bonds holding the β-pleated sheets together, and are not involved in maintaining the β-pleated sheet structure.
Tertiary Structure
The tertiary structure of a polypeptide chain is its overall three-dimensional shape, once all the secondary structure elements have folded together among each other. Interactions between polar, nonpolar, acidic, and basic R group within the polypeptide chain create the complex three-dimensional tertiary structure of a protein. When protein folding takes place in the aqueous environment of the body, the hydrophobic R groups of nonpolar amino acids mostly lie in the interior of the protein, while the hydrophilic R groups lie mostly on the outside. Cysteine side chains form disulfide linkages in the presence of oxygen, the only covalent bond forming during protein folding. All of these interactions, weak and strong, determine the final three-dimensional shape of the protein. When a protein loses its three-dimensional shape, it will no longer be functional.
Quaternary Structure
The quaternary structure of a protein is how its subunits are oriented and arranged with respect to one another. As a result, quaternary structure only applies to multi-subunit proteins; that is, proteins made from more than one polypeptide chain. Proteins made from a single polypeptide will not have a quaternary structure.
In proteins with more than one subunit, weak interactions between the subunits help to stabilize the overall structure. Enzymes often play key roles in bonding subunits to form the final, functioning protein.
For example, insulin is a ball-shaped, globular protein that contains both hydrogen bonds and disulfide bonds that hold its two polypeptide chains together. Silk is a fibrous protein that results from hydrogen bonding between different β-pleated chains.
Key Points
• Protein structure depends on its amino acid sequence and local, low-energy chemical bonds between atoms in both the polypeptide backbone and in amino acid side chains.
• Protein structure plays a key role in its function; if a protein loses its shape at any structural level, it may no longer be functional.
• Primary structure is the amino acid sequence.
• Secondary structure is local interactions between stretches of a polypeptide chain and includes α-helix and β-pleated sheet structures.
• Tertiary structure is the overall the three-dimension folding driven largely by interactions between R groups.
• Quarternary structures is the orientation and arrangement of subunits in a multi-subunit protein.
Key Terms
• antiparallel: The nature of the opposite orientations of the two strands of DNA or two beta strands that comprise a protein’s secondary structure
• disulfide bond: A bond, consisting of a covalent bond between two sulfur atoms, formed by the reaction of two thiol groups, especially between the thiol groups of two proteins
• β-pleated sheet: secondary structure of proteins where N-H groups in the backbone of one fully-extended strand establish hydrogen bonds with C=O groups in the backbone of an adjacent fully-extended strand
• α-helix: secondary structure of proteins where every backbone N-H creates a hydrogen bond with the C=O group of the amino acid four residues earlier in the same helix.
3.4D: Denaturation and Protein Folding
Learning Objectives
• Discuss the process of protein denaturation
Each protein has its own unique sequence of amino acids and the interactions between these amino acids create a specify shape. This shape determines the protein’s function, from digesting protein in the stomach to carrying oxygen in the blood.
Changing the Shape of a Protein
If the protein is subject to changes in temperature, pH, or exposure to chemicals, the internal interactions between the protein’s amino acids can be altered, which in turn may alter the shape of the protein. Although the amino acid sequence (also known as the protein’s primary structure) does not change, the protein’s shape may change so much that it becomes dysfunctional, in which case the protein is considered denatured. Pepsin, the enzyme that breaks down protein in the stomach, only operates at a very low pH. At higher pHs pepsin’s conformation, the way its polypeptide chain is folded up in three dimensions, begins to change. The stomach maintains a very low pH to ensure that pepsin continues to digest protein and does not denature.
Because almost all biochemical reactions require enzymes, and because almost all enzymes only work optimally within relatively narrow temperature and pH ranges, many homeostatic mechanisms regulate appropriate temperatures and pH so that the enzymes can maintain the shape of their active site.
Reversing Denaturation
It is often possible to reverse denaturation because the primary structure of the polypeptide, the covalent bonds holding the amino acids in their correct sequence, is intact. Once the denaturing agent is removed, the original interactions between amino acids return the protein to its original conformation and it can resume its function. However, denaturation can be irreversible in extreme situations, like frying an egg. The heat from a pan denatures the albumin protein in the liquid egg white and it becomes insoluble. The protein in meat also denatures and becomes firm when cooked.
Chaperone proteins (or chaperonins ) are helper proteins that provide favorable conditions for protein folding to take place. The chaperonins clump around the forming protein and prevent other polypeptide chains from aggregating. Once the target protein folds, the chaperonins disassociate.
Key Points
• Proteins change their shape when exposed to different pH or temperatures.
• The body strictly regulates pH and temperature to prevent proteins such as enzymes from denaturing.
• Some proteins can refold after denaturation while others cannot.
• Chaperone proteins help some proteins fold into the correct shape.
Key Terms
• chaperonin: proteins that provide favorable conditions for the correct folding of other proteins, thus preventing aggregation
• denaturation: the change of folding structure of a protein (and thus of physical properties) caused by heating, changes in pH, or exposure to certain chemicals | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.04%3A_Proteins-_Molecules_with_Diverse_Structures_and_Functions/3.4C%3A_Protein_Structure.txt |
Learning Objectives
• Differentiate between saturated and unsaturated fatty acids
Glycerol and Fatty Acids
A fat molecule consists of two main components: glycerol and fatty acids. Glycerol is an alcohol with three carbons, five hydrogens, and three hydroxyl (OH) groups. Fatty acids have a long chain of hydrocarbons with a carboxyl group attached and may have 4-36 carbons; however, most of them have 12-18. In a fat molecule, the fatty acids are attached to each of the three carbons of the glycerol molecule with an ester bond through the oxygen atom. During the ester bond formation, three molecules are released. Since fats consist of three fatty acids and a glycerol, they are also called triacylglycerols or triglycerides.
Saturated vs. Unsaturated Fatty Acids
Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between neighboring carbons in the hydrocarbon chain, the fatty acid is said to be saturated. Saturated fatty acids are saturated with hydrogen since single bonds increase the number of hydrogens on each carbon. Stearic acid and palmitic acid, which are commonly found in meat, are examples of saturated fats.
When the hydrocarbon chain contains a double bond, the fatty acid is said to be unsaturated. Oleic acid is an example of an unsaturated fatty acid. Most unsaturated fats are liquid at room temperature and are called oils. If there is only one double bond in the molecule, then it is known as a monounsaturated fat; e.g. olive oil. If there is more than one double bond, then it is known as a polyunsaturated fat; e.g. canola oil. Unsaturated fats help to lower blood cholesterol levels whereas saturated fats contribute to plaque formation in the arteries.
Unsaturated fats or oils are usually of plant origin and contain cis unsaturated fatty acids. Cis and trans indicate the configuration of the molecule around the double bond. If hydrogens are present in the same plane, it is referred to as a cis fat; if the hydrogen atoms are on two different planes, it is referred to as a trans fat. The cis double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature.
Trans Fats
In the food industry, oils are artificially hydrogenated to make them semi-solid and of a consistency desirable for many processed food products. During this hydrogenation process, gas is bubbled through oils to solidify them, and the double bonds of the cis-conformation in the hydrocarbon chain may be converted to double bonds in the trans-conformation.
Margarine, some types of peanut butter, and shortening are examples of artificially-hydrogenated trans fats. Recent studies have shown that an increase in trans fats in the human diet may lead to an increase in levels of low-density lipoproteins (LDL), or “bad” cholesterol, which in turn may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have recently banned the use of trans fats, and food labels are required to display the trans fat content.
Essential Fatty Acids
Essential fatty acids are fatty acids required for biological processes, but not synthesized by the human body. Consequently, they have to be supplemented through ingestion via the diet and are nutritionally very important. Omega-3 fatty acid, or alpha-linoleic acid (ALA), falls into this category and is one of only two fatty acids known to be essential for humans (the other being omega-6 fatty acid, or linoleic acid). These polyunsaturated fatty acids are called omega-3 because the third carbon from the end of the hydrocarbon chain is connected to its neighboring carbon by a double bond. Salmon, trout, and tuna are good sources of omega-3 fatty acids.
Research indicates that omega-3 fatty acids reduce the risk of sudden death from heart attacks, reduce triglycerides in the blood, lower blood pressure, and prevent thrombosis by inhibiting blood clotting. They also reduce inflammation and may help reduce the risk of some cancers in animals.
Key Points
• Fats provide energy, insulation, and storage of fatty acids for many organisms.
• Fats may be saturated (having single bonds) or unsaturated (having double bonds).
• Unsaturated fats may be cis (hydrogens in same plane) or trans (hydrogens in two different planes).
• Olive oil, a monounsaturated fat, has a single double bond whereas canola oil, a polyunsaturated fat, has more than one double bond.
• Omega-3 fatty acid and omega-6 fatty acid are essential for human biological processes, but they must be ingested in the diet because they cannot be synthesized.
Key Terms
• hydrogenation: The chemical reaction of hydrogen with another substance, especially with an unsaturated organic compound, and usually under the influence of temperature, pressure and catalysts.
• ester: Compound most often formed by the condensation of an alcohol and an acid, by removing water. It contains the functional group carbon-oxygen double bond joined via carbon to another oxygen atom.
• carboxyl: A univalent functional group consisting of a carbonyl and a hydroxyl functional group (-CO.OH); characteristic of carboxylic acids.
Fats have important functions, and many vitamins are fat soluble. Fats serve as a long-term storage form of fatty acids and act as a source of energy. They also provide insulation for the body. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.05%3A_Lipids-_Hydrophobic_Molecules/3.5A%3A_Lipid_Molecules.txt |
Learning Objectives
• Describe phospholipids and their role in cells
Defining Characteristics of Phospholipids
Phospholipids are major components of the plasma membrane, the outermost layer of animal cells. Like fats, they are composed of fatty acid chains attached to a glycerol backbone. Unlike triglycerides, which have three fatty acids, phospholipids have two fatty acids that help form a diacylglycerol. The third carbon of the glycerol backbone is also occupied by a modified phosphate group. However, just a phosphate group attached to a diacylglycerol does not qualify as a phospholipid. This would be considered a phosphatidate (diacylglycerol 3-phosphate), the precursor to phospholipids. To qualify as a phospholipid, the phosphate group should be modified by an alcohol. Phosphatidylcholine and phosphatidylserine are examples of two important phospholipids that are found in plasma membranes.
Structure of a Phospholipid Molecule
A phospholipid is an amphipathic molecule which means it has both a hydrophobic and a hydrophilic component. A single phospholipid molecule has a phosphate group on one end, called the “head,” and two side-by-side chains of fatty acids that make up the lipid “tails. ” The phosphate group is negatively charged, making the head polar and hydrophilic, or “water loving.” The phosphate heads are thus attracted to the water molecules in their environment.
The lipid tails, on the other hand, are uncharged, nonpolar, and hydrophobic, or “water fearing.” A hydrophobic molecule repels and is repelled by water. Some lipid tails consist of saturated fatty acids and some contain unsaturated fatty acids. This combination adds to the fluidity of the tails that are constantly in motion.
Phospholipids and Biological Membranes
The cell membrane consists of two adjacent layers of phospholipids, which form a bilayer. The fatty acid tails of phospholipids face inside, away from water, whereas the phosphate heads face the outward aqueous side. Since the heads face outward, one layer is exposed to the interior of the cell and one layer is exposed to the exterior. As the phosphate groups are polar and hydrophilic, they are attracted to water in the intracellular fluid.
Because of the phospholipds’ chemical and physical characteristics, the lipid bilayer acts as a semipermeable membrane; only lipophilic solutes can easily pass the phospholipd bilayer. As a result, there are two distinct aqueous compartments on each side of the membrane. This separation is essential for many biological functions, including cell communication and metabolism.
Membrane Fluidity
A cell’s plasma membrane contain proteins and other lipids (such as cholesterol) within the phospholipid bilayer. Biological membranes remain fluid because of the unsaturated hydrophobic tails, which prevent phospholipid molecules from packing together and forming a solid.
If a drop of phospholipids is placed in water, the phospholipids spontaneously form a structure known as a micelle, with their hydrophilic heads oriented toward the water. Micelles are lipid molecules that arrange themselves in a spherical form in aqueous solution. The formation of a micelle is a response to the amphipathic nature of fatty acids, meaning that they contain both hydrophilic and hydrophobic regions.
Key Points
• Phospholipids consist of a glycerol molecule, two fatty acids, and a phosphate group that is modified by an alcohol.
• The phosphate group is the negatively-charged polar head, which is hydrophilic.
• The fatty acid chains are the uncharged, nonpolar tails, which are hydrophobic.
• Since the tails are hydrophobic, they face the inside, away from the water and meet in the inner region of the membrane.
• Since the heads are hydrophilic, they face outward and are attracted to the intracellular and extracellular fluid.
• If phospholipids are placed in water, they form into micelles, which are lipid molecules that arrange themselves in a spherical form in aqueous solutions.
Key Terms
• micelle: Lipid molecules that arrange themselves in a spherical form in aqueous solutions.
• amphipathic: Describing a molecule, such as a detergent, which has both hydrophobic and hydrophilic groups.
3.5D: Steroids
Learning Objectives
• Describe some functions of steroids
Structure of Steroid Molecules
Unlike phospholipids and fats, steroids have a fused ring structure. Although they do not resemble the other lipids, they are grouped with them because they are also hydrophobic and insoluble in water. All steroids have four linked carbon rings, and many of them, like cholesterol, have a short tail. Many steroids also have the –OH functional group, and these steroids are classified as alcohols called sterols.
Cholesterol
Cholesterol is the most common steroid and is mainly synthesized in the liver; it is the precursor to vitamin D. Cholesterol is also a precursor to many important steroid hormones like estrogen, testosterone, and progesterone, which are secreted by the gonads and endocrine glands. Therefore, steroids play very important roles in the body’s reproductive system. Cholesterol also plays a role in synthesizing the steroid hormones aldosterone, which is used for osmoregulation, and cortisol, which plays a role in metabolism.
Cholesterol is also the precursor to bile salts, which help in the emulsification of fats and their absorption by cells. It is a component of the plasma membrane of animal cells and the phospholipid bilayer. Being the outermost structure in animal cells, the plasma membrane is responsible for the transport of materials and cellular recognition; and it is involved in cell-to-cell communication. Thus, steroids also play an important role in the structure and function of membranes.
It has also been discovered that steroids can be active in the brain where they affect the nervous system, These neurosteroids alter electrical activity in the brain. They can either activate or tone down receptors that communicate messages from neurotransmitters. Since these neurosteroids can tone down receptors and decrease brain activity, steroids are often used in anesthetic medicines.
Key Points
• Steroids are lipids because they are hydrophobic and insoluble in water, but they do not resemble lipids since they have a structure composed of four fused rings.
• Cholesterol is the most common steroid and is the precursor to vitamin D, testosterone, estrogen, progesterone, aldosterone, cortisol, and bile salts.
• Cholesterol is a component of the phospholipid bilayer and plays a role in the structure and function of membranes.
• Steroids are found in the brain and alter electrical activity in the brain.
• Because they can tone down receptors that communicate messages from neurotransmitters, steroids are often used in anesthetic medicines.
Key Terms
• neurotransmitter: any substance, such as acetylcholine or dopamine, responsible for sending nerve signals across a synapse between two neurons
• osmoregulation: the homeostatic regulation of osmotic pressure in the body in order to maintain a constant water content
• hormone: any substance produced by one tissue and conveyed by the bloodstream to another to affect physiological activity | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/03%3A_The_Chemical_Building_Blocks_of_Life/3.05%3A_Lipids-_Hydrophobic_Molecules/3.5C%3A_Phospholipids.txt |
Learning Objectives
• State the general characteristics of a cell
Close your eyes and picture a brick wall. What is the basic building block of that wall? A single brick, of course. Like a brick wall, your body is composed of basic building blocks, and the building blocks of your body are cells.
Cells as Building Blocks
A cell is the smallest unit of a living thing. A living thing, whether made of one cell (like bacteria) or many cells (like a human), is called an organism. Thus, cells are the basic building blocks of all organisms. Several cells of one kind that interconnect with each other and perform a shared function form tissues; several tissues combine to form an organ (your stomach, heart, or brain); and several organs make up an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being). There are many types of cells all grouped into one of two broad categories: prokaryotic and eukaryotic. For example, both animal and plant cells are classified as eukaryotic cells, whereas bacterial cells are classified as prokaryotic.
Types of Specialized Cells
Your body has many kinds of cells, each specialized for a specific purpose. Just as a home is made from a variety of building materials, the human body is constructed from many cell types. For example, epithelial cells protect the surface of the body and cover the organs and body cavities within. Bone cells help to support and protect the body. Cells of the immune system fight invading bacteria. Additionally, blood and blood cells carry nutrients and oxygen throughout the body while removing carbon dioxide. Each of these cell types plays a vital role during the growth, development, and day-to-day maintenance of the body. In spite of their enormous variety, however, cells from all organisms—even ones as diverse as bacteria, onion, and human—share certain fundamental characteristics.
Key Points
• A living thing can be composed of either one cell or many cells.
• There are two broad categories of cells: prokaryotic and eukaryotic cells.
• Cells can be highly specialized with specific functions and characteristics.
Key Terms
• prokaryotic: Small cells in the domains Bacteria and Archaea that do not contain a membrane-bound nucleus or other membrane-bound organelles.
• eukaryotic: Having complex cells in which the genetic material is contained within membrane-bound nuclei.
• cell: The basic unit of a living organism, consisting of a quantity of protoplasm surrounded by a cell membrane, which is able to synthesize proteins and replicate itself.
4.1B: Microscopy
Learning Objectives
• Compare and contrast light and electron microscopy.
Microscopy
Cells vary in size. With few exceptions, individual cells cannot be seen with the naked eye, so scientists use microscopes (micro- = “small”; -scope = “to look at”) to study them. A microscope is an instrument that magnifies an object. Most photographs of cells are taken with a microscope; these images can also be called micrographs.
The optics of a microscope’s lenses change the orientation of the image that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when viewed through a microscope, and vice versa. Similarly, if the slide is moved left while looking through the microscope, it will appear to move right, and if moved down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image. Because of the manner by which light travels through the lenses, this system of two lenses produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but they include an additional magnification system that makes the final image appear to be upright).
Light Microscopes
To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter; the head of a pin of is about two thousandths of a meter (two mm) in diameter. That means about 250 red blood cells could fit on the head of a pin.
Most student microscopes are classified as light microscopes. Visible light passes and is bent through the lens system to enable the user to see the specimen. Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells.
Light microscopes, commonly used in undergraduate college laboratories, magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the ability of a microscope to distinguish two adjacent structures as separate: the higher the resolution, the better the clarity and detail of the image. When oil immersion lenses are used for the study of small objects, magnification is usually increased to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes.
Electron Microscopes
In contrast to light microscopes, electron microscopes use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail, it also provides higher resolving power. The method used to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so living cells cannot be viewed with an electron microscope.
In a scanning electron microscope, a beam of electrons moves back and forth across a cell’s surface, creating details of cell surface characteristics. In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell’s internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes.
Key Points
• Light microscopes allow for magnification of an object approximately up to 400-1000 times depending on whether the high power or oil immersion objective is used.
• Light microscopes use visible light which passes and bends through the lens system.
• Electron microscopes use a beam of electrons, opposed to visible light, for magnification.
• Electron microscopes allow for higher magnification in comparison to a light microscope thus, allowing for visualization of cell internal structures.
Key Terms
• resolution: The degree of fineness with which an image can be recorded or produced, often expressed as the number of pixels per unit of length (typically an inch).
• electron: The subatomic particle having a negative charge and orbiting the nucleus; the flow of electrons in a conductor constitutes electricity. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.01%3A_Cell_Theory/4.1A%3A_Cells_as_the_Basic_Unit_of_Life.txt |
Learning Objectives
• Identify the components of cell theory
Cell Theory
The microscopes we use today are far more complex than those used in the 1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the movements of protista (a type of single-celled organism) and sperm, which he collectively termed “animalcules. ”
In a 1665 publication called Micrographia, experimental scientist Robert Hooke coined the term “cell” for the box-like structures he observed when viewing cork tissue through a lens. In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells.
By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory. The unified cell theory states that: all living things are composed of one or more cells; the cell is the basic unit of life; and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory.
Schleiden and Schwann proposed spontaneous generation as the method for cell origination, but spontaneous generation (also called abiogenesis) was later disproven. Rudolf Virchow famously stated “Omnis cellula e cellula”… “All cells only arise from pre-existing cells. “The parts of the theory that did not have to do with the origin of cells, however, held up to scientific scrutiny and are widely agreed upon by the scientific community today. The generally accepted portions of the modern Cell Theory are as follows:
1. The cell is the fundamental unit of structure and function in living things.
2. All organisms are made up of one or more cells.
3. Cells arise from other cells through cellular division.
The expanded version of the cell theory can also include:
• Cells carry genetic material passed to daughter cells during cellular division
• All cells are essentially the same in chemical composition
• Energy flow (metabolism and biochemistry) occurs within cells
Key Points
• The cell theory describes the basic properties of all cells.
• The three scientists that contributed to the development of cell theory are Matthias Schleiden, Theodor Schwann, and Rudolf Virchow.
• A component of the cell theory is that all living things are composed of one or more cells.
• A component of the cell theory is that the cell is the basic unit of life.
• A component of the cell theory is that all new cells arise from existing cells.
Key Terms
• cell theory: The scientific theory that all living organisms are made of cells as the smallest functional unit.
4.1D: Cell Size
Learning Objectives
• Describe the factors limiting cell size and the adaptations cells make to overcome the surface area to volume issue
At 0.1 to 5.0 μm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10 to 100 μm. The small size of prokaryotes allows ions and organic molecules that enter them to quickly diffuse to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly diffuse out. This is not the case in eukaryotic cells, which have developed different structural adaptations to enhance intracellular transport.
In general, small size is necessary for all cells, whether prokaryotic or eukaryotic. Consider the area and volume of a typical cell. Not all cells are spherical in shape, but most tend to approximate a sphere. The formula for the surface area of a sphere is 4πr2, while the formula for its volume is 4πr3/3. As the radius of a cell increases, its surface area increases as the square of its radius, but its volume increases as the cube of its radius (much more rapidly).
Therefore, as a cell increases in size, its surface area-to-volume ratio decreases. This same principle would apply if the cell had the shape of a cube (below). If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume. In other words, as a cell grows, it becomes less efficient. One way to become more efficient is to divide; another way is to develop organelles that perform specific tasks. These adaptations lead to the development of more sophisticated cells called eukaryotic cells.
Smaller single-celled organisms have a high surface area to volume ratio, which allows them to rely on oxygen and material diffusing into the cell (and wastes diffusing out) in order to survive. The higher the surface area to volume ratio they have, the more effective this process can be. Larger animals require specialized organs (lungs, kidneys, intestines, etc.) that effectively increase the surface area available for exchange processes, and a circulatory system to move material and heat energy between the surface and the core of the organism.
Increased volume can lead to biological problems. King Kong, the fictional giant gorilla, would have insufficient lung surface area to meet his oxygen needs, and could not survive. For small organisms with their high surface area to volume ratio, friction and fluid dynamics (wind, water flow) are relatively much more important, and gravity much less important, than for large animals.
However, increased surface area can cause problems as well. More contact with the environment through the surface of a cell or an organ (relative to its volume) increases loss of water and dissolved substances. High surface area to volume ratios also present problems of temperature control in unfavorable environments.
Key Points
• As a cell grows, its volume increases much more rapidly than its surface area. Since the surface of the cell is what allows the entry of oxygen, large cells cannot get as much oxygen as they would need to support themselves.
• As animals increase in size they require specialized organs that effectively increase the surface area available for exchange processes.
Key Terms
• surface area: The total area on the surface of an object. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.01%3A_Cell_Theory/4.1C%3A_Cell_Theory.txt |
Does the shape matter?
It does if you're a bacterium. Prokaryotic cells are distinguished by their shape. And as you can imagine, shape may have something to do with mobility.
Prokaryote Structure
Most prokaryotic cells are much smaller than eukaryotic cells. Although they are tiny, prokaryotic cells can be distinguished by their shapes. The most common shapes are helices, spheres, and rods (see Figure below).
Prokaryotic Cell Shapes. The three most common prokaryotic cell shapes are shown here.
Plasma Membrane and Cell Wall
Like other cells, prokaryotic cells have a plasma membrane (see Figure below). It controls what enters and leaves the cell. It is also the site of many metabolic reactions. For example, cellular respiration and photosynthesis take place in the plasma membrane.
Most prokaryotes also have a cell wall. It lies just outside the plasma membrane. It gives strength and rigidity to the cell. Bacteria and Archaea differ in the makeup of their cell wall. The cell wall of Bacteria contains peptidoglycan, composed of sugars and amino acids. The cell wall of most Archaea lacks peptidoglycan.
Prokaryotic Cell. The main parts of a prokaryotic cell are shown in this diagram. The structure called a mesosome was once thought to be an organelle. More evidence has convinced most scientists that it is not a true cell structure at all. Instead, it seems to be an artifact of cell preparation. This is a good example of how scientific knowledge is revised as more evidence becomes available. Can you identify each of the labeled structures?
Cytoplasm and Cell Structures
Inside the plasma membrane of prokaryotic cells is the cytoplasm. It contains several structures, including ribosomes, a cytoskeleton, and genetic material. Ribosomes are sites where proteins are made. The cytoskeleton helps the cell keep its shape. The genetic material is usually a single loop of DNA. There may also be small, circular pieces of DNA, called plasmids. (see Figure below). The cytoplasm may contain microcompartments as well. These are tiny structures enclosed by proteins. They contain enzymes and are involved in metabolic processes.
Prokaryotic DNA. The DNA of a prokaryotic cell is in the cytoplasm because the cell lacks a nucleus.
Extracellular Structures
Many prokaryotes have an extra layer, called a capsule, outside the cell wall. The capsuleprotects the cell from chemicals and from drying out. It also allows the cell to stick to surfaces and to other cells. Because of this, many prokaryotes can form biofilms, like the one shown in Figure below. A biofilm is a colony of prokaryotes that is stuck to a surface such as a rock or a host’s tissues. The sticky plaque that collects on your teeth between brushings is a biofilm. It consists of millions of bacteria.
Most prokaryotes also have long, thin protein structures called flagella (singular, flagellum). They extend from the plasma membrane. Flagella help prokaryotes move. They spin around a fixed base, causing the cell to roll and tumble. As shown in Figure below, prokaryotes may have one or more flagella.
Bacterial Biofilm. The greatly magnified biofilm shown here was found on a medical catheter (tubing) removed from a patient’s body.
Variations in the Flagella of Bacteria. Flagella in prokaryotes may be located at one or both ends of the cell or all around it. They help prokaryotes move toward food or away from toxins.
Endospores
Many organisms form spores for reproduction. Some prokaryotes form spores for survival. Called endospores, they form inside prokaryotic cells when they are under stress. The stress could be UV radiation, high temperatures, or harsh chemicals. Endospores enclose the DNA and help it survive under conditions that may kill the cell. Endospores are commonly found in soil and water. They may survive for long periods of time.
Summary
• Most prokaryotic cells are much smaller than eukaryotic cells.
• Prokaryotic cells have a cell wall outside their plasma membrane.
• Prokaryotic DNA consists of a single loop. Some prokaryotes also have small, circular pieces of DNA called plasmids.
Review
1. Identify the three most common shapes of prokaryotic cells.
2. Describe a typical prokaryotic cell.
3. What are the roles of flagella and endospores in prokaryotes? | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.02%3A_Prokaryotic_Cells/4.2.01%3A_Prokaryotic_Structure.txt |
With so many different bacteria, how are they all classified?
By shape? By size? By some other criteria? As you can imagine, classifying bacteria is probably not an easy task. Bacteria are classified by their traits, some of which have to do with their shape, others with the cell wall, and even additional traits.
The Prokaryotic Domains
Domain Bacteria
Bacteria are the most diverse and abundant group of organisms on Earth. They live in almost all environments. They are found in the ocean, the soil, and the intestines of animals. They are even found in rocks deep below Earth’s surface. Any surface that has not been sterilized is likely to be covered with bacteria. The total number of bacteria in the world is amazing. It’s estimated to be 5 × 1030, or five million trillion. You have more bacteria in and on your body than you have body cells!
Bacteria called cyanobacteria are very important. They are bluish green in color (see Figure below) because they contain chlorophyll (but not chloroplasts, of course). They make food through photosynthesis and release oxygen into the air. These bacteria were probably responsible for adding oxygen to the air on early Earth. This changed the planet’s atmosphere. It also changed the direction of evolution. Ancient cyanobacteria also may have evolved into the chloroplasts of plant cells.
Cyanobacteria Bloom. The green streaks in this lake consist of trillions of cyanobacteria. Excessive nutrients in the water led to overgrowth of the bacteria.
Thousands of species of bacteria have been discovered, and many more are thought to exist. The known species can be classified on the basis of various traits. One classification is based on differences in their cell walls and outer membranes. It groups bacteria into Gram-positiveand Gram-negative bacteria, as described in Figure below.
Classification of Bacteria. Different types of bacteria stain a different color when stained with Gram stain. This makes them easy to identify.
Domain Archaea
Scientists still know relatively little about Archaea. This is partly because they are hard to grow in the lab. Many live inside the bodies of animals, including humans. However, none are known for certain to cause disease.
Archaea were first discovered in extreme environments. For example, some were found in hot springs. Others were found around deep sea vents. Such Archaea are called extremophiles, or “lovers of extremes.” Figure below describes three different types of Archaean extremophiles. The places where some of them live are thought to be similar to the environment on ancient Earth. This suggests that they may have evolved very early in Earth’s history.
Extremophile Archaea. Many Archaea are specialized to live in extreme environments. Just three types are described here.
Archaea are now known to live just about everywhere on Earth. They are particularly numerous in the ocean. Archaea in plankton may be one of the most abundant types of organisms on the planet. Archaea are also thought to play important roles in the carbon and nitrogen cycles. For these reasons, Archaea are now recognized as a major aspect of life on Earth.
Summary
• Bacteria live in virtually all environments on Earth.
• Archaea live everywhere on Earth, including extreme environments.
Review
1. Distinguish between Gram-positive and Gram-negative bacteria, and give an example of each.
2. Summarize the evolutionary significance of cyanobacteria.
3. What are extremophiles? Name three types.
4. Describe the habitat of extreme halophiles. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.02%3A_Prokaryotic_Cells/4.2.02%3A_Prokaryotic_Classification.txt |
Skills to Develop
• Name examples of prokaryotic and eukaryotic organisms
• Compare and contrast prokaryotic cells and eukaryotic cells
• Describe the relative sizes of different kinds of cells
• Explain why cells must be small
Cells fall into one of two broad categories: prokaryotic and eukaryotic. Only the predominantly single-celled organisms of the domains Bacteria and Archaea are classified as prokaryotes (pro- = “before”; -kary- = “nucleus”). Cells of animals, plants, fungi, and protists are all eukaryotes (eu- = “true”) and are made up of eukaryotic cells.
Components of Prokaryotic Cells
All cells share four common components: 1) a plasma membrane, an outer covering that separates the cell’s interior from its surrounding environment; 2) cytoplasm, consisting of a jelly-like cytosol within the cell in which other cellular components are found; 3) DNA, the genetic material of the cell; and 4) ribosomes, which synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways.
A prokaryote is a simple, mostly single-celled (unicellular) organism that lacks a nucleus, or any other membrane-bound organelle. We will shortly come to see that this is significantly different in eukaryotes. Prokaryotic DNA is found in a central part of the cell: the nucleoid (Figure $1$).
Most prokaryotes have a peptidoglycan cell wall and many have a polysaccharide capsule (Figure $1$). The cell wall acts as an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. The capsule enables the cell to attach to surfaces in its environment. Some prokaryotes have flagella, pili, or fimbriae. Flagella are used for locomotion. Pili are used to exchange genetic material during a type of reproduction called conjugation. Fimbriae are used by bacteria to attach to a host cell.
Career Connection: Microbiologist
The most effective action anyone can take to prevent the spread of contagious illnesses is to wash his or her hands. Why? Because microbes (organisms so tiny that they can only be seen with microscopes) are ubiquitous. They live on doorknobs, money, your hands, and many other surfaces. If someone sneezes into his hand and touches a doorknob, and afterwards you touch that same doorknob, the microbes from the sneezer’s mucus are now on your hands. If you touch your hands to your mouth, nose, or eyes, those microbes can enter your body and could make you sick.
However, not all microbes (also called microorganisms) cause disease; most are actually beneficial. You have microbes in your gut that make vitamin K. Other microorganisms are used to ferment beer and wine.
Microbiologists are scientists who study microbes. Microbiologists can pursue a number of careers. Not only do they work in the food industry, they are also employed in the veterinary and medical fields. They can work in the pharmaceutical sector, serving key roles in research and development by identifying new sources of antibiotics that could be used to treat bacterial infections.
Environmental microbiologists may look for new ways to use specially selected or genetically engineered microbes for the removal of pollutants from soil or groundwater, as well as hazardous elements from contaminated sites. These uses of microbes are called bioremediation technologies. Microbiologists can also work in the field of bioinformatics, providing specialized knowledge and insight for the design, development, and specificity of computer models of, for example, bacterial epidemics.
Cell Size
At 0.1 to 5.0 μm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10 to 100 μm (Figure $2$). The small size of prokaryotes allows ions and organic molecules that enter them to quickly diffuse to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly diffuse out. This is not the case in eukaryotic cells, which have developed different structural adaptations to enhance intracellular transport.
Small size, in general, is necessary for all cells, whether prokaryotic or eukaryotic. Let’s examine why that is so. First, we’ll consider the area and volume of a typical cell. Not all cells are spherical in shape, but most tend to approximate a sphere. You may remember from your high school geometry course that the formula for the surface area of a sphere is $4\pi r^2$, while the formula for its volume is $4\pi r^2/3$. Thus, as the radius of a cell increases, its surface area increases as the square of its radius, but its volume increases as the cube of its radius (much more rapidly). Therefore, as a cell increases in size, its surface area-to-volume ratio decreases. This same principle would apply if the cell had the shape of a cube (Figure $3$). If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume. In other words, as a cell grows, it becomes less efficient. One way to become more efficient is to divide; another way is to develop organelles that perform specific tasks. These adaptations lead to the development of more sophisticated cells called eukaryotic cells.
Art Connection
Prokaryotic cells are much smaller than eukaryotic cells. What advantages might small cell size confer on a cell? What advantages might large cell size have?
Summary
Prokaryotes are predominantly single-celled organisms of the domains Bacteria and Archaea. All prokaryotes have plasma membranes, cytoplasm, ribosomes, and DNA that is not membrane-bound. Most have peptidoglycan cell walls and many have polysaccharide capsules. Prokaryotic cells range in diameter from 0.1 to 5.0 μm.
As a cell increases in size, its surface area-to-volume ratio decreases. If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume.
Art Connections
Figure $3$: Prokaryotic cells are much smaller than eukaryotic cells. What advantages might small cell size confer on a cell? What advantages might large cell size have?
Answer
Substances can diffuse more quickly through small cells. Small cells have no need for organelles and therefore do not need to expend energy getting substances across organelle membranes. Large cells have organelles that can separate cellular processes, enabling them to build molecules that are more complex.
Glossary
nucleoid
central part of a prokaryotic cell in which the chromosome is found
prokaryote
unicellular organism that lacks a nucleus or any other membrane-bound organelle | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.02%3A_Prokaryotic_Cells/4.2.03%3A_Prokaryotic_Cells.txt |
At this point, it should be clear that eukaryotic cells have a more complex structure than do prokaryotic cells. Organelles allow for various functions to occur in the cell at the same time. Before discussing the functions of organelles within a eukaryotic cell, let us first examine two important components of the cell: the plasma membrane and the cytoplasm.
ART CONNECTION
What structures does a plant cell have that an animal cell does not have? What structures does an animal cell have that a plant cell does not have?
The Plasma Membrane
Like prokaryotes, eukaryotic cells have a plasma membrane (Figure \(2\)) made up of a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule composed of two fatty acid chains, a glycerol backbone, and a phosphate group. The plasma membrane regulates the passage of some substances, such as organic molecules, ions, and water, preventing the passage of some to maintain internal conditions, while actively bringing in or removing others. Other compounds move passively across the membrane.
The plasma membranes of cells that specialize in absorption are folded into fingerlike projections called microvilli (singular = microvillus). This folding increases the surface area of the plasma membrane. Such cells are typically found lining the small intestine, the organ that absorbs nutrients from digested food. This is an excellent example of form matching the function of a structure.
People with celiac disease have an immune response to gluten, which is a protein found in wheat, barley, and rye. The immune response damages microvilli, and thus, afflicted individuals cannot absorb nutrients. This leads to malnutrition, cramping, and diarrhea. Patients suffering from celiac disease must follow a gluten-free diet.
The Cytoplasm
The cytoplasm comprises the contents of a cell between the plasma membrane and the nuclear envelope (a structure to be discussed shortly). It is made up of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals (Figure \(1\)). Even though the cytoplasm consists of 70 to 80 percent water, it has a semi-solid consistency, which comes from the proteins within it. However, proteins are not the only organic molecules found in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found there too. Ions of sodium, potassium, calcium, and many other elements are also dissolved in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm.
The Cytoskeleton
If you were to remove all the organelles from a cell, would the plasma membrane and the cytoplasm be the only components left? No. Within the cytoplasm, there would still be ions and organic molecules, plus a network of protein fibers that helps to maintain the shape of the cell, secures certain organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently. Collectively, this network of protein fibers is known as the cytoskeleton. There are three types of fibers within the cytoskeleton: microfilaments, also known as actin filaments, intermediate filaments, and microtubules (Figure \(3\)).
Microfilaments are the thinnest of the cytoskeletal fibers and function in moving cellular components, for example, during cell division. They also maintain the structure of microvilli, the extensive folding of the plasma membrane found in cells dedicated to absorption. These components are also common in muscle cells and are responsible for muscle cell contraction. Intermediate filaments are of intermediate diameter and have structural functions, such as maintaining the shape of the cell and anchoring organelles. Keratin, the compound that strengthens hair and nails, forms one type of intermediate filament. Microtubules are the thickest of the cytoskeletal fibers. These are hollow tubes that can dissolve and reform quickly. Microtubules guide organelle movement and are the structures that pull chromosomes to their poles during cell division. They are also the structural components of flagella and cilia. In cilia and flagella, the microtubules are organized as a circle of nine double microtubules on the outside and two microtubules in the center.
The centrosome is a region near the nucleus of animal cells that functions as a microtubule-organizing center. It contains a pair of centrioles, two structures that lie perpendicular to each other. Each centriole is a cylinder of nine triplets of microtubules.
The centrosome replicates itself before a cell divides, and the centrioles play a role in pulling the duplicated chromosomes to opposite ends of the dividing cell. However, the exact function of the centrioles in cell division is not clear, since cells that have the centrioles removed can still divide, and plant cells, which lack centrioles, are capable of cell division.
Flagella and Cilia
Flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell, (for example, sperm, Euglena). When present, the cell has just one flagellum or a few flagella. When cilia (singular = cilium) are present, however, they are many in number and extend along the entire surface of the plasma membrane. They are short, hair-like structures that are used to move entire cells (such as paramecium) or move substances along the outer surface of the cell (for example, the cilia of cells lining the fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory tract that move particulate matter toward the throat that mucus has trapped).
The Endomembrane System
The endomembrane system (endo = within) is a group of membranes and organelles (Figure \(3\)) in eukaryotic cells that work together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, the endoplasmic reticulum and Golgi apparatus, which we will cover shortly. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles.
The Nucleus
Typically, the nucleus is the most prominent organelle in a cell (Figure \(1\)). The nucleus (plural = nuclei) houses the cell’s DNA in the form of chromatin and directs the synthesis of ribosomes and proteins. Let us look at it in more detail (Figure \(4\)).
The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus (Figure \(4\)). Both the inner and outer membranes of the nuclear envelope are phospholipid bilayers.
The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and the cytoplasm.
To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the nucleus that are made up of DNA, the hereditary material, and proteins. This combination of DNA and proteins is called chromatin. In eukaryotes, chromosomes are linear structures. Every species has a specific number of chromosomes in the nucleus of its body cells. For example, in humans, the chromosome number is 46, whereas in fruit flies, the chromosome number is eight.
Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. When the cell is in the growth and maintenance phases of its life cycle, the chromosomes resemble an unwound, jumbled bunch of threads.
We already know that the nucleus directs the synthesis of ribosomes, but how does it do this? Some chromosomes have sections of DNA that encode ribosomal RNA. A darkly staining area within the nucleus, called the nucleolus (plural = nucleoli), aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported through the nuclear pores into the cytoplasm.
The Endoplasmic Reticulum
The endoplasmic reticulum (ER) (Figure \(7\)) is a series of interconnected membranous tubules that collectively modify proteins and synthesize lipids. However, these two functions are performed in separate areas of the endoplasmic reticulum: the rough endoplasmic reticulum and the smooth endoplasmic reticulum, respectively.
The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope.
The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope.
The ribosomes synthesize proteins while attached to the ER, resulting in transfer of their newly synthesized proteins into the lumen of the RER where they undergo modifications such as folding or addition of sugars. The RER also makes phospholipids for cell membranes.
If the phospholipids or modified proteins are not destined to stay in the RER, they will be packaged within vesicles and transported from the RER by budding from the membrane (Figure \(7\)). Since the RER is engaged in modifying proteins that will be secreted from the cell, it is abundant in cells that secrete proteins, such as the liver.
The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface (see Figure \(1\)). The SER’s functions include synthesis of carbohydrates, lipids (including phospholipids), and steroid hormones; detoxification of medications and poisons; alcohol metabolism; and storage of calcium ions.
The Golgi Apparatus
We have already mentioned that vesicles can bud from the ER, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles need to be sorted, packaged, and tagged so that they wind up in the right place. The sorting, tagging, packaging, and distribution of lipids and proteins take place in the Golgi apparatus (also called the Golgi body), a series of flattened membranous sacs (Figure \(5\)).
The Golgi apparatus has a receiving face near the endoplasmic reticulum and a releasing face on the side away from the ER, toward the cell membrane. The transport vesicles that form from the ER travel to the receiving face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications. The most frequent modification is the addition of short chains of sugar molecules. The newly modified proteins and lipids are then tagged with small molecular groups to enable them to be routed to their proper destinations.
Finally, the modified and tagged proteins are packaged into vesicles that bud from the opposite face of the Golgi. While some of these vesicles, transport vesicles, deposit their contents into other parts of the cell where they will be used, others, secretory vesicles, fuse with the plasma membrane and release their contents outside the cell.
The amount of Golgi in different cell types again illustrates that form follows function within cells. Cells that engage in a great deal of secretory activity (such as cells of the salivary glands that secrete digestive enzymes or cells of the immune system that secrete antibodies) have an abundant number of Golgi.
In plant cells, the Golgi has an additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which are used in other parts of the cell.
Lysosomes
In animal cells, the lysosomes are the cell’s “garbage disposal.” Digestive enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. In single-celled eukaryotes, lysosomes are important for digestion of the food they ingest and the recycling of organelles. These enzymes are active at a much lower pH (more acidic) than those located in the cytoplasm. Many reactions that take place in the cytoplasm could not occur at a low pH, thus the advantage of compartmentalizing the eukaryotic cell into organelles is apparent.
Lysosomes also use their hydrolytic enzymes to destroy disease-causing organisms that might enter the cell. A good example of this occurs in a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known as phagocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen (Figure \(6\)).
Vesicles and Vacuoles
Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Vacuoles are somewhat larger than vesicles, and the membrane of a vacuole does not fuse with the membranes of other cellular components. Vesicles can fuse with other membranes within the cell system. Additionally, enzymes within plant vacuoles can break down macromolecules.
ART CONNECTION
Why does the cis face of the Golgi not face the plasma membrane?
Ribosomes
Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, free ribosomes appear as either clusters or single tiny dots floating freely in the cytoplasm. Ribosomes may be attached to either the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum (Figure \(7\)). Electron microscopy has shown that ribosomes consist of large and small subunits. Ribosomes are enzyme complexes that are responsible for protein synthesis.
Because protein synthesis is essential for all cells, ribosomes are found in practically every cell, although they are smaller in prokaryotic cells. They are particularly abundant in immature red blood cells for the synthesis of hemoglobin, which functions in the transport of oxygen throughout the body.
Mitochondria
Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. The formation of ATP from the breakdown of glucose is known as cellular respiration. Mitochondria are oval-shaped, double-membrane organelles (Figure \(8\)) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae, which increase the surface area of the inner membrane. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.
In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration of mitochondria because muscle cells need a lot of energy to contract.
Peroxisomes
Peroxisomes are small, round organelles enclosed by single membranes. They carry out oxidation reactions that break down fatty acids and amino acids. They also detoxify many poisons that may enter the body. Alcohol is detoxified by peroxisomes in liver cells. A byproduct of these oxidation reactions is hydrogen peroxide, H2O2, which is contained within the peroxisomes to prevent the chemical from causing damage to cellular components outside of the organelle. Hydrogen peroxide is safely broken down by peroxisomal enzymes into water and oxygen.
Animal Cells versus Plant Cells
Despite their fundamental similarities, there are some striking differences between animal and plant cells (see Table \(1\)). Animal cells have centrioles, centrosomes (discussed under the cytoskeleton), and lysosomes, whereas plant cells do not. Plant cells have a cell wall, chloroplasts, plasmodesmata, and plastids used for storage, and a large central vacuole, whereas animal cells do not.
The Cell Wall
In Figure \(1\)b, the diagram of a plant cell, you see a structure external to the plasma membrane called the cell wall. The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and protist cells also have cell walls.
While the chief component of prokaryotic cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose, a polysaccharide made up of long, straight chains of glucose units. When nutritional information refers to dietary fiber, it is referring to the cellulose content of food.
Chloroplasts
Like mitochondria, chloroplasts also have their own DNA and ribosomes. Chloroplasts function in photosynthesis and can be found in eukaryotic cells such as plants and algae. In photosynthesis, carbon dioxide, water, and light energy are used to make glucose and oxygen. This is the major difference between plants and animals: Plants (autotrophs) are able to make their own food, like glucose, whereas animals (heterotrophs) must rely on other organisms for their organic compounds or food source.
Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked, fluid-filled membrane sacs called thylakoids (Figure \(9\)). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane and surrounding the grana is called the stroma.
The chloroplasts contain a green pigment called chlorophyll, which captures the energy of sunlight for photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria also perform photosynthesis, but they do not have chloroplasts. Their photosynthetic pigments are located in the thylakoid membrane within the cell itself.
EVOLUTION IN ACTION: Endosymbiosis
We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation.
Symbiosis is a relationship in which organisms from two separate species live in close association and typically exhibit specific adaptations to each other. Endosymbiosis (endo-= within) is a relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. Microbes that produce vitamin K live inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and are provided a stable habitat and abundant food by living within the large intestine.
Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that mitochondria and chloroplasts have DNA and ribosomes, just as bacteria do. Scientists believe that host cells and bacteria formed a mutually beneficial endosymbiotic relationship when the host cells ingested aerobic bacteria and cyanobacteria but did not destroy them. Through evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the photosynthetic bacteria becoming chloroplasts.
The Central Vacuole
Previously, we mentioned vacuoles as essential components of plant cells. If you look at Figure \(1\), you will see that plant cells each have a large, central vacuole that occupies most of the cell. The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. In plant cells, the liquid inside the central vacuole provides turgor pressure, which is the outward pressure caused by the fluid inside the cell. Have you ever noticed that if you forget to water a plant for a few days, it wilts? That is because as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm and into the soil. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the cell walls of a plant results in the wilted appearance. Additionally, this fluid has a very bitter taste, which discourages consumption by insects and animals. The central vacuole also functions to store proteins in developing seed cells.
Extracellular Matrix of Animal Cells
Most animal cells release materials into the extracellular space. The primary components of these materials are glycoproteins and the protein collagen. Collectively, these materials are called the extracellular matrix (Figure \(10\)). Not only does the extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each other.
Blood clotting provides an example of the role of the extracellular matrix in cell communication. When the cells lining a blood vessel are damaged, they display a protein receptor called tissue factor. When tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the wall of the damaged blood vessel, stimulates adjacent smooth muscle cells in the blood vessel to contract (thus constricting the blood vessel), and initiates a series of steps that stimulate the platelets to produce clotting factors.
Intercellular Junctions
Cells can also communicate with each other by direct contact, referred to as intercellular junctions. There are some differences in the ways that plant and animal cells do this. Plasmodesmata (singular = plasmodesma) are junctions between plant cells, whereas animal cell contacts include tight and gap junctions, and desmosomes.
In general, long stretches of the plasma membranes of neighboring plant cells cannot touch one another because they are separated by the cell walls surrounding each cell. Plasmodesmata are numerous channels that pass between the cell walls of adjacent plant cells, connecting their cytoplasm and enabling signal molecules and nutrients to be transported from cell to cell (Figure \(11\)a).
A tight junction is a watertight seal between two adjacent animal cells (Figure \(11\)b). Proteins hold the cells tightly against each other. This tight adhesion prevents materials from leaking between the cells. Tight junctions are typically found in the epithelial tissue that lines internal organs and cavities, and composes most of the skin. For example, the tight junctions of the epithelial cells lining the urinary bladder prevent urine from leaking into the extracellular space.
Also found only in animal cells are desmosomes, which act like spot welds between adjacent epithelial cells (Figure \(11\)c). They keep cells together in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles.
Gap junctions in animal cells are like plasmodesmata in plant cells in that they are channels between adjacent cells that allow for the transport of ions, nutrients, and other substances that enable cells to communicate (Figure \(11\)d). Structurally, however, gap junctions and plasmodesmata differ.
Table \(1\): This table provides the components of prokaryotic and eukaryotic cells and their respective functions.
Cell Component Function Present in Prokaryotes? Present in Animal Cells? Present in Plant Cells?
Plasma membrane Separates cell from external environment; controls passage of organic molecules, ions, water, oxygen, and wastes into and out of the cell Yes Yes Yes
Cytoplasm Provides structure to cell; site of many metabolic reactions; medium in which organelles are found Yes Yes Yes
Nucleoid Location of DNA Yes No No
Nucleus Cell organelle that houses DNA and directs synthesis of ribosomes and proteins No Yes Yes
Ribosomes Protein synthesis Yes Yes Yes
Mitochondria ATP production/cellular respiration No Yes Yes
Peroxisomes Oxidizes and breaks down fatty acids and amino acids, and detoxifies poisons No Yes Yes
Vesicles and vacuoles Storage and transport; digestive function in plant cells No Yes Yes
Centrosome Unspecified role in cell division in animal cells; organizing center of microtubules in animal cells No Yes No
Lysosomes Digestion of macromolecules; recycling of worn-out organelles No Yes No
Cell wall Protection, structural support and maintenance of cell shape Yes, primarily peptidoglycan in bacteria but not Archaea No Yes, primarily cellulose
Chloroplasts Photosynthesis No No Yes
Endoplasmic reticulum Modifies proteins and synthesizes lipids No Yes Yes
Golgi apparatus Modifies, sorts, tags, packages, and distributes lipids and proteins No Yes Yes
Cytoskeleton Maintains cell’s shape, secures organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently Yes Yes Yes
Flagella Cellular locomotion Some Some No, except for some plant sperm
Cilia Cellular locomotion, movement of particles along extracellular surface of plasma membrane, and filtration No Some No
Summary
Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleolus within the nucleus is the site for ribosome assembly. Ribosomes are found in the cytoplasm or are attached to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria perform cellular respiration and produce ATP. Peroxisomes break down fatty acids, amino acids, and some toxins. Vesicles and vacuoles are storage and transport compartments. In plant cells, vacuoles also help break down macromolecules.
Animal cells also have a centrosome and lysosomes. The centrosome has two bodies, the centrioles, with an unknown role in cell division. Lysosomes are the digestive organelles of animal cells.
Plant cells have a cell wall, chloroplasts, and a central vacuole. The plant cell wall, whose primary component is cellulose, protects the cell, provides structural support, and gives shape to the cell. Photosynthesis takes place in chloroplasts. The central vacuole expands, enlarging the cell without the need to produce more cytoplasm.
The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, as well as the plasma membrane. These cellular components work together to modify, package, tag, and transport membrane lipids and proteins.
The cytoskeleton has three different types of protein elements. Microfilaments provide rigidity and shape to the cell, and facilitate cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. They are also the structural elements of centrioles, flagella, and cilia.
Animal cells communicate through their extracellular matrices and are connected to each other by tight junctions, desmosomes, and gap junctions. Plant cells are connected and communicate with each other by plasmodesmata.
Art Connections
Figure \(1\): What structures does a plant cell have that an animal cell does not have? What structures does an animal cell have that a plant cell does not have?
Answer
Plant cells have plasmodesmata, a cell wall, a large central vacuole, chloroplasts, and plastids. Animal cells have lysosomes and centrosomes.
Figure \(7\): Why does the cis face of the Golgi not face the plasma membrane?
Answer
Because that face receives chemicals from the ER, which is toward the center of the cell.
Glossary
cell wall
a rigid cell covering made of cellulose in plants, peptidoglycan in bacteria, non-peptidoglycan compounds in Archaea, and chitin in fungi that protects the cell, provides structural support, and gives shape to the cell
central vacuole
a large plant cell organelle that acts as a storage compartment, water reservoir, and site of macromolecule degradation
chloroplast
a plant cell organelle that carries out photosynthesis
cilium
(plural: cilia) a short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire cell or move substances along the outer surface of the cell
cytoplasm
the entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals
cytoskeleton
the network of protein fibers that collectively maintains the shape of the cell, secures some organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move
cytosol
the gel-like material of the cytoplasm in which cell structures are suspended
desmosome
a linkage between adjacent epithelial cells that forms when cadherins in the plasma membrane attach to intermediate filaments
endomembrane system
the group of organelles and membranes in eukaryotic cells that work together to modify, package, and transport lipids and proteins
endoplasmic reticulum (ER)
a series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids
extracellular matrix
the material, primarily collagen, glycoproteins, and proteoglycans, secreted from animal cells that holds cells together as a tissue, allows cells to communicate with each other, and provides mechanical protection and anchoring for cells in the tissue
flagellum
(plural: flagella) the long, hair-like structure that extends from the plasma membrane and is used to move the cell
gap junction
a channel between two adjacent animal cells that allows ions, nutrients, and other low-molecular weight substances to pass between the cells, enabling the cells to communicate
Golgi apparatus
a eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution
lysosome
an organelle in an animal cell that functions as the cell’s digestive component; it breaks down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles
mitochondria
(singular: mitochondrion) the cellular organelles responsible for carrying out cellular respiration, resulting in the production of ATP, the cell’s main energy-carrying molecule
nuclear envelope
the double-membrane structure that constitutes the outermost portion of the nucleus
nucleolus
the darkly staining body within the nucleus that is responsible for assembling ribosomal subunits
nucleus
the cell organelle that houses the cell’s DNA and directs the synthesis of ribosomes and proteins
peroxisome
a small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons
plasma membrane
a phospholipid bilayer with embedded (integral) or attached (peripheral) proteins that separates the internal contents of the cell from its surrounding environment
plasmodesma
(plural: plasmodesmata) a channel that passes between the cell walls of adjacent plant cells, connects their cytoplasm, and allows materials to be transported from cell to cell
ribosome
a cellular structure that carries out protein synthesis
rough endoplasmic reticulum (RER)
the region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification
smooth endoplasmic reticulum (SER)
the region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies chemicals like pesticides, preservatives, medications, and environmental pollutants, and stores calcium ions
tight junction
a firm seal between two adjacent animal cells created by protein adherence
vacuole
a membrane-bound sac, somewhat larger than a vesicle, that functions in cellular storage and transport
vesicle
a small, membrane-bound sac that functions in cellular storage and transport; its membrane is capable of fusing with the plasma membrane and the membranes of the endoplasmic reticulum and Golgi apparatus | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.03%3A_Eukaryotic_Cells.txt |
Skills to Develop
• List the components of the endomembrane system
• Recognize the relationship between the endomembrane system and its functions
The endomembrane system (endo = “within”) is a group of membranes and organelles (Figure \(1\)) in eukaryotic cells that works together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, which we’ve already mentioned, and the endoplasmic reticulum and Golgi apparatus, which we will cover shortly. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles. The endomembrane system does not include the membranes of either mitochondria or chloroplasts.
Art Connection
If a peripheral membrane protein were synthesized in the lumen (inside) of the ER, would it end up on the inside or outside of the plasma membrane?
The Endoplasmic Reticulum
The endoplasmic reticulum (ER) (Figure \(1\)) is a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids. However, these two functions are performed in separate areas of the ER: the rough ER and the smooth ER, respectively.
The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope.
Rough ER
The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope (Figure \(2\)).
Ribosomes transfer their newly synthesized proteins into the lumen of the RER where they undergo structural modifications, such as folding or the acquisition of side chains. These modified proteins will be incorporated into cellular membranes—the membrane of the ER or those of other organelles—or secreted from the cell (such as protein hormones, enzymes). The RER also makes phospholipids for cellular membranes.
If the phospholipids or modified proteins are not destined to stay in the RER, they will reach their destinations via transport vesicles that bud from the RER’s membrane (Figure \(1\)).
Since the RER is engaged in modifying proteins (such as enzymes, for example) that will be secreted from the cell, you would be correct in assuming that the RER is abundant in cells that secrete proteins. This is the case with cells of the liver, for example.
Smooth ER
The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface (Figure \(1\)). Functions of the SER include synthesis of carbohydrates, lipids, and steroid hormones; detoxification of medications and poisons; and storage of calcium ions.
In muscle cells, a specialized SER called the sarcoplasmic reticulum is responsible for storage of the calcium ions that are needed to trigger the coordinated contractions of the muscle cells.
Link to Learning
Video \(1\): You can watch an excellent animation of the endomembrane system here.
Career Connection: Cardiologist
Heart disease is the leading cause of death in the United States. This is primarily due to our sedentary lifestyle and our high trans-fat diets.
Heart failure is just one of many disabling heart conditions. Heart failure does not mean that the heart has stopped working. Rather, it means that the heart can’t pump with sufficient force to transport oxygenated blood to all the vital organs. Left untreated, heart failure can lead to kidney failure and failure of other organs.
The wall of the heart is composed of cardiac muscle tissue. Heart failure occurs when the endoplasmic reticula of cardiac muscle cells do not function properly. As a result, an insufficient number of calcium ions are available to trigger a sufficient contractile force.
Cardiologists (cardi- = “heart”; -ologist = “one who studies”) are doctors who specialize in treating heart diseases, including heart failure. Cardiologists can make a diagnosis of heart failure via physical examination, results from an electrocardiogram (ECG, a test that measures the electrical activity of the heart), a chest X-ray to see whether the heart is enlarged, and other tests. If heart failure is diagnosed, the cardiologist will typically prescribe appropriate medications and recommend a reduction in table salt intake and a supervised exercise program.
The Golgi Apparatus
We have already mentioned that vesicles can bud from the ER and transport their contents elsewhere, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles still need to be sorted, packaged, and tagged so that they wind up in the right place. Sorting, tagging, packaging, and distribution of lipids and proteins takes place in the Golgi apparatus (also called the Golgi body), a series of flattened membranes (Figure \(3\)).
The receiving side of the Golgi apparatus is called the cis face. The opposite side is called the trans face. The transport vesicles that formed from the ER travel to the cis face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications that allow them to be sorted. The most frequent modification is the addition of short chains of sugar molecules. These newly modified proteins and lipids are then tagged with phosphate groups or other small molecules so that they can be routed to their proper destinations.
Finally, the modified and tagged proteins are packaged into secretory vesicles that bud from the trans face of the Golgi. While some of these vesicles deposit their contents into other parts of the cell where they will be used, other secretory vesicles fuse with the plasma membrane and release their contents outside the cell.
In another example of form following function, cells that engage in a great deal of secretory activity (such as cells of the salivary glands that secrete digestive enzymes or cells of the immune system that secrete antibodies) have an abundance of Golgi.
In plant cells, the Golgi apparatus has the additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which are used in other parts of the cell.
Career Connection: Geneticist
Many diseases arise from genetic mutations that prevent the synthesis of critical proteins. One such disease is Lowe disease (also called oculocerebrorenal syndrome, because it affects the eyes, brain, and kidneys). In Lowe disease, there is a deficiency in an enzyme localized to the Golgi apparatus. Children with Lowe disease are born with cataracts, typically develop kidney disease after the first year of life, and may have impaired mental abilities.
Lowe disease is a genetic disease caused by a mutation on the X chromosome. The X chromosome is one of the two human sex chromosome, as these chromosomes determine a person's sex. Females possess two X chromosomes while males possess one X and one Y chromosome. In females, the genes on only one of the two X chromosomes are expressed. Therefore, females who carry the Lowe disease gene on one of their X chromosomes have a 50/50 chance of having the disease. However, males only have one X chromosome and the genes on this chromosome are always expressed. Therefore, males will always have Lowe disease if their X chromosome carries the Lowe disease gene. The location of the mutated gene, as well as the locations of many other mutations that cause genetic diseases, has now been identified. Through prenatal testing, a woman can find out if the fetus she is carrying may be afflicted with one of several genetic diseases.
Geneticists analyze the results of prenatal genetic tests and may counsel pregnant women on available options. They may also conduct genetic research that leads to new drugs or foods, or perform DNA analyses that are used in forensic investigations.
Lysosomes
In addition to their role as the digestive component and organelle-recycling facility of animal cells, lysosomes are considered to be parts of the endomembrane system. Lysosomes also use their hydrolytic enzymes to destroy pathogens (disease-causing organisms) that might enter the cell. A good example of this occurs in a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known as phagocytosis or endocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen (Figure \(4\)).
Summary
The endomembrane system includes the nuclear envelope, lysosomes, vesicles, the ER, and Golgi apparatus, as well as the plasma membrane. These cellular components work together to modify, package, tag, and transport proteins and lipids that form the membranes.
The RER modifies proteins and synthesizes phospholipids used in cell membranes. The SER synthesizes carbohydrates, lipids, and steroid hormones; engages in the detoxification of medications and poisons; and stores calcium ions. Sorting, tagging, packaging, and distribution of lipids and proteins take place in the Golgi apparatus. Lysosomes are created by the budding of the membranes of the RER and Golgi. Lysosomes digest macromolecules, recycle worn-out organelles, and destroy pathogens.
Art Connections
Figure \(1\): If a peripheral membrane protein were synthesized in the lumen (inside) of the ER, would it end up on the inside or outside of the plasma membrane?
Answer
It would end up on the outside. After the vesicle passes through the Golgi apparatus and fuses with the plasma membrane, it turns inside out.
Glossary
endomembrane system
group of organelles and membranes in eukaryotic cells that work together modifying, packaging, and transporting lipids and proteins
endoplasmic reticulum (ER)
series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids
Golgi apparatus
eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution
rough endoplasmic reticulum (RER)
region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification and phospholipid synthesis
smooth endoplasmic reticulum (SER)
region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies certain chemicals (like pesticides, preservatives, medications, and environmental pollutants), and stores calcium ions | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.04%3A_The_Endomembrane_System.txt |
Sperm cells and muscle cells need lots of energy. What do they have in common?
They have lots of mitochondria. Mitochondria are called the power plants of the cell, as these organelles are where most of the cell's energy is produced. Cells that need lots of energy have lots of mitochondria.
Other Organelles
In addition to the nucleus, eukaryotic cells have many other organelles, including ribosomes and mitochondria. Ribosomes are present in all cells.
Ribosomes
Ribosomes are small organelles and are the sites of protein synthesis (or assembly). They are made of ribosomal protein and ribosomal RNA, and are found in both eukaryotic and prokaryotic cells. Unlike other organelles, ribosomes are not surrounded by a membrane. Each ribosome has two parts, a large and a small subunit, as shown in Figure below. The subunits are attached to one another. Ribosomes can be found alone or in groups within the cytoplasm. Some ribosomes are attached to the endoplasmic reticulum (ER) (as shown in Figure below), and others are attached to the nuclear envelope.
The two subunits that make up a ribosome, small organelles that are intercellular protein factories.
Ribozymes are RNA molecules that catalyze chemical reactions, such as translation.Translation is the process of ordering the amino acids in the assembly of a protein, and translation will be discussed more in another concept. Briefly, the ribosomes interact with other RNA molecules to make chains of amino acids called polypeptide chains, due to the peptide bond that forms between individual amino acids. Polypeptide chains are built from the genetic instructions held within a messenger RNA (mRNA) molecule. Polypeptide chains that are made on the rough ER (discussed below) are inserted directly into the ER and then are transported to their various cellular destinations. Ribosomes on the rough ER usually produce proteins that are destined for the cell membrane.
Ribosomes are found in both eukaryotic and prokaryotic cells. Ribosomes are not surrounded by a membrane. The other organelles found in eukaryotic cells are surrounded by a membrane.
Mitochondria
A mitochondrion (mitochondria, plural), is a membrane-enclosed organelle that is found in most eukaryotic cells. Mitochondria are called the "power plants" of the cell because they are the sites of cellular respiration, where they use energy from organic compounds to make ATP (adenosine triphosphate). ATP is the cell's energy source that is used for such things such as movement and cell division. Some ATP is made in the cytosol of the cell, but most of it is made inside mitochondria. The number of mitochondria in a cell depends on the cell’s energy needs. For example, active human muscle cells may have thousands of mitochondria, while less active red blood cells do not have any.
(a): Electron micrograph of a single mitochondrion, within which you can see many cristae. Mitochondria range from 1 to 10 μm in size. (b): This model of a mitochondrion shows the organized arrangement of the inner and outer membranes, the protein matrix, and the folded inner mitochondrial membranes.
As Figure above (a) and (b) show, a mitochondrion has two phospholipid membranes. The smooth outer membrane separates the mitochondrion from the cytosol. The inner membrane has many folds, called cristae. The fluid-filled inside of the mitochondrion, called matrix, is where most of the cell’s ATP is made.
Although most of a cell's DNA is contained in the cell nucleus, mitochondria have their own DNA. Mitochondria are able to reproduce asexually, and scientists think that they are descended from prokaryotes. According to the endosymbiotic theory, mitochondria were once free-living prokaryotes that infected or were engulfed by ancient eukaryotic cells. The invading prokaryotes were protected inside the eukaryotic host cell, and in turn the prokaryote supplied extra ATP to its host.
Summary
• Ribosomes are small organelles and are the site of protein synthesis. Ribosomes are found in all cells.
• Mitochondria are where energy from organic compounds is used to make ATP.
Explore More
Use this resource to answer the following questions.
1. List three characteristics of mitochondria.
2. Describe how mitochondria originated?
3. What is the general function of proteins embedded within the mitochondria inner membrane?
4. What occurs in the mitochondrial matrix?
5. How do mitochondria divide?
Review
1. What is the function of a ribosome?
2. What is a significant difference between the structure of a ribosome and other organelles?
3. Identify the reason why mitochondria are called "power plants" of the cell.
4. Describe the structure of a mitochondrion. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.05%3A_Mitochondria_and_Chloroplasts-_Cellular_Generators/4.5.01%3A_Mitochondria.txt |
What do pancakes and chloroplasts have in common?
The chloroplast is the site of photosynthesis. Part of the photosynthesis reactions occur in an internal membrane within the organelle. The chloroplast contains many of these internal membranes, making photosynthesis very efficient. These internal membranes stack on top of each other, just like a stack of pancakes.
Stages of Photosynthesis
Photosynthesis occurs in two stages, which are shown in Figure below.
1. Stage I is called the light reactions. This stage uses water and changes light energy from the sun into chemical energy stored in ATP and NADPH (another energy-carrying molecule). This stage also releases oxygen as a waste product.
2. Stage II is called the Calvin cycle. This stage combines carbon from carbon dioxide in the air and uses the chemical energy in ATP and NADPH to make glucose.
The two stages of photosynthesis are the light reactions and the Calvin cycle. Do you see how the two stages are related?
Before you read about these two stages of photosynthesis in greater detail, you need to know more about the chloroplast, where the two stages take place.
The Chloroplast
Chloroplasts: Theaters for Photosynthesis
Photosynthesis, the process of turning the energy of sunlight into ‘‘food,’’ is divided into two basic sets of reactions, known as the light reactions and the Calvin cycle, which uses carbon dioxide. As you study the details in other concepts, refer frequently to the chemical equation of photosynthesis: 6CO2 + 6H2O + Light Energy → C6H12O6 + 6O2. Photosynthesis occurs in the chloroplast, an organelle specific to plant cells.
If you examine a single leaf of a Winter Jasmine leaf, shown in Figure below, under a microscope, you will see within each cell dozens of small green ovals. These are chloroplasts, the organelles which conduct photosynthesis in plants and algae. Chloroplasts closely resemble some types of bacteria and even contain their own circular DNA and ribosomes. In fact, the endosymbiotic theory holds that chloroplasts were once independently living bacteria (prokaryotes). So when we say that photosynthesis occurs within chloroplasts, we speak not only of the organelles within plants and algae, but also of some bacteria – in other words, virtually all photosynthetic autotrophs.
High power microscopic photo of the upper part of a Winter Jasmine leaf. Viewed under a microscope, many green chloroplasts are visible.
Each chloroplast contains neat stacks called grana (singular, granum). The grana consist of sac-like membranes, known as thylakoid membranes. These membranes contain photosystems, which are groups of molecules that include chlorophyll, a green pigment. The light reactions of photosynthesis occur in the thylakoid membranes. The stroma is the space outside the thylakoid membranes, as shown in Figure below. This is where the reactions of the Calvin cycle take place. In addition to enzymes, two basic types of molecules - pigments and electron carriers – are key players in this process and are also found in the thylakoid membranes.
You can take a video tour of a chloroplast at Encyclopedia Britannica: Chloroplast:www.britannica.com/EBchecked/...in-plant-cells.
A chloroplast consists of thylakoid membranes surrounded by stroma. The thylakoid membranes contain molecules of the green pigment chlorophyll.
Electron carrier molecules are usually arranged in electron transport chains (ETCs). These accept and pass along energy-carrying electrons in small steps (Figure below). In this way, they produce ATP and NADPH, which temporarily store chemical energy. Electrons in transport chains behave much like a ball bouncing down a set of stairs – a little energy is lost with each bounce. However, the energy “lost” at each step in an electron transport chain accomplishes a little bit of work, which eventually results in the synthesis of ATP.
This figure shows the light reactions of photosynthesis. This stage of photosynthesis begins with photosystem II (so named because it was discovered after photosystem I). Find the two electrons (2 e-) in photosystem II, and then follow them through the electron transport chain (also called the electron transfer chain) to the formation of NADPH. Where do the hydrogen ions (H+) come from that help make ATP?
Summary
• Photosynthesis occurs in the chloroplast, an organelle specific to plant cells.
• The light reactions of photosynthesis occur in the thylakoid membranes of the chloroplast.
• Electron carrier molecules are arranged in electron transport chains that produce ATP and NADPH, which temporarily store chemical energy.
Explore More
Use this resource to answer the questions that follow.
1. What are the functions of a plant's leaves?
2. Where do the photosynthetic reactions occur?
3. What is a stomata? What is their role?
4. Describe the internal structure of a chloroplast.
5. What reactions occur in the thylakoid membranes?
Review
1. Describe the chloroplast's role in photosynthesis.
2. Explain how the structure of a chloroplast (its membranes and thylakoids) makes its function (the chemical reactions of photosynthesis) more efficient.
3. Describe electron carriers and the electron transport chain. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.05%3A_Mitochondria_and_Chloroplasts-_Cellular_Generators/4.5.02%3A_Chloroplasts.txt |
Does a cell have, or even need, a "skeleton"?
What do you get if you take some tubing, and make the tubes smaller and smaller and smaller? You get very small tubes, or microtubes. Very small tubes, or microtubules, together with microfilaments, form the basis of the "skeleton" inside the cell.
The Cytoplasm and Cytoskeleton
The cytoplasm consists of everything inside the plasma membrane of the cell, excluding the nucleus in a eukaryotic cell. It includes the watery, gel-like material called cytosol, as well as various structures. The water in the cytoplasm makes up about two thirds of the cell’s weight and gives the cell many of its properties.
Functions of the Cytoplasm
The cytoplasm has several important functions, including:
1. suspending cell organelles.
2. pushing against the plasma membrane to help the cell keep its shape.
3. providing a site for many of the biochemical reactions of the cell.
The Cytoskeleton
The cytoskeleton is a cellular "scaffolding" or "skeleton" that crisscrosses the cytoplasm. All eukaryotic cells have a cytoskeleton, and recent research has shown that prokaryotic cells also have a cytoskeleton. The eukaryotic cytoskeleton is made up of a network of long, thin protein fibers and has many functions. It helps to maintain cell shape. It holds organelles in place, and for some cells, it enables cell movement. The cytoskeleton also plays important roles in both the intracellular movement of substances and in cell division. Certain proteins act like a path that vesicles and organelles move along within the cell. The threadlike proteins that make up the cytoskeleton continually rebuild to adapt to the cell's constantly changing needs. Three main kinds of cytoskeleton fibers are microtubules, intermediate filaments, and microfilaments.
• Microtubules, shown in Figure below (a), are hollow cylinders and are the thickest of the cytoskeleton structures. They are most commonly made of filaments which are polymers of alpha and beta tubulin, and radiate outwards from an area near the nucleus called the centrosome. Tubulin is the protein that forms microtubules. Two forms of tubulin, alpha and beta, form dimers (pairs) which come together to form the hollow cylinders. The cylinders are twisted around each other to form the microtubules. Microtubules help the cell keep its shape. They hold organelles in place and allow them to move around the cell, and they form the mitotic spindle during cell division. Microtubules also make up parts of cilia and flagella, the organelles that help a cell move.
• Microfilaments, shown in Figure below (b), are made of two thin actin chains that are twisted around one another. Microfilaments are mostly concentrated just beneath the cell membrane, where they support the cell and help the cell keep its shape. Microfilaments form cytoplasmatic extensions, such as pseudopodia and microvilli, which allow certain cells to move. The actin of the microfilaments interacts with the protein myosin to cause contraction in muscle cells. Microfilaments are found in almost every cell, and are numerous in muscle cells and in cells that move by changing shape, such as phagocytes (white blood cells that search the body for bacteria and other invaders).
• Intermediate filaments differ in make-up from one cell type to another. Intermediate filaments organize the inside structure of the cell by holding organelles and providing strength. They are also structural components of the nuclear envelope. Intermediate filaments made of the protein keratin are found in skin, hair, and nails cells.
(a) The eukaryotic cytoskeleton. Microfilaments are shown in red, microtubules in green, and the nuclei are in blue. By linking regions of the cell together, the cytoskeleton helps support the shape of the cell. (b) Microscopy of microfilaments (actin filaments), shown in green, inside cells. The nucleus is shown in blue.
Cytoskeleton Structure
Microtubules Intermediate Filaments Microfilaments
Fiber Diameter About 25 nm 8 to 11 nm Around 7 nm
Protein Composition Tubulin, with two subunits, alpha and beta tubulin One of different types of proteins such as lamin, vimentin, and keratin Actin
Shape Hollow cylinders made of two protein chains twisted around each other Protein fiber coils twisted into each other Two actin chains twisted around one another
Main Functions Organelle and vesicle movement; form mitotic spindles during cell reproduction; cell motility (in cilia and flagella) Organize cell shape; positions organelles in cytoplasm structural support of the nuclear envelope and sarcomeres; involved in cell-to-cell and cell-to-matrix junctions Keep cellular shape; allows movement of certain cells by forming cytoplasmatic extensions or contraction of actin fibers; involved in some cell-to-cell or cell-to-matrix junctions
Representation
The cytoskeleton is discussed in the following video: http://www.youtube.com/watch?v=5rqbmLiSkpk (4:50).
Summary
• The cytoplasm consists of everything inside the plasma membrane of the cell.
• The cytoskeleton is a cellular "skeleton" that crisscrosses the cytoplasm. Three main cytoskeleton fibers are microtubules, intermediate filaments, and microfilaments.
• Microtubules are the thickest of the cytoskeleton structures and are most commonly made of filaments which are polymers of alpha and beta tubulin.
• Microfilament are the thinnest of the cytoskeleton structures and are made of two thin actin chains that are twisted around one another.
Explore More
Use this resource to answer the following questions.
1. What is the role of the cytoskeleton?
2. What is the subunit of microfilaments and microtubules?
3. Describe the main function of microtubules.
4. What is the role of microtubules during mitosis?
5. How are microtubules associated with locomotion?
6. Describe the roles of microfilaments.
Review
1. What is the difference between cytoplasm and cytosol?
2. List two roles of the cytoplasm.
3. Name the three main types of cytoskeleton fibers.
4. List two functions of the eukaryotic cytoskeleton. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.06%3A_The_Cytoskeleton/4.6.01%3A_Cytoplasm_and_Cytoskeletons.txt |
Skills to Develop
• Describe the cytoskeleton
• Compare the roles of microfilaments, intermediate filaments, and microtubules
• Compare and contrast cilia and flagella
• Summarize the differences among the components of prokaryotic cells, animal cells, and plant cells
If you were to remove all the organelles from a cell, would the plasma membrane and the cytoplasm be the only components left? No. Within the cytoplasm, there would still be ions and organic molecules, plus a network of protein fibers that help maintain the shape of the cell, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable cells within multicellular organisms to move. Collectively, this network of protein fibers is known as the cytoskeleton. There are three types of fibers within the cytoskeleton: microfilaments, intermediate filaments, and microtubules (Figure \(1\)). Here, we will examine each.
Microfilaments
Of the three types of protein fibers in the cytoskeleton, microfilaments are the narrowest. They function in cellular movement, have a diameter of about 7 nm, and are made of two intertwined strands of a globular protein called actin (Figure \(2\)). For this reason, microfilaments are also known as actin filaments.
Actin is powered by ATP to assemble its filamentous form, which serves as a track for the movement of a motor protein called myosin. This enables actin to engage in cellular events requiring motion, such as cell division in animal cells and cytoplasmic streaming, which is the circular movement of the cell cytoplasm in plant cells. Actin and myosin are plentiful in muscle cells. When your actin and myosin filaments slide past each other, your muscles contract.
Microfilaments also provide some rigidity and shape to the cell. They can depolymerize (disassemble) and reform quickly, thus enabling a cell to change its shape and move. White blood cells (your body’s infection-fighting cells) make good use of this ability. They can move to the site of an infection and phagocytize the pathogen.
Link to Learning
Video \(1\): To see an example of a white blood cell in action, watch a short time-lapse video of the cell capturing two bacteria. It engulfs one and then moves on to the other.
Intermediate Filaments
Intermediate filaments are made of several strands of fibrous proteins that are wound together (Figure \(3\)). These elements of the cytoskeleton get their name from the fact that their diameter, 8 to 10 nm, is between those of microfilaments and microtubules.
Intermediate filaments have no role in cell movement. Their function is purely structural. They bear tension, thus maintaining the shape of the cell, and anchor the nucleus and other organelles in place. Figure \(1\) shows how intermediate filaments create a supportive scaffolding inside the cell.
The intermediate filaments are the most diverse group of cytoskeletal elements. Several types of fibrous proteins are found in the intermediate filaments. You are probably most familiar with keratin, the fibrous protein that strengthens your hair, nails, and the epidermis of the skin.
Microtubules
As their name implies, microtubules are small hollow tubes. The walls of the microtubule are made of polymerized dimers of α-tubulin and β-tubulin, two globular proteins (Figure \(4\)). With a diameter of about 25 nm, microtubules are the widest components of the cytoskeleton. They help the cell resist compression, provide a track along which vesicles move through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. Like microfilaments, microtubules can dissolve and reform quickly.
Microtubules are also the structural elements of flagella, cilia, and centrioles (the latter are the two perpendicular bodies of the centrosome). In fact, in animal cells, the centrosome is the microtubule-organizing center. In eukaryotic cells, flagella and cilia are quite different structurally from their counterparts in prokaryotes, as discussed below.
Flagella and Cilia
To refresh your memory, flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell (for example, sperm, Euglena). When present, the cell has just one flagellum or a few flagella. When cilia (singular = cilium) are present, however, many of them extend along the entire surface of the plasma membrane. They are short, hair-like structures that are used to move entire cells (such as paramecia) or substances along the outer surface of the cell (for example, the cilia of cells lining the Fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory tract that trap particulate matter and move it toward your nostrils.)
Despite their differences in length and number, flagella and cilia share a common structural arrangement of microtubules called a “9 + 2 array.” This is an appropriate name because a single flagellum or cilium is made of a ring of nine microtubule doublets, surrounding a single microtubule doublet in the center (Figure \(5\)).
You have now completed a broad survey of the components of prokaryotic and eukaryotic cells. For a summary of cellular components in prokaryotic and eukaryotic cells, see Table \(1\).
Table \(1\): Cellular components in prokaryotic and eukaryotic cells.
Cell Component Function Present in Prokaryotes? Present in Animal Cells? Present in Plant Cells?
Plasma membrane Separates cell from external environment; controls passage of organic molecules, ions, water, oxygen, and wastes into and out of cell Yes Yes Yes
Cytoplasm Provides turgor pressure to plant cells as fluid inside the central vacuole; site of many metabolic reactions; medium in which organelles are found Yes Yes Yes
Nucleolus Darkened area within the nucleus where ribosomal subunits are synthesized. No Yes Yes
Nucleus Cell organelle that houses DNA and directs synthesis of ribosomes and proteins No Yes Yes
Ribosomes Protein synthesis Yes Yes Yes
Mitochondria ATP production/cellular respiration No Yes Yes
Peroxisomes Oxidizes and thus breaks down fatty acids and amino acids, and detoxifies poisons No Yes Yes
Vesicles and vacuoles Storage and transport; digestive function in plant cells No Yes Yes
Centrosome Unspecified role in cell division in animal cells; source of microtubules in animal cells No Yes No
Lysosomes Digestion of macromolecules; recycling of worn-out organelles No Yes No
Cell wall Protection, structural support and maintenance of cell shape Yes, primarily peptidoglycan No Yes, primarily cellulose
Chloroplasts Photosynthesis No No Yes
Endoplasmic reticulum Modifies proteins and synthesizes lipids No Yes Yes
Golgi apparatus Modifies, sorts, tags, packages, and distributes lipids and proteins No Yes Yes
Cytoskeleton Maintains cell’s shape, secures organelles in specific positions, allows cytoplasm and vesicles to move within cell, and enables unicellular organisms to move independently Yes Yes Yes
Flagella Cellular locomotion Some Some No, except for some plant sperm cells.
Cilia Cellular locomotion, movement of particles along extracellular surface of plasma membrane, and filtration Some Some No
Summary
The cytoskeleton has three different types of protein elements. From narrowest to widest, they are the microfilaments (actin filaments), intermediate filaments, and microtubules. Microfilaments are often associated with myosin. They provide rigidity and shape to the cell and facilitate cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. They are also the structural element of centrioles, flagella, and cilia.
Glossary
cilium
(plural = cilia) short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire cell or move substances along the outer surface of the cell
cytoskeleton
network of protein fibers that collectively maintain the shape of the cell, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable unicellular organisms to move independently
flagellum
(plural = flagella) long, hair-like structure that extends from the plasma membrane and is used to move the cell
intermediate filament
cytoskeletal component, composed of several intertwined strands of fibrous protein, that bears tension, supports cell-cell junctions, and anchors cells to extracellular structures
microfilament
narrowest element of the cytoskeleton system; it provides rigidity and shape to the cell and enables cellular movements
microtubule
widest element of the cytoskeleton system; it helps the cell resist compression, provides a track along which vesicles move through the cell, pulls replicated chromosomes to opposite ends of a dividing cell, and is the structural element of centrioles, flagella, and cilia | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.06%3A_The_Cytoskeleton/4.6.02%3A_The_Cytoskeleton.txt |
Learning Objectives
• Explain the role of the extracellular matrix in animal cells
Extracellular Matrix of Animal Cells
Most animal cells release materials into the extracellular space. The primary components of these materials are proteins. Collagen is the most abundant of the proteins. Its fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. Collectively, these materials are called the extracellular matrix. Not only does the extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each other.
How does this cell communication occur? Cells have protein receptors on the extracellular surfaces of their plasma membranes. When a molecule within the matrix binds to the receptor, it changes the molecular structure of the receptor. The receptor, in turn, changes the conformation of the microfilaments positioned just inside the plasma membrane. These conformational changes induce chemical signals inside the cell that reach the nucleus and turn “on” or “off” the transcription of specific sections of DNA. This affects the production of associated proteins, thus changing the activities within the cell.
An example of the role of the extracellular matrix in cell communication can be seen in blood clotting. When the cells lining a blood vessel are damaged, they display a protein receptor called tissue factor. When a tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the wall of the damaged blood vessel and stimulates the adjacent smooth muscle cells in the blood vessel to contract (thus constricting the blood vessel). Subsequently, a series of steps are initiated which then prompt the platelets to produce clotting factors.
Key Points
• The extracellular matrix of animal cells is made up of proteins and carbohydrates.
• Cell communication within tissue and tissue formation are main functions of the extracellular matrix of animal cells.
• Tissue communication is kick-started when a molecule within the matrix binds a receptor; the end results are conformational changes that induce chemical signals that ultimately change activities within the cell.
Key Terms
• collagen: Any of more than 28 types of glycoprotein that forms elongated fibers, usually found in the extracellular matrix of connective tissue.
• proteoglycan: Any of many glycoproteins that have heteropolysaccharide side chains
• extracellular matrix: All the connective tissues and fibres that are not part of a cell, but rather provide support.
4.8B: Intercellular Junctions
Learning Objectives
• Describe the purpose of intercellular junctions in the structure of cells
Intercellular Junctions
The extracellular matrix allows cellular communication within tissues through conformational changes that induce chemical signals, which ultimately transform activities within the cell. However, cells are also capable of communicating with each other via direct contact through intercellular junctions.
There are some differences in the ways that plant and animal cells communicate directly. Plasmodesmata are junctions between plant cells, whereas animal cell contacts are carried out through tight junctions, gap junctions, and desmosomes.
Junctions in Plant Cells
In general, long stretches of the plasma membranes of neighboring plant cells cannot touch one another because they are separated by the cell wall that surrounds each cell. How then can a plant transfer water and other soil nutrients from its roots, through its stems, and to its leaves? This transport primarily uses the vascular tissues (xylem and phloem); however, there are also structural modifications called plasmodesmata (singular: plasmodesma) that facilitate direct communication in plant cells. Plasmodesmata are numerous channels that pass between cell walls of adjacent plant cells and connect their cytoplasm; thereby, enabling materials to be transported from cell to cell, and thus throughout the plant.
Junctions in Animal Cells
Communication between animal cells can be carried out through three types of junctions. The first, a tight junction, is a watertight seal between two adjacent animal cells. The cells are held tightly against each other by proteins (predominantly two proteins called claudins and occludins). This tight adherence prevents materials from leaking between the cells. These junctions are typically found in epithelial tissues that line internal organs and cavities and comprise most of the skin. For example, the tight junctions of the epithelial cells lining your urinary bladder prevent urine from leaking out into the extracellular space.
Also found only in animal cells are desmosomes, the second type of intercellular junctions in these cell types. Desmosomes act like spot welds between adjacent epithelial cells, connecting them. Short proteins called cadherins in the plasma membrane connect to intermediate filaments to create desmosomes. The cadherins join two adjacent cells together and maintain the cells in a sheet-like formation in organs and tissues that stretch, such as the skin, heart, and muscles.
Lastly, similar to plasmodesmata in plant cells, gap junctions are the third type of direct junction found within animal cells. These junctions are channels between adjacent cells that allow for the transport of ions, nutrients, and other substances that enable cells to communicate. Structurally, however, gap junctions and plasmodesmata differ. Gap junctions develop when a set of six proteins (called connexins) in the plasma membrane arrange themselves in an elongated doughnut-like configuration called a connexon. When the pores (“doughnut holes”) of connexons in adjacent animal cells align, a channel between the two cells forms. Gap junctions are particularly important in cardiac muscle. The electrical signal for the muscle to contract is passed efficiently through gap junctions, which allows the heart muscle cells to contract in tandem.
Key Points
• Plasmodesmata are intercellular junctions between plant cells that enable the transportation of materials between cells.
• A tight junction is a watertight seal between two adjacent animal cells, which prevents materials from leaking out of cells.
• Desmosomes connect adjacent cells when cadherins in the plasma membrane connect to intermediate filaments.
• Similar to plasmodesmata, gap junctions are channels between adjacent cells that allow for the transport of ions, nutrients, and other substances.
Key Terms
• plasmodesma: A microscopic channel traversing the cell walls of plant cells and some algal cells, enabling transport and communication between them.
• connexon: An assembly of six connexins forming a bridge called a gap junction between the cytoplasms of two adjacent cells.
• occludin: Together with the claudin group of proteins, it is the main component of the tight junctions. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/04%3A_Cell_Structure/4.07%3A_Extracellular_Structures_and_Cell_Movement/4.7A%3A_Extracellular_Matrix_of_Animal_Cells.txt |
• 5.1: The Structure of Membranes
Among the most sophisticated functions of the plasma membrane is the ability to transmit signals by means of complex, integral proteins known as receptors. These proteins act both as receivers of extracellular inputs and as activators of intracellular processes. These membrane receptors provide extracellular attachment sites for effectors like hormones and growth factors, and they activate intracellular response cascades when their effectors are bound. Occasionally, receptors are hijacked by vir
• 5.2: Phospholipids- The Membrane's Foundation
• 5.3: Proteins- Multifunctional Components
• 5.4: Passive Transport Across Membranes
The most direct forms of membrane transport are passive. Passive transport is a naturally occurring phenomenon and does not require the cell to expend energy to accomplish the movement. In passive transport, substances move from an area of higher concentration to an area of lower concentration in a process called diffusion. A physical space in which there is a different concentration of a single substance is said to have a concentration gradient.
• 5.5: Active Transport Across Membranes
• 5.6: Bulk Transport by Endocytosis and Exocytosis
In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and particles (see Table 5.4.1 for examples). Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that the uptake and release of large particles by the cell requires energy. A large particle, however, cannot pass through the membrane, even with energy supplied by the cell.
05: Membranes
Skills to Develop
• Understand the fluid mosaic model of cell membranes
• Describe the functions of phospholipids, proteins, and carbohydrates in membranes
• Discuss membrane fluidity
A cell’s plasma membrane defines the cell, outlines its borders, and determines the nature of its interaction with its environment (see Table \(1\) for a summary). Cells exclude some substances, take in others, and excrete still others, all in controlled quantities. The plasma membrane must be very flexible to allow certain cells, such as red blood cells and white blood cells, to change shape as they pass through narrow capillaries. These are the more obvious functions of a plasma membrane. In addition, the surface of the plasma membrane carries markers that allow cells to recognize one another, which is vital for tissue and organ formation during early development, and which later plays a role in the “self” versus “non-self” distinction of the immune response.
Among the most sophisticated functions of the plasma membrane is the ability to transmit signals by means of complex, integral proteins known as receptors. These proteins act both as receivers of extracellular inputs and as activators of intracellular processes. These membrane receptors provide extracellular attachment sites for effectors like hormones and growth factors, and they activate intracellular response cascades when their effectors are bound. Occasionally, receptors are hijacked by viruses (HIV, human immunodeficiency virus, is one example) that use them to gain entry into cells, and at times, the genes encoding receptors become mutated, causing the process of signal transduction to malfunction with disastrous consequences.
Fluid Mosaic Model
The existence of the plasma membrane was identified in the 1890s, and its chemical components were identified in 1915. The principal components identified at that time were lipids and proteins. The first widely accepted model of the plasma membrane’s structure was proposed in 1935 by Hugh Davson and James Danielli; it was based on the “railroad track” appearance of the plasma membrane in early electron micrographs. They theorized that the structure of the plasma membrane resembles a sandwich, with protein being analogous to the bread, and lipids being analogous to the filling. In the 1950s, advances in microscopy, notably transmission electron microscopy (TEM), allowed researchers to see that the core of the plasma membrane consisted of a double, rather than a single, layer. A new model that better explains both the microscopic observations and the function of that plasma membrane was proposed by S.J. Singer and Garth L. Nicolson in 1972.
The explanation proposed by Singer and Nicolson is called the fluid mosaic model. The model has evolved somewhat over time, but it still best accounts for the structure and functions of the plasma membrane as we now understand them. The fluid mosaic model describes the structure of the plasma membrane as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character. Plasma membranes range from 5 to 10 nm in thickness. For comparison, human red blood cells, visible via light microscopy, are approximately 8 µm wide, or approximately 1,000 times wider than a plasma membrane. The membrane does look a bit like a sandwich (Figure \(1\)).
The principal components of a plasma membrane are lipids (phospholipids and cholesterol), proteins, and carbohydrates attached to some of the lipids and some of the proteins. A phospholipid is a molecule consisting of glycerol, two fatty acids, and a phosphate-linked head group. Cholesterol, another lipid composed of four fused carbon rings, is found alongside the phospholipids in the core of the membrane. The proportions of proteins, lipids, and carbohydrates in the plasma membrane vary with cell type, but for a typical human cell, protein accounts for about 50 percent of the composition by mass, lipids (of all types) account for about 40 percent of the composition by mass, with the remaining 10 percent of the composition by mass being carbohydrates. However, the concentration of proteins and lipids varies with different cell membranes. For example, myelin, an outgrowth of the membrane of specialized cells that insulates the axons of the peripheral nerves, contains only 18 percent protein and 76 percent lipid. The mitochondrial inner membrane contains 76 percent protein and only 24 percent lipid. The plasma membrane of human red blood cells is 30 percent lipid. Carbohydrates are present only on the exterior surface of the plasma membrane and are attached to proteins, forming glycoproteins, or attached to lipids, forming glycolipids.
Phospholipids
The main fabric of the membrane is composed of amphiphilic, phospholipid molecules. The hydrophilic or “water-loving” areas of these molecules (which look like a collection of balls in an artist’s rendition of the model) (Figure \(1\)) are in contact with the aqueous fluid both inside and outside the cell. Hydrophobic, or water-hating molecules, tend to be non-polar. They interact with other non-polar molecules in chemical reactions, but generally do not interact with polar molecules. When placed in water, hydrophobic molecules tend to form a ball or cluster. The hydrophilic regions of the phospholipids tend to form hydrogen bonds with water and other polar molecules on both the exterior and interior of the cell. Thus, the membrane surfaces that face the interior and exterior of the cell are hydrophilic. In contrast, the interior of the cell membrane is hydrophobic and will not interact with water. Therefore, phospholipids form an excellent two-layer cell membrane that separates fluid within the cell from the fluid outside of the cell.
A phospholipid molecule (Figure \(2\)) consists of a three-carbon glycerol backbone with two fatty acid molecules attached to carbons 1 and 2, and a phosphate-containing group attached to the third carbon. This arrangement gives the overall molecule an area described as its head (the phosphate-containing group), which has a polar character or negative charge, and an area called the tail (the fatty acids), which has no charge. The head can form hydrogen bonds, but the tail cannot. A molecule with this arrangement of a positively or negatively charged area and an uncharged, or non-polar, area is referred to as amphiphilic or “dual-loving.”
This characteristic is vital to the structure of a plasma membrane because, in water, phospholipids tend to become arranged with their hydrophobic tails facing each other and their hydrophilic heads facing out. In this way, they form a lipid bilayer—a barrier composed of a double layer of phospholipids that separates the water and other materials on one side of the barrier from the water and other materials on the other side. In fact, phospholipids heated in an aqueous solution tend to spontaneously form small spheres or droplets (called micelles or liposomes), with their hydrophilic heads forming the exterior and their hydrophobic tails on the inside (Figure \(3\)).
Proteins
Proteins make up the second major component of plasma membranes. Integral proteins (some specialized types are called integrins) are, as their name suggests, integrated completely into the membrane structure, and their hydrophobic membrane-spanning regions interact with the hydrophobic region of the the phospholipid bilayer (Figure \(1\)). Single-pass integral membrane proteins usually have a hydrophobic transmembrane segment that consists of 20–25 amino acids. Some span only part of the membrane—associating with a single layer—while others stretch from one side of the membrane to the other, and are exposed on either side. Some complex proteins are composed of up to 12 segments of a single protein, which are extensively folded and embedded in the membrane (Figure \(4\)). This type of protein has a hydrophilic region or regions, and one or several mildly hydrophobic regions. This arrangement of regions of the protein tends to orient the protein alongside the phospholipids, with the hydrophobic region of the protein adjacent to the tails of the phospholipids and the hydrophilic region or regions of the protein protruding from the membrane and in contact with the cytosol or extracellular fluid.
Peripheral proteins are found on the exterior and interior surfaces of membranes, attached either to integral proteins or to phospholipids. Peripheral proteins, along with integral proteins, may serve as enzymes, as structural attachments for the fibers of the cytoskeleton, or as part of the cell’s recognition sites. These are sometimes referred to as “cell-specific” proteins. The body recognizes its own proteins and attacks foreign proteins associated with invasive pathogens.
Carbohydrates
Carbohydrates are the third major component of plasma membranes. They are always found on the exterior surface of cells and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids) (Figure \(1\)). These carbohydrate chains may consist of 2–60 monosaccharide units and can be either straight or branched. Along with peripheral proteins, carbohydrates form specialized sites on the cell surface that allow cells to recognize each other. These sites have unique patterns that allow the cell to be recognized, much the way that the facial features unique to each person allow him or her to be recognized. This recognition function is very important to cells, as it allows the immune system to differentiate between body cells (called “self”) and foreign cells or tissues (called “non-self”). Similar types of glycoproteins and glycolipids are found on the surfaces of viruses and may change frequently, preventing immune cells from recognizing and attacking them.
These carbohydrates on the exterior surface of the cell—the carbohydrate components of both glycoproteins and glycolipids—are collectively referred to as the glycocalyx (meaning “sugar coating”). The glycocalyx is highly hydrophilic and attracts large amounts of water to the surface of the cell. This aids in the interaction of the cell with its watery environment and in the cell’s ability to obtain substances dissolved in the water. As discussed above, the glycocalyx is also important for cell identification, self/non-self determination, and embryonic development, and is used in cell-cell attachments to form tissues.
Evolution Connection: How Viruses Infect Specific Organs
Glycoprotein and glycolipid patterns on the surfaces of cells give many viruses an opportunity for infection. HIV and hepatitis viruses infect only specific organs or cells in the human body. HIV is able to penetrate the plasma membranes of a subtype of lymphocytes called T-helper cells, as well as some monocytes and central nervous system cells. The hepatitis virus attacks liver cells.
These viruses are able to invade these cells, because the cells have binding sites on their surfaces that are specific to and compatible with certain viruses (Figure \(5\)). Other recognition sites on the virus’s surface interact with the human immune system, prompting the body to produce antibodies. Antibodies are made in response to the antigens or proteins associated with invasive pathogens, or in response to foreign cells, such as might occur with an organ transplant. These same sites serve as places for antibodies to attach and either destroy or inhibit the activity of the virus. Unfortunately, these recognition sites on HIV change at a rapid rate because of mutations, making the production of an effective vaccine against the virus very difficult, as the virus evolves and adapts. A person infected with HIV will quickly develop different populations, or variants, of the virus that are distinguished by differences in these recognition sites. This rapid change of surface markers decreases the effectiveness of the person’s immune system in attacking the virus, because the antibodies will not recognize the new variations of the surface patterns. In the case of HIV, the problem is compounded by the fact that the virus specifically infects and destroys cells involved in the immune response, further incapacitating the host.
Membrane Fluidity
The mosaic characteristic of the membrane, described in the fluid mosaic model, helps to illustrate its nature. The integral proteins and lipids exist in the membrane as separate but loosely attached molecules. These resemble the separate, multicolored tiles of a mosaic picture, and they float, moving somewhat with respect to one another. The membrane is not like a balloon, however, that can expand and contract; rather, it is fairly rigid and can burst if penetrated or if a cell takes in too much water. However, because of its mosaic nature, a very fine needle can easily penetrate a plasma membrane without causing it to burst, and the membrane will flow and self-seal when the needle is extracted.
The mosaic characteristics of the membrane explain some but not all of its fluidity. There are two other factors that help maintain this fluid characteristic. One factor is the nature of the phospholipids themselves. In their saturated form, the fatty acids in phospholipid tails are saturated with bound hydrogen atoms. There are no double bonds between adjacent carbon atoms. This results in tails that are relatively straight. In contrast, unsaturated fatty acids do not contain a maximal number of hydrogen atoms, but they do contain some double bonds between adjacent carbon atoms; a double bond results in a bend in the string of carbons of approximately 30 degrees (Figure \(2\)).
Thus, if saturated fatty acids, with their straight tails, are compressed by decreasing temperatures, they press in on each other, making a dense and fairly rigid membrane. If unsaturated fatty acids are compressed, the “kinks” in their tails elbow adjacent phospholipid molecules away, maintaining some space between the phospholipid molecules. This “elbow room” helps to maintain fluidity in the membrane at temperatures at which membranes with saturated fatty acid tails in their phospholipids would “freeze” or solidify. The relative fluidity of the membrane is particularly important in a cold environment. A cold environment tends to compress membranes composed largely of saturated fatty acids, making them less fluid and more susceptible to rupturing. Many organisms (fish are one example) are capable of adapting to cold environments by changing the proportion of unsaturated fatty acids in their membranes in response to the lowering of the temperature.
Link to Learning
Visit this site to see animations of the fluidity and mosaic quality of membranes.
Animals have an additional membrane constituent that assists in maintaining fluidity. Cholesterol, which lies alongside the phospholipids in the membrane, tends to dampen the effects of temperature on the membrane. Thus, this lipid functions as a buffer, preventing lower temperatures from inhibiting fluidity and preventing increased temperatures from increasing fluidity too much. Thus, cholesterol extends, in both directions, the range of temperature in which the membrane is appropriately fluid and consequently functional. Cholesterol also serves other functions, such as organizing clusters of transmembrane proteins into lipid rafts.
Table \(1\): The Components and Functions of the Plasma Membrane.
Component Location
Phospholipid Main fabric of the membrane
Cholesterol Attached between phospholipids and between the two phospholipid layers
Integral proteins (for example, integrins) Embedded within the phospholipid layer(s). May or may not penetrate through both layers
Peripheral proteins On the inner or outer surface of the phospholipid bilayer; not embedded within the phospholipids
Carbohydrates (components of glycoproteins and glycolipids) Generally attached to proteins on the outside membrane layer
Career Connection: Immunologist
The variations in peripheral proteins and carbohydrates that affect a cell’s recognition sites are of prime interest in immunology. These changes are taken into consideration in vaccine development. Many infectious diseases, such as smallpox, polio, diphtheria, and tetanus, were conquered by the use of vaccines.
Immunologists are the physicians and scientists who research and develop vaccines, as well as treat and study allergies or other immune problems. Some immunologists study and treat autoimmune problems (diseases in which a person’s immune system attacks his or her own cells or tissues, such as lupus) and immunodeficiencies, whether acquired (such as acquired immunodeficiency syndrome, or AIDS) or hereditary (such as severe combined immunodeficiency, or SCID). Immunologists are called in to help treat organ transplantation patients, who must have their immune systems suppressed so that their bodies will not reject a transplanted organ. Some immunologists work to understand natural immunity and the effects of a person’s environment on it. Others work on questions about how the immune system affects diseases such as cancer. In the past, the importance of having a healthy immune system in preventing cancer was not at all understood.
To work as an immunologist, a PhD or MD is required. In addition, immunologists undertake at least 2–3 years of training in an accredited program and must pass an examination given by the American Board of Allergy and Immunology. Immunologists must possess knowledge of the functions of the human body as they relate to issues beyond immunization, and knowledge of pharmacology and medical technology, such as medications, therapies, test materials, and surgical procedures.
Summary
The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of which span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some of the proteins and lipids on the outward-facing surface of the membrane, forming complexes that function to identify the cell to other cells. The fluid nature of the membrane is due to temperature, the configuration of the fatty acid tails (some kinked by double bonds), the presence of cholesterol embedded in the membrane, and the mosaic nature of the proteins and protein-carbohydrate combinations, which are not firmly fixed in place. Plasma membranes enclose and define the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux.
Glossary
amphiphilic
molecule possessing a polar or charged area and a nonpolar or uncharged area capable of interacting with both hydrophilic and hydrophobic environments
fluid mosaic model
describes the structure of the plasma membrane as a mosaic of components including phospholipids, cholesterol, proteins, glycoproteins, and glycolipids (sugar chains attached to proteins or lipids, respectively), resulting in a fluid character (fluidity)
glycolipid
combination of carbohydrates and lipids
glycoprotein
combination of carbohydrates and proteins
hydrophilic
molecule with the ability to bond with water; “water-loving”
hydrophobic
molecule that does not have the ability to bond with water; “water-hating”
integral protein
protein integrated into the membrane structure that interacts extensively with the hydrocarbon chains of membrane lipids and often spans the membrane; these proteins can be removed only by the disruption of the membrane by detergents
peripheral protein
protein found at the surface of a plasma membrane either on its exterior or interior side; these proteins can be removed (washed off of the membrane) by a high-salt wash | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/05%3A_Membranes/5.01%3A_The_Structure_of_Membranes.txt |
All cells have a plasma membrane. This membrane surrounds the cell. So what is its role?
Can molecules enter and leave the cell? Yes. Can anything or everything enter or leave? No. So, what determines what can go in or out? Is it the nucleus? The DNA? Or the plasma membrane?
The Plasma Membrane
The plasma membrane (also known as the cell membrane) forms a barrier between the cytoplasm inside the cell and the environment outside the cell. It protects and supports the cell and also controls everything that enters and leaves the cell. It allows only certain substances to pass through, while keeping others in or out. The ability to allow only certain molecules in or out of the cell is referred to as selective permeability or semipermeability. To understand how the plasma membrane controls what crosses into or out of the cell, you need to know its composition.
The plasma membrane is discussed at http://www.youtube.com/watch?v=-aSfoB8Cmic (6:16).
A Phospholipid Bilayer
The plasma membrane is composed mainly of phospholipids, which consist of fatty acids and alcohol. The phospholipids in the plasma membrane are arranged in two layers, called aphospholipid bilayer. As shown in Figure below, each phospholipid molecule has a head and two tails. The head “loves” water (hydrophilic) and the tails “hate” water (hydrophobic). The water-hating tails are on the interior of the membrane, whereas the water-loving heads point outwards, toward either the cytoplasm or the fluid that surrounds the cell.
Molecules that are hydrophobic can easily pass through the plasma membrane, if they are small enough, because they are water-hating like the interior of the membrane. Molecules that are hydrophilic, on the other hand, cannot pass through the plasma membrane—at least not without help—because they are water-loving like the exterior of the membrane, and are therefore excluded from the interior of the membrane.
Phospholipid Bilayer. The phospholipid bilayer consists of two layers of phospholipids, with a hydrophobic, or water-hating, interior and a hydrophilic, or water-loving, exterior. The hydrophilic (polar) head group and hydrophobic tails (fatty acid chains) are depicted in the single phospholipid molecule. The polar head group and fatty acid chains are attached by a 3-carbon glycerol unit.
See Insights into cell membranes via dish detergent at http://ed.ted.com/lessons/insights-into-cell-membranes-via-dish-detergent-ethan-perlstein for additional information on the cell membrane.
Summary
• The plasma membrane forms a barrier between the cytoplasm and the environment outside the cell. The plasma membrane has selective permeability.
• The plasma membrane is primarily composed of phospholipids arranged in a bilayer, with the hydrophobic tails on the interior of the membrane, and the hydrophilic heads pointing outwards.
Explore More
Use these resources to answer the questions that follow.
Explore More I
1. What are the two main components of the cell membrane?
2. Describe the types of proteins that live in the cell membrane.
3. Describe the orientation of the phospholipid molecule in the cell membrane.
Explore More II
1. Are all cells surrounded by a membrane?
2. Why are phospholipids considered an amphipathic molecule?
3. What is a glycolipid?
4. Describe the role of cholesterol in the cell membrane.
Explore More III
1. What are the roles of the plasma membrane?
2. What are the functions of proteins associated with the cell membrane?
3. Why is the structure of the cell membrane described as "fluid mosaic"?
Review
1. Describe the role of the plasma membrane.
2. What is meant by semipermeability?
3. Describe the composition of the plasma membrane.
4. Explain why hydrophobic molecules can easily cross the plasma membrane, while hydrophilic molecules cannot. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/05%3A_Membranes/5.02%3A_Phospholipids-_The_Membrane%27s_Foundation.txt |
Can anything or everything move in or out of the cell?
No. It is the semipermeable plasma membrane that determines what can enter and leave the cell. So, if not everything can cross the membrane, how do certain things get across?
Membrane Proteins
The plasma membrane contains molecules other than phospholipids, primarily other lipids and proteins. The green molecules in Figure below, for example, are the lipid cholesterol. Molecules of cholesterol help the plasma membrane keep its shape. Many of the proteins in the plasma membrane assist other substances in crossing the membrane.
The plasma membranes also contain certain types of proteins. A membrane protein is a protein molecule that is attached to, or associated with, the membrane of a cell or an organelle. Membrane proteins can be put into two groups based on how the protein is associated with the membrane.
Integral membrane proteins are permanently embedded within the plasma membrane. They have a range of important functions. Such functions include channeling or transporting molecules across the membrane. Other integral proteins act as cell receptors. Integral membrane proteins can be classified according to their relationship with the bilayer:
• Transmembrane proteins span the entire plasma membrane. Transmembrane proteins are found in all types of biological membranes.
• Integral monotopic proteins are permanently attached to the membrane from only one side.
Some integral membrane proteins are responsible for cell adhesion (sticking of a cell to another cell or surface). On the outside of cell membranes and attached to some of the proteins are carbohydrate chains that act as labels that identify the cell type. Shown in Figure below are two different types of membrane proteins and associated molecules.
Peripheral membrane proteins are proteins that are only temporarily associated with the membrane. They can be easily removed, which allows them to be involved in cell signaling. Peripheral proteins can also be attached to integral membrane proteins, or they can stick into a small portion of the lipid bilayer by themselves. Peripheral membrane proteins are often associated with ion channels and transmembrane receptors. Most peripheral membrane proteins are hydrophilic.
Some of the membrane proteins make up a major transport system that moves molecules and ions through the polar phospholipid bilayer.
The Fluid Mosaic Model
In 1972 S.J. Singer and G.L. Nicolson proposed the now widely accepted Fluid Mosaic Modelof the structure of cell membranes. The model proposes that integral membrane proteins are embedded in the phospholipid bilayer, as seen in Figure above. Some of these proteins extend all the way through the bilayer, and some only partially across it. These membrane proteins act as transport proteins and receptors proteins.
Their model also proposed that the membrane behaves like a fluid, rather than a solid. The proteins and lipids of the membrane move around the membrane, much like buoys in water. Such movement causes a constant change in the "mosaic pattern" of the plasma membrane.
A further description of the Fluid Mosaic Model can be viewed athttp://www.youtube.com/watch?v=Qqsf_UJcfBc (1:27).
Extensions of the Plasma Membrane
The plasma membrane may have extensions, such as whip-like flagella or brush-like cilia. In single-celled organisms, like those shown in Figure below, the membrane extensions may help the organisms move. In multicellular organisms, the extensions have other functions. For example, the cilia on human lung cells sweep foreign particles and mucus toward the mouth and nose.
Flagella and Cilia. Cilia and flagella are extensions of the plasma membrane of many cells.
Summary
• The plasma membrane has many proteins that assist other substances in crossing the membrane.
• The Fluid Mosaic Model depicts the biological nature of the plasma membrane.
• Cilia and flagella are extensions of the plasma membrane.
Explore More
Use these resources to answer the questions that follow.
Explore More I
1. What is the major role of many membrane proteins?
2. How much of a cell's genetic material may code for membrane proteins?
3. What are transmembrane proteins, and what is their main function?
4. How can a protein "tunnel" form through the membrane?
5. How can a protein "channel" form through the membrane?
Explore More II
1. How may water molecules enter the cell?
2. How may ions enter the cell?
3. What type(s) of protein(s) identify the cell?
4. What molecule is found in the membrane of animal cells but not plant cells?
Review
1. What is the main difference between the two main types of proteins associated with the plasma membrane?
2. What are two functions of integral membrane proteins?
3. Discuss the Fluid Mosaic Model.
4. What are flagella and cilia? | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/05%3A_Membranes/5.03%3A_Proteins-_Multifunctional_Components.txt |
Plasma membranes must allow certain substances to enter and leave a cell, while preventing harmful material from entering and essential material from leaving. In other words, plasma membranes are selectively permeable—they allow some substances through but not others. If they were to lose this selectivity, the cell would no longer be able to sustain itself, and it would be destroyed. Some cells require larger amounts of specific substances than do other cells; they must have a way of obtaining these materials from the extracellular fluids. This may happen passively, as certain materials move back and forth, or the cell may have special mechanisms that ensure transport. Most cells expend most of their energy, in the form of adenosine triphosphate (ATP), to create and maintain an uneven distribution of ions on the opposite sides of their membranes. The structure of the plasma membrane contributes to these functions, but it also presents some problems.
The most direct forms of membrane transport are passive. Passive transport is a naturally occurring phenomenon and does not require the cell to expend energy to accomplish the movement. In passive transport, substances move from an area of higher concentration to an area of lower concentration in a process called diffusion. A physical space in which there is a different concentration of a single substance is said to have a concentration gradient.
Selective Permeability
Plasma membranes are asymmetric, meaning that despite the mirror image formed by the phospholipids, the interior of the membrane is not identical to the exterior of the membrane. Integral proteins that act as channels or pumps work in one direction. Carbohydrates, attached to lipids or proteins, are also found on the exterior surface of the plasma membrane. These carbohydrate complexes help the cell bind substances that the cell needs in the extracellular fluid. This adds considerably to the selective nature of plasma membranes.
Recall that plasma membranes have hydrophilic and hydrophobic regions. This characteristic helps the movement of certain materials through the membrane and hinders the movement of others. Lipid-soluble material can easily slip through the hydrophobic lipid core of the membrane. Substances such as the fat-soluble vitamins A, D, E, and K readily pass through the plasma membranes in the digestive tract and other tissues. Fat-soluble drugs also gain easy entry into cells and are readily transported into the body’s tissues and organs. Molecules of oxygen and carbon dioxide have no charge and pass through by simple diffusion.
Polar substances, with the exception of water, present problems for the membrane. While some polar molecules connect easily with the outside of a cell, they cannot readily pass through the lipid core of the plasma membrane. Additionally, whereas small ions could easily slip through the spaces in the mosaic of the membrane, their charge prevents them from doing so. Ions such as sodium, potassium, calcium, and chloride must have a special means of penetrating plasma membranes. Simple sugars and amino acids also need help with transport across plasma membranes.
Diffusion
Diffusion is a passive process of transport. A single substance tends to move from an area of high concentration to an area of low concentration until the concentration is equal across the space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of perfume in a room filled with people. The perfume is at its highest concentration in the bottle and is at its lowest at the edges of the room. The perfume vapor will diffuse, or spread away, from the bottle, and gradually, more and more people will smell the perfume as it spreads. Materials move within the cell’s cytosol by diffusion, and certain materials move through the plasma membrane by diffusion (Figure \(1\)). Diffusion expends no energy. Rather the different concentrations of materials in different areas are a form of potential energy, and diffusion is the dissipation of that potential energy as materials move down their concentration gradients, from high to low.
Each separate substance in a medium, such as the extracellular fluid, has its own concentration gradient, independent of the concentration gradients of other materials. Additionally, each substance will diffuse according to that gradient.
Several factors affect the rate of diffusion.
• Extent of the concentration gradient: The greater the difference in concentration, the more rapid the diffusion. The closer the distribution of the material gets to equilibrium, the slower the rate of diffusion becomes.
• Mass of the molecules diffusing: More massive molecules move more slowly, because it is more difficult for them to move between the molecules of the substance they are moving through; therefore, they diffuse more slowly.
• Temperature: Higher temperatures increase the energy and therefore the movement of the molecules, increasing the rate of diffusion.
• Solvent density: As the density of the solvent increases, the rate of diffusion decreases. The molecules slow down because they have a more difficult time getting through the denser medium.
CONCEPT IN ACTION
For an animation of the diffusion process in action, view this short video on cell membrane transport.
Facilitated transport
In facilitated transport, also called facilitated diffusion, material moves across the plasma membrane with the assistance of transmembrane proteins down a concentration gradient (from high to low concentration) without the expenditure of cellular energy. However, the substances that undergo facilitated transport would otherwise not diffuse easily or quickly across the plasma membrane. The solution to moving polar substances and other substances across the plasma membrane rests in the proteins that span its surface. The material being transported is first attached to protein or glycoprotein receptors on the exterior surface of the plasma membrane. This allows the material that is needed by the cell to be removed from the extracellular fluid. The substances are then passed to specific integral proteins that facilitate their passage, because they form channels or pores that allow certain substances to pass through the membrane. The integral proteins involved in facilitated transport are collectively referred to as transport proteins, and they function as either channels for the material or carriers.
Osmosis
Osmosis is the diffusion of water through a semipermeable membrane according to the concentration gradient of water across the membrane. Whereas diffusion transports material across membranes and within cells, osmosis transports only water across a membrane and the membrane limits the diffusion of solutes in the water. Osmosis is a special case of diffusion. Water, like other substances, moves from an area of higher concentration to one of lower concentration. Imagine a beaker with a semipermeable membrane, separating the two sides or halves (Figure \(2\)). On both sides of the membrane, the water level is the same, but there are different concentrations on each side of a dissolved substance, or solute, that cannot cross the membrane. If the volume of the water is the same, but the concentrations of solute are different, then there are also different concentrations of water, the solvent, on either side of the membrane.
A principle of diffusion is that the molecules move around and will spread evenly throughout the medium if they can. However, only the material capable of getting through the membrane will diffuse through it. In this example, the solute cannot diffuse through the membrane, but the water can. Water has a concentration gradient in this system. Therefore, water will diffuse down its concentration gradient, crossing the membrane to the side where it is less concentrated. This diffusion of water through the membrane—osmosis—will continue until the concentration gradient of water goes to zero. Osmosis proceeds constantly in living systems.
Tonicity
Tonicity describes the amount of solute in a solution. The measure of the tonicity of a solution, or the total amount of solutes dissolved in a specific amount of solution, is called its osmolarity. Three terms—hypotonic, isotonic, and hypertonic—are used to relate the osmolarity of a cell to the osmolarity of the extracellular fluid that contains the cells. In a hypotonic solution, such as tap water, the extracellular fluid has a lower concentration of solutes than the fluid inside the cell, and water enters the cell. (In living systems, the point of reference is always the cytoplasm, so the prefix hypo- means that the extracellular fluid has a lower concentration of solutes, or a lower osmolarity, than the cell cytoplasm.) It also means that the extracellular fluid has a higher concentration of water than does the cell. In this situation, water will follow its concentration gradient and enter the cell. This may cause an animal cell to burst, or lyse.
In a hypertonic solution (the prefix hyper- refers to the extracellular fluid having a higher concentration of solutes than the cell’s cytoplasm), the fluid contains less water than the cell does, such as seawater. Because the cell has a lower concentration of solutes, the water will leave the cell. In effect, the solute is drawing the water out of the cell. This may cause an animal cell to shrivel, or crenate.
In an isotonic solution, the extracellular fluid has the same osmolarity as the cell. If the concentration of solutes of the cell matches that of the extracellular fluid, there will be no net movement of water into or out of the cell. Blood cells in hypertonic, isotonic, and hypotonic solutions take on characteristic appearances (Figure \(3\)).
ART CONNECTION
A doctor injects a patient with what the doctor thinks is isotonic saline solution. The patient dies, and autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?
Some organisms, such as plants, fungi, bacteria, and some protists, have cell walls that surround the plasma membrane and prevent cell lysis. The plasma membrane can only expand to the limit of the cell wall, so the cell will not lyse. In fact, the cytoplasm in plants is always slightly hypertonic compared to the cellular environment, and water will always enter a cell if water is available. This influx of water produces turgor pressure, which stiffens the cell walls of the plant (Figure \(4\)). In nonwoody plants, turgor pressure supports the plant. If the plant cells become hypertonic, as occurs in drought or if a plant is not watered adequately, water will leave the cell. Plants lose turgor pressure in this condition and wilt.
Section Summary
The passive forms of transport, diffusion and osmosis, move material of small molecular weight. Substances diffuse from areas of high concentration to areas of low concentration, and this process continues until the substance is evenly distributed in a system. In solutions of more than one substance, each type of molecule diffuses according to its own concentration gradient. Many factors can affect the rate of diffusion, including concentration gradient, the sizes of the particles that are diffusing, and the temperature of the system.
In living systems, diffusion of substances into and out of cells is mediated by the plasma membrane. Some materials diffuse readily through the membrane, but others are hindered, and their passage is only made possible by protein channels and carriers. The chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem. In living systems, diffusion of some substances would be slow or difficult without membrane proteins.
Art Connections
Figure \(3\): A doctor injects a patient with what he thinks is isotonic saline solution. The patient dies, and autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?
Answer
No, it must have been hypotonic, as a hypotonic solution would cause water to enter the cells, thereby making them burst.
Glossary
concentration gradient
an area of high concentration across from an area of low concentration
diffusion
a passive process of transport of low-molecular weight material down its concentration gradient
facilitated transport
a process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins
hypertonic
describes a solution in which extracellular fluid has higher osmolarity than the fluid inside the cell
hypotonic
describes a solution in which extracellular fluid has lower osmolarity than the fluid inside the cell
isotonic
describes a solution in which the extracellular fluid has the same osmolarity as the fluid inside the cell
osmolarity
the total amount of substances dissolved in a specific amount of solution
osmosis
the transport of water through a semipermeable membrane from an area of high water concentration to an area of low water concentration across a membrane
passive transport
a method of transporting material that does not require energy
selectively permeable
the characteristic of a membrane that allows some substances through but not others
solute
a substance dissolved in another to form a solution
tonicity
the amount of solute in a solution. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/05%3A_Membranes/5.04%3A_Passive_Transport_Across_Membranes.txt |
Active transport mechanisms require the use of the cell’s energy, usually in the form of adenosine triphosphate (ATP). If a substance must move into the cell against its concentration gradient, that is, if the concentration of the substance inside the cell must be greater than its concentration in the extracellular fluid, the cell must use energy to move the substance. Some active transport mechanisms move small-molecular weight material, such as ions, through the membrane.
In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and particles. Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that the uptake and release of large particles by the cell requires energy. A large particle, however, cannot pass through the membrane, even with energy supplied by the cell.
Electrochemical Gradient
We have discussed simple concentration gradients—differential concentrations of a substance across a space or a membrane—but in living systems, gradients are more complex. Because cells contain proteins, most of which are negatively charged, and because ions move into and out of cells, there is an electrical gradient, a difference of charge, across the plasma membrane. The interior of living cells is electrically negative with respect to the extracellular fluid in which they are bathed; at the same time, cells have higher concentrations of potassium (K+) and lower concentrations of sodium (Na+) than does the extracellular fluid. Thus, in a living cell, the concentration gradient and electrical gradient of Na+ promotes diffusion of the ion into the cell, and the electrical gradient of Na+ (a positive ion) tends to drive it inward to the negatively charged interior. The situation is more complex, however, for other elements such as potassium. The electrical gradient of K+ promotes diffusion of the ion into the cell, but the concentration gradient of K+ promotes diffusion out of the cell (Figure \(1\)). The combined gradient that affects an ion is called its electrochemical gradient, and it is especially important to muscle and nerve cells.
Moving Against a Gradient
To move substances against a concentration or an electrochemical gradient, the cell must use energy. This energy is harvested from ATP that is generated through cellular metabolism. Active transport mechanisms, collectively called pumps or carrier proteins, work against electrochemical gradients. With the exception of ions, small substances constantly pass through plasma membranes. Active transport maintains concentrations of ions and other substances needed by living cells in the face of these passive changes. Much of a cell’s supply of metabolic energy may be spent maintaining these processes. Because active transport mechanisms depend on cellular metabolism for energy, they are sensitive to many metabolic poisons that interfere with the supply of ATP.
Two mechanisms exist for the transport of small-molecular weight material and macromolecules. Primary active transport moves ions across a membrane and creates a difference in charge across that membrane. The primary active transport system uses ATP to move a substance, such as an ion, into the cell, and often at the same time, a second substance is moved out of the cell. The sodium-potassium pump, an important pump in animal cells, expends energy to move potassium ions into the cell and a different number of sodium ions out of the cell (Figure \(2\)). The action of this pump results in a concentration and charge difference across the membrane.
Secondary active transport describes the movement of material using the energy of the electrochemical gradient established by primary active transport. Using the energy of the electrochemical gradient created by the primary active transport system, other substances such as amino acids and glucose can be brought into the cell through membrane channels. ATP itself is formed through secondary active transport using a hydrogen ion gradient in the mitochondrion.
Endocytosis
Endocytosis is a type of active transport that moves particles, such as large molecules, parts of cells, and even whole cells, into a cell. There are different variations of endocytosis, but all share a common characteristic: The plasma membrane of the cell invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly created vacuole that is formed from the plasma membrane.
Phagocytosis is the process by which large particles, such as cells, are taken in by a cell. For example, when microorganisms invade the human body, a type of white blood cell called a neutrophil removes the invader through this process, surrounding and engulfing the microorganism, which is then destroyed by the neutrophil (Figure \(3\)).
A variation of endocytosis is called pinocytosis. This literally means “cell drinking” and was named at a time when the assumption was that the cell was purposefully taking in extracellular fluid. In reality, this process takes in solutes that the cell needs from the extracellular fluid (Figure \(3\)).
A targeted variation of endocytosis employs binding proteins in the plasma membrane that are specific for certain substances (Figure \(3\)). The particles bind to the proteins and the plasma membrane invaginates, bringing the substance and the proteins into the cell. If passage across the membrane of the target of receptor-mediated endocytosis is ineffective, it will not be removed from the tissue fluids or blood. Instead, it will stay in those fluids and increase in concentration. Some human diseases are caused by a failure of receptor-mediated endocytosis. For example, the form of cholesterol termed low-density lipoprotein or LDL (also referred to as “bad” cholesterol) is removed from the blood by receptor-mediated endocytosis. In the human genetic disease familial hypercholesterolemia, the LDL receptors are defective or missing entirely. People with this condition have life-threatening levels of cholesterol in their blood, because their cells cannot clear the chemical from their blood.
CONCEPT IN ACTION
See receptor-mediated endocytosis animation in action.
Exocytosis
In contrast to these methods of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes discussed above in that its purpose is to expel material from the cell into the extracellular fluid. A particle enveloped in membrane fuses with the interior of the plasma membrane. This fusion opens the membranous envelope to the exterior of the cell, and the particle is expelled into the extracellular space (Figure \(4\)).
Section Summary
The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. Living cells need certain substances in concentrations greater than they exist in the extracellular space. Moving substances up their electrochemical gradients requires energy from the cell. Active transport uses energy stored in ATP to fuel the transport. Active transport of small molecular-size material uses integral proteins in the cell membrane to move the material—these proteins are analogous to pumps. Some pumps, which carry out primary active transport, couple directly with ATP to drive their action. In secondary transport, energy from primary transport can be used to move another substance into the cell and up its concentration gradient.
Endocytosis methods require the direct use of ATP to fuel the transport of large particles such as macromolecules; parts of cells or whole cells can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle wholly enclosed by an envelope of plasma membrane. Vacuoles are broken down by the cell, with the particles used as food or dispatched in some other way. Pinocytosis is a similar process on a smaller scale. The cell expels waste and other particles through the reverse process, exocytosis. Wastes are moved outside the cell, pushing a membranous vesicle to the plasma membrane, allowing the vesicle to fuse with the membrane and incorporating itself into the membrane structure, releasing its contents to the exterior of the cell.
Glossary
active transport
the method of transporting material that requires energy
electrochemical gradient
a gradient produced by the combined forces of the electrical gradient and the chemical gradient
endocytosis
a type of active transport that moves substances, including fluids and particles, into a cell
exocytosis
a process of passing material out of a cell
phagocytosis
a process that takes macromolecules that the cell needs from the extracellular fluid; a variation of endocytosis
pinocytosis
a process that takes solutes that the cell needs from the extracellular fluid; a variation of endocytosis
receptor-mediated endocytosis
a variant of endocytosis that involves the use of specific binding proteins in the plasma membrane for specific molecules or particles | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/05%3A_Membranes/5.05%3A_Active_Transport_Across_Membranes/5.5.02%3A_Active_Transport.txt |
Skills to Develop
• Describe endocytosis, including phagocytosis, pinocytosis, and receptor-mediated endocytosis
• Understand the process of exocytosis
In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and particles (see Table \(1\) for examples). Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that the uptake and release of large particles by the cell requires energy. A large particle, however, cannot pass through the membrane, even with energy supplied by the cell.
Endocytosis
Endocytosis is a type of active transport that moves particles, such as large molecules, parts of cells, and even whole cells, into a cell. There are different variations of endocytosis, but all share a common characteristic: The plasma membrane of the cell invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly created intracellular vesicle formed from the plasma membrane.
Phagocytosis
Phagocytosis (the condition of “cell eating”) is the process by which large particles, such as cells or relatively large particles, are taken in by a cell. For example, when microorganisms invade the human body, a type of white blood cell called a neutrophil will remove the invaders through this process, surrounding and engulfing the microorganism, which is then destroyed by the neutrophil (Figure \(1\)).
In preparation for phagocytosis, a portion of the inward-facing surface of the plasma membrane becomes coated with a protein called clathrin, which stabilizes this section of the membrane. The coated portion of the membrane then extends from the body of the cell and surrounds the particle, eventually enclosing it. Once the vesicle containing the particle is enclosed within the cell, the clathrin disengages from the membrane and the vesicle merges with a lysosome for the breakdown of the material in the newly formed compartment (endosome). When accessible nutrients from the degradation of the vesicular contents have been extracted, the newly formed endosome merges with the plasma membrane and releases its contents into the extracellular fluid. The endosomal membrane again becomes part of the plasma membrane.
Pinocytosis
A variation of endocytosis is called pinocytosis. This literally means “cell drinking” and was named at a time when the assumption was that the cell was purposefully taking in extracellular fluid. In reality, this is a process that takes in molecules, including water, which the cell needs from the extracellular fluid. Pinocytosis results in a much smaller vesicle than does phagocytosis, and the vesicle does not need to merge with a lysosome (Figure \(2\)).
A variation of pinocytosis is called potocytosis. This process uses a coating protein, called caveolin, on the cytoplasmic side of the plasma membrane, which performs a similar function to clathrin. The cavities in the plasma membrane that form the vacuoles have membrane receptors and lipid rafts in addition to caveolin. The vacuoles or vesicles formed in caveolae (singular caveola) are smaller than those in pinocytosis. Potocytosis is used to bring small molecules into the cell and to transport these molecules through the cell for their release on the other side of the cell, a process called transcytosis.
Receptor-mediated Endocytosis
A targeted variation of endocytosis employs receptor proteins in the plasma membrane that have a specific binding affinity for certain substances (Figure \(3\)).
In receptor-mediated endocytosis, as in phagocytosis, clathrin is attached to the cytoplasmic side of the plasma membrane. If uptake of a compound is dependent on receptor-mediated endocytosis and the process is ineffective, the material will not be removed from the tissue fluids or blood. Instead, it will stay in those fluids and increase in concentration. Some human diseases are caused by the failure of receptor-mediated endocytosis. For example, the form of cholesterol termed low-density lipoprotein or LDL (also referred to as “bad” cholesterol) is removed from the blood by receptor-mediated endocytosis. In the human genetic disease familial hypercholesterolemia, the LDL receptors are defective or missing entirely. People with this condition have life-threatening levels of cholesterol in their blood, because their cells cannot clear LDL particles from their blood.
Although receptor-mediated endocytosis is designed to bring specific substances that are normally found in the extracellular fluid into the cell, other substances may gain entry into the cell at the same site. Flu viruses, diphtheria, and cholera toxin all have sites that cross-react with normal receptor-binding sites and gain entry into cells.
Link to Learning
Video \(1\): See receptor-mediated endocytosis in action, and click on different parts for a focused animation.
Exocytosis
The reverse process of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes discussed above in that its purpose is to expel material from the cell into the extracellular fluid. Waste material is enveloped in a membrane and fuses with the interior of the plasma membrane. This fusion opens the membranous envelope on the exterior of the cell, and the waste material is expelled into the extracellular space (Figure \(4\)). Other examples of cells releasing molecules via exocytosis include the secretion of proteins of the extracellular matrix and secretion of neurotransmitters into the synaptic cleft by synaptic vesicles.
Table \(1\): Methods of transport, Energy requirements and types of Material transported.
Transport Method Active/Passive Material Transported
Diffusion Passive Small-molecular weight material
Osmosis Passive Water
Facilitated transport/diffusion Passive Sodium, potassium, calcium, glucose
Primary active transport Active Sodium, potassium, calcium
Secondary active transport Active Amino acids, lactose
Phagocytosis Active Large macromolecules, whole cells, or cellular structures
Pinocytosis and potocytosis Active Small molecules (liquids/water)
Receptor-mediated endocytosis Active Large quantities of macromolecules
Summary
Active transport methods require the direct use of ATP to fuel the transport. Large particles, such as macromolecules, parts of cells, or whole cells, can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle entirely enclosed by an envelope of plasma membrane. Vesicle contents are broken down by the cell, with the particles either used as food or dispatched. Pinocytosis is a similar process on a smaller scale. The plasma membrane invaginates and pinches off, producing a small envelope of fluid from outside the cell. Pinocytosis imports substances that the cell needs from the extracellular fluid. The cell expels waste in a similar but reverse manner: it pushes a membranous vacuole to the plasma membrane, allowing the vacuole to fuse with the membrane and incorporate itself into the membrane structure, releasing its contents to the exterior.
Glossary
caveolin
protein that coats the cytoplasmic side of the plasma membrane and participates in the process of liquid update by potocytosis
clathrin
protein that coats the inward-facing surface of the plasma membrane and assists in the formation of specialized structures, like coated pits, for phagocytosis
endocytosis
type of active transport that moves substances, including fluids and particles, into a cell
exocytosis
process of passing bulk material out of a cell
pinocytosis
a variation of endocytosis that imports macromolecules that the cell needs from the extracellular fluid
potocytosis
variation of pinocytosis that uses a different coating protein (caveolin) on the cytoplasmic side of the plasma membrane
receptor-mediated endocytosis
variation of endocytosis that involves the use of specific binding proteins in the plasma membrane for specific molecules or particles, and clathrin-coated pits that become clathrin-coated vesicles | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/05%3A_Membranes/5.06%3A_Bulk_Transport_by_Endocytosis_and_Exocytosis.txt |
Learning Objectives
• Explain the importance of metabolism
Energy and Metabolism
All living organisms need energy to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is the set of life-sustaining chemical processes that enables organisms transform the chemical energy stored in molecules into energy that can be used for cellular processes. Animals consume food to replenish energy; their metabolism breaks down the carbohydrates, lipids, proteins, and nucleic acids to provide chemical energy for these processes. Plants convert light energy from the sun into chemical energy stored in molecules during the process of photosynthesis.
Bioenergetics and Chemical Reactions
Scientists use the term bioenergetics to discuss the concept of energy flow through living systems such as cells. Cellular processes such as the building and breaking down of complex molecules occur through step-by-step chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. All of the chemical reactions that take place inside cells, including those that use energy and those that release energy, are the cell’s metabolism.
Cellular Metabolism
Every task performed by living organisms requires energy. Energy is needed to perform heavy labor and exercise, but humans also use a great deal of energy while thinking and even while sleeping. For every action that requires energy, many chemical reactions take place to provide chemical energy to the systems of the body, including muscles, nerves, heart, lungs, and brain.
The living cells of every organism constantly use energy to survive and grow. Cells break down complex carbohydrates into simple sugars that the cell can use for energy. Muscle cells may consumer energy to build long muscle proteins from small amino acid molecules. Molecules can be modified and transported around the cell or may be distributed to the entire organism. Just as energy is required to both build and demolish a building, energy is required for both the synthesis and breakdown of molecules.
Many cellular process require a steady supply of energy provided by the cell’s metabolism. Signaling molecules such as hormones and neurotransmitters must be synthesized and then transported between cells. Pathogenic bacteria and viruses are ingested and broken down by cells. Cells must also export waste and toxins to stay healthy, and many cells must swim or move surrounding materials via the beating motion of cellular appendages like cilia and flagella.
Key Points
• All living organisms need energy to grow and reproduce, maintain their structures, and respond to their environments; metabolism is the set of the processes that makes energy available for cellular processes.
• Metabolism is a combination of chemical reactions that are spontaneous and release energy and chemical reactions that are non-spontaneous and require energy in order to proceed.
• Living organisms must take in energy via food, nutrients, or sunlight in order to carry out cellular processes.
• The transport, synthesis, and breakdown of nutrients and molecules in a cell require the use of energy.
Key Terms
• metabolism: the complete set of chemical reactions that occur in living cells
• bioenergetics: the study of the energy transformations that take place in living organisms
• energy: the capacity to do work | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/06%3A_Energy_and_Metabolism/6.01%3A_The_Flow_of_Energy_in_Living_Systems/6.1A%3A_The_Role_of_Energy_and_Metabolism.txt |
Learning Objectives
• Differentiate between types of energy
Energy is a property of objects which can be transferred to other objects or converted into different forms, but cannot be created or destroyed. Organisms use energy to survive, grow, respond to stimuli, reproduce, and for every type of biological process. The potential energy stored in molecules can be converted to chemical energy, which can ultimately be converted to kinetic energy, enabling an organism to move. Eventually, most of energy used by organisms is transformed into heat and dissipated.
Kinetic Energy
Energy associated with objects in motion is called kinetic energy. For example, when an airplane is in flight, the airplane is moving through air very quickly—doing work to enact change on its surroundings. The jet engines are converting potential energy in fuel to the kinetic energy of movement. A wrecking ball can perform a large amount of damage, even when moving slowly. However, a still wrecking ball cannot perform any work and therefore has no kinetic energy. A speeding bullet, a walking person, the rapid movement of molecules in the air that produces heat, and electromagnetic radiation, such as sunlight, all have kinetic energy.
Potential Energy
What if that same motionless wrecking ball is lifted two stories above a car with a crane? If the suspended wrecking ball is not moving, is there energy associated with it? Yes, the wrecking ball has energy because the wrecking ball has the potential to do work. This form of energy is called potential energy because it is possible for that object to do work in a given state.
Objects transfer their energy between potential and kinetic states. As the wrecking ball hangs motionlessly, it has 0%0% kinetic and 100%100%potential energy. Once the ball is released, its kinetic energy increases as the ball picks up speed. At the same time, the ball loses potential energy as it nears the ground. Other examples of potential energy include the energy of water held behind a dam or a person about to skydive out of an airplane.
Chemical Energy
Potential energy is not only associated with the location of matter, but also with the structure of matter. A spring on the ground has potential energy if it is compressed, as does a rubber band that is pulled taut. The same principle applies to molecules. On a chemical level, the bonds that hold the atoms of molecules together have potential energy. This type of potential energy is called chemical energy, and like all potential energy, it can be used to do work.
For example, chemical energy is contained in the gasoline molecules that are used to power cars. When gas ignites in the engine, the bonds within its molecules are broken, and the energy released is used to drive the pistons. The potential energy stored within chemical bonds can be harnessed to perform work for biological processes. Different metabolic processes break down organic molecules to release the energy for an organism to grow and survive.
Key Points
• All organisms use different forms of energy to power the biological processes that allow them to grow and survive.
• Kinetic energy is the energy associated with objects in motion.
• Potential energy is the type of energy associated with an object’s potential to do work.
• Chemical energy is the type of energy released from the breakdown of chemical bonds and can be harnessed for metabolic processes.
Key Terms
• chemical energy: The net potential energy liberated or absorbed during the course of a chemical reaction.
• potential energy: Energy possessed by an object because of its position (in a gravitational or electric field), or its condition (as a stretched or compressed spring, as a chemical reactant, or by having rest mass).
• kinetic energy: The energy possessed by an object because of its motion, equal to one half the mass of the body times the square of its velocity. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/06%3A_Energy_and_Metabolism/6.01%3A_The_Flow_of_Energy_in_Living_Systems/6.1B%3A_Types_of_Energy.txt |
Learning Objectives
• Discuss the concept of free energy.
Free Energy
Since chemical reactions release energy when energy-storing bonds are broken, how is the energy associated with chemical reactions quantified and expressed? How can the energy released from one reaction be compared to that of another reaction?
A measurement of free energy is used to quantitate these energy transfers. Free energy is called Gibbs free energy (G) after Josiah Willard Gibbs, the scientist who developed the measurement. Recall that according to the second law of thermodynamics, all energy transfers involve the loss of some amount of energy in an unusable form such as heat, resulting in entropy. Gibbs free energy specifically refers to the energy associated with a chemical reaction that is available after accounting for entropy. In other words, Gibbs free energy is usable energy or energy that is available to do work.
Calculating ∆G
Every chemical reaction involves a change in free energy, called delta G (∆G). The change in free energy can be calculated for any system that undergoes a change, such as a chemical reaction. To calculate ∆G, subtract the amount of energy lost to entropy (denoted as ∆S) from the total energy change of the system. This total energy change in the system is called enthalpy and is denoted as ∆H. The formula for calculating ∆G is as follows, where the symbol T refers to absolute temperature in Kelvin (degrees Celsius + 273): G=ΔH−TΔS.
The standard free energy change of a chemical reaction is expressed as an amount of energy per mole of the reaction product (either in kilojoules or kilocalories, kJ/mol or kcal/mol; 1 kJ = 0.239 kcal) under standard pH, temperature, and pressure conditions. Standard pH, temperature, and pressure conditions are generally calculated at pH 7.0 in biological systems, 25 degrees Celsius, and 100 kilopascals (1 atm pressure), respectively. It is important to note that cellular conditions vary considerably from these standard conditions; therefore, standard calculated ∆G values for biological reactions will be different inside the cell.
Endergonic and Exergonic Reactions
If energy is released during a chemical reaction, then the resulting value from the above equation will be a negative number. In other words, reactions that release energy have a ∆G < 0. A negative ∆G also means that the products of the reaction have less free energy than the reactants because they gave off some free energy during the reaction. Reactions that have a negative ∆G and, consequently, release free energy, are called exergonic reactions. Exergonic means energy is exiting the system. These reactions are also referred to as spontaneous reactions because they can occur without the addition of energy into the system. Understanding which chemical reactions are spontaneous and release free energy is extremely useful for biologists because these reactions can be harnessed to perform work inside the cell. An important distinction must be drawn between the term spontaneous and the idea of a chemical reaction that occurs immediately. Contrary to the everyday use of the term, a spontaneous reaction is not one that suddenly or quickly occurs. The rusting of iron is an example of a spontaneous reaction that occurs slowly, little by little, over time.
If a chemical reaction requires an input of energy rather than releasing energy, then the ∆G for that reaction will be a positive value. In this case, the products have more free energy than the reactants. Thus, the products of these reactions can be thought of as energy-storing molecules. These chemical reactions are called endergonic reactions; they are non-spontaneous. An endergonic reaction will not take place on its own without the addition of free energy.
Free Energy and Biological Processes
In a living cell, chemical reactions are constantly moving towards equilibrium, but never reach it. A living cell is an open system: materials pass in and out, the cell recycles the products of certain chemical reactions into other reactions, and chemical equilibrium is never reached. In this way, living organisms are in a constant energy-requiring, uphill battle against equilibrium and entropy.
When complex molecules, such as starches, are built from simpler molecules, such as sugars, the anabolic process requires energy. Therefore, the chemical reactions involved in anabolic processes are endergonic reactions. On the other hand, the catabolic process of breaking sugar down into simpler molecules releases energy in a series of exergonic reactions. As in the example of rust above, the breakdown of sugar involves spontaneous reactions, but these reactions don’t occur instantaneously. An important concept in the study of metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in both directions, releasing energy into their environment in one direction, and absorbing it from the environment in the other direction.
Key Points
• Every chemical reaction involves a change in free energy, called delta G (∆G).
• To calculate ∆G, subtract the amount of energy lost to entropy (∆S) from the total energy change of the system; this total energy change in the system is called enthalpy (∆H ): ΔG=ΔH−TΔS.
• Endergonic reactions require an input of energy; the ∆G for that reaction will be a positive value.
• Exergonic reactions release free energy; the ∆G for that reaction will be a negative value.
Key Terms
• exergonic reaction: A chemical reaction where the change in the Gibbs free energy is negative, indicating a spontaneous reaction
• endergonic reaction: A chemical reaction in which the standard change in free energy is positive, and energy is absorbed
• Gibbs free energy: The difference between the enthalpy of a system and the product of its entropy and absolute temperature | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/06%3A_Energy_and_Metabolism/6.02%3A_The_Laws_of_Thermodynamics_and_Free_Energy/6.2A%3A__Free_Energy.txt |
Learning Objectives
• Describe the first law of thermodynamics
Thermodynamics is the study of heat energy and other types of energy, such as work, and the various ways energy is transferred within chemical systems. “Thermo-” refers to heat, while “dynamics” refers to motion.
The First Law of Thermodynamics
The first law of thermodynamics deals with the total amount of energy in the universe. The law states that this total amount of energy is constant. In other words, there has always been, and always will be, exactly the same amount of energy in the universe.
Energy exists in many different forms. According to the first law of thermodynamics, energy can be transferred from place to place or changed between different forms, but it cannot be created or destroyed. The transfers and transformations of energy take place around us all the time. For instance, light bulbs transform electrical energy into light energy, and gas stoves transform chemical energy from natural gas into heat energy. Plants perform one of the most biologically useful transformations of energy on Earth: they convert the energy of sunlight into the chemical energy stored within organic molecules.
The System and Surroundings
Thermodynamics often divides the universe into two categories: the system and its surroundings. In chemistry, the system almost always refers to a given chemical reaction and the container in which it takes place. The first law of thermodynamics tells us that energy can neither be created nor destroyed, so we know that the energy that is absorbed in an endothermic chemical reaction must have been lost from the surroundings. Conversely, in an exothermic reaction, the heat that is released in the reaction is given off and absorbed by the surroundings. Stated mathematically, we have:
ΔE=ΔEsys+ΔEsurr=0
Heat and Work
We know that chemical systems can either absorb heat from their surroundings, if the reaction is endothermic, or release heat to their surroundings, if the reaction is exothermic. However, chemical reactions are often used to do work instead of just exchanging heat. For instance, when rocket fuel burns and causes a space shuttle to lift off from the ground, the chemical reaction, by propelling the rocket, is doing work by applying a force over a distance.
If you’ve ever witnessed a video of a space shuttle lifting off, the chemical reaction that occurs also releases tremendous amounts of heat and light. Another useful form of the first law of thermodynamics relates heat and work for the change in energy of the internal system:
ΔEsys=Q+W
While this formulation is more commonly used in physics, it is still important to know for chemistry.
Key Points
• According to the first law of thermodynamics, the total amount of energy in the universe is constant.
• Energy can be transferred from place to place or transformed into different forms, but it cannot be created or destroyed.
• Living organisms have evolved to obtain energy from their surroundings in forms that they can transfer or transform into usable energy to do work.
Key Terms
• first law of thermodynamics: A version of the law of conservation of energy, specialized for thermodynamical systems, that states that the energy of an isolated system is constant and can neither be created nor destroyed.
• work: A measure of energy expended by moving an object, usually considered to be force times distance. No work is done if the object does not move. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/06%3A_Energy_and_Metabolism/6.02%3A_The_Laws_of_Thermodynamics_and_Free_Energy/6.2B%3A_The_First_Law_of_Thermodynamics.txt |
Learning Objectives
• Explain how living organisms can increase their order despite the second law of thermodynamics
The Second Law of Thermodynamics
A living cell ‘s primary tasks of obtaining, transforming, and using energy to do work may seem simple enough, but they are more problematic than they appear. The second law of thermodynamics explains why: No energy transfers or transformations in the universe are completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. In most cases, this energy is in the form of heat. Thermodynamically, heat energy is defined as the energy transferred from one system to another that is not doing work. For example, when an airplane flies through the air, some of the energy of the flying plane is lost as heat energy due to friction with the surrounding air. This friction heats the air by temporarily increasing the speed of air molecules. Likewise, some energy is lost in the form of heat during cellular metabolic reactions. This is good for warm-blooded creatures like us because heat energy helps to maintain our body temperature. Strictly speaking, no energy transfer is completely efficient because some energy is lost in an unusable form.
Entropy
An important concept in physical systems is disorder (also known as randomness). The more energy that is lost by a system to its surroundings, the less ordered and more random the system is. Scientists define the measure of randomness or disorder within a system as entropy. High entropy means high disorder and low energy. To better understand entropy, remember that it requires energy to maintain structure. For example, think about an ice cube. It is made of water molecules bound together in an orderly lattice. This arrangement takes energy to maintain. When the ice cube melts and becomes water, its molecules are more disordered, in a random arrangement as opposed to a structure. Overall, there is less energy in the system inside the molecular bonds. Therefore, water can be said to have greater entropy than ice.
This holds true for solids, liquids, and gases in general. Solids have the highest internal energy holding them together and therefore the lowest entropy. Liquids are more disordered and it takes less energy to hold them together. Therefore they are higher in entropy than solids, but lower than gases, which are so disordered that they have the highest entropy and lowest amount of energy spent holding them together.
Entropy changes also occur in chemical reactions. In an exergonic chemical reaction where energy is released, entropy increases because the final products have less energy inside them holding their chemical bonds together. That energy has been lost to the environment, usually in the form of heat.
All physical systems can be thought of in this way. Living things are highly ordered, requiring constant energy input to be maintained in a state of low entropy. As living systems take in energy-storing molecules and transform them through chemical reactions, they lose some amount of usable energy in the process because no reaction is completely efficient. They also produce waste and by-products that are not useful energy sources. This process increases the entropy of the system’s surroundings. Since all energy transfers result in the loss of some usable energy, the second law of thermodynamics states that every energy transfer or transformation increases the entropy of the universe. Even though living things are highly ordered and maintain a state of low entropy, the entropy of the universe in total is constantly increasing due to the loss of usable energy with each energy transfer that occurs. Essentially, living things are in a continuous uphill battle against this constant increase in universal entropy.
Key Points
• During energy transfer, some amount of energy is lost in the form of unusable heat energy.
• Because energy is lost in an unusable form, no energy transfer is completely efficient.
• The more energy that is lost by a system to its surroundings, the less ordered and more random the system is.
• Entropy is a measure of randomness and disorder; high entropy means high disorder and low energy.
• As chemical reactions reach a state of equilibrium, entropy increases; and as molecules at a high concentration in one place diffuse and spread out, entropy also increases.
Key Terms
• second law of thermodynamics: Every energy transfer or transformation increases the entropy of the universe since all energy transfers result in the loss of some usable energy.
• entropy: A measure of randomness and disorder in a system. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/06%3A_Energy_and_Metabolism/6.02%3A_The_Laws_of_Thermodynamics_and_Free_Energy/6.2C%3A_The_Second_Law_of_Thermodynamics.txt |
Learning Objectives
• Discuss the concept of activation energy
Many chemical reactions, and almost all biochemical reactions do not occur spontaneously and must have an initial input of energy (called the activation energy) to get started. Activation energy must be considered when analyzing both endergonic and exergonic reactions. Exergonic reactions have a net release of energy, but they still require a small amount of energy input before they can proceed with their energy-releasing steps. This small amount of energy input necessary for all chemical reactions to occur is called the activation energy (or free energy of activation) and is abbreviated EA.
Activation Energy in Chemical Reactions
Why would an energy-releasing, negative ∆G reaction actually require some energy to proceed? The reason lies in the steps that take place during a chemical reaction. During chemical reactions, certain chemical bonds are broken and new ones are formed. For example, when a glucose molecule is broken down, bonds between the carbon atoms of the molecule are broken. Since these are energy-storing bonds, they release energy when broken. However, to get them into a state that allows the bonds to break, the molecule must be somewhat contorted. A small energy input is required to achieve this contorted state, which is called the transition state: it is a high-energy, unstable state. For this reason, reactant molecules don’t last long in their transition state, but very quickly proceed to the next steps of the chemical reaction.
Cells will at times couple an exergonic reaction (ΔG<0) with endergonic reactions (ΔG>0), allowing them to proceed. This spontaneous shift from one reaction to another is called energy coupling. The free energy released from the exergonic reaction is absorbed by the
endergonic reaction. One example of energy coupling using ATP involves a transmembrane ion pump that is extremely important for cellular function.
Free Energy Diagrams
Free energy diagrams illustrate the energy profiles for a given reaction. Whether the reaction is exergonic (ΔG<0) or endergonic (ΔG>0) determines whether the products in the diagram will exist at a lower or higher energy state than the reactants. However, the measure of the activation energy is independent of the reaction’s ΔG. In other words, at a given temperature, the activation energy depends on the nature of the chemical transformation that takes place, but not on the relative energy state of the reactants and products.
Although the image above discusses the concept of activation energy within the context of the exergonic forward reaction, the same principles apply to the reverse reaction, which must be endergonic. Notice that the activation energy for the reverse reaction is larger than for the forward reaction.
Heat Energy
The source of the activation energy needed to push reactions forward is typically heat energy from the surroundings. Heat energy (the total bond energy of reactants or products in a chemical reaction) speeds up the motion of molecules, increasing the frequency and force with which they collide. It also moves atoms and bonds within the molecule slightly, helping them reach their transition state. For this reason, heating up a system will cause chemical reactants within that system to react more frequently. Increasing the pressure on a system has the same effect. Once reactants have absorbed enough heat energy from their surroundings to reach the transition state, the reaction will proceed.
The activation energy of a particular reaction determines the rate at which it will proceed. The higher the activation energy, the slower the chemical reaction will be. The example of iron rusting illustrates an inherently slow reaction. This reaction occurs slowly over time because of its high EA. Additionally, the burning of many fuels, which is strongly exergonic, will take place at a negligible rate unless their activation energy is overcome by sufficient heat from a spark. Once they begin to burn, however, the chemical reactions release enough heat to continue the burning process, supplying the activation energy for surrounding fuel molecules.
Like these reactions outside of cells, the activation energy for most cellular reactions is too high for heat energy to overcome at efficient rates. In other words, in order for important cellular reactions to occur at significant rates (number of reactions per unit time), their activation energies must be lowered; this is referred to as catalysis. This is a very good thing as far as living cells are concerned. Important macromolecules, such as proteins, DNA, and RNA, store considerable energy, and their breakdown is exergonic. If cellular temperatures alone provided enough heat energy for these exergonic reactions to overcome their activation barriers, the essential components of a cell would disintegrate.
The Arrhenius Equation
The Arrhenius equations relates the rate of a chemical reaction to the magnitude of the activation energy:
k=AeEa/RT
where
• k is the reaction rate coefficient or constant
• A is the frequency factor of the reaction. It is determined experimentally.
• R is the Universal Gas constant
• T is the temperature in Kelvin
Key Points
• Reactions require an input of energy to initiate the reaction; this is called the activation energy (EA).
• Activation energy is the amount of energy required to reach the transition state.
• The source of the activation energy needed to push reactions forward is typically heat energy from the surroundings.
• For cellular reactions to occur fast enough over short time scales, their activation energies are lowered by molecules called catalysts.
• Enzymes are catalysts.
Key Terms
• activation energy: The minimum energy required for a reaction to occur.
• catalysis: The increase in the rate of a chemical reaction by lowering its activation energy.
• transition state: An intermediate state during a chemical reaction that has a higher energy than the reactants or the products. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/06%3A_Energy_and_Metabolism/6.02%3A_The_Laws_of_Thermodynamics_and_Free_Energy/6.2D%3A_Activation_Energy.txt |
Skills to Develop
• Explain the role of ATP as the cellular energy currency
• Describe how energy is released through hydrolysis of ATP
Even exergonic, energy-releasing reactions require a small amount of activation energy in order to proceed. However, consider endergonic reactions, which require much more energy input, because their products have more free energy than their reactants. Within the cell, where does energy to power such reactions come from? The answer lies with an energy-supplying molecule called adenosine triphosphate, or ATP. ATP is a small, relatively simple molecule (Figure $1$), but within some of its bonds, it contains the potential for a quick burst of energy that can be harnessed to perform cellular work. This molecule can be thought of as the primary energy currency of cells in much the same way that money is the currency that people exchange for things they need. ATP is used to power the majority of energy-requiring cellular reactions.
As its name suggests, adenosine triphosphate is comprised of adenosine bound to three phosphate groups (Figure $1$). Adenosine is a nucleoside consisting of the nitrogenous base adenine and a five-carbon sugar, ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are labeled alpha, beta, and gamma. Together, these chemical groups constitute an energy powerhouse. However, not all bonds within this molecule exist in a particularly high-energy state. Both bonds that link the phosphates are equally high-energy bonds (phosphoanhydride bonds) that, when broken, release sufficient energy to power a variety of cellular reactions and processes. These high-energy bonds are the bonds between the second and third (or beta and gamma) phosphate groups and between the first and second phosphate groups. The reason that these bonds are considered “high-energy” is because the products of such bond breaking—adenosine diphosphate (ADP) and one inorganic phosphate group (Pi)—have considerably lower free energy than the reactants: ATP and a water molecule. Because this reaction takes place with the use of a water molecule, it is considered a hydrolysis reaction. In other words, ATP is hydrolyzed into ADP in the following reaction:
$\ce{ATP + H_2O \rightarrow ADP + P_{i} + free\: energy} \nonumber$
Like most chemical reactions, the hydrolysis of ATP to ADP is reversible. The reverse reaction regenerates ATP from ADP + Pi. Indeed, cells rely on the regeneration of ATP just as people rely on the regeneration of spent money through some sort of income. Since ATP hydrolysis releases energy, ATP regeneration must require an input of free energy. The formation of ATP is expressed in this equation:
$\ce{ADP + P_{i} + free\: energy \rightarrow ATP + H_2O} \nonumber$
Two prominent questions remain with regard to the use of ATP as an energy source. Exactly how much free energy is released with the hydrolysis of ATP, and how is that free energy used to do cellular work? The calculated ∆G for the hydrolysis of one mole of ATP into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol). Since this calculation is true under standard conditions, it would be expected that a different value exists under cellular conditions. In fact, the ∆G for the hydrolysis of one mole of ATP in a living cell is almost double the value at standard conditions: 14 kcal/mol (−57 kJ/mol).
ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + Pi, and the free energy released during this process is lost as heat. The second question posed above, that is, how the energy released by ATP hydrolysis is used to perform work inside the cell, depends on a strategy called energy coupling. Cells couple the exergonic reaction of ATP hydrolysis with endergonic reactions, allowing them to proceed. One example of energy coupling using ATP involves a transmembrane ion pump that is extremely important for cellular function. This sodium-potassium pump (Na+/K+ pump) drives sodium out of the cell and potassium into the cell (Figure $2$). A large percentage of a cell’s ATP is spent powering this pump, because cellular processes bring a great deal of sodium into the cell and potassium out of the cell. The pump works constantly to stabilize cellular concentrations of sodium and potassium. In order for the pump to turn one cycle (exporting three Na+ ions and importing two K+ ions), one molecule of ATP must be hydrolyzed. When ATP is hydrolyzed, its gamma phosphate doesn’t simply float away, but is actually transferred onto the pump protein. This process of a phosphate group binding to a molecule is called phosphorylation. As with most cases of ATP hydrolysis, a phosphate from ATP is transferred onto another molecule. In a phosphorylated state, the Na+/K+ pump has more free energy and is triggered to undergo a conformational change. This change allows it to release Na+ to the outside of the cell. It then binds extracellular K+, which, through another conformational change, causes the phosphate to detach from the pump. This release of phosphate triggers the K+ to be released to the inside of the cell. Essentially, the energy released from the hydrolysis of ATP is coupled with the energy required to power the pump and transport Na+ and K+ ions. ATP performs cellular work using this basic form of energy coupling through phosphorylation.
Art Connection
The hydrolysis of one ATP molecule releases 7.3 kcal/mol of energy (∆G = −7.3 kcal/mol of energy). If it takes 2.1 kcal/mol of energy to move one Na+ across the membrane (∆G = +2.1 kcal/mol of energy), how many sodium ions could be moved by the hydrolysis of one ATP molecule?
Often during cellular metabolic reactions, such as the synthesis and breakdown of nutrients, certain molecules must be altered slightly in their conformation to become substrates for the next step in the reaction series. One example is during the very first steps of cellular respiration, when a molecule of the sugar glucose is broken down in the process of glycolysis. In the first step of this process, ATP is required for the phosphorylation of glucose, creating a high-energy but unstable intermediate. This phosphorylation reaction powers a conformational change that allows the phosphorylated glucose molecule to be converted to the phosphorylated sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward. Here, the exergonic reaction of ATP hydrolysis is coupled with the endergonic reaction of converting glucose into a phosphorylated intermediate in the pathway. Once again, the energy released by breaking a phosphate bond within ATP was used for the phosphorylation of another molecule, creating an unstable intermediate and powering an important conformational change.
Link to Learning
See an interactive animation of the ATP-producing glycolysis process at this site.
Summary
ATP is the primary energy-supplying molecule for living cells. ATP is made up of a nucleotide, a five-carbon sugar, and three phosphate groups. The bonds that connect the phosphates (phosphoanhydride bonds) have high-energy content. The energy released from the hydrolysis of ATP into ADP + Pi is used to perform cellular work. Cells use ATP to perform work by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions. ATP donates its phosphate group to another molecule via a process known as phosphorylation. The phosphorylated molecule is at a higher-energy state and is less stable than its unphosphorylated form, and this added energy from the addition of the phosphate allows the molecule to undergo its endergonic reaction.
Art Connections
Figure $2$: The hydrolysis of one ATP molecule releases 7.3 kcal/mol of energy (∆G = −7.3 kcal/mol of energy). If it takes 2.1 kcal/mol of energy to move one Na+ across the membrane (∆G = +2.1 kcal/mol of energy), how many sodium ions could be moved by the hydrolysis of one ATP molecule?
Answer
Three sodium ions could be moved by the hydrolysis of one ATP molecule. The ∆G of the coupled reaction must be negative. Movement of three sodium ions across the membrane will take 6.3 kcal of energy (2.1 kcal × 3 Na+ ions = 6.3 kcal). Hydrolysis of ATP provides 7.3 kcal of energy, more than enough to power this reaction. Movement of four sodium ions across the membrane, however, would require 8.4 kcal of energy, more than one ATP molecule can provide.
Glossary
ATP
adenosine triphosphate, the cell’s energy currency
phosphoanhydride bond
bond that connects phosphates in an ATP molecule | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/06%3A_Energy_and_Metabolism/6.03%3A_ATP-_The_Energy_Currency_of_Cells/6.3.01%3A_Adenosine_Triphosphate.txt |
Skills to Develop
• Describe the role of enzymes in metabolic pathways
• Explain how enzymes function as molecular catalysts
• Discuss enzyme regulation by various factors
A substance that helps a chemical reaction to occur is a catalyst, and the special molecules that catalyze biochemical reactions are called enzymes. Almost all enzymes are proteins, made up of chains of amino acids, and they perform the critical task of lowering the activation energies of chemical reactions inside the cell. Enzymes do this by binding to the reactant molecules, and holding them in such a way as to make the chemical bond-breaking and bond-forming processes take place more readily. It is important to remember that enzymes don’t change the ∆G of a reaction. In other words, they don’t change whether a reaction is exergonic (spontaneous) or endergonic. This is because they don’t change the free energy of the reactants or products. They only reduce the activation energy required to reach the transition state (Figure \(1\)).
Enzyme Active Site and Substrate Specificity
The chemical reactants to which an enzyme binds are the enzyme’s substrates. There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single-reactant substrate is broken down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified, and leave the reaction as two products. The location within the enzyme where the substrate binds is called the enzyme’s active site. The active site is where the “action” happens, so to speak. Since enzymes are proteins, there is a unique combination of amino acid residues (also called side chains, or R groups) within the active site. Each residue is characterized by different properties. Residues can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of amino acid residues, their positions, sequences, structures, and properties, creates a very specific chemical environment within the active site. This specific environment is suited to bind, albeit briefly, to a specific chemical substrate (or substrates). Due to this jigsaw puzzle-like match between an enzyme and its substrates (which adapts to find the best fit between the transition state and the active site), enzymes are known for their specificity. The “best fit” results from the shape and the amino acid functional group’s attraction to the substrate. There is a specifically matched enzyme for each substrate and, thus, for each chemical reaction; however, there is flexibility as well.
The fact that active sites are so perfectly suited to provide specific environmental conditions also means that they are subject to influences by the local environment. It is true that increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site in such a way that they are less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature, a process that changes the natural properties of a substance. Likewise, the pH of the local environment can also affect enzyme function. Active site amino acid residues have their own acidic or basic properties that are optimal for catalysis. These residues are sensitive to changes in pH that can impair the way substrate molecules bind. Enzymes are suited to function best within a certain pH range, and, as with temperature, extreme pH values (acidic or basic) of the environment can cause enzymes to denature.
Induced Fit and Enzyme Function
For many years, scientists thought that enzyme-substrate binding took place in a simple “lock-and-key” fashion. This model asserted that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view called induced fit (Figure \(2\)). The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that confirms an ideal binding arrangement between the enzyme and the transition state of the substrate. This ideal binding maximizes the enzyme’s ability to catalyze its reaction.
When an enzyme binds its substrate, an enzyme-substrate complex is formed. This complex lowers the activation energy of the reaction and promotes its rapid progression in one of many ways. On a basic level, enzymes promote chemical reactions that involve more than one substrate by bringing the substrates together in an optimal orientation. The appropriate region (atoms and bonds) of one molecule is juxtaposed to the appropriate region of the other molecule with which it must react. Another way in which enzymes promote the reaction of their substrates is by creating an optimal environment within the active site for the reaction to occur. Certain chemical reactions might proceed best in a slightly acidic or non-polar environment. The chemical properties that emerge from the particular arrangement of amino acid residues within an active site create the perfect environment for an enzyme’s specific substrates to react.
You’ve learned that the activation energy required for many reactions includes the energy involved in manipulating or slightly contorting chemical bonds so that they can easily break and allow others to reform. Enzymatic action can aid this process. The enzyme-substrate complex can lower the activation energy by contorting substrate molecules in such a way as to facilitate bond-breaking, helping to reach the transition state. Finally, enzymes can also lower activation energies by taking part in the chemical reaction itself. The amino acid residues can provide certain ions or chemical groups that actually form covalent bonds with substrate molecules as a necessary step of the reaction process. In these cases, it is important to remember that the enzyme will always return to its original state at the completion of the reaction. One of the hallmark properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme is done catalyzing a reaction, it releases its product(s).
Control of Metabolism Through Enzyme Regulation
It would seem ideal to have a scenario in which all of the enzymes encoded in an organism’s genome existed in abundant supply and functioned optimally under all cellular conditions, in all cells, at all times. In reality, this is far from the case. A variety of mechanisms ensure that this does not happen. Cellular needs and conditions vary from cell to cell, and change within individual cells over time. The required enzymes and energetic demands of stomach cells are different from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so do the amounts and functionality of different enzymes.
Since the rates of biochemical reactions are controlled by activation energy, and enzymes lower and determine activation energies for chemical reactions, the relative amounts and functioning of the variety of enzymes within a cell ultimately determine which reactions will proceed and at which rates. This determination is tightly controlled. In certain cellular environments, enzyme activity is partly controlled by environmental factors, like pH and temperature. There are other mechanisms through which cells control the activity of enzymes and determine the rates at which various biochemical reactions will occur.
Regulation of Enzymes by Molecules
Enzymes can be regulated in ways that either promote or reduce their activity. There are many different kinds of molecules that inhibit or promote enzyme function, and various mechanisms exist for doing so. In some cases of enzyme inhibition, for example, an inhibitor molecule is similar enough to a substrate that it can bind to the active site and simply block the substrate from binding. When this happens, the enzyme is inhibited through competitive inhibition, because an inhibitor molecule competes with the substrate for active site binding (Figure \(3\)). On the other hand, in noncompetitive inhibition, an inhibitor molecule binds to the enzyme in a location other than an allosteric site and still manages to block substrate binding to the active site.
Some inhibitor molecules bind to enzymes in a location where their binding induces a conformational change that reduces the affinity of the enzyme for its substrate. This type of inhibition is called allosteric inhibition (Figure \(4\)). Most allosterically regulated enzymes are made up of more than one polypeptide, meaning that they have more than one protein subunit. When an allosteric inhibitor binds to an enzyme, all active sites on the protein subunits are changed slightly such that they bind their substrates with less efficiency. There are allosteric activators as well as inhibitors. Allosteric activators bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme’s active site(s) for its substrate(s).
Everyday Connection: Drug Discovery by Looking for Inhibitors of Key Enzymes in Specific Pathways
Enzymes are key components of metabolic pathways. Understanding how enzymes work and how they can be regulated is a key principle behind the development of many of the pharmaceutical drugs (Figure \(5\)) on the market today. Biologists working in this field collaborate with other scientists, usually chemists, to design drugs.
Consider statins for example—which is the name given to the class of drugs that reduces cholesterol levels. These compounds are essentially inhibitors of the enzyme HMG-CoA reductase. HMG-CoA reductase is the enzyme that synthesizes cholesterol from lipids in the body. By inhibiting this enzyme, the levels of cholesterol synthesized in the body can be reduced. Similarly, acetaminophen, popularly marketed under the brand name Tylenol, is an inhibitor of the enzyme cyclooxygenase. While it is effective in providing relief from fever and inflammation (pain), its mechanism of action is still not completely understood.
How are drugs developed? One of the first challenges in drug development is identifying the specific molecule that the drug is intended to target. In the case of statins, HMG-CoA reductase is the drug target. Drug targets are identified through painstaking research in the laboratory. Identifying the target alone is not sufficient; scientists also need to know how the target acts inside the cell and which reactions go awry in the case of disease. Once the target and the pathway are identified, then the actual process of drug design begins. During this stage, chemists and biologists work together to design and synthesize molecules that can either block or activate a particular reaction. However, this is only the beginning: both if and when a drug prototype is successful in performing its function, then it must undergo many tests from in vitro experiments to clinical trials before it can get FDA approval to be on the market.
Many enzymes don’t work optimally, or even at all, unless bound to other specific non-protein helper molecules, either temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds. Two types of helper molecules are cofactors and coenzymes. Binding to these molecules promotes optimal conformation and function for their respective enzymes. Cofactors are inorganic ions such as iron (Fe++) and magnesium (Mg++). One example of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules, DNA polymerase, which requires bound zinc ion (Zn++) to function. Coenzymes are organic helper molecules, with a basic atomic structure made up of carbon and hydrogen, which are required for enzyme action. The most common sources of coenzymes are dietary vitamins (Figure \(6\)). Some vitamins are precursors to coenzymes and others act directly as coenzymes. Vitamin C is a coenzyme for multiple enzymes that take part in building the important connective tissue component, collagen. An important step in the breakdown of glucose to yield energy is catalysis by a multi-enzyme complex called pyruvate dehydrogenase. Pyruvate dehydrogenase is a complex of several enzymes that actually requires one cofactor (a magnesium ion) and five different organic coenzymes to catalyze its specific chemical reaction. Therefore, enzyme function is, in part, regulated by an abundance of various cofactors and coenzymes, which are supplied primarily by the diets of most organisms.
Enzyme Compartmentalization
In eukaryotic cells, molecules such as enzymes are usually compartmentalized into different organelles. This allows for yet another level of regulation of enzyme activity. Enzymes required only for certain cellular processes can be housed separately along with their substrates, allowing for more efficient chemical reactions. Examples of this sort of enzyme regulation based on location and proximity include the enzymes involved in the latter stages of cellular respiration, which take place exclusively in the mitochondria, and the enzymes involved in the digestion of cellular debris and foreign materials, located within lysosomes.
Feedback Inhibition in Metabolic Pathways
Molecules can regulate enzyme function in many ways. A major question remains, however: What are these molecules and where do they come from? Some are cofactors and coenzymes, ions, and organic molecules, as you’ve learned. What other molecules in the cell provide enzymatic regulation, such as allosteric modulation, and competitive and noncompetitive inhibition? The answer is that a wide variety of molecules can perform these roles. Some of these molecules include pharmaceutical and non-pharmaceutical drugs, toxins, and poisons from the environment. Perhaps the most relevant sources of enzyme regulatory molecules, with respect to cellular metabolism, are the products of the cellular metabolic reactions themselves. In a most efficient and elegant way, cells have evolved to use the products of their own reactions for feedback inhibition of enzyme activity. Feedback inhibition involves the use of a reaction product to regulate its own further production (Figure \(7\)). The cell responds to the abundance of specific products by slowing down production during anabolic or catabolic reactions. Such reaction products may inhibit the enzymes that catalyzed their production through the mechanisms described above.
The production of both amino acids and nucleotides is controlled through feedback inhibition. Additionally, ATP is an allosteric regulator of some of the enzymes involved in the catabolic breakdown of sugar, the process that produces ATP. In this way, when ATP is abundant, the cell can prevent its further production. Remember that ATP is an unstable molecule that can spontaneously dissociate into ADP. If too much ATP were present in a cell, much of it would go to waste. On the other hand, ADP serves as a positive allosteric regulator (an allosteric activator) for some of the same enzymes that are inhibited by ATP. Thus, when relative levels of ADP are high compared to ATP, the cell is triggered to produce more ATP through the catabolism of sugar.
Summary
Enzymes are chemical catalysts that accelerate chemical reactions at physiological temperatures by lowering their activation energy. Enzymes are usually proteins consisting of one or more polypeptide chains. Enzymes have an active site that provides a unique chemical environment, made up of certain amino acid R groups (residues). This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, called substrates, into unstable intermediates called transition states. Enzymes and substrates are thought to bind with an induced fit, which means that enzymes undergo slight conformational adjustments upon substrate contact, leading to full, optimal binding. Enzymes bind to substrates and catalyze reactions in four different ways: bringing substrates together in an optimal orientation, compromising the bond structures of substrates so that bonds can be more easily broken, providing optimal environmental conditions for a reaction to occur, or participating directly in their chemical reaction by forming transient covalent bonds with the substrates.
Enzyme action must be regulated so that in a given cell at a given time, the desired reactions are being catalyzed and the undesired reactions are not. Enzymes are regulated by cellular conditions, such as temperature and pH. They are also regulated through their location within a cell, sometimes being compartmentalized so that they can only catalyze reactions under certain circumstances. Inhibition and activation of enzymes via other molecules are other important ways that enzymes are regulated. Inhibitors can act competitively, noncompetitively, or allosterically; noncompetitive inhibitors are usually allosteric. Activators can also enhance the function of enzymes allosterically. The most common method by which cells regulate the enzymes in metabolic pathways is through feedback inhibition. During feedback inhibition, the products of a metabolic pathway serve as inhibitors (usually allosteric) of one or more of the enzymes (usually the first committed enzyme of the pathway) involved in the pathway that produces them.
Glossary
active site
specific region of the enzyme to which the substrate binds
allosteric inhibition
inhibition by a binding event at a site different from the active site, which induces a conformational change and reduces the affinity of the enzyme for its substrate
coenzyme
small organic molecule, such as a vitamin or its derivative, which is required to enhance the activity of an enzyme
cofactor
inorganic ion, such as iron and magnesium ions, required for optimal regulation of enzyme activity
competitive inhibition
type of inhibition in which the inhibitor competes with the substrate molecule by binding to the active site of the enzyme
denature
process that changes the natural properties of a substance
feedback inhibition
effect of a product of a reaction sequence to decrease its further production by inhibiting the activity of the first enzyme in the pathway that produces it
induced fit
dynamic fit between the enzyme and its substrate, in which both components modify their structures to allow for ideal binding
substrate
molecule on which the enzyme acts
6.05: Metabolism- The Chemical Description of Cell Function
All living things must have an unceasing supply of energy and matter. The transformation of this energy and matter within the body is called metabolism.
Catabolism and Anabolism
Catabolism is destructive metabolism. Typically, in catabolism, larger organic molecules are broken down into smaller constituents. This usually occurs with the release of energy (usually as ATP). Anabolism is constructive metabolism. Typically, in anabolism, small precursor molecules are assembled into larger organic molecules. This always requires the input of energy (often as ATP).
Autotrophic vs. Heterotrophic Nutrition
Green plants, algae, and some bacteria are autotrophs ("self-feeders"). Most of them use the energy of sunlight to assemble inorganic precursors, chiefly carbon dioxide and water, into the array of organic macromolecules of which they are made. The process is photosynthesis. Photosynthesis makes the ATP needed for the anabolic reactions in the cell. All other organisms, including ourselves, are heterotrophs. We secure all our energy from organic molecules taken in from our surroundings ("food"). Although heterotrophs may feed partially (as most of us do) or exclusively on other heterotrophs, all the food molecules come ultimately from autotrophs. We may eat beef but the steer ate grass. Heterotrophs degrade some of the organic molecules they take in (catabolism) to make the ATP that they need to synthesize the others into the macromolecules of which they are made (anabolism).
How humans (and other animals) do it
Humans are heterotrophs. We are totally dependent on ingested preformed organic molecules to meet all our energy needs. We are also dependent on preformed organic molecules as the building blocks to meet our anabolic needs.
The steps for converting food to energy in animals:
1. Ingestion: taking food within the body (although as the figure shows, it is still topologically in the external world, not the internal).
2. Digestion: The enzyme-catalyzed hydrolysis of polysaccharides (e.g., starch) to sugars, proteins to amino acids, fats to fatty acids and glycerol, and nucleic acids to nucleotides.
3. Absorption into the body and transport to the cells.
4. Absorption into cells.
Within cells, these molecules are further degraded into still simpler molecules containing two to four carbon atoms. These fragments (acetyl-CoA for example) face one of two alternatives. They may proceed up various metabolic pathways and serve as the building blocks of, for example, sugars and fatty acids. From these will be assembled the macromolecules of the cell (e.g., polysaccharides, fats, proteins, and nucleic acids). Alternatively, the molecules in this pool of two- to four-carbon fragments may be still further degraded — ultimately to simple inorganic molecules such as carbon dioxide (CO2), H2O, and ammonia (NH3). This phase of catabolism releases large amounts of energy (in the form of ATP). One use to which this energy is put is to run the anabolic activities of the cell. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/06%3A_Energy_and_Metabolism/6.04%3A_Enzymes-_Biological_Catalysts.txt |
Learning Objectives
• Discuss the importance of cellular respiration
Introduction: Cellular Respiration
An electrical energy plant converts energy from one form to another form that can be more easily used. For example, geothermal energy plants start with underground thermal energy (heat) and transform it into electrical energy that will be transported to homes and factories.
Like a generating plant, living organisms must take in energy from their environment and convert it into to a form their cells can use. Organisms ingest large molecules, like carbohydrates, proteins, and fats, and convert them into smaller molecules like carbon dioxide and water. This process is called cellular respiration, a form of catabolism, and makes energy available for the cell to use. The energy released by cellular respiration is temporarily captured by the formation of adenosine triphosphate (ATP) within the cell. ATP is the principle form of stored energy used for cellular functions and is frequently referred to as the energy currency of the cell.
The nutrients broken down through cellular respiration lose electrons throughout the process and are said to be oxidized. When oxygen is used to help drive the oxidation of nutrients the process is called aerobic respiration. Aerobic respiration is common among the eukaryotes, including humans, and takes place mostly within the mitochondria. Respiration occurs within the cytoplasm of prokaryotes. Several prokaryotes and a few eukaryotes use an inorganic molecule other than oxygen to drive the oxidation of their nutrients in a process called anaerobic respiration. Electron acceptors for anaerobic respiration include nitrate, sulfate, carbon dioxide, and several metal ions.
The energy released during cellular respiration is then used in other biological processes. These processes build larger molecules that are essential to an organism’s survival, such as amino acids, DNA, and proteins. Because they synthesize new molecules, these processes are examples of anabolism.
Key Points
• Organisms ingest organic molecules like the carbohydrate glucose to obtain the energy needed for cellular functions.
• The energy in glucose can be extracted in a series of chemical reactions known as cellular respiration.
• Cellular respiration produces energy in the form of ATP, which is the universal energy currency for cells.
Key Terms
• aerobic respiration: the process of converting the biochemical energy in nutrients to ATP in the presence of oxygen
• adenosine triphosphate: a multifunctional nucleoside triphosphate used in cells as a coenzyme, often called the “molecular unit of energy currency” in intracellular energy transfer
• cellular respiration: the set of the metabolic reactions and processes that take place in the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP)
• catabolism: the breakdown of large molecules into smaller ones usually accompanied by the release of energy
7.1B: Electrons and Energy
Learning Objectives
• Describe the role played by electrons in energy production and storage
Electrons and Energy
The removal of an electron from a molecule via a process called oxidation results in a decrease in the potential energy stored in the oxidized compound. When oxidation occurs in the cell, the electron (sometimes as part of a hydrogen atom) does not remain un-bonded in the cytoplasm. Instead, the electron shifts to a second compound, reducing the second compound (oxidation of one species always occurs in tandem with reduction of another).
The shift of an electron from one compound to another removes some potential energy from the first compound (the oxidized compound) and increases the potential energy of the second compound (the reduced compound). The transfer of electrons between molecules via oxidation and reduction is important because most of the energy stored in atoms is in the form of high-energy electrons; it is this energy that is used to fuel cellular functions. The transfer of energy in the form of electrons allows the cell to transfer and use energy in an incremental fashion: in small packages rather than as a single, destructive burst.
Electron carriers
In living systems, a small class of molecules functions as electron shuttles: they bind and carry high-energy electrons between compounds in cellular pathways. The principal electron carriers we will consider are derived from the vitamin B group, which are derivatives of nucleotides. These compounds can be easily reduced (that is, they accept electrons) or oxidized (they lose electrons). Nicotinamide adenine dinucleotide (NAD) is derived from vitamin B3, niacin. NAD+ is the oxidized form of niacin; NADH is the reduced form after it has accepted two electrons and a proton (which together are the equivalent of a hydrogen atom with an extra electron). It is noteworthy that NAD+must accept two electrons at once; it cannot serve as a one-electron carrier.
NAD+ can accept electrons from an organic molecule according to the general equation:
RH (Reducing agent) + NAD+ (Oxidizing agent) → NADH (Reduced) + R (Oxidized)
When electrons are added to a compound, the compound is reduced. A compound that reduces another is called a reducing agent. In the above equation, RH is a reducing agent and NAD+ is reduced to NADH. When electrons are removed from a compound, the compound is oxidized. In the above equation, NAD+ is an oxidizing agent and RH is oxidized to R. The molecule NADH is critical for cellular respiration and other metabolic pathways.
Similarly, flavin adenine dinucleotide (FAD+) is derived from vitamin B2, also called riboflavin. Its reduced form is FADH2. A second variation of NAD, NADP, contains an extra phosphate group. Both NAD+ and FAD+ are extensively used in energy extraction from sugars, and NADP plays an important role in anabolic reactions and photosynthesis.
Key Points
• When electrons are added to a compound, the compound is reduced; a compound that reduces another is called a reducing agent.
• When electrons are removed from a compound, the compound is considered oxidized; a compound that oxidizes another is called an oxidizing agent.
• The transfer of energy in the form of electrons allows the cell to transfer and use energy in an incremental fashion.
• The principle electron carriers are NAD+ and NADH because they can be easily oxidized and reduced, respectively.
• NAD+ is the oxidized form of the niacin and NADH is the reduced form after it has accepted two electrons and a proton.
Key Terms
• oxidation: A reaction in which the atoms of an element lose electrons and the valence of the element increases.
• reduction: A reaction in which electrons are gained and valence is reduced; often by the removal of oxygen or the addition of hydrogen.
• nicotinamide adenine dinucleotide: (NAD) An organic coenzyme involved in biological oxidation and reduction reactions.
• electron shuttle: molecules that bind and carry high-energy electrons between compounds in cellular pathways | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/07%3A_How_Cells_Harvest_Energy/7.01%3A_Overview_of_Respiration/7.1A%3A_Transforming_Chemical_Energy.txt |
Learning Objectives
• Compare the two methods by which cells utilize ATP for energy.
ATP in Living Systems
A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would lead to excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store energy safely and release it for use as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell and can be used to fill any energy need of the cell.
ATP Structure and Function
The core of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and to a single phosphate group. Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine diphosphate (ADP); the addition of a third phosphate group forms adenosine triphosphate (ATP).
The addition of a phosphate group to a molecule requires energy. Phosphate groups are negatively charged and, thus, repel one another when they are arranged in a series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process called dephosphorylation, releases energy.
Energy from ATP
Hydrolysis is the process of breaking complex macromolecules apart. During hydrolysis, water is split, or lysed, and the resulting hydrogen atom (H+) and a hydroxyl group (OH) are added to the larger molecule. The hydrolysis of ATP produces ADP, together with an inorganic phosphate ion (Pi), and the release of free energy. To carry out life processes, ATP is continuously broken down into ADP, and, like a rechargeable battery, ADP is continuously regenerated into ATP by the reattachment of a third phosphate group. Water, which was broken down into its hydrogen atom and hydroxyl group during ATP hydrolysis, is regenerated when a third phosphate is added to the ADP molecule, reforming ATP.
Obviously, energy must be infused into the system to regenerate ATP. In nearly every living thing on earth, the energy comes from the metabolism of glucose. In this way, ATP is a direct link between the limited set of exergonic pathways of glucose catabolism and the multitude of endergonic pathways that power living cells.
Phosphorylation
When ATP is broken down by the removal of its terminal phosphate group, energy is released and can be used to do work by the cell. Often the released phosphate is directly transferred to another molecule, such as a protein, activating it. For example, ATP supplies the energy to move the contractile muscle proteins during the mechanical work of muscle contraction. Recall the active transport work of the sodium-potassium pump in cell membranes. Phosphorylation by ATP alters the structure of the integral protein that functions as the pump, changing its affinity for sodium and potassium. In this way, the cell performs work, using energy from ATP to pump ions against their electrochemical gradients.
Sometimes phosphorylation of an enzyme leads to its inhibition. For example, the pyruvate dehydrogenase (PDH) complex could be phosphorylated by pyruvate dehydrogenase kinase (PDHK). This reaction leads to inhibition of PDH and its inability to convert pyruvate into acetyl-CoA.
Energy from ATP hydrolysis
The energy from ATP can also be used to drive chemical reactions by coupling ATP hydrolysis with another reaction process in an enzyme. In many cellular chemical reactions, enzymes bind to several substrates or reactants to form a temporary intermediate complex that allow the substrates and reactants to more readily react with each other. In reactions where ATP is involved, ATP is one of the substrates and ADP is a product. During an endergonic chemical reaction, ATP forms an intermediate complex with the substrate and enzyme in the reaction. This intermediate complex allows the ATP to transfer its third phosphate group, with its energy, to the substrate, a process called phosphorylation. Phosphorylation refers to the addition of the phosphate (~P). When the intermediate complex breaks apart, the energy is used to modify the substrate and convert it into a product of the reaction. The ADP molecule and a free phosphate ion are released into the medium and are available for recycling through cell metabolism. This is illustrated by the following generic reaction:
A + enzyme + ATP→[ A enzyme −P ] B + enzyme + ADP + phosphate ion
Key Points
• Cells require a constant supply of energy to survive, but cannot store this energy as free energy as this would result in elevated temperatures and would destroy the cell.
• Cells store energy in the form of adenosine triphosphate, or ATP.
• Energy is released when the terminal phosphate group is removed from ATP.
• To utilize the energy stored as ATP, cells either couple ATP hydrolysis to an energetically unfavorable reaction to allow it to proceed or transfer one of the phosphate groups from ATP to a protein substrate, causing it to change conformations and hence energetic preference.
Key Terms
• phosphorylation: the addition of a phosphate group to a compound; often catalyzed by enzymes
• adenosine triphosphate: a multifunctional nucleoside triphosphate used in cells as a coenzyme, often called the “molecular unit of energy currency” in intracellular energy transfer
• phosphate: Any salt or ester of phosphoric acid
Contributions and Attributions
• adenosine triphosphate. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/adenosine%20triphosphate. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44430/latest...ol11448/latest. License: CC BY: Attribution
• cellular respiration. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/cellular%20respiration. License: CC BY-SA: Attribution-ShareAlike
• photosynthesis. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/photosynthesis. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Introduction. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44430/latest...e_07_00_01.jpg. License: CC BY: Attribution
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44431/latest...ol11448/latest. License: CC BY: Attribution
• reduction. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/reduction. License: CC BY-SA: Attribution-ShareAlike
• oxidation. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/oxidation. License: CC BY-SA: Attribution-ShareAlike
• Boundless. Provided by: Boundless Learning. Located at: www.boundless.com//biology/de...ectron-shuttle. License: CC BY-SA: Attribution-ShareAlike
• nicotinamide adenine dinucleotide. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/nicoti...e_dinucleotide. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Introduction. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44430/latest...e_07_00_01.jpg. License: CC BY: Attribution
• OpenStax College, Energy in Living Systems. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44431/latest...07_01_01ab.jpg. License: CC BY: Attribution
• adenosine triphosphate. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/adenosine%20triphosphate. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44431/latest...ol11448/latest. License: CC BY: Attribution
• phosphorylation. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/phosphorylation. License: CC BY-SA: Attribution-ShareAlike
• phosphate. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/phosphate. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Introduction. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44430/latest...e_07_00_01.jpg. License: CC BY: Attribution
• OpenStax College, Energy in Living Systems. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44431/latest...07_01_01ab.jpg. License: CC BY: Attribution
• OpenStax College, Energy in Living Systems. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44431/latest...e_07_01_03.jpg. License: CC BY: Attribution
• OpenStax College, Energy in Living Systems. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44431/latest...e_07_01_02.jpg. License: CC BY: Attribution | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/07%3A_How_Cells_Harvest_Energy/7.01%3A_Overview_of_Respiration/7.1C%3A_ATP_in_Metabolism.txt |
Skills to Develop
• Describe the overall result in terms of molecules produced in the breakdown of glucose by glycolysis
• Compare the output of glycolysis in terms of ATP molecules and NADH molecules produced
You have read that nearly all of the energy used by living cells comes to them in the bonds of the sugar, glucose. Glycolysis is the first step in the breakdown of glucose to extract energy for cellular metabolism. Nearly all living organisms carry out glycolysis as part of their metabolism. The process does not use oxygen and is therefore anaerobic. Glycolysis takes place in the cytoplasm of both prokaryotic and eukaryotic cells. Glucose enters heterotrophic cells in two ways. One method is through secondary active transport in which the transport takes place against the glucose concentration gradient. The other mechanism uses a group of integral proteins called GLUT proteins, also known as glucose transporter proteins. These transporters assist in the facilitated diffusion of glucose.
Glycolysis begins with the six carbon ring-shaped structure of a single glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate. Glycolysis consists of two distinct phases. The first part of the glycolysis pathway traps the glucose molecule in the cell and uses energy to modify it so that the six-carbon sugar molecule can be split evenly into the two three-carbon molecules. The second part of glycolysis extracts energy from the molecules and stores it in the form of ATP and NADH, the reduced form of NAD.
First Half of Glycolysis (Energy-Requiring Steps)
Step 1. The first step in glycolysis (Figure \(1\)) is catalyzed by hexokinase, an enzyme with broad specificity that catalyzes the phosphorylation of six-carbon sugars. Hexokinase phosphorylates glucose using ATP as the source of the phosphate, producing glucose-6-phosphate, a more reactive form of glucose. This reaction prevents the phosphorylated glucose molecule from continuing to interact with the GLUT proteins, and it can no longer leave the cell because the negatively charged phosphate will not allow it to cross the hydrophobic interior of the plasma membrane.
Step 2. In the second step of glycolysis, an isomerase converts glucose-6-phosphate into one of its isomers, fructose-6-phosphate. An isomerase is an enzyme that catalyzes the conversion of a molecule into one of its isomers. (This change from phosphoglucose to phosphofructose allows the eventual split of the sugar into two three-carbon molecules.).
Step 3. The third step is the phosphorylation of fructose-6-phosphate, catalyzed by the enzyme phosphofructokinase. A second ATP molecule donates a high-energy phosphate to fructose-6-phosphate, producing fructose-1,6-bisphosphate. In this pathway, phosphofructokinase is a rate-limiting enzyme. It is active when the concentration of ADP is high; it is less active when ADP levels are low and the concentration of ATP is high. Thus, if there is “sufficient” ATP in the system, the pathway slows down. This is a type of end product inhibition, since ATP is the end product of glucose catabolism.
Step 4. The newly added high-energy phosphates further destabilize fructose-1,6-bisphosphate. The fourth step in glycolysis employs an enzyme, aldolase, to cleave 1,6-bisphosphate into two three-carbon isomers: dihydroxyacetone-phosphate and glyceraldehyde-3-phosphate.
Step 5. In the fifth step, an isomerase transforms the dihydroxyacetone-phosphate into its isomer, glyceraldehyde-3-phosphate. Thus, the pathway will continue with two molecules of a single isomer. At this point in the pathway, there is a net investment of energy from two ATP molecules in the breakdown of one glucose molecule.
Second Half of Glycolysis (Energy-Releasing Steps)
So far, glycolysis has cost the cell two ATP molecules and produced two small, three-carbon sugar molecules. Both of these molecules will proceed through the second half of the pathway, and sufficient energy will be extracted to pay back the two ATP molecules used as an initial investment and produce a profit for the cell of two additional ATP molecules and two even higher-energy NADH molecules.
Step 6. The sixth step in glycolysis (Figure \(2\)) oxidizes the sugar (glyceraldehyde-3-phosphate), extracting high-energy electrons, which are picked up by the electron carrier NAD+, producing NADH. The sugar is then phosphorylated by the addition of a second phosphate group, producing 1,3-bisphosphoglycerate. Note that the second phosphate group does not require another ATP molecule.
Here again is a potential limiting factor for this pathway. The continuation of the reaction depends upon the availability of the oxidized form of the electron carrier, NAD+. Thus, NADH must be continuously oxidized back into NAD+ in order to keep this step going. If NAD+ is not available, the second half of glycolysis slows down or stops. If oxygen is available in the system, the NADH will be oxidized readily, though indirectly, and the high-energy electrons from the hydrogen released in this process will be used to produce ATP. In an environment without oxygen, an alternate pathway (fermentation) can provide the oxidation of NADH to NAD+.
Step 7. In the seventh step, catalyzed by phosphoglycerate kinase (an enzyme named for the reverse reaction), 1,3-bisphosphoglycerate donates a high-energy phosphate to ADP, forming one molecule of ATP. (This is an example of substrate-level phosphorylation.) A carbonyl group on the 1,3-bisphosphoglycerate is oxidized to a carboxyl group, and 3-phosphoglycerate is formed.
Step 8. In the eighth step, the remaining phosphate group in 3-phosphoglycerate moves from the third carbon to the second carbon, producing 2-phosphoglycerate (an isomer of 3-phosphoglycerate). The enzyme catalyzing this step is a mutase (isomerase).
Step 9. Enolase catalyzes the ninth step. This enzyme causes 2-phosphoglycerate to lose water from its structure; this is a dehydration reaction, resulting in the formation of a double bond that increases the potential energy in the remaining phosphate bond and produces phosphoenolpyruvate (PEP).
Step 10. The last step in glycolysis is catalyzed by the enzyme pyruvate kinase (the enzyme in this case is named for the reverse reaction of pyruvate’s conversion into PEP) and results in the production of a second ATP molecule by substrate-level phosphorylation and the compound pyruvic acid (or its salt form, pyruvate). Many enzymes in enzymatic pathways are named for the reverse reactions, since the enzyme can catalyze both forward and reverse reactions (these may have been described initially by the reverse reaction that takes place in vitro, under non-physiological conditions).
Link to Learning
Gain a better understanding of the breakdown of glucose by glycolysis by visiting this site to see the process in action.
Outcomes of Glycolysis
Glycolysis starts with glucose and ends with two pyruvate molecules, a total of four ATP molecules and two molecules of NADH. Two ATP molecules were used in the first half of the pathway to prepare the six-carbon ring for cleavage, so the cell has a net gain of two ATP molecules and 2 NADH molecules for its use. If the cell cannot catabolize the pyruvate molecules further, it will harvest only two ATP molecules from one molecule of glucose. Mature mammalian red blood cells are not capable of aerobic respiration—the process in which organisms convert energy in the presence of oxygen—and glycolysis is their sole source of ATP. If glycolysis is interrupted, these cells lose their ability to maintain their sodium-potassium pumps, and eventually, they die.
The last step in glycolysis will not occur if pyruvate kinase, the enzyme that catalyzes the formation of pyruvate, is not available in sufficient quantities. In this situation, the entire glycolysis pathway will proceed, but only two ATP molecules will be made in the second half. Thus, pyruvate kinase is a rate-limiting enzyme for glycolysis.
Summary
Glycolysis is the first pathway used in the breakdown of glucose to extract energy. It was probably one of the earliest metabolic pathways to evolve and is used by nearly all of the organisms on earth. Glycolysis consists of two parts: The first part prepares the six-carbon ring of glucose for cleavage into two three-carbon sugars. ATP is invested in the process during this half to energize the separation. The second half of glycolysis extracts ATP and high-energy electrons from hydrogen atoms and attaches them to NAD+. Two ATP molecules are invested in the first half and four ATP molecules are formed by substrate phosphorylation during the second half. This produces a net gain of two ATP and two NADH molecules for the cell.
Glossary
aerobic respiration
process in which organisms convert energy in the presence of oxygen
anaerobic
process that does not use oxygen
glycolysis
process of breaking glucose into two three-carbon molecules with the production of ATP and NADH
isomerase
enzyme that converts a molecule into its isomer
pyruvate
three-carbon sugar that can be decarboxylated and oxidized to make acetyl CoA, which enters the citric acid cycle under aerobic conditions; the end product of glycolysis | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/07%3A_How_Cells_Harvest_Energy/7.02%3A_Glycolysis-_Splitting_Glucose/7.2.01%3A_Glycolysis.txt |
Even exergonic, energy-releasing reactions require a small amount of activation energy to proceed. However, consider endergonic reactions, which require much more energy input because their products have more free energy than their reactants. Within the cell, where does energy to power such reactions come from? The answer lies with an energy-supplying molecule called adenosine triphosphate, or ATP. ATP is a small, relatively simple molecule, but within its bonds contains the potential for a quick burst of energy that can be harnessed to perform cellular work. This molecule can be thought of as the primary energy currency of cells in the same way that money is the currency that people exchange for things they need. ATP is used to power the majority of energy-requiring cellular reactions.
ATP in Living Systems
A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would denature enzymes and other proteins, and thus destroy the cell. Rather, a cell must be able to store energy safely and release it for use only as needed. Living cells accomplish this using ATP, which can be used to fill any energy need of the cell. How? It functions as a rechargeable battery.
When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. This energy is used to do work by the cell, usually by the binding of the released phosphate to another molecule, thus activating it. For example, in the mechanical work of muscle contraction, ATP supplies energy to move the contractile muscle proteins.
ATP Structure and Function
At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to both a ribose molecule and a single phosphate group (Figure \(1\)). Ribose is a five-carbon sugar found in RNA and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in adenosine diphosphate (ADP); the addition of a third phosphate group forms adenosine triphosphate (ATP).
The addition of a phosphate group to a molecule requires a high amount of energy and results in a high-energy bond. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process called hydrolysis, releases energy.
Glycolysis
You have read that nearly all of the energy used by living things comes to them in the bonds of the sugar, glucose. Glycolysis is the first step in the breakdown of glucose to extract energy for cell metabolism. Many living organisms carry out glycolysis as part of their metabolism. Glycolysis takes place in the cytoplasm of most prokaryotic and all eukaryotic cells.
Glycolysis begins with the six-carbon, ring-shaped structure of a single glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate. Glycolysis consists of two distinct phases. In the first part of the glycolysis pathway, energy is used to make adjustments so that the six-carbon sugar molecule can be split evenly into two three-carbon pyruvate molecules. In the second part of glycolysis, ATP and nicotinamide-adenine dinucleotide (NADH) are produced (Figure \(2\)).
If the cell cannot catabolize the pyruvate molecules further, it will harvest only two ATP molecules from one molecule of glucose. For example, mature mammalian red blood cells are only capable of glycolysis, which is their sole source of ATP. If glycolysis is interrupted, these cells would eventually die.
Summary
ATP functions as the energy currency for cells. It allows cells to store energy briefly and transport it within itself to support endergonic chemical reactions. The structure of ATP is that of an RNA nucleotide with three phosphate groups attached. As ATP is used for energy, a phosphate group is detached, and ADP is produced. Energy derived from glucose catabolism is used to recharge ADP into ATP.
Glycolysis is the first pathway used in the breakdown of glucose to extract energy. Because it is used by nearly all organisms on earth, it must have evolved early in the history of life. Glycolysis consists of two parts: The first part prepares the six-carbon ring of glucose for separation into two three-carbon sugars. Energy from ATP is invested into the molecule during this step to energize the separation. The second half of glycolysis extracts ATP and high-energy electrons from hydrogen atoms and attaches them to NAD+. Two ATP molecules are invested in the first half and four ATP molecules are formed during the second half. This produces a net gain of two ATP molecules per molecule of glucose for the cell.
Glossary
ATP
(also, adenosine triphosphate) the cell’s energy currency
glycolysis
the process of breaking glucose into two three-carbon molecules with the production of ATP and NADH
7.03: The Oxidation of Pyruvate Produces Acetyl-CoA
Learning Objectives
• Explain why cells break down pyruvate
Breakdown of Pyruvate
In order for pyruvate, the product of glycolysis, to enter the next pathway, it must undergo several changes to become acetyl Coenzyme A (acetyl CoA). Acetyl CoA is a molecule that is further converted to oxaloacetate, which enters the citric acid cycle (Krebs cycle). The conversion of pyruvate to acetyl CoA is a three-step process.
Step 1. A carboxyl group is removed from pyruvate, releasing a molecule of carbon dioxide into the surrounding medium. (Note: carbon dioxide is one carbon attached to two oxygen atoms and is one of the major end products of cellular respiration. ) The result of this step is a two-carbon hydroxyethyl group bound to the enzyme pyruvate dehydrogenase; the lost carbon dioxide is the first of the six carbons from the original glucose molecule to be removed. This step proceeds twice for every molecule of glucose metabolized (remember: there are two pyruvate molecules produced at the end of glycolysis); thus, two of the six carbons will have been removed at the end of both of these steps.
Step 2. The hydroxyethyl group is oxidized to an acetyl group, and the electrons are picked up by NAD+, forming NADH (the reduced form of NAD+). The high- energy electrons from NADH will be used later by the cell to generate ATP for energy.
Step 3. The enzyme-bound acetyl group is transferred to CoA, producing a molecule of acetyl CoA. This molecule of acetyl CoA is then further converted to be used in the next pathway of metabolism, the citric acid cycle.
Key Points
• In the conversion of pyruvate to acetyl CoA, each pyruvate molecule loses one carbon atom with the release of carbon dioxide.
• During the breakdown of pyruvate, electrons are transferred to NAD+ to produce NADH, which will be used by the cell to produce ATP.
• In the final step of the breakdown of pyruvate, an acetyl group is transferred to Coenzyme A to produce acetyl CoA.
Key Terms
• acetyl CoA: a molecule that conveys the carbon atoms from glycolysis (pyruvate) to the citric acid cycle to be oxidized for energy production | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/07%3A_How_Cells_Harvest_Energy/7.02%3A_Glycolysis-_Splitting_Glucose/7.2.02%3A_Glycolysis.txt |
Learning Objectives
• List the steps of the Krebs (or citric acid) cycle
Citric Acid Cycle (Krebs Cycle)
Like the conversion of pyruvate to acetyl CoA, the citric acid cycle takes place in the matrix of the mitochondria. Almost all of the enzymes of the citric acid cycle are soluble, with the single exception of the enzyme succinate dehydrogenase, which is embedded in the inner membrane of the mitochondrion. Unlike glycolysis, the citric acid cycle is a closed loop: the last part of the pathway regenerates the compound used in the first step. The eight steps of the cycle are a series of redox, dehydration, hydration, and decarboxylation reactions that produce two carbon dioxide molecules, one GTP/ATP, and reduced forms of NADH and FADH2. This is considered an aerobic pathway because the NADH and FADH2 produced must transfer their electrons to the next pathway in the system, which will use oxygen. If this transfer does not occur, the oxidation steps of the citric acid cycle also do not occur. Note that the citric acid cycle produces very little ATP directly and does not directly consume oxygen.
Steps in the Citric Acid Cycle
Step 1. The first step is a condensation step, combining the two-carbon acetyl group (from acetyl CoA) with a four-carbon oxaloacetate molecule to form a six-carbon molecule of citrate. CoA is bound to a sulfhydryl group (-SH) and diffuses away to eventually combine with another acetyl group. This step is irreversible because it is highly exergonic. The rate of this reaction is controlled by negative feedback and the amount of ATP available. If ATP levels increase, the rate of this reaction decreases. If ATP is in short supply, the rate increases.
Step 2. Citrate loses one water molecule and gains another as citrate is converted into its isomer, isocitrate.
Steps 3 and 4. In step three, isocitrate is oxidized, producing a five-carbon molecule, α-ketoglutarate, together with a molecule of CO2and two electrons, which reduce NAD+ to NADH. This step is also regulated by negative feedback from ATP and NADH and by a positive effect of ADP. Steps three and four are both oxidation and decarboxylation steps, which release electrons that reduce NAD+ to NADH and release carboxyl groups that form CO2 molecules. α-Ketoglutarate is the product of step three, and a succinyl group is the product of step four. CoA binds the succinyl group to form succinyl CoA. The enzyme that catalyzes step four is regulated by feedback inhibition of ATP, succinyl CoA, and NADH.
Step 5. A phosphate group is substituted for coenzyme A, and a high- energy bond is formed. This energy is used in substrate-level phosphorylation (during the conversion of the succinyl group to succinate) to form either guanine triphosphate (GTP) or ATP. There are two forms of the enzyme, called isoenzymes, for this step, depending upon the type of animal tissue in which they are found. One form is found in tissues that use large amounts of ATP, such as heart and skeletal muscle. This form produces ATP. The second form of the enzyme is found in tissues that have a high number of anabolic pathways, such as liver. This form produces GTP. GTP is energetically equivalent to ATP; however, its use is more restricted. In particular, protein synthesis primarily uses GTP.
Step 6. Step six is a dehydration process that converts succinate into fumarate. Two hydrogen atoms are transferred to FAD, producing FADH2. The energy contained in the electrons of these atoms is insufficient to reduce NAD+ but adequate to reduce FAD. Unlike NADH, this carrier remains attached to the enzyme and transfers the electrons to the electron transport chain directly. This process is made possible by the localization of the enzyme catalyzing this step inside the inner membrane of the mitochondrion.
Step 7. Water is added to fumarate during step seven, and malate is produced. The last step in the citric acid cycle regenerates oxaloacetate by oxidizing malate. Another molecule of NADH is produced.
Products of the Citric Acid Cycle
Two carbon atoms come into the citric acid cycle from each acetyl group, representing four out of the six carbons of one glucose molecule. Two carbon dioxide molecules are released on each turn of the cycle; however, these do not necessarily contain the most recently-added carbon atoms. The two acetyl carbon atoms will eventually be released on later turns of the cycle; thus, all six carbon atoms from the original glucose molecule are eventually incorporated into carbon dioxide. Each turn of the cycle forms three NADH molecules and one FADH2 molecule. These carriers will connect with the last portion of aerobic respiration to produce ATP molecules. One GTP or ATP is also made in each cycle. Several of the intermediate compounds in the citric acid cycle can be used in synthesizing non-essential amino acids; therefore, the cycle is amphibolic (both catabolic and anabolic).
Key Points
• The four-carbon molecule, oxaloacetate, that began the cycle is regenerated after the eight steps of the citric acid cycle.
• The eight steps of the citric acid cycle are a series of redox, dehydration, hydration, and decarboxylation reactions.
• Each turn of the cycle forms one GTP or ATP as well as three NADH molecules and one FADH2 molecule, which will be used in further steps of cellular respiration to produce ATP for the cell.
Key Terms
• citric acid cycle: a series of chemical reactions used by all aerobic organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats, and proteins into carbon dioxide
• Krebs cycle: a series of enzymatic reactions that occurs in all aerobic organisms; it involves the oxidative metabolism of acetyl units and serves as the main source of cellular energy
• mitochondria: in cell biology, a mitochondrion (plural mitochondria) is a membrane-enclosed organelle, often described as “cellular power plants” because they generate most of the ATP
Contributions and Attributions
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44433/latest...ol11448/latest. License: CC BY: Attribution
• acetyl CoA. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/acetyl%20CoA. License: CC BY-SA: Attribution-ShareAlike
• 09 10PyruvateToAcetylCoA-L. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/Fi...cetylCoA-L.jpg. License: CC BY: Attribution
• Krebs cycle. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/Krebs_cycle. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Biology. October 29, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44433/latest...ol11448/latest. License: CC BY: Attribution
• Boundless. Provided by: Boundless Learning. Located at: www.boundless.com//biology/de...tion/tca-cycle. License: CC BY-SA: Attribution-ShareAlike
• Boundless. Provided by: Boundless Learning. Located at: www.boundless.com//biology/de...n/oxaloacetate. License: CC BY-SA: Attribution-ShareAlike
• 09 10PyruvateToAcetylCoA-L. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/Fi...cetylCoA-L.jpg. License: CC BY: Attribution
• OpenStax College, Oxidation of Pyruvate and the Citric Acid Cycle. November 10, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44433/latest/. License: CC BY: Attribution
• Krebs cycle. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/Krebs_cycle. License: CC BY-SA: Attribution-ShareAlike
• OpenStax College, Biology. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44433/latest...ol11448/latest. License: CC BY: Attribution
• mitochondria. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/mitochondria. License: CC BY-SA: Attribution-ShareAlike
• citric acid cycle. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/citric%20acid%20cycle. License: CC BY-SA: Attribution-ShareAlike
• 09 10PyruvateToAcetylCoA-L. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/Fi...cetylCoA-L.jpg. License: CC BY: Attribution
• OpenStax College, Oxidation of Pyruvate and the Citric Acid Cycle. November 10, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44433/latest/. License: CC BY: Attribution
• OpenStax College, Oxidation of Pyruvate and the Citric Acid Cycle. October 16, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44433/latest...e_07_03_02.jpg. License: CC BY: Attribution | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/07%3A_How_Cells_Harvest_Energy/7.04%3A_The_Citric_Acid_Cycle.txt |
The electron transport chain uses the electrons from electron carriers to create a chemical gradient that can be used to power oxidative phosphorylation.
Learning Objectives
• Describe how electrons move through the electron transport chain
Key Points
• Oxidative phosphorylation is the metabolic pathway in which electrons are transferred from electron donors to electron acceptors in redox reactions; this series of reactions releases energy which is used to form ATP.
• There are four protein complexes (labeled complex I-IV) in the electron transport chain, which are involved in moving electrons from NADH and FADH2 to molecular oxygen.
• Complex I establishes the hydrogen ion gradient by pumping four hydrogen ions across the membrane from the matrix into the intermembrane space.
• Complex II receives FADH2, which bypasses complex I, and delivers electrons directly to the electron transport chain.
• Ubiquinone (Q) accepts the electrons from both complex I and complex II and delivers them to complex III.
• Complex III pumps protons through the membrane and passes its electrons to cytochrome c for transport to the fourth complex of proteins and enzymes.
• Complex IV reduces oxygen; the reduced oxygen then picks up two hydrogen ions from the surrounding medium to make water.
Key Terms
• prosthetic group: The non-protein component of a conjugated protein.
• complex: A structure consisting of a central atom, molecule, or protein weakly connected to surrounding atoms, molecules, or proteins.
• ubiquinone: A lipid soluble substance that is a component of the electron transport chain and accepts electrons from complexes I and II.
Oxidative phosphorylation is a highly efficient method of producing large amounts of ATP, the basic unit of energy for metabolic processes. During this process electrons are exchanged between molecules, which creates a chemical gradient that allows for the production of ATP. The most vital part of this process is the electron transport chain, which produces more ATP than any other part of cellular respiration.
Electron Transport Chain
The electron transport chain is the final component of aerobic respiration and is the only part of glucose metabolism that uses atmospheric oxygen. Electron transport is a series of redox reactions that resemble a relay race. Electrons are passed rapidly from one component to the next to the endpoint of the chain, where the electrons reduce molecular oxygen, producing water. This requirement for oxygen in the final stages of the chain can be seen in the overall equation for cellular respiration, which requires both glucose and oxygen.
A complex is a structure consisting of a central atom, molecule, or protein weakly connected to surrounding atoms, molecules, or proteins. The electron transport chain is an aggregation of four of these complexes (labeled I through IV), together with associated mobile electron carriers. The electron transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes and the plasma membrane of prokaryotes.
Complex I
To start, two electrons are carried to the first complex aboard NADH. Complex I is composed of flavin mononucleotide (FMN) and an enzyme containing iron-sulfur (Fe-S). FMN, which is derived from vitamin B2 (also called riboflavin), is one of several prosthetic groups or co-factors in the electron transport chain. A prosthetic group is a non-protein molecule required for the activity of a protein. Prosthetic groups can be organic or inorganic and are non-peptide molecules bound to a protein that facilitate its function.
Prosthetic groups include co-enzymes, which are the prosthetic groups of enzymes. The enzyme in complex I is NADH dehydrogenase, a very large protein containing 45 amino acid chains. Complex I can pump four hydrogen ions across the membrane from the matrix into the intermembrane space; it is in this way that the hydrogen ion gradient is established and maintained between the two compartments separated by the inner mitochondrial membrane.
Q and Complex II
Complex II directly receives FADH2, which does not pass through complex I. The compound connecting the first and second complexes to the third is ubiquinone (Q). The Q molecule is lipid soluble and freely moves through the hydrophobic core of the membrane. Once it is reduced to QH2, ubiquinone delivers its electrons to the next complex in the electron transport chain. Q receives the electrons derived from NADH from complex I and the electrons derived from FADH2 from complex II, including succinate dehydrogenase. This enzyme and FADH2 form a small complex that delivers electrons directly to the electron transport chain, bypassing the first complex. Since these electrons bypass, and thus do not energize, the proton pump in the first complex, fewer ATP molecules are made from the FADH2 electrons. The number of ATP molecules ultimately obtained is directly proportional to the number of protons pumped across the inner mitochondrial membrane.
Complex III
The third complex is composed of cytochrome b, another Fe-S protein, Rieske center (2Fe-2S center), and cytochrome c proteins; this complex is also called cytochrome oxidoreductase. Cytochrome proteins have a prosthetic heme group. The heme molecule is similar to the heme in hemoglobin, but it carries electrons, not oxygen. As a result, the iron ion at its core is reduced and oxidized as it passes the electrons, fluctuating between different oxidation states: Fe2+ (reduced) and Fe3+ (oxidized). The heme molecules in the cytochromes have slightly different characteristics due to the effects of the different proteins binding them, which makes each complex. Complex III pumps protons through the membrane and passes its electrons to cytochrome c for transport to the fourth complex of proteins and enzymes. Cytochrome c is the acceptor of electrons from Q; however, whereas Q carries pairs of electrons, cytochrome c can accept only one at a time.
Complex IV
The fourth complex is composed of cytochrome proteins c, a, and a3. This complex contains two heme groups (one in each of the cytochromes a and a3) and three copper ions (a pair of CuA and one CuB in cytochrome a3). The cytochromes hold an oxygen molecule very tightly between the iron and copper ions until the oxygen is completely reduced. The reduced oxygen then picks up two hydrogen ions from the surrounding medium to produce water (H2O). The removal of the hydrogen ions from the system also contributes to the ion gradient used in the process of chemiosmosis.
7.5B: Chemiosmosis and Oxidative Phosphorylation
Learning Objectives
• Describe how the energy obtained from the electron transport chain powers chemiosmosis and discuss the role of hydrogen ions in the synthesis of ATP
During chemiosmosis, electron carriers like NADH and FADH donate electrons to the electron transport chain. The electrons cause conformation changes in the shapes of the proteins to pump H+ across a selectively permeable cell membrane. The uneven distribution of H+ ions across the membrane establishes both concentration and electrical gradients (thus, an electrochemical gradient) owing to the hydrogen ions’ positive charge and their aggregation on one side of the membrane.
If the membrane were open to diffusion by the hydrogen ions, the ions would tend to spontaneously diffuse back across into the matrix, driven by their electrochemical gradient. However, many ions cannot diffuse through the nonpolar regions of phospholipid membranes without the aid of ion channels. Similarly, hydrogen ions in the matrix space can only pass through the inner mitochondrial membrane through a membrane protein called ATP synthase. This protein acts as a tiny generator turned by the force of the hydrogen ions diffusing through it, down their electrochemical gradient. The turning of this molecular machine harnesses the potential energy stored in the hydrogen ion gradient to add a phosphate to ADP, forming ATP.
Chemiosmosis is used to generate 90 percent of the ATP made during aerobic glucose catabolism. The production of ATP using the process of chemiosmosis in mitochondria is called oxidative phosphorylation. It is also the method used in the light reactions of photosynthesis to harness the energy of sunlight in the process of photophosphorylation. The overall result of these reactions is the production of ATP from the energy of the electrons removed from hydrogen atoms. These atoms were originally part of a glucose molecule. At the end of the pathway, the electrons are used to reduce an oxygen molecule to oxygen ions. The extra electrons on the oxygen attract hydrogen ions (protons) from the surrounding medium and water is formed.
Key Points
• During chemiosmosis, the free energy from the series of reactions that make up the electron transport chain is used to pump hydrogen ions across the membrane, establishing an electrochemical gradient.
• Hydrogen ions in the matrix space can only pass through the inner mitochondrial membrane through a membrane protein called ATP synthase.
• As protons move through ATP synthase, ADP is turned into ATP.
• The production of ATP using the process of chemiosmosis in mitochondria is called oxidative phosphorylation.
Key Terms
• ATP synthase: An important enzyme that provides energy for the cell to use through the synthesis of adenosine triphosphate (ATP).
• oxidative phosphorylation: A metabolic pathway that uses energy released by the oxidation of nutrients to produce adenosine triphosphate (ATP).
• chemiosmosis: The movement of ions across a selectively permeable membrane, down their electrochemical gradient. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/07%3A_How_Cells_Harvest_Energy/7.05%3A_Electron_Transport_Chain_and_Chemiosmosis/7.5A%3A_Electron_Transport_Chain.txt |
ese atoms were originally part of a glucose molecule. At the end of the pathway, the electrons are used to reduce an oxygen molecule to oxygen ions. The extra electrons on the oxygen attract hydrogen ions (protons) from the surrounding medium and water is formed.
ATP Yield
The amount of energy (as ATP) gained from glucose catabolism varies across species and depends on other related cellular processes.
LEARNING OBJECTIVES
Describe the origins of variability in the amount of ATP that is produced per molecule of glucose consumed
Key Points
• While glucose catabolism always produces energy, the amount of energy (in terms of ATP equivalents) produced can vary, especially across different species.
• The number of hydrogen ions the electron transport chain complexes can pump through the membrane varies between species.
• NAD+ provides more ATP than FAD+ in the electron transport chain and can lead to variance in ATP production.
• The use of intermediates from glucose catabolism in other biosynthetic pathways, such as amino acid synthesis, can lower the yield of ATP.
Key Terms
• catabolism: Destructive metabolism, usually including the release of energy and breakdown of materials.
ATP Yield
In a eukaryotic cell, the process of cellular respiration can metabolize one molecule of glucose into 30 to 32 ATP. The process of glycolysis only produces two ATP, while all the rest are produced during the electron transport chain. Clearly, the electron transport chain is vastly more efficient, but it can only be carried out in the presence of oxygen.
The number of ATP molecules generated via the catabolism of glucose can vary substantially. For example, the number of hydrogen ions the electron transport chain complexes can pump through the membrane varies between species. Another source of variance occurs during the shuttle of electrons across the membranes of the mitochondria. The NADH generated from glycolysis cannot easily enter mitochondria. Thus, electrons are picked up on the inside of mitochondria by either NAD+ or FAD+. These FAD+ molecules can transport fewer ions; consequently, fewer ATP molecules are generated when FAD+ acts as a carrier. NAD+ is used as the electron transporter in the liver, and FAD+ acts in the brain.
Another factor that affects the yield of ATP molecules generated from glucose is the fact that intermediate compounds in these pathways are used for other purposes. Glucose catabolism connects with the pathways that build or break down all other biochemical compounds in cells, but the result is not always ideal. For example, sugars other than glucose are fed into the glycolytic pathway for energy extraction. Moreover, the five-carbon sugars that form nucleic acids are made from intermediates in glycolysis. Certain nonessential amino acids can be made from intermediates of both glycolysis and the citric acid cycle. Lipids, such as cholesterol and triglycerides, are also made from intermediates in these pathways, and both amino acids and triglycerides are broken down for energy through these pathways. Overall, in living systems, these pathways of glucose catabolism extract about 34 percent of the energy contained in glucose.
7.7.01: Connections of Carbohydrate Protein and Lipid Metabolic Pathways
Skills to Develop
• Discuss the ways in which carbohydrate metabolic pathways, glycolysis, and the citric acid cycle interrelate with protein and lipid metabolic pathways
• Explain why metabolic pathways are not considered closed systems
You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume more than glucose for food. How does a turkey sandwich end up as ATP in your cells? This happens because all of the catabolic pathways for carbohydrates, proteins, and lipids eventually connect into glycolysis and the citric acid cycle pathways (see Figure \(2\)). Metabolic pathways should be thought of as porous—that is, substances enter from other pathways, and intermediates leave for other pathways. These pathways are not closed systems. Many of the substrates, intermediates, and products in a particular pathway are reactants in other pathways.
Connections of Other Sugars to Glucose Metabolism
Glycogen, a polymer of glucose, is an energy storage molecule in animals. When there is adequate ATP present, excess glucose is shunted into glycogen for storage. Glycogen is made and stored in both liver and muscle. The glycogen will be hydrolyzed into glucose monomers (G-1-P) if blood sugar levels drop. The presence of glycogen as a source of glucose allows ATP to be produced for a longer period of time during exercise. Glycogen is broken down into G-1-P and converted into G-6-P in both muscle and liver cells, and this product enters the glycolytic pathway.
Sucrose is a disaccharide with a molecule of glucose and a molecule of fructose bonded together with a glycosidic linkage. Fructose is one of the three dietary monosaccharides, along with glucose and galactose (which is part of the milk sugar, the disaccharide lactose), which are absorbed directly into the bloodstream during digestion. The catabolism of both fructose and galactose produces the same number of ATP molecules as glucose.
Connections of Proteins to Glucose Metabolism
Proteins are hydrolyzed by a variety of enzymes in cells. Most of the time, the amino acids are recycled into the synthesis of new proteins. If there are excess amino acids, however, or if the body is in a state of starvation, some amino acids will be shunted into the pathways of glucose catabolism (Figure \(1\)). Each amino acid must have its amino group removed prior to entry into these pathways. The amino group is converted into ammonia. In mammals, the liver synthesizes urea from two ammonia molecules and a carbon dioxide molecule. Thus, urea is the principal waste product in mammals produced from the nitrogen originating in amino acids, and it leaves the body in urine.
Connections of Lipid and Glucose Metabolisms
The lipids that are connected to the glucose pathways are cholesterol and triglycerides. Cholesterol is a lipid that contributes to cell membrane flexibility and is a precursor of steroid hormones. The synthesis of cholesterol starts with acetyl groups and proceeds in only one direction. The process cannot be reversed.
Triglycerides are a form of long-term energy storage in animals. Triglycerides are made of glycerol and three fatty acids. Animals can make most of the fatty acids they need. Triglycerides can be both made and broken down through parts of the glucose catabolism pathways. Glycerol can be phosphorylated to glycerol-3-phosphate, which continues through glycolysis. Fatty acids are catabolized in a process called beta-oxidation that takes place in the matrix of the mitochondria and converts their fatty acid chains into two carbon units of acetyl groups. The acetyl groups are picked up by CoA to form acetyl CoA that proceeds into the citric acid cycle.
Evolution Connection: Pathways of Photosynthesis and Cellular Metabolism
The processes of photosynthesis and cellular metabolism consist of several very complex pathways. It is generally thought that the first cells arose in an aqueous environment—a “soup” of nutrients—probably on the surface of some porous clays. If these cells reproduced successfully and their numbers climbed steadily, it follows that the cells would begin to deplete the nutrients from the medium in which they lived as they shifted the nutrients into the components of their own bodies. This hypothetical situation would have resulted in natural selection favoring those organisms that could exist by using the nutrients that remained in their environment and by manipulating these nutrients into materials upon which they could survive. Selection would favor those organisms that could extract maximal value from the nutrients to which they had access.
An early form of photosynthesis developed that harnessed the sun’s energy using water as a source of hydrogen atoms, but this pathway did not produce free oxygen (anoxygenic photosynthesis). (Early photosynthesis did not produce free oxygen because it did not use water as the source of hydrogen ions; instead, it used materials like hydrogen sulfide and consequently produced sulfur). It is thought that glycolysis developed at this time and could take advantage of the simple sugars being produced, but these reactions were unable to fully extract the energy stored in the carbohydrates. The development of glycolysis probably predated the evolution of photosynthesis, as it was well suited to extract energy from materials spontaneously accumulating in the “primeval soup.” A later form of photosynthesis used water as a source of electrons and hydrogen, and generated free oxygen. Over time, the atmosphere became oxygenated, but not before the oxygen released oxidized metals in the ocean and created a “rust” layer in the sediment, permitting the dating of the rise of the first oxygenic photosynthesizers. Living things adapted to exploit this new atmosphere that allowed aerobic respiration as we know it to evolve. When the full process of oxygenic photosynthesis developed and the atmosphere became oxygenated, cells were finally able to use the oxygen expelled by photosynthesis to extract considerably more energy from the sugar molecules using the citric acid cycle and oxidative phosphorylation.
Summary
The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism. The simple sugars are galactose, fructose, glycogen, and pentose. These are catabolized during glycolysis. The amino acids from proteins connect with glucose catabolism through pyruvate, acetyl CoA, and components of the citric acid cycle. Cholesterol synthesis starts with acetyl groups, and the components of triglycerides come from glycerol-3-phosphate from glycolysis and acetyl groups produced in the mitochondria from pyruvate.
Contributors and Attributions
• Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski (Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY 4.0; Download for free at http://cnx.org/contents/[email protected]). | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/07%3A_How_Cells_Harvest_Energy/7.06%3A_Energy_Yield_of_Aerobic_Respiration/7.6C%3A_ATP_Yield.txt |
Skills to Develop
• Discuss the fundamental difference between anaerobic cellular respiration and fermentation
• Describe the type of fermentation that readily occurs in animal cells and the conditions that initiate that fermentation
In aerobic respiration, the final electron acceptor is an oxygen molecule, O2. If aerobic respiration occurs, then ATP will be produced using the energy of high-energy electrons carried by NADH or FADH2 to the electron transport chain. If aerobic respiration does not occur, NADH must be reoxidized to NAD+ for reuse as an electron carrier for the glycolytic pathway to continue. How is this done? Some living systems use an organic molecule as the final electron acceptor. Processes that use an organic molecule to regenerate NAD+ from NADH are collectively referred to as fermentation. In contrast, some living systems use an inorganic molecule as a final electron acceptor. Both methods are called anaerobic cellular respiration in which organisms convert energy for their use in the absence of oxygen.
Anaerobic Cellular Respiration
Certain prokaryotes, including some species of bacteria and Archaea, use anaerobic respiration. For example, the group of Archaea called methanogens reduces carbon dioxide to methane to oxidize NADH. These microorganisms are found in soil and in the digestive tracts of ruminants, such as cows and sheep. Similarly, sulfate-reducing bacteria and Archaea, most of which are anaerobic (Figure $1$), reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH.
Link to Learning
Video $1$: Watch this video to see anaerobic cellular respiration in action.
Lactic Acid Fermentation
The fermentation method used by animals and certain bacteria, like those in yogurt, is lactic acid fermentation (Figure $2$). This type of fermentation is used routinely in mammalian red blood cells and in skeletal muscle that has an insufficient oxygen supply to allow aerobic respiration to continue (that is, in muscles used to the point of fatigue). In muscles, lactic acid accumulation must be removed by the blood circulation and the lactate brought to the liver for further metabolism. The chemical reactions of lactic acid fermentation are the following:
$\text{Pyruvic} \enspace \text{acid} + \text{NADH} \leftrightarrow \text{lactic} \enspace \text{acid} + \text{NAD}^+ \nonumber$
The enzyme used in this reaction is lactate dehydrogenase (LDH). The reaction can proceed in either direction, but the reaction from left to right is inhibited by acidic conditions. Such lactic acid accumulation was once believed to cause muscle stiffness, fatigue, and soreness, although more recent research disputes this hypothesis. Once the lactic acid has been removed from the muscle and circulated to the liver, it can be reconverted into pyruvic acid and further catabolized for energy.
Exercise $1$
Tremetol, a metabolic poison found in the white snake root plant, prevents the metabolism of lactate. When cows eat this plant, it is concentrated in the milk they produce. Humans who consume the milk become ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?
Answer
The illness is caused by lactate accumulation. Lactate levels rise after exercise, making the symptoms worse. Milk sickness is rare today, but was common in the Midwestern United States in the early 1800s.
Alcohol Fermentation
Another familiar fermentation process is alcohol fermentation (Figure $3$) that produces ethanol, an alcohol. The first chemical reaction of alcohol fermentation is the following (CO2 does not participate in the second reaction):
$\text{Pyruvic} \enspace \text{acid} \rightarrow \ce{CO_2} + \text{acetaldehyde} + \text{NADH} \rightarrow \text{ethanol} + \text{NAD}^+ \nonumber$
The first reaction is catalyzed by pyruvate decarboxylase, a cytoplasmic enzyme, with a coenzyme of thiamine pyrophosphate (TPP, derived from vitamin B1 and also called thiamine). A carboxyl group is removed from pyruvic acid, releasing carbon dioxide as a gas. The loss of carbon dioxide reduces the size of the molecule by one carbon, making acetaldehyde. The second reaction is catalyzed by alcohol dehydrogenase to oxidize NADH to NAD+ and reduce acetaldehyde to ethanol. The fermentation of pyruvic acid by yeast produces the ethanol found in alcoholic beverages. Ethanol tolerance of yeast is variable, ranging from about 5 percent to 21 percent, depending on the yeast strain and environmental conditions.
Other Types of Fermentation
Other fermentation methods occur in bacteria. Many prokaryotes are facultatively anaerobic. This means that they can switch between aerobic respiration and fermentation, depending on the availability of oxygen. Certain prokaryotes, like Clostridia, are obligate anaerobes. Obligate anaerobes live and grow in the absence of molecular oxygen. Oxygen is a poison to these microorganisms and kills them on exposure. It should be noted that all forms of fermentation, except lactic acid fermentation, produce gas. The production of particular types of gas is used as an indicator of the fermentation of specific carbohydrates, which plays a role in the laboratory identification of the bacteria. Various methods of fermentation are used by assorted organisms to ensure an adequate supply of NAD+ for the sixth step in glycolysis. Without these pathways, that step would not occur and no ATP would be harvested from the breakdown of glucose.
Summary
If NADH cannot be oxidized through aerobic respiration, another electron acceptor is used. Most organisms will use some form of fermentation to accomplish the regeneration of NAD+, ensuring the continuation of glycolysis. The regeneration of NAD+ in fermentation is not accompanied by ATP production; therefore, the potential of NADH to produce ATP using an electron transport chain is not utilized.
Glossary
anaerobic cellular respiration
process in which organisms convert energy for their use in the absence of oxygen
fermentation
process of regenerating NAD+ with either an inorganic or organic compound serving as the final electron acceptor, occurs in the absence; occurs in the absence of oxygen | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/07%3A_How_Cells_Harvest_Energy/7.08%3A_Oxidation_without_O2.txt |
Excess amino acids are converted into molecules that can enter the pathways of glucose catabolism.
Learning Objectives
• Describe the role played by proteins in glucose metabolism
Key Points
• Amino acids must be deaminated before entering any of the pathways of glucose catabolism: the amino group is converted to ammonia, which is used by the liver in the synthesis of urea.
• Deaminated amino acids can be converted into pyruvate, acetyl CoA, or some components of the citric acid cycle to enter the pathways of glucose catabolism.
• Several amino acids can enter the glucose catabolism pathways at multiple locations.
Key Terms
• catabolism: Destructive metabolism, usually including the release of energy and breakdown of materials.
• keto acid: Any carboxylic acid that also contains a ketone group.
• deamination: The removal of an amino group from a compound.
Metabolic pathways should be thought of as porous; that is, substances enter from other pathways and intermediates leave for other pathways. These pathways are not closed systems. Many of the substrates, intermediates, and products in a particular pathway are reactants in other pathways. Proteins are a good example of this phenomenon. They can be broken down into their constituent amino acids and used at various steps of the pathway of glucose catabolism.
Proteins are hydrolyzed by a variety of enzymes in cells. Most of the time, the amino acids are recycled into the synthesis of new proteins or are used as precursors in the synthesis of other important biological molecules, such as hormones, nucleotides, or neurotransmitters. However, if there are excess amino acids, or if the body is in a state of starvation, some amino acids will be shunted into the pathways of glucose catabolism.
Each amino acid must have its amino group removed (deamination) prior to the carbon chain’s entry into these pathways. When the amino group is removed from an amino acid, it is converted into ammonia through the urea cycle. The remaining atoms of the amino acid result in a keto acid: a carbon chain with one ketone and one carboxylic acid group. In mammals, the liver synthesizes urea from two ammonia molecules and a carbon dioxide molecule. Thus, urea is the principal waste product in mammals produced from the nitrogen originating in amino acids; it leaves the body in urine. The keto acid can then enter the citric acid cycle.
When deaminated, amino acids can enter the pathways of glucose metabolism as pyruvate, acetyl CoA, or several components of the citric acid cycle. For example, deaminated asparagine and aspartate are converted into oxaloacetate and enter glucose catabolism in the citric acid cycle. Deaminated amino acids can also be converted into another intermediate molecule before entering the pathways. Several amino acids can enter glucose catabolism at multiple locations.
7.9C: Connecting Lipids to Glucose Metabolism
Lipids can be both made and broken down through parts of the glucose catabolism pathways.
Learning Objectives
• Explain the connection of lipids to glucose metabolism
Key Points
• Many types of lipids exist, but cholesterol and triglycerides are the lipids that enter the pathways of glucose catabolism.
• Through the process of phosphorylation, glycerol can be converted to glycerol-3-phosphate during the glycolytic pathway.
• When fatty acids are broken down into acetyl groups through beta-oxidation, the acetyl groups are used by CoA to form acetyl-CoA, which enters the citric acid cycle to produce ATP.
• Beta-oxidation produces FADH2 and NADH, which are used by the electron transport chain for ATP production.
Key Terms
• beta-oxidation: A process that takes place in the matrix of the mitochondria and catabolizes fatty acids by converting them to acetyl groups while producing NADH and FADH2.
• lipid: A group of organic compounds including fats, oils, waxes, sterols, and triglycerides; characterized by being insoluble in water; account for most of the fat present in the human body.
Like sugars and amino acids, the catabolic pathways of lipids are also connected to the glucose catabolism pathways. The lipids that are connected to the glucose pathways are cholesterol and triglycerides.
Cholesterol
Cholesterol contributes to cell membrane flexibility and is a precursor to steroid hormones. The synthesis of cholesterol starts with acetyl groups, which are transferred from acetyl CoA, and proceeds in only one direction; the process cannot be reversed. Thus, synthesis of cholesterol requires an intermediate of glucose metabolism.
Triglycerides
Triglycerides, a form of long-term energy storage in animals, are made of glycerol and three fatty acids. Animals can make most of the fatty acids they need. Triglycerides can be both made and broken down through parts of the glucose catabolism pathways. Glycerol can be phosphorylated to glycerol-3-phosphate, which continues through glycolysis.
Fatty acids are catabolized in a process called beta-oxidation that takes place in the matrix of the mitochondria and converts their fatty acid chains into two carbon units of acetyl groups, while producing NADH and FADH2. The acetyl groups are picked up by CoA to form acetyl CoA that proceeds into the citric acid cycle as it combines with oxaloacetate. The NADH and FADH2 are then used by the electron transport chain. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/07%3A_How_Cells_Harvest_Energy/7.09%3A_Catabolism_of_Proteins_and_Fats/7.9B%3A_Connecting_Proteins_to_Glucose_Metabolism.txt |
Learning Objectives
• Describe the process of photosynthesis
The Importance of Photosynthesis
The processes of all organisms—from bacteria to humans—require energy. To get this energy, many organisms access stored energy by eating food. Carnivores eat other animals and herbivores eat plants. But where does the stored energy in food originate? All of this energy can be traced back to the process of photosynthesis and light energy from the sun.
Photosynthesis is essential to all life on earth. It is the only biological process that captures energy from outer space (sunlight) and converts it into chemical energy in the form of G3P (
Glyceraldehyde 3-phosphate) which in turn can be made into sugars and other molecular compounds. Plants use these compounds in all of their metabolic processes; plants do not need to consume other organisms for food because they build all the molecules they need. Unlike plants, animals need to consume other organisms to consume the molecules they need for their metabolic processes.
The Process of Photosynthesis
During photosynthesis, molecules in leaves capture sunlight and energize electrons, which are then stored in the covalent bonds of carbohydrate molecules. That energy within those covalent bonds will be released when they are broken during cell respiration. How long lasting and stable are those covalent bonds? The energy extracted today by the burning of coal and petroleum products represents sunlight energy captured and stored by photosynthesis almost 200 million years ago.
Plants, algae, and a group of bacteria called cyanobacteria are the only organisms capable of performing photosynthesis. Because they use light to manufacture their own food, they are called photoautotrophs (“self-feeders using light”). Other organisms, such as animals, fungi, and most other bacteria, are termed heterotrophs (“other feeders”) because they must rely on the sugars produced by photosynthetic organisms for their energy needs. A third very interesting group of bacteria synthesize sugars, not by using sunlight’s energy, but by extracting energy from inorganic chemical compounds; hence, they are referred to as chemoautotrophs.
The importance of photosynthesis is not just that it can capture sunlight’s energy. A lizard sunning itself on a cold day can use the sun’s energy to warm up. Photosynthesis is vital because it evolved as a way to store the energy in solar radiation (the “photo-” part) as high-energy electrons in the carbon-carbon bonds of carbohydrate molecules (the “-synthesis” part). Those carbohydrates are the energy source that heterotrophs use to power the synthesis of ATP via respiration. Therefore, photosynthesis powers 99 percent of Earth’s ecosystems. When a top predator, such as a wolf, preys on a deer, the wolf is at the end of an energy path that went from nuclear reactions on the surface of the sun, to light, to photosynthesis, to vegetation, to deer, and finally to wolf.
Key Points
• Photosynthesis evolved as a way to store the energy in solar radiation as high-energy electrons in carbohydrate molecules.
• Plants, algae, and cyanobacteria, known as photoautotrophs, are the only organisms capable of performing photosynthesis.
• Heterotrophs, unable to produce their own food, rely on the carbohydrates produced by photosynthetic organisms for their energy needs.
Key Terms
• photosynthesis: the process by which plants and other photoautotrophs generate carbohydrates and oxygen from carbon dioxide, water, and light energy in chloroplasts
• photoautotroph: an organism that can synthesize its own food by using light as a source of energy
• chemoautotroph: a simple organism, such as a protozoan, that derives its energy from chemical processes rather than photosynthesis | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/08%3A_Photosynthesis/8.01%3A_Overview_of_Photosynthesis/8.1.1A%3A_The_Purpose_and_Process_of_Photosynthesis.txt |
Learning Objectives
• Describe the main structures involved in photosynthesis and recall the chemical equation that summarizes the process of photosynthesis
Overview of Photosynthesis
Photosynthesis is a multi-step process that requires sunlight, carbon dioxide, and water as substrates. It produces oxygen and glyceraldehyde-3-phosphate (G3P or GA3P), simple carbohydrate molecules that are high in energy and can subsequently be converted into glucose, sucrose, or other sugar molecules. These sugar molecules contain covalent bonds that store energy. Organisms break down these molecules to release energy for use in cellular work.
The energy from sunlight drives the reaction of carbon dioxide and water molecules to produce sugar and oxygen, as seen in the chemical equation for photosynthesis. Though the equation looks simple, it is carried out through many complex steps. Before learning the details of how photoautotrophs convert light energy into chemical energy, it is important to become familiar with the structures involved.
Photosynthesis and the Leaf
In plants, photosynthesis generally takes place in leaves, which consist of several layers of cells. The process of photosynthesis occurs in a middle layer called the mesophyll. The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata (singular: stoma ), which also play a role in the plant’s regulation of water balance. The stomata are typically located on the underside of the leaf, which minimizes water loss. Each stoma is flanked by guard cells that regulate the opening and closing of the stomata by swelling or shrinking in response to osmotic changes.
Photosynthesis within the Chloroplast
In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast. For plants, chloroplast-containing cells exist in the mesophyll. Chloroplasts have a double membrane envelope composed of an outer membrane and an inner membrane. Within the double membrane are stacked, disc-shaped structures called thylakoids.
Embedded in the thylakoid membrane is chlorophyll, a pigment that absorbs certain portions of the visible spectrum and captures energy from sunlight. Chlorophyll gives plants their green color and is responsible for the initial interaction between light and plant material, as well as numerous proteins that make up the electron transport chain. The thylakoid membrane encloses an internal space called the thylakoid lumen. A stack of thylakoids is called a granum, and the liquid-filled space surrounding the granum is the stroma or “bed.”
Key Points
• The chemical equation for photosynthesis is 6CO2+6H2O→C6H12O6+6O2.6CO2+6H2O→C6H12O6+6O2.
• In plants, the process of photosynthesis takes place in the mesophyll of the leaves, inside the chloroplasts.
• Chloroplasts contain disc-shaped structures called thylakoids, which contain the pigment chlorophyll.
• Chlorophyll absorbs certain portions of the visible spectrum and captures energy from sunlight.
Key Terms
• chloroplast: An organelle found in the cells of green plants and photosynthetic algae where photosynthesis takes place.
• mesophyll: A layer of cells that comprises most of the interior of the leaf between the upper and lower layers of epidermis.
• stoma: A pore in the leaf and stem epidermis that is used for gaseous exchange.
8.1.1C: The Two Parts of Photosynthesis
Learning Objectives
• Distinguish between the two parts of photosynthesis
Light-Dependent Reactions
Just as the name implies, light-dependent reactions require sunlight. In the light-dependent reactions, energy from sunlight is absorbed by chlorophyll and converted into stored chemical energy, in the form of the electron carrier molecule NADPH (nicotinamide adenine dinucleotide phosphate) and the energy currency molecule ATP (adenosine triphosphate). The light-dependent reactions take place in the thylakoid membranes in the granum (stack of thylakoids), within the chloroplast.
Photosystems
The process that converts light energy into chemical energy takes place in a multi-protein complex called a photosystem. Two types of photosystems are embedded in the thylakoid membrane: photosystem II ( PSII) and photosystem I (PSI). Each photosystem plays a key role in capturing the energy from sunlight by exciting electrons. These energized electrons are transported by “energy carrier” molecules, which power the light-independent reactions.
Photosystems consist of a light-harvesting complex and a reaction center. Pigments in the light-harvesting complex pass light energy to two special chlorophyll a molecules in the reaction center. The light excites an electron from the chlorophyll a pair, which passes to the primary electron acceptor. The excited electron must then be replaced. In photosystem II, the electron comes from the splitting of water, which releases oxygen as a waste product. In photosystem I, the electron comes from the chloroplast electron transport chain.
The two photosystems oxidize different sources of the low-energy electron supply, deliver their energized electrons to different places, and respond to different wavelengths of light.
Light-Independent Reactions
In the light-independent reactions or Calvin cycle, the energized electrons from the light-dependent reactions provide the energy to form carbohydrates from carbon dioxide molecules. The light-independent reactions are sometimes called the Calvin cycle because of the cyclical nature of the process.
Although the light-independent reactions do not use light as a reactant (and as a result can take place at day or night), they require the products of the light-dependent reactions to function. The light-independent molecules depend on the energy carrier molecules, ATP and NADPH, to drive the construction of new carbohydrate molecules. After the energy is transferred, the energy carrier molecules return to the light-dependent reactions to obtain more energized electrons. In addition, several enzymes of the light-independent reactions are activated by light.
Key Points
• In light-dependent reactions, the energy from sunlight is absorbed by chlorophyll and converted into chemical energy in the form of electron carrier molecules like ATP and NADPH.
• Light energy is harnessed in Photosystems I and II, both of which are present in the thylakoid membranes of chloroplasts.
• In light-independent reactions (the Calvin cycle), carbohydrate molecules are assembled from carbon dioxide using the chemical energy harvested during the light-dependent reactions.
Key Terms
• photosystem: Either of two biochemical systems active in chloroplasts that are part of photosynthesis.
Photosynthesis takes place in two sequential stages:
1. The light-dependent reactions;
2. The light-independent reactions, or Calvin Cycle. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/08%3A_Photosynthesis/8.01%3A_Overview_of_Photosynthesis/8.1.1B%3A_Main_Structures_and_Summary_of_Photosynthesis.txt |
This chapter talks about various scientists and their path towards discovering photosynthesis.
van Helmont
Perhaps the first experiment designed to explore the nature of photosynthesis was that reported by the Dutch physician van Helmont in 1648. Some years earlier, van Helmont had placed in a large pot exactly 200 pounds (91 kg) of soil that had been thoroughly dried in an oven. Then he moistened the soil with rain water and planted a 5-pound (2.3 kg) willow shoot in it. He then placed the pot in the ground and covered its rim with a perforated iron plate. The perforations allowed water and air to reach the soil but lessened the chance that dirt or other debris would be blown into the pot from the outside.
For five years, van Helmont kept his plant watered with rain water or distilled water. At the end of that time, he carefully removed the young tree and found that it had gained 164 pound, 3 ounces (74.5 kg). (This figure did not include the weight of the leaves that had been shed during the previous four autumns.) He then redried the soil and found that it weighed only 2 ounces (57 g) less that the original 200 pounds (91 kg). Faced with these experimental facts, van Helmont theorized that the increase in weight of the willow arose from the water alone. He did not consider the possibility that gases in the air might be involved.
Joseph Priestley
The first evidence that gases participate in photosynthesis was reported by Joseph Priestley in 1772. He knew that if a burning candle is placed in a sealed chamber, the candle soon goes out. If a mouse is then placed in the chamber, it soon suffocates because the process of combustion has used up all the oxygen in the air — the gas on which animal respiration depends. However, Priestley discovered that if a plant is placed in an atmosphere lacking oxygen, it soon replenishes the oxygen, and a mouse can survive in the resulting mixture. Priestley thought (erroneously) that it was simply the growth of the plant that accounted for this.
Ingen-Housz
It was another Dutch physician, Ingen-Housz, who discovered in 1778 that the effect observed by Priestley occurred only when the plant was illuminated. A plant kept in the dark in a sealed chamber consumes oxygen just as a mouse (or candle) does.
Ingen-Housz also demonstrated that only green parts of plants liberated oxygen during photosynthesis. Nongreen plant structure, such as woody stems, roots, flowers, and fruits actually consume oxygen in the process of respiration. We now know that this is because photosynthesis can go on only in the presence of the green pigment chlorophyll.
Jean Senebier
The growth of plants is accompanied by an increase in their carbon content. A Swiss minister, Jean Senebier, discovered that the source of this carbon is carbon dioxide and that the release of oxygen during photosynthesis accompanies the uptake of carbon dioxide. Senebier concluded (erroneously as it turned out) that in photosynthesis carbon dioxide is decomposed, with the carbon becoming incorporated in the organic matter of the plant and the oxygen being released.
CO2 + H2O → (CH2O) + O2
(The parentheses around the CH2O signify that no specific molecule is being indicated but, instead, the ratio of atoms in some carbohydrate, e.g., glucose, C6H12O6.) The equation also indicates that the ratio of carbon dioxide consumed to oxygen release is 1:1, a finding that was carefully demonstrated in the years following Senebier's work. Using glucose as the carbohydrate product, we can write the equation for photosynthesis as
6CO2 + 6H2O → C6H12O6 + 6O2
F. F. Blackman
The above equation shows the relationship between the substances used in and produced by the process. It tells us nothing about the intermediate steps. That photosynthesis does involve at least two quite distinct processes became apparent from the experiments of the British plant physiologist F. F. Blackman. His results can easily be duplicated by using the setup in Figure 4.9.1. The green water plant Elodea (available wherever aquarium supplies are sold) is the test organism. When a sprig is placed upside down in a dilute solution of NaHCO3 (which serves as a source of CO2) and illuminated with a flood lamp, oxygen bubbles are soon given off from the cut portion of the stem. One then counts the number of bubbles given off in a fixed interval of time at each of several light intensities. Plotting these data produces a graph like the one in Figure 4.9.2.
Since the rate of photosynthesis does not continue to increase indefinitely with increased illumination, Blackman concluded that at least two distinct processes are involved: one, a reaction that requires light and the other, a reaction that does not. This latter is called a "dark" reaction although it can go on in the light. Blackman theorized that at moderate light intensities, the "light" reaction limits or "paces" the entire process. In other words, at these intensities the dark reaction is capable of handling all the intermediate substances produced by the light reaction. With increasing light intensities, however, a point is eventually reached when the dark reaction is working at maximum capacity. Any further illumination is ineffective, and the process reaches a steady rate.
This interpretation is strengthened by repeating the experiment as a somewhat higher temperature. Most chemical reactions proceed more rapidly at higher temperatures (up to a point). At 35°C, the rate of photosynthesis does not level off until greater light intensities are present. This suggest that the dark reaction is now working faster. The fact that at low light intensities the rate of photosynthesis is no greater at 35°C than at 20°C also supports the idea that it is a light reaction that is limiting the process in this range. Light reactions depend, not on temperature, but simply on the intensity of illumination.
The increased rate of photosynthesis with increased temperature does not occur if the supply of CO2 is limited. As the figure shows, the overall rate of photosynthesis reaches a steady value at lower light intensities if the amount of CO2 available is limited. Thus CO2 concentration must be added as a third factor regulating the rate at which photosynthesis occurs. As a practical matter, however, the concentration available to terrestrial plants is simply that found in the atmosphere: 0.035%.
Van Niel
It was the American microbiologist Van Niel who first glimpsed the role that light plays in photosynthesis. He studied photosynthesis in purple sulfur bacteria. These microorganisms synthesize glucose from CO2 as do green plants, and they need light to do so. Water, however, is not the starting material. Instead they use hydrogen sulfide (H2S). Furthermore, no oxygen is liberated during this photosynthesis but rather elemental sulfur. Van Niel reasoned that the action of light caused a decomposition of H2S into hydrogen and sulfur atoms. Then, in a series of dark reactions, the hydrogen atoms were used to reduce CO2 to carbohydrate:
\[\ce{CO2 + 2H2S → (CH2O) + H2O + 2S}\]
Van Niel envisioned a parallel to the process of photosynthesis as it occurs in green plants. There the energy of light causes water to break up into hydrogen and oxygen. The hydrogen atoms are then used to reduce CO2 in a series of dark reactions:
\[\ce{CO2 + 2H2O → (CH2O) + H2O + O2}\]
If this theory is correct, then it follows that all of the oxygen released during photosynthesis comes from water just as all the sulfur produced by the purple sulfur bacteria comes from H2S. This conclusion directly contradicts Senebier's theory that the oxygen liberated in photosynthesis comes from the carbon dioxide. If Van Niel's theory is correct, then the equation for photosynthesis would have to be rewritten:
\[\ce{6CO2 + 12H2O → C6H12O6 + 6 H2O + 6O2}\]
In science, a theory should be testable. By deduction, one can make a prediction of how a particular experiment will come out if the theory is sound. In this case, the crucial experiments needed to test the two theories had to await the time when the growth of atomic research made it possible to produce isotopes other than those found naturally or in greater concentrations than are found naturally.
Samuel Ruben
In air, water and other natural materials containing oxygen, 99.76% of the oxygen atoms are 16O and only 0.20% of them are the heavier isotope 18O. In 1941, Samuel Ruben and his coworkers at the University of California were able to prepare specially "labeled" water in which the 0.85% of the molecules contained 18O atoms. When this water was supplied to a suspension of photosynthesizing algae, the proportion of 18O in the oxygen gas that was evolved was 0.85%, the same as that of the water supplied, and not simply the 0.20% found in all natural samples of oxygen (and its compounds like CO2).
% 18O FOUND IN
EXPERIMENT H2O CO2 O2
1. START 0.85 0.20
FINISH 0.85 0.61* 0.86
2. START 0.20 0.68
FINISH 0.20 0.57 0.20
* A non-biochemical exchange of oxygen atoms between the water and the bicarbonate ions used as a source of CO2 explains the uptake of the isotope by CO2 in the first experiment.
These results clearly demonstrated that Senebier's interpretation was in error. If all the oxygen liberated during photosynthesis comes from the carbon dioxide, we would expect the oxygen evolved in Ruben's experiment to contain simply the 0.20% found naturally. If, on the other hand, both the carbon dioxide and the water contribute to the oxygen released, we would expect its isotopic composition to have been some intermediate figure. In fact, the isotopic composition of the evolved oxygen was the same as that of the water used.
Ruben and his colleagues also prepared a source of carbon dioxide that was enriched in 18O atoms. When algae carried out photosynthesis using this material and natural water, the oxygen that was given off was not enriched in 18O. It contained simply the 0.20% 18O found in the natural water used. The heavy atoms presumably became incorporated in the other two products (carbohydrate and by-product water).
These experiments lent great support to Van Niel's idea that one function of light in photosynthesis was the separation of the hydrogen and oxygen atoms of water molecules. But there remained to work out just how the hydrogen atoms were made available to the dark reactions. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/08%3A_Photosynthesis/8.02%3A_The_Discovery_of_Photosynthetic_Processes/8.2.01%3A_Photosynthesis_-_Dicovering_the_Secrets.txt |
Learning Objectives
• Explain the difference between short and long wavelengths.
What Is Light Energy?
The sun emits an enormous amount of electromagnetic radiation (solar or light energy). Humans can see only a fraction of this energy, which is referred to as “visible light.” The manner in which solar energy travels is described as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength, the distance between consecutive points of a wave, such as from crest to crest or from trough to trough.
Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun and other stars. The electromagnetic spectrum is the range of all possible frequencies of radiation. The electromagnetic spectrum shows several types of electromagnetic radiation originating from the sun, including X-rays and ultraviolet (UV) rays. The higher-energy waves can penetrate tissues and damage cells and DNA, which explains why both X-rays and UV rays can be harmful to living organisms. Scientists differentiate the various types of radiant energy from the sun within the electromagnetic spectrum.The difference between wavelengths relates to the amount of energy carried by them.
Each type of electromagnetic radiation travels at a particular wavelength. The longer the wavelength, the less energy is carried. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a person moving a heavy rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy.
Key Points
• The amount of energy of a wave can be determined by measuring its wavelength, the distance between consecutive points of a wave.
• Visible light is a type of radiant energy within the electromagnetic spectrum; other types of electromagnetic radiation include UV, infrared, gamma, and radio rays as well as X-rays.
• The difference between wavelengths relates to the amount of energy carried by them; short, tight waves carry more energy than long, wide waves.
Key Terms
• electromagnetic spectrum: the entire range of wavelengths of all known radiations consisting of oscillating electric and magnetic fields, including gamma rays, visible light, infrared, radio waves, and X-rays
• wavelength: the length of a single cycle of a wave, as measured by the distance between one peak or trough of a wave and the next; it corresponds to the velocity of the wave divided by its frequency
• visible light: the part of the electromagnetic spectrum, between infrared and ultraviolet, that is visible to the human eye
8.3B: Absorption of Light
Learning Objectives
• Differentiate between chlorophyll and carotenoids.
Absorption of Light
Light energy initiates the process of photosynthesis when pigments absorb the light. Organic pigments have a narrow range of energy levels that they can absorb. Energy levels lower than those represented by red light are insufficient to raise an orbital electron to an excited, or quantum, state. Energy levels higher than those in blue light will physically tear the molecules apart, a process called bleaching. For example, retinal pigments can only “see” (absorb) 700 nm to 400 nm light; this is visible light. For the same reasons, plant pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm; plant physiologists refer to this range for plants as photosynthetically-active radiation.
The visible light seen by humans as the color white light actually exists in a rainbow of colors in the electromagnetic spectrum, with violet and blue having shorter wavelengths and, thus, higher energy. At the other end of the spectrum, toward red, the wavelengths are longer and have lower energy.
Understanding Pigments
Different kinds of pigments exist, each of which has evolved to absorb only certain wavelengths or colors of visible light. Pigments reflect or transmit the wavelengths they cannot absorb, making them appear in the corresponding color.
Chlorophylls and carotenoids are the two major classes of photosynthetic pigments found in plants and algae; each class has multiple types of pigment molecules. There are five major chlorophylls: a, b, c and d, along with a related molecule found in prokaryotes called bacteriochlorophyll.
With dozens of different forms, carotenoids are a much larger group of pigments. The carotenoids found in fruit, such as the red of tomato (lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an orange peel (β-carotene), are used to attract seed-dispersing organisms. In photosynthesis, carotenoids function as photosynthetic pigments that are very efficient molecules for the disposal of excess energy. When a leaf is exposed to full sun, the light-dependent reactions are required to process an enormous amount of energy; if that energy is not handled properly, it can do significant damage. Therefore, many carotenoids are stored in the thylakoid membrane to absorb excess energy and safely release that energy as heat.
Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is the absorption spectrum. Chlorophyll a absorbs light in the blue-violet region, while chlorophyll b absorbs red-blue light. Neither a or b absorb green light; because green is reflected or transmitted, chlorophyll appears green. Carotenoids absorb light in the blue-green and violet region and reflect the longer yellow, red, and orange wavelengths.
Many photosynthetic organisms have a mixture of pigments. In this way organisms can absorb energy from a wider range of wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity and quality decrease and change with depth. Other organisms grow in competition for light. Plants on the rainforest floor must be able to absorb any light that comes through because the taller trees absorb most of the sunlight and scatter the remaining solar radiation
When studying a photosynthetic organism, scientists can determine the types of pigments present by using a spectrophotometer. These instruments can differentiate which wavelengths of light a substance can absorb. Spectrophotometers measure transmitted light and compute its absorption. By extracting pigments from leaves and placing these samples into a spectrophotometer, scientists can identify which wavelengths of light an organism can absorb.
Key Points
• Plant pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm; this range is referred to as photosynthetically-active radiation.
• Violet and blue have the shortest wavelengths and the most energy, whereas red has the longest wavelengths and carries the least amount of energy.
• Pigments reflect or transmit the wavelengths they cannot absorb, making them appear in the corresponding color.
• Chorophylls and carotenoids are the major pigments in plants; while there are dozens of carotenoids, there are only five important chorophylls: a, b, c, d, and bacteriochlorophyll.
• Chlorophyll a absorbs light in the blue-violet region, chlorophyll b absorbs red-blue light, and both a and b reflect green light (which is why chlorophyll appears green).
• Carotenoids absorb light in the blue-green and violet region and reflect the longer yellow, red, and orange wavelengths; these pigments also dispose excess energy out of the cell.
Key Terms
• chlorophyll: Any of a group of green pigments that are found in the chloroplasts of plants and in other photosynthetic organisms such as cyanobacteria.
• carotenoid: Any of a class of yellow to red plant pigments including the carotenes and xanthophylls.
• spectrophotometer: An instrument used to measure the intensity of electromagnetic radiation at different wavelengths. | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/08%3A_Photosynthesis/8.03%3A_Pigments/8.3A%3A_Introduction_to_Light_Energy.txt |
How can light be used to make food? It is easy to think of light as something that exists and allows living organisms, such as humans, to see, but light is a form of energy. Like all energy, light can travel, change form, and be harnessed to do work. In the case of photosynthesis, light energy is transformed into chemical energy, which autotrophs use to build carbohydrate molecules. However, autotrophs only use a specific component of sunlight (Figure \(1\)).
CONCEPT IN ACTION
Watch the process of photosynthesis within a leaf in this video.
What Is Light Energy?
The sun emits an enormous amount of electromagnetic radiation (solar energy). Humans can see only a fraction of this energy, which is referred to as “visible light.” The manner in which solar energy travels can be described and measured as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength, the distance between two consecutive, similar points in a series of waves, such as from crest to crest or trough to trough (Figure \(2\)).
Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun. The electromagnetic spectrum is the range of all possible wavelengths of radiation (Figure \(3\)). Each wavelength corresponds to a different amount of energy carried.
Each type of electromagnetic radiation has a characteristic range of wavelengths. The longer the wavelength (or the more stretched out it appears), the less energy is carried. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy.
The sun emits (Figure \(3\)) a broad range of electromagnetic radiation, including X-rays and ultraviolet (UV) rays. The higher-energy waves are dangerous to living things; for example, X-rays and UV rays can be harmful to humans.
Absorption of Light
Light energy enters the process of photosynthesis when pigments absorb the light. In plants, pigment molecules absorb only visible light for photosynthesis. The visible light seen by humans as white light actually exists in a rainbow of colors. Certain objects, such as a prism or a drop of water, disperse white light to reveal these colors to the human eye. The visible light portion of the electromagnetic spectrum is perceived by the human eye as a rainbow of colors, with violet and blue having shorter wavelengths and, therefore, higher energy. At the other end of the spectrum toward red, the wavelengths are longer and have lower energy.
Understanding Pigments
Different kinds of pigments exist, and each absorbs only certain wavelengths (colors) of visible light. Pigments reflect the color of the wavelengths that they cannot absorb.
All photosynthetic organisms contain a pigment called chlorophyll a, which humans see as the common green color associated with plants. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not from green. Because green is reflected, chlorophyll appears green.
Other pigment types include chlorophyll b (which absorbs blue and red-orange light) and the carotenoids. Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is its absorption spectrum.
Many photosynthetic organisms have a mixture of pigments; between them, the organism can absorb energy from a wider range of visible-light wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity decreases with depth, and certain wavelengths are absorbed by the water. Other organisms grow in competition for light. Plants on the rainforest floor must be able to absorb any bit of light that comes through, because the taller trees block most of the sunlight (Figure \(4\)).
How Light-Dependent Reactions Work
The overall purpose of the light-dependent reactions is to convert light energy into chemical energy. This chemical energy will be used by the Calvin cycle to fuel the assembly of sugar molecules.
The light-dependent reactions begin in a grouping of pigment molecules and proteins called a photosystem. Photosystems exist in the membranes of thylakoids. A pigment molecule in the photosystem absorbs one photon, a quantity or “packet” of light energy, at a time.
A photon of light energy travels until it reaches a molecule of chlorophyll. The photon causes an electron in the chlorophyll to become “excited.” The energy given to the electron allows it to break free from an atom of the chlorophyll molecule. Chlorophyll is therefore said to “donate” an electron (Figure \(5\)).
To replace the electron in the chlorophyll, a molecule of water is split. This splitting releases an electron and results in the formation of oxygen (O2) and hydrogen ions (H+) in the thylakoid space. Technically, each breaking of a water molecule releases a pair of electrons, and therefore can replace two donated electrons.
The replacing of the electron enables chlorophyll to respond to another photon. The oxygen molecules produced as byproducts find their way to the surrounding environment. The hydrogen ions play critical roles in the remainder of the light-dependent reactions.
Keep in mind that the purpose of the light-dependent reactions is to convert solar energy into chemical carriers that will be used in the Calvin cycle. In eukaryotes and some prokaryotes, two photosystems exist. The first is called photosystem II, which was named for the order of its discovery rather than for the order of the function.
After the photon hits, photosystem II transfers the free electron to the first in a series of proteins inside the thylakoid membrane called the electron transport chain. As the electron passes along these proteins, energy from the electron fuels membrane pumps that actively move hydrogen ions against their concentration gradient from the stroma into the thylakoid space. This is quite analogous to the process that occurs in the mitochondrion in which an electron transport chain pumps hydrogen ions from the mitochondrial stroma across the inner membrane and into the intermembrane space, creating an electrochemical gradient. After the energy is used, the electron is accepted by a pigment molecule in the next photosystem, which is called photosystem I (Figure \(6\)).
Generating an Energy Carrier: ATP
In the light-dependent reactions, energy absorbed by sunlight is stored by two types of energy-carrier molecules: ATP and NADPH. The energy that these molecules carry is stored in a bond that holds a single atom to the molecule. For ATP, it is a phosphate atom, and for NADPH, it is a hydrogen atom. Recall that NADH was a similar molecule that carried energy in the mitochondrion from the citric acid cycle to the electron transport chain. When these molecules release energy into the Calvin cycle, they each lose atoms to become the lower-energy molecules ADP and NADP+.
The buildup of hydrogen ions in the thylakoid space forms an electrochemical gradient because of the difference in the concentration of protons (H+) and the difference in the charge across the membrane that they create. This potential energy is harvested and stored as chemical energy in ATP through chemiosmosis, the movement of hydrogen ions down their electrochemical gradient through the transmembrane enzyme ATP synthase, just as in the mitochondrion.
The hydrogen ions are allowed to pass through the thylakoid membrane through an embedded protein complex called ATP synthase. This same protein generated ATP from ADP in the mitochondrion. The energy generated by the hydrogen ion stream allows ATP synthase to attach a third phosphate to ADP, which forms a molecule of ATP in a process called photophosphorylation. The flow of hydrogen ions through ATP synthase is called chemiosmosis, because the ions move from an area of high to low concentration through a semi-permeable structure.
Generating Another Energy Carrier: NADPH
The remaining function of the light-dependent reaction is to generate the other energy-carrier molecule, NADPH. As the electron from the electron transport chain arrives at photosystem I, it is re-energized with another photon captured by chlorophyll. The energy from this electron drives the formation of NADPH from NADP+ and a hydrogen ion (H+). Now that the solar energy is stored in energy carriers, it can be used to make a sugar molecule.
Summary
In the first part of photosynthesis, the light-dependent reaction, pigment molecules absorb energy from sunlight. The most common and abundant pigment is chlorophyll a. A photon strikes photosystem II to initiate photosynthesis. Energy travels through the electron transport chain, which pumps hydrogen ions into the thylakoid space. This forms an electrochemical gradient. The ions flow through ATP synthase from the thylakoid space into the stroma in a process called chemiosmosis to form molecules of ATP, which are used for the formation of sugar molecules in the second stage of photosynthesis. Photosystem I absorbs a second photon, which results in the formation of an NADPH molecule, another energy carrier for the Calvin cycle reactions.
Glossary
absorption spectrum
the specific pattern of absorption for a substance that absorbs electromagnetic radiation
chlorophyll a
the form of chlorophyll that absorbs violet-blue and red light
chlorophyll b
the form of chlorophyll that absorbs blue and red-orange light
electromagnetic spectrum
the range of all possible frequencies of radiation
photon
a distinct quantity or “packet” of light energy
photosystem
a group of proteins, chlorophyll, and other pigments that are used in the light-dependent reactions of photosynthesis to absorb light energy and convert it into chemical energy
wavelength
the distance between consecutive points of a wave | textbooks/bio/Introductory_and_General_Biology/Map%3A_Raven_Biology_12th_Edition/08%3A_Photosynthesis/8.04%3A_Photosystem_Organization/8.4.01%3A_The_Light-Dependent_Reactions_of_Photosynthesis.txt |
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