General Biology Chapter 2
Describe the physical interaction between an enzyme and its substrate.
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Explain how these degrees of structure for proteins relate to the function of a protein or enzyme.
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List and describe the four degrees of structure for proteins.
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List six different functions of proteins.
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Molecules and Bond Energy
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What are the possible fates of glucose once digested/ingested within/into the human body?
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What are the two types of nucleic acids and what function do they serve?
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What is the source of most of our circulating cholesterol? What are some positive and negative implications of cholesterol in our bodies?
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What pairs of bases interact with each other in a DNA molecule? In an RNA molecule?
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Why does the carbohydrate starch fail to provide you with the quick burst of energy that the carbohydrate glucose can provide?
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Why have humans evolved a preference for fats in their diets?
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phospholipid
A type of lipid that is the major component of the plasma membrane. Phospholipids are structurally similar to fats, but contain a phosphorus atom and have two, not three, fatty acid chains.
hydrogen bond
A type of weak chemical bond formed between the slightly positively charged hydrogen atoms of one molecule and the slightly negatively charged atoms (often oxygen or nitrogen) of another. Hydrogen bonds are important in building complex molecules, such as large proteins and DNA, and are responsible for many of the unique and important features of water.
Water: Strong Cohesiveness Cohesion Adhesion
Cohesion Water molecules bind to each other due to hydrogen bonding Adhesion Water molecules stick to other surfaces due to its polar nature
polysaccharide
Complex carbohydrates formed by the union of many simple sugars.
There are three types of chemical bonding. Briefly define each type and their strength relative to each other.
Covalent Bond: a strong bond formed when atoms share electrons in order to become more stable, forming a molecule Ionic Bond: an attraction between two oppositely charged ions, forming an ionic compound. Hydrogen Bond: an attraction between the slightly positively charged hydrogen atom of one molecule and the slightly negatively charged atom of another.
buffer
A chemical that can quickly absorb excess H+ ions in a solution (preventing it from becoming too acidic) or quickly release H+ ions (to counteract increases in OH- concentration).
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Nucleic acids are made up of nucleotide monomers
hydrophobic
Repelled by water, as, for example, nonpolar molecules that tend to minimize contact with water.
Universal Solvent
If you put a bit of table salt into a glass of water, it will quickly dissolve. This means that the charged sodium (Na+) and the chloride (Cl) ions that were ionically bonded together all become separated from each other. The sodium and chloride ions were initially attracted to each other because they are polar molecules, each carrying a slight charge. Water is able to pry them apart because, as a polar molecule, it too carries charges. The positively charged sodium ions are attracted to the negatively charged side of the water molecule, and the negatively charged chloride ions are attracted to the positively charged side (Figure 2-17 Solutions). Many substances are polar like water. That is why, like salt, they easily dissolve into it. Non-polar molecules (such as oil) have neither positively charged regions nor negatively charged regions. Consequently, the polar water molecules are not attracted to them. Instead, when oil is poured into a container of water, the water molecules distance themselves from the oil, leaving the oil molecules in isolated aggregations that never dissolve.
Surface Tension
LINK: ants Predators chasing after Green Basilisk lizards in Central America sometimes get the shock of a lifetime (and lose their lunch in the process). When chased, the lizards run quickly across rocks and dirt—nothing unusual for a lizard. When they come to the edge of a stream or river, however, these fleeing lizards show their uniqueness and earn their nickname, the "Jesus" lizard. Without stopping, the Jesus lizard runs right across the surface of the water, leaving stunned predators behind at the water's edge. How do they do it? The Jesus lizard makes use of the fact that water molecules have tremendous cohesion. That is, they stick together with unusual strength. This molecular cohesiveness is due to hydrogen bonds between the water molecules. Insects such as the water strider can take advantage of this and literally stride over the water surface.
Describe how the polar covalent bonds in water molecules lead to the formation of hydrogen bonds between water molecules.
Large numbers of water molecules orient themselves so that the negative side of one molecule is near the positive side of another. Hydrogen bonds form between the relatively positively charged hydrogen atoms and the relatively negatively charged oxygen atoms of adjacent water molecules.
Lipids are macromolecules with several functions, including energy storage.
Lipids are insoluble in water because, in sharp contrast to water, they consist mostly of hydrocarbons, which are nonpolar. Nonpolar molecules (or parts of molecules) tend to minimize contact with water and are considered hydrophobic. Instead, lipids cluster together when mixed with water, never fully dissolving. Molecules that readily form hydrogen bonds with water, on the other hand, are considered hydrophilic (meaning "water loving").
nucleus
the center of an atom and is usually made up of two types of particles called protons and neutrons
In what three ways does RNA differ from DNA?
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List and describe the four key properties of water conferred by its ability to form hydrogen bonds. Be sure to give examples. 1)
1. Cohesion: Water molecules bind to each other due to hydrogen bonding. Water molecules can pull up adjacent water molecules to which they have hydrogen-bonded.
List and describe the four key properties of water conferred by its ability to form hydrogen bonds. Be sure to give examples. 2)
2. Large heat capacity: because water resists warming, it takes a lot of energy to change the temperature of water even a small amount. When we heat water, the added energy doesn't immediately increase the movement of the individual water molecules. Rather, it disrupts some of the hydrogen bonds between the molecules. The hydrogen bonds form again somewhere else, and since the water molecules themselves don't increase their movement, the temperature doesn't increase.
List and describe the four key properties of water conferred by its ability to form hydrogen bonds. Be sure to give examples. 3)
3. Low density as a solid: As the cooling molecules slow down, they pack together more and more efficiently-and densely. Water, however, becomes less dense, this unusual property is due to hydrogen bonding. As the temperature drops and water molecules slow down, each V-shaped water molecule bonds with four partners, via hydrogen bonds, forming a crystalline lattice in which the molecules are held slightly farther apart than in the liquid, causing ice to be less dense than water.
List and describe the four key properties of water conferred by its ability to form hydrogen bonds. Be sure to give examples. 4)
4. Good solvent: If you put a pinch of table salt into a glass of water, it will quickly dissolve. This means that all the charged sodium (Na+) and chloride (Cl-) ions that were ionically bonded together become separated from one another. The sodium and chloride ions were initially attracted to each other because they carry a slight opposing charge. Water is able to pry them apart because, as a polar molecule, it, too carries charges. The positively charged sodium ions are attracted to the negatively charged side of the water molecules, and the negatively charged chloride ions are attracted to the positively charged side. The ionic bonds holding together the ions are broken, and each ion becomes surrounded by water molecules. Water pries apart ionic bonds, dissolving ionic compounds.
peptide bond
A bond in which the amino group of one amino acid is bonded to the carboxyl group of another; two amino acids so joined form a dipeptide, several amino acids so joined form a polypeptide.
complex carbohydrate
A carbohydrate that contains multiple simple carbohydrates linked together; examples are starch, which is the primary form of energy storage in plants, and glycogen, which is the primary form of short-term energy storage in animals.
glycogen
A complex carbohydrate consisting of stored glucose molecules linked to form a large web, which breaks down to release glucose when it is needed for energy.
cellulose
A complex carbohydrate, indigestible by humans, that serve as the structural material for a huge variety of plant structures. It is the single most prevalent organic compound on earth.
molecule
A group of atoms held together by covalent bonds
macromolecule
A large molecule, made up of smaller building blocks or subunits; the four main types of biological macromolecules are carbohydrates, lipids, proteins, and nucleic acids.
pH
A logarithmic scale that measures the concentration of hydrogen ions (H+) in a solution, which decreasing values indicating increasing acidity. Water, in which the concentration of hydrogen ions (H+) equals the concentration of hydroxyl ions (OH-), has pH=7, the midpoint of the scale.
nucleotide
A molecule containing a phosphate group, a sugar molecule, and a nitrogen-containing molecule. Nucleotides are the individual units that together, in a unique sequence, constitute a nucleic acid.
deoxyribonucleic acid (DNA)
A nucleic acid that carries information, in the sequences of its nucleotide bases, about the production of particular proteins.
The Effects of Hydrogen Bonds
Ability to make water a liquid at room temperature Hold the molecules together, so more energy (heat) is needed to form steam. Water in its liquid form is a key component for life on Earth
What are the three main types of lipids and what function do they serve in the body?
fats, sterols and phospholipids
What is an ion and how does one form?
An atom that carries an electrical charge, positive or negative, because it has either lost or gained an electron or electrons from its normal, stable configuration.
base (chemistry)
Any fluid with a pH above 7.0, that is, with more OH- ions than H+ ions in solution.
hydrophilic
Attracted to water, as, for example, polar molecules that readily form hydrogen bonds with water.
Carbohydrates C, H, and O Primary fuel for organisms Cell structure
Carbohydrates are molecules that contain mostly carbon, hydrogen, and oxygen: they are the primary fuel for running all of the cellular machinery and also form much of the structure of cells in all life forms. Sometimes they contain atoms of other elements, but they must have carbon, hydrogen, and oxygen to be considered a carbohydrate. Further, a carbohydrate generally has approximately the same number of carbon atoms as it does H2O units. For instance, the best-known carbohydrate, glucose, has the composition C6H12O6 (6 carbons and a little math will show us that it also has 6 H2O units; notice that 6 x H2 = H12 and 6 x O = O6). A carbohydrate called maltose has the composition C12H22O11 (Figure 2-20 All carbohydrates have a similar structure and function).
disaccharide
Carbohydrates formed by the union of two simple sugars, such as sucrose (table sugar) and lactose (the sugar found in milk).
Carbohydrates Make a bond... ...store energy. Break a bond... ...release energy
Carbohydrates function well as fuels because their many carbon-hydrogen bonds store a great deal of energy. These C-H bonds are easily broken and organisms can capture the energy released when the bond is broken and put it to use.
The Versatility of Carbon
Carbon's electron configuration gives it considerable versatility when it comes to bonding with other atoms and making important compounds Carbon has 6 electrons overall: 2 in the first electron shell and 4 in the second electron shell. Because the second electron shell has a capacity of 8 electrons, carbon can share its 4 electrons in its outermost shell. This gives it an ability to bond with other atoms in a large number of different ways—including in four different directions—and makes a huge variety of complex molecules possible (Fig. 2-7). Carbon most commonly bonds with oxygen, hydrogen, and nitrogen. And because carbon atoms often bind to other carbon atoms, carbon chains are very common—and each carbon bound to two other carbon atoms can still bind with one or two additional atoms. These carbon chains are present in most organic molecules.
Macromolecules
Carbon..... "backbone" of all organic molecules.... because it can covalently bond 4 times
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Cholesterol is an important component of most cell membranes. For this reason, it is an essential molecule to living organisms. It has a bad reputation in most Western cultures, though, that is mostly well-deserved. When humans ingest too much cholesterol (present in animal-based foods such as egg yolks, red meat, and cream) and high levels of cholesterol circulate in our bloodstream, the cholesterol can attach to blood vessel walls and cause them to thicken. In turn, this thickening can lead to high blood pressure, a major contributor to strokes and heart attacks. For these reasons, nutritionists advise limiting the consumption of foods high in cholesterol. Surprisingly, most of the cholesterol in our blood doesn't come from actually consuming it directly. Instead, cells in our liver produce almost 90% of the circulating cholesterol. How do they do it? By transforming the saturated fats in our diet. For this reason, the best way to reduce cholesterol levels may be to consume fewer saturated fats.
Water: High Surface Tension
Each water molecule is "V"-shaped (Figure 2-13 Walking on water!). The hydrogen atoms are at the end of each arm and the oxygen is at the bottom end of the "V" between the two hydrogen atoms. Oxygen's strongly, positively charged nucleus pulls the circling electrons toward itself and holds onto them for more than its fair share of the time. Consequently, the oxygen at the bottom of the "V" has a slight negative charge and the end of the water molecule containing the hydrogen atoms has a slight positive charge. Hydrogen bonds are much weaker than covalent bonds and they don't last very long. Nonetheless, to the Jesus lizard, the cumulative effect of all of the hydrogen bonds is to link together all of the water molecules in the stream just enough to give the water a surface tension with some net-like properties. If the lizard was too fat or too slow, its weight would overwhelm the hydrogen bonds and the lizard would push the molecules apart and sink like a rock.
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Enzymes are very choosy: they bind only with their appropriate substrate molecules, much like a lock that can be opened with one key (Figure 2-42 part 2 Lock and key). It is important that an enzyme have the right configuration (ultimately the correct sequence of aa's). The exposed atoms in the active site have electrical charges that attract rather than repel the substrate molecules, and only the substrate molecules can fit into the active site groove. Once the substrate is bound to the active site, a reaction can take place—and usually does very quickly. An enzyme can help to bring about the reaction in a variety of ways. These include: 1) By stressing, bending, or stretching critical chemical bonds, increasing their likelihood of breaking. 2) By directly participating in the reaction, perhaps temporarily sharing one or more electrons with the substrate molecule, thereby giving it chemical features that increase its ability to make or break other bonds. 3) By creating a microhabitat that is conducive to the reaction. For instance, the active site might be a water-free, nonpolar environment, or it might have a slightly higher or lower pH than the surrounding fluid. Both of these slight alterations might increase the likelihood that a particular reaction occurs. 4) By simply orienting or holding substrate molecules in place so that they can be modified.
Energy is stored within molecules
Example: glucose Plants produce glucose via photosynthesis using energy from the sun Organisms produce ATP via cellular respiration using energy from glucose
Lipids are macromolecules with several functions, including energy storage. Non-soluble in water Insulation Membrane formation Hormones Long term high energy storage
Fat molecules contain much more stored energy than carbohydrate molecules. That is, the chemical breakdown of fat molecules releases significantly more energy. A single gram of carbohydrates stores about four calories of energy, while the exact same amount of fat stores about 9 calories—not unlike the difference between a five dollar bill and a ten dollar bill. Because fats store such a large amount of energy, animals have evolved a strong taste preference for fats over other energy sources (Figure 2-30 Animals (including humans!) prefer the taste of fats). Organisms evolving in an environment of uncertain food supply will build the largest surplus by consuming molecules that hold the most amount of energy in the smallest mass. This feature helped humans to survive millions of years ago, but today puts us in danger from the health risks of obesity now that fats are all too readily available.
Types of Carbohydrates
Monosaccharides Glucose & fructose Disaccharides Lactose & sucrose Polysaccharides Starch & cellulose Glycogen
Why wouldn't your blood and other fluids become significantly acidic after you drink a half gallon of orange juice?
Most of the chemicals that aid in the chemical reactions within our blood or cells stop functioning well if the pH swings by less than half a point. Fortunately there are some chemicals that act like bank accounts for H+ ions (Figure 2-19 Maintaining a constant internal environment). Called buffers, these chemicals can quickly absorb excess H+ ions to keep a solution from becoming too acidic and they can quickly release H+ ions to counteract any increases in OH concentration.
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Not all lipids are fats, nor do they necessarily function in energy storage. A second group of lipids, called the sterols plays an important role in regulating growth and development (Fig. 2-34). Steroids (Sterols) are made up of 4 carbon rings Cholesterol, estrogen, and testosterone are examples. Waxes are present on the outside of plants and insects (prevents desication); also present on wing feathers of some birds.
amino acid
One of 20 molecules built of an amino group, a carboxyl group, and a unique side chain. Proteins are constructed of combinations of amino acids linked together.
carbohydrate
One of the four types of biological macromolecules containing mostly carbon, hydrogen, and oxygen. It is the primary fuel for cellular activity and form much of the cell structure in all life forms.
protein
One of the four types of biological macromolecules, constructed of unique combinations of 20 amino acids that result in unique structures and chemical behavior. Proteins are the chief building blocks of tissues in most organisms.
lipid
One of the four types of biological macromolecules, insoluble in water and greasy to the touch. Lipids are important in energy storage and insulation (fats), membrane formation (phospholipids), and regulating growth and development (sterols).
nucleic acid
One of the four types of biological macromolecules, involved in information storage and transfer. The nucleic acids DNA and RNA store genetic information in unique sequences of nucleotides.
base (of DNA)
One of the nitrogen-containing side-chain molecules attached to a sugar molecule in the sugar-phosphate backbone of DNA and RNA. The four bases in DNA are adenine (A), thymine (T), guanine (G), and cytosine (C); the four bases in RNA are adenine (A), uracil (U), guanine (G), and cytosine (C). The information in a molecule of DNA and RNA is determined by its sequence of bases.
cholesterol
One of the sterols, a group of lipids important in regulating growth and development; an important component of most cell membranes, helping the membrane maintain its flexibility.
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One protein "misspelling" is responsible for the condition called lactose intolerance. Remember, DNA/RNA codes to build the aa's and proteins. The sequence of amino acids determines how the enzyme will fold upon itself. It must be a perfect match for the substrate and enzyme to "fit together". Normally, during digestion the lactose in milk is broken down into its component parts, glucose and galactose. The simple sugars are then used for energy. But some people are unable to break the bond linking the two simple sugars because they lack a functioning version of the enzyme lactase that assists in this process. Consequently, the lactose passes through their stomach and small intestine undigested. Then, when it reaches the large intestine, bacteria living inside us consume it. The problem is, as they break down the lactose, they produce some carbon dioxide and other hydrogen gases. These gases are trapped in the intestine and lead to severe discomfort. These unpleasant symptoms can be avoided by not consuming milk, cheese, yogurt, ice cream or any other dairy products, but they can also be avoided by taking a pill containing the enzyme lactase. It doesn't matter how the enzyme gets there, as long as it is in your digestive system the lactose in the milk can be broken down.
Which elements are most abundant in organisms ("The Big Four")?
Oxygen, Carbon, Hydrogen, Nitrogen and they make up more than 96% of your body mass
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Protein shape is particularly critical in enzymes, molecules that help initiate and accelerate the chemical reactions in our bodies. Enzymes emerge in their original form when the reaction is complete and thus can be used again and again.
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Proteins are formed by linking individual amino acids together with a peptide bond, in which the amino group of one amino acid is bonded to the carboxyl group of another (Figure 2-39 Protein structure). Two amino acids joined together is a dipeptide, and several amino acids joined together is a polypeptide.
List and describe the three subatomic particles that make up an atom.
Protons: particles that have a positive electrical charge. Neutrons: particles that have no electrical charge. Electrons: negatively charged particle that moves around the atomic nucleus.
Hydrogen bonds give water special qualities. 2. Water has features that enables it to support all life.
Section 2-2 Opener Water flowing down a Japanese waterfall. All life on earth depends on water; organisms are made up mostly from water and require it more than any other molecule. Hydrogen bonding among water molecules gives water several important properties that contribute to its important role in the biology of all organisms
Four Types of Macromolecules 1. Carbohydrates
Section 2-3 Opener Worldwide, more corn is produced (by weight) than any other grain.
Four Types of Macromolecules 2. Lipids
Section 2-4 Opener A well-insulated harbor seal, in Alaska. Lipids are a second group of macromolecules important to all living organisms. Lipids are made primarily from atoms of carbon, hydrogen, and oxygen, just as carbohydrates are, but the atoms are in different proportions. In particular, while carbohydrates usually have two hydrogen atoms for every oxygen, lipids have more hydrogen atoms for each carbon. As a result, there are significantly more C-H bonds and significantly more energy stored in lipid molecules. What exactly is a lipid? That's not as easy to answer as you might expect. Lipids come in a wide variety of structures. They don't have any unique subunits (like the simple sugars that make up di- and polysaccharides) or a particular ratio of atoms that serve as defining features. Consequently, lipids are defined based on their physical characteristics. Most notably, lipids do not dissolve in water and are greasy to the touch, like salad dressings.
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Section 2-5 Opener Hair and feathers are built from proteins.
What is pH? Draw a pH scale and label it with the following: high concentration of H+, low concentration of H+, acidic, neutral, basic, numbers 0-14
The amount of H+ or OH in a fluid gives it some important properties. In particular, the amount of H+ in a solution is a measure of its acidity and is called pH. The more free hydrogen ions floating around, the more acidic the solution is. Pure water is in the middle of the pH scale, with a pH of 7.0. Any fluid with a pH below 7.0 has more H+ ions (and fewer OH ions) and is considered an acid. Any fluid with a pH above 7.0 has fewer H+ ions (and more OH ions) and is considered a base. The pH scale is logarithmic, like the Richter Scale for earthquakes: an increase in 1 on the scale represents a ten-fold increase in the hydrogen ion concentration. An increase of 2 represents a hundred-fold increase. This means that Coke, with a pH of about 3.0, is 10,000 times (!) more acidic than a glass of water, with a pH of 7.0.
Living systems are highly sensitive to acidic and basic conditions. pH Scales Acids Bases
The amount of H+ or OH in a fluid gives it some important properties. In particular, the amount of H+ in a solution is a measure of its acidity and is called pH. The more free hydrogen ions floating around, the more acidic the solution is. Pure water is in the middle of the pH scale, with a pH of 7.0. Any fluid with a pH below 7.0 has more H+ ions (and fewer OH ions) and is considered an acid. Any fluid with a pH above 7.0 has fewer H+ ions (and more OH ions) and is considered a base. The pH scale is logarithmic, like the Richter Scale for earthquakes: an increase in 1 on the scale represents a ten-fold increase in the hydrogen ion concentration. An increase of 2 represents a hundred-fold increase. This means that Coke, with a pH of about 3.0, is 10,000 times (!) more acidic than a glass of water, with a pH of 7.0.
Four Types of Macromolecules (Organic Molecules) 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids
The are four types of macromolecules—large molecules made up from smaller building blocks—found in living organisms: carbohydrates, lipids, proteins, and nucleic acids.
denaturation
The disruption of protein folding, in which secondary and tertiary structures are lost, caused by exposure to extreme conditions in the environment such as heat or extreme pH.
Blood pH Buffers
The pH of blood is usually 7.4. Given that most cellular reactions produce or consume H+ molecules, there ought to be great swings in the pH of our blood. Unfortunately, our bodies can't tolerate such swings. Most of the chemicals that aid in the chemical reactions within our blood or cells stop functioning well if the pH swings by less than half a point. Fortunately there are some chemicals that act like bank accounts for H+ ions (Figure 2-19 Maintaining a constant internal environment). Called buffers, these chemicals can quickly absorb excess H+ ions to keep a solution from becoming too acidic and they can quickly release H+ ions to counteract any increases in OH concentration.
active site
The part of an enzyme to which reactants (or substrates) bind and undergo a chemical reaction.
primary structure
The sequence of amino acids in a polypeptide chain.
monosaccharides
The simplest carbohydrates and the building blocks of more complex carbohydrates; they cannot be broken down into other monosaccharides; examples are glucose, fructose, and galactose; also known as simple sugars.
double helix
The spiraling ladder-like structure of DNA composed of two strands of nucleotides; the bases protruding from each strand like "half-rungs" meet in the center and bind to each other (via hydrogen bonds), holding the ladder together.
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The steroid hormones estrogen and testosterone are built by slight chemical modifications to cholesterol. These are among the primary molecules that direct and regulate sexual development, maturation, and sperm and egg production. In both males and females, estrogen influences memory and mood, among other traits. Testosterone has numerous effects, one of which is to stimulate muscle growth. As a consequence, athletes often take synthetic variants of testosterone to increase their muscularity. But the usage of these supplements is often accompanied by dangerous side effects, though, including extreme aggressiveness ("'roid rage"), high cholesterol, and, following long-term use, cancer. As a consequence, nearly all athletic organizations have banned their use. Figure 2-34 Dangerous bulk.
bond energy
The strength of a bond between two atoms, defined as the energy required to break the bond.
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The two intertwining spirals fit together because only two combinations of bases pair up together. The base A always pairs with T and C always pairs with G. Consequently, if the base sequence of one of the spirals is CCCCTTAGGAACC, the base sequence of the other must be GGGGAATCCTTGG. That is why researchers working on the Human Genome Project describe only one sequence of nucleotides when presenting a DNA sequence. With that sequence, we can infer the identity of the bases in the complementary sequence and thus we know the exact structure of the nucleic acid. The sequence of base pairs containing the information about how to produce a particular protein may be anywhere from a hundred bases to several thousand. In a human, all of the DNA in a cell, containing all of the instructions for every protein that a human must produce, contains about three billion base pairs. This DNA is generally in the nucleus of a cell.
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There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Both play central roles in directing the production of proteins in living organisms, and by doing so play a central role in determining all of the inherited characteristics of an individual. In both types of nucleic acids, the molecule has a consistent backbone: a sugar molecule attached to a phosphate group attached to another sugar, then another phosphate, and so on. Attached to each sugar is one of the nitrogen-containing molecules, called DNA bases due to their chemical structure. A ten-unit nucleic acid therefore would have ten bases, one attached to each sugar within the sugar-phosphate backbone. But the base attached to each sugar is not always the same. It can be one of several different bases. For this reason, a nucleic acid is often described by the sequence of bases attached to the sugar-phosphate backbone.
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Think of an enzyme as a big piece of popcorn. Its tertiary or quaternary structure gives it a complex shape with lots of nooks and crannies. Within one of those nooks is a small area called the "active site" (Figure 2-42 part 1 Lock and key). Based on the chemical properties of the atoms lining this pocket, the active site provides a place for the reactants, called substrate molecules, to nestle briefly
quaternary structure
Two or more polypeptide chains bonded together in a single protein; an example is hemoglobin.
Large Heat Capacity
Walking across a sandy beach on a hot day, you can feel how easily sand heats up. By comparison, stepping into the cooler ocean that same day reveals that water resists warming. It takes a lot of energy to change the temperature of water even a small amount. Why? Again, we must look to hydrogen bonding for our answer. The temperature of a substance is a measure of how quickly all of the molecules are moving. The molecules move more quickly when energy is added in the form of heat. When we heat water, the added energy doesn't immediately increase the movement of the individual water molecules. Rather, it disrupts some of the hydrogen bonds between the molecules (Figure 2-15 Water as a moderator of temperature change). As quickly as they can be disrupted, though, they form again somewhere else. And since the water molecules themselves don't increase their movement, the temperature doesn't increase. The net effect is that even if you release a lot of energy into water, the temperature doesn't change much. Because so much of your body is water, you are able to maintain relatively constant body temperatures.
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We have examined three of life's macromolecules: carbohydrates, lipids, and proteins. We turn our attention now to the fourth: nucleic acids, macromolecules that store information and are made up of individual units called nucleotides. All nucleotides have three components: a molecule of sugar, a phosphate group (containing a phosphorous atom bound to four oxygen atoms), and a nitrogen-containing molecule (Figure 2-43 The molecules that carry genetic information).
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You can't look at a living organism and not see proteins (Figure 2-36 Proteins everywhere!). Inside and out, proteins are the chief building blocks of all life. They make up skin and feathers and horns. They make up bones and muscles. In your bloodstream, proteins fight invading microorganisms and stop you from bleeding to death from a shaving cut. Proteins control the levels of sugar and other chemicals in your bloodstream and carry oxygen from one place in your body to another. And in just about every cell in every living organism, proteins called enzymes initiate and assist all chemical reactions that occur.
What are atoms and elements?
a bit of matter that cannot be subdivided any further without losing its essential properties.
electron
a negatively charged particle that moves around the atomic nucleus
enzyme
a protein that initiates and accelerates a chemical reaction in a living organism. It is found throughout the cell; enzymatic proteins take part in chemical reactions on the inside and outside surfaces of the plasma membrane.
What are elements?
a substance that cannot be broken down chemically into any other substances. Whatever the element, if you keep cutting it into ever smaller pieces, each of the pieces behaves exactly the same as any other piece.
What is the difference between atoms and elements?
an element will stay an element until the tiny pieces can no longer be divided without losing its property, then it becomes an atom
acid
any fluid with pH below 7.0, indicating the presence of more H+ ions than OH- ions in solution
proton
particles that have a positive electrical charge
neutron
particles that have no electric charge
All nucleotides contain 3 parts
phosphate, pentose sugar (5-carbon sugar), nitrogen containing base
What is a polar molecule?
when water molecules have unequally shared electrons