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Most covalent bonds involve the sharing of two electrons, one donated by each participating atom; these are called *single bonds*. Some covalent bonds, however, involve the sharing of more than one pair of electrons. Four electrons can be shared, for example, two coming from each participating atom; such a bond is call... | {
"Header 1": "Chemical Components of Cells",
"Header 3": "There Are Different Types of Covalent Bonds",
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(A) The spatial arrangement of the covalent bonds that can be formed by oxygen, nitrogen, and carbon. (B) Molecules formed from these atoms therefore have a precise three-dimensional structure defined by the bond angles and bond lengths for each covalent linkage. A water molecule, for example, forms a "V" shape with an... | {
"Header 1": "Chemical Components of Cells",
"Header 2": "Figure 2–9 Covalent bonds are characterized by particular geometries.",
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We have already seen that the covalent bond between two atoms has a characteristic length that depends on the atoms involved. A further crucial property of any chemical bond is its strength. Bond strength is measured by the amount of energy that must be supplied to break the bond, usually expressed in units of either k... | {
"Header 1": "is relatively nonpolar. Covalent Bonds Vary in Strength",
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**Ionic bonds** are usually formed between atoms that can attain a completely filled outer shell most easily by donating electrons to—or accepting electrons from—another atom, rather than by sharing them. For example, returning to Figure 2–5, we see that a sodium (Na) atom can achieve a filled outer shell by giving up ... | {
"Header 1": "is relatively nonpolar. Covalent Bonds Vary in Strength",
"Header 3": "Ionic Bonds Form by the Gain and Loss of Electrons",
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In aqueous solution, ionic bonds are 10–100 times weaker than the covalent bonds that hold atoms together in molecules. But this weakness has its place: much of biology depends on specific but transient interactions between one molecule and another. These associations are mediated by noncovalent bonds. Although noncova... | {
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"Header 3": "Noncovalent Bonds Help Bring Molecules Together in Cells",
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Water accounts for about 70% of a cell's weight, and most intracellular reactions occur in an aqueous environment. Life on Earth is thought to have begun in the ocean. Thus the properties of water have put a permanent stamp on the chemistry of living things.
In each molecule of water (H2O), the two H atoms are linked... | {
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"Header 3": "Hydrogen Bonds Are Important Noncovalent Bonds For Many Biological Molecules",
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If we disregard water, nearly all the molecules in a cell are based on carbon. Carbon is outstanding among all the elements in its ability to form large molecules; silicon—an element with the same number of electrons in its outer shell—is a poor second. Because a carbon atom is small and
#### Question 2–5
A. Are th... | {
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"Header 3": "A Cell Is Formed from Carbon Compounds",
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The small organic molecules of the cell are carbon compounds with molecular weights in the range 100–1000 that contain up to 30 or so carbon atoms. They are usually found free in solution in the cytosol and have many different roles. Some are used as *monomer* subunits to construct the cell's giant polymeric *macromole... | {
"Header 1": "is relatively nonpolar. Covalent Bonds Vary in Strength",
"Header 3": "Cells Contain Four Major Families of Small Organic Molecules",
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The simplest sugars—the *monosaccharides*—are compounds with the general formula (CH2O)*n*, where *n* is usually 3, 4, 5, or 6. Sugars, and the larger molecules made from them, are also called *carbohydrates* because of this simple formula. Glucose, for example, has the formula C6H12O6 (Figure 2–17). The formula, howev... | {
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"Header 3": "Sugars Are Both Energy Sources and Subunits of Polysaccharides",
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A **fatty acid** molecule, such as *palmitic acid*, has two chemically distinct regions. One is a long hydrocarbon chain, which is hydrophobic and not very reactive chemically. The other is a carboxyl (–COOH) group,
Figure 2–18 Two monosaccharides can be linked by a covalent glycosidic ... | {
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"Header 3": "Fatty Acid Chains Are Components of Cell Membranes",
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Amino acids are small organic molecules with one defining property: they all possess a carboxylic acid group and an amino group, both linked to their α-carbon atom (Figure 2–22). Each amino acid also has a side chain attached to its α-carbon. The identity of this side chain is what distinguishes one amino acid from ano... | {
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"Header 3": "Amino Acids Are the Subunits of Proteins",
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Why do you suppose only l-amino acids and not a random mixture of the l- and d-forms of each amino acid are used to make proteins?
Figure 2–23 Amino acids in a protein are held together by peptide bonds. The four amino acids shown are linked together by three peptide bonds, one of which is highlighted in *yellow*. On... | {
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"Header 3": "Question 2–6",
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DNA and RNA are built from subunits called nucleotides. *Nucleosides* are made of a nitrogen-containing ring compound linked to a five-carbon sugar, which can be either ribose or deoxyribose (Panel 2–6, pp. 76–77). Nucleotides are nucleosides that contain one or more phosphate groups attached to the sugar, and they com... | {
"Header 1": "is relatively nonpolar. Covalent Bonds Vary in Strength",
"Header 3": "Nucleotides Are the Subunits of DNA and RNA",
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On the basis of weight, macromolecules are by far the most abundant of the organic molecules in a living cell (Figure 2–27). They are the principal building blocks from which a cell is constructed and also the components that confer the most distinctive properties on living things. Intermediate in size and complexity b... | {
"Header 1": "is relatively nonpolar. Covalent Bonds Vary in Strength",
"Header 3": "Macromolecules in Cells",
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Although the chemical reactions for adding subunits to each polymer are different in detail for proteins, nucleic acids, and polysaccharides, they share important features. Each polymer grows by the addition of a monomer onto one end of the polymer chain via a condensation reaction, in which a molecule of water is lost... | {
"Header 1": "Each Macromolecule Contains a Specific Sequence of Subunits",
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The idea that proteins, polysaccharides, and nucleic acids are large molecules that are constructed from smaller subunits, linked one after another into long molecular chains, may seem fairly obvious today. But this was not always the case. In the early part of the twentieth century, few scientists believed in the exis... | {
"Header 1": "Each Macromolecule Contains a Specific Sequence of Subunits",
"Header 3": "what are macromolecules?",
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Most of the single covalent bonds that link together the subunits in a macromolecule allow rotation of the atoms they join; thus the polymer chain has great flexibility. In principle, this allows a single-chain macromolecule to adopt an almost unlimited number of shapes, or conformations, as the polymer chain writhes a... | {
"Header 1": "Each Macromolecule Contains a Specific Sequence of Subunits",
"Header 3": "Noncovalent Bonds Specify the Precise Shape of a Macromolecule",
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As we discussed earlier, although noncovalent bonds are individually weak, they can add up to create a strong attraction between two molecules when these molecules fit together very closely, like a hand in a glove, so that many noncovalent bonds can occur between them (see Panel 2–7). This form of molecular interaction... | {
"Header 1": "Each Macromolecule Contains a Specific Sequence of Subunits",
"Header 3": "Noncovalent Bonds Allow a Macromolecule to Bind Other Selected Molecules",
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- • Living cells obey the same chemical and physical laws as nonliving things. Like all other forms of matter, they are made of atoms, which are the smallest unit of a chemical element that retain the distinctive chemical properties of that element.
- • Cells are made up of a limited number of elements, four of which—C... | {
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"Header 3": "Essential Concepts",
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acid inorganic molecule amino acid ion
atom ionic bond atomic weight lipid
ATP lipid bilayer Avogadro's number macromolecule base molecule
buffer molecular weight chemical bond monomer
chemical group noncovalent bond
condensation reaction nucleotide conformation organic molecule covalent bond pH scale
DNA p... | {
"Header 1": "Each Macromolecule Contains a Specific Sequence of Subunits",
"Header 3": "Key terms",
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A covalent bond forms when two atoms come very close together and share one or more of their outer-shell electrons. Each atom forms a fixed number of covalent bonds in a defined spatial arrangement.
SINGLE BONDS: two electrons shared per bond
![](_page... | {
"Header 1": "Each Macromolecule Contains a Specific Sequence of Subunits",
"Header 3": "**COVALENT BONDS**",
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A carbon chain can include double bonds. If these are on alternate carbon atoms, the bonding electrons move within the molecule, stabilizing the structure by a phenomenon called resonance.
the truth is somewhere between these two structures
Alternating double bonds in a ring can generate a very stable structure.
... | {
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"Header 3": "ALTERNATING DOUBLE BONDS",
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#### WATER STRUCTURE
Molecules of water join together transiently in a hydrogen-bonded lattice.
The cohesive nature of water is responsible for many of its unusual properties, such as high surface tension, high specific heat, and high heat of vaporization.
#### HYDROPHILIC MOLECU... | {
"Header 1": "Each Macromolecule Contains a Specific Sequence of Subunits",
"Header 3": "ALTERNATING DOUBLE BONDS",
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Monosaccharides usually have the general formula $(CH_2O)_n$ , where n can be 3, 4, 5, or 6, and have two or more hydroxyl groups. They either contain an aldehyde group $(-c \leqslant_H^0)$ and are called aldoses, or a ketone group (>c=0) and are called ketoses.
| | 3-carbon (TRIOSES) | 5... | {
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"Header 3": "MONOSACCHARIDES",
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All fatty acids have carboxyl groups at one end and long hydrocarbon tails at the other.
Hundreds of different kinds of fatty acids exist. Some have one or more double bonds in their hydrocarbon tail and are said to be unsaturated. Fatty acids with no double bonds are saturated.
![](_p... | {
"Header 1": "Each Macromolecule Contains a Specific Sequence of Subunits",
"Header 3": "**FATTY ACIDS**",
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Steroids have a common multiple-ring structure.
cholesterol—found in many cell membranes testosterone—male sex hormone
#### GLYCOLIPIDS
Like phospholipids, these compounds are composed of a hydrophobic region, containing two long hydrocarbon tails, an... | {
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"Header 3": "STEROIDS",
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The general formula of an amino acid is
R is commonly one of 20 different side chains. At pH 7, both the amino and carboxyl groups are ionized.
#### OPTICAL ISOMERS
The $\alpha$ -carbon atom is asymmetric, allowing for two mirror-image (or stereo-) isomers, L and D.
![](_page_98_P... | {
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"Header 3": "THE AMINO ACID",
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(Val, or V)
H C C O N H CH3 CH3 CH
#### leucine
(Leu, or L)
H C C O N H CH2 CH CH3 CH3
#### isoleucine
(Ile, or I)
H C C O N H CH3 CH2 CH CH3
#### proline
(Pro, or P)
$$\begin{array}{cccccccccccccccccccccccccccccccccccc$$
#### phenylalanine
(Phe, or F)
H C C O N H CH2
#### methionine
(Met,... | {
"Header 1": "Each Macromolecule Contains a Specific Sequence of Subunits",
"Header 3": "valine",
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The base is linked to the same carbon (C1) used in sugar–sugar bonds.
#### **NOMENCLATURE**
The names can be confusing, but the abbreviations are clear.
| BASE | NUCLEOSIDE | ABBR. |
|----------|------------|-------|
| adenine | adenosine | Α ... | {
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"Header 3": "BASE-SUGAR LINKAGE",
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Charged groups are shielded by their interactions with water molecules. Electrostatic attractions are therefore quite weak in water.
Inorganic ions in solution can also cluster around charged groups and further weaken these electrostatic
Despite bein... | {
"Header 1": "ELECTROSTATIC ATTRACTIONS IN AQUEOUS SOLUTIONS",
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#### Question 2–10
Which of the following statements are correct? Explain your answers.
- A. An atomic nucleus contains protons and neutrons.
- B. An atom has more electrons than protons.
- C. The nucleus is surrounded by a double membrane.
- D. All atoms of the same element have the same number of neutrons.
- E. T... | {
"Header 1": "ELECTROSTATIC ATTRACTIONS IN AQUEOUS SOLUTIONS",
"Header 3": "Questions",
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One property above all makes living things seem almost miraculously different from nonliving matter: they create and maintain order in a universe that is tending always toward greater disorder. To accomplish this remarkable feat, the cells in a living organism must carry out a neverending stream of chemical reactions t... | {
"Header 1": "Energy, Catalysis, and Biosynthesis",
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The universal tendency of things to become disordered is expressed in a fundamental law of physics, the *second law of thermodynamics*. This law states that, in the universe or in any isolated system (a collection of matter that is completely isolated from the rest of the universe), the degree of disorder can only incr... | {
"Header 1": "Energy, Catalysis, and Biosynthesis",
"Header 3": "Biological Order Is Made Possible by the Release of Heat Energy from Cells",
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According to the *first law of thermodynamics*, energy cannot be created or destroyed—but it can be converted from one form to another (Figure 3–6). Cells take advantage of this law of thermodynamics, for example, when they convert the energy from sunlight into the energy in the chemical bonds of sugars and other small... | {
"Header 1": "Energy, Catalysis, and Biosynthesis",
"Header 3": "Cells Can Convert Energy from One Form to Another",
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All animals live on energy stored in the chemical bonds of organic molecules, which they take in as food. These food molecules also provide the atoms that animals need to construct new living matter. Some animals obtain their food by eating other animals, others by eating plants. Plants, by contrast, obtain their energ... | {
"Header 1": "Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules",
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All animal and plant cells require the chemical energy stored in the chemical bonds of organic molecules—either the sugars that a plant has produced by photosynthesis as food for itself or the mixture of large and small molecules that an animal has eaten. To use this energy to live, grow, and reproduce, organisms must ... | {
"Header 1": "Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules",
"Header 3": "Cells Obtain Energy by the Oxidation of Organic Molecules",
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Paper burns readily, releasing into the atmosphere water and carbon dioxide as gases, while simultaneously releasing energy as heat:
paper +
$$O_2 \rightarrow smoke + ashes + heat + CO_2 + H_2O$$
This reaction occurs in only one direction: smoke and ashes never spontaneously gather carbon dioxide and water from the... | {
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"Header 3": "Chemical Reactions Proceed in the Direction that Causes a Loss of Free Energy",
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In which of the following reactions does the *red* atom undergo an oxidation?
- A. Na → Na+ (Na atom → Na+ ion)
- B. Cl → Cl– (Cl atom → Cl– ion)
- C. CH3CH2OH → CH3CHO (ethanol → acetaldehyde)
- D. CH3CHO → CH3COO–
- (acetaldehyde → acetic acid)
- E. CH2=CH2 → CH3CH3
- (ethene → ethane)
Figure 3–12 Even energetica... | {
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"Header 2": "Question 3–2",
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According to the second law of thermodynamics, a chemical reaction can proceed only if it results in a net (overall) increase in the disorder of the universe (see Figure 3–5). Disorder increases when useful energy that could be harnessed to do work is dissipated as heat. The useful energy in a system is known as its fr... | {
"Header 1": "Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules",
"Header 2": "Question 3–2",
"Header 3": "The Free-Energy Change for a Reaction Determines Whether It Can Occur",
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It's easy to see how a tensed spring, when left to itself, will relax and release its stored energy to the environment as heat. But chemical reactions are a bit more complex—and harder to intuit. That's because whether a reaction will proceed depends not only on the energy stored in each individual molecule, but also o... | {
"Header 1": "Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules",
"Header 2": "Question 3–2",
"Header 3": "Δ*G* Changes As a Reaction Proceeds Toward Equilibrium",
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Because Δ*G* depends on the concentrations of the molecules in the reaction mixture at any given time, it is not a particularly useful value for comparing the relative energies of different types of reactions. But such energetic assessments are necessary, for example, to predict whether an energetically favorable react... | {
"Header 1": "Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules",
"Header 2": "Question 3–2",
"Header 3": "The Standard Free-Energy Change, Δ*G*°, Makes it Possible to Compare the Energetics of Different Reactions",
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As mentioned earlier, all chemical reactions tend to proceed toward equilibrium. Knowing where that equilibrium lies for any given reaction will tell you which way the reaction will proceed—and how far it will go. For example, if a reaction is at equilibrium when the concentration of the product is ten times the concen... | {
"Header 1": "Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules",
"Header 2": "Question 3–2",
"Header 3": "The Equilibrium Constant Is Directly Proportional to Δ*G*°",
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Consider, for example, the combustion of glucose in oxygen:
$$CH_2OH$$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_2OH$
$CH_... | {
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"Header 2": "Question 3–2",
"Header 3": "The Equilibrium Constant Is Directly Proportional to Δ*G*°",
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| | | | $\Delta G^\circ$ (kcal/mole) |
|------------|---------------|--------------------------|------------------------------|
| acetyl P | <b>-</b> | acetate + Pi | -10.3 |
| ATP | $\rightarrow$ | ADP + Pi ... | {
"Header 1": "Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules",
"Header 2": "Question 3–2",
"Header 3": "The Equilibrium Constant Is Directly Proportional to Δ*G*°",
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The concept of free-energy change does not only apply to chemical reactions where covalent bonds are being broken and formed, but also to interactions where one molecule binds to another by means of noncovalent interactions (see Chapter 2, p. 63). Noncovalent interactions are immensely important to cells. They include ... | {
"Header 1": "Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules",
"Header 2": "Question 3–2",
"Header 3": "The Equilibrium Constant Indicates the Strength of Molecular Interactions",
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Now we return to our original concern: how can enzymes catalyze reactions that are energetically unfavorable? One way they do so is by directly coupling energetically unfavorable reactions with energetically favorable ones. Consider, for example, two sequential reactions,
$$X \rightarrow Y$$
and $Y \rightarrow Z$
... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
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Enzymes and their substrates are both present in relatively small amounts in the cytosol of a cell, yet a typical enzyme can capture and process about a thousand substrate molecules every second. This means that an enzyme can release its product and bind a new substrate in a fraction of a millisecond. How do these mole... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "Thermal Motion Allows Enzymes to Find Their Substrates",
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To catalyze a reaction, an enzyme must first bind its substrate. The substrate then undergoes a reaction to form the product, which initially remains bound to the enzyme. Finally, the product is released and diffuses away, leaving the enzyme free to bind another substrate molecule and catalyze another reaction (see Fig... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "*V*max and *K*M Measure Enzyme Performance",
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The energy released by energetically favorable reactions such as the oxidation of food molecules must be stored temporarily before it can be used by cells to fuel energetically unfavorable reactions, such as the synthesis of all the other molecules needed by the cell. In most cases, the energy is stored as chemical-bon... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "Activated Carriers and Biosynthesis",
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When a fuel molecule such as glucose is oxidized in a cell, enzyme-catalyzed reactions ensure that a large part of the free energy released is captured in a chemically useful form, rather than being released wastefully as heat. (Oxidizing sugar in a cell allows you to power metabolic reactions, whereas burning a chocol... | {
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"Header 3": "The Formation of an Activated Carrier Is Coupled to an Energetically Favorable Reaction",
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At first glance, it seems that a cell's metabolic pathways have been pretty well mapped out, with each reaction proceeding predictably to the next—substrate X is converted to product Y, which is passed along to enzyme Z. So why would anyone need to know exactly how tightly a particular enzyme clutches its substrate or ... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "measuring enzyme performance",
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The first step to understanding how an enzyme performs involves determining the maximal velocity, *V*max, for the reaction it catalyzes. This is accomplished by measuring, in a test tube, how rapidly the reaction proceeds in the presence of different concentrations of substrate (Figure 3–27A): the rate should increase ... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "Speed",
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Substrates are not the only molecules that can influence how well or how quickly an enzyme works. In many cases, products, substrate lookalikes, inhibitors, and other small molecules can also increase or decrease enzyme activity. Such regulation allows cells to control when and how rapidly various reactions occur, a pr... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "Control",
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With the kinetic data in hand, we can use computer modeling programs to predict how an enzyme will perform, and even how a cell will respond when exposed to different conditions—such as the addition of a particular sugar or amino acid to the culture medium, or the addition of a poison or a pollutant. Seeing how a cell ... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "Design",
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The most important and versatile of the activated carriers in cells is ATP (adenosine 5'-triphosphate). Just as the energy stored in the raised bucket of water in Figure 3–30B can be used to drive a wide variety of hydraulic machines, ATP serves as a convenient and versatile store, or currency, of energy that can be us... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "ATP Is the Most Widely Used Activated Carrier",
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A common type of reaction that is needed for biosynthesis is one in which two molecules, A and B, are joined together by a covalent bond to produce A–B in the energetically unfavorable condensation reaction:
$$A-H + B-OH \rightarrow A-B + H_2O$$
ATP hydrolysis can be coupled indirectly to this reaction to make it g... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "Energy Stored in ATP Is Often Harnessed to Join Two Molecules Together",
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Other important activated carriers participate in oxidation–reduction reactions and are commonly part of coupled reactions in cells. These activated carriers are specialized to carry both high-energy electrons and hydrogen atoms. The most important of these *electron carriers* are NADH (nicotinamide adenine dinucleotid... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "NADH and NADPH Are Both Activated Carriers of Electrons",
"token_count": 272,
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The phosphoanhydride bond that links two phosphate groups in ATP in a high-energy linkage has a Δ*G*° of –7.3 kcal/mole. Hydrolysis of this bond in a cell liberates from 11 to 13 kcal/mole of usable energy. How can this be? Why do you think a range of energies is given, rather than a precise number as for Δ*G*°?
![](... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "Question 3–8",
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In addition to ATP (which transfers a phosphate) and NADPH and NADH (which transfer electrons and hydrogen), cells make use of other activated carriers that pick up and carry a chemical group in an easily transferred, high-energy linkage. *FADH2*, like NADH and NADPH, carries hydrogen and high-energy electrons (see Fig... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "Cells Make Use of Many Other Activated Carriers",
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The macromolecules of the cell constitute the vast majority of its dry mass—that is, the mass not due to water. These molecules are made from *subunits* (or monomers) that are linked together by bonds formed during an enzyme-catalyzed condensation reaction. The reverse reaction—the breakdown of polymers—occurs through ... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "The Synthesis of Biological Polymers Requires an Energy Input",
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- • Living organisms are able to exist because of a continual input of energy. Part of this energy is used to carry out essential reactions that support cell metabolism, growth, movement, and reproduction; the remainder is lost in the form of heat.
- • The ultimate source of energy for most living organisms is the sun.... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "Essential Concepts",
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#### Question 3–10
Which of the following statements are correct? Explain your answers.
- A. Some enzyme-catalyzed reactions cease completely if their enzyme is absent.
- B. High-energy electrons (such as those found in the activated carriers NADH and NADPH) move faster around the atomic nucleus.
- C. Hydrolysis of... | {
"Header 1": "For Sequential Reactions, the Changes in Free Energy Are Additive",
"Header 3": "Questions",
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Use this graph to estimate the *K*M and the *V*max for this enzyme.
B. Recall from the How We Know essay (pp. 104–106) that to determine these values more precisely, a trick is generally used in which the Michaelis–Menten equation is transformed so that it is possible to plot the data as a straight line. A simple rea... | {
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"Header 3": "Questions",
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When we look at a cell in a microscope or analyze its electrical or biochemical activity, we are, in essence, observing the handiwork of proteins. Proteins are the main building blocks from which cells are assembled, and they constitute most of the cell's dry mass. In addition to providing the cell with shape and struc... | {
"Header 1": "Protein Structure and Function",
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Proteins, as you may recall from Chapter 2, are assembled mainly from a set of 20 different amino acids, each with different chemical properties. A protein molecule is made from a long chain of these amino acids, held together by covalent peptide bonds (Figure 4–1). Proteins are therefore referred to as polypeptides, a... | {
"Header 1": "Protein Structure and Function",
"Header 3": "The Shape of a Protein Is Specified by Its Amino Acid Sequence",
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Each type of protein has a particular three-dimensional structure, which is determined by the order of the amino acids in its polypeptide chain. The final folded structure, or conformation, adopted by any polypeptide chain is determined by energetic considerations: a protein generally folds into the shape in which its ... | {
"Header 1": "Protein Structure and Function",
"Header 3": "Proteins Fold into a Conformation of Lowest Energy",
"token_count": 925,
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Urea used in the experiment shown in Figure 4–7 is a molecule that disrupts the hydrogen-bonded network of water molecules. Why might high concentrations of urea unfold proteins? The structure of urea is shown here.
$$\begin{array}{c} O \\ \parallel \\ C \\ H_2N \end{array}$$
$NH_2$
(A) normal protein can, on occas... | {
"Header 1": "Protein Structure and Function",
"Header 3": "Question 4–1",
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More than 60 years ago, scientists studying hair and silk discovered two common folding patterns present in many different proteins. The first to be discovered, called the **α** helix, was found in the protein *α-keratin*, which is abundant in skin and its derivatives—such as hair, nails, and horns. Within a year of th... | {
"Header 1": "Protein Structure and Function",
"Header 3": "The α Helix and the β Sheet Are Common Folding Patterns",
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The abundance of helices in proteins is, in a way, not surprising. A helix is a regular structure that resembles a spiral staircase. It is generated simply by placing many similar subunits next to one another, each in the same strictly repeated relationship to the one before. Because it is very rare for subunits to joi... | {
"Header 1": "Protein Structure and Function",
"Header 3": "Helices Form Readily in Biological Structures",
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A $\beta$ sheet is made when hydrogen bonds form between segments of a polypeptide chain that lie side by side (see Figure 4–13D). When the neighboring segments run in the same orientation (say, from the N-terminus to the C-terminus), the structure is a *parallel* $\beta$ *sheet*; when they run in opposite directio... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
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A protein's structure does not end with $\alpha$ helices and $\beta$ sheets; there are additional levels of organization. These levels are not independent but are built one upon the next to establish the three-dimensional structure of the entire protein. A protein's structure begins with its amino acid sequence, wh... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 3": "Proteins Have Several Levels of Organization",
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Small protein molecules, such as the oxygen-carrying muscle protein myoglobin, contain only a single domain (see Figure 4–11). Larger proteins can contain as many as several dozen domains, which are usually connected by relatively unstructured lengths of polypeptide chain. Such regions of polypeptide chain lacking any ... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 3": "Many Proteins Also Contain Unstructured Regions",
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Random mutations only very rarely result in changes in a protein that improve its usefulness for the cell, yet useful mutations are selected in evolution. Because these changes are so rare, for each useful mutation there are innumerable mutations that lead to either no improvement or inactive proteins. Why, then, do ce... | {
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"Header 3": "Question 4–3",
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Once a protein had evolved a stable conformation with useful properties, its structure could be modified over time to enable it to perform new functions. We know that this occurred quite often during evolution, because many present-day proteins can be grouped into protein families, in which each family member has an am... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 3": "Proteins Can Be Classified into Families",
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The same type of weak noncovalent bonds that enable a polypeptide chain to fold into a specific conformation also allow proteins to bind to each other to produce larger structures in the cell. Any region on a protein's surface that interacts with another molecule through sets of noncovalent bonds is termed a *binding s... | {
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"Header 3": "Large Protein Molecules Often Contain More Than One Polypeptide Chain",
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Proteins can form even larger assemblies than those discussed so far. Most simply, a chain of identical protein molecules can be formed if the binding site on one protein molecule is complementary to another region on the surface of another protein molecule of the same type. Because each protein molecule is bound to it... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 3": "Proteins Can Assemble into Filaments, Sheets, or Spheres",
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Most of the proteins we have discussed so far are **globular proteins**, in which the polypeptide chain folds up into a compact shape like a ball with an irregular surface. Enzymes, for example, tend to be globular proteins: even though many are large and complicated, with multiple subunits, most have a quaternary stru... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 3": "Some Types of Proteins Have Elongated Fibrous Shapes",
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The helical array of actin molecules in a filament often contains thousands of molecules and extends for micrometers in the cell.
ECB4 m3.30/4.27 Figure 4–28 Many viral capsids are more or less spherical protein assemblies. They are formed from many copies of a small set of protein sub... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 2": "Figure 4–26 An actin filament is composed of identical protein subunits.",
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Many protein molecules are either attached to the outside of a cell's plasma membrane or secreted as part of the extracellular matrix, which exposes them to extracellular conditions. To help maintain their structures, the polypeptide chains in such proteins are often stabilized by covalent cross-linkages. These linkage... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 2": "Figure 4–26 An actin filament is composed of identical protein subunits.",
"Header 3": "Extracellular Proteins Are Often Stabilized by Covalent Cross-Linkages",
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The biological properties of a protein molecule depend on its physical interaction with other molecules. Antibodies attach to viruses or bacteria as part of the body's defenses; the enzyme hexokinase binds glucose and ATP to catalyze a reaction between them; actin molecules bind to one another to assemble into long fil... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 2": "Figure 4–26 An actin filament is composed of identical protein subunits.",
"Header 3": "All Proteins Bind to Other Molecules",
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All proteins must bind to particular ligands to carry out their various functions. For antibodies, the universe of possible ligands is limitless. Each of us has the capacity to produce a huge variety of antibodies, among which there will be one that is capable of recognizing and binding tightly to almost any molecule i... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 2": "Figure 4–26 An actin filament is composed of identical protein subunits.",
"Header 3": "There Are Billions of Different Antibodies, Each with a Different Binding Site",
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"source_pd... |
For many proteins, binding to another molecule is their main function. An actin molecule, for example, need only associate with other actin molecules to form a filament. There are proteins, however, for which ligand binding is simply a necessary first step in their function. This is the case for the large and very impo... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 2": "Figure 4–26 An actin filament is composed of identical protein subunits.",
"Header 3": "Enzymes Are Powerful and Highly Specific Catalysts",
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To explain how enzymes catalyze chemical reactions, we will use the example of lysozyme—an enzyme that acts as a natural antibiotic in egg white, saliva, tears, and other secretions. Lysozyme severs the polysaccharide chains that form the cell walls of bacteria. Because the bacterial cell is under pressure due to intra... | {
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"Header 2": "Figure 4–26 An actin filament is composed of identical protein subunits.",
"Header 3": "Lysozyme Illustrates How an Enzyme Works",
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"source_pdf": "datasets/websources/biochem/Alber... |
#### B CELLS PRODUCE ANTIBODIES
Antibodies are made by a class of white blood cells called B lymphocytes, or B cells. Each resting B cell carries a different membrane-bound antibody molecule on its surface that serves as a receptor for recognizing a specific antigen. When antigen binds to this receptor, the B cell is... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 2": "ANTIBODIES DEFEND US AGAINST INFECTION foreign molecules viruses bacteria ANTIBODIES ( ) CROSS-LINK ANTIGENS INTO AGGREGATES Antibody–antigen aggregates are ingested by phagocytic cells. Special proteins i... |
In the active site of lysozyme, a covalent bond in a polysaccharide molecule is bent and then broken. The top row shows the free substrate and the free products. The three lower panels depict sequential events at the enzyme active site, during which a sugar-sugar covalent bond is broken. Note the change in the conforma... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 2": "ANTIBODIES DEFEND US AGAINST INFECTION foreign molecules viruses bacteria ANTIBODIES ( ) CROSS-LINK ANTIGENS INTO AGGREGATES Antibody–antigen aggregates are ingested by phagocytic cells. Special proteins i... |
Many of the drugs we take to treat or prevent illness work by blocking the activity of a particular enzyme. Cholesterol-lowering *statins* inhibit HMG-CoA reductase, an enzyme involved in the synthesis of cholesterol by the liver. *Methotrexate* kills some types of cancer cells by shutting down dihydrofolate reductase,... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 2": "ANTIBODIES DEFEND US AGAINST INFECTION foreign molecules viruses bacteria ANTIBODIES ( ) CROSS-LINK ANTIGENS INTO AGGREGATES Antibody–antigen aggregates are ingested by phagocytic cells. Special proteins i... |
Although the order of amino acids in proteins gives these macromolecules their shape and functional versatility, sometimes the amino acids by themselves are not enough for a protein to do its job. Just as we use tools to enhance and extend the capabilities of our hands, so proteins often employ small, nonprotein molecu... | {
"Header 1": "$\\boldsymbol{\\beta}$ Sheets Form Rigid Structures at the Core of Many Proteins",
"Header 2": "ANTIBODIES DEFEND US AGAINST INFECTION foreign molecules viruses bacteria ANTIBODIES ( ) CROSS-LINK ANTIGENS INTO AGGREGATES Antibody–antigen aggregates are ingested by phagocytic cells. Special proteins i... |
A living cell contains thousands of different enzymes, many of which are operating at the same time in the same small volume of the cytosol. By their catalytic action, enzymes generate a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the subst... | {
"Header 1": "The Catalytic Activities of Enzymes Are Often Regulated by Other Molecules",
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One feature of feedback inhibition was initially puzzling to those who discovered it. Unlike what one expects to see for a competitive inhibitor (see Figure 3–29), the regulatory molecule often has a shape that is totally different from the shape of the enzyme's preferred substrate. Indeed, when this form of regulation... | {
"Header 1": "Allosteric Enzymes Have Two or More Binding Sites That Influence One Another",
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Enzymes are regulated solely by the binding of small molecules. Another method that eukaryotic cells use with great frequency to regulate protein
activity involves attaching a phosphate group covalently to one or more of the protein's amino acid side chains. Because each phosphate grou... | {
"Header 1": "Phosphorylation Can Control Protein Activity by Causing a Conformational Change",
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Phosphorylation can do more than control a protein's activity; it can create docking sites where other proteins can bind, thus promoting the assembly of proteins into larger complexes. For example, when extracellular signals stimulate a class of cell-surface, transmembrane proteins called *receptor tyrosine kinases*, t... | {
"Header 1": "Phosphorylation Can Control Protein Activity by Causing a Conformational Change",
"Header 3": "Covalent Modifications Also Control the Location and Interaction of Proteins",
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Eukaryotic cells have a second way to regulate protein activity by phosphate addition and removal. In this case, however, the phosphate is not enzymatically transferred from ATP to the protein. Instead, the phosphate is part of a guanine nucleotide—guanosine triphosphate (GTP)—that is bound tightly to various types of ... | {
"Header 1": "Phosphorylation Can Control Protein Activity by Causing a Conformational Change",
"Header 3": "GTP-Binding Proteins Are Also Regulated by the Cyclic Gain and Loss of a Phosphate Group",
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... |
We have seen how conformational changes in proteins play a central part in enzyme regulation and cell signaling. But conformational changes also play another important role in the operation of the eukaryotic cell: they enable certain specialized proteins to drive directed movements of cells and their components. These ... | {
"Header 1": "Phosphorylation Can Control Protein Activity by Causing a Conformational Change",
"Header 3": "ATP Hydrolysis Allows Motor Proteins to Produce Directed Movements in Cells",
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As one progresses from small, single-domain proteins to large proteins formed from many domains, the functions that the proteins can perform become more elaborate. The most complex tasks, however, are carried out by large protein assemblies formed from many protein molecules. Now that it is possible to reconstruct biol... | {
"Header 1": "Phosphorylation Can Control Protein Activity by Causing a Conformational Change",
"Header 3": "Proteins Often Form Large Complexes That Function as Protein Machines",
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Understanding how a particular protein functions calls for detailed structural and biochemical analyses—both of which require large amounts of pure protein. But isolating a single type of protein from the thousands of other proteins present in a cell is a formidable task. For many years, proteins had to be purified dir... | {
"Header 1": "Phosphorylation Can Control Protein Activity by Causing a Conformational Change",
"Header 3": "How Proteins Are Studied",
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Explain why the hypothetical enzymes in Figure 4–47 have a great advantage in opening the safe if they work together in a protein complex, as opposed to working individually in an unlinked, sequential manner.
Figure 4–48 Affinity chromatography can be used to isolate the binding partner... | {
"Header 1": "Phosphorylation Can Control Protein Activity by Causing a Conformational Change",
"Header 3": "Question 4–8",
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The task of determining the amino acid sequence of a protein can be accomplished in several ways. For many years, sequencing a protein was done by directly analyzing the amino acids in the purified protein. First, the protein was broken down into smaller pieces using a selective protease; the enzyme trypsin, for exampl... | {
"Header 1": "Phosphorylation Can Control Protein Activity by Causing a Conformational Change",
"Header 3": "Determining a Protein's Structure Begins with Determining Its Amino Acid Sequence",
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Advances in genetic engineering techniques now permit the production of large quantities of almost any desired protein. In addition to making life much easier for biochemists interested in purifying specific proteins, this ability to churn out huge quantities of a protein has given rise to an entire biotechnology indus... | {
"Header 1": "Phosphorylation Can Control Protein Activity by Causing a Conformational Change",
"Header 3": "Genetic Engineering Techniques Permit the Large-Scale Production, Design, and Analysis of Almost Any Protein",
"token_count": 355,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Bio... |
Biochemists have made enormous progress in understanding the structure and function of proteins over the past 150 years (see Table 4–2, p. 159). These advances are the fruits of decades of painstaking research on isolated proteins, performed by individual scientists working tirelessly on single proteins or protein fami... | {
"Header 1": "The Relatedness of Proteins Aids the Prediction of Protein Structure and Function",
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As you've no doubt already concluded in reading this chapter, for many proteins, their three-dimensional shape determines their function. So to learn more about how a protein works, it helps to know exactly what it looks like.
The problem is that most proteins are too small to be seen in any detail, even with a power... | {
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"Header 3": "PROBING PROTEIN STRUCTURE",
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} |
Subsets and Splits
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