Biochemistry Test 1

Front 1

Cysteine residues play an important role in the structure of many proteins by

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providing covalent links between parts of a protein molecule or between two different protein chains

Front 2

L-alanine and D-alanine are:

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enantiomers.

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The level of protein structure that describes all aspects of the three-dimensional folding of a polypeptide is referred to as the

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tertiary structure

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The level of protein structure that describes all covalent bonds (peptide and disulfide bonds) that link amino acids residues in a polypeptide chain.

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primary structure

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The level of protein structure that refers to stable arrangements of amino acid residues that give rise to recurring structural patterns, such as an α-helix.

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secondary structure

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The level of protein structure that describes the arrangement in space of the polypeptide subunits of a protein that consists of two or more polypeptides.

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quaternary structure

Front 7

A protein retained on an affinity chromatography column is usually eluted off the column by

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adding the protein's free ligand.
Affinity chromatography uses a specific ligand that is cross-linked to the column beads. After specific binding of a protein to its ligand on the column, the protein can be eluted from the column by adding a solution containing the protein's free ligand.

Front 8

Sodium dodecyl sulfate (SDS) is used in the electrophoresis of proteins to

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separate the subunits of a multisubunit protein.
SDS, which is an ionic detergent, will disrupt the noncovalent bonds that allow the association between most subunits of a multisubunit protein. In addition, SDS binds proteins and contributes a large net negative charge, rendering the intrinsic charge of the protein insignificant and conferring on each protein a similar charge-to-mass ratio. This allows electrophoresis to separate proteins on the basis of their mass (molecular weight) rather than on their intrinsic charge.

Front 9

Two proteins that have the same molecular weight but differ in their pI are best separated by

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two-dimensional electrophoresis.
Two-dimensional electrophoresis separates proteins of identical molecular weight that differ in pI or proteins with similar pI values but different molecular weights. In two-dimensional electrophoresis, proteins are first subjected to isoelectric focusing to separate them by their pI, then they are subjected to SDS electrophoresis to separate them by molecular weight.

Front 10

Affinity chromatography separates proteins according to

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their binding specificities.

Front 11

Size exclusion chromatography separates proteins according to

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size

Front 12

SDS polyacrylamide gel electrophoresis can resolve proteins that

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differ in molecular weight.

Front 13

When an enzymatic activity is purified from a complex mixture of proteins what usually happens to the total amount of protein and the specific activity during the purification process?

Back 13

The total amount protein decreases and the specific activity increases.
s the particular enzymatic activity is purified, the unwanted proteins are discarded and the protein with the specific activity is concentrated at each step. Therefore, with successive purification steps the total amount of protein decreases, but the specific activity increases.

Front 14

T/F: Peptides are synthesized on an insoluble support.

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True. Peptides are synthesized while being attached at one end to a solid support of an insoluble polymer. This technique, invented by R. Bruce Merrifield, obviated the need to purify the product after each step.

Front 15

T/F: Peptides are synthesized in an N-terminal to C-terminal direction.

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False. Chemical synthesis proceeds from the carboxyl terminus to the amino terminus, in which the α-amino group of the N-terminal amino acid is chemically protected to block unwanted reactions.

Front 16

T/F: Peptides must be purified (isolated) after each addition cycle.

Back 16

False. Peptides are not synthesized in solution, so they do not need to be purified after each addition cycle. Peptides are synthesized while being attached at one end to a solid support. This technique, invented by R. Bruce Merrifield, obviated the need to purify the product after each step.

Front 17

T/F: Peptides of any length can be synthesized.

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False. The practical limit of peptide length is approximately 100 amino acids. Because the yield of addition of each amino acid is less than 100%, the overall yield of the final peptide decreases with peptide length.

Front 18

T/F: The Edman degradation system will work on any size polypeptide.

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False. Because the efficiency of each cycle is not 100%, the peptides that did not react in earlier cycles would contribute amino acids to an ever-increasing background. Therefore, the Edman degradation system does not work with large polypeptides, which necessitates the cleavage of a large polypeptide with proteases, followed by the sequencing and ordering of the sequences of the peptides to determine the sequence of the original polypeptide.

Front 19

T/F: In the Edman degradation system the amino-terminal residue is labeled and the polypeptide is hydrolyzed to its constituent amino acids.

Back 19

False. In the Edman degradation system, the amino-terminal residue is labeled, cleaved, and identified, and the remaining polypeptide chain is kept intact for the next cycle.

Front 20

T/F: In the Edman degradation system the amino-terminal residue is labeled, cleaved and identified in each successive cycle.

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True. The polypeptide is treated with a reagent that labels the amino-terminal residue, then that residue is removed and identified. In the next cycle, the identity of the new amino-terminal residue is similarly determined, and the procedure is repeated until the entire sequence is determined.

Front 21

T/F: In a hypotonic solution, cells will swell.

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True. In a hypotonic solution the osmolarity is lower than in the cytosol, which causes the cell to swell as water enters.

Front 22

T/F: In an isotonic solution, cells will shrink.

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False. In an isotonic solution, the cell stays the same. Because the cytosol and the solution have the same osmolarity, the cell neither gains nor loses water.

Front 23

T/F: In a hypertonic solution, cells will stay the same.

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False. In a hypertonic solution the osmolarity is higher than in the cytosol, which causes the cell to shrink as water flows out.

Front 24

T/F: Cells can neither shrink nor swell because water cannot penetrate the plasma membrane.

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False. Water can shrink or swell depending on the osmolarity of the solution that they are in. Because of the plasma membrane, cells are more permeable to water than to other small molecules, ions and macromolecules. Thus water can pass freely, but these other molecules usually cannot.

Front 25

T/F: When bases ionize, they donate protons.

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False. Bases are proton acceptors; acids are proton donors.

Front 26

T/F: Strong acids and bases are completely ionized in dilute aqueous solutions.

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True. Strong acids and bases are completely ionized in dilute aqueous solutions, while weak acids and bases are not completely ionized.

Front 27

T/F: The dissociation constant of a strong acid is lower than that for a weak acid.

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False. The dissociation constant, K a, equals [H+][A-]/[HA]. Because strong acids are more completely ionized than weak acids, Ka will be larger for a strong acid.

Front 28

T/F: The pK a of a strong acid will be higher than that for a weak acid.

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False. Strong acids dissociate more completely and therefore have a high Ka (Ka = [H+][A-]/[HA]). Because the pK a is the -logK a, the stronger the acid, the lower the pKa.

Front 29

Cells need to be buffered because

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they need to maintain a specific cytosolic pH to keep biomolecules at their optimal ionic state.
Because all biological processes are pH dependent, cells need a mechanism to maintain the optimal pH (usually near pH 7) at which the cell's biomolecules best function.

Front 30

T/F: Condensation reactions are invariably exergonic.

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False. Hydrolysis reactions are exergonic. Condensation reactions require energy (are endergonic) and therefore must be coupled to the hydrolysis of ATP.

Front 31

T/F: Condensation reactions involve the depolymerizion of macromolecules.

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False. Condensation reactions involve the polymerization of macromolecules.

Front 32

T/F: Condensation reactions involve the loss of the elements of water.

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True. Condensation reactions, such as the formation of ATP from ADP and inorganic phosphate, involve the loss of water.

Front 33

T/F: A typical condensation reaction is the formation of ADP from ATP and inorganic phosphate.

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False. A typical condensation is the formation of ATP from ADP and inorganic phosphate.

Front 34

Hydrophobic interactions account for

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why the nonpolar regions of molecules cluster together in water.
Hydrophobic interactions are the forces that hold the nonpolar regions of molecules together in water. Hydrophobic interactions provide thermodynamic stability to a system by minimizing the number of ordered water molecules required to surround hydrophobic portions of the solute molecules.

Front 35

T/F: Water can form hydrogen bonds with NaCl.

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False. Water cannot form hydrogen bonds with NaCl. Hydrogen bonds form between an electronegative atom, such as oxygen or nitrogen, and a hydrogen atom covalently bonded to another electronegative atom.

Front 36

T/F: NaCl does not spontaneously dissolve in water because the Na+ and Cl- ions are in the form of a stable crystalline lattice.

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False.NaCl readily dissolves in water because this results in an increase in entropy.

Front 37

T/F: Crystalline salts dissolve in water because it results in an increase in entropy.

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True. Crystalline salts such as NaCl readily dissolve in water because it results in an increase in entropy of the system.

Front 38

T/F: Crystalline salts dissolve in water because water adds to the electrostatic attractions of Na+ and Cl- ions.

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False. Na+ and Cl- ions are hydrated by water, which neutralizes the ionic charges and weakens the electrostatic attractions necessary for lattice formation.

Front 39

A buffer system consists of

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a weak acid and its conjugate base.
A buffer system, which resists changes in pH when small amounts of acid or base are added, consists of a weak acid (a proton donor) and its conjugate base (a proton acceptor). The weak acid, which is a proton donor, contains a reserve of H+, which can be released to neutralize an addition of OH- to the system, forming H2O; similarly, the conjugate base can react with H+ ions added to the system.

Front 40

T/F: The pH for optimal buffering power of a weak acid is 7.00

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False. The pH for optimal buffering power of a weak acid is its pKa. Recall that buffer systems consist of a weak acid and its conjugate base. At the pK a the weak acid is at a one-to-one molar ratio with its conjugate base, providing maximal buffering capacity to absorb small amounts of added acid or base.

Front 41

T/F: You can calculate the pKa of an acid, given the pH and the molar ratio of the acid and its conjugate base.

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True. Using the Henderson-Hasselbalch equation.

Front 42

T/F: The pK a of a weak acid is the pH at which the acid is completely dissociated.

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False. The pK a of a weak acid is the pH at which the acid is half dissociated, such that the concentrations of an acid and its conjugate base are equal.

Front 43

T/F: At a pH below the pK a of a weak acid, its conjugate base will predominate.

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False. The conjugate base of a weak acid will predominate above the pKa.

Front 44

A dynamic steady state results when

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the rate of intake or synthesis of a molecule equals the rate of its disappearance.
A dynamic steady state results when the rate of synthesis or intake of a molecule equals the rate of its breakdown, consumption, or conversion into some other product. For example, a dynamic steady state in the blood maintains constant levels of hemoglobin and glucose.

Front 45

An open system is one

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that exchanges both matter and energy with its surroundings.
If a system exchanges energy and matter with its surroundings, it is called an open system. A living organism, for example, is an open system because it exchanges matter and energy with its surroundings.

Front 46

T/F: All organisms obtain their energy directly from the radiant energy of sunlight.

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False. Many organisms and cells obtain their energy only indirectly from solar energy by consuming the products of photosynthetic cells, such as starch and sucrose.

Front 47

T/F: Photosynthetic cells use light energy to drive electrons from one molecule to another.

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True. Photosynthetic cells absorb light energy and use it to drive electrons from water to carbon dioxide to form energy-rich products such as glucose, starch, and sucrose.

Front 48

T/F: Photosynthetic cells use light energy to produce CO2 that can be used as energy by non-photosynthetic cells.

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False. Photosynthetic cells use light energy to not to produce CO2 but to convert it into energy-rich products such as glucose, starch, and sucrose that can be used by non-photosynthetic cells.

Front 49

T/F: Photosynthetic cells absorb light energy and use it to break down compounds such as starch and sucrose.

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False. Photosynthetic cells absorb light energy and use it to drive electrons from water to carbon dioxide to form energy-rich products such as glucose, starch, and sucrose.

Front 50

T/F: Carbon-carbon double bonds have freedom of rotation.

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False. Carbon-carbon double bonds have no freedom of rotation.

Front 51

T/F: Carbon atoms can form covalent bonds with up to four other atoms.

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True. Carbon atoms have four unpaired electrons and therefore can share electron pairs (covalent bonds) with up to four other atoms. In addition to forming single covalent bonds with four atoms, carbon can form two single and one double bond, etc.

Front 52

T/F: Carbon can form double bonds with hydrogen.

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False. Carbon can form only a single bond with hydrogen because hydrogen has only one unpaired electron available for forming a covalent bond.

Front 53

T/F: Carbon-carbon single bonds cannot rotate.

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False. Carbon-carbon single bonds have freedom of rotation.

Front 54

The difference between phototrophs and chemotrophs is

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their energy source.
Phototrophs obtain energy from sunlight and chemotrophs obtain their energy from chemical compounds.

Front 55

Both prokaryotic and eukaryotic cells possess which of the following?

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a plasma membrane.
Prokaryotic and eukaryotic cells both have a plasma membrane that encloses the cytoplasm.

Front 56

Exergonic and endergonic reactions differ in that

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exergonic reactions produce products with less free energy than the reactants; endergonic reactions produce products with more free energy than the reactants.
Exergonic reactions produce products with less free energy than the reactants; endergonic reactions produce products with more free energy than the reactants. Because the products of an exergonic reaction have less free energy than the reactants, the reaction releases free energy that is available to do work.

Front 57

The three-dimensional structure (native conformation) of proteins is determined primarily by

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its amino acid sequence.
The three-dimensional structure of proteins is dictated by its amino acid sequence.

Front 58

T/F: Degradative reactions require an input of energy.

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False. Degradative, or catabolic, reactions yield free energy, which can be harnessed into the synthesis of high-energy ATP.

Front 59

T/F: Synthetic pathways are anabolic.

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True. Anabolic reactions include the synthesis of complex molecules such as proteins and nucleic acids.

Front 60

T/F: Catabolism and anabolism are linked by O2.

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False. Overall, catabolism and anabolism are linked by ATP. The nutrients and foods broken down in catabolic reactions generate energy in the form of ATP, which drives anabolic reactions needed to synthesize biomolecules.

Front 61

T/F: Catabolic reactions require the breakdown of ATP, and anabolic reactions generate ATP.

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False. Catabolic reactions, being exergonic, use the free energy of catabolism to generate ATP. Anabolic reactions, being endergonic, require the energy of ATP.

Front 62

T/F: Enzymes are consumed in the process of converting one molecule to another.

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False. Enzymes are catalysts, which means that they are not consumed in a cellular chemical reaction and can act repeatedly to convert particular molecules into other molecules.

Front 63

T/F: Enzymes are needed to carry out only endergonic reactions.

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False. Enzymes are needed to increase the rate of virtually all cellular chemical reactions. Even the rate of exergonic reactions in the cell proceeds too slowly and therefore must be increased.

Front 64

T/F: Enzymes are needed in the cell to increase the rate of a chemical reaction.

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True. Enzymes are catalysts that increase the rate of virtually all cellular chemical reactions, which would not otherwise occur at any measurable rate.

Front 65

T/F: Enzymes eliminate the activation barrier.

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False. Reactants must overcome an activation barrier in order to be converted to products. Enzymes catalyze reactions by lowering (but not eliminating) the activation barrier.

Front 66

How can thermodynamically unfavorable reactions, such as the synthesis of DNA and protein polymers, occur in cells?

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Cells couple thermodynamically unfavorable reactions to the hydrolysis of ATP.
The free-energy deficit of a thermodynamically unfavorable reaction (with a positive ΔG) can be overcome by coupling the reaction to one that is favorable (with a negative ΔG), such as the hydrolysis of ATP, so that the overall process is exergonic (the sum of the ΔG's is negative).

Front 67

Under what conditions is a carbon atom a chiral center?

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if it has four different substituent groups.
A carbon atom with four different substituent groups is said to be asymmetric, and asymmetric carbons are called chiral centers.

Front 68

T/F: Stereoisomers have different configurations.

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True. Stereoisomers, which are molecules with a different spatial arrangement of atoms, have different configurations.

Front 69

T/F: Stereoisomers are indistinguishable by enzymes.

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False. Enzymes are able to distinguish between stereoisomers.

Front 70

T/F: Stereoisomers have different chemical bonds.

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False. Stereoisomers have the same chemical bonds, but differ in their spatial arrangement of atoms.

Front 71

T/F: Stereoisomers exist in equal amounts in living organisms.

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False. In living organisms, chiral molecules are usually present in only one of their stereoisomer forms. For example, the amino acids in proteins occur only in their L isomers.

Front 72

Paralogs and orthologs differ in that

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Paralogs exist in the same species and orthologs exist in different species.
If two homologous genes occur in the same species, they are said to be paralogous and their protein products are paralogs. Two homologous genes (or proteins) found in different species are said to be orthologous, and their protein products are orthologs.

Front 73

Supramolecular complexes of proteins, nucleic acids, and polysaccharides are not held together by

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covalent bonds.
The monomeric subunits of proteins, nucleic acids, and polysaccharides are joined by covalent bonds, whereas the supramolecular complexes of these molecules are held together by much weaker noncovalent interactions such as ionic interactions, hydrogen bonds, hydrophobic interactions, and van der Waals interactions. Because they are held together by weak interactions, supramolecular complexes are easier to form and dissociate as needed.

Front 74

Aromatic R Groups

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Phenylalanine
Tyrosine
Tryptophan

Front 75

NonPolar, Aliphatic R Groups

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Glycine
Alanine
Proline
Valine
Leucine
Isoleucine
Methionine

Front 76

Polar, Uncharged R Groups

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Serine
Threonine
Cysteine
Asparagine
Glutamine

Front 77

Positively Charged (Basic) R Groups

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Lysine
Arginine
Histidine

Front 78

Negatively Charged (Acidic) R Groups

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Aspartate
Glutamate