Exam 4 Flashcards by Alexandra Miranda

2008

Which of these statements about the composition of biological membranes is false?

In a given eukaryote cell type (for example, hepatocyte), all intracellular membranes have essentially the same complement of lipids and proteins
The carbohydrate found in membranes is virtually all part of either glycolipids or glycoproteins
The plasma membranes of the cells of which vertebrate animals contain more cholesterol than the mitochondrial membranes
The ratio of lipid to protein varies widely among cell types in a single organism
Triacylglycerols are not commonly found in membranes

In a given eukaryote cell type (for example, hepatocyte), all intracellular membranes have essentially the same complement of lipids and proteins

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2008

Why is it surprising that the side chains of tryptophan residues in proteins can interact with lectins?

because the side chain of tryptophan is hydrophilic and lectins are hydrophobic
because the side chain of tryptophan is (-) charged and lectins are generally (+) charged or neutral
because the side chain of tryptophan can make hydrogen bonds and lectins cannot
because the side chain of tryptophan is hydrophobic and lectins are generally hydrophilic
none of the above

because the side chain of tryptophan is hydrophobic and lectins are generally hydrophilic

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2008

In which of the following can inhibition be overcome at very high substrate concentrations?

noncompetitive inhibition
inhibition in which Lineweaver-Burk lines meet at a point on the I/[S] axis
inhibition in which Lineweaver-Burk lines meet at a point on the I/v axis
inhibition in which Lineweaver-Burk lines never meet
none of the above

inhibition in which Lineweaver-Burk lines meet at a point on the I/v axis

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2008

Sucrose on hydrolysis (in H2O) gives ______ monosaccharides; the product will exist in cyclic forms

1, 2
2, 4
2, 2
2, 6
1, 1

2,6

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2008

Peripheral membrane proteins

are generally noncovalently bound to membrane lipids
are usually denatured when released from membranes
can be released from membranes only by treatment with detergent(s)
may have functional units on both sides of the membrane
penetrate deeply into the lipid bilayer

are generally noncovalently bound to membrane lipids

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2008

Mercury is toxic. Its mechanism of toxicity involves primarily

reaction with protein amino groups
causing extreme fever (The mercury is rising.)
binding to DNA bases
reaction with protein sulfhydryl groups
disruption of membranes

reaction with protein sulfhydryl groups

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2008

The drug methotrexate inhibits dihydrofolate reductase, an enzyme essential for DNA synthesis in cells. It thus prevents cell division. Methotrexate is therefore used in the treatment of cancer, as it inhibits growth of rapidly dividing cells. When tested in vitro, the drug’s inhibition of the enzyme is overcome at saturating substrate concentrations, although Km for substrate is larger in the presence of the inhibitor than in its absence. One can conclude that

methotrexate binds to the enzyme only in the substrate is already bound
methotrexate binds to the enzyme either in the absence or in the presence of the substrate
methotrexate is an allosteric effector of the enzyme
methotrexate is bound to the enzyme only if substrate is not bound
Michaelis-Menten kinetics do not apply

methotrexate is bound to the enzyme only if substrate is not bound

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Glycosamino glycans are negatively charged at pH 7. What components of these polymers confer negative charge?

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2008

Which of these statements is generally true of integral membrane proteins?

A hydropathy plot reveals one or more regions with a high hydorpathy index
The domains that protrude on the cytoplasmic face of the plasma membrane nearly always have covalently attached oligosaccharides
They are unusually susceptible to degradation by trypsin
They can be removed from the membrane with high salt or mild denaturing agents
They undergo constant rotational motion that moves a given domain from the outer face of a membrane to the inner face and then back to the outer

A hydropathy plot reveals one or more regions with a high hydorpathy index

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2008

Which of the following solutions would have the greatest ionic strength?

NaCl at 0.05 M
Na₂SO₄ at 0.05 M
Ribonuclease at pH 2 and 0.05M. The protein has a net charge of +19 at this pH. Its counterion is chloride, so it may be represented as RibonucleaseCl₁₉
Distilled water
Cannot tell from available data

Ribonuclease at pH 2 and 0.05M. The protein has a net charge of +19 at this pH. Its counterion is chloride, so it may be represented as RibonucleaseCl₁₉

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2008

The observation of parallel lines in a series of Lineweaver-Bruk plots severa inhibitor concentrations implies that

the substrate and inhibitor bind at the same site, the binding of one preventing the binding of the other
the substrate and inhibitor can bind in either order, the binding of one having no effect on the binding of the other
the substrate can bind only if the inhibitor is already bound
inihibitor can bind only if substrate is already bound
cannot tell from data given

the substrate can bind only if the inhibitor is already bound

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2008

N-acetyl neuraminic acid is formed from phosphoenol pyruvate and an N-acetyl hexosamine. The latter is

NacGlc
NacGal
NAcFru
NAcMan
None of the above

NAcMan

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2008

The fluidity of the lipid side chains in the interior of a bilayer is generally increased by

a decrease in temperature
an increase in fatty acyl chain length
an increase in the number of double bonds in fatty acids
an increase in the percentage of phosphatidyl membrane
teh binding of water to the fatty acyl side chains

an increase in the number of double bonds in fatty acids

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2008

A plant virus binds to a receptor protein on its target plant cell by means of the interaction between its coat protein and the receptor protein. An experimenter wishes to study the binding reaction in tissue culture in the laboratory. At the pH of the experiment, the receptor has a net negative charge, while the coat protein has a net positive charge. All other factors being equal, at which ionic strength would the binding be strongest?

0.01 M
0.02 M
0.05 M
0.1 M
0.15 M

0.01 M

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2008

In the serine protease reaction mechanism

distortion of the carbonyl of the peptide bond to be cleaved toward tetrahedral geometry lowers the activation energy of the reaction
stabilization of the carbonyl of the peptide bond to be cleaved in its normal planar geometry lowers the activation energy of the reaction
reaction of the enzyme with DIPF will increase activity toward a protein substrate
hydrogen bonds play no significant role
none of the above is true

distortion of the carbonyl of the peptide bond to be cleaved toward tetrahedral geometry lowers the activation energy of the reaction

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2008

A process not involving the fusion of two membranes or two regions of the same membrane is

endocytosis
entry of enveloped viruses into cells
entry of glucose into cells
exocytosis
reproductive budding in yeast

entry of glucose into cells

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2008

How many of the 20 amino acids found in proteins have at least one atom of nitrogen in their side chians? Do not count proline, its nitrogen is part of the backbone

Three
Five
Six
Fewer than three
More than six

Six

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In the serine protease reaction mechanism, which of the following has the highest free energy?

the initial ES complex
the acyl enzyme complex
the tetrahedral intermediate
the first product
the second product

the tetrahedral intermediate

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2008

From the abbreviation name Glcα1→2βFru, which of the following is false?

Fru is at the reducing end
Glc is at the non-reducing end
Fru is at the non-reducing end
Fru and Glc are both at non-reducing ends
A solution in H2) will not display mutarotation

Fru is at the reducing end

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2008

The αβ-barrel protein folding motif is found in many hundreds of proteins which have no sequence similarity whatsoever, and when their gene sequence are examined, these, too, show no sequence similarity. This suggests that

all such proteins are descended from a common αβ-barrel protein ancestral protein
nature “invented” the αβ-barrel protein structure more than once
the genes for αβ-barrel proteins have been transferred among different species
the sequence data must not be correct
none of the above could be correct

nature “invented” the αβ-barrel protein structure more than once

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2008

Which of the following makes serine 195 in chymotrypsin into a strong nucleophile when serives are not normally highly nucleophilic?

reaction with DIPF
the development of negative charge on the Ser195 hydroxyl oxygen by the charge relay system
binding of the substrate
a rise in pH
none of the above

the development of negative charge on the Ser195 hydroxyl oxygen by the charge relay system

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2008

sphingosine is not a component of

cardiolipin
ceramide
cerebrosides
gangliosides
sphingomyelin

cardiolipin

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2008

In doing site specific mutagenesis experiments, the absorbance of a DNA solution is used to determine the DNA concentration. When the DNA from a cell preparation is measured in a 0.1 cm cell, the absorbance is so high, the spectrophotometer cannot obtain a reading. Which of the following would be the researcher’s best course of action?

Use a 1 cm cell
Dilute the solution with buffer
Use a 0.2 cm cell
Denature the DNA prior to measuring its concentration
none of these would help at all

Dilute the solution with buffer

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2008

The activity of a normal allosteric enzyme is

high at low substrate [] and low at high substrate []
low at low substrate [] and low at high substrate []
low at low substrate [] and high at high substrate []
high at low substrate [] and high at high substrate []
the same at all substrate []

low at low substrate [] and high at high substrate []

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# 2008 Which of the following statements about membrane lipids is true * Glycerophospholipids are found only in the membranes of plant cells * Glycerophospholipids contain fatty acids linked to glycerol through amide bonds * Lecithin (phosphatidylcholine), which is used as an emulsifier in margarine and chocolate, is a shpingolipd * Some sphingolipids include oligosaccharides in their structure * Triacylglycerols are the principal components of erythrocyte memranes.

Some sphingolipids include oligosaccharides in their structure

# 2008 A ligand-gated ion channel (such as the nicotinic acetylchlroide receptor) is * A. a charged lipid in the membrane bilayer that allows ions to pass through. * B. a membrane protein that permits a ligand to pass through the membrane only when opened by the appropriate ion. * C. a membrane protein that permits an ion to pass through the membrane only when opened by the appropriate ligand. * D. a molecule that binds to the membrane, thereby allowing ions to pass through. * E. requiring a second ligand to close the channel once it is opened

C. a membrane protein that permits an ion to pass through the membrane only when opened by the appropriate ligand.

# 2008 Imagine a tripeptide which does not contain proline. If each phi and psi bond has three possible allowed positions, how many backbone conformations can the tripeptide assume? The first phi and last psi may be ignored, as rotation about them does not change the spatial relationship of backbone atoms to one another. * A. Three * B. Four * C. 3⁴ * D. 4³ * E. none of these

C. 3⁴

# 2008 Which of the following is true of an allosteric enzyme? * Allosteric enzymes allow particular steps in metabolism to be revesible depending on which effectors are present * Allosteric enzymes allow for feedback inhibition of metabolic pathways by catalyzing the first committed step in the path whose final product acts as allosteric inhibitor * Allosteric enzymes show Michaelis-Menten kinetics in the presence of their effectors but not in the absence * None of the above is true

Allosteric enzymes allow for feedback inhibition of metabolic pathways by catalyzing the first committed step in the path whose final product acts as allosteric inhibitor

# 2008 Fatty acids are a component of * carotenes * cerebrosides * sterols * vitamin D * vitamin K

cerebrosides

# 2008 Teh specificity of the potassium channel for K+ over Na+ is mainly the result of the * differential interaction with the selectivity filter protein * hydrophobicity of the channel * phospholipid composition of the channel * presence of carbohydrates in the channel * presence of cholesterol in the channel

differential interaction with the selectivity filter protein

# 2008 How many amino acid residues are required to make a tight turn (one in which the direction of the polypeptide chain changes by approximately 180 degrees) * one * two * three * four * more than four

four

# 2008 Consider a double stranded piece of DNA one of whose strands has the sequence GATTACA as in the movie of that name. How many hydrogen bonds connect the bases of one strand to those of the other? * A. None * B. Seven * C. Fourteen * D. Sixteen * E. Twenty-one

D. Sixteen

# 2008 An example of a glycerophospholipid that is involved in cell signaling is * arachidonic acid * ceramide * phosphatidylinositol * testosterone * Vitamin A (retinol)

phosphatidylinositol

# 2008 Consider the transport of K+ from the blood (where its concentration is about 4mM) into an erythrocyte that contains 150 mM K+. The transmembrane potential is about 60 mV, inside negative relative to outside. The free energy change for this transport process is: (These values may be of use to you: R = 8.315 J/mol -K; T = 298 K; 9 (Faraday constant) = 96,480 J/V; N = 6.022 x 10²³/mol) * about 3 J/mol * about -15 J/mol * about -3 kJ/mol * about 15 kJ/mol * about +3 kJ/mol

about +3 kJ/mol

# 2008 Where in a protein’s three dimensional structure would the mutation of an alanine residue to leucine be least likely to lead to a stable, biochemically active enzyme? * A. at the amino terminus * B. at the carboxy terminus * C. on the surface * D. deep in the protein interior * E. Such mutations are tolerated throughout protein structures.

D. deep in the protein interior

# 2008 Which of the following has the highest melting point? * C_20:4^Δ5,8,11,14 * C_18:0 * C_18:1^Δ9 * C_15:0

C_18:0

# 2008 What is the unity principle in biology? * An organism's set of proteins and the substances with which they interact constitute a unified network of materials * All organisms of a given species funciton in essentially the same way and differ from the organisms of a differnet species in how they function * All living things share the same basic sets of molecule, the same basic metabolic processes and the same basic genetic apparatus * The biosphere is so diverse there is no such thing as a unity principle * None of the above

All living things share the same basic sets of molecule, the same basic metabolic processes and the same basic genetic apparatus

# 2008 Urea is often used as an unfolding (denaturing) agent in studies of protein folding. According to a paper published in teh journal Protein Science, the enzyme glutamine synthase unfolds slowly in 4 M urea, following first order kinetics as it does so. The half life for loss both of activity and of native secondary structure is 1,030 sec. How long will it take for the activity to fall to 25% of its initial value? * 1,030 sec * 2,060 sec * 3,090 sec * less than 1030 sec * more than 3,090 sec

2,060 sec

# 2008 Supercoiled DNA * A. travels faster in gel electrophoresis than relaxed DNA. * B. travels at the same rate as relaxed DNA in gel electrophoresis. * C. travels more slowly than relaxed DNA in gel electrophoresis. * D. travels at rates which have nothing to do with the supercoiling. * E. cannot enter electrophoresis gels.

A. travels faster in gel electrophoresis than relaxed DNA.

# 2008 The inner (plasma) membrane of E. coli is about 75% lipid and 25% protein by weight. How many molecules of membrane lipid are there for each molecule of protein? (Assume that the average protein is Mr 50,000 and the average lipid is 750.) * A. 1 * B. 50 * C. 200 * D. 10,000 * E. 50,000

C. 200

# 2008 A protein is known to have its amino terminus blocked by an acetyl group, which makes the terminus unreactive. The protein is reacted with a very large excess of an aldehyde to form Schiff's bases, and the resulting product is reduced with sodium borotritide (NaBT₄). The tritium (T) is radioactive. When the radioactivity is measured it is found that fourteen atoms of tritium have been introduced per molecule of protein. How many lysine residues does the protein contain? * 14 * 7 * 21 * 2 * None, there is no reaction under these conditions with NaBT₄

# 2008 In first order reactions the half life is * A. proportional to the reactant concentration. * B. proportional to the square of the reactant concentration. * C. proportional to the logarithm of the reactant concentration n * D. proportional to the time * E. independent of the reactant concentration.

E. independent of the reactant concentration.

# 2008 Which of the following is not a characteristic of living organisms? * They extract chemical energy form the sun and/or radiant energy from the sun * They produce their own structural components and the organization of these components * They may do chemical work, mechanical work, and osmotic work (pumping materials against their concentration gradients) * They increase their own overall entropy, using the resulting free energy to drive theri metabolic reactions * all of the above are characteristics of living organism

They increase their own overall entropy, using the resulting free energy to drive theri metabolic reactions

# 2008 Which is the closes biochemical equivalent to money within an organism * carbon dioxide * water * glucose * ATP * all of these can serve as biochemical money

ATP

# 2008 In the structure of t-RNA the anticodon and the amino acid acceptor site are * at the 5' and 3' ends of the polynucleotide chain respectively * close to one another in the three dimensional space of the molecule * buried in the interior of the molecule * as far from one another as the molecular structure will allow * are adjacent to the unclecodon

as far from one another as the molecular structure will allow

# 2011 Sucrose is a product of photosynthesis and is synthesized by a number of enzymes. However, glucose (glc) in water exists as a mixture of α and β pyranoses whereas fructose (fru) exists as a mixture of α and β pyranoses and α and β furanoses. Sucrose is glc (pyranose) α1 - 2β fru (furanose). This is because * A - In water the main isomers are a glucopyranose and β fructofuranose. * B - The sucrose synthetic enzymes are very specific and only use as substrates a glucopyranose and β fructofuranose out of the complex equilibrium mixture. * The synthetic enzymes specifically form glc α1→2β fru linkage. * A and B * B and C

B and C

# 2011 α-D-glucopyranose has a specific rotation [α] = + 112.2° where as β-D-glucopyranose has a specific rotation of +18.7 °. What is the composition of a mixture which has a specific rotation of 83.0 °? * 50% α and 50% β * 60% α and 40% β * 68% α and 32% β * 80% α and 20% β * 32% α and 68% β

68% α and 32% β

# 2011 The commercial product Beano contains enzymes that hydrolyse stachyose completely. To give complete hydrolysis of stachyose the enzymes (exoglycosidases) have to include: 1. β glucosidase. 2. invertase 3. α galactosidase 4. β-galactosidase 5. B, C, and D

B, C, and D

# 2011 Which of the following disaccharides can be extended to form a cellulose polymer? 1. Sucrose 2. Trehalose 3. Maltose 4. Lactose 5. None of the above

None of the above

# 2011 How many isomers of D-Glucopyranose are possible? ## Footnote A. 2 B. 4 C. 8 D. 16 E. 32

D. 16

# 2011 A cell surface receptor 1. reacts only with molecules too large to cross the lasma membrane. 2. when bound to its ligand, could result in activation of an enzymatic cascade. 3. always opens an ion channel when bound to its ligand. 4. must produce a second messenger when it binds to its ligand.

when bound to its ligand, could result in activation of an enzymatic cascade.

# 2011 Cells can terminate signal transduction by cell surface receptors by 1. reducing agonist availability in the vicinity of the target cell. 2. internalizing and degrading the receptor-agonist complex. 3. modifying the receptor so that it is inactive or desensitized. 4. All of the above 5. None of the above

All of the above

# 2011 Calmodulin is 1. a nonspecific kinase. 2. a protein that binds Ca²⁺ 3. a second messenger 4. an activator of nitric oxide synthase 5. a protein channel that facilitates the influx of Ca²⁺

a protein that binds Ca²

# 2011 The PI system begins with activation of phospholipase C, which initiates a sequence of events including all of the following except 1. activation of lP3 by action of a phosphotase 2. increase in intracellular Ca²⁺ concentration 3. release of diacylglycerol (DAG) from a phospholipid 4. activation of protein kinase C 5. phosphorylation of certain cytoplasmic proteins

activation of lP3 by action of a phosphotase

# 2011 Which of the following statements concerning G proteins is correct? 1. G proteins bind the appropriate hormone at the cell surface. 2. GTP is bound to G rotein in the resting state. 3. α-Subunit may be either stimulatory or inhibitory because it has two forms. 4. Adenylate cyclase can be activated only if a- and P-subunits of G protein are associated with each other. 5. Hydrolysis of GTP is necessary for G protein subunits to separate.

α-Subunit may be either stimulatory or inhibitory because it has two forms.

# 2011 The shortest a helix segment in a protein that will span a membrane bilayer has about residues. ## Footnote A. 5 B. 20 C. 50 D. 100 E. 200

# 2011 How many phospholipid molecules are there in a 1 m² region of a phospholipid bilayer membrane? Assume that a phospholipid molecule occupies 70A² (lA = 10^-8cm) of the surface area. A. 7 X 10⁴ B. 7 X 10⁶ C. 2.89 x 10⁶ D. 1.43 x 10⁶ E. 1.43 x 10²

2.89 x 10⁶

# 2011 Although proteins rarely if ever flip-flop across a membrane, distribu tion of membrane lipids between the two membrane layers does occur except in the case of glycolipids. Why are glycolipids less likely to flip-flop? 1. Glycolipids are larger than lipids. 2. Glycolipids are smaller than lipids. 3. Hydrophobic nature of glycolipids. 4. shifting from aerobic to anaerobic metabolism 5. synthesizing thicker membranes to insulate the cell

Hydrophobic nature of glycolipids.

# 2011 An ion conducting channel exhibits a currency increment of 5p ampere at a membrane potential of -50mV (positive outside). How many univalent ions flow through the channel when open for 1 m second? Note 1 ampere represents a flow of 6.24 x 10¹⁸ charges/second 1. 3. l x lO⁴ 2. 3. l x lO⁷ 3. 1550 4. 6.2 X 10⁵ 5. 3. l x lO²

3. l x lO⁴

# 2011 Consider the transport of glucose into an erythrocyte by facilitated diffusion. When the glucose concentrations are 5 mM on the outside and 0.1 mM on the inside, the free-energy change for glucose uptake into the cell is: (These values may be of use to you: R = 8.315 J/mol-K; T= 298 K; 9 (Faraday constant)= 96,480 J/V; *N=* 6.022 x 10²³/mol.) 1. less than 2 kJ/mol. 2. about - lOkJ/mol. 3. about 30kJ/mol. 4. about -30 kJoule/mol. 5. impossible to calculate without knowledge of the membrane potential.

about - lOkJ/mol

# 2011 The rates of transport for two compounds indole and glucose across a cell membrane are shown in the figure; This suggests: 1. Two different transporters, one of indole the other for glucose. 2. Both compounds are simply diffusing. 3. Both use the same transporter which has different K_t for indole and glucose 4. Giucose has has a specific transporter whereas indole simply diffuses 5. Indole is transported by active transport

Giucose has has a specific transporter whereas indole simply diffuses

# 2011 Acetycholine esterase has k_cat 25000 sec^-1 and k_cat/Km 1.6 x10⁸ s-¹ M. The rate of diffusion of enzyme and substrate is 10⁸ to 10⁹ s^-1 m^-1_. This tells us that acetylcholine esterase 1. Operates close to the maximum so as to limit the time that acetylcholine lasts in the synaptic cleft. 2. Acetylcholine esterase operates too slowly. 3. would open the ion channels for a short period. 4. would open the ion channels for a long period. 5. A and C IE. **A and C**

A and C

# 2011 Which of the following vitalist statements did J. B. Sumner's crystallization of the enzyme urease disprove? 1. The substances composing living matter are qualitatively different from those of the non-living world. 2. Living matter may be like non-living, but organisms arise from non-living matter by spontaneous generation through the intervention of the "vital force." 3. We may be able to make some of the substances of living matter, but the reactions constituting life occur only in living cells. 4. Structure of "ferments" is too complex to be described in chemical terms, and the nature of catalysis is not comprehensible 5. none of the above

Structure of "ferments" is too complex to be described in chemical terms, and the nature of catalysis is not comprehensible

# 2011 The low packing density of liquid water is due to 1. the hydrophobic effect 2. re:eulsion between ionic charges of the same sign 3. the geometry and rigidity of hydrogen bonds 4. the attraction between ionic charges of opposite sign 5. more than one of the above

the geometry and rigidity of hydrogen bonds

# 2011 Which of the following statements about buffers is true? 1. The pH of a buffered solution remains constant no matter how much acid or base is added to the solution. 2. The strongest buffers are those composed of strong acids and strong bases. 3. A buffer composed of a weak acid of pKa = 5 is stronger at H 4 than at pH 6. 4. When pH = pKa, the weak acid and its salt concentrations are equal 5. None of the above is true

When pH = pKa, the weak acid and its salt concentrations are equal

# 2011 A solution containing these proteins is applied at pH 3 to a cation exchange column and eluted with a buffer gradient whose pH rises from 3 to 11.5. In what order will the proteins elute? 1. CYT C, CBP, HHB, HSA, HGG, CAT 2. CYT C, HHB, HGG, CBP, CAT, HSA 3. HSA, CAT, CBP, HGG, HHB, CYT C 4. CAT, HGG, HSA, HHB, CBP, CYT C 5. none of the above

HSA, CAT, CBP, HGG, HHB, CYT C

# 2011 A solution containing these proteins is applied to a molecular sieve (gel filtration) column in phosphate buffered saline at pH 7.2 and eluted with the same buffer. In which order do they elute? 1. CYT C, CBP, HHB, HSA, HGG, CAT 2. CYT C, HHB, HGG, CBP, CAT, HSA 3. HSA, CAT, CBP, HGG, HHB, CYT C 4. CAT, HGG, HSA, HHB, CBP, CYT C 5. none of the above

CAT, HGG, HSA, HHB, CBP, CYT C

# 2011 A solution containing these proteins is applied at pH 3 to an anion exchange column and eluted with a buffer gradient whose pH rises from 3 to 11.5. In what order will the proteins elute? 1. CYT C, CBP, HHB, HSA, HGG, CAT 2. CYT C, HHB, HGG, CBP, CAT, HSA 3. HSA, CAT, CBP, HGG, HHB, CYT C 4. CAT, HGG, HSA, HHB, CBP, CYT C 5. none of the above

none of the above

# 2011 Which of the following do not occur in native globular proteins? 1. side chain to side chain hydrogen bonds 2. side chain to backbone hydrogen bonds 3. backbone to backbone hydrogen bonds 4. disulfide bonds between methionine side chains 5. All of the above occur in globular proteins

disulfide bonds between methionine side chains (2014 exam says its E. google it)

# 2011 Most of the area of the Ramachandran plot is "forbidden” because of 1. unfavorable electrostatic interactions of the amino acid side chains. 2. poor hydrogen bonding. 3. excessive flexibility at glycine residues. 4. L chirality at the n carbons of the amino acids except for glycine. 5. steric overlaps of atoms on neighboring amino acids

steric overlaps of atoms on neighboring amino acids

# 2011 Serine proteases catalyze the hydrolysis of esters as well as of peptides, and this fact has been utilized to make small molecular weight ester substrates for use as test reagents in laboratory assays. In the hydrolysis of these ester substrates the rate limiting step is hydrolysis of the acyl-enzyme complex. This implies that 1. the acyl-enzyme complex is more stable than the original substrate. 2. the activation energy barrier for formation of the acyl-enzyme complex is greater than that of its hydrolysis. 3. the activation energy barrier for hydrolysis of the acyl-enzyme complex is greater than that of its formation 4. activation energies have nothing to do with the rates. 5. none of the above

the activation energy barrier for hydrolysis of the acyl-enzyme complex is greater than that of its formation

# 2011 When substrates bind to enzymes, it is often observed that the enzyme molecule becomes more rigid. This increase in rigidity involves 1. a rise in the enzymes's entropy. 2. a rise in the enzyme's enthalpy. 3. a decrease in the enzyme's entropy 4. a decrease in the enzyme's enthalpy. 5. a decrease in the enzyme's free energy.

a decrease in the enzyme's entropy

# 2011 Which of the following correctly shows the intrachain hydrogen bonding (JJJ) in an n helix? 1. -N-H ||| H-N- 2. -C=O ||| H-C- 3. -C=O ||| H-N- 4. -N-H ||| H-R- 5. -C=O ||| H-O-

-C=O ||| H-N-

# 2011 Which amino acid side chain looks most like that of valine in shape, although not in polarity? 1. leucine 2. isoleucine 3. serine 4. threonine 5. none of these looks at all like valine

threonine

# 2011 The observation of parallel lines in a series of Lineweaver-Burk plots at several inhibitor concentrations implies that 1. the substrate and inhibitor bind at the same site, the binding of one preventing the binding of the other. 2. the substrate and inhibitor can bind in either order, the binding of one having no effect on the binding of the other. 3. the substrate can bind only if the inhibitor is already bound. 4. the inhibitor can bind only if the substrate is already bound. 5. cannot tell from data given.

the inhibitor can bind only if the substrate is already bound.

# 2011 A mutation of an active site residue in an enzyme which increases the binding affinity for substrate without having any other effects would cause which of the following? 1. It would increase k_cat 2. It would decrease k_cat 3. It would increase K_m 4. It would decrease k_m 5. none of the above

It would decrease k_m

# 2011 Buffers are best at holding the pH nearly constant when 1. the pH = the pKa 2. the pH = the pI 3. The pH is alkaline 4. the pH is acidic 5. none of these is correct

the pH = the pKa

# 2011 Under which of the following conditions would the rate of an enzyme catalyzed reaction appear to be first order in the enzyme concentration but not in the concentration of anything else? 1. very low substrate concentration, many times less than Km. 2. at Vmax. 3. at substrate concentrations near Km. 4. none of the above; a catalyzed reaction can never be first order in catalyst. 5. cannot tell from data given.

at Vmax.

# 2011 In the Bohr effect of hemoglobin, lowering the pH reduces the affinity of the protein for oxygen. Which of the following therefore has a higher affinity for protons? 1. the R (relaxed) form 2. the T (tense) form 3. the alpha chains 4. the beta chains 5. all these have the same proton affinity

the T (tense) form

# 2011 A "residue” in the biochemical sense is 1. what remains after the complete oxidation of a substance. 2. a monomer unit within a biopolymer. 3. the result of polymer cleavage into monomers. 4. the part of a biopolymer which is not exposed to the solvent. 5. what's left in a student's mind after an exam.

a monomer unit within a biopolymer.

# 2013 The fact that oil and water don’t mix, otherwise called the hydrophobic effect, is due to * A. unfavorable enthalpic interactions between water molecules and hydrophobic molecules. * B. an increase in the ordering of water molecules around hydrophobic molecules when the latter dissolve in water. * C. a decrease in the ordering of water molecules around hydrophobic molecules when the latter dissolve in water. * D. more than one of the above. * E. none of the above.

B. an increase in the ordering of water molecules around hydrophobic molecules when the latter dissolve in water.

# 2013 In biochemistry we often study “model systems” because they illustrate principles which are broadly applicable. Why is formic acid a useful model system for studying buffering in biochemical systems? * A. It is a simple compound which shows all the buffering properties of a weak acid. * B. It is cheap and easy to work with in the laboratory. * C. Its multiple carboxyl groups are a good model for proteins. * D. Its pKa, 3.75, is in the physiological range very near neutrality. * E. It is toxic to baboons.

A. It is a simple compound which shows all the buffering properties of a weak acid.

# 2013 Which will show the greater degree of dissociation: formic acid (pKa = 3.75) or acetic acid (pKa = 4.76) if dissolved at 0.1 M concentrations in solutions whose pH is 11.0? * A. Formic acid * B. Acetic acid * C. Within the accuracy of measurement they will be equally dissociated. * D. Cannot tell from data given

C. Within the accuracy of measurement they will be equally dissociated.

# 2013 Imagine two groups each of which carries a single positive charge. In one situation they are fully exposed to the aqueous solvent, while in another they are buried in the interior of a folded protein and unable to contact the solvent at all. In both situations they are separated by the same distance, r. The dielectric constant of water is 80, while that of the protein interior is 20. It follows that * A. the force of attraction between the two groups is four times greater in water than in the protein interior. * B. the force of repulsion between the two groups is four times greater in water than in the protein interior. * C. the force of repulsion between the two groups is four times greater in the protein interior than in water. * D. the two groups do not interact in either situation. * E. none of the above is true.

C. the force of repulsion between the two groups is four times greater in the protein interior than in water. (Exam 2018 and 2014: both say its none of the above is true)

# 2013 Which of the following molecules would have at least one chiral atom? * A. glycine * B. adenine (the base) * C. palmitic acid * D. glycerol * E. None of these contains a chiral atom.

E. None of these contains a chiral atom

# 2013 The first page of this exam contains approximately 340 words and weighs approximately 17 grams. What is the page’s information density? * A. 20 * B. 0.05 * C. 340 * D. 17 * E. none of these.

A. 20

# 2013 The solubility of β-lactoglobulin, a protein found in milk, is lowest at pH 5.2. Its solubility at pH 4.8 and pH 5.8 is much higher, however. Which of the following best explains these observations? * A. At pH 5.2 the protein molecules have an extended conformation, causing them to become tangled and precipitate from solution, but this is not the case at the other pHs. * B. At pH 4.8 the protein molecules have a net positive charge while at pH 5.8 they have a net negative charge. As a result in both cases the molecules repel one another and don’t aggregate, whereas at pH 5.2 they have zero net charge and can thus come together and precipitate. * C. The structure of the water changes as the pH changes, and this favors solubility at the low and high pH values but not at the intermediate value. * D. more than one of the above * E. none of the above

B. At pH 4.8 the protein molecules have a net positive charge while at pH 5.8 they have a net negative charge. As a result in both cases the molecules repel one another and don’t aggregate, whereas at pH 5.2 they have zero net charge and can thus come together and precipitate.

# 2013 A protein has its isoelectric point at pH 9.6. In which direction will it migrate in an electric field if the pH is 8.6? * A. toward the anode * B. toward the cathode * C. it won’t migrate in either direction * D. the direction will depend on the protein’s size * E. cannot tell from data given

B. toward the cathode

# 2013 Molecule for molecule, which of the following will have the greatest contribution to the solution’s ionic strength? * A. sodium DNA in which the nucleic acid is 1000 base pairs long. (One can buy this from a scientific supply company. The sodium ions neutralize the DNA phosphates.) * B. the protein ribonuclease at pH 2, at which it has a net charge of +19 with chloride ions present to make the solution electrically neutral. * C. palmitic acid as the sodium salt * D. sucrose * E. All these contribute the same amount to the ionic strength

A. sodium DNA in which the nucleic acid is 1000 base pairs long. (One can buy this from a scientific supply company. The sodium ions neutralize the DNA phosphates.)

# 2013 How many of the standard twenty amino acids have one or more atoms of oxygen in their side chains? * A. one * B. three * C. five * D. an even number * E. none of these answers is correct

E. none of these answers is correct

# 2013 How many of the standard twenty amino acids have no atoms other than carbon and hydrogen in their side chains? * A. one * B. three * C. five * D. an even number * E. none of these answers is correct

E. none of these answers is correct (answer is seven, but it's not listed as an answer)

# 2013 If you were to look down the axis of an -helix in a four helix bundle protein you would see what is called a "helical wheel" in which * A. hydrophobic and hydrophilic side chains would project inward towards the helical axis and be scattered more or less randomly about it. * B. hydrophobic and hydrophilic side chains would project outward from the helix and be scattered more or less randomly about the circumference. * C. the side chains would project inward towards the helical axis with hydrophobic side chains mostly on one side and hydrophilics mostly on the opposite side. * D. hydrophobic and hydrophilic side chains would project outward from the helix with hydrophobic side chains mostly on one side and hydrophilics mostly on the opposite side. * E. none of the above.

D. hydrophobic and hydrophilic side chains would project outward from the helix with hydrophobic side chains mostly on one side and hydrophilics mostly on the opposite side.

# 2013 All other factors being equal, which of the following mutational changes is/are most likely to disrupt the three dimensional structure of a protein? * A. asp to glu in a surface residue * B. ala to ile in the interior * C. ile to ala in the interior * D. thr to ser in the interior * E. ile to val in the interior

B. ala to ile in the interior

# 2013 When the sequences of a protein from two different species is compared, which of the following differences would be considered the most conservative? * A. gly versus trp * B. val versus leu * C. his versus asp * D. none of these is conservative * E. all are conservative

B. val versus leu

# 2013 The pKa of the phosphate in nucleic acids is approximately 3. At neutral pH one would expect that * A. nearly all these phosphates would be protonated. * B. approximately half of them would be protonated and half would be charged. * C. nearly all would be charged. * D. all would be esterified at three of the phosphate oxygen atoms. * E. none of the above

C. nearly all would be charged.

# 2013 Methanol (wood alcohol) is highly toxic because it is converted to the toxic compound formaldehyde in a reaction catalyzed by the liver enzyme, alcohol dehydrogenase: NAD+ + methanol ----\> NADH + H+ + formaldehyde. Part of the medical treatment for methanol poisoning is to administer ethanol (grain alcohol) in amounts large enough to cause intoxication under normal circumstances. What is the most likely reason why this is done? * A. The ethanol stimulates conversion of the formaldehyde to nontoxic products. * B. The ethanol competes for the active site of the enzyme, slowing conversion to formaldehyde, which allows the time for the kidneys to excrete the methanol. * C. The ethanol inhibits reaction of formaldehyde with cellular components. * D. The ethanol makes the patient feel better. * E. The ethanol makes the doctor feel better.

B. The ethanol competes for the active site of the enzyme, slowing conversion to formaldehyde, which allows the time for the kidneys to excrete the methanol.

# 2013 Exons are * A. DNA sequences which code for protein sequences. * B. DNA sequences which do not appear in the m-RNA after the RNA is processed and therefore not in the protein either. * C. artifacts of the DNA preparation introduced by the experimental procedure. * D. gas stations * E. none of the above

B. A. DNA sequences which code for protein sequences.

# 2013 The conformational stress introduced into a closed circular DNA molecule by supercoiling can be relieved by * A. treatment with a topoisomerase. * B. underwinding. * C. overwinding. * D. unwinding. * E. treatment of the experimenter with ethanol.

A. treatment with a topoisomerase.

# 2013 In Anfinsen's ribonuclease experiment he and his coworkers observed that when native, catalytically active enzyme was dissolved in concentrated urea containing mercaptoethanol, it lost all its activity, but when the urea and mercaptoethanol were dialyzed away, the protein regained all its original activity. They concluded that * A. protein folding is very fast. * B. the gene sequence for ribonuclease specifies the amino acid sequence of the protein. * C. the amino acid sequence contains all the information needed for formation of the native fold. * D. auxiliary proteins are necessary for unfolded proteins to reach their native conformations. * E. ribonuclease is a peculiar protein.

C. the amino acid sequence contains all the information needed for formation of the native fold.

# 2013 Glycine is often used as a buffer in biochemical work. Its pKa values are 2.34 and 9.6. Which of the solutions listed below would be the best buffer, i.e. be best able to resist changes in pH? * A. 0.01 M gly at pH 5.97 * B. 0.01 M gly at pH 2.34 * C. 0.01 M gly at pH 11.6 * D. 0.01 M gly at pH 7 * E. all these are equally good as buffers.

B. 0.01 M gly at pH 2.34

# 2013 What is the function of this molecule? * A. It controls the movement of water across the plasma membrane. * B. It controls the movement of sodium and potassium ions across the plasma membrane. * C. It controls the transport of maltose into the cell. * D. It acts as a proton-driven symport. * E. none of the above (Hint: there is a clue embedded in the image.)

C. It controls the transport of maltose into the cell.

# 2013 What do the four spheres, three of which are outside the main structure, represent? * A. Sodium ions * B. Potassium ions * C. Manganese ions * D. Magnesium ions * E. none of these

D. Magnesium ions

# 2014 The low packing density of water arises primarily from * A. repulsion of hydrogen atoms from one another * B. hydrogen bond geometry * C. repulsion of oxygen atoms from one another * D. the absence of attractive forces * E. None of these; water does not have a low packing density

B. hydrogen bond geometry

# 2014 Which of the following involves a decrease in the entropy of water? * A. the unfolding of a native protein * B. shaking olive oil and vinegar together to make salad dressing * C. dissolcing sodium chloride in water * D. removal of histone proteins from DNA * E. more than one of the above

E. more than one of the above

# 2014 Which of the following solutions has the smallest concentration of hydrogen ions? * A. a 50 mM phosphate buffer at pH 7.2 * B. a 100 mM acetate buffer at pH 4.76 * C. a glycine buffer at pH 2.35 * D. a glycine buffer at pH 9.6 * E. Cannot teel from data given

D. a glycine buffer at pH 9.6 (E4-2016, states a glycine buffer at pH 2.35)

# 2014 Under which of the following conditions would 25% of a weak acid in solution be in the dissociated form while the rest is protonated (HA)? * A. when the pH is approximately 0.48 units lower than the pKa * B. when the pH is approximately 0.48 units above the pKa * C. when the pH equals the pKa * D. when the pH and the pKa differ by 2 pH units * E. cannot tell from data given

A. when the pH is approximately 0.48 units lower than the pKa

# 2014 Two different types of protein are present in a solution undergoing electrophoresis. Protein X migrates toward the cathode, while protein Y moves toward the anode. Which of the two proteins has the higher isoelectric point? * A. Protein X * B. Protein Y * C. They have the same pI. * D. Cannot tell from data given, as it depends on the pH.

A. Protein X

# 2014 When proteins are synthesized in cells, cysteine residues are often part of the resulting polypeptide chain. After synthesis some of these may form disulfide bonds. The reaction by which the disulfides are formed from cysteines is * A. an oxidation * B. a reduction * C. a dehydration * D. a hydrolysis * E. none of these

A. an oxidation

# 2014 Which of the following statements about cAMP and its functioning in hormone action is correct? * A. Most effects of cAMP in eukaryotic cells are exerted through the activation of all protein kinase. * B. Cyclic AMP binds the catalytic subunits of PKA and activates the enzyme allosterically. * C. Cyclic AMP binds the regulatory subunits of PKA and activates the enzyme by releasing the catalytic subunits. * D. Cyclic AMP is bound by the activated hormone receptor and PKA simultaneously to convey the hormonal signal in order to activate the kinase. * E. None of the above.

C. Cyclic AMP binds the regulatory subunits of PKA and activates the enzyme by releasing the catalytic subunits.

# 2014 Deamination of cytosine occurs spontaneously and is usually detected by the DNA repair system, which restores the cytosine. Occasionally the lesion is not detected. What would be the most likely effect in this case? (This question is from the third hour exam.) * A. An AT base pair would be replaced by a GC base pair at the next cell division. * B. A GC base pair would be replaced by an AT base pair at the next cell division. * C. The resulting base would be deleted from the DNA. * D. The cell would be unable to replicate its DNA. * E. none of the above.

B. A GC base pair would be replaced by an AT base pair at the next cell division.

# 2014 From which end of a protein being subjected to Edman degradation are amino acids removed? (From the first hour exam) * A. the amino terminus * B. the carboxyterminus * C. It depends on which end is available to reagents * D. from both ends * E. cannot tell without more information

A. the amino terminus

# 2014 How many of the four bases found in DNA do not contain any atoms of oxygen? (The question refers to the bases alone, not to the nucleosides or nucleotides.) * A. None * B. One * C. Two * D. Three * E. Four

B. One

# 2014 The function of topoisomerase is * A. to change the linking number of DNA. * B. to reduce strain in supercoiled DNA. * C. to aid in packaging DNA within the cell. * D. more than one of the above. * E. none of the above.

D. more than one of the above.

# 2014 Histone proteins, if dissolved at physiological pH and subjected to electrophoresis, will * A. migrate to the anode * B. migrate to the cathode * C. not migrate, as their net charge will be zero * D. cannot tell from data given, as it depends on the species from which the histones come

B. migrate to the cathode

# 2014 Planarity of the peptide bond in proteins is maintained by * A. steric hindrance. * B. π electrons. * C. hydrogen bonding. * D. electrostatic repulsion of negatively charged side chains * E. squashing them flat in a press.

B. π electrons.

# 2014 An α/β barrel structure such as is found in triose phosphate isomerase contains eight parallel β-strands and eight α-helices. If the structure were to begin with a strand and end with a helix, how many loops or turns would be needed to connect the repeating secondary structures? * A. Eight * B. Seven * C. Fifteen * D. Sixteen * E. none of the above

C. Fifteen

# 2014 The type of motion least common in biological membranes is: * A. flip-flop diffusion of phospholipid from one monolayer to the other. * B. lateral diffusion of individual lipid molecules within the plane of each monolayer. * C. lateral diffusion of membrane proteins in the bilayer. * D. random motion of the fatty acyl side chains in the interior of the phospholipid bilayer. * E. All these occur equally

A. flip-flop diffusion of phospholipid from one monolayer to the other.

# 2014 Which of the following is true of a βαβ structure which is part of an αβ barrel protein? * A. The β-strands are antiparallel. * B. The helix is left handed. * C. The β-strands are parallel. * D. βαβ structures do not occur in αβ barrels. * E. None of the above.

C. The β-strands are parallel.

# 2014 In the diagram used in class to illustrate the structure of the peptide bond, the sausage shaped shading above and below the plane of the peptide group's atoms represents * A. a non-covalent bond * B. π electrons * C. a hot dog * D. a σ bond * E. none of these

B. π electrons

# 2014 An α/β-barrel protein and an α/β-saddle protein are found to catalyze the same reaction. Their structures are an example of * A. divergent evolution * B. gene duplication * C. convergent evolution * D. lack of evolution * E. coincidence

C. convergent evolution

# 2014 The tendency of hydrophobic amino acid side chains to be found in the protein interior is due primarily to * A. conformational entropy. * B. Van der Waals attractions. * C. the entropy change of the water expelled from the side chains' surfaces on folding. * D. charge repulsions. * E. none of the above

C. the entropy change of the water expelled from the side chains' surfaces on folding.

# 2014 At the melting temperature (the tm) of DNA * A. the free energy of unfolding is zero. * B. the enthalpy of unfolding is zero. * C. the entropy of unfolding is zero. * D. all of the above are zero * E. none of these is zero

A. the free energy of unfolding is zero.

# 2018 If dissolved in water, at what pH would the amino acid arginine have no net charge? * A. 2.17 * B. 9.04 * C. 12.48 * D. 10.76 * E. Cannot tell from available data

D. 10.76

# 2018 Consider the acid dissociations of phosphoric acid: (a) H3PO4 ⇌ H2PO4 - + H+ (b) H2PO4 - ⇌ HPO4 -2 + H+ (c) HPO4 -2 ⇌ PO4 -3 + H+ Which of these reactions involve phosphorous-containing forms that can act only as a proton donor or only as an acceptor? * A. (a) * B. (b) * C. (c) * D. (a) and (c) * E. none of these

D. (a) and (c)

# 2018 The components of poison ivy and poison oak that produce the characteristic rash are catechols substituted with long-chain alkyl groups. Catechols are benzene rings with two hydroxyl groups substituted for ring hydrogens. These hydroxyls are weak acids like the hydroxyl of tyrosine. The poison ivy/oak catechol is shown below. Its first pKa is 8.0. If you were exposed to poison ivy, which of the treatments below if applied immediately would best reduce or eliminate the itchy rash in the affected area? (From the end of chapter 2 in the text) * A. Wash the affected area with cold water. * B. Wash the area with dilute vinegar or lemon juice. * C. Wash the area with soap and water. * D. Wash the area with soap, water and baking soda (sodium bicarbonate). * E. Nothing can reduce or eliminate the rash.

D. Wash the area with soap, water and baking soda (sodium bicarbonate).

# 2018 Heavy atoms in proteins are defined as all non-hydrogen atoms, i.e. all C, N, O, S and any other nonhydrogens covalently attached to the protein. Consider a pentapeptide. Would rotation about phi of residue 4 change the distance between any heavy atoms of residue 2 and residue 3? * A. Yes. * B. No. * C. It would depend on the values of other phi and psi. * D. Yes provided that residue 4 is proline * E. cannot tell from data given.

B. No.

# 2018 Phosphofructokinase, which puts the second phosphate onto fructose 6-phosphate during glycolysis, is an allosteric enzyme. Which of the following is most likely to act as an allosteric inhibitor? * A. ATP * B. phosphoenol pyruvate * C. ADP * D. glucose * E. A and C

E. A and C

# 2018 Which of the following, if in the Watson-Crick double helix with its complementary DNA strand, would have the highest melting temperature? * A. AGGTTACAT * B. AAGAATCAT * C. TACTATAGC * D. TACCTGGAT * E. TATAGAGAT

D. TACCTGGAT

# 2018 Which of the following could form a double stranded B-form DNA with 5’-ATTGCCA-3’? * A. 5’-ATTGCCA-3’ * B. 3’-ATTGCCA-5’ * C. 5’-TAACGGT-3’ * D. 3’-TAACGGT-5’ * E. more than one of these

D. 3’-TAACGGT-5’

# 2018 You are given two containers of polysaccharide by a colleague who has labeled one container as cellulose and one as glycogen. In his haste he may have mislabeled them and has asked you to verify which is which by methylation analysis. Indicate what product(s) you would expect from exhaustive methylation and mild acid hydrolysis of each polysaccharide and how the products could be used to differentiate the samples. * A. Both give 2,3,6-tri-O-methyl-D-glucose and very little other methylated glucoses. * B. Both give 2,4,6-tri-O-methyl-D-glucose mainly * C. Cellulose would give 2,4,6-tri-O-methyl-D-glucose mainly * D. Glycogen would give 2,3,6-tri-O-methyl-D-glucose and an appreciable amount of 2,3,4,6-tetra-O-methyl-D-glucose * E. Could not tell them apart by this method

D. Glycogen would give 2,3,6-tri-O-methyl-D-glucose and an appreciable amount of 2,3,4,6-tetra-O-methyl-D-glucose

# 2018 Why do unsaturated fatty acids with cis double bonds in a bilayer membrane make the membrane more fluid? * A. They don’t pack as well against neighboring fatty acids, allowing more room to move. * B. They pack better against one another that saturated fatty acids do. * C. Fatty acids with cis double bonds isomerize rapidly to trans and back to cis, which creates fluidity * D. They force adjacent saturated fatty acids to move with them. * E. None of the abov

A. They don’t pack as well against neighboring fatty acids, allowing more room to move.

# 2018 In cryo-EM of unstained specimens, macromolecules are embedded in: * A. Water * B. Crystalline ice * C. Vitreous or amorphous ice * D. Uranyl acetate * E. Silicone

C. Vitreous or amorphous ice

# 2018 Energy filters are used in cryo-EM to: * A. Eliminate elastic scattering * B. Increase inelastic scattering * C. Eliminate Rayleigh scattering * D. Enhance Compton scattering * E. Decrease inelastic scattering

E. Decrease inelastic scattering

# 2016 In the Miller-Urey experiment a spark discharge was passed through a closed system containing ammonia, methane, hydrogen gas, water vapor, and hydrogen sulfide and the products recycled back to the spark chamber through a condenser. The products contained * A. monosaccharides * B. fatty acids * C. mononucleotides * D. amino acids * E. none of these.

D. amino acids

# 2016 Why is aerobic energy metabolism more efficient than anerobic energy metabolism? * A. Aerobic mitochondria are more efficient than anerobic. * B. Aerobes can oxidize glucose fully to CO2, while anerobes are only able to oxidize such compounds partially. * C. Aerobes metabolize faster than anerobes. * D. Aerobic photosynthesis makes aerobes more efficient than anerobes lacking phiotosynthesis * E. The statement is incorrect, as anerobes are more efficient because they suffer less oxidative damage from molecular oxygen.

B. Aerobes can oxidize glucose fully to CO2, while anerobes are only able to oxidize such compounds partially.

# 2016 How many water molecules would be removed in monosaccharides to an oligosaccharide whose main chain contains five sugar residues and which contains a single branch three residues in length? * A. eight * B. four * C. three * D. seven * E. none of these

D. seven

# 2016 The van der Waals radii of carbon and oxygen are 1.70 Å and 1.52 Å respectively. Which of the two terms in the Lennard-Jones potential would predominate if a carbon and oxygen that are not covalently bonded to one another were to have an interatomic distance, r, of 2.5 Å. * A. the attractive term (dependent on 1/r6 ) * B. the repulsive term (dependent on 1/r12) * C. the two terms would be equal another, they can’t interact at all. * D. neither, as the atoms would form a hydrogen bond * E. since the atoms are not covalently bonded to one

B. the repulsive term (dependent on 1/r12)

# 2016 How many of the twenty amino acids contain neither oxygen nor nitrogen in their side chains? * A. 3 * B. 6 * C. 9 * D. 12 * E. none of these is correct

C. 9

# 2016 Which of the following can transport a solute against its concentration gradient? (“Mediated” means a membrane protein is involved in the transport. From the posted exam.) * A. active mediated transport * B. passive mediated transport * C. both of the above systems the membrane * D. neither of the above systems * E. passive diffusion directly through

A. active mediated transport

# 2016 In first order reactions the half-life is * A. proportional to the reactant concentration. * B. proportional to the square of the reactant concentration. * C. proportional to the logarithm of the reactant concentration n * D. proportional to the time * E. independent of the reactant concentration

E. independent of the reactant concentration

# 2016 How many half-lives of a first order reaction would have to pass for the reactant concentration to fall to less than 2% of its initial value? * A. 1 * B. 3 * C. 5 * D. an even number of half-lives * E. none of these

C. 5

# 2016 Which of the following sequeNces would have the highest Tm if base paired with its complementary sequence? * A. ATTACCGT * B. CGCTACC * C. GTACCTAT * D. ATCAGAGT (Contributed by a member of the class) * E. They would all have the same Tm.

B. CGCTACC

# 2016 38. Consider the transport of glucose into an erythrocyte by facilitated diffusion. When the glucose concentrations are 5 mM on the outside and 0.1 mM on the inside, the free-energy change for glucose uptake into the cell is: (These values may be of use to you: R = 8.315 J/mol·K; T= 298 K; 9 (Faraday constant) = 96,480 J/V; N= 6.022 x 1023/mol.) * A. less than 2 kJ/mol. * B. about -10kJ/mol. * C. about 30kJ/mol. * D. about -30 kJoule/mol. * E. impossible to calculate without knowledge of the membrane potential

B. about -10kJ/mol.

# 2016 Which of the following solutions will have the greatest ionic strength? * A. 0.1 M NaCl * B. 0.1 M CaCl2 * C. 0.1 M FeCl3 * D. All these will have the same ionic strength. (You can answer this by inspection; no calculation is needed.) * E. cannot tell from data given

C. 0.1 M FeCl3

Plants store energy in the form of starch (amylose), while animals store energy in the form of glycogen. Which of the following is true concerning these two compounds? * A. Both are homopolysaccharides * B. One is a heteropolysaccharide, and one is a homopolysaccharide. * C. Gylcogen is formed for short term energy storage, while amylose is formed for long term storage. * D. Amylose is unbranched, while glycogen is branched * E. more than one of the above (Contributed by a member of the class.)

E. more than one of the above

# 2019 Given the data in the table below, estimate the number of residues in hemoglobin. * A. 2100 * B. 9900 * C. 4500 * D. 564,500 * E. None of these is even close to correct.

E. None of these is even close to correct.

# 2019 In the Miller-Urey experiments electric sparks were passed through what was then believed to be a mixture of gases similar to the atmosphere of the primitive Earth. Which of the following was NOT produced as a result? * A. amino acids * B. fatty acids * C. nucleotides * D. deoxynucleotides * E. more than one of these *

E. more than one of these

# 2019 Which of the following solutions has the lowest concentration of hydrogen ions? * A. a 50 mM phosphate buffer at pH 7.2 * B. a 100 mM acetate buffer at pH 4.76 * C. a 50 mM glycine buffer at pH 2.35 (Adapted from last year’s exam) * D. a 50 mM glycine buffer at pH 9.6 * E. Cannot tell from data given

D. a 50 mM glycine buffer at pH 9.6

# 2019 Consider the acid dissociations of phosphoric acid: (a) H3PO4 ⇌ H2PO4 - + H+ (b) H2PO4 - ⇌ HPO4 -2 + H+ (c) HPO4 -2 ⇌ PO4 -3 + H+ Which of these reactions involve phosphorous-containing forms that can act only as a proton donor or only as an acceptor? * A. (a) * B. (b) * C. (c) * D. (a) and (c) * E. none of these

B. (b)

# 2019 If the individual hydrogen bonds in the following four structures are compared, which will contain the strongest H-bond? * A. 1 * B. 2 * C. 3 * D. * 4 E. cannot tell from data given

4 E. cannot tell from data given

# 2019 To which sodium chloride concentration would 0.04 M ammonium sulfate, (NH4)2SO4, be equivalent in ionic strength? * A. 0.04 M * B. 0.08 M * C. 0.16 M * D. 0.24 M * E. none of these

E. none of these

# 2019 Fatty acids are not very soluble in water, but a few molecules can be dissolved and remain as single fatty acid molecules not associated with other fatty acids. What effect will these fatty acids have on the water near them? * A. The water molecules will form a loose, open cage around the hydrocarbon part of the fatty acid. * B. The waters will be closer to one another than they were before the fatty acid arrived. * C. The water molecules will be excited in energy due to a rise in their enthalpy and will undergo more rapid motions than they did before the fatty acid arrived. * D. The water molecules will become completely inert as a result of interaction with the fatty acid. * E. None of the above

B. The waters will be closer to one another than they were before the fatty acid arrived.

# 2019 Why do olive oil and vinegar separate from one another when shaken together to make salad dressing? * A. The heat generated by the mixing drives them apart. * B. The hydrocarbon molecules in the olive oil attract one another more strongly than they attract water molecules. * C. The water molecules adjacent to the hydrocarbons of the olive oil undergo a drop in free energy when they separate, and this drives the separation. * D. The water molecules adjacent to the hydrocarbons become more restricted in their movements due to the formation of hydrogen bonds to other waters. * E. more than one of the above

C. The water molecules adjacent to the hydrocarbons of the olive oil undergo a drop in free energy when they separate, and this drives the separation.

# 2019 Which of the reactions in the figure below would be favored by an increase in the temperature? * A. Reaction (a) * B. Reaction (b) * C. Reaction (c) * D. none of them * E. more than one of them

E. more than one of them

# 2019 Two protein sequences have been aligned and the amino acid differences between corresponding positions are examined. Which of the following substitutions would be the most conservative? * A. D for E * B. E for S * C. K for Y * D. I for C * E. N for T

A. D for E

Consider the following table. Which of the proteins would not stick to a cation exchange column at pH 6? * A. pepsin * B. cytochrome c * C. myoglobin * D. urease * E. pepsin and urease

E. pepsin and urease

# 2019 Which of the following, if in the Watson-Crick double helix with its complementary DNA strand, would have the lowest melting temperature? * A. AGGTTACAT * B. AAGAATAAT * C. TACTATAGC * D. TACCTGGAT * E. TATAGAGAT

B. AAGAATAAT

# 2019 In the epinephrine cascade, one epinephrine binds to a β-adrenergic receptor, whose binding site is on the outside of the cell membrane. That triggers a conformational change in the receptor protein, causing it to release a bound G-protein (called GSα) on the inside of the membrane. Once released the GSα releases a bound GDP, replacing it with a GTP from the cytosol. That activates the GSα, which then binds to another membrane protein, adenylyl cyclase. The cyclase catalyzes conversion of ATP to c-AMP. Each cyclase yields 60 c-AMP molecules before it is inactivated. Four c-AMP molecules bind to one c-AMP-dependent protein kinase A (PKA) molecule. This changes the conformation of the two regulatory subunits of PKA, releasing its two catalytic subunits. These each phosphorylate 100 enzyme molecules of various sorts before the catalytic subunits are inactivated. Each of these enzymes catalyzes 200 reactions before it, too, is inactivated by hydrolysis of the phosphate which activated it. How many reactions are catalyzed by these enzyme molecules before they are inactivated? * A. 15 * B. 600,000 * C. 60,000 * D. 3000 * E. none of these is correct.

B. 600,000

# 2019 A voltage gated ion channel uses one ATP to pump three Na+ ions out of the cell and bring two K+ ions in. It is likely that * A. the concentration of Na+ outside is lower than its concentration inside. * B. the concentration of K+ outside is lower than its concentration inside. * C. the pumping equalizes the internal and external ion concentrations for both ions. * D. the pumping maintains the voltage difference between the inside and outside. * E. More than one of these is correct.

E. More than one of these is correct.

# 2019 In the reaction ATP + glucose ⇌ ADP + glucose-6-phosphate, a hydroxyl of the glucose interacts with the terminal phosphate of the ATP. Which of the following is a correct statement about the reaction? * A. The hydroxyl conducts an electrophilic attack on the negatively charged phosphate. * B. The slight positive charge on the P atom of the terminal phosphate attracts attack by the OH. * C. A pair of unshared electrons on the hydroxyl group performs a nucleophilic attack on the phosphorous atom of the phosphate. * D. The ATP hydrolysis in this reaction could be called ‘glucolysis’, as the hydroxyl acts as an OH of water would. * E. B, C, and D are all correct

E. B, C, and D are all correct

# 2019 Which of the following reactions is catalyzed by nucleoside diphosphate kinase? * A. ATP + Enzyme-histidine → ADP + Enzyme-histidine-phosphate * B. ADP + H2O → AMP + Pi * C. ATP + AMP → 2 ADP * D. 2 AMP → ADP + adenosine * E. None of the above

C. ATP + AMP → 2 ADP