Biochemistry 244-Midterm 1

October 16th 2014

Time: 4:30 pm-5:30 pm

Lecturer: Cristina C. Clement, Ph.D.

For each of the questions below choose the best answer:

R (gas constant) = 8.315 J•mol–1•Kelvin–1 = 8.315 x 10–3 kJ•mol–1•Kelvin–1

(25 °C) T = 298 K; human physiological temperature (37 °C) T = 310 K.
1. What is the pI of valine, shown below? (thepKa's are shown):

A. 2.32; B. 4.81; C.9.62; D. 5.96.

2. Which of the following amino acids lacks a center of asymmetry?

A) Alanine; B) Glycine; C) Valine; D) Isoleucine; E) Aspartic acid

3. Which of the following is the zwitterion form of alanine?

A.A; B. B; C. C; D. D

4. The isoelectronic point of an amino acid is the point where:

A) The pK of the carboxylic acid is the same as the amino group; B) Sodium ions are attracted
to the amino groups; C) the amino acid carries no net electrical charge; D) the solubility of the
amino acid is maximized; E) the amino acid racemizes;

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5. The disulfide bond between two cysteine (-S-S-) molecules:
A) is a peptide bond.; B) is an ionic bond that is stable at physiological pH.
C) is a covalent bond formed by oxidation.; D) is a hydrogen bond between the two sulfhydryl
groups.; E) is a weak ion-induced dipole attraction.
6. Which of the following amino acids has an uncharged polar side chain at pH 7?
A) Arg; B) Thr; C) Glu; D) Pro; E) Ile
7. Which of the following amino acids has a sulfur atom in its side chain?
A) Asn; B) Ser; C) Phe; D) Met; E) Tyr
8.Some proteins have amino acids that are modified after synthesis (post-translational
modifications). In the figure below identify the post-translation modification and the
amino acids on which they occurred:

A. 1=4-hydroxy-proline; 2=gamma-carboxyglutamate; 3= O-phosphoserine; 4=5-

hydroxylysine

B. 1= gamma-carboxyglutamate; 2=4-hydroxy-proline; 3= O-phosphoserine; 4=5-

hydroxylysine

C. 1=4-hydroxy-proline; 2=gamma-carboxyglutamate; 3=5-hydroxylysine;4= O-

phosphoserine

D. 1=gamma-carboxyglutamate; 2=4-hydroxy-proline; 3=5-hydroxylysine;4= O-

phosphoserine

9.At pH 11, glutamic acid (pKs are alpha-carboxylate 2.1, alpha-amino 9.47, alpha-
carboxylate 4.07. would be charged as follows:
A) +1 alpha-carboxylate, 0 alpha-amino, +1 alpha-carboxylate, +2 net charge
B) -1 alpha-carboxylate, +1 alpha-amino, -1 alpha-carboxylate, -1 net charge
C) 0 alpha-carboxylate, 0 alpha-amino, 0 alpha-carboxylate, 0 net charge

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D) -1 alpha-carboxylate, 0 alpha-amino, -1 alpha-carboxylate, -2 net charge
E) +1 alpha-carboxylate, -1 alpha-amino, +1 alpha-carboxylate, +1 net charge

10.What is the net charge on L-aspartic acid (R = –CH2CO2H) at a pH of 11.0?

A.–2; B.+1 ; C.+2 ; D.–1 ;

11.In strongly acidic solution L-lysine is primarily a dication as shown below. As the pH is
raised, which proton is lost to form the monocation?

A.A ;B.C ; C.D; D.B

12.Which structures are shown below?

1 2 3

A) 1=Ser, 2=Thr, 3=Trp; B) 1=Tyr; 2=Phe; 3=Trp; C) 1=Tyr, 2=Thr; 3=Ser; D)1=Phe;
2=Tyr; 3=Trp
13.In the following table, which column has the isoelectric points (pI) correctly matched
with the amino acids on the left? (Note: The side chains are given for each.)

A.D; B.A; C.B; D.C;

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14. Linus Pauling is credited with describing the -helix structure of a polypeptide. The -helix is
an example of a polypeptide's

A. primary structure; B.tertiary structure; C. quaternary structure; D.secondary structure

15.The peptide linkage in proteins and peptides is planar and has restricted rotation about the
carbon-nitrogen bond because

A.hydrogen bonding requires a planar arrangement and restricts bond rotation; B.the peptide
bond has partial double bond character ;C. the steric hindrance of the large side chains; D.the
carbonyl is predominately in the enol form.

16.Why is the peptide bond stronger than the ester bond?

A) Resonance stabilization of the amide bond; B) Greater electronegativity of nitrogen; C)

Greater electronegativity of oxygen; D) Increased basicity of nitrogen; E) Size of the nitrogen
atom compared to the oxygen atom.

17. In the figure below secondary structure elements are shown.

A) 1=alpha-helix, 2=beta- sheet; B) 1=beta- sheet, 2=alpha-helix; C) 1=‘parallel’ beta-sheets,

2=‘anti-paralllel’ beta-sheets; D) 1=‘anti-paralllel’ beta-sheets, 2=‘parallel’ beta-sheets

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18. Hemoglobin contains two α chains of protein and two β chains. The maximum degree of
protein structure shown by hemoglobin is:

a. Quaternary b. Primary c. Tertiary d. Secondary

19. Given the graph below for the hemoglobin binding to O2 in presence of 2,3-
biphosphoglycerate (BPG), the following conclusions can be outline about BPG:

A) BPG is a negative allosteric effector; B) BPG is a positive allosteric effector

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 C) BPG is decreasing the affinity of hemoglobin for O2; D) Both A) and C) are correct; E)
BPG is increasing the affinity of hemoglobin for O2;

20. The Bohr effect describes the cooperative binding of oxygen by hemoglobin. At low
oxygen concentrations, hemoglobin binds oxygen poorly, but at high oxygen
concentrations, oxygen is readily taken up by hemoglobin. In addition, oxygen is bound
readily at high pH and released readily at low pH. Using this model, you could predict that:
A. Hemoglobin will absorb oxygen readily in lungs and release oxygen readily in working
muscle
B. Hemoglobin will release oxygen readily in lungs and absorb oxygen readily in working
muscle
C. Hemoglobin will take up oxygen best when there is very little available
D. Under very acidic conditions in lungs, hemoglobin will release oxygen

21. What is the net charge on the dipeptide lys-asp at a pH of 1.0?

aspartic acid (R = –CH2CO2H)

lysine (R = CH2CH2CH2CH2NH2)

A. +1; B. +2; C.+3 ; D.+4

22. A polypeptide 5 amino acids long is split into various smaller fragments, and the amino
acid sequences of some of the fragments are determined. The identified fragments include:
his-gly-ser, ala-his, and ala-ala.
Predict the primary sequence of the polypeptide.

A. his-gly-ser-ala-alaB. ala-his-gly-ser-ala; C. ala-ala-his-gly-ser; D. his-gly-ser-ala-ala

E. cannot be determined without more information.

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23. The major classes of amino acids are shown below. Identify the correct assignment for
each number:

1 2 3
A) 1=polar, uncharged R; 2) polar charged R; 3)=hydrophobic R;

B) 1=hydrophobic R; 2) polar charged R; 3)=polar uncharged R;

C) 1=polar, charged R; 2) polar uncharged R; 3)=hydrophobic R

D) C) 1=polar, uncharged R; 2) hydrophobic R; 3=polar charged R

24. The tertiary structure of a protein refers to the:

A. Sequence of amino acids

B. Presence of alpha-helices or beta-sheets
C. Unique three dimensional folding of the molecule
D. Interactions of a protein with other subunits of enzymes
E. Interaction of a protein with a nucleic acid

25. Which statement is true concerning the structure of proteins?

A. The primary structure is the sequence of amino acids.

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B. Alpha helices and beta sheets are examples of secondary structure.
C. Side chains (R-groups) of amino acids can be hydrophilic or hydrophobic.
D. Proteins made of two or more polypeptide chains have quaternary structure.
E. All statements are true.

26.) A hydrogen bond is best defined as:

A) A strong chemical bond between hydrogen and another element; B) A weak chemical bond
between hydrogen and another element; C) A relatively strong electrostatic bond between
hydrogen and oxygen or nitrogen; D) A weak electrostatic bond between hydrogen and oxygen
or nitrogen; E) A bond between two hydrogens

27) Which of the following compounds is capable of hydrogen bonding with like molecules
?

A) CH3CH2CH2CH2CH3; B) CH3CH2OCH2CH3; C) CH3NH2; D) HOCH2CH2OH; E) Both C

and D are correct

28) Which of the following is not an example of noncovalent interactions between

molecules?

A) Salt bridges; B) Hydrogen bonds; C) Hydrophobic interactions; D) Ionic bonds

E) Chemicalcovalent bonds

29) The tendency of nonpolar molecules to aggregate in a water medium is called ________.

A) Crenation; B) Hydrophobic effect; C) Hydrophillic effect; D) Micellular effect; E)

Amphiatic

30) The carbohydrate coat of a cell is called the:

A) Extracellular matrix; B) Glycocalyx; C) Cell cortex; D) Fibroblast; E) Both A and C are

correct

31) Which of the following organelles is involved in aerobic metabolism?

A) Mitochondria; B) Peroxisomes; C) Glyoxysomes; D) Ribosomes; E) Lysosomes

32) The ability of water to form hydrogen bonds with other water molecules or with
other polar compounds is important for two reasons:

A) It gives water great cohesion and resistance to vaporization,

B) It allows for solvation of biomolecules which can also form hydrogen bonds.

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 C) Both A) and B) are correct
D) None of the above is correct

33) If the concentration of H+ in a solution is 10 - 3 M, what will the concentration of

OH - be in the same solution at 25° C?

A. 10 - 3 M
B. 10 - 11 M
C. 1011 M
D. 2 x 10 - 11 M
E. 10 - 14 M
Hint: [H +] [OH - ] = 10 - 14

34) The correct operational relationship between pKa and pH is that:

pH = pKa + log [A-] / [HA]

A. both are log functions.

B. both are always < 7 for acids, and >7 for bases.
C. These two concepts are not operationally related in any way since biological fluids contains
mixtures of too many acids and bases.
D. When pH = pKa , the compound in question will have a charge of +0.5.
E. When pH = pKa , the ionizable compound in question (whether acid or base) will be half
protonated and half deprotonated.

35)The binding between a specific antibody and a virus is very tight. If the forces that allow
interactions between molecules are said to be weak, how can electrostatic attractions,
hydrogen bonds, van der Waals bonds and hydrophobic attractions lead to a very strong
interaction?

A. The structure of the antibody allows the formation of a large number of weak interactions.
B. Weak interaction is the precursor to the formation of covalent bonds.
C. The weak forces lead to condensation reactions converting the interaction to a very tight
bond.

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D. The electrostatic attractions become very strong once water is excluded from the bound
molecules.
36) Amphiphilic molecules:
A) have both oxidizing and reducing groups.; B) are micelles.; C) have chromophores in two
different wavelength regions.; D) have both acidic and basic groups.; E) have both hydrophilic
and hydrophobic groups.

37). The strongest non-covalent interactions are:

A) ionic interactions; B) hydrogen bonds; C) dipole-dipole interaction; D) London
dispersion forces; E) van der Waal forces

38) How is the following structure classified?

A. A. DNA base; B. nucleoside; C. nucleotide; D. nucleic acid

39) Which of the following are purines?

I. adenine II.cytosine III. guanine IV. thymine

A. I and II ; B.I and III ; C. II and III ; D. II and IV

40)Which of the following is the abbreviated name for the structure shown below?

A. dAMP; B. dADP; C. AMP; D. ADP

41) What type of bond is being cleaved during the conversion of ATP to ADP?

A) Ester; B) Ether; C) Hydrogen; D) Anhydride; E) Amide

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42) The structure shown in the diagram is an example of a monomer unit used in the
formation of:

A. RNA

B. protein

C. DNA

D. polysaccharides

E. lipids
43) In order for two reactions to be coupled what conditions must be met?

A) They must both be spontaneous; B) One of the reactions must be spontaneous

C) A product of one of the reactions must be a reactant in the second reaction; D) They both
must have ATP as a reactant; E) Both B and C must be true.

44) The structure on the left is a(n) _________________, and the structure on the right is
a(n)_________________.

A. lipid, polypeptide ; B. carbohydrate, lipid ; C. carbohydrate, amino acid ; D. nucleotide,

amino acid ; E. nucleotide, carbohydrate
B.
45) Which of the following statements regarding free energy changes is true?
A) At equilibrium deltaG0 = 0; B) For the reaction to be spontaneous deltaGo must be
positive; C) Free energy is a state function; D) Both A and C are true; E) All of the
above are true

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46. The tendency of ATP to undergo hydrolysis is called __________.

A) Free energy of hydrolysis; B) Cleavage rate; C) Phosphoryl group transfer potential;

D) High energy bond potential; E) None of the above is correct

47) The body performs many processes that depend upon energy and could not occur
without a supply of ATP. How does the energy from ATP power the cellular reactions?

a) The cellular processes are coupled to hydrolysis of ATP, an exergonic process

b. Cellular processes are coupled to hydrolysis of ATP, an endergonic process
c. Energy from ATP hydrolysis is stored in cellular chambers
d. ATP hydrolysis absorbs the remaining energy from formation of glucose-6-phosphate
e. All of the energy from hydrolysis of ATP is released as heat

48)ΔG for an exothermic reaction is:

A. >0 ; B. <0 ; C. =0 ; D. Never a value that can be numerically

determined;E. A value that varies with the temperature of the reaction

49) For a reaction with H = 20 kJ/mol and S =20 J/K•mol, the G is ______ at 27°C.

A) 14 J/mol; B) 140 J/mol; C) 1400 J/mol; D) 14,000 J/mol; E) none of the above

50)What is the ratio of citric acid (pK1 = 3.09) to monosodium citrate in a 1.0 M citric acid
solution with a pH = 2.09?
A) 10:1; B) 1:1; C) 1:10; D) 10:11; E) 1:11

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