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Biochem Exam 1 > Biochem Final > Flashcards

Biochem Final Flashcards

1
Q

The shift from the deoxy to the oxy state of hemoglobin happens simultaneously in all binding sites, even if some of these sites don’t have oxygen present. T or F

A

True

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2
Q

In the structure of Oxy-myoglobin, 4 ligands are bound to iron from the heme, one from the protein, and the 6th ligand is provided by the distal histidine. T or F

A

False

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3
Q

The hydrogen bonding pattern in a beta sheet occurs between beta strands rather than within the same strand. T or F

A

True

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4
Q

A biochemical reaction (A converted to B) has a delta G = -116 kJ/mol. Which of the following can you conclude about this reaction?
a. The reaction does require thermodynamic coupling.
b. The delta H (enthalpy change is likely to be small.
c. The reaction does not require thermodynamic coupling.
d. The delta S is likely to be the driving force of the reaction.

A

c. The reaction does not require thermodynamic coupling.

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5
Q

A mutation in several cultured cells renders their ribosomes unable to include proline in any amino acid sequences. Which one of the following would be unaffected by this mutation?
a. Tropocollagen production.
b. Production of proteins containing beta-turns in their secondary structure.
c. Amphipathic alpha-helix production.

A

c. Amphipathic alpha-helix production.

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6
Q

A positive delta S for water is the driving force behind the tendency of nonpolar molecules to self-associate, otherwise known as the hydrophobic effect. T or F

A

True

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7
Q

Which structural technique does not work well for studying large proteins?
a. NMR spectroscopy
b. Structural prediction
c. X-ray crystallography
d. SDS page
e. Cyro-EM

A

a. NMR spectroscopy

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8
Q

Fibroin is composed of stacks of beta sheets made of a hydrophobic 7 residue pseudo repeat in which every third residue is nonpolar. T or F

A

False

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9
Q

Flattening of the heme plane (upon binding to oxygen) is the basis of positive cooperativity in hemoglobin. T or F

A

True

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10
Q

In exclusion chromotography, small proteins elute before big proteins. T or F

A

False

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11
Q

The primary role of the distal histidine in Myoglobin is to:
a. Provide favorable delta H interactions to help the protein fold.
b. Promote positive cooperativity through allostery.
c. Promote oxygen binding via a hydrogen bond
d. Hold the heme in place by forming a covalent bond with the iron.

A

c. Promote oxygen binding via a hydrogen bond.

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12
Q

Which of the following is not an example of heterotropic regulation of hemoglobin?
a. Low pH resulting in the stabilization of the deoxy state of hemoglobin
b. The Bohr effect.
c. 2,3-BPG binding to the deoxy state of hemoglobin
d. Oxygen binding to alpha1 chain of hemoglobin.

A

d. Oxygen binding to alpha1 chain of hemoglobin.

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13
Q

A solution of carbonic acid (pKa=6.37) that is set to a pH of 8.0 is at its maximum buffering capacity (i.e., most effective at resisting changes in pH). T or F

A

False

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14
Q

A solution of L-cysteine at 50 mM concentration is adjusted to a pH of 5. What is the net charge of L-cysteine in this solution? (chart is shown)
a. -1
b. +1
c. +2
d. 0

A

d. 0

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15
Q

Among all the amino acids with an ionizable side chain, histidine is unique in which way? (chart is given)
a. It is small in comparison to the aromatic amino acids.
b. It can be covalently linked in the active site of some enzymes.
c. It can dissociate a proton near physiological pH.
d. It is the only titratable amino acid that has a ring structure on its side chain.

A

c. It can dissaciate a proton near physiological pH.

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16
Q

Hydrogen bonding is used to stabilize which of the following?
a. Intrinsically disordered proteins.
b. Beta turns
c. Disulfide bonds
d. Van der Waals interactions

A

b. Beta turns

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17
Q

What is the purpose of the amphipathic detergent in SDS PAGE?
a. Ensure that proteins are positively charged, and therefore migrate on the acrylamide matrix.
b. Ensure that proteins remain folded during electrophoresis.
c. Ensure that the disulfide bonds in a protein are all reduced.
d. Ensure that proteins are negatively charged, and therefore migrate on the acrylamide matrix.

A

d. Ensure that proteins are negatively charged, and therefore migrate on the acrylamide matrix.

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18
Q

You try to purify a protein using ion exchange chromatography, but you find that your protein did not “stick” to the column. What is a possible cause?
a. The protein has no affinity tag.
b. The protein was too big to enter the column matrix.
c. The pH of the buffer puts the protein close to its isoelectric point.
d. The protein is misfolded.

A

c. The pH of the buffer puts the protein close to its isoelectric point.

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19
Q

A chemical reaction is found to have an equilibrium constant (Keq) that is very, very small. Which of the following can you conclude regarding the reaction?
a. The acid involved in the reaction is only partially dissociated.
b. The concentrations of the reactants and products are equal.
c. The concentrations of the reactants are higher than the products.
d. The concentrations of the reactants are lower than the products.

A

c. The concentrations of the reactants are higher than the products.

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20
Q

A mutation of Myoglobin is discovered that results in stronger binding to oxygen. What can you expect from this new protein?
a. The P50 will decrease.
b. The P50 will increase.
c. This form of myoglobin will be an effective substitute for hemoglobin.
d. The Hill coefficient (nH) will increase.

A

a. The P50 will decease.

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21
Q

The classic experiment with Ribonuclease A demonstrated which of the following?
a. That disulfides promote misfolded structures of proteins.
b. That using urea to unfold proteins is a useful research tool
c. That the information needed to fold a protein is contained in the primary amino acid sequence.
d. That the information needed to form quaternary structures is contained in the primary amino acid sequence.

A

c. That the information needed to fold a protein is contained in the primary amino acid sequence.

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22
Q

Which of the following does not stabilize the structure of tropocollagen?
a. Hydroxylation of proline
b. The activity of lysyl oxidase.
c. The hydrophobic effect.
d. Disulfide bonds.

A

d. Disulfide bonds.

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23
Q

The following amino acid sequence is ⍺ helical. How many separate ⍺ helices are there? MAKLLGVEPETVHELAAHVDAAMSVCSTAEIGDDVVIAWTALSARSPAFLSITSANFDS
a. 4
b. 5
c. 3
d. 2

A

c. 3

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24
Q

An enzyme catalyst can only change which of the following?
a. hydrophobic effect
b. ΔG°‡
c. Keq
d. ΔG°

A

b. ΔG°‡

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25
Q

Lysine cross-linking, lysine hydroxylation, and proline hydroxylation are all examples of post-translational modifications that stabilize the structure of tropocollagen. T or F

A

True

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26
Q

A simple first order reaction is directly proportional to the concentration of the reactant. T or F

A

True

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27
Q

The following shows the Michaelis-Menten plot for an enzyme. Which of the following is true regarding the reaction order at the red arrow (i.e., concentration of substrate is much larger than Km)? (chart is given)
a. The reaction is second order overall.
b. The reaction is zero order overall.
c. The reaction is first order overall.
d. The reaction is first order with respect to substrate.

A

c. The reaction is first order overall.

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28
Q

A carbonyl oxygen of one residue that is hydrogen bonding to an amine hydrogen from 4 resiudes away is an example of this:
a. Tertiary structure
b. Primary structure.
c. Secondary structure.
d. An intrinsically disordered protein.

A

c. Secondary structure

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29
Q

A mutant form of hemoglobin is found that has negative charges lining the central (water-filled) cavity of the structure. What would you predict regarding this hemoglobin?
a. The P50 will be smaller than normal hemoglobin.
It will display a hyperbolic binding curve.
c. The P50 will be larger than normal hemoglobin.
d. It will have a higher denaturation temperature.

A

a. The P50 will be smaller than normal hemoglobin.

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30
Q

Transport across a membrane that is active and primary:
a. Requires symport with a solute that is going down a concentration gradient
b. Requires a solute to move up a concentration gradient
c. Is not classified as “facilitated”
d. Has transport kinetics that are linear

A

b. Requires a solute to move up a concentration gradient

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31
Q

The enzyme chymotrypsin has evolved to cleave a peptide bond right after which of the following residues:
a. Residues that are negatively charged
b. Residues that are large and hydrophobic
c. Residues that are small and neutral
d. Residues that are large and hydrophobic and located at the C-terminal end of a protein

A

b. Residues that are large and hydrophobic

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32
Q

Which molecule is an example of convergent evolution when compared to Chymotrypsin?
a. Elastase
b. Papain
c. Trypsin
d. Subtilisin

A

d. Subtilisin

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33
Q

Which of the following best describes a protein signal sequence?
a. A sequence in the mature protein that identifies the protein as a secreted protein
b. A polar, C-terminal sequence of resiudes that is cleaved by the signal peptidase
c. The part of the SRP that “signals” recognition of the SRP receptor
d. A nonpolar, N-terminal sequence of residues that is recognized by the SRP

A

d. A nonpolar, N-terminal sequence of residues that is recognized by the SRP

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34
Q

Which of the following coenzymes are NOT involved in oxidation, reduction reactions?
a. Nicotinamide adenine dinucleotide
b. Flavin adenine dinucleotide
c. Thiamine pyrophosphate
d. Lipoamide

A

c. Thiamine pyrophosphate

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35
Q

The signal sequence explains which of the following observations:
a. The C-terminal side of membrane proteins sometimes face the extracellular side of the plasma membrane
b. Membrane proteins with multiple hydrophobic helices are rarely found at the plasma membrane
c. The N-terminal side of membrane proteins are facing the extracellular side of the plasma membrane
d. The C-terminal side of the membrane proteins are modified to contain oligosaccharides

A

c. The N-terminal side of membrane proteins are facing the extracellular side of the plasma membrane

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36
Q

What describes the “steady state assumption” of enzyme kinetics?
a. The [ES] is assumed to be constant
b. The free [E] is assumed to be decrease as the enzyme resets
c. The [S] is assumed to be increasing
d. The [P] is assumed to be steady

A

a. The [ES] is assumed to be constant

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37
Q

When an enzyme is activated by a molecule other than its substrate, this is an example of:
a. Heteroallostery
b. Noncompetitive inhibition
c. Homoallostery
d. Competitive activation

A

a. Heteroallostery

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38
Q

An ES complex that does not require E and S to change shape is best explained by the induced-fit model of substrate binding. T or F

A

False

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39
Q

An enzyme accepts both cholesterol and pregnenolone as its substrates. According to the following table, the enzyme is most efficient with cholesterol as its substrate (table shown with cholesterol and pregnenolone values). T or F

A

True

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40
Q

You identify an new enzyme and find that it has a relatively large turnover number (kcat). Which of the following is also likely to be true?
a. There is not enough information to determine if the reaction velocity (Vo) is high
b. The Km must be small compared to the kcat
c. The Km must also large
d. The reaction velocity (Vo) is high

A

a. There is not enough information to determine if the reaction velocity (Vo) is high

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41
Q

Thiamine pyrophosphate is an example of a prosthetic group. T or F

A

True

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42
Q

Which of the following do not contribute to the favorable thermodynamics of a phospholipid bilayer?
a. Favorable enthalp resulting from van der Waals interactions
b. Favorable enthalpy resulting from disulfide bond formation between head group
c. Favorable entropy resulting from the hydrophobic effect
d. Favorable enthalpy resulting from hydrogen bonding

A

b. Favorable enthalpy resulting from disulfide bond formation between head groups

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43
Q

Which of the following amino acids is not capable of acid base catalysis:
a. Histidine
b. Cysteine
c. Phenylalanine
d. Tyrosine

A

c. Phenylalanine

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44
Q

The prosthetic group that is directly involved in formation of Acetyl-CoA is:
a. Lipoamide (LA)
b. Flavin adenine dinucleotide (FAD)
c. Thiamine Pyrophosphate (TPP)
d. Coenzyme A

A

a. Lipoamide (LA)

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45
Q

A Tm is measured for a bilayer that is made of the lipid PI (18/1:18/1). A second bilayer is determined to have a Tm that is 10 degrees higher. What is the likeliest composition of the second bilayer?
a. PI (18:2/18:2)
b. PI (20:1/20:1)
c. PI (18:1/18:1) with 10 % cholesterol
d. PI (16:1/16:1)

A

b. PI (20:1/20:1)

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46
Q

In which way are Carboxypeptidase A and trypsin similar?
a. They both use zinc to stabilize the transitions state
b. They both display a rapid burst phase followed by a slower stead state phase
c. They both recognize large, bulky hydrophobic groups in their specificity pockets
d. They both cleave at a peptide bond

A

d. They both cleave at a peptide bond

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47
Q

A membrane protein that moves two solutes in opposite directions of one another is an example of:
a. Active unipot
b. Facilitates symport
c. Passive antiport
d. Facilitated antiport

A

d. Facilitated antiport

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48
Q

Cholesterol “blurs the transition” between the gel phase and the liquid crystal phase of a bilayer. How does it do this?
a. It inverts between leaflets of the bilayer
b. It lowers the Tm to a more physiologically relevant level
c. It promotes more efficient tail packing between fatty acid tails
d. It decreases motional freedom between the neighboring fatty acid tails

A

d. It decreases motional freedom between the neighboring fatty acid tails

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49
Q

In serine proteases, the role of the serine residue is to serve as an essential nucleophile. T or F

A

True

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50
Q

Which of the following is an example of desensitization of a signaling event:
a. The activity of phosphodiesterases
b. The conversion of ATP into cAMP
c. The activation of adenylate cyclase
d. G-protein degradation

A

a. The activity of phosphodiesterases

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51
Q

The following structure is an example of a glycerophospholipid (shows an image of lipid with two tails). T or F

A

False

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52
Q

What is the correct label for the following fatty acid?
(shows image)
a. 20:5 c∆ 5, 8, 11, 14, 17
b. 20:5 t∆ 5, 8, 11, 14, 17
c. 19:5 c∆ 5, 8, 11, 14, 17
d. 20:5 c∆ 3, 6, 9, 12, 15

A

a. 20:5 c∆ 5, 8, 11, 14, 17

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53
Q

Which of the following is true regarding competitive inhibition?
a. It requires some form of allostery
b. The inhibitor is not likely to “look like” the substrate
c. The apparent Vmax decreases
d. The apparent Km increases

A

d. The apparent Km increases

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54
Q

Which of the following result in a more fluid membrane?
a. Increase in the fatty acid tail length
b. Decrease the size of the polar head group
c. Increasing the size of the polar head group
d. Decreasing the number of double bonds

A

c. Increasing the size of the polar head group

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55
Q

Triglycerols are not amphipathic and therefore are not components of membranes. T or F

A

True

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56
Q

The enzyme triose phosphate isomerase is a very efficient enzyme. Therefore, its ΔΔG°‡ must be a small number. T or F

A

False

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57
Q

In the “signal hypothesis”, the outcome of a deficient SRP receptor would be finding protein that is secreted, but still has an intact signal sequence. T or F

A

False

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58
Q

Lactate dehydrogenase in skeletal muscles:
a. Replenishes ADP so that glycolysis can continue to run
b. Maximizes energy production by oxidizing pyruvate
c. Generates NADH so that gluconeogenesis can run
d. Generates ATP so that gluconeogenesis can run
e. Replenishes NAD+ so that glycolysis can continue to run

A

e. Replenishes NAD+ so that glycolysis can continue to run

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59
Q

Under high blood glucose concentrations, ___ effectively traps glucose in liver cells.
a. Glucose-6-phosphate
b. Glucokinase
c. GLU2
d. Hexokinase
e. Phosphofructokinase-1

A

b. Glucokinase

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60
Q

In Complex V (ATP synthase; FOF1 complex), the proton pump consists of:
a. αβ-subunits
b. Oligomycin sensitivity conferral protein (OSCP)
c. Stator
d. a- and c-subunits
e. γδε-subunit

A

d. a- and c- subunits

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61
Q

In glycogenesis, almost all α(1→4) linkages are synthesized by:
a. Glycogen synthase
b. Branching enzyme
c. Debranching enzyme
d. Glycogen phosphorylase
e. Glycogenin

A

a. Glycogen synthase

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62
Q

Substrate level phosphorylation involves transferring a high energy phosphate bond from __________.
a. A phosphorylated molecule of ATP
b. ATP to another molecule

A

a. A phosphorylated molecule of ATP

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63
Q

A metabolic accident leads to 1 electron being transferred onto O2. The resulting molecule is:
a. Water (H20)
b. Hydrogen peroxide (H2O2)
c. Superoxide (●O2-)
d. Hydroxyl radical (●OH)
d. Elemental oxygen (O)

A

c. Superoxide (●O2-)

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64
Q

In glycogenesis, α(1→6) linkages are synthesized by:
a. Glycogen synthase
b. Glycogenin
c. Debranching enyzme
d. Branching enzyme
e. Glycogen phosphorylase

A

d. Branching enzyme

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65
Q

In skeletal muscles, electrons from cytoplasmic NADH are transported into the mitochondria via __________.
a. Glycerol-3-phosphate shuttle
b. Malate / Aspartate shuttle

A

a. Glycerol-3-phosphate shuttle

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66
Q

The two enzymes that directly digest dietary glycogen are __________ and isomaltase.
a. Maltase
b. α-amylase

A

b. α-amylase

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67
Q

The rate-limiting step in the TCA cycle is:
a. Succinate dehydrogenase
b. Isocitrate dehydrogenase
c. Citrate synthase
d. Malate dehydrogenase
e. α-ketoglutarate dehydrogenase

A

b. Isocitrate dehydrogenase

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68
Q

Fructose-2,6-bisphophate promotes the activation of __________ while inactivating __________.
a. phosphofructokinase-1; fructose-1,6-bisphosphatase
b. glycogen phosphorylase; glycogen synthase
c. glycogen synthase;
glycogen phosphorylase
d. fructose-1,6-bisphosphatase;
phosphofructokinase-1
e. pyruvate kinase;
pyruvate decarboxylase

A

a. phosphofructokinase-1;
fructose-1,6-bisphosphatase

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69
Q

ATP is exported out of the mitochondrial matrix by:
a. Adenine nucleotide translocase
b. ATP / ADP symport protein
c. Phosphate translocase
d. Complex VI
e. Complex V

A

a. Adenine nucleotide translocase

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70
Q

__________ decreases pyruvate kinase activity and increases the activity of pyruvate carboxylase.
a. ATP
b. Acetyl-CoA

A

b. Acetyl-CoA

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71
Q

Complex I is a flavoprotein and __________.
a. Iron sulfur protein
b. c-type cytochrome

A

a. Iron sulfur protein

72
Q

Hexokinase, but not glucokinase, is allosterically regulated by:
a. ADP
b. ATP
c. AMP
d. Glucose-6-phosphate
e. Glucose

A

d. Glucose-6-phosphate

73
Q

The __________ is the primary site of gluconeogenesis to raise blood glucose concentrations.
a. Liver
b. Kidney cortex

A

a. Liver

74
Q

The flow of carbon through glycolysis is largely regulated by the activity of:
a. Phosphofructokinase-1
b. Pyruvate kinase
c. Hexokinase
d. Glucose-6-phosphatase
e. Fructose-1,6-bisphosphatase

A

a. Phosphofructokinase-1

75
Q

Skeletal muscles are __________ of synthesizing glucose from gluconeogenic intermediates.
a. Not capable
b. Capable

A

a. Not capable

76
Q

The gluconeogenic enzyme found in the endoplasmic reticulum is:
a. Glucose-6-phosphatase
b. Glucokinase
c. Fructose-2,6-bisphosphatase
d. Phosphoenolpyruvate carboxykinase
e. Pyruvate carboxylase

A

a. Glucose-6-phosphatase

77
Q

The starting point of glycolysis is ___.
a. Glucose-6-phosphate
b. Glucose

A

b. Glucose

78
Q

Metabolic pathways:
a. Always end at a specific molecule
b. Never share common enzymes
c. Are only found in higher eukaryotes, such as humans
d. Usually flow in both directions
e. Are only viable when delta G is highly positive

A

a. Always end at a specific molecule

79
Q

Glycogen synthase b is:
a. Phosphorylated and usually active
b. Phosphorylated and usually inactive
c. Never active
d. Unphosphorylated and usually inactive
e. Unphosphorylated and usually active

A

b. Phosphorylated and usually inactive

80
Q

In glycogenolysis, __________ uses a phosphate to cleave α(1→4) linkages.
a. Debranching enzyme
b. Glycogen phosphorylase
c. Glycogen synthase
d. alpha-amylase
e. Branching enzyme

A

b. Glycogen phosphorylase

81
Q

Pyruvate dehydrogenase complex is found in the __________.
a. Cytoplasm
b. Mitochondria

A

b. Mitochondria

82
Q

__________ are the most common cofactor in dehydrogenase reactions.
a. NADH / NAD+
b. NADPH / NADP+

A

a. NADH / NAD+

83
Q

The most important regulated step of gluconeogenesis is:
a. Phosphofructokinase-1
b. Hexokinase
c. Fructose-1,6-bisphosphatase
d. Glucose-6-phosphatase
e. Phosphoenolpyruvate carboxykinase

A

c. Fructose-1,6-bisphosphatase

84
Q

Pyruvate dehydrogenase is NOT regulated by:
a. Pyruvate dehydrogenase phosphatase
b. Acetyl-CoA
c. Glucagon
d. Insulin
e. Pyruvate dehydrogenase kinase

A

c. Glucagon

85
Q

Glycogen phosphorylase a is:
a. Never active
b. Unphosphorylated and usually inactive
c. Phosphorylated and usually active
d. Unphosphorylated and usually active
e. Phosphorylated and usually inactive

A

c. Phosphorylated and usually active

86
Q

__________ is a bidirectional glucose transporter.
a. GLUT3
b. GLUT2
c. GLUT4
d. GLUT1
c. GLUT5

A

b. GLUT2

87
Q

The respiratory complex that transfers electrons from mitochondrial NADH to CoQ is:
a. Complex V
b. Complex III
c. Complex I
d. Complex IV
e. Complex II

A

c. Complex I

88
Q

The starting materials needed to synthesize cholesterol are
a. Acetyl-CoA and more Acetyl-CoA
b. Acetyl-CoA and dimethylallyl pyrophosphate
c. Acetyl-CoA and squalene
d. Acetyl-CoA and mevalonate
e. Acetyl-CoA and Malonyl-CoA

A

a. Acetyl-CoA and more Acetyl-CoA

89
Q

Which of the following correctly matches the hormones to their function?
a. Ghrelin → Activates food intake signal
b. Adiponectin → Inactivates food intake signal
c. Leptin → Activates food intake signal
d. Insulin → Activates food intake signal

A

a. Ghrelin → Activates food intake signal

90
Q

Ammonia (NH3) enters the Urea cycle attached to the amino acid __________.
a. Oxaloacetate
b. Glutamate
c. Fumarate
d. Arginine
e. Aspartate

A

e. Aspartate

91
Q

Lipoprotein lipases are activated by __________.
a. ApoC-II
b. ApoE

A

a. ApoC-II

92
Q

The __________ can synthesize various types of fuels and redistribute them to other organs.
a. Liver
b. Skeletal muscles
c. Brain
d. Cardiac muscles
e. Adipose tissue

A

a. Liver

93
Q

The carbon carrier used in fatty acid biosynthesis is __________.
a. Coenzyme A (CoA)
b. Acyl carrier protein (ACP)

A

b. Acyl carrier protein

94
Q

Cathepsins are involved in protein degradation in the __________.
a. Small intestines
b. Lysosome

A

b. Lysosome

95
Q

The following molecule is (shows a picture)
a. Cholesterol
b. Steroid hormone
c. Vitamin D3
d. Cholesteryl ester
e. Bile salt

A

e. Bile salt

96
Q

One round of β-oxidation will yield: (assume saturated fatty acid and NOT
the final round)
a. 1 NADH and 2 acetyl-CoA
b. 1 FADH2, 1 NADH, and 1 acetyl-CoA
c. NADP+, NADH, and one acetyl-CoA
d. FADH2, NADH, 1 acetyl-CoA, 1 one malonyl-CoA
e. 1 FADH2, 1 NADH, and 2 Acetyl-CoA

A

b. 1 FADH2, 1 NADH, and 1 acetyl-CoA

97
Q

In humans, the NAD+-dependent conversion of glutamate to α-ketoglutarate is catalyzed by:
a. Glutaminase
b. Glutamine synthetase
c. Carbamoyl phosphate synthase
d. Glutamate dehydrogenase
e. Transaminase

A

d. Glutamate dehydrogenase

98
Q

Dietary triacylglycerol is mostly digested by __________.
a. Pancreatic lipase
b. Gastric lipase

A

a. Pancreatic lipase

99
Q

Type 2 diabetes arises when insulin signal transduction does not occur because there is:
a. No insulin
b. Something blocking the signal transduction pathway

A

b. Something blocking the signal transduction pathway

100
Q

To synthesize palmitate (16 carbon saturated fatty acid) via the fatty acid synthase, we need __ molecules of NADPH per round.
a. 7
b. 14
c. 8
d. 1
e. 2

A

e. 2

101
Q

During exertion, skeletal muscles will utilize glucose as fuel and release __________ as waste.
a. Lactate
b. Alanine

A

a. Lactate

102
Q

Carnitine acyltransferase I is inhibited by __________.
a. Malonyl-CoA
b. Acetyl-CoA
c. Carnitine
d. Citrate
e. Glucagon

A

a. Malonyl-CoA

103
Q

Transaminases require __________ as a coenzyme.
a. Cobalamin (B12)
b. NAD+
c. NADH
d. Tetrahydrofolate
e. Pyridoxal phoasphate

A

e. Pyridoxal phosphate

104
Q

The reversible conversion between alanine and pyruvate is catalyzed by __________.
a. Alanine dehydrogenase
b. Alanine transaminase

A

b. Alanine transaminase

105
Q

The preferred fuel for cardiac muscle is:
a. Fatty acids
b. Ketone bodies
c. Amino acids
d. Lactate
e. Glucose

A

a. Fatty acids

106
Q

Glucagon signals the fast state when:
a. blood glucose is low or at homeostatic levels
b. Ketone bodies are high
c. Blood glucose is lower than what is needed to maintain life
d. Blood glucose is high, but cells do not respond
e. Blood glucose is high

A

a. Blood glucose is low or at homeostatic levels

107
Q

Excess nitrogen from skeletal muscles is safely shipped to the liver as:
a. Carbamoyl phosphate
b. Alanine
c. Glutamine
d. Glutamate
e. Urea

A

b. Alanine

108
Q

Methyl groups enter one-carbon metabolsim as:
a. Glycine
b. Serine
c. Methylated B12
d. 5-methyl-tetrahydrofolate
e. S-adenosylmethionine

A

b. Serine

109
Q

Ketogenesis can only occur in the liver as it is the only tissue that has __________.
a. HMG-CoA lyase
b. 3-oxoacid CoA-transferase

A

a. HMG-CoA lyase

110
Q

Prostaglandins are derivates of:
a. Cholesterol
b. Arachidonic acid

A

b. Arachidonic acid

111
Q

The biosynthesis of triacylglycerol and glycerophospholipids are activated by:
a. Glucagon
b. Acetyl-CoA
c. Insulin
d. Phosphatidic acid
e. Citrate

A

c. Insulin

112
Q

Epinephrine signals to:
a. Raise blood glucose to maintain homeostatic levels
b. Inhibit food intake
c. Activate food intake
d. Increases fuel supply to muscles
e. Lower blood glucose by increasing storage of metabolites

A

d. Increase fuel supply to muscles

113
Q

__________ is synthesize by the liver to collect unwanted lipids from the bloodstream and cells.
a. Very low density lipoprotein
b. Intermediate density lipoprotein
c. Low density lipoproteins
d. Chylomicron
e. High density lipoprotein

A

e. High density lipoprotein

114
Q

Acetyl-CoA carboxylase is activated by:
a. Malonyl-CoA
b. Acetyl-CoA
c. Oxaloacetate
d. Glucagon
e. Insulin

A

e. Insulin

115
Q

A regulated enzyme of fat mobilization (lipolysis) is:
a. Pancreatic lipase
b. Lipoprotein lipase
c. Hepatic lipase
d. Adipose triglyceride lipase
e. Monoaceylglycerol lipase

A

d. Adipose triglyceride lipase

116
Q

Triacylglycerol (fat) is packaged into _________ in mucosal cells of the small intestine so that it can be safely transported through the bloodstream.
a. Intermediate density lipoprotein
b. High density lipoprotein
c. Very low density lipoprotein
d. Chylomicron
e. Low density lipoproteins

A

d. Chylomicron

117
Q

__________ results in the synthesis of glutamate.
a. Glutaminase
b. Glutamine synthetase

A

a. Glutaminase

118
Q

A piece of DNA has 15 base pairs per twists (bp/twist). This DNA will exhibit:
a. Right-handed writhes
b. Left-handed writhes

A

a. Right-handed writhes

119
Q

Large damage to a single DNA bases is removed using:
a. Non-homologous end joining
b. Nucleotide excision repair
c. Base excision repair
d. Mismatch repair
e. Direct reversal

A

b. Nucleotide excision repair

120
Q

Decatenation of the circular chromosomes in E. coli is performed by:
a. TOP2
b. DNA gyrase
c. TOP1
d. Topoisomerase IV
e. DnaB

A

d. Topoisomerase IV

121
Q

RNA polymerase:
a. Requires a primer before it can be loaded onto the DNA template
b. Reads the sense strand of DNA
c. Synthesizes RNA in the 3 to 5 direction
d. Reads RNA and reads DNA
e. Has an intrinsic helicase

A

e. Has an intrinsic helicase

122
Q

Epigenetic marks:
a. Are never reversible
b. Only promote heterochromatin
c. Are not inheritable during mitosis
d. Ensure stable pattern of gene expression across mitosis
e. Do not affect transcription

A

d. Ensure stable pattern of gene expression across mitosis

123
Q

N-glycosidic bonds form between __________ of the purine and __________ of deoxyribose.
a. Nitrogen 9 (N9); 1’ carbon (1’C)
b. Nitrogen 9 (N9); 5’ carbon (5’C)
c. Carbon-1 (C1); 1’ carbon (1’C)
d. Nitrogen 1 (N1); 1’ carbon (1’C)
e. Nitrogen 1 (N1); 5’ carbon (5’C)

A

a. Nitrogen 9 (N9); 1’ carbon (1’C)

124
Q

Hypoacetylated histones are associated with areas of:
a. Euchromatin
b. Heterochromatin

A

b. Heterochromatin

125
Q

Holliday junction resolution requires
a. Resolvase
b. Dissolvasome

A

a. Resolvase

126
Q

In E. coli, the promoter is recognized and bound by:
a. β’ (beta prime) subunit
b. TFID
c. σ (sigma) factor
d. TFIIH
e. β (beta) subunit

A

c. σ (sigma) factor

127
Q

Secondary structure of RNA:
a. Is represented by the linear sequence of nitrogenous bases written in 5’ to 3’ direction.
b. Is double stranded of RNA.
c. Occurs between one strand of RNA and a protein.
d. Occurs between one strand of RNA and one strand of DNA.
e. Results due to complementary base pairings within the same strand of RNA.

A

e. Results due to complementary base pairings within the same strand of RNA.

128
Q

The use of a specialized polymerase to read through DNA lesions is called:
a. Translesion synthesis
b. Mismatch repair
c. Damage avoidance
d. Homologous recombination
e. Polymerase switch

A

a. Translesion synthesis

129
Q

CpG islands are:
a. Part of the Galapagos.
b. Binding sites of prokaryotic transcription factors.
c. cis-acting elements commonly found near eukaryotic genes.
d. Transcriptional termination sites in prokaryotes.
e. Trans-acting elements.

A

c. cis-acting elements commonly found near eukaryotic genes.

130
Q

Immediately after initiation of DNA replication in E. coli, the Initiator Binding Element is __________, which results in __________ binding to that DNA element.
a. Hemi-methylated; SeqA
b. Methylated; SeqA
c. Methylated; DnaA-ATP
d. Hemi-methylated; DnaA-ATP
e. Methylated; DnaA-ADP

A

a. Hemi-methylated; SeqA

131
Q

Before loading the sliding clamp onto DNA, we need a double stranded template. The initial double stranded template is made possible by:
a. Type I topoisomerase
b. DNA primase
c. DNA polymerase
d. DNA helicase
e. Single stranded DNA binding proteins

A

b. DNA primase

132
Q

The correct order of DNA polymerase function for lagging strand synthesis in humans is:
a. DNA polymerase delta (δ) → DNA polymerase epsilon (ε) → DNA polymerase alpha (α)
b. DNA polymerase alpha (α) → DNA polymerase epsilon (ε)
c. DNA polymerase alpha (α) → DNA polymerase epsilon (ε) → DNA polymerase delta (δ)
d. DNA polymerase alpha (α) → DNA polymerase delta (δ) → DNA polymerase epsilon (ε)
e. DNA polymerase alpha (α) → DNA polymerase delta (δ)

A

e. DNA polymerase alpha (α) → DNA polymerase delta (δ)

133
Q

In eukaryotes, the transcription factor that initially unwinds DNA so that RNA II polymerase can be loaded is:
a. TFIIF
b. Mediator
c. TFIIB
d. TFIIH
e. TFIID

A

d. TFIIH

134
Q

DNA polymerases can directly interact with __________ to increase processivity.
a. Single stranded DNA binding protein
b. Sliding clamp
c. Clamp loading complex
d. Type II topoisomerases
e. DNA helicase

A

b. Sliding clamp

135
Q

In ribonucleotides, the 2’ carbon is attached to:
a. No functional groups
b. An alcohol (-OH) group

A

b. An alcohol (-OH) group

136
Q

Methyl groups are added to histones by a class of enzymes called:
a. Histone acetyltransferase
b. Maintenance methylase
c. Histone deacetylase
d. Histone methyltransferase
e. Histone demethylase

A

d. Histone methyltransferase

137
Q

The __________ strand of DNA looks nearly identical to the transcribed RNA.
a. Antisense
b. Sense

A

b. Sense

138
Q

During initiation of DNA replication in humans, Cdc6 and Cdt1 recruit __________to the replication origin.
a. Origin recognition complex
b. DnaB
c. Cyclin D
d. TOP2
e. Minichromosome maintenance protein (MCM) complex

A

e. Minichromosome maintenance protein (MCM) complex

139
Q

Clamp loading complex will directly load __________ onto the DNA template.
a. Sliding clamp
b. DNA polymerase

A

a. Sliding clamp

140
Q

DNA lisgase:
a. catalyze phosphodiester bonds between two strands of DNA.
b. may have proofreading ability.
c. synthesizes the new DNA strand in 3’ to 5’ direction.
d. are processive.
e. catalyze phosphodiester bonds between one strand of DNA and a deoxyribonucleotide (dNTP).

A

a. catalyze phosphodiester bonds between two strands of DNA.

141
Q

Type II Topoisomerases:
a. Utilizes ATP to cut double stranded DNA to relieve writhes.
b. Protect single stranded DNA from damage.
c. Utilizes ATP to break hydrogen bonds between complementary base pairing.
d. Relieves supercoiled DNA without the need of ATP.
e. Generates a small RNA primer to aid in loading the DNA polymerase.

A

a. Utilizes ATP to cut double stranded DNA to relieve writhes.

142
Q

DNA polymerases with smaller active sites are typically __________.
a. More processive
b. Less processive

A

a. More processive

143
Q

Telomeres protects:
a. Tips of eukaryotic chromosomes
b. 5 ends of prokaryotic mRNA c. 3 ends of prokaryotic mMRNA
d. 5` ends of eukaryotic mRNA
e. Tips of prokaryotic chromosomes

A

a. Tips of eukaryotic chromosomes

144
Q

The leading strand in E. coli is primarily synthesized by:
a. DNA polymerase II
b. DNA polymerase ε (epsilon)
c. DNA polymerase I
d. DNA polymerase δ (delta)
e. DNA polymerase III

A

e. DNA polymerase III

145
Q

The termination of DNA replication in E. coli occurs at:
a. Non-specific sites of DNA
b. Tus/Ter complexes

A

b. Tus/Ter complexes

146
Q

DnaA-ATP binds to the DNA element called __________ in OriC.
a. Initiator binding element
b. DNA unwinding element

A

a. Initiator binding element

147
Q

Factor Independent Termination involves the transcription of:
a. Rho-recognition site
b. Symmetrical GC-rich sequences

A

b. Symmetrical GC-rich sequences

148
Q

For this question, please refer to the follow mRNA sequence:
ACCGGAUAUUGACGCUACUG
The fourth (4th) codon in reading frame 2 (RF2) encodes for:
a. Isoleucine (Iso, I)
b. Alanine (Ala, A)
c. Threonine (Thr, T)
d. Stop codon
e. Aspartate (Asp, D)

A

e. Aspartate (Asp, D)

149
Q

An indel mutation that does NOT cause a frameshift will result in:
a. an insertion or deletion of one or more amino acids in the encoded protein sequence.
b. a change of one amino acid to a different amino acid.
c. a change of one amino acid encoding codon to a stop codon.
d. a change to an amino acid encoding codon, but no change to the encoded amino acid.
e. a change in the sequence and length in the encoded protein sequence.

A

a. an insertion or deletion of one or more amino acids in the encoded protein sequence.

150
Q

The anticodon sequence 5’ UGG 3’ can form a Wobble interaction
with the codon ________. (please note the direction (5’ to 3’) of the codon and anticodon):
a. 5’ CCA 3’
b. 5’ CCG 3’

A

b. 5’ CCG 3’

151
Q

Proteins targeted to the mitochondria are expressed by ________ and transported into the mitochondria via __________.
a. Free ribosomes; Nuclear pores
b. Rough endoplasmic reticulum-bound ribosomes; TOM barrels
c. Free ribosomes; TOM barrels
d. Free ribosomes; Vesicles
e. Rough endoplasmic reticulum-bound ribosomes; Vesicles

A

c. Free ribosomes; TOM barrels

152
Q

Which sequence represents a fragment of DNA that was cut with a restriction enzyme to produce a sticky end? (Note: ▼represents site of cut DNA)
a. 5’ CATA▼TG
b. 5’ CAT▼ATG

A

a. 5’ CATA▼TG

153
Q

Prokaryotic rRNA __________ processed.
a. Is
b. Is not

A

a. Is

154
Q

Polymerase Chain Reaction (PCR) uses high temperatures (95°C) to replace the need for:
a. DNA polymerase
b. Sliding clamp
c. DNA helicase
d. DNA primase
e. Clamp loader

A

c. DNA helicase

155
Q

Which one of the following is not synthesized by rough endoplasmic reticulum-bound ribosomes?
a. Mitochondrial proteins
b. Lysosomal proteins
c. Extracellular proteins
d. Golgi proteins
e. Cellular membrane proteins

A

a. Mitochondrial proteins

156
Q

Translocation of an unfolded protein in bacteria requires ________.
a. TAT pathway
b. Sec pathway

A

b. Sec pathway

157
Q

The 5’ cap is added to the 5’ end of RNA by __________.
a. RNA polymerase II (RNAPII)
b. RNA guanylyltransferase (GTase)
c. RNA (guanine-N7)-methylatransferase (N7MTase)
d. RNA (nucleoside-2`-O) methyltransferase (2’OMTase)
e. RNA triphosphatase (RTPase)

A

b. RNA guanylyltransferase (GTase)

158
Q

__________ can be used to find the DNA-binding site of a protein.
a. Immunohistochemistry
b. Southern Blot
c. Western Blot
d. Electrophoretic Mobility Shift Assay
e. DNase I footprinting

A

e. DNase I footprinting

159
Q

To sort proteins by net charge and shape of their folded structure, you should use __________.
a. Native polyacrylamide gel electrophoresis
b. SDS-polyacrylamide gel electrophoresis

A

a. Native polyacrylamide gel electrophoresis

160
Q

Small interfering RNA (siRNA):
a. Is an exogenour source of RNA used in RNAi
b. Is the RNA portion of SnRNPs
c. Is an endogenous source of RNA used in RNAi
d. Is an endonuclease involved in anti-viral response
e. Forms a complex with Dicer to form RNA-induced silencing complex (RISC)

A

a. Is an exogenous source of RNA used in RNAi

161
Q

__________ can be used to determine if a protein of interest is present in an intact sample.
a. Protein immunoprecipitation
b. Western blot
c. Immunohistochemistry
d. Chromatin immunoprecipitation
e. ELISA

A

c. Immunohistochemistry

162
Q

Chromatin Immunoprecipitation (ChIP) can be used to study __________ in vivo.
a. DNA-protein interactions for any DNA-binding protein
b. DNA-histone interactions only

A

a. DNA-protein interactions for any DNA-binding protein

163
Q

During processing of microRNA (miRNA), Argonaute:
a. Selects which strand of miRNA will be used to target mRNA.
b. Degrades the strand of miRNA that is not chosen to target mRNA.
c. Stabilizes aptamers to form a riboswitch.
d. Deaminates cytosine to form uracil.
e. Cleaves miRNA in the nucleus.

A

a. Selects which strand of miRNA will be used to target mRNA.

164
Q

__________ can be used to detect a protein of interest after the sample has been run on a gel.
a. ELISA
b. Western blot
c. Immunohistochemistry
d. Northern blot
e. Southern blot

A

b. Western blot

165
Q

To accurately measure gene expression at the level of RNA (i.e., to determine how much RNA is present in your sample), you should use:
a. qPCR
b. A reporter construct
c. Southern blot
d. Northern blot
e. Western blot

A

a. qPCR

166
Q

A CAG codon is mutated to TAG (assume coding strand of DNA). This is an example of:
a. Nonsense mutation
b. Missense (or non-synonymous) mutation

A

a. Nonsense mutation

167
Q

During elongation in eukaryotes, __________ is recharged by __________.
a. eEF-1α; eEF-1βγ
b. eEF-1βγ; eEF-1α
c. EF-Tu; EF-Ts
d. eEF-2; eEF-1βγ
e. EF-G; EF-Ts

A

a. eEF-1α; eEF-1βγ

168
Q

eEF1α loads an aminoacyl-tRNA into the __________ of the ribosome.
a. P-site
b. A-site

A

b. A-site

169
Q

The Kozak Sequence is recognized by:
a. 16S rRNA
b. 18S rRNA

A

b. 18S rRNA

170
Q

A technique that amplifies and isolates a specific DNA fragment is called:
a. Agarose gel electrophoresis
b. Polymerase Chain Reaction (PCR)
c. Southern blot
d. Restriction digestion
e. In vivo experiments

A

b. Polymerase chain reaction (PCR)

171
Q

A technique used to push DNA through non-uniform pores to separate molecules by length is called:
a. SDS-Agarose gel electrophoresis
b. Agarose gel electrophoresis
c. Native Polyacrylamide gel electrophoresis
d. Polyacrylamide gel electrophoresis
e. SDS-Polyacrylamide gel electrophoresis

A

b. Agarose gel electrophoresis

172
Q

eIF2 helps attach:
a. an N-formylmethionyl-tRNA to the 50S subunit of the ribosome.
b. a methionyl-tRNA to the 40S subunit of the ribosome.
c. a methionyl-tRNA to the 60S subunit of the ribosome.
d. an N-formylmethionyl-tRNA to the 30S subunit of the ribosome.
e. aa-tRNA into the A site of the ribosome.

A

b. a methionyl-tRNA to the 40S subunit of the ribosome.

173
Q

The substrates for amino acyl-tRNA synthetases are:
a. an amino acid, ATP, and tRNA
b. Amino acyl-tRNA and Peptidyl-tRNA
c. an amino acid and tRNA
d. two amino acids and tRNA
e. an amino acid, GTP, and tRNA

A

a. an amino acid, ATP, and tRNA

174
Q

In prokaryotes, the formation of a peptide bond is catalyzed by a catalytic adenosine residue found on the ________.
a. 16S rRNA
b. 28S rRNA
c. 18S rRNA
d. 5.8S rRNA
e. 23S rRNA

A

e. 23S rRNA

175
Q

The first snRNP to bind to the target mRNA during spliceosome formation is:
a. SnRNP U4
b. SnRNP U1
c. SnRNP U2
d. SnRNP U5
e. SnRNP U6

A

b. SnRNP U1

176
Q

During electrophoretic mobility shift assays (EMSA, gel shift), a DNA fragment __________ will migrate fastest (e.g., farther) through the gel?
a. Not bound to a protein
b. Bound to a protein

A

a. Not bound to a protein

177
Q

The polyA tail is added to the end of eukaryotic mRNA by:
a. Polyadenylate Binding Protein (PABP)
b. Cleavage Factor I (CFI)
c. Poly A Polymerase
d. Cleavage factor II (CFII)
e. Cleavage / Polyadenylation Specificity Factor (CPSF)

A

c. Poly A Polymerase

Biochem Exam 1 (3 decks)

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