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Concepts of Biochem > PROTEINS: Homework & Tophat > Flashcards

PROTEINS: Homework & Tophat Flashcards

1
Q

How can you find the alpha carbon in a structure?

A

where the amine groups stems from and the carboxylic acid connects to as well

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2
Q

A scientist has synthesized a new amino acid that is hydrophilic and has an overall neutral charge (i.e., 0) at physiological pH. Based on the information provided, this amino acid would likely be classified as:

A

polar

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3
Q

How can you check for an amino acid’s overall charge?

A
  1. Check for zwitterion state (carboxylic acid has a negative charge and amine has a positive charge) these will cancel
  2. Check for the remaining charge left on the side chain, often the amine group
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4
Q

True or false: All 20 standard proteinogenic amino acids are chiral.

A

this is false

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5
Q

Your friend works in a research lab on campus. He wants to conduct an experiment using the WEAKEST possible acid. His choices are: Furo-hydroxamic acid (pKa of 8.5), Nicotinehydroxamic acid methiodide (pKa of 6.5) or Tropo-hydroxamic acid (pKa of 9.1). Which acid should he use?

A

Tropo-hydroxamic acid (largest pKa)

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6
Q

What is the rule to remember amino acid charge with changes to pKa and pH?

A

pH>pKa: deprotonated
pH<pKa: protonated
-pKa amine: 9
-pKa carboxylic acid: 2
-go group by group and compare the number values first then apply the rules

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7
Q

True or false: A protein’s primary structure is stabilized by covalent peptide bonds.

A

true

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8
Q

The amino acid below has a side chain with a pKa of 11. In a neutral pH solution (i.e., pH 7), it has the ionization state shown.
Under what pH condition would the amino acid have a net charge of -1? ( side chain is protonated/amine, the carboxylic acid is negative, the amine is positive)

A

pH 13

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9
Q

True or false: Both tertiary structure and quaternary structure are stabilized by non-covalent interactions between amino acid side chains.

A

True

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10
Q

Most snake venom contains metalloproteinase, a type of proteolytic enzyme that requires zinc (Zn+2) or cobalt (Co+3) for catalysis. Based on this information, and your knowledge of biochemistry, which statement below is true?

A

The enzyme is using metal ion catalysis with a mineral.

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11
Q

Allopurinol is commonly prescribed to people to treat gout (a form of arthritis caused by excess uric acid). After the drug binds to the active site of Xanthine oxidase, it is converted by the enzyme into alloxanthine. This intermediate then covalently modifies the active site, permanently disabling the enzyme. Drug dosing reflects the fact that the enzyme-drug complex dissociates slowly.

Based on this information, Allopurinol is a/an:

A

suicide inhibitor

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12
Q

Select the best explanation for why the reaction shown below increases the entropy of the system.

NH4NO2 (s) -> N2 (g) + 2H2O (l)

A

The number of products is greater than the number of reactants.

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13
Q

The committed step in fatty acid synthesis is shown below. What is the most likely reason for why this reaction includes ATP hydrolysis?

A

Condensing acetyl CoA with bicarbonate (HCO3-) is endergonic.

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14
Q

A pharmaceutical company has developed three versions of a drug: Version A (KM = 1.2x10-1 M), Version B (KM = 2.4x10-1 M), and Version C (KM = 4.8x10-1 M). The enzyme of interest can catalyze its reaction using any version of the drug. Based on KM values, the enzyme’s preferred substrate is:

A

Version A

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15
Q

True or false: Michaelis-Menten enzymes are controlled via feedback inhibition.

A

false

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16
Q

What do cofactors and positive effectors have in common?

A

Both interact with the enzyme to facilitate the reaction

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17
Q

True or false: Dietary protein digestion involves lipases.

A

false

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18
Q

Below we see cleavage of viral and host proteins by a viral protease. The viral protease always cleaves between glutamine (Q) and glycine (G) amino acid residues. Based on this information, this enzyme is a:

A

specific protease

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19
Q

On Monday, you worked on generating a true/false question for the amino acid shown (at pH 7). Below are four collated options. Select the one you like best. (zwitterion state with amine and a carboxylic acid, the side chain is benzene with negative Oxygen )

A

true: at this pH, the amino acid’s net charge is -1

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20
Q

how does entropy increase in reactions?

A

As the reactant in the reaction freezes, it undergoes a phase change toward a higher internal energy.

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21
Q

For the amino acid shown below, select the functional group that is removed during amino acid metabolism.

A

amine group, stemming off the alpha carbon

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22
Q

Carbamoyl phosphate synthetase I catalyzes the committed step of the urea cycle. Consequently, this enzyme is a/an:

A

allosteric enzyme with complex sigmoid kinetics

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23
Q

True or false: All proteinogenic amino acids generate major metabolic intermediates for cellular respiration.

A

true

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24
Q

What do fatty acids and amino acids have in common?

A

Both are comprised of carbon, hydrogen and oxygen.

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25
Q

Proteins have a variety of roles. Which role is shared with ligand lipids?

A

Being primary messengers in signal transduction pathways.

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26
Q

Which component of the general amino acid structure differs between amino acids?

A

The side chain (R group)

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27
Q

Although cysteine and methionine (shown below) are both standard amino acids, their structure differs from most proteinogenic amino acids. What makes them unusual?

A

They contain sulfur, a major element required for life.

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28
Q

Bicarbonate (shown below) functions as a conjugate base within the plasma’s bicarbonate buffer system. Bicarbonate also was important for the:

A

committed step in fatty acid synthesis

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29
Q

The amino acid shown below does not have an ionizable side chain. However, when this amino acid is in a basic solution (i.e., pH 13), it would resemble:

A

both are less than the rule, deprotonated, state C

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30
Q

Amino acids with ionizable side chains are found in all groups except:

A

hydrophobic, are found in negatively-charged/polar/positively-charged

31
Q

The side chain for the amino acid shown below has a pKa of 4.

Which ionization state is correct for this amino acid, when it is in a more neutral solution (i.e., pH 7)?

A

both the side chain and carboxylic acid would deprotonate and the amine would protonate

32
Q

Your friend works in a research lab on campus. He wants to conduct an experiment using the strongest possible acid. His choices are: Furo-hydroxamic acid (pKa of 8.5), Nicotinehydroxamic acid methiodide (pKa of 6.5) or Tropo-hydroxamic acid (pKa of 9.1). Which acid should he use?

A

Nicotinehydroxamic acid methiodide

33
Q

[ Select ]
is achiral because its side chain is a/an
[ Select ]

A

glycine, hydrogen atom

34
Q

True or false: Changes in pH will impact both protein structure and function.

A

True

35
Q

The amino acid shown below has a side chain with a pKa of 11.

In an acidic solution (i.e., pH 1), the amino acid would look like
[ Select ]
and have a net charge of
[ Select ]

A

The side chain amine would protonate, the amine from the alpha carbon would protonate, and the carboxylic acid would protonate or keep the hydrogen

36
Q

The amino acid below has a side chain with a pKa of 4. In a neutral pH solution (i.e., pH 7), it has the ionization state shown.

Under what pH condition would the amino acid have a net charge of 0? (same as usual)

A

pH 3 (has to be smaller to deprotonate)

37
Q

Which statement about the proteolipid shown below is true?

A

It contains a saturated fatty acid that could be synthesized by human enzymes.

38
Q

Sodium dodecyl sulfate (SDS) is often used as a detergent in laboratory cleaning procedures. SDS contains sulfate ions (SO42-), which bind strongly to positively-charged amino acid residues and alter the protein’s net charge.

Which level(s) of protein structure is/are adversely impacted by SDS? Select all that apply.

A

tertiary and quaternary structure

39
Q

Below is a list of different chemical bonds that help stabilize protein structure. Select the covalent bond.

A

Disulfide bond

40
Q

Which level of protein structure is retained (i.e., still present) in a denatured protein?

A

primary structure

41
Q

A macromolecular complex formed by two identical proteins (in terms of primary structure and subsequent folding) is called a homodimer. A macromolecular complex formed by two different proteins is called a heterodimer.

Based on that information, the macromolecular complex shown below is a:

A

homodimer

42
Q

Gastric lipase - which cleaves ester linkages within triacylglycerols - has an optimal pH of 4. Based on your knowledge of biochemistry, at a pH of 7 this enzyme would:

A

be less catalytically active than at pH 4

43
Q

What do coenzymes and minerals have in common?

A

Both facilitate diverse enzymatic reactions.

44
Q

Methotrexate is commonly prescribed to treat rheumatoid arthritis. This drug binds to the active site of dihydrofolate reductase, preventing the enzyme from converting dihydrofolate to tetrahydrofolate. Methotrexate must be taken often because the enzyme-drug complex dissociates rapidly.

Structure of substrate (DHF) and inhibitor (MTX)

Based on this information and the diagram above (showing the structures of dihydrofolate and methotrexate), this drug is most likely a/an:

A

competitive inhibitor

45
Q

Select the best explanation for why each reaction increases the entropy of the system.

NaCl (s) -> NaCl (aq) is accompanied by an increase in entropy because
[ Select ]

SO2Cl2 (g) -> SO2 (g) + Cl2 (g) is accompanied by an increase in entropy because
[ Select ]

H2O (s) -> H2O (l) is accompanied by an increase in entropy because the phase change from melting is towards a higher internal energy

A

Answer 1:
a solute was dissolved in water, forming a solution
Answer 2:
the number of products is greater than the number of reactants
Answer 3:
the phase change from melting is towards a higher internal energy

46
Q

True or false: Transition states are only formed in enzyme-catalyzed reactions.

A

false

47
Q

1,3-bisphosphoglycerate can phosphorylate ADP, generating ATP, because 1,3-bisphosphoglycerate has a
[ Select ] than ADP.

In contrast, glycerol 3-phosphate cannot phosphorylate ADP because glycerol 3-phosphate has a
[ Select ] than ADP.

A

Answer 1:
higher phosphoryl-transfer potential
Answer 2:
lower phosphoryl-transfer potential

48
Q

In the diagram below, an orange circle represents an effector, and a purple diamond or rod represents a substrate. Effectors are small molecules that regulate enzyme activity.

Based on this information and the diagram itself, which statement is true?

A

The active site is the location where a substrate binds to the enzyme.

49
Q

Which reactions would occur spontaneously

A

negative G values; exothermic

50
Q

True or false: At equilibrium, the concentration of products and reactants are always the same.

A

False

51
Q

Based on the reaction schematic below, which enzyme conforms to allosteric kinetics?

A

Single arrow pointing to a product

52
Q

A pharmaceutical company has developed three versions of a drug: Version A (KM = 2.3x10-1 M), Version B (KM = 2.3x10-3 M), and Version C (KM = 2.3x10-2 M). The enzyme of interest can catalyze its reaction using any version of the drug.

Based on KM values, the enzyme’s preferred substrate is:

A

Version B: Smaller KM values show a greater affinity

53
Q

True or false: Enzymes alter the ΔG°’ of the reactants and/or products.

A

False

54
Q

Dietary protein digestion involves: peptidase, bile salts, pepsin, and chymotrypsin. For each molecule listed, indicate where in the human body it participates in digestion.

peptidase, bile salts, pepsin, chymotrypsin

A

Bile salts, Peptidase, Chrymotrypsin: SI
Pepsin: Stomach

55
Q

True or false: Digestive enzymes break covalent bonds in protein containing foods.

A

True

56
Q

Serine and threonine can both be directly deaminated during amino acid metabolism. What else do these two amino acids have in common?

A

Both can be phosphorylated or glycosylated.

57
Q

Amino acid metabolism generates 7 major metabolic intermediates: pyruvate, fumarate, oxaloacetate, acetyl CoA, succinyl CoA, acetoacetyl CoA, and alpha-ketoglutarate.

Which intermediate can be generated from cleaving arginosuccinate in the urea cycle?
Which intermediate can be generated from metabolizing an even chain fatty acid?

A

fumarate, acetyl CoA

58
Q

True or false: Dietary amino acids are stored in the liver for later use.

A

False

59
Q

If you wanted to synthesize glucose, you could use the keto acid from a glucogenic amino acid.

A

glucogenic

60
Q

The urea cycle happens exclusively in the
[ Select ] , which is the same location where
[ Select ]

A

liver, cholesterol synthesis occurs

61
Q

Where do humans obtain most of the nitrogen our bodies need?

A

through the food we eat

62
Q

True or false: Human enzymes can synthesize both essential and nonessential amino acids.

A

false: humans can only synthesize nonessential amino acids

63
Q

The committed step in fatty acid synthesis is shown below. What is the most likely reason for why this reaction includes ATP hydrolysis?

A

Condensing acetyl CoA with bicarbonate (HCO3-) is endergonic.

64
Q

True or false: Michaelis-Menten enzymes are controlled via feedback inhibition.

A

false

65
Q

What do cofactors and positive effectors have in common?

A

Both interact with the enzyme to facilitate the reaction.

66
Q

True or false: Dietary protein digestion involves lipases.

A

False

67
Q

For the amino acid shown below, select the functional group that is removed during amino acid metabolism.

A

amine group from the alpha carbon

68
Q

Carbamoyl phosphate synthetase I catalyzes the committed step of the urea cycle. Consequently, this enzyme is a/an:

A

allosteric enzyme with complex sigmoid kinetics

69
Q

True or false: All proteinogenic amino acids generate major metabolic intermediates for cellular respiration.

A

This is true

70
Q

In humans, amino acid synthesis often involves:

A

transamination and cofactors

71
Q

True or false: Translation is the process by which all genes on a chromosome are expressed at once.

A

false

72
Q

True or false: Humans can synthesize proteins that contain both essential and nonessential amino acids.

A

true

73
Q

Kirromycin is an antibiotic that immobilizes and degrades elongation factor Tu (EF-Tu) in prokaryotes. Consequently, administering kirromycin prevents bacterial translation by interfering with the:

A

Elongation stage

74
Q

In eukaryotes, confining mRNA to the cytoplasm would:

A

hinder translation

Concepts of Biochem (8 decks)

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