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MCAT BIOCHEM $ > 2. Amino Acids and Proteins > Flashcards

2. Amino Acids and Proteins Flashcards

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1
Q

What are the non-polar, hydrophobic amino acids? For each explain their shape, and their single letter name

A

GAVLIMP

glycine - no R 
alanine - CH3
valine - isopropyl
leucine - methyl-isopropyl 
isoleucine - secondary-butyl
methionine - C-C-S-C
proline - attaches to itself
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2
Q

T or false, phenylalanine and tryptophan are also hydrophobic.

A

True,

they are not a part of GAVLIMP b/c they are aromatic

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3
Q

What are the polar, hydrophilic amino acids? For each explain their shape, briefly.

A

STNC-Q

Serine - S - OH group 
Threonine - T - ethanol 
Asparagine - N - amino group (shorter)
Cysteine - C - SH 
Glutamine - Q - amino group (longer)

tyrosine (Y) is also polar, but placed with the aromatic compounds. Polar amino acids form H-bonds with water.

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4
Q

What are the basic amino acids?

A

Lysine - K - Long tail to an NH3
Arginine - R - shorter tail to an NHNH2=NH
Histidine - H - ring containing two Ns

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5
Q

What are the acidic amino acids?

A

Aspartic Acid - D - shorter COOH

Glutamic Acid - E - longer COOH

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6
Q

How can we differentiate E from D and Q from N?

A

Q and N are polar. Q (glutamine) is longer
E and D are acidic. E (glutamate) is longer

glut = longer.

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7
Q

Explain the protonation status of D, E, K, R, and H ar physiological pH (7.4)

A

D and E are acidic (low pKa values). These are deprotonated (anionic) at physiological pH

K and R are basic (higher pKa values). These are protonated (cationic) at physiological pH.

H (pKa = 6.5) exists equally in protonated and deprotonated forms at 7.4. (His goes both ways)

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8
Q

What are the aromatic amino acids?

A

tyrosine - Y - phenol group - polar
Tryrptophan - W - two aromatic rings - nonpolar
phenylalanine - F - benzene ring - nonpolar

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9
Q

What amino acids are phosphorylated by kinases?

A

hydroxyl-containing amino acids: tyrosine, serine, and threonine.

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10
Q

What amino acids contain sulfur?

A

Cysteine - C - SH

methionine - M - CCSC

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11
Q

What is an essential amino acid?

A

An AA that we cannot synthesize and must be obtained by our diets. Most non-polar AAs are essential.

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12
Q

What are the pKa values for the carboxyl group and amino group of the amino acid backbone?

A

COOH - pKa = 2

NH2 - pKa = 9/10

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13
Q

What is the Henderson-Hasselbalch equation?

A

pH = pKa + log ([base] / [acid])

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14
Q

Henderson-Hasselbalch equation: What happens if pH = pKa?

A

pH = pKa + log ([base] / [acid])

if pH = pKa, then log ([base] / [acid]) = 0. This means that [base] = [acid] since log(1) = 0

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15
Q

Explain the relationship of pH and pKa with the protonation status of an R group.

A

pH < pKa; the acidic group will be mostly protonated

pH > pKa; the acidic group will be mostly deprotonated

e.g. at physiological pH (7.3), carboxylic acid groups of the AA backbone (pKa = 2) are almost entirely deprotonated.

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16
Q

What is an isoelectronic point? What is a zwitterion?

A

isoelectronic point (pI) - the pH at which a molecule has a neutral net charge.

An amino acid that is at its isoelectronic point (glycine at 7.4 has a + and a - charge) is called a zwitterion.

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17
Q

How can we calculate the isoelectronic point for an amino acid with two functional groups?

A

We just take the average of the pKa values. For glycine, we take

(9 + 2) / 2 = 5.5

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18
Q

during polypeptide synthesis, what end is made first?

A

The amino end is made first and the COOH is made last.

Read N –> C

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19
Q

In the dipeptide, is ALA - GLY the same molecule as GLY - ALA?

A

NO, since the amino acid terminals are different

H3N - ALA - GLY - COOH

H3N - GLY - ALA - COOH

connectivity is different.

20
Q

Why does peptide bond formation require a dehydration reaction?

A

It requires energy input = dehydration. Hydrolysis releases energy

NH2 attacks carbonyl oxygen

21
Q

T or f, cystine formation is an oxidation reaction.

A

True, since they reactants lost hydrogen

oxidation = lose electrons, lose hydrogens, or gain oxygen

22
Q

t or f, the inside of the cell is called a reducing environment because it contains many anti-oxidants.

A

True!

23
Q

What is the implication of the cells reducing environment on disulfide bridges?

A

The formation of a disulfide bond (cystine) is an oxidation reaction. However, because the inside of the cell is a reducing environment, the cell will reduce the bond back to two thiol groups.

Thus, Disulfide bridges are only found in extracellular proteins!!!

24
Q

What is capable of protein denaturation (protein unfolding)?

A

urea, extreme temperature, pH, or salt concentrations.

peptide bonds are NOT broken, only protein shape

25
Q

What holds together protein secondary structure?

A

Amino acid backbone hydrogen bonding

The alpha-carboxyl oxygen of one amino acid, hydrogen bonds with the alpha-amino proton of an amino acid three residues away.

26
Q

Why are proline residues not found within an alpha-helix (n=2)?

A
  1. proline binds to its own backbone, which removes the only hydrogen on its amino group. Thus, proline residues cannot hydrogen bond (which holds together helixes)
  2. proline causes a physical kink in the peptide chain
27
Q

How does an enzyme work?

A

Enzymes are biological catalysts: They increase the rate of a reaction by lowering the activation energy (which is done by stabilizing the transition state). They DO NOT effect the ΔG or the Eq.

enzymes are kinetic not thermodynamic

28
Q 
What does each enzyme do? 
Kinase
Polymerase
Phosphatase
Lyase
Hydrolase
Ligase
A

Kinase - adds (transfers) phosphate groups
Polymerase - extends nucleotide chains
Phosphatase - removes phosphate groups
Lyase - breaks chemical bonds by means other than REDOX or hydrolysis
Hydrolase - hydrolyzes chemical bonds
Ligase - forms chemical bonds (e.g. in DNA lagging strand)

29
Q

What is reaction coupling?

A

Enzymes facilitate ΔG (-) reactions. However, many reactions are ΔG (+). Therefore, the cell couples very negative reactions with positive reactions, which drive the positive reaction.

ATP hydrolysis is the primary reaction coupler.

30
Q

T or f, enzymes selectively promote unfavorable reactions via reaction coupling.

A

True. Enzymes only have a kinetic role in the reaction itself. But since they are designed for specific reactions, they are selective.

31
Q

Amino acids and sugars. Which isomers are found in animals / humans (D/L)?

A

D-sugars (think Delicious)

L-amino acids

32
Q

What are co-factors and what are co-enzymes?

A

co-factor: A small molecule or metal ion that facilitates enzyme catalysis. Vitamins are co-factors.
co-enzyme: An organic (Carbon-containing) co-factor

33
Q

What is allosteric regulation?

A

The modification of an enzymes active site via interactions that occur at a different site on the enzyme (called the allosteric site).

34
Q

The reaction rate (mols of product per second) of an enzyme catalyzed reaction is dependent on what?

A

the [enzyme]
the [substrate]

however, the enzyme concentration is usually fixed, and therefore, the substrate concentration is only considered.

35
Q

On a V (rate) vs [S] curve, explain how changing [S] effects V?

A

At low [S], they are proportional. If you double [S], you double V. However, as you consistently increase [S], eventually the enzymes all become saturated. At this point, any increase in [S] does not change V. This is Vmax.

36
Q

What is Km on a V (rate) vs [S] curve?

A

Km is the [S] at which we are at Vmax / 2

how much substrate is needed to get to half maximum velocity.

37
Q

What is the implication of a high / low km?

A

A low Km indicates that not much substrate is required to get to half Vmax. If this is the case, then the enzyme affinity for that substrate must be high.

If the Km is high, then the affinity must be low.

38
Q

Certain enzymes do not follow normal Vmax, Km kinetics. Explain enzyme cooperativity.

A

Cooperativity is a special form of allosteric regulation. An enzyme or multienzyme complex that has two or more active sites is capable of this. Essentially, the binding of one active site regulates the substrate affinity (+ or -) of the other active site.

Positive cooperation: Oxygen binding on hemoglobin

39
Q

What curve is made with positive cooperation?

A

A sigmoid curve. At the start [S] effects V a little. Then once one AS is bound, the other AS is in a relaxed state, so the curve shoots up. It then plateaus at saturation.

40
Q

Enzyme inhibition: Explain Km and Vmax.

Competitive inhibition

A

Competitive inhibition, the inhibitor directly binds the enzymes active site. Thus, we need to increase the [S] to compete with this inhibitor.

Vmax is unchanged
Km - increases (since you need more substrate to get to half Vmax)

41
Q

Enzyme inhibition: Explain Km and Vmax.

Non-Competitive inhibition

A

Non-competitive inhibition, the inhibitor binds an allosteric site that alters the active site. Adding more substrate will not displace the allosteric inhibitor and therefore does not change anything.

Vmax - decreased while the inhibitor is bound
Km - unchanged (since the affinity of the active site has not changed). The AS can still bind the substrate, but ithe reaction will proceed more slowly.

42
Q

Enzyme inhibition: Explain Km and Vmax.

Un-Competitive inhibition

A

Un-competitive inhibition, the inhibitor can only bind the Enzyme once the substrate has already bound the AS (i.e. the inhibitor binds the enzyme-substrate complex at an allosteric site).

Vmax - decreased since the inhibitor cannot be displaced.
Km - decreased (the apparent affinity for the E has increased - the E-S complex is favored).

43
Q

Enzyme inhibition: Explain Km and Vmax.

Mixed inhibition

A

Mixed inhibition is a combination of non-competitive and un-competitive inhibition. It can bind E alone or the E-S complex.

Vmax - decreased
Km - varies on inhibitor

44
Q

Explain the Lineweaver-Burke plot. Slope, y-axis, x-axis.

A

A Lineweaver-Burke plot is a double reciprocal plot that plots enzyme kinetics on a linear graph.

Slope = Km / Vmax

y-intercept = 1/Vmax

x-intercept = -1/Km

45
Q

How is an increase in reaction rate or an increase in Km represented on a Lineweaver-Burke plot.

A

Since a Lineweaver-Burke plot is a double reciprocal,

increases in Vmax are seen as a decrease in y-value.
increases in Km are seen as a decrease in x-value.

Vice versa,
if Km decreases, x-values increase.

46
Q

What is the slope of a Lineweaver-Burke plot?

A

Km / Vmax

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