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Kaplan: Biochemistry Part I > Chapter 8: Amino Acids, Proteins, and Enzymes > Flashcards

Chapter 8: Amino Acids, Proteins, and Enzymes Flashcards

1
Q

Describe and draw out the general structure of an amino acids?

A
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2
Q

How do amino acids differ from one another?

A

only in the chemical nature of the side chains

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3
Q

How many amino acids in nature are used as building blocks of proteins?

A

20

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4
Q

In general how do proteins fold in respect to their hydrophobic and hydrophilic side chains?

A

hydrophobic side chains are in the interior of the molecule where they are protected from water, while those with hydrophilic side chains on the surface

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5
Q

What are the amino acids which are precursors for catecholamines?

A

phenylalanine and tyrosine

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6
Q

Which amino acid can form serotonin and niacin?

A

tryptophan

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7
Q

Which amino acids have abnormal metabolism in maple syrup urine disease?

A

Valine, leucine, and isoluecine

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8
Q

Which amino acids is a secondary amine whose presence in a protein disrupts normal secondary structure?

A

proline

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9
Q

Hydrophilic amino acids have side chains that contain which atoms?

A

O or N atoms

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10
Q

What are the names of the acidic amino acids who have carboxyl groups that are negatively charged?

A

aspartic and glutamic acid

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11
Q

What are the basic amino acids that have nitrogen atoms that are positively charged?

A

lysine, arginine, and histidine

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12
Q

What are the amino acids that are sites for O-linked glycosylation of proteins, a post-translational modification that should be associated with the golgi apparatus?

A

serine and theronine

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13
Q

What is the amino acid site for N-linked glycosylation of proteins? What organelle is it associated with

A

Asparagine and is associated with co-translational modification occuring in the ER

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14
Q

Cysteine contains what atom and bonds?

A

sulfur and disulfide bonds to stabilize the shape

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15
Q

Besides cysteine what is another sulfer containing amino acid?

A

methionine

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16
Q

SAM is a methyl donor of which methionine is part of, that is used in biochemical pathways. What does it stand for?

A

S-adenosylmethionine

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17
Q

List the hydrophobic/ nonpolar amino acids.

A

Glycine Gly G
Alanine Ala A
Valine Val V
Leucine Leu L
Isoleucine Ile I
Proline Pro P
phenylalanine Phe F
tyrosine (sometimes) can be polar or non-polar because of the ability of the OH group to form a H bond) Tyr Y
tryptophan Trp W

Grandma Always Visits London in May For Winstons Party

Glycine, Gly, G
Alanine, Ala, A
Valine, Val, V
Leucine, Leu, L
Isoleucine, Ile, I
Methionine, Met, M Sometimes because it contains a sulfer
Phenylalanine, Phe, F
Tryptophan, Trp, W
Proline, Pro, P

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18
Q

List the amino acids with aromatic side chains.

A

phenylalanine phe F
Tyrosine Tyr Y
Tryptophan Trp W

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19
Q

List the amino acids with positively charged R groups

A

Lysine Lys K
Arginine Arg R
Histidine His H

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20
Q

What is the definition of aliphatic?

A

relating to or denoting organic compounds in which carbon atoms form open chains (as in the alkanes), not aromatic rings.

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21
Q

List the amino acids with negatively charged R groups?

A

Aspartate Asp (D)
Glutamate Glu (E)

which form aspartic acid and glutamic acid

22
Q

List the essential amino acids.

A

PVT TIM HALL
Phenylalainine phe (F)
Valine Val (V)
Tryptophan Trp (W)
Threonine Thr (T)
Isoleucine Ile (I)
Methionine Met (M)
Histidine His (H)
Arginine Arg (R)
Lysine Lys (K)
Leucine Leu (L)

23
Q

What are the polar uncharged R group amino acids?

A

Serine Ser (S)
Threonine Thr (T)
Cysteine Cys (C)
Methionine Met (M) sometimes polar
Asparagine Asn (N)
Glutamine Gln (Q)

24
Q

When is arginine an essential amino acid?

A

during times of positive nitrogen balance

25
Q

Proteins tend to be broken down in what 2 cellular locations?

A

lysosomal proteases which digest endocytosed proteins
Large cytoplasmic complexes (or proteasomes) which digest older or abnormal proteins that have been covalently tagged with a protein (called ubiquitin for destruction)

26
Q

What is nitrogen balance?

A

the normal condition in which the amount of nitrogen incorporated into the body each day exactly equals the amount excreted

27
Q

Negative nitrogen balance conditions?

A

occurs when nitrogen loss exceeds incorporation:

  • protein malnutrition (kwashiorkor)
  • dietary deficiency of even 1 essential amino acid
  • starvation
  • uncontrolled diabetes
  • infection
28
Q

What are conditions in which you would have positive nitrogen balance?

A

growth
pregnancy
convalescence (recovery phase of injury or surgery)
Recovery from condition associate with negative N balance

29
Q

Difference between kwashiorkor and marasmus?

A

marasmus is a chronic deficiency of calories where patients do not present with edema as they do kwashiorkor which is protein malnutrition

30
Q

What are the 2 chemical properties of chemical reactions?

A

energy and rate

31
Q

Which is thermodynamically spontaneous? (ΔG > 0 or ΔG < 0)?

A

ΔG < 0

32
Q

What does ΔG = 0 mean?

A

reaction is at equilibrium

33
Q

What does the Michaelis Menten equation describe?

A

how the rate of the reaction depends on the concentration of both the enzyme E and the substrate

34
Q

What is the only way to increase Vmax?

A

by increasing E (enzyme)

35
Q

What is Km?

A

substrate concentration required to produce half the max velocity; in certain conditions Km is a measure of the affinity of the enzyme for its substrate

36
Q

T/F. A missense mutation in the coding region of a gene may yield an enzyme with a different Km?

A

True

37
Q

What is the Lineweaver-Burk equation?

A

a reciprocal form of the Michaelis-Menten equation. Same data graphed yields a straight line

38
Q

What does the x intercept of a Lineweaver Burk plot tell you?

A

-1/Km value

39
Q

What does the y-intercept on a Lineweaver Burk plot tell you?

A

the value of 1/Vmax

40
Q

Difference between competitive and noncompetitive inhibitors?

A

competitive resemble the substrate and compete for binding to active site;
noncompetitive inhibitors do not bind to the active site

41
Q

How does Km and Vmax change based on the effects of a competitive inhibitor?

A

Km increases: Vmax no effect

42
Q

How does Km and Vmax change based on the effects of non-competitive inhibitors?

A

Km will have no effect and Vmax will decrease

43
Q

Is allopurinol an example of a competitive or noncompetitive inhibitor? MOA?

A

noncompetitive inhibitor which inhibits xanthine oxidase

44
Q

What is an enzyme activator?

A

a molecule that binds to an enzyme and increases its activity

45
Q

In cases where an enzyme or activator is added to a reaction, on a Lineweaver-Burk plot where would your line be relative to your control?

A

curve would always be below the control curve in the right-hand quadrant

46
Q

What is occurring when certain enzymes show sigmoid kinetics upon being graphed on a Michaelis-Menten plot?

A

it may be a cooperative enzyme

47
Q

What are cooperative enzymes? (Give an example)

A

Enzymes with multiple subunits and multiple active sites. They are often regulatory enzymes in pathways

i.e phosphofructokinase-1 PFK-1 in glycolysis

48
Q

What are cooperative enzymes often also referred to as?

A

allosteric enzymes

49
Q

MOA by which alcohol treats methanol poisoning?

A

ethanol has much lower Km for alcohol dehydrogenase which prevents breakdown of methanol down its toxic metabolite formaldehyde. Therefore that metabolite is not metabolized any further.

50
Q

What does Km refer to when dealing with transporters?

A

Km is the solute concentration at which the transporter is functioning at half its max activity

Kaplan: Biochemistry Part I (27 decks)

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