Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MCAT Biochemistry > Chapter 1: Amino Acids, Peptides, and Proteins > Flashcards

Chapter 1: Amino Acids, Peptides, and Proteins Flashcards

You may prefer our related Brainscape-certified flashcards:
MCAT flashcards
1
Q

Amino acids contain what 2 functional groups?

A
  1. Amino group
  2. Carboxyl group
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is the formula for an amino group?

A

-NH2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is a formula for a carboxyl group?

A

-COOH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is an α-amino acid?

A

Amino group and carboxyl group are bonded to the same carbon, the α-carbon of the carboxylic acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

You can think of the α-carbon as the ____________ carbon of the amino acid.

A

central

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

In addition to the amino and carboxyl groups, the α-carbon also has what 2 other groups attached to it?

A
  1. A hydrogen atom
  2. A side chain (R group)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What determines the properites of amino acids?

A

The side chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

For most amino acids, the α-carbon is a ____________ center, as it has 4 different groups attached to it. This means that most amino acids are _______________ __________.

A

chiral/stereogenic
optically active

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the only achiral amino acid? Why?

A

glycine; it has a hydrogen atom as its R group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

All chiral amino acids are (L/D?)-amino acids, so the amino group is drawn on the ______ in a Fischer projection.

A

L; left

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

In the Cahn-Ingold-Prelog system, L (Fischer) translates to an (R/S?) absolut configuration for almost all chiral amino acids.

A

S

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Even though it is an L-amino acid, this amino acid has an R absolute configuration because the –CH2SH group has priority over the –COOH group.

A

cysteine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

____________ has a single hydrogen atom as its side chain and is therefore achiral.

A

Glycine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

The smallest amino acid is ____________.

A

Glycine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Which four amino acids have alkyl side chains containing 1 to 4 carbons?

AVaIL = alkyl

A
  1. Alanine
  2. Valine
  3. Isoleucine
  4. Leucine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Which are the only 2 amino acids that have a sulfur atom in its side chain?

A

Methionine and cysteine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Since sulfur has a methyl group attached, it is considered relatively ____________. Why?

A

nonpolar; sulfur has approximately the same electronegativity as carbon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Which amino acid is the only cyclic AA?

A

Proline

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

In proline, the ________ ____________ becomes part of the side chain, forming a 5-membered ring. What does this do?

A

amino nitrogen; makes it less flexible, limits where it can be in a protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

3 amino acids have uncharged aromatic side chains. What are they?

Try PT

A
  1. Tryptophan
  2. Phenylalanine
  3. Tyrosine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Which is the largest amino acid with an aromatic side chain? What does it have?

A

tryptophan; has a double-ring system that contains a nitrogen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Which amino acid with an aromatic side chain is the smallest? What does it have?

A

phenylalanine; has a benzyl side chain

(benzyl = benzene ring + CH2)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Adding an -OH group to phenylalanine gives ____________.

A

tyrosine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

While phenylalanine is relatively ____________, the -OH group makes tyrosine relatively ____________.

A

nonpolar; polar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What are the 5 amino acids whose R side chains are polar but not aromatic?

STNQC

A
  1. Serine
  2. Threonine
  3. Asparagine
  4. Glutamine
  5. Cysteine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

________ and ____________ both have -OH groups in their side chains, which makes them highly polar. Can H bond.

(non-alipathic)

A

serine, threonine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

____________ and ____________ have amide side chains.

A

Asparagine, glutamine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Unlike the amino group common to all amino acids, the ________ nitrogens do not gain or lose protons. What does this mean?

A

amide; There is no change in pH and they do not become charged.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

The last amino acid with a polar side chain is ____________, which has a thiol (-SH) in its side chain.

A

cysteine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Because sulfur is larger than oxygen, the S-H bond is longer and weaker than the O-H bond. Sulfur is also more EN than oxygen. What does this mean for the thiol group in cysteine?

A

It is more prone to oxidation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Only 2 of the amino acids have negative charges on their side chains at body pH. What are they and what other AA are they related to?

A

aspartate (aspartic acid) and glutamate (glutamic acid)

asparagine, glutamine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Unlike asparagine and glutamine, asparate and glutamate have ________________ (-COO-) groups in their side chains, rather than ________.

A

carboxylate, amide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Asparate and glutamate are the ____________________ forms of aspartic and glutamic acid.

A

deprotonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What are the 3 amino acids with positively charged nitrogen atoms?

Stay positive, his lys aren’t real

A
  1. Histidine
  2. Lysine
  3. Arginine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

________ has a terminal primary amino group

A

Lysine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

____________ has 3 nitrogen atoms in its side chain

A

Arginine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Where is the positive charge on lysine?

A

It is delocalized over all 3 nitrogen atoms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

____________ has an aromatic ring with 2 nitrogen atoms. This ring is an ________________.

A

histidine; imidazole

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Histine’s side chain pKa is relatively close to 7.4, about 6, so at physiologic pH, one ________________ atom is protonated and the other isn’t.

A

nitrogen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Amino acids with long alkyl side chains are strongly hydrophobic and are more likely to be found in the interior of proteins. Which are they? Why are they in the interior?

A
  1. Alanine
  2. Isoleucine
  3. Leucine
  4. Valine
  5. Phenylalanine

Away from water

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

All amino acids with charged side chains are (hydrophobic/hydrophilic?), along with the amides, which are ________________. What are the amino acids with charged side chains.

A

Positively charged:
1. Histidine
2. Arginine
3. Lysine
Negatively charged:
1. Glutamate
2. Aspartate
Amides:
1. Asparagine
2. Glutamine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

Amino acids are ________________ species, as they can either accept a proton or donate a proton; how they react depends on the pH of their environment.

A

amphoteric

43
Q

Ionizable groups tend to (lose/gain?) protons under acidic conditions and (lose/gain?) them under basic conditions.

A

gain; lose

44
Q

The pKa of a group is the pH at which, on average, ____________ are deprotonated.

A

half of the molecules of that species

[deprotonated] = [protonated] or [HA] = [A-]

45
Q

If pH < pKa, a majority of an AA species will be ________________.

A

protonated

46
Q

If pH > pKa, a majority of an AA species will be ____________________.

A

deprotonated

47
Q

Because all amino acids have 2+ groups that can be deprotonated, they all have at least (how many?) pKa values?

A

2

48
Q

The first pKa, pKa1 is for the ____________ group and is usually around ____.

A

carboxyl; 2

49
Q

For most amino acids, the second pKa value, pKa2, is the pKa for the ____________ group, which is usually between ____ and ____.

A

amino; 9 and 10

50
Q

Under very acidic conditions, the amino group will be fully ____________ and will be ____________ charged. What is its formula?

A

protonated; positively; -NH3+

51
Q

Under very acidic conditions, the carboxyl group will also be fully ________________ and will be ________________. What is its formula?

A

protonated; neutral; -COOH

52
Q

At the physiologic pH, the carboxylic acid is ________________ and the amino acid is ________________. What are their formulas?

A

deprotonated; protonated
-COO- and -NH3+

53
Q

At physiologic pH, an amino acid has both a positive and negative charge. This means it is electrically ____________ and is referred to as a ________________, which is a dipolar ion.

A

neutral; zwitterion

exist in water as internal salts

54
Q

At very basic conditions, the carboxylate group and amino group are ________________. The carboxylate is ____________ charged and the amino is ____________.

A

deprotonated; negatively charged, neutral

55
Q

Titration of amino acids looks like that of 2 ________________ acids, with 2 curves. It could also be 3 if the ________ ____________ is charged.

A

monoprotic; side chain

56
Q

When pH is close to pKa value of a solute, the solution acts as a ________, and the titration curve is relatively ________.

A

buffer; flat

protonated and zwitterion concentrations are equal

57
Q

When you start adding base where pH = pKa, the carboxylate group goes from half-protonated to fully protonated. Once 1.0 equivalent of base is added, the AA is only in zwitterion form. Every molecule is electrically ____________, and thus the pH equals the ________________ point of the AA.

A

neutral; isoelectric point

58
Q

The ________________ ________ is the pH at which the molecule is electrically neutral.

A

isoelectric point

59
Q

For neutral amino acids, you can calculate the isoelectric point how?

A

Average the 2 pKa values for the amino and carboxyl group

60
Q

When 1.5 equivalents of base have been added to a solution of neutral amino acid, the concentration of ____________ form equals the concentration of the fully ____________________ form (because amino acid has started to deprotonate).

A

zwitterion, deprotonated

61
Q

When 2.0 equivalents of base have been added to a solution of neutral amino acid, the amino acid has become fully ________________.

A

deprotonated

62
Q

____________ are composed of amino acid subunits, sometimes called ____________.

A

Peptides; residues

63
Q

____________ consist of 2 amino acid residues; ____________ have three.

A

dipeptides; tripeptides

64
Q

The term ____________ is used for relatively small peptides, up to about 20 residues, while longer chains are called ____________.

A

oligopeptide; polypeptide

65
Q

The residues in peptides are joined together through ________ ________, a specialized form of an amide bond, which form between what?

A

peptide bond; forms between the COO- group of one amino acid and the NH3+ of another amino acid.

66
Q

What functional group is formed in a peptide bond?

A

-C(O)NH-

67
Q

Peptide bond formation is an example of a ________________ or ________________ reaction, because it results in the removal of a water molecule.

A

condensation; hydration

68
Q

Peptide bond formation can also be viewed as an ________ ________________ reaction, which can occur with all carboxylic acid derivatives.

A

acyl substition

69
Q

When a peptide bond forms, the ____________ carbonyl carbon on the first amino acid is attacked by the ____________ amino group on the second amino acid. After that attack, the ____________ group of the carboxylic acid is kicked off.

A

electrophilic; nucleophilic; hydroxyl

70
Q

Because amide groups have delocalizable pi electrons in the carbonyl and lone pair on the amino nitrogen, they can exhibit ________________.

A

resonance

See Figure 1.11

71
Q

Rotation of the protein backbone around its C-N amide bonds is restricted, which makes the protein more ________.

A

rigid

72
Q

When a peptide bond forms, the free amino end is known as the ________ terminus or ____-terminus. The free carboxyl end is known as the ________ terminus or ____-terminus.

A

amino, N; carboxy, C

73
Q

To break down peptide bonds, this requires ________________. This can be catalyzed by hydrolytic enzymes like trypsin or chymotrypsin.

A

hydrolysis

74
Q

Trypsin cleaves at the carboxyl end of ____________ and ________, while chymotrypsin cleaves at the carboxyl end of ________________, ____________ and ________.

A

arginine and lysine; phenylalanine, tryptophan, and tyrosine

75
Q

High yield

How do trypsin and chymotrypsin catalyze hydrolysis?

A

They break apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon.

76
Q

________ are polypeptides that range from just a few amino acids in length up to thousands.

A

proteins

77
Q

The ____________ structure of a protein is the linear arrangement of amino acids coded in an organism’s DNA. It’s the sequence of amino acids from N-terminus to C-terminus.

A

primary

78
Q

What stabilizes primary structures?

A

The formation of covalent peptide bonds between adjacent amino acids

79
Q

The primary structure of a protein is determined by ____________ (either the protein or DNA).

A

sequencing

80
Q

A protein’s ________________ structure is the local structure of neighboring amino acids. They are the result of ____________ bonding between nearby amino acids.

A

secondary; hydrogen

81
Q

What are the 2 most common secondary structures?

A

alpha-helices and beta-pleated sheets

82
Q

The ____-____________ is a rodlike structure in which the peptide chain coils clockwise around a central axis.

A

alpha-helix

83
Q

What stabilizes the alpha-helix?

A

intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom 4 residues down the chain

84
Q

The alpha-helix is an important component in the structure of ____________, a fibrous structural protein found in skin, hair, and nails.

A

keratin

85
Q

The ____-________ sheets, which can be parallel or antiparallel, have peptide chains that lie alongside one another, forming rows or strands.

A

beta-pleated

86
Q

What holds beta-pleated sheets together?

A

intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain

87
Q

Why do beta-pleated sheets have pleats?

A

to accommodate as many hydrogen bonds as possible

88
Q

The R groups of amino acids point where in the plane of the beta-pleated sheet?

A

Above and below

89
Q

Because of its rigid cyclic structure, ________ will introduce a kink in the peptide chain when it is found in the middle of an alpha-helix. Thus, they are rarely found in alpha-helices, unless they cross the cell membrane. Also rarely found in the middle of pleated sheets.

A

proline

90
Q

Where is proline often found?

A
  1. In turns between the chains of a beta-pleated sheet
  2. The residue at the start of an alpha-helix
91
Q

Proteins can be broadly divided into ________ proteins (structures that resemble sheets or long strands) and ________ proteins (that tend to be spherical). What are examples of each?

A

fibrous, collagen; globular, myoglobin

92
Q

A protein’s ____________ structure is its 3D shape. What determines this?

A

tertiary; hydrophilic and hydrophobic interactions between R groups of amino acids

93
Q

Hydrophilic N-H and C=O bonds found in the polypeptide chain get pulled in by hydrophobic residues found in the protein’s interior. What do these hydrophilic residues do?

A

They stabilize the protein from the inside through electrostatic interactions and hydrogen bonds

94
Q

As a result of hydrophobic interactions, most amino acids on the surface of proteins have ____________ R groups.

A

hydrophilic

95
Q

If a protein loses its tertiary structure, it loses its function. This is called ____________________.

A

denaturation

96
Q

Whenever a solute dissolves in a solvent, the nearby solvent molecules form a ________________ ________ around that solute.

A

solvation layer

97
Q

When a hydrophobic side chain is placed in an aqueous solution, the water molecules in the solvation layer cannot do what? What happens instead?

A

Cannot form hydrogen bonds with the side chain; the nearby water molecules have to rearrange themselves into specific arrangements to maximize hydrogen bonding

98
Q

Putting hydrophilic residues on the exterior of a protein allows nearby water molecules to have more latitidue in their positioning, thus (decreasing/increasing?) their entropy.

A

increasing

99
Q

____________ structures only exist for proteins that contain more than one polypeptide chain. These structures are an aggregate of smaller globular peptides, or ____________, and represent the functional form of the protein. Example?

A

Quaternary; subunits

Example is hemoglobin, which has 4 distinc subunits

100
Q

Quaternary structures have 4 possible roles. What are they?

A
  1. Stabilize by reducing surface area
  2. Reduce amount of DNA needed to encode
  3. Bring catalytic sites close together (less travel for intermediates)
  4. Induce cooperativity or allosteric effects (one subunit can undergo conformational change to enhance/reduce other subunits’ activity)
101
Q

____________ proteins derive part of their function from covalently attached molecules called ____________ groups.

A

Conjugated; prosthetic

102
Q

Denaturation is often irreversible. Unfolded proteins cannot catalyze reactions. What are the 2 main causes of denaturation?

A

Heat and solutes

103
Q

When the temperature of a protein increases, its average kinetic energy increases. When temperature gets high enough, what can happen to the protein?

A

The hydrophobic interactions that hold the protein together can be overcome, causing the protein to unfold

104
Q

Solutes can denature proteins by disrupting what?

A

The forces that hold the protein together, e.g. disulfide bridges, hydrogen bonds, noncovalent bonds etc.

MCAT Biochemistry (13 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions