Brainscape's Knowledge GenomeTM

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


See full index

Biochem > 1: Amino Acids, Peptides and Proteins > Flashcards

1: Amino Acids, Peptides and Proteins Flashcards

1
Q

Amino acids are molecules that contain two functional groups: ______ and _______.

A

amino group (-NH2), carboxyl group (-COOH)

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

What are alpha-amino acids?

A

amino group and carboxyl group attached to the SAME carbon–the alpha-carbon of the carboxylic acid

(Think of the alpha carbon as the central carbon of the amino acid)

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

Another name for the 20 alpha-amino acids encoded by the human genetic code

A

proteinogenic amino acids

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

Most amino acids are ____ due to the 4 different substituent groups attached to the alpha-carbon. This makes amino acids ________.

A

Chiral (stereogenic), optically active

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

Name the achiral amino acid. What does it have attached in place of the R group?

A

Glycine, Hydrogen atom

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

All chiral amino acids used in eukaryotes are _________.

This translates to an (__) absolute configuration for almost all chiral amino acids.

A

L-amino acids (amino group is drawn o the left), (S) absolute configuration

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Name the only L-amino acid that has an (R) absolute configuration.

A

Cysteine, because the -CH2SH group has priority over the -COOH grp

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

Except for ____, all amino acids are chiral–and except for ____, all amino acids have an (S) absolute configuration.

A

glycine, cysteine

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

List the Nonpolar, Nonaromatic Side Chains amino acids.

A

1) Glycine
2) Alanine
3) Valine
4) Leucine
5) Isoleucine
6) Methionine
7) Proline

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

Describe the amino acid GLYCINE

A
  • Nonpolar, nonaromatic
  • achiral, due to single Hydrogen as its side chain/R-group
  • smallest amino acid
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Nonpolar, Nonaromatic side chains:

These 4 other amino acids have alkyl side chains containing 1-4 carbons.

A

VAIL:

1) Valine
2) Alanine
3) Isoleucine
4) Leucine

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

Nonpolar, Nonaromatic side chains:

_______ is one of only two amino acids that contains a sulfur atom in its side chain.

A

Methionine

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

Methionine’s sulfur has a ______ group attached, making it relatively NONpolar.

A

methyl

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

_____ is unique because it forms a cyclic amino acid.

A

Proline

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

How is proline different from the other amino acids?

A

The amino nitrogen becomes a part of the side chain, forming a five-membered ring. In the other amino acids, the amino nitrogen is only attached to the alpha-carbon.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

List the Aromatic Side Chains

A

1) Tryptophan
2) Phenylalanine
3) Tyrosine

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

_____ has a double-ring system that contains a nitrogen atom.

A

Tryptophan

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

Name the largest Aromatic (Side Chain) Amino Acid.

A

Tryptophan

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

Describe Phenylalanine.

A
  • Part of the Aromatic Side Chain group
  • Smallest of the 3
  • has a benzyl side chain (benzene ring with a -CH2 group)
  • relatively NONpolar
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Describe Tyrosine

A
  • Part of the Aromatic Side Chain group
  • Phenylalanine with an -OH group attached
  • the addition of the -OH makes it relatively polar
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

List the Polar (Side Chain) Amino Acids

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
22
Q

____ and ____ both have -OH groups in their side chains, which makes them highly polar and able to participate in hydrogen bonding.

A

Serine and Threonine

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

_____ and _______ have amide side chains. What is significant about their amide nitrogens?

A

Asparagine and Glutamine
Unlike the amino group common to all amino acids, the amide nitrogens do NOT gain or lose protons with changes in pH; they do NOT become charged.

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

____ has a thiol group (-SH) in its side chain.

A

Cysteine

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

Which bond is stronger in Cysteine– the S–H bond or the O–H bond?

A

O–H.
Because sulfur is larger and less electronegative than oxygen, the S–H bond is weaker than the O–H bond. This leaves the thiol group in cysteine prone to oxidation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Name the Negatively Charged/Acidic Side Chains Amino Acids

A

1) Aspartic Acid (Aspartate)

2) Glutamic Acid (Glutamate)

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

Unlike asparagine and glutamine, aspartate and glutamate have _____ groups in their side chains, rather than amides.

A

carboxylate (-COO-)

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

What is the difference b/w aspartic acid vs. aspartate?

glutamic acid vs. glutamate?

A

Aspartate is the deprotonated form of aspartic acid
Glutamate is the deprotonated form of glutamic acid

*Likely to see these anion names because most of the acids exist in cells in the deprotonated form. (This also applies to molecules other than amino acids; malate instead of malic acid).

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

Positively Charged (Basic) Side Chains

A

1) Lysine
2) Arginine
3) Histidine

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

____ has a terminal primary amino group side chain

A

Lysine

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

_____ has 3 nitrogen atoms in its side chain.

The positive charge is delocalized over all 3 nitrogen atoms

A

Arginine

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

_____ has an aromatic ring with two nitrogen atoms (ring is called “Imidazole”)

A

Histidine

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

How does histidine acquire a positive charge?

A

The pKa of the aromatic side chain is relatively close to 7.4 (~6). At physiologic pH, one nitrogen atom is protonated and the other is not. Under more acidic conditions, the second nitrogen atom can become protonated, giving the side chain a positive charge.

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

The amino acids w/long alkyl side chains (alanine, isoleucine, leucine, valine, phenylalanine) are all strongly ______.
Where are they likely to be found?

A

Hydrophobic

-More likely to be found in the interior of the proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

All of these amino acids are hydrophilic.

A

All of the charged AA (positive and negative side chains) as are the amides asparagine and glutamine.

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

The surface of a protein tends to be rich in amino acids with ____ side chains. Strongly hydrophobic amino acids (____ side chains) tend to be found in the interior of the protein.

A

charged, alkyl

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

What are the four groups attached to the central alpha-carbon of a proteinogenic amino acid?

A
  • amino group (-NH2)
  • carboxyl group (-COOH)
  • R group/side chain
  • H atom
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What is the stereochemistry of the chiral amino acids that appear in eukaryotic proteins?

  • L/D?
  • R/S?
A
  • L

- S, except for cysteine which is R and glycine which is achiral.

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

Amino acids contain both an acidic carboxylic acid group and a basic amino group, making them _______, as they can either accept a proton or donate a proton.
(How they react depends on the pH of their environment.)

A

amphoteric (species)

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

Ionizable groups tend to gain protons under acidic conditions and lose them under basic conditions.
So, in general:
At low pH, ionizable groups tend to be _______.
At high pH, ionizable groups tend to be ________.

A

protonated, deprotonated

if group is in acidic solution, there are already enough protons floating around, so it wants to keep it.
If the group is in basic soln, there aren’t enough protons in the environment, so it wants to make the environment more acidic, thus donate its proton. (becoming deprotonated).

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

The pKa of a group is the pH at which ____ of the molecules of that species are deprotonated.

A

half

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

if the pH is LESS than the pKa, a majority of the species will be _______

A

protonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

if the pH is HIGHER than the pKa, a majority of the species will be ______

A

deprotonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

Because all amino acids have at least two groups that can be deprotonated, they all have _______

A

at least two pKa values

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

What is the pKa for the carboxyl group? (pKa1)

A

~2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What is the pKa for the amino group? (pKa2)

A

between 9-10

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

For amino acids with an ionizable side chain, how many pKa values will you expect?

A

3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

At very acidic pH values, amino acids tend to be _______ charged.

A

positively

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

At pH 1, there are plenty of protons in solution. Because we’re far below the pKa of the amino group, the amino group will be ___ _____.
Charge?

A

fully protonated (-NH3+) and thus positively charged

50
Q

At pH 1, there are plenty of protons in solution. Because we’re below the pKa of the carboxylic group, the carboxyl group will be ___ _____.
Charge?

A

fully protonated (-COOH) and thus neutral

51
Q

At very alkaline pH values, the amino acids tend to be _____ charged.

A

negatively

52
Q

At very acidic pH values, amino acids tend to be ______ charged.

A

positively

53
Q

At physiologic pH, amino acids tend to be _______ charged.

A

neutral(ly)

54
Q

A name for dipolar ions

A

Zwitterions

55
Q

The two charges neutralize one another (at physiologic pH) and zwitterions exist in water as ______.

A

internal salts

56
Q

When the pH of a solution is approximately equal to the pKa of the solute, the solution acts as a ____, and the titration curve is relatively ____.

A

buffer, flat

57
Q

Titration curves of amino acids looks like a combination of ____ ______ titration curves

A

two monoprotic acid

*or three curves if the side chain is charged

58
Q

This is true for all amino acids: the ______ ____ is the pH at which the molecule is electrically neutral.

A

isoelectric point (pI)

59
Q

What is the equation for pI?

A

pI(neutral amino acid) = (pKa1 + pKa2)/2
pKa1 = carboxyl group
pKa2 = amino group

60
Q

Because glutamic acid has two carboxyl groups and one amino group, its charge in its fully protonated state is still ______.

A

+1

61
Q

Isolelectric point of an acidic amino acid

A

pI = (pKa,R grp + pKa,COOH)/2

62
Q

Titration Steps of Amino Acids w/Charged Side Chains:

A

1) It undergoes FIRST deprotonation, losing the proton from its main carboxyl group, just as glycine does. (Neutral at this point)
2) When it loses its second proton, its overall charge will be -1.
HOWEVER, the second proton that is removed in this case comes from the side chain carboxyl group, NOT the amino group!!!! (This is a relatively acidic group, with a pKa ~4.2).
The result is that the pI of glutamic acid is much lower than that of glycine, ~3.2.

63
Q

When does lysine become electrically neutral?

A

When it loses the proton from its main amino group

64
Q

Amino acids with acidic side chains have relatively _____ isoelectric points, while those with basic side chains have relatively ____ pIs.

A

low, (well below 6)

high, well above 6

65
Q

the pI is calculated as the average of the

A

two nearest pKa values.

66
Q

____ (a.k.a residues) are composed of amino acid subunits

A

Peptides

67
Q

Two amino acid residues?
Three?
Small peptides (up to ~20)?
long chains?

A

Dipeptides, Tripeptides, Oligopeptides, Polypeptides

68
Q

residues in peptides are joined together thru ______, specialized form of an ____ bond

A

peptide bonds, amide

69
Q

Amide bond is formed from:

A

the -COO- group of one amino acid and the NH3+ group of another amino acid.
Functional group: -C(O)NH-

70
Q

Peptide bond formation is an example of a ________ or ______ reaction. Why?
It can also be viewed as a(n):

A

condensation, dehydration
results in the removal of a water molecule
-acyl substitution reaction (which can occur with all carboxylic acid derivatives)

71
Q

When a peptide bond forms,

A

the electrophilic carbonyl carbon on the 1st amino acid is attached by the nucleophilic amino group on the 2nd amino acid.
After the attack, the hydroxyl group of the carboxylic acid is kicked off.
Result: formation of peptide (amide) bond

72
Q

Because amide groups have delocalizable pi electrons in the carbonyl and in the lone pair on the amino group, they can exhibit ______.
Thus, the C–N bond in the amide has _________

A

resonance.

-partial double bond character

73
Q

When a peptide bond forms, the free amino end is known as the ________

A

amino terminus/N-terminus

74
Q

When a peptide bond forms, the free carboxyl end is known as the ________

A

Carboxy terminus/C-Terminus

75
Q

By convention, peptides are drawn with the _____ on the left and _____ on the right. They are also read in this manner.

A

N-Terminus on the left, C-Terminus on the right

The peptide bond is drawn in the same order that it is synthesized by ribosomes!

76
Q

_____ cleaves at the carboxyl end of arginine and lysine

A

trypsin

77
Q

_____ cleaves at the carboxyl end of phenylalanine, tryptophan, tyrosine

A

chymotrypsin

78
Q

How do trypsin and chymotrypsin work?

A

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

79
Q

What molecule is released during formation of a peptide bond?

A

Water molecule

80
Q

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

A

Proteins

81
Q

What is the primary structure of a protein?

How is it stabilized?

A

The linear arrangement of amino acids encoded in an organism’s DNA. (the sequence of amino acids)
-Stabilized by the formation of covalent peptide bonds between adjacent amino acids

82
Q

How can the primary structure be determined?

A

Sequencing

83
Q

The primary structure alone encodes ____

A

all the information needed for folding at all the higher structural levels

84
Q

What is the secondary structure?

A

Local structure of neighboring amino acids.

85
Q

Hydrogen bonding between nearby amino acids primarily results in

A

the protein’s secondary structure

86
Q

What are the two most common secondary structures?

A

alpha- helices and beta-pleated sheets

87
Q

What are the key to stability for the secondary structures?

A

formation of intramolecular hydrogen bonds between the different residues

88
Q

the alpha helix is a rodlike structure in which the peptide chain

A

coils clockwise around a central axis

89
Q

The alpha helix is stabilized by

A

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

90
Q

The side chains of the amino acids in the alpha-helical conformation point ____ from the helix core.

A

away

91
Q

The alpha helix is an important component in the structure of _____

A

keratin, fibrous structural protein

92
Q

beta-pleated sheets can be _____ or ______

A

parallel or antiparallel

93
Q

Beta-pleated sheets:

the peptide chains lie alongside one another, forming rows or strands held together by intramolecular hydrogen bonds between

A

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

94
Q

To accomodate as many ______ as possible, the beta-pleated sheets assume a pleated, or rippled shape.

A

hydrogen bonds

95
Q

The R groups of the amino residues point ______ the plain of the Beta-pleated sheet.

A

above and below

96
Q

Because of its rigid cyclic structure, ____ will introduce kinks in the peptide chain when it is found in the middle of an alpha-helix.
Thus, they’re rarely found here, except in helices that cross the cell membrane.

A

proline

97
Q

Where is proline typically found in terms of secondary structures?

A

In the turns between the chains of a beta-pleated sheet or as the residue at the start of an alpha-helix

98
Q

How can proteins be divided?

A

Fibrous or globular

99
Q

____ proteins (i.e. collagen) have structures that resemble sheets or long strands

A

Fibrous

100
Q

Tertiary and quarternary protein structures are the result of _____

A

protein folding

101
Q

_____ proteins (myoglobin) tend to be spherical/globe.

A

Globular

102
Q

Describe Tertiary structure

A
  • 3D shape

- determined by hydrophilic and hydrophobic interactions between R groups of amino acids

103
Q

Hydrophilic ___ and ___ bonds found in the polypeptide chain get pulled in by these hydrophobic residues.

A

N–H and C=O bonds

104
Q

These ___ bonds can form electrostatic interactions and hydrogen bonds that further stabilize the protein from the inside.

A

hydrophilic

105
Q

As a result of these hydrophobic interactions, most of the amino acids on the surface of the protein have _________ (_________) R groups.

A

Hydrophilic (polar or charged)

106
Q

Highly hyrdrophobic R groups, such as ____________, are almost never found in the surface of a protein.

A

Phenylalanine

107
Q

A particularly important component of tertiary structure is the presence of ________.
How do these bonds form?

A

Disulfide bonds;

Bonds that form when two cysteine molecules become oxidized to form cysteine

108
Q

The ______ structure is primarily just the result of moving hydrophobic amino acid side chains into the interior of a protein.

A

Tertiary

109
Q

Sequence of protein folding?

What does it develop (into) during the process?

A

The secondary structure (probably) forms first, then hydrophobic interactions and hydrogen bonds cause the protein to “collapse” into its proper form.
Along the way, it adopts intermediate states known as “molten globules”

110
Q

If a protein loses its tertiary structure, a process called ___________, it loses its function.

A

Denaturation

111
Q

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

A

Solvation Layer

112
Q

What happens when a hydrophobic side chain, such as phenylalanine and leucine are placed in an aqueous solution?

A

The water molecules in the solvation layer cannot form hydrogen bonds with the side chain.

This forces the nearby water molecules to rearrange themselves into specific arrangements to maximize hydrogen bonding–which means a NEGATIVE change in entropy.

113
Q

What do negative changes in entropy represent?

Is the reaction spontaneous or non-spontaneous?

A 
Increasing order (decreasing disorder) and thus UNfavorable.
-Non spontaneous (delta G > 0)
114
Q

What would happen if there were hydrophilic residues, such as serine or lysine, on the exterior of the protein?

A

Allows nearby water molecules more latitude in their positioning, thus INCREASING their entropy (S>0)
Spontaneous reaction

115
Q

What structures do all proteins process? (primary-quartnerary)

A

Primary, secondary, tertiary

Only some possess quartnerary

116
Q

When do quarternary structures exist?

A

For proteins contain more than 1 polypeptide chain

For these proteins, the quarternary structure is an aggregate of smaller globular peptides (subunits) and represents the functional form of a protein.

117
Q

Give two examples of quarternary structure.

A

Hemoglobin and immunoglobulins

Hemoglobin consists of four distinct subunits, each of which can bind one molecule of oxygen.

Similarly, immunoglobulin G (IgG) antibodies also contain a total of 4 subunits each.

118
Q

4 roles of quarternary structure?

A

1) can be more stable by reducing the surface area of the protein complex
2) can reduce the amount of DNA needed to encode a protein complex
3) can bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction
4) can induce cooperativity or allosteric effects**

**basic idea: one subunit can undergo conformational or structure changes, which either enhance or reduce the activity of other subunits.

119
Q

Describe prosthetic groups

A
  • can be organic molecules (vitamins) or even metal ions
  • have major roles in determining the function of their respective proteins
  • can also direct the protein to be delivered to a certain location
120
Q

What is the primary motivation for hydrophobic residues in a polypeptide to move to the inferior of the protein?

A

Moving hydrophobic residues to the interior of a protein increases entropy by allowing water molecules on the surface of the protein to have more possible positions and configurations. This positive S makes G < 0, stabilizing the protein.

Biochem (4 decks)

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