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

Ch. 1: Amino Acids, Peptides, and Proteins Flashcards

1
Q

defn: amino acids

A

molecules that contain two specific functional groups: an amino group (-NH2) and a carboxyl group (-COOH)

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2
Q

defn + components: alpha-amino acid

diagram: basic amino acid structure

A

the amino group and the carboxyl group are bonded to the same C, the alpha-C of the carboxylic acid

the alpha-C has 2 other groups attached to it: a H atom and a side chain (R group), which is specific to each amino acid

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3
Q

what do the side chains of amino acids determine?

A

the properties of the amino acids, and thus their functions

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4
Q

do amino acids need to have both the amino and carboxyl groups bonded to the same C?

A

no, for example GABA has the amino group on the gamma C

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5
Q

is every amino acid found in the human body specified by a codon in the genetic code or incorporated into proteins?

A

no, for example ornithine

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6
Q

however, the AAMC focuses on the proteinogenic amino acids (defn)

A

the 20 alpha-amino acids encoded by the genetic human code

THIS is what “amino acid” refers to generally

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7
Q

almost all amino acids have a chiral alpha-C and are optically active, what is the one exception to the rule and why?

A

GLYCINE

it has H as its R group

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8
Q

all chiral amino acids used in eukaryotes are L or D amino acids? what does this mean for the Fischer projection? S or R absolute configuration?

what is the only exception to this?

A

L-amino acids

the amino group is drawn on the left in a Fischer projection

(S) absolute configuration

exception: cysteine which is an L-amino acid but has an (R) absolute configuration

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9
Q

why does cysteine have an (R) absolute configuration?

A

because the -CH2SH group has priority over the -COOH group

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10
Q

what are the 7 nonpolar, nonaromatic side chains amino acids

A
  1. Glycine
  2. Alanine
  3. Valine
  4. Leucine
  5. Isoleucine
  6. Methionine
  7. Proline
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11
Q

what is the smallest amino acid?

A

glycine

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12
Q

what are the common characteristics across alanine, valine, leucine, and isoleucine?

A

they have alkyl side chains containing 1-4 carbons

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13
Q

char (2): methionine

A
  1. one of only 2 amino acids that contains a sulfur in its R group
  2. considered nonpolar because the sulfur has a methyl group attached
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14
Q

char (4): proline

A
  1. cyclic amino acid (the amino nitrogen becomes a part of the side chain, forming a 5 membered ring)
  2. the ring leads to notable constraints on proline’s flexibility
  3. this impacts where it can appear in a protein
  4. and has significant effects on proline’s role in secondary structure
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15
Q

what are the 3 amino acids with uncharged aromatic side chains?

A
  1. tryptophan
  2. phenylalanine
  3. tyrosine
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16
Q

char (2): tryptophan

A
  1. the largest aromatic amino acid
  2. has a double-ring system that contains a nitrogen atom
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17
Q

char (3): phenylalanine

A
  1. the smallest aromatic amino acid
  2. has a benzyl side chain (a benzene side ring plus a -CH2 group)
  3. relatively nonpolar
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18
Q

what happens when you add an -OH group to phenylalanine?

A

it gives you tyrosine! and the -OH group makes it relatively polar

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19
Q

what are the 5 amino acids with polar nonaromatic side chains?

A
  1. serine
  2. threonine
  3. asparagine
  4. glutamine
  5. cysteine
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20
Q

char (3): serine and threonine

A
  1. have -OH groups in their side chains
  2. highly polar
  3. able to participate in H-bonding
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21
Q

char (2): asparagine and glutamine

A
  1. have amide side chains
  2. these amide nitrogens do not gain or lose protons with changes in pH, they do not become charged
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22
Q

char (4): cysteine

A
  1. has a thiol (-SH) group in its side chain
  2. the thiol group is longer and weaker than an OH bond
  3. sulfur is more electronegative than oxygen
  4. the thiol group is prone to oxidation
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23
Q

what are the 2 amino acids with negatively charged (acidic) side chains at physiological pH?

A
  1. aspartic acid (aspartate), related to asparagine
  2. glutamic acid (glutamate), related to glutamine
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24
Q

what is the relationship between aspartate and aspartic acid?

between glutamate and glutamic acid?

A

aspartate = the deprotonated form of aspartic acid

glutamate = the deprotonated form of glutamic acid

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25
Q

what are the 3 amino acids with positively charged (basic) side chains?

A
  1. lysine
  2. arginine
  3. histidine
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26
Q

char (1): lysine

A
  1. has a terminal primary amino group
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27
Q

char (2): arginine

A
  1. has 3 nitrogen atoms in its side chain
  2. the positive charge is delocalized over all 3 nitrogen atoms
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28
Q

char (1): histidine

A

has an aromatic ring with 2 nitrogen atoms (imidazole)

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29
Q

how can histidine acquire a positive charge?

A

the pKa of the side chain is relatively close to 7.4 (it’s about 6) so at physiologic pH, one nitrogen atom is protonated and the other isn’t

under more acidic conditions, the second nitrogen atom can become protonated, giving the side chain a positive charge

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30
Q

classifying amino acids as hydrophobic or hydrophilic is quite complicated. what are 3 conclusions that we can draw for certain?

A
  1. amino acids with LONG ALKYL side chains (alanine, isoleucine, leucine, valine, and phenylalanine) are all strongly hydroPHOBIC and more likely to be found in the interior of proteins, away from water on the surface of the protein
  2. all the amino acids with CHARGED side chains (histidine, arginine, lysine + glutamate, aspartate) are hydroPHILIC
  3. asparagine and glutamine are hydroPHILIC
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31
Q

what are the 8 remaining amino acids that lie somewhere n the middle and are neither particularly hydrophilic nor particularly hydrophobic?

A
  1. Serine
  2. Threonine
  3. Cysteine
  4. Glycine
  5. Proline
  6. Methionine
  7. Tyrosine
  8. Tryptophan
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32
Q

what makes amino acids an amphoteric species and a reminder of what that means?

A

what makes them: they have both an acidic carboxylic acid group and a basic amino group

amphoteric: they can either accept a proton or donate a proton, how they react depends on the pH of their environment

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33
Q

what are the 2 key facts you should remember to understand the behavior of amino acids?

A
  1. 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 protonated; at high pH, they tend to be deprotonated.
  2. the pKa of a group is the pH at which, on average, half of the molecules of that species are deprotonated; that is [protonated version of the ionizable group] = [deprotonated version of the ionizable group] or [HA] = [A-]. if the pH is less than the pKa, a majority of the species will be protonated. if the pH is higher than the pKa, a majority of the species will be deprotonated.
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34
Q

why do all amino acids have at least 2 pKa values and what are they?

A

because they all have at least 2 groups that can be deprotonated

first = pKa1 = pKa for the carboxyl group = around 2

second = pKa2 = pKa for amino group = between 9-10

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35
Q

what types of amino acids have 3 pKa values?

A

amino acids that have an ionizable side chain

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36
Q

what effect do very acidic conditions have on amino acids and why? (overall amino acid, amino group, carboxylic acid group)

A

amino acids tend to be POSitively charged at very acidic pH values

at pH 1, below even the stomach, there are plenty of protons in solution

we are far below the pKa of the amino group –> so the amino group will be fully protonated (-NH3+) and positively charged

we are below the pKa of the carboxylic acid group –> so it will be fully protonated (-COOH) and neutral

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37
Q

what is the effect of physiologic pH (7.4) on amino acids and why? (overall amino acid, amino group, carboxylic acid group)

A

we are far above the pKa of the carboxylic acid group –> the carboxyl group will be in its conjugate form and deprotonated (-COO-)

we’re still well below the pKa of the amino group –> it will remain fully protonated and in its conjugate acid form (-NH3+)

there is a positive charge and a negative charge in the overall molecule, but the molecule as a whole is electrically neutral

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38
Q

defn: zwitterion

A

dipolar ions with a positive and negative charge, but overall electrically neutral

the two charges neutralize each other, and they exist in water as internal salts

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39
Q

what is the effect of very basic conditions on amino acids and why? (overall amino acid, amino group, carboxylic acid group)

A

the carboxylate group is already deprotonated –> remains as -COO-

we are now well above the pKa for the amino group –> it deprotonates too to become -NH2

the amino acid is now negatively charged

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40
Q

why do amino acids make great candidates for titration?

A

because of their acid-base properties

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41
Q

what do we assume with how titration of amino acids occurs?

A

the titration of each proton occurs at each distinct step, resembling a titration of a simple monoprotic acid

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42
Q

what does the titration curve for an amino acid look like?

A

a combination of two monoprotic acid titration curves (or three curves if the side chain is charged)

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43
Q

Let’s talk through the titration of glycine, starting with an acidic 1 M glycine solution. (8 steps)

A
  1. at low pH values, glycine exists predominantly as +NH3CH2COOH, it is fully protonated with a positive charge
  2. as the solution is titrated with NaOH, the carboxyl group will deprotonate first because it is more acidic than the amino group
  3. when 0.5 equivalents of base have been added to the solution, the concentrations of the fully protonated glycine and its zwitterion +NH3CH2COO- are equal and the pH = pka1
  4. as we add more base, the carboxylate group goes from half-deprotonated to fully deprotonated, the amino acid stop as acting like a buffer, and pH starts to increase rapidly
  5. when we’ve added 1.0 equivalent of base, glycine exists exclusively as the zwitterion form. Every molecule is now electrically neutral and the pH = the isoelectric point (pI) of glycine
  6. as we continue adding base, glycine passes through a 2nd buffering phase as the amino group deprotonates, the pH is relatively constant
  7. when 1.5 equivalents of base have been added, the concentration of the zwitterion form equals the concentration of the fully deprotonated form and the pH = pKa2 and the titration curve is flat
  8. when we’ve added 2.0 equivalents of base, the amino acid has become fully deprotonated and all that remains is NH2CH2COO-; additional base will only increase the pH further
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44
Q

what is important to remember about titrations when the pH is close to the pKa value of the solute?

A

the solution is acting as a buffer and the titration curve is relatively flat

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45
Q

what is true about the isoelectric point of all amino acids?

A

it is the pH at which the molecule is electrically neutral

at this point, it is also especially sensitive to pH changes and the titration curve is nearly vertical

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46
Q

eqn: pI of a neutral amino acid

A
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47
Q

explain the impact of the extra “step” in the titration curve for amino acids with charged side chains. let’s look at glutamic acid first. (4)

A
  1. glutamic acid has 2 carboxyl groups and one amino group, so its charge in its fully protonated state is still +1
  2. it undergoes the first deprotonation, losing the proton from its main carboxyl group, just as glycine does. it is now electrically neutral.
  3. when it loses its second proton, just as with glycine, 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
  4. this is a relatively acidic group. so the pI of glutamic acid is much lower than that of glycine
48
Q

eqn: pI for an acidic amino acid

A
49
Q

explain the impact of the extra “step” in the titration curve for amino acids with charged side chains. now let’s look at lysine.

A
  1. lysine has 2 amino groups and one carboxyl group ,so its charge in its fully protonated state is +2
  2. losing the carboxyl proton brings the charge down to +1 (this occurs around pH 2)
  3. lysine does not become electrically neutral until it loses the proton from its main amino group (happens around pH 9)
  4. it gets a negative charge when it loses the proton on the amino group in its side chain (happens around pH 10.5), so the pI is higher
50
Q

eqn: pI basic amino acid

A
51
Q

net, what do we know about the isoelectric points of acidic and basic amino acids

A

amino acids with acidic side chains –> relatively LOW isoelectric points

amino acids with basic side chains –> relatively HIGH isoelectric points

52
Q

what are peptides composed of?

A

amino acid subunits, which are sometimes called residues

53
Q

defn: dipeptide vs.

tripeptide vs.

oligopeptide vs.

polypeptide

A

DIPEPTIDE = 2 amino acid residues

TRIPEPTIDE = 3 amino acid residues

OLIGOPEPTIDE = relatively small peptides (4-20 residues)

POLYPEPTIDE = longer chain peptides

54
Q

what joins the residues in peptides together?

A

peptide bonds

55
Q

defn: peptide bond

A

a specialized form of an amide bond, which forms between the -COO- group of one amino acid and the NH3+ group of another amino acid, forming the functional group -C(O)NH-

56
Q

what are the 3 categories of reactions that peptide bond formation can be categorized as?

A
  1. condensation
  2. dehydration
  3. acyl substitution reaction
57
Q

explain how a peptide bond forms from the perspective of an acyl substitution reaction (2 steps)

A
  1. the electrophilic carbonyl C on the first amino acid is attacked by the nucleophilic amino group on the second amino acid
  2. after the attack, the hydroxyl group of the carboxylic acid is kicked off, forming a peptide (amide) bond
58
Q

diagram: peptide bond formation and cleavage

A
59
Q

why can amide groups exhibit resonance and what is the implication of this?

A

they can exhibit resonance because they have delocalizable pi electrons in the carbonyl and in the lone pair on the amino nitrogen

because there is resonance, the C-N bond in the amide has partial double bond character

60
Q

diagram: resonance in the peptide bond

A
61
Q

what is the impact of having partial double bond character in the amide?

A

rotation of the protein backbone around its C-N amide bond is restricted, making the protein rigid

rotation around the remaining bonds in the backbone, is not, as those are still single (sigma) bonds

62
Q

defn: N-terminus and C-terminus

A

N-terminus = amino terminus = free amino end

C-terminus = carboxy terminus = free carboxyl end

63
Q

from what terminus to what are peptides drawn and read?

A

N-terminus left, C-terminus right

read from N to C

64
Q

why do peptides need to be relatively stable in solution?

A

for enzymes to carry out their function

65
Q

but, in order to digest proteins, we do need to be able to break them down into their component amino acids, how is this done in organic chemistry? how is this done in living organisms?

A

ORGO: amides can be hydrolyzed using acid or base catalysis

LIVING: hydrolysis is catalyzed by hydrolytic enzymes such as trypsin and chymotrypsin

66
Q

what is the main idea behind how hydrolytic enzymes catalyze peptide bond hydrolysis?

A

they break apart the amide bond by adding a H atom to the amide nitrogen and an OH group to the carbonyl C

67
Q

defn: proteins

A

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

68
Q

what are 4 major roles of proteins in biological systems?

A
  1. enzymes
  2. hormones
  3. membrane pores and receptors
  4. elements of cell structure

they are the main actors in cells

69
Q

how many levels of structure do proteins have?

A

4!

70
Q

defn: primary structure of a protein

A

the linear arrangement/sequence of amino acids, listed from N-terminus to C-terminus, coded in an organism’s DNA

71
Q

what is primary structure stabilized by?

A

the formation of covalent peptide bonds between adjacent amino acids

72
Q

func: primary structure of a protein

A

encodes alone all the information needed for folding at all of the higher structural levels

73
Q

what are the secondary, tertiary, and quaternary structures in relation to the primary structure?

A

the secondary, tertiary, and quaternary structures a protein adopts are the most energetically favorable arrangements of the primary structure in a given environment

74
Q

how can the primary structure of a protein be determined?

A

sequencing

75
Q

is sequencing done from the DNA or the protein?

A

it can be done from both, but is more easily done using the DNA that coded for the protein

76
Q

defn: secondary structure

A

the local structure of the neighboring amino acids

77
Q

what are secondary structures primarily the result of?

A

hydrogen bonding between nearby amino acids

78
Q

what are the 2 most common secondary structures?

A

alpha-helices

beta-pleated sheets

79
Q

what is the key to the stability of both types of secondary structures?

A

the formation of intramolecular hydrogen bonds between different residues

80
Q

defn + direction of R groups: alpha-helix

A

a rodlike structure in which the peptide chain coils clockwise down a central axis

the side chains of the amino acids in the alpha-helical conformation point away from the helix core

81
Q

what stabilizes the helix?

A

intramolecular hydrogen bonds between a carbonyl O atom and an amide H atom four residues down the chain

82
Q

the alpha-helix is an important component in structure of what protein? what is the func/defn of that protein?

A

keratin

a fibrous structural protein found in human skin, hair, and fingernails

83
Q

are beta-pleated sheets parallel or anitparallel?

A

they can be either

84
Q

structure + direction of R groups: beta-pleated sheets

A

the peptide chains lie alongside one another, forming rows or strands held together by intramolecular hydrogen bonds between carbonyl O atoms on one chain and amide H atoms in an adjacent chain

the R groups of amino residues point above and below the plane of the Beta-pleated sheet

85
Q

why are beta-pleated sheets pleated (rippled)?

A

to accommodate as many H bonds as possible

86
Q

in what part of each secondary structure is proline often found? why is it not found elsewhere?

A

FOUND:
1. in the turns between the chains of a Beta-pleated sheet
2. as the residue at the start of an alpha-helix

NOT FOUND:
1. in the middle of an alpha helix (except in helices that cross the cell membrane)
2. in the middle of beta pleated sheets

BECAUSE
it has a rigid cyclic structure, which will introduce a kink in the peptide chain when it is found in the middle of secondary structures

87
Q

defn + example: fibrous vs. globular proteins

A

FIBROUS proteins = have structures that resemble sheets or long strands – example: collagen

GLOBULAR proteins = tend to be spherical – example: myoglobin

88
Q

what level of protein structure causes the structures of fibrous and globular proteins?

A

tertiary and quaternary protein structures

89
Q

denf: protein’s tertiary structure

A

its 3-D shape

90
Q

what are tertiary structures mostly determined by?

A

hydrophilic and hydrophobic interactions between R groups of amino acids

91
Q

talk through the hydrophilic and hydrophobic interactions of amino acids (4)

A
  1. hydrophobic residues prefer to be on the interior of proteins, reducing their proximity to water
  2. hydrophilic N-H and C=O bonds found in the polypeptide chain get pulled in by these hydrophobic residues
  3. these hydrophilic bonds can then form electrostatic interactions and hydrogen bonds that further stabilize the protein from the inside
  4. as a result, most of the amino acids on the surface of the proteins have hydrophilic (polar or charged) R groups. Highly hydrophobic R groups, such as phenylalanine, are almost never found on the surface of a protein
92
Q

what else (2) can 3-D structure be determined by?

A
  1. hydrogen bonding
  2. acid-base interactions between amino acids with charged R groups, creating salt bridges
93
Q

defn: disulfide bonds

A

the bonds that form when two cysteine molecules become oxidized to form cystine

94
Q

why are disulfide bonds a particularly important component of tertiary structure?

A

disulfide bonds create loops in the protein chain

95
Q

what role do disulfide bonds have in curly hair?

A

the more disulfide bonds, the curlier the hair is

96
Q

what electrons or protons are lost or gained in the formation of a disulfide bond?

A

the loss of two protons and two electrons (oxidation)

97
Q

What are the basics behind protein folding? (3)

A
  1. the secondary structures probably form first
  2. hydrophobic interactions and hydrogen bonds cause the protein to “collapse” into its proper 3-D structure
  3. along the way, it adopts intermediate states known as “molten globules”
98
Q

is protein folding fast or slow?

A

it is an extremely rapid process
from start to finish it takes much less than a second

99
Q

defn + effect: denaturation

A

the process by which a protein loses its tertiary structure

effect: the protein loses its function

100
Q

one word + longer answer: why do hydrophobic residues tend to occupy the interior of a protein, while hydrophilic residues tend to accumulate on the exterior of proteins?

A

entropy

by moving hydrophobic residues away from water molecules and hydrophilic residues toward water molecules, a protein achieves maximum stability

101
Q

explain further: why do hydrophobic residues tend to occupy the interior of a protein?

A
  1. whenever a solute dissolves in a solvent, the nearby solvent molecules form a solvation layer around that solute
  2. from an enthalpy standpoint, even hydrocarbons are more stable in aqeous solution than in organic ones
  3. however, when a hydrophobic side chain is placed in aqueous solution, the water molecules in the solvation layer cannot form hydrogen bonds with the side chain
  4. This forces the nearby water molecules to rearrange themselves into specific arrangements to maximize hydrogen bonding, which means a negative change in entropy (this represents increasing order, decreasing disorder), and are thus unfavorable
  5. this entropy change makes the overall process nonspontaneous
102
Q

explain further: why do hydrophilic residues tend to occupy the exterior of a protein?

A

allows nearby water molecules more latitude in their positioning, thus increasing their entropy, and making the overall solvation process spontaneous

103
Q

do all proteins have quaternary structure?

A

no

104
Q

for what types of proteins does quaternary structure exist?

A

only proteins that contain more than one polypeptide chain

105
Q

what is quaternary structure for those proteins that DO have it?

A

an aggregate of smaller globular peptides, or subunits, and represents the functional form of the protein

106
Q

what are the classic examples of quaternary structure?

A

hemoglobin and immunoglobulins

107
Q

the formation of quaternary structure can serve several roles, what are these roles? (4)

A
  1. they can be more stable by further reducing the surface area of the protein complex
  2. they can reduce the amount of DNA needed to encode the protein complex
  3. they can bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction
  4. they can induce cooperativity, or allosteric effects (basically: one subunit can undergo conformational or structural changes, which either enhance or reduce the activity of other subunits)
108
Q

defn: prosthetic groups

A

covalently attached molecules that conjugated proteins derive part of their function from and can also direct the protein to be delivered to a certain location

109
Q

what types of molecules can prosthetic groups be? (2)

A
  1. organic molecules (such as vitamins)
  2. metal ions (such as iron)
110
Q

defn: lipoproteins, glycoproteins, and nucleoproteins

A

proteins with lipid, carbohydrate, and nucleic acid prosthetic groups, respectively

111
Q

defn + func (2): heme

A

a prosthetic group that is contained within each of hemoglobin’s subunits

  1. the heme group (which contains an iron atom in its core) binds to and carries oxygen
  2. so hemoglobin is inactive without the heme group
112
Q

can unfolded proteins catalyze reactions?

A

no, whether its denaturation is reversible or not

113
Q

is denaturation reversible or irreversible?

A

it is sometimes reversible, but often irreversible

114
Q

what are the 2 main causes of denaturation?

A
  1. heat
  2. solutes
115
Q

explain denaturation via heat (2)

A
  1. when the temperature of a protein increases, its average kinetic energy increases
  2. when the temperature gets high enough, this extra energy can be enough to overcome the hydrophobic interactions that hold a protein together, causing the protein to unfold
116
Q

explain denaturation via solutes: summary + examples (3)

A

summary: denature proteins by directly interfering with the forces that hold the protein together
1. they can disrupt tertiary and quaternary structures by breaking disulfide bridges, reducing cystine back to two cysteine residues
2. they can overcome hydrogen bonds and other side chain interactions that hold alpha-helices and beta-pleated sheets intact
3. detergents can solubilize proteins, disrupting noncovalent bonds and promoting denaturation

Biochem (12 decks)

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