Chapter 1: Amino Acids, Peptides, and Proteins (Kaplan) Flashcards

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1
Q

Remarkably, the difference between the normal form of hemoglobin (HbA) and the one that causes sickle cell disease (HbS), is a seemingly minor one. All it takes is a change in a single amino acid on the surface of hemoglobin: the ___ amino acid in 2 of its 4 chains is changed from ________ acid to ______. That minor difference allows the deoxygenated form of HbS to aggregate and precipitate, which leads to the sickled shape – and all the symptoms – of sickle cell disease.

A

6th glutamic acid to valine p. 3

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2
Q

Amino acids are molecules that contain two functional groups: an amino group (____) and a carboxyl group (_____).

A
  • NH2
  • COOH
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3
Q

The alpha-amino acids are the group in which the amino group and the carboxyl group are bonded to the same carbon, the _____-______ of the carboxylic acid. This means the carbon that is ________ to the carboxyl carbon.

A

alpha-carbon

adjacent

p. 4

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4
Q

Amino acids DO/ DO NOT need to have both the amino and carboxyl groups bonded to the same carbon.

A

do NOT

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5
Q

Name an example of an amino acid in the body which is not specified by a codon in the genetic code or incorporated into proteins.

A

ornithine, one of the intermediates in the urea cycle, which is the metabolic process by which the body excretes excess nitrogen

p. 4

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6
Q

The AAMC has specifically stated they’ll focus on the 20 alpha-amino acids encoded by the human genetic code, also called ____________ amino acids.

A

proteinogenic

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7
Q

What does chiral/ achiral mean?

A

Chiral means it’s asymmetric in such a way that the structure and its mirror image are not superimposable.

Achiral means that the object IS superimposable on its mirror image.

The term chiral comes from the Greek word for hand.

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8
Q

All chiral amino acids used in eukaryotes are _-amino acids.

A

L-amino acids

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9
Q

Name the 7 amino acids that fall into the category of nonpolar, nonaromatic side chains.

A

GAVLIMP

glycine

alanine

valine

leucine

isoleucine

methionine

proline

p. 6

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10
Q

Name the 3 amino acids that have uncharged aromatic side chains.

A

tryptophan, phenylalanine, tyrosine

(TPT)

p. 6

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11
Q

Which amino acid is achiral and also the smallest amino acid?

A

glycine

p. 5

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12
Q

Proline is unique in that it forms a ______ amino acid. In all the other amino acids, the amino group is attached ____ to the alpha-carbon. In proline, however, the amino nitrogen becomes a part of the side chain, forming a 5-membered ring. That ring places notable constraints on the flexibility of proline, which limits where it can appear in a protein and can have significant effects on the proline’s role in secondary structure.

A

cyclic

only

p. 6

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13
Q

Except for _______, all amino acids are chiral – and except for ________, all of them have an (S) absolute configuration.

A

glycine

cysteine

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14
Q

An imine is specifically a molecule with a…

Some textbooks problematically describe proline as an imino acid bc the amino nitrogen forms 2 bonds to carbon.

A

…carbon-nitrogen double bond.

p. 6

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15
Q

Phenylalanine has a benzyl side chain. What does that mean?

A

Benzyl means a benzene ring plus a -CH2 group.

p. 6

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16
Q

5 amino acids have side chains that are polar but not aromatic. Name them.

Which is the 1 polar amino acid that is aromatic and has a neutral charge?

A

(Mnemonic: SAG-C-2T)

Serine, Asparagine, Glutamine, Cysteine, Threonine

Tyrosine is aromatic and neutral.

(Remember also that tyrosine is aromatic, but asparagus is not, which is how you can remember that asparagine is the A in the mnemonic, since there are 3 other amino acids that start with A.)

p. 7

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17
Q

Asparagine and glutamine have amide side chains. What is unique amount these amino acids?

A

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.

p. 7

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18
Q

Cysteine contains a thiol (-SH) group in its side chain. Why is the S-H bond weaker than the O-H bond?

What is the significance of this?

A

because sulfur is larger and less electronegative than oxygen

It leaves the thiol group in cysteine prone to oxidation.

p. 7

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19
Q

Only 2 of the 20 amino acids have negative charges on their side chains at physiological pH (7.4). What are they?

A

aspartic acid and glutamic acid

p. 8

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20
Q

Note that ________ is simply the deprotonated form of aspartic acid, and _________ is the deprotonated form of glutamic acid.

A

aspartate

glutamate

*on the MCAT you are likely to see these anion names instead of acid names because most acids in cells exist in the deprotonated form.

p. 8

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21
Q

Strongly hydrophobic amino acids tend to be found in the ________ of proteins.

A

interior

p. 9

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22
Q

The amino acids with long _____ side chains – alanine, isoleucine, leucine, valine, and phenylalanine – are all strongly hydrophobic, and thus more likely to be found in the interior of proteins.

A

alkyl

p. 9

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23
Q

All the amino acids with charged side chains – __________ charged histidine, arginine, and lysine, plus __________ charged glutamate and aspartate – are hydrophilic, as are the amides asparagine and glutamine. The remaining amino acids lie somewhere in the middle and are neither particularly hydrophilic nor particularly hydrophobic.

A

POSITIVELY

NEGATIVELY

p. 9

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24
Q

The histidine residue in chymotrypsin’s ______ ____ removes a proton from the -COOH group in an aspartic acid residue, which can then deprotonate a serine residue.

A

active site

p. 8

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25
Q

What is the aromatic ring in histidine with 2 nitrogen atoms called?

A

an imidazole

p. 8

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26
Q

What does the notation “E6V” mean in turns of a mutation by substitution?

A

That the sixth amino acid, glutamic acid (E), has been changed to valine (V).

p. 10

27
Q

Because amino acids have both an acidic carboxylic acid group and a basic amino group, this makes them an __________ species.

A

amphoteric

p. 12

28
Q

The pKa of a group is the pH at which, on average, half of the molecules of that species are deprotonated.

If the pH is LESS than the pKa, a majority of the species will be ________. If the pH is HIGHER than the pKa, a majority of the species will be ________.

A

protonated

deprotonated

p. 12

29
Q

Because all amino acids have at least 2 groups that can be deprotonated, they all have at least 2 pKa values. The first one, pKa1, is the pKa for the _____ group, and usually around _. For most amino acids, the second pKa value, pKa2, is the pKa for the amino group, and is usually around _ or _.

If the amino acid has an ionizable side chain, there will be more than 2 pKa values.

A

carboxyl, 2

9 or 10

p. 12

30
Q

At very acidic pH values (such as that of the environment of the stomach), amino acids tend to be ________ charged.

A

positively

p. 12

31
Q

At physiological pH, you will not find amino acids with the carboxylate group protonated (-COOH), AND the amino group unprotonated (-NH2). In what form will be find these groups?

A

The carboxyl group will be deprotonated (-COO-) and the amino group will be protonated (in its conjugate acid form: -NH3+)

32
Q

At very alkaline pH values, amino acids tend to be…

A

…negatively charged.

p. 13

33
Q

The isoelectric point is the pH at which the molecule is electrically _______.

A

neutral

p. 15

34
Q

The pI is calculated as the average of the 2 nearest pKa values. For amino acids with non-ionizable side chains, the pI is usually around _.

A

6

35
Q

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

A

+1

36
Q

the pI of an acidic amino acid = [pKa,R group + pKa,COOH group] / 2

What is the pI of a basic amino acid?

A

pI = [pKa,R group + pKa,NH3+ group] / 2

37
Q

We think of peptide bond formation as a condensation or dehydration reaction, but it can also be viewed as an ____ substitution reaction, which can occur with all carboxylic acid derivatives.

A

acyl

p. 17

38
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. The hydroxyl group of the carboxylic acid is then kicked off, and the result is the formation of a peptide (amide) bond.

A

electrophilic

nucleophilic

p. 17

39
Q

Do amide groups exhibit resonance? And why?

A

Yes, because they have delocalizable pi electrons in the carbonyl and in the lone pair on the amino nitrogen, thus the C-N bond in the amide has partial double bond character.

p. 18

40
Q

Why do we draw peptide bonds in a certain order, from NH3 on the left to COOH group on the right?

A

They are drawn in the same order that they are synthesized by ribosomes!

p. 18

41
Q

Because of the double bond character, rotation of the protein backbone around the C-N amide bonds is ________, which makes the protein rigid, however the rest of the bonds are sigma with free rotation.

A

restricted

p. 18

42
Q

What is an oligopeptide?

A

a string of 2 or more amino acids, up to 20 amino acids

2 amino acids may be called a dipeptide, and 3 may be called a tripeptide

p. 19, 33

43
Q

True or false, in organic chemistry, amides can be hydrolyzed using acid or base catalysis.

A

True

p. 18

44
Q

The primary structure alone encodes all the information needed for folding at all of the higher structural levels; the secondary, tertiary, and quaternary structures a protein adopts are the most _______ _______ arrangements of the primary structure in a given environment.

A

energetically favorable

p. 20

45
Q

Which amino acid forms a kink in a peptide chain, and thus is rarely found in the middle of beta pleated sheets, but often found in the turns between the chains of a beta pleated sheet or at the start of an alpha helix?

A

proline

p. 21

46
Q

in an alpha helix, the helix is stabilized by intermolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom 4 residues down the chain. This means the side chains of the amino acids point ____ from the helix core.

A

away

p. 20

47
Q

Conjugated proteins derive part of their function from covalently attached molecules called _________ groups. These groups can be organic molecules, vitamins, metal ions, lipids, carbohydrates, or nucleic acids.

A

prosthetic

E.g. lipoproteins, glycoproteins, nucleoproteins

p. 25

48
Q

Hemoglobin is an example of a conjugated protein. Each of its subunits contains a prosthetic group. What is this prosthetic group called?

A

heme

p. 25

49
Q

What is tertiary structure?

What are the subtypes of tertiary structure?

A

The 3-D shape of a protein.

hydrophobic interactions, acid-base/ salt bridges, disulfide links

p. 34

50
Q

What bonds stabilize the tertiary structure of a protein?

(Note: quaternary structure is stabilized by these same forces.)

A

van der Waals forces, hydrogen bonds, ionic bonds, and covalent bonds

p. 34

51
Q

What is quaternary structure of a protein?

A

the interactions between separate subunits of a multisubunit protein.

p. 34

52
Q

What is the primary motivation for hydrophobic residues in a polypeptide to move to the interior 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 ΔS makes ΔG < 0, stabilizing the protein.

p. 34

53
Q

If a protein loses its ________ structure, a process called denaturation, it loses its function.

A

tertiary

p. 23

54
Q

The 2 main causes of denaturation are…

A

….heat and solutes.

Heat is energy which, if high enough, can overcome the hydrophobic interactions that hold a protein together, causing it to unfold.

p. 28

55
Q

What is an example of a solute that can denature proteins by directly interfering with the forces that hold the protein together.

A

urea

p. 29

56
Q

D-amino acids can exist in __________.

A

prokaryotes

p. 30

57
Q

Amino acids can be titrated; the titration curve is nearly _______ at the pKa values of the amino acid, and nearly _______ at the pI of the amino acid.

A

flat

vertical

p. 30

58
Q

Breaking a peptide bond is a _________ reaction.

A

hydrolysis

p. 31

59
Q

α-helices are _________ coils around a central axis.

A

clockwise

p. 31

60
Q

Why is cysteine the only amino acid with an S absolute configuration?

A

Because it is the only one that has an R group that has a higher priority than a carboxylic acid according to Cahn-Ingold-Prelog rules.

p. 33

61
Q

Glutamic acid and aspartic acid are acidic amino acids bc they have an extra ________ group. At neutral pH, both of these groups are deprotonated and thus negatively charged.

A

carboxyl

p. 38

62
Q

What type of structure may or may not be disrupted by denaturation?

A

secondary structure

p. 38

63
Q

Which 2 amino acids also have a chiral carbon in their side chain?

A

threonine and isoleucine

p. 39

64
Q

Which amino acid is most likely to be found in the highest concentration in the triple helix structure of collagen?

A

glycine, bc it has the smallest side chain of all, and steric hindrance is the biggest potential problem with the other larger amino acids.

p. 39