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MCAT BIochem > Amino Acids > Flashcards

Amino Acids Flashcards

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MCAT flashcards
1
Q

Amino acids

A

Molecules hat contain functional groups amino and carboxyl (COOH)

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2
Q

Where is the alpha carbon located on an amino acid?

A

Next to carboxyl group carbon

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3
Q

Parts of amino acid

A

Amino group
Side chain/R group
alpha carbon
Carboxyl group

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4
Q

Which amino acid is achiral?

A

Glycine

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5
Q

Eukaryotes use which form of amino acids?

A

L-amino acids (counter clockwise)

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6
Q

Which amino acid has R absolute configuration?

A

Cysteine (still an L amino acid)

CH2SH has priority over COOH

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7
Q

What amino acids are nonpolar, nonaromatic

A

Glycine, alanine, valine, leucine, isoleucine, methionine, proline

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8
Q

Which amino acid contains sulfur in its side chain & is nonpolar

A

Methionine

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9
Q

Which amino acid has a five member nitrogen ring & is nonpolar- significant effect on structure?

A

Proline

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10
Q

Which amino acid has a methyl group attached to alpha carbon?

A

Alanine

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11
Q

Which amino acids have uncharged aromatic side chains?

A

Tryptophan, phenylalanine, tyrosine

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12
Q

Which amino acid has a double ring and contains nitrogen?

A

Tryptophan

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13
Q

Which amino acid has a benzyl side chain?

A

Phenylalanine

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14
Q

Which amino acid has a benzyl ring plus an -OH group?

A

Tyrosine

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15
Q

Which amino acids have polar side chains?

A

Serine, threonine, asparagine, glutamine, cysteine

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16
Q

Which polar amino acids have -OH side chains that can participate in hydrogen bonding

A

Serine, threonine

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17
Q

Which polar amino acids have amide groups ?

A

Asparagine & Glutamine

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18
Q

What happens to amide side chains when pH changes?

A

Do not gain or lose protons

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19
Q

Which polar amino acid has a thiol group as its side chain?

A

Cysteine

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20
Q

Which is stronger -SH or -OH?

A

-OH

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21
Q

Which is more prone of oxidation -SH or -OH?

A

-SH

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22
Q

Which amino acids are negatively charged/acidic?

A

Aspartic acid/aspartate & glutamic acid/glutamate

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23
Q

What physiological pH of aspartate & glutamate side chains become negatively charged?

A

pH 7.4

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24
Q

Which amino acids are positively charged/basic?

A

Lysine, arginine, histidine

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25
Q

Which amino acid has three nitrogens in its side chain?

A

arginine

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26
Q

Which amino acid has two nitrogens in an aromatic ring?

A

Histidine

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27
Q

Aromatic ring with two nitrogens?

A

Imidazole

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28
Q

pKa of histidine side chain?

A

pH 6

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29
Q

Under physiological pKa what how is histidine protonated?

A

One nitrogen is protonated and the other isnt

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30
Q

How to make an amino acid more positively charged?

A

Lower pH

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31
Q

How to make an amino acid more negatively charged

A

Increase pH

32
Q

Which amino acids are more hydrophobic?

A

Alanine, isoleucine, leucine, valine, phenylalanine

33
Q

Which amino acids are hydrophilic?

A

Histidine, arginine, lysine, glutamnie, aspartate, glutamate, asparagine

34
Q

What is an amphoteric species?

A

Can accept or release a proton

35
Q

pKa

A

pH where on average half of the molecule of that species are deprotonated , [HA]={A-}

36
Q

If the pH is less than the pKa?

A

Majority of species is protonated

37
Q

If pH is greater than pKa?

A

Majority of species is deprotonated

38
Q

What is the first pKa for?

A

Carboxyl group

39
Q

What is the carboxylic group pKa?

A

pH of 2

40
Q

What is the second pKa for?

A

Amino group

41
Q

What is the pKa of the amino group?

A

9-10

42
Q

What kind of charge would glycine have at pH 1?

A

1+

43
Q

What is a zwitterion?

A

A molecules that have both positive and negative charge, but overall the molecule is electrically neutral.

44
Q

At a pH of 7.4 what kind of charge would glycine have?

A

0

45
Q

At a pH of 10.5 what kind of charge would glycine have?

A

-1

46
Q

What happens when pH equals pKa?

A

The solution will act as a buffer and the line will become more flat

47
Q

Isoelectric point

A

pH at which the molecule is electrically neutral

48
Q

pI(neutral amino acids)

A

pKa, NH+ group + pKa COOH / 2 (usually around 6)

49
Q

pI (acidic amino acid)

A

pKa R group + pKa COOH group / 2

50
Q

pI (basic amino acid)

A

pKa NH+ group + pKa R group /2

51
Q

What amino acid configuration has groups organized clockwise?

A

D -configuration

52
Q

What is physiological pH?

A

pH 7.4

53
Q

Oligiopeptide

A

Peptide of up to 20 amino acid residues

54
Q

In peptide bond formation, what is the neucleophile?

A

Amine group

55
Q

In peptide bond formation, what is the electrophile?

A

Carbonyl group

56
Q

What is kicked off of an amino acid in peptide formation?

A

Hydroxyl of carboxyl group

57
Q

Where is there partial double bond character in an peptide bond?

A

From the carbonyl to the C-N bond

58
Q

Where is an amino acid rigid?

A

On the C-N bond of the amide linkage

59
Q

How are amino acids read from their termini?

A

N-terminus to C-terminus

60
Q

How is an amino acid broken apart?

A

Hydrolysis, adding water back into the molecule

61
Q

What is the main kind of bonding involved in secondary structures?

A

Hydrogen bonding between carbonyl oxygen and amide hydrogen bonds

62
Q

What structure is important in keratin?

A

a-helices

63
Q

Where do the R groups point in B-pleated sheets?

A

Above and below the sheet

64
Q

Where is proline often found?

A

In between chains of B-pleated sheet and start of a-helices

65
Q

What interactions occur during tertiary structures?

A

R groups- Hydrophobic, hydrophilic interactions, cystine bonds

66
Q

What causes loops in the protein chain?

A

Disulfide bonds (oxidation)

67
Q

When hydrophobic side chains group together and form a group, what is the effect on entropy & spontaneity?

A

Negative effect, more order & less disorder & is non-spontaneous

68
Q

When hydrophilic side chains group together and form a group, what is the effect on entropy & spontaneity?

A

Entropy increases and it is spontaneous

69
Q

Examples of tertiary structures?

A

Hemoglobin & antibodies

70
Q

Effects of tertiary structures

A

Reduce SA & increase stability
Reduce DNA needed to encode protein
Bring catalytic sites close together
Cooperativity/allosteric effects

71
Q

Two main causes of denaturation?

A

Heat and solutes

72
Q

What are reasons for conjugating proteins

A
  1. ) Direct delivery to particular organelle
  2. )Direct delivery to cell membrane
  3. ) Add cofactor needed for activity
73
Q

Which amino acids have chiral side chains?

A

Theronine & Isoleucine

74
Q

What can strong base do to proteins?

A

Denature them by cleaving peptide residues through hydrolysis

75
Q

What is the charge on a cathode?

A

Negative

76
Q

What is the charge on the anode?

A

Positive

MCAT BIochem (8 decks)

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