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SP MCAT Biochem > Amino Acids > Flashcards

Amino Acids Flashcards

1
Q

What functional groups make-up amino acids?

A
  • amino group (-NH2)

- carboxyl group (-COOH)

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2
Q

What are proteinogenic amino acids?

A

20 alpha amino acids that are L isomers (means that they occur in nature)

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3
Q

What is the one amino acid that isn’t chiral (which means it is also the only AA that does not have both a L- and D- form)?

A

glycine

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4
Q

What are the two amino acids that don’t have a (S) absolute configuration at their alpha carbon?

A

cysteine and glycine

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5
Q

Which amino acids have non-polar, non-aromatic side chains?

A
  • LIMPGAV*
  • Leucine (alkyl side chain)
  • Isoleucine (alkyl side chain)
  • Methionine (sulfur atom in side chain)
  • Proline (forms a cyclic AA)
  • Glycine (single H)
  • Alanine (alkyl side chain)
  • Valine (alkyl side chain)
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6
Q

Which amino acids have aromatic side chains?

A
  • TTP*
  • Tyrosine (contains -OH group making it relatively polar)
  • Tryptophan (contains two rings)
  • Phenylalanine (relatively nonpolar)
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7
Q

Which amino acids have polar side chains?

A
  • CATSG*
  • Cysteine (contain a thiol -SH in side chain which is prone to oxidation)
  • Asparagine (amide side chain, nitrogen in amide doesn’t gain or lose protons with changes in pH)
  • Threonine (-OH groups in side chain so highly polar and able to participate in H-bonding)
  • Serine (-OH groups in side chains so highly polar and able to participate in H-bonding)
  • Glutamine (amide side chain, nitrogen in amide doesn’t gain or lose protons with changes in pH)
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8
Q

Which amino acids have negatively charged (acidic) side chains?

A
  • GA*
  • Glutamate (negative charge on side chain at pH of 7.4)
  • Aspartate (negative charge on side chain at pH of 7.4)
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9
Q

Which amino acids have positively charged (basic) side chains?

A
  • LAH*
  • Lysine
  • Arginine (3 nitrogen atoms that delocalizes + charge)
  • Histidine (aromatic ring with 2 nitrogen atoms called imidazole)
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10
Q

What amino acids contain a chiral atom in their side chain?

A
  • Threonine

- Isoleucine

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11
Q

What type of amino acids are found on the surface of a protein?

A
  • amino acids with charged side chains
  • histine, arginine, lysine
  • aspartate, glutamate
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12
Q

What type of amino acids are found inside a protein?

A
  • hydrophobic amino acids

- alanine, isoleucine, leucine, valine, phenylalanine

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13
Q

Why are amino acids considered amphoteric species?

A
  • they have an acidic carboxylic acid group and a basic amino group
  • they can either accept a proton or donate a proton
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14
Q

What happens to ionizable groups at a low pH?

A

protonated (NH3+, COOH)

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15
Q

What happens to ionizable groups at a high pH?

A

deprotonated (NH2, COO-)

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16
Q

What is the pKa?

A

pH at which half the molecules are deprotonated

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17
Q

pH < pKa

A

majority of species is protonated

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18
Q

pH > pKa

A

majority of species is deprotonated

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19
Q

What is the pKa of the amino acid carboxyl group (COOH)?

A

pKa1 = 2

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20
Q

What is the pKa of the amino acid amino group (NH3+)?

A

pKa2 = 9-10ish

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21
Q

How protonated are amino acids in acidic conditions?

A
  • amino group fully protonated (NH3+)

- carboxylic acid protonated (COOH)

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22
Q

How protonated are amino acids in basic conditions?

A
  • amino group deprotonates (NH2)

- carboxylic acid deprotonated (COO-)

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23
Q

What are amino acids like at physiological pH?

A
  • most carboxylic acids are protonated (COOH)

- amino group is deprotonated (NH2)

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24
Q

What occurs when pH is near the pI of the amino acid?

A

the amino acid is a neutral zwitterion – molecule contains charges but is neutral overall

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25
Q

Titration curve is nearly _____ at the pka values of an amino acid

A

flat

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26
Q

Titration curve is nearly _____ at the pI of the amino acid

A

vertical

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27
Q

When does a solution act as a buffer?

A

when the pH of the solution is approximately equal to teh pKa of the solute

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28
Q

What is the pI of amino acids with nonionizable side chains?

A
  • pH at which an amino acid is predominately in zwitterionic form
  • electronically neutral
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29
Q

What are the pI values of amino acids with acidic side chains?

A

well below 6

30
Q

What are the pI values of amino acids with basic side chains?

A

well above 6

31
Q

Dipeptides

A

consist of 2 amino acid residues

32
Q

Tripeptides

A

consist of 3 amino acid residues

33
Q

Oligopeptides

A

relatively small peptides with up to 20 amino acid residues

34
Q

Polypeptides

A

longer peptides with >20 amino acid residues

35
Q

What is a peptide bond?

A
  • join peptide residues
  • form of an amide bond that forms between the COO- group and the NH3 group of another amino acid
  • forms the functional group C(O)NH
36
Q

What type of reaction forms peptide bonds?

A

condensation/dehydration reaction

37
Q

What order are peptides drawn/read from?

A

N terminus on the left to the C terminus on the right

38
Q

What type of reaction breaks peptide bonds?

A

hydrolysis using an acid or base catalysis

39
Q

What enzymes in humans catalyze the hydrolysis of peptide bonds?

A
  • hydrolytic enzymes like trypsin and chymotrypsin
  • both these enzymes function by breaking apart the amide bond by adding a H atom to the amide N and an OH group to the carbonyl carbon
40
Q

Where does the enzyme trypsin cleave a peptide bond?

A

at the carboxyl end of arginine and lysine

41
Q

Where does the enzyme chymotrypsin cleave a peptide bond?

A

at the carboxyl end of phenylalanine, tryptophan and/or tyrosine

42
Q

pH=pKa

A

50% of protonated form, and 50% of deprotonated form

43
Q

Zwitterion has both ___ and ___ species in the same ion

A

negative and positive

44
Q

What are the ? beta-branched AAs?

A
  • Valine
  • Isoleucine
  • Threonine
45
Q

What are beta branched AAs?

A

AAs that have a branch at the C that is 2C’s away from the carbonyl

46
Q

What can be said about beta-branched amino acids?

A

they are not favored in some secondary structures (i.e. alpha helix)

47
Q

What two amino acids will never be found in alpha helices?

A
  • glycine

- proline

48
Q

Which amino acid introduces a kink in the amino acid chain?

A

Proline

49
Q

What 3 AAs can be phosphorylated at their R group -OH?

A
  • Serine
  • Threonine
  • Tyrosine
50
Q

What two things can be said about Tyrosine?

A

it is aromatic and nonpolar

51
Q

What two amino acids contain sulfur?

A
  • Cysteine

- Methionine

52
Q

What amino acid can form disulfide bonds under oxidizing conditions?

A

Cysteine

53
Q

What type of agent is needed to break covalent disulfide bonds? (like the one formed btw two cysteines)

A

Reducing agent

54
Q

What protein structures are disulfide bonds found in?

A
  • secondary
  • tertiary
  • quaternary
55
Q

What is the pKa of Lysine’s R-group?

A

10.5

56
Q

What is the pKa of Arginine’s R-group?

A

12.5

57
Q

What is the pKa of Histidine’s R-group?

A

6

58
Q

Arginine contains a ____ group

A

guanidinium

59
Q

Histidine contains a ____ group

A

imidazole

60
Q

Is Histidine aromatic?

A

yes

61
Q

What is the pKa of Aspartate’s (Aspartic Acid) R-group?

A

4

62
Q

What is the pKa of Glutamate’s (Glutamic Acid) R-group?

A

4

63
Q

Does histidine ionize?

A

Yes

64
Q

What is a wild-type variant?

A

normal peptide, no changes

65
Q

What is a T7K variant?

A

changing the threonine at position 7 in a peptide to lysine

66
Q

What is the pKa of Histidine’s side group?

A

6

67
Q

In an acidic amino acid that is transitioning above it’s pKa, its charge goes from __ to ___

A

neutral to negative
[below its pKa of 4 the R group COOH is protonated and neutral, above its pKa the R group COO- is deprotonated and negative]

68
Q

In a basic amino acid that is transitioning above it’s pKa, it’s charge goes from ___ to ___

A

positive to neutral
[below its pKa the R group NH is protonated with a positive charge, above its pKa the R group N is deprotonated and neutral]

69
Q

What is an Isoelectric Point?

A

the pH that gives an overall net neutral charge

70
Q

How do you find the isoelectric point of a polypeptide?

A

average all the pKas of the amino acids in the molecule (make sure to include the N-terminus, 9, and C-terminus, 2, pKas!!!)

71
Q

What is a dipolar molecule?

A

A molecule that is electrically neutral but still carries a positive and negative charge

72
Q

Proteins are molecules that contain 50 or more amino acid residues, and they can act as excellent buffers because of their:

A

H-bonding capabilities in forming secondary and tertiary structures

SP MCAT Biochem (16 decks)

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