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Biochemistry MCAT > Ch. 1: Amino Acids and Proteins > Flashcards

Ch. 1: Amino Acids and Proteins Flashcards

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MCAT flashcards
1
Q

What are the four groups attached to the central (a) carbon of a proteinogenic amino acid?

A

Carboxylic acid (COOH)
Amino group (NH2)
Hydrogen (H)
Side group (R)

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2
Q

What is the stereochemistry of the amino acids that appear in eukaryotic proteins?
L or D?
R or S?

A

L
S (exception: cysteine)

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3
Q

What are the hydrophobic/nonpolar amino acids?

A

GAV LIM FWP

Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Proline

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4
Q

What are the hydrophillic/polar amino acids?

A

DESTY HKR NQ

Aspartic Acid, Glutamic Acid, Serine, Threonine, Tyrosine, Histidine,
Lysine, Arginine, Asparagine, Glutamine

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5
Q

What are the Aromatic amino acids?

A

FWP

Phenylalanine, Tyrosine, Tryptophan

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6
Q

What the Acidic amino acids?

A

DE
Aspartate, Glutamate

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7
Q

What are the Basic Amino Acids?

A

HKR

Arginine, Lysine, Histidine

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8
Q

What makes an amino acid an amphoteric species?

A

Amino acids can accept a proton or donate a proton

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9
Q

Describe what happens to ionizable groups in amino under acidic and basic conditions.

A

Ionizable groups tend to gain protons under acidic conditions and lose them during basic conditions

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10
Q

If the pH is less than the pKa, ________________________.

A

a majority of the species will be protonated

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11
Q

If the pH is greater than the pKa, ________________________.

A

the majority of the species will be deprotonated

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12
Q

What is the pKa of the carboxyl group in an amino acid?

A

2

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13
Q

What is the pKa of the amino group in an amino acid?

A

10

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14
Q

For a generic amino acid, NH2CRHCOOH, with an uncharged side chain, what would be the predominant form at each of the following pH values?
pH = 1
pH = 7
pH = 11

A

1: NH3CRHCOOH
7: NH3CRHCOO-
11:NH2CRHCOO-

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15
Q

Given the following pka values, what is the value of the pI for each of the amino acids listed below?
Aspartic acid: pka1 = 1.88, pka2 = 3.65, pka3 = 9.60
Arginine: pka1 = 2.17, pka2 = 9.04, pka3 = 12.48
Valine: pka1 = 2.32, pka2 = 9.62

A

Aspartic acid: 2.77
Arginine: 10.8
Valine: 5.97

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16
Q

dipeptide

A

two amino acids

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17
Q

tripeptide

A

three amino acids

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18
Q

Write the pI of a neutral amino acid.

A
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19
Q

Write the pI of an acidic amino acid.

A
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20
Q

What are Peptide bonds?

A

Bond between the amino group of one amino acid and the carboxyl group of another amino acid

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21
Q

What molecule is released during formation of a peptide bond?

A

Water

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22
Q

Describe what happens during a condensation/dehydration reaction.

A

Reaction that results in removal of a water molecule and formation of a peptide bond between two amino acids

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23
Q

Draw the reaction mechanism of a condensation/dehydration reaction.

A
24
Q

Describe what happens during a hydrolysis reaction.

A

Reaction where a peptide bond is broken by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl atom.

25
Q

What is the definition, subtypes and stabilizing bonds of the primary structure of a protein?

A
  • linear sequence of amino acids
  • no subtypes
  • peptide bond
26
Q

What is the definition, subtypes and stabilizing bonds of the secondary structure of a protein?

A
  • local structure
  • alpha helices and beta sheets
  • hydrogen bond
27
Q

What role does Proline serve in the secondary structure?

A

Its rigid structure introduces kinks in alpha helices and creates turns in beta sheets

28
Q

What is the definition, subtypes and stabilizing bonds of the tertiary structure of a protein?

A
  • 3-D shape
  • hydrophobic interactions, acid-base/salt bridges, disulfide bond
  • van der Waals forces, hydrogen bonding, ionic bonds, covalent bonds
29
Q

What is the definition, subtypes and stabilizing bonds of the quaternary structure of a protein?

A
  • multiple polypeptides
  • no subtypes
  • van der Waals forces, hydrogen bonding, ionic bonds, covalent bonds
30
Q

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

A

increase in entropy
decrease in free energy

31
Q

Why are proteins denatured by heat?

A

increasing temperature increases kinetic energy, disrupting hydrogen interactions

32
Q

Why are proteins denatured by solutes?

A

disrupts elements of the secondary, tertiary, and quaternary structures

33
Q

In a neutral solution, most amino acids exist as
(A) positively charged compounds
(B) zwitterions
(C) negatively charged compounds
(D) hydrophobic molecules

A

(B) zwitterions

34
Q

At pH 7, the charge on a glutamic acid molecule is
(A) -2
(B) -1
(C) 0
(D) +1

A

(B) -1

35
Q

Which of the following statements is most likely to be true of nonpolar R groups in aqueous solution?
(A) they are hydrophilic and found buried within proteins
(B) they are hydrophobic and found on protein surfaces
(C) they are hydrophobic and found buried within proteins
(D) they are hydrophobic and found don protein surfaces

A

(C) they are hydrophobic and found buried within proteins

36
Q

Glycine

A

G
Gly

37
Q

Alanine

A

A
Ala

38
Q

Valine

A

V
Val

39
Q

Leucine

A

L
Leu

40
Q

Isoleucine

A

I
Ile

41
Q

Methionine

A

M
Met

42
Q

Phenylalanine

A

F
Phe

43
Q

Tryptophan

A

W
Trp

44
Q

Proline

A

P
Pro

45
Q

Cysteine

A

C
Cys

46
Q

Aspartic Acid

A

D
Asp

47
Q

Glutamic Acid

A

E
Glu

48
Q

Serine

A

S
Ser

49
Q

Threonine

A

T
Thr

50
Q

Tyrosine

A

Y
Tyr

51
Q

Histidine

A

H
His

52
Q

Lysine

A

K
Lys

53
Q

Arginine

A

R
Arg

54
Q

Asparagine

A

N
Asn

55
Q

Glutamine

A

Q
Gln

Biochemistry MCAT (8 decks)

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