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Biochemistry MCAT > Amino Acids, Peptides and Proteins > Flashcards

Amino Acids, Peptides and Proteins Flashcards

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MCAT flashcards
1
Q

What determines the properties of the amino acids

A

side chain – R group

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2
Q

What are proteinogenic amino acids?

A

20 alpha oleic amino acids that are encoded but the human genetic code

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3
Q

What type of amino acids have the carboxyl group and the amino group attached to the same carbon?

A

alpha amino acids

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4
Q

Do the carboxyl group and the amino group have to be connected to the same carbon to be an amino acid?

A

no the carboxyl group and the amino group do not have to be connected to the same carbon to be an amino acid

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5
Q

What determines the chemical properties of amino acids

A

R group

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6
Q

Of the 20 proteinogenic amino acids, which are chiral

A

19
chiral - four different group attached to it
optically active

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7
Q

Of the 20 proteinogenic amino acids, which are achiral

A

glycine – because the hydrogen atom is its R group so it does not have four different groups attached to it

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8
Q

All chiral amino acids used in eukaryotes are _____

A

L-amino acids

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9
Q

Which amino acids have an absolute S configuration

A

All the amino acids besides glycine and cysteine

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10
Q

Which amino acids have an absolute R configuration

A

cysteine – the -CH2SH group has priority over the –COOH group

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11
Q

What are D-amino acids

A

not in eukaryotes – found in antibiotics

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12
Q

Alanine abbreviations

A

Ala

A

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13
Q

Arginine abbreviations

A

Arg

R

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14
Q

Asparagine abbreviations

A

Asn

N

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15
Q

Aspartic Acid abbreviations

A

Asp

D

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16
Q

Cysteine abbreviations

A

Cys

C

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17
Q

Glutamic Acid abbreviations

A

Glu

E

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18
Q

Glutamine abbreviations

A

Gln

Q

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19
Q

Histidine abbreviations

A

His

H

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20
Q

Isoleucine abbreviations

A

lle

I

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21
Q

Leucine abbreviations

A

Leu

L

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22
Q

Methionine abbreviations

A

Met

M

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23
Q

Phenylalanine abbreviations

A

Phe

F

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24
Q

Proline abbreviations

A

Pro

P

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25
Q

Serine abbreviations

A

Ser

S

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26
Q

Threonine abbreviations

A

Thr

T

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27
Q

Tryptophan abbreviations

A

Trp

W

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28
Q

Tyrosine abbreviations

A

Tyr

Y

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29
Q

Valine abbreviations

A

Val

V

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30
Q

Which amino acids are non polar and non aromatic (7)

A

gal v mip

glycine g 
valine   v 
alanine  a 
leucine  l 
methionine m 
isoleucine i 
proline  p
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31
Q

What is the smallest amino acid

A

glycine – single hydrogen atom as its R group

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32
Q

What are the aromatic amino acids

A

tryptophan
phenylalanine
tyrosine

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33
Q

What amino acids have polar side chains and are not aromatic

A

q cn st

Serine      s 
Threonine  t
Asparagine n 
Glutamine   q 
Cysteine     c
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34
Q

Which amino acids have negatively charged acidic side chains

A

Aspartate – aspartic acid

Glutamate – glutamic acid

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35
Q

Which amino acids have positively charged basic side chains

A

Lysine
Arginine
Histidine

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36
Q

What are some common properties of hydrophobic amino acids

A

long alkyl side chains
interior proteins
alaine, isoleucine, leucine, valine, phenylalanine

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37
Q

What are some common properties of hydrophilic amino acids

A 
charged side chains 
(positive - histidine, lysine,arginine)
(negative - aspartic acid and glutamic acid) 
amides - asparagine and glutamine
surface proteins
38
Q

What type of amino acids would be found on the interior of proteins

A

hydrophobic

39
Q

What type of proteins would be found on the surface of proteins

A

hydrophilic

40
Q

What is an amino acid

A 
have four groups attached to an central carbon 
an amino group
a carboxylic group 
a hydrogen 
an R group
41
Q

Amino acids are amphoteric meaning

A

they can accept or donate protons

42
Q

What is pKa of a group

A

is the pH at which half of the species are deprotonated

43
Q

Do amino acids change based on the pH

A

yes, amino acids exist in different forms at different pH values

44
Q

What happens to an amino acid at a low pH

A

at a low acidic pH the amino acid is fully protonated

45
Q

What happens to an amino acid at a high pH

A

at a high basic pH the amino acid is fully deprotonated

46
Q

What happens to an amino acid if the pH is near the pI of the amino acid

A

the amino acid is a neural zwitterion

47
Q

What is the pI of an amino acid, what does pI stand for

A

pI is the isoelectric point

48
Q

How do you determine the pI of an amino acid that does to have a charged side chain

A

pI of an amino acid without a charged side chain can be calculated by averaging the two pKa values

49
Q

How do you determine the pI of an amino acid with a charged side chain

A

calculated by averaging the two pKa values that correspond to protonation and deprotonation of the zwitteron

50
Q

Generally amino acids without charged side chains have a pI of about

A

6

51
Q

Generally amino acids that are acidic and negatively charged have a pI

A

well below 6

52
Q

Generally amino acids that are basic and positively charged have a pI of

A

well above 6

53
Q

What reaction occurs when a peptide bond is formed

A

condensation or dehydration

releasing one molecule of water

54
Q

How many amino acid residues are in dipeptides

A

two amino acids

55
Q

How many amino acid residues are in tripepties

A

three amino acids

56
Q

How many amino acids are in Oligopeptides

A

more than 3 but less than 20

57
Q

How many amino acids are in polypeptides

A

more than 20

58
Q

When a peptide bond is broken, what reaction occurs

A

hydrolysis

59
Q

What is the Primary structure of proteins and how is it stabilized

A

linear sequence of amino acids in a peptide

stabilized by peptide bonds

60
Q

What is the secondary structure of proteins and how is it stabilized

A

local structure of neighboring amino acids and is stabilized by hydrogen bonding between amino groups and nonadjacent carboxyl groups

alpha helices
beta sheets

61
Q

What is Tertiary structure of a protein and how is it stabilized

A

3D shape of a single polypeptide chain

stabilized by hydrophobic interactions, acid-base interactions, hydrogen bonding, and disulfide bonds

62
Q

What is quaternary protein structure and how is it stabilized

A

interaction between peptides in proteins that contain multiple subunits

63
Q

What is denaturation

A

loss of the 3D dimensional protein structure

64
Q

How can proteins become denatured

A

heat and increasing solute concentrations

65
Q

What are alpha helices, which type of protein structure does this correlate to

A

clockwise coils around a central axis

secondary

66
Q

What are beta pleated sheets, which type of protein structure do they correlate to

A

rippled strands that can be parallel or antiparallel

67
Q

How does proline interrupt secondary protein structure

A

because of its rigid cyclic structure

68
Q

When the pH is less than the pka, a majority of the species will be ____

A

protonated

69
Q

When the pH is more than the pka, a majority of the species will be ____

A

deprotonated

70
Q

All amino acids have ___ groups that can become deprotonated, so they have ___ pka values

A

two, two

71
Q

The pka1 refers to the ___ group becoming deprotonated and the pka2 refers to the ___ group becoming deprotonated

A

pka1 - carboxyl group usually around 2

pka 2 - amino group usually 9-10

72
Q

The pka1 of the carboxyl group is usually around

A

2

73
Q

The pka2 of the amino group is usually around

A

9-10

74
Q

At a pH of 1, what happens to the amino acid

A
  • usually becomes positively charged
  • pka is below 9-10 so the NH group is positively charges so it is NH3+
  • pka is below 2 so the COOH group is fully protonated and will be neutral
75
Q

At a pH greater than 10, what happens to the amino acid

A
  • usually becomes negatively charged
  • pka is above 10 so the NH group is deprotonated and becomes NH2
  • pka is above 2 so the COOH group is deprotonated and becomes COO-
76
Q

At a intermediate pH of 7, what happens to the amino acid

A
  • usually becomes neutral
  • pka is below 9 so the NH group becomes protonated forming NH3
  • pka is above 2 so the COOH group becomes deprotonated forming COO-
  • overall the charge is neural, these are called zwitterions
  • exist in water as internal salts
77
Q

In a neural solution, most amino acids exist as

  • positively charged compounds
  • zwitterions
  • negatively charged compounds
  • hydrophobic molecules
A
  • zwitterions
78
Q

At pH 7, the charge on a glutamic acid molecule is

  • -2
  • -1
  • 0
    • 1
A
  • -1
79
Q

Which of these statements concerning peptide bonds is false

  • their formation involves a reaction between and amino group and a carboxyl group
  • they are the primary bonds that hold amino acids together
  • they have partial double bond character
  • their formation involves hydration reactions
A
  • their formation involves hydration reactions
80
Q

How many distinct tripeptides can be formed form one valine molecule, one alanine molecule and one leucine molecule

  • 1
  • 3
  • 6
  • 27
A
  • 6
81
Q

Which of these is most likely to be preserved when a protein is denatured

  • primary structure
  • secondary structure
  • tertiary structure
  • quaternary structure
A
  • primary
82
Q

An alpha helix is most likely to be held together by

  • disulfide bonds
  • hydrophobic effects
  • hydrogen bonds
  • ionic attraction between side chains
A
  • hydrogen bonds
83
Q

Which of the following is least likely to cause denaturation of proteins

  • heating the protein to 100C
  • adding 8 M urea
  • moving it to a more hypotonic environment
  • adding a detergent such as sodium didecyl sulfate
A

-

84
Q

Which of the following is least likely to cause denaturation of proteins

  • heating the protein to 100C
  • adding 8 M urea
  • moving it to a more hypotonic environment
  • adding a detergent such as sodium didecyl sulfate
A
  • moving it to a more hypotonic environment
85
Q

Which of these amino acids has a chiral carbon in its side chain

  • serine
  • threonine
  • isoleucine
  • I only
  • II only
  • II and III only
  • I, II, and III
A
  • II and III only
86
Q

Adding concentrated strain base to a solution containing an enzyme often reduces enzyme activity to zero. In addition to causing protein denaturation, which of the following is another plausible reason for the loss of enzyme activity

  • enzyme activity, once lost, cannot be recovered
  • the base can cleave peptide residues
  • adding a base catalyzes protein polymerization
  • adding a base tends to deprotonated amino acids on the surface of proteins
A
  • the base can cleave peptide residues
87
Q

Which of these amino acids has a side chain that can become ionized in cells

  • histidine
  • leucine
  • proline
  • threonine
A
  • histidine
88
Q

In lysine, the pka of the side chain is about 10.5. Assuming the pka of the carboxyl and amino group are 2 and 9 respectively, the pI of lysine is closet to 5.5

  • 5.5
  • 6.2
  • 7.4
  • 9.8
A
  • 9.8
89
Q

Which of the following is a reason for conjugating proteins

  • to direct their delivery to a particular organelle
  • to direct their delivery to the cell membrane
  • to add a cofactor needed for their activity
  • I only
  • II only
  • II and III only
  • I, II, and III
A
  • I, II, and III
  • to direct their delivery to a particular organelle
  • to direct their delivery to the cell membrane
  • to add a cofactor needed for their activity
90
Q

Collagen consist of three helices with carbon backbones that are tightly wrapped around one another in a triple helix. which of these amino acids is most likely to be found in the highest concentration in collagen

  • proline
  • glycine
  • threonine
  • cysteine
A
  • glycine

Biochemistry MCAT (7 decks)

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