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MCAT Biochem (Mine) > Chapter 4: Amino Acids & Proteins > Flashcards

Chapter 4: Amino Acids & Proteins Flashcards

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MCAT flashcards
1
Q

What are the two acidic amino acids?

A

Aspartic Acid & Glutamic acid ( they both have a carboxylic acid functional group (pKa about 4) (Asparate & glutamate are their depronated forms)

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2
Q

What is the 3 letter abbreviation for Aspartic Acid?

A

Asp

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3
Q

What is the 3 letter abbreviation for Glutamic Acid?

A

Glu

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4
Q

What is the one-letter abbreviation for Aspartic Acid?

A

D

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5
Q

What is the one-letter abbreviation for Glutamic Acid?

A

E

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6
Q

What are the Basic Amino Acids?

A

Lysine, Arginine, & histidine

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7
Q

What is the pKa for the lysine R-group side chain?

A

10

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8
Q

What is the pKa for the Arginine R-group side chain?

A

12

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9
Q

What is the pKa for the Histidine R-group side chain?

A

6.5

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10
Q

What is special about histidine?

A

Its side chain has a pKa close to physiological pH so unlike other amino acids its either protonated or deprotonated at pH 7.4 so it can act as both an acid or base (“His goes both ways”)

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11
Q

What is the 3 letter abbreviation for Lysine?

A

Lys

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12
Q

What is the 3 letter abbreviation for Arginine?

A

Arg

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13
Q

What is the 3 letter abbreviation for Histidine?

A

His

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14
Q

What is the 1 letter abbreviation for Lysine?

A

K

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15
Q

What is the 1 letter abbreviation for Arginine?

A

R

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16
Q

What is the 1 letter abbreviation for Histdine?

A

H

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17
Q

Nonpolar (Hydrophobic amino acids) have either ____________ or aromatic side chains

A

Aliphatic (Alkyl)

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18
Q

Within the nonpolar amino acids which ones have an aliphatic (alkyl) side chain?

A

Glycine, Alanine, Valine, Leucine, & Isoleucine

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19
Q

Within the nonpolar amino acids which ones have an aromatic side chain?

A

Phenylalanine, Tryptophan, & Proline

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20
Q

The ______________ the hydrophobic group the greater the hydrophobic force repelling it from water

A

Larger

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21
Q

What is the 3 letter abbreviation for Glycine?

A

Gly

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22
Q

What is the 3 letter abbreviation for Alanine?

A

Ala

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23
Q

What is the 3 letter abbreviation for Valine?

A

Val

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24
Q

What is the 3 letter abbreviation for Leucine?

A

Leu

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25
Q

What is the 3 letter abbreviation for Isolecuine?

A

Ile

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26
Q

What is the 3 letter abbreviation for Phenylalanine?

A

Phe

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27
Q

What is the 3 letter abbreviation for Trypotphan?

A

Trp

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28
Q

What is the 1 letter abbreviation for Glycine?

A

G

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29
Q

What is the 1 letter abbreviation for Alanine?

A

A

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30
Q

What is the 1 letter abbreviation for Valine?

A

V

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31
Q

What is the 1 letter abbreviation for Leucine?

A

L

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32
Q

What is the 1 letter abbreviation for Isoleucine?

A

I

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33
Q

What is the 1 letter abbreviation for Phenylalanine?

A

F

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34
Q

What is the 1 letter abbreviation for Tryptophan?

A

W

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35
Q

___________ amino acids can form H bonds with water but doesn’t act as an acid or base

A

Polar amino acids

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36
Q

What are the polar amino acids

A

Serine, threonine, tyrosine, Asparagine, Glutamine

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37
Q

The hydroxyl group of the polar amino acids is usually modified by the attachment of a phosphate group by a regular enzyme called ______________

A

kinase

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38
Q

What is the 3 letter abbreviation for Serine?

A

Ser

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39
Q

What is the 3 letter abbreviation for Threonine?

A

Thr

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40
Q

What is the 3 letter abbreviation for Tyrosine?

A

Tyr

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41
Q

What is the 3 letter abbreviation for Asparagine?

A

Asn

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42
Q

What is the 3 letter abbreviation for Glutamine?

A

Gln

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43
Q

What is the 1 letter abbreviation for Serine?

A

S

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44
Q

What is the 1 letter abbreviation for Threonine?

A

T

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45
Q

What is the 1 letter abbreviation for Tyrosine?

A

Y

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46
Q

What is the 1 letter abbreviation for Asparagine?

A

N

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47
Q

What is the 1 letter abbreviation for Glutamine?

A

Q

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48
Q

What are the amino acids that contain sulfur side chains?

A

Cysteine & Methionine

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49
Q

Cysteine is fairly ___________ whereas methionine is fairly ___________

A

Polar, nonpolar

50
Q

Proline is what type of amino acid?

A

Nonpolar amino acid & has a ring structure

51
Q

What is the 3 letter abbreviation for Proline?

A

Pro

52
Q

What is the 1 letter abbreviation for Proline?

A

P

53
Q

What equation is used to used related to acid-base reactions?

A

Henderson -Hasselbalch equation (pH= pKa + log [A-/HA]

54
Q

When the pH of the solution is ________ than the pKa of an acidic group the acidic group will mostly be in its protonated form

A

Less

55
Q

When the Ph of the solution is __________ than the pKa of an acidic group the acidic group will mostly be in its deprotonated form

A

Greater

56
Q

The alpha-amino group of amino acids have a pka of what?

A

9-10

57
Q

The alpha-carboxyl group of amino acids have a pKa of what?

A

2

58
Q

When an amino has no net charge (both groups cancel each other out) its called what?

A

The Zwiterion (dipolar)

59
Q

The zwitterion is referred to as what?

A

Isoelectric point (pI)

60
Q

What is the point of calculating the pI

A

To figure out the pH value at which the (+) & (-) charges balance (cancel out)

61
Q

What are the two types of covalent bonds in proteins?

A
  1. Peptide bonds that link amino acids together into polypeptides
  2. Disulfides bridges between cysteine R - groups
62
Q

Why can’t you use proline residues to form an alpha helix?

A
  1. The formation of a peptide bond with proline eliminates the only hydrogen atom on the nitrogen of proline. The absence of the N-H bond disrupts the backbone hydrgen bonding in the polypeptide chain
  2. The unique structureof proline forces it to kink the polypeptide chain
63
Q

Thermodynamically unfavorable reactions that take place in the cell are driven by what?

A

Reaction coupling

64
Q

In _______________ one very favorable reaction is used to drive an unfavorable one

A

Reaction coupling (since free energy changes are additive)

65
Q

___________ is a type of reaction coupling that drives unfavorable reactions

A

ATP hydrolysis

66
Q

The active site model

A

Known as “The lock & Key model” which states that the substrate and active site are perfectly complementary

67
Q

Induced fit model

A

States that the substrate and active site differ slightly in structure and that the binding of the substrate induces a conformational change in the enzyme

68
Q

Cofactors

A

Are metal ions or small molecules that are used in enzyme activity

69
Q

Coenzyme

A

Often bind to the substrate during the catalyzed reaction (ex. Coenzyme A (CoA)

70
Q

The activity of enzymes are regulated in metabolic pathwaysin what ways?

A
  1. Covalent modifications
  2. Proteolytic Cleavage
  3. Association with other polypeptides
  4. Allosteric regulation
71
Q

Covalent Modifications

A

Proteins can have several different groups covalently attached to them which can regulate their activity

72
Q

Proteolytic cleavage

A

Enzymes that are synthesized in inactive forms that are activated by cleavage by a protease

73
Q

Association with other polypeptides

A

Some enzymes have catalytic activity in one poly peptide subunit that is regulated with a separate regulatory subunit.

74
Q

Constitutive activity ( continuous or unregulated)

A

When proteins have a continuous rapid catlysis if their their regulatory subunit is removed

75
Q

Allosteric Regulation

A

The modification of active site activity through the interaction of molecules with other specific sites on the enzyme

76
Q

When bound the ____________ regulator can alter the conformation of the enzyme to increase or decrease catalysis even though it may be bound to the enzyme at a site distant from the active site or even on a separate polypeptide

A

allosteric

77
Q

___________________ (feedback inhibition, feedback regulation) is used in the regulation of substrates & involves enzymes

A

Negative feedback

78
Q

Enzyme kinetics

A

Is the study of the rate of formation of products from substrates in the presence of an enzyme

79
Q

The reaction rate (V (mol/s))

A

Is the amount of product formed per unit of time & it depends on [S] & enzyme

80
Q

If there is only a little substrate then the rate V is ___________ proportional to the amount of substrate added

A

directly (double the amount of substrate & the reaction doubles)

81
Q

Vmax

A

Is when the enzyme is saturated so, therefore, adding more substrate won’t increase the reaction at all

82
Q

Km (Michaelis constant)

A

A low Km means that the enzyme has a high affinity for the substrate

83
Q

Km is found how?

A

1/2 Vmax

84
Q

Cooperativity (related to enzymes)

A

The binding of substrate to one subunit modulates the affinity of other subunitsfor substances

85
Q

What is the main type of Cooperativity related to enzymes?

A

Positive Cooperativity

86
Q

In _____________ cooperativity the binding of a substrate to one subunit increases the affinity of other subunits for the substrate

A

Positive ( Usually referred to as “tense” for the conformation of enzyme prior to substrate binding & referred as “relaxed” for the conformation of enzyme with increased affinity

87
Q

A _________ curve results from positive cooperactive binding

A

Sigmodial

88
Q

Describe the sigmodial curve

A

The beginning flat part of the curve means at low [S] the enzyme complex has low affinity for substrate (its in the tense state) & as you add more substrate it increase the rate so the steep part of the middle curve represents the part where adding more substrate increases the rate (in the relaxed state) & the top level part represent the Vmax part

89
Q

Cooperativity is a special kind of _________ interaction, one active site acts like an allosteric regulatory site for the other active sites & cooperative enzyme complexes are often allosterically regulated also

A

Allosteric

90
Q

Enzyme inhibitors can reduce enzyme activity by what mechanisms?

A
  1. Competitive inhibition
  2. Noncompetitive inhibition
  3. Uncompetitive inhibition
  4. Mixed-type inhibition inhibition
91
Q

Competitive Inhibitors

A

Are molecules that compete with the substrate for binding at the active sites

92
Q

How can competitive Inhibitors inhibition be overcome?

A

By adding more substrate, where if the [S] is high enough it can outcompete the inhibitor (Vmax is not affected)

93
Q

When you are dealing with competitive inhibitor what happens to Km?

A

The Km increases, Vmax doesnt change

94
Q

When dealing with a noncompetitive inhibitor

A

The Vmax decreases & the Km doesnt change

95
Q

Noncompeptive inhibitors bind at an ___________ site

A

Allosteric site (another site) so an “allosteric inhibitor”

96
Q

Uncompetitive inhibitors also bind to __________ sites

A

Allosteric

97
Q

How does uncompetitive inhibitors affect Vmax & Km

A

It decreases Vmax & decrease Km

98
Q

Mixed type inhibitors bind to __________ sites but additional substrates cant overcome inhibition

A

Allosteric

99
Q

How does mixed type inhibition affect Vmax & Km

A

It decrease Vmax but varies with Km where if the enzyme has lower affinity for the substrate then the Km increases & if the enzyme has a greater affinity for the substrate then Km decreases

100
Q

When dealing with the double reciprocal plot (Lineweaver plot) how do you interpret it?

A
  1. The slope of the graph is Km/ Vmax
  2. The y-intercept of the graph is 1/Vmax
  3. The x-intercept of the graph is -1/Km
101
Q

What is the 3 letter abbreviation for Cysteine?

A

Cys

102
Q

What is the 1 letter abbreviation for Cysteine?

A

C

103
Q

What is the 3 letter abbreviation for Methionine?

A

Met

104
Q

What is the 1 letter abbreviation for Methionine?

A

M

105
Q

What is the common structure of all 20 amino acids?

A

They have the N-C-C backbone & have an amino group, carboxyl group, & a side chain (side chain is what makes them different)

106
Q

Hydrophobic residues tend to be found in the ___________ of the globular protein ( the larger the hydrophobic group the greater the hydrophobic force repelling it from water)

A

Interior

107
Q

When the amino group is protonated its called an _______________________ group

A

Ammonium group

108
Q

Isoelectric point (pI)

A

The pH which a molecule is uncharged

109
Q

When a molecule just has 2 functional groups (no side that is acidic or basic) then the pI can be calculated by just ________________ the 2 functional groups

A

Averaging

110
Q

In a pI If the pH is higher than the pKa the site is mostly __________________________

A

Deprotonated

111
Q

In a pI If the pH is lower than the pKa the site is mostly ____________________

A

protonated

112
Q

Peptide bonds

A

Link amino acids together into polypeptide chains (by a loss of water)

113
Q

Disulfides bonds

A

Bonds between cysteine R groups

114
Q

How is a peptide bond formed?

A

Its formed between the carboxyl group of one amino acids & the amino groups of the other amino acids & a loss of water in the process

115
Q

In a polypeptide chain what is its backbone pattern?

A

N-C-C-N-C-C

116
Q

The ____________________ residue side is always written first floor a polypeptide or just a peptide bond

A

Amino- terminal

117
Q

Denatured proteins are __________________

A

Non-functional

118
Q

Denaturation

A

The disruption of a protein shape without breaking the peptide bond

119
Q

Primary sequence

A

The linear sequence of amino acids residues (determined by the peptide bond)

120
Q

The secondary structure is stabilized by what?

A

Hydrogen bonds between the backbone

MCAT Biochem (Mine) (4 decks)

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