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MCAT BIOCHEMISTRY FLASHCARDS > BIO CHEM CH.4 PART 1 > Flashcards

BIO CHEM CH.4 PART 1 Flashcards

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MCAT flashcards
1
Q

What is the unique feature of all twenty amino acids?

A

Side chain which gives it its physical and chemical properties that distinguish it from the other nineteen

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2
Q

What are the two acidic amino acids?

A
  1. Aspartic acid

2. Glutamic acid

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3
Q

What is the side chain of the two acidic amino acids?

A

Carboxylic acid functional group with a pKa of 4

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4
Q

What is the difference between glutamate and glutamic acid?

A

Refer to the anionic form (deprotonated)

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5
Q

Which amino acids are considered basic?

A

Lysine, arginine and histidine

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6
Q

What is the pKa value of the 3 basic amino acids?

A

Lysine: 10 Arginine: 12 and Histidine: 6.5

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7
Q

What is the three letter code fo glutamic acid and aspartic acid?

A

Glu and Asp

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8
Q

What is the one letter code for glutamic acid and aspartic acid?

A

E and D

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9
Q

What is unique about histidine?

A

Unique in having a side chain with a pKa close to physiological pH and can be protonated or deprotonated at pH 7.4

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10
Q

Amino acids containing -COOH side chains are always…

A

Anionic

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11
Q

Amino acids containing -NH2 side chains are always….

A

Cationic

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12
Q

What is the three letter code for histidine, lysine and arginine?

A

His, Lys and Arg

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13
Q

What is the one letter code for histidine, lysine and arginine?

A

H, L, and R

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14
Q

What do the hydrophobic amino acids contain for their side chains?

A

aliphatic (alkyl) or aromatic side chains

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15
Q

What are the amino acids with an aromatic side chain?

A

Phenylalanine, tryptophan and tyrosine

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16
Q

What are the amino acids with an aliphatic side chain?

A

Glycine, alanine, valine, leucine and isoleucine

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17
Q

Why are hydrophobic side chains found on the interior of folded globular proteins?

A

Hydrophobic residues tend to associate with each other rather than with water

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18
Q

The large the hydrophobic group of the amino acid…..

A

The greater the hydrophobic force repelling it from water

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19
Q

What is the three letter code for glycine, alanine, valine, leucine?

A

Gly, Ala, Val and Leu

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20
Q

What is the three letter code for isoleucine, phenylalanine, tryptophan?

A

Ile, Phe and Trp

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21
Q

What is the one letter code for glycine, alanine, valine, leucine?

A

G, A, V and L

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22
Q

What is the one letter code for isoleucine, phenylalanine, tryptophan?

A

I, F and W

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23
Q

How are the polar amino acids characterized?

A

R-group polar enough to form H bonds with water but does not act as an acid or base

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24
Q

What do the side chains of polar amino acids usually have?

A

Hydroxyl or single double bonded O

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25
Q

Which amino acids have a hydroxyl group on their side chains?

A

Serine, threonine and tyrosine

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26
Q

What happens to the hydroxyl group of serine, threonine and tyrosine?

A

Often modified by a kinase to attach a phosphate

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27
Q

What are the five amino acids corresponding to the polar amino acid groups?

A

Serine, threonine, tyrosine, asparagine and glutamine

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28
Q

What is the three letter code for serine, threonine, tyrosine, asparagine and glutamine?

A

Ser, Thr, Tyr, Aan and Gln

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29
Q

What is the one letter code for serine, threonine, tyrosine, asparagine and glutamine?

A

S, T, Y, N and Q

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30
Q

What are the two amino acids that have sulfur-containing side chains?

A

Cysteine and methionine

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31
Q

What type of side chain does cysteine include?

A

Contains a thiol

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32
Q

What type of side chain does methionine include?

A

Thioether

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33
Q

What type of amino acid polarity does cysteine have? What about methionine?

A

Polar; nonpolar

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34
Q

Why is proline unique?

A

Its amino group is covalently bound to its non polar side chain, creating a secondary alpha-amino group and distinctive ring structure

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35
Q

What type of polarity does proline have?

A

Nonpolar

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36
Q

What is the one letter code for cysteine, methionine and proline?

A

C, M and P

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37
Q

What is the three letter code for cysteine, methionine and proline?

A

Cys, Met and Pro

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38
Q

What are the nine essential amino acids that cannot be synthesized by humans?

A
  1. Lysine 2. Histidine 3. Threionine 4. Valine 5. Leucine 6. Isoleucine 7. Phenyalanine 8. Tryptophan 9. Methionine
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39
Q

Are amino acids amphoteric?

A

Yes

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40
Q

What is the pKa of carboxyl groups on amino acids?

A

2

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41
Q

What is the pKa of ammonium groups on amino acids?

A

9 or 10

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42
Q

What does the Henderson-Hasselbach explain?

A

Mathematical formula that describes the relationship between pH, pKa and the position of equilibrium in an acid-base reaction

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43
Q

What is the Henderson-Hasselbach equation?

A

pH = pKa + log [A-]/[HA] = pKa + log([base form]/[acid form])

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44
Q

What happens to the acidic group when the solution is less than the pKa of the acidic group?

A

Protonated form

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45
Q

What happens to the acidic group when the solution is more than the pKa of the acidic group?

A

Deprotonated form

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46
Q

Acids with low pKa tend to _______ more easily….

A

Deprotonated

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47
Q

Alll amino acids contain what two groups? What do they act as based on acids and bases?

A

Amino and carboxyl group; amino as a base and carboxyl as an acid

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48
Q

What is the protonated or acidic form of the amino group?

A

Ammonium group

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49
Q

What’s the pKa of the ammonium group?

A

Between 9-10

50
Q

A molecule with a positive and negative charges that balance is referred to as a ….

A

Dipolar ion or zwitterionic

51
Q

What is the name of the pH at which a molecule is uncharged (zwitterionic)?

A

Isoelectric point (pI)

52
Q

How to determine the pI of an amino acid?

A

Figure out the pH value at which the positive and negative charges balances

53
Q

If the p is higher than the pKa, the group is mostly….?

A

Deprotonated

54
Q

If the p is higher than the pKa, the group is mostly….?

A

Protonated

55
Q

What are the two common bond between amino acids in proteins?

A
  1. Peptide bonds linking amino acids together into polypeptide chains
  2. Disulfide bridges between cysteine R-groups
56
Q

How are polypeptides formed?

A

Formed by linking amino acids

57
Q

Where is a peptide bond formed based on two amino acids forming it?

A

Between the carboxyl group and alpha-amino group of amino acids

58
Q

What is lost during peptide formation?

A

Water

59
Q

Based on the polypeptide chain, what’s always first and what’s always last?

A

Amino terminus is first and carboxyl terminus is last

60
Q

What is the term to explain hydrolysis of a protein?

A

Proteolysis or proteolytic cleavage

61
Q

What is protease?

A

Protein that complete proteolysis

62
Q

What is the reactive group on the cysteine?

A

Thiol (sulhydryl SH) in its side chain

63
Q

What is the importance of a disulfide bridge?

A

Stabilizing tertiary protein structure

64
Q

What does denaturation refer to?

A

Disruption of a protein’s shape without breaking peptide bonds

65
Q

What can cause a protein denaturation?

A
  1. Urea 2. Extreme pH 3. Extreme temperature or 4. Changes in salt concentration
66
Q

What is the primary structure in protein folding?

A

The order of amino acids bonded to each other in the polypeptide chain

67
Q

What is the secondary structure in protein folding?

A

Initial folding of a polypeptide chain into shapes

68
Q

What is the secondary structure stabilized by?

A

Stabilized by hydrogen bonds between backbone

69
Q

The hydrogen bonds are stabilized between what, based on secondary structure?

A

Between backbone NH and CO groups

70
Q

What are the two common motifs of the secondary structure in protein folding?

A

Alpha-helix and beta pleated sheets

71
Q

The alpha helixes of proteins are always…..?

A

Right-handed, 5 angstroms in width with each subsequent amino acid rising 1.5 angstroms

72
Q

How many amino acids are present per turn in an alpha helix shape?

A

3.6 amino acid residues per turn

73
Q

Which amino acid has a problem in the polypeptide chains during secondary structure of protein folding?

A

Proline

74
Q

Why does proline disrupt the backbone hydrogen bonding in the polypeptide chain?

A

Because the formation of peptide bond with proline eliminates the only H atom on the nitrogen atom of proline

75
Q

What does the structure of proline force the polypeptide chain to do?

A

Kink

76
Q

Prolines can be present in alpha and beta pleated sheets. T/F

A

False: proline residues never appear within the alpha-helix

77
Q

Hormone receptors and ion channels are often found where, based on secondary structure?

A

With α-helical transmembrane regions integrated into the hydrophobic membranes of cells

78
Q

Why is the α-helic a favorable structure for a hydrophobic transmembrane region?

A

Because all polar NH and CO groups in the backbone are hydrogen-bonded to each other on the inside of the helix

79
Q

What do α-helical regions have that allow them interact with the hydrophobic interior of the membrane?

A

Hydrophobic R-groups

80
Q

Where do the NH and CO groups bonding happen in the beta-pleated sheets?

A

Bonding occurs between residues distant from each other in the chain or even on separate polypeptide chains

81
Q

What are the two types of beta pleated sheets?

A

Parallel and antiparallel

82
Q

What is a parallel beta pleated sheet?

A

Adjacent polypeptide strands running in the same direction

83
Q

What is an anti-parallel beta pleated sheet?

A

Adjacent polypeptide strands running in opposite directions

84
Q

What is the tertiary protein folding?

A

Interactions between amino acid residues located more distantly rom each other in the polypeptide chain

85
Q

In which protein folding is there electrostatic interactions between acidic and basic side chains?

A

Tertiary folding

86
Q

What is the tertiary structure folding driven by?

A

Interactions between R groups and with the solvent (water)

87
Q

What is the hydrophobic effect?

A

During tertiary structure, hydrophobic R-groups tend to fold inwards while hydrophilic fold outwards

88
Q

What is quaternary structure in protein folding?

A

Describes interaction between polypeptides

89
Q

What bond cannot be involved in quaternary structure and why?

A

Peptide bond because this bond defines sequence; primary structure

90
Q

As catalysts, enzymes have a _____ role and not a ____ one.

A

Kinetic role, not thermodynamic

91
Q

Enzymes can control the direction, therefore can go forward or backwards when demanded. T/F

A

False: Enzymes cannot control the direction in which a reaction proceeds

92
Q

What are hydrolases?

A

Hydrolyzes chemical bonds

93
Q

What are isomerases?

A

Rearranges bonds within a molecule to form an isomer

94
Q

What are ligase?

A

Forms a chemical bond

95
Q

What are lyases?

A

Breaks chemical bonds by means other than oxidation or hydrolysis

96
Q

What are kinases?

A

Transfers a phosphate group to a molecule from a high energy carrier

97
Q

What are oxidoreductases?

A

Runs redox reactions

98
Q

What are polymerases?

A

Polymerization

99
Q

What are phosphatase?

A

Removes a phosphate group from a molecule

100
Q

What are phosphorylase?

A

Transfers a phosphate group to a molecule from inorganic phosphate

101
Q

What are proteases?

A

Hydrolyzes peptide bonds

102
Q

What is a reaction coupling?

A

One very favorable reaction is used to drive an unfavorable one

103
Q

Why is reaction coupling possible?

A

Because free energy changes are additive

104
Q

What is a favorable reaction the cell can us to drive unfavorable reactions?

A

ATP hydrolysis

105
Q

What are the two ways ATP hydrolysis can drive an unfavorable reaction?

A
  1. Causing a conformational change in a protein

2. Transfer of a phosphate group from ATP to a substrate

106
Q

What is the active site model theory?

A

The substrate and the active site are perfectly complementary

107
Q

What is the induced fit model?

A

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

108
Q

How does enzymes accelerate the rate of given reaction?

A

Helping stabilize the transition state

109
Q

Which configuration of amino acids are found in animals?

A

L amino acids

110
Q

Many proteases have an actives site with…?

A

Serine residue whose OH group can act as a nucleophile,

111
Q

How does the serine residue’s OH group act as a nucleophile?

A

Attacks the carbonyl carbon of an amino acid residue in a polypeptide

112
Q

What are examples of the proteases with a OH serine group nucleophile ?

A

Trypsin, chymotrypsin and elastase

113
Q

Why is pH important for enzymes to function?

A

Several amino acids possess ionizable R groups that change charge depending on pH

114
Q

What is a cofactor?

A

An associative additional molecule for an enzyme to run

115
Q

What is a coenzyme?

A

When the cofactor is an organic molecule

116
Q

How are enzyme regulated by proteolytic cleavage?

A

Enzymes synthesized in inactive forms at are then activated by protease cleavage

117
Q

How are enzymes regulated by covalent modification?

A

Different groups covalently attached them which can regulate their activity

118
Q

What is the most common example of covalent modification

A

Phosphoryl group from ATP by a protein kinase to the hydroxyl of serine, threonine or tyrosine

119
Q

How does protein phophorylases does its work?

A

Uses free-floating inorganic phosphate in the cell

120
Q

How can protein phosphorylation be reversed?

A

By a protein phosphatase

121
Q

How are enzymes regulated by association with other polypeptides?

A

Some enzymes have catalytic activity in one polypeptide subunit that is regulated by association with a separate regulatory subunit

MCAT BIOCHEMISTRY FLASHCARDS (2 decks)

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