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MCAT Biochemistry > Chapter 1: Amino Acids, Peptides, and Proteins > Flashcards

Chapter 1: Amino Acids, Peptides, and Proteins Flashcards

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MCAT flashcards
1
Q

Amino Acid Structure

A

-Four substituents attached to central alpha carbon

  • Four substituents:
    1. Amino group (-NH2)
    2. Carboxylic acid group (-COOH)
    3. Hydrogen
    4. Unique “R” or side chain group (specific to each AA) -> Determines chemical properties and their functions
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2
Q

Proteinogenic Amino Acids

A

20 amino acids encoded by the human genetic code

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3
Q

Are amino acids chiral or achiral?

A

Chiral: Optically active

Exception: Glycine which is achiral

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4
Q

Which is amino acids are used in eukaryotes, L-amino acids or D-amino acids?

A

L-amino acids

-NH2 group is on the left side

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5
Q

What is the absolute configuration of amino acids?

A

(S) configuration

Exception: Cysteine is (R) configuration

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6
Q

Nonpolar Amino Acids

A
  1. Glycine (Gly, G)
  2. Alanine (Ala, A)
  3. Valine (Val, V)
  4. Leucine (Leu, L)
  5. Isoleucine (Ile, I)
  6. Methionine (Met, M)
  7. Proline (Pro, P) (Amino nitrogen becomes part of the
    side chain)
  8. Phenylalanine (Phe, F)
  9. Tryptophan (Trp, W)

Mneumonic: GAVaLIMP PT

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7
Q

Polar, Uncharged Amino Acids

A
  1. Serine (Ser, S)
  2. Threonine (Thr, T)
  3. Cysteine (Cys, C)
  4. Tyrosine (Tyr, Y)
  5. Asparagine (Asn, N)
  6. Glutamine (Gln, Q)

Mneumonic: SomeTimes Cats Try A Growl

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8
Q

Acidic, Negatively Charged Amino Acids

A
  1. Aspartic Acid (Asp, D)
  2. Glutamic Acid (Glu, E)

Mneumonic: A Good

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9
Q

Basic, Positively Charged Amino Acids

A
  1. Lysine (Lys, K)
  2. Arginine (Arg, R)
  3. Histidine (His, H)

Mneumonic: Lawyer Aims High

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10
Q

Aromatic Amino Acids

A
  1. Phenylalanine
  2. Tryptophan
  3. Tyrosine
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11
Q

pKa of COOH group

A

pKa = 2

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12
Q

pKa of NH2 group

A

pKa = 9-10

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13
Q

Isoelectric Point (pI) of Non Polar and Polar, Uncharged Amino Acids

A

pI = 5-6

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14
Q

pKa and pI for Negatively Charged Amino Acid

A 
1. Aspartic Acid
pKa (-NH2) = 2
pKa (-COOH) = 9-10
pKa3 = 3.7
pI = 2.8
2. Glutamic Acid
pKa (-NH2) = 2
pKa (-COOH) = 9-10
pKa3 = 4.3
pI = 3.2
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15
Q

pKa and pI for Positively Charged Amino Acid

A 
1. Lysine
pKa (-NH2) = 2
pKa (-COOH) = 9-10
pKa3 = 10.5
pI = 9.7
2. Arginine
pKa (-NH2) = 2
pKa (-COOH) = 9-10
pKa3 = 12.5
pI = 10.7
3. Histidine
pKa (-NH2) = 2
pKa (-COOH) = 9-10
pKa3 = 6.00
pI = 7.59
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16
Q

Hydrophobic Amino Acids

A 
Alanine
Valine
Leucine
Isoleucine
Phenylalanine
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17
Q

Essential Amino Acids

A 
Valine
Histidine 
Methionine
Isoleucine
Leucine
Lysine
Tryptophan
Threonine
Phenylalanine

Mneumonic: VH MILK WTF

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18
Q

Where can hydrophobic AAs be found?

A

On the interior of proteins

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19
Q

Where can hydrophilic AAs be found?

A

On the surface of proteins

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20
Q

Does the amino and carboxylic acid group need to be bonded to the same alpha carbon in an AA?

A

No.

Gamma-aminobutyric acid (GABA) is an AA where amino group is on gamma carbon from carboxyl group.

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21
Q

Is every amino acid specified by a codon in the genetic code?

A

No.

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22
Q

Is every amino acid incorporated into proteins?

A

No.

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23
Q

What is an example of an amino acid that is not specified by a codon in the genetic code, and is not incorporated in proteins?

A

Ornithine

*Ornithine is an urea cycle intermediate.

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24
Q

Which amino acid is optically inactive or achiral?

A

Glycine

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25
Q

Which amino acid does NOT have a (S) configuration?

A

Cysteine

  • The -CH2SH group takes higher priority than the carboxylic acid group.
  • Cysteine has (R) configuration.
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26
Q

What is the smallest AA?

A

Glycine

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27
Q

What effect does proline have?

A

It has constraints on flexibility.

It has limits on secondary structure.

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28
Q

Aspartate

A

Anion of Aspartic Acid

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29
Q

Glutamate

A

Anion of Glutamic Acid

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30
Q

Which amino acids have alkyl side chains?

A

Alanine, Valine, Leucine, and Isoleucine

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31
Q

What is the smallest aromatic side chain?

A

Phenylalanine

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32
Q

Which aromatic side chain is polar?

A

Tyrosine

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33
Q

Does the amide nitrogens in asparagine and glutamine, gain or lose protons with changes in pH?

A

NO

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34
Q

What is AA has a thiol (-SH) group?

A

Cysteine

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35
Q

Which bond is stronger, O-H or S-H?

A
  • O-H bond is stronger

* S-H bond is weaker and more prone to oxidation.

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36
Q

What type of bonds form between 2 cysteine AAs?

A

Disulfide bonds

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37
Q

What form of acidic AAs exist in cells?

A

The anion or deprotonated form exists in cells.

*Applies to other molecules.

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38
Q

What AAs are hydrophilic?

A 
Serine
Threonine
Asparagine
Glutamine
Aspartic Acid
Glutamic Acid
Lysine
Arginine
Histidine
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39
Q

Glucogenic AAs

A

AA that can be converted into glucose via gluconeogenesis

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40
Q

Which AAs are glucogenic?

A 
Alanine 
Arginine
Asparagine
Aspartic Acid
Cysteine
Glutamine
Glutamic Acid
Glycine
Histidine
Methionine 
Proline
Serine
Valine
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41
Q

Ketogenic AAs

A

An AA that can be degraded directly into acetyl-coA

*Acetyl-coA is a precursor of ketone bodies

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42
Q

Which AAs are ketogenic?

A

Leucine

Lysine

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43
Q

Which AAs are ketogenic and glucogenic?

A 
Phenylalanine
Isoleucine
Threonine
Tryptophan
Tyrosine

Mneumonic: PITTT

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44
Q

Amphoteric Species

A
  • Can either accept or donate proton.
  • How they react depends on the pH of the environment.
  • Can act as a base or acid.
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45
Q

Bronsted-Lowry Acid

A

Species that donates H+

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46
Q

Bronsted-Lowry Base

A

Species that accepts H+

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47
Q

What happens to ionizable groups at a low pH, acidic conditions?

A

Groups gets protonated

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48
Q

What happens to ionizable groups at a high pH, basic conditions?

A

Groups gets deprotonated

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49
Q

pKa

A

[HA] = [A-]

[protonated version of ionizable group] = [deprotonated version of ionizable group]

*half of species deprotonated

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50
Q

Under what conditions are the majority of the species protonated?

A

pH < pKa

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51
Q

Under what conditions are the majority of the species deprotonated?

A

pH > pKa

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52
Q

What is physiological pH?

A

7.4

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53
Q

Zwitterion

A
  • Dipolar ions that have a (+) and a (-) charge

* Overall charge would be electrically neutral

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54
Q

At very acidic pH, AAs tend to be

A

(+) charged

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55
Q

At very basic pH, AAs tend to be

A

(-) charged

56
Q

When does solution act as a buffer in terms of pH?

A

When pH of soln. = pKa of solute

57
Q

Isoelectric point (pI)

A

pH at which all molecules are electrically neutral/exist as zwitterions

58
Q

pI (neutral AA)

A

1/2 * [pKa (NH2) + pKa (COOH)]

59
Q

pI of AA with non-ionizable chains

A

approximately 6

60
Q

What are neutral molecules sensitive to?

A
  • They are sensitive to pH changes.

* Curve is nearly vertical at pI

61
Q

What is the pI of AAs with acidic side chains?

A

pI < 6

62
Q

What is the pI of AAs with basic side chains?

A

pI > 6

63
Q

pI (acidic AA)

A

1/2 [pKa (R group) + pKa (COOH)]

64
Q

pI (basic AA)

A

1/2 [pKa (NH2) + pKA (R group)]

65
Q

Peptides

A

Composed of AA subunits

66
Q

Residues

A

AA subunit

67
Q

Dipeptide

A

Consists of 2 AA residues

68
Q

Tripeptides

A

Consists of 3 AA residues

69
Q

Oligopeptides

A

Relatively small peptides of up to 20 residues

70
Q

Polypeptides

A

Larger peptides of more than 20 residues

71
Q

Peptide Bonds

A
  • An amide bond that joins 2 AA resides together

* Forms between carboxyl group of 1 AA and amino group of another AA via loss of H2O

72
Q

What type of rxn is peptide formation?

A

Dehydration or condensation rxn (removal of H2O)

73
Q

What functional group is a peptide bond?

A

Amide

74
Q

Which group is the nucleophile in peptide bond formation?

A

Amino group

75
Q

Which group is the electrophile in peptide bond formation?

A

Carbonyl carbon of Carboxyl group

76
Q

Can the peptide bond rotate?

A

Bond rotation is restricted because of partial double bond character. Has delocalizable pi e-

77
Q

How are AAs written?

A

Written from N-terminus to C-terminus

78
Q

How can amide bonds be broken?

A

*They can be hydrolyzed using acid or base catalysis.

OR

*Via hydrolytic enzymes

79
Q

Hydrolysis of Peptide Bond

A
  • Amide bond breaks apart
  • Hydrogen added to amide nitrogen
  • -OH group added to carbonyl carbon
80
Q

Proteins

A

Polypeptides that range from a few AAs in length to up to thousands of AAs.

81
Q

What are the levels of protein structure?

A

Primary
Secondary
Tertiary
Quaternary

82
Q

Primary Structure of Protein

A
  • Linear arrangement of amino acids

- Written from N-terminus (amino group) to C-terminus (carboxyl group)

83
Q

What stabilizes the primary structure of a protein?

A

Covalent peptide bond between adjacent AAs

84
Q

Protein structure is energetically favorable or unfavorable?

A

It is most energetically favorable.

85
Q

Sequencing

A
  • Determines the primary structure of a protein

- DNA or protein can be used for sequencing

86
Q

Secondary Structure of Protein

A

-Local structure of neighboring AAs.

87
Q

What bond is involved in the secondary structure of proteins?

A

Hydrogen bonds between nearby AAs

88
Q

What are the 2 most common secondary structures?

A
  1. Alpha-helix

2. Beta-pleated sheet

89
Q

What stabilizes the alpha-helices and beta-pleated sheets?

A

-Formation of intramolecular hydrogen bonds between different residues.

90
Q

Alpha-Helix

A
  • Rodlike structure in which the peptide chain coils CLOCKWISE around a central axis.
  • Hydrogen bonding between a carbonyl oxygen atom and an amide hydrogen atom 4 residues down the chain.
  • R groups point away from the helix core
91
Q

What protein structure does the alpha-helix play a major role in?

A

Keratin

92
Q

What is keratin?

A

A fibrous structural protein found in human skin, hair, and fingernails.

93
Q

Beta-Pleated Sheet

A
  • Can be parallel or anti-parallel
  • Hydrogen bonding between carbonyl oxygen of one chain and amide hydrogen of another adjacent chain
  • R groups above and below plane
  • Pleated or rippled shape
94
Q

What protein structure does the beta-pleated sheet play a role in?

A

Fibroin

95
Q

Fibroin

A

Primary protein component of silk fibers

96
Q

What role does Proline play in secondary structure?

A
  • Introduces a kink in the peptide chain when in the middle of an alpha-helix
  • Often found in the turns between the chains of a beta-pleated sheet
  • Often found as the residue at the start of an alpha-helix
97
Q

What categories can proteins be divided into?

A
  1. Fibrous

2. Globular

98
Q

Fibrous proteins

A
  • Structures that resemble sheets or long strands

- Ex: collagen

99
Q

Globular proteins

A
  • Tend to be spherical

- Ex: myosin

100
Q

What factors cause the shape of fibrous and globular proteins?

A

Tertiary and quaternary structures of protein structures.

101
Q

What levels of protein structure result in protein folding?

A

Tertiary and Quarternary Structures of Proteins

102
Q

Tertiary Structure

A

-3-dimensional shape of a protein

103
Q

What determines tertiary structure?

A
  • Hydrophobic and hydrophilic interactions between R groups of AAs.
  • Hydrogen bonding
  • Acid-Base Interactions
104
Q

Where are the hydrophobic residues mostly located?

A
  • They are located on the interior of proteins.

- It reduces its proximity to H2O.

105
Q

Where are the hydrophilic residues mostly located?

A

-They are located on the surface of proteins

106
Q

What further stabilizes the interior of proteins?

A
  • Electrostatic interactions between hydrophilic N-H + C=O bonds and the hydrophobic residues
  • Hydrogen bonding
107
Q

What is created as a result of acid-base interactions between R groups in tertiary structure of proteins?

A

Salt Bridges

108
Q

What is an example of a component involved in tertiary structures?

A

Disulfide Bonds

109
Q

Disulfide Bonds

A
  • Bond that forms between 2 cysteine molecules that are oxidized to form cystine.
  • Involves the loss of 2 protons and 2 electrons
110
Q

Molten globules

A

Intermediate states in tertiary structures

111
Q

Denaturation

A
  • When a protein loses its tertiary structure or three-dimensional structure
  • Loss of function results
112
Q

Why do hydrophobic residues reside on the interior and hydrophilic residues on the surface?

A

Entropy

113
Q

Would hydrophobic residues in aqueous solutions be energetically favorable or unfavorable?

A

Energetically unfavorable

delta S < 0 : increasing order, decreasing order

114
Q

Would hydrophilic residues in aqueous solutions be energetically favorable or unfavorable?

A
  • Energetically favorable
  • Allows H2O molecules more latitude in their positioning

delta S > 0: decreasing order, increasing entropy

115
Q

What would happen if hydrophobic residues are placed in an aqueous solution?

A

Solvation layer forms

116
Q

What position of residues provides maximum stability?

A

Hydrophilic: toward H2O
Hydrophobic: away H2O

117
Q

Does all proteins have primary structure?

A

Yes

118
Q

Does all proteins have secondary structure?

A

Yes

119
Q

Does all proteins have tertiary structure?

A

Yes

120
Q

Does all proteins have quaternary structure?

A

No

121
Q

Quarternary Structures

A

-Only in proteins with multiple polypeptide
chains
-Is an aggregate of smaller globular peptides, or subunits
-Represents the functional form of the protein

122
Q

What examples of proteins have quaternary structures?

A

Hemoglobin and immunoglobulins

123
Q

How many subunits does hemoglobin have?

A

4 subunits

124
Q

What purposes do quarternary structures serve?

A
  1. Provides more stability by further reducing the surface area of the protein complex
  2. Can reduce the amount of DNA needed to encode the protein complex
  3. Can bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction
  4. Can induce cooperativity and allosteric effects
125
Q

Cooperativity

A
  • Involves multiple subunits
  • When one subunit undergoes conformational or structural changes, it can either enhance or reduce the activity of the other subunits
126
Q

Can denatured proteins catalyze reactions?

A

No, they CAN NOT,

127
Q

What are the 2 main causes of denaturation?

A

Heat and solutes

128
Q

How does increase in temperature or heat cause denaturation?

A
  • Temperature increases, average KE increases
  • Increase in average KE allows overcoming of hydrophobic interactions that hold protein together.
  • This causes protein to unfold
129
Q

What is an example of a solute that unfolds protein?

A

Urea and SDS (sodium dodecyl sulfate or sodium lauryl sulfate)

130
Q

How does urea cause proteins to denature?

A
  • They directly interfere with the forces that hold the protein together.
  • They break disulfide bridges in which cystine is reduced to 2 cysteine residues.
  • They can also overcome hydrogen bonds and other side chain interactions that hold alpha-helices and beta-pleated sheets intact.
131
Q

Conjugated Proteins

A

Derives part of their function from prosthetic groups.

132
Q

Prosthetic groups

A
  • Covalently attached molecules to proteins
  • Can be organic molecules (i.e. vitamins) or metal ions (i.e. iron)
  • Major role in determining function of their respective proteins
133
Q

Heme

A
  • A prosthetic group for each hemoglobin subunit.
  • Contains an iron atom in the core
  • Binds to and carries oxygen
134
Q

Denaturation

A
  • Protein loses its three-dimensional structure

* Thus loses its function

135
Q

Is denaturation reversible or irreversible?

A
  • Often it is irreversible

* Sometimes it is reversible

136
Q

How does SDS denature proteins?

A

Can solubilize proteins by disrupting non-covalent bonds

MCAT Biochemistry (7 decks)

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