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1) Biochemistry I > Amino Acids, Peptides, and Proteins > Flashcards

Amino Acids, Peptides, and Proteins Flashcards

1
Q

What are the four different roles of proteins?

A

1) Catalysis
2) Transport
3) Structure
4) Motion

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2
Q

Does each cell make a similar or different repertoire of proteins?

A

Different

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3
Q

Define genome.

A

Refers to all the genes encoded in a cell’s DNA.

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4
Q

Define transcriptome.

A

Refers to complete RNA profile.

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5
Q

Define proteome. How do proteomes vary by tissue?

A

Refers to protein complement expressed by a cell.

ex: proteome of liver not the same as heart.

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6
Q

Subsets of proteins depend on what?

A

They are tissue dependant

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7
Q

How many genes do we have? And proteins?

A

30 000 genes

50 000-100 000 proteins

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8
Q

Define peptide.

A

Small protein containing 2-50 amino acids

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9
Q

Define polypeptide.

A

More than 50 amino acids

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10
Q

How many naturally occurring amino acids are there?

A

20

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11
Q

Name the three classes of protein.

A

1) Soluble Proteins
2) Membrane Proteins
3) Fibrous/Structural Proteins

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12
Q

What is the chemical composition of an amino acid?

A

Amino Group + Side Chain (R) + Carboxyl Group

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13
Q

Name two properties of amino acids.

A
  • Can function as buffers

- Capacity to polymerize

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14
Q

Define a chiral molecule.

A

Non-superimposable on its mirror image; possesses an asymmetric carbon center.

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15
Q

How do you achieve chirality?

A

If you attach 4 different groups to an alpha carbon

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16
Q

Which amino acid is the only non-chiral one?

A

Glycine (2 hydrogens)

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17
Q

Define enantiomers. Give an example of an enantiomer.

A

Non-superimposable mirror image.

Amino acids are enantiomers

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18
Q

Define racemization.

A

Conversion of an enantiomerically pure mixture into a mixture with more enantiomers.

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19
Q

Define a racemic mixture.

A

D and L configurations present in equal quantities.

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20
Q

How does racemization between L and D isomers occur? Is it fast?

A

Spontaneously

Reaching equilibrium is a VERY slow process

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21
Q

What is the most abundant configuration of amino acids?

A

CORN configuration (L configuration)

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22
Q

What biological compound can back convert?

A

Enzymes but ONLY in living cells (D to L)

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23
Q

How many essential amino acids are there?

A

8

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24
Q

Which two amino acids are considered essential for infants?

A

Arginine and HIstidine

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25
Q

Name the 5 classes of amino acids.

A

1) Non-polar, aliphatic
2) Aromatic
3) Polar, uncharged
4) Positively charged
5) Negatively charged

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26
Q

Which classes of amino acids are hydrophobic?

A

1) Non-polar, aliphatic

2) Aromatic

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27
Q

Which classes of amino acids are hydrophilic?

A

1) Polar, uncharged
2) Positively charged
3) Negatively charged

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28
Q

Which amino acid is referred to as a secondary amine? Why?

A

Proline, since it cycles back and reacts with the alpha amino group

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29
Q

Which group of amino acid has a strong ultraviolet light absorption properties?

A

Aromatic group

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30
Q

Which amino acid in the aromatic group does not have strong ultraviolet light properties? Why?

A

Phenylalanine, since it does not have conjugation

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31
Q

Which amino acid can be involved with covalent disulfide bonds?

A

Cysteine

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32
Q

What are cysteine bonds (disulfide bonds) critical for?

A

Controlling the structure of proteins when they are released outside the cell

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33
Q

Where do cysteine bonds occur?

A

In an oxidizing environment

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34
Q

Which amino acids are always positively charged under biological systems? Why?

A

Arginine and Lysine

Since they have high pKas

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35
Q

Which amino acid is not always positively charged under biological systems, but can be?

A

Histidine, pKa=6

Neutral at pKa>6, Positively charged at pKa

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36
Q

If you add a proton to Histidine, what becomes positively charged?

A

the N will undergo protonation

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37
Q

At neutral pH, the carboxyl group is ______ but the amino group is ______. The net charge is ___.

A

deprotonated, protonated, 0

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38
Q

At acidic pH, the carboxyl group is ______ but the amino acid is in its ______ form. The net charge is ___.

A

protonated, cationic, +1

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39
Q

At alkaline pH, the amino group is ______ but the amino acid is in its ______ form. The net charge is ___.

A

neutral, anionic, -1

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40
Q

Define Zwitterions.

A

Positive and negative ions that can act as either an acid or a base

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41
Q

Define isoelectric point.

A

pH where the net charge on the molecule is 0.

Occurs at 1 equivalence, no net charge

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42
Q

What is the equation to define the isoelectric point?

A

pI = (pK1 + pK2)/2

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43
Q

If it is an acidic amino acid, which range will the pI be in?

A

Acidic range

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44
Q

If it is a basic amino acid, which range will the pI be in?

A

Alkaline range

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45
Q

How do amino acids undergo polymerization?

A

In a head to tail fashion.

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46
Q

How are peptides formed? What does it result in?

A

By condensation, results in the loss of water

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47
Q

What is the primary structure of a protein?

A

The linear sequence of amino acids.

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48
Q

Where does the primary structure being? End?

A

Begin: free amino end (or N-terminal)
End: free carboxyl end (C-terminal)

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49
Q

What does the primary structure contain?

A

Information that allows 2nd and 3rd structure.

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50
Q

What character do peptide bonds display? Why?

A

Partial double bond character due to electron delocalization

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51
Q

What does the partial double bond character cause?

A

Restricts rotation around the peptide bond.

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52
Q

How do single, double, and peptide bond lengths differ?

A

Peptide bond lengths are right in between the two

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53
Q

Which type of peptide rotations are permitted? Which aren’t?

A

Permitted: rotation around bonds connected to the alpha carbon
Not permitted: rotation around the peptide bond

54
Q

The phi angle refers to which bond?

A

Amide nitrogen bond (N-C)

55
Q

The psi angle refers to which bond?

A

Carbonyl carbon bond (C-C)

56
Q

Which configuration is conformationally favorable? Why?

A

Trans since atoms can’t occupy the same space

57
Q

What angles can psi and phi angles never be? Why?

A

0 or 180 since atoms can’t occupy the same space

58
Q

Why is Proline conformationally unique? Why?

A

Since it switches between cis and trans configurations (second amine)

59
Q

What gives rise to secondary structure?

A

Phi and psi angles

60
Q

Name the three secondary structures.

A
  1. a-helix
  2. B-sheets
  3. B-turn
61
Q

What defines and stabilizes the secondary structure?

A
  • Hydrogen bonds between the main chain peptide groups

- R-chain helps stabilize as well

62
Q

What stabilizes the a-helix?

A

Intra-hellical hydrogen bonds

63
Q

What is the pitch of the a-helix per turn?

A

3.6

64
Q

What atoms are hydrogen bonded in an a-helix?

A

H-bond between the hydrogen atom attached to the electronegative nitrogen atom of a peptide linkage and the electronegative carbonyl oxygen atom

65
Q

Which amino acid likes to form helices? Which don’t?

A

Like: Alanine

Don’t like: Proline and Glycine

66
Q

How can R-groups affect the structure of a helix.

A

They will either stabilize (attraction) or destabilize (repulsion)

67
Q

How does pH influence the structure of a helix?

A

For ex, putting a protein into an acid will disrupt the hydrogen bonds (protonation) and cause the protein to unravel

68
Q

What is the driving force for proteins to fold?

A

Hydrophobic interactions

69
Q

Which hand is the most common helix

A

Right hand

70
Q

Name a biological molecule that has a left-handed helix.

A

Collagen

71
Q

Where is the - end on a helix? And _?

A

Carboxyl (-)

Amino (+)

72
Q

What’s the difference between parallel and antiparallel B-sheets?

A

Parallel: amino groups point in the same direction
Antiparallel: amino groups point in opposite directions

73
Q

What’s critical for antiparallel B-sheets?

A

To have a tight-turn to allow the protein strand to do an 180o turn

74
Q

Which type of B-sheet cannot be contiguous?

A

Parallel

75
Q

What does the Ramachandran plot dictate?

A

Protein structure is dictated by the phi and psi angles

76
Q

How many amino acids do B-Turns involve?

A

4 amino acids

77
Q

Where are proline and glycine situated on a B-turn?

A

Proline (2) Glycine (3)

78
Q

What is the function of the B-turn?

A

Allows the proteins to do an 180o turn

79
Q

What are the characteristics of spider silk?

A

Stronger than steel, stretches

80
Q

What is spider silk stabilized by?

A

Hydrogen bonds & Van der Waals interactions

81
Q

What amino acids are in high abundance in spider silk?

A

Glycine and Alanine

82
Q

What is the MAIN driving force of tertiary structure?

A

Bury hydrophobic interactions

83
Q

Are B-sheets flat? Why/Why not?

A

B-sheets are flat, but not completely planar because of angles (tend to have a twist)

84
Q

Name some favorable interactions in proteins.

A
  • Hydrophobic Effect
  • Hydrogen Bonds
  • Van der Waals Interactions
  • Electrostatic Interactions
  • Disulfide Bonds
85
Q

How is the tertiary structure of proteins held together?

A

Electrostatic interactions

86
Q

How does protein structure evolve?

A

To accommodate the environment

87
Q

Define homomeric.

A

Same subunits

88
Q

Define heteromeric.

A

Different subunits

89
Q

Define oligomeric.

A

More than one subunit (could be homo or hetero)

90
Q

Provide examples of how quaternary structures bind together.

A
  • Hydrophobic interactions
  • Hydrogen bonds
  • Disulfide bonds
91
Q

Describe the function of the Allosteric effect.

A
  • Easier to load and unload oxygen

- Allows to more tightly regulate the activity of an enzyme

92
Q

If there is a change in amino acid, which protein structure would it affect the most?

A

Quaternary

93
Q

Describe briefly the 4 levels of protein structure.

A

Primary: amino acid residues (important order of polymerization)
Secondary: a-Helix
Tertiary: polypeptide chains
Quaternary: assembled subunits

94
Q

For a generic amino acid, NH2CRHCOOH (uncharged), what would be the predominant form at:

a) pH=1
b) pH=7
c) pH=11

A

a) +NH2CRHCOOH
b) +NH2CRHCOOH-
c) NH2CRHCOOH-

95
Q

What determines how curly a human’s hair is?

A

Disulfide bonds

96
Q

What do disulfide bonds create?

A

Loops in the protein chain

97
Q

Do all proteins have quaternary structure? In what case?

A

No, exist for proteins that contain more than one polypeptide chain

98
Q

In a neutral solution, most amino acids exist as ____?

A

Zwitterions

99
Q

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

A

2x negative because of 2x carboxyl
1x positive because of amino
so -1

100
Q

What holds up tertiary structure?

A

Disulfide bridges and hydrophobic effects

101
Q

Which amino acids would be likely to be found in a transmembrane portion of the a-helix?

A

Amino acids with a hydrophobic side chain

102
Q

Which amino acid is likely to be found in high concentration in collagen?

A

Glycine, reduce steric hindrance

103
Q

Why can amino acids ionize?

A

Since both the carboxyl and amino groups (sometimes side chains as well) can ionize

104
Q

Why is glycine not optically active?

A

It does not have a D and L isomer, not chiral

105
Q

Which amino acid allows the most structural flexibility (least amount of steric hindrance)? Which the least?

A

Most: Glycine
Least: Proline

106
Q

What happens to an R-group when pH < pka? When pH pka?

A

pH smaller than pka: protonation

pH higher than pka: deprotonation

107
Q

Name the amino acids that are positively charged at physiological pH.

A

Lysine and arginine

Histidine (possibly, but low pKa)

108
Q

Name the amino acids that are part of the aromatic R group, hydrophobic and neutral at any pH

A

Phenylalanine and tryptophan

not tyrosine since it has an OH

109
Q

Name the amino acids that have saturated hydrocarbon R groups.

A

Alanine, valine, leucine, isoleucine

110
Q

Name the only amino acid having an R group with a pKa near 7.

A

Histidine

111
Q

Name the only amino acid with a substituted a-amino group.

A

Proline

112
Q

Why are all individual amino acids soluble in water but not all peptides are soluble?

A

Individual amino acids are zwitterions at physiological pHs

113
Q

What do the amino acids threonine and tyrosine have in common?

A

Both have an OH group (contributes to polarity and hydrogen bonding)

114
Q

What makes amino acid cysteine so important? Can methionine perform the same function?

A

Cysteine can form disulfide bridges to stabilize the structures of proteins, methionine cannot

115
Q

Are protein structures static?

A

No, they undergo changes in conformation

116
Q

Where do phi and psi angles occur?

A

In the peptide backbone

117
Q

How many residues per turn does an alpha helix have?

A

3.6 residues/turn

118
Q

The rise along the helical axis for each amino acid residue is ____?

A

Rise: 5.4/3.6 residues per turn = 1.5

119
Q

Where are the amino acid sidechains on an a-helix?

A

The amino-acid side-chains are on the outside of the helix, and point roughly “downward”

120
Q

Where are the R groups located in a B-sheet?

A

Opposite directions, either below or above the peptide chain (alternating)

121
Q

What noncovalent forces stabilize B-sheet structures?

A

Hydrogen bonds

122
Q

What is unusual about peptide bonds involving the nitrogen of proline in B turns?

A

It readily assumes the cis configuration, a form that is particularly amenable to a tight turn.

123
Q

How can we permanently wave someones hair?

A

1) Reduce disulfide bonds to seperate cysteines
2) Curl the hair with heat
3) Oxidize the hair to form new disulfide bonds with the curled formation

124
Q

What are the roles of soluble proteins (globular)?

A

Antibodies, enzymes, structural

125
Q

What are the roles of membrane proteins?

A

Hydrophobic proteins, transporters, receptors

126
Q

What are the roles of fibrous/structural proteins?

A

Keratin, muscles (myosin), spider webs (silk)

127
Q

How many pKa values does glycine have? It can act as a buffer in how many regions?

A
  • Two pKa values (carboxyl and amino group)

- Buffer in two regions

128
Q

What is the most likely charge of tyrosine at pH 7?

A

Neutral

129
Q

What is the probability of histidine to have a positive charge at ph=7? ph=6?

A

pH7: 10%
pH6: 50%
Very sensitive to pH change in the physiological range

130
Q

What is the phi angle between? Psi? Peptide bond?

A

Phi: N-Ca
Psi: Ca-C
Peptide bond: C-N

1) Biochemistry I (12 decks)

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