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Biochem Exam 1 > Chapter 5 - Amino Acids and Proteins > Flashcards

Chapter 5 - Amino Acids and Proteins Flashcards

1
Q

Describe the general structure of an amino acid.

A

Alpha Carbon bonded to a carboxyl group (COO-), and amine group (most commonly primary:NH3+), hydrogen atom, and an R side chain

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2
Q

Why is the middle carbon of an amino acid assigned as “alpha” carbon?

A

It’s the carbon directly adjacent to the carboxyl group

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3
Q

The alpha carbon is chiral in all 20 amino acids except for 1. Which one?

A

Glycine

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4
Q

Virtually all amino acids are present in the D or L form??

A

L

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5
Q

What are the acidic amino acids?

A

Aspartate (Asp, D), glutamate (Glu,E)

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6
Q

Which are the basic amino acids?

A

Lysine, arginine, histidine

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7
Q

Which amino acid can act both as an acid AND a base?

A

Histidine

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8
Q

What are the 3 amino acids with hydroxyl groups? Which is primary, which is secondary, and which is aromatic?

A

Primary hydroxyl - Serine
Secondary hydroxyl-Threonine
Aromatic hydroxyl - Tyrosine

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9
Q

When going from serine to threonine to tyrosine, do rates of dephosphorylation increase or decrease?

A

Increase

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10
Q

Are primary, secondary or tertiary alcohols more reactive?

A

Tertiary is the most reactive

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11
Q

Sulfur appears in 2 amino acids. Which ones and explain how they are incorporated into the structure.

A

Cysteine - sulfhydryl
Methionine - thioether

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12
Q

What is a thioether?

A

S bonded to 2 R groups

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13
Q

What is a sulfhydryl?

A

S bonded to an H and an R group

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14
Q

Why is Sulfur considered a SOFT nucleophile?

A

Its valence electrons are more shielded and distant from the nucleus. Thus, it will readily reverse its nucleophilic additions

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15
Q

What is significant about 2 cysteine molecules interacting in the protein structure?

A

-HS and -SH can form a DISULFIDE BRIDGE -S-S-.
This further stabilizes protein structure

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16
Q

Why do alterations in pH affect amino acids??

A

Changes in pH affect the charges of the dissociable acid and base groups.

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17
Q

At a minimum, how many dissociable groups will an amino acid have and what are they?

A

2 - Carboxyl group is a weak acid and will lose its H, NH2 (amine) is a base and will accept a proton

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18
Q

How many common amino acids are there that are used as the building blocks of proteins?

A

20

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19
Q

How many amino acids have an L conformation?

A

19 - Glycine is neither not chiral

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20
Q

What are the 2 acidic amino acids??

A

Aspartate (Asp,D)
Glutamate (Glu, E)

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21
Q

Which 2 amino acids contain sulfur in the side chain??

A

Methionine (Met,M)
Cysteine (Cys, C)

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22
Q

What is the largest amino acid??

A

Tryptophan

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23
Q

Which 3 amino acids can be an O glycosylation site?? (Oxygen attached to sugar)

A

Serine, Threonine, tyrosine

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24
Q

Which is more reactive to N glycosylation - R or Q??

A

R is more reactive. Arginine is a base

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25
Q

Which are the 3 aromatic amino acids??

A

Phenylalanine (phe,F)
Tyrosine (tyr, y)
Tryptophan (trp, W)

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26
Q

Lysine gives ____plateaus when titrated. Why??

A

3 plateaus. It has 3 polarizable groups

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27
Q

What are the 3 base amino acids??

A

Lysine (Lys,K)
Histidine (His,H)
Arginine (Arg, R)

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28
Q

What could be the precursor of dopamine??

A

Tyrosine

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29
Q

What is the function of a disulfide bond in a protein??

A

Stabilizes protein structure

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30
Q

primary structure determines _________structure

A

3D

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31
Q

What are the 3 things that make up the secondary structure of a protein

A

Alpha helix
Beta sheet
Beta turns

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32
Q

Most proteins are ______soluble

A

water

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33
Q

Proteins embedded in the cell membrane are _______soluble

A

lipid

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34
Q

Is the main chain or side chain involved in Hydrogen bonding in alpha helix/beta sheet?

A

ALWAYS main chain

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35
Q

Since side chains do not engage in Hydrogen bonding, what is their role in secondary structure formation?

A

They might prevent it from forming. They can clash and prevent H bonds if the side chain is too big (ex: tryptophan)

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36
Q

What 4 intermolecular forces are involved in folding to form the 3D structure?

A
  1. Disulfide bond (covalent)
  2. Salt bonds
  3. Hydrogen bonds
  4. Van der Waals forces
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37
Q

Among the 4 intermolecular forces that fold a protein into its 3D structure, which is the strongest??

A

Disulfide bridge. The other forces are not covalent

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38
Q

Does protein folding involve absorbing or releasing heat????

A

releasing. folded structure is more stable (less energy)

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39
Q

Protein denaturation involves the _____ of heat

A

absorption

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40
Q

The enzyme Rnase can be unfolded by heating. When the solution is cooled slowly, the enzyme regains its function. What does this suggest??

A

Folded protein is at a low energy state
Primary structure determines 3D structure

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41
Q

Which amino acid has a sulfhydrl (SH) functional grouo?

A

Cysteine

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42
Q

Which 3 amino acids have hydroxyl groups?

A

Tyrosine (Tyr, Y)
Serine (Ser,S)
Threonine (Thr, T)

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43
Q

What is the most reactive amino acid with a hydroxyl group?

A

Tyrosine

44
Q

What are Zwitterions??

A

Molecule that has 2 charged groups but a net charge of zero

45
Q

Most amino acids are _______at a physiological pH

A

zwitterions

46
Q

Which has a better chance at penetrating the cell membrane?? COO- or COOH

A

COOH

47
Q

What is isoelectric point??

A

pH at which the zwitterion has exactly a zero charge

48
Q

How do we determine pI? (isoelectric point)

A

average the 2pka’s

49
Q

How is the peptide bond linked?

A

alpha amine of 1 amino acid linked by dehydration synthesis to alpha carboxyl group of another amino acid

50
Q

What 2 things do we need to input before forming a peptide bond?

A

energy (ATP) and an enzyme

51
Q

Amide bond in an amino acid is commonly referred to as a ___________

A

peptide bond

52
Q

Which is on the left side?? N-terminus or C-terminus?

A

N terminus on the left, C terminus on the right (both carry a charge)

53
Q

What is the amide (peptide) bond?

A

C-N

54
Q

What is another name for N-terminus?

A

Amino

55
Q

What is another name for C-terminus?

A

Carboxyl

56
Q

What exists at the peptide bond which makes it very stable?

A

Delocalization (resonance) between O,C,N

57
Q

Peptide bonds are more stable than _______

A

esters

58
Q

C-N has partial _______ character. Why?

A

C-N has partial double bond character due to resonance. They can’t freely rotate. Restricts 3D arrangement

59
Q

Amino acids start being numbered at the __________side

A

N-terminus

60
Q

Short chains have _____or less amino acids. They’re called ________

A

short chains have 25 or less amino acids. They’re called peptides

61
Q

What is a LINEAR peptide that causes vasoconstriction and increased blood pressure?

A

Angiotensin II

62
Q

2 cysteine molecules can form a _____bond. In which peptide does this occur??

A

can form a disulfide bond. occurs in vasopressin

63
Q

Short peptides are often utilized as ______

A

hormones

64
Q

Longer chains with ____or more amino acids are no longer called peptides, but _______

A

25 or more, proteins

65
Q

Proteins can be broken down into smaller pieces by _______. Do they require ATP?

A

proteases,no

66
Q

proteases break peptide bonds through….?

A

Hydrolysis - addition of water

67
Q

What is the primary structure of a protein?

A

SEQUENCE and IDENTITY of amino acids in a linear protein chain

68
Q

What is the secondary structure of a protein?

A

Regular, repeating structural element formed when a segment folds into 3D shape. (alpha helix,beta sheet)

69
Q

What is the tertiary structure of a protein?

A

The entire 3D arrangement or conformation

70
Q

Most proteins function in their ______structure

A

tertiary

71
Q

What is the quaternary structure?

A

3D arrangement of multi subunit protein chains that associate NONCOVALENTLY

72
Q

When is a protein in its lowest energy state?

A

in its 3D structure

73
Q

What is the function of random coils?? What structure are they categorized under?

A

random coils link secondary structures together.
THEY DO NOT BELONG TO A STRUCTURE

74
Q

Alpha helices are joined by

A

N-O hydrogen bonds

75
Q

The inner core of an alpha helix is _______

A

hydrophobic

76
Q

Water solubility is determined by ____groups

A

R

77
Q

Which 2 properties of amino acids PERMIT helix formation??

A

Hydrophobic amino acids
Side chains have ISOLATED charges

78
Q

Which property of amino acids PREVENTS helix formation?

A

Neighboring charges (electrical repulsion)

79
Q

What are the 2 different alignments of beta pleated sheets?

A

parallel and antiparallel

80
Q

What are beta sheets stabilized by?

A

Hydrogen bonds

81
Q

Do amino acids hydrogen bond at the turn?

A

NO

82
Q

Domains exist between _______ and ______levels of structure

A

secondary and tertiary

83
Q

What is a domain?

A

a combination of secondary structural elements that has a specific finction

84
Q

What is an example of a domain?

A

binding pocket in an enzyme

85
Q

The core of an alpha helix is ________. Why?

A

Hydrophobic because there are already numerous hydrogen bonds between N and O , leaving nothing to interact with water

86
Q

What are helix breakers??

A

amino acids with neighboring charges causing electrical repulsion, preventing alpha helices from forming

87
Q

Domains often correspond to a certain ________

A

function

88
Q

What are 2 names for domain structure?

A

motif, supersecondary structure

89
Q

what is a prosthetic group

A

a small molecule which is bound to a protein to assist its function

90
Q

what is an example of a prosthetic group

A

heme

91
Q

explain the structure of heme

A

4 linked pyrrole rings each with a nitrogen attached to a central fe2+. fe2+ has a coordination number of 6

92
Q

what 6 things is fe2+ bound to

A

4 nitrogen, 1 histidine residue of myoglobin. 6th is either occupied by oxygen (oxygen bound myoglobin) or unoccupied in free myoglobin

93
Q

which binds oxygen more avidly??

A

myoglobin

94
Q

myoglobin provided oxygen for ____use when the concentration is very ____.

A

intercellular, low. binds more tightly

95
Q

what is the bohr effect?

A

diminished binding of oxygen to hemoglobin in response to an increase in concentration of protons

96
Q

protons _____the binding of oxygen to hemoglobin and shift the curve to the ____

A

decrease, right

97
Q

the oxygen saturation curve for hemoglobin is a ___shaped curve

A

s

98
Q

in order to purify a protein what must happen first?

A

must be extracted from its natural environment

99
Q

what is an assay

A

specific measure of a protein. must be easy to perform

100
Q

what are some measures taken to prevent denaturation during extraction and purification?

A

cold room, buffers, inclusion of protease inhibitors to prevent hydrolysis, reagents to prevent oxidation of cysteine side groups

101
Q

the methods of separation of molecules are based on what 3 differences?

A

solubility
size
charge

102
Q

the main purification is usually achieved by a form of _____

A

chromatography

103
Q

what is chromatography?

A

separation of components due to their different affinities towards 2 distinct phases - mobile phase and stationary phase

104
Q

what is affinity chromatography?

A

attaching a molecule to the stationary phase known to strongly bind the protein

105
Q

what is electrophoresis?

A

form of chromatography in which the mobile phase is driven by an electrical field imposed by electrodes. used to IDENTIFY proteins present

106
Q

what do chaperones too?

A

they are proteins that assist and accelerate the process of folding

107
Q

name 3 analysis methods applied to proteins

A

NMR, mass spectroscopy, X Ray crystallography

Biochem Exam 1 (7 decks)

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