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Biochem > Lecture 2 > Flashcards

Lecture 2 Flashcards

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1
Q

What is the protein structure hierarchy?

A

Primary -> Secondary -> Tertiary -> Quartenary

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2
Q

What is the primary structure of protein structure?

A

The amino acid sequence of the peptide or protein

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3
Q

What is the secondary structure of protein structure?

A

Folded structures with only local contacts

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4
Q

What is the tertiary structure of protein structure?

A

Global folding of secondary structure units

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5
Q

What is the quarternary structure of protein structure?

A

Multi-subunit assemblies

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6
Q

In what amino acids is the aC NOT an S stereocenter?

A

Glycine (achiral) and cysteine (R because S has higher priority than COOH)

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7
Q

What is an S stereocenter amino acid called (blank-Alanine)

A

L-Alanine, the other is D

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8
Q

At a neutral pH, when the carboxyl and amine is deprotonated, what is created?

A

A Zwitterion

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9
Q

For amino acids without ionizable sidechains, what is the Isoelectric Point (pI)?

A

pI = pKa1 + pKa2/2

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10
Q

What happens to an amino acid when pH = pI?

A

Amino acid does not migrate in electric field and solubility is poor

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11
Q

How do you find the pI for a ionizable sidechain?

A

pI = pK1 + pKr/2
pI is between the pK acidic and pK basic

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12
Q

What is the pKa of the N-terminus?

A

7.8

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13
Q

What is the pKa of the C-terminus?

A

4.0

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14
Q

What can amino acid modifications do?

A

Alter acid conformation, cross-link peptide strands, or change sidechain electrostatic character

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15
Q

How are peptides formed?

A

Amino acids being condensed (H2O eliminated)

Nucleophillic attack of an amine at an activated carbonyl

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16
Q

Peptides have ~_ amino acids, Proteins have ____ amino acids

A

20
thousands

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17
Q

What are the steps of Solid Phase Peptide Synthesis?

A
  1. Load resin to an amino acid attached to a Fmoc (protective group)
  2. Remove Fmoc
  3. With another amino acid, activate it with DCC
  4. Couple the two amino acids
  5. Repeat
  6. Remove Fmoc, cleave peptide from resin
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18
Q

How is DNA transcribed into mRNA?

A

RNA polymerase enzyme

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19
Q

How are amino acids placed on tRNA?

A

tRNA synthetase enzymes

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20
Q

How do ribosomes add amino acids to a chain?

A

Pairs codons in mRNA with anti-codons on tRNA

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21
Q

Can you rotate around the peptide bond? How about Calpha bonds?

A

No it is forbidden
Yes you can do those

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22
Q

What angle is phi referring to in a peptide backbone?

A

Dihedral angle between the two carbonyls

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23
Q

What angle is omega referring to in a peptide backbone?

A

Dihedral angle between the two nitrogens

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24
Q

What are the angles of omega and phi in a fully extended peptide?

A

Both 180

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25
What is a Ramachandran plot?
Distribution of phi and omega angles found in a protein, (omega y-axis, phi x-axis)
26
What makes certain phi and omega combinations favorable?
H-bonding interactions along the backbone and minimizing steric crowding
27
What is a peptide bond?
H-N-C=O
28
What can be used as a sidechain protection?
A t-Butyl on the OH of the amino acid to prevent it from being used as an electrophile
29
What are the approximate phi and omega angles of a-Helices?
Phi - 60 degrees Omega - 45 degrees
30
For a right-handed helix, how many residues are there per turn?
3.6 residues (5.4 angstroms)
31
Which residues should roughly align?
i and i+7
32
Can anything fit inside an a-Helix?
No it's too compact
33
Describe the net-dipole in an alpha helix
Positive dipole at the N-terminus, negative dipole at the C-terminus
34
Where would you often find negatively charged residues in an alpha helix?
Near the positive end of the helix dipole (N-terminus), this is called helix capping
35
Where would you often find positively charged residues in an alpha helix?
Near the negative end of the helix dipole (C-terminus), this is called helix capping
36
Do peptide bonds have a strong or weak dipole moment?
STRONG
37
Are all of the peptide bonds in the alpha helix in a similar or different orientation?
Similar
38
What causes the macroscopic dipole moment of the alpha helix?
Polarity of the amide bond, uncompensated H-bonds at the ends, and parallel alignment
39
What are strong helix formers? (amino acids)
Ala and Leu
40
What are strong helix breakers?
Pro (cannot rotate around N-Ca bond) and Gly (too flexible)
41
What are the two variations of a beta sheet?
Parallel and Antiparallel -> <- -> -> -> <-
42
What are the phi and omega angles of beta sheets?
Both ~135 degrees
43
Is there a regular relationship for backbone H-bonds in beta sheets?
no, its more distal
44
How many acids does it take to make a 180 degree turn in a beta sheet?
Four
45
How is a turn stabilized?
A hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence
46
What is a type 1 turn in a beta sheet?
180 degree turn with proline in the 2 position causing a kink in the ring 3 4 2 1
47
What is a type 2 turn in a beta sheet?
180 degree turn with glycine in the 3 position using its flexibility to stabilize the turn 3 4 2 1
48
Why are cis non-proline peptide bonds so rare?
So much steric hindrance
49
Why is there 6% cis proline peptide bonds vs 0.05% other cis peptide bonds? Why is it beneficial? Why does it happen?
Cis proline is very hard to switch back to trans so it can act as a switch Creating the cis conformation requires proline isomerases or external energy to create the configuration (cis configuration occurs in 6% of its occurrences in
50
Right alpha helices purely contain _ amino acids
L
51
How do proteins mechanically fold?
They keep folding until reach the lowest potential energy structure where it stays that way (remember the mariana trench diagram)
52
What bonds does urea break?
Disulfide bonds
53
In the case of ribonuclease A, what does exposing it to Urea and beta-mercaptoethanol do?
Fully denatures it
54
In the case of ribonuclease A, what does removing to Urea and beta-mercaptoethanol do to protein folding?
The protein refolds and the proper disulfide bonds form
55
What does the Anfinsen Dogma state?
Native protein structure is determined only by the protein's primary amino acid sequence
56
What are the exceptions that proteins reach their natural state on their own?
Some proteins need chaperone proteins and energy to be properly folded
57
What can happen if proteins partially misfold?
They can polymerize and form amyloid fibrils (plaques) that are toxic
58
For a reversible unfolding protein, what is the rate of going from native to denatured?
Equal
59
How can unfolding be accomplished?
Thermally or chemically
60
What are the conditions of reversible protein denaturation?
That folding is effectively a two state process with no intermediate, this means the curve should be identical from either direction
61
What is a van't Hoff Plot?
lnKu vs 1/T
62
What equation regarding dH and dS reflect a y=mx+b equation?
ln Ku = -dHu/RT + dSu/R x = 1/T m = -dHu/R b = dS/R
63
What are some protein folding motifs?
beta barrels Ca2+ binding loop beta-alpha-B loop a/beta barrel
64
What is a coiled coil? How is it formed?
Two alpha-helixes twisted together Formed by a left-handed twist of right handed helices
65
What is a parallel coiled coil? How about a anti-parallel coiled coil?
Parallel has their N terminuses together (CC and NN) Antiparallel has their N and C terminuses together instead (CN)
66
Why are coiled coils often referred to as leucine zippers?
First characterized coils had leucine-rich interfaces
67
What is the heptad repeat?
a - hydrophobic b - alanine c - alanine d - hydrophobic e - charged f - alanine g - charged
68
How do you pair heptad repeats?
A - D' D - A' Forms hydrophobic core G - E' E - G' Forms ion pairs with oppositely charged amino acids on opposing coil and establishes register of helices and parallel anti-parallel orientation
69
What is the parallel coiled-coil packing described as?
"Knobs into holes" packing The hydrophobic core runs straight up axis of major helix which is a superhelical axis
70
Proteins with molecular weights > ___ kDa are oligomers
100
71
How can oligomers arise?
Spontaneously and association stabilizes fold of individual subunits
72
Oligomers refer to the ____ structure of a protein
quartnary
73

Biochem (4 decks)

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