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Protein Structure & Function > Protein Structures > Flashcards

Protein Structures Flashcards

1
Q

What is the difference between positive and negative sense RNA?

A

Positive-sense viral RNA is similar to mRNA and thus can be immediately translated by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA polymerase before translation

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2
Q

What does 1HHO stand for?

A

Human Hemoglobin

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3
Q

What type of pKa does the carboxyl group have and what happens at ~7pH?

A

COOH/Coo- has low pKa ~2
Tends to deprotonate and become negatively charged at physiological pH

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4
Q

What type of pKa does the amino group have and what happens at ~7pH?

A

NH2/NH3+ has a high pKa ~9-10
Tends to protonate and become positively charged at physiological pH

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5
Q

What is a chiral center?

A

An atom that has 4 different groups bonded to it in such a manner that it has a non-superimposable mirror image

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6
Q

Define enantiomer

A

Aka stereoisomer have the same molecular formula and sequence of bonded atoms but differ in the way the atoms are arranged in space

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7
Q

What are the two enantiomers for each amino acid, and which is more common?

A

D and L forms

In proteins, the L form is predominantly used

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8
Q

What are the exceptions, where L-amino acids is not used?

A

Non-ribosomal system uses D-amino acid (Microbial peptides)
Post translational enzymatic conversion of L to D (Euk peptides/proteins)

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9
Q

What are the polar side chains?

A

Chains charged at pH7 or groups that can H bond
OH
SH
CO-NH (amide)
NH
COOH

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10
Q

What are the non-polar side chains?

A

Alkyl hydrophobic groups which cannot H bond

C-H
C-C
C-S-C

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11
Q

Describe electronegativities of atoms in non-polar groups

A

Low electronegativities = low difference

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12
Q

Define amphipathic

A

A molecular having both hydrophilic and hydrophobic

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13
Q

What are the two amphipathic amino acids?

A

Tryptophan and methionine = non-polar side chain

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14
Q

What are the 6 hydrophobic amino acids?

A

Alanine + Phenylalanine
Proline
Valine
Leucine + Isoleucine

All non-polar side chains

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15
Q

What is the charge of glycine?

A

Neutral
So counts as a non-polar side chain

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16
Q

Which amino acids with polar side-chains are amphipathic?

A

Threonine
Tyrosine
Lysine

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17
Q

Which amino acids with polar size chains are basic?

A

Arginine
Lysine
Histidine

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18
Q

Which amino acids with polar side chains are acidic?

A

Aspartate
Glutamate

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19
Q

Where are non-polar and polar amino acids found in a channel?

A

Non-polar tend to be located on the surface in contact with the membrane

Polar will line interior pores to great hydrophilic channels

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20
Q

What functions do serine & threonine do?

A

Phosphorylation
Glycosylation
Deprotonation -> nucleophilic catalysis

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21
Q

What are the 3 roles of cysteine and why?

A
  1. Nucleophilic catalysis
  2. Metal coordination
  3. S-S bonds

The first two because S has more shells than O/N so electrons are held weakly. This means Cys has a low pKa(8.6) so deprotonates.

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22
Q

What are engineered disulphide bonds used for?

A

To stabilize or eliminate protein dynamics

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23
Q

What bonding does Asparagine perform?

A

N-linked glycosylation

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24
Q

How is SARS-CoV-2 affected by varying pH?

A

Virus particles are assembled in their low pH vesicles
Once the virus makes contact with neutral pH outside the cell, the spike protein changes from closed conformation to open conformation

Important the timing it right, premature opening can cause spike protein to decay too early

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25
Q

Name the 3 aromatic amino acids

A

Phenylalanine
Tyrosine
Tryptophan

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26
Q

What are the two interactions aromatic amino acids do?

A

Pi-Pi interactions
Cation-Pi interactions

27
Q

What property does glycine give proteins?

A

Flexibility

28
Q

What property does proline give proteins?

A

Rigidity because of its very rigid side chains

29
Q

What property does methionine give proteins?

A

Ability to participate in enzymatic metal catalysis

30
Q

What property do aromatic amino acids give proteins?

A

Form gates in ion channels & transporters
UV light absorptions
Ligand binding via non-covalent interactions

31
Q

What property does tyrosine give proteins?

A

Regulation of protein and cellular functions via phosphorylation
Facilitates protein secretion, viral entry into cells & metal binding via sulfation

32
Q

What property does tryptophan have?

A

Largest side chain of all amino acids
Low frequency in proteins
Participates in electron transport (aromatic)
Fluorescent

33
Q

Define amino acid residues

A

Amino acids in the peptide bond/chain

34
Q

Define resonance and what role it plays in peptide bond

A

Resonance = delocalization of electron within a molecule
Resonance stabilizes the peptide bond

35
Q

What type of bond is a peptide bond?

A

Partial double bond

36
Q

Which conformation do peptide groups more commonly assume, and why?

A

Trans conformation = partly due to steric interference
Cis conformation is less stable than trans

37
Q

—– Secondary structure —–

A
38
Q

What restricts rotation freedom of a peptide bond?

A

Rotations around backbone bonds
Atomic steric clashes

39
Q

What atoms are in a Phi bond?

A

Cα-N

40
Q

What atoms are in a Psi bond?

A

Cα-C

41
Q

What conformation does a Phi angle of 0 make?

A

Cis conformation
N-H and Cα-R point in the same direction

So 180 degree angle = trans

42
Q

What is a Ramachandram diagram used for?

A

Plot sterically favourable combinations of Phi and Psi angles = to predict preferred secondary structures

43
Q

What are the exception in a Ramachandran diagram and why?

A

Glycine = has more regions because more flexible
Proline = has fewer regions because geometrically limited

44
Q

What is the pattern in a right-handed α-helix?

A

Carbonyl O of x amino acid
H bonds with amid H of x+4 amino acid

45
Q

RH α-helix radius?

A

~2.3 angstrom

46
Q

RH α-helix residues per turn?

A

3.6 (5.4 angstrom)

47
Q

RH α-helix phi and psi angles

A

-57
-47

48
Q

In globular proteins, what % of resides are in RH α-helix?

A

~30%

49
Q

Top 5 residues in α-helices and why?

A

M = methionine
A = alanine
R = arginine
K = lysine
L = leucine

Short side chains = produce less steric clashes

50
Q

Unfavourable residues in α-helices, and why?

A

Proline is a helix breaker cuz rigid
Glycine is too flexible

Polar side chains = Ser, Aspartate & Asparagine
Might form H bonds with backbone other than amide H

Beta-branch side chains = Thr, Val, Isoleucine
Favoured in beta-sheets because of branching

51
Q

Proline substitution in vaccine development

A

Proline’s rigid cyclic structure restricts flexibility locking it in a specific confirmation

This stabilises the prefusion confirmation of the antigen for vaccines

Reduces chances of proteins changing shape so makes vaccines more effective and safe

52
Q

Where is 3-10 helix found?

A

As a single turn at the beginning or end of α-helices (3% of proteins)

53
Q

Role of 3-10 helix?

A

Connecting secondary elements & fixing distortions formed within α-helix (by Proline***)

54
Q

Which is the tighter helix?

A

3-10 is tighter than α-helix

With 3.0 resides per turn instead of 3.6

55
Q

What type of β-strand are there?

A

Parallel and antiparallel

56
Q

Do β-strands appear in proteins?

A

No normally in their isolated form = they arrange into β-sheet

57
Q

In globular proteins, what % are β-sheets?

A

~20%

58
Q

Name 3 structural motifs using beta sheets

A

β-a-β motif
Twisted β-sheet (thioredoxin)
β-barrel

59
Q

What is the function of helices & sheets?

A

Compaction of polypeptide chain = keeps proteins soluble in dense cytoplasm

Reduce the cost of burying polar backbone groups = pair polar groups efficiently

60
Q

How does burying a peptide bond work? ***

A
61
Q

What is the function of β-turn(reverse turn) structure?

A

Usually connects anti-parallel b-strands

Allows peptide chain to reverse direction

62
Q

What is the difference between type I and type II β-turn?

A

Different dihedral angles

63
Q

Describe the bonding in beta-turn (reverse turn) structure

A

Carbonyl O (i ) is H bonded to
Amide H of residue i + 3

64
Q

What amino acids are most commonly found in reverse-turns?

A

Proline because of cyclic structure
Glycine because most sterically flexible

Both accommodate a kink

Protein Structure & Function (11 decks)

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