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BS2091 Biochemistry I: from genes to proteins > Amino acids and protein structure > Flashcards

Amino acids and protein structure Flashcards

1
Q

Describe the general structure of an alpha amino acid

A

C-H
N-H2: amine group
C-O2-H: carboxylic acid group
R: side chain/variable group

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2
Q

What are the charges on an alpha amino acid at pH 7?

A

Positive charge on N of the amine group

Negative charge across the O2 of the carboxylic acid group

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3
Q

What is the charge on a protonated alpha amino acid (i.e. below pH 5)?

A

Positive charge on N of the amine group

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4
Q

What form is an alpha amino acid in between pH 3 and pH 8?

A

Zwitterionic form

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5
Q

What is the charge on a deprotonated alpha amino acid (i.e. above pH 7)?

A

Negative charge across the O2 of the carboxylic acid group

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6
Q

Using ‘CO-R-(H)-N’ law, a clockwise CO-R-(H)-N is known as what type of isomer?

A

A D isomer

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7
Q

Using ‘CO-R-(H)-N’ law, an anticlockwise CO-R-(H)-N is known as what type of isomer?

A

An L isomer

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8
Q

What type of bond forms between 2 amino acids?

A

A peptide bond

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9
Q

How would we describe a C omega bond angle of 180 degrees?

A

Trans

Favoured

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10
Q

How would we describe a C omega bond angle of 0 degrees?

A

Cis

Disfavoured

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11
Q

Is the change from free rotation about the C-N bond to a planar C-N bond reversible or irreversible?

A

Reversible

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12
Q

Describe the C-N bond when there is free rotation

A

Single bond, no charge

Double bond on C=O

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13
Q

Describe the C-N bond when it is planar

A

Double bond, negative charge on the O, positive charge on the N
(Single bond on C-O)

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14
Q

Name some important bonds/interactions in protein structure in order of decreasing strength

A 
Covalent bonds
Ionic (electrostatic) interactions
Hydrogen bonds
Hydrophobic interactions
Van der Waals forces
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15
Q

Define covalent bonds

A

Strong bond, arising from the sharing of one or more pairs of electrons between atoms

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16
Q

Define ionic (electrostatic) interactions

A

Between 2 charged groups

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17
Q

Define hydrogen bonds

A

Sharing of a hydrogen atom between 2 other atoms (= hydrogen donor and acceptor)

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18
Q

Define hydrophobic interactions

A

Tendency for ‘water-hating’ molecules to cluster together to exclude water

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19
Q

Define van der Waals forces

A

Non-specific attractive force when 2 atoms are in close proximity (0.3-0.4nm)

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20
Q

Give an example of where a disulphide bond could form

A

Between 2 cysteines

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21
Q

What type of reaction forms a disulphide bond?

A

Oxidation reaction

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22
Q

What type of reaction breaks a disulphide bond?

A

Reduction reaction

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23
Q

What is released when a disulphide bond forms between 2 cysteines?

A

2H+ ions

2e-

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24
Q

Use chemical equations to demonstrate how an ionic interaction works

A

HA + H2O A- + H3O+

HA+ A + H3O+

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25
Q

What is the equation for Ka?

A

Ka = ([A-][H3O+]) / ([HA])
OR
Ka = ([A][H3O+]) / ([HA+])

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26
Q

What is the equation for pKa?

A

pKa = -log(Ka)

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27
Q

What is the equation for pH?

A

pH = -log(H3O+)

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28
Q

What is pKa?

A

The pH were 50% is ionised

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29
Q

What does a low pKa indicate?

A

Acidic

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30
Q

What can ionic interactions occur between?

A

Negative (acid) charged side chains - negatively charged, hydrophilic residues
Positive (basic) charged side chains - positively charged, hydrophilic residues

31
Q

What is significant about ionic interactions?

A

Between charged groups
Positive attracts negative
Importance of environment

32
Q

What is the distance between hydrogen-bond donors and acceptors?

A

~2.8 An = 0.28 nm

33
Q

Give examples of hydrogen-bond donor and acceptor interactions

A 
(-)dipole - (+)dipole _ (-)dipole
N-H_N
N-H_O
O-H_N
O-H_O
34
Q

What is significant about hydrogen bonds?

A

They are directional, weakening as the (donor-H-lone pair) becomes less linear

35
Q

What do 4 sp3 hybrid orbitals form?

A

A tetrahedron

36
Q

Give examples of amino acids with side chains that can form hydrogen bonds

A 
Residues with polar groups:
Asparagine
Cysteine
Glutamine
Neutral histidine
Serine
Threonine
Tryptophan
Tyrosine
37
Q

What can’t hydrophobic groups form?

A

Hydrogen bonds

38
Q

What do co-locating hydrophobic regions allow?

A

Water to maximise both hydrogen bonding and entropic potential

39
Q

Give examples of amino acids with side chains that can form hydrophobic interactions

A 
Nonpolar, hydrophobic residues
Alanine
Isoleucine
Glycine
Leucine
Methionine
Phenylalanine
Proline
Valine
40
Q

In terms of van der Waals forces, what does a positive charge cause?

A

An induced dipole on a neighbouring atom

41
Q

In terms of van der Waals forces, what does an induced dipole cause?

A

Mutually induced dipoles (transient) on neighbouring atoms

42
Q

Define primary structure

A

The sequence of amino acids linked by covalent peptide bonds. Amino (N-) and carboxy (C-) termini.

43
Q

Why is the peptide group rigid and planar?

A

Because the carbon-nitrogen bond has partial double-bond character. Also:
Peptide has dipole
Peptide N is a hydrogen bond donor, the carbonyl O an acceptor

44
Q

Where is there freedom of rotation about bonds?

A

Either side of C alpha - dihedrals phi and psi

45
Q

Define secondary structure

A

Regular structural motifs alpha-helix and beta-strand/sheet

H-bonding between -NH and -CO groups in protein backbone

46
Q

Describe the properties of an alpha-helix

A

The peptide N is a hydrogen bond donor, the carbonyl O an acceptor
Main chain carbonyl group is H-bonded to main chain amino group four residues away
All polar groups of main chain are H-bonded so compatible with hydrophobic environment inside a protein, e.g. can have hydrophobic one side and hydrophilic the other side

47
Q

At what ends are the positive and negative dipoles of the alpha-helix?

A

Positive dipole is at the N-terminal end

Negative dipole is at the C-terminal end

48
Q

What binds to the heme group of myoglobin?

A

An iron atom

49
Q

What secondary structural make up myoglobin?

A

Helix-turn-helix

50
Q

Which side of the Ramachandran plot do beta-strands and alpha-helices lie?

A

Beta-strands at the top left

Alpha-helices at the bottom left

51
Q

What is the Ramchandran plot a plot of?

A

psi vs. phi

52
Q

In what orientation can beta-sheets lie?

A

Parallel or antiparallel

53
Q

How do beta-strands combine and give and example of a molecule where this combination may occur?

A

In various ways with both parallel and antiparallel parts in a sheet
E.g. in part of an antibody molecule

54
Q

What are the various ways secondary structures combine known as?

A

Motifs

55
Q

What can the hairpin be extended to form?

A

The Greek-key

56
Q

What forms the beta-alpha-beta motif? And what can this motif form?

A

The simple combination of a beta-sheet and a helix forms the motif
The motif can form larger structures, e.g. the TIM barrel

57
Q

Is the barrel structure common or uncommon?

A

Very common, as it provides a good structural scaffold for forming an active site in an enzyme

58
Q

In the right-handed beta-alpha-beta unit, where does the helix lie ?

A

The helix lies above the plane of the strands

59
Q

Beta-alpha-beta can double up to form what?

A

Nucleotide binding domain with signature g-x-g-x-x-g found in e.g. dehydrogenases
(Known as the Rossman fold)

60
Q

Describe how a barrel might form

A

Trimer of left-handed beta-helices with alpha-helical region at C-terminus

61
Q

Alpha-helices can also combine to form what? And give an example of one of the most important

A

Form motifs

One of the most important is the helix-turn-helix that has been found in many DNA-binding proteins

62
Q

Where can you fins a similar helix-loop-helix motif?

A

The calcium-binding EF hand

Electronegative oxygens around Ca2+

63
Q

Give examples of other motifs worth knowing about

A

The four-helix-bundle

The leucine zipper

64
Q

What might proteins also have bound?

A

Metal ions, they may be important for the structure, and an example is the zinc finger found in DNA binding proteins

65
Q

What can some large polypeptides fold into?

A

Domains

66
Q

What is the fundamental unit of tertiary structure?

A

Domains

67
Q

Define domain

A

A polypeptide chain or part of a polypeptide chain that can fold independently into a stable tertiary structure

68
Q

What are domains also units of?

A

Also units of function, they may be recognisable from an analysis of sequence
May be subunits, if the oligomeric protein consists of more than one chain

69
Q

Give examples of a domain

A

SH2 (Src-homology-2) and SH3 (Src-homology-3) domains

70
Q

Define tertiary structure

A

Folding of polypeptide, stabilised by side chain interactions (covalent, ionic, H-bonding, hydrophobic, van der Waals)

71
Q

Describe the properties of the amino acids in myoglobin

A

Hydrophilic and polar amino acids on the outside, hydrophobic amino acids on the inside

72
Q

Describe the distribution of amino acids in a membrane protein

A

‘Inside out’
Water-filled hydrophobic channel
Largely hydrophobic exterior

73
Q

Define quaternary structure

A

Associations between polypeptides - multisubunit molecules, e.g. Hb.
Mainly side chain interactions (covalent, ionic, H-bonding, hydrophobic, van der Waals)

74
Q

Where do disulphide bonds primarily occur? And give an example of a biological molecule that contains disulphide bonds

A

Primarily occur in extracellular proteins
Can be intra- or intersubunit
Can be found in insulin

BS2091 Biochemistry I: from genes to proteins (16 decks)

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