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Molecular biochemistry > Proteins and amino acids > Flashcards

Proteins and amino acids Flashcards

1
Q

What differentiates small molecules or macromolecules?

A

Mr of 1000

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2
Q

What isoform is AA always in (mammalian AA)?

A

L form

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3
Q

What isoform are mammalian carbs always in?

A

D form

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4
Q

What are stereoisomers?

A

Non super imposable mirror images (D and L form) with chiral carbon

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5
Q

What are 4 functions of protein?

A

Structural (e.g. collagen, actin)

Globular (e.g. Hb, enzymes)

Plasma membrane proteins (e.g. transporters, receptors)

Regulatory protein (e.g. calmodulin)

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6
Q

Describe globular proteins, why are they like this?

A

Compact, folding of PP chain

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7
Q

Describe properties of plasma membrane proteins?

A

Hydrophobic domains in lipid membrane and hydrophilic domains in cytoplasm/ECF

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8
Q

What are the +ve charge/basic AA?

A

Arginine, lysine

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9
Q

Why are arginine and lysine always +ve charged?

A

Amino group of side chain has pk14 so always positively charge (side chain fully protonated at pH7)

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10
Q

What are the acidic/-ve charged amino acids?

A

Aspartate, glutamate

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11
Q

Why are glutamate and aspartate negatively charged?

A

Carboxyl group side chain has pK 4 so always -ve charged, COOH group ionised at pH7

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12
Q

What are the uncharged hydrophilic amino acids (6)?

A

Glutamine, asparagine, serine, threonine, tyrosine, cysteine

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13
Q

What is way to remember uncharged hydrophilic amino acids?

A

Give all sugary treats to clara

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14
Q

What are hydrophobic amino acids (9)?

A

Alanine, phenylalanine, leucine, isoleucine, valine, proline, glycine, methionine, tryptophan

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15
Q

What is way to remember hydrophobic amino acids?

A

Alanine phenylalanine

Leucine, isoleucine

Valine, proline, glycine, methionine

Tryptophan

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16
Q

What does proline do to PP chains?

A

Puts kink in PP chain - structural amino acid

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17
Q

What is unique around histidine?

A

Side chain can either be protonated/unprotonated

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18
Q

Why is glycine useful?

A

Allow flexibility in PP chain due to small R group (H atom)

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19
Q

What constitutes peptide bond?

A

C=O-N-H (amino group and carboxyl group - amide bond)

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20
Q

How is peptide bond formed?

A

Condensation reaction where molecule of water lost

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21
Q

Where does peptide bond form (where in cell)?

A

In ribosomes

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22
Q

What is the starting AA of proteins?

A

Methionine

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23
Q

C-N bond has characteristics of a …

A

Double bond

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24
Q

Describe electron distribution along CO-NH system?

A

Resonance

Electrons shared along the CO-NH system so partial charges on H + O atoms

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25
Q

How much rotation is there around peptide bond , what’s the consequence?

A

None - creates rigid, planar structure

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26
Q

Where do you have rotational flexibility around the amide bond?

A

alpha C-C (psi) and alpha carbon-nitrogen (phi)

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27
Q

What is psi and phi bond?

A

psi - alpha C-C bond

phi - alpha C-N bond

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28
Q

Why is there only a few ways in which a PP chain can fold?

A

Only psi and phi rotate around peptide bond

Electron clouds cannot overlap and the bonds can only rotate certain ways.

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29
Q

What specifies how PP chain forms 3d structure of protein?

A

Angles of rotation around C-C and C-N (alpha carbons) (torsion angles)

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30
Q

What direction is the alpha helix, why?

A

Right handed

All AA are in L-form

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31
Q

What isoform AA do bacteria have?

A

D isoform

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32
Q

Which AA doesn’t have chiral carbon?

A

Glycine

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33
Q

What are the weakest interactions to stabilise protein structure?

A

Van der Waals

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34
Q

What does extent of repulsive/attractive VdWs forces depend on?

A

Distance between atoms

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35
Q

What causes attractive forces for VdWs?

A

Fluctuations in electron charge densities of neighbouring bonding atoms

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36
Q

What causes repulsive forces of VdwS?

A

Close approach of electron density clouds

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37
Q

What do VdW forces favour?

A

Tight packing arrangement in macromolcules .

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38
Q

What drives protein folding?

A

Hydrophobic interaction

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39
Q

What is the most common type of bond stabilising protein structure?

A

Hydrogen bonds

40
Q

What does H bond form between?

A

C=O and N-H

41
Q

What is Hydrogen bond important for?

A

Secondary structure stabilisation

42
Q

What do hydrophobic interactions do?

A

Fold proteins

Reduce water associated with hydrophobic amino acids

Increase thermodynamic stability of structure - forms globular proteins

43
Q

What are ionic interactions stabilising protein structure?

A

Oppositely charged amino acid side chains

44
Q

What do disulphide bonds form between?

A

Side chains of cysteine residues

i.e. SH groups - S-S bond

45
Q

Where can disulphide chains be found relative to PP chains?

A

Intrachain or interchain

46
Q

Why is ultimate mean PP structure dynamic and flexible?

A

Lots of weak, bonds non directional

47
Q

What is primary structure of protein?

A

Order of AA held by peptide bonds

48
Q

What is secondary structure of protein?

A

Local interactions of AA in PP chain - hydrogen bonded arrangement of backbone

49
Q

What defines conformation of protein backbone?

A

Planar peptide bond and 2 freely rotating bonds (psi and phi)

50
Q

Describe structure of alpha helix?

A

Involves one PP chain, highly coiled and side chains extend outwards from axis of spiral

51
Q

Describe side chains in alpha helix?

A

Extend outwards from axis of spiral

52
Q

What stabilises alpha helix?

A

Stabilised by hydrogen bonds between every 4th peptide bond (between C=O and N-H)

53
Q

Describe alignment of hydrogen bonds in alpha helix?

A

Linear arrangement of atoms involved in hydrogen atoms

54
Q

Describe vDWs forces in alpha helix?

A

Interactions in the core of the helix

55
Q

What does proline do to alpha helix?

A

Helix breaker and causes a kink in the chain

This is because one of the amino H is used in the bond to the R group and one in the peptide bond.

Therefore it cannot hydrogen bond with the n+4th amino acid.

56
Q

What are the rough angles of psi and phi in alpha helix?

A

60 degrees

57
Q

What stabilises Beta sheet?

A

Hydrogen bonds between peptide bonds of adjacent polypeptide chains

58
Q

What are the rough angles of psi and phi in beta sheet?

A

psi -135 phi 135

59
Q

Describe different types of beta sheet, describe the peptide chain orientations and the hydrogen bond formation

A

Parallel - peptide chains run in same direction (N-termini together). H bonds at an angle (less stable)

Antiparallel - alternating chains in opposite direction (N-terminus next to C-terminus). H bonds aligned (most stable)

60
Q

Why is antiparallel beta sheet more stable?

A

H-bonds aligned

61
Q

Describe arrangement of side chains in beta pleated sheet?

A

Side chains alternate on either side of plane on sheet

62
Q

What forms a connecting loop/turn , describe what they do and how are they stabilised?

A

4 AA, ensure PP chain makes 180 degree change in direction.

Link secondary structures. H bonds between residues 1 and 4 - stabilise hairpin bend.

63
Q

What is a motif?

A

3d structure of several secondary structure elements

64
Q

Describe a motif relative to domain, secondary and tertiary structures?

A

Smaller than protein domain

Intermediate between secondary and tertiatry structure

65
Q

What is a structural domain?

A

Section of protein sufficient to perform chemical/physical task (e.g. bind ligand)

66
Q

What are domains formed from?

A

Several motifs combining

67
Q

What do several domains do?

A

Form functional protein

68
Q

How does structural domain fold?

A

Autonomously (unlike motif)

69
Q

What is the tertiary structure?

A

Overall structure formed by PP chain (arrangements of region of secondary structure proteins forming domains via side chain interactions)

70
Q

What stabilises tertiary structure?

A

Bonds between side chains, non covalent bonds, stabilised by disulphide bonds

71
Q

What is most important intramolecular interaction for globular protein formation?

A

Hydrophobic forces: cluster hydrophobic residues on inside of protein to reduce amount of water associated with them for greater thermodynamic stability.

72
Q

What is quaternary structure and what interactions hold it together?

A

Multiple PP chains normally held together by weak non covalent bonds

73
Q

Describe structure of different Quaternary structures?

A

Form homooligomers (identical subunits) or heterooligomers (different subunits)

74
Q

Describe dissociation curve for myoglobin, why?

A

Hyperbolic affinity curve, single PP chain (no cooperativity)

75
Q

Describe dissociation curve for haemoglobin, describe why it’s like this?

A

Sigmoidal curve

Cooperation between 4 binding sites/PP chains

Binding of first oxygen causes allosteric change making binding of next one easier

76
Q

What are the different post translational modifications, describe them? (not non peptide attachments)

A

Disulphide bonding

Cross linking - covalent cross links

Peptidolysis - enzymatic removal of part of protein

77
Q

Describe the non peptide attachments involved in post translational modification

A

Glycosylation: adding carb group

Phosphorylation

Adenylation: add AMP

Farnesylation: add C15 group - inserts into plasma membrane

78
Q

How does modifying protein affect function (4)?

A

Regulation: i.e. phosphorylation to turn on/off

Targeting: molecules conjugated to protein - act as signals for intracellular sorting

Turnover: glycosylation regulate half life of protein

Structural: cross link molecules in collagen for strength

79
Q

Give an example of a fibrous protein

A

Collagen

80
Q

Example of globular protein

A

Histone

81
Q

Which structures is collagen found in

A

Tendons and ligaments, also the protein component onto which minerals are deposited - gives bone high tensile strength

82
Q

Describe structure of collagen

A

3 PP chains (left hand twists) form triple helix with right hand twist

Gly is every third AA as it has smallest R group to fit into centre of helical structure - allows tight packing.

Collagen contains hydroxyproline and hydroxylysine

83
Q

Describe bonding in collagen?

A

Stabilised by interchain hydrogen bonding between N-H from glycine (every 3rd AA)

O-H of Hydroxyproline forms hydrogen bonds to other PP strands - stabilise helix

Lysine modified to allysine aldehyde. Form cross links between the chains of collagen. allysine - lysine = Schiff base. Two allysine = aldol condensation cross link.

84
Q

What are symptoms of Ehlers Danlos?

A

Hyperextenisve skin and recurrent dislocation

85
Q

Describe structure of tropocollagen?

A

Tropocollagen form bundles of parallel 50nm (diameter) fibres which are staggered in assembly and cross linked between lysine and hydroxylisne residues - form collagen fibrils

86
Q

What is Ehlers Danlos caused by?

A

Deficient cross linking due to defective enzyme forming hydroxylysine resiudes

Failure to cut procollagen to tropocollagen

87
Q

What AAs are sulfur containing?

A

Methionine and Cysteine

88
Q

What are aliphatic AAs?

A

Side chain aliphatic

Alanine, isoleucine, leucine, proline, methionine and valine

89
Q

What are aromatic AAs?

A

Side chain aromatic

Phenylalanine, tryptophan and tyrosine

90
Q

What AAs are polar?

A

Asparagine, glutamine, serine, threonine and tyrosine.

91
Q

Which of the following amino acids forms hydrophobic interactions with other non-polar amino acids?

A

isoleucine

92
Q

The AA … is least likely to be included in an alpha helix

A

Proline

93
Q

ATP synthase is an example of which protein structure?

A

Quaternary

94
Q

Are there hydrophobic interactions between side groups in an alpha helix?

A

No

95
Q

What is a characteristic feature of the protein domain?

A

Folds independently

96
Q

Disulfide bridges are formed from pairs of cysteine residues by the chemical process of…

A

Oxidation

Molecular biochemistry (5 decks)

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