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proteins Flashcards

1
Q

what is the proteome?

A

full set of proteins encoded by the human genome – NOT the same as the number of genes.

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2
Q

what are the 4 groups amino acids have?

A

hydrogen atom
α-amino group
α -carboxyl group
distinctive R group

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3
Q

how many ways are there of naming an amino acid?

A

3 - full name, three letter abbreviation and 1 letter abbreviation.

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4
Q

name the nonpolar amino acids

A 
glycine
alanine
valine
leucine
isoleucine
methionine
phenylalanine
tryptophan
proline
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5
Q

name the polar amino acids

A 
serine
threonine
cysteine
tyrosine
asparagine
glutamine
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6
Q

name the acidic amino acids

A

aspartate

glutamate

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7
Q

name the basic amino acids

A

lysine
arginine
histidine

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8
Q

which form of amino acids are found in proteiins?

A

L optical isomer

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9
Q

describe the primary structure of a protein.

A

the sequence of amino acids

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10
Q

describe the secondary structure of a protein.

A

local spatial arrangements of amino acids in the peptide chain into pleated sheets and helices

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11
Q

describe the secondary structure of a protein.

A

local spatial arrangements of amino acids in the peptide chain into pleated sheets and helices

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12
Q

describe the tertiary structure of a protein.

A

organisation of the primary and secondary structures into the 3D protein shape.

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13
Q

describe the quaternary structure of a protein.

A

arrangement of different subunits in a protein

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14
Q

what is an amino acid in a polypeptide called?

A

a residue

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15
Q

why does a polypeptide have direction?

A

because each amino acid has a N-Terminal and a C-terminal.

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16
Q

which end is seen to be the start of the protein chain?

A

N-terminal

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17
Q

what type of bond links amino acids?

A

covalent peptide bond

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18
Q

what characteristic does a peptide bond have?

A

partial double bond - can resonate between two forms

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19
Q

describe the structure of an alpha helix

A

The main chain forms the inner part of the rod, the side chains extend outwards
Hydrogen bonds between the N-H and C=O groups of the main chain stabilise the helix. These are intrachain H-bonds.

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20
Q

describe the structure of an alpha helix

A

The main chain forms the inner part of the rod, the side chains extend outwards
Hydrogen bonds between the N-H and C=O groups of the main chain stabilise the helix. These are intrachain H-bonds.

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21
Q

how does the helix form a rod like structure?

A

Each C=O oxygen is hydrogen bonded to the NH of the amino acid 4 residues ahead in the linear sequence.

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22
Q

what are the characteristics of beta pleated sheet?

A

fully extended polypeptide chain
no elasticity
zigzag/pleated shape
R-groups lie outside the plane of the sheet

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23
Q

how many different ways can beta pleated sheets form?

A

interchain
intrachain
parallel
antiparallel

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24
Q

is the interior of proteins hydrophilic/phobic?

A

hydrophobic

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25
Q

give examples of proteins with quaternary structures

A

structural proteins (collagen monomers join together to form collagen fibres)

multi-enzyme complexes (mitochondrial ATPase)

immune system proteins (antibodies)

transport proteins (haemoglobin)

motility proteins (myosin)

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26
Q

give examples of proteins with quaternary structures

A

structural proteins (collagen monomers join together to form collagen fibres)

multi-enzyme complexes (mitochondrial ATPase)

immune system proteins (antibodies)

transport proteins (haemoglobin)

motility proteins (myosin)

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27
Q

list the forces that stabilise tertiary and quaternary structures

A 
Electrostatic interactions
Van der Waals forces 
H-bonds 
Burial of hydrophobic residues
Disulphide bonds
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28
Q

how do disulphide bonds form?

A

oxidation of 2 cysteines to form cysteine

have to be adjacent in space but not in sequence

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29
Q

what is the other name for electrostatic interactions?

A

salt bridges

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30
Q

what kind of molecules do Van de Waals forces occur in?

A

neutral molecules

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31
Q

list the three types of Van de Waals forces.

A

permanent dipole-permanent dipole
dipole induced dipole
London dispersion forces

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32
Q

which amino acids can form amino acids?

A

Most polar residues can H-bond (twelve of the amino acids).

asp, glu, lys, arg, his, tyr, ser, thr, asn, gln, trp, cys (SH).

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33
Q

which is the most important effect in stabilising proteins?

A

burying hydrophobic amino acids

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34
Q

how do proteins fold?

A

Small sequences of secondary structure form.
Stabilising forces tend to retain these
Less stable structures unravel and alternative structures form in quick succession until a more stable conformation occurs.
Folding continues in a hierarchical manner.

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35
Q

how do proteins fold?

A

Small sequences of secondary structure form.
Stabilising forces tend to retain these
Less stable structures unravel and alternative structures form in quick succession until a more stable conformation occurs.
Folding continues in a hierarchical manner.

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36
Q

what are the possible outcomes for a protein being incorrectly folded?

A

Cellular processes relying on the presence of the correct protein will not continue (e.g. phenylketonuria)

The misfolded protein may accumulate and hinder normal cellular processes (e.g. Alzheimer’s disease)

The misfolded protein may cause conformational changes in other proteins (e.g. Creutzfelt-Jacob disease)

The cell may identify the peptide for early destruction

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37
Q

what is the biochemical basis for alzheimers?

A

A fragment from a normal membrane protein, amyloid precursor protein, accumulates and aggregates forming insoluble fibrils of amyloid β protein in the brain.

The fibrils aggregate to form plaques.

These plaques damage and destroy neurons

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38
Q

what is the biochemical basis for Creutzfeldt Jacob Disease?

A

PrPSc has an identical primary sequence to a normal membrane protein PrPc but has a much higher proportion of β-pleated sheet.
Contact of normal soluble PrPc protein (mostly α-helical) with abnormal form PrPSc (mostly β-pleated sheet ) causes the PrPc protein to acquire the abnormal PrPSc structure and it accumulates

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39
Q

what are the characteristics of globular proteins?

A

compact, soluble – hydrophilic residues outside, hydrophobic residues hidden

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40
Q

what are the characteristics of fibrous proteins?

A

elongated, often have repeating amino acid sequences, insoluble due to high hydrophobic amino acid content

41
Q

how many mutant Hbs are known?

A

> 400

42
Q

why do we need oxygen carrying proteins?

A

Cells require O2 for oxidation of foodstuffs

O2 only sparingly soluble in blood, therefore need transport and storage system.

43
Q

what is the function of myoglobin and where is it at highest conc?

A

stores O2 in tissues

highest concentration in muscle

44
Q

what components make up a haem molecule?

A

porphyrin ring with Fe2+ at the centre

Non-covalently bound in a hydrophobic crevice in protein

45
Q

what components make up a haem molecule?

A

porphyrin ring with Fe2+ at the centre

Non-covalently bound in a hydrophobic crevice in protein

46
Q

how many ligands can Fe2+ coordinate with?

A

6

47
Q

describe the binding of oxygen within myoglobin molecule

A

proximal histidine F8 binds to Fe directly
oxygen binds to last ligand site
changes the position of Fe
allows distal Histidine E7 to bind to oxygen as well

48
Q

what are the advantages of the haem group being associated within a protein?

A

Fe atoms are kept in Fe2+ form

Binding of other small molecules e.g. carbon monoxide is inhibited

49
Q

what chains are found in adult Hb?

A

2 alpha , 2β chains

50
Q

what does Hb being allosteric mean?

A

the binding of O2 to one subunit affects interactions with the other subunits

51
Q

what is Hb dependent on?

A

pH and CO2 levels

52
Q

what is Hb regulated by?

A

BPG

53
Q

is O2 binding cooperative or non cooperative in Hb?

A

cooperative

54
Q

does Mb or Hb have a higher affinity for oxygen?

A

Mb

55
Q

why does the O2 affinity for oxygen produce a sigmoidal curve?

A

Binding of O2 to Hb is co-operative – binding curve is sigmoidal

Binding of one O2 makes binding of next easier

56
Q

why does the O2 affinity for oxygen produce a sigmoidal curve?

A

Binding of O2 to Hb is co-operative – binding curve is sigmoidal

Binding of one O2 makes binding of next easier

57
Q

what is the effect of one O2 binding to one Hb subunit?

A

proximal His F8 is pulled in
shifts helix F, EF and FG corners
altered shape transmitted to subunit surfaces
some interchain salt bridges rupture

As the subunit changes shape, it therefore changes the relationship between the 4 subunits

The β pairs slide and rotate relative to one another

58
Q

what are the two states an Hb subunit can be in and which has a higher affinity?

A

T state – ‘tense state’ – more salt bridges between subunits
Low affinity for O2

R-state – ‘relaxed state’ – fewer salt bridges
High affinity for O2

59
Q

what is the bohr effect?

A

lowering of pH decreases affinity of Hb for O2

60
Q

why is the bohr effect important in the body?

A

Increased CO2 in blood or increased lactic acid will lower pH

Increased release of O2 to respiring rapidly tissues or muscle releasing lactic acid

61
Q

how do H+ ions effect the binding of oxygen?

A

affects the protonation state of amino acid residues
additional residues are protonated – particularly histidine residues
Additional positively charged residues can form new salt bridges – these stabilise the T-state and decrease affinity for O2

62
Q

how do H+ ions effect the binding of oxygen?

A

affects the protonation state of amino acid residues
additional residues are protonated – particularly histidine residues
Additional positively charged residues can form new salt bridges – these stabilise the T-state and decrease affinity for O2

63
Q

what is BPGs effect on oxygen?

A

decreases affinity of Hb for O2 so causing more oxygen release in these conditions

64
Q

where does BPG bind?

A

space between the β subunits – in the T-state only

65
Q

how does BPG bind to Hb?

A

Negative charges on BPG interact with positive amino acid residues lining the space

66
Q

how is foetal haemoglobin different to adult haemoglobin?

A

Foetal HbF 2γ2
Adult HbA 2β2
HbF binds BPG less effectively, so has higher affinity for O2

Allows efficient transfer of O2 across the placenta

67
Q

what are the 9 critical residues of Hb?

A 
F8			His			Proximal His
E7			His			Distal His
CD1			Phe			Haem contact
F4			Leu			Haem contact
B6			Gly			B and E helices contact
C2			Pro			Helix termination
HC2			Tyr			H-bonds between H and 						        F helices
68
Q

what is conservative substitution?

A

maintains hydrophobic interior of molecule

Interior of Hb often see change of one non-polar residue for another

69
Q

what is Non-conservative substitution?

A

a substitution that will have a major effect on protein structure and function.

70
Q

what is Non-conservative substitution?

A

a substitution that will have a major effect on protein structure and function.

71
Q

where is collagen present and what does it form?

A

Major fibrous element of skin, bone, tendon, cartilage,
blood vessels, teeth
Present in most organs
Holds cells together in discrete units – basement membranes
Also a directive role in developing tissue

72
Q

how many different types of collagen are there?

A

at least 12

73
Q

what are the three categories of collagen?

A

fibril-forming collagens - form long fibrils

network-forming collagens - form 2-dimensional matrix – important in basal lamina

fibril-associated collagens - involved in crosslinking

74
Q

how many chains do all collagens have?

A

3 protein chains

75
Q

what is the chain composition of type 1 collagen and where is it found?

A

[a1(I)]2[alpha(I)] skin, tendon, bone, etc.

76
Q

what is the chain composition of type 2 collagen and where is it found?

A

[alpha1(II)]3 cartilage, vitreous humor

77
Q

what is the chain composition of type 3 collagen and where is it found?

A

[alpha1(III)]3 skin, muscle, often with type I

78
Q

what is the chain composition of type 4 collagen and where is it found?

A

[alpha1(IV)2[alpha2(IV)] all basal lamina

79
Q

describe the steps of collagen synthesis before secretion

A

Post-translational modifications
Procollagen triple helical cable (Within
fibroblasts)

80
Q

describe the steps of collagen synthesis before secretion

A

Post-translational modifications
Procollagen triple helical cable (Within
fibroblasts)

81
Q

describe the steps of collagen synthesis after secretion

A 
Removal of extension peptides
Tropocollagen
Aggregation into microfibril
Cross-linking to form collagen fibre
(all in In extracellular spaces of connective tissue.)
82
Q

describe the steps of collagen synthesis after secretion

A 
Removal of extension peptides
Tropocollagen
Aggregation into microfibril
Cross-linking to form collagen fibre
(all in In extracellular spaces of connective tissue.)
83
Q

what is the repeating sequence in collagen?

A

(Gly – X – Y)n

84
Q

what are the most frequent X and Y amino acids in collagen

A

X often Pro
(Gly-Pro-Y)

Y often Hyp
(Gly-X-Hyp)

85
Q

which two amino acids are hydroxilated in collagen and what is the co factor needed?

A

proline and lysine

need vitamin C

86
Q

what does hydroxyproline do?

A

involved in H-bond formation, which helps to stabilise the triple helix

87
Q

what does hydroxylysine do?

A

attachment sites for sugar residues, and are involved in cross-linking between collagen chains

88
Q

which direction does each polypeptide of collagen wind?

A

left at 3.3 residues per turn

89
Q

which direction does each triple helix of tropocollagen wind?

A

right

90
Q

which residues are on the inside and outside of a helix?

A

Gly on the centre, Pro and Hyp on the outside

91
Q

how does the assembly of collagen start?

A

disulphide bond formation between C-terminal extensions – facilitates triple helix assembly

92
Q

what are extension peptides

A

additional amino acids at each end of a chain of collagen

93
Q

which enzyme removes the extension peptides from collagen?

A

Peptidase enzymes

94
Q

how and why do cross links form in collagen?

A

Allysine has a reactive aldehyde group which then reacts spontaneously with the amino group on other lysine molecules, forming cross-links between adjacent chains

Covalent cross-links between and within tropocollagen molecules give strength and rigidity

95
Q

how and why do cross links form in collagen?

A

Allysine has a reactive aldehyde group which then reacts spontaneously with the amino group on other lysine molecules, forming cross-links between adjacent chains

Covalent cross-links between and within tropocollagen molecules give strength and rigidity

96
Q

why are nucleation sites important?

A

for calcium deposition

97
Q

why?

A

just because

98
Q

why are collegenases important?

A

important in tumour invasion and metastasis (spreading) – often produced at high levels by tumour cells

Dupuytren’s contracture

99
Q

what is the cause of osteogenesis imperfect?

A

mutations in type 1 collagen

IMS (13 decks)

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