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IMS > Proteins > Flashcards

Proteins Flashcards

1
Q

define the genome

A

full set of genes in an organism

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2
Q

define proteome

A

full set of proteins encoded by the genome

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3
Q

define non polar

A

hydrophobic

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4
Q

define polar

A

hydrophilic

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5
Q

which amino acids are hydrophobic (non - polar)

A

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

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6
Q

which amino acids are polar (hydrophilic)

A

serine, threonine, cysteine, tyrosine, asparagine, glutamine

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7
Q

which amino acids have electrically charged side chains

A

aspartate, glutamate, lysine, arginine, histidine

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8
Q

which amino acids are acidic

A

aspartate, glutamate

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9
Q

which amino acids are basic

A

lysine, arginine, histidine

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10
Q

where do you find polar or charged amino acid residues in a protein

A

on the outside

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11
Q

all amino acids are chiral apart from

A

glycine

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12
Q

which chiral amino acids are found in proteins

A

only L

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13
Q

what bonds are present causing the a helix

A

hydrogen bonds form between and N-H every 4 residues

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14
Q

which parts of the tertiary structure are polar (philic) and non-polar (phobic)

A

the interior of the tertiary structure is usually non polar and the exterior / outside is usually polar (hydrophilic)

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15
Q

what bonds occur between cysteine

A

disulphide bonds

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16
Q

which disease is associated with alzheimers

A

amyloid disease

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17
Q

what is the basic pathology of alzheimers

A

amyloid precursor protein accumulates and aggregates forming insoluble fibrils of amyloid B protein which then form plaques causes atrophy of neurones

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18
Q

what causes Creutzfeldt-jacob disease

A

prion disease - in may be inherited or caused by ingestion of infectious proteins - causes abnormal PrPsc structure

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19
Q

what is the polarity of globular proteins

A

polar outside and non-polar inside

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20
Q

what time of binding is o2 to Hb and what shape is the graph

A

co-operative binding and is sigmoidal

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21
Q

does Mb or Hb have the higher affinity for o2

A

Mb

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22
Q

what occurs during the T state in Hb

A

T state - Tense state - more salt bridges and a low affinity for O2 - binding sites aren’t accessible

23
Q

What occurs during the R state of Hb

A

Relaxed state - less salt bridges and higher affinity

24
Q

describe what happens in the bohr effect

A

increase in H+ means more acidity and and lower ph - this decreases Hb’ affinity for O2 and therefore O2 is released

25
Q

why does an increase in H+ cause O2 unloading

A

H+ protonates amino acids (mainly histidine) making them more prone to forming salt bridges ie a better T state

26
Q

what does BPG do

A

decreases the affinity of O2 at high altitude and in states of hypoxia

27
Q

how do BPG bind to O2

A

binds to the space between the B subunits in the T state only and secures the T state

28
Q

what is BPG effect on foetal Hb

A

binds less effectively so HbF has higher affinity for oxygen

29
Q

what is the terminating amino acid in Hb

A

proline terminates the helical structure at C2

30
Q

what is a conservative substitution

A

a sub to another amino acid with similar properties so there is no effect on function

31
Q

what is a non conservative substitution

A

substitution which change the properties of the molecule due to a residue with a different side chain amino acid

32
Q

how many chains does collagen have

A

3 chains - 2 a-1 and 1 a-2

33
Q

what is the structure of collagen

A

has a glycine every 3 residue so that it can fold easily as glycine is very small - glycine pack inside while proline and 4HP are on the outside

34
Q

what bonds are formed in collagen

A

hydroxyproline forms hydrogen bonds and hydroxylysine forms cross linking

35
Q

in collagen it requires vitamin C for bonding, what does it do

A

hydroxylation of proline and lysine require ascorbic acid as a co factor which is vitamin C

36
Q

when does a helix become left handed in collagen?

A

lysl oxidase deaminates some lysine and hydroxylysine residues to allysine which can form cross links with lysine or allysine (3.3 residues per turn rather than a normal 3.6)

37
Q

what is dupuytrens contracture

A

excess collagen production hands - permanently bend fingers

38
Q

what is osteogenesis imperfecta and what are the different types

A

mutation in type 1 collagen - brittle bone disease - break easily
type 1 - mild
type 2 fatal after birth
type 3/4 - severe deformities

39
Q

what is ehlers danlos syndrome type IV

A

translucent skin around eyes so you can see the veins - lyssl oxidase deficiency

40
Q

what is sickle cell anaemia

A

substitution of glutamate to valine causing hydrophobic sticky patches and sickle cell shape causing vein obstruction

41
Q

what effect would changing lysine with argenine have

A

no effect - it is a conservative substitution as they are both basic

42
Q

what are all the bonds that stabilise the secondary structure

A

they are all weak bonds

43
Q

what would happen to the affinity for Hb and oxygen if you increased levels of BPG

A

high BPG = lower affinity for o2 and more unloading

44
Q

collagen formation requires what

A

vitamin c

45
Q

what reaction bonds amino acids in a polypeptide and what are the characteristics

A

peptide bond via condensation reaction and the production of water - partial double bond which causes rigidity and limited rotation going from CN to CO

46
Q

differences between alpha helix and beta sheet

A

alpha helix - stabilised by H bonds - has some elasticity

beta - no elasticity

47
Q

describe primary secondary and tertiary quaternary

A

primary - amino acid sequence
secondary - local spatial arrangement of amino acids
tertiary - formation of 3D shape
quat - arrangements of different subunits in a protein

48
Q

where is myoglobin highest in conc

A

skeletal muscle and cardiac muscle

49
Q

difference between myoglobin and haemoglobin

A

myoglobin has only pone subunit mostly alpha helical

hb - binding is sigmoidal, it is pH and CO2 dependant and regulated by BPG - Mb is not

50
Q

difference between foetal hb and adult hb

A

foetal has 2 alpha and 2 gamma chains which bind to o2 more tightly

51
Q

when o2 is bound to hb which state is the iron in

A

Fe2+

52
Q

describe the synthesis of collagen

A

polypeptide synthesis, post translational modifications, pro collagen triple helix within fibroblasts - secretion from fibroblasts - removal of extension peptides - aggregation of microfibril - cross linking

53
Q

how long is the half life of collagen

A

a few months

IMS (20 decks)

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