Proteins

Question 1

define the genome

Answer 1

full set of genes in an organism

Question 2

define proteome

Answer 2

full set of proteins encoded by the genome

Question 3

define non polar

Answer 3

hydrophobic

Question 4

define polar

Answer 4

hydrophilic

Question 5

which amino acids are hydrophobic (non - polar)

Answer 5

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

Question 6

which amino acids are polar (hydrophilic)

Answer 6

serine, threonine, cysteine, tyrosine, asparagine, glutamine

Question 7

which amino acids have electrically charged side chains

Answer 7

aspartate, glutamate, lysine, arginine, histidine

Question 8

which amino acids are acidic

Answer 8

aspartate, glutamate

Question 9

which amino acids are basic

Answer 9

lysine, arginine, histidine

Question 10

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

Answer 10

on the outside

Question 11

all amino acids are chiral apart from

Answer 11

glycine

Question 12

which chiral amino acids are found in proteins

Answer 12

only L

Question 13

what bonds are present causing the a helix

Answer 13

hydrogen bonds form between and N-H every 4 residues

Question 14

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

Answer 14

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

Question 15

what bonds occur between cysteine

Answer 15

disulphide bonds

Question 16

which disease is associated with alzheimers

Answer 16

amyloid disease

Question 17

what is the basic pathology of alzheimers

Answer 17

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

Question 18

what causes Creutzfeldt-jacob disease

Answer 18

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

Question 19

what is the polarity of globular proteins

Answer 19

polar outside and non-polar inside

Question 20

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

Answer 20

co-operative binding and is sigmoidal

Question 21

does Mb or Hb have the higher affinity for o2

Answer 21

Mb

Question 22

what occurs during the T state in Hb

Answer 22

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

Question 23

What occurs during the R state of Hb

Answer 23

Relaxed state - less salt bridges and higher affinity

Question 24

describe what happens in the bohr effect

Answer 24

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

Question 25

why does an increase in H+ cause O2 unloading

Answer 25

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

Question 26

what does BPG do

Answer 26

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

Question 27

how do BPG bind to O2

Answer 27

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

Question 28

what is BPG effect on foetal Hb

Answer 28

binds less effectively so HbF has higher affinity for oxygen

Question 29

what is the terminating amino acid in Hb

Answer 29

proline terminates the helical structure at C2

Question 30

what is a conservative substitution

Answer 30

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

Question 31

what is a non conservative substitution

Answer 31

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

Question 32

how many chains does collagen have

Answer 32

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

Question 33

what is the structure of collagen

Answer 33

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

Question 34

what bonds are formed in collagen

Answer 34

hydroxyproline forms hydrogen bonds and hydroxylysine forms cross linking

Question 35

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

Answer 35

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

Question 36

when does a helix become left handed in collagen?

Answer 36

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)

Question 37

what is dupuytrens contracture

Answer 37

excess collagen production hands - permanently bend fingers

Question 38

what is osteogenesis imperfecta and what are the different types

Answer 38

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

Question 39

what is ehlers danlos syndrome type IV

Answer 39

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

Question 40

what is sickle cell anaemia

Answer 40

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

Question 41

what effect would changing lysine with argenine have

Answer 41

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

Question 42

what are all the bonds that stabilise the secondary structure

Answer 42

they are all weak bonds

Question 43

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

Answer 43

high BPG = lower affinity for o2 and more unloading

Question 44

collagen formation requires what

Answer 44

vitamin c

Question 45

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

Answer 45

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

Question 46

differences between alpha helix and beta sheet

Answer 46

alpha helix - stabilised by H bonds - has some elasticity | beta - no elasticity

Question 47

describe primary secondary and tertiary quaternary

Answer 47

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

Question 48

where is myoglobin highest in conc

Answer 48

skeletal muscle and cardiac muscle

Question 49

difference between myoglobin and haemoglobin

Answer 49

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

Question 50

difference between foetal hb and adult hb

Answer 50

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

Question 51

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

Answer 51

Fe2+

Question 52

describe the synthesis of collagen

Answer 52

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

Question 53

how long is the half life of collagen

Answer 53

a few months