Protein structure and function

Question 1

Are peptide linkages in b strands and alpha helices

• cis or trans
• what geometry

Answer 1

trans, planar

Question 2

describe direction of alpha helix

Answer 2

right handed (anticlockwise)

Question 3

how many aa’s per turn of the helix

Answer 3

3.6

Question 4

H bond form between peptide linkages that are __ aa’s apart

Answer 4

4

Question 5

direction of NH, CO and R groups?

Answer 5

NH up
CO down
R out.

Question 6

effect of proline?

Answer 6

forms N, not NH in peptide. Hence can’t form H bond with CO, so causes kink

Question 7

describe effect of ionic R groups

Answer 7

if on aa 1 and 4 and are oppositely charged, it can stabilise the helix.

Question 8

how are b turns formed

Answer 8

type 1: proline

type 2: glycine.

Question 9

what are the 2 types of beta sheets

Answer 9

parallel and antiparallel beta sheets

Question 10

globular proteins are said to have

Answer 10

confromation

Question 11

what is native conformation

Answer 11

lowest energy state of a protein, formed by maximising H bonds and burying hydrophobic residues

Question 12

experiment involing urea, mercaptoethanol and RNA enzyme

Answer 12

urea breaks H bonds and forms new ones
mercaptoethanol breaks disulfide bridges
after this, protein spontaneously refolds into native state, regaining catalytic acitivyt

Question 13

3 key concepts regarding proteins spontaneously folding into native state?

Answer 13

• -folding takes place through intermediate steps
• folding involves different pathways
• proteins fold and unfold to find lowest energy native state

Question 14

describe myoglobin structure

Answer 14

monomer
many alpha helices
alpha helices and hydrophobic residues form pocket for heme group

Question 15

describe heme group

Answer 15

octahedral iron bonded to planar ring

• 4 bonds to ring
• 1 bond to oxygen
• 1 bond to N in histidine in R group

Question 16

what happens when oxygen binds to iron in heme group in myoglobin

Answer 16

turns from tense state (no O2 bound, and low O2 affinity) to relaxed state (O2 bond, high O2 affinity)

Question 17

describe haemoglobin.

Answer 17

individual proteins have similar structure to myoglobin - slightly different however.
2 alpha and 2 beta chains - tetramer
if one subunit is bound to O2, then all units turn to R state.

Question 18

what are the 3 types of proteins?

Answer 18

globular
fibrous
membrane

Question 19

haemoglobin is a

Answer 19

globular protein

Question 20

describe sickle cell anemia

Answer 20

mutation of 6th aa in beta chain
turns glutamate (acidic) to valine (hydrophobic)
creates hydrophobic patches on surface of molecule
attaches via hydrophobic interactions to form strands which form fibres. this creates sickle cell shape.

Question 21

4 key features of fibrous proteins?

Answer 21

atleast 2 pp chains
often a lot of a single secondary structure element
not water soluble
often cross linkages

Question 22

describe collagen

Answer 22

3 left handed coils (clockwise) containing repeating glycine-x-(hydroxy)proline units; form a right handed superhelix which is stabilised by crossl inkages and hydrogen bonds.

Question 23

what happens when we age

Answer 23

more collagen cross linkages - less elastic

Question 24

describe scurvy

Answer 24

vit C deficiency
a cofactor for enzyme converting proline to hydroxyproline
can cause collagen molecules to just fall apart.

Question 25

4 types of membrane proteins?

Answer 25

integral proteins
peripheral proteins
amphitropic protein (either in cytosol or associated with pm)
membrane linked proteins

Question 26

for integral proteins, which parts are hydrophobic and which parts are hydrophilic

Answer 26

philic - inside

phobic - outside

Question 27

how can integral proteins be separated from plb?

Answer 27

detergent (lipid part of detergent next to lipid part of plbb)

Question 28

3 main functions of integral proteins?

Answer 28

signal transduction
transport
give cell a property

Question 29

describe glycophorin

Answer 29

found in rbc’s
N terminal outside, C terminal inside cell. Both hydrophilic
part of protein inside cell is hydrophobic
N terminal contains serine and threonine, which enzymes add sugar groups to. THe sugar groups become ionised, and repel other rbc’s

Question 30

describe bacteriorhodopsin

Answer 30

7 subunits; made of alpha helices. Attached by loops.

Contains retinal, which responds to light

Question 31

describe hydropathy plot

Answer 31

Y axis: bottom is hydrophilic, top is hydrophobic

X axis: tells us which residue it is.