Protein structure and function Flashcards
Are peptide linkages in b strands and alpha helices
- cis or trans
- what geometry
trans, planar
describe direction of alpha helix
right handed (anticlockwise)
how many aa’s per turn of the helix
3.6
H bond form between peptide linkages that are __ aa’s apart
4
direction of NH, CO and R groups?
NH up
CO down
R out.
effect of proline?
forms N, not NH in peptide. Hence can’t form H bond with CO, so causes kink
describe effect of ionic R groups
if on aa 1 and 4 and are oppositely charged, it can stabilise the helix.
how are b turns formed
type 1: proline
type 2: glycine.
what are the 2 types of beta sheets
parallel and antiparallel beta sheets
globular proteins are said to have
confromation
what is native conformation
lowest energy state of a protein, formed by maximising H bonds and burying hydrophobic residues
experiment involing urea, mercaptoethanol and RNA enzyme
urea breaks H bonds and forms new ones
mercaptoethanol breaks disulfide bridges
after this, protein spontaneously refolds into native state, regaining catalytic acitivyt
3 key concepts regarding proteins spontaneously folding into native state?
- -folding takes place through intermediate steps
- folding involves different pathways
- proteins fold and unfold to find lowest energy native state
describe myoglobin structure
monomer
many alpha helices
alpha helices and hydrophobic residues form pocket for heme group
describe heme group
octahedral iron bonded to planar ring
- 4 bonds to ring
- 1 bond to oxygen
- 1 bond to N in histidine in R group
what happens when oxygen binds to iron in heme group in myoglobin
turns from tense state (no O2 bound, and low O2 affinity) to relaxed state (O2 bond, high O2 affinity)
describe haemoglobin.
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.
what are the 3 types of proteins?
globular
fibrous
membrane
haemoglobin is a
globular protein
describe sickle cell anemia
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.
4 key features of fibrous proteins?
atleast 2 pp chains
often a lot of a single secondary structure element
not water soluble
often cross linkages
describe collagen
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.
what happens when we age
more collagen cross linkages - less elastic
describe scurvy
vit C deficiency
a cofactor for enzyme converting proline to hydroxyproline
can cause collagen molecules to just fall apart.
4 types of membrane proteins?
integral proteins
peripheral proteins
amphitropic protein (either in cytosol or associated with pm)
membrane linked proteins
for integral proteins, which parts are hydrophobic and which parts are hydrophilic
philic - inside
phobic - outside
how can integral proteins be separated from plb?
detergent (lipid part of detergent next to lipid part of plbb)
3 main functions of integral proteins?
signal transduction
transport
give cell a property
describe glycophorin
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
describe bacteriorhodopsin
7 subunits; made of alpha helices. Attached by loops.
Contains retinal, which responds to light
describe hydropathy plot
Y axis: bottom is hydrophilic, top is hydrophobic
X axis: tells us which residue it is.
