protein structure & function

Question 1

What is primary structure of polypeptide ?

Answer 1

sequence of amino acids
polypeptides-unbranched polymers of amino acid residue which are linked togwther by the ribosome
-primary structuyre looks like this :ABFDIKHF
this sequence adopts certain 3D structure detemining reactivity

Question 2

What are proteins made from ?

Answer 2

made from L-amino acids
-S enantiomers (unless cysteine)
-polypeptide 3D strcutures begins with the atomic position around backbone -backbone generously
Peptide bonds
cant rotate
typicaly trans configuration
180 between H & O

Question 3

How can we describe backbone geometry ?

Answer 3

with 2 torsion angles
only peptide bond that is fixed
atoms around other 2 bonds can adopt diff conformations
phi adn psi angles

Question 4

What angle is the phi angle ?

Answer 4

between the successive backbone carbonyl atoms ?

Question 5

What angle is the Psi angle ?

Answer 5

between succesive backbone nitrogens

Question 6

why are some values of phi and psi more stable than others ?

Answer 6

phi is unlikely to be zero
-steric repulsion between bulky groups
common recurring combinations are particularly favoured by hydrogen bonding
-see in ramachandran plot

Question 7

what is a ramachandran plot ?

Answer 7

visualizes energetically allowed and forbidden regions for the dihedral angles

Question 8

Beta sheets are what ?

Answer 8

psi is near 180; 3.5 Å between residues
e.g:antiparralell beta sheet

Question 9

A-helix and blah ?

Answer 9

more compact structure
“i + 4–>i” hydrogen bonding
-3.6 residues/turn
-1.5 Å between residues
-Hairpins (B) turn between helices stabilised by i + 3—> hydrogen bonding

Question 10

What do different amino acids prefer ?

Answer 10

differents econdary structures
1. Pro-disrupts a-helices and B-sheets
2. Gly & Pro are comman in B-turns ,although Gly can adopt many psi and phi angles
3. Bulkier,hydrophobic sidechains-Val,Ile tend to favour B-sheets
4. Ser,Asp,Asn sidechains tend to disrupt a-helices

Question 11

What is a tertiary structure ?

Answer 11

overall 3D structure of polypetide
-involves the precise positioning of secondary structural units
-tertiary structure is stabilised by
non-covalent interactions
disulphide bridges

Question 12

What are loops ?

Answer 12

random coils used as flexible binding sites in many proteins
-antibodies can bind antigens strongly loop regions
very low dissociation constant
some (many )proteins are mostly disturbed until they bind to a partner

Question 13

Define Structural protein ?

Answer 13

proteins may form insoluble extended structures by bonding to themselves

Question 14

What are binding & transport proteins ?

Answer 14

proteins may bond with other molecules at their binding sites
eg.)myoglobin,haemoglobin

Question 15

Define catalytic proteins ?

Answer 15

proteins may bond with transition states at their active sites to increase reaction rates

Question 16

1st example of of structural protein ?

Answer 16

α Keratin-main componant of hair,epidermis & fingernails
-fibrous,insoluble structure based on RH α-complex
-these helices are coiled together in a long left-handed super-helix

Question 17

How do keratin α-helices bind to each other ?

Answer 17

helix is slightly distorted :3.5 residues / turn
every 7th residue is similar position in helix
chosen to bind non-covalently with one another – hydrophobic effect important
-“heptad repeats “
-helices also attached covalently via disulphide bonds
HAIR STINKS WHEN BURNED

Question 18

2nd example of structural protein ?

Answer 18

Collagen
-main component of connective tissue in mammals
-tendon,cartlidge & dermis
long-triple helix
near β-sheets in ramachandran plot
-Vanderwaals interaction within helices & hydrogen bonds between helices
-every 3rd residue-glycine-make helix compact
proline and hydroxyproline are comman too

Question 19

What is the collagen triple helix ?

Answer 19

Gly is small enough to fit in helix centre
-Hyp also stablises structure by using its hydroxyl group to form inter-strand hydrogen bonds
-hyp synthesis depends on vitamin C (ascorbate)

Question 20

What is protein pathological aggregation ?

Answer 20

water soluble proteins may mis-fold and bind to 1 another to form insoluble fibres
eg.)amyloid fibrils in alzheimers ,type 2 diabetes & prion diseases

Question 21

How do enzymes work ?

Answer 21

-proteins are biological catalysts
-they lower the energy barrier(Activation energy) on a reaction
speeds it up

Question 22

What do enzymes do to transition states ?

Answer 22

stabilise them
transition state-highest energy structure on reaction pathway
a reaction may happen in diff ways with diff transition state
enzymes provide reaction pathway with lower energy TS
enzymes bind to TS to catalyse reaction
active site forms bonds with TS2
release energy and therefore stabilises transition state

Question 23

Serine proteases & hydrolysase stabilising -vely charged TS

Answer 23

TS for this step develops negative charge on carbonyl oxygen
oxyonion hole stabilises charge with 2 hydrogen bonds
reaction goes fast