6b

Question 1

the geometry of the peptide bond and their functional group interactions gives rise to what

Answer 1

complex protein structures

Question 2

diff protein structures

Answer 2

• primary
• secondary
• tertiary
• quaternary

Question 3

whats the primary structure

Answer 3

linear sequency of amino acids

Question 4

bonds involved in the primary structure

Answer 4

covalent peptide bonds : amide bonds

Question 5

secondary structure

Answer 5

alpha helix or beta plated sheet

spatial arrangement of the polypeptide chain in a well defined structure

Question 6

bonds in secondary structure

Answer 6

hydrogen bonds between the NH and CO in the ppc backbond

electrostatic ion interactions

VDW and hydrophobic effect

Question 7

tertiary structure

Answer 7

overall 3d structure of the polypeptide chain

Question 8

bonds in tertiary structure

Answer 8

hydrogen
electrostatic
vdw
disulphide

Question 9

quaternary structure

Answer 9

combo of multiple ppc // subunits

the quaternary structure is the way the subunits are arranged

Question 10

bonds in quaternary structure

Answer 10

h bonds
electrostatic
vdw
disulphide

Question 11

what bonds are important in determining the protein structure

Answer 11

non covalent forcesssss

Question 12

what is the primary sequence determines by

Answer 12

the primary sequencee of amino acids is determined by the dan of the gene that encodes that protein

Question 13

the primary structure starts with what

Answer 13

n terminus to C terminus

Question 14

what does the alpha helix look like

Answer 14

like a telephone cord

with the R groups pointing outwards bc theyre hydrophobic

and the H bonds between the N and H of the backbond being inside the helix bc theyre hydrophilic

Question 15

is the alpha helix a clockwise or anticlockwise thing

Answer 15

its a clockwise rotation!!1

Question 16

whats the wall of the helix made up of

Answer 16

the wall of the helix is made up of the peptide bonds

Question 17

whats the stability of the alpha helix bc of

Answer 17

bc the side chains are well separated + point towards the N terminus

bc each peptide link is involved in 2 hydrogen bonds ,, aka in a peptide bond,, the N and CO are both invloved in diff H bonding

Question 18

describe fully the alpha helix

Answer 18

each spiral is 5.4A away from the axis

there are about3.6aa per turn

a normal alpha helix normally has around 35 aa residues

Question 19

the NH and CO in an aloha helix make H bonds how many aa away

Answer 19

4 aa away.

so aa 1 is h bonded to aa 5

Question 20

why is alpha helix clockwise and not anticlockwise

Answer 20

bc the anticlockwise helix would have the side chains near the CO making it too overcrowded.

Question 21

theres a small electric dipole in the peptide bond meaning what

Answer 21

theres a net dipole along the helical axis

aka the N terminus is delta +

the C terminus is delta -

Question 22

the structure of the alpha helix depends on what

Answer 22

the correct repeating torsion angles!!

aka the angles of the peptide bonds.

Question 23

why is the alpha helix picky when it comes to aa and their side r chains

Answer 23

bc a a too big // too small one can destabilise the alpha helix.

Question 24

why is proline not used in the alpha helix

Answer 24

bc the r group bonds back onto the n

meaning it will create kinks in the chain

and there will be steric hinderance and no h bonds will be made

Question 25

alpha helixes are favourable to what

Answer 25

theyre favourable structures for a hydrophobic transmembrane region

Question 26

why are alpha helixes favourable for a transmembrane hydrophobic region

Answer 26

- r groups are hydrophobic and point out - NH and CO are inside the helix and form h bonds in the hydrophilic version.

Question 27

describe the alpha helix and transmembrane image

Answer 27

u have the membrane which obvs is hydrophobic on the inside bc its phospholipids and all that. the alpha helix kinda sits in it but also peaks out the top thats why theyre good bc they help communicate things from the outside and inside of cells.

Question 28

describe a beta pleated sheet

Answer 28

the backbone and individual polypeptide strand forms a zigzag which gives it the pleated appreance

Question 29

what happens to beta pleated sheets

Answer 29

u laterally associate strands to it

Question 30

do beta pleated sheets like larger of small amino acids

Answer 30

they like large amino acids

Question 31

type of beta pleated sheets

Answer 31

u have antiparallel sheets and parallel sheets

Question 32

descibe antiparallel sheets

Answer 32

allows well aligned h bonds u kinda keep inverting the ppc as u add more laterally also allows VDW to occur between the side r chains

Question 33

describe parallel beta pleated shets

Answer 33

this is where u have unaligned h bonds between the NH and CO of ppc. this is bc u dont invert the ppc as u add them laterally. u keep placing them the same as the previous one.

Question 34

a long beta strand is usually made up of how many amino acids

Answer 34

usually around 15 aa residues

Question 35

describe the tertiary strcutre

Answer 35

its the 3d shape of the protein u have the single ppc backbpne and the secondary alpha helix and beta pleated sheets kinda packed against eachother u have the beta pleated sheets and the alpha helix packed ontop of eachother

Question 36

the tertiary structure has 2 diff domains,, what are they

Answer 36

the alpha and beta domains

Question 37

decribe quaternary structure

Answer 37

many subunits!! the alpha and beta subunits

Question 38

describe haemoglobin

Answer 38

quaternary structure u have the alpha and beta subunits

Question 39

if a protein is made up of n residues,, how many possible aa sequences are there

Answer 39

20^n bc theres 20 possible amino acids

Question 40

the structure of the protein relates to what

Answer 40

its function

Question 41

what are the 2 diff types of protein

Answer 41

fibrous globular

Question 42

describe a fibrous protein

Answer 42

they have a structural function they provide support, strength , shape and flexibility ppc arranged in long strands // sheets single type of secondary unit insoluble in water collagen is an example