Lecture 6 - Teritary & Quaternary Structure

Question 1

wha type of non-cov interactions can stabilise a tertial structure

Answer 1

H bonds
Disulphide bridges
or even the hydrophobic on inside and hydrophillic on outside can be stabilising

Question 2

how many AAs are there per turn of alpha helix

Answer 2

3.6

Question 3

how many nm does one AA take up (ie the Rise)

Answer 3

0.15nm

Question 4

what are 2 folding patterns in tertiary sturctures

Answer 4

motifs/supersecondary structures
and
domains

Question 5

what are motifs

Answer 5

at least 2 connected secondary structures
this is observed in many proteins
(theyre the ones with all the different types: hairpin, helix bundle etc)

Question 6

what is a helix-turn-helix and where commonly found

Answer 6

aka helix-loop-helix
two helices connected by a turn (looks like little string in between them)

found in many proteins that bind to DNA

Question 7

what is a coiled coil and where commonly found

Answer 7

two AMPHIPATHIC alpha helices
they interact in parallel via hydrophobic edges

it’s like two coils twisted around each other

• found in proteins that bind to DNA
  and also structural proteins

Question 8

what is a beta-alpha-beta unit

Answer 8

2 parallel beta strands with an aplha helix in between - bound by two loops

Question 9

what is a helix bundle

Answer 9

many alpha helices associated in antiparallel way to form a bundle

found in cytoskeleton

Question 10

what is a beta hairpin

Answer 10

two adjacent antiparallel beta strands connected via beta turn

this is the smallest form of beta that’s stable by itself

Question 11

what is a greek key

Answer 11

4 antiparallel strands that dont neighbour in priamry structure but neighbour in this tertiary stucture

see diagram, hard to explain

Question 12

what is a domain

Answer 12

independently fodled sections in a protein
may be multiple secitons that are individually folded or just one domain
and these sections are connected by loops and associated via non-cov interactions between side chains

Question 13

how is pyruvate kinase an example on a multi domain proteins

Answer 13

main chain folds into 3 distinct domains

Question 14

how can domains allow a multi-function protein

Answer 14

multiple domains in one protein mean each section can have a standalone fucntion

Question 15

[how do domains show evolutionary conservstion and give an example

Answer 15

the way a protein is folded into a domain can be conserved, even if the primary structure changes

e.g. cytochrome C

Question 16

what are the 4 common domain folds

Answer 16

parallel twisted sheet
beta barrel
alpha/beta barrel
beta helix

Question 17

motifs and domains allow us to classify protein structures into how many catergories

Answer 17

4

Question 18

what are the 4 categories of protein structure

Answer 18

1. all alpha
2. all beta
3. mixed alpha and beta (where a and B are interdispersed)
4. alpha + beta (where there are clustes of a helices and B sheets in distinct regions)

Question 19

how do subunits associate in quaternary structure

Answer 19

via many weak, non-cov interactions
e.g. hydrophobic, electrostatic, H-bonds

and covalent disulphide bonds (rare)

Question 20

what type of proteins usually have quat structure

Answer 20

regulated proteins
e.g. metabolic enzymes

Question 21

what structure catergory are immunoglobulin G in

Answer 21

quaternary structure
all beta protein

Question 22

what is immunoglobuling G made up of

Answer 22

2 heavy and 2 light chains
connected via disulphide bridges

Question 23

how many domains do each chain have in IG G

Answer 23

each heavy chain has 2 chains
and each light chain has 4 chains

Question 24

oh yea forgot, what is a beta sandwich

Answer 24

stacked beta strands/sheets