Protein Structure

Question 1

What are proteins used for in the body?

Answer 1

Enzymes
Transporters 
Machines 
Immune protection 
Ion channels 
Receptors 
Ligands

Question 2

General structure of an amino acid

Answer 2

H,NH2,COOH,R attached to a central carbon group. R group distinguishes the type of amino acid.

Question 3

What is a zwitterion

Answer 3

When both the NH2 and COOH group are charged. (NH3+ and COO-)
NH2=base proton acceptor
COOH=acid proton donor

Question 4

How are amino acids classified?

Answer 4

According to chemical properties of the R groups

Question 5

Which is the N terminal and C terminal of a protein?

Answer 5

N= NH3+end (amino end) and C=COO- end (carboxyl end)

Question 6

What is amino acid residue

Answer 6

An amino acid after its bonded. What’s left of it w.g NH-CHR-CO

Question 7

Categories by which amino acids are categorised

Answer 7

Chemical properties: 
Hydrophobic 
hydrophilic 
Polar 
Non polar 
Acidic 
Basic 
Neutral 

Physical properties:
Aliphatic
Aromatic

Question 8

If the pH of the solution < the Pk value then the side chain will be…..?

Answer 8

Protonated

Question 9

Is the pH of a solution> the pK value then…..?

Answer 9

The group will be deprotonated

Question 10

Are positively charged R groups basic or acidic?

Answer 10

Basic - high pK and NH3 = positive charge. Are protonated as a base accepts a proton

Same fo reverse

Question 11

How is a polypeptide bond formed

Answer 11

Between COOH and NH3. Cones nation reaction- loss of h2o.

Question 12

in which plane do peptide bonds (C-N) lie in a polypeptide

Answer 12

all in the same plane, they are planar

Question 13

why are all peptide bonds(C-N) in the same plane and what advantages does this give?

Answer 13

peptide bonds C-N has partial double bond characteristics meaning they are unable to rotate. This makes the bonds more rigid. The other bonds are free to rotate (N-CHR and C-CO)

Question 14

What is cis/trans conformation

Answer 14

whether the side chain(Rgroup) is on the same side of the bond(cis) or opposite sides on the peptide bond(trans)

Question 15

what is the isoelectric point (pI) of proteins

Answer 15

pH at which a protein forms a zwitterion. A molecule with both a positive and negative charge

Question 16

pI>7 = acidic or basic protein?

Answer 16

basic because contain mainly positively charged proteins. lower pH required to deprotonate the COOH

Question 17

pI<7 = basic or acidic?

Answer 17

acidic because protein contains mainly negatively charged amino acids and pH needs to be raised considerably to protonate

Question 18

if proteins pHpI?

Answer 18

pHpI protein is deprotonated

Question 19

what type of bond are peptide bond and what do they hold together

Answer 19

covalent bonds and they hold together primary sequence

Question 20

structure of alpha helix?

Answer 20

H bonds stabilise structure and its shaped by the sugar phosphate backbone. Also hydrophobic residues are strong helix formers

Question 21

structure of beta sheet

Answer 21

R groups alternate, each R group is on opposite side to last R group on chain. they are arranged anitparrallely to form beta sheet. hydrogen bonds form between sheets to stabilise structure. can also line up parallel or a mix of both.

Question 22

example of beta sheet and alpha helix

Answer 22

beta sheet- fatty acid binding protein

alpha helix- iron storage protein ferritin

Question 23

structure, role and example of a fibrous protein

Answer 23

long strands/sheets of repaying structures. role is to support and protect shape. e.g collagen

Question 24

structure, role and example of a globular protein

Answer 24

compact shape and made of mixture of secondary structures. role is in catalysis and regulation. e.g carbonic anhydrase

Question 25

Structure of collagen

Answer 25

triple helical arrangement of collagen chains. contains glycine every 3rd amino acid. hydrogen bonds between chains stabilise it.

Question 26

how do proteins fold?

Answer 26

primary= covalent bonds 
secondary= hydrogen bonds 
tertiary= other interactions including disulphide and hydrophi/pho (hydrophobic R groups on inside of proteins) 
quaternary= same but joins multiple polypeptides together.