amino acids

Question 1

pKa values amino acids

values of positively charged R groups and negatively charged

Answer 1

low pka - act as acids donate protons –> negatively charged
high pka - acts as bases and accept protons –> positively charged

Acidic negatively charged amino acids have low pKA

Basic Positively charged amino acids have a high pKa

Question 2

if ph of solution is less than pKa

if ph of solution is greater than pKa

Answer 2

if pH of solution is less than pKa the amino acids will be protonated .

if ph of solution is greater than pKa the amino acids will be deprotonated

Question 3

if pH is less than pI

if pH is greater than pI

Answer 3

if pH is less than pI the amino acid will be protonated

if the pH is greater than the pI the amino acid will be deprotonated.

Question 4

isoelectric point

acidic and basic proteins with charge and pI

Answer 4

is the ph at which a protein has no overall net charge.

acidic proteins have a negatively charged amino acid and a low pI less than 7

basic proteins have postiviely charged amino acids and have a high pI greater than 7

Question 5

features of a peptide bond

Answer 5

the peptide bond C-N has partial double bond characteristics

makes bond rigid and planar

Question 6

what orientation of peptide bond is seen?

Answer 6

trans peptide bond with carbona on opposite sides of peptide bond

Question 7

define primary, secondary, tertiary and quaternary structures of proteins

Answer 7

primary structure - the linear amino acid sequence of a polypeptide chain.

secondary - the local spatial arrangement of the polypeptide backbone

tertiary the 3D arrangement of all the atoms in a polypeptide chain

quaternary - the 3D arrangement of a multi subunit protein

Question 8

What bonds are involved in the primary, secondary, tertiary and quaternary structure?

Answer 8

Primary - peptide

secondary - hydrogen

tertiary - hydrogen, VDW’s, covalent disulphide, hydrophobic interactions and ionic

quaternary - hydrogen, VDWs, covalent disulphide, ionic and hydrophobic interactions.

Question 9

describe the collagen tertiary structure

Answer 9

collagen alpha chains that form a helical structure.

Question 10

what is the difference between motifs and domains?

Answer 10

motifs are folding patterns containing one or more elements of secondary structures

domains are part of a polypeptide that folds into a distinct shape with a functional role

Question 11

give the key features of an alpha helix

Answer 11

right handed helix

3. 6 amino acids per turn (distance of each repeating pattern
4. 54nm pitch

r groups are on outside so not involved in structure
small hydrophobic residues form strong alpha helixes
proline and glycine are helix breakers

Question 12

give the key features of a beta pleated sheet

Answer 12

0.35nm between adjacent amino acids when fully extended
can be antiparrellel - side by side arrangement of beta strands with them running in opposite directions
or parallel where strands run in same directions
or a mix

r groups on opposite sides of chain

Question 13

how do disulphide bonds form?

Answer 13

oxidation reactions as hydrogen is being lost

being cysteine r groups

Question 14

which bonds are more common in proteins that are secreted?

Answer 14

covalent

Question 15

give three ways of denaturing proteins

Answer 15

heat
ph - alters the ionisation states of amino acids - affects ionic and hydrogen bonds

detergents - distrupt hydrophobic interactions