Protein structure and function

Question 1

what occurs with the functional groups of proteins at PH 7

Answer 1

Amino and carboxyl groups are ionized

deprotonated

Question 2

what carbon in amino acid is chiral and what do they dispaly

Answer 2

the central carbon is chiral
exist in L- or D- confromations

Question 3

How do you identify which AA sidechain is , nonpolar, uncharged polar, negative and postive

Answer 3

postive sidechains - protons ( arginine,lysine,histidine)
negative sidechains- COO- ( aspartic acid,glutami acid

Uncharged polar sidechains - NH2 -OH

Nonpolar sidechains - CH3 , SH

Question 4

what are essential AA

Answer 4

humans cannot synthesis and is provided by diet instead

histidine, isoleucine, leucine, lysine, methionine, phenlyalnine, threonine, tryptophan, valine

Question 5

list examples of conditional essential and none essential AA

Answer 5

Conditionally essential- argingine,cysteine,glutamine,glycine,proline,tyrosine

Non-essential - alanine, aspartic acid, asparagine, glutamic acid, serine ,selonocysteine, pyrrolysine

Question 6

How do AA mediate protein folding through their sidechains

Answer 6

polar sidechains can from h bond with water
Non polar sidechains form a hydrophobic core region

Question 7

what attractiosn and bonds do protein folding involve

Answer 7

electrostatic attractions- very strong
VDW attractions - relatively weak, amongst nonpolar molecules with lots of atoms
H bonds- formed in polar sidechains with oxygen, crucial for secondary structure
Disulphide bonds- covalent bonds, very strong, permanent

Question 8

what are peptide bonds and how are they formed

Answer 8

peptide bonds- amide linkage- join together AA into dipeptides and polypeptides

the N-terminus is the amino end
The C-terminus is the carboxyl end

C-N bond rigid and behaves liek a double bond

Question 9

why are the long polypeptide chians flexible

Answer 9

the single bonds between the central carbon atoms and the amide linkages allow rotation
only central C can rotate

peptide bonds between AA are rigid and cannot rotate

Question 10

what are phi and psi

Answer 10

dihedral angles of C-N and C-C

Question 11

describe the primary structure of a protein

Answer 11

sequence of AA joining by peptide bonding
polypeptide chain- polar
N terminus beginning, c-terminus is the end

Question 12

describe the secondary structure (alpha helices)

Answer 12

alpha helices
- a polypeptide chain can fold in an alpha helix by H bonding
- between oxygen atom of amide and hydrogen of amino group
- right handed spiral
- helices wind around one another to form coiled- coil superhelix
These superhelices are found in keratin i.e hair quills claws horns

Question 13

describe the secondary structure of a protein - beta sheets

Answer 13

• sheets formed by H bonding between oxygen and hydrogen
  beta strands aligned parallel or antiparallel

antiparallel- H bonds between NH and CO groups connect each AA with single AA on adjacent strand stabilising structure

Parallel - H bonds connect each AA on one strand with 2 diff AA on adjacent strand

Question 14

describe the tertiary structure of proteins

Answer 14

Final 3-D folding of polypeptide chains
▪ Often devoid of (free from) symmetry
▪ For globular proteins – nonpolar residues on the interior, charged residues on the surface

Question 15

describe the quaternary structure of proteins

Answer 15

❖ Proteins containing more than one polypeptide chain have quaternary structures
❖ Each substituent polypeptide chain is known as a subunit
❖ Subunits assemble into multi-subunit structures
❖ Multi-subunit structures can contain identical or differing subunits

Question 16

how many subunits do human insulin and heamogloblin have

Answer 16

Human insulin has 2 subunits - connected by disulfide bonds
Haemoglobin has 4 subunits ( 2 alpha and 2 beta chains, each has its own Haem group