proteins

Question 1

protein chain folds

Answer 1

3d conformation depends on the constituent amino acids

due to non-covalent interactions

Question 2

protein function

Answer 2

Function depends on 3D structure

• 3D structure depends on sequence
• Sequence is determined genetically

Question 3

protein organisation

Answer 3

primary: amino acid sequences
secondary: local packing, regular occurring
arrangements
tertiary: 3d packing of secondary structure elements
quaternary: number and position of polypeptide subunits

Question 4

structure of amino acids

Answer 4

Peptide bonds form between the amino & carboxyl groups of amino acids

Question 5

Uncharged polar side chains

Answer 5

Methionine
(Met or M)
Cysteine
(Cys or C

Question 6

Methionine

Answer 6

relatively unreactive but always at the beginning of a protein (tRNA charged with methionine binds to the translation start signal)

Question 7

Cysteine

Answer 7

form complexes with various metal ions can form disulfide binds

Question 8

disulfide bonds

Answer 8

form in between two cysteine residues to form cystine: very stable
oxidation and reduction

Question 9

peptide bond

Answer 9

One loses a hydrogen and oxygen from its carboxyl group (COOH) and the other loses a hydrogen from its amino group (NH2). This reaction produces a molecule of water (H2O) and two amino acids joined by a peptide bond (-CO-NH-). The two joined amino acids are called a dipeptide
Delocalisation of π electrons over entire peptide bond, rather than simply over the C=O bond= planar structure
partial double bond character because of the restricted rotation

Question 10

peptide bond conformation

Answer 10

trans or cis conformation (one of the infinite number of possible spatial arrangements of atoms in a molecule )

Question 11

secondary structure overview

Answer 11

described as the local organisation of polypeptide backbone (excluding constituent’s side-chains).

Question 12

α-helix & β-sheet

Answer 12

Strands are normally 5-10 amino acids in length
2 strands
Side chains point alternatively up and down
favorises hydrogen bonds between adjacent strands for sheet and amino acids close together for helix
parrallel or antiparallel strands
n-c n-c or n-c c-n

Question 13

tertiary structure

Answer 13

refers to its exact 3D structure, and the packing of secondary structural elements within it

Question 14

domains

Answer 14

Polypeptides greater than 200 amino acids often display multiple ‘Domains’
- Often serve as independent units of function

Question 15

modular structures

Answer 15

Proteins are made up from combinations of structural & functional folds/domains that can be repeated within the same protein structure and found in other proteins

Question 16

structural motifs

Answer 16

building blocks many domains are composed of: super-secondary structures, can be found in a wide variety of related or unrelated polypeptides
ex: the greek key: linked by loops in a specific 3d structure

Question 17

stabilisation of structure

Answer 17

domains are achieved after biosynthesis: conformation attained depends on the amino acids present+folding constraints and extent of secondary structure

Question 18

major stabilising forces:

Answer 18

hydrophobic interactions 
electrostatic interactions (salt bridge, hydrogen bounding) 
covalent linkages

Question 19

hydrophobic interactions

Answer 19

occur between 2 or more non polar molecules when they are in polar environments: non polar residues are buried inside of a polypeptides interior
very powerful interactions

Question 20

hydration shell

Answer 20

form an order : polar, main chain, hydrophobic

Question 21

electrostatic attractions

Answer 21

van der walls forces
hydrogen bonds
ionic interactions: slat bridges+ between oppositely charged amino acid side chains

Question 22

proteins movement

Answer 22

0.2 mm

Question 23

evolution

Answer 23

optimised protein for it’s role

Question 24

mutations

Answer 24

deleterious:
leading to an absent/ 1.dysfunctional protein
2.cutting a metabolic pathway
3.dysfunction of a regulatory protein or receptor
4. protein aggregation(alzheimers)
5.impairment or loss of defence against infection

Question 25

sickle cell anaemia

Answer 25

sickle cells obstruct capillaries causing intense pain and organ damage:
normal haemoglobin: molecules do not interact
exposed hydrophobic pocket (consequence of mutation): Hb molecules associate to form fibres under low oxygen condition