C. PROTEIN CHEMISTRY 1

Question 1

how many amino acids are in peptides

Answer 1

less than 50 linked by peptide bonds eg - Vasopressin
(often don’t possess well-defined 3D structures due to short chain length)
can be referred to as polypeptides

Question 2

how many amino acids are in proteins

Answer 2

more than 50 eg - insulin

Question 3

what can exist as peptides

Answer 3

antibiotics, hormones, poisons, pain killers

Question 4

examples of peptides in renal and endocrine disease

Answer 4

somatostatin
glucagon
TRH (hypothalamic releasing factor)
TSH, ACTH, LH (anterior pituitary hormone)
Oxytocin, vasopressin (posterior pituitary hormone)

Question 5

how are peptides used as therapeutics

Answer 5

Ozempic, Rybelsus, Wegovy for weight loss and diabetes
ie - Semaglutide modified from GLP-1 with a change in aa 8 so it can’t be cleaved and a linker added to aa 26

Question 6

how are peptides/proteins made

Answer 6

ribosome
DNA to mRNA to protein

Question 7

how are peptides read

Answer 7

from N-terminus to C-terminus

Question 8

why does combining Ala and Phe result in 4 rather than 1 dipeptide

Answer 8

both peptides have an amine and CA so there is different combinations

Question 9

what are the 3 problems with synthesising peptides

Answer 9

1. the amino acids can react either way round
2. the amino acids could self-condense
3. some amino acids have reactive side chains ie - an ester may form

Question 10

what do protecting groups do

Answer 10

• prevent unwanted side reactions and are removed until mild conditions when required
• they protect the NH2 and COOH and can protect reactive R-groups
  1. there is condensation of 2 protected amino acids to form peptide bond
  2. the protecting groups are removed

Question 11

why do we attach a leaving group to the acyl carbon of the carboxyl component to facilitate attack of amino component

Answer 11

because at ambient temperature an amine will form a salt with a carboxylic acid (acid + base = salt + water)

Question 12

what is the leaving group

Answer 12

conjugate base of a strong acid
ie - halide to form a acyl halide, ester etc

Question 13

what do we consider for peptide formation reaction

Answer 13

• rapidly and quantitatively
• under mild conditions
• avoiding side effects
• without affecting chirality
• producing easily removed co-products

Question 14

what determines function of a protein

Answer 14

structure (tertiary and maybe quaternary shape)

Question 15

what is the primary structure

Answer 15

unique amino acid sequence of a protein

Question 16

what type of bond is a peptide bond

Answer 16

amide bond

Question 17

how does resonance affect amide bond

Answer 17

NH+ and O- = due to mesomeric effect (nitrogen lone pair is conjugated with carbonyl group)
it has some double bond character

Question 18

what are the consequences of the resonance stabilisation of the amide bond

Answer 18

1. the peptide bond is chemically inert
2. amide group is planar (due to double bond character)

Question 19

what is a dihedral angle

Answer 19

involves 4 atoms and is measured clockwise
(0 or 120 degrees = eclipsed and 60 or 180 degrees = staggered)

Question 20

what staggered angle is more stable and favourable

Answer 20

180 degrees as sterically further away and hence not in the way

Question 21

what is a torsion (dihedral) angle

Answer 21

defined by 4 atoms
(+ = clockwise and - = counterclockwise)

Question 22

when is the angle positive

Answer 22

when the bond to front must be rotated clockwise to eclipse the bond at the rear ie - turn A in order to be in front of D or
the angle between 2 intersecting planes

Question 23

what are the 3 dihedral angles in proteins and peptides

Answer 23

phi, psi and omega

Question 24

what is the angle about the N-Cα bond

Answer 24

phi Φ

Question 25

what is the angle about the Cα-C bond

Answer 25

psi Ψ

Question 26

what’s the angle about the peptide bond

Answer 26

omega ω
(partial double bond character and is planar)

Question 27

what is the conformation when the omega angle is 180 (staggered)

Answer 27

trans = more favourable

Question 28

what is the conformation when the omega angle is 0 (eclipsed)

Answer 28

cis = unfavourable, due to steric clashed
(99% ω angles are trans due to high energy cost of eclipsing)

Question 29

what are the angles φ and ψ take up

Answer 29

they are co-dependent ie if φ = 0 degrees then ψ can’t equal 0 degrees due to steric clashes

Question 30

where does hydrogen bonding occur in the α-helix

Answer 30

between ci and ci+3

Question 30

what plot are φ and ψ summarised in

Answer 30

Ramachandran plot which shows that alpha helices, beta strands, and turns are the most likely conformations for a polypeptide chain to adopt, because most other conformations are impossible due to steric collisions between atoms

Question 31

what does hydrogen bonding cause in β-strand/sheet

Answer 31

creates antiparallel or parallel sheets

Question 32

what are the properties of α-helices

Answer 32

• right handed helix
• the carbonyl oxygen of residue ‘i’ forms a hydrogen bond with the amide of residue ‘i+4’. There are 3.6 amino acid residues per turn of the helix
• although each hydrogen bond is relatively weak in isolation, the sum of the hydrogen bonds in a helix makes it quite stable
• side chains point outwards and towards the N-terminus of the chain (lower residue numbers)
• α-helices form when φ ≈ -60°and ψ ≈ -50°

Question 32

what are the properties of β-strand/sheet

Answer 32

• C=O, N-H groups form H-bonds between neighbouring strands
  (same chain or different chain)
• Two types: Strands may be parallel or antiparallel
• Sheets pleat to maintain correct H-bond stereochemistry
• Side chains point alternatively on opposite sides of the sheet
• The polypeptide chain is much more extended in comparison to the alpha helix
• β-sheets form when φ ≈ -140° and ψ ≈ +130°

Question 33

what do β-turns in beta-sheets allow

Answer 33

the protein backbone to make abrupt turns

Question 34

what determines the 3D structure of a protein

Answer 34

the amino acid sequence
(the same protein can adopt different structures -e.g. native proteins refold into a different stable conformation such as happens in Alzheimer’s and Parkinson’s disease)

Question 35

what is unique about glycine

Answer 35

no chiral centre hence polypeptide chain is more flexible as no bulky side chain and adopts a larger range of phi and psi angles

Question 36

what is unique about cysteine

Answer 36

thiol group (SH) which allows disulfide bond formation within the same polypeptide chain or between different chains

proteins secreted into the extracellular environment often contain disulphide bridges due to oxidation occurring but the environment within a cell is reducing and therefore these proteins do not generally contain disulfide bridge

Question 37

what is unique about proline

Answer 37

secondary amine which is cyclic (-NH-) and creates a tertiary amide bond and makes polypeptide more rigid and hence restricts torsion angles in chain

Question 38

what is quaternary structure

Answer 38

> 1 polypeptide chains
(communication or structural role like haemoglobin and actin)