C. PROTEIN CHEMISTRY 1 Flashcards
how many amino acids are in peptides
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
how many amino acids are in proteins
more than 50 eg - insulin
what can exist as peptides
antibiotics, hormones, poisons, pain killers
examples of peptides in renal and endocrine disease
somatostatin
glucagon
TRH (hypothalamic releasing factor)
TSH, ACTH, LH (anterior pituitary hormone)
Oxytocin, vasopressin (posterior pituitary hormone)
how are peptides used as therapeutics
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
how are peptides/proteins made
ribosome
DNA to mRNA to protein
how are peptides read
from N-terminus to C-terminus
why does combining Ala and Phe result in 4 rather than 1 dipeptide
both peptides have an amine and CA so there is different combinations
what are the 3 problems with synthesising peptides
- the amino acids can react either way round
- the amino acids could self-condense
- some amino acids have reactive side chains ie - an ester may form
what do protecting groups do
- 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
why do we attach a leaving group to the acyl carbon of the carboxyl component to facilitate attack of amino component
because at ambient temperature an amine will form a salt with a carboxylic acid (acid + base = salt + water)
what is the leaving group
conjugate base of a strong acid
ie - halide to form a acyl halide, ester etc
what do we consider for peptide formation reaction
- rapidly and quantitatively
- under mild conditions
- avoiding side effects
- without affecting chirality
- producing easily removed co-products
what determines function of a protein
structure (tertiary and maybe quaternary shape)
what is the primary structure
unique amino acid sequence of a protein
what type of bond is a peptide bond
amide bond
how does resonance affect amide bond
NH+ and O- = due to mesomeric effect (nitrogen lone pair is conjugated with carbonyl group)
it has some double bond character
what are the consequences of the resonance stabilisation of the amide bond
- the peptide bond is chemically inert
- amide group is planar (due to double bond character)
what is a dihedral angle
involves 4 atoms and is measured clockwise
(0 or 120 degrees = eclipsed and 60 or 180 degrees = staggered)
what staggered angle is more stable and favourable
180 degrees as sterically further away and hence not in the way
what is a torsion (dihedral) angle
defined by 4 atoms
(+ = clockwise and - = counterclockwise)
when is the angle positive
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
what are the 3 dihedral angles in proteins and peptides
phi, psi and omega
what is the angle about the N-Cα bond
phi Φ
what is the angle about the Cα-C bond
psi Ψ
what’s the angle about the peptide bond
omega ω
(partial double bond character and is planar)
what is the conformation when the omega angle is 180 (staggered)
trans = more favourable
what is the conformation when the omega angle is 0 (eclipsed)
cis = unfavourable, due to steric clashed
(99% ω angles are trans due to high energy cost of eclipsing)
what are the angles φ and ψ take up
they are co-dependent ie if φ = 0 degrees then ψ can’t equal 0 degrees due to steric clashes
where does hydrogen bonding occur in the α-helix
between ci and ci+3
what plot are φ and ψ summarised in
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
what does hydrogen bonding cause in β-strand/sheet
creates antiparallel or parallel sheets
what are the properties of α-helices
- 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°
what are the properties of β-strand/sheet
- 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°
what do β-turns in beta-sheets allow
the protein backbone to make abrupt turns
what determines the 3D structure of a protein
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)
what is unique about glycine
no chiral centre hence polypeptide chain is more flexible as no bulky side chain and adopts a larger range of phi and psi angles
what is unique about cysteine
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
what is unique about proline
secondary amine which is cyclic (-NH-) and creates a tertiary amide bond and makes polypeptide more rigid and hence restricts torsion angles in chain
what is quaternary structure
> 1 polypeptide chains
(communication or structural role like haemoglobin and actin)
