Lecture notes
Lecture notes Year 1 MBChB: Introduction to Medical Sciences (IMS)
Concise lecture notes from the proteins strand of the IMS module taught in the first year of the MBChB course at the University of Leeds!
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PROTEINSPROTEIN DIVERSITY
Proteome: full set of proteins encoded but not the human genome – not the same as number of genes
Polymorphism give rise to proteins that differ by one amino acid – functions differently
Alternative splicing during the maturing process for mRNA can give rise to completely different proteins based
on the same gene
Modification (e.g. adding sugar) causes difference in the final protein
Known proteins – translation factors, transporters, binding, structural, signalling, receptors, binding and enzymes
Type Disease Cause
Enzyme Haemophilia Defective/absent blood clotting factor
Catalase metabolic reactions Phenylketonuria Absence of phenylalanine hydroxylase (breakdown of
phenylalanine) – causes metabolic problems – babies can end
up with permanent brain damage
Transport/storage Sickle cell anaemia Hb not synthesised correctly
Muscle proteins Duchenne muscular Dystrophin is absent/ineffective – lose ability to use muscle –
Physical movement, dystrophy often wheel chair bound, don’t survive beyond teen years
movement of food in the gut
Communication Type 2 diabetes Insulin receptor is faulty, insulin can’t bind, raised blood
Receptors for hormones and glucose
neurotransmitters
Structure Osteogenesis imperfecta Mutation in type 1 collagen – increases risk of bone fractures
Keratin, collagen Scurvy Poor synthesis of collagen when vitamin C isn’t present to
support that process
Channels/transporters Cystic fibrosis Defective CFTR Cl- channel protein- problems with lungs,
Facilitate movement across digestive system, reproductive system
membranes
Regulation Type 1 diabetes Cells that synthesis insulin have been destroyed so no insulin
Cell division, protein present
synthesis hormones
Immunity Myasthenia gravis Body unintentionally creates antibodies that bind to
Antibodies, self-recognition neurotransmitter receptors- difficulty getting muscles to
respond to neurological signals
AMINO ACID STRUCTURE & PROPERTIES
Properties of amino acids
Categorising R groups- large/small, aliphatic/aromatic, polar/non-polar,
acidic/basic, sulphur-containing (cysteine & methionine), imino (proline)
Proline – secondary amine, alpha amino group is covalently bonded to
side-chain
o Makes the C – N very inflexible, limits conformations
All amino acids have a chiral α-carbon apart from glycine
o This makes amino acids optically active- L-isomer and D-isomer
o L-isomer found in proteins
o An enzyme won’t be able to catalyse a reaction of D or L because different groups wouldn’t sit right in the
active site
The charge on amino acids with ionisable R groups is pH – dependant
o pKa: pH at which a group is 50% ionised
o pH is below pKa – group will have H attached
o pH is above pKa – group will lose H+
, PRIMARY AND SECONDARY STRUCTURE
PRIMARY - number, sequence and order of amino acids in a peptide chain
Determined by gene which codes for protein, gene transcribed to produce mRNA, then translated on the ribosome
Unique properties of proteins are determined by the order of amino acids and their R groups
Amino acid polymers
Backbone – amino acid chain
Residue – an amino acid in a polypeptide chain
Side chains – R groups
A polypeptide chain has direction as the amino acids have different ends
Formation of peptide bonds (amide bonds)
Formed at ribosome
The peptide bond resonates between two forms – makes the bond quite rigid
C-N shows double bond characteristics, limited rotation
O and H positioned at opposite sides of the bond – trans position – maintains maximum distance between them
which is sterically most advantageous
SECONDARY- local spatial arrangements of amino acids in the peptide chain
Stabilised by H-bonds arising between O in peptide bond and N in another peptide bond
α- helix
o Formed by backbone of the chain, set number of residues per term
o H-bonds between the N-H and C=O groups (intrachain H-bonds) of the main chain
stabilise the helix
o Side-chains stick out form the helical structure
o Each C=O oxygen is H-bonded to N – H of amino acid 4 residues ahead: 1-5, 3-7, 2-6
o H-bonds nearly parallel to helix axis – gives some elasticity to the helix
-pleated sheet
o Stabilised by H-bonding between adjacent strands; between 2 part of the same chain
(intrachain) or between different amino acid chains (interchain)
o Side-chain lie above/below plane of sheet
o Fully extended polypeptide chain
o No elasticity
o Tetrahedral angles separating bonds of the carbon give a pleated appearance
o Loops and turns allow for the change in direction of the chains
TERTIARY AND QUATERNARY STRUCTURE
TERTIARY - organisation of primary and secondary structures into the 3D protein shape
Interior of soluble proteins is hydrophobic (e.g. Leu, Val, Met)
Exterior of soluble proteins is mostly hydrophilic (e.g. Arg, Lys, Glu)
o Most proteins have small exposed hydrophobic regions
Amino acids are brought together in the folded protein to assemble the
active site of an enzyme
o Each of the amino acid residue interacts with the substrate to
position it correctly and catalyse the conversion of substrate to
product
QUATERNARY - arrangement of different subunits in space
Multi-enzyme complexes – mitochondrial ATPase
Motility proteins – myosin
The interfaces between subunits contain closely packed non-polar side chains, hydrogen bonds and sometimes
disulphide bonds
Forces that stabilise tertiary and quaternary structure
Packing of helices, sheets and different subunits are stabilised by sidechain interactions
Interactions vary in strength
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