David O'Connell lecture notes

Compartmentation

an enclosed system that maintains high local concentrations of components that would otherwise diffuse away

Amphipathic

Describes a molecule that has both hydrophilic and hydrophobic parts

The hydrophobic effect

The tendency of non polar molecules to minimise their contact with water.

Water molecules form more ordered ‘cages’ around hydrophobic groups.

Micelles

Tiny spherical structures formed by amphipathic molecules in water. Hydrophobic core, hydrophobic molecules insert into the micelles core effectively hiding from water.

Disulfide bond formation mechanism 

1. Two cysteine thiol groups (-SH) come close together

2. Oxidation occurs: electrons are removed and a bond forms between the sulfurs

3. Result: stable -S-S- linkage 

Enzymes like protein disulphide isomerase (PDI) in the endoplasmic reticulum can catalyse bond formation and rearrangement. 

Amino acids being modified after incorporation into proteins: Hydroxylation

Adds a hydroxyl group to a side chain of a protein

Amino acids are also precursors to a number of neurotransmitters, hormones, cofactors, antixoxidants and signalling molecules, for example

GABA, histamine, dopamine and thyroxine 

Methylation

Adds a methyl group, usually at lysine or arginine residues

Phosphorylation

adds a phosphate to serine, threonine or tyrosine

Glycosylation

attaches a sugar, usually to a nitrogen or oxygen in an amino acid side chain

Ubitiquitation

adds ubiquitin to lysine residue of a target for degradation

SUMOylation

adds a small protein SUMO (small ubiquitin-like modifier) to a target protein.

Angstrom

Unit of length used to measure very small distances, especially in atoms, molecules and light wavelength. 

The alpha helix right handed conformation has how many residues per turn and a pitch of how many angstroms 

• 3.6 residues 

• 5.4 angstroms 

Oligomeric protein

a protein composed of two or more polypeptide chains, called subunits, that assemble into a functional structure known as an oligomer.

Beta sheets

• formed by hydrogen bonding between the backbone atoms of adjacent polypeptide chains or segments.

• polypeptide chains in B-sheets are almost fully extended, unlike the coiled alpha-helix 

Parallel Beta sheets

• Strands run in the same N to C direction

• Hydrogen bonds are slightly angled, so sheet is less stable than antiparallel 

Anti parallel Beta sheets

• Strands run in the opposite N to C directions

• Hydrogen bonds are linear and therefore stronger

Formation of Fluorophore of Green Fluorescent Protein (GFP)

• Carbonyl C atom of Serine forms a covalent bond to the amino N atom of Glycine 

• Elimination of water occurs and oxidation of alpha carbon to beta carbon bond of Tyrosine to a double bond.

• Resulting structure gives conjugated double bonds giving the protein its fluorescent properties

Dimer

a complex made of two identical or similar units, called monomers, joined by a covalent bond

Protofilaments

• Definition: Protofilaments are linear chains of protein subunits that assemble to form the basic building blocks of certain larger structures, such as microtubules or amyloid fibrils.

• Example: In microtubules, each protofilament is a chain of α- and β-tubulin dimers stacked head-to-tail.

• Key point: Protofilaments are one-dimensional (linear) and provide the scaffold for more complex filament structures.

Protofibrils 

• Definition: Protofibrils are intermediate fibrillar aggregates formed by the lateral or longitudinal association of protofilaments.

• Example: In amyloid formation, multiple protofilaments twist together to form a protofibril.

• Key point: Protofibrils are larger than protofilaments and often have a helical or twisted appearance.

Microfibrils

• Definition: Microfibrils are small, fiber-like structures composed of multiple fibrils or protofibrils, often forming a part of larger extracellular or cytoskeletal networks.

• Example: In plant cell walls, cellulose microfibrils consist of many cellulose chains (β-glucose polymers) bundled together. In the cytoskeleton, actin microfibrils are bundles of actin filaments.

• Key point: Microfibrils are higher-order structures with a fibrous appearance and usually provide mechanical strength.

Myoglobin 

• 153 amino acid monomer 

• 8 alpha helices connected by short peptide loops 

• Iron containing Haeme group

• Major physiological role is to facilitate oxygen diffusion in muscle 

The Haeme group containing Iron in Myoglobin

• Central Fe(II) atom is liganded to four N atoms of the Porphoryin ring

• Pyrrole groups of the ring are labelled A-D

• The Fe(II) is also liganded to a His side chain

• This structure binds Oxygen

• Heame is wedged in a hydrophobic pocket between the E and F helices in myoglobin

• Histidine E7 hydrogen bonds to the oxygen

• Two hydrophobic side chains on the O2 binding side of the haeme Val E11 and Phe CD1 help hold the haeme in place

Haemoglobin 

a tetramer with two conformations 

• Responsible for oxygen transport in the blood -from the lungs to the tissues 

• The protein quaternary structure is a tetramer -a2B2- a and B subunits are structurally related to each other and to myoglobin. 

Deoxyheamoglobin

The a1B1 protomer is related to the a2B2 protomer by a two fold axis of symmetry