describe proteins
- Make up more then 50% of cells dry weight
- Made of ONLY L-amino acids
- Made of amino acids joined by peptide bonds
- When the peptide bonds break, releases H2O
- Note: Ca is the alpha carbon, while Co si the carbonyl carbon
- Note: the number of amino acid differences in amino acid chains is proprtional to phylogenetic differences between species, so can be used as a basis for studying molecular evolution
what configuration are amino acids?
Most peptide bonds between amino acids are trans configuration (opposite sides) to create less steric hindrance
* However, by changing the conformation to cis, can regulate proteins
○ E.g.
§ At proline, cis and trans have almost same stability, so can be either
Used in the folding of newly synthesised proteins
define N-terminal and C-terminal
- N-terminal
○ Start point of a amino chain- C-terminal
○ End point
- C-terminal
describe residue and conserved residue
- Residue
○ A amino acid unit (what’s left after the release of water)
○ 2 residues- dipeptide
○ 3 residues- tripeptide
○ + = oligopeptide
○ ‘many’ = polypeptide- Conserved residues
Invovled in active site of amino acids
- Conserved residues
what are the 3 classes of proteins?
classed based on shape + solubility
fibrous, globular, membrane proteins
describe fibrous proteins
§ Simple, linear
§ Serve structural roles
§ Insoluble in H2O + dilute salts
describe globular protein
§ Roughly spherical due to compact folding
§ Hydrophobic amino acids on inside, and hydrophilic on outside
Soluble in H2O
describe membrane proteins
§ Hydrophobic face outwards
NOT soluble in H2O
describe primary structure of proteins
- Primary
○ Chain of amino acids
Made up of a mix of the 3 classes of proteins
describe secondary structure of amino acids
- Folding into 3D structure due to interactions of backbone
- Note: b-sheets add strength + rigidity, a-helices provide flexibility
- Note: if amino acids have cysteines, will have a even no. Because pair up to make disulphide bridges
describe super-secondary structure: motif
Intermediate between secondary and tertiary structure
describe domains
- Units that make up tertiary structure
- Made of up several motifs
- Can be used to group organism because can see a common protein domain
- Domains identified by proteolysis- (breakdown of proteins back into amino acids using enzymes)
- Can have functions, e.g.
- EF-hand
- Binds calcium
- SH2
- Bind tyrosine for tyrosine kinase signalling cascades
- EF-hand
describe tertiary structures of proteins + Leventhal paradox
- Further folding due to intermolecular forces
- In order to become more stable
- Stability come from the larger no. Of hydrogen bonds + less SA + van der waals forces - Effected by hydrogen bonds, salt bridges (between NH3+ and O-), hydrophobic interactions (see image), and disulphide bonds (between 2 S)
- Note: Leventhal’s paradox: a protein cannot try every possible structure until it find the perfect one (because would take literally forever), therefore its implied that their is a folding pathway that it follows to find the most energetically favourable fold- the protein folding energy landscape
- In order to become more stable
describe quaternary structure of proteins
- Joining of multiple tertiary structures
- E.g. Haemoglobin, immunoglobulin G antibody, lactose dehydrogenase (can be used for malaria drugs to target)
describe open quaternary structure fo proteins
- Can polymerase
- Make up cytoskeletal system in cells
- Shaped like a wall or a funnel
advantages of quaternary structure of proteins
- Stability
- Due to reduction in protein Surface to volume ratio - genetic economy + efficiency
- shields hydrophobic residues
Less DNA required for monomer units
- shields hydrophobic residues
disadvantages of quaternary structure of proteins
- Brings catalytic sites together
- Catalase different by related reactions on different subunits
- Regulation/cooperation
- Binding of ligands in 1 site alters the binding ability at another
