Module 1.1 - Amino acids and protein structure Flashcards
Gibbs Free Energy
The energy of the reaction that is available to do work - also called “available” energy. Spontaneous reactions have a negative change in Gibbs free energy
Exergonic
ΔG is negative: free energy released. Favourable, spontaneous
Endergonic
ΔG is positive: free energy absorbed. Unfavourable, not spontaneous
Exothermic
ΔH is negative: heat released
Endothermic
ΔH is positive: heat absorbed
ΔS is negative
less disorder
ΔS is positive
more disorder
Keq
the thermodynamic equilibrium constant for the reaction. it describes the ‘position’ of the reaction at equilibrium i.e. the relative concentrations of components at equilibrium
What are some of the functions of proteins?
Catalysis
- Enolase (in the glycolytic pathway)
- DNA polymerase (in DNA replication)
Transport
- Haemoglobin (transports oxygen in the blood)
- GLUT1 (transports glucose across the cell membrane)
Structure
- Collagen (connective tissue)
- Keratin (hair, nails, feathers, horns)
Motion
- Myosin (muscle tissue)
- Actin (muscle tissue, cell motility)
Signalling (transduction)
- Insulin receptor (detects hormones in blood)
- Glucagon receptor (detects hormones in blood)
Altering cellular metabolism
What are the overarching properties of amino acids?
○ Capacity to polymerise
○ Useful acid-base properties
○ Varied physical properties
Varied chemical functionality
Features of Aspartic acid (Asp, D)
Side chain: one methylene capped by a carboxylic group
It is completely ionised negatively charged at physiological pH (carboxylate favoured). Very polar. Often acts as chelators of metal ions. pKa of 4.4 - deprotonated form dominates, can get resonance structures
Features of glutamic acid (Glu, E)
Side chain: two methylene capped by a carboxylic group
It is completely ionised negatively charged at physiological pH (carboxylate favoured). Very polar. Often acts as chelators of metal ions. pKa of 4.4 - deprotonated form dominates, can get resonance structures
Features of Lysine (Lys, K)
Basic amino acid. Long aliphatic side chain of 4 methylene groups capped with amino group. Completely ionised, positively charged at physiological pH. Nh3+ form predominates. Very polar. pKa of 10.
Features of Arginine (Arg, R)
Basic. Long aliphatic chain side chain of 3 methylene groups capped with guanidino group. Completely ionised at physiological pH (pKa 12). Very polar. Guanidino group is planar stabilised by resonance. Charge is delocalised over whole group (partial double bonds)
Features of histidine (His, H)
Basic. 5 membered ring with two nitrogens. Both states dominate at pH 7 (pKa roughly 7). Highly used in enzyme active sites. Imidazole ring has special properties. H-bond donor or acceptor, electrophile or nucleophile (chemically ambidextrous). Tertiary amine.
Features of Asparagine (Asn, N)
Uncharged, polar. One methylene capped by an amide group. Not very chemically reactive. H-bond donor and acceptor. Deamidate to aspartic acid and high and low pH.
Glutamine (Gln, Q)
Uncharged, polar. Two methylene capped by an amide group. Not very chemically reactive. H-bond donor and acceptor. Deamidate to glutamic acid and high and low pH.
Features of Serine (Ser, S)
Uncharged, polar. Hydroxyl on side chain. Not very chemically reactive. H -bond donor and acceptor.
Features of threonine (Thr, T)
Uncharged, polar. Hydroxyl on side chain. Not very chemically reactive. H -bond donor and acceptor.
Features of phenylalanine (Phe, F)
Aromatic side chain (benzene ring). Nonpolar, unreactive. Only reactive under extreme conditions. Absorbs UV weakly.
features of tyrosine (Tyr, Y)
aromatic with some characteristics of uncharged polars. Largely nonpolar (ring). Somewhat polar (OH) can form H-bonds. Hydroxyl group pKa of roughly 10 (deprotonates below). Fluoresces weakly, absorbs UV moderately
Features of Tryptophan (Trp, W)
Aromatic. Largely nonpolar. Indole ring (6 member and 5 member ring). Largest and rarest side chain (1% occurrance). Conjugated double bonds. Absorbs UV strongly and fluorescent. Indole Nh H-bond donor. Electron rich - charge transfer
Features of alanine (Ala, A)
Nonpolar, aliphatic side chain. No reactive groups, hydrophobic, interact favourably with other nonpolar groups.
Features of Valine (Val, V)
Nonpolar, aliphatic side chain. No reactive groups, hydrophobic, interact favourably with other nonpolar groups. Beta branched (has additional methyl groups)
