Table of Contents

Table of Contents

Module 1 Amino Acid & Peptides 1

Module 2 Proteins 2

Module 3 Protein function

2

Module 4 Lipids & Carbohydrates 3

Module 5 Enzymes

5

Module 6 Metabolic Pathways 6

Module 7 Metabolic regulations

10

Module 8 DNA structure and function 12

Module 9 Information processing

13

Module 10 Gene Regulation

16

Module 11 Genome Maintenance 18

1 Module Key term Explanation

Module 1 Amino Acid & Peptides 1 Gibbs Free energy DG=DH-TDS; DG=DG product - DG reactant

Energy of the reaction available to do work

1 Exergonic DG=-ve; Free energy released; favourable, spontaneous

1 Endergonic DG=+ve; Free energy absorbed, unfavourable, non-spontaneous

1 Enthalpy DH; heat

1 Exothermic DH=-ve, heat released 1 Endothermic DH=+ve, heat absorbed

1 Entropy DS=-ve: less disorder; DS=+ve: more disorder

1 Amino acid = central C + alpha C + amino (NH2) + R group (characteristic) 1 Chiral Molecules that is not superimposable on its mirror image (4 group

) 1 Aspartic Acid

[D, Asp]

Acidic; chelators, completely ionised, H bond acceptor Neutralß4.4à-ve

1 Glutamic Acid [E, Glu]

Acidic; chelators, completely ionised, H bond acceptor Neutralß3.1à-ve

1 Lysine

[K, Lys] Basic; 1 NH group (high pH: HH2) +veß10àNeutral

1 Arginine

[R, Arg] Basic, 3 NH group (guanidino), partial double bond +veß12àNeutral

1 Histidine

[H, His] Imidazole ring; H donor/acceptor; aromatic +veß7.4àNeutral

1 Asparagine

[N, Asn] Uncharged, polar; partial double bond; not chemically reactive;

H bond & acceptor 1 Glutamine

[Q, Gln] Uncharged, polar; partial double bond; not chemically reactive H bond & acceptor

1 Serine

[S, Ser] Uncharged, polar; partial double bond; not chemically reactive H bond & acceptor

1 Threonine

[T, Thr] Uncharged, polar; partial double bond; not chemically reactive H bond & acceptor; extra chiral centre; 多一个 methyl group 1 Phenylalanine

[F, Phe] Aromatic, non-polar, unreactive, resonance structure 1 Tyrosine

[Y, Tyr] Aromatic, non-polar和Phe差一个OH, OH can H bond, uncharged-polar Neutralß10à-ve

1 Tryptophan

[W, Trp] Aromatic, largely nonpolar, conjugated double bond, Absorbs UV light, fluorescent, Indole NH H-bond donor, electron-richà charge transfer, 280nm

1 Alanine [A, Ala]

Non-polar, hydrophobic, aliphatic, interact with other non-polar, no reactive groups

1 Valine [V, Val]

Non-polar, hydrophobic, aliphatic, interact with other non-polar, no reactive groups, 比 Ala 多一个 beta branch

1 Leucine

[L, Leu] Non-polar, hydrophobic, aliphatic, interact with other non-polar, no reactive groups, longer version of Val

1 Isoleucine

[I, Ile] Non-polar, hydrophobic, aliphatic, interact with other non-polar, no reactive groups, beta-branched, extra chiral center, structural isomer of Leu

1 Proline

[P, Pro] Non-polar, hydrophobic, aliphatic, interact with other non-polar, no reactive groups, cyclic five membered ring, no NH groups, helix breaker, f=60

2 1 Glycine

[G, Gly] Non-polar, hydrophobic, aliphatic, interact with other non-polar, no reactive groups, side chain=H, Non-chiral, less steric clashed/restrictions on f&y 1 Cysteine

[C, Cys] Sulfur-containing à disulphide bridges, thiol polar, deprotonated=very polar Neutralß8.5à-ve

1 Methionine [M, Met]

Sulfur-containing à disulphide bridges, thioester, non-polar, air-oxidised to sulfoxide

1 Omega Trans = -180˚; Cis = 0˚, C-N

1 Phi N-Ca, Dàclockwiseà+ve, Làantià -ve

1 Psi C-Ca

Module 2 Proteins

2 Folding More favoured, cooperative, polar side chain 在外，nonpolar 在内 2 Unfolding Less favoured, denatured

2 Anfinsen’s Protein folding/refolding is reversible

2 Misfolding Molecular crowding à inappropriate interactions before folding (Nascent) 2 Chaperones Help avoid misfolding

2 Molecular crowding Cells containing high concentration of proteins/nucleic acid/sugar/lipids 2 Electrostatic

interactions

Interactions between charged molecules (Salt bridges/Hydrogen bonding/ dipole-dipole)

2 Van der Waals London dispersion, electrostatic, atoms very close to each other

2 Hydrogen bond Two electronegative atoms compete for the same H atom, O>N>C>S>H 2 Hydrophobic effect Interactions between water and non-polar atoms

2 Ramachandran plot The distribution of phi and psi dihedral angles that are found in a protein, shows common 2˚ structure elements

2 Secondary structure A local spatial arrangement of the polypeptide backbone, stabilized by H bond

2 Alpha-helix Phi, psi=-57˚, -47˚, 3.6 residues/turn, HxxHxxx Ala & Leu = helix former, Pro & Gly = helix breaker

2 Beta-sheet Phi, psi = -130˚, +130˚, antiparallel, ≥2 beta strands, HxHxHx 2 Beta/reverse turn Beta strands转弯的地方, 有Proline/Glycine

2 Super 2˚ aa-hairpin, bb-hairpin, bab

2 Tertiary structure Overall spatial arrangement of atoms in a protein, stabilised by hydrophobic/disulphide bond

2 Folds How 2˚ structure folds relative to each other in space 2 Domains Independently folded region

2 Module A repeating domain with same fold

2 Quaternary structure Formed by assembly of individual polypeptides into a larger functional cluster 2 Intragenic mutation Point mutations, insertions, deletions

2 Gene duplication Whole/part of genome is duplicated

2 DNA segment shuffle ≥ 2 existing gene can be broken & recombined

2 Gene lateral transfer One organism acquires part of the genome of another 2 Similarity Different AA, similar property, >25% identity

2 Gap Better alignment, result in loop insertion 2 Homologue Same folds, > 25% identity

2 Orthologue Same function, different species 2 Paralogue Different performance, 1 organism

Module 3 Protein function 3 Haemoglobin 4˚ structure, tetramer = 2a+2b

3 Immunoglobin 2 heavy chain + 2 light chain, promoter = heavy-light chain

3 Myoglobin Dense hydrophobic core, high proportion of a helix, O2 binds to Fe2+ heme,