Lecture 3 & 5 Aminos Peptides And Prim-quat Structure

Question 1

Amino acids

Answer 1

Amino group+alpha carbon+ hydroxyl group+ side chain + hydrog

Question 2

Iso electric point

Answer 2

Equal/ no charge
Least soluble condition of protein
Most proteins neg charged
Some proteins have pH+ and are attracted to neg phosphate backbone of DNA or RNA

Question 3

Peptide bond

Answer 3

Ribosome connects aminos by condensation reaction forming a covalent C-N peptide bond - planar due to electronic ‘resonance’

Question 4

Primary protein structure

Answer 4

Condensation forms polypep chains
Weak non cov interactions:
H-H, ion-ion, dispersion & dipole

E.g. Si-O, C-F, C-H, C-OH, C-NH2, C-C, C-I, C-NO

Many more non cov than cov bonds form in any macromolecule

Cov bonds form framework and shape is due to non cov bonds

Electrostatic - not based on geometry except H bonds

Depend on proximity of charges

Bonds:
charge - charge
Charge-dipole (polarised molecules)
Dipole - dipole
Flux in adjacent electronclouds

Question 5

Primary protein structure H bonds

Answer 5

Non-cov polarised bond
Due to electoneg atoms having “lone pair” of electrons
Directional w/defined length like cov bonds

Usually N-H-N N-H-O O-H-N or O-H-O

Question 6

Secondary protein structure

Answer 6

alpha helix
Right hand most common
Strengthened by H bonds in backbone
Ampiphatic helices have
Hydrophobic/ polar side chains on one helix face
Hydrophilic/ nonpolar side chains on other helix face

Aminos that favour alpha helix:
Ala, Cys, Leu, Met, Glu, Gln, His, Lys

Beta sheets:
same direction chains - parallel
Opposite direction - antiparallel
Stabilised by H bonds (N-H / C-O)
Side chains project above & below sheet

Aminos that favour them: Val,Ile, Phe, Tyr,Trp, Thr

Other structures:
Random coiled regions

Turns- reverse, beta or hairpin bends
Tight loops change shape of polypep backbone often connect chains in beta sheets

Loops- more flexible extended turns

Favoured by: Gly, Ser, Asp, Asn, Pro

Pro and Gly are helix breakers

Question 7

Tertiary protein structure

Answer 7

Overall folding shape of protein
Contains regions of secondary structure assembled into overall shape
Structural domains contain ~1400 folds
Domains usually 80-150 amino acids
Diff domains have diff functions

Motifs - amino sequences linked to functions e.g. ef hand found in Ca binding proteins

Soluble globular proteins have polar hydrophilic residues outside and hydrophobic residues inside

Tertiary structure maintained by
H bonds to amino side chains
Ion pair interactions amino- amino (“salt bridges”)
Charge - dipole and dipole - dipole bonds between amino chains
Dispersible forces- induced dipoles
Protein w/water interaction
Hydrophobic effect directs amino chains in/out
May have ligands e.g. metal ions for stability or function

Question 8

Quaternary structure

Answer 8

Formed by combination of protein subunits each made up of one or more polypep chain and shaped by weak non-cov bonds

Question 9

Math

Answer 9

Power law y=Kx^a or logy= alogx+logk

E.g. metabolic rate Vs animal mass a=~0.75.

Logarithm scales allow huge data range - plot clearly on graph

Exponentials 10=10^1 333=10^2.5524
E= ~2.72
10=10^1= e^2.3026
e is transc