Biochemistry Flashcards
Covalent bonds
Shared pairs of electrons - strong (200-800kJ/mol), defined length + direction
O-4, N-3, S-2, P-5.
Single bonds allow rotation, different conformations more energetically favourable than others.
Functional groups
Mols w/ carboxyl -CO groups are acids.
Amino groups +ve charged, phosphate groups -ve charge in neutral conditions
Non covalent bonds
Weaker (<30kJ/mol), unequal sharing of electrons between nuclei.
Inc. hydrogen, electrostatic, van der waals, hydrophobic
Differing electronegativity of elements causes polarity: F > O»_space;S = C > H.
S-H has moderate polar bond, C-H non-polar covalent
Hydrogen bonds
Most common dipole-dipole bond, acceptor must be around 1.8nm away + in straight line. 30kJ to break H bonds.
Water mol can form 4 H bonds w/ other mols, 2 as acceptor + 2 as donor.
Donors: amino group, hydroxyl group.
Acceptors: imine, ether, ketone
Electrostatic interactions
Between opposite charges, stringer than H bond + greater distances than other non-covalent bonds.
e.g. acidic + basic a. acids (glutamate + lysine) -> salt bridge or ion pair
Attraction can be weakened by screening of water mol/other ions on protein surface, pairs in hydrophobic interior stronger/more stable
Van der waals
Between permanent or inducible dipoles (C-H), depends strongly on distance.
Inducible dipoles come due to random asymmetry/fluctuations, sum of vdw radius is optimum distance for inducible dipole interaction, force v. small (< 1kJ/mol) - large numbers can stabilise mol e.g. DNA
Hydrophobic interactions
Not bonds, cant engage in H binding as few/no polar bonds in hydrophobic mols.
Increase in entropy, every CH2 group out of water increases entropy (s) by +3kJ/mol so its favourable.
Molecules in water
Water determines shape molecules assume. Is molecular dipole so forms H bonds w/ itself. Can disrupt NaCl lattice by forming hydration shell around ions.
Alanine (carboxyl + amino) very polarised so more soluble, can form H bonds w/ water (solvation), hydrophilic.
Benzene is non-polar + hydrophobic -> reduces entropy as water has reduced motility around it.
Phospholipids amphipathic/amphiphilic, can migrate into micelles/vesicles.
Titration curves
Can study pH of a solution of weak acid by gradually adding small vols of strong base - until molar equivalent reached.
Flattest parts of curve where pH = pKa -> strongest buffering capacity e.g. buffers normally have pK of 6.5-7.5
A. acids (esp glycine) have acidic carboxyl & basic amino so titration curve has 2 pKa values -> amphoteric/amphiprotic.
If pKa > pH then more acid then base, vise versa
Amino acid structure
Zwitterion - under normal conditions have + and - charge.
C is chiral asymmetric. Enantiomers are stereoisomers that are mirror images of each other.
If carboxyl on left then it is L, if on right then it is D enantiomer.
-> mainly L amino acids in proteins
Glycine only a. acid without enantiomeric form (not chiral)
Fischer projection
Positions carboxyl group at top, R group at bottom of central C atom.
If amino group on left it is an L enantiomer, if on right then it is a D enantiomer.
Aliphatic a. acids
Non-aromatic hydrocarbon side chains.
G, A, V, L, I -> V to I have branched side chain
More hydrophobic as you go along.
Proline
Aliphatic a. acid (3C chain) BUT has heterocycle, much less hydrophobic + rotation restricted around N-C
Aromatic a.acids
Ring structures w/ alternating double bonds (delocalised pi electrons), varying hydrophobicity.
F, Y, W, H
-> H can have +ve charge, is a weak acid pKa =6
Both H & W engage in H bonding
Hydroxyl a. acids
Polar groups involved in H bonding as donor + acceptor.
- can from phosphate esters
Y, S, T
Sulphur containing a. acids
C - similar to serine, weak H bonds, much stronger acid, forms disulphide bonds
M - fairly hydrophobic, AUG start codon
Acidic a. acids + their amides
Form salt bridges + polar interactions w/ water (H bonding), negatively charged
D & E
- pKa of side chain ~ 4
Amides are N & Q - not ionisable but highly polar, strong H bond donor/acceptor
Basic amino acids
N atoms w/ free electron pair, +ve charges.
R & K
Arg pK =12.5, Lys pK = 10
Peptide bonds
Formation eliminates ionizable carboxyl + amino groups (removes charge)
Repeating N-C-C unit makes up backbone of peptide chain
Secondary structure
A. acid sequence determines regularly repeating conformations.
a -helices + B strands/sheets
Native conformation is single stable shape of polypeptide chain
Affected by bond rotations + weak non-covalent interactions.
Peptide group always planar/flat, C-N bond has double bond character -> resonance
So no rotation at peptide bond, 6 atoms lie in same plane
Trans + cis conformations of peptide groups
Double bond character means distinct conformations possible about C-N.
Cis is less favourable due to steric interference of a-C side chains
Rotation of N-C(a) bind in proline restricted due to ring structure.
Ramachandran plot can model possible phi (N-C(a))+ psi (C(a)-C) rotations
a-helix
Right handed - backbone turns clockwise from N terminus.
- each C=O (n) from H bind w/ amide hydrogen on residue (n+4)
- all C=O groups point towards C terminus, helix is dipole
- stabilised by many H bonds
Pitch is advance along long helical axis per turn (0.54nm)
Rise is the advance of each residue along long helical axis (0.15nm)
-> 3.6 amino acids per turn
B strands/sheets
Strands - polypeptide chains almost fully extended
Sheets - many strands arranged side by side, stabilised by H bonds between adjacent strands (C=O & -NH), if antiparallel more stability.
-> side chains project alternately above + below B sheet plane -> pleated
Loops - contain hydrophilic residues + found on protein surfaces
Turns - loops w/ 5 residues or less
^^ have both B-strands + a-helices
Tertiary structure
Stabilised mainly by non-covalent interactions + disulphide bridge formation.
Hydrophobic residues on isde (entropically favourable)
Determined by X-ray + NMR, sorted patterns into motifs/supersecondary structure + domains