Module 1 Flashcards
Amino acids and peptides
What does exergonic mean
Delta G is negative: Free energy released, favourable, spontaneous
What does endergonic mean
Delta G is positive: Free energy absorbed. Unfavourable, not spontaneous
What does exothermic mean
Delta H is negative: Heat released
What does endothermic mean
Delta H is positive: heat absorbed
What does positive delta S mean
less disorder, low entropy, not spontaneous
What does negative delta S mean
more disorder, high entropy, spontaneous
What is the equation to find delta G
Delta G= Delta Gnode + RTln([C][D]/[A][B])
What are the 3 ways to make unfavourable reaction go
Remove products faster than it produce, Add reactants faster than it removes, Couple unfavourable reaction with highly favourable reaction
What is a nucleotide
base + sugar + phosphate
What is nucleoside
base + sugar
What are the properties that amino acid have to carry out biological functions
Able to polymerise, useful acid-base properties, varied physical properties, varied chemical functionality
Alanine
CH3, A, Ala, nonpolar
Cysteine
CH2-SH, C, Cys, polar uncharged
Aspartate
CH2-COO-, D, Asp. negatively charged
Glutamate
CH2-CH2-COO-, E, Glu, Negatively charged
Phenylalanine
CH2-cyclic, F, Phe, Aromatic
Gylcine
H, G, Gly, nonpolar
Histidine
CH2-C=-CH NH-CH=N, H, His, Positively charged
Isoleucine
C—H CH3 CH2-CH3, I, Ile, nonpolar
Lysine
CH2-CH2-CH2-CH2-NH3+, K, Lys, positively charged
Leucine
CH2-CH–CH3 CH3, L, Leu, nonpolar
Methionine
CH2-CH2-S-CH3, M, Met, nonpolar
Asparagine
CH2-C-=NH2 O, N, Asn, polar uncharged
Proline
CH2-CH2-CH2(connects to amine), P, Pro, nonpolar
Glutamine
CH2-CH2-C-=NH2 O, Q, Gln, polar uncharged
Arginine
CH2-CH2-CH2-NH-C-=NH2 NH2, R, Arg, positively charged
Serine
CH2OH, S, Ser, polar
Threonine
C—H OH CH3, T, Thr, polar
Valine
CH–CH3 CH3, V, Val, nonpolar
Tryptophan
CH2-C=CH-NH-(Cyclic), W, Trp, aromatic
Tyrosine
CH2-(cyclic)-OH, Y, Tyr, aromatic
pKa of Asp/Glu
4.4
pKa of C-ter
3.1
pKa of N-ter
8.0
pKa of His
7
pKa of Cys
8.5
pKa of Tyr
10
pKa of Lys
10
pKa of Arg
12
What acts as a chelate
Acidic side chains
Which 2 aa are not very chemically reactive
Ser and Thr
what are the aliphatic side chains
Leu, Ile, ala, val, pro
What aa can form disulfide bonds
Cysteine
Types representing protein structures
Worm/tube backbone, ribbon backbone, space-filling heavy atoms, line
What peptide linkages is more favourable
trans
Where is the omega angle
the carbon with a oxygen and nitrogen
Where is the phi angle
N-C alpha
Where is the psi angle
C alpha - C
What are the polar amino acid
Serine, threonine, cysteine, asparagine, glutamine 5aa
What are the non-polar aa
glycine,alanine, proline, valine, leucine, isoleucine, methionine 7aa
Aromatic aa
phenylalanine, tyrosine, tryptophan 3aa
Positively charged aa
lysine, arginine, histidine 3aa
Negative charge aa
aspartate, glutamate 2aa
