W1 Proteins, DNA structure and synthesis Flashcards
What are proteins, what do they provide
Polymers made by RS during translation and provide both structural + functional elements that underlie dynamic processes of the cell
Residue
Each repeating unit of the PP chain
0.1% peptide bonds have less energetically favourable cis arrangement
AA at low, neutral + high pH
Low = AA acts as a base + accepts H+
Neutral = zwitterion
High = AA acts as an acid w/ loss of H+
Overall charge depends on R group thus ratio of charged groups
Folding to form beta sheets
Continuous folding of PP chain, b/een strands intraM H bonds formed = stabilise sheet.
Strands antip/p - loops connect strands in either a-p/p arrangement→ b-turns v.specific arrangement stabilised by H bonds + sometimes not connected by b-turn
Functions products of genome
Carrier → trafficking O2
Metabolic → enzymes producing/utilising energy
Parts of cellular machinery → spliceosomes (removes introns from transcribed pre-mRNA, made up of about 80 proteins and snRNAs). snRNAs → nucleus, in splicing/RNA processing
Structural scaffold → microtubules
Sensing molecules → receptors + their glands
Secondary structure alpha helix
- Right handed
- Stabilised by H bonds b/een 2 AAs 4 residues apart
- 3.6 residues per turn
- 0.54 nm per turn
Why water soluble proteins often globular
Hydrophilic residues mostly on external, Hphobic buried inside protein
May assemble into filaments/tubes
DNA structure
Bases are store of genetic info → seen in pneumococcal transformation (Griffith’s experiment) and bacteriophage infection of E coli
Double helix → complementary PNs w/major and minor grooves → receptors for drugs
Major grooves appear where backbones are further apart and vice versa → easier for DNA binding proteins to interact w/bases as backbones not in the way
DNA present as chromatin in nucleus → chromatin = DNA + histones → chromatins function is to pack DNA into small vol so can fit inside nucleus, protect DNA structure, allow mitosis/meiosis to happen, prevents CS breakage, controls gene expression + DNA replication
A form
- Shorter + more compact → base pairs not perpendicular (tilted instead) to helix axis as in B-DNA
Grooves v.similar - 11 bp per helical turn = smaller twist angle than B (20/25% shorter than B)
- Right handed
- DNA driven into A form in dehydrating conditions
- Same helical structure in double-stranded RNAs + DNA-RNA hybrid double helices
- Major = deep/narrow, minor = shallow/wide
- C-3’ lies outside the plane = C-3’-endo
- tRNA in A form
B form
Most cells’ DNA
Right handed
10 bp per helical turn
Base pairs perpendicular to helix axis
Longer/narrower due to less bp per turn
C-2’ lies outside plane = C-2’-endo
Phosphates + other groups bind to greater water molecules than A hence hydration favours B form
Why major/minor grooves present
2 GSD bonds not being diametrically opp each other → grooves lined by potential H-bond donors
Z form
Left handed
Does not exist as a stable feature of double helix
Conformation repeats every other base pair
Little diff in width b/een M/M
Formation = alternating purine-pyrimidine sequence, negative DNA supercoiling
C (pyrimidine) - G (purine) bp bond
3 H bonds:
NH (C) - O=C (G)
N (C) - H-N (G)
O (C) - H-N-H (G)
Total length 1.08 nm
T (pyrimidine) - A (purine) bp bond
2 H bonds:
C=O (T) - H-N-H (A)
N-H (T) - N-C (A)
Total length 1.11 nm
Holliday junction
4 stranded junction
In genetic recombination → 2 double stranded DNA molecules separate into 4 = exchange segments of genetic info
HJ travels along DNA unzipping one strand + reforming H bonds on second strand
Conformation of arms depends on [buffer salt] + sequence of nucleobases closest to the junction
