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
Tetraplex DNA
Formed at telomeres, involves G rich sequences
Occur near ends of CSs + transcriptional regulatory regions of multiple genes + oncogenes
Stabilised by presence of cation (K+)
DNA recombination and the packaging of retroviral genome
Bacterial DNA
E.coli DNA circular + 3*10^6 BP
Supercoiled + DNA ribbon twisted caused by DNA gyrase
Nucleosome
Length of DNA coiled around histone
Nucleosome building block of chromatin
DNA double helix wound around octamer of histones (two molecules each of 2A, 2B, 3 and 4). Histone 1 binds to outside of this core particle + to linker DNA
Histones’ +vely charged interact w/-ve charge on phosphate
Higher order chromatin structure
DNA → beads on a string → 30 nm fibre → higher order coiling/looping → chromosomes
Xeroderma pigmentosum
Defect in excision repair that deals with UV damage
to DNA. Very prone to skin cancer
Replication origins
A specific site (sequence) where DNA replication is initiated + recognised by initiation complex
Larger DNAs has many origins unlike bacterial plasmids/small viruses where one is sufficient
DNA origin unwinds (DNA helicase) to form a replication bubble + allow access to replication machinery
DNA polymerase (transferase category)
- Adds nucleotide to pre existing 3` OH group, primer needed to add first nucleotide, first 2 bases are always RNA - enzyme which provides RNA primer is primase
- Primase = RNA polymerase as uses DNA template to synthesise RNA
- Reaction forms PPD bonds b/een 3
end of growing DNA chain + 5phosphate group of incoming nucleotide (enters as a deoxyribonucleoside triphosphate dNTP *4) + Mg2+ also required
Stays associated w/DNA - Proofreads DNA in 3’ to 5’ direction → removes mismatched nucleotides + remove unpaired 3’ overhanging nucleotides to create blunt ends
- Proofreading done by nuclease which cleaves PPD backbone
- Only if match is correct then catalyzes nucleotide-addition reaction
dNTP hydrolysis
Pyrophosphate released
Further hydrolysed to inOG phosphate = polymerisation irreversible
Replication fork
- Asymmetrical
- 2 replication forks move away in opp directions at each replication origin
- Lagging strand made discontinuously on fork as DNA P moves backwards so strand still made in 5’ to 3’ direction → Okazaki fragments joined to make continuous strand
- Keeps moving to expose bases
- DNA binding protein prevents nucleases from cleaving
Topoisomerase = +vely charged and removes intertwining
