DNA and Mutations

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Nucleoacids

Purine: Adenine -NH2 -N, Guanine -NH2 =O -N (2 Rings)
Pyrimidine: Cytosine -NH2 -N =O, Thymine =O =O -CH3 -N (1 Ring) 
Uracil =O, =O, -N

Base- 1'- Ribose (2'(OH or H) 5'-CH2OH- Phosphate

5'-3' end 

0.34nm internucleotide distance
3.4nm one full twist (10 nucleotide turn-1)
2.0nm diameter of helix

RIGHT-HANDED 

G-C: 3 hydrogen bonds 
A-T: 2 hydrogen bonds

3 x 10^9 nucleotide pairs: 5um diameter: 146bp of DNA wrapped around a protein core of 8 histones = nucleosome 

Genes: 4.6 x 10^7 nucleotides (1.5% of genome encodes protein)

23,000 genes (2,000 bases each)

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Nucleoacids

Exons 1.5%

Introns 23%

Untranscribed areas near genes 2%

Repetitive DNA 50% 

-Viral (LINES L1 6500bp)

-Non-Viral (SINES Alu repeat 160bp)

Satellite DNA (8%)

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Semi-Conservative Replication

1. Helicase separate to form two replication forks

2. Primase makes RNA 5'-3' DNA polymerase 3 extends the primers DNA polymerase 1 removes the RNA and replaces with DNA 

3. DNA ligase makes 5'-3' phosphodiester bond (join adjacent fragments)

3'-5' exonuclease 

Telomerase makes telomeres at the ends (extends 3' end) 

N-Ras (oncogene in rhabdosarcoma) - Gln-> His 

CCR5 loss of 32 bp (individuals homozygous for 32 CCR5 allele are resistant to HIV-1)

CAG 36> Huntingtin (Htt) Huntigton's disease

Cri-du-Chat: Deletion chromosome 5
CML: 9/22 pieces chromosome swap

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Mutations

Deamination: C->U (Pairs with A) A->Hypoxanthine (Pairs with C)

UV: Thymine dimers
UV-B (290-320nm) major mutagenic
UV-C: (180-290nm) lethal

Nitrous acid: C->U

Alkylating agents: Guanine modification

Free radicals: strand breaks

Repair:

Dealkylation by MTase 

Nucleotide excision repair (NER)

NER defect: xeroderma pigmentosum (XP-D mutation)
HIV: AZT targets reverse transcriptase 

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Genetics and Inheritance

Down's: 21: Retard growth and development, cardiac abnormalities, acute leukaemia
Patau's: 13: Heart defects, incomplete brain development, spinal defects and seizures, small or missing eyes
Edward's: 18: Heart defects, intestines protruding outside body, kidney (5-10% survive 1 year)

XXY Klinefelter's: Small testes, infertility
X Turner's: Amenorrhoea, infertility
XYY: Increased growth
XX Male: SRY (Transfer to X) (1/2000)

X Linked: Red-green colour blindness, Duchenne muscular dystrophy, X-linked ichthyosis

Mitochondria: 13 polypeptides r/tRNA

MELAS myopathy encephalopathy lactic acidosis stroke like episodes
LHONS Leber's herediatary optic neuropathy 

-passed on by mother

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Transcription/ Translation

RNA polymerase 5'-3' direction in phosphodiester bonds 

Promoter Region + sigma factor + RNA polymerase 

Termination Region + rho GC rich stem loop (STOP)

Eukaryotes

Capping 5' (mRNA) methylation at 7' end Guanosine 

Polyadenylation (Poly A tail) 

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Transcription/ Translation

Translation

CCA-OH 3' end + 61 amino acids
A.A + tRNA + ATP -> aminoacyl-tRNA + PPi + AMP 

 70S Ribosome: 50S (23S rRNA + 5S rRNA + 34 proteins) 
30S (16S rRNA  + 21 proteins)

AUG- Shine-Dalgarno 16S rRNA 

Initiaition: IF1/IF3 + 30S fmet-tRNAfmet AUG initiation codon + GTP-IF2 (Bind 50S subunit GDP + Pi) 

Elongation: AA2 + EF-Tu GTP --> Peptidyl transferase --> 

Translocation EF-G-GTP-->GDP + Pi 

Termination: Stop codon: RF1/2 + IF3 + Ribosomal recycling factor + GTP hydrolysis 


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Transcription/ Translation

Translation

CCA-OH 3' end + 61 amino acids
A.A + tRNA + ATP -> aminoacyl-tRNA + PPi + AMP 

 70S Ribosome: 50S (23S rRNA + 5S rRNA + 34 proteins) 
30S (16S rRNA  + 21 proteins)

AUG- Shine-Dalgarno 16S rRNA 

Initiaition: IF1/IF3 + 30S fmet-tRNAfmet AUG initiation codon + GTP-IF2 (Bind 50S subunit GDP + Pi) 

Elongation: AA2 + EF-Tu GTP --> Peptidyl transferase --> 

Translocation EF-G-GTP-->GDP + Pi 

Termination: Stop codon: RF1/2 + IF3 + Ribosomal recycling factor + GTP hydrolysis 


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Antibiotics

Actinomycin: Bind to DNA prevent elongation by RNA polymerase

Rifamycin: Bind to RNA polymerase inhibit RNA synthesis

Streptomycin: 30S

Erythromycin: 50S (prevent translocation)

Chloramphenicol: peptidyl transferase inhibition by binding onto 50S

Tetracycline: inhibit aminoacyl-tRNAs by binding to ribosome

Puromycin: premature chain termination

a-aminitin: RNA polymerase II inhibitor

Cycloheximide: Translocation 

Diphteria: RNA translational inhibitor by EF-2

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Haemoglobin

yo2= po2/p50+po2 Sigmoidal curve 

Increase in pH and decrease pCO2 increases affinity for O2 and BPG lowers it

HbF a2y2
HbA a2b2 

Proximal His F8- O2Fe-His F8 Distal makes Co 200x not 20000x stronger 

Moves 0.4Ao towards heme plane (F helix moving)

Hb transports 40% of H+ produced CO2 binds with Hb N-termini to produce carbamino terminal residues 

transports 15% CO2 produced 

Protonated His HC3 and Asp FG1 bind (stabilise T form) deoxy 

p50 increases as BPG increases 

HbF has H143S mutation and therefore BPG is less efficient 

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Regulation of Cell cycle

G1 (in absence of growth factors- G0) / S / G2 /

Prophase: chromosomes condense, nucelolus disappears, cytoplasmic MT breakdown, spindle
Prometaphase: nuclear envelope breakdown, chromosome attach to spindle via. kinetochores
Metaphase: line up 
Anaphase: sister chromatids split 
Telophase: chromosomes decondense, nucleolus reforming and cytoplasmic MT reform 
Cytokinesis: actin 

Centrosome: pair of centrioles (0.5 x 0.2 um diameter) wall made up of 9 triplets of MT 

MPF: Cdk1 cyclin B 

SPF: Cdk 2 cyclin A/E 

Rb represses E2F (p107 p130) Rb-P by Kinase Cyclin D1  

Ras-GTP (low -ase activity) point mutation 12, 13, 61 

HER2 EGFR 

p53-p21-inhibits Cdk (S/M)

Mad1 prevents anaphase onset at kinetochores 


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Protein Synthesis

ER: Signal sequence: Non-Polar + Glu repeats

Mitochondria: Chaperones: Polar/Non-Polar + Arg repeats

Nucleus: Positive Lys/Arg + Importin 

Lysosome: Mannose-6-Phosphate Inclusion cell disease

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