DNA + RNA Flashcards
(38 cards)
What is a nucleoside?
What is a nucleotide?
What is the difference between ribose and deoxyribose sugars?
Nucleoside: base and sugar
Nucleotide: base and sugar and phosphate group
Deoxyribose: Carbon-2 OH group is replaced by H
Ribose: 2 OH groups on the Carbon-2 and Carbon-3
What are the purines and what are the pyrimidines and what is their feature?
Purines (2 rings): Adenine and Guanine
Pyrimidines (1 ring): Cytosine and Thymine
Which bases form 3 hydrogen bonds and which form 2 hydrogen bonds?
3: Guanine and Cytosine
2: Adenine and Thymine
Where do major grooves and minor grooves arise?
Major: 5’ — 3’ (phosphodiester bonds above:below H-bonds)
Minor: 3’ — 5’ (phosphodiester bonds below:above H-bonds)
Define: Gene Exons Introns Regulatory sequence
Gene: Unit of DNA that codes for a protein
Exons: Coding region of DNA
Introns: Non-coding region of DNA
Regulatory sequence: Region on DNA that controls gene expression
Define: Codon Anticodon Allele Telomere Kinetchore
Codon: Sequence of 3 bases on mRNA (Amino Acids)
Anticodon: Sequence of 3 bases on translated protein
Allele: Different form of the same gene
Telomere: Repeated Sequence coding the end of a chromosome (TTAGGG)
Kinetchore: Area on the centromere spindle fibres attach to during prometaphase of cell division
Where are the various locations centromeres can be found on chromosomes?
Metacentric: middle (50%)
Sub-metacentric: slightly above the middle (60%)
Acrocentric: above the middle (75%)
Telocentric: closer to the telomeres (85%)
How is DNA packaged?
DNA forms double helix from right-sided twist
DNA coils twice around (positively charged) histones to form Nucleosomes (with linker proteins in between)
Euchromatin (transcriptionally active) stay as histones links
Heterochromatina (transcriptionally inactive) become solenoids of histone
What happens to DNA packaging during cell division?
During prophase of cell division DNA is super-condensed into X-shaped chromosomes by scaffolding proteins
How does chromatin change between euchromatin and heterochromatin?
Euchromatin: surrounded by methyl groups (activate DNA)
Heterochromatin: surrounded by acetyl groups (inactivate DNA)
Switch between by methylation and acetylation
What are the three ways in which DNA accumulates damage?
Defective replication machinery factors (Nucleoside mis-incorporation)
Replication fork progression inhibitors (Fork slippage (can lead to repetitive DNA))
Defective response pathways (Irregular/missing cell cycle checkpoints)
Define DNA stress
Inefficient replication that leads to the replication fork slowing, stalling or breaking and consequentially further mutations
What is the DNA damage response?
How can this lead to cancer?
If DNA damage irreparable: senescence or apoptosis
If DNA damage reparable: cell cycle arrest and repair
If these pathways(senescence, apoptosis, arrest, repair) fail cell could become cancerous
What are the two types of DNA repair?
Double strand break
Mis-match Repair
How does double strand break repair work?
Non-homologous end joining:
KU70/80 dimer protects the ends of the break
Activates DNA-Pk to bridge the two stands together
Ligase joins the stands
Homology directed repair:
Resection or faulty nucleotides leaving single strand overhangs
Polymerase resynthesises missing/resected strand
Strands re-integrated into homologous pair (can cause crossing-over)
What is mis-match repair?
Works on single-strand (usually newly synthesised)
Recognition, Excision, Removal, Resynthesis, Ligation
How does mutations in the DNA Damage Response lead to cancer evolution?
Mutations in the DDR lead to higher number of mutations (greater susceptibility)
Mutations cannot be corrected
Continued mutation accumulation —> heterogenous tumour
What happens when a heterogenous tumour is exposed to therapy?
Clonal expansion of resistant tumour cells
Therapy induced mutagenecity (DNA damage —> mutations that resist therapy)
What are the molecular techniques used to detect DNA nucleotide mutations?
DNA sequencing
DNA gel electrophoresis
PCR
What are the molecular techniques used to detect DNA gene mutations?
Electrophoresis Southern blot Microarray DNA fingerprinting Northern blot Reverse Transcriptase PCR Gene Cloning
What are the molecular techniques used to detect DNA chromosome mutations?
Karyotyping
FISH
What are the molecular techniques used to detect protein mutations?
Electrophoresis
Western blot
Enzyme assays
ELISA
How does DNA sequencing work?
Sanger-Chain termination:
Dideoxy-NTP’s with fluorescent markers are used to anneal to replicating DNA strand (no elongation of strand - cannot form phosphodiester bonds)
Mixture of strands produced each dd-NTP’s binds at different point resulting in strands of different length
Electrophoresis separates strands and DNA sequence can be read
How does DNA gel electrophoresis work?
DNA is separated into fragments by endonucleases and placed into a gel (buffered: constant pH)
An electric field is placed over the gel and the fragments move to the anode separating based on their size
