6. DNA Flashcards
Nucleosides vs nucleotides
pentose (5 carbon sugar) + nitrogenous base at C1 vs phosphate at C5 + pentose (5 carbon sugar) + nitrogenous base at C1
Ribose vs deoxyribose
Has -OH at C2 vs has -H at C2
Know Chargaff’s rule
A + G = C + T. Purines = Pyrimidines (ie. A%=T%, C%=G%)
Purines vs pyrimidines. Are purines ever seen on opposite sides of DNA strands?
A,G; cyclohexane + cyclopentane ring vs C, U ,T; cyclohexane ring. BOTH ARE AROMATIC —> very stable and unreactive which is important when storing and analyzing them. Purines are NEVER seen on opposite sides of DNA strands b/c they never pair together (ie. purines bond w/ pyrimidines)
What does Watson-Crick model tell you?
double helix with antiparallel strands, bases facing inside and phosphate groups facing outside
B DNA vs Z DNA. Major groove vs minor groove
Right handed helix vs left handed helix (has zigzag appearance). Big gap vs little gap
Histones vs nucleosome vs chromatin
The protein around which DNA winds itself VIA ELECTROSTATIC INTERACTIONS vs a bunch of histones + wound DNA together vs a bunch of nucleosomes
Heterochromatin vs euchromatin. Constitutive vs facultative heterochromatin
compacted chromatin during interphase, dark light microscopy, genetically inactive vs dispersed chromatin during interphase, light microscopy, genetically active. Repetitive DNA for structural roles (ex: centromeres and telomeres) vs coding regions of DNA that are silenced
Topoisomerase vs DNA helicase vs DNA primase (or just primease, it’s a RNA polymerase) vs DNA polymerase vs replisome/replication complex vs DNA ligase vs RNAse H vs telomerase vs DNA gyrase
Untangles supercoils vs UNWINDS aka splits up H bond b/w bases vs attaches on RNA primers vs adds bases from 5’ to 3’ direction vs set of proteins assisting DNA polymerase vs puts Okazaki fragments together and zips DNA strands together vs removes RNA primers vs prevents DNA degradation and maintains stability by adding on telomeres at 3’ ends of DNA, a reverse transcriptase (ie. RNA dependent DNA polymerase) vs supercoils bacterial circular chrm
Know leading strand vs lagging strand and Okazaki fragment. Which is more prone to mutations?
strand in which DNA polymerase adds bases straightforward vs strand in which DNA polymerase adds bases in chunks => Okazaki fragments. Lagging strand is more prone to mutations cuz of constant start/stops
Name types of DNA polymerases in prok vs euk
DNA polymerase I, II, III, IV vs DNA polymerase alpha, delta and epsilon
Oncogenes vs proto-oncogenes vs antioncogenes. What’s angiogenesis?
mutated genes that causes cancer vs genes before they became oncogenes vs tumor suppressor genes. When tumor cells induce new blood vessel growth to obtain nutrients and O2 —> metastasis
Describe mismatch repair mechanism
- DNA polymerase does 3’ -> 5’ exonuclease activity by cutting out wrong nucleotide
- DNA polymerase puts in correct nucleotide
- DNA ligase glues nucleotides and strands together
This usually occurs on 1 of the 2 strands since the unaffected strand can act as a template strand for the affected nucleotide
Describe nucleotide excision repair mechanism
- AP Endonuclease cuts out affected nucleotide and leaves behind apyrimidic/apuric site aka abasic site
- DNA polymerase puts in correct nucleotide
- DNA ligase glues nucleotides and strands together
This usually occurs on 1 of the 2 strands since the unaffected strand can act as a template strand for the affect nucleotide
What types of factors can cause DNA damage?
Endogenous/internal factors (ex: reactive O2 species) and exogenous/external factors (ex: UV rays by forming pyr dimers, gamma rays, and x-rays by causing double stranded breaks)
Name 3 things that can occur if nucleotide excision repair doesn’t work
- Cell doesn’t grow and goes to dormant state => senescence
- Apoptosis
- Unregulated cell division => cancer
Which as higher melting pt: purines or pyrimidines?
Purines b/c double ring and complex bonding
