Molecular Biology week 1 Flashcards
Semi conservative Replication
Replication that produces two copies that each contained one of the original parent strand and one new strand
Important because it maintains DNA integrity from generation to generation
DNA Polymerase
Catalyzes DNA synthesis
Elongation in 5’-3’ direction
Need a free 3’-OH
Replication Fork
site of the origin of replication
Okazaki Fragment
short newly synthesized fragments that are formed on the lagging strand during DNA replication
S-phase
Part of cell cycle where DNA replication takes place
DNA Primase
RNA polymerase that creates RNA primer
RNAse H
digests the RNA primer
DNA ligase
seals fragment
DNA Helicase
pries apart the double helix through the hydrolysis of ATP
Single Strand DNA binding protein (SSBP)
prevents single strands from forming “hairpins”
Sliding-clamp protein complex
holds the DNA polymerase on the DNA template
DNA topoisomerase
creates ds breaks to relieve supercoiling induced by DNA helicase and prevent DNA tangling during replication
What are the essential elements of DNA replication?
3’-OH, ATP, primer
DNA Polymerase target drugs
AZT for HIV
Acyclovir
DNA topoisomerase target drug
Irinotecan, Ciproflaxicin, Etoposide, Doxorubicin
Endogenous causes of DNA Damage
attack by reactive oxygen species
replication errors
Exogenous Causes of DNA Damage
UV and ionizing radiation including x-rays and gamma rays, plant toxins
man-made mutagenic chemicals that act as DNA intercalating agents, cancer chemotherapy and radiotherapy
Viruses
DNA Damaging Agent: x-rays, oxygen radicals, alkylating agents, spontaneous reactions
Results in: uracil, abasic site, gamma-oxoguanine, single strand breaks
Repaired via base excision repair
DNA Damaging Agent: UV light, polycyclic aromatic hydrocarbons
Results in: bulky adducts, pyrimidine dimer
Repaired via nucleotide excision repair
DNA damaging agent: IR, UV light, x-rays, anti-tumor agents, HU
Results in interstrand crosslink, double strand breaks
Repaired via Recombinatorial repair (HR/NHEJ)
DNA damaging Agent: replication error
Results in: A-G, T-C mismatch, insertion, deletion
Repaired via mismatch repair (MMR)
Depurination
When the glycosidic bond between the purine (A or G) and the sugar is hydrolytically cleaved and the purine base is removed. Can result in deletion mutation
Deamination
Removal of an amine group.
In cytosine, the NH2 is hydrolytically cleaved thus forming Uracil which preferentially binds to adenine
Base excision repair
cellular mechanism that repairs damaged DNA, it removes small, non-helix distorting base lesions (removes incorrect base)
ex. uracil DNA glycosylase
Nucleotide excision repair
DNA repair mechanism that looks for bulky lesions (ex. pyrimidine dimers)
The portion of DNA is cut out by nuclease
Nonhomologous End Joining (NHEJ)
DNA repair mechanism that trim broken DNA ends and ligate the trimmed ends together. Method to to repair ds DNA breaks
May result in mutation due to DNA loss
Homologous end joining
DNA repair mechanism that uses sequence from the other identical c-some to fix error
HNPCC
caused by defective DNA mismatch error
Xeroderma pigmentosum
caused by defective nucleotide excision repair
Ataxia-telangiextasia (AT)
caused by defective ATM gene which is responsible for multiple form of stress including ds breaks
Enzyme affected: ATM protein kinase
BRCA-2
gene involved in homologous end joining, when defective, leads to increase risk of breast cancer
Fanconi anemia
results from defective enzymes involved in DNA interstrand cross-link repair
site specific recombination
the movement of specialized nucleotide sequences called transposons between non-homologous sites
Genome
Genomes carry the information for all the RNA and protein that an organism will ever synthesize
Viral genomes
some viral genomes are DNA, other are RNA
some are single stranded, others are double stranded
some integrate their genetic material into their host cell’s genome (HIV) others do not (Flu, Herpes)
Much smaller than human genome
no introns
Bacterial Genomes
Prokaryotic genomes are dsDNA
Most have single c-some, either circular or linear
Smaller than human genome
No introns
Human genome
A haploid cell contains 3 billion bps
Approx. 1.5% of genome encodes for proteins
~27k protein coding genes
Human are 99.9% identical at DNA level
Human mitochondrial genome
circular duplex molecule of 16.5kb
encodes 13 proteins, 22tRNAs, and 2 rRNAs
Transcription and translation take place in mitochondria
Purifying selection
selective removal of alleles that are deleterious
survival of the fittest
Do the number of genes correlate with biological complexity
Yes, the more genes you have the more biologically complex the organism is
Which of the following is more conserved: gene sequence or genomic structure?
gene sequence is more conserved than genomic structure
Homologous genes
genes with similar sequence and function can be recognized across vast phylogenetic distances
synteny
stretches of conserved gene order on chromosomes
Mechanisms of creating ‘new’ genes
Intragenic mutation
Gene duplication - duplicated genes diverge independently
DNA segment shuffling - via recombination
Horizontal transfer - organism a and organism b shuffle genes around
pseudogenes
genes that lose function or are irreversibly inactivated by mutation
Single nucleotide polymorphisms (SNPs)
positions in a genome where some individuals have one nucleotide and others have a different nucleotide
Simple sequence length polymorphisms
tandem repeat sequences that display length variations
4Ps in P4 medicine
Predictive, Preventative, Personalized, Participatory
