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Block 1 > Molecular Biology week 1 > Flashcards

Molecular Biology week 1 Flashcards

(48 cards)

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1
Q

Semi conservative Replication

A

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

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2
Q

DNA Polymerase

A

Catalyzes DNA synthesis

Elongation in 5’-3’ direction

Need a free 3’-OH

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3
Q

Replication Fork

A

site of the origin of replication

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4
Q

Okazaki Fragment

A

short newly synthesized fragments that are formed on the lagging strand during DNA replication

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5
Q

S-phase

A

Part of cell cycle where DNA replication takes place

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6
Q

DNA Primase

A

RNA polymerase that creates RNA primer

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7
Q

RNAse H

A

digests the RNA primer

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8
Q

DNA ligase

A

seals fragment

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9
Q

DNA Helicase

A

pries apart the double helix through the hydrolysis of ATP

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10
Q

Single Strand DNA binding protein (SSBP)

A

prevents single strands from forming “hairpins”

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11
Q

Sliding-clamp protein complex

A

holds the DNA polymerase on the DNA template

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12
Q

DNA topoisomerase

A

creates ds breaks to relieve supercoiling induced by DNA helicase and prevent DNA tangling during replication

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13
Q

What are the essential elements of DNA replication?

A

3’-OH, ATP, primer

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14
Q

DNA Polymerase target drugs

A

AZT for HIV

Acyclovir

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15
Q

DNA topoisomerase target drug

A

Irinotecan, Ciproflaxicin, Etoposide, Doxorubicin

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16
Q

Endogenous causes of DNA Damage

A

attack by reactive oxygen species

replication errors

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17
Q

Exogenous Causes of DNA Damage

A

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

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18
Q

DNA Damaging Agent: x-rays, oxygen radicals, alkylating agents, spontaneous reactions

A

Results in: uracil, abasic site, gamma-oxoguanine, single strand breaks

Repaired via base excision repair

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19
Q

DNA Damaging Agent: UV light, polycyclic aromatic hydrocarbons

A

Results in: bulky adducts, pyrimidine dimer

Repaired via nucleotide excision repair

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20
Q

DNA damaging agent: IR, UV light, x-rays, anti-tumor agents, HU

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A

Results in interstrand crosslink, double strand breaks

Repaired via Recombinatorial repair (HR/NHEJ)

21
Q

DNA damaging Agent: replication error

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A

Results in: A-G, T-C mismatch, insertion, deletion

Repaired via mismatch repair (MMR)

22
Q

Depurination

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A

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

23
Q

Deamination

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A

Removal of an amine group.

In cytosine, the NH2 is hydrolytically cleaved thus forming Uracil which preferentially binds to adenine

24
Q

Base excision repair

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A

cellular mechanism that repairs damaged DNA, it removes small, non-helix distorting base lesions (removes incorrect base)

ex. uracil DNA glycosylase

25
Nucleotide excision repair
DNA repair mechanism that looks for bulky lesions (ex. pyrimidine dimers) The portion of DNA is cut out by nuclease
26
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
27
Homologous end joining
DNA repair mechanism that uses sequence from the other identical c-some to fix error
28
HNPCC
caused by defective DNA mismatch error
29
Xeroderma pigmentosum
caused by defective nucleotide excision repair
30
Ataxia-telangiextasia (AT)
caused by defective ATM gene which is responsible for multiple form of stress including ds breaks Enzyme affected: ATM protein kinase
31
BRCA-2
gene involved in homologous end joining, when defective, leads to increase risk of breast cancer
32
Fanconi anemia
results from defective enzymes involved in DNA interstrand cross-link repair
33
site specific recombination
the movement of specialized nucleotide sequences called transposons between non-homologous sites
34
Genome
Genomes carry the information for all the RNA and protein that an organism will ever synthesize
35
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
36
Bacterial Genomes
Prokaryotic genomes are dsDNA Most have single c-some, either circular or linear Smaller than human genome No introns
37
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
38
Human mitochondrial genome
circular duplex molecule of 16.5kb encodes 13 proteins, 22tRNAs, and 2 rRNAs Transcription and translation take place in mitochondria
39
Purifying selection
selective removal of alleles that are deleterious survival of the fittest
40
Do the number of genes correlate with biological complexity
Yes, the more genes you have the more biologically complex the organism is
41
Which of the following is more conserved: gene sequence or genomic structure?
gene sequence is more conserved than genomic structure
42
Homologous genes
genes with similar sequence and function can be recognized across vast phylogenetic distances
43
synteny
stretches of conserved gene order on chromosomes
44
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
45
pseudogenes
genes that lose function or are irreversibly inactivated by mutation
46
Single nucleotide polymorphisms (SNPs)
positions in a genome where some individuals have one nucleotide and others have a different nucleotide
47
Simple sequence length polymorphisms
tandem repeat sequences that display length variations
48
4Ps in P4 medicine
Predictive, Preventative, Personalized, Participatory

Block 1 (9 decks)

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