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Block 1 > Molecular Biology week 1 > Flashcards

Molecular Biology week 1 Flashcards

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

A

Results in interstrand crosslink, double strand breaks

Repaired via Recombinatorial repair (HR/NHEJ)

21
Q

DNA damaging Agent: replication error

A

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

Repaired via mismatch repair (MMR)

22
Q

Depurination

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

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

A

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

ex. uracil DNA glycosylase

25
Q

Nucleotide excision repair

A

DNA repair mechanism that looks for bulky lesions (ex. pyrimidine dimers)

The portion of DNA is cut out by nuclease

26
Q

Nonhomologous End Joining (NHEJ)

A

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
Q

Homologous end joining

A

DNA repair mechanism that uses sequence from the other identical c-some to fix error

28
Q

HNPCC

A

caused by defective DNA mismatch error

29
Q

Xeroderma pigmentosum

A

caused by defective nucleotide excision repair

30
Q

Ataxia-telangiextasia (AT)

A

caused by defective ATM gene which is responsible for multiple form of stress including ds breaks

Enzyme affected: ATM protein kinase

31
Q

BRCA-2

A

gene involved in homologous end joining, when defective, leads to increase risk of breast cancer

32
Q

Fanconi anemia

A

results from defective enzymes involved in DNA interstrand cross-link repair

33
Q

site specific recombination

A

the movement of specialized nucleotide sequences called transposons between non-homologous sites

34
Q

Genome

A

Genomes carry the information for all the RNA and protein that an organism will ever synthesize

35
Q

Viral genomes

A

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
Q

Bacterial Genomes

A

Prokaryotic genomes are dsDNA

Most have single c-some, either circular or linear

Smaller than human genome

No introns

37
Q

Human genome

A

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
Q

Human mitochondrial genome

A

circular duplex molecule of 16.5kb

encodes 13 proteins, 22tRNAs, and 2 rRNAs

Transcription and translation take place in mitochondria

39
Q

Purifying selection

A

selective removal of alleles that are deleterious

survival of the fittest

40
Q

Do the number of genes correlate with biological complexity

A

Yes, the more genes you have the more biologically complex the organism is

41
Q

Which of the following is more conserved: gene sequence or genomic structure?

A

gene sequence is more conserved than genomic structure

42
Q

Homologous genes

A

genes with similar sequence and function can be recognized across vast phylogenetic distances

43
Q

synteny

A

stretches of conserved gene order on chromosomes

44
Q

Mechanisms of creating ‘new’ genes

A

Intragenic mutation

Gene duplication - duplicated genes diverge independently

DNA segment shuffling - via recombination

Horizontal transfer - organism a and organism b shuffle genes around

45
Q

pseudogenes

A

genes that lose function or are irreversibly inactivated by mutation

46
Q

Single nucleotide polymorphisms (SNPs)

A

positions in a genome where some individuals have one nucleotide and others have a different nucleotide

47
Q

Simple sequence length polymorphisms

A

tandem repeat sequences that display length variations

48
Q

4Ps in P4 medicine

A

Predictive, Preventative, Personalized, Participatory

Block 1 (9 decks)

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