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Biochemistry > Qiao 1 > Flashcards

Qiao 1 Flashcards

0
Q

What is the role of caretaker genes? Gatekeeper genes?

A

Caretaker: DNA repair, chromosome segregation. These genes control the stability of the genome and prevent accumulation of mutations (oncogenes)

Gatekeeper: inhibit growth/promote death of tumor (tumor suppressor genes)

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1
Q

In general, what threatens genomic integrity?

A
  1. Mutations
  2. Replication errors
  3. Persistent DNA damage
  4. Genomic instability

(The source of these threats can be either endogenous or exogenous.)

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2
Q

What is necessary for tumor suppressor genes and oncogenes to lead to cancer?

A

One ‘activating mutation’ in an oncogene; two ‘inactivating mutations’ in tumor suppressor gene.

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3
Q

DNA is a polymer of _______ __________ covalently linked by ________________________.

A

deoxyribonucleoside monophosphates; 3’→5’–phosphodiester bonds

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4
Q

Describe the hydrophobicity of the DNA helix.

A

The deoxyribose-phosphate backbone (exterior) is hydrophilic and the bases (interior) are hydrophobic.

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5
Q

What types of forces stabilize the DNA structure?

A

Hydrogen bonds between base pairs; hydrophobic effect between stacks of bases (vertical).

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6
Q

How does the anti cancer drug Actinomycin D work?

A

It intercalates into the minor groove of DNA helices, blocking replication and transcription.

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7
Q

What are the 3 enzymatic capabilities of DNA Pol I?

A

5’ to 3’ DNA polymerizing activity (removes RNA primer created by primase on lagging strand and then fills gaps between Okazaki fragments)
5’ to 3’ exonuclease activity (5’ RNA removal)
3’ to 5’ exonuclease activity

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8
Q

What are the 4 essential requirements of DNA Pol I activity?

A
  1. TEMPLATE strand
  2. PRIMER
  3. The primer must have a FREE 3’ OH terminus.
  4. dNTP’s (bases are dNMPs, PPi is lost)
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9
Q

Why is the replication fork considered asymmetrical?

A

Synthesis of one strand is continuous (leading strand) and the other is discontinuous (lagging strand, Okazaki fragments).

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10
Q

What is required for the initiation of replication?

A

ori binding protein (DnaA, binds oriC sequence)
DNA Helicase (DnaB hexamer encircles DNA and provides unlimited processivity)
Primase (DnaG, low processivity, ~12 RNA nt primer)
ssDNA binding proteins (SSB, straightens ssDNA and prevents reannealing)
Polymerases (the replisome holoenzyme)
DNA ligase
DNA topoisomerase

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11
Q

Camptothecin targets _________ causing cytotoxic activity in the __ phase.

A

Topoisomerase I; S phase.

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12
Q

Which drug commonly used to treat breast cancer works by targeting DNA Topoisomerase II activity?

A

Doxorubicin (adriamycin)

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13
Q

On which strand does DNA Pol III function?

A

Both, leading and lagging.

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14
Q

What are the proteins of the eukaryotic replication fork?

A 
ORC = origin recognition
MCM = helicase activity
RPA = ssDNA protection
Pol A/Primase - primer synthesis
PCNA = sliding clamp
RNase H, FEN 1 - primer removal
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15
Q

What are the steps of lagging strand synthesis in E. coli?

A
  1. Partial disassembly of Pol III complex from lagging strand
  2. Synthesis of new RNA primers by Primase, which is closely associated with Helicase (DnaB)
  3. Reassembly of Pol III complex and elongation of primer (Okazaki fragments)
  4. Removal of RNA primer by DNA Pol I (5’ to 3’ exonuclease)
  5. Space vacated by primer is filled by DNA Pol I
  6. Bonding of 5’ phosphate on DNA made by Pol III to 3’ OH on DNA made by Pol I by DNA ligase
16
Q

What are the major differences between eukaryotic and prokaryotic DNA replication (in general terms)?

A

Machinery, multiple replication origins in euk, linear euk DNA

17
Q 
Name the eukaryotic equivalents:
Helicase
Polymerase (Pol III equiv)
Primase
Primer removal (Pol I)
Proofreading (Pol I)
Sliding clamp
Clamp loader
SSB
DNA ligase
DNA topoisomerase
A 
Helicase = MCM proteins
Polymerase (Pol III equiv) = pol delta for lagging strand, pol epsilon for leading, pol gamma for mitochondrial 
Primase = Primase-pol alpha (RNA-DNA pol complex)
Primer removal (Pol I) = RNase H, FEN 1
Proofreading capabilities (Pol I) = pol delta, epsilon, gamma
Sliding clamp = PCNA
Clamp loader = RFC
SSB = RPA
DNA ligase = Lig 1
DNA topoisomerase = topoisomerase I, II
18
Q

Which human DNA pol subunit is central to base excision repair and is thus often mutated in tumors?

A

pol β

19
Q

Ophthalmoplegia, Alper syndrome, and other neurodegenerative disorders are caused by homozygous mutations of which enzyme?

A

DNA pol γ (mitochondrial DNA synthesis)

20
Q

What is the substrate of the Cdk-cyclin enzyme complex?

A

Helicase (MCM in euk). Control cell cycle phase transitions.

21
Q

Histones carry a ____ charge at physiologic pH because of their high content of ______ and ______ amino acids. With the help of ____, histones neutralize the ______ charge of DNA ______ groups.

A

positive, lysine, arginine, Mg+ and other cations, negative, phosphate

22
Q

Which diseases are associated with trinucleotide repeat expansion?

A

In exon: Huntington’s, Kennedy’s, spinocerebellar ataxias (SCA)
In UTR: Fragile X, myotonic dystrophy

23
Q

The _____ enzyme overcomes the end-replication problem, where the removal of the last RNA primer on the ___ end of the lagging strand creates a gap that cannot be filled because there is no ____ group, which is a requirement for priming of DNA polymerase

A

Telomerase, 5’, 3’ OH

24
Q

What general type of enzyme is telomerase and what are its two subunits?

A

Ribonucleoprotein; TR (RNA subunit, complementary to DNA seq at 3’ end of telomere) and TERT (reverse transcriptase protein subunit)

25
Q

What is the Hayflick limit?

A

The number of times a cell population will divide until telomeres shorten to a critical length and cells senesce.

26
Q

Which factors accelerate telomere loss?

A

Stress, smoking, obesity

27
Q

How do telomeres and telomerase activity differ between healthy adults and those with premature aging syndromes, cancerous cells, and germ lines?

A

Telomeres of people with premature aging syndromes shorten more rapidly and enter disease stages earlier. Telomeres of cancer cells grow rather than shorten because of telomerase activity. Germ cell telomeres shorten at a slower rate than somatic cells.

28
Q

What are arabinosides?

A

Nucleoside analogs that block DNA replication (anti cancer, anti viral)

Biochemistry (12 decks)

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