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Foundation Unit 1 > Lectures 1.8-1.9 > Flashcards

Lectures 1.8-1.9 Flashcards

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1
Q

What are the types of chemical modifications that cause DNA damage?

A
  • Single strand break
  • Double strand break
  • Deamination
  • intercalation (binding of chemicals between base pairs)
  • Depurination
  • Thymine dimer
  • Inter strand crosslinks
  • mismatches
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2
Q

What happens in cells to convert a damaged DNA to a genetic mutation?

A

When DNA gets replicated, the chemical change becomes a mutation

  • there is now a fixed change in the genome as the DNA sequence is altered due to improperly paired bases
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3
Q

What DNA repair pathways/processes occur prior to DNA replication?

A
  • Enzyme selectivity (shape of the enzyme is specific and only watson crick base pairs will fit into it)
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4
Q

Nucleotide excision repair (NER)

A
  • occurs anytime throughout replication
  • repairs damaged bases (pyrimidine dimers, alkylated DNA, and other bulky adducts)
  1. excinuclease binds to site of damage and cuts damaged strand on either side
  2. Helicase separates the damaged strand to create a gap
  3. polymerase comes to fill in the gap and ligase seals the strand
    * Xeroderma pigmentosum caused by mutations involved in NER*
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5
Q

Base excision repair (BER)

A
  • occurs anytime
  • repairs modified or damaged bases (alkylated DNA, oxidative damage)
  1. glycosylase cleaves the bond between the base and sugar
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6
Q

Base excision repair (BER)

A
  • occurs anytime
  • repairs modified or damaged bases (alkylated DNA, oxidative damage)
  1. glycosylase cleaves the bond between the base and sugar
  2. removes damaged base creating abasic site (site without base)
  3. AP endonuclease binds and creates a nick
  4. polymerase comes and synthesizes across AP site and ligase seals strand
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7
Q

Direct reversal

A

enzyme that reverses a specific type of damage

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8
Q

Transcription coupled repair

A

transcribed strand is repaired more efficiently than the non-transcribed strand (NER proteins are involved)

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9
Q

Error Prone Repair

A
  • When the replication fork encounters an unrepaired lesion or a strand break, it stalls.
  • occurs during replication
  1. Translesion DNA polymerases are much less specific in the shape and size of bases that can fit in them
  2. these different polymerases are used to incorporate nucleotides opposite of the damaged DNA template
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10
Q

Double strand break repair

A
  • nonhomologous end-joining (can occur anytime)

- homologous end-joining or recombination (S and G2 phase)

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11
Q

nonhomologous end-joining

A
  • type of dsDNA break repair
  • repair with loss of several bases
  • two ends get put back together and ligated

-predominant pathway in mammalian cells

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12
Q

Recombinational ds-break repair (homologous end-joining / recombination)

A
  • type of dsDNA break repair
  • requires resection of the DNA ends and then general recombination
  • Holliday junction results in a repaired break and recombined DNA
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13
Q

Xeroderma pigmentosum

A

caused by mutations in proteins involved in NER (nucleotide excision repair)

-thin, unevenly pigmented skin with very high sensitivity to the sun

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14
Q

Fanconi’s Anemia

A

caused by a defect in proteins involved in repair of inter-strand cross-links

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15
Q

HNPCC (hereditary nonpolyposis colon cancer)

A

caused by mutations in one of the genes involved in mismatch repair

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16
Q

How do the two pathways for repairing double-stranded DNA breaks differ?

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A

in nonhomologous end-joining there is a loss of several bases and the region has an altered segment/sequence.

homologous end-joining completely restores the broken sequence by copying it from the second chromosome.

17
Q

Why T in DNA but U in RNA?

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A
  • cytosine undergoes spontaneous deanimation which yields uracil
  • if uracil were found in DNA, the cell would not be able to differenciate between a normal uracil and a deaminated cytosine
  • uracil in DNA is recognized as a damaged cytosine and it is repaired
18
Q

What is a gene?

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A

units of genetic information that directly encode a molecule used by the cell

  • segment of DNA that includes genetic information that is expressed
19
Q

What are the classes of RNA found in human cells?

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A
  • mRNA (messenger) (Pol II)
  • rRNA (ribosomal) (Pol I)
  • tRNA (transfer) (Pol III)
20
Q

How do genes get expressed?

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A

genetic information turned into RNA being transcribed

21
Q

mRNA

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A
  • synthesized by RNA polymerase II
  • encode protein
  • templates for translation that get made into proteins
  • diverse and complex
22
Q

How are genes arranged differently in prokaryotes and eukaryotes?

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A
  • prokaryotes arrange genes in groups for similar function

- eukaryotes’ genes are separate and expressed on different chromosomes. Transcription is complicated.

23
Q

rRNA

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A
  • synthesized by RNA polymerase I
  • make up 80-90% of RNA in the cell
  • part of the ribosomes and carry out protein synthesis
24
Q

tRNA

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A
  • synthesized by RNA Polymerase III
  • carry amino acids that become proteins to the translating mRNA
  • very stabile, short, and heavily modified
  • used in translation
25
Template strand
the DNA strand that acts as a synthesis template
26
coding stand
the DNA strand that corresponds to the sequence of RNA transcript -sequence identical to RNA that is produced except contains T instead of U)
27
RNA transcript
A primary transcript is the single-stranded ribonucleic acid (RNA) product synthesized by transcription of DNA, and processed to yield various mature RNA products such as mRNAs, tRNAs, and rRNAs. The primary transcripts designated to be mRNAs are modified in preparation for translation
28
How does RNA polymerase II initiate transcription?
- occurs at the promoter - TBP (TATA-binding protein) binds to the TATA box and other initiation factors come to form bigger complex on the promoter resulting in closed complex (DNA still closed/double stranded) - TFIIH activated and opens up DNA (with helicase) to make open complex - TFIIH and CDK9 phosphorylates C-terminal domain (CTD) (catalytic subunit) activating RNA pol. II transcription
29
What is the 5' cap?
an unusual 5', 5' triphosphate linkage where the 5' nucleotide of mRNA is linked to a 7-methy-guanosine residue -increase mRNA stability
30
What are the roles of polyadenylation in eukaryotic transcription?
- multiple adenine nucleotides added on the end - there is no defined termination sequence in eukaryotes thus polyA complex recognizes a certain sequence and cleaves the transcript downstream from this specific sequence and then adds a string of A's to the end of the mRNA - enhances stability and translation of mRNA
31
Promoter
- region of DNA that initiates transcription of a particular gene - located at transcription start site
32
RNA Polymerase
- synthesizes RNA in 5' to 3' direction (same as DNA pol) - doesn't have proofreading - require DNA template - doesn't require a primer (unlike DNA pol) - unwinding and rewinding DNA at the site of transcription changes the topology of the DNA (creates pos. supercoils in front and neg. supercoils behind)
33
RNA Polymerase
- synthesizes RNA in 5' to 3' direction (same as DNA pol) - doesn't have proofreading - require DNA template - doesn't require a primer (unlike DNA pol) - unwinding and rewinding DNA at the site of transcription changes the topology of the DNA (creates pos. supercoils in front and neg. supercoils behind)
34
What does mature mRNA contain?
- 5' cap - coding sequences (exons) - untranslated 3' sequences and polyA tail
35
What roles does the C-terminal domain (CTD) of RNA polymerase II have in transcription?
It is phosphorylated by TFIIH and CDK9 which is essential for initiation and other events in transcription
36
What are the functions of snRNAs (small nuclear) in splicing?
- snRNA help make up a nucleoprotein complex called spliceosome - spliceosome binds to transcript - snRNA recognizes junctions and orient RNA in spliceosome - Assembly of complex requires ATP but the actual catalysis of splicing comes from RNA
37
How does alternate splicing contribute to the diversity of proteins expressed in human cells?
- results in multiple messages from a single gene - leads to multiple gene products (different mature mRNAs) - mRNAs can be differentially processed - these different genes allow for different functions in different cells
38
What is the life cycle of a retrovirus and how does it differ from retrotransposons?
- retroviruses have an RNA genome that is copied into DNA and integrated into the genome of the cell - viral sequences are then transcribed into mRNA and viral RNA - retrotransposons are similar but may not form virion-like particles - if particles are formed, they remain in the cell

Foundation Unit 1 (6 decks)

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