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sem 1- MCBG > DNA & Inheritance > Flashcards

DNA & Inheritance Flashcards

1
Q

Breakdown DNA into the base pairs in order.

A
  • DNA (double helix, condensed around histones)
  • Chromatin (heterochromatin & euchromatin)
  • chromosomes (one X chromosome is 2 DNA molecules, A chromatid is 1)
  • genes
  • genomes
  • base pairs eg A&T, G&C
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2
Q

What is heterochromatin and how does it appear?

What is euchromatin & how does it appear in a stain ?

A
  • heterochromatin= solenoid 30nm fibre, genes are not expressed, tightly packed or condensed (methylation of DNA), stains DARK
  • euchromatin= beads on a string, genes are expressed, loosely packed (acetylation of DNA), stains LIGHT
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3
Q

Define the following:

  • gene
  • genome
  • DNA
A
  • genes carry the code for a protein & have a chromosomal location, humans have around 25,000
  • genome is the entire DNA sequence of a species eg humans is 23 pairs of chromosomes, of which 22 pairs are autosomes and 1 pair is the sex chromosomes (X &Y)
  • deoxyribonucleic acid, polynucleotide, contains pentose sugar, phosphate group & nitrogenous base (ATCG), differs from RNA (ribose sugar, phosphate & bases AUCG)
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4
Q

Define; nucleoside, nucleotide, pyrimidine, purine

A
  • nucleoside= base + sugar
  • nucleotide= base + sugar + phosphate
  • pyrimidine= smaller, single ringed bases eg CTU
  • purine= bigger, double ring bases eg AG
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5
Q

How are nucleotides joined? In which direction does DNA synthesis happen? Which direction do we read & write the sequence?

A
  • via hydrolysis reaction expelling H2O & forming a phosphodiester bond, between C=O & NH2 groups, specific orientation needed
  • synthesis of DNA= 5’ to 3’
  • read= 3’ to 5’ eg 5’ACCTG3’ is synthesised as a new strand to 5’CAGGT3’
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6
Q

What is the properties of base pairings between

a) C &G
b) A&T
c) A&U
- what does this base pairing allow DNA to do?

A

a) forms x3 H bonds
b) forms x2 H bonds
c) forms x2 H bonds
- base pairings allow DNA to form duplex structures

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7
Q

Give properties of DNA in

  • 2’ structure
  • 3’ structure
  • 4’ structure
A
  • 2’ DNA strands are complimentary & anti parallel, each strand held together by covalent bonds between sugar-phosphates, double stand held by H bonds
  • 3’ forms a right handed helix w anti parallel strands
  • 4’ forms double helix to nucleosomes, then nuclesomes to hetero & euchromatin
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8
Q

Give some features of DNA replication

A
  • Each DNA strand acts as a template for a new strand
  • It takes place during the S phase of the cell cycle
  • it is semiconservative
  • from 5’ to 3’
  • Catalysed by DNA polymerase
  • DNTP’s needed (hydrolysis of pi bond in pyrophosphatase drives the reaction)
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9
Q

Using three steps initiation, elongation and termination, outline DNA replication in prokaryotes.
prokaryotes have a circular, naked chromosome

A

1) Initiation=
- Recognition of origin of replication, it requires recruitment of DNA polymerase and a kickstart by DNA primase that makes an RNA primer w -OH that DNA polymerase can extend its 3’ prime end(reads template strand from 3’ to 5’), one origin of replication results in two replication forks
- Elongation= Moving replication forks, DNA helicase unwinds the double helix, forms a replication bubble, DNA polymerase adds nucleotides on 3’ ends only, leading to a leading strand-5’ to 3’(continuous), the lagging strand -3’ to 5’(discontinuous) and Okazaki fragments joined by DNA ligase
- Termination= Replication is happening at different parts of the DNA & the direction of replication for these parts is towards each other. When two facing replication forks meet, the DNA ligase joins final fragments resulting in two identical DNA molecules

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10
Q

What is cell division in prokaryotes & eukaryotes?
What is cell division in somatic cells?
What is cell division in germline cells?

A
  • In prokaryotes the process going from one mother cell to 2 daughter cells
  • In eukaryotes the process going from one mother cell to 2 daughter cells
  • In somatic cells, it includes cell division mitosis from one cell to 2 identical daughter cells
  • In germline cells there are specialised cell division process (meiosis) from one cell to four non-identical sex cells
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11
Q

Name what happens at each stage of the cell cycle

A
  • M stage =mitosis (nuclear division) or cellular division (cytokinesis) only stage not in interphase (<1hr)
  • G1= Cell contents duplication e.g. organelles (10-12 hours)
  • G0= stationary phase
  • S phase= DNA replication (6-8hrs)
  • G2= double check and repair (3-4hrs)
  • very complex
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12
Q

What is DNA integrity and at which level is it important

A

Keeping DNA strands intact

  • important at nucleotide, gene and chromosome level
  • protecting DNA from single-strand and double strand damage
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13
Q

Name some types of damage that can happen in DNA

A

Single-strand break, bulky adduct, interstrand cross-link, double-stranded break, mismatch, insertion , deletion, intercalating agent

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14
Q

Name some exogenous & endogenous sources of DNA damage.

A
  • exogenous= ionising radiation, UV, alkylating agents, mutagenic chemicals, anti-cancer drugs, free radicals
  • endogenous= free radicals (formed in mitochondria during metabolism, in WBC during inflammation), replication errors
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15
Q

How does DNA replication stress happen?

A
  • Inefficient replication that leads to replication fork slowing, stalling and/ or breakage
  • replication machinery defects eg
  • replication fork progression hindrance e.g. limited number of nucleotides, lesions, transcription, repetitive DNA
  • defects in response pathways
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16
Q

Fork slippage is one example of DNA replication stress. how does this happen?

A
  • When there is lots of repetitions of bases eg AAA they can loop out
  • if on the newly synthesised strand, there is an extra nucleotide on the new strand, if on template strand, the new strand will be missing a nucleotide & there’ll be an extra on the template strand
  • backwards slippage means the new strands will be longer (insertion)
  • forward slippage means the new strands will be shorter (deletion)
17
Q

Huntington’s disease is an example of a trinucleotide repeat disorder. outline how this happens.

A
  • CAG repeats in HTT gene leading to polyglutamine repeats in Huntington’s
  • Effects neurons, progressive, late onset disease
18
Q

What is the DNA damage response?

What are the 3 outcomes?

A
  • includes the cellular pathways that sense, signal and repair DNA damage
  • when DNA damage is sensed there are three outcomes:
    1) senescence- permanent cell cycle arrest
    2) proliferation- cells divide after DNA is repaired
    3) apoptosis- programmed cell death
19
Q

DNA can be repaired. Give 3 ways this happens.

A

1) Base excision repair= removal of the wrong base (should be C but becomes U) replaced with the correct one (C) by DNA polymerase and gap sealed by DNA ligase.
2) nucleotide excision repair= UV radiation forms a thymine dimer that loops out (more than one base damaged) is cut out and replaced with new undamaged DNA.
3) mismatch repair= mismatched base and its neighbours are removed and replaced with the correct complimentary nucleotides

20
Q

DNA can be damaged by a single strand break and double-stranded breaks.
describe both.

A
  • single-strand break= Relatively simple, many different mechanisms, integrity of DNA molecule intact, damage removed on one strand only, homology of the other strand used to repair damaged, not error free but not error prone
  • double strand break= complex, integrity of DNA lost, most likely error prone, use of homology may be possible.
21
Q

What are the two methods by which double-stranded breaks can be repaired?
Why is one method sometimes used although it has no apparent benefits?

A

1) non-homologous end joining= broken ends recognised and protected, complex formed, damaged ends removed, broken ends ligated, error prone (mutations likely)
2) homologous end-joining= invading DNA helix can make new DNA using homologous DNA molecule to repair perfectly, no mutations can arise from this.
* In some stages of the cell cycle, nonhomologous end-joining will be favoured

22
Q
  • outline the multistep cancer model -what are the consequences of lack of cell cycle control?
  • how can the DNA damage response stop this?
A
  • mutation accumulation, normal-> premalignant-> malignant.
  • DNA replication stress stimulates carcinogenesis
  • loss of cell cycle control leads to cancer
  • dna damage response repairs defects, stopping carcinogenesis.
23
Q

What are some DNA repair defects?

A

DDR defect
Mutated gene
Syndrome
Cancer predisposition

24
Q

Define tumour heterogeneity.
Define differential sensitivity in regards to chemotherapy.
Define chemotherapy induced mutagenesis & cancer evolution

A
  • one tumour will have many subclones of which there are many different cell types
  • chemotherapy may only be effective against some types of cells within the tumour.
  • chemotherapy can cause the cells it is not effective against to mutate and induce further growth thereby resulting in cancer evolution

sem 1- MCBG (10 decks)

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