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Molarcular men biology > Shafter > Flashcards

Shafter Flashcards

1
Q

(1) Interphase chromatin is mainly existing of wat

A

Euchromatin

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2
Q

(1) Differences between euchromatin and heterochromatin

A

Euchromatin: Decondenses during interphase, most expressed sequences
Heterochromatin: Remains condensed, few expressed sequences (contains elements essential to chromosome stability and inheritance)

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3
Q

(1) Characteristics of histones

A
  • Small basic and highly conserved

- Form a solenoid structure with DNA wound core of histone protein

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4
Q

(1) 3 main types of functional elements of chromosomes

A

Telomere
Replication origin
Centromere

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5
Q

(1) Telomere characteristics

A
  • Vertebrate sequence is TTAGGG repeated over several kb
  • Telomere gets shorter after each replication as end of lagging strand cannot be replaced as DNA can’t put a primer
  • Telomerase can replace telomere sequence
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6
Q

(1) Example of creating new genes by duplication during evolution

A

Globin gene family

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7
Q

(1) First evidence for Eukaryotic transposable elements

A

MAIZE

  • Change in pigmentation during development (variegation)
  • Results in sector tissue with altered phenotype
  • Proposed due to rearrangement of genome
  • Unstable alleles
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8
Q

(1) 3 types of reassociation kinetics used to predict number of genes per genome

A

1) Highly repetitive DNA: High copy number seq, repetitive very short sequences
2) Moderately repetitive DNA: Moderate short sequences (e.g. histones, ribosomal genes, transposons)
4) Non repetitive DNA: Unique sequences, genes, gene families.

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9
Q

(2) 7 stages gene expression can be controlled

A

1) Histone modification (acetylation, methylation)
2) Translational control (RNA polymerase, TFs)
3) RNA processing control
4) RNA transport and localisation control
5) mRNA degradation
6) Translation control
7) Protein activity control

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10
Q

(2) WAT is histone code hypothesis

A

Proposes that specific combinations to histones and DNA of chromatin help determine chromatin configuration and influence transcription

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11
Q

(2) 3 histone modifications

A

1) Acetylation: Loosens chromatin and promotes initiation of trans. (Acetyl groups attached to +ve lysines in histone tails)
2) Methylation: condenses chromatin
3) Phosphorylation (next to methylated aa): Loosens chromatin

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12
Q

(2) 3 types of RNA Polymerase

A

Pol I: rRNA
Pol II: All protein-coding genes (mRNA)
Pol III: tRNA genes

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13
Q

(2) Eukaryotes consensus sequence

A

TATA box, -25 relative to transcriptional start

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14
Q

(2) RNA Pol II Initiation complex subunits

A

1) TFIID: TBP (TATA box recognised), TAF (regs DNA-binding)
2) TFIIB: Positions RNA Pol
3) TFIIF: Stabilises RNA polymerase
4) TFIIE: Attracts and regs TFIIH
5) TFIIH: Unwinds DNA, phos Ser5

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15
Q

(2) Role of Activators, enhancers

A
  • Enhancers are distal control elements away from gene

- Activators: proteins that binds to enhancers and stim trans of gene.

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16
Q

(2) How are different genes activated in different tissues?

A

There are different activators in different cells to determine which specific gene is expressed

17
Q

(2) Role of Leu zipper TFs

A
  • Mediates both DNA and protein binding

- Bind to DNA as homo or deterodimers

18
Q

(3) Methods for analysing expression of single gene

A

1) RT-PCR
2) Live cell imaging
3) Promoter studies

19
Q

(3) Methods for analysing expression of all genes

A

1) Microarrays analysis (Tiling or Affymetrix)

2) RNA seq: using next gen sequencing

20
Q

(3) Method for analysing TF binding site

A

1) Add reporter gene to promoter construct: encodes an easily assayed enzyme (e.g. B-galactosidase)
2) Transfect reporter DNA construct to cultured cells
3) Allow time for expression
4) Extract protein
5) Assay for reporter enzyme activity
ALSO CHROMATIN IMMUNOPRECIPITATON

21
Q

(3) Method to test promoter function

A

TRANSFECTION

  • Modify reporter construct and repeat experiement
  • Find TF binding sites by PCR or expression of reporter gene/protein
22
Q

(3) Modifications to make mature mRNA from pre-mRNA

A

1) 5’ Cap
2) Polyadenylation at 3’ end
3) RNA splicing

23
Q

(3) Why do modifications to mRNA?

A

1) Distinguishes mRNA from other RNA
2) Helps mRNA to process and export to cytosol
3) Stabilises mRNA
4) required for efficient translation

24
Q

(3) Principle of splicing

A 
A TWO STEP TRANSESTERIFICATION
1) 5' end splice site
2) 3' end splice site
3) Branch point in intron sequence
MUST BE PRECISE
25
Q

(3) Alternative splicing principles

A

A mechanism for cells to generate diversity by creating alternative mRNA.

26
Q

(4) 3 types of RNA editing

A

1) Base insertion (Uracil)
2) C deamination to U
3) A deamination to Inosine

27
Q

(4) C deamination to U, what subunits are needed in editosome

A

1) APOBEC (ApoB mRNA editing enzyme catalytic subunit)
2) ACF (APOBEC complementation factor)
BOTH recognise seq flanking C to be edited

28
Q

(4) Affect of RNA editing of glutmate receptor subunit GluR-B

A
  • A to I editing of pre-mRNA codes for transmitter gated ion channel in brain
  • Causes glutamine to arginine that alters Ca2+ permeability of channel
29
Q

(4) Examples of proteins from edited mRNA

A

Gluamate R
Serotonin R
DNA repair enzymes
ADAR mutant flies suffer from neurodegeneration

30
Q

(4) Explanations for RNA editing

A

System to revise mistakes in trans
Enhancements of genome plasticity
Once evolved as defence system to inactivate retroviral mRNA

31
Q

(4) Def Ribozymes (Ribonucleic acid enzymes)

A

RNA molecules that possess catalytic activities

32
Q

(4) Nuclease activity of ribozyme

A

Peptidyl transferase function of ribosome is encoded by RNA molecule (Ribozyme)

33
Q

(4) Role of snoRNAs

A

Guide RNAs used as template to conduct modifications

34
Q

(4) WAT are + Function of miRNAs

A

Can stifle production of a protein by interacting with true mRNA, thereby preventing its translation
-Small noncoding RNA molecules that can regulate eukaryotic gene expression (degradation and translatability)

35
Q

(4) miRNA function in development

A
  • Dicer disrupted in fertilised eggs (block generation of all miRNAs at stage_
  • Dicer inactivated in development in specific tissues, severe growth defects are seen (miRNAs are able to fine tune protein levels)

Molarcular men biology (8 decks)

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