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Zoology Semester 1 > APS138 Cell And Molecular Biology - Ton > Flashcards

APS138 Cell And Molecular Biology - Ton Flashcards

1
Q

Prokaryotic genes are often organised in…

A

Functional operons

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2
Q

What is the operator region?

A

A segment of DNA that the repressor or activator protein binds to

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3
Q

2 parts to a functional operon:

A

Promoter and functional genes

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4
Q

Activator proteins (which activate RNA polymerase) coded by…

A

Activator genes

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5
Q

How can the activator protein stability affect the expression of a gene?

A

If activator protein unstable then it is degraded more easily and won’t activate RNA polymerase as much, so the gene won’t be expressed as much

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6
Q

What is the lac operon found in?

A

E. coli gram negative bacteria

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7
Q

What is the lac operon expression regulated by?

A

Repressor protein coded for by Lac I repressor gene

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8
Q

What does lactose bind to?

A

Lac I repressor protein - inactivates and no longer fits operator, operon is expressed - lactose can be broken down - negative feedback regulation
- b-galactosidase is the enzyme

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9
Q

What does Trp stand for?

A

Tryptophan - an amino acid

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10
Q

What does the trpR repressor gene code for?

A 
An inactive (by default) repressor protein - tprR
- activated by tryptophan - binds to operator and blocks expression of tryptophan - negative feedback
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11
Q

Explain quorum sensing in bacteria

A

When cell density is low bacteria display individual behaviour. They constantly release low levels of auto-inducer compounds (often homoserine lactone), which naturally diffuse when bacteria are at low levels. However, when cell density is higher, group behaviours are displayed, such as virulence, microfilm formation or luminescence, as the concentration of the auto-inducer compounds are higher and diffuse back into cells, triggering reactions and gene expression.
- Hawaiian bobtail squid lives in symbiosis with bioluminescent bacteria (Aliivibrio fescheri) - lux operon - luxR repressor activated by enzyme Lux I which is constantly secreted at a low rate.

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12
Q

What is a nucleosome?

A

8 histones + 146 base pairs of DNA

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13
Q

What is heterochromatin?

A

Dense, tightly packed chromatin - inaccessible for transcription

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14
Q

What is lightly packed chromatin called?

A

Euchromatin

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15
Q

How is heterochromatin converted into euchromatin?

A

Histone acetyl transferases and histone methyl transferases

acetylation

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16
Q

How is euchromatin converted into heterochromatin?

A

Histone deacetylase and histone demethylase

methylation

17
Q

In the paused state of RNA polymerase II what is phosporylated?

A

Serine 5

18
Q

In the active state of RNA polymerase II what is phosphorylated?

A

Serines 2 and 5

19
Q

Where does alternative splicing occur?

A

In the nucleus

20
Q

What are the two types of small RNAs?

A

microRNA (miRNA) and small interfering RNA (siRNA)

21
Q

What are small RNAs?

A

Double stranded RNA between 20 and 30 nucleotides long - can regulate heterochromatin methylation

22
Q

What is microRNA and siRNA used for

A

Repressing gene expression via three mechanisms:
1. repression of gene translation
2. Promoting mRNA degradation
(post-transcriptional silencing)
3. Repression of gene transcription via chromatin remodelling and DNA methylation (siRNA) - thought to be ancient way of protecting plants from retroviruses

23
Q

What enzymes cut pre-miRNA into miRNA?

A

Dicers

24
Q

What degrades unneeded proteins?

A

Proteasome

Breaks them down in to small protein fragments (peptides)

25
Q

What are proteins tagged with before degradation?

A

Multiple Ubiquitins

26
Q

Miss out Figure 5 of the paper

A

Zooweemama

27
Q

What does reverse-transcriptase quantitative PCR (RT-qPCR) measure?

A

Relative mRNA levels in tissues/cells

28
Q

What are the 3 stages of PCR? What temperatures are required

A
  1. Denature at 95 degrees
  2. Anneal gene-specific primers are 55 degrees
  3. Extend primers using taq DNA polymerase at 72 degrees

Repeat cycle 35 times

29
Q

What do nuclear run-on assays measure?

A

Rates of mRNA production from the nucleus

30
Q

How do you carry out a run on assay?

A
  1. Rapidly extract nuclei
  2. Add biotin-U and unlabelled A, G and C
  3. Extract biotin-labelled mRNA (mRNA which has been produced since extracting the nucleus) using streptvidin-coated beads
  4. Measure biotin labelled mRNA by RT-qPCR
31
Q

What is ChIP?

A

Chromatin-immuno-precipitation. Used to quantify binding between specific gene DNA sequences and a protein - measures the amount of any specific DNA sequence attached to a protein

32
Q

How is ChIP carried out?

A

Chromatin extracted from nuclei and sonicated to chop into chunks. Immunoprecipitated using a specific antibody against the protein. Extract DNA from chromatin. qPCR to determine levels of DNA in chromatin before and after immunoprecipitation.

33
Q

What is H3K4me3 a good marker for?

A

Open euchromatin

Zoology Semester 1 (16 decks)

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