Gene Expression 1 Flashcards

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1
Q

What are housekeeping genes?

A

Cells often have some of the same proteins that keep it working such as histones, RNA polymerase. If these genes were taken away then the cell would die

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2
Q

Why are some genes not found in all cells still vitally important?

A

Specialised proteins not essential for cell viability but are for the organism
Therefore the cell will have the same housekeeping genes but some different genes for the main cells specialisations

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3
Q

How many genes do most cells express?

A

10 000-15 000

Housekeeping proteins are needed by all cells

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4
Q

What is the concept unequal gene expression

A

Not all genes are expressed at an equal rate. Some genes are abundant such as mRNAs where as other genes may be scarce in other cells.

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5
Q

What is the concept of constitutively or conditionally expressed genes?

A

Constitutively expressed genes - genes that are always on such as the housekeeping genes.

Conditionally expressed genes - inducible expression from external environmental signals telling the genes to be switched on.

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6
Q

How do cells regulate gene expression?

A
  1. Transcriptional control
  2. RNA processing control
  3. RNA transport and localisation control
  4. Translation control
  5. mRNA degradation control
  6. Protein activity control
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7
Q

What is transcriptional control?

A

mRNA population is regulated by:
which genes are transcribed (active vs repressed)
the rate at which they are transcribed
the transcriptional start site used.

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8
Q

What is mRNA processing control?

A
Splicing:
Introns (intervening sequence) are removed and exons (expressed sequence) are kept in determining what kind of protein forms.
Capping:
Addition of 5' methyl cap place on
Polyadenylation: 
Addition of a 3' poly A tail.
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9
Q

What is the idea of alternative splicing?

A

Determining on where the splicing occurs, different proteins can be made (eg. different forms of insulin) depending on where on the gene splicing occurs.

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10
Q

What is Pol II?

A

Acts as a transcription factory allowing RNA processing to be carried out co-transcriptionally.

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11
Q

Why is there variation in gene organisation?

A

Intron and exon size varies and the number of exons/introns present in a gene varies.
24-28% of the human genome are introns and only 1% of the human genome is exon.

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12
Q

Why do we have introns?

A

Exons often encode discrete protein functional domains.
Exon shuffling can only occur due to having introns.
This allows different proteins to be formed from the same gene (alternative splicing) (idea of multiple types of insulin)

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13
Q

what defines an intron?

A

Most introns contain STOP codons in all reading frames.

Have conserved sequences at the intron-exon boundaries (splice sites)

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14
Q

What are snRNPs?

A

They recognise intron-exon boundaries
They are structural RNAs due to RNA-RNA interaction.
U1 and U2 snRNPs bind to 5’ and 3’ splice sites to splice out the introns

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15
Q

What is the concept of alternative splicing?

A

The idea that the same gene can create related proteins that have similar but not the same functional properties

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16
Q

How does alternative splicing occur?

A

Alternative selection of promoters
Alternative selection of cleavage/polyadenylation sites
Intron retaining mode
Exon cassette mode

(different exons = different protein domains)

(additional exons = larger proteins with additional functionality)

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17
Q

What is the concept of tissue specific expression?

A

Different proteins are produced from the same gene but they occur in different locations of tissue

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18
Q

What is the predominant level of control for gene expression?

A

Transcription

19
Q

What kind of regulatory sequences can be found within an intron?

A

Sequences telling which genes will be turned on and which will be silenced.
Also tell the rate of transcription.

20
Q

What is a gene composed of?

A

Structural information coding for a protein

Regulatory sequences giving instructions for expression.

21
Q

What do the 5’ Regulatory sequences do?

A

Controls the transcription initiation = Gene promotor.

Turns the genes on or off.

22
Q

What are the promotors?

A

Chunks of DNA which initiate transcription.

23
Q

What is the polymerase that makes the mRNA?

A

RNA polymerase II

24
Q

What are the main concepts of RNA polymerase II?

A

RNA pol II holoenzyme:
where many proteins (enzymes) come along and integrate together in order for transcription to work. Enzymes may be involved in binding to DNA, regulating the enzyme,

25
Q

What defines where a gene starts?

A

TATA BOX

26
Q

Where does the first basal machinery factor bind to?

A

TATA BOX.
This site is recognised by the TBP (TATA Binding Protein) which is in a multi protein complex with TAFs (TBP associated factors)

27
Q

What is TFIID?

A

Transcription Factor II D

This is the TF that binds to the TATA box and initiates transcription by recruiting polymerase II to this site.

28
Q

How does TBP work?

A

TBP distorts the promotor DNA as when it binds, it induces a kink (90 degree bend) producing a saddle shaped protein.

29
Q

How does TFIID work?

A

TFIID forms a horseshoe shaped structure around the DNA with TBP at the top cavity.
TFIIA and TFIIB alter the shape of the cavity and stabilise the interactions.

30
Q

What is TFIIH involved in?

A

DNA helicase that opens up the DNA and pulls the strands apart.

Also has protein kinase activity which phosphorylates CTD.

Releases Pol II from other general TFs.

TFIID remains to promote re-initiation

31
Q

What does TFIIE do?

A

Involved in DNA melting at the promotor

32
Q

What is transcriptional initiation?

A

Initiation complex assembly at the basal level of transcription.

Transcription with only basal factors is very inefficient.

33
Q

How can activated transcription occur?

A

Transcription + gene specific transcription factors

34
Q

What are transcriptional activators

A

bind to a specific sequence in DNA with an activate domain that the TAFs bind to.

35
Q

What are gene enhancers?

A

DNA sequence elements that are specifically associated with gene promotors.
They can be a considerable distance away from the promotor.

36
Q

What do gene enhancers do?

A

Bind to DNA sequence specific transcription factors and therefore can act as switches.

37
Q

How do transcription activators work?

A

They are modular proteins.

They have a DNA binding domain and this activation domain interacts with the basal transcription complex typically TAFs

38
Q

What do transcriptional repressors do?

A

Turn genes off

39
Q

What is the CREB protein?

A

Leucine zipper motif:

Has a DNA binding basic aa domain and a transcriptional activation domain.

40
Q

What controls the rates of transcription?

A
Multiple enhances (both up and downstream)
Multiple transcription activators
41
Q

Why is spacer DNA crucial?

A

to allow flexibility (bending/looping)

Allows interaction with basal transcription machinery.

42
Q

What is the concept of the RNA polymerase Holoenzyme?

A

The idea that there are lots of proteins helping the RNA polmerase enzyme to do its job

43
Q

What is the TATA BOX?

A

A DNA sequence found upstream which is about 25 B.P from the start site of transcription and therefore the ATG coming after is the start of transcription and is important.

44
Q

What maes up TFIID?

A

Multi protein complex comprising of:
TBPs (TATA bind porteins
TAFs (TBP Associated Factors) - TFIIA/TFIIB