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Lec 5 Flashcards

1
Q

Where are the cis- and trans- elements located?

A

The cis-elements are on the DNA

The trans-elements are on the opposite

trans-acting elements:
transcription factors (proteins that will bind to DNA)
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2
Q

What is one of the mRNA degradation pathways

A

mRNA degradation has 4 different pathways

  1. nonsense-mediated mRNA decay (NMD)
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3
Q

What pathway does protein degradation undergo?

A

protein degration

ubiquitin proteasome pathway

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4
Q

During the exonuclease decay pathway, mRNA degradation starts at the ________ of mRNA

A

During the exonuclease decay pathway, mRNA degradation starts at the 3’ end of mRNA

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5
Q

Is mRNA degradation a simple process

A

no, mRNA degradation is a complex of many diff proteins

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6
Q

why is RNA sometimes degraded?

A

There is a splice mutation so there is a partial intron in the mRNA seq that hasn’t been spliced out correctly
therefore this surveilance system (mRNA degradation pathway) picks up and degrades mRNA and not made into protein.

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7
Q

What is the purpose of methylated guanosine cap on mRNA

A

Methylated guanosine cap on the 5’ end for stability

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8
Q

Decsribe the exonuclease decay pathway

A

In the exonuclease decay pathway

We have a mature mRNA transcript with a methylated guanosine cap on the 5’ end for stability and a poly(A) tail on the 3’ end.

Proteins come in to the 3’ end of the mRNA at the poly(A) tail.

Poly(A) tail is for stability of the mRNA and helps for the export of the mRNA into the cytoplasm.

A range of protein bind to remove the poly(A) tail. Once the tail has been removed, another set of proteins come in to remove the 5’ guanosine cap.

Then, 2 enzymes start degraded the mRNA from each side.

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9
Q

template strand direction

A

3’=>5’

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10
Q

If the promoter is on the left of the coding region is it located upstream/downstream of the coding region

A

upstream<=======>downstream

promoter = upstream of coding region

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11
Q

define cds

A

coding sequence

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12
Q

Where can regulatory elements be located?

give an example of a regulatory element

A

upstream of coding region and/or promoter

enhancer

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13
Q

Define an enhancer

A

A regulatory element where the transcription factor can bind to and increase the transcription levels

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14
Q

Define an enhancer

A

A short DNA seq where the transcription factor can bind to and increase the transcription levels

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15
Q

Define transcription factors

A

They are proteins that bind to the enhancer (region of DNA) to promote transcription levels of a particular gene

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16
Q

Define repressors

A

Repressors are proteins that bind to the enhancer (DNA seq) and lower the transcription rate

aka transcription factor

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17
Q

Define silencers

A

If a repressor bind to a silencer that can inhibit gene expression

A silencer is a DNA seq that can be bound to transcription regulatory factors

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18
Q

Define insulator

A

Another regulatory factor that can be located upstream or downstream of the coding region is an insulator.

Insulator regulates the expression of an enhancer.

Therefore, the insulator can block the enhancer

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19
Q

When RNA is transcribe from DNA it can be transcribed as:

A 
When RNA is transcribe from DNA it can be transcribed as:
lncDNA
rRNA
tRNA
miRNA
mRNA
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20
Q

T/F

the combination of gene that are expressed or repressed determine cellular form and function

A

T

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21
Q

Cell-intrinsic regulation can be divided into __ groups what are they?

A

Cell-intrinsic regulation can be divided into 2 groups

  1. environmental cures (outside the cell)

2.

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22
Q

Define environmental cues

A

They are cell-extrinsic regulation factors

  • small molecules, secreted proteins, temp and oxygen act as input materials which affect a receptor protein on the cell membrane. Once the membrane receptors have bound to the receptor proteins, they will start a cascade of protein reactions where a lot of proteins are activated by being phosphorylated by protein kinase
    e. g the activation of a transcription factor will occur which then binds somewhere depending on the consensus sequences in the DNA

There is a specific sequence on the DNA that the transcription factor binds to.

23
Q

How do we activate a DNA to be transcribed into an RNA transcript

A

1 way= environmental signals that come from outside the cell

24
Q

T/F

Within the organism, cells communicate with each other by sending and receiving secreted proteins (growth factors, morphogens (pattern formation) cytokines, or signalling molecules)

A

T

25
Q

Explain cell-intrinsic regulation

A

Intracellular cues (inside the cell)

  • DNA can be modified which can affect gene expression
  • DNA and its associated histone proteins can be chemically modified by a cell’s own machiner
  • chromatin modifications can affect gene expression by changing the accessibility of genes to transcription factors

2 major classes of chemical modifications

  1. DNA methylation
  2. histone modification
26
Q

What are the 2 major classes of chemical modification?

A
  1. DNA methylation

2. histone modification

27
Q

What are the types of gene expression?

A
  1. constitutive expression (house-keeping genes)
  2. Induced expression
  3. repressed expression
28
Q

Define constitutive expression

A

Constitutive expression is a type of gene expression aka house-keeping genes

  • some genes are essential and necessary for life
  • they are continuously expressed - function of the gene is very important for cell function/maintenance

eg gene =
beta-actin
gapTh?

29
Q

Define induced expression

A

Induced expression is a type of gene expression in which some genes have higher expression levels once activated

30
Q

Define repressed expression

A

Repressed expression is a type of gene expression in which some genes are repressed and their expression levels are lowered

31
Q

Why are the genes in constitutive expression called house-keeping genes

A

Because they are required for the normal function of the cell and tissue

in RTQ-PCR the house-keeping genes are called reference genes

32
Q

What are reference genes also known as

A

house-keeping genes

33
Q

What are reference genes used for?

A

reference genes are used to compare gene expression against

34
Q

Define temporal specificity

A

Temporal specificity aka stage specificity

  • different genes expressed at diff times
    e. g a particular gene is expressed during pregnancy but not after birth
  • some genes expressed in infant but not adult
35
Q

Gene expression can be categorised into _groups based on specificity.

What are they?

A

Gene expression can be categorised into 2 groups based on specificity

  1. temporal specificity (stage specificity)
  2. spatial/tissue specificity
36
Q

Define tissue specificity

A

spatial/tissue specificty

  • not every gene product needed in every cell type
  • why in heart not in brain
37
Q

What regulatory mechanism is required for the following

  1. area around a prospective transcription zone needs to be accessible
  2. controlling the amount of gene product synthesised during the initiation of transcription
A
  1. epigenetics

2. cis- and trans- acting elements

38
Q

Describe the regulation that occurs at the structural level

A

eukaryotic DNA is packaged into chromatin. Chromatin structure is directly related to the control of gene expression. Chromatin structure begins with the organization of DNA into nucleosomes.

Nucleosomes may block RNA pol 2 from gaining access to promoters

39
Q

Describe cis-acting elements

A

Cis-acting elements are specific DNA sequences which regulate transcription of 1 or more genes

they are made up of 2 interacting parts:

  1. basal promoter elements
  2. enhancer elements

The elements functionally and physically interact

40
Q

Describe basal promoter elements

A

They are components of cis-acting elements.

-they bind accessory transcription initiation factors

100-1000bp long and are adjacent and typically upstream of the transcribed gene

41
Q

___ is close to a gene’s initiation site (upstream of the gene)

A

the promoter is close to a gene’s initiation site (upstream of the gene)

42
Q

The _____retains function even when reversed or moved far from the gene whose transcription it influences

A

The enhancer retains function even when reversed or moved far from the gene whose transcription it influences

43
Q

The ___ has 3 main components

A

The basal promoter has 3 main areas that provide a consensus sequence that allow the activation of transcription without the RNAse polymerase

44
Q

The _____ has 3 main areas that provide a _______ that allow the activation of transcription with the RNAse polymerase

A

The basal promoter has 3 main areas that provide a consensus sequence that allow the activation of transcription with the RNAse polymerase

  1. TATA box
  2. CAAT box
  3. GC box
45
Q

what is the order of the consensus sequences from the mRNA start site

A

upstream of the mRNA start site is the TATA box. Upstream of that is the GC box. Upstream of that is the CAAT box (-110).

46
Q

TATA box

A

tbc..

47
Q

Define the consensus sequence

A

Consensus sequence = specific set of nucleotides that are required for protein to bind to

48
Q

Where is the start site of mRNA

A

mRNA start site is at +1

because +1 is the adenine for the first ATG start codon (methionine)

49
Q

Describe the TATA box

A

it is TATAAAA

located between -25 and -30bp from 1st mRNA start site at adenine (+1)

function:

  • binding site for transcription factor II D (TFIID)
  • composed of TATA binding protein (TBP) and TBP-associated factors (TAFs)

-controls the accuracy and frequency of transcriptional initiation

50
Q

Do prokaryotes have a TATA box?

A

prokaryotes contain a sequence functionally equak to the TATA box, called the Pribnow box which usually consists of 6 nucleotides

TATAAT

51
Q

Describe the CAAT box

A

GCCAAT

location= -70bp

function:
binding site for CAAT-binding transcription factor (CTF1) and CAAT enhancer binding protein (C/EBP)

52
Q

describe GC box

A

GGGCGG

53
Q

methods to identify rna

A 
1. qpcr
rna seq
3. in situ hybridisation
4. reporter assay
5. chip

. (12 decks)

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