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Y1 Genes, Molecules and Cells > Transcription in Prokaryotes and Eukaryotes > Flashcards

Transcription in Prokaryotes and Eukaryotes Flashcards

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Organic Chemistry 101 flashcards
1
Q

What is the nucleoiod

A

The bacterial ‘equivalent’ (sort of) of the nucleus
NOT membrane bound
Contains DNA and proteins (HU and H1)

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2
Q

In prokaryotes: DNA is arranged how?

A

DNA is assembled in loops
Supercoiling allows DNA to coil up on itself
Loops in bateria - 10-50 kb
Loops contain DNA that is condensed by interacting with basic (positively charged proteins). DNA is negatively charged so interacts well

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3
Q

What is Transcription

A

Synthesis of RNA from a DNA template
RNA polymerase copies one strand of DNA into RNA
RNA is identical to coding strand (but U replaces T) and coplimentary to the template strand

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4
Q

What is a gene

A

Region of double stranded DNA that codes a peptide chain (protein) (OR functional RNA)

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5
Q

True or False?
All genes encode proteins

A

False
Genes encode tRNA and rRNA (involved in translation to produce proteins)
Some genes encode RNAs to help process mRNA
Some genes encode RNAs that regulate other genes

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6
Q

Why is the translational start codon (AUG) not found exactly at the start of the mRNA

A

The region before AUG does not encode protein called an untranslated region or UTR

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7
Q

RNA is always synthesised in which direction
What is the length of mRNA relative to the protein coding regions

A

5’ to 3’ direction
mRNA is longer than the protein coding regions because of the 5’ and 3’ untranslated regions

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8
Q

What is the Promoter

A

is the control region found at the start of the gene
The point where transcription starts is within the promoter
The promoter is a key control region for controlling transcription in the gene

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9
Q

Relative to the promoter and terminator, which way is mRNA synthesised

A

in the direction from promoter to terminator
i.e. information flows through the gene from left to right

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10
Q

Anything in the direction of the promoter is said to be …..

A

Upstream (against the flow of RNA polymerase)

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11
Q

Anything towards the terminator is …..

A

Downstream (with the flow of the RNA polymerase)

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12
Q

In bacteria, genes are often clustered together with several genes transcribed from one promoter
This is called what?

A

An operon

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13
Q

Genes whose products have related functions are often what?

A

Arranged together
This is however very unusual to occur in eukaryotes

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14
Q

What is polycistronic mRNA

A

Codes more than one protein
In prokaryotes

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15
Q

How are common signals in the DNA sequence (conserved elements) identified

A

100s of different promoters from different genes were aligned

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16
Q

For each gene, transcription always starts at a particular positon called

A

the promoter

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17
Q

RNA polymerase does what
It has how many types of subunit?

A

Synthesises RNA
4 types of subunit

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18
Q

What is the consensus sequence

A

Most common bases observed at these areas

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19
Q

A -10 sequence is relatively rich in AT base pairs which allow what

A

Stands to seperate more easily
(2 hydrogen bonds instead of 3)

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20
Q

Is or isn’t there variation within the -35 and -10 sequences

A

Yes there is variation

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20
Q

How does RNA polymerase interact with the promoter region

A

RNA polymerase binds to the -35 sequence
Closed complex forms over the promoter region
and unwinds the -10 sequence by melting which turn complex to open form

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21
Q

The promoter region has 3 componenets
What are they?

A
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22
Q

Describe the main features of RNA sysnthesis in prokaryotes

A

One strand used as a templated
Transcription 5’-3’ (like DNA replication)
No primer needed

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23
Q

The first ribonucleotide has a what
What bonds are formed between the ribonucleotides

A

triphosphate at 5’ end (usually an A base)
Forms a phosphodiester bond in the same way as DNA synthesis

24
Q

Describe the transcrption process

A
  • Template recognised: RNA polymerase bonds to duplex DNA and DNA is unwound at the promoter
  • Initiation: Several abortive attempts are made to get going (makes short chains and then releases them) until eventually
  • Elongation Polymerase synthesises RNA of a certain minimum size that is stably associated with a template DNA which it then goes on to elongate
  • Termination: RNA polymerase and RNA are released
25
Q

Describe how RNA moves through RNA polymerase

A

DNA is unwound in front, template DNA passes through active site and RNA is synthesised then passes out the back
At the active site, there is a hybrid of newly synthesised RNA and DNA (9bp)
This is why RNA polymerase takes time to get going as it needs to have something longer than 9 nucleotides to get started

26
Q

Describe the coupled transcription and translation within bacteria

A

As RNA polymerase moves through the gene making the mRNA, ribosomes latch onto the mRNA to make protein at the same time before mRNA sythesis (transcription) completed
Makes process very fast (relative to eukaryotes because once mRNA is formed in the nucleus it must then move to the cytoplasm)

27
Q

Transcription terminated at specific signals in the DNA called terminators.
What are the two types of terminators

A
  • Intrinsic terminators
  • Rho dependent terminators
  • Both are 50:50 in bacteria
28
Q

What are intrinsic terminators
What is the two features which it has

A
  • All information to bring about termination is in the gene itself. Bacterial termination occurs at a discrete site. All sequences required for termination are in transcribe region, leading to RNA polymerase and RNA being released.
  • Loop and stem
29
Q

During intrisnsic termination newly synthesied mRNA folds into a hairpain structure, How?

A

A hairpin shape is formed as part of coiling over through strong G-C bond
Forms a stem loop strucutre
Causes process to stop
Single stranded U run setion which are very weakly bonded between DNA and RNA and enzymes to fall off

29
Q

What causes Rho factor-dependant termination

A

Rho is a hexameric RNA binding protein
Recognises a rho utilisation (RUT) site in the newly synthesised mRNA
Rho-dependent terminator sequence (RUT site) rich in C and poor in G
Forms a signal in the RNA which the Rho factor can interact with

30
Q

What is the process of Rho-dependent termination

A
  • RNA polymerase transcribes the DNA incorperating the rut site into the RNA
  • Rho factor recognises the rut site and interacts with RNA
  • It translocates along the RNA towards the RNA polymerase
  • RNA polymerase pauses at hairpin structure (similar to intrinsic terminator)
  • Rho cataches up with RNA polymerase and unwinds DNA and RNA hybrid at which point everything is released and transcription is terminated
31
Q

Eukaryotes: Describe the packaging of DNA

A

DNA is tightly packaged to fit in nucleus of cell ( has profound implications for transcription)
Packaging of DNA is done by organising FNA into chromatin (DNA + histone) using strucutres called nucleosomes

32
Q

Eukaryotes: Core nucleosomes contains what?

A

Core nucleosome contains 2 copies of H2a, H2B, H3 and H4 - DNA wound round outside of core nucleosome
H1 associated with DNA between nucleosomes - linker histone ‘beads on a string structure’

33
Q

How can 10nm Chromatin fibres condense further

A

nucleosome string coils around itself - solenoid forming a 30nm fibre

34
Q

Eukaryotic genes are often interupted by what?
How are they removed

A

Introns
Introns are transcribed from DNA into RNA but removed by a processing reaction to generate the final mRNA

35
Q

Eukaryotes: Which form of RNA polymerase transcribes DNA (if the gene is a protein-coding gene)

A

RNA polymerase ll

36
Q

What is the polyadenylation site

A

Marks end of mRNA product

37
Q

What is RNA processing reactions

A

Introns removed - extra regions at the 3’ end back to the polyadenylation site as well as the introns
Exons joined together to produce the final mRNA
Known as RNA splicing
Only exons are preset in the final mRNA

38
Q

What is the primary transcript

A

Contains introns as well as extra sequence at the 3’ end (beyond the polyadenylation site)

39
Q

What is the protein start codon

A

ATG
not the same as the RNA start point

40
Q

What are the three protein stop codons

A

TAG
TAA
TGA

41
Q

Why is the process of transcription and translation slower in eukaryotoes than it is in prokaryotes

A

Transcription occurs in the nucleus and translation occurs in the cytoplasm so mRNA must move through nuclear membrane making process slower - eukaryotes
In prokaryotes you get couples transcription and translation

42
Q

What are the 5 different transcriptional machinery in eukaryotes and their role

A

RNA polymerase l - synthesis rRNA
RNA polymerase ll - synthesis mRNA
RNA polymerase lll - synthesis tRNA, snRNA, 5SRNA
General transcription factos - promoter location
Activator proteins - stimulation of transcription

43
Q

RNA polymerase ll transcribes what

A

Protein coding genes (has 10+ subunits)
Needs general transcription factors and activator proteins to find promoters and to aid transciption at a higher level

44
Q

What is the core promoter

A

Region where transcription starts. Contains RNA initiation site (start site) and in some core promoters there is a TATA box 25bp upstream of the RNA start site

45
Q

What is the proximal promoter

A

next 100-200 bp upstream of the RNA start site

46
Q

What is the enhancer

A

Often many 1000s of bases upstream - plays a role in regulating transcription from the core promoter
The DNA elements are recognised by proteins (transcription factors and activators) that target RNA polymerase ll (this polymerase cannot bind without help)

47
Q

What are general transcription factors

A

Interact with DNA at the core promoter
Present in all cell and forms the transcription ‘machine’ in combination with RNA polymerase

48
Q

What are activators

A

Interact with DNA and proximal promoter and enhancer
Maybe tissue specific. Regulate the level and timing of transcription of indvidual genes

49
Q

Where ar the enhancers, activators, proximal and core promoters and transcription factors relative to another on DNA

A

General transcription factors assemble a transcription complex at the core promoter
This allows RNA polymerase II to associate
Known as a STEPWISE ASSEMBLY model

50
Q

General transcription factos are called what

A

TFIIA
TFIIB
TFIID
TFIIE
TFIIF
where TF = transcription factor
II = RNA polymerase II associated

51
Q

Which is the first transcription factor to bind
Why is the order the transcription factors bind important

A

First transcription factor to bind is TFIID (mix of proteins - TBP and several TAF proteins)
TBP binds in minor groove of DNA and brings TFIID into the core promoter
Followed by TFIIA
Assemble in a defined order on the core promoter to establish the transcription complex (TC)

52
Q

Activators influence what?

A

the assembly of the transcription complex and strucuture of chromatin
They work in two ways: make assembly of the transcription complex more efficient and unpack chromatin to allow transcription

53
Q

Activators are a long way from the promoter. How therefore can they react with the promoter

A

One model suggests they interact and influence the core promoter is by the DNA between the enhancer and core promoter looping around so the proteins attached to the enhancer make contact with the general TFs assembling at the core promoter

54
Q

What are Hemingway cats

A

They have 6 rather than 5 toes
Results from mutation in an enhancer that regulates expression of a gene called sonic hedgehod involved in development

55
Q

How does the process of eukaryotic mRNA being capped work

A

Capping of the 5’ end of the Eukaryotic DNA
Adds a 7-methyl Guanine Ribose to the 5’ end of the mRNA (modified G nucleotide)
Added on by an unusual 5’ to 5’ triphosphate bond

56
Q

Why is mRNA capped

A
  • The cap protects the 5’ end of the mRNA from degradation and is important for mRNA stability
  • The cap interacts with translation factors which recruit ribosomes for protein synthesis
  • The cap interacts with the cap binding complex involved in export of mRNA from the nucleus
  • The cap may be important in splicingg introns near the 5’ end of the mRNA
57
Q

Polyadenlylation occurs at the 3’ end of mRNA
How

A

At the 3’ end, transcription goes past the position of the end of the mRNA to make a longer RNA, which is the cut and then polyadenylated
The sequence AAU AAA in the mRNA targets a protein complex
This complex cuts the mRNA 11-30 bases past the AAU AAA
The removed part of the RNA is degraded and the remaining mRNA is polyadenylated
The poly A tail is important in determining mRNA stability and aiding translation

Y1 Genes, Molecules and Cells (16 decks)

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