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Molecular Biology of the Gene > Alasdair MacKenzie > Flashcards

Alasdair MacKenzie Flashcards

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1
Q

What are the three kinds of RNA?

What are their purposes?

A
  • Messenger RNA (mRNA); encodes for proteins
  • Ribosomal RNA (rRNA); forms part of ribosomal structure
  • Transfer RNA (tRNA); adaptor for protein synthesis
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2
Q

What is RNA synthesised by?

A

a DNA dependent RNA polymerase (RNA pol.)

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3
Q

What is required for RNA synthesis?

A
  • DNA template
  • All 4 NTP’s (ATP, GTP, UTP & CTP)
  • Mg^2+
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4
Q

What is NTP? Give examples

A

NTP = Nucleotide triphosphate

ATP
GTP
UTP
CTP

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5
Q

How many subunits does the core enzyme of E.coli RNA pol have? What are they?

A

5 subunits;
2 alpha;
2 beta;
1 omega

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6
Q

What is the name of the resultant molecule when the core enzyme of E.coli RNA pol associated with a sigma subunit?

A

Holoenzyme

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7
Q

What is the role of sigma factor?

A

Guides RNA polymerase to promotor binding specificity

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8
Q

Which promotor element is important for high gene expression? Which subunit does this bind?

A

Upstream Promotor (UP)

Binds the alpha subunit of RNA polymerase

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9
Q

Briefly describe prokaryotic transcriptional initiation

A
  1. RNA pol. binds promotor
  2. Forms “closed” complex
  3. Forms an “open” complex (transcription bubble)
  4. Polymerase undergoes conformational change
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10
Q

Initiation is characterised by the formation of what? What is this also known as?

A

(i) small RNA oligonucleotides

(ii) Abortive events

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11
Q

Can the use of different sigma factors alter the cells response to environmental factors?

A

Yes

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12
Q

Transcription requires the unwinding of how many base pairs of DNA at a time?
Briefly describe the consequence of this

A

(i) 17 base pairs

(ii) this generates torsional stress that is relieved by topoisomerases

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13
Q

What are the two types of termination signal?

Briefly describe

A
  • Rho p-independent; occurs in region that can form a “hairpin”; Found 20bp from the end of RNA strand; Strings of adenine with weak hydrogen bonds to uracil are also present; combination of both terminates transcription
  • P-dependent terminator; does not involve the repeated sequence of adenine; sometimes encodes a short “hairpin”; involves a p-protein which binds RNA and migrates 3’; Once it reaches the paused RNA pol. P contributes to release mRNA; Exact mechanism of action is unknown
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14
Q

What are the 4 main types of classification of genes?

Briefly describe them

A
  • House-keeping genes; Essential for cell survival
  • Constitutive gene expression; Expression of gene never varies
  • Inducible gene expression; Gene products increase in concentration
  • Repressible gene expression; Gene products decrease in expression following repression by a repressor molecule
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15
Q

What are the two main types of prokaryotic gene regulation?

A
  • Repressors

- Activators

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16
Q

Briefly describe repressors

A
  • DNA-binding proteins that physically impede the activity of RNA pol. at the promotor.

Two types:

  1. Binding the effector molecule changes repressor protein conformation that then release the operator
  2. Binding of effector molecule changes repressor protein conformation that then binds the operator
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17
Q

Briefly describe activators

A
  • DNA-binding transactivators that enhance the activity of RNA pol. at the promotor.

Two types:

  1. Binding of effector molecule changes the activator protein conformation releasing the DNA
  2. Binding of the effector molecule changes activator protein conformation binding the DNA
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18
Q

What is an operon?

A
  • Clusters of genes involved in a set of related processes which share the same promotor and are transcribed together
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19
Q

In the absence of lactose, the lac-repressor binds to what protein sequence?

A

the Operator sequence (O1)

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20
Q

Briefly describe the de-repression of the lac-operon

A
  • When lactose is present, it is converted to allolactose

- Allolactose binds the lac-repressor protein causing its release from the operator

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21
Q

Why is lactose considered “hard” to break down?

A

It has to be broken down into glucose and galactose

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22
Q

What is CRP?

A

cAMP Receptor Protein ( a DNA binding transactivator)

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23
Q

CRP binds the DNA of the CRP-site only when cAMP is…

A

abundant

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24
Q

cAMP is abundant when glucose is absent. True of false?

A

True

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25
Q

What are the three different types of RNA pol. present in eukaryotes and what do they synethesise?

A
  • RNA pol. I synthesises rRNA
  • RNA pol. II synthesises mRNA
  • RNA pol. III synthesises tRNA
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26
Q

What type of transcription factors are required at every promotor for transcription in eukaryotes?

A

RNA pol. II Basal Transcription Factors (TFII)

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27
Q

What does TBP stand for?

A

TATA Binding Protein

28
Q

What does TAFs stand for?

A

TBP Associated Factors

29
Q

What is TFIID made of?

A

TBP & TAFs combined

30
Q

Which transcriptional factor is responsible for stabilising the DNA binding of TBP?

A

TFIIB

31
Q

What is the purpose of TFIIF?

A

Binds to RNA Pol. II and escorts it to TBP & TFIIB

32
Q

Which two transcriptional factors bind to create a “closed” complex?

A

TFIIE & TFIIH

33
Q

What is the purpose of protein kinase in the assembly of the pre-initiation complex?

A

Phosphorylates the Carboxyl-terminal domain of RNA pol. II

34
Q

After how many base pairs have been synthesised will TFIIE and TFIIH be released?

A

70 base pairs

35
Q

Which transcription factor binds with RNA pol. II through elongation?

A

TFIIF

36
Q

What are the DNA components used in transcriptional regulation?

A
  • Enhancers
  • Core promoters
  • Exons
37
Q

What are enhancers bound by?

A

Activated DNA dependent transactivators

38
Q

What is the function of an enhancer?

A

To increase RNA pol. II activity at the promoter.

39
Q

How do we detect enhancer activity?

A

Through “reporter constructs”; they are isolated and placed next to an easily detectable gene using gene cloning.

40
Q

Where are promoters found in a DNA sequence?

A

Immediately next to transcriptional start site of the exons.

41
Q

What is the main difference between enhancers and promoters?

A

Promoters are orientation and distance dependent.

42
Q

What are the three protein components used in transcriptional regulation?

A
  1. DNA-binding transactivator proteins
  2. Mediator
  3. Pre-initiation complex
43
Q

Most DNA-binding transactivators need to be “activated” or modified before they can bind enhancers. These modifications are regulated by what?

A
  • Signal transduction pathways
44
Q

What is the mediator?

A

(Often referred to as co-activator)

- Transmits information from a bound and activated DNA-binding transactivators to pre-initiation complex

45
Q

What is the role of histones and chromatin in the transcriptional regulation of eukaryotes?

A
  • DNA is wrapped around histones into a DNA-protein complex called chromatin
  • When chromatin binds to transcriptional initiation sites, it represses transcription in eukaryotes
  • so, histones must be removed from the promoter prior to initiation.
46
Q

Which proteins add acetyl groups to histones?

What is the result of this addition?

A

(i) HAT proteins (Histone Acetyl Transferases)

(ii) Acetylated histones do not bind DNA so tightly; known as chromatin remodelling or enhancesome

47
Q

Newly synthesised RNA is called what?

A

Primary transcript

48
Q

How is the primary transcript processed?

A
  1. 5’ end is “capped”
  2. 3’ end given a “poly A tail”
  3. Introns removed by splicing
49
Q

What is used to cap the 5’ end of the primary transcript?

What is its purpose?

A

(i)7-methylguanosine

(ii) Linked to 5’ terminal with 5’-5’ triphosphate link
Maybe involved with binding mRNA to ribosome
Protects mRNA from degradation

50
Q

What are the three steps of the addition of the Poly A tail?

A
  1. Release of RNA pol. & binding of poly A enzyme
  2. Digestion of mRNA end
  3. Addition of ATP to form tail
51
Q

What are the majority of eukaryotic mRNAs spliced by?

A

Small Nuclear Ribonuclearproteins (snRNP’s) (snurps)

52
Q

Many tRNAs contain a nucleotide called what?
Where is it positioned?
What bases can it pair with?

A

(i) inosinate
(ii) Position 1 of the aniticodon
(iii) Adenine, Uracil & Cytosine

53
Q

Briefly describe the prokaryotic ribosome

A
  • Comprises 25% of the dry weight of the cell
  • 35% protein & 65% RNA
  • Made of a 30s and 50s subunit
54
Q

Briefly describe the eukaryotic ribosome

A
  • Comprised of 60s and 40 subunit

- Larger and more complex than the prokaryotic ribosome

55
Q

What are the 5 major stages of protein synthesis?

A
  1. Amino acid activation
  2. Initiation
  3. Elongation
  4. Termination
  5. Folding & Post-Translational Modification
56
Q

Where does amino acid activation occur?

A

In the cytoplasm

57
Q

What is the name of the enzyme that covalently links the correct amino acid to their corresponding tRNA?

A

aminoacyl-tRNA synthtases

58
Q

Finish the following reaction:

Amino acid + tRNA + ATP –Mg^2+–>

A

Amino acid + tRNA + ATP –Mg^2+–> Aminoacyl-tRNA + AMP + PPi

59
Q

Protein synthesis always begins at which end of the polypeptide?

A

The amino terminal end

60
Q

What is the purpose of tRNA^Met?

A

It is used for inseting methionine WITHIN the polypeptide chain

61
Q

What is the purpose of tRNA^fMet?

A

It is used for inserting methionine at the beginning of the polypeptide chain

62
Q

What are the three steps of elongation?

A
  1. Binding of incoming aminoacyl-tRNA
  2. Peptide bond formation
  3. Translocation
63
Q

Briefly describe each of the three steps of elongation

A
  1. Binding of incoming aminoacyl-tRNA
    - Involves the formation of peptide bonds
    - New aminoacyl-tRNAs are bound by EF-Tu and are escorted to the A-site of the ribosome
  2. Peptide bond formation
    - Peptide bonds form between the amino acids bound to the tRNAs occupying the A and P sites
    - This step is catalysed by an enzyme called PEPTIDYL TRANSFERASE within the 50s subunit
  3. Translocation
    - The ribosome moves towards to 3’ end of the mRNA molecule
    - Shifts the dipeptidyl-tRNA bound at the mRNA into the P site of the ribosome
64
Q

What are the main types of post-translational processing?

A
  • Removal of signal peptides
  • Formation of disulphide cross links
  • Proteolytic cleavage
  • Glycosylation
  • Phosphorylation
65
Q

Insulin is produced as a prepropeptide with a signal sequence. What are the two main stages that are needed in order for the prepropeptide to produce active insulin?

A
  • Preproinsulin requires disulphide bonds to form between its cystein amino acids (to become proinsulin)
  • Proinsulin then needs to be proteolytically cleaved to produce active insulin
66
Q

Briefly describe protein degradation in eukaryotes

A
  • Proteins targeted for degradation are linked to a 76 amino acid long protein called UBIQUITIN
  • Once covalently linked, ubiquitin directs the protein to the 26s proteosome
  • Ubiquitinated proteins are fed through and broken down into individual amino acids.

Molecular Biology of the Gene (3 decks)

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