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Molecular Biology > Mod 4- From DNA To RNA > Flashcards

Mod 4- From DNA To RNA Flashcards

1
Q

What is a gene?

A

A genetic unit containing information to make a functional product (RNA and/or Protein)

Genes can carry information for structural, temporal, positional, and inducible functions.

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2
Q

What information does a gene contain?

A
  • Structural - coding DNA
  • Temporal (developmental= when gene switches on/off)
  • Positional (tissue/cell specific= when it switches on/off)
  • Inducible (nutrients, stress, hormones= switching genes on/off due to environment)

These categories help define the role and regulation of genes in different contexts.

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3
Q

What is a cistron?

A

A segment of DNA corresponding to one polypeptide (stop and start signals)

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4
Q

What is the role of a promoter in gene transcription?

A

Defines transcription start site and its direction (for RNA polymerase)

Promoters are essential for the binding of RNA polymerase

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5
Q

What is the difference between sense and antisense strands?

A
  • Sense (coding) strand: 5’ - 3’ sequence matches RNA product
  • Antisense (template) strand: 3’ - 5’ sequence is complementary to RNA product

Understanding these strands is crucial for studying transcription.

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6
Q

What are the key features of eukaryotic Class II genes?

A
  • Enhancer = sometimes distal from promoter, contains transcription factor binding sites (works in a 5’ direction)
  • Promoter
  • Exons = in mature transcript
  • Introns = in primary transcript but removed from mature transcript
  • 5’-UTR
  • 3’-UTR
    UTR = untranslated region

Eukaryotic genes are more complex than prokaryotic genes and include regulatory elements.

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7
Q

What is a polycistronic mRNA?

A

An mRNA that contains multiple cistrons, allowing for the expression of multiple proteins

This is a common feature in prokaryotic gene organization.

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8
Q

Fill in the blank: Eukaryotic genes can be quite large, approximately _______ kB.

A

50

Most of this size is due to non-coding regions.

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9
Q

What is the general mechanism of transcription?

A
  • Coding strand (sense): 5’ - 3’ = same sequence as RNA product = leading strand
  • Template strand (antisense): 3’ - 5’ = complementary to RNA product = lagging strand
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10
Q

What is the function of RNA polymerase?

A

Binds to DNA, melts double strand, and polymerizes RNA in the 5’ to 3’ direction

RNA produced is copy of the coding strand and complementary to template strand

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11
Q

What is the significance of the TATAAATG sequence?

A

It is part of the promoter region that helps RNA polymerase bind to DNA

This sequence is crucial for the initiation of transcription.

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12
Q

True or False: All genes contain a regulatory element.

A

True

This is the promoter/ enhancer

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13
Q

What distinguishes prokaryotic gene organization from eukaryotic gene organization?

A
  • Cistrons vs. introns/exons
  • Lack of complex regulatory elements in prokaryotes

Understanding these differences is important for molecular biology.

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14
Q

What are the untranslated regions (UTR) in eukaryotic genes?

A
  • 5’-UTR
  • 3’-UTR

UTRs are crucial for the regulation of translation and stability of mRNA.

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15
Q

How many RNA polymerases are present in prokaryotes and eukaryotes?

A

Prokaryotes have one RNA polymerase - multi-protein complex that does all of the functions and makes all types of RNA

Eukaryotes have three

Eukaryotic RNA polymerases include Pol I, Pol II, and Pol III

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16
Q

What are the roles of the components in the prokaryotic RNA polymerase holoenzyme?

A

RNA polymerase holoenzyme is composed of 6 subunits

sigma (σ)
- promoter recognition
- recognises and binds to promoter region of a gene to unwind the DNA slightly allowing transcription to begin (‘guiding’ factor)
- recognises specific DNA sequences (promoter) and gives direction

2 x alpha (α)
- assembly, activation
- smaller
- activates the polymerase by assembling the core of the enzyme

2 x beta (β + β’)
- catalysis, termination
- opens and polymerises DNA to make RNA copy
- large
- builds the RNA chain
- holds the DNA template in place within the active site and binds incoming RNA nucleotides
- signals end of transcription

Omega (ω)
- assembly, folding, required for some genes
- doesn’t do much in terms of function
- stabilises structure of the polymerase and protects it from denaturing

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17
Q

What is TFIID composed of?

A

TATA binding protein (TBP) + TBP-Associated Factors (TAFs)

TBP is A-T rich

TFIID is involved in the assembly of the RNA polymerase II initiation complex

It recognises the TATA sequence on DNA

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18
Q

What is the function of TFIIA?

A

Helps TFIID to bind to DNA

It facilitates the interaction of TBP with DNA

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19
Q

What does TFIIB do in the transcription initiation process?

A

An accessory factor

This is a single polypeptide

Sets distance from TATA element (where core promoter sequence is) to start site of transcription

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20
Q

What is the structure of the TBP-TFIIB-DNA complex?

A

Saddle structure

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21
Q

What is the role of the Upstream Binding Factor (UBF) in RNA Polymerase I transcription?

A

Binds to UCE and core element in DNA (loops DNA together)

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22
Q

Fill in the blank: RNA polymerase III is recruited and initiates transcription after the recruitment of _______.

A

TFIIIB

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23
Q

What is the function of TFIIIC in RNA polymerase III transcription?

A

Binds to B box and is recruited upstream of start site

Once TFIIIB is recruited, TFIIIC is dispensable

24
Q

True or False: Eukaryotic RNA polymerases are specialized and gene-type specific.

A

True

25
Q

What are the key differences in transcriptional apparatus between prokaryotes and eukaryotes?

A

Complexity and organization; prokaryotes have one polymerase, eukaryotes have three

Eukaryotic polymerases use general transcription factors

26
Q

Identify the general transcription factors associated with eukaryotic RNA polymerases.

A
  • TFIIA
  • TFIIB
  • TFIID
  • TFIIE
  • TFIIF
  • TFIIH
  • Others (TFIIJ, etc.)
27
Q

What is the significance of the TATA box in transcription?

A

Recognized by TBP, crucial for the assembly of the transcription initiation complex

28
Q

What is the function of the RNA polymerase II?

A

Has 10 subunits IN EUKARYOTES and has 6 subunits IN PROKARYOTES

TF2E,F,H,J,K

  • Facilitate interaction with D-A-B complex and recruitment of polymerase II
  • Blocks non-specific binding of polymerase II to DNA
  • Promoter clearance = opens DNA and reads and makes RNA
  • Helicase = mostly done by TFIIE
  • Processivity and elongation = checks for errors, mostly done by TF2H
  • Transcription-coupled DNA repair = done by TF2H
29
Q

What is an operon?

A

A cluster of genes transcribed by the same promoter that gives rise to a polycistronic mRNA

Operons usually consist of genes that are related in function.

30
Q

What does the lac operon do?

A

Hydrolyses lactose to galactose and glucose

31
Q

What occurs when there is no lactose present in the lac operon?

A

The lac operon is repressed as the repressor binds to the operator, preventing RNA polymerase from clearing the promoter.

32
Q

What role does allolactose play in the lac operon?

A

Allolactose binds to the repressor, causing it to dissociate from the operator, thus inducing transcription.

33
Q

True or False: Allolactose is considered an inducer of the lac operon.

A

True

Gene only works if lactose is present

It is under negative feedback control ( basically self-regulating)

34
Q

What are cis-acting elements?

A

DNA sequences that regulate only the genes to which they are directly joined.

These are dominant if mutated

‘Cis’ = next to/ alongside/ adjacent to

35
Q

What are trans-acting factors?

A

Regulatory proteins that can regulate genes anywhere in the genome.

Mostly protein transcription factors

Recessive (mostly - phenotype can be rescued)

36
Q

Define cis-acting mutations.

A

Mutations in regulatory elements that cannot be complemented and affect only the operon they are part of.

37
Q

Define trans-acting mutations.

A

Mutations that can be complemented and may affect many genes.

38
Q

What is catabolite repression?

A

The phenomenon where several operons are repressed by glucose and activate only when glucose is exhausted.

39
Q

What is the role of CRP in the lac operon?

A

RNA polymerase requires CRP

CRP (Catabolite Repressor Protein) binds to cAMP, permitting DNA binding

High glucose = low cAMP so lac operon is off even if lactose is available

Low glucose = high cAMP so lac operon is on IF lactose is present

Glucose preferentially used as a carbon source

40
Q

What happens to cAMP levels when glucose is high?

A

cAMP levels are low, causing the lac operon to be off, even if lactose is available.

Only produced when there is no glucose

cAMP = signalling molecule

41
Q

What does the trp operon do?

A

Contains genes for the synthesis of the amino acid tryptophan.

42
Q

What is the trp repressor?

A

The trp repressor binds to the operator in the presence of tryptophan and prevents transcription

43
Q

Compare the lac and trp operons regarding their inducers and repressors.

A

Lac operon is induced by lactose (substrate), while trp operon is repressed by tryptophan (biosynthetic product).

44
Q

Fill in the blank: Products of biosynthetic operons ______ their operons.

A

[repress]

45
Q

Fill in the blank: Substrates for metabolism ______ their operons.

A

[induce]

46
Q

What interactions are emphasized in the mechanism of regulation by operons?

A
  • DNA-protein interactions
  • Protein-protein interactions
  • Protein-small molecule interactions
  • Conformational change
  • Inducers/co-repressors
47
Q

What is a leader/ spacer?

A

Section of DNA which is non-translated

Transcribed into mRNA for regulating gene expression

NOT translated into protein

48
Q

What is the organisation of a prokaryotic gene?

A

Start (AUG), leader, coding region (cistron), spacer (UGA) terminator

49
Q

What happens in transcription initiation by prokaryotic RNA polymerase?

A

The sigma factor is released and the core enzyme (aabb’) is competent for elongation

Polymerase starts making RNA whilst still sat at the promoter = promoter clearance (to error check)

50
Q

What are the 3 RNA Polymerases in eukaryotes?

A

Pol I - ribosomal RNA genes (rRNA)

Pol II - protein coding genes (mRNA) and small nuclear RNA (snRNA)

Pol III - transfer RNA (tRNA) and rRNA and snRNA

51
Q

What do genes which make different types of RNA have?

A
  • different architecture
  • use different RNA polymerases (recognises different promoter sequences)
  • each type of RNA polymerase needs a distinct set of accessory factors (in eukaryotes)
52
Q

What is SL1 composed of in RNA polymerase I?

A

TBP (TATA binding protein) + pol I- specific TAFs (TBP-associated factors)

TBP & the TAF bind the promoter

53
Q

What is the role of SL1?

A

Selectivity factor 1

This is specific to the species

Recognises promoter of the rRNA genes and initiates transcription when RNA Polymerase I binds to the complex

54
Q

Explain the mechanism of RNA polymerase III

A
  • Promoter is within the coding region
  • TF3C (found to the right) binds to the B box and recruits TF3B
  • TF3B (TBP sits at the centre of this) is recruited upstream of the start site
  • TBP is non-contacting DNA acting as a saddle
  • TF3B = TBP + 2 pol III- specific TAFs
  • Once TF3B is recruited, TF3C is dispensable (not needed as transcription has started so gets displaced)
  • RNA polymerase III is recruited and initiates transcription
55
Q

What are other RNA polymerase III genes?

A
  • 5S rRNA genes are similar to tRNA genes (has promoter sequence after the transcription start site) but use an extra factor TF3A to recruit TF3C
  • snRNA genes have a similar structure to pol II genes = have an upstream promoter and TATA box
56
Q

What are lacZ, lacY and lacA?

A

All code for a single RNA and each bit of this RNA codes for a separate polypeptide

lacZ - b-galactosidase = hydrolyses lactose (a disaccharide) to galactose and glucose (monosaccharides of lactose)

lacY - Permease = facilitates diffusion of lactose

lacA - Acetylase

57
Q

What are cis-acting sequences?

A

Directly regulate the gene i.e. promoters

These are part of the gene

These are binding sites for trans-acting factors

Molecular Biology (10 decks)

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