22. Transcription Flashcards

1
Q

Define DNA transcription

A

DNA transcription: mRNA synthesis from a DNA gene

  • in interphase (S) - only in this phase chromosomes despiralise - can be read
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Sequence of transcription + enzymes

A
  1. INITIATION: RNA polymerase binds to promoter sequence - unwinds DNA - NTPs (E) used for mRNA synthesis from template strand (antisense)
  2. ELONGATION: synthesis of mRNA in 5’ to 3’ end
  3. TERMINATION: gene synthesised until terminator sequence - RNA polymerase and mRNA detach from template strand (antisense)

RNA transcript is identical to sense strand (5’-3’) and complementary to antisense strand (3’-5’)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Sections of a gene

A
  • Promoter: non-coding, initiates trasncription, binding site for RNA polymerase (controlled by transcription factors in euk.)
  • Coding sequence: transcribed by RNA polymerase into mRNA
  • Terminator: non-coding, stops transcription, RNA polymerase detaches
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Sense strand vs antisense strand

A

SENSE strand: coding strand, not transcribed, identical to mRNA (T→U)

ANTISENSE strand: template strand, transcribed, complementary to mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Post-transcriptional modifications

A
  1. Capping: addition of methyl group to 5’ end, protection against exonucleases, can be recognised by cell’s translation machinery
  2. Polyadenylation: addition of poly-A tail to 3’ end, improves stability, facilitates export out of nucleus
  3. Splicing: introns are removed - mature mRNA
  4. Alternative splicing: removal of some exons - different proteins from same gene
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Exons vs introns

A

INTRONS - intruding sequence

EXONS - expressing sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What regulates gene expression?

A

TRANSCRIPTION FACTORS: from a complex with RNA polymerase - transcription cannot be started without - levels regulate expression

REGULATORY PROTEINS: bind to DNA sequences (control elements) and interact with transcription factors, enhancer (activator, increases rate of transcription) - silencer (repressor, decreases rate of transcription)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Types of control elements in transcription

A

Distal control elements: distant from promoter, regulatory proteins bind

Proximal control elements: close to promoter, transcription factors bind

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Examples of environmental influences on gene expression

A
  1. Hydrangeas: pH of soil determines - pink/blue flowers
  2. Himalayan rabit produces different fur colour depending on the temperature
  3. Humans produce different amounts of melanin depending on light exposure
  4. Certain fish/reptiles change sex depending on social cues
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Histone tail modifications and their influence on gene expression

A

ACTIVATION - DEACTIVATION of genes by nucleosome packing

  1. Acetylation: neutralises the + charge of histone tails - DNA less tightly coiled - increases transcription of those genes - EUCHROMATIN
  2. Methylation: maintains + charge of histone tails - DNA more coiled - transcription of those genes reduced - HETEROCHROMATIN
  3. Phosphorylation: phosphate group addition
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

DNA methylation

A

DNA methylation decreases gene expression - prevents transcription factor binding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Define epigenetics

A

EPIGENETICS: study of changes in phenotype due to variation in gene expression levels

Shows DNA methylation patterns - change over life

Methylation influenced by:

  • heritability but not genetically pre-determined (identical twins different methylation patterns)
  • environmental effects (diet, exercise, smoking)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Reverse transcription

A

In retroviruses - by reverse transcriptase - cDNA (complementary) transcribed from mRNA - cDNA represent sequences which are actively transcribed

  • used to determined gene expression in healthy - diseased
  • cDNA used in gene transfer (don’t possess introns)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Explain codons how many of them

A
  • codons code for specific amino acids, three bases translated into one amino acid (reading frame)
  • 64 codons in total: 61 code for the 20 possible amino acids, 3 STOP codons
  • Several codons can code for the same amino acid, but one codon corresponds only to one amino acid
  • AUG (Met) start codon
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What are the three RNA polymerases and what to they synthesise?

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Explain how transcription is initiated: promoters, transcription factors, RNA polymerase

A
  1. Promoter regions in DNA - upstream (earlier) the gene
  2. Transcription factors bind to the promoter regions
  3. RNA polymerase II can bind to the DNA strand when transcription factors indicates where - transcription initiation complex
  4. TATA box - DNA sequences crucial for forming transcription initiation complexes in eukaryotes
17
Q

Explain how distant elements promote transcription during initiation stage

A
  • Away from the gene region activator proteins bind to specific regions - act as enhancers in transcription
  • Distant elements (activator proteins) come in contact with transcription via a mediator complex to which both of them bind → initiation of transcription (once activator proteins come in contact RNA polymerase II is released to transcribe)
18
Q

Termination in eukaryotes vs prokaryotes

A
  • in bacteria transcription ends at the terminator region - mRNA can be translated
  • in eukaryotes polyadenylation sequence must be transcribed and termination happens when 10-35 more nucleotides are added post adenylation transcript in mRNA
19
Q

What are the post transcriptional modifications of mRNA?

A
  • when only transcribed - pre-mRNA - RNA processing modifies pre-mRNA in nucleus before sending off to cytoplam: both ends of pre-mRNA are changed: 5’ end 5’ cap, 3’ end poly-A tail
  • Splicing occurs to form mature mRNA
20
Q

What are the functions of modifying mRNA ends? Poly-A tail and 5’ cap

A
  • facilitate transport out of the nucleus
  • protect mRNA from hydrolytics enzymes
  • help ribosomes attach to 5’ end
21
Q

Structure of a mature mRNA ready for transcription

A

the start and stop codons in the sequence are for translation

22
Q

Explain split genes and RNA splicing

A
23
Q

What is the evidence for mRNA splicing?

A
24
Q

What are the signals on mRNA for splicing?

A

Always in eukaryotes: AG-GU (A) AG-G signal splicing

25
Q

What is the mechanism for splicing?

A
  • occurs in splicosomes
  • 2 nucleophilic attacks to get rid of an intron in a lariet structure (the loop) - small nuclear ribonuclear proteins (snRNP) form the splicosome
26
Q

What allows RNA to function as an enzyme?

A
  • can form 3D structures with itself due to base pairing
  • some RNA abses functional groups that may act in catalysis
  • RNA can form hydrogen bonds with other nucelic acid molecules
  • Examples: snRNAs, ribozymes are catalytic RNAS
27
Q

What are self splicing RNA introns?

A
  • tetrahymena, some mitochondrial and chloroplast genes contain these introns
  • don’t require additional molecules
  • rely on extensive base pairing with intron sequence
  • 2 possible groups of self splicing
  • 2 group mechanism resembles mammalian splicing in splicosomes (A performs nucleophilic attack, repeated nucleophilic attack on another part in intron - lariet structure)
  • splicosomal splicing may have originated from group 2 self splicing (same mechanism)
28
Q

What are the uses of introns in transcription?

A
  • regulate gene expression
  • alternative RNA splicing may result in different mRNAS from the same DNA sequence (depends which sections are treated as exons)