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2024 SEM 1 BIOCHEMISTRY (LEC) > transcription > Flashcards

transcription Flashcards

1
Q

Enzyme that catalyzes the production of RNA on a DNA template

A

RNA polymerase

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2
Q

briefly explain the multisubunit structure in rna polymerase

A

core enzyme:
α (alpha): There are two of these.
β (beta): There is one of these.
β′ (beta prime): There is one of these.
ω (omega): There is one of these.

holoenzyme:
same as core and
σ (sigma): This one is special and helps the enzyme find where to start.

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3
Q

α, β, β′, ω - why are all these combine and which subunit is loosely bound

A

to make active site for polymerization [process where small units, called monomers, join together to form a larger, chain-like structure known as a polymer. ]

loosely bound - σ

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4
Q

template strand is also known as -
coding strand is also known as -

A

template strand is also known as - antisense or -ve strand
coding strand is also known as - sense or +ve or nontemplate strand

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5
Q

briefly explain the differences between template strand and coding strand

A

template strand:
template for rna synthesis
rna polymerase reads it from 3’ to 5’
= builds complementary rna strand in 5’ to 3’

coding strand:
same sequence as the rna that is produced (except for one difference, rna has uracil)
not used in the actual process of making rna but contains the information needed to determine what proteins will be made

In simple terms: the template strand is like the instructions for building RNA, while the coding strand is similar to the final product that shows what the RNA will look like.

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6
Q

what is the role of the σ subunit

A

recognize the promoter (signal start of rna and provide direction)
released after transcription begins

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7
Q

in which dna strand can the promoter be found

A

template strand

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8
Q

true or false:
In even the simplest organisms, there is a lot of DNA that doesn’t get turned into RNA. This means that not all parts of the DNA are used to make proteins.

A

true

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9
Q

what are some of the guidance that rna polymerase needs

A
  1. needs to known which strand of the dna is the template strand
  2. needs to know which parts of the dna to transcribe
  3. needs to find the exact spor where the transcription shld start
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10
Q

DNA sequences that provide direction for RNA polymerase

A

promoters

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11
Q

what are the sequence of representative promoters from E. coli

A

-35region:
35 bases awayy from the TSS, upstream

pribnow box:
10 bases awayy from TSS

transcription start site:
marked as +1
where the actual gene reading begins

‘upstream’ - 35 region and pribnow box (they are part of the promoters)
‘reference point’ - tss

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12
Q

explain promoters that are upstream

A

5’ to the side of the coding strand and ‘3 to the template strand

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13
Q

it is the % of occurrence of indicated bases

A

consensus bases

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14
Q

the base sequence of promoter regions has been determined to contain many bases in common

A

consensus bases
* promoter regions are rich in A-T than C-G

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15
Q

Part of transcription where RNA polymerase binds to DNA, the strands are separated, and the first nucleotide binds to its complement

A

chain initiation

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16
Q

chain initiation
closed complex:
open complex:

A

closed complex: (bind lang)
rna polymerase binds to the promoter and forms closed complex
complex that initially forms between rna polymerase and dna before transcription begins
rna polymerase able to distinguish coding and template strand

open complex:
form rna polymerase and dna that occurs during transcription
once the open complex is formed, rna polymerase can add the first nucleotide to the growing RNA strand

*a purine ribonucleoside triphosphate is the first base in RNA and binds to its complementary dna base at position +1(TSS)

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17
Q

chain initiation vs chain elongation in simple terms

A

Chain Initiation
1. Binding: The enzyme RNA polymerase attaches to a specific region of DNA called the promoter.
2. Opening: The DNA strands unwind and separate to form an open complex.
3.Starting RNA Production:
RNA polymerase adds the first nucleotide (the building block of RNA) to the growing RNA strand by pairing it with its complementary DNA base.

Chain Elongation
1. Adding Nucleotides: RNA polymerase continues to add nucleotides one by one to the growing RNA strand. Each new nucleotide matches with the DNA template strand.
2. Moving Along: As RNA polymerase moves along the DNA, the RNA strand gets longer, and the DNA strands re-anneal (come back together) behind it.
3. Completing the RNA Strand: This process continues until RNA polymerase reaches a termination signal, marking the end of the gene.

In summary, chain initiation is about starting the RNA copy, while chain elongation is about building that RNA strand by adding more nucleotides.

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18
Q

briefly explain chain elongation process
(refer to slides)

A

after dna has separated,
transcription bubble forms (at 17 base pairs wide) - this is whr rna is made

rna polymerase moves along the dna strand and adds nucleotides to the growing rna strand
- connects the ribonucleotides by forming phosphodiester bonds

after 10 ribonucleotides have been added, σ-subunit separates from the enzyme = recycled and used again

as rna polymeras move alon the dna, it twist and coils
negative supercoiling: (gg to 3’) in front of the transcription bubble
positive supercoiling: (gg to 5’)
twisting in the same direction

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19
Q

relax the supercoils in front of and behind the transcription bubble

A

Topoisomerases

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20
Q

briefly explain the 2 types of termination

A
  1. Intrinsic Termination
    does not require any extra proteins (like rho) and is controlled by termination sites
  2. Rho-Dependent Termination
    require extra proteins, rho (ρ)
    - ρ binds to the rna and chases the polymerase
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21
Q

Certain areas in the DNA which help end transcription.

A

termination sites
-by generating hairpin loops and a zone of weak binding between dna and rna (between A & U bases)

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22
Q

true or false:
rho-dependent termination sequences cause a hairpin loop to form

A

true

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23
Q

Ways to Control Transcription in Prokaryotes

A

Alternative σ factors
Enhancers
Operons
Transcription attenuation

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24
Q

Viruses and bacteria exert control over which genes are expressed by producing different σ-subunits that direct the RNA polymerase to different genes
(example)

A

Alternative σ Factors

example:
σ32 > σ70 @ higher T
[E. coli (a type of bacteria) is exposed to high temperatures (heat shock), it switches from using a regular σ factor (σ70) to a different one (σ32). This new σ factor helps activate genes that help the bacteria cope with the stress of heat, ensuring they survive the harsh conditions.]

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25
Q

DNA sequences that bind to a transcription factor and increase the rate of transcription

A

enhancers

  • they are DNA sequences that increase transcription rates by binding transcription factors, which then help RNA polymerase do its job more effectively
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26
Q

what are transcription factors

A

Proteins or other complexes that bind to DNA sequences and alter the basal level of transcription (makes them )

RNA polymerase does not bind directly to enhancers, these enhancers interact with transcription factors. When a transcription factor binds to an enhancer, it helps recruit RNA polymerase to the promoter (the starting point for transcription), boosting the transcription of nearby genes.

27
Q

what are the three upstream sites of E. coli genes

A

they are called Fis sites
- binding sites for the protein called Fis

28
Q

enhancers vs promoters
(refer to slides)

A

enhancers:
fis sites
bind to transcription factors
increase rate of transcription

promoters:
pribnow box (core promoter)
-35 (core promoter)
UP element (-60 to -40)
bind to RNA polymerase
does not enhance TSS
determine TSS

29
Q

Group of operator, promoter, and structural genes

A

operon

  • physically adjacent to the
    structural gene in the dna (located next to each other on the DNA and are usually transcribed together)
  • not transcribes all the time
30
Q

Directs the synthesis of a protein under the control of some regulatory gene

A

structural gene

31
Q

Triggering of the production of an enzyme by the presence of a specific inducer

A

induction

32
Q

is a set of genes in E. coli that helps the bacteria digest lactose, a sugar found in milk

A

lac operon

33
Q

Molecule that turns on the transcription of a gene

A

inducer

For example, if a bacterium needs to break down a sugar, the presence of that sugar can act as an inducer to turn on the operon responsible for making the necessary enzymes.

34
Q

lac operon consists of

A

lacZ: Codes for β-galactosidase, an enzyme that breaks down lactose.
lacY: Codes for lactose permease, a protein that helps transport lactose into the cell.
lacA: Codes for transacetylase, an enzyme involved in lactose metabolism.

35
Q

this gene produces a repressor protein that can block transcription of the structural genes. The repressor can be located some distance away from the operon.

A

lacI

36
Q

When the lacI gene is expressed, it produces a repressor protein that can form a complex (tetramer) and binds to the operator (O) region of the lac operon.

A

repressor protein

37
Q

This is a specific DNA sequence where the repressor attaches, blocking RNA polymerase from binding to the promoter (the starting point for transcription).

A

operator

38
Q

The operator and promoter together help control whether the lac operon genes are turned on or off.

A

control sites

39
Q

Repression of the synthesis of lac proteins by glucose

A

catabolite repression

40
Q

binds to cAMP and then attaches to the promoter, enhancing the binding of RNA polymerase to the promoter. This promotes the transcription of the lac operon when lactose is available.

A

Catabolite Activator Protein (CAP)

41
Q

Type of transcription control in which the transcription is controlled after it has begun via pausing and early release of incomplete RNA sequences

A

Transcription Attenuation

42
Q

Transcription Attenuation possible hairpin loops

A

Pause Structures:
1·2 Pause Structure: When the RNA polymerase encounters this structure, it causes a pause in transcription. If this happens, transcription can terminate prematurely, stopping the production of the RNA.

Terminators:
3·4 Terminator: This structure can cause the RNA polymerase to release the RNA transcript early, preventing the full RNA molecule from being made.

Antiterminators:
2·3 Antiterminator: When this structure forms, it allows transcription to continue instead of stopping. This means the complete RNA sequence is produced.

43
Q

true or false:
transcription in prokaryotes, single rna polymerase does all the work

A

true
-can switch sigma factor to interact w different promoters

44
Q

true or false:
transcription in eukaryotes,
3 primary RNA polymerases with
different activities and recognize a same set of promoters

A

false - recognize a different set
of promoters

45
Q

what are the 3 RNA polymerase (location)
- function

A

RNA polymerase I (nucleolus):
- synthesis precursors of most but not all
- ribosomal RNAs

RNA polymerase II (nucleoplasm):
- synthesis mRNA precursors

RNA polymerase III (nucleoplasm):
- synthesis tRNA
- precursors of 5S ribosomal RNA and a variety of other small RNA molecules involved in mRNA processing and protein transport

RNA Polymerase I synthesizes ribosomal RNA (rRNA)
RNA Polymerase II produces messenger RNA (mRNA) for protein coding
RNA Polymerase III generates transfer RNA (tRNA) and other small RNAs.

46
Q

what are the pol II promoters

A

eukaryotic promoters:
they bind to transcription factors

1) upstream elements
- GC box (-40)
- CAAT box (extending -100)
2) TATAA box (25 base upstream)
3) initiator element - loosely conserved
4) downstream regulator - rare

47
Q

genes that do not have TATA boxes

A

TATA-less promoters

48
Q

why is TATA box necessary for transcription

A

as it orients the RNA polymerase correctly
it eliminated the TATA box in these genes causes transcription at random starting points

49
Q

briefly explain the initiation of transcription

A

forms PIC, preinitiation complex, whr control of transcription occurs

PIC: RNA pol + GTFs, general transcription factors

GTFs: 6 transcription factors that bind to DNA

50
Q

order of events of transcription

A

index card

51
Q

what is the eukaryotic consensus sequence for termination

A

AAUAAA

52
Q

Giant protein complex that bridges the promoter and general transcription factors with remote silencers and enhancers

A

Mediator

53
Q

a structure where the eukaryotic DNA is supercoiled

A

chromatin
- tightly packed state, RNA polymerase II has no access to the promoter regions and transcription cannot occur

54
Q

chromatin structure depends on what for the relied of repression

A

chromatin remodeling complexes:
uses ATP to change the structure of nucleosomes
= dna more open and accessible

histone-modifying enzymes:
make chemical changes to histones of dna
= rna polymerase access for transcription

to activate transcription, cells need to open up tightly packed dna using chromatin remodeling and histones modifications

55
Q

acetylation vs deacetylation in the modifications of histones

A

acetylation:
HATs histone acetyltransferases adds acetyl groups to the histones
removes + charge
reduces the attraction to -ve charged dna
= less tightly bound n more open, allow transcription

deacetylation:
reversed by HDAC histone deacetylase
restores the charges on histones
= tightly packed, stops transcription

56
Q

true or false:
98% of transcriptional output of human genomes comprises noncoding RNAs

A

true

57
Q

these are small double-stranded RNA (dsRNA) that are involved in control of gene expression via several related mechanisms

A

noncoding RNAs, NcRNAs

58
Q

what are the 2 types of noncoding RNAs

A

miRNA, micro:
endogenous (naturally produced inside the cell)
22 nucleotides long

  • affects gene expression
  • growth and development

siRNA, small:
exogenous (come from outside the cell)
21-25 nucleotides long

  • control gene expression
  • selective suppression of genes

help both regulate how genes are turned on and off

59
Q

what are the different types of binding domains

A

dna-binding domains: part of a transcription factor that binds to the dna

  • helix-turn-helix HTH
    alpha helix tht fits into the major grooves
    20 aa
  • zinc finger
    transcription factor of rna polymerase III, TFIIIA
    9 repeating structures of 30 aa
    2 cys & 2 hid spaced after 12 aa
  • basic region leucine zipper bZIP
    residues of lys, arg and his
60
Q

what are the modification in tRNA and rRNA

A

tRNA:
methylation
subs of sulfur for oxygen

rRNA:
methylation in prokaryotes and eukaryotes

61
Q

what are the modifications in mRNA

A
  1. capping 5’ end
    guanylate residue - methylated at N-7 position
    to form a protective cap from exonuclease degradation
  2. polyadenylating 3’ end
    100 - 200 (A) nucleotides long = poly-A tail
    protects the mRNA being degraded by nucleases and phosphates
    help mRNA exits
  3. splicing of coding sequences
    exons - expressed
    introns - not expressed
    hence removal of introns and join the exons tgt = fully functional

splicing - guided by small proteins and snRPS, small nuclear ribonuclear proteins

62
Q

different forms of a protein produced by alternative splicing reactions
what are the 2 possible differences

A

isoforms

  1. 2 forms of the mRNA in the same cell
  2. 1 form in one tissue but a diff from in another tissue
63
Q

it catalyze their own self-splicing

A

ribozymes

64
Q

what are the 2 types of ribozymes

A

group I ribozymes:
require external nucleotide, Guanosine

group II ribozymes:
do not require external nucleotide
display a lariat mechanism

2024 SEM 1 BIOCHEMISTRY (LEC) (19 decks)

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