genetics chapter 10.1

trascription

the process by which a DNA template is used to synthesize messenger RNA

transcript

transcribed RNA

RNA purines

Adenine and Guanine

RNA pyrimidines

cytosine and uracil

characteristics of RNA

- Ribose sugar
- 2'- OH group present
- nucleotides joined via phosphodiester bonds
- single stranded
- many types of secondary structure
- not stable

what shape is RNA in in its primary form?

a linear single strand

what shape is RNA in in its secondary form?

many shapes, it is twisted and folded due to the pairing of its bases with complementary parts on the structure

which is more reactive, RNA or DNA, and why?

RNA because it has an OH group instead of just a H on the 2' carbon and the un-bonded oxygen makes it more reactive

what causes an RNA molecule to fold and pair with itself?

hydrogen bonding between complementary bases on the same strand

Messenger RNA (mRNA)

carries the genetic code necessary for synthesizing proteins

transfer RNA (tRNA)

brings the correct amino acid to the mRNA so that the mRNA can synthesize proteins; helps incorporate amino acids into the polypeptide chain

Ribosomal RNA (rRNA)

RNA that makes up the major part of ribosomes

small nuclear RNA (snRNA)

RNA processing components of spliceosome; processing of pre-mRNA

micro-RNA (miRNA)

regulates gene expression; inhibits translation of mRNA

small interfering RNA (siRNA)

triggers degradation of other RNA molecules to defend the genome

where are all eukaryotic RNAs synthesized?

nucleus

transcription overview

- DNA double strands seperate
- Template DNA is used to synthesize RNA
- no primer is needed

how is the synthesis of RNA related to DNA?

RNA is synthesized by using one strand of unwound DNA as a template to synthesize a new strand of RNA

how does RNA seperate from DNA?

as the replication fork proceeds, RNA is displaced as the DNA closes. a few nucleotides remain attached and move forward with RNA polymerase and the transcription bubble

in what direction is RNA synthesized?

5' to 3'

how are the non-template strand of DNA and the newly synthesized RNA strand relate?

they are the same except for the differences in T and U

how are nucleotides added to the 3' end of the RNA molecule?

RNA does not require a primer. Nucleotides are added to the 3' end and DNA unwinds in front of the transcription bubble so that more nucleotides can be added.

what part of the mRNA is translated?

the coding sequence with 2 untranslated regions on either side of it

initiation site

nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a "+1"

mutations to which two regions of DNA cause transcription to not occur?

-10 and -35

which regions of DNA does RNA polymerase bind to?

-10 and -35

what are the core enzymes that initiate transcription?

alpha, ß, ß',

ɑ enzyme

helps assembly and promotes interactions with regulatory proteins

ß enzyme function function

active in catalysis

ß' enzyme function

binds to DNA

ω enzyme function (omega)

assembles enzymes

holo-enzyme

all the enzymes needed for transcription initiation in prokaryotes

σ enzyme (sigma)

binds to -35 and -10 to correctly positino holoenzyme and begin seperation the DNA strands around the -10 region

do different σ factors recognize the same promoters?

no they recognize different promoters

does the σ enzyme stay on the DNA strand after transcription begins?

no

what is the consensus sequence?

This is a DNA promoter sequence whose position relative to the transcription start and whose sequence is largely conserved across species

transcription elongation formula

NTP + (NMP)n -------> PPi + (NMP)n+1

what metal has to be present in order for transcription to occur?

Mg2+

does the σ factor stay attatched to teh DNA as RNA polymerase moves past the promoter?

no

what is the conclusion of transcription in bacteria?

RNA transcription is initiated when core RNA polymerase binds to the promoter with the help of ∂

ϱ (rho) independent terminaiton mechanism conclusion

transcription terminates when inverted repeats form a haripin followed by a string of uracils

what are the requirements for ϱ independent termination to occur?

there must be a hairpin structure in the RNA followed by a string of uracils

what causes a string of uracils to occur?

a string of adenine in the DNA template sequence

how many H-bonds form between A and U?

2

how many H-bonds form between G and C?

3

what does a string of A and U pairings cause?

a weakening in the connection between the template DNA and transcribed RNA due to less H-bonds forming

what shape hairpin must occur to stop ϱ independent termination?

inverted repeat hairpin

what happens in ϱ dependent termination mechanism?

ϱ bind to an unstructure region of RNA and moves to the 3' end. when RNA polymeras encounters a terminator sequence (hairpin) it stops and ϱ catches up. ϱ then uses helicase activity to unwind the DNA-RNA hybrid and transcription ends

terminator sequence

signals the end of RNA synthesis (hairpin)

what type of activity does ϱ use to unwind DNA and RNA?

helicase

in what type of organisms does transcription and translation occur simultaneously?

prokaryotic organisms

can more than one RNA be simultanously transcribed from a gene?

yes

what shape does multiple RNA being transcribed from one gene form?

christmas tree

do transcription and translation occur simultaneously in eukaryotes?

no

what does RNA polymerase II transcribe?

pre-mRNA, some snRNAs, snoRNAs, some miRNAs

what is the core promoter?

a basic promotor that is necessary for transcription to occur but is not sufficient to complete it on its own

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex

TATA box, CAAT box, GC box, OCT box

eukaryotic promoter sites

are all eukaryotic promotor sites consensus sequences?

yes

where is the TATA box located?

-30 bp region

what part of the eukaryotic initiation complex is equivalent to the σ factor in prokaryotes?

TBP

TBP

TATA binding protein

what all does TBP attract?

other GFT's adn RNA polymerase II

TFIID

the first general transcription factor to bind the promoter, binds to the TATA box through the TATA binding protein (TBP)

enhancer

A DNA segment containing multiple control elements that can recognize certain transcription factors that stimulate the transcription of nearby genes

are the enhancer and initiation complex close together?

no

PIC

preinitiated complex (RNA polymerase II + GFTs)

GFTs

general transcription factors

CTD

C' terminal domain of RNA polymerase II carries all the elongation and processing factors it needs for transcription. It is activated by phosphorylation

phosphorylation

The transfer of a phosphate group, usually from ATP, to a molecule. Nearly all cellular work depends on ATP energizing other molecules by phosphorylation

what is the beginning of the promoter equivalent to?

the beginning of a gene

what is the terminal equivalent to?

end of a gene

which of the following is true of RNA copmared to DNA?

RNA has a hydroxyl group on the 2' carbon atom of its sugar component

When RNA is transcribed from a gene, which strand of DNA is used?

the template strand

the transcription unit includes three essential regions. What is the proper order of these regions?

promoter, RNA coding sequence, terminator

what woudl the result be if a specific sigma subunit were mutated?

RNA polymerase would fail to initiate transcription at the promoter specific to the sigma subunit

the bacterial holoenzyem binds to which part of the promotor?

-10 adn -35 consensus sequence

in rho-depended transcription termination, the rho factor binds to _______

mRNA

in eukaryotes, what initilally binds to the TATA box on the ther DNA template?

TFIID