Lecture 6 and 7 Transcription and RNA

Genetic information directs synthesis of

protein

the flow of genetic information in cells from DNA to RNA is so fundamental that it has been termed the

central dogma of molecular biology

the central dogma of molecular biology was first articulated in 1958 by

Francis Crick

what is transcription

copy nucleotide sequence of DNA into RNA

what is translation

information in RNA to make protein

central dogma slide

what does the central dogma describe

the flow of genetic info

genes can be expressed with different

efficiencies

efficiencies of gene expression slide

___% of genome is coding for protein but not expression all at the same time

1-2%

we are roughly expressing _ genes at any time

10-15,000

diff __ types express diff genes

cell

the chemical structure of RNA _ from DNA

differs

what is the sugar difference between RNA and DNA

RNA uses ribose but DNA uses deoxyribose

base differences between uracil and thymine

is chemical bonds in RNA the same as DNA

yes

Chemical structure of RNA differs from DNA

uracil forms a base pair with

adenine

do U-A base pairs closely resemble T-A base pairs

yes

how many bonds does uracil form with adenine

2 bonds

uracil forms a base pair with adenine

RNA molecules can form intramolecular

base pairs and fold into specific structures

RNA is ___ but it is often contains stretches of nucleotides that can basepair with complementary sequences found elsewhere on same molecule

single-stranded

RNA folding on itself slide

some RNAs can have halflifes as little as

20 minutes

RNA often times has some _ structures

secondary

Non-template strand of DNA is sometimes called

coding strand because sequence is equivalent to RNA product

The RNA chain produced by transcription is called _ and has nucleotide sequence exactly complementary to template strand

transcript

transcription produces an RNA complement to one strand of DNA

DNA is transcribed by the enzyme

RNA polymerase

what does RNA polymerase do

it catalyzes formation of phosphodiester bonds linking nucleotides together, forming sugar-phosphate backbone of RNA chain

RNA pol moves along the _ doing what

DNA, unwinding the DNA helix in front of it

Using an exposed DNA as a template polymerase does what

adds nucleotides one by one to RNA chain at polymerization site

as it moves along the DNA template, polymerase displaces ___

formed RNA, allowing the two strands of DNA behind the polymerase to rewind

a short region of hybrid DNA/RNA helix forms transiently causing a ‘___

‘Window‘ of DNA/RNA helix to move along DNA with polymerase

RNA transcription slide

visualizing transcription slide

when talking about translating RNA to proteins what RNA are we talking about

mRNAs

types of RNA produced in cells slide

__ in sequence of a gene determine where bacterial RNA polymerase starts and stops transcription

signals

bacterial RNA pol contains a subunit called _ that recognizes the —- on the DNA

sigma factor, promoter region

once transcription begins ___ is released and polymerase continues synthesizing RNA

sigma facor

chain elongation continues until

polymerase encounters a termination signal (terminator or stop site) in the DNA

when RNA pol reaches a stop what happens

the enzyme halts and releases both DNA template and newly made mRNA

after the enzyme halts and releases both DNA template and newly made mRNA polymerase reassociates with a

free sigma factor and searchers for another promoter to begin process again

RNA pol associating with DNA and dissociating slide

bacterial _ and - have specific sequences that are recognized by RNA pol

promoters and terminators

first nucleotide is designated as

+1

terminator is a _ for trasncription

stop signal

the asymmetry of the promoter with conserved -35 sequence located upstream of -10 sequence _

orients RNA pol and determines direction of transcription

specific sequences slide

some genes are transcribed using _

one DNA strand as a template, others are transcribed using other DNA strand

the direction of transcription is determined by

orientation of promoter at beginning of each gene

direction of transcription slide

how any eukaryotic RNA pols are there

3

what are the names of the 3 RNA pols

I, II, III

RNA pol 1 is for

most rRNA genes

RNA pol II is for

all protein coding genes, miRNA, plus genes for other noncoding RNAs

RNA pol III is for

tRNA, 5S rRNA gene, genes for many other small RNAs

prokaryotic RNA pol (along with its sigma subunit) can initiate _

transcription on its own whereas eukaryotic RNA pol requires the assistance of a large set of accessory proteins

eukaryotic RNA pol requires the assistance of a large set of accessory proteins, principle among these are

general transcription factors, which must assemble at each promoter along with polymerase before transcription can begin

three eukaryotic RNA pols slide

RNA pol is the star for all protein coding genes

RNA pol II

Eukaryotic RNA pol 2 requires _ for tarsncription initiation

general transcription factors

many promoters for RNA pol II contain DNA sequence called _

TATA box

TATA box is _

recognized and bound by general transcription factor TFIID through one of its subunits called TATA binding protein

After TFIID, TATA box-binding of TFIID then enables the adjacent binding of

TFIIB, a general transcription factor

The rest of the general transcription factors including - and - assemble at

TFIIH and RNA pol, promoter to form a complete transcription initiation complex

what dos TFIIH do

pries apart double helix of DNA at transcription start point, using energy of ATP hydrolysis, allowing template strand to be exposed

TFIIH does what

phosphorylates long polypeptide “tail“ of RNA pol II

TFIIH phosphorylates long polypeptide “tail“ of RNA pol II which _

releases it from general transcription factors so it can begin the elongation phase of transcription

eukaryote RNA pol transcription factor slide

transcription initiation flow slide

TATA binding protein (TBP) does what

binds to TATA box sequences and distorts the DNA

TBP is the subunit of the general transcription factor __

TF2D

TBP is the subunit of the general transcription factor TFIID that is responsible for

recognizing and binding to TATA box sequence

The unique DNA bending caused by TBP may help

attarct other general tarnscription factors

TBP is a

single polynucleotide chain that is folded into two very similar domains

what part of TBP sits atop the DNA helix

its eight beta sheets sit atop the DNA helix like a saddle on a horse

TBP slide

what do we need to add to mRNA to get it out of the nucleus

5’ cap and 3’ poly-A tail

Phosphorylation of RNA polymerase II allows

RNA-processing proteins to assemble on its tail

when is phosphorylation of RNA pol tail happening

as elongation is occurring

phosphorylation helps _

recruit important enzymes for RNA processing

eukaryotic RNAs are — and —- simultaneously in the nucleus

transcribed and processed

what does phosphorylation mean

covalently attaching phosphate group in order to signal to other enzymes that something is happening

— and — are modifications made to RNA during processing

capping at the 5’ ends with a guanine polyadenylation at the 3’ ends with poly-A tail and splicing are modifications made to RNA during processing

need wait until _ in order for poly-A-tail to be added to 3’ end

transcription is complete

phosphorylation of RNA pol II slide

eukaryotic mRNA molecules ar emodified by

capping and polyadenylation

what is the 5’ cap

7-methyl gauanine

what is the poly-A-tail

series of repeated adenine nucletides to the cut end

5’ cap and poly-A tail slide

how is the 7-methyl guanine attached to the RNA

through a 5’-5’ linkage

5’ cap slide

are eukaryotic and bacterial genes organized the same

no

the bacterial gene consists of

a single stretch of uninterrupted nucleotide sequence that encodes amino acid sequence of a protein

prokaryote genes are _ and -

small and efficient

which has a greater percentage of coding DNA in their genes prokaryotes and eukaryotes

prokaryotes

prokaryotic gene is called an

operon