9 - From DNA to RNA Part I

Transcription

DNA does not direct protein synthesis directly, instead it copies into RNA

Translation

RNA copies of DNA segments direct synthesis of protein

What is a difference in the processing of RNA transcripts in euk cells

Splicing; which can change the meaning of an RNA molecule

What is RNA

A linear polymer made of four different nucleotides

Three main differences in RNA and DNA

1. Sugar group is ribose

2. Uracil replaces thymines

3. Sometimes there are unique base pairings

How does uracil replace thymines

Loses methyl group

What are some unique base pairings in RNA

G with U

Is uracil a pyrimidine or purine

Primitive

Is RNA ss or ds

Ss

5 main similarities between transcription compared to replication

1. Unwinding of DNA helix at a specific point

2. One of the two strands serves as a template

3. Ribonucleotides base-pair with template if there is a good match, then the nucleotide is covalently linked via an enzyme reaction

4. RNA is polymerized in the 5’ to 3’ direction

5. Template-dependent polymerization

3 main differences in transcription compared to replication

1. RNA ss is removed from the DNA strand close to where transcription begins

2. RNA strand is much shorter than DNA replicants (usually only a few thousand nucleotides long)

3. RNA polymerases are the transcribers

What are RNA polymerases

A group of enzymes that form phosphodiester bonds between ribonuclotides

How fast are RNA strands synthesized

20-50 nucleotides/sec

Why is no primer required for transcription

• RNA doesn’t need to have a free 3’ hydroxyl base pair in place to begin with

• Only modest proofreading capability and a different reaction is carried out

• RNA pol cannot dissociate from strand until finished

What are most RNAs

Noncoding with unclear function

Transcription units

A transcribed segment of DNA: information in just one gene for just one RNA molecule or single protein

What do RNA poly require

General transcription factors

What are general transcription factors

Proteins that initiate transcription

What presents a problem for RNA poly

DNA packaging into nucleosomes

What do general transcription factors do

Help position RNA poly at the promoter

What is a promoter

A sequence of DNA nucleotides that signal the starting point for RNA synthesis

First step of transcription factors

Binding of TFII subunit to double strand of DNA begins at TATA box

What is the TATA box

Sequence of DNA Ts and As located ~30 nucleotides upstream from transcription start site

What is the TFIID subunit called

TBP, for TATA Binding Protein

Is TATA the only sequence that signals the starting point of transcription

Nope

Second step of transcription factors

Binding of TFIID causes distortion in DNA helix that shows there is activity going on here

More facets gather, then RNA pol II to form a complete “transcription initiation complex”

What is the most complex transcription factor and has most work to do

TFIIH

What does TFIIH do

Uses ATP to pry apart the double strands of DNA like helicase

Phosphorylates RNA poly II at its tail so it can be released from the factors (conformational change in pol) and can begin to transcribe

What sequences do transcriptional activators bind to

Specific sequences called enhancer” sequences

What do activators need to do

Communicate with the transcription complex

How do the activators and transcription complex communicate

Through a mediator

What are recruited with mediator

Chromatin and histone remodeling proteins and enzymes

How does RNA pol move

In a jerky way, pausing at some sequences

What do elongation factors do

Determine when RNA pol will dissociate from the helix

What does elongation do and why

Because of the need to unwind the helix, produces supercools

Every how often does a supercoil form in elongation

Every 10 nucleotides that open

What might elongation supercoiling aid in eukaryotes

Unwinding DNA from nucleosomes

How many RNA polymerases

3