BIOL 3200 Bacterial Transcription, Regulation, and RNA

What is RNA?

Ribonucleic acid

Is RNA double or single stranded?

Single-stranded

What are hairpins?

RNA-RNA double strand

What is different about the nucleotide bases in RNA and DNA?

Uracil replaces thymine

Does RNA contain ribose sugar?

Yes

What is different about RNA and DNA in regards to its sugars?

Every single sugar is missing an oxygen at the carbon #2

What is mRNA?

Messenger RNA that encodes proteins

What is rRNA?

Ribosomal RNA that is an integral part of ribosomes

What is tRNA?

Transfer RNA that shuttles amino acids

What is sRNA?

Small RNA that regulates transcription or translation

What is tmRNA?

A mix between tRNA and mRNA that frees ribosomes stuck on damaged mRNA

What is catalytic RNA?

Carries out enzymatic reactions

Coding strand can be what?

A template strand

What is the template strand?

The strand directly involved in transcription

What way does the template strand go?

3' to 5'

What way does RNA grow?

5' to 3'

What direction does transcription go? (not using 3' or 5' ends)

From our left to our right

What is RNA polymerase?

A complex enzyme that carries out transcription by making RNA copies (transcripts) of a DNA template strand

What is the shape of RNA polymerase?

Snail-like enzyme that contains 5 subunits

Is RNA polymerase bigger or smaller than DNA polymerase?

Bigger

What is transcription?

The synthesis of a strand of RNA from a DNA template

When does transcription begin?

When RNA polymerase binds to the promoter on DNA

What is a promoter?

A sequence of DNA upstream of transcription start site (+)

What is a sigma factor?

A protein required for the initiation phase of RNA synthesis

What does a sigma factor contain?

- Two alpha subunits
- One Beta subunit
- One Beta prime subunit

What is sigma-70?

A housekeeping sigma factor

What is the function of sigma-70?

It helps core enzymes detect the promoter which signals the beginning of the gene

What is a housekeeping sigma factor?

A protein in bacteria that is responsible for initiating transcription that transcribes all the time

True or False
A single bacterial species can make several different sigma factors.

True

What does sigma-70 do once starting RNA transcription?

-10 and -35 positions

When does transcription start?

At +1 position on a strand

What do all sigma factors compete for?

The same core RNA polymerase

What are the three phases of transcription from DNA to RNA?

- Initiation
- Elongation
- Termination

What is initiation?

RNA polymerase binds to the promoter

What is elongation?

The RNA chain is extended

What is termination?

RNA polymerase detaches from DNA, after transcript is made

Describe initiation

1) RNA polymerase, by help of sigma factor, binds to the promoter region. Results in the unwinding of one helical turn
2) RNA polymerase then starts transcription
3) Scans for -35 to -10 of the promoter region

Describe elongation

1) DNA unwinds ahead, forming a 17-bp transcription bubble
2) DNA unwinding results in positive supercoils ahead which are removed by DNA topoisomerases
3) RNA polymerase move along the template, synthesizing RNA at ~45 bases per second

Describe termination

All bacterial genes use one of two known transcription termination signals: rho-dependent or rho-independent

What is rho-dependent?

Relies on protein called Rho. The contact between Rho and RNA polymerase cause termination

What is Rho-independent?

Relies on the inverted repeat sequence on DNA template. It forms a stem-loop structure

What is a repressible operon?

Transcription is controlled by the binding of repressors to operator regions. By default, on

What is tryptophan (trp)?

When it binds to repressible operon, it blocks transcription

What is inducible operon?

Transcription is controlled by the presence of the substrate. By default, off

What binds to the operator to stop transcription?

The lac repressor

How does lactose begin transcription?

The lac repressor is released from the operator

Why do scientists work with prokaryotic systems?

It is less complex

Eukaryotic transcription regulation is ...

Too complicated

What two fundamental criteria must antibiotics meet?

1) They must kill or retard growth of a pathogen
2) They must not harm the host

What is rifamycin B?

Amycolatopsis mediterrane that selectively binds to the bacterial RNA polymerase

What does rifamycin B do?

It inhibits transcription in humans

What is actinomycin D?

Actinomycete that non-selectively binds to DNA

What does actinomycin D do?

It inhibits transcription in humans