DNA TRANSCRIPTION

What are proteins considered in organisms

Important molecules because they carry out many different jobs

What is one of the jobs of proteins

Production of other molecules

Where is the information for making proteins carried

In each cell's DNA

What does the sequence of bases in a gene encode

The sequence of amino acids that should be joined to make a protein

What happens when amino acids are joined together in sequence

They fold into a specific shape

Why is the folding of amino acids into a specific shape important

It allows the protein to carry out its specific job

What is protein synthesis composed of

A two-step process

What are the two steps of protein synthesis

Transcription and Translation

What happens during transcription

A temporary copy of information in RNA is made using DNA as a template

What happens during translation

The base sequence of mRNA is decoded to make a sequence of amino acids

Why are transcription and translation only carried out when needed

To save energy, they occur only when a particular protein is needed

What is transcription

The synthesis of RNA from a DNA template

What does transcription create

An equivalent RNA copy of a sequence of DNA

What is the first step leading to gene expression

Transcription

What reads the DNA sequence during transcription

RNA polymerase

What does RNA polymerase produce

A complementary, antiparallel RNA strand

What base is included in RNA instead of thymine (T)

Uracil (U)

What enzyme performs transcription

RNA polymerase

What does RNA polymerase need to help initiate and produce the transcript

Assisting proteins

What are the assisting proteins for transcription called

Transcription factors

How do transcription factors assist RNA polymerase

They either associate directly with RNA polymerase or aid in building the transcription complex apparatus

What is the general term for proteins associated with RNA polymerase during transcription

Transcription factors

What is the stretch of DNA transcribed into an RNA molecule called

Transcription unit

What does a transcription unit encode

At least one gene

If the transcribed gene encodes a protein, what is the result of transcription

Messenger RNA (mRNA)

What is mRNA used for

To create a protein via the process of translation

What else may the transcribed gene encode besides mRNA

Ribosomal RNA (rRNA) or transfer RNA (tRNA)

What does a DNA transcription unit encoding for a protein contain

The coding sequence and regulatory sequences that direct and regulate the synthesis of that protein

What is the regulatory sequence before the coding sequence called

Five prime untranslated region (5'UTR)

What is the sequence following the coding sequence called

Three prime untranslated region (3'UTR)

From which direction is DNA read during transcription

3'-5'

From which direction is complementary RNA created during transcription

5'-3'

Which DNA strand is used for transcription

Template strand

What is the other DNA strand called that has the same sequence as the RNA transcript

Coding strand

What is the difference between the coding strand and the RNA transcript

RNA contains uracil (U) instead of thymine (T)

What does the use of only the 3'-5' strand during transcription eliminate

The need for Okazaki fragments

What are the five stages of transcription

Pre-initiation, Initiation, Promoter clearance, Elongation, Termination

What does RNA polymerase require for the initiation of transcription

the presence of a core promoter sequence in the DNA

Where are promoters found upstream from the start site of transcription

-30, -75, and -90 base pairs

What are core promoters

sequences within the promoter essential for transcription initiation

When can RNA polymerase bind to core promoters

in the presence of various specific transcription factors

What is the most common type of core promoter

TATA box (short DNA sequence)

Where is the TATA box found

-30 base pairs from the start site of transcription

What is the TATA box the binding site for

TATA Binding Protein (TBP)

What is TATA Binding Protein (TBP) a subunit of

Transcription Factor IID (TFIID)

What happens after TFIID binds to the TATA Box via TBP

five more transcription factors and RNA polymerase combine around the TATA box in a series of stages to form a pre-initiation complex

Which transcription factor is involved in separating opposing strands of double-stranded DNA

DNA Helicase

Why does DNA Helicase separate the DNA strands

to provide access to a single-stranded DNA template

What kind of transcription rate is driven by the pre-initiation complex alone

a low, or basal, rate

Which proteins modulate the transcription rate

activators and repressors, along with any associated coactivators or corepressors

What happens during initiation in transcription

Binding of the RNA polymerase (RNAP) and association of the initiation complex to promoter and enhancer regions on double-stranded DNA

What does RNA polymerase not directly recognize

The core promoter sequences

What mediates the binding of RNA polymerase and the initiation of transcription

Transcription factors

When does RNA polymerase bind to the promoter

Only after certain transcription factors are attached to the promoter

What is formed by the completed assembly in initiation

The transcription initiation complex

What must RNA polymerase do after the first bond is synthesized

Clear the promoter

What tendency occurs during promoter clearance

To release the RNA transcript and produce truncated/premature transcripts (abortive initiation)

Until when does abortive initiation continue

Until the sigma factor rearranges, resulting in the transcription elongation complex

What footprint does the transcription elongation complex give

35 base pairs moving footprint

Before how many nucleotides of mRNA are synthesized is the sigma factor released

Before 80 nucleotides

At approximately how many nucleotides does the transcript no longer slip

23 nucleotides

What type of process is elongation during transcription

An energy-dependent process consuming adenosine triphosphate (ATP)

With what does the process coincide

Phosphorylation by TFIIH (transcription factor) of serine 5 on the carboxy terminal domain of RNAP

What happens during elongation in transcription

Covalent addition of ribonucleic bases to the 3' end of a growing chain pairing with a single stranded DNA template

Which strand is used as a template during elongation

The template strand (or noncoding strand)

In what direction is the RNA molecule produced

From 5' to 3'

What is the RNA molecule in elongation

An exact copy of the coding strand

What base replaces thymine in RNA

Uracil

What type of sugar do RNA nucleotides have

Ribose (5-carbon) sugar

What type of sugar do DNA nucleotides have

Deoxyribose (one less oxygen atom in its sugar-phosphate backbone)

How does RNA differ from DNA in structure

RNA is single-stranded while DNA is double-stranded

Unlike DNA replication, what can mRNA transcription involve

Multiple RNA polymerases on a single DNA template and multiple rounds of transcription

What is the result of multiple rounds of transcription

Many mRNA molecules can be rapidly produced from a single copy of a gene

What mechanism is involved in elongation to ensure accuracy

A proofreading mechanism that can replace incorrectly incorporated bases

What does the proofreading mechanism involve

A short pause allowing appropriate RNA editing factors to bind

What may the proofreading mechanism be intrinsic to

The RNA polymerase or due to chromatin structure

What happens during transcription termination

Recognition of the transcription termination sequence and the release of RNA polymerase and the newly formed RNA polymer

What happens to the double-stranded DNA after transcription termination

It can close back after single-stranded RNA is produced

What question arises about transcription termination

How does our cell know when to stop

What do bacteria (prokaryotes) use for transcription termination

Two different strategies

What happens in Rho-independent transcription termination

RNA transcription stops when the newly synthesized RNA molecule forms a G-C rich hairpin loop followed by a run of U's, which makes it detach from the DNA template

What causes RNA transcription to stop in Rho-independent termination

The newly synthesized RNA molecule forms a G-C rich hairpin loop

What follows the hairpin loop in Rho-independent termination

A run of U's

What effect does the run of U's have in Rho-independent termination

It makes the RNA detach from the DNA template

What is the structural feature in RNA that signals Rho-independent termination

G-C rich hairpin loop

What happens in Rho-dependent transcription termination

A protein factor called Rho destabilizes the interaction between the template and the mRNA, releasing the newly synthesized mRNA from the elongation complex

What protein factor is required in Rho-dependent transcription termination

Rho

What does Rho do during transcription termination

It destabilizes the interaction between the template and the mRNA

What is the result of Rho destabilizing the template-mRNA interaction

Release of the newly synthesized mRNA from the elongation complex

In which type of termination is Rho involved

Rho-dependent transcription termination

How is transcription termination in eukaryotes described

Less understood but involves cleavage of the new transcript followed by template-independent addition of As at its new 3' end, in a process called polyadenylation

What tool can be used to observe the ribosomal transcription process

Electron micrograph

What process can be seen in an electron micrograph

Ribosomal transcription process

What appears as branches from the main DNA strand in transcription

Forming mRNA strands

What does a Nuclear Run-on assay measure

The relative abundance of newly formed transcripts

What is detected by RNase protection assay

Active transcription sites

What is detected by ChIP-Chip of RNAP

Active transcription sites

What does RT-PCR measure

The absolute abundance of total or nuclear RNA levels

What process in eukaryotes is less understood but linked to transcript cleavage

Transcription termination

What follows cleavage in eukaryotic transcription termination

Template-independent addition of As at the new 3' end (polyadenylation)