BIOL 306 - Chapter Thirteen: Transcription

True or False: Evidence suggests that RNA was the original genetic material

True

Ribozymes

Catalytic RNA

Components of Ribonucleotides

1. Ribose sugar

2. Phosphate

3. Nitrogenous base

RNA has a ____________ structure and ____________ structure

primary; secondary

RNA Primary Structure

Linear sequence of ribonucleotides

RNA Secondary Structure

Pairing of complementary bases in single strand of RNA via hydrogen bonding

RNA secondary structure results from _____________________

an RNA molecule folding in on itself

RNA Secondary Structure Examples

Stem-loop & Hairpin

RNA Classes

Ribosomal RNA: rRNA

Messenger RNA: mRNA

Transfer RNA: tRNA

Pre-Messenger RNA: pre-mRNA

Small Nuclear RNA: snRNA

Small Nuclear Ribonucleoproteins: snRNP

Small Nucleolar RNA: snoRNA

Small Cytoplasmic RNA: scRNA

MicroRNA: miRNA

Small Interfering RNA: siRNA

Piwi-Interacting RNA: piRNA

Long Noncoding RNA: lncRNA

CRISPR RNA: crRNA

What RNAs are produced in both prokaryotes and eukaryotes?

mRNA, rRNA, tRNA

What RNAs are produced in only eukaryotes?

pre-mRNA, snRNA, snoRNA, miRNA, siRNA, piRNA

What RNA is produced in only prokaryotes?

crRNA

Some viruses copy RNA directly from ___________

RNA

All eukaryotic RNAs are synthesized in the _____________

nucleus

What RNAs are located in only the cytoplasm in eukaryotic cells?

rRNA, tRNA

What RNAs are located in only the nucleus in eukaryotic cells?

snRNA, snoRNA

What RNAs are located in both the cytoplasm and nucleus in eukaryotic cells?

mRNA, miRNA, siRNA, piRNA, lncRNA

rRNA Function

Structural and functional components of ribosome

tRNA Function

Carries genetic code (amino acids) for proteins

mRNA Function

Helps incorporate amino acids into polypeptide chain

snRNA Function

Processing of pre-mRNA

snoRNA Function

Processing and assembly of rRNA

miRNA Function

Inhibits translation of mRNA

siRNA Function

Triggers degradation of other RNA molecules

piRNA Function

Suppresses transcription of transposable elements in reproductive cells

crRNA Function

Assists destruction of foreign DNA

lncRNA Function

Eukaryotic nulceus and cytoplasm; Variety of functions

Required Components of Transcription

1. DNA Template

2. Ribonucleotides

3. Transcription Apparatus

Transcription Apparatus

Consists of proteins neceessary for catalyzing synthesis of RNA

True or False: Transcription requires a primer for initiation

False

In transcription, the transcribed strand is the __________ strand

template

Components of the Transcription Unit

1. Promoter

2. RNA-Coding Sequence

3. Terminator

RNA molecules become ___________ the further the transcription apparatus moves down the DNA and _______________

longer; transcribes more of the template

The RNA molecule is ____________ & ____________ to the template DNA strand

complementary; antiparallel

The DNA template strand is ______________, while the RNA transcribed strand is ______________

3' to 5'; 5' to 3'

Components of Ribonucleoside Triphosphates (rNTP)

1. Ribose sugar

2. Nucleoside base

3. Three phosphate groups

rNTPs are added to the ______ end of the RNA molecule

3'

Subunits of Bacterial RNA Polymerase Core Enzyme

1. Two copies of ɑ

2. One copy of β

3. One copy of β'

4. Stabilizing enzyme: ⍵

When transcription starts, the _________________ binds to the promoter

sigma (σ) factor

In transcription, nucleotides are always added to the ________ end of the RNA molecule

3'

The core enzyme catalyzes the __________________________

elongation of the RNA molecule by the addition of RNA nucleotides

The holoenzyme is composed of the _________________ & the _________________

sigma factor; core enzyme

True or False: The holoenzyme is capable of binding to a promoter and initiating transcription

True

Consensus Sequence

Sequence that compromises most commonly encountered nucleotides found at specific location in DNA or RNA

Common Bacterial Promoter Consensus Sequences

-10 Consensus & -35 Consensus

-10 Consensus/Pribnow Box

Consensus sequence found 10 bp upstream of transcription start site

-35 Consensus

Consensus sequence found 35 bp upstream of transcription start site

-10 Consensus vs. -35 Consensus

-10 Consensus: TATAAT

-35 Consensus: TTGACA

Location of the consensus sequence determines position of _____________

transcription start site

Transcription is initiated by the binding of _____________ & _____________

RNA Polymerase; sigma factor

The holoenzyme binds to the ____________________

-35 and -10 consensus sequences in the promoter

The _____________ unwinds the double-stranded DNA

holoenzyme

What is cleaved from each subsequent rNTP?

Two phosphate groups

As the RNA polymerase moves beyond the promoter, the ________________ is released

sigma factor

RNA elongation is carried out by _____________________

RNA polymerase

Rho-Dependent Termination vs. Rho-Independent Termination

Rho-Dependent: Uses Rho factor

Rho-Independent: Inverted repeats form hairpin structure, followed by string of uracils

In Rho-dependent termination, Rho binds to the _____________

rut site

True or False: Rho-independent termination is a single-step process

False: It is multistep

Eukaryotic Transcription: Key Differences

1. Chromatin modification occurs before transcription

2. Three RNA polymerases

3. Promoter recognition carried out by accessory proteins that bind to promoter and recruit one of three RNA polymerases

4. Basal transcription apparatus

5. Core promoter is TATA box (TATAAAA), -25 to -30 bp

Basal Transcription Apparatus

Complex of transcription factors, RNA polymerase, and other proteins that assemble on promoter and are capable of initiating minimal levels of transcription

True or False: RNA Polymerase Ⅲ is involved in mRNA synthesis

False: RNA Polymerase Ⅱ

Gene promoters transcribed by RNA Polymerase Ⅱ consist of a __________ promoter and __________ promoter

core; regulatory

Promoters in Eukaryotic Transcription

1. Regulatory Promoters

2. Enhancers

3. Polymerase Ⅰ and Ⅲ Promoters

In _____________ promoters, a variety of different consensus sequences may be found

regulatory

Eukaryotic Transcription Initiation

1. Binding of TFIID transcription factor to TATA box with help of TATA binding protein (TBP)

2. Binding of preassembled holoenzyme containing general transcription factors, RNA Polymerase Ⅱ, and mediator

In eukaryotes, transcription is initiated at RNA Polymerase ____ promoters

Ⅱ

Where do the steps of eukaryotic transcription initiation take place?

1. TFIID transcription factor and TATA box bind in core promoter

2. Transcription factors and RNA Polymerase Ⅱ bind to core promoter

3. Transcriptional activator proteins bind to sequences in enhancers, then interact with basal transcriptional apparatus, then bind to sequences in regulatory promoter and interact with basal transcriptional apparatus again, now through mediator

True or False: The TATA-binding protein binds to the major groove of DNA

False: It binds to the minor groove

Eukaryotic Transcription Elongation

1. DNA double helix enters RNA polymerase Ⅱ through cleft in enzyme and unwinds

2. DNA-RNA duplex angles 3' to active site of enzyme

3. New nucleotides added to 3' end of growing RNA molecule

What RNA polymerases are present in all eukaryotes?

RNA Polymerase Ⅰ, Ⅱ, and Ⅲ

What RNA polymerases are present in plants?

RNA Polymerase Ⅳ & Ⅴ

What do the RNA polymerases transcribe?

1. RPⅠ: Large rRNAs

2. RPⅡ: Pre-mRNA, some snRNAs and miRNAs, snoRNAs

3. RPⅢ: tRNAs, small rRNAs, some snRNAs and miRNAs

4. RPⅣ: Some sniRNAs

5. RPⅤ: RNA molecules taking part in heterochromatin formation

True or False: The RNA polymerases found in eukaryotes all use different mechanisms of transcription termination

True

Eukaryotic Transcription Termination: RNA Polymerase Ⅱ

Rat1 exonuclease enzyme attaches to RNA's cleaved 5' end and moves down RNA until it reaches the polymerase enzyme

Rat1 exonuclease degrades RNA in the ______ to ______ direction

5' to 3'