Exam 2: RNA Synthesis & Processing

Transcription

Synthesis of RNA using a DNA strand as the template.

Coding RNA

RNA that carries information used to synthesize a protein; mRNA is the major example.

Noncoding RNA (ncRNA)

RNA that is not translated into protein and may have structural, catalytic, or regulatory functions.

mRNA

Which major RNA is coding and carries genetic information from DNA for protein synthesis?

rRNA and tRNA

Which major RNAs involved in translation are noncoding?

snRNA, miRNA, and snoRNA

Which additional groups of small noncoding RNAs are listed in the lecture?

RNA or protein

What can be the final functional product of gene expression?

~2%

Approximately what percentage of the genome does the professor state encodes proteins?

Transcriptome

All coding and noncoding RNA transcripts expressed by a genome.

Different cell types can have different transcriptomes

Why can two cells with the same genome have different transcriptomes?

Time of day, disease, and chemical/drug exposure

What factors does the lecture say can alter a cell's transcriptome?

DNA elements

Specific DNA sequences that tell RNA polymerase where to start, how often to start, and where to stop transcription.

Regulatory proteins

Besides DNA elements, what molecules help make transcription a highly selective process?

Single-stranded RNA

What type of nucleic-acid product is produced by RNA polymerase?

Primary transcript

The initial RNA copy produced by transcription before necessary processing.

Nascent transcript

An RNA molecule that is currently being synthesized by RNA polymerase.

Mature transcript

An RNA transcript that has undergone the processing required to become functional.

Terminal additions, base modifications, trimming, and internal-segment removal

What types of changes can convert an inactive primary RNA transcript into a functional molecule?

RNA processing

Modifications that convert an initial RNA transcript into its mature functional form.

3′→5′ phosphodiester bonds

What type of covalent bonds connect nucleoside monophosphates in an RNA chain?

Ribose with a 2′-OH

What sugar feature distinguishes RNA from DNA?

Uracil

RNA contains what base in place of thymine?

RNA is generally shorter, single-stranded, and able to fold into complex structures

How does the overall physical structure of RNA differ from DNA?

snoRNA = nucleolus; snRNA = nucleus; miRNA = cytoplasm

Where does the lecture associate these three specialized eukaryotic ncRNAs?

rRNA, tRNA, and mRNA

Which three major types of RNA have important roles in translation?

Ribosomal RNA (rRNA)

The major noncoding RNA that forms structural and catalytic components of ribosomes.

~80%

Approximately what percentage of total cellular RNA is rRNA?

Ribozyme

An RNA molecule that possesses catalytic activity.

Scaffolding for ribosome assembly and catalysis of peptide-bond formation

Explain the two major roles of rRNA in protein synthesis.

Peptide-bond formation

What catalytic reaction does rRNA perform during protein synthesis?

Svedberg unit

What does the “S” in 23S, 16S, 28S, etc. stand for?

23S, 16S, and 5S

Which three rRNA species are found in prokaryotes?

28S, 18S, 5.8S, and 5S

Which four rRNA species are found in eukaryotes?

80S ribosome = 60S + 40S

How is the eukaryotic ribosome divided into large and small subunits?

28S, 5.8S, 5S rRNA + proteins

What makes up the eukaryotic 60S ribosomal subunit?

18S rRNA + proteins

What makes up the eukaryotic 40S ribosomal subunit?

Methylation and pseudouridylation

Which modified-base processes are particularly common in rRNA?

rRNA species and ribosomal subunits (IMAGE NEEDED — SLIDE 18)

Identify the prokaryotic/eukaryotic rRNAs and the components of the 40S and 60S subunits.

Transfer RNA (tRNA)

The noncoding adaptor RNA that carries an amino acid to the site of protein synthesis.

~15%

Approximately what percentage of total cellular RNA is tRNA?

At least one tRNA for each amino acid

What general relationship exists between tRNAs and the 20 amino acids?

Posttranscriptional chemical modification

When are many of tRNA's unusual bases generated?

Cloverleaf secondary structure and L-shaped tertiary structure

What 2° and 3° structures result from extensive intrachain base pairing in tRNA?

3′ end

To what end of tRNA is its amino acid covalently attached?

Anticodon

The tRNA sequence that recognizes the corresponding genetic code on mRNA.

Adaptor function

Explain why tRNA is called an adaptor molecule.

tRNA structure (IMAGE NEEDED — SLIDE 22)

Identify the anticodon loop, 3′ amino-acid attachment end, D loop, TΨC loop, and variable loop.

Messenger RNA (mRNA)

The coding RNA that directly carries genetic information from DNA for protein synthesis.

~5%

Approximately what percentage of total cellular RNA is mRNA?

Polycistronic mRNA

A single mRNA transcript containing coding information for more than one gene.

Monocistronic mRNA

A single mRNA transcript containing coding information for one gene.

Prokaryotic mRNA is generally polycistronic; eukaryotic mRNA is monocistronic

Compare prokaryotic and eukaryotic mRNA by number of genes encoded.

5′ UTR and 3′ UTR

What nontranslated regions flank the protein-coding region of mature mRNA?

5′ cap and 3′ poly-A tail

Which two structural modifications are found on eukaryotic mRNA but not typical prokaryotic mRNA?

7-methylguanosine-triphosphate

What molecule forms the 5′ cap of eukaryotic mRNA?

Poly-A tail

A long sequence of adenylates attached to the 3′ end of most mature eukaryotic mRNAs.

Structure of mature eukaryotic mRNA (IMAGE NEEDED — SLIDE 26)

Identify the 5′ cap, 5′ UTR, coding region, 3′ UTR, and poly-A tail.

One RNA polymerase species

In prokaryotes, how many RNA polymerase species synthesize the major cellular RNAs?

Primase

What is the important exception to the statement that one prokaryotic RNA polymerase synthesizes RNA?

RNA polymerase recognizes promoter/termination sequences and makes a complementary RNA copy

Explain the overall function of prokaryotic RNA polymerase.

5′→3′

In what direction is RNA synthesized?

3′→5′

In what direction does RNA polymerase move/read along the DNA template?

Template strand

The DNA strand directly read by RNA polymerase to synthesize complementary RNA.

Antisense/minus strand

What other names are used for the DNA template strand?

Coding strand

The DNA strand whose sequence matches the RNA transcript except that DNA contains T instead of U.

Sense/plus strand

What other names are used for the DNA coding strand?

RNA is complementary to template DNA and essentially identical to coding DNA except U replaces T

Explain the relationship among the template strand, coding strand, and RNA transcript.

Only one DNA strand serves as the template for a particular gene

Although regions of either DNA strand can be transcribed, what is true for one specific gene?

Coding strand

According to the lecture, on which DNA strand is the gene promoter element located?

Coding vs template strand (IMAGE NEEDED — SLIDE 31)

Given coding DNA, template DNA, and RNA, determine which strand is which and explain their sequence relationships.

RNA polymerase core enzyme

The five-subunit prokaryotic polymerase lacking sigma factor.

2 α + 1 Ω

Which prokaryotic RNA polymerase core subunits are required for enzyme assembly?

β′ subunit

Which prokaryotic RNA polymerase subunit is required for template binding?

β subunit

Which prokaryotic RNA polymerase subunit provides 5′→3′ polymerase activity?

Sigma factor (σ)

The additional RNA polymerase subunit that enables recognition of the promoter region.

Holoenzyme

Core RNA polymerase plus sigma factor.

Core enzyme vs holoenzyme

Explain the key difference between the prokaryotic RNA polymerase core enzyme and holoenzyme.

Prokaryotic RNA polymerase holoenzyme (IMAGE NEEDED — SLIDE 33)

Identify α, β, β′, Ω, and σ and state the function of each.

Initiation → elongation → termination

What are the three major phases of transcription?

Transcription unit

The DNA segment extending from the promoter region to the termination region.

Primary transcript

The initial nascent product generated from a transcription unit.

Promoter

A DNA region where RNA polymerase and associated proteins bind to initiate transcription.

Consensus sequence

A conserved DNA sequence shared among many promoters and recognized by transcription machinery.

The promoter is not transcribed

Is the prokaryotic promoter sequence included in the RNA transcript?

Pribnow box

The prokaryotic promoter element with sequence 5′-TATAAT-3′ located about 10 bases upstream of the TSS.

−35 sequence

The prokaryotic promoter element 5′-TTGACA-3′ located about 35 bases upstream of the TSS.

Essential for starting transcription

What role does the −10 Pribnow box play?

Allows a high transcription rate

What role is associated with the prokaryotic −35 sequence?

Pribnow box vs −35 sequence

Compare the sequence, location, and emphasized function of the two conserved prokaryotic promoter elements.

Transcription start site (TSS)

The +1 position at which synthesis of the RNA transcript begins.

RNA pol holoenzyme binds promoter and locally unwinds DNA at the TSS

What is the first major event of prokaryotic transcription initiation?

Nucleoside triphosphates (NTPs)

What substrates does RNA polymerase use during transcription?

NMPs

What units from the NTP substrates are incorporated into the growing RNA chain?

Short transcripts are initially synthesized and discarded

What occurs early after promoter binding before productive elongation begins?

After the transcript exceeds ~10 nucleotides

When is sigma factor released from prokaryotic RNA polymerase?

The core enzyme clears the promoter and moves along the template

What happens after sigma factor is released?

DNA-RNA hybrid

What temporary hybrid structure exists within the transcription complex during elongation?

Promoter binding/unwinding → short transcripts → >10 nt → sigma release → promoter clearance → elongation

Explain the major sequence of events as prokaryotic transcription transitions from initiation to elongation.

No primer required

How does RNA polymerase differ from DNA polymerase regarding initiation of synthesis?

No conventional proofreading activity

How does RNA polymerase differ from DNA polymerase in error checking?