Molecular Biology: Transcription and RNA Processing

Comprehensive practice flashcards covering transcription in prokaryotes and eukaryotes, RNA polymerase functions, RNA types, promoter architectures, transcription factor assembly, and post-transcriptional processing.

How is a gene defined according to the lecture notes?

A linear stretch of instructions that directs the production of a particular product (a protein or a functional RNA molecule).

What is the definition of transcription?

The process in which RNA polymerase uses one strand of DNA as a template to synthesize a complementary RNA sequence.

What is the definition of translation?

The process by which the sequence of nucleotides in an mRNA molecule directs the incorporation of amino acids into a protein.

What chemical structural difference distinguishes ribose (in RNA) from deoxyribose (in DNA)?

Ribose has a hydroxyl group ($-\text{OH}$) at the $2'$ carbon, whereas deoxyribose has a hydrogen ($-\text{H}$) at the $2'$ carbon.

What chemical functional group distinguishes thymine from uracil?

Thymine possesses a methyl group ($-\text{CH}_3$) on its pyrimidine ring, whereas uracil possesses a hydrogen ($-\text{H}$) at that position.

What type of chemical bond links ribonucleotides together into an RNA chain?

A phosphodiester bond linking the $3'$ carbon of one ribose to the $5'$ carbon of the adjacent ribose.

What key catalytic properties distinguish RNA polymerase during transcription?

It unwinds the DNA duplex, catalyzes phosphodiester bond formation, synthesizes RNA in the $5' \rightarrow 3'$ direction, can start synthesis without a primer, and lacks proofreading activity.

What provides the driving energy for the polymerization reaction catalyzed by RNA polymerase?

Incoming ribonucleoside triphosphates (ATP, CTP, UTP, or GTP).

In this electron micrograph showing active transcription, what is represented by the multiple branches extending from the central DNA strand?

Growing RNA transcripts simultaneously synthesized by multiple RNA polymerase molecules moving along the gene.

What are the primary functions of ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs)?

rRNAs form the core of the ribosome's structure and catalyze protein synthesis; tRNAs serve as adaptors between mRNA and amino acids during protein synthesis.

What are the biological functions of microRNAs (miRNAs) and small interfering RNAs (siRNAs)?

miRNAs regulate gene expression; siRNAs provide protection from viruses and proliferating transposable elements.

What is the primary role of the sigma ($\sigma$) factor in bacterial transcription?

It recognizes the promoter sequence to guide bacterial RNA polymerase to the transcription start site, and is released once RNA synthesis begins.

Which two conserved DNA sequence regions are found in bacterial promoters to direct RNA polymerase binding?

The $-10$ and $-35$ consensus sequence elements located upstream of the $+1$ transcription start site.

In what direction does RNA polymerase read the template DNA strand, and what dictates which strand serves as the template?

RNA polymerase reads the template strand in the $3' \rightarrow 5'$ direction; the orientation and polarity of the promoter sequence dictate which strand is transcribed.

Which classes of genes are transcribed by eukaryotic RNA polymerase I, II, and III?

RNA polymerase I transcribes most rRNA genes; RNA polymerase II transcribes all protein-coding genes (mRNAs), miRNA genes, and other noncoding RNAs (such as spliceosomal RNAs); RNA polymerase III transcribes tRNA genes, the 5S rRNA gene, and many other small RNAs.

What are the rRNA and protein components of the eukaryotic 60S and 40S ribosomal subunits?

The 60S subunit contains 28S, 5.8S, and 5S rRNAs (~46 proteins); the 40S subunit contains 18S rRNA (33 proteins).

Where is RNA polymerase I localized within the eukaryotic nucleus, and what chromosomal contributions form this structure?

It is localized in the nucleolus, where $10$ chromosomes each contribute a loop containing rRNA genes.

What is the sequential assembly order of general transcription factors at a eukaryotic TATA-box-containing promoter?

TFIID (via TBP) binds first, followed by TFIIB, then RNA polymerase II accompanied by TFIIF, followed by TFIIE and TFIIH.

What two critical functions does TFIIH carry out during eukaryotic transcription initiation?

It unwinds the promoter DNA and phosphorylates the C-terminal domain tail of RNA polymerase II, releasing it from the transcription factors to begin elongation.

How does the TATA-binding protein (TBP) subunit of TFIID alter DNA structure upon binding?

TBP binds the TATA box sequence and introduces a sharp bend in the DNA double helix to facilitate assembly of other transcription factors.

How do elongation factors assist RNA polymerase II in traversing chromatin?

They assemble on the actively transcribing RNA polymerase II and form a wedge that pries DNA off the histone core of the nucleosome as the enzyme progresses.

How are pre-mRNA processing factors recruited to the newly synthesized transcript?

Phosphorylation of the C-terminal tail of RNA polymerase II allows capping factors, splicing factors, and polyadenylation factors to assemble directly onto the tail.

What are the four sequential modification steps required during eukaryotic tRNA processing?

1) Removal of the $5'$ leader sequence, 2) Replacement of $3'$ nucleotides with CCA, 3) Chemical modification of specific bases, and 4) Excision of an intron.

What is the unique chemical structure of the eukaryotic mRNA 5' cap?

A 7-methylguanosine connected via an unusual $5' \rightarrow 5'$ triphosphate bridge to the initial nucleotide, accompanied by methylation of the $2'$ hydroxyl groups of the next two sugars.

What are the two major functional roles of the 5' cap on eukaryotic mRNA?

It protects the mRNA against exonuclease degradation (enhancing stability) and positions the mRNA on the ribosome for translation initiation.

What sequence marks the cleavage site for polyadenylation, and what enzyme synthesizes the poly(A) tail?

The AAUAAA polyadenylation signal sequence directs cleavage, after which poly(A) polymerase adds $50$ to $250$ adenine nucleotides to the $3'$ end.

How does the poly(A) tail cooperate with the 5' cap to facilitate eukaryotic translation initiation?

Poly(A) binding proteins (PABPs) bound to the poly(A) tail interact with initiation factors (such as eIF4E at the $5'$ cap) and the 40S ribosomal subunit, circularizing the mRNA to stimulate translation.