Exam 3

What is transcriptional regulation in prokaryotes responsible for?

It controls cellular state, mRNA levels of genes, and thereby protein levels in the cell.

What is the function of sigma factor in prokaryotic transcription?

Sigma factor is required for RNA polymerase to initiate transcription by binding to promoter regions.

What are the two major types of proteins involved in transcription regulation?

Activator proteins, which promote transcription, and repressor proteins, which inhibit transcription.

What sequence is recognized by sigma factor 70 in prokaryotes?

The minus 10 and minus 35 regions of the promoter region.

What is the difference between rho-independent and rho-dependent termination of transcription?

Rho-independent termination involves a hairpin structure in the mRNA, while rho-dependent termination involves the binding of the Rho helicase to the rut site.

What is the lac operon responsible for?

The lac operon is responsible for the breakdown of lactose in bacterial cells.

How does allolactose affect the lac operon?

Allolactose binds to the lac repressor, inactivating it and allowing transcription of the lac operon.

What is the role of cyclic AMP in the regulation of the lac operon?

Cyclic AMP binds to the CAP protein, which helps recruit RNA polymerase to the promoter when glucose levels are low.

What happens to the lac operon when glucose is high and lactose is present?

The lac repressor is not bound to the operator, allowing low-level transcription of the lac operon due to the presence of glucose.

What is the role of AraC in the arabinose operon?

AraC acts as both an activator when arabinose is present and a repressor when it is absent, regulating transcription.

What is the function of the trp operon?

The trp operon is involved in the biosynthesis of tryptophan in bacteria.

How does the presence of tryptophan affect the trp operon?

High levels of tryptophan activate the trp repressor, which binds to the operator and prevents transcription.

What is the significance of the attenuator sequence in the trp operon?

It determines whether transcription should be terminated early or allowed to continue based on tryptophan levels.

What happens when tryptophan levels are low in the trp operon?

The ribosome stalls at tryptophan codons, allowing transcription to continue through the structural genes.

What is the difference between transacting and cisacting factors in the regulation of the lac operon?

Transacting factors are proteins (like the lac repressor) that regulate gene expression, while cisacting factors are DNA sequences (like the operator) that are recognized by these proteins.

What is the function of transfer RNA (tRNA) in protein translation?

tRNA serves as an adapter molecule that reads nucleotide codons in mRNA and inserts the appropriate amino acid into the growing polypeptide chain.

What structure is formed by tRNA due to internal base pairing?

The tRNA folds into a cloverleaf structure with four arms.

What is the role of the anticodon in tRNA?

The anticodon forms complementary base pairs with the codon in mRNA.

What is the function of tRNA synthetases?

tRNA synthetases are enzymes that covalently attach the appropriate amino acid to its corresponding tRNA.

What are ribosomal RNAs (rRNAs) and why are they important?

Ribosomal RNAs are noncoding RNAs that are the most abundant RNA in living organisms and play a crucial role in the formation of ribosomes for protein translation.

How is ribosomal RNA structured in prokaryotes compared to eukaryotes?

In prokaryotes, the large subunit consists of 23S and 5S rRNA; while in eukaryotes, it includes 28S, 5S, and 5.8S rRNA.

What is RNA interference (RNAi)?

RNAi is a phenomenon where RNA molecules inhibit gene expression by binding to complementary mRNA, preventing protein translation.

What effect did overexpressing the chalcone synthase gene in petunias have?

It caused white patches instead of a deeper purple color, indicating suppression of both the transgene and the endogenous gene.

What is the significance of Craig Mello and Andrew Fire in the study of RNA interference?

They discovered the RNA interference pathway and demonstrated its mechanism using C. elegans, for which they won a Nobel Prize.

What are the two types of RNA molecules that elicit RNA interference?

Short interfering RNA (siRNA) and microRNA (miRNA).

What is the role of Dicer in RNA interference?

Dicer processes long double-stranded RNA into short double-stranded RNA fragments, which are involved in the RNAi pathway.

What is the role of the RISC complex in RNA interference?

RISC (RNA-induced silencing complex) incorporates short RNA and facilitates the degradation or translational inhibition of complementary mRNA.

How do microRNAs typically interact with their target mRNAs?

MicroRNAs usually have partial complementarity with target mRNAs, leading to translational inhibition or degradation.

How is RNA interference used in molecular biology?

It is used to manipulate gene expression by knocking down specific genes post-transcriptionally without altering the genome.

What are the two pathways of post-transcriptional processing, and how do they differ?

The two pathways are exogenous, which involves external RNA (like siRNA) introduced to modulate gene expression (used in viral infections), and endogenous, which involves RNA produced within the cell.

What is Dicer and its role in RNA interference?

Dicer is an enzyme that processes long double-stranded RNA into short double-stranded RNA fragments, which are essential components in the RNA interference pathway.

What is the RISC complex and its function in RNA interference?

The RISC (RNA-induced silencing complex) is a multi-protein complex that incorporates small RNA molecules and guides those RNAs to complementary mRNA targets, facilitating mRNA degradation or inhibiting translation.

What molecules do RNA interference (RNAi) and Cas9 target?

RNA interference targets complementary mRNA molecules to inhibit gene expression, while Cas9 targets DNA sequences to create double-strand breaks, leading to gene knockout or modification.

What happens to molecules when they are targeted by RNA interference (RNAi) or Cas9?

When mRNA is targeted by RNAi, it undergoes degradation or translational inhibition. Meanwhile, when DNA sequences are targeted by Cas9, double-strand breaks are created, leading to gene knockout or modification.

How does targeting mRNA lead to gene expression knockdown?

Targeting mRNA with RNA interference (RNAi) leads to knockdown by degrading the mRNA, resulting in a reduction of protein production without eliminating the gene itself.

How does targeting DNA lead to gene knockout?

Targeting DNA with methods like Cas9 results in gene knockout by creating double-strand breaks, which can lead to gene deletion and completely abolish protein production.

What are the three different RNA polymerases in eukaryotes?

RNA Polymerase 1, RNA Polymerase 2, and RNA Polymerase 3.

What is the primary function of RNA Polymerase 2?

Transcribes messenger RNA, protein coding genes, many micro RNAs, and some noncoding RNAs.

What is the TATA box and its significance?

A sequence located about 30 nucleotides upstream of the transcription start site; it is important for the binding of the TATA binding protein.

What is the role of the BRE element in transcription?

It is recognized by transcription factor 2 B and is located about 30 to 37 nucleotides upstream of the transcription start site.

What are general transcription factors?

Proteins required to help RNA polymerase bind to the promoter and initiate transcription.

What does the mediator complex do in transcription regulation?

It facilitates interactions between RNA polymerase and transcription factors, helping to coordinate transcriptional regulation.

How do enhancers function in gene expression?

Enhancers can be located distant from a gene and, when bound by specific transcription factors, they help promote transcription of that gene.

What is combinatorial control in eukaryotic gene expression?

The requirement of multiple transcription factors working together to achieve high levels of gene activation.

What is the effect of insulator sequences in transcriptional regulation?

Insulators block enhancer signals from activating neighboring gene promoters, allowing for specific gene expression.

What is imprinting in genetics?

The phenomenon where only one of the two inherited alleles is expressed.

in eukaryotes RNA polymerase requires _____ to bind to promotor sequences

transcription factors

In eukaryotes, there are DNA sequences distant from the gene that can bind transcription factors to activate or repress gene expression called

enhancers

In eukaryotes, there are DNA sequences between gene promoters of different genes called _______ which prevent enhancers from one gene from affecting expression of the other gene.

insulators

Scientists can use __________ enzymes to chew up DNA that is unbound by transcription factors to find the transcription factor "footprint", or region of the DNA bound and therefore protected from digestion by the transcription factor.

DNase

What is DNA footprinting?

A technique used to identify the specific regions of DNA that are bound by proteins, typically transcription factors, by comparing digestion patterns of DNA with and without bound proteins.

What is RNA processing and why is it important for eukaryotic cells?

RNA processing is required to convert pre-mRNA into mature mRNA for translation, involving adding a 5' cap, splicing out introns, and adding a poly A tail.

What happens during transcription in prokaryotes?

RNA polymerase binds to the promoter, transcribes mRNA from the template strand, producing a molecule that can be directly translated into a protein without processing.

What are the three major steps of RNA processing in eukaryotes?

1. Addition of a 5' cap 2. Splicing to remove introns and connect exons 3. Addition of a poly A tail at the 3' end.

Why is RNA processing not required in prokaryotes?

Prokaryotic genes lack introns and transcription and translation occur simultaneously in the cytoplasm.

What role does the 5' methylated guanine cap play in mRNA?

It protects mRNA from degradation by exonucleases and assists in ribosome binding for translation.

What is polyadenylation?

The process of adding 80 to 250 adenine nucleotides to the 3' end of mRNA, facilitating stability and export from the nucleus.

What are cis regulatory elements and their function?

RNA sequences in the 3' UTR that are bound by proteins, influencing translation regulation and mRNA localization.

Describe the role of the spliceosome in RNA processing.

The spliceosome, made of snRNPs, recognizes splice sites, removes introns, and ligates exons together during RNA splicing.

What is alternative splicing?

A process where different splice sites are used to produce multiple mature mRNA variants from a single gene, leading to different proteins.

What are snRNPs and their function in splicing?

Small nuclear ribonucleoproteins (snRNPs) are components of the spliceosome that help identify splice sites and catalyze the splicing reaction.

RNA Transcription

The process by which messenger RNA (mRNA) is synthesized from a DNA template.

Messenger RNA (mRNA)

A type of RNA that carries genetic information from DNA to the ribosome for protein synthesis.

Genes

Sequences of DNA that contain the instructions for making proteins.

Exons

Coding regions of a gene that are retained in the final mRNA after splicing.

Introns

Non-coding regions of a gene that are removed during mRNA processing.

Regulatory DNA

DNA sequences that control the rate of transcription of genes.

MicroRNAs

Small non-coding RNA molecules that regulate gene expression post-transcriptionally.

Transfer RNA (tRNA)

A type of non-coding RNA that helps translate mRNA into proteins by bringing amino acids to the ribosome.

Ribosomal RNA (rRNA)

A type of non-coding RNA that is a component of ribosomes, essential for protein synthesis.

RNA Polymerase

The enzyme responsible for synthesizing RNA from a DNA template during transcription.

Promoter

A DNA sequence that initiates transcription by providing a binding site for RNA polymerase.

Terminator

A sequence in DNA that signals the end of transcription.

Transcription Start Site (TSS)

The location on the DNA where RNA polymerase begins transcription.

Untranslated Regions (UTRs)

Portions of mRNA that are transcribed but not translated into protein, including the 5' UTR and 3' UTR.

Pre-mRNA

The initial RNA transcript that contains both exons and introns before processing.

Methylated Guanine (5' cap)

A modified guanine nucleotide added to the 5' end of mRNA during processing to protect it and assist in ribosome binding.

Poly A Tail

A stretch of adenine nucleotides added to the 3' end of mRNA during processing, important for stability and export from the nucleus.

Splicing

The process of removing introns and joining exons in pre-mRNA to form mature mRNA.

Heteroduplex

A region where an RNA strand is base-paired with a DNA strand during transcription.