Molecular Biology: Transcription and RNA Processing

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Questions and Answers

What is the main difference in mRNA processing between prokaryotes and eukaryotes?

Eukaryotes have no mRNA processing.

Prokaryotes perform 5’ capping.

Prokaryotes utilize RNA Pol II for processing.

Eukaryotes undergo 5’ capping, polyadenylation, and splicing. (correct)

Which RNA polymerase is responsible for transcribing mRNA in eukaryotes?

RNA Pol I

RNA Pol IV

RNA Pol II (correct)

RNA Pol III

What additional structure must eukaryotic mRNA pass through before being translated?

Ribosome

Nucleolus

Endoplasmic reticulum

Nuclear pore (correct)

Which element is recognized by the TATA Binding Protein (TBP) during eukaryotic transcription initiation?

TATA Box Signup and view all the answers

How is transcription regulation in eukaryotes primarily achieved?

By transcription factors and enhancers Signup and view all the answers

Which statement about RNA polymerase III is true?

It transcribes small RNA genes. Signup and view all the answers

What characterizes the process of transcription in prokaryotes compared to eukaryotes?

Occurs simultaneously with translation Signup and view all the answers

What is the role of the consensus sequence in eukaryotic transcription?

To bind specific transcription factors Signup and view all the answers

What does Chargaff’s Rule state about base pairing?

The amount of A equals the amount of T. Signup and view all the answers

What provides the ideal thickness for the DNA double helix?

Purine + Pyrimidine pairing Signup and view all the answers

Which experimental evidence supported the semiconservative model of DNA replication?

Cesium chloride centrifugation Signup and view all the answers

What stabilizes the structure of the DNA double helix?

Hydrogen bonds between complementary bases Signup and view all the answers

In DNA structure, what direction do the two anti-parallel strands run?

One runs 5’ to 3’ and the other 3’ to 5’ Signup and view all the answers

During which type of DNA replication do parent strands remain intact?

Conservative replication Signup and view all the answers

What characterizes the hydrophobic base stacking in DNA?

It helps exclude water from the bases Signup and view all the answers

Which enzyme is primarily responsible for DNA synthesis during replication?

DNA Polymerase Signup and view all the answers

What initiates the self-splicing process of introns without protein assistance?

RNA acts as a ribozyme Signup and view all the answers

Which of the following is NOT a mechanism of alternative splicing?

Mutually exclusive introns Signup and view all the answers

What is the role of the guanosine cofactor in self-splicing introns?

It facilitates reactive hydroxyl transfer Signup and view all the answers

What role does the RISC play in miRNA functionality?

It separates miRNA strands for activation Signup and view all the answers

Which type of mRNA decay enzyme removes the poly-A tail?

Deadenylase Signup and view all the answers

How do miRNA and siRNA differ in their mechanism of action?

miRNA uses imperfect complementarity, siRNA uses perfect complementarity Signup and view all the answers

What is the primary function of alternative splicing?

To produce different protein isoforms from a single gene Signup and view all the answers

What happens to introns during the splicing process?

They are cleaved out and degrade outside the cell Signup and view all the answers

What is the primary role of the TATA box in eukaryotic transcription?

Recruits TBP and GTFs to form the PIC Signup and view all the answers

Which of the following processes primarily involves co-transcriptional modifications?

Processing Signup and view all the answers

What do the 5’ splice donor and the 3’ splice acceptor sequences have in common?

They are located at the exon-intron boundaries Signup and view all the answers

Which model leads to the release of RNA polymerase II during termination?

Both torpedo and allosteric models Signup and view all the answers

What is the primary purpose of introns in eukaryotic genes?

To provide a regulatory role via siRNAs Signup and view all the answers

In the two-step transesterification process of splicing, what initiates the first step?

2’-OH of branch point A attacking the 5’ splice site phosphate Signup and view all the answers

Which complex is primarily responsible for mRNA silencing?

RNA-induced silencing complex (RISC) Signup and view all the answers

What characterizes the splicing mechanism of introns in eukaryotic transcription?

It involves a transesterification mechanism with two steps Signup and view all the answers

What was the primary outcome of inserting a viral gene into tobacco plants?

The plants remained healthy and showed no symptoms of viral infection. Signup and view all the answers

How do antibiotics work in relation to ribosomes?

They specifically target bacterial ribosomes. Signup and view all the answers

What defines the primary structure of a protein?

The sequence of amino acids in a linear form. Signup and view all the answers

Which of the following best describes frameshift mutations?

Alterations that change the reading frame of the genetic code. Signup and view all the answers

What was a key finding from Nirenberg's synthetic RNA experiment?

Identified UUU as the codon for phenylalanine. Signup and view all the answers

What defines the secondary structure of proteins?

Alpha helix and beta-pleated sheet formations. Signup and view all the answers

What is one consequence of antibiotic resistance in bacteria?

Mutations can alter bacterial rRNA or ribosomal proteins. Signup and view all the answers

What does an overlapping genetic code mean?

A single nucleotide can belong to more than one codon. Signup and view all the answers

What is the optimal growth temperature range for thermophiles?

60°C–108°C Signup and view all the answers

Which polymerase is known for its higher fidelity during DNA synthesis in PCR?

Pfu Polymerase Signup and view all the answers

What is the purpose of the denaturation step in the PCR process?

To separate the DNA strands Signup and view all the answers

How many cycles are typically repeated in a PCR process for effective amplification?

25–30 cycles Signup and view all the answers

What is the function of EcoRI in PCR product processing?

To create sticky ends for cloning Signup and view all the answers

What must be included in the forward primer for in vitro transcription with T7 polymerase?

A T7 promoter sequence Signup and view all the answers

Why do eukaryotic genes need to be converted into cDNA when expressing them in bacteria?

Eukaryotic mRNA contains introns Signup and view all the answers

Which component is essential for reverse transcription of mRNA to cDNA?

Reverse transcriptase Signup and view all the answers

Study Notes

DNA Structure and Replication

DNA is essential for all organisms, carrying the necessary information for building and functioning.
It transmits information from parents to offspring.
It replicates to create copies for inheritance.
It exhibits variation to explain phenotypic diversity.

Central Dogma

DNA acts as a template for RNA production (transcription).
RNA then directs protein synthesis (translation).
Epigenetics involves modifications to DNA that can be inherited.
Non-coding RNAs (miRNA, siRNA, IncRNA, piRNA) play diverse regulatory roles.

Key Experiments

Griffith (1928): Demonstrated transformation in bacteria, implying a genetic material.
Avery, MacLeod, and McCarty (1944): Confirmed DNA's role as the transforming agent.
Hershey and Chase (1952): Provided evidence that DNA, not protein, enters bacteria during viral infection.

DNA Structure (1953)

Watson and Crick's model: DNA is a double helix with two strands running antiparallel (5' to 3' and 3' to 5').
Nucleotides are the building blocks, each consisting of a phosphate group, deoxyribose sugar, and a nitrogenous base (A, T, C, G).
A pairs with T, and C pairs with G through hydrogen bonds.

DNA Double Helix

Two antiparallel strands are coiled around each other.
Key interactions: hydrogen bonds between base pairs and hydrophobic interactions between stacked bases.
DNA has a hydrophilic sugar-phosphate backbone that interacts with water and proteins.

DNA Replication

Semiconservative Replication: Each new DNA molecule consists of one original strand and one new strand.
Enzymes like helicase, DNA polymerase, primase, and ligase are crucial for this process.
Replication proceeds in both directions along the replication fork.

DNA Replication Speed and Accuracy

DNA polymerase III synthesizes 2,000 nucleotides per second.
Proofreading mechanisms ensure high accuracy (approximately 1 error in 10^10 nucleotides).
DNA Polymerases in E. coli: Pol I (repair), Pol II (backup), Pol III (main replication).

Key Enzymes and Proteins in DNA Replication

Helicase: unwinds DNA double helix ahead of replication fork.
DNA gyrase (topoisomerase): relieves supercoiling tension.
Primase: synthesizes RNA primers (starting points for DNA synthesis).
DNA polymerase III: extends RNA primers with new DNA.
DNA polymerase I: removes RNA primers and replaces them with DNA.
Ligase: joins Okazaki fragments on the lagging strand.
Single-strand binding protein (SSB): prevents re-annealing of separated DNA strands.

DNA Replication in Eukaryotes

Multiple origins of replication along each chromosome
Replication occurs during S phase of the cell cycle.
Telomeres are involved in protecting the ends of linear chromosomes.

Key Concepts of DNA Replication

DNA replication fork location where DNA unwinding occurs
RNA primer as starting point for replication by DNA polymerase
Leading strand synthesizes continuously 5’-> 3’
Lagging strand synthesizes in short fragments (Okazaki fragments).

RNA Structure and Function

RNA consists of ribose sugar, a phosphate group, and uracil instead of thymine.
Various RNA types have diverse roles: mRNA (template for protein synthesis), tRNA (transfers amino acids), rRNA (part of ribosome), and non-coding RNAs.
RNA plays a crucial role in gene expression.

RNA Synthesis and Translation, Prokaryotic and Eukaryotic

RNA synthesis occurs in the cytoplasm for prokaryotes and in the nucleus for eukaryotes.
Transcription and translation are coupled in prokaryotes.
Processing steps are needed before translation in eukaryotes.

RNA Replication, Process and Function

RNA polymerase utilizes one strand as a template for transcription.
Synthesizes new RNA from 5’-> 3’,
RNA is produced and exported to the cytoplasm from the nucleus
RNA is processed through different steps and functions in different ways in various processes.

RNA vs DNA

RNA has ribose, DNA has deoxyribose
RNA is typically single-stranded, DNA is double-stranded
RNA is less stable than DNA.

RNA Polymerase in Eukaryotes

Three types utilized (Pol I, Pol II, and Pol III).
Pol I synthesizes rRNA; Pol II synthesizes mRNA, and Pol III synthesizes tRNA and other small RNAs.

RNA Polymerase II Transcribed Genes

Promoter and control elements play a role in gene-specific expression.

Transcription Initiation

Pre-initiation complex (PIC) comprises multiple transcription factors and RNA polymerase II.

Transcription in a eukaryotic organism

RNA is produced, processed and exported out of the nucleus.
Transcription Initiation factors recruit the transcription machinery to the promotor region and RNA polymerase.
Transcription Elongation by RNA polymerase elongates the mRNA.
Termination mechanisms cause the release of RNA and transcription machinery from the DNA.

Protein Protein Interactions

Yeast two-hybrid system is used to screen libraries of proteins to find interactions.
This system is able to find protein-protein partners.
Screening protein-protein interactions may help to better understand complicated biological systems.

Comparative Genomics

Comparisons between genomes of pathogens and non-pathogens, and between humans and other species provide insights into gene function and evolution.
Gene duplications through retroviral insertions,
Changes between multiple species can reveal relationships and evolutionary pathways.

Protein Structure

Primary structure: amino acid sequence.
Secondary structure: alpha helix, beta sheet.
Tertiary structure: 3D shape of a single polypeptide chain.
Quaternary structure: arrangement of multiple polypeptide chains to form a functional protein.

Point Mutations

Transition (purine to purine or pyrimidine to pyrimidine).
Transversion (purine to pyrimidine or vice versa).
Effects on protein structure and function can vary from no effect to complete loss of function.

Gene mutations and regulation

Mutations can affect gene expression by altering regulatory regions (enhancers, promoters), splicing sites, and microRNA binding sites.
Spontaneous mutations can occur due to errors in DNA replication, tautomeric shifts, deamination, etc.
Trinucleotide repeats cause genetic disorders.

DNA Damage and Repair

DNA can be damaged by physical or chemical agents, leading to mutations and severe problems.
Cells utilize dedicated repair mechanisms to correct these damages.
Defects in DNA repair systems lead to certain genetic diseases.

Gene Cloning and PCR

Gene cloning involves isolating a specific gene and creating multiple identical copies.
Polymerase Chain Reaction (PCR) is a method for amplifying DNA sequences.
These methods have critical applications in research, medicine, etc.

Other genetic concepts

Other details involved in mutations, replication, and gene cloning

Chromosomal Rearrangements

Deletions, duplications, inversions, and translocations: changes in chromosome structure
these disrupt genes, potentially leading to disease.
these events can bring distant genes together.

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Description

This quiz examines the key concepts of transcription and RNA processing in prokaryotes and eukaryotes. Participants will explore differences in mRNA processing, RNA polymerases, and the structural elements of DNA. Test your understanding of these fundamental biological processes!