Slides - Ch 7 Part 1 - Intro & From DNA to RNA

Page 1: Learning Objectives

• Central Dogma & Gene Expression

  • Discuss steps involved in gene expression.

  • Possible steps include transcription, splicing, and translation.

• Comparison of DNA & RNA

  • Compare their structures, functions, and roles in cells.

• DNA Replication vs. Transcription

  • Contrast the mechanisms and end products of each process.

• RNA Production by Transcription

  • Describe mRNA, rRNA, tRNA, and other RNA types produced.

• Transcription Start & Stop Sequences

  • Specialized sequences inform where transcription begins and ends.

• Bacterial vs. Eukaryotic Transcription Initiation

  • Compare initiation mechanisms in prokaryotes and eukaryotes.

• Eukaryotic RNA Processing

  • Steps taken to process RNA after transcription and their purpose.

Page 2: Central Dogma of Molecular Biology

• Fundamental Principle

  • Describes how cells decode and utilize hereditary information in DNA.

  • Directs organismal development and maintenance.

  • Encodes proteins necessary for cellular functions.

• Genetic Information Flow Variations

  • Some genes yield RNA as final products.

  • Some organisms involve additional processing steps.

Page 3: Gene Expression Regulation

• Regulation at Transcription Level

  • Multiple RNA molecules can arise from one gene.

• Regulation at Translation Level

  • Each RNA can lead to the synthesis of many proteins.

• Variability in Gene Transcription/Translation

  • Genes can be expressed at differing rates, allowing for varied protein levels.

Page 4: Transcription Process

• Initial Step of Gene Expression

  • DNA sequence is converted into RNA (DNA → RNA).

• Opening DNA Helix

  • A small section of the double helix unwinds.

• Template Strand Usage

  • One DNA strand serves as the template for complementary RNA strand synthesis.

• Base Pairing & RNA Assembly

  • Assembles RNA via complementary base pairing.

• RNA Displacement

  • Newly synthesized RNA displaces from the template and the double helix re-forms.

Page 5: RNA Characteristics

• Definition

  • Ribonucleic acid, produced during transcription as a chemical form of information.

• Structural Features

  • Linear polymer composed of four nucleotide subunits linked by phosphodiester bonds.

• Comparison to DNA

  • Shorter than DNA, contains ribose sugar, and uracil base replaces thymine.

Page 6: RNA Structure

• Folding of RNA

  • Typically single-stranded, can form 3D structures through intra-molecular base pairing.

• Functional Roles

  • Can serve structural, catalytic, or regulatory roles within cells.

Page 7: Types of RNA in Cells

• Messenger RNAs (mRNAs)

  • Function: Code for proteins.

• Ribosomal RNAs (rRNAs)

  • Function: Make up the ribosome structure and catalyze protein synthesis.

• MicroRNAs (miRNAs)

  • Function: Regulate gene expression.

• Transfer RNAs (tRNAs)

  • Function: Adaptor molecules during protein synthesis.

• Small interfering RNAs (siRNAs)

  • Function: Protect from viruses and transposable elements.

• Long noncoding RNAs (IncRNAs)

  • Function: Diverse roles including scaffolding.

Page 8: Template Strand in Transcription

• Transcription Mechanics

  • The template strand produces complementary RNA.

• Strands Defined

  • Template Strand: Guides RNA synthesis.

  • Coding Strand: Sequence equivalent to the RNA product, with T replaced by U.

Page 9: RNA Polymerase Role

• RNA Polymerase Function

  • Utilizes one DNA strand as a template for RNA synthesis.

• Base Pairing and Polymerization

  • Synthesizes RNA in the 5’-to-3’ direction.

  • Hydrolysis of nucleoside triphosphates fuels bond formation.

Page 10: Multiple RNA Copies

• Simultaneous Transcription

  • Many RNA polymerases can transcribe the same gene simultaneously, allowing rapid RNA synthesis.

Page 11: Transcription Start & Stop Signals

• Promoter Sequences

  • Initiate transcription; located upstream of the starting point and not transcribed.

• Terminator Sequences

  • Indicate where transcription should halt; transcribed into the RNA and causes the release of new RNA and DNA template.

Page 12: Promoter Polarity**

• Orientation of RNA Polymerase

  • Different sequences on each DNA strand lead RNA polymerase to bind and transcribe the correct strand as the template.

  • Determines direction of synthesis to maintain 5’-to-3’ synthesis.

Page 13: Direction of Transcription Variability

• Transcription Directionality

  • Can vary between genes based on promoter orientation.

Page 14: Bacterial Transcription Process

• Initiation by RNA Polymerase

  • Scans DNA for promoter sequences, recognized by sigma factors.

• Opening the Helix

  • Once the promoter is found, RNA polymerase tightly binds, opens the helix, and begins transcription.

• Termination Process

  • Transcription stops after reading terminator sequences, releasing RNA and template.

Page 15: Eukaryotic Transcription Complexity

• Multifaceted Initiation

  • Utilizes multiple RNA polymerases and accessory proteins for transcription initiation, influenced by regulatory DNA sequences.

Page 16: Eukaryotic RNA Polymerases**

• Types of Eukaryotic RNA Polymerases

  • RNA Polymerase I: Transcribes most rRNA genes.

  • RNA Polymerase II: Transcribes protein-coding genes and miRNA genes.

  • RNA Polymerase III: Transcribes tRNA genes and some small RNAs.

Page 17: General Transcription Factors in Eukaryotes

• Role of TFIID

  • Binds to TATA box and recruits other factors needed for transcription initiation.

• Function of TFIIH

  • Opens the double helix, phosphorylates RNA polymerase II, and starts transcription.

Page 18: mRNA Production Complexity**

• In Prokaryotes

  • Transcription and translation occur simultaneously in the same compartment.

• In Eukaryotes

  • Transcription occurs within the nucleus, requiring additional processing steps before translation in the cytoplasm.

Page 19: RNA Processing in Eukaryotes**

• During Synthesis

  • RNA transcripts are modified during synthesis by processing enzymes.

• Types of Processing

  • Capping, splicing, and polyadenylation of RNA.

Page 20: RNA Capping and Polyadenylation

• 5’ Capping

  • Involves modification to the 5’ end with a special nucleotide (7-methylguanosine).

• 3’ Polyadenylation

  • Addition of adenine nucleotides to the 3’ end.

• Purpose of Modifications

  • Enhance RNA stability, facilitate export from the nucleus, and indicate that the RNA is mature for translation.

Page 21: Gene Organization in Prokaryotes vs. Eukaryotes

• Prokaryotic Organization

  • Most proteins encoded by uninterrupted DNA sequences.

• Eukaryotic Organization

  • Genes often interrupted by introns (noncoding) and exons (coding).

  • Introns are removed through splicing, exons are expressed sequences.

Page 22: RNA Splicing

• Mechanism

  • Spliceosome recognizes sequences at intron boundaries and removes introns, combining exons.

Page 23: Spliceosome Composition**

• Structure

  • Large assembly of RNA and protein that carries out RNA splicing by forming "lariat" structures for intron removal.

Page 24: Intron-Exon Cleavage**

• Intron Removal Process

  • Involves adenine in the intron attacking the splice site, cleaving the pre-mRNA, and forming a branched "lariat" followed by exon joining.

Page 25: Alternative Splicing**

• Increasing Coding Potential

  • Allows for splicing variations that enable different proteins to be synthesized from a single gene by skipping certain exons.

Page 26: mRNA Export from Nucleus

• Selective Export Process

  • Only properly processed mRNAs are moved to cytoplasm, involving various binding proteins (cap-binding, poly-A-binding, exon junction complex) mediated through nuclear pore complexes.