Chapter 11 Lecture PDF

Uses an RNA to Nov 26, guide a DNA- 2018 cutting protein to the correct sequence of DNA. The cut deactivates the gene and prevents protein being made. sciencemag.org Chapter 11 – The Expression of Genetic Information via...

Uses an RNA to Nov 26, guide a DNA- 2018 cutting protein to the correct sequence of DNA. The cut deactivates the gene and prevents protein being made. sciencemag.org Chapter 11 – The Expression of Genetic Information via Genes II: Non-coding RNAs Chapter Outline 1. Overview of non-coding RNAs 2. Role of ncRNAs in eukaryotic DNA replication 3. Effects of ncRNAs on chromatin structure and transcription 4. Effects of ncRNAs on translation and mRNA degradation 5. ncRNAs and protein sorting 6. ncRNAs and genome defense 7. Roles of ncRNAs in human disease and plan health 11.1 Overview of Non-coding RNAs Section 11.1 Learning Outcomes 1. Describe the ability of ncRNAs to bind to other molecules and macromolecules 2. Outline the general functions of ncRNAs 3. Define ribozyme 4. List several examples of ncRNAs, and describe their functions  In a typical human cell, only about 20% of transcription involves the production of mRNAs, whereas 80% is associated with making ncRNAs! Need to know (summary) Non coding RNA binds to Small molecules DNA RNA To 1 or multiple proteins They bind through complimentary bas pairing What are some of the ncRnas functions - They act as a scaffold - AS a guide; guiding one molecule to another location - Can change the structure and hence change the function of a protein - Some RNA’s have catalytic functions; - Blocker - Decoy; a decoy binds to Rna’s to prevent them from binding to anything else 11.1 Overview of Non-coding RNAs ncRNAs Can Bind to Different Types of Molecules 1-2. Bind to DNA or another RNA through complimentary base pairing Allows ncRNAs to affect the processes of DNA replication, transcription, and translation 3-4. Bind proteins or small molecules Stem-loop structures may bind or scaffold proteins or may form a binding site for a small molecule 11.1 Overview of Non-coding RNAs ncRNAs Can Perform a Diverse Set of Functions Common functions of ncRNAs include: 1. Scaffold – bind to multiple components such as proteins, act as scaffold for formation of a complex 2. Guide – guide one molecule to a specific location in the cell, for example guiding a protein to a particular site on DNA 3. Alteration of protein function or stability – binding of ncRNA can affect the ability of the protein to be a catalyst, the ability of the protein to bind other 11.1 Overview of Non-coding RNAs ncRNAs Can Perform a Diverse Set of Functions Common functions of ncRNAs include: 4. Ribozyme – RNA molecule with catalytic function, for example peptidyltransferase activity of ribosome 5. Blocker – the ncRNA physically prevents or blocks a cellular process from happening, for example blocks the binding of a ribosome, thereby inhibiting translation 11.1 Overview of Non-coding RNAs ncRNAs Can Perform a Diverse Set of Functions Common functions of ncRNAs include: 6. Decoy – recognize other ncRNAs and sequester them, preventing them from working The key difference between a blocker and decoy is what they bind to; a blocker binds a molecule that is not an ncRNA and a 11.1 Overview of Non-coding RNAs The Functions of Some ncRNAs Are Understood 11.2 Role of ncRNAs in Eukaryotic DNA Replication Section 11.2 Learning Outcomes 1. Describe the structure and function of telomeres 2. Explain how an ncRNA plays a role in the replication of telomeres in eukaryotes 11.2 Role of ncRNAs in Eukaryotic DNA Replication The ends of linear eukaryotic chromosomes have telomeres composed of repeat sequences In humans, the repeat sequence is 5ʹ–GGGTTA–3ʹ and it is typically present hundreds of times Telomeres protect the ends of the chromosomes from becoming tangled or broken As cells divide, the telomeres typically become shorter and eventually they are so short that the cell can no longer successfully divide; this causes the cell to go through a process of programmed cell death Some cells that divide rapidly express an enzyme called telomerase, which adds the https://www.genome.gov/genetics-glossary/ 11.2 Role of ncRNAs in Eukaryotic DNA Replication The ends of the chromosomes cannot be fully replicated by DNA polymerase Primer- required for DNA polymerase to build the red daughter strand - remember that DNA polymerase cannot begin Primer is removed during DNA its own work replication This strand is left shorter than the other 11.2 Role of ncRNAs in Eukaryotic DNA Replication The ends of the chromosomes cannot be fully replicated by DNA polymerase Primer- required for DNA polymerase to build the red daughter strand - remember that DNA polymerase cannot begin Primer is removed during DNA its own work replication This strand is left shorter than the other But telomerase is the solution. It allows this strand to be synthesized to the full length of the top strand. 11.2 Role of ncRNAs in Eukaryotic DNA Replication 11.2 Role of ncRNAs in Eukaryotic DNA Replication vide o Telomere lengthening occurs in 3 steps: 1. Binding of telomerase to end of chromosome 1. TERC acts as a guide, bringing telomerase to end of chromosome 2. Telomerase adds “excess DNA” to the long strand of DNA at the end of chromosome 1. Makes room for future primer 2. TERC acts as a template for telomerase extend the existing DNA strand 3. Build primer on “excess DNA” 4. Fully replicate the chromosome 11.3 Effects of ncRNAs on Chromatin Structure and Transcription Section 11.3 Learning Outcomes 1. Explain how the ncRNA known as HOTAIR plays a role in gene expression 11.3 Effects of ncRNAs on Chromatin Structure and Transcription HOTAIR (Hox transcript antisense intergenic RNA) is an ncRNA in humans and other mammals that regulates transcription by forming a scaffold that binds 2 proteins complexes and guides them to particular genes The protein complexes covalently modify histones, and these modifications silence the target genes 11.3 Effects of ncRNAs on Chromatin Structure and Transcription 11.4 Effects of ncRNAs on Translation and mRNA Degradation Section 11.4 Learning Outcomes 1. Analyze experimental evidence that double- stranded RNA is more potent at inhibiting mRNA than is antisense RNA 2. Compare and contrast microRNAs (miRNAs) and small-interfering RNAs (siRNAs) 3. Outline the steps of RNA interference and explain what happens during each step 11.4 Effects of ncRNAs on Translation and mRNA Degradation Double-Stranded RNA Is More Potent Than Antisense RNA ncRNAs can affect the ability of mRNAs to be translated or degraded The phenomenon was termed RNA interference (RNAi) Degradation RNA Interference Is Mediated by MicroRNAs or Small- Interfering RNAs via the RNA-Induced RNA interference Silencing Complex is found in most eukaryotic species, including animals and plants; there are 2 sources of ncRNA that can promote RNA interference 1.MicroRNAs (miRNAs) are ncRNAs that are transcribed from endogenous eukaryotic genes that play key roles in regulating gene expression miRNAs are partially complementary to their mRNA targets It is estimated that 60% of human protein-coding genes are regulated by miRNAs 2.Small-interfering RNAs (siRNAs) come from exogenous sources – viruses that infect a cell or from researchers siRNAs are usually perfectly complimentary to their target mRNA; they play a role in preventing viral Degradation RNA Interference Is Mediated by MicroRNAs or Small- Interfering RNAs via the RNA-Induced Silencing Complex vide o 11.5 Non-coding RNAs and Protein Sorting Section 11.5 Learning Outcomes 1. Describe the function of the signal recognition particle (SRP) 2. Explain the roles of SRP RNA with regard to SRP function 11.5 Non-coding RNAs and Protein Sorting Signal recognitio n protein binds this and chaperone s ribosome to ER  11.5 Non-coding RNAs and Protein Targeting Signal recognition particle (SRP) Composed of protein and ncRNA It chaperones the ribosome to 2. SRP binds to an SRP receptor in the ER the ER membrane, which is located next to a channel. For this binding to occur, proteins within SRP and the SRP receptor must also bind GTP 3. The GTP-binding proteins within SRP and the SRP receptor hydrolyze their GTP, causing the release of SRP. This allows 1. As a polypeptide is translation to resume, and being made, SRP binds the polypeptide is to an ER signal threaded through a sequence and causes channel into the ER lumen translation to pause 11.6 Non-coding RNAs and Genome Defense Section 11.6 Learning Outcomes 1. Outline the genes that are part of the type II CRISPR-Cas system 2. Explain how the CRISPR-Cas system defends bacteria against bacteriophages 3. Explain the events of the adaptation, expression, and interference stages 11.6 Non-coding RNAs and Genome Defense Some species of bacteria and archaea have a system called the CRISPR-Cas system that provides defense against bacteriophages and transposons There are 3 general types, designated type I, II, and III The type II CRISPR-Cas system provides bacteria with defense against bacteriophages Short sequence of phage dna from prior phage infection 11.6 Non-coding RNAs and Genome Defense The CRISPR-Cas System Provides Bacteria with Defense Against Bacteriophages The CRISPR-Cas type II system contains: Crispr gene with repeats interspersed with short, unique sequences called spacers A gene that encodes an ncRNA called tracrRNA (pronounced “tracer RNA”) Several protein-encoding CRISPR-associated genes (Cas genes) The defense occurs in 3 phases: adaptation, expression, and interference 11.6 Non-coding RNAs and Genome Defense The CRISPR-Cas System Provides Bacteria with Defense Against Bacteriophages Adaptation occurs after the bacterial cell has been exposed to a bacteriophage The Cas1 and Cas2 proteins form a complex that recognizes the bacteriophage DNA as being foreign and cleaves it into small pieces A piece of bacteriophage DNA is inserted into the Crispr gene 11.6 Non-coding RNAs and Genome Defense The CRISPR-Cas System Provides Bacteria with Defense Against Bacteriophages If a bacterial cell has already been adapted to a bacteriophage, a subsequent infection will result in the expression phase The Crispr, tracr, and Cas9 genes are transcribed (expressed) The tracrRNA is an ncRNA with a region that is complimentary to the repeat sequences of the pre- crRNA The pre-crRNA is cleaved into Is going to “guide” cas 9 A scaffold to many small crRNA molecules to the invading hold cas 9 + the crRNA The tracrRNA acts as a guide that phage causes the tracrRNA-crRNA complex to bind to a Cas9 protein 11.6 Non-coding RNAs and Genome Defense The CRISPR-Cas System Provides Bacteria with Defense Against Bacteriophages After the tracrRNA-crRNA- Cas9 complex has formed, the bacterial cell is ready to destroy the bacteriophage DNA This phase is called interference because it resembles the process of RNA interference Each spacer is complementary to one of the strands of bacterio- phage DNA; the crRNA acts as a guide that causes the complex to 11.7 Role of ncRNAs in Human Disease and Plant Health Section 11.7 Learning Outcomes 1. List examples in which ncRNAs are associated with human diseases 2. List examples in which ncRNAs play a role in plant health 11.7 Role of ncRNAs in Human Disease and Plant Health ncRNAs Play a Role in Many Forms of Cancer and Other Human Diseases Abnormal expression levels of certain miRNAs are found in nearly all forms of human cancer Some miRNAs are tumor-suppressors, others act as oncogenes HOTAIR is highly expressed in several cancers; when overexpressed, it behaves as an oncogene Various ncRNAs are associated with neurological disorders (Alzheimer disease) and cardiovascular diseases (arrhythmias) 11.7 Role of ncRNAs in Human Disease and Plant Health ncRNAs Are Essential to Plant Health In parallel to the study of human disease, plant biologists are discovering that abnormalities in ncRNAs play essential roles in plant health (seed development, growth, stress responses) This knowledge is important for agriculture