Chapter 12 Notes - Exam 3 PDF

Chapter 12 – The Control of Genetic Information via Gene Regulation Chapter Outline 1. Overview of gene regulation 2. Regulation of transcription...

Chapter 12 – The Control of Genetic Information via Gene Regulation Chapter Outline 1. Overview of gene regulation 2. Regulation of transcription in bacteria 3. Regulation of transcription in eukaryotes: roles of transcription factors 4. Regulation of transcription in eukaryotes: changes in chromatin structure and DNA methylation 5. Regulation of RNA splicing and translation in eukaryotes 12.1 Overview of Gene Regulation Section 12.1 Learning Outcomes 1. Discuss the various ways that organisms benefit from gene regulation 2. Identify where gene regulation can occur in the pathway of gene expression for bacteria and eukaryotes 12.1 Overview of Gene Regulation Gene regulation refers to the ability of cells to control the expression of their genes Most genes are regulated to ensure proteins are produced at the correct time and in the correct amount Regulation conserves energy by producing only what is needed Some genes have relatively constant levels of expression; such Loading… constitutive genes frequently encode proteins that are constantly required (like enzymes for carbohydrate metabolism) Many proteins regulate gene expression through binding to DNA 12.1 Overview of Gene Regulation Eukaryotic Gene Regulation Enables Multicellular Organisms to Proceed Through Developmental Stages For multicellular organisms that progress through developmental stages, certain genes are expressed at particular stages Embryo ζ ζ e e These bind O2 with high affinity Fetal a a e e Birth+ Bind O2 with a a lesser affinity b b since lots of O2 in blood Practice: Three different cell types from the same human are shown below. How do the genomes differ among these cells (or do they differ)? How do the proteomes differ among these cells (or do they)? Loading… 12.1 Overview of Gene Regulation Eukaryotic Gene Regulation Produces Different Cell Types in a Single Organism Cell differentiation is the process by which cells become specialized into particular types 12.1 Overview of Gene Regulation Gene Regulation Occurs at Different Points in the Process from DNA to Protein 12.3 Regulation in Eukaryotes: Transcription Factors Section 12.3 Learning Outcomes 1. Explain the concept of combinatorial control 2. Describe how RNA polymerase and general transcription factors initiate transcription at the core promoter 3. Discuss how activators, coactivators, repressors, and TFIID play a role in gene regulation 12.3 Regulation in Eukaryotes: Eukaryotic Protein-Encoding Genes Have a Core Promoter and Regulatory Elements Most promoters include a core promoter and regulatory elements The core promoter contains the TATA box and the transcription start site The core promoter alone results in a low level basal transcription 12.3 Regulation in Eukaryotes: Transcription Factors Transcription factors Bind to the gene regulatory elements Two types: enhancers and silencers How do enhancers and silencers effect gene expression? 12.3 Regulation in Eukaryotes: Transcription Factors RNA Polymerase II requires Transcription factors RNA polymerase II transcribes genes that encode proteins RNA polymerase II requires 5 different general transcription factors (GTFs) to initiate transcription These GTFs ensure that RNA polymerase starts in the right place and facing the correct direction Loading… 12.3 Regulation in Eukaryotes: Transcription Factors Activators and Repressors May Influence the Function of General Transcription Factors (GTFs) Activators bind to enhancer sequences; repressors bind to silencer sequences Activators and repressors commonly regulate transcription by affecting the function of GTFs In this example an activator and a coactivator are involved TFIID binds the TATA box and is a common target for activators and repressors TFIID plays the important role of ensuring that RNA polymerase is facing the correct direction 12.3 Regulation in Eukaryotes: Transcription Factors Activators and Repressors May Influence the Function of General Transcription Factors (GTFs) TFIID binds the TATA box and is a common target for activators and repressors TFIID plays the important role of ensuring that RNA polymerase is facing the correct direction 12.3 Regulation in Eukaryotes: Transcription Factors Most eukaryotic genes are under combinatorial control, where expression is regulated by the combination of many factors inhibit RNA polymerase from initiating Activators transcription small effector molecules, protein–protein Modulation interactions, and covalent modifications can effect activators and repressors Repressors promotion loosening up of the region in the chromosome where a gene is located, making it easier for RNA polymerase to transcribe the gene DNA Methylation stimulate RNA polymerase to initiate transcription Chromatin usually inhibits transcription, either by blocking structure an activator protein or by recruiting proteins that inhibit transcription 12.4 Regulation in Eukaryotes: Chromatin Structure Section 12.4 Learning Outcomes 1. Describe the flanking of eukaryotic genes by nucleosome-free regions and how nucleosomes are altered during gene transcription 2. Explain how DNA methylation affects transcription 3. Describe how the formation of facultative heterochromatin can silence genes in a tissue- specific manner  12.4 Regulation in Eukaryotes: Chromatin Structure Some genes are buried in tight chromatin which RNApol cannot reach A region in a closed conformation is difficult or impossible to transcribe; transcription requires changes in chromatin structure A region in an open conformation is accessible to GTFs and RNA polymerase II and can therefore be transcribed 12.4 Regulation in Eukaryotes Goal: Make the DNA more accessible for RNA polymerase II. But How? 1. Many eukaryotic genes show a common pattern of nucleosome organization: a nucleosome-free region (NFR) is found at the beginning and end of the gene Question: Why do you think that nucleosome-free regions exist? To make/leave space for RNA polymerase 12.4 Regulation in Eukaryotes: Chromatin Structure Goal: Make the DNA more accessible for RNA polymerase II. 2. change chromatin structure is through chromatin-remodeling complexes They can move nucleosomes around as shown in this figure. 12.4 Regulation in Eukaryotes: Chromatin Structure Goal: Make the DNA more accessible for RNA polymerase II Two Ways: 2a) Modify histone tails 2b) Directly methylate cytosines in DNA 12.4 Regulation in Eukaryotes: Chromatin Structure Two Ways: 1) Modify histone tails 2) Directly methylate cytosines in DNA Ok, so RNA pol is bound to the promoter…what happens to nucleosomes during transcription elongation?? Ok, so RNA pol is bound to the promoter…what happens to nucleosomes during transcription elongation?? 12.4 Regulation in Eukaryotes: Chromatin Structure DNA Methylation Inhibits Gene Transcription 12.4 Regulation in Eukaryotes: Chromatin Structure DNA Methylation Inhibits Gene Transcription 12.5 Eukaryotic Regulation of RNA Splicing and Translation Section 12.5 Learning Outcomes 1. Outline the process of alternative splicing, and explain how it increases protein diversity 2. Explain how RNA- binding proteins regulate the translation of specific mRNAs, using the regulation of iron absorption in mammals as an example 12.5 Eukaryotic Regulation of RNA Splicing and Translation Alternative Splicing of Pre-mRNAs Increases Protein Diversity Alternative splicing allows an organism to use the same gene to make different proteins at different stages of development 12.5 Eukaryotic Regulation of RNA Splicing and Translation The Fastest Way to Regulate Proteins Iron is a vital Iron cofactor for many levels The mRNA that encodes enzymes however, it ferritin is controlled by is toxic at high levels an RNA binding protein The protein ferritin known as iron prevents toxicity by regulatory protein HIG storing excess iron LO H (IRP) W 12.2 Regulation of Transcription in Bacteria Section 12.2 Learning Outcomes 1. Explain how regulatory transcription factors and small effector molecules are involved in the regulation of transcription 2. Describe the organization of the lac operon 3. Explain, in detail, how the lac operon is regulated by negative and positive control 12.2 Regulation of Transcription in Bacteria Transcriptional Regulation Involves Regulatory Transcription Factors and Small Effector Molecules Regulatory transcription factors, proteins that bind to regulatory sequences in DNA, are frequently used to change levels of gene expression Repressor are transcription factors that exert negative ___________ control s and decrease transcription _________ and Loading… Activator are transcription factors that exert positive control s increase transcription 12.2 Regulation of Transcription in Bacteria The lac Operon Contains Genes That Encode Proteins Involved in Lactose Metabolism An operon is a cluster of genes under the control of a single promoter Ex. lac operon 12.2 Regulation of Transcription in Bacteria The lac Operon Contains Genes That Encode Proteins Involved in Lactose Metabolism Why does the cell need to produce glucose? 12.2 Regulation of Transcription in Bacteria The lac Operon Is Under Negative Control by a Repressor Protein The lacI gene encodes the lac repressor, and it is constitutively expressed at a low level In the absence of lactose, the lac repressor binds the operator and prevents RNA polymerase from transcribing the structural genes 12.2 Regulation of Transcription in Bacteria The lac Operon Is Under Negative Control by a Repressor Protein When E. coli is exposed to lactose: 12.2 Regulation of Transcription in Bacteria The lac Operon Is Under Negative Control by a Repressor Protein Regulation of the lac operon allows E. coli to conserve energy, making proteins for lactose utilization only when needed The lac operon is inducible (normally “off”, turned “on” as needed) and allolactose is an inducer (effector that increases transcription) 12.2 Regulation of Transcription in Bacteria The lac Operon Is Also Under Positive Control by an Activator Protein CAP (catabolite activator protein) is an activator of the lac operon CAP is controlled by a small effector, cyclic AMP (cAMP), which is produced from ATP The cAMP-CAP complex binds to the CAP site and enhances the ability of RNA polymerase to bind the promoter The level of cAMP, and associated CAP activity, is influenced by glucose Glucose present low cAMP Glucose absent high cAMP 12.2 Regulation of Transcription in Bacteria The lac Operon Is Also Under Positive Control by an Activator Protein Glucose blocks activation of the lac operon; lactose relieves repression of the lac operon c 12.3 Regulation in Eukaryotes: Transcription Factors If eukaryotes do not have operons… how do they turn on (express) multiple genes at one time?