Biology Chapter 18 Lecture Notes (gene expression) PDF

Chapter 18 Regulation of Gene Expression Instructor: Erin Heine, PhD Lecture Presentations by Nicole T...

Chapter 18 Regulation of Gene Expression Instructor: Erin Heine, PhD Lecture Presentations by Nicole Tunbridge and © 2021 Pearson Education, Inc. Kathleen Fitzpatrick Figure 18.1a © 2021 Pearson Education, Inc. Figure 18.1b © 2021 Pearson Education, Inc. CONCEPT 18.1: Bacteria often respond to environmental change by regulating transcription Natural selection has favored bacteria that express only the genes that encode products needed by the cell A cell can regulate the production of enzymes by feedback inhibition or by gene regulation In feedback inhibition, the end product of a metabolic pathway shuts down further synthesis of the product by inhibiting enzyme activity © 2021 Pearson Education, Inc.  Cells can adjust the production level of certain enzymes by regulating expression of the genes encoding the enzymes The control of enzyme production is thus at the level of transcription One basic mechanism for this type of regulation of groups of genes is called the operon model © 2021 Pearson Education, Inc. Operons: The Basic Concept A cluster of functionally related genes can be coordinately controlled by a single “on-off switch” The switch is a segment of DNA called an operator, usually positioned within the promoter An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control © 2021 Pearson Education, Inc.  The operon can be switched off by a protein repressor The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase The repressor is the product of a separate regulatory gene, located some distance from the operon itself © 2021 Pearson Education, Inc.  The repressor can be in an active or inactive form, depending on the presence of other molecules A corepressor is a molecule that cooperates with a repressor protein to switch an operon off For example, E. coli can synthesize the amino acid tryptophan when it has insufficient tryptophan © 2021 Pearson Education, Inc.  By default, the trp operon is on and the genes for tryptophan synthesis are transcribed When tryptophan is present, it binds to the trp repressor protein, which turns the operon off The repressor is in the active state only in the presence of its corepressor tryptophan Thus the trp operon is turned off (repressed) if tryptophan levels are high © 2021 Pearson Education, Inc. Figure 18.3 © 2021 Pearson Education, Inc. Repressible and Inducible Operons: Two Types of Negative Gene Regulation A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription – The trp operon is a repressible operon An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription – The lac operon is an inducible operon © 2021 Pearson Education, Inc.  The lac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose By itself, the lac repressor is active and switches the lac operon off A molecule called an inducer inactivates the repressor to turn the lac operon on – In the case of the lac operon, the inducer is allolactose, an isomer of lactose – Allolactose binds the repressor protein, altering its shape of the repressor so it can no longer bind to the operator sequence © 2021 Pearson Education, Inc. Figure 18.4 © 2021 Pearson Education, Inc.  Inducible enzymes usually function in catabolic pathways; their synthesis is induced by a chemical signal Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high levels of the end product Regulation of both the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor © 2021 Pearson Education, Inc. Positive Gene Regulation Some operons are also subject to positive control through a stimulatory protein, such as cyclic AMP receptor protein (CRP), an activator of transcription When glucose (a preferred food source of E. coli) is scarce, CRP is activated by binding with cyclic AMP (cAMP) – CRP is like a glucose sensor, telling the cell when there is not a lot around to do something about it! © 2021 Pearson Education, Inc.  Activated CRP (low glucose) attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription When glucose levels increase, CRP detaches from the lac operon, and transcription returns to a normal, low level CRP helps regulate other operons that encode enzymes used in catabolic pathways The ability to catalyze compounds like lactose enables cells deprived of glucose to survive The compounds present in any given cell determine which genes are switched on © 2021 Pearson Education, Inc. CONCEPT 18.2: Eukaryotic gene expression is regulated at many stages All organisms must regulate which genes are expressed at any given time Genes are turned on and off in response to signals from their external and internal environments In multicellular organisms, regulation of gene expression is essential for cell specialization © 2021 Pearson Education, Inc. Differential Gene Expression Almost all the cells in an organism contain an identical genome Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome © 2021 Pearson Education, Inc. Differential Gene Expression Abnormalities in gene expression can lead to diseases including cancer Gene expression is regulated at many stages, but is often equated with transcription © 2021 Pearson Education, Inc. Regulation of Chromatin Structure The structural organization of chromatin helps regulate gene expression in several ways – Genes within highly packed heterochromatin are usually not expressed – In euchromatin, gene transcription is affected by the location of nucleosomes along the promoter and the sites where DNA attaches to the protein scaffolding of the chromosome – Chromatin structure and gene expression can be influenced by chemical modifications of the histone proteins of the nucleosome © 2021 Pearson Education, Inc. Histone Modifications and DNA Methylation In histone acetylation, acetyl groups are attached to an amino acid in a histone tail – This appears to open up the chromatin structure, thereby promoting the initiation of transcription The addition of methyl groups (methylation) can condense chromatin and reduce transcription © 2021 Pearson Education, Inc.  DNA methylation -addition of methyl groups to certain bases in DNA – associated with reduced transcription – DNA methylation can cause long-term inactivation of genes in cellular differentiation In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development © 2021 Pearson Education, Inc. Epigenetic Inheritance Although the chromatin modifications do not alter DNA sequence, they may be passed to future generations of cells epigenetic inheritance- the inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence Epigenetic variations might explain cases where one identical twin develops a https:// genetically based disease, whyy.org/episodes/d while the other does not © 2021 Pearson Education, Inc. na-adapted Regulation of Transcription Initiation Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery © 2021 Pearson Education, Inc. Organization of a Typical Eukaryotic Gene and Its Transcript Associated with most eukaryotic genes are multiple control elements, segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription Control elements and the transcription factors they bind are critical to the precise regulation of gene expression in different cell types © 2021 Pearson Education, Inc. The Roles of General and Specific Transcription Factors General transcription factors are essential for the transcription of all protein-coding genes Some genes require specific transcription factors that bind to control elements that may be close to or farther away from the promoter © 2021 Pearson Education, Inc. General Transcription Factors at the Promoter General transcription factors are essential for the transcription of all protein- coding genes – RNA polymerase II requires the assistance of transcription factors to initiate transcription – A few bind to the TATA box within the promoter – Many bind to proteins, including other transcription factors and RNA polymerase II – Only when the complete initiation complex has assembled can the RNA polymerase begin to move along the template strand of the DNA © 2021 Pearson Education, Inc. Enhancers and Specific Transcription Factors High levels of transcription depend on the presence of another set of factors, specific transcription factors Proximal control elements are located close to the promoter Distal control elements, groupings of which are called enhancers, may be far away from a gene or even located in an intron Each enhancer is generally associated with only one gene and no other © 2021 Pearson Education, Inc.  An activator is a protein that binds to an enhancer and stimulates transcription of a gene Other transcription Activators have two factors domains, one that binds RNA pol. II DNA and a second that activates transcription Bound activators facilitate a transcription sequence of protein−protein interactions Site of DNA control element that result in enhanced transcription of a given gene © 2021 Pearson Education, Inc.  The currently accepted model suggests that protein-mediated bending of the DNA brings the bound activators into contact with a group of mediator proteins The mediator proteins interact with general transcription factors at the promoter This helps assemble and position the preinitiation complex © 2021 Pearson Education, Inc. Animation: Regulation of Transcription by Transcription Activators and Enhancers © 2021 Pearson Education, Inc.  Some transcription factors function as repressors, inhibiting expression of a particular gene in several different ways – Some repressors bind directly to control elements, and block activator binding – Others interfere with activators, so they cannot bind the DNA Some activators and repressors my indirectly affect transcription by altering chromatin structure © 2021 Pearson Education, Inc. Combinatorial Control of Gene Activation A particular combination of control elements can activate transcription only when the appropriate activator proteins are present With only a dozen or so control elements, a large number of potential combinations is possible © 2021 Pearson Education, Inc. Coordinately Controlled Genes in Eukaryotes Co-expressed eukaryotic genes are not organized in operons (with a few exceptions) These genes can be scattered over different chromosomes, but each has the same combination of control elements Activator proteins in the nucleus recognize specific control elements and promote simultaneous transcription of the genes © 2021 Pearson Education, Inc. Nuclear Architecture and Gene Expression Loops of chromatin from different chromosomes may congregate at particular sites, some of which are rich in transcription factors and RNA polymerases These transcription factories are thought to be areas specialized for a common function © 2021 Pearson Education, Inc. Mechanisms of Post-Transcriptional Regulation Transcription alone does not constitute gene expression Regulatory mechanisms can operate at various stages after transcription Such mechanisms allow a cell to rapidly fine-tune gene expression in response to environmental changes © 2021 Pearson Education, Inc. RNA Processing In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns – Alternative RNA splicing can significantly expand the repertoire of a eukaryotic genome – It is a proposed explanation for the surprisingly low number of genes in the human genome More than 90% of the human protein-coding genes undergo alternative splicing © 2021 Pearson Education, Inc. Figure 18.14 © 2021 Pearson Education, Inc. Initiation of Translation and mRNA Degradation The initiation of translation of selected mRNAs can be blocked by: – regulatory proteins that bind to sequences or structures of the mRNA – miRNA that bind to the sequences Alternatively, translation of all mRNAs in a cell may be regulated simultaneously – ex: translation initiation factors are simultaneously activated in an egg following fertilization © 2021 Pearson Education, Inc.  The life span of mRNA molecules in the cytoplasm is important in determining the pattern of protein synthesis in a cell Eukaryotic mRNA is more long-lived than prokaryotic mRNA Nucleotide sequences that influence the life span of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3′ end of the molecule © 2021 Pearson Education, Inc. Animation: mRNA Degradation © 2021 Pearson Education, Inc. Protein Processing and Degradation After translation, polypeptides undergo processing: – cleavage – chemical modifications The enzymes controlling these modifications are also subject to control. © 2021 Pearson Education, Inc. Animation: Protein Processing © 2021 Pearson Education, Inc. Protein Processing and Degradation The length of time each protein functions is regulated by selective degradation Cells mark proteins for degradation by attaching ubiquitin to them This mark is recognized by proteasomes, which recognize and degrade the proteins © 2021 Pearson Education, Inc. CONCEPT 18.3: Noncoding RNAs play multiple roles in controlling gene expression Roughly 75% of the human genome is transcribed in at some point in any given cell – A small fraction of DNA codes for proteins – A very small fraction of the non-protein-coding DNA consists of genes for RNA such as rRNA and tRNA – At least some of the genome is transcribed into noncoding RNAs (ncRNAs) Researchers are uncovering more evidence of biological roles for these ncRNAs every day This represents a major shift in the thinking of biologists © 2021 Pearson Education, Inc. Effects on mRNAs by MicroRNAs and Small Interfering RNAs MicroRNAs (miRNAs) are small, single- stranded RNA molecules that can bind complementary sequences in mRNA These can cause degradation of the target mRNA or sometimes block its translation Biologists estimate that expression of at least one-half of human genes may be regulated by miRNAs © 2021 Pearson Education, Inc.  Small interfering RNAs (siRNAs) are similar to miRNAs in size and function The blocking of gene expression by siRNAs is called RNA interference (RNAi) RNAi is used in the laboratory as a means of disabling genes to investigate their function Small ncRNAs are also used by bacteria as a defense system, called the CRISPR-Cas9 system, against viruses that infect them © 2021 Pearson Education, Inc. Chromatin Remodeling and Effects on Transcription by ncRNAs Some ncRNAs can cause remodeling of chromatin structure – In some yeasts, siRNAs re- form heterochromatin at centromeres after chromosome replication Small ncRNAs called piwi- interacting RNAs (piRNAs) induce formation of heterochromatin, blocking the expression of parasitic DNA elements in the genome known as transposons piRNAs help to reestablish appropriate methylation patterns during gamete formation in many animal species © 2021 Pearson Education, Inc.  Long noncoding RNAs (lncRNAs) range from 200 to hundreds of thousands of nucleotides in length – One type of lncRNA is responsible for X chromosome inactivation Because chromatin structure affects transcription and thus gene expression, RNA-based regulation of chromatin must play an important role in gene regulation Some experimental evidence suggest that lncRNAs can act as a scaffold, bringing DNA, proteins, and other RNAs together into complexes These may consequently promote gene expression, directly or indirectly © 2021 Pearson Education, Inc. CONCEPT 18.4: A program of differential gene expression leads to the different cell types in a multicellular organism During embryonic development, a fertilized egg gives rise to many different cell types Cells are organized successively into tissues, organs, organ systems, and the whole organism Gene expression orchestrates the developmental programs of animals © 2021 Pearson Education, Inc. A Genetic Program for Embryonic Development The transformation from zygote to adult results from cell division, cell differentiation, and morphogenesis Cell differentiation is the process by which cells become specialized in structure and function The physical processes that give an organism its shape constitute morphogenesis Differential gene expression results from genes being regulated differently in each cell type Materials placed in the egg by maternal cells set up a program of gene regulation that is carried out as cells divide © 2021 Pearson Education, Inc. Cytoplasmic Determinants and Inductive Signals An egg’s cytoplasm contains RNA, proteins, and other substances that are distributed unevenly in the unfertilized egg Cytoplasmic determinants are maternal substances in the egg that influence early development As the zygote divides by mitosis, cells contain different cytoplasmic determinants, which lead to different gene expression © 2021 Pearson Education, Inc.  The other major source of developmental information is the environment around the cell, especially signals from nearby embryonic cells In the process called induction, signal molecules from embryonic cells cause changes in nearby target cells Thus, interactions between cells induce differentiation of specialized cell types © 2021 Pearson Education, Inc. Sequential Regulation of Gene Expression During Cellular Differentiation Determination irreversibly commits a cell to becoming a particular cell type Determination precedes differentiation Cell differentiation is the process by which a cell attains its determined fate © 2021 Pearson Education, Inc.  Myoblasts are cells determined to form muscle cells and produce large amounts of muscle-specific proteins MyoD is a “master regulatory gene” that encodes a transcription factor that commits the cell to becoming skeletal muscle Some target genes for MyoD (protein) encode additional muscle-specific transcription factors © 2021 Pearson Education, Inc. Figure 18.18 © 2021 Pearson Education, Inc. Pattern Formation: Setting Up the Body Plan Pattern formation is the development of a spatial organization of tissues and organs In animals, pattern formation begins with the establishment of the major axes Positional information, the molecular cues that control pattern formation, tells a cell its location relative to the body axes and to neighboring cells © 2021 Pearson Education, Inc.  Pattern formation has been extensively studied in the fruit fly Drosophila melanogaster Combining anatomical, genetic, and biochemical approaches, researchers have discovered developmental principles common to many other species, including humans © 2021 Pearson Education, Inc. The Life Cycle of Drosophila Flies and other organisms have a modular construction, an ordered series of segments In Drosophila, cytoplasmic determinants in the unfertilized egg provide positional information for placement of body axes even before fertilization After fertilization, the embryo develops into a segmented larva with three larval stages The larva then forms a pupa, which undergoes metamorphosis into the adult fly © 2021 Pearson Education, Inc. Genetic Analysis of Early Development: Scientific Inquiry Edward B. Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus won a Nobel Prize in 1995 for decoding pattern formation in Drosophila Lewis discovered homeotic genes, which control pattern formation in the late embryo, larva, and adult stages © 2021 Pearson Education, Inc. Axis Establishment Maternal effect genes encode cytoplasmic determinants that initially establish the axes of the body of Drosophila These maternal effect genes are also called egg- polarity genes because they control orientation of the egg and consequently the fly © 2021 Pearson Education, Inc. Bicoid: A Morphogen That Determines Head Structures One maternal effect gene, the bicoid gene, affects the front half of the body An embryo whose mother has no functional bicoid gene lacks the front half of its body and has duplicate posterior structures at both ends © 2021 Pearson Education, Inc.  This phenotype suggests that the product of the mother’s bicoid gene is essential for setting up the anterior end of the embryo This hypothesis is an example of the morphogen gradient hypothesis, in which gradients of substances called morphogens establish an embryo’s axes and other features of its form – Experiments showed that bicoid protein is distributed in an anterior to posterior gradient in the early embryo © 2021 Pearson Education, Inc. Figure 18.22 © 2021 Pearson Education, Inc.  The bicoid research was groundbreaking for three reasons: 1. It identified a specific protein required for some early steps in pattern formation 2. It increased understanding of the mother’s role in embryo development 3. It demonstrated that a gradient of molecules can determine polarity and position in the embryo © 2021 Pearson Education, Inc. Evolutionary Developmental Biology (“Evo-Devo”) The fly with legs emerging from its head is the result of a single mutation in one gene Some scientists considered whether these types of mutations could contribute to evolution by generating novel body shapes This line of inquiry gave rise to the field of evolutionary developmental biology, “evo- devo” © 2021 Pearson Education, Inc. CONCEPT 18.5: Cancer results from genetic changes that affect cell cycle control The gene regulation systems that go wrong during cancer are the very same systems involved in embryonic development Mutations that alter normal cell growth and division can lead to cancer © 2021 Pearson Education, Inc. Oncogenes and Proto-oncogenes: cancer ON switches Proto-oncogenes are normal cellular genes that are responsible for normal cell growth and division Oncogenes are mutations in proto-oncogenes that lead to abnormal stimulation of the cell cycle – An oncogene arises from a change that either increases the amount of the proto-oncogene’s product or in the activity of the protein © 2021 Pearson Education, Inc.  The genetic changes that convert proto- oncogenes to oncogenes fall into four main categories – Epigenetic changes – Translocations – Gene amplification – Point mutations © 2021 Pearson Education, Inc. Tumor-Suppressor Genes: cancer OFF switches Tumor-suppressor genes normally inhibit cell division Mutations that decrease protein products of tumor- suppressor genes may contribute to cancer onset Tumor-suppressor proteins normally – repair damaged DNA – control cell adhesion – act in cell-signaling pathways that inhibit the cell cycle © 2021 Pearson Education, Inc. Interference with Normal Cell-Signaling Pathways Mutations in the ras proto-oncogene and p53 tumor-suppressor gene are common in human cancers Mutations in the ras gene can lead to production of a hyperactive Ras protein and increased cell division The Ras protein is a G protein that relays a signal from a growth factor receptor on the cell surface The response to the resulting cascade stimulates cell division © 2021 Pearson Education, Inc. Figure 18.24 © 2021 Pearson Education, Inc.  Mutations in the p53 gene prevent suppression of the cell cycle Suppression of the cell cycle can be important in the case of damage to a cell’s DNA; normal p53 prevents a cell from passing on mutations It also activates expression of miRNAs that inhibit the cell cycle, and can turn on genes directly involved in DNA repair If DNA is irreparable, p53 activates cell “suicide” genes © 2021 Pearson Education, Inc. Figure 18.25 © 2021 Pearson Education, Inc. The Multistep Model of Cancer Development Multiple mutations are generally needed for full- fledged cancer; thus the incidence increases with age At the DNA level, a cancerous cell is usually characterized by at least one active oncogene and the mutation of several tumor-suppressor genes © 2021 Pearson Education, Inc.  Routine screening for some cancers, such as colorectal cancer, is recommended – Suspicious polyps may be removed before cancer progresses Breast cancer is a heterogeneous disease that is the second most common form of cancer in women in the United States; it also occurs in some men – A genomics approach to profiling breast tumors has identified four major types of breast cancer © 2021 Pearson Education, Inc. Figure 18.27 © 2021 Pearson Education, Inc. Inherited Predisposition and Environmental Factors Contributing to Cancer Individuals can inherit oncogenes or mutant alleles of tumor-suppressor genes – Inherited mutations in the tumor-suppressor gene adenomatous polyposis coli are common in individuals with colorectal cancer – Mutations in the BRCA1 or BRCA2 gene are found in at least half of inherited breast cancers, and tests using DNA sequencing can detect these mutations © 2021 Pearson Education, Inc. The Role of Viruses in Cancer A number of tumor viruses can also cause cancer in humans and animals Viruses can interfere with normal gene regulation in several ways if they integrate into the DNA of a cell Viruses are powerful biological agents © 2021 Pearson Education, Inc. Figure 18.UN06 © 2021 Pearson Education, Inc. Figure 18.UN07 © 2021 Pearson Education, Inc.