Regulation of Gene Expression 11

Concept 11.1 Several Strategies Are Used to Regulate Gene Expression Gene expression is tightly regulated. Gene expression may be modified to counteract environmental changes, or gene expression may change to alter function in the cell. Constitutive proteins are actively expressed all the time. Inducible genes are expressed only when their proteins are needed by the cell. It is based on a feedback mechanism Negative regulation—a repressor protein prevents transcription Positive regulation—an activator protein binds to stimulate transcription

Figure 11.1 Potential Points for the Regulation of Gene Expression Points of Potential Regulation of Genes Transcription Processing of mRNA Translation Post-translational

Gene Expression is precisely regulated Maintain stable conditions -hormones To perform cellular functions, keratin in skin, hemoglobin in RBC’s

Concept 11.4 Eukaryotic Gene Expression Can Be Regulated after Transcription Three ways to regulate mRNA translation: Inhibition of translation with miRNAs Modification of the 5′ cap end of mRNA can be modified — if cap is unmodified mRNA is not translated. Repressor proteins can block translation directly— translational repressors

Concept 11.4 Eukaryotic Gene Expression Can Be Regulated after Transcription MicroRNAs(miRNAs)—small molecules of noncoding RNA—are regulators of gene expression. example In C. elegans, soil worm, lin-14 mutations cause the larvae to skip the first lin-4 mutations cause cells to repeat stage one events— thus the normal role for lin-4 is to negatively regulate lin-14, so that cells can progress to the next stage of development. lin-4 codes for miRNA that inhibits lin-14 expression posttranscriptionally by binding to its mRNA. once miRNAs’ transcribed they are guided to a target mRNA to inhibit its translation and to degrade the mRNA.

Figure mRNA Degradation Caused by MicroRNAs

Figure A Repressor of Translation

Protein Stability can be RegulatedRegulated Proteins can be targeted for destruction Begins when an enzyme attaches to a 76 amino acid protein called Ubiquitin (it is ubiquitous in cells) More ubiquitins attach to form a polyubiquitin chain This then binds to a proteasome, a protein complex which contains enzymes. The polyubiquitin is removed and ATP is used to unfold the protein. It is digested into peptides and amino acids. Cyclins in the cell cycle are regulated in this way.

Figure 11.2 Positive and Negative Regulation Gene expression begins at the Promoter where RNA Polymerase binds to initiate transcription A gene cluster with a single promoter is an operon An operator is a short stretch of DNA near the promoter that controls transcription of the structural genes. General Operon Model

Two types of regulatory proteins—transcription factors—control whether a gene is active. Repressors are Negative Activators are Positive, AKA Inducers

Example of gene control Prokaryotes conserve energy by making proteins only when needed. In a rapidly changing environment, the most efficient gene regulation is at the level of transcription. E. coli must adapt quickly to food supply changes in Glucose or lactose.

Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons Generally, inducible (positive) systems control catabolic pathways—turned on when substrate is available Repressible systems (negative) control anabolic pathways—turned on until product becomes excessive

Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons Lac Operon encodes for the lactose enzymes Lac Operon is an Inducible operon (Positive)—turned off unless needed If lactose is present and glucose is low, E. coli synthesizes enzymes. If lactose is absent, synthesis stops. A compound that induces protein synthesis (transcription) is an inducer.

Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons Uptake and metabolism of lactose by E. coli involve three proteins:  -galactoside permease—a carrier protein that moves sugar into the cell  -galactosidase—an enzyme that hydrolyses lactose  -galactoside transacetylase—transfers acetyl groups to certain  -galactosides If E. coli is grown with no lactose present, no enzymes for lactose conversion are produced.

Lac Operon Inducible Gene operon Model Active Repressor-no Transcriptionoperon Gene region

Gene Activation Inactivate Repressor Transcription takes place

Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons The lac operon is only transcribed when a  -galactoside predominates in the cell: In the presence of a  -galactoside, the repressor detaches and allows RNA polymerase to initiate transcription. A repressor protein is normally bound to the operator, which blocks transcription. The key to this regulatory system is the repressor protein.

Repressor Gene Trp Operon A repressible operon is switched off when its repressor is bound to its operator. However, the repressor only binds in the presence of a co-repressor. The co-repressor causes the repressor to change shape in order to bind to the promoter and inhibit transcription. Tryptophan functions as its own co-repressor, binding to the repressor of the trp operon.

Figure 11.9 The trp Operon: A Repressible System Catalysis of Amino Acid TryptophanOperon

Figure 11.9 The trp Operon: A Repressible System

Figure 11.6 Two Ways to Regulate a Metabolic Pathway

To Summaryize Difference in two types of operons: In inducible systems—a metabolic substrate (inducer) interacts with a regulatory protein (repressor); the repressor cannot bind and allows transcription. In repressible systems—a metabolic product (co- repressor) binds to regulatory protein, which then binds to the operator and blocks transcription.

Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes Transcription factors act at eukaryotic promoters. Each promoter contains a core promoter sequence where RNA polymerase binds. TATA box is a common core promoter sequence—rich in A-T base pairs. Only after general transcription factors (TF) bind to the core promoter, can RNA polymerase II bind and initiate transcription.

Figure The Initiation of Transcription in Eukaryotes

Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes Transcription factors recognize particular nucleotide sequences: NFATs (nuclear factors of activated T cells) are transcription factors that control genes in the immune system. They bind to a recognition sequence near the genes’ promoters. The binding produces an induced fit—the protein changes conformation.

Viral Regulation of Genes Viruses are non-living entities which become activated when they have infected a host cell They can contain DNA or RNA as their genetic material They have a protein coat to protect the genetic material

Concept 11.1 Several Strategies Are Used to Regulate Gene Expression Acellular viruses use gene regulation to take over host cells. A bacteriophage will infect bacteria A phage injects a host cell with nucleic acid that takes over synthesis. New viral particles (virions) appear rapidly and are soon released from the lysed cell. This lytic cycle is a typical viral reproductive cycle lysogenic cycle, the viral genome is incorporated into the host genome (prophage DNA) and is replicated too. However, something will trigger this to occur.lysogenic

Concept 11.1 Several Strategies Are Used to Regulate Gene Expression The lytic cycle has two stages: Early stage—promoter in the viral genome binds host RNA polymerase and adjacent viral genes are transcribed Early genes shut down transcription of host genes, and stimulate viral replication and transcription of viral late genes. Host genes are shut down by a posttranscriptional mechanism. Viral nucleases digest the host’s chromosome for synthesis in new viral particles.

Concept 11.1 Several Strategies Are Used to Regulate Gene Expression Late stage—viral late genes are transcribed They encode the viral capsid proteins and enzymes to lyse the host cell and release new virions. The whole process from binding and infection to release of new particles takes about 30 minutes.

Figure 11.3 A Gene Regulation Strategy for Viral Reproduction

Concept 11.1 Several Strategies Are Used to Regulate Gene Expression Human immunodeficiency virus (HIV) is a retrovirus with single-stranded RNA. It infects white blood cells.immunodeficiency HIV is enclosed in a membrane from the previous host cell—it fuses with the new host cell’s membrane. After infection, RNA-directed DNA synthesis is catalyzed by reverse transcriptase. Two strands of DNA are synthesized and reside in the host’s chromosome as a provirus.

Concept 11.1 Several Strategies Are Used to Regulate Gene Expression Host cells have systems to repress the invading viral genes. One system uses transcription “terminator” proteins that interfere with RNA polymerase. HIV counteracts this negative regulation with Tat (Transactivator of transcription), which allows RNA polymerase to transcribe the viral genome.

Figure 11.4 The Reproductive Cycle of HIV

Figure 11.5 Regulation of Transcription by HIV

Table 11.1 Transcription in Bacteria and Eukaryotes