Week 8.1_Prokaryotic Gene Expression

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Gene Expression I: Prokaryotes Week 8 – Monday, October 9, 2023
Quiz #2 will be open on Friday, October 13, 2023, after class, at 10:30AM and close the same day at 11:59PM. The quiz will be on Laulima, under Test and Quizzes. There will be 10 questions. Once you start the quiz, you will have 15 minutes to complete the quiz. Covers the first two weeks of Module #2 Open books and open notes. Updates and reminders
Week 8 Learning Objectives Understand how prokaryotes use operons to regular gene expression. Understand how chromatin affects how eukaryotic genes are expressed Learn the stages of the cell cycle and how it is regulated (and becomes dysregulated in disease)
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Review: Central Dogma Central Dogma: Transcription: DNA to RNA. Translation: RNA to Protein. What is getting transcribed? Genes! DNA RNA Protein
Remember the differences between prokaryotes and eukaryotes Prokaryotes Eukaryotes DNA free in cytoplasm. Transcription and translation occur almost simultaneously in cytoplasm. No processing! DNA packaged into chromatin (around histones). RNA is processed. Transcription and translation occur in different locations.
Gene Expression Are genes always on? Some are, but most are only ‘on’ when needed. Why would a cell want to express some genes only sometimes? Different cell types require different genes Rapid response to changes in the environment DNA RNA Protein DNA RNA Protein
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How does a cell know to turn a gene on or off? Promoters are part of gene that is responsible for the beginning of transcription. Activator proteins attach to the promoter and result in RNA polymerase attaching and starting transcription Gene Promoter RNA polymerase
To understand gene expression, lets start with an example in prokaryotes How many genes are in E. coli ? There are around 5,000 genes. But their organization is unique. And not all of them are always. Expressed. In a bacterium, like E. coli , glucose is usually used as energy source. If glucose isn’t around – they will use lactose. But lactose is a disaccharide. It needs to be enzymatically broken down to monosaccharides, glucose and galactose before E. coli can utilize the sugars for energy. Glucose Lactose a disaccharide a monosaccharide
E. coli Gene Expression: How To Turn on Lactose Metabolism Genes? Prokaryotes arrange genes into operons: A collection of genes whose proteins work in same pathway. These genes are lined up one after the other and therefore are controlled by the same promoter. An additional regulatory sequence called the operator works with promoter to control gene expression. Regulate the amount of transcription Three genes for lactose metabolism
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When are genes expressed? A. All genes are always expressed. B. Genes are only expressed when they are needed. C. Some genes are always expressed, but mostly they are only expressed when they are needed.
How Does the lac Operon Control Gene Expression of These Three Genes? The lac operon is an example of a typical inducible operon . It has proteins that bind to activate or repress transcription depending on the need of the cell. For example, Escherichia coli , by default, utilize glucose as its energy source. But when glucose is unavailable or low, other sugars can be used as energy sources. One that is commonly utilized is lactose. That’s where the lac operon comes in. Two conditions must be met for lac operon to be activated: Level of glucose must be low or absent. Lactose must be present!
How Does the lac Operon Control Gene Expression of These Three Genes? When glucose is available (default), a repressor protein normally binds to a sequence of the operator between the promoter and structural genes blocks transcription in lac operon. This blocks the lacZ of lac operon from transcription of beta-galactosidase, the enzyme that breaks down lactose into glucose and galactose. When glucose is available, lactose is not needed. Blocking formation of beta-galactosidase save cellular energy.
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Glucose is typically utilized by E. coli for energy. When glucose levels are low, it can go to other sources for energy. Typically, lactose is utilized, but new genes to process lactose must be transcribed. When glucose levels drop, cyclic AMP (cAMP) accumulates in the cell. Accumulating cAMP binds to positive activator protein, catabolite activator protein (CAP): A protein that binds to the promoters of operons that control processing of alternative sugars, lactose in this case. cAMP binds to CAP, which then binds to the promoter region of genes that are needed to use lactose. Without cAMP, CAP is unable to bind to the promoter and transcription of lactose occurs slowly. Catabolite Activator Protein (CAP)
Transcription of lactose without and with cAMP. Catabolite Activator Protein (CAP) In the absence of cAMP, CAP cannot bind the promoter. Transcription of lactose occurs very slowly. In the presence of cAMP, CAP bind the promoter and transcription of lactose activity increase.
How Does the lac Operon Control Gene Expression of Three Lactose Genes? The lac operon is an inducible operon where proteins bind to activate transcription. The lac operon encodes genes to acquire and process lactose from the environment. In order for this to occur: Glucose level must be low or absent . This allows cAMP to accumulate that binds to CAP that makes transcription more effective. Lactose must be present . When present, allolactose, derived from lactose, binds to the lac repressor, changing its shape so that it cannot bind to the lac operator, allow transcription of the genes to occur. Without CAP and cAMP transcription is slow! allolactose
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When CAP binds cAMP, then bind to promoter, transcription increases significantly. How Does the lac Operon Control Gene Expression of These Three Genes?
What Is Produced From the lac Operon? DNA RNA Proteins The lac operon produces a single polycistronic mRNA molecule This mRNA gets translated into the three different proteins!
Operons encode genes that work in the same pathway lacY allows lactose to pass into the cell lacA encodes galactoside acetyltransferase (function is not fully understood!) beta-galactosidase lacZ cleaves lactose into two monosaccharides
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Summarizing the Lac operon Signals that Induce or Repress Transcription of lac Operon Transcription of lac Operon occurs only when glucose is absent and lactose is present.
When is the rate of the genes transcription of lactose most rapid? A. When glucose is present, but lactose is absent. B. When glucose is present and lactose is present. C. When glucose is absent and lactose is present. D. When glucose is absent and lactose is present and cAMP binds to CAP and they bind to the promoter. E. When some glucose is present and lactose is present.
The trp Operon Bacteria needs amino acids to make their protein and are able to synthesize many amino acids and can absorb them from the environment as well. One example of such an amino acid is Tryptophan . The tryptophan operon consist of five genes. Genes are transcribed into a single mRNA, which is translated to all five enzyme.
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The trp Operona When tryptophan is present in the environment, tryptophan molecule binds to repressor, changes its shape and enable tryptophan to bind to the operator preventing transcription. When tryptophan is not present, repressor by itself cannot bind to operator and transcription can occur in the trp operon.
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Summarizing Gene Expression in Prokaryotes The lac operon: lac operon is regulated by a repressor. If lactose is absent and glucose is present, repressor binds to operator preventing transcription of lac operon. Lactose and glucose is present, allolactose binds to repressor, changes its shape and it cannot bind to operator, allowing transcription to occur, but at a slow rate because presence of glucose prevents cAMP from accumulating and binding to CAP and promoter. Only when glucose is absent and lactose is present will transcription occur at more rapid rate because cAMP accumulates and binds to CAP and then to promoter and presence of lactose will prevent binding of repressor to operator.
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Human Genome Has 20,000+ Genes Remember: genes are stretches of DNA that encode proteins Organisms vary widely in how many genes are present Species Number of genes Homo sapiens 21,000 Mus musculus 24,000 Saccharomyces cerevisiae 6,000 Caenorhabditis elegans 20,000 Drosophila melanogaster 13,000 Escherichia coli 5,000 1918 flu virus 8 Adapted from: Pray 2008, Nature Education Tumpey et al., 2005 Science
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A Few Words About Chromosomes Chromosomes: Threadlike structure of nucleic acids and protein found in the nucleus of eukaryotic cells, carrying genetic information in the form of genes. Humans have 46 (23 pairs) chromosomes. Each pair is said to be homologous , each having the same genes. One of each chromosome pair is inherited from your mom and the other from your dad.
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A Few Words About Chromosomes Karyotype of 23 pairs of human chromosomes . One of each chromosome pair is inherited from your mom and the other from your dad . Each pair are homologous chromosomes. Black bands are the genes. A gene is the segment of DNA that controls all traits of organisms. mom dad
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A Few Words About Chromosomes Homologous chromosomes: Provides 2 copies of each gene Order of genes on each chromosome is the same. One from dad and one from mom in each pair. Does the genes on each homologous carry the same information?
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A Few Words About Chromosomes No, usually they will have different information. The corresponding genes of homologous chromosomes are called alleles : One of two or more alternative forms of a gene that found in the same place on homologous chromosomes. Example of coat colors in Labrador dogs, alleles of the parents are the same. Parents BB bb The BB and bb represents pairs of alleles in the dad and mom labs that codes for their coat color, black and chocolate, respectively. If you cross the parents.
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A Few Words About Chromosomes The puppies will be all black, but now carry the alleles Bb because they inherited B from one parent and b from the other. All black coated puppies, but each carry an allele for black and chocolate coat color. b B
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Phenotypes: measurable traits Biologists use the term phenotype to refer to visible traits such as coat color of the labs. Phenotype traits can also be chemical: Concentration of calcium, ability to produce a toxin. The genetic makeup of a trait is its genotype . For example, the genotype of the puppies in the last slide is Bb, indicating that the puppies are heterozygous for coat color. This means that the alleles are different, B=black coat and b=chocolate coat. Why didn’t any of the puppies have chocolate coats? The parents of the puppies were homozygous for coat color, meaning that both alleles were the same, BB=black coat and bb=chocolate coat. Some traits are influenced by one gene, but most involve MANY genes.
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Genotype and environment affect phenotypes Our traits are controlled by our genetics (G) as well as the environment (E).
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