Ap Bio Gene Regulation

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Importance of gene regulation

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To control the amount of gene product present in the cell, to allow cells to adjust with changing conditions, expression of appropriate genes at proper times and to prevent the waste of cellular resources and energy

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Prokaryotic Regulation

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Bacterial cells regulate the turning of genes “on” or “off” for transcription and translation, so that the appropriate amount of protein is produced

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Feedback mechanisms

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To control the amount of gene product made, bacterial cells are able to use these which allow them to repress (“off”) gene expression of a constantly made protein or induce (“on”) gene expression of a protein that is not constantly made

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Operon

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In bacterial regulation, this is repressed or induced to undergo transcription and translation, is a cluster of genes and DNA that functions as a single unit in the transcription of mRNA

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Structural genes

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The genes to be expressed

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Operator

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A segment of DNA between the promoter and the structural genes to be expressed, that acts as an “on” or “off” switch for transcription

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Regulator gene

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Codes for production of a repressor and is found upstream of the operon

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Repressor

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A protein that turns the operon “on” or “off”, is an allosteric enzyme that had an active form and inactive form

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Active repressor

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Will turn the operon “off.” By binding to the operator the repressor blocks RNA polymerase from binding, so the operon is “on” for transcription

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Inactive repressor

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Cannot bind to the operator therefore RNA polymerase is not blocked from binding, so the operon is “on” for transcription

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Repressible operon

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Is the one that is normally “on” to constantly manufacture a product from gene expression but is able to be turned “off” when the product isn’t needed, the repressor is inactive and does not block RNA Polymerase from binding for transcription Ex: trp operon

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Repressible enzymes

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Are produced continuously until production is repressed by a corepressor, are for the synthesis of materials in a cell (anabolic pathways) Ex: The enzymes for the synthesis of Tryptophan

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Inducible operon

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Is the operon that by default the switch is “off” and does not allow transcription of the genes, the repressor is active, blocking RNA Polymerase from binding for transcription Ex: Lac Operon

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Inducible enzymes

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Enzymes whose production requires an induced which is an allosteric inhibitor that binds to the repressor, causing it to assume an inactive form, are used in catabolic pathways Ex: Lactase

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Lactase

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The enzyme for lactose metabolism

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Trp operon

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In E.Coli, it codes for 5 enzymes needed for the production of tryptophan, the 5 genes that code for the enzymes are next to each other and are served by one promoter which allows all of the genes to be expressed/not expressed together

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Trp operon

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By default it is continuously on, the repressor is inactive so the genes are on for expression

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Tryptophan

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When an excess of this is present, these molecules act as the corepressor binding to the allosteric site of the repressor which causes the repressor to take its active form, the active repressor binds to the operator, switching the operon “off” and no more of this is made

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Lac operon

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Is an inducible operon, by default it is switched “off”, the regulatory gene in this operon produces the repressor in its active form, it immediately binds to the operator blocking RNA polymerase which prevents transcription of the genes involved in lactose metabolism

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Lac operon

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Contains 3 lac genes that code for enzymes used in the metabolism of lactose a disaccharide milk sugar

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Lac operon

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To turn this “on” an inducer will bind to the repressor causing it to assume an inactive form, the inactive form can no longer bind to the operator and block RNA polymerase, so Transcription can occur

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Allolactose

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The inducer for the lac operon, the presence of lactose induces the production of enzymes necessary for its own digestion

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Inducer

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Induces the system to produce necessary proteins

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Eukaryotic organisms

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can be unicellular or multicellular, they include protists, fungi, plants and animals, they have multiple chromosomes inside a nucleus, the typical genome is much larger than prokaryotic genomes

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Eukaryotes

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Have histones associated with DNA, have membrane bound organelles specialized for different functions, in the multicellular types cell specialization is crucial, have simple polysaccharide cell walls (algae, fungi and plants)

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Eukaryotes

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Carry out cell division by mitosis (nuclear division) and meiosis (egg and sperm production)

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Eukaryotic cells

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Are larger and more complex than prokaryotic cells

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Noncoding RNA molecules

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Play many roles in regulating gene expression in eukaryotes

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Mutlicellular Eukaryotes

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In these, gene expression plays a vital role in regulation of embryo development and cell differentiation

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Cancer

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Results from accumulated mutations in proto-oncogenes and tumor suppressor genes

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Purposes of eukaryotic gene regulation

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To prevent the waste of cellular resources and energy, and to maintain stable internal conditions otherwise known as homeostasis while facing changing conditions

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Unicellular and multicellular Eukaryotes

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Both must continually turn genes on and off in response to signals from their external and internal environments

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Points of control

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The chromatin structure, transcription, post-transcription mRNA processing, Post-Translation and protein degradation

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DNA Packing

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As well as the location of the promoter to the nucleosomes, it controls which genes are available for transcription, if genes are not accessible to RNA polymerase then they cannot be transcribed

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Euchromatin structures

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Allows RNA polymerase access to the promoter so transcription occurs

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Heterochromatin

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The DNA is tightly wrapped around histones and there is no access to the promoter so there is no transcription and the genes are turned "off"

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Chemical modifications

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Are done to the histones or the DNA and also influence both chromatin structure and gene expression

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Histone acetylation

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Is an epigenetic process in which acetyl groups (-COCH3) attach to histone tails which causes a conformational change in histone protein structure so DNA unwinds, transcription factors have access to the genes which enables transcription and so the genes are turned "on"

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Epigenetics

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The study of changes in gene expression that occur without any changes to DNA sequences, there are chemical modifications that alter the expression of genes

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Methylation

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IS the addition of methyl groups (-CH3) to the 5th carbon of the cytosine bases in DNA by the enzyme DNA methyltransferase, this can cause long term inactivation of genes or chromosomes

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DNA Methylation

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Is an epigentic mechanism used by cells to control gene expressuon, usually suppressing expression, it commonly silences the gene and keeps it in the "off' position, the methylated cytosine blocks transcription factors and the genes are turned off, no transcription

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Methylation

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To date, genes involved in the regulation of the cell cycle, DNA repair, growth, angiogenesis, and apoptosis are all inactivated by this

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Tumor suppressor genes

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The methylation of these genes turns the genes off and promotes the formation o cancer cells

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Genomic imprinting

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In this, methylation regulates which genes either the maternal or paternal are silenced and not expressed during embryo development

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Epigenome

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Consists of the chemical compounds that modify or mark the DNA and change the way genes are expressed

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Epigenetic markers

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Can be passed on during cell division from one generation to the next, it is believed that these can be passed on for two generations at least

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DNA Methylation

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Regulates gene by inhibiting the binding of transcription factors and RNA polymerase to DNA

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Histone modification

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Activates expression

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RNA Associated silencing

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Is a process in which genes can be turned off by small non-coding RNAs

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promoter

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A control sequence on DNA for the binding of RNA polymerase and transcription factors for the "base" rate of transcription

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Enhancers

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Control sequences on DNA, upstream of the promoter and gene

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Activators

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Proteins (transcription factors) specific for cell type, gene function and enhancers specific in order to bind the enhancer and increase the rate of transcription

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Activators and enhancers

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The binding of these facilitates DNA bending bringing the enhancer in contact with the promoter region

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Post-transcription control

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The addition of the 5' and 3' caps to pre-mRNA, excision of introns and splicing of exons, and alternative mRNA splicing, involves protein processing and protein degradation

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Proteolytic processing

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The inactive protein is converted to an active form by the removal of a portion of the polypeptide chain

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Chemical modification

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Especially for cell communcation is by adding or removing functional phosphate groups to alter the activity of a protein

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Kinases

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Enzymes that add a phosphate group and activate a protein

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Phosphatases

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Remove phosphate groups which inactivates a protein

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proteases

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Enzymes that degrade proteins

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mRNA

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The life span of this determines the amount of protein synthesis, the 5' and 3' caps stabilize it so it can last from hours to weeks for protein synthesis

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mRNA degradation

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AKA blocking of translation ( gene silencing) occurs as a result of RNA interference (RNAi) by the actions of small interfering RNA (siRNA) and micro RNA (miRNA)

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siRNA and miRNA

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They can bind to mRNA and block translation, they can bind to, cleave and degrade mRNA, binding to euchromatin promotes the formation of heterochromatin preventing transcription

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cell differentiation

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In multicellular organisms during embryo development, a zygote gives rise to many different cell types by a process of specialization in structure and function called....

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Cell types

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Are organized into tissues, organs, organ systems, and the whole organism through morphogenesis

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Morphogenesis

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physical processes that produce structures and shape

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Differential gene expression

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The expression of different sets of genes by cells with the same genome, each cell of a multicellular eukaryote expresses only a fraction of its genes. In each type of differentiated cell a unique subset of genes is expressed.

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Cytoplasm

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_________________________ of an unfertilized egg contains maternal mRNA, proteins, and other substances that are unevenly distributed.

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Cytoplasmic determinants

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are the maternal substances in the egg that influence early embryo development, As the zygote divides by mitosis, cells will receive different cytoplasmic determinants

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Determination

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commits a cell to its final fate. “they still look like each other, have not yet undergone differentiation," precedes Differentiation

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Induction

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In this process, signal molecules from embryonic cells cause transcriptional changes in nearby target cells, The other important source of developmental control is the environment around the cell, induction signals from nearby embryonic cells.

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Embryonic induction

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plays a role in the development of tissues and organs in most animals.

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Cell differentiation

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is the process by which cells become specialized in structure and function, occurs through differential gene expression

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differentiated

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When a cell becomes_______________, a specific set of genes are turned “on” and expresses for tissue-specific proteins, This expression is controlled at the level of transcription.

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Morphogenesis

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is the development of spatial organization of tissues, organs and systems into their locations (pattern formation) under the control of body plan genes, known as homeotic genes.

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homeotic genes

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The three main active in early embryo development are: HOX genes, Sonic Hedgehog genes and SHOX genes.

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Hox genes

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A highly conserved group of developmental genes involved in establishing the anterior-posterior axis (longitudinal axis) and the identity of each body segment, The first was discovered in Drosophila

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Sonic hedgehog gene

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plays a critical role in patterning of vertebrates, including the brain and spinal cord, the axial skeleton and limb formation.

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SHOX gene

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is located on each of the sex chromosomes ( X and Y) in an area called the pseudoautosomal region, is part of the family of homeobox genes, which act during early embryonic development to control the formation of the skeleton.

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Cancer

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The genes that normally regulate cell growth and division are the types of genes when mutated are associated with this disease, There are two families of genes associated with this disease

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Proto-oncogenes

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are normal cellular genes that code for proteins that stimulate normal cell growth and cell division. Ex: ras gene, A mutation that makes this excessively active, converts it to an oncogene, which promotes uncontrolled cell division, cancer.

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Tumor-suppressor genes

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These genes code for proteins that inhibit abnormal cell division & repair of damaged DNA. Ex: p53 gene – If the damage in DNA is irreparable, p53 activates “suicide genes” that initiate apoptosis .

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p3 gene

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A mutation in this reduces the activity of the p53 protein, which can lead to uncontrolled cell division, cancer, is mutated in about 50% of human cancers

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Normal cells

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are converted to cancer cells by the accumulation of multiple mutations affecting proto-oncogenes and tumor suppressor genes

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Certain viruses

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promote cancer by integration of viral DNA into a cell’s genome

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HeLa cells

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HPV DNA was inserted into the most active proto-oncogene in the cells of the cervix, resulting in the aggressive form of cervical cancer

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Viral proteins

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can also inactivate p53 or other tumor suppressor genes.

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Cancer

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Individuals who inherit a mutant oncogene or tumor suppressor allele have an increased risk of developing certain types of_______________.

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Colon cancers

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About 15% of these involve inherited mutations in the tumor-suppressor gene APC.

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Breast cancer

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About 5-10% of these cases are linked to an inherited mutant allele for either the BRCA1 or BRCA2 genes, both of which are tumor suppressor genes involved in DNA damage repair.

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UV radiation

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_________________ in sunlight and cigarette smoking may contribute to cancer through their DNA-damaging effects