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This 23 page Study Guide was uploaded by Tatiana Tabares on Monday December 14, 2015. The Study Guide belongs to EBIO 1210-001 at University of Colorado taught by Dr. Barbara Demmig-Adams in Fall 2015. Since its upload, it has received 248 views. For similar materials see General Biology 1 in Biology at University of Colorado.
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Date Created: 12/14/15
EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations EXAM 4 ● Gene expression: how information stored in your DNA sequences comes to life in universal processes. Gene Expression = DNA directs the synthesis of proteins Two Universal Steps 1. Transcription 2. Translation 1. Easing in How do we get from a sequence of nucleotides to a trait in the organism? ● The Central Dogma: ○ DNA > RNA > PROTEIN ● Protein is a polymer of amino acids ○ Transcription > RNA Processing > Translation ● In Eukaryotes ○ There is a PremRNA ○ Then there is a final mRNA ○ Transcription and RNA processing occurs in the nuclear envelope ○ Translation occurs in the cytoplasm 2. Transcription in Detail Successful transcription requires 3 basic processes 1. Initiation (1) figure out where to start reading DNA and (2) actually begin making mRNA 2. Elongation make the full length mRNA transcript 3. Termination INITIATION ● promoter the start here signal ● the promoter is not transcribed or translated ● "upstream" of where the gene is a promoter ● whole promoter = several dozen nucleotides How build mRNA with an enzyme right? RNA polymerase ● reads one strand of DNA and builds the mRNA ● it can’t bind to the promoter on its own (in eukaryotes) ● only binds when certain transcription factors are present ● RNA can only synthesize in a 5' to 3' direction EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ○ therefore its template goes 3' to 5' reads antiparallel ● with transcription factors in place, RNA polymerase can now bind to DNA at the right place and begin transcription of the gene ELONGATION ● RNA polymerase untwists DNA, makes mRNA 1020 base pairs of DNA ● you get a U to pair with an A but T still pairs with A ○ Uracil ● RNA polymerase moves along, the new RNA molecule peels away from the DNA, and the helix retwists TERMINATION ● bacteria termination sequence ● Describe the relationship between a DNA molecule and a gene. In doing so, define what a gene is in molecular terms. ● The molecule of heredity ● DNA that directs the program that takes raw materials and turns them into YOU ● Contains your genome, genes Known: ● much about cell chemistry ● the work of Mendel, Morgan, and many others > many findings suggesting chromosomes/DNA contain heredity molecule 1. DNA is a double stranded molecule 2. Two strands form a double helix DNA is A nucleic acid is a polymer of made of nucleotide monomers A nucleotide consists of: 1. a nitrogenous base 2. a sugar 3. a phosphate group EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ● The sugar and phosphate group are the same for all nucleotides ● The base is what varies ● The sequence of nucleotides with different bases forms the code containing all hereditary information There are only 4 nitrogenous bases > four possible nucleotides ● diff sequences of the 4 possible nucleotides are what make them different ● Describe how information is stored in a nucleic acid sequence. Erwin Chargaff looking at chemical composition of DNA in any particular species: % adenine (A) = % thymine (T) % guanine (G) = % cytosine (C) ● Chargaff's Rule (above) In an UNPUBLISHED REPORT, Franklin postulated ● The strands of DNA run in an antiparallel manner (one is upside down relative to the other one) ● The phosphate group in a single nucleotide is attached to the 5' (five prime) carbon atom of the sugar ● Sugar (deoxyribose) 3' (three prime end) ○ Like lego bricks top has dots (5') bottom has holes (3') ● adjacent nucleotides are linked phosphate to 3' carbon atom ○ forms the backbone ● antiparallel arrangement allows proper base pairing ○ hydrogen bonding keeps the two strands together and Chargaff's rule DNA replication is not trivial 1. Open the replication bubble , separate the two strands 2. Unwind the helix Specialized enzymes keep the process running smoothly The unity of all life EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ● The genetic code is shared by all life on Earth ● Genes are nucleotide sequences, hundred or thousands of nucleotides long ● List the major steps of gene expression. see above ● List the major steps and molecules involved during “transcription”; describe the roles played by the main molecules that are involved; describe what is accomplished by transcription. 3. RNA processing in Eukaryotes Before RNA transcripts leave the nucleus, they are modified 1. alteration of ends 2. cutting out some of the middle R NA Splicing ○ introns in the middle ● cut out ○ exons will be expressed ● spliced back together ○ Spliceosome ○ Any mutation that alters splicing can cause a different protein, or different form of a protein, to be produced. ○ Some introns are "selfsplicing" catalyze their own excision 3. ● offers cell a way of controlling when and where protein is produced ● Alternative splicing: multiple control mechanisms and involvement to human disease ● Alternative splicing occurs NORMALLY for MORE THAN HALF of our proteins 4. The Genetic Code ● Amino Acids 20 are commonly used by most organisms ● The genetic code consists of 3 letter codons: ○ sequence of 3 nucleotides = specification of amino acid ○ each triplet is called a odon Some notes on Codons: 1. When we say "codon", we are referring implicitly to the RNA triplets EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations 2. Codons are read in the 5' to 3' direction, because that is how they are read by the translation machinery 3. Codons don't overlap (300 nucleotides encode 100 codons) Transcription Factors ● The first step in transcription is binding transcription factors (proteins) to the promoter of the gene. (BUT THIS WASN'T THE WHOLE STORY) ● In addition to the promoter, and additional regulatory sequence, called an enhancer, is generally involved ○ An enhancer for a specific gene tends to be located far from the gene ○ For TFs to bind the enhancer and the promoter at the same time, the DNA between the enhancer and the promoter bends ● All cells have the same genomes, so they all have the same enhancers and promoters ○ Cells are ultimately diff. from each other because they have different transcription factors ● There are only several thousand TFs, but millions of cell types ○ Cells are defined by the combination of TFs they have ● an enhancer often has around 10 c ontrol elements ● the same individual control element may be used in the regulation of many different genes ○ different cell types will have some of the same TFs present, but not all ○ Cells acquire their unique set of TFs during DEVELOPMENT ● List the major steps and molecules involved during “translation”; describe the roles played by the main molecules that are involved; describe what is accomplished by translation. 5. Translation in detail Translation (bacterial example): ● The structure of tRNA ● The ribosome ○ initiate EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ○ elongate ○ terminate The Ribosome What does it do? ● Facilitates the coupling of mRNA codons with tRNA anticodons ● Provides a physical site for translation in which all the participating moecules find their proper spatial arrangement ● Catalyzes formation of peptide bonds All those RNA molecules... ● RNA = ribonucleic acid ● premRNA = the RNA transcript produced initially during transcription in eukaryotes ● mRNA = messenger RNA = the (processed) RNA transcript molecule that will actually be translated ● tRNA = transfer RNA = the RNA molecule that brings amino acids to the ribosome ● rRNA = ribosomal RNA = RNA = RNA that forms the structure of the ribosome initiation of translation ● small ribosomal subunit binds both mRNA and initiator tRNA, then "scans" for start codon correct reading frame ● we are now ready to elongate ● Define what a virus is; compare and contrast the major properties of viruses with those of living organisms. 1. Viral Structure What is a Virus? ● particles that infect cells ● nucleic acids with protein coats ○ nucleic acid contains instructions for....making more virus particles ● obligate intracellular parasites ● Must have a well defined host range ● Viruses are NOT considered to be living things How does a virus do its business? EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations 1. Virus enters cell cell manufacturers viral proteins AND copies of virus' genome 2. Virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP,... 3. assembly of new viruses 4. new virus particles break out of the cell ● Describe different ways that the genetic information of viruses can be stored. Give and explain examples of viruses in which the process of gene expression is different from the “central dogma”. 2. Animal Viruses ● There are 2 key variables used to classify viruses that infect animals: ○ DNA or RNA? ○ single stranded or double stranded ● Many viruses that infect animals have a membranous "envelope" derived from host cell ● Viruses have many ways of parasitizing the host cell's machinery ● SOME VIRUSES DEFY THE CENTRAL DOGMA 3. How viruses make you sick A) damage or kill cells (with enzymes) B) Cause infected cells to produce toxins C) Envelope proteins that are toxic ● Symptoms come from your own immune system (this is most of what you are feeling) D) However MOST symptoms and most of the damage to the body comes from your own immune system! E) The immune system detects virusinfected cells and mounts and inflammatory response ● infected cells kill themselves by apoptosis ● Fluids, immune cells accumulate in tissues to clean out dead cells (inflammation) ● Fever, mucus, soreness are all caused by the strong inflammatory response ● Death can result from uncontrolled inflammation Vaccines are Overwhelmingly Safe ● Easily preventable illnesses are happening because of MISINFORMATION and unfounded fears about vaccines EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ● If you care about your own health, and the health of the people around you you should get all the vaccinations that are recommended by the vast majority of doctors 4. The Origin of new viruses and H1N1 Novel Pathogens in the Modern Day 1. Most newlyemerging pathogens are viruses, especially RNA viruses 2. Most that are new to humans come from animal reservoirs (wild or agriculture) 3. Emergence of new pathogens often associated with changes in human ecology a. exotic trade b. agriculture c. "bushmeat" d. population density and travel 4. When newly acquired from animals, most pathogens are NOT highly transmissible between humans at the beginning H1N1 ● What are influenza viruses? What is in the name? ● Why have they repeatedly reached pandemic status in humans? ● Humans are infected by 3 main groups of influenza viruses: ○ influenza A ○ influenza B ○ influenza C ● H1N1 is influenza A What does H1N1 stand for? ● Naming convention referring to two proteins in viral envelope of influenza type A viruses ● These are Hemagglutinin and Neuraminidase ● There are 16 types of "H" and 9 types of "N" in birds ● Only 3 types of H (1,2,3) and 2 types of N (1,2) are common in humans ● A recent scare in far eastern Asia involved the jump of H5N1 influenza virus from birds to humans Mutation = any change in 1. Where do mutations come from? ● Damage to the DNA molecule (toxins, carcinogens, etc.) EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ● Errors in DNA replication 1. How do mutations affect gene expression? ● Substitution ○ switching one nucleotide for another can cause a different amino acid to be attached. ○ switching one nucleotide for another can cause NO CHANGE in the protein because there are multiple ways to code for certain proteins ● Insertions or Deletions ○ Inserting an extra nucleotide, or deleting a nucleotide causes a frameshift. This almost always results in a shortened protein being made. ○ Frameshift can cause a change downstream for the rest of the DNA strand ● How do we know what "reading frame" to use, that is where to start translating the mRNA and how to break it into codons? ○ Some kind of start signal in the mRNA sequence. ● The first codon (AUG) establishes the START POINT and the READING FRAME ● (AUG) = start codon ● Define “reassortment” and explain the consequences it can have for the evolution of new viruses. Gene regulation and development: how genes are “switched on” and “switched off” to maintain a healthy organism. Reassortment possible when multiple virus types infect the same individual host and get into the same cell ○ think "viral sex" ● Vaccines are derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the actual microbe ● Overwhelming benefits:disease reduction ● We actually exploit reassortment in the production of "live attenuated" influenza vaccine ● Explain why gene regulation is necessary in all organisms, even those that are single celled. EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ● Explain why gene regulation is essential for multicellular organisms (a) during development and (b) with regard to the existence of specialized tissues. Gene Regulation t urning genes on and off when needed Why do genes need to be regulated? ● Every cell in our body has the same genome (set of genes) ● However, our body consists of trillions of cells and millions of distinct cell types. Why not express all your genes in every cells? 1. It would be impossible to have differentiated structures/organs 2. Within one cell, not all of that cell's functions are needed all the time 3. Waste of energy/molecules to express genes whose products are not needed 4. Some functions are mutually exclusive; two enzymes may have opposite functions Examples: different cell types within a human ● Muscle cells express muscle actin and myosin ● Hair and nail cells express k eratin ● Blood cells express hemoglobin ● Describe ways in which cells and tissues “know” how to develop during the growth of an organism. see above ● Compare and contrast general mechanisms of gene regulation in bacteria and eukaryotes. ● Describe the basic features of a bacterial operon; using the example of the trp operon, explain how the genes of an operon can be “turned on” or “turned off” as needed by a bacterial cell. ● Molecules can act as signals by directly influencing transcription ● many bacterial genes are switched "on" or "off" by metabolic status of cell EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations Tryptophan synthesis in E. Coli: a specific example meant to illuminate general principles 1. turning multiple genes "on" and "off" in concert a. all 5 genes are clustered together b. single promoter serves all 5 genes one big transcriptional unit c. one long mRNA is translated into 5 polypeptides 1. doing so at the appropriate times / expressing the genes of the operon at the right time a. the operator is the "onoff switch" that controls the access of RNA polymerase to the genes b. For the trp operon, RNA polymerase can bind when nothing is bound to the operator i. Operons are generally NOT a feature of Eukaryotes ii. Operator is part of the promoter (controls on/off) iii. regulatory gene that codes for a repressor protein (inactive at first until there is a lot of it in the system) c. d. A system of negative feedback How do we stop repression? ● binding of tryptophan to repressor is reversible ● Whether most repressor molecules are active or inactive depends upon relative concentrations of tryptophan and repressor protein ● Transcriptional regulation is the most important level of gene regulation, since it is the main on/off/dimmer switch ● Transcriptional regulation determines whether a gene is turned on/off and at what level (i.e. how much protein is ultimately expressed). 1. Bacterial Example 2. Eukaryotes a. A few generalities b. Example: Insulin regulation and diabetes ● There are many points at which gene expression can be regulated in eukaryotes EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ● Transcriptional regulation is the most important level of gene regulation, since it is the main on/off/dimmer switch ● Transcriptional regulation determines whether a gene is turned on/off and at what level (how much protein is ultimately expressed) ● Define the terms “hypothesis” and “theory” as used in scientific disciplines Hypothesis, theories, and facts, as used in the domain of SCIENCE Hypothesis ● a testable, falsifiable explanation for a phenomenon of interest Theory ● a framework of internally consistent ideas used for generating hypotheses (our best current understanding of something) Fact ● a piece of information about circumstances that exist or events that have occurred; an actual occurrence ● Explain the difference between “evolution” and “evolutionary theory”; explain the difference between evolution and natural selection What is Evolution? ● change over time in a population's genetic makeup ● descent with modification ● examples of evolution: ○ modern forms are not present in the early fossil record ○ novel flu viruses arise ○ populations of many species have gone extinct in our lifetimes Natural Selection ● Evolution refers to patterns and processes of descent with modification; natural selection is a mechanisms that can produce the processes of evolution ● natural selection and evolution are NOT SYNONYMOUS ● Explain what evolution is to a nonscientist and how a researcher can actually observe evolution happening Patterns EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ● observations of the natural world ● factual descriptions of change Processes ● mechanisms that produce a pattern ● List the two main contributions that Darwin made in The Origin of Species Patterns ● observations of the natural world ● factual descriptions of change Processes ● mechanisms that produce a pattern Also the idea of Darwinism or natural selection as a theory of evolution Controlling Blood Sugar (what happens when you eat a donut) ● Normal human blood sugar levels: 70100 mg/dL ● So, when you eat a donut, there's a temporary surge in your blood sugar ○ need to return to "normal" to keep tissues and organs working properly ○ part of homeostasis Two Aspects of Homeostasis in this example 1. Release of insulin 2. Make more insulin (get ready for the next donut) gene regulation problem Development ● Embryonic development ○ zygote > developed animal ● Determination (cell division, mitosis) ○ cell committed to its fate ● Differentiation ○ cell specialization in structure and function ○ production of tissuespecific proteins ● Morphogenesis EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ○ tissues, organs, and organism take shape *This involves lots of precise gene expression. Molecules in the early "environment" > Certain genes "switched on" > determination of cell fate ● A process critically dependent upon gene regulation ● * differential gene regulation set up by molecules in the cytoplasm of the zygote First General Problem ● Within one cell type, how can a cell turn on a bunch of genes in a coordinated manner? ○ Cascading effects of transcription factors Pattern Formation: Setting up the Body Plan ● Pattern formation = development of spatial organization of tissues and organs ○ establishment of major axes ● Positional information = molecular cues that tell a cell its location Two Complementary Mechanisms of Pattern Formation ● Cytoplasmic Determinants ○ before fertilization, when eggs are made ○ maternally derived ○ seeds of differential gene expression ● Inductive Signals ○ once there are multiple cells ○ substance from outside a cell (e.g., signal from nearby cell) influences cell's gene expression How to eggs get their molecules in the first place? MADE THAT WAY BY MOM! "Nurse" Cells ● provide nutrients, mRNAs, and other substances for development of egg cell (BEFORE fertilization) ● make egg shell ● deposits bicoid genes on the left it is more concentrated EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations Fruit fly egg 1. Egg cell developing within ovarian follicle 2. Unfertilized egg 3. Fertilized egg 4. Segmented embryo 5. Larval Stage Bicoid Gene highest concentrations turns on "head genes"; lowest concentrations turns on "tail" genes Gradient of bicoid protein determines anteriorposterior axis ● The wings and legs begin as bumps of tissue called limb buds Proper pattern formation requires 3 axes of specification: 1. proximaldistal ("shoulder to fingertip") 2. anteriorposterior ("thumb to pinky") 3. dorsalventral ("knuckle to palm") Cells in two regions secrete proteins (inducers) providing positional information: 1. ZPA ( = zone of polarizing activity ) a. anteriorposterior b. ZPA side = posterior = pinky c. other side = anterior = thumb d. if you take out ZPA you get two thumbs e. if you add an extra ZPA you get two pinkies 2. AER ( = apical ectodermal ridge) a. proximaldistal b. if the AER cells are removed no limb outgrowth Conclusions: ● Cells of ZPA secrete proteins (inducer) ● anteriorposterior inducer gradient creates anteriorposterior pattern What about wings (arms) vs. legs? ● wings vs legs are differentiated based on PREVIOUS events in histories of respective limb bud cells EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations Helpful photos: Why are there 3 species in this cartoon? This is a triple reassortment swine virus EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations Do this exercise to review mutations EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ________________________________________________________________ EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations Helpful iClicker Question: The best explanation for the pattern of inheritance seen in the F2 generation is: Answer: The eye color gene is sexlinked, on the X chromosome Counterintuitive > Question: Given the conclusion from Morgan's work: If Morgan's parental generation had been whiteeyed FEMALES and redeyed MALES, then ____ of the males and ___ of the females in the F1 generation would have had white eyes. Answer: All;None Is it advantageous for a VIRUS to make us sick or to even kill us? Answer: it depends We can cure ourselves of BACTERIAL infections by taking antibiotics. Antibiotics kill bacteria by disrupting their cellular processes. Why can't we take antibiotics to successfully cure ourselves of VIRAL infections? Answer: Viruses use our own cellular machinery Why are vaccines effective in preventing viral illnesses? Answer: Vaccines teach your immune system how to recognize specific viruses Why don't all influenza A viruses readily jump back and forth between humans, birds, pigs, dogs, etc? Answer: Most viruses are host specific; specializing to infect one species can make a virus unable to infect another When a single premRNA molecule is made in one of your cells, how much info does it contain? Answer: B) the genetic code for one allele from one chromosome Which cells in the albino deer have the albino mutation Answer: B) all of the cells RNA molecules can: Answer: ● be information carriers ● catalyze chemical reactions ● be carriers of the building blocks for proteins EBIO 1210 Exam 4 Study Guide: Gene Expression, Gene Regulation, Viruses, & Mutations ● have complex three dimensional structure
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