Study Guide for Exam #4
Study Guide for Exam #4 LIFE 102-220
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This 9 page Study Guide was uploaded by Bailey Sniffin on Thursday January 21, 2016. The Study Guide belongs to LIFE 102-220 at Colorado State University taught by Dr. Patricia Bedinger in Fall 2015. Since its upload, it has received 190 views. For similar materials see Attributes of Living Systems (Honors) in Biology at Colorado State University.
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Date Created: 01/21/16
STUDY GUIDE FOR EXAM IV (FINAL) The final will be worth 130 points, 90 from new material, 30 cumulative (see below) and 10 about stem cells GENES TO PROTEINS– CHAPTER 17 Translation all phases: A charged tRNA binds to the A site A peptide bond forms mRNA shifts relative to the ribosome (translocation) Uncharged tRNA is released 1. Initiation: (formation of the initiation complex) o mRNA o Special initiator tRNA in the P site o Ribosomal subunits o Requires Initiation Factors and GTP hydrolysis 2. Elongation: o A charged tRNA enter the A (amino acid) site, the anticodon Hbonds with the codon of the mRNA o A peptide bond forms between aa at P site and aa at A site o Translocation: mRNA, with tRNA with attached polypeptide shifts to the P site, “naked” tRNA at P site moves to E, exits site and leaves 3. Termination: o Stop codon is reached in the mRNA There is no charged tRNA that recognizes it o A release factor binds, releases protein, and disrupts the complex Po/ly(ribo)somes: On any single mRNA, there are usually many ribosomes translating at one time Mutagens: Agents that increase mutation frequency Is an agent (light, chemical, radiation) that causes mutations Types and notations of mutations; silent, missense, nonsense, frameshift, deletions, insertions: Mutation: a heritable change in a gene = DNA Can be inherited by offspring or arises in a somatic cell o May or may not cause problems Occur because: o Errors made during DNA replication (wrong base pairs) Very rare o Errors during repair Mutagens Point mutations: o Not chromosomal arrangements o NT substitutions: silent (often third base) o Missense (substitution of aa) o Nonsense (a stop codon is produced so premature termination of the protein) o Nucleotide insertions or deletions cause a frameshift Unless it’s 3 or multiples of 3 Sickle Cell Anemia: o The 6 amino acid is usually Glu but the mutation causes a substitution of Val Getting proteins into the endomembrane system on the RER: The first few aa are very specific and are recognized as a “signal” by a Signal Recognition Particle o SRP, a proteinRNA complex SRP attaches the translation complex to the RER and the growing peptide is “fed” into the center (cisternal space) of the RER o The “signal” is clipped off How DNA repair can cause mutations Mutagens are agents that increase mutation frequency REGULATION OF GENE EXPRESSION – CHAPTER 18 What is a gene? A segment of DNA that is transcribed to produce a functional RNA product Operons in bacteria – polycistronic mRNAs Genes are clustered and transcribed together in operon Operon: multiple gene, single promoter o Functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter Lactose: o The repressor of transcription is inactivated o RNA polymerase will bind to the promoter and transcribe all 3 genes in a polycistronic mRNA containing three start codons for 3 separate proteins Can encode more than one polypeptide separately within the same RNA molecule Usually bacterial mRNA Chromatin modification/epigenetics (histone modification and DNA methylation): DNA can be methylated: o Affects its expression o Involved in genomic imprinting, Xinactivation o Prevents transcription DNA can be acetylated: o Chromatin is looser o Easier to transcribe Chromatin modification: o Histone proteins can be acetylated or methylated Enhancers: Often tissuespecific, so whether or not a gene gets transcribed often depends on whether the enhancerbinding transcription factors are present in the cell A typical eukaryotic gene has enhancers + promoters Promoter = on DNA Enhancer = can be far away from DNA strand Transcription factors: Proteins that bind to promoters and enhancers o Allows RNA polymerase to “load” onto a gene and begin transcription Alternative splicing: >92% of human genes A regulated process during gene expression that results in a single gene coding for multiple proteins MicroRNAs, what are they, how do they work to inhibit gene expression: miRNA, siRNA, RNAi Small noncoding (nc) that can interfere with gene expression by inhibiting translation or causing degradation of target mRNAs Cell fate, determination, differentiation, morphogenesis, and Morphogen: Differentiation: cells become specialized o Structurally and biochemically Cell fate: final differentiated state of a cell Determination: a cell has become committed to a cell fate o Stem cells are NOT determined Morphogenesis: the creation of form o The shape of an organism Morphogen: a factor that influences morphogenesis Importance of transcription factors: Proteins that bind DNA and influence transcription Homeotic genes and mutations (what do mutants look like?) Homeotic genes discovered in Drosophila encode transcription factors that determine the structures in different body segments Fly with legs for eyes o Organs in the wrong place Cytoplasmic determinants in development, example: Factors that are asymmetrically distributed in the cytoplasm and influence development Ex. Body plan in drosophila (fruit fly) Induction in development, example: Process by which one cell influences the development of a neighboring cell Ex. Stem cell connection A neighboring cell may emit signals differently to one daughter cell that will influence its cell fate o A cellcell signaling during development Apoptosis, example in development: Cell suicide Ex: webbed hands in fetus Cancer causes: viruses and mutations: Viruses: Have transcription factors that transcribe where it shouldn’t Most cancers are caused by mutations in genomes of somatic cells o More rarely: occur in cells that will produce gametes Can then be inherited About 15% of human cancers are genital warts Difference between sporadic vs. inherited cancer: Sporadic: mutation occurs in somatic cells o 2 normal copies of the gene in every cell one copy mutated in cell (acquired) second copy mutated in cell (also acquired) Inherited: one of the 2 homologous genes is already mutated in gametes o The first mutational “hit” is already present at birth o The second “hit” sometimes called “loss of heterozygosity” can occur to another mutation, a deletion, or epigenetic silencing Resulting in cancer at a younger age Oncogenes; what is their normal function, what goes wrong when mutated, example: Normal, nonmutated version: protooncogene: promote cell division/growth; lthe “gas pedal” of the cell cycle Oncogenes are dominant mutations in protooncogenes o Gas pedal gets stuck Ex. Ras What causes a protooncogene to become an oncogene? Figure on page 15 of notes Translocation or transposition: gene is moved to a new locus and under new controls Gene amplification: multiple copies of the gene Point mutation within a control element oncogene Tumor Suppressor Genes – what is their normal function, what goes wrong when mutated, example Normal function: inhibit cell division – “brakes” on the cell cycle o Cell cycle checkpoints Recessive mutations: no gene product or dysfunctional gene product = “loss of function” In order to see effect, BOTH alleles must be mutated Ex. p53 Additional issues in cancer; multiple mutations, apoptosis, angiogenesis, telomeres, metastasis: At the molecular level of cancer: multiple mutations The next mutation may be in a more “general” protooncogene like ras (in about 25% of all human tumors) or loss of a “general” tumor suppressor gene like p53 or RB (in about 50% of all human tumors) Apoptosis: last lines of defense – even if a cell acquires a series of mutations in cancer genes, DNA damage can trigger cell suicide Angiogenesis: development of new blood vessels o Tumor size is limited unless blood vessels develop in tumor Metastasis: secondary site of tumor If a cell escapes apoptosis, there is normally still a “shutoff” system for cell division = shortening of telomeres causes cells to stop after 2060 divisions BIOTECHNOLOGY – CHAPTER 20 DNA cloning (recombinant DNA) as opposed to organism cloning: Recombinant DNA: 2 molecules of DNA (vector and insert DNA) that combine DNA cloning: o Restriction enzyme cuts sugarphosphate backbones Produces sticky ends o DNA fragment added from another molecule cut by same enzyme. Base pairing occurs o DNA ligase seals strands covalently Organism cloning: o Organisms that receive recombinant DNA are GMO Dolly was a cloned organism, but not a GMO Restriction enzymes – be able to recognize sticky ends: Enzymes that cut doublestranded DNA at a specific DNA sequence These and DNA ligase make it possible to recombine DNA in the lab Insert, vector, plasmid, recombinant DNA, transformation, transgenic or GM organisms: Insert: can be from any kind of organism; the vector DNA mixes with insert DNA Vector: can replicate in bacterial cells o A smaller circular plasmid or viral DNA o Has 3 things: Bacterial replication origin A cloning site for the insert DNA A “selectable marker” gene that allows bacteria to grow only if they contain the vector Transformation: getting the recombinant DNA into the cells Transgenic: DNA from a separate organism has been introduced o Gene therapy is a transient (so far) kind of genetic modification Bubble boy = gene therapy is being used Applications of recombinant DNA technology including GMOs and gene therapy: Bubble boy Bone marrow transplants PCR – how is it done (including steps and ingredients) and what are applications? Denatures anneals (primers attach) elongation (RNA polymerase) GENOMES – Chapter 21 Approximate # genes are found in prokaryotes vs. multicellular eukaryotes like humans: 2,000 – 4,000 genes in bacteria 20,000 – 40,000 genes in multicellular eukaryotes How much of the human genome sequence consists of exons (encodes proteins or functional RNAs)? 1.5% exons o Encodes proteins/functional RNA 22% introns 15%psueudogenes 15% SSR (simple sequence repeats) 44% transposons What are transposons? “Jumping genes” Transposable elements Occur in all major life forms What other kinds of sequences are found in the human genome? More “junk” DNA Simple sequence repeats (SSRs) of 113 bases ~19,000 pseudogenes (mutated nonfunctional genes) DESCENT WITH MODIFICATION — Chapter 22 4 common misconceptions about the Theory of Evolution: Evolution is “just a theory” Evolution is about the origins of life Evolution means atheism “Survival of the fittest” What is Intelligent Design? No natural explanation, life form is caused by an intelligent power Historic views of the relationships of organisms: Aristotle, Lamarck (how did it differ from Darwin’s?) Aristotle: great chain of being o Primitive to complex organisms in a chain Humans at the top No interactions of the rings of the chains Lamarck: father of evolution o Evolution is sporadic o No exchange between generations Darwin: naturalist for the captain o Galapagos islands o Darwin and his journey, Wallace as codiscoverer Darwin’s “context”: taxonomy (role of Linnaeus), fossils, geology/uniformitarianism, and artificial selection Grouped by common characteristics Artificial selection: o Breeding types of crops, etc. Two postulates of Darwinian Evolution Natural selection Descent with modification Adaptation Being fit for the environment Fitness (what is the equation?) Survival + reproductive success What two conditions are necessary for natural selection to work? Genetic variation in a population Limits to survival How does each of these support Darwinian Evolution: Biogeography (what is this), Fossil Record, Comparative Morphology, Molecular Biology, Direct observation (examples): Biogeography: where you are located o Might not be the same species but they seem alike Fossil record: species past vs. now Comparative morphology: comparing bones from then vs. now Molecular biology: looking at genes Direct observation: observing What are fossils and how are they produced Preserved remnants of a life form o Form when something interferes with the natural process of decomposition The evolutionary relationship of apes and humans Humans are not descendants of modern apes EVOLUTION OF POPULATIONS – CHAPTER 23 Modern synthesis Genetics as applied to populations Locus, gene, allele, gene pool, population, species, microevolution Locus: position on a gene Gene: a segment of DNA that encodes a functional protein or functional RNA product Gene pool: ALL of the alleles of ALL of the genes of ALL the individuals in a population Population: a localized group of freely interbreeding individuals of the same species Species: according to the biological species concept: a group that freely interbreeds and produces fertile offspring in a natural setting and is reproductively isolated from other groups Microevolution: changes in a gene pool which = changes in allele frequencies = evolution of populations HardyWeinberg Theorem, be able to do simple calculations of allele and genotype frequencies, e.g. frequency of all genotypes if know frequency of recessive trait (homozygous recessive genotype) Genotype frequency: p and q 2 Allele frequency: p and q What conditions need to exist for HardyWeinberg to apply to a population? Not changing, not evolving Allele frequencies do not change 3 things that can cause microevolution; genetic drift (bottleneck and founder effect), gene flow, natural selection (how do each of these increase or decrease alleles in a population?) Bottleneck: catastrophe decreased alleles Founder effect: some break off and move somewhere else decrease alleles Gene flow: immigration – introduction of new alleles o Increases gene pool Natural selection: gene pool decreases o But more fit o Remaining alleles are adaptive ORIGIN OF SPECIESCHAPTER 24 Macroevolution, speciation Macro: the origin of new groups, such as species, genera, families, etc. Speciation: formation of new species Biological species concept: A group that freely interbreeds and produces fertile offspring in a natural setting and is reproductively isolated from other groups Examples of pre and postzygotic barriers: Pre: habitat, temporal, behavioral, mechanical, Gametic Post: reduced hybrid viability, hybrid breakdown, reduced hybrid fertility Allopatric vs sympatric speciation, examples Allopatric: An original group becomes separated by formation of geographical barriers or by migration of a splinter group o Peripheral isolate Sympatric: new species can arise within an original population at the same location o Especially well documented in plants STEM CELLS (10 points) What are 2 ways to get stem cells to differentiate? 1. Get embryonic stem cells to grow and then differentiate in culture o Different treatments with small peptide growth factors cause the cells to divide and differentiate o Remember cell division and cell communication and induction 2. Inject the undifferentiated stem cells into an organism and let the other cells within the body cause the embryonic stem cells to differentiate by induction, just like in normal development What are potential uses for stem cells, know at least one for both disease/age and injury: Regenerative medicine: or cellbased medicine to replace dead or injured cells Help with Parkinson’s, diabetes, osteoarthritis, blindness, heart disease, stroke, spinal cord injuries, burns How are stem cells being used in research for human genetic diseases? Can make iPCs from people with a genetic disease including neurodegenerative diseases o Including Alzheimer’s o Can use for drug discovery Cumulative (40 points): Summary figures; Cell structure, Respiration (equation, locations, steps with inputs and outputs), and Photosynthesis (equation, steps with inputs and outputs), Transcription vs. Translation
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