Bio 2 Final Review
Bio 2 Final Review BIOL 1362
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Final Exam Review Biodiversity – Chapters 24 27 ● List characteristics shared by Archaea & Bacteria, but not Eukarya ○ No nuclear envelope ○ No membrane bound organelles ○ One (1) circular chromosome ● List characteristics shared by Archaea & Eukarya, but not Bacteria ○ No peptidoglycan cell wall ○ More than 1 (>1) RNA polymerase ○ Initiator amino acid: methionine ○ No ribosome assembly sensitive to antibiotics ● List characteristics unique to each domain ○ Archaea ■ Extremophiles: can live in harsh environments (salty, hot, freezing) ■ Methanogens: producers, use CO to oxidize H to CH, hydrothermal vents, cow and 2 2 4 termite guts ■ Growth at temperatures greater than 100°C ○ Bacteria ■ Peptidoglycan cell wall ■ One (1) RNA polymerase ■ No introns or histones ○ Eukaryotes ■ Nuclear envelope ■ Membrane bound organelles ■ No circular chromosomes ■ Many introns, one histone ● Histones are proteins that coil with DNA ● Introns are noncoding DNA sequences Bacteria Archaea Eukarya nuclear envelope 0 0 1 membranebound organelles 0 0 1 circular chromosome 1 1 0 peptidoglycan cell wall 1 0 0 RNA polymerase 1 >1 >1 initiator aa formyl Met Met Met Ribosome assembly sens to antibio1 cs 0 0 growth at > 100°C 0 1 0 membrane lipids unbranched hc tail some branched hc tail unbranched hc tail introns rare some many histones 0 0/1 1 ● Name the 5 kingdoms within Domain Bacteria and be able to draw a phylogenetic tree showing relationships among the 5 kingdoms ○ Proteobacteria ■ Salmonella ■ Vibrio ■ Helicobacteria pylori ■ Rhizobium ○ Chlamydia ○ Spiro parasitic ■ Barrelia burgdorferi ■ Treponema pallidum ○ Cyano=parasitic ■ lichen ○ GramPositive ■ Streptomyces ■ Bacillus antrhacis ■ Clostridium botulinum ● ● Know the kingdom for each species of bacteria listed in lecture ● ● Know characteristic that differentiates grampositive and gramnegative bacteria and which kingdoms belong to which category ○ Grampositive ■ No additional membrane covering cell wall ■ thick layer of peptidoglycan ■ dark stained ■ Pathogenic vs. Nonpathogenic ○ Gramnegative ■ Proteobacteria ■ Cell wall, thin layer of peptidoglycan, with additional membrane ■ Autotrophs (chemo and photo) vs. Heterotrophs can be pathogenic vs. nonpathogenic ■ Pathogenic vs nonpathogenic ● Name the 4 supergroups within Domain Eukarya and be able to draw a phylogenetic tree showing relationships among the supergroups ○ Animalia ○ Fungi ○ Plant ○ Charophyte algae ● Know the supergroup to which each singlecelled eukaryote listed in lecture belongs ● Explain what the branching pattern on a phylogenetic tree indicates about evolutionary relationships ○ The branch point represents a pattern of divergence ○ unknown shared traits ● Compare phylogenetic trees to see if they represent the same or different relationships between groups ● Use a phylogenetic tree to identify which groups descend from a more recent or more ancient common ancestor ● Define the ancestral characteristics that unite the Archaeplastida ○ Shared with green algae: chlorophyll a and b ● Define the shared derived traits that unite the plant kingdom ○ Alternation of generationsfertilization ○ Sporangiamulticellular organs that produce desiccation resistant spores ○ Gametangiaembryo ○ Apical meristem cell division at the tip of the root ● Draw the cycle of alternation of generations – name each generation, indicate ploidy (1n or 2n) and type of cell division that produces the single cells that develop into the next generation ● Name the 7 phyla within Kingdom Plantae and be able to match the name of plants listed in lecture to the correct phylum ○ Liverworts ○ Hornworts ○ Mosses ○ Lycophytes ○ Monilophytes ○ Gymnosperms ○ Angiosperms ● Draw a phylogenetic tree showing relationships among the 7 plant phyla ● Draw a phylogenetic tree showing relationships among these animal phyla: Porifera, Cnidaria, Chordata, Mollusca, Annelida, Nematoda, Arthropoda ● Be able to indicate on the phylogenetic tree which groups are part of the BilateriaDeuterostomia, Lophotrochozoa, Ecdysozoa ● List ancestral characteristics common to all animals and choanoflagellates, distinguish animals from choanoflagellates by shared derived characteristic of animals ○ Genes encoding rRNA ○ Chaperone proteins ○ Tubulin ● List and map shared derived characteristics of Eumetazoa, Bilateria, Deuterostomia, and the rotostomes onto a phylogenetic tree ● List the 4 protostome phyla discussed in lecture ○ Ecdysozoa ○ Lophotrochozoa ○ Cnidaria ○ Deuterostomes ● List shared derived characteristics of Lophotrochozoaand list 2 phyla that belong to this group ○ Spiral cleavage pattern of embryonic cells ○ Hox genes ○ Annelida and Mollusca ● List shared derived characteristics of Ecdysozoa and 2 phyla that belong to this group ○ Shedding exoskeleton to grow larger ○ Invertebrates ○ Arthropoda and Nematoda ● List the 4 classes of arthropods and be able to match the name of arthropods listed in class (and in the Life video) to the correct class ○ Chelicerata ○ Myriapoda ○ Crustacea ○ Insecta Darwin and Natural Selection: Chapter 19 ● Describe Lyell’s ideas about geologic processes and inferences about Earth’s age ○ Lyell believed that geologic processes operate today at the same rate as in the past. ● Compare & contrast Lamarck’s ideas vs Darwin’s idea regarding mechanisms of change in living organisms ○ Lamarck ■ Species can change into new species ■ Use and disuse ■ Inheritance of acquired characteristics ○ Darwin ■ Adaptation ■ Species are changing due to natural selection ■ Survival of the fittest ■ Descent with modification: all species descend from a common ancestor ■ Artificial Selection ● Define descent with modification ○ All living spp descended from one ancestor ● List and recognize examples of descent with modification in living organisms, both within and between species, and fossil organisms ● Define 2 conditions necessary for natural selection and give examples that satisfy each condition ○ Variation in inherited traits ○ More offspring than environment can support ● Evaluate conditions under which natural selection could occur ● Understand that natural selection acts on individuals, but causes changes in populations ● Compare and contrast natural selection and artificial selection: conditions necessary, selection pressure, result ○ Both: variation in heritable trait ○ Artificial selection ● trait desired by humans ● desired trait increases ○ Natural selection ● selection pressure ● trait desired by environment ● favorable trait increases Chapters 11: Heredity ● Define Mendel’s Law of segregation ○ Principles that governs heredity ● Define Mendel’s Law of independent assortment ○ When two or more characteristics are inherited, individual hereditary factors assort independently during gamete production, giving different traits an equal opportunity of occurring together. ● Monohybrid cross – use Punnett square to detail possible genotype of gametes and progeny and indicate progeny phenotypes ○ Two individuals two or multiple alleles for a single locus. ● Dihybrid cross – use Punnett square to show possible genotypes of gametes and progeny and indicate progeny phenotype ○ Cross between two different lines (varieties, strains) that differ in two observed traits. ● Identify dominant or recessive modes of inheritance from the notation (example: A is the dominant allele, a is the recessive allele) ● Analyze a pedigree to determine whether a trait is dominant or recessive ○ http://www.cs.cmu.edu/~genetics/units/instructions/instructionsPBA.pdf ■ Dominance whether the disease alleles are dominant or recessive; (2) ■ Linkage whether disease alleles are Xlinked or autosomal ■ utosomal chromosomes The 22 chromosome pairs other than the XX (female) or XY (male) sex chromosomes. ■ Allele A version of a gene. Humans have 2 alleles of all their autosomal genes; females have 2 alleles of X linked genes; males have one allele of Xlinked genes (and one allele of Ylinked genes). ■ Recessiveif any affected individual has 2 unaffected parents. ■ Dominant if every affected child of nonfounding parents has an affected parent. ● Use information in a pedigree to determine genotype and calculate the probability of a dominant or recessive trait being inherited by a son or daughter ● Use a Punnett square to figure out possible gamete genotype and progeny genotypes for autosomal traits ● Use genotype and phenotype of parents to figure out genotype and phenotype of offspring (vice versa) ● Use correct notation for dominant, recessive, codominant, wildtype, mutant, sexlinked ○ codominant relationship between two versions of a gene. ○ wildtype characteristic that prevails among individuals in natural conditions, as distinct from an atypical mutant type. ○ mutant organism or a new genetic character arising or resulting from an instance of mutation, which is a basepair sequence change within DNA or chromosome ○ sexlinked trait associated with gene that is carried only by male or female parent. ● Define gene, locus, and allele. Know how many alleles an individual diploid organism can have for each locus. ○ Gene: the biological code of all traits ○ Locus: location on a chromosome where a gene sits ○ Allel: version of gene that codes for specific version of a character ○ An individual can have 2 alleles, one from each parent, in each locus. ● Explain why the number of alleles per gene in an individual can be different from the number of alleles per gene in a population ○ An individual has one allele per gene in each chromosome, meaning the individual exhibits only one trait. Vocabulary Phylogenetic tree branching diagram representing the evolutionary history, group of organisms Archaea unicellular prokaryot distinguished by cell walls made of certain polysaccharides not found in bacterial or eukaryotic cell walls plasma membranes composed of unique isoprenecontaining phospholipids, ribosomes and RNA polymerase similar to those of eukaryotes Bacteria consisting of unicellular prokaryotes distinguished by cell walls composed largely of peptidoglycan, plasma membranes similar to those of eukaryotic cells, ribosomes and RNA polymerase that differ from those in archaeans or eukaryotes. Eukarya unicellular to multicellular organisms that have a membranebound nucleus containing several chromosomes. Sexual reproduction is common. Cyanobacteria unicellular organisms photosynthetic oldest fossil autotroph ancestor of chloroplast form soil crust forms a symbiotic relationship with fungi resulting in lichen early cyanobacteria began releasing oxygen into the Earth’s atmosphere. With this rising concentration of atmospheric O2, several prokaryotic groups went extinct Excavata Feeding groove along one side of cell mitochondria that do not use O2 many are heterotrophs and many are parasites Giardia Intestinalis intestinal parasite in mammals, transmitted by infected feces Trypanosoma parasite that causes sleeping sickness in mammals; transmitted by tsetse fly bites. Stramenopileunicellular diatoms 2part silicon dioxide wall Photosynthetic Alveolate Dinoflagellates Photosynthetic Some are symbiotic with corals (ex. Cnidaria) Red tide Some are bioluminescent Plastid organelle surrounded by multiple organelles Diatom unicellular, major group of algae DinoflagellatePhotosynthetic Some are symbiotic with corals (ex. Cnidaria) Red tide Some are bioluminescent Giardiaintestinal parasite in mammals, transmitted by feces Trypanosoma parasite that causes sleeping sickness in mammals, transmitted by tsetse fly bites Plasmodium causes malaria Autotroph able to make its own food and energy HeterotrophConsumes other organisms for energy Saprotroph acquiring energy by absorbing nutrients from the environment Archaeplastidaland plants Ancestral characteristishared by the ancestral and current descendants Shared derived trait shared by descendants Apical meristemcell division at roots Sporangia multicellular organs that produce desiccationresistant spores Gametangia either makes eggs OR sperm Sporophyte is dominant generation, spores develops into a microscopic gametophyte within the parent sporophyte Gametophyte produces sperm or egg Sporopollenin resistant polymer that prevents spore from drying out or being crushed Unikonta Fungi/Animalia Metazoa nimalia Eumetazoa eukaryotic clad in Kingdom Animalia that contains most major groups Bilateria twosided symmetry Lophotrochozoa Spiral cleavage pattern of embryonic cells Hox genes Annelida and Mollusca Ecdysozoa hedding of the exoskeleton to grow larger Gastrulation tissue formation Mycorrhizae symbiotic relationship between fungus and plant roots Adaptationinherited trait that enhances survival and reproduction in the envi Natural selectionDarwin mechanism of descent with modification Individuals that inherit certain traits will survive better and produce more offspring in current local environment Artificial selectiintentional reproduction of individuals to have certain traits Evolution theory that individuals descend from a common ancestor into better and more diverse forms Homology existence of shared characteristics between structures or genes in different species. Analogy similarity of function and resemblance of structures that have different origins Biogeography tudy of species in different environments Hutton Earth’s physical features are changing Lyell Geological process operate today at the same rate as the past LamarckSpecies can change into new species CuvierSpecies go extinct due to a catastrophe Extantopposite of extinct Allelealternative version of the gene Blending hypothesismixing of the two parents Particulate hypothesismixing of the particles Charactervaries between individuals Traitariant of character P generationarent F1 generationst offspring F2 generationnd offspring Law of segregation Alleles separate from each other in the formation of gametes Law of independent assortment Individual hereditary factors assort independently, so it gives an equal chance of occurring together Genotypeenetic makeup Phenotype What they look like Dominant allel is heterozygous for that trait, or possesses one of each allele, then the dominant trait is expressed. Recessive alleleis only expressed if an organism is homozygous for that trait, or possesses two recessive alleles. Heterozygous having 2 different versions of hereditary particles for a character Homozygous having the same version of hereditary particles for a character Punnett squaremethod to predict possible combinations of gametes and offspring Monohybrid cross one mixture of traits Dihybrid crossmating between parents heterozygous for 2 characters Chapters 9 & 10: Cell division ● Cell cycle: name the phases, describe the events in each phanow relative length of each phase with the cycle ● Interphase 90% of the cell cycle, high metabolic activity. The cell grows by producing proteins and organelles, and chromosomes are replicated, Nucleoli are present ○ G1 This is the portion of the cell cycle just after division, but before DNA synthesis. The cell grows by producing proteins and organelles ○ S phase ■ DNA synthesis (or replication) occurs during this phase. At the beginning of the phase, each chromosome is single. At the end, after DNA replication, each chromosome consists of two sister chromatids. ■ most DNA from the cell cycle. ● # of chromosomes = 4 ● # of DNA =8 ● # of sister chromatids = 4 ○ G2 growth and preparation for cell division ● M phase Cell division occurs during this short phase, which generally involves two discrete processes: the contents of the nucleus (mainly the duplicated chromosomes) are evenly distributed to two daughter nuclei, and the cytoplasm divides in two. ● Mitosisivision of chromosomes of the nucleus occurs. he chromosomes that have been replicated are distributed to two daughter nuclei. ■ Prophase ● include the condensation of chromatin and the dispersal of nucleoli ● Spindle forms ● Centrosomes begins to move away from each other ● Chromosomes become visible the chromatin fibers become discrete chromosome ■ Prometaphase ● the attachment of spindle fibers to kinetochores. ● Spindle fibers attach to kinetochores ■ Metaphase chromosomes align along the metaphase plate. ■ Anaphase ● Centromeres divide and sister chromatids become fullfledged chromosome, sister chromatids separate and daughter chromosomes migrate to opposite poles. ● centromeres come apart, and sister chromatids become fullfledged chromosomes, which migrate to opposite poles of the cell. ■ Telophaseboth nuclear envelopes+nucleoli reform. ● Cytokinesis:plant vs animal ○ Cytoplasm divides in two ○ Cytokinesis in plant cells involves the formation of a cell plate. ○ Cytokinesis in animal cells involves formation of a cleavage furrow. ○ each one has: ■ # of chromosomes = 4, ■ # of DNA =8) ● Cell division: list the 3 main steps required, list the 3 major functions of cell division ○ Roles of Cell Division ■ Reproduction (equal distribution of genetic material to two daughter cells) ■ Growth; sexually reproducing organisms develop from a single cell ■ Renewal and Repair: replacing cells that die from normal wear and tear or accidents ● Mitosis in eukaryotes: Identify the ploidy level at the beginning and end of cell division; Name the 5 phases and describe the events in each phase, including what happens to chromosomes, nucleus, and cytoskeleton ● Explain how chromosomes move along spindle & where spindle attaches ○ Motor proteins and the elongating and shortening of spindle attaches ● Identify organs in which mitosis occurs. ○ every organ except the nervous system (brain and nerves) ○ sex organs do have mitosis too, but they produce sex cells (sperm and ova) by meiosis. ● Define the terms: ploidy, haploid, and diploid ○ Ploidy ■ number of sets of chromosomes in a cell. Usually a gamete(sperm or egg, which fuse into a single cell during the fertilization phase of sexual reproduction) carries a full set of chromosomes that includes a single copy of each chromosome ○ haploid number(n) ■ number of chromosomes in a gamete. Two gametes form a diploidzygote with twice this number (2n, the zygotic or diploid number) ■ 2n= 1 chromosomes 2(23)=46 chromosomes ● ame the phases of meiosis I, describe the events of each phase, identify the ploidy level of cells at the end of meiosis I. ● Name the phases of meiosis II, describe the events of each phase, identify the ploidy level of cells at the end of meiosis II. ● Indicate when homologous chromosomes separate and when sister chromatids separate during meiosis. ● Explain what occurs during crossing over ○ It is the process by which two chromosomes pair up and exchange sections of their DNA between nonsister chromatids. This often occurs during prophase 1 of meiosis in a process called synapsis. ● Name the products of meiosis and describe their chromosome content and their genetic makeup compared to each other ● Identify organs in which meiosis occurs ● Identify the key steps during meiosis that result in genetically different daughter cells from the same parent cell ● Compare and contrast mitosis, meiosis I and meiosis II. Fill in text descriptions in a chart similar to the one below. Mitosis Meiosis I Meiosis II Ploidy level BEFORE division 2n=46chromosomes 46 chromo 23 End 23 92 chromatid 92 46 23 2n cells =46 2n=46 2n Homologous chromo =23 1st stage prophase 2nd stage proprophase 3rd stage metaphase 4th stage Sister chromatids anaphase separate 5th stage telophase Product – number of cells 2 genetically identical 2n 2 daughter cells 4(n) daughter cells Genetic makeup cells=46 sister 2n=23 chromo in each cell N cells=23 chromo 46 sister Chapter 12: Heredity ● Define Mendel’s Law of segregation & explain its physical basis in chromosome movement during Anaphase I ● Define Mendel’s Law of independent assortment & its physical basis in chromosome movement during Metaphase I Chapter 13: DNA structure & replication ● Griffith, Avery et al, Hershey & Chase, Meselson & Stahl experiments for each experiment: ○ Hershey and Chase: T2 Phage and E. Coli 35 Sulfur coated the proteins and the 32p was for the DNA. They proved that DNA was the genetic material not proteins. ○ Chargaff: different compositions of the nitrogenous bases ○ Griffith transformation, used streptococcus pneumoniae. Mouse thing with S cells and R cells and Heat ○ Avery:DNA, RNA or protein from dead S cells was transforming R cells ○ Watson and Crick : DNA replicationdouble helix (discovered by Rosalind Franklin) ○ Meselson and Stahl: U sed E. Coli, worked with the 3 models (dispersive, semiconservative, etc) ● Explain the purpose of each treatment in the experimental design ● State the hypothesis (or hypotheses, if there is more than one) ● Predict the likely results if a hypothesis is true ● Evaluate whether results are consistent with or contrary to a hypothesis ● Apply Chargaff’s rule to calculate the percentage of the other 3 nucleotides when given the percentage of 1 of the 4 DNA nucleotides ● Apply complementary base pairing & antiparallel arrangement of the 2 DNA helices to predict the sequence of one DNA strand from the other ● List the observations about DNA structure that led to Watson & Crick’s hypothesis for DNA structure and replication ● State Watson & Crick’s description of DNA structure and their hypothesis for replication ● *Mechanics of DNA replication: Describe the molecules involved, the steps of the process on the leading strand and on the lagging strand AMINO ACID STRUCTURE ● For each step, predict the outcome if a particular molecule were limited or inhibited: e.g. a shortage of nitrogenous bases, or inhibition of primase, DNA polymerase, DNA ligase, or helicase Big picture: Identify cellular process(es) that require DNA replication Know when DNA replication occurs in life cycle of cell DNA STRUCTURE Vocabulary Centrosome a structure that is present in the cytoplasm of animal cells that functions as a microtubule organizing center. Contains two centrioles Centromere the region on each sister chromatid where they are most likely attached to each other by proteins that bind to specific DNA sequences, causes constriction in chromosome Chromatidcolored stuff Prophase the first stage of mitosis; chromatin condenses into discrete chromosomes; mitotic spindle forms, and nucleolus disappears Spindle Array of microtubules Prometaphase it the second stage of the mitosis. Nuclear envelope disappears. Chromosomes are now even more condensed and chromatids have kinetochores. Kinetochore Protein structure that is attached to centromere, connects centromeres to spindle fibers. Metaphase Centrosomes are now at the opposite poles of the cell and they align on an imaginary central line. Anaphase the fourth stage of mitosis; chromatids of each chromosome have separated and the daughter chromosomes are moving to the poles cell Telophase two daughter nuclei form in cell. Nucleoli reappear. Mitotic division is now complete. Cleavage furrow groove around the animal cell near the old metaphase plate Traits ariant of a character Gene specifi sequence of DNA nucleotides of the molecule of a chromosome Locus ocation of a gene on a chromosomes Chromosome consists of one DNA molecule and are associated with protein molecules. Eukaryotes have multiple, linear chromosomes located in the nucleus. Prokaryotes have a single, circular chromosome located in the nucleoid. Homologous chromosome same length and pattern, one from father and one for mother Karyotype icture thing in our bio lab manual Autosome a chromosome that is not a sex chromosome Sex chromosome last pair on the karyotype picture, determine the sex Haploid n gametes Diploid 2n zygote Meiosis reduces 2n to n Meiosis I Meiosis I Cell division that reduces a 2n(diploid) number of chromosomes to a haploid number. Allele alternative versions of a gene that may produce distinguishable phenotypic effects Chiasma A point where crossovers occur Synaptonemal Complex Is a protein structure that forms between homologous chromosomes during meiosis and is thought to mediate chromosome pairing, synapsis and recombination. Law of segregatio Mendel's 1st law; 2 alleles sepaanaphase I Law of independent assortment Mendel’s 2nd law; each pair of alleles assort independently of each other duringgamete formation;enes for 2 characters may act as if on different chromosometaphase I Sexlinked genea gene located on either sex chromosome Carrier individual who is heterozygous at any given locus for a recessive disorder. Can pass gene onto offspring Pyrimidine A and G Purine U, T and C 3’ end of nucleotide 5’ end of nucleotide Antiparallelrefers to arrangement of sugarphosphate backbones in a DNA double helix; run opposite (3’ → 5’) Rosalind Franklin discovered DNA double helix James Watson & Francis Crick worked and experimented using the idea of a double helix Replication fork the y shaped region, where the parental strand are being unwound DNA polymerase enzyme that catalyzes elongation of new DNA by addition of nucleotides to the 3’ end of an existing chain. Helicase enzymes that unwinds Primer short pieces of complementary RNA, it starts replication Leading strand the new complementary DNA strand synthesized continuously along the template strand toward the replication fork in a 5’ → 3’ direction Lagging strand a discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5’ → 3’ direction away from the replication fork DNA ligase a linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3’ end of one DNA strand to the 5’ end of another Nucleosome basic unit of DNA; consists of DNA wrapped around a protein core composed of two copies of each of the four types of histone Histone small protein with high proportion of highly charged amino acids that binds to negatively charged DNA ● Drawings to help you prepare: ○ Assume a cell with 2n = 2. ○ Draw the chromosomes at prophase, prometaphase, metaphase, anaphase, and telophase of mitosis. ● Draw the chromosomes at each stage of Meiosis I and Meiosis II. Assume a cell with 2n = 6. Draw each stage of mitosis and each stage of meiosis. ● Draw a DNA replication bubble showing the origin of replication, the replication fork, and the position of the RNA primer on the leading strand and on the lagging strand (more than 1 RNA primer). Be sure to show the leading strand and lagging strand for both parent strands of DNA (top and bottom of the bubble). Indicate the direction of elongation of the new DNA strand. This exam covers Chapters 14, 15.1 & 16.1, 20, 21, and 23. Concepts Chapter 14: Transcription & Translation ● Apply complementary base pairing of DNA & RNA nucleotides and antiparallel arrangement of RNA in relation to DNA to predict RNA primer or messenger RNA sequence in the correct 5’ to 3’ orientation Coding strands 53 Template strand 35 mRNA 53 ● Know the number of different DNA bases, number of bases in a codon (3) DNA ACTG RNA UGAC ● Know where translation begins on the mRNA (5’) ● Use codon table (will be provided) to figure out which amino acids are coded for by a given DNA or mRNA sequence ● *Mechanics of transcription: Describe the molecules involved, the steps of the process, and location within the cell ● *Mechanics of translation: Describe the molecules, steps of process, location within the cell, importance of GTP ● For each step in transcription or translation, predict the outcome if a particular molecule were limited or inhibited: e.g.a shortage of GTP or tRNA, RNA polymerase inhibition, or inhibited enzymatic activity of large ribosomal subunit ● Explain how multiple copies of a protein molecule are made from one molecule of mRNA ● Big picture: ○ Identify several examples of cellular processes that require transcription & translation ○ Know when transcription and translation occur in the life cycle of cell Chapters 15 & 16 (selected sections): Regulating Gene Expression ● Describe inducible regulation of an operon in prokaryotes ○ Gene expression is usually “off” because a repressor gene is present and attached to an operator.This blocks transcription. If an inducer binds to a repressor protein, it cannot attach to an operator. Gene expression is now “on” and transcription proceeds. ● Explain how transcription factors and chromatin modification regulate gene expression in eukaryotes ○ Transcription factors: attach to DNA at control elements and either enhance or reduce interaction of RNA polymerase with promoter. ○ Chromatin modification: chemical changes in histone proteins or to DNA can alter transcription rate ■ Histone acetylation: adding an acetyl group to histone protein reduces binding between nucleosomes → increases transcription ■ DNA methylation: enzymes add methyl group to cytosine → decrease transcription ● ● Define transcription factor, explain how function differs between general and specific transcription factors with regard to where they attach to DNA and how they regulate gene expression ○ Transcription factor proteins that interact with control elements of genes ○ General: can interact with promoters of any proteincoding gene ○ Specific: works only on specific promoters Big picture: ● Give examples of changing environmental or physiological conditions that turn on or turn off gene expression ○ Glucose Lactose Other sugar ○ Nutrients Hormone signal O2 ● Inducible gene expression turn on ○ Gene expression is usually off as the repressor proteins is there, attached to the operator, blocking transcription ○ If an inducer binds to the repressor protein, it can no longer attach to the operator ● 3 ways to change eukaryotic gene expression ○ Chromosomes structure histone acetylation , DNA methylation ○ Transcription control elements ○ Translation Microevolution: Chapter 21 ● Graph each mode of natural selection stabilizing selection, disruptive selection, and directional selection ● Analyze frequency distributions of a trait in original and evolved populations to identify the type of selection occurring ● List 5 conditions that lead to changes in allele frequency in a population and explain the difference between random and adaptive evolution ● Define the sources of genetic variation, explain how each source contributes to genetic variation ○ Behavior of chromosomes during the meiosis and fertilization is the most of the variation that arise each generation. ○ Independent assortment at metaphase (meiosis I) and meiosis II ■ chromosomes contributes to genetic variability due to the random orientation of tetrads at the metaphase plate.(2^n) n= haploid ) ○ Crossing over recombinant chromosomes prophase I homologous chromosomes (nonsister chromatids) pair up gene by gene ○ Fertilization ovum * sperm ○ Mutation process of mutation does not itself drive evolution. The rate of change in gene frequency from the mutation process is very low because spontaneous mutation rates are low. The mutation rate is defined as the probability that a copy of an allele changes to some other allelic form in one generation. ● Given the genotypes in a population, calculate the frequency of each allele for a single locus with only 2 alleles ○ Use HardyWeinberg Principle ○ p^2 + 2pq + q^2 = 1.0 ● Explain why the number of alleles per gene inndividuacan be different from the number of alleles per gene in population ○ There may be several alleles in a population, but an individual can only inherit 2 alleles (one from mom, one from dad) ● Define and give examples of genetic drift, founder effect, bottleneck effect ○ Genetic drifis when chance events cause changes in frequencies of alleles in a population. ○ Acts more quickly to reduce genetic variation in small populations, underottleneckcan reduce a population's genetic variation by a lot, even if the bottleneck does not last for very many generations ○ Founder effectsoccurs when a new colony is started by a few members of the original population. This small population size means that the colony may have: ■ reduced genetic variation from the original population. ■ a nonrandom sample of the genes in the original population. Phylogenetic Hypotheses: Chapter 20 ● List the kinds of characters used to construct a phylogenetic tree ○ Shared ancestral characters ○ Clade ○ Outgroup ● Interpret relationships shown in a phylogenetic tree: ○ Homologies/analogies ○ Morphology ○ Biochemistry ○ Pattern of embryonic development ○ DNA sequence data ● Which species share a common ancestor? Which group of species shares a more recent common ancestor than another group? Compare trees and determine which show the same hypotheses for relationships among species and which show a different hypothesis of relationships ● Estimate time when common ancestor of a group of species lived in relative terms (beforeafter) and based on branch length (millions of years ago) ● Compare parsimony between 2 phylogenetic trees ○ Identify whether 2 trees show the same or different numbers of evolutionary changes ● Evaluate whether 2 structurally similar characteristics in 2 different organisms are more likely homologous or analogous structures ○ Define homologous structure; define analogous structure ■ Homologous: same structure, different function ■ Analogous: same function, different structure ○ Identify criteria needed to decide ■ Homology: recent common ancestor ■ Analogy: Common ancestor is long time ago ○ Know how to use the criteria to make your decision Macroevolution – Chapter 23 ● Radiometric dating: explain what is measured and how time elapsed is calculated; choose appropriate halflife duration for determining potential age of rocks or fossils ○ Measures the time passed since death ○ Expressed as half lives ○ Usually Carbon14 (t½ = 5730 years) ● O2 production – who made it, when, and what are the consequences? ○ Aerobic cyanobacteria ○ 1 BYA ○ O2 concentration increased, more life on Earth ● List biochemical evidence supporting 3 domains of life and use characters to draw a phylogenetic tree showing relationships between the 3 domains ● Describe the endosymbiont theory of mitochondria and chloroplast origins and list 4 types of evidence supporting it ○ Host cell (archaeal) ingested but did not digest another cell (aproteobacterium) ○ Evidence: ■ Replication, transcription, translation similar in archaea and eukarya ■ Mitochondrial genome and translation system similar to proteobacteria ■ Circular DNA ■ rRNA genes ■ Ribosome assembly sensitive to streptomycin and chloramphenicol ■ Membrane transport system ■ Reproduce by binary fission ● Identify the corphylum for species we have discussed this semester using a resource such as Encyclopedia of Life (eol.org) and be able to place these phyla in the correct kingdom and domain on a phylogenetic tree. ○ Sea urchin, sand dollaAmoeba, newt, human, pea plant, dog, fruit fly, Streptococcus pneumoniae, Escherichia col mourning dove, mouse, pocket mouse, grasshopper, rtemia, American robin, finch, flower mantid, pigeon, mustard plant, soapberry bug, Tiktaalik, cougar, cattle egret, grackle, humpback whale, leopard ● Know the shared derived characteristics supporting the animal and plant phylogenetic trees shown in Fig. 26.16 (plants) and 27.10 (animals) Vocabulary Pyrimidine C, T, and U; 1 ring Purine A and G; 2 rings 3’ end of nucleoti OH group 5’ end of nucleoti links to PO4 group Antiparall two complementary DNA strands running opposite of each other Transcriptio copying DNA info to mRNA RNA polymerase enzyme that binds to promoter; unwinds DNA double helix Translatio making a protein from the instructions on mRNA Codon 3 base sequence on the mRNA that specifies an amino acid; read 5’ to 3’ Transfer RNA tRNA; matched amino acids to codons on mRNA Messenger RNA mRNA; copy of the DNA code Ribosome organelle containing protein and rRNA; facilitates coupling of tRNA and mRNA Template strand strand of DNA read from 3’ to 5’ by RNA polymerase to make mRNA Coding strand strand of DNA complementary to the template strand; written 5’ to 3’ Anticodon complementary sequence to mRNA codon Point mutatio single DNA nucleotide pair is changed Operon DNA sequence on aprokaryotic chromosome including (in 3’ to 5’ order): a promoter, operator, enzymes Promoter specific DNA nucleotide sequence making start site for transcription of a gene Operator DNA sequence that controls access of RNA polymerase to start transcription Enhancer region of DNA that can be bound by proteins (activators) to activate transcription of a gene. These proteins are usually referred to as transcription actors. Gene expression making a functional product from a gene Transcription facto enhancer proteins; interact with control elements of genes; can enhance or reduce rate of transcription by RNA polymerase Control elements aka response elements; specific binding sites for transcription factors Differentiati becoming specialized in structure and function Cytoplasmic determinant molecules in egg cytoplasm produced by mother and added to eggs; begins process of cell differentiation Histone acetylatio adding an acetyl group to a histone protein reduces binding between nucleosomes DNA methylation enzymes add methyl groups to cytosine; decreases transcription of heavily methylated genes Inductive signa chemical signals secreted by neighboring cells Morphogenesis development of spatial organization in an organism Homeotic genes Hox genes; genes that control anteriorposterior position of limbs, developments of digits and organs HomeobOX DNA sequence in hox genes Homeodomain DNA binding domain in the transcription factor protein EvolutionChange in an population over time Homology characters shared because they were inherited from a common ancestor; may not have same function Analogy characters with similar function because of similar selection, not due to gradual modification of an ancestral structure Biogeography current distributions of species reflect historical locations of continents Gene pool allele frequencies in a population Gene flow individuals from a geographically distinct population bring new alleles into the local population Binomial nomenclature 2 part nameGenus species Classificatio hierarchy of more inclusive categories Taxon names unit at any level of hierarchy Phylogeny evolutionary relationships among organisms Locus location of a gene on a chromosome Gene sequence of DNA nucleotides that codes for a protein Allel version of a gene; codes for a specific version of a character selection pressure some aspect of the environment that reduces survival and reproduction of a phenotype stabilizing selectio extreme characteristics are selected against, intermediate phenotype is favored disruptive selectio environment changes and intermediate phenotype is selected against directional selecti environment changes and a more extreme phenotype is favored Microevolution change in allele frequency in a population over generations genetic drif random events that change allele frequency without regard to whether traits provide a reproductive advantage founder effec potion of a population founds a new colony bottleneck effec population size is drastically reduced; allele frequency changes from one generation to next; population stays in same place after dieoff Parsimony simplest explanation if the most likely; tree with fewest evolutionary changes to get from ancestor to descendent most likely sister tax are each other’s closest relatives because they share an immediate common ancestor Outgroup basal taxon; lineage that diverges early in the evolutionary history of a group shared ancestral character characters originated in the ancestor shared derived character characters different from ancestor and unique to the clade Clade complete group of descendents from a single ancestor Cyanobacteria first prokaryotes; produce oxygen Radiometric dating measures time passed since death using Carbon14 (commonly) Halflife (t time required for half of a substance to decay Endosymbiosis host cell ingested but did not digest other cell Archaea ● Draw a phylogenetic tree consisting of 5 taxa, A, B, C, D, E: ○ Show 1 taxon as an outgroup and show 2 pairs of sister taxa 2 of which are sister taxa. Comparing Transcription and Translation
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