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AGBU – HIGH SCHOOL (PASADENA) AP BIOLOGY OBJECTIVES AND KEY TERMS (Study Guide) UNIT I Chapter 2: The Chemical Context of Life Key Terms: Matter electron Mass atomic number Element mass number Trace element isotope Compound radioactive Atom half life Proton energy Neutron potential energy electron shell orbital valence electrons chemical bond molecule electronegativity covalent bond polar covalent bond ionic bond cation anion ion hydrogen bond Objectives: 1. Define element and compound. 2. State four elements essential to life that make up 96% of living matter. 3. Describe the structure of an atom. 4. Define and distinguish among atomic number, mass number, atomic weight and valence. 5. Given the atomic number and mass number of an atom, determine the number of neutrons. 6. Explain why radioisotopes are important to biologists. 7. Explain how electron configuration influences the chemical behavior of an atom. 8. Explain the octet rule and predict how many bonds an atom might form. 9. Explain why the noble gases are so unreactive. 10. Define electronegativity and explain how it influences the formation of chemical bonds. 11. Distinguish among nonpolar covalent, polar covalent and ionic bonds. 12. Describe the formation of a hydrogen bond and explain how it differs from a covalent or ionic bond. 13. Explain why weak bonds are important to living organisms. 14. Describe how the relative concentrations of reactants and products affect a chemical reaction 15. Describe the chemical conditions on early Earth and explain how they were different from today. Chapter 3: Water and the Fitness of the Environment Key Terms: Cohesion temperature solvent Surface tension calorie solute Adhesion kilocalorie aqueous solution Hydrophilic specific heat mole Hydrophobic heat of vaporization molecular weight Kinetic energy evaporative cooling hydronium ion Heat solution hydroxide ion Objectives: dissociation acid base pH scale buffer acid precipitation 1. Describe how water contributes to the fitness of the environment to support life. 2. Describe the structure and geometry of a water molecule, and explain what properties emerge as a result of this structure. 3. Explain the relationship between the polar nature of water and its ability to form hydrogen bonds. 4. List five characteristics of water that are emergent properties resulting from hydrogen bonding. 5. Describe the biological significance of the cohesiveness of water. 6. Distinguish between heat and temperature. 7. Explain how water’s high specific heat, high heat of vaporization and expansion upon freezing affect both aquatic and terrestrial ecosystems. 8. Explain how the polarity of the water molecule makes it a versatile solvent. 9. Define molarity and list some advantages of measuring substances in moles. 10. Write the equation for the dissociation of water, and explain what is actually transferred from one molecule to another. 11. Explain how acids and bases directly or indirectly affect the hydrogen ion concentration of a solution. 12. Explain how acids and bases directly or indirectly affect the hydrogen ion concentration of a solution. 13. Using the bicarbonate buffer system as an example, explain how buffers work. 14. Describe the causes of acid precipitation, and explain how it adversely affects the fitness of the environment. Chapter 4: Carbon and the Molecular Diversity of Life Key Terms: Organic chemistry structural isomer alcohol Organic molecules geometric isomer carbonyl Vitalism enantiomer aldehyde Mechanism asymmetric carbon ketone Hydrocarbons functional group carboxyl Isomer hydroxyl carboxylic acid amino group amine sulfhydryl thiol phosphater Objectives: 1. Summarize the philosophies of vitalism and mechanism, and explain how they influenced the development of organic chemistry, as well as mainstream biological thought. 2. Explain how carbon’s electron configuration determines the kinds and number bonds carbon will form. 3. Describe how carbon skeletons may vary, and explain how this variation contributes to the diversity and complexity of organic molecules. 4. Distinguish among the three types of isomers: structural, geometric and enantiomers. 5. Recognize the major functional groups, and describe the chemical properties of organic molecules in which they occur. Chapter 5: The Structure and Function of Macromolecules Key Terms: Polymer glycogen protein denaturation Monomer Macromolecule Peptide bond Hydrolysis Carbohydrates Monosaccharide Disaccharide Polysaccharide Glycosidic linkage cellulose chitin condensation reaction protein conformation lipid fat phopholipid tertiary structure ester linkage amino acid polypeptide pyrimidine phophodiester bond native conformation primary structure secondary structure disulfide bridge quaternary structure nucleic acid nucleotide purine DNA RNA pentose starch steroid Objectives: 1. List the levels of biological hierarchy from subatomic particles to macromolecules. 2. Explain how organic polymers contribute to biological diversity. 3. Describe how covalent linkages are formed and broken in organic polymers. 4. Describe the distinguishing characteristics of carbohydrates, and explain how they are classified. 5. List four characteristics of a sugar. 6. Identify a glycosidic linkage and describe how it is formed. 7. Describe the important biological functions of polysaccharides. 8. Distinguish between the glycosidic linkages found in starch and cellulose, and explain why the difference is biologically important. 9. Explain what distinguishes lipids from other major classes of macromolecules. 10. Describe the unique properties, building block molecules and biological importance of the three important groups of lipids: fats, phospholipids and steroids. 11. Identify an ester linkage and describe how it if formed. 12. Distinguish between a saturated and unsaturated fat, and list some unique emergent properties that are consequence of these structural differences. 13. Describe the characteristics that distinguish proteins from the other major classes of macromolecules, and explain the biologically important functions of this group. 14. List and recognize four major components of amino acid, and explain how amino acids may be grouped according to the physical and chemical properties of the side chains. 15. Identify a peptide bond and explain how it is formed. 16. Explain what determines protein conformation and why it is important. 17. Define primary structure and describe how it may be deduced in the laboratory. 18. Describe the two types of secondary protein structure, and explain the role of hydrogen bonds in maintaining the structure. 19. Explain how weak interactions and disulfide bridges contribute to tertiary protein structure. 20. Using collagen and hemoglobin as examples, describe quaternary protein structure. 21. Define denaturation and explain how proteins may be denatured. 22. Describe the characteristics that distinguish nucleic acids from the other major groups of macromolecules. 23. Summarize the functions of nucleic acids. 24. List the major components of a nucleotide, and describe how these monomers are linked together to form a nucleic acid. 25. Distinguish between a pyrimidine and a purine. 26. List the functions of nucleotides. 27. Briefly describe the three-dimensional structure of DNA. Chapter 6: An Introduction to Metabolism Key Terms: Metabolism bond energy Catabolic pathways heat of reaction Anabolic pathways enthalpy Kinetic energy exothermic Potential energy endothermic Thermodynamics spontaneous reaction Closed system free energy Open system exergonic Entropy endergonic equilibrium catalyst enzyme activation energy transition state substrate active site feedback inhibition saturation cofactors coenzymes competitive inhibitors noncompetitive inhibitors cooperativity induced fit Objectives: 1. Explain the role of catabolic and anabolic pathways in the energy exchanges of cellular metabolism. 2. Distinguish between kinetic and potential energy. 3. Distinguish between open and closed systems. 4. Explain, in their own words, the First and Second Laws of Thermodynamics. 5. Explain why highly ordered living organisms do not violate the Second Law of Thermodynamics. 6. Distinguish between entropy and enthalpy. 7. Write the Gibbs equation for free energy change. 8. Explain how changes in enthalpy, entropy and temperature influence the maximum amount of useable energy that can be harvested from a reaction. 9. Explain the usefulness of free energy. 10. List two major factors capable of driving spontaneous processes. 11. Distinguish between exergonic and endergonic reactions. 12. Describe the relationship between equilibrium and free energy change for a reaction. 13. Describe the function of ATP in the cell. 14. List the three components of ATP and identify the major classes of macromolecules to which it belongs. 15. Explain how ATP performs cellular work. 16. Explain why chemical disequilibrium is essential for life. 17. Describe the energy profile of a chemical reaction including activation energy (E A), free energy change (deltaG) and transition state. 18. Describe the function of enzymes in biological systems. 19. Explain the relationship between enzyme structure and enzyme specificity. 20. Explain the induced fit model of enzyme function and describe the catalytic cycle of an enzyme. 21. Describe several mechanisms by which enzymes lower activation energy. 22. Explain how substrate concentration affects the rate of an enzyme-controlled reaction. 23. Explain how enzyme activity can be regulated or controlled by environmental conditions, cofactors, enzyme inhibitors and allosteric activation regulators. 24. Distinguish between allosteric activation and cooperativity. 25. Explain how metabolic pathways are regulated. UNIT II Chapter 7: A Tour of the Cell Key Terms: Magnification Resolving power Light microscope SEM TEM Cell fractionation Cytoplasm Cytosol Nucleus Nuclear envelope Chromatin Chromosome Nucleolus Ribosome Endomembrane system Vesicles Mitochondrial matrix Gap junctions endoplasmic reticulum smooth ER rough ER Golgi apparatus cis face trans face lysosomes phagocytosis macrophages food vacuole contractile vacuole central vacuole tonoplast peroxisome mitochondria intermembrane space extracellular matrix Plasmodesmata plastid amyloplast chromoplast chloroplast thylakoid thylakoid space grana cytoskeleton flagella microtubules microfilaments intermediate filaments centriole cilia centrosome desmosomes tight junctions actin myosin basal body cell wall collagen integrin stroma tubulin Objectives: 1. Describe techniques used to study cell structure and function. 2. Distinguish between magnification and resolving power. 3. Describe the principles, advantages and limitations of the light microscope, transmission electron microscope and scanning electron microscope. 4. Describe the major steps of cell fractionation and explain why it is a useful technique. 5. Distinguish between prokaryotic and eukaryotic cells. 6. Explain why there are both upper and lower limits to cell size. 7. Explain why compartmentalization is important in eukaryotic cells. 8. Describe the structure and function of the nucleus, and briefly explain how the nucleus controls protein synthesis in the cytoplasm. 9. Describe the structure and function of a eukaryotic ribosome. 10. List the components of the endomembrane system, describe their structures and functions and summarize the relationships among them. 11. Explain how impaired lysosomal function causes the symptoms of storage diseases. 12. Describe the types of vacuoles and explain how their functions differ. 13. Explain the role of peroxisomes in eukaryotic cells. 14. Describe the structure of a mitochondrion and explain the importance of compartmentalization in mitochondrial function. 15. Distinguish among amyloplast, chromoplast and chloroplast. 16. Identify the three functional compartments of a chloroplast, and explain the importance of compartmentalization in chloroplast function. 17. Describe probable functions of the cytoskeleton. 18. Describe the structure, monomers and functions of microtubules, microfilaments and intermediate filaments. 19. Explain how the ultrastructure of cilia and flagella relates to their function. 20. Describe the structure and list some functions of the extracellular matrix in animal cells. 21. Describe the structure of intercellular junctions found in plant and animal cells, and relate their structure to function. Chapter 8: Membrane Structure and Function Key Terms: Phospholipids bilayer carrier-mediated Amphipathic transport Fluid mosaic model permease Integral protein diffusion Peripheral proteins osmosis Selective permeability dialysis Facilitated diffusion active transport Concentration gradient bulk flow Membrane potential electrogenic pump Signal-transduction second messenger Pathway water potential osmotic potential solution solvent solute hypertonic hypotonic isotonic sodium-potassium pump proton pump cotransport exocytosis endocytosis phagocytosis pinocytosis receptormediated endocytosis Objectives: 1. Describe the function of the plasma membrane. 2. Explain how scientists used early experimental evidence to make deductions about membrane structure and function. 3. Describe the fluid properties of the cell membrane and explain how membrane fluidity is influenced by membrane composition. 4. Explain how hydrophobic interactions determine membrane structure and function. 5. Describe how proteins are spatially arranged in the cell membrane and how they contribute to membrane function. 6. Describe factors that affect selective permeability of membranes. 7. Define diffusion: explain what causes it and why it is a spontaneous process. 8. Explain what regulates the rate of passive transport. 9. Explain why a concentration gradient across membrane represents potential energy. 10. Define osmosis and predict the direction of water movement based upon differences in solute concentration. 11. Explain how bound water affects the osmotic behavior of dilute biological fluids. 12. Describe how living cells with and without walls regulate water balance. 13. Explain how transport proteins are similar to enzymes. 14. Describe one model for facilitated diffusion. 15. Explain how active transport differs from diffusion. 16. Explain how large molecules are transported across the cell membrane. 17. Give an example of receptor-mediated endocytosis. 18. Explain how membrane proteins interface with and respond to changes in the extracellular environment. 19. Describe a simple signal-transduction pathway across the membrane including the roles of first and second messengers. Chapter 9: Cellular Respiration: Harvesting Chemical Energy Key Terms: Fermentation NAD+ cytochrome Cellular respiration FADH2 heme group Phophorylation ETC dehydrogenase Oxidative phophorylation ubiquinone proton pump Substrate-level cristae proton gradient Phophorylation intermembrane chemiosmosis Coenzyme space electon carrier proton-motive force ATP synthase aerobic anaerobic oxidation reduction Kreb’s cycle Objectives: 1. Diagram energy flow through the biosphere. 2. Describe the overall summary equation for cellular respiration. 3. Destinguish between substrate-level phosphorylation and oxidative phosphorylation. 4. Explain how exergonic oxidation of glucose is coupled by endergonic synthesis of ATP. 5. Define oxidation and reduction. 6. Explain how redox reactions are involved in energy exchanges. 7. Define coenzyme and list those involved in respiration. 8. Describe the role of ATP in coupled reactions. 9. Describe the structure of coenzymes and explain how they function in redox reactions. 10. Explain why ATP is required for the preparatory steps of glycolysis. 11. Write a summary equation for glycolysis and describe where it occurs in the cell. 12. Describe how pyruvate links glycolysis to Kreb’s cycle. 13. Describe the location and the molecules out of Kreb’s cycle. 14. Explain how the exergonic slide of electrons down the ETC is coupled in the endergonic production of ATP by chemiosmosis. 15. Summarize the net ATP yield from the oxidation of a glucose molecule. 16. Describe the fate of pyruvate in the absence of oxygen. 17. Explain why fermentation is necessary. 18. Distinguish between aerobic and anaerobic metabolism. Chapter 10: Photosynthesis Key Terms: Autotrophic electromagnetic radiation Photoautotroph wavelength Chemoautotroph electromagnetic spectrum Heterotrophic photon Chloroplast pigments Chlorophyll spectrophotometer Mesophyll absorption spectrum Stomata chlorophyll a Vascular bundles stroma Thylakoid thylakoid membrane Thylakoid space CAM pathway accessory pigments chlorophyll b carotenoids ground state excited state photosystem antenna assembly reaction center primary elec. acceptor P700 P680 cyclic electron flow noncyclic el. flow photophosphorylation Calvin cycle PGAL rubisco RuBP Melvin Calvin photorespiration C4 pathway Objectives: 1. Distinguish between autotrophic and heterotrophic nutrition. 2. Distinguish between photosynthetic autotrophs and chemosynthetic autotrophs. 3. Describe the location and structure of the chloroplast. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. Explain how chloroplast structure relates to its function. Write a summary equation for photosynthesis. Describe the wavelike and particlelike behaviors of light. List the wavelengths of light that are most effective for photosynthesis. Explain what happens when chlorophyll or accessory pigments absorb photons. List the components of a photosystem and explain their function. Trace electron flow through photosystems II and I. Compare cyclic and noncyclic electron flow and explain the relationship between these components of the light reactions. Summarize the light reactions with an equation and describe where they occur. Summarize the carbon-fixing reactions of the Calvin cycle. Describe the role of ATP and NADPH in the Calvin cycle. Describe what happens to rubisco when the O2 concentration is much higher than CO2. Describe the major consequences of photorespiration. Describe two important photosynthetic adaptations that minimize photorespiration. Describe the fate of photosynthetic products. Chapter11: The Reproduction of Cells Key Terms: Cell division mitosis Genome cytokinesis Density-dependent interphase Inhibition S phase Somatic cells G1 phase Chromosomes G2 phase Chromatin prophase Sister chromatids metaphase Centromere anaphase Centriole telophase M phase mitotic spindle centrosome kinetochore microtubules nonkinetochore micro. asters metaphase plate cleavage cleavage furrow MPF transformation cell plate binary fission growth factor restriction point kinase cyclin Cdk cancer cell cycle Objectives: 1. Define genome and state what major events must occur during cell division for the entire genome to be passed on to daughter cells. 2. Describe the process of binary fission in prokaryotes. 3. Describe the composition of chromosomes and explain how chromosomal structure changes in preparation for cell division. 4. Describe how chromosome number changes throughout the human life cycle. 5. List the phases of the cell cycle and describe the sequence of events that occurs during each phase. 6. Describe what major events occur during the G1, S and G2 periods of interphase, and describe what characterizes a G2 interphase cell. 7. Distinguish between interphase and mitosis phase. 8. List the phases of mitosis and describe the events characteristic of each phase. 9. Recognize the phases of mitosis from diagrams. 10. Compare cytokinesis in plants and animals. 11. List several factors, identified from cell tissue-culture studies, which stimulate or inhibit cell growth. 12. Describe what point in the cell cycle determines whether a cell will. 13. Explain how MPF induces the changes that occur in mitosis and describe what causes the cyclical change in MPF concentration. 14. Explain how abnormal cell division of cancerous cells differs from normal cell division. UNIT III Chapter 12: Meiosis and Sexual Life Cycles Key Terms: Heredity homologous chromosomes Genetics variation Gene sex chromosomes Life cycle diploid Somatic cell haploid Asexual repr. Gamete Sexual repr. Fertilization zygote meiosis meiosis I synapsis tetrad sporophyte karyotype chiasmata locus autosome independent assortment sister chromatid crossing over Objectives: 1. Explain why organisms only reproduce their own kind, and why offspring more closely resemble their parents than unrelated individuals of the same species. 2. Explain what makes heredity possible. 3. Distinguish between asexual and sexual reproduction. 4. Indicate where in the human body mitosis and meiosis occur; which cells are the result of mitosis and meiosis; and which cells are diploid or haploid. 5. Distinguish sporophyte and gametophyte. 6. List the phases of meiosis I and meiosis II and describe the events characteristics of each phase. 7. Recognize the phases of meiosis from diagrams. 8. Describe the process of synapsis during prophase I and explain how genetic recombination occurs. 9. Describe key differences between mitosis and meiosis and distinguish between the chromosomal arrangement during metaphase of both processes. 10. Distinguish between mitotic interphase and meiotic interphase. 11. Explain how independent assortment, crossing over and random fertilization contribute to genetic variation in sexually reproducing organisms. 12. Explain why inheritable variation was crucial to Darwin’s theory of evolution. 13. List the sources of genetic variation. Chapter 13: Mendel and the Gene Idea Key Terms: Blending theory heterozygous Gregor Mendel phenotype True-breeding genotype P generation monohybrid F1 generation testcross F2 generation dihybrid Mendel’s law of law of independent Segragation assortment Recessive allele incomplete dominant ABO blood system pleiotropy epistasis quantitative character polygenic inheritance norm of reaction lethal recessive carriers cystic fibrosis lethal dominant Huntington’s disease amniocentesis chorionic villi sampling ultrasound alleles dominant allele codominance Homozygous multiple alleles sickle-cell disease Tay-Sachs disease Objectives: 1. Describe the favored model of heredity in the 19th century prior to Mendel, and explain how this model was inconsistent with observations. 2. Explain how Mendel’s hypothesis of inheritance differed from the blending theory of inheritance. 3. List several features of Mendel’s methods that contributed to his success. 4. List four components of Mendel’s hypothesis that led him to deduce the law of segregation. 5. State, in their own words, Mendel’s law of segregation. 6. Use a Punnett square to predict the results of a monohybrid cross and state the phenotypic and genotypic ratios of F2 generation. 7. Distinguish between genotype and phenotype; heterozygous and homozygous; dominant and recessive. 8. Explain how a testcross can be used to determine if a dominant phenotype is homozygous or heterozygous. 9. Define random event, and explain why it is significant that allele segregation during meiosis and fusion of gametes at fertilization are random events. 10. Use the rule of multiplication to calculate the probability that a particular F2 individual will be homozygous recessive or dominant. 11. Given a Mendelian cross, use the rule of addition to calculate the probability that a particular F2 individual will be heterozygous. 12. State Mendel’s law of independent assortment. 13. Use a Punnett square to predict the results of a dihybrid cross and state the phenotypic and genotypic ratios of the F2 generation. 14. Give an example of incomplete dominance and explain why it is not evidence for the blending theory of inheritance. 15. Explain how the phenotypic expression of the heterozygote is affected by complete dominance, incomplete dominance and codominance. 16. Describe the inheritance of the ABO blood system and explain why the IA and IB alleles are said to be codominant. 17. Define and give examples of pleiotropy. 18. Explain what is meant by “one gene is epistatic to another.” 19. Describe a simple model for polygenic inheritance, and explain why most polygenic characters are described in quantitative terms. 20. Describe how environmental conditions can influence the phenotypic expression of a character. 21. Given a simple example of a pedigree, deduce the genotypes for some of the family members. 22. Describe the inheritance and expression of cystic fibrosis, Tay-Sachs disease and sickle-cell disease. 23. Explain how a lethal recessive gene can be maintained in a population. 24. Explain why lethal dominant genes are much more rare than lethal recessive genes. 25. Explain how carrier recognition, fetal testing and newborn screening can be used in genetic screening and counseling. Chapter 14: The Chromosomal Basis of Inheritance Key Terms: Morgan locus Drosophila melanogaster chromosome map Wild type map unit Mutant phenotype point mutation Linkage chromosomal Sex linkage mutation Genetic autosome Recombination sex chromosome Recombinant deletion translocation Barr body nondisjunction aneuploidy polyploidy trisomy triploidy duplication inversion amniocentesis Down Syndrome genomic imprinting Fragile-X syndrome Huntington’s disease parental type Objectives: 1. Explain how the observations of cytologists and geneticists provided the basis for the chromosome theory of inheritance. 2. Explain why Drosophila melanogaster is a good experimental organism. 3. Define linkage and explain why linkage interferes with independent assortment. 4. Explain how crossing over can unlink genes. 5. Map a linear sequence of genes on a chromosome using given recombination frequencies from experimental crosses. 6. Describe sex determination in humans. 7. Describe the inheritance of a sex-linked gene such as color-blindness. 8. Explain why a recessive sex-linked gene is always expressed in human males. 9. Distinguish among nondisjunction, aneuploidy and polyploidy; explain how these major chromosomal changes occur and describe the consequences. 10. Distinguish between trisomy and triploidy. 11. Distinguish among deletions, duplications, translocations and inversions. 12. Describe the effects of alterations in chromosome structure, and explain the role of position effects in altering the phenotype. 13. Describe the type of chromosomal alterations implicated in the following human disorders: Down syndrome, Klineferlter syndrome, extra X, triple-X syndrome, Turner syndrome, cri du chat syndrome and chronic myelogenous leukemia. Chapter 15: The Molecular Basis of Inheritance Key Terms: Griffith deoxyribose Transromation ribose Bacteriophage nitrogen base Hershey purine Chase pyrimidine Chargaff adenine Chargaff’s rules thymine Watson guanine Crick cytosine Franklin nucleoside Nucleotide triphosphate Nucleic acids semiconservative replication conservative replication ultracentrifugation origin of replication replication fork replication bubble helicase ligase excision repair single-strand binding protein primer primase DNA polymerase replication complex Okazaki fragments leading strand lagging strand mismatch repair antiparallel Objectives: 1. Explain why researchers originally thought protein was the genetic material. 2. Summarize experiments performed by the following scientists, which provided evidence that DNA is the genetic material: a. Griffith b. Hershey and Chase c. Chargaff 3. List the three components of a nucleotide. 4. List the nitrogen bases found in DNA and distinguish between pyrimidines and purines. 5. Explain how Watson and Crick deduced the structure of DNA and describe what evidence they used. 6. Explain the “base-pairing rule” and describe its significance. 7. Describe the structure of DNA and explain what kind of chemical bond connects the nucleotides of each strand and what type of bond holds the two strands together. 8. Explain semiconservative replication. 9. Describe the process of DNA replication and explain the role of helicase, single strand binding protein, DNA polymerase, ligase and primase. 10. Explain what energy source drives endergonic synthesis of DNA. 11. Define antiparallel and explain why continuous synthesis of both DNA strands is not possible. 12. Distinguish between the leading strand and the lagging strand. 13. Explain how the lagging strand is synthesized when DNA polymerase can add nucleotides only to the 3’ end. 14. Explain the role of DNA polymerase, ligase and repair enzymes in DNA proofreading and repair. Chapter 16: From Gene to Protein Key Terms: “one gene-one enzyme” “one gene-one polypeptide” transcription codon mRNA RNA polymerase Promoter P site A site Initiation factors Deletion Mutagens terminator tRNA anticodon triphosphate nucleotide ribosome rRNA intron exon start codon snRNA elongation factor CAP(mRNA) translocation termination codon release factor wobble effect redundance hnRNA RNA splicing reading frame frameshift mut. splicesome ribozyme Poly-A-tail point mutation base-pair sub missense mut nonsense mut insertion snRNPS Mutagenesis Objectives: 1. Distinguish between “one gene-one enzyme” hypothesis and “one gene-one polypeptide”, and explain why the original hypothesis was changed. 2. Explain how RNA differs from DNA. 3. Briefly explain how information flows from gene to protein. 4. Distinguish between transcription and translation. 5. Describe where transcription and translation occur in eukaryotes; explain why it is significant that, in eukaryotes, transcription and translation are separated in space and time. 6. Define codon, and explain what relationship exists between the linear sequence of codons on mRNA and the linear sequence of amino acids in a polypeptide chain. 7. Explain in what way is the genetic code redundant and unambiguous. 8. Explain the evolutionary significance of a nearly universal genetic code. 9. Explain the process of transcription including the three major steps of initiation, elongation and termination. 10. Describe the general role of RNA polymerase in transcription. 11. Explain how RNA polymerase recognizes where transcription should begin. 12. Distinguish among mRNA, tRNA and rRNA. 13. Describe the structure of tRNA and explain how the structure is related to function. 14. Given a sequence of bases in DNA, predict the corresponding codons transcribed on mRNA and the corresponding anticodons of tRNA. 15. Describe the wobble effect. 16. Describe the structure of ribosome, and explain how this structure relates to function. 17. Describe the process of translation, including initiation, elongation and termination and explain what enzymes, protein factors and energy sources are needed for each step. 18. Describe what determines whether a ribosome will be free in the cytosol or attached to rough ER. 19. Explain how eukaryotic mRNA is processed before it leaves the nucleus. 20. Describe some biological functions of introns and gene splicing. 21. Explain why base-pair insertions or deletions usually have a greater effect than base-pair substitutions. UNIT IV Chapter 22: Descent with Modification: A Darwinian View of Life Key Terms: On the Origin of Species by Means of Natural Selection Darwin evolution idealism Linneaus taxonomy fossils Paleontology Cuvier gradualism Lyell uniformitarianism Lamarck HMS Beagle Galapagos islands natural selection Common descent descent with Malthus Population modification modern synthesis Orthogenesis population genetics biogeography Homology vestigial organ phylogeny natural theology catastrophism Hutton inheritance of aquired charac Wallace artificial selection mutations homologous structures Objectives: 1. State the two major points Darwin made in The Origin of Species concerning the Earth’s biota. 2. Describe Cuvier’s contribution to paleontology. 3. Explain how Cuvier and his followers used the concept of catastrophism to oppose evolution. 4. Explain how the principle of gradualism and Lyell’s theory of uniformitarianism influenced Darwin’s ideas about evolution. 5. Describe Lamarck’s model for how adaptations evolve. 6. Describe how Wallace influenced Darwin. 7. Explain what Darwin meant by the principle of common descent and “descent with modification.” 8. Explain what evidence convinced Darwin that species change over time. 9. State three inferences Darwin made from his observations, which led him to propose natural selection as mechanism for evolutionary change. 10. Explain why variation was so important to Darwin’s theory. 11. Explain how Malthus’ essay influenced Darwin. 12. Distinguish between artificial and natural selection. 13. Explain why the population is the smallest unit that can evolve. 14. Explain how natural selection results in evolutionary change. 15. Explain why the emergence of population genetics was an important turning point for evolutionary theory. 16. Describe the lines of evidence Darwin used to support the principle of common descent. 17. Describe how molecular biology can be used to study the evolutionary relationships among organisms. 18. Explain the problem with the statement that Darwinism is “just a theory.” 19. Distinguish between the scientific and colloquial use of the word “theory.” Chapter 23: The Evolution of Population Key Terms: Species inbreeding Gene flow assortative mating Gene pool polygenic traits Fixed allele morphs Microevolution polymorphic Hardy-Weinberg geographic variation Equilibrium cline Nonadaptive point-mutation Sampling error bottleneck effect sexual recombination balanced polymorphism heterozygous advantage sickle-cell anemia frequency-dependent selection neutral variation adaptive evolution founder effect relative fitness pleiotropy stabilizing selection directional selection diversifying select. sexual dimorphism sexual selection genetic drift Objectives: 1. Explain how microevolutionary change can affect gene pool. 2. State the Hardy-Weinberg theorem. 3. Write the general Hardy-Weinberg equation and use it to calculate allele and genotype frequencies. 4. Explain the consequences of Hardy-Weinberg equilibrium. 5. Describe the usefulness of the Hardy-Weinberg model to population geneticists. 6. List the conditions a population must meet in order to maintain Hardy-Weinberg equilibrium. 7. Explain how genetic drift, gene flow, mutation, nonrandom mating and natural selection can cause microevolution. 8. Explain the role of population size in genetic drift. 9. Distinguish between the bottleneck effect and the founder effect. 10. Explain why mutation has little quantitative effect on a large population. 11. Describe how inbreeding and assortative mating affect a population’s allele frequencies and genotype frequencies. 12. List some factors that can produce geographical variation among closely related populations. 13. Explain why even though mutation can be a source of genetic variability, it contributes a negligible amount to genetic variation in a population. 14. Explain how genetic variation may be preserved in a natural population. 15. Give the cause of nearly all genetic variation in a population. 16. Describe what selection works on and what factors contribute to the overall fitness of a genotype. 17. Distinguish among stabilizing selection, directional selection and diversifying selection. 18. Define sexual dimorphism and explain how it can influence evolutionary change. 19. Give at least four reasons why natural selection cannot breed perfect organisms. Chapter 24: The Origin of Species Key Terms: Anagenesis mechanical isolation Cladogenesis gametic isolation Morphospecies postzygotic Biological species reduced hybrid Reproductive barrier fertility Prezygotic reduced hybrid Habitat isolation viability Temporal isolation behavioral isolation adaptive radiation sympatric speciation peripheral isolate polyploidy autopolyploidy tetraploid allopolyploidy adaptive landscape adaptive peak peak shift hybrid zone gradualism punctuated equil. allopatric speciation Objectives: 1. Distinguish between anagenesis and cladogenesis. 2. Define morphospecies and explain how this concept can be useful to biologists. 3. Define biological species. 4. Describe some limitations of the biological species concept. 5. Explain how gene flow between closely related species can be prevented. 6. Distinguish between prezygotic and postzygotic isolating mechanisms. 7. Describe five prezygotic isolating mechanisms and give an example of each. 8. Explain why many hybrids are sterile. 9. Explain how hybrid breakdown maintains separate species even if gene flow occurs. 10. Distinguish between allopatric and sympatric speciation. 11. Explain the allopatric speciation model and describe the role of intraspecific variation and geographical isolation. 12. Describe the adaptive radiation model and use it to describe how it might be possible to have many sympatric closely related species even if geographic isolation is necessary for them to evolve. 13. Define sympatric speciation and explain how polyploidy can cause reproductive isolation. 14. List some points of agreement and disagreement between the two schools of thought about the tempo of speciation (gradualism vs punctuated equilibrium). Chapter 24: Tracing Phylogeny: Macroevolution, the Fossil Record, and Systematics Key Terms: Macroevolution allometric growth systematics DNA sequencing Fossil taxonomy paleontologists molecular clocks Sedimentary rock binomial nomenclature divergence sedimentation Genus convergence trace fossils species selection Petrification geological time scale relative dating index fossil Absolute dating radiometric dating half-life carbon-14 Racemization preadaptation biogeography continental drift Pangaea adaptive zone adaptive radiation phylogeny Phylogenetic tree taxon Homology analogy Cladogram classical evolutionary Taxonomy polyphyletic paraphyletic convergent evolution cladistics shared primitive modern synthesis character Objectives: 1. Explain the importance of the fossil record to the study of evolution. 2. Describe how fossils form. 3. Distinguish between relative and absolute dating. 4. Explain how isotopes can be used in absolute dating. 5. Explain how preadaptation can result in macroevolutionary change. 6. Explain how modification of regulatory genes can result in macroevolutionary change. 7. Explain how continental drift may have played a role in macroevolutionary change. 8. Describe how radiation into new adaptive zones could result in macroevolutionary change. 9. Explain how mass extinctions could occur and affect evolution of surviving forms. 10. Distinguish between a taxon and taxonomy. 11. Describe the contribution Linneaus made to biology. 12. Distinguish between a taxon and a category. 13. List the major taxonomic categories from the most to least inclusive. 14. Explain why it is important when constructing a phylogeny to distinguish between homologous and analogous character traits. 15. Distinguish between homologous and analogous structures. 16. Distinguish between a monophyletic and polyphyletic group, and explain what is meant by a “natural taxon.”