Courses

LS 1

Course Description

LS 1: Evolution, Ecology, and Biodiversity (5)

Lecture, three hours; laboratory, two hours; one field trip. Introduction to principles and
mechanisms of evolution by natural selection; population, behavioral, and community ecology; and
biodiversity, including major taxa and their evolutionary, ecological, and physiological
relationships. P/NP or letter grading.

List of Topics

ORIGINS OF LIFE

  1. Why do we think life originally evolved from non-living materials on this planet? How might this have occurred?
  2. What are the oldest fossils? Explain their importance both evolutionarily and ecologically. How did these early organisms change the world?
  3. What is the endosymbiotic theory for the evolution of eukaryotic cells? How does it account for the nucleus, mitochondria, chloroplasts and plasma membranes?

EVOLUTIONARY PROCESSES

  1. Using modern genetic terms, define evolution.
  2. How did Darwin formulate his ideas about evolution via natural selection? How were the following relevant to him: variation, inheritance patterns, and population growth?
  3. By what mechanisms can evolution occur?
  4. What is sexual selection? Give examples of behaviors and physical traits it has produced.
  5. Giving examples, discuss how physical sexual dimorphism gives insight into mating systems.
  6. Why is creationism not a scientific alternative to evolution?
  7. Describe and provide examples of the following evolutionary patterns: divergence, convergence, and adaptive radiation.
  8. From an evolutionary perspective, what is a “successful” organism? How is this related to the concept of “fitness”?
  9. Demonstrate how to predict the phenotypes in a population from data on allele frequencies. Using the Hardy Weinberg equations, determine whether a population is undergoing evolutionary change. What assumptions and variables does this equation rely upon?
  10. What is the significance of genetic drift and the bottleneck effect for populations?
  11. What is the relationship between a phenotype and a genotype?
  12. Be able to discuss the evolution of and differences between instinctive and learned behaviors.
  13. What is inclusive fitness?
  14. How can natural selection produce complex organs such as eyes or wings?
  15. Describe evidence that natural selection can influence behaviors as well as physical traits.

SPECIATION AND EXTINCTION

  1. What is a species? What difficulties can arise in applying this definition in nature?
  2. How is a population distinct from a species? Why is this distinction important?
  3. What is necessary for speciation to occur?
  4. What factors influence extinction?
  5. Why has the evolution of a species or higher taxon so rarely been observed?
  6. Describe some of the causes of population and species extinctions.
  7. Discuss mass extinctions. How do we know they have occurred? What has caused them?

PHYLOGENY AND SYSTEMATICS

  1. Using the concepts of cladistic analysis, explain why the Protista are not a valid taxonomic unit (clade).
  2. How is DNA used to infer evolutionary relationships?
  3. What is the primary goal of modern systematics? How is this related to the system of binomial nomenclature?
  4. What are shared derived characters and what is their relevance to establishing phylogenies?
  5. Giving examples of each, distinguish between monophyletic and polyphyletic groups of organisms.
  6. What are the three domains of life? Where are they found, and why is this important?

THE EVOLUTION OF BIODIVERSITY

  1. How do organisms gather information from their environment? Discuss the range of solutions seen in nature.
  2. How do surface-area-to-volume ratios influence the evolution of body plans and organs in animals and plants?
  3. At least 5 groups of the Protista are common and important members of local ecosystems. Comment briefly upon the biology and or importance of one or more members of each of the following groups: (a) Protozoa (b) Green Algae (c) Red Algae (d) Brown Algae (e) Dinoflagellates
  4. What characteristics separate the plants, algae, animals and fungi?
  5. Discuss the evolutionary origin of the animals, include the importance of multicellularity, organs, body cavities, sensory systems and cephalization.
  6. Discuss the ecological importance of the fungi, mentioning mycorrhizal associations, recycling of organic materials and competition with bacteria.
  7. The least organized of all animal groups are the members of the sponges. What characteristics distinguish the Phylum Porifera from all other animals?
  8. Cnidaria are distinguished from other animals by the possession of nematocysts, and having only two cell layers, endoderm and ectoderm. Discuss the evolutionary or ecological importance of each of these traits.
  9. Explain both the differences and similarities between the polyp and medusa phases in the cnidarians.
  10. Explain how the radula is used by mollusks. Which group of mollusks has no radula? Why?
  11. Distinguish the feeding habits of the following groups of mollusks: (a) Snails (b) Clams (c) Cephalopods (d) Chitons
  12. Explain the function of the mantle and foot in each of the mollusks listed above.
  13. Discuss the advantages and disadvantages of the exoskeleton of the Arthropods. Make sure you discuss growth, gas exchange, water relations, muscle attachment and excretion.
  14. Explain why flight helped the insects to become such a successful group.
  15. Describe the water vascular system of the Echinoderms. How is it used?
  16. How does the skeletal system of the Echinoderms differ from that of the Vertebrates and the Arthropods?
  17. Describe the feeding habits and anatomical specializations for feeding in the following groups: (a) Sea Stars (b) Sea Cucumbers (c) Sea Urchins
  18. Using examples from a variety of taxa, describe the relative advantages and disadvantages of sexual and asexual reproduction.

PLANT FUNCTION AND EVOLUTION

  1. Discuss the evolutionary origin of the plants.
  2. What are the characteristics which separate animals from plants and fungi?
  3. What adaptations were most important as plants and animals moved from the water onto land? Address the significance of water use, support structures, reproductive strategies, and temperature regulation. (You need not go into detail on life cycles or double fertilization.)
  4. Discuss the fertilization strategies of gymnosperms and compare them with those of angiosperms and ferns.
  5. Discuss the co-evolution of angiosperm flowers and pollinators.
  6. Explain the evolutionary and ecological significance of fruits.
  7. What is the significance of “alternation of generations” to sexual reproduction in plants?

EVOLUTION OF VERTEBRATES

  1. Explain why birds are more likely to migrate than are small mammals.
  2. What adaptations make reptiles better able to colonize terrestrial niches than their amphibian ancestors?
  3. Discuss the importance of the evolution of jaws in the fishes.
  4. Which two vertebrate groups are phylogenetically closest to the dinosaurs?
  5. Describe three separate evolutionary origins of flight among the vertebrates.
  6. You should be able to construct a cladogram for all of the groups named in the questions above, and be able to explain why each clade (group) is separated from the others.

ECOLOGY

  1. What are energy flow and biomass pyramids? What are the consequences of inefficient energy transfer?
  2. What is the theory of island biogeography? How are island size and distance from the mainland related to colonization and extinction rates?
  3. Describe and illustrate curves for logistic and exponential growth. Include in your discussion the concept of carrying capacity and difficulties in determining it.
  4. What is a life history strategy? Give examples of organisms that exhibit vastly different life histories.
  5. Describe the past and present growth pattern of the human population.
  6. Discuss the importance of competition, predation, and symbiosis in the structuring of natural communities.
  7. Discuss the ecological similarities and differences between the insects and crustaceans.

CONSERVATION BIOLOGY

  1. What is the importance of algal symbionts to coral reefs? How might this relationship be affected by global warming?
  2. Discuss the endosymbiotic relationship that results in the formation of coral reefs. Explain why coral reefs are considered so important ecologically.
  3. How does the theory of island biogeography give insight into maintaining biodiversity in the face of increased human population sizes?
  4. Explain the differences in effectiveness of preserving individual species versus habitats.
  5. Describe how humans have affected our biotic and abiotic environment, touching on agriculture, desertification, atmospheric changes, and biodiversity.
  6. Explain the idea of Maximum Sustained Yield and discuss why it is difficult to implement.
  7. Discuss how human behavior might be responsible for global warming and ozone depletion?
  8. Why is the preservation of biodiversity in our best interest?

 

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LS 2

Course Description

LS 2: Cells, Tissues, and Organs (4 credits)

Lecture, three hours; discussion, 75 minutes. Enforced requisite: Chemistry 14A or 20A. Introduction to basic principles of cell structure, organization of cells into tissues and organs, and principles of organ systems. Letter grading.

List of Topics

INTRODUCTION TO BIOLOGICAL MOLECULES AND MACROMOLECULES

  1. What is hydrogen bonding? What properties does it give water that make it an important biological molecule?
  2. Using examples, describe three different types of carbohydrates. Why are carbohydrates so effective as energy sources for living organisms?
  3. Using an example, describe what a lipid is. Why do they function so well as energy storage molecules for living organisms?
  4. Using an example, describe what a protein is. What are they chiefly used for in living organisms?
  5. What are the two most important types of nucleic acids found in living organisms? How does their structure enable them to serve as information storage macromolecules?

CELL ORGANIZATION AND MEMBRANES

  1. What is the relationship between the surface area and the volume of a cell? Why does it limit the size a cell can be? How is this related to multicellularity?
  2. Describe the three chief features that distinguish prokaryote and eukaryotic cells.
  3. Describe each of the following important landmarks in eukaryotic cells: nucleus, cytoskeleton, mitochondrion, lysosome, endoplasmic reticulum, Golgi apparatus, cell wall, vacuole, chloroplasts.
  4. What is the structure of cell membranes? How do they resemble a fluid mosaic of lipids, proteins, and carbohydrates?
  5. Using an example for each, describe passive and active transport.
  6. What is osmosis? How does it influence pressure differently in plant and animal cells?
  7. Describe the connections that link cells together and how they facilitate communication.

ENZYMES AND ENERGETICS

  1. Describe two laws govern all conversions of energy from one form to another.
  2. Define and compare potential and kinetic energy.
  3. What is ATP? What features of it suit it to serving as the energy currency in all living organisms?
  4. Describe how organisms use coupled reactions to make unlikely events possible.
  5. Using an example, describe what an enzyme is? By what chemical methods do they help to start reactions?
  6. What factors can enhance or disrupt enzyme function?
  7. What are metabolic pathways? What is the role of enzymes in them?

MITOCHONDRIA AND CELLULAR RESPIRATION

  1. Describe the overall process of cell respiration?
  2. Describe the structure of the mitochondrion. How is the structure related to its function?
  3. Describe the relationship between glycolysis, the Krebs cycles, and chemiosmosis.
  4. What is fermentation? How does it differ from glycolysis?
  5. What are redox reactions? How are they used to help organisms generating usable energy?
  6. What is an electron transport chain? How do cells create concentration gradients and utilize their potential energy?

PHOTOSYNTHESIS

  1. How do pigment molecules “capture” energy from light?
  2. Describe the process by which energy in a photon of light is ultimately harnessed by a photosystem in a plant.
  3. Trace the path of an electron from its donor to its ultimate recipient during photosynthesis.
  4. Describe and distinguish the light reactions of photosynthesis from the dark reactions? What molecules are required and what molecules are produced by set of reactions?
  5. How and where are electrochemical gradients used to produce ATP during photosynthesis?
  6. Distinguish between cyclic and non-cyclic photophosphorylation. Why do plants use both types?
  7. What is photorespiration? Describe two ways in which plants reduce its effects.

HOMEOSTASIS

  1. What is homeostasis? How does it differ between single-celled and multi-cellular organisms?
  2. Describe different strategies by which endothermic and exothermic animals maintain optimal body temperature.
  3. What is basal metabolic rate? How is it related to the thermoneutral zone?

THE ENDOCRINE SYSTEM

  1. What are hormones? Describe two different ways in which they influence target cells.
  2. Using examples describe four major endocrine glands and the hormones that they produce.
  3. Using examples, describe how positive and negative feedback control are used in the endocrine system.
  4. Describe how sex steroids influence the developing fetus to develop as a male or female.
  5. Trace the changes in sex hormones throughout an ovulatory cycle in a woman. How do they initiate and trigger various steps in the cycle?

THE NERVOUS SYSTEM

  1. Describe the components and functions of a nervous system, using the simplest and most complex nervous systems as examples.
  2. Describe the structure and function of a typical motor neuron.
  3. How does a neuron generate and conduct a nerve impulse?
  4. Describe the events that occur at a synapse.
  5. Using examples, describe the structure and function of neurotransmitters.
  6. Using an example, describe how many drugs can interfere with signal transmission at the synapse.
  7. Using an example, describe how sensory cells receive and transmit information.
  8. What are effectors? Using an example, describe how they function.

REPRODUCTION AND ANIMAL DEVELOPMENT

  1. How do sexual and asexual reproduction differ from each other?
  2. Describe the process of fertilization. How does an egg prevent fertilization by multiple sperm cells?
  3. Using examples, describe and distinguish ovipary and vivipary.
  4. Describe the different patterns of cleavage during early development of a sea urchin, frog, and a chicken.
  5. What is gastrulation? Describing the three germ layers, explain how gastrulation influences the ultimate body plan of an individual?
  6. Describe the process of neurulation in vertebrates.
  7. What is totipotency? Distinguish between determination and differentiation in animal development.

RESPIRATION

  1. What is a respiratory surface? What physical factors influence the rate of gas exchange across a respiratory surface?
  2. Describe the variety of respiratory surfaces that occur among insects, fish, and birds.
  3. How does countercurrent flow influence the rate of gas exchange?
  4. Describe the process by which oxygen binds to hemoglobin and to myoglobin. How do the oxygen binding dynamics of these molecules affect respiration?
  5. Describe some changes in the oxygen binding curves of
    hemoglobin in different species and different environments,
    including those seen in low-oxygen environments and those seen
    in human fetuses.

CIRCULATION

  1. Describe what a circulatory system is and when one needed in an organism.
  2. Compare and distinguish open versus closed circulatory systems, giving examples of each.
  3. What is blood? Discuss its components and its functions.
  4. Trace the flow of blood through the human heart and circulatory system, indicating its pressure and oxygen concentration at various points.
  5. Describe the electrical and muscular events involved in the contraction of a human heart.
  6. How do gases and nutrients in the blood get into body tissues? Distinguish between arteries, veins, and capillaries.
  7. What is cardiovascular disease? How does it occur and why does it lead to health problems?

 

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LS 3

Course Description

LS 3: Introduction to Molecular Biology (4 credits)

Lecture, three hours; discussion, 75 Minutes. Enforced requisites: course 2, and Chemistry 14C or 30A. Introduction to basic principles of biochemistry and molecular biology. Letter grading.

List of Topics

STRUCTURE OF DNA, RNA

  1. What is the experimental evidence that DNA is the genetic material?
  2. Describe the structure of DNA and RNA, highlighting their similarities and differences.
  3. What is RNA secondary structure and how is it related to ribozymes?
  4. What is meant by the terms denaturation, renaturation, and hybridization?
  5. What is a probe?

STRUCTURE AND BIOCHEMISTRY OF PROTEINS

  1. Be familiar with properties of all 20 amino acids and know both the three letter and one letter abbreviations
  2. Be able to draw a peptide bond and describe the major features of alpha-helices and beta-sheets.
  3. What is the difference between tertiary structure and quaternary structure? What are domains and motifs?
  4. What is a disulfide bond? What are the other major post-translational modifications?
  5. What is an example of protein processing? How is it important for protein function?
  6. What are the basic structural features of antibodies and how are they used as tools in molecular biology?
  7. How can enzyme activity be regulated?

PROTEIN PURIFICATION AND ANALYSIS

  1. Using an example, describe a biochemical assay.
  2. What is the basis of separation of proteins by SDS polyacrylamide gel electrophoresis? How does 2-D gel electrophoresis separate proteins?
  3. How are specific proteins detected from crude extracts using western blots?
  4. How are proteins purified by immunoprecipitation? How can protein tags facilitate purification?
  5. How are protein sequences determined?
  6. What does proteomics refer to?
  7. How is mass spectrometry used to analyze multiprotein complexes?

GENOMES AND CHROMATIN

  1. What is a genome? How are prokaryotic and eukaryotic genomes organized?
  2. How are eukaryotic genomes packaged?
  3. What is repetitive DNA and where is it found?
  4. What is FISH and how does it work?

TRANSCRIPTION

  1. What are the major subunits of RNA polymerase? How do prokaryotic and eukaryotic polymerases differ?
  2. What are the major features of a prokaryotic promoter?
  3. Describe all the steps in transcription initiation.
  4. What are the substrates for RNA synthesis?
  5. What is the chemical reaction for synthesis of a phosphodiester bond?
  6. How is prokaryotic transcription terminated? What are the general transcription factors?
  7. What are the elements found in Pol II promoters? How is the pre-initiation complex formed?
  8. What is unique about TBP and its association with DNA?
  9. What role does phosphorylation of the C-terminal domain of Pol II play in transcription?
  10. What is the 5’cap and poly A tail and why are they important?

SPLICING

  1. What is an intron?
  2. What sites in the mRNA are important for splicing?
  3. What is a lariat and when is it formed?
  4. Describe the assembly of the spliceosome. What component of the spliceosome is involved in both recognition of splice sites and in catalysis?
  5. Describe the two transesterification reactions.
  6. What is alternative splicing? How does this differ from exon shuffling?

TRANSLATION

  1. What is the genetic code and what is meant by a degenerate code?
  2. What is an ORF and why are there six reading frames on any given DNA sequence?
  3. What is the function of tRNAs? Why are they called adaptors?
  4. Describe the general structure of tRNAs and specify where the anticodon loop is.
  5. What is the difference between a charged and uncharged tRNA? Be able to write the chemical reaction involved in charging of tRNAs catalyzed by tRNA synthetases.
  6. What is a wobble pair? How does it relate to the degenerate genetic code?
  7. Describe the role of the ribosomal subunits in translation.
  8. What are the A, P and E sites?
  9. What is the ribosome binding site in prokaryotes? Where do ribosomes initially bind in eukaryotes?
  10. How do ribosomes distinguish between AUG signaling the start of a protein and AUG found in the middle of an ORF?
  11. What role do initiation factors play in translation?
  12. Describe the formation of the ternary complex in prokaryotes? How does initiation differ in eukaryotes?
  13. What are the three main steps occurring during elongation?
  14. What is the role of GTP in translation?
  15. What component of the ribosome catalyzes peptide bond formation?
  16. Describe the process of translation termination.

REGULATION OF TRANSCRIPTION

  1. What determines whether a promoter is weak or strong?
  2. What are some of the mechanisms by which activators function to increase transcription initiation and by which repressors function to decrease transcription initiation?
  3. Why are prokaryotic genes frequently organized into operons?
  4. Using an example, describe induction.
  5. Be able to describe the lac operon and how it is regulated by both lactose and glucose.
  6. Give two examples of allosteric regulation in regards to the lac operon.
  7. What is the difference between I- and Oc mutations, and how is the cis/trans test used to distinguish between them? Distinguish between trans-acting and cis-dominant.
  8. Be familiar with the common types of DNA binding motifs found in activators and repressors.
  9. What is the role of nucleosome remodeling and post-translational modifications in transcription initiation in eukaryotes?

DNA REPLICATION

  1. What is the difference between conservative and semi-conservative replication? How did the Meselson-Stahl experiment distinguish between these two models?
  2. What is the difference in substrate requirements between RNA polymerases and DNA polymerases? What other proteins are required for DNA replication?
  3. What is the lagging strand? What is the leading strand?
  4. What type of exonuclease activity is associated with proofreading?
  5. Why is RNA used as a primer in DNA synthesis? Does RNA remain in the final product?
  6. What is the difference between a helicase and a topoisomerase?
  7. What is the structure and function of eukaryotic telomeres? What type of enzyme is telomerase?
  8. What is the difference between mismatch repair and nucleotide excision repair?

VIRUSES

  1. What types of genomes have been found in viruses?
  2. How do RNA viruses alter the central dogma of molecular biology?
  3. Describe the life cycle of a retrovirus.
  4. How are viruses used in molecular biology?

RECOMBINANT DNA TECHNOLOGY

  1. What are restriction enzymes and what is their natural role in prokaryotes?
  2. How does methylation protect the genome from restriction enzymes?
  3. What is the difference between a sticky end and a blunt end?
  4. What is a plasmid and how are these used to make recombinant DNA?
  5. What is the difference between cloning a gene and cloning an organism?
  6. What is PCR and how does it work? How can PCR be used to clone specific genes?
  7. What is a genomic library? What is a cDNA library? How can libraries be screened for specific genes?
  8. Why are bacteriophage useful for cloning genes? What are YAC and BAC vectors and when are they used?
  9. What is an oligonucleotide?
  10. What is the difference between a Southern blot and a northern blot?
  11. Describe the dideoxy sequencing method commonly used today. How are fluorescent labels used in automated sequencing?
  12. What is the principle of chemical synthesis of DNA and how does it differ from DNA synthesis by DNA polymerase?
  13. How do you express genes to overproduce proteins?
  14. What information can be obtained by comparing genomes from different organisms?
  15. What is microarray analysis and how can it be used to study gene expression?

 

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LS 4

Course Description

LS 4: Genetics (5)

Lecture, three hours; discussion, two hours. Enforced
requisite: course 3. Principles of Mendelian inheritance and
chromosomal basis of heredity in prokaryotes and eukaryotes,
recombination, biochemical genetics, mutation, DNA, genetic
code, gene regulation, genes in populations. Letter grading.

List of Topics

MENDELIAN GENETICS

  1. How did Mendel formulate his ideas on heredity? How did his findings relate to Darwin’s theory on evolution by natural selection?
  2. What is a test cross? When is it used?
  3. Describe Mendel’s law of segregation and its role in inheritance.
  4. Describe Mendel’s law of independent assortment.
  5. Using specific examples, describe how genetics has allowed us to understand and minimize the negative impact of rare genetic disorders.
  6. What is a pedigree? How is pedigree analysis used to infer the mode of inheritance of given traits?

CHROMOSOMAL INHERITANCE

  1. What evidence suggests that genes are located on chromosomes?
  2. What is a karyotype? In what ways are karyotypes useful for genetic analyses?
  3. Describe the behavior of chromosomes during mitosis and during meiosis. How do they differ? What is the role of each process in eukaryotic organisms?
  4. In what ways and at what phases does meiosis enhance the genetic variation in a population?
  5. Distinguish sister chromatids from homologous chromosomes.
  6. What are sex-linked traits? How can they be identified?
  7. Why are males more likely to exhibit sex-linked recessive traits?
  8. What is Down syndrome? How is the incidence of the disorder related to the mother’s age?

MUTATION

  1. What are mutations and where do they occur?
  2. Distinguish between point mutations and chromosomal mutations, giving an example of a disease caused by each.
  3. Distinguish between loss-of-function mutations and gain-of-function mutations.
  4. Using the example of malaria resistance and sickle cell anemia, define and describe pleiotropy. How does pleiotropy ensure that certain mutations are able to accumulate in our DNA?
  5. How can mutations nearly always decrease fitness yet at the same time lead to evolution via natural selection?

THE RELATIONSHIP OF GENOTYPES TO PHENOTYPES

  1. What phenomena lead to variations in Mendelian phenotypic ratios? Using examples, be sure to discuss: (a) codominance (b) incomplete dominance (c) epistasis (d) suppression (e) duplication (f) homozygous lethality
  2. Do most traits show full dominance or recessiveness? How do we know this?
  3. Describe suppression and duplication and explain the ramifications of each on evolution.
  4. Using an example, describe complementation and its role in determining genotypes.
  5. What is inbreeding? Why does it increase the frequency of phenotypic expression of recessive traits? Why does this sometimes reduce fitness?
  6. Be able to calculate the probable outcomes of multi-character crosses of diploid organisms.
  7. Distinguish between continuous and discontinuous variation in a population and cite examples of each.

LINKAGE ANALYSIS

  1. What is a three-way cross? How is it useful in determining the linkage patterns of genes?
  2. What are recombination frequencies? How do they reflect patterns of linkage?
  3. How have observations of phenotypes in nature challenged Mendel’s law of independent assortment?
  4. What is a chi-square analysis? Why is such a test for goodness-of-fit necessary for geneticists

POPULATION GENETICS

  1. What is “heterozygote superiority”? How does this explain why a deleterious allele can remain in a population despite the fact that the homozygous dominant genotype is harmful?
  2. Be able to describe and cite examples of the four agents of evolutionary change: (a) mutation (b) migration (c) genetic drift (d) natural selection
  3. Do recessive alleles decrease in frequency in a population over time?
  4. What is Hardy-Weinberg equilibrium? What does it mean if a population is in Hardy-Weinberg equilibrium (or is not)?

BACTERIAL AND PHAGE GENETICS

  1. Distinguish between a selective medium and a non-selective medium, giving examples of each.
  2. What features of bacteria make them good model organisms in genetics?
  3. What three methods of genetic exchange occur in bacteria?
  4. Describe an interrupted mating study and its purpose.
  5. Why is conjugation the most efficient mechanism of gene transfer in bacteria?
  6. Why does an antibiotic resistance highlight a mechanism for genetic exchange in bacteria?
  7. Describe replica plating and its uses in bacterial genetics.
  8. Discuss the life cycle of a bacteriophage. How can bacteriophage infection lead to genetic recombination?
  9. What is a bacterial map? How are map distances measured?
  10. Describe Benzer’s experimental protocols and discuss how his work bridged the gulf between classical genetics and the knowledge of the chemical structure of DNA.
  11. What is intragenic recombination? Why is this important in understanding gene mutations?
  12. Discuss the process of deletion mapping. How does this facilitate the process of mapping point mutation sites at the rII locus?
  13. What is auxotrophic mutation and how is it useful?

GENE STRUCTURE AND FUNCTION

  1. Using the universal genetic code, describe the sequence of amino acids that would result from a given sequence of codons.
  2. Giving an example, define and describe transposons.
  3. Defining both, distinguish introns from exons.
  4. Using PKU as an example, describe the relationship between genetic disease and biosynthetic pathways.
  5. How can the steps in a biosynthetic pathway be determined using nutritional supplementation?
  6. Though each cell contains every gene, only some are active. Why is this?
  7. How is gene regulation controlled?
  8. Using an example, distinguish between positive and negative gene regulation.
  9. What is an open reading frame (ORF) and how is it predicted?

GENOMICS AND GENETIC APPLICATIONS

  1. How are molecular markers used for linkage studies to locate a disease gene and to start the positional cloning of the gene?
  2. Discuss the magnitude, variety, and significance of repetitive sequences in the Eukaryotic genome.
  3. What are restriction fragment length polymorphisms (RFLPs) and short tandem repeat polymorphisms (STRPs) and how are they used in DNA fingerprinting?
  4. What techniques are used to detect variations within a defined chromosome region?
  5. What is meant by DNA fingerprinting? Describe the process.
  6. What is a transgenic organism? How are transgenic organisms used in genetics?
  7. What are genetic screens? How are they used to investigate biological processes?
  8. What is the human genome project and what is its purpose?
  9. What are genetically modified organisms (GMOs)? Describe and discuss their potential benefits?

 

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LS 7A

Course Description

LS 7A. Cell and Molecular Biology (5 Units)

Lecture, three hours; discussion 75 minutes. Enforced requisite: none. Introduction to basic principles of cell structure and cell biology, basic principles of biochemistry and molecular biology. P/NP or letter grading.


 

LS 7B

Course Description

Genetics, Evolution and Ecology (5 Units)

Lecture, three hours; discussion 110 minutes. Enforced requisite: LS 7A. Principles of Mendelian inheritance and population genetics; Introduction to principles and mechanisms of evolution by natural selection; population, behavioral, and community ecology; and biodiversity, including major taxa and their evolutionary, ecological and physiological relationships. Letter grading.


 

LS 7C

Course Description

Physiology and Human Biology (5 Units)

Lecture, three hours; discussion 75 minutes. Enforced requisite: LS 7B. Organization of cells into tissues and organs, and principles of physiology of organ systems. Introduction to human genetics and genomics. Letter grading.


 

LS 10H

Course Description

LS 10H: Research Training in Genes, Genetics, and Genomics (6)

Lecture, 90 minutes; laboratory, six hours; computer laboratory, 90
minutes. Limited to 30 students. Basic training in biological research,
including techniques in genetics, model organism, bioinformatics,
functional genomics, electron microscopy. Part of Undergraduate Research
Consortium in Functional Genomics sponsored by Howard Hughes Medical
Institute Professors Program. Letter grading.

 

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LS 15

Course Description

LS 15: Life: Concepts and Issues (5)

Lecture, three hours; discussion, two hours. Introduction to important
concepts and issues in the field for non-life sciences majors. Topics
include chemistry of life, genetics, physiology, evolution, and ecology
— all explored in lecture and debates, with a writing component. P/NP
or letter grading.

List of Topics

  • The nature of science
  • Science and its relation to human activity
  • Darwin story Basic Evolution
  • Patterns of Evolution
  • Coevolution and symbiosis
  • DNA replication and inheritance
  • Genetic Engineering
  • Sexual reproduction and Genetic Diseases
  • Patterns of sexual reproduction
  • Evolutionary basis of Behavior
  • Sociobiology
  • Human Evolution and behavior
  • Principles of Ecology
  • Biodiversity
  • Global warming, materials cycles & climatic patterns
  • Biogeography & Introduced species
  • Water resources
  • Environmental Legislation and Action
  • Environmental Success Stories and Failures

 

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LS 20

Course Description

LS 20: Quantitative Concepts for Life Sciences (4)

Quantitative skills are essential for success in the life sciences, chemistry, mathematics and physics classes that make up the core curriculum for Life Science majors at UCLA. The LS 20 is a unique interdisciplinary course designed to introduce a variety of quantitative/mathematical concepts and modeling using inquiry-based active learning styles. Mathematical concepts focus on precalculus algebra and introductory statistics required for quantification, analyses, interpretation and modeling of biological data. In addition to learning the approaches and application of mathematical modeling of biological data, students acquire skillsets in computer-based computations and visualization of data using available tools such as Microsoft Excel and Apps on mobile electronic devices. Students are further introduced to computer programming (MIT Scratch) and digital imaging and image processing through hands-on projects to gain an appreciation for the use of technology in scientific investigation. An emphasis will also be placed on learning study skills and time management behaviors to improve student success. (This course prepares students for more advanced Calculus courses LS 30A and LS 30B and also provides them the necessary foundation in quantitative biology to perform well in other courses of the life sciences curriculum)

Lecture, 3 hours.
Discussion/laboratory, 1 hour
Preparation : three years of high school mathematics (up to Algebra II), some basic
familiarity with computers.

Textbook

Activities and notes prepared specifically for this course. These will be made available on the course website.

Major topics, by Week

1. Introduction to biological data and measurements: understanding the
importance of quantification and scientific representation of data in biology.

2-3. Experimentation, probability and statistics: understanding experimental
design, probability distribution, descriptive and inferential statistics.

4-5 Biological Variables, Relationships and Mathematical Functions:
understanding biological variables and their relationships through mathematical functions and
their properties; function domain and range, graphing, evaluation and solving; linear, quadratic
and higher order polynomials, exponential, logarithmic, power and logistic functions.

5-6 Curve fitting and modeling: understanding linear fits and goodness of fit
through linear regression and correlations (residuals, least square error minimization),
developing exponential, logarithmic, polynomial and power function based models.

7-8 Rate of change of biological variables: observing change and estimating
rate of change using exponential growth and decay equations; calculating velocity; understanding
absolute and relative changes.

9-10 Periodicity in biology and trigonometry: understanding oscillating
phenomena and periodicity in biology through trigonometry; some geometry, trigonometric sine,
cosine and tangent functions; trigonometric identities; power spectrum and Fourier series.

 

 


 

LS 23L

Course Description

LS 23L:Introduction to Laboratory & Scientific Methodology (2 credits)

One hour online lecture; three hours laboratory each week. Enforced requisites: Course 2, and Chemistry 14C or 30A. LS23L offers the opportunity to conduct wet-lab and cutting edge bioinformatics laboratory experiments. Undergraduate students will work in groups of three conducting experiments in the areas of physiology, metabolism, cell biology, molecular biology, genotyping and bioinformatics. Letter grading. This course is taken concurrently with the life sciences course “Introduction to Molecular Biology” (LS3).

List of Topics

Introduction to Scientific Methodology

This introductory lab will help you develop the concepts and skills you need to perform scientific investigations, carry out experiments
appropriately, and write reports. You will apply what you learn from this lab to the Pigments of Photosynthesis and
Metabolism labs later in the course.

The Pigments of Photosynthesis

Working with several taxa of photosynthetic organisms, you will explore the physical nature of the pigments that allow the organisms
to trap light energy and convert it into chemical energy. You will utilize thin layer chromatography and spectrophotometry to
examine the pigment composition of these photosynthetic pigments and relate your results to environmental and evolutionary
factors that influence pigment composition in these organisms.

Metabolism in Goldfish

You will use electronic data acquisition tools to explore respiration in animals. Computerized tutorials will guide you in the use of
probeware, oxygen electrodes, and oxygen chambers as you formulate your own predictions about metabolic rates in goldfish
and develop experimental strategies by which to test them.

Rat Dissection

During this lab you will dissect a rat, focusing on the relationship between structure and function in approximately a dozen
major organ systems. In addition to providing detailed guidance with the dissection procedures, computer enhancements will
facilitate comparisons to other mammals.

Microscopy and Histology

This is an introduction to the dissecting and compound microscopes, incorporated into a laboratory investigation of histology.
While becoming familiar with the use of these tools and with the aid of information describing the function of various tissues
and cells, you will relate structure to function as you attempt to deduce the identities of a variety of unknown mammalian
cell and tissue samples. This exercise will enhance your understanding of cell, tissue, and organ systems explored in the rat
dissection lab.

Pipetter Exercise and Analysis of Protein Size Using SDS-PAGE

In this lab you are going to get to know the most commonly used instrument in molecular biology. You will get to learn the proper
ways of operating pipetters during the pipetting exercise. You will then continue on to the SDS-PAGE experiment. One of the
basic ways to understand a protein is to know its mass. There are a few methods to learn the mass of a protein. In this exercise
you will use gel electrophoresis to estimate the mass of the subunits of an unknown protein. In conjunction with information
gathered from other methods, you will also determine the number of subunits of the unknown protein.

Biochemical Assay of b-Galactosidase Activity

b-galactosidase is an enzyme that breaks down lactose into two monosaccharides. You will learn to measure the activity of the
enzyme by measuring the rate at which products appear and the time required for this enzyme to be synthesized. You will also
learn the important concept of using a control in an experiment.

DNA Isolation and Amplification

Polymerase Chain Reaction (PCR) is a technique that allows scientists to make many copies of DNA from a small sample. In
this lab, you will isolate DNA from your cheek cells and then prepare the sample for PCR. The samples will be amplified and
sent out for sequencing for use in lab 5. Good primer design is a vital part of developing a PCR protocol, so you will be asked
to practice creating your own primer pair in the primer design exercise.

Agarose Gel Electrophoresis and Molecular Clocks

In this lab you will receive a portion of your amplified DNA sample from lab 3. You will check for PCR product in two ways: by
visualizing the product on an agarose gel and by checking the concentration using the spectrophotometer. You will also learn
how to use BLAST, ClustalX and Mega4, programs that you will need to be familiar with in order to work with your individual
sequence in lab 5.

Sequence Analysis and Maternal Lineages

In this lab you will receive your mitochondrial DNA sequence, which was sequenced off site after the PCR amplification. You
will then compare it to many other sequences, which will allow you to determine your maternal lineage, based on human
migration patterns. You will learn how to annotate your sequence, and you will re-visit the programs used in lab 4 to create
phylogenetic trees with your own sequence.

 

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LS 30A

Course Description

LS 30A: Mathematics for Life Scientists (5)

This course teaches mathematical modeling as a tool for
understanding the dynamics of biological systems. We will begin with
the fundamental concepts of single-variable calculus, and then
develop single- and multi-variable differential equation models of
dynamical processes in ecology, physiology and other subjects in
which quantities change with time. The laboratory will use the free
computer program Sage for problem-solving, plotting and dynamical
simulation. The necessary basic programming concepts and skills,
such as program flow control and data structures, will be
introduced. (No prior programming experience is assumed.)

Lecture, 3 hours.
Computational laboratory, 2 hours
Preparation : three years of high school mathematics (up to Algebra II), some basic
familiarity with computers.

Textbook

A set of notes, mostly written specifically for this course. These will be made available on the course website.

Major topics, by Week

1. Introduction to modeling and differential equations. The importance of dynamics in biology.

2. State spaces, vector fields and trajectories. Differential
equations as instructions for constructing vector fields. Behavior
as a trajectory through state space. Attractors and forms of
behavior.

3-4 The derivative. Algebraic and geometric interpretations.
Simple rules for differentiation. The shapes of functions. Maxima,
minima and inflection points. Optimization as an application of the
derivative.

4-5 Integration; linear approximation and Euler’s method. How
trajectories arise from vector fields. Numerical integration.
Recovering f from f′: integration as the area under f′.

Fundamental Theorem of Calculus.

6 Exponential growth and decay. From discrete to continuous
time. Linear differential equations.

7 Equilibrium points and graphical stability analysis. The concept of
dynamical stability. Assessing the stability of equilibria in 1-D.

8 Types of equilibria in 2-D. Stability and instability of equilibria.

9 Bifurcations of fixed points: qualitative changes in behavior from
quantitative changes in parameters. Simple examples of saddle-node and
pitchfork bifurcations in 1- and 2-D. Biological examples.

10 Limit cycle attractors. Oscillations in biology. Negative feedback
as a cause of oscillation. Introduction to Hopf Bifurcation.

 


 

LS 30B

Course Description

LS 30B: Mathematics for Life Scientists (5)

LS30B will continue the dynamics focus of LS30A, while
introducing the concept of matrices and linear transformations.
The goals are to equip the student with some basic tools for
understand the dynamics of multi-variable, non-linear systems.
Examples will come from ecological, physiological, chemical and
other systems.

Lecture, 3 hours.
Computational laboratory, 2 hours.
Preparation: LS 30A (enforced)

Textbook

A set of notes, mostly written specifically for this course.

Major topics, by Week

1 Delay differential equations. Time delays as a cause of oscillation.

2 Nonlinear difference equations and chaos. Discrete logistic equation.
Introduction to properties of chaos. Erratic and aperiodic behavior from
deterministic models

3 Chaos in systems of differential equations. Examples of chaotic
behavior in biology and physiology.

4-5 Concept of a linear function. Vectors and linear transformations of
vectors. Matrices as representing linear transformations in N-space.
Operations on matrices. Matrix multiplication representing the
composition of linear functions.

6 The dynamics of matrix models. Iterated matrices and discrete time
systems: steady states, growth and decay, oscillations.

7 Eigenvalues and eigenvectors. Dynamical significance of eigenvalues
and eigenvectors of matrices that represent linear ODEs.

8 The stability of equilibria in 2D and in N dimensions. Linearization:
analytical approach to stability of nonlinear equations in one
dimension.

9 Partial derivatives. Linear approximations to functions in higher
dimensions.

10 The stability of equilibria in higher dimensions. The Jacobian
matrix in stability analysis. Hopf bifurcation: the role of complex
conjugate eigenvalues.


 

LS 107

Course Description

LS 107. Genetics (5 Units)

Lecture, three hours; discussion 75 minutes. Enforced requisite: Chem14a or 20A; Chem14C or 30A; LS7C and LS23L. Advanced Mendelian genetics, recombination, biochemical genetics, mutation, DNA, genetic code, gene regulation, genes in populations. Letter grading.


 

LS 110

Course Description

LS 110. Career Exploration in Life Sciences

Seminar, two hours. Recommended for sophomore and incoming transfer students. Designed to help life sciences students expand awareness of their interests, needs, and skills to make deliberate career choices. Introduction to many components that go into making effective career decisions to help students explore diversity of career options for life sciences majors. P/NP grading.


 

LS 192A & LS 192B

Course Description

LS 192A: Undergraduate Practicum in Life Sciences (4)

Seminar, two hours. Requisite: course 2 or 3. Limited to
sophomores/juniors/seniors. Training and supervised practicum in
laboratory setting for advanced undergraduate students in courses
related to life sciences. Students work on oral presentation skills and
assist in preparation and presentation of materials and development of
programs under guidance of faculty members. May be repeated once for
credit. Letter grading.

LS 192B: Undergraduate Practicum in Life Sciences (4)

Seminar, two hours. Requisite: course 2 or 3. Limited to
sophomores/juniors/seniors. Training and supervised practicum
for advanced undergraduate students in courses related to life
sciences. Students work on oral presentation skills and assist
in preparation and presentation of materials and development of
programs under guidance of faculty members. Letter grading.

 

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