LAGUARDIA COMMUNITY COLLEGE

CITY UNIVERSITY OF NEW YORK

DEPARTMENT OF NATURAL AND APPLIED SCIENCE

FUNDAMENTALS OF BIOLOGY I

SCB 201

COURSE INFORMATION

Course Coordinator: Professor Joseph McPhee

Fall I 2005

Fundamentals of Biology I SCB 201

Course Coordinator: Professor McPhee Fall I 2005

Fundamentals of Biology I SCB 201

Course Coordinator: Professor McPhee Fall I 2005

* Students are required to complete the study questions listed below in a timely manner. The instructor will periodically check your answers and the resulting grade is worth 10% of your final laboratory grade.

Laboratory Manual must be brought to each laboratory Lecture. Students should read the laboratory exercise prior to entering laboratory. No eating, drinking or smoking in lab.

Laboratory attendance is mandatory. Excessive absences will be deducted from final grade. Completion of Laboratory Reports and individual effort in the laboratory will be considered in the laboratory portion of the final grade.

Fundamentals of Biology I SCB 201

Course Coordinator: Professor McPhee Fall I 2005

SESSION 1 - INTRODUCTION Chapter 1

State the Cell Theory and describe the experiments that support it.

Describe the Darwinian theory of Evolution.

Describe the levels of organization in living systems and some of the methods of classification.

List the steps of the scientific method and apply them to a specific problem.

Define hypothesis, experiment, control, theory, and scientific law.

Describe how the Universe formed and the origin of the molecules of life.

Define what is meant by the terms, matter and energy.

List the stages in the development of the Earth and the formation of Life on Earth.

Define the terms, elements, atom, proton, electron, neutron, isotope and ion.

Define atomic number, and atomic mass.

Draw and describe an electron shell configuration.

Define molecule, compound, single and double bonds.

Describe ionic, covalent, polar, non-polar, hydrogen bonds.

Describe how bonds are formed and broken through the transfer of energy.

Define the term chemical energy and how it relates to bond strength.

Describe the properties of water and its importance in chemical evolution.

Describe the relationship and properties of acids, bases and salts.

Describe the importance of the carbon atom to organic chemistry.

List the components and steps in Miller's Experiment.

Describe the structure of the functional groups: amino, carboxyl, sulfhydryl, aldehyde, alcohol, and ketone.

List the four main classes of biological macromolecules (saccharides, lipids, proteins and nucleic acids), stating their chemical elements, subunits, and role they play in living systems.

Define amino acid, peptide bond, polypeptide, and protein.

Describe the four levels of protein structure.

Describe the mechanism by which enzymes work as organic catalysts.

Compare and contrast the structures of RNA and DNA.

Describe the role of RNA and DNA in the synthesis of macromolecules.

Define monomer, polymer, carbohydrate, monosaccharide, disaccharide, polysaccharide, starch, glycogen, cellulose, pentose and hexose sugars.

Describe the role of carbohydrates in cell structure and metabolism.

Describe the basic chemical structure of the biological membrane.

Define lipid, glycerol, fatty acid, triglyceride, saturated, unsaturated, phospholipid, and steroid.

Describe how phospholipids assemble spontaneously to form the basic membrane.

Define what is meant by the terms permeability and semipermeability.

List and describe methods by which molecules cross the membrane; impermeable, selective permeability, passive transport, diffusion, facilitated diffusion, carrier proteins, pores, osmosis, active transport, sodium-potassium pump, phagocytosis, and pinocytosis.

Describe the three states of osmosis.

Describe the Fluid Mosaic Model.

Describe the different methods used to study cells and their organelles.

Describe the main differences between prokaryotic and eukaryotic cells, as well as between plant and animal cells.

Describe the structure and function of the following nuclear organelles: nucleus, chromosome, nucleolus, and nuclear envelope.

Describe the structure and function of the following organelles: ribosome, endoplasmic reticulum, Golgi complex, lysosome, peroxisome, mitochondrion, vesicle, vacuole, plastid, chloroplast and cell wall.

Define the three classes of transport vesicles.

Describe the structure and function of the following parts of the cytoskeleton: microtubules, microvilli, cilia, flagella, and centriole.

Define the terms respiration, aerobic, anaerobic and fermentation.

Define the term coenzyme, list four and explain the function of each.

Diagram and describe the overall reaction for the oxidation of glucose stating the number of ATP's produced, and why oxygen is needed.

List the starting materials, the end products, and key chemicals in glycolysis and the formation of Acetyl-CoA.

Describe the Chemiosmotic Theory of ATP synthesis, including the role of the electron transport system, the membrane, the electrochemical gradient, and ATP synthetase.

Summarize the number of ATP molecules produced from each step in fermentation.

Contrast aerobic respiration with yeast alcoholic fermentation and muscle lactate fermentation.

Explain how and why muscles go into oxygen debt.

Explain how other nutrients, such as lipids, proteins and polysaccharides enter into the glucose oxidative pathway.

Describe the relationship between cellular respiration and photosynthesis, autotroph and heterotroph, oxidation and reduction.

Name the three main groups of photosynthetic pigments and state the function of each.

Describe the structure of the plant leaf and chloroplast. Define cuticle, epidermis, mesophyll, stomata, vascular bundle, grana, thylakoid, and stroma.

State the colors of light most effective in promoting photosynthesis, and explain why.

Write the overall reaction summary for photosynthesis.

Summarize the input and output for the four steps of photosynthesis: photochemical reactions, electron transport, chemiosmosis, carbon fixation (dark reaction), light reaction.

Describe the two photosystems, including chlorophyll a, P700, P680, antenna pigment, light trap, and reaction center.

Draw the two photosystems and show the energy flow relationships between them.

Explain the C3 cycle of carbon fixation, stating the importance of ribulose bisphosphate, RuBP carboxylase, and the number of turns of the cycle needed to produce a molecule of glucose.

Discuss how various environmental factors control the rate of photosynthesis.

Compare and contrast the C4 and C3 cycles and the relative benefits of each.

Describe the parts of the cell cycle and the three periods of interphase.

Describe the events in each of the stages of mitosis: prophase, metaphase, anaphase, telophase.

Define poles, centrioles, mitotic spindle, colchicine, cleavage furrow, and cell plate.

Describe how the kinetochore controls chromosome partitioning.

List the regulatory factors of the cell cycle and the function of each.

Describe the events in meiosis; include tetrad, synapsis, and separation of homologous chromosomes.

Distinguish between spermatogenesis and oogenesis.

Describe the significance of 'crossing over' in heredity.

Describe how the process of meiosis influences genetic variation.

Describe Mendel's experiments and give reasons why he was successful in discovering the laws governing the inheritance of genetic traits. State his three laws.

Define the terms genotype and phenotype, and their relationship to dominant and recessive.

Define parental (P1), first filial (F1), and second filial (F2) generations; homozygous, heterozygous, allele, monohybrid cross, dihybrid cross, homologous chromosomes, segregation, independent assortment, and linked genes.

Use the Punnett square to predict the results of monohybrid and dihybrid crosses, giving both genotype and phenotype ratios.

Describe the test cross and discuss its use as a genetic tool to distinguish between homozygous and heterozygous genotypes.

Describe how the discovery of linkage and the chromosome theory altered Mendel's original theory.

List and describe the mechanism of some non-Mendelian patterns of inheritance including incomplete dominance, multiple allelism and environmentally-influenced genes.

Describe the structure of the DNA molecule. Define purine, pyrimidine, complementary bases, double helix, antiparallel strands, 3' and 5' ends.

Describe how DNA is coiled and complexed with histones to form chromatin

Define mutation, list some kinds of mutations, and describe the importance of mutations.

Describe Griffith's experiment and how it was able to relate DNA to heredity.

Describe DNA replication, touching on DNA helicase, DNA polymerase, direction of replication, Okazaki fragments, DNA ligase, and replication bubbles.

Compare and contrast the structure of prokaryotic vs. eukaryotic DNA

List three differences between DNA and RNA.

State the "one-gene, one-enzyme" hypothesis.

Define what is meant by the genetic code.

Describe how the genetic code differs between DNA and RNA.

Describe the underlying principal of the Central Dogma.

Define what is meant by the transcription.

Describe the role of the promoter in transcription.

Describe the structure and origin of mRNA, tRNA and rRNA.

Describe the role of RNA polymerase and how it functions in transcription

Describe the structure of pre-mRNA

Describe the post-transcriptional processing of pre-mRNA

Define the terms start and termination signals, pre-mRNA, snRNAs, cap poly-A tail, introns, and exons.

Define what is meant by translation

Describe how the ribosome functions as the site for protein synthesis

Describe the basic structure of tRNA and its role in translation.

List the stages of translation and the processes that occur at each stage.

Define the terms, P site, A site and catalytic site

Describe what is meant by post-translational processing and its role in protein synthesis.

Describe the experimental basis of the lac operon theory.

Define the terms operator, repressor, and functional genes.

Define the role of CAP in transcriptional regulation.

Describe the structure of a typical eukaryotic gene and the DNA sequences involved in the regulation of that gene.

Describe how the altering of chromatin structure can be a regulatory mechanism.

Describe what is meant by 'flanking sequences' and what they do in gene regulation.

Identify some of the post-transcriptional and post-translational regulatory controls on gene expression.

Describe the characteristics of prokaryotic and karyotic genomes.

Define the term transposable element and describe its function.

List some of the uses that may be made of genomics.

Describe how Vg1 gene influences early embryonic development.

List the stages of fertilization and describe how each stage is regulated.

Describe how the zygotic genome is activated.

Define what is meant by the term 'Organizer'.

Describe the role of cell adhesion proteins in differentiation.

Define the process of induction and apoptosis.

Describe the function of bicoid and maternal effect genes in development.

Describe how the gap, pair-rule and segment polarity genes organize the embryo.

Explain how the differential expression of homeotic genes results in the formation of different structures from different body segments.

Contrast the processes of determination and differentiation.

Define evolution, gene pool, and natural selection.

Describe the 4 premises of evolution by natural selection.

Explain the LaMarck and the Darwin/Wallace theories of evolution.

Define homologous, analogous, and vestigial structures, adaptive radiation.

Explain the following evidence for the occurrence of evolution: artificial selection, fossil record, comparative anatomy, embryology, and biogeography. Give an example of each.

Explain why genetic diversity is essential in a species.

State the Hardy-Weinberg Law and use it to determine allele frequencies in a population.

State and explain the 5 situations in which the Hardy-Weinberg Law is invalid.

Describe evolution as deviation from the Hardy-Weinberg equilibrium through mutation, gene flow, genetic drift, founder effect, and natural selection.

Define what is meant by directional, stabilizing and disruptive selection and compare and contrast their respective mechanisms.

Define speciation and distinguish between allopatric and sympatric speciation.

List the different types of premating and postmating isolating mechanisms.

Describe the mechanisms of polyploidy and hybridization.

Describe the environment on earth, which led to the formation of the first living organisms.

Trace the steps by which life may have originated on earth from the formation of organic monomers to the rise of eukaryotic organisms.

Describe some of the techniques that are used to discover the evolution of Life.

LAGUARDIA COMMUNITY COLLEGE

CITY UNIVERSITY OF NEW YORK

DEPARTMENT OF NATURAL AND APPLIED SCIENCE

FUNDAMENTALS OF BIOLOGY I

SCB 201

COURSE INFORMATION

Course Coordinator: Professor Joseph McPhee

Fall I 2005

Fundamentals of Biology I SCB 201

Course Coordinator: Professor McPhee Fall I 2005

Fundamentals of Biology I SCB 201

Course Coordinator: Professor McPhee Fall I 2005

* Students are required to complete the study questions listed below in a timely manner. The instructor will periodically check your answers and the resulting grade is worth 10% of your final laboratory grade.

Laboratory Manual must be brought to each laboratory Lecture. Students should read the laboratory exercise prior to entering laboratory. No eating, drinking or smoking in lab.

Laboratory attendance is mandatory. Excessive absences will be deducted from final grade. Completion of Laboratory Reports and individual effort in the laboratory will be considered in the laboratory portion of the final grade.

Fundamentals of Biology I SCB 201

Course Coordinator: Professor McPhee Fall I 2005

There will be 4 lecture seminars during the semester. The topics include:

Cancer and The Cell Cycle

The Promise and Threat of Eugenics

The Biological Revolution and The Future of Biotechnology

Modern Evolutionary Theory and Its Alternatives

During the first week of classes, students will be divided into 4 groups. Each group will be assigned one of the topics listed above. The students in each group will meet to discuss how to cover the topic, with each student preparing his or her own 10 minute oral presentation on his/her specific part of the topic. A minimum 3 page synopsis of each student's presentation must be submitted to the instructor on or before the day of the seminar.

In addition to the standard laboratory assignments, students in this course will be expected to design and carry out a research project. Students in the laboratory will be divided into groups of four and they will be asked to submit a research project based on one or more of the laboratory experiments performed as part of their normal curriculum. The project topic must be submitted and approved by the laboratory instructor before Laboratory 6 (see laboratory outline on previous page). . They will be expected to write up a formal research protocol, based on the scientific method (establish a hypothesis, determine the experimental methodology with appropriate controls and identified variables, and appropriate presentation of results). During Lab 8, student groups will carry out the approved research design. At the end of the research, they will be required to turn in a 5-10 page report by Lab 10, using the scientific format. The research and the report are counted as 10% of the final course grade.

Fundamentals of Biology I SCB 201

Course Coordinator: Professor McPhee Fall I 2005

SESSION 1 - INTRODUCTION Chapter 1

State the Cell Theory and describe the experiments that support it.

Describe the Darwinian theory of Evolution.

Describe the levels of organization in living systems and some of the methods of classification.

List the steps of the scientific method and apply them to a specific problem.

Define hypothesis, experiment, control, theory, and scientific law.

Describe how the Universe formed and the origin of the molecules of life.

Define what is meant by the terms, matter and energy.

List the stages in the development of the Earth and the formation of Life on Earth.

Define the terms, elements, atom, proton, electron, neutron, isotope and ion.

Define atomic number, and atomic mass.

Draw and describe an electron shell configuration.

Define molecule, compound, single and double bonds.

Describe ionic, covalent, polar, non-polar, hydrogen bonds.

Describe how bonds are formed and broken through the transfer of energy.

Define the term chemical energy and how it relates to bond strength.

Describe the properties of water and its importance in chemical evolution.

Describe the relationship and properties of acids, bases and salts.

Describe the importance of the carbon atom to organic chemistry.

List the components and steps in Miller's Experiment.

Describe the structure of the functional groups: amino, carboxyl, sulfhydryl, aldehyde, alcohol, and ketone.

List the four main classes of biological macromolecules (saccharides, lipids, proteins and nucleic acids), stating their chemical elements, subunits, and role they play in living systems.

Define amino acid, peptide bond, polypeptide, and protein.

Describe the four levels of protein structure.

Describe the mechanism by which enzymes work as organic catalysts.

Compare and contrast the structures of RNA and DNA.

Describe the role of RNA and DNA in the synthesis of macromolecules.

Define monomer, polymer, carbohydrate, monosaccharide, disaccharide, polysaccharide, starch, glycogen, cellulose, pentose and hexose sugars.

Describe the role of carbohydrates in cell structure and metabolism.

Describe the basic chemical structure of the biological membrane.

Define lipid, glycerol, fatty acid, triglyceride, saturated, unsaturated, phospholipid, and steroid.

Describe how phospholipids assemble spontaneously to form the basic membrane.

Define what is meant by the terms permeability and semipermeability.

List and describe methods by which molecules cross the membrane; impermeable, selective permeability, passive transport, diffusion, facilitated diffusion, carrier proteins, pores, osmosis, active transport, sodium-potassium pump, phagocytosis, and pinocytosis.

Describe the three states of osmosis.

Describe the Fluid Mosaic Model.

Describe the different methods used to study cells and their organelles.

Describe the main differences between prokaryotic and eukaryotic cells, as well as between plant and animal cells.

Describe the structure and function of the following nuclear organelles: nucleus, chromosome, nucleolus, and nuclear envelope.

Describe the structure and function of the following organelles: ribosome, endoplasmic reticulum, Golgi complex, lysosome, peroxisome, mitochondrion, vesicle, vacuole, plastid, chloroplast and cell wall.

Define the three classes of transport vesicles.

Describe the structure and function of the following parts of the cytoskeleton: microtubules, microvilli, cilia, flagella, and centriole.

Define the terms respiration, aerobic, anaerobic and fermentation.

Define the term coenzyme, list four and explain the function of each.

Diagram and describe the overall reaction for the oxidation of glucose stating the number of ATP's produced, and why oxygen is needed.

List the starting materials, the end products, and key chemicals in glycolysis and the formation of Acetyl-CoA.

Describe the Chemiosmotic Theory of ATP synthesis, including the role of the electron transport system, the membrane, the electrochemical gradient, and ATP synthetase.

Summarize the number of ATP molecules produced from each step in fermentation.

Contrast aerobic respiration with yeast alcoholic fermentation and muscle lactate fermentation.

Explain how and why muscles go into oxygen debt.

Explain how other nutrients, such as lipids, proteins and polysaccharides enter into the glucose oxidative pathway.

Describe the relationship between cellular respiration and photosynthesis, autotroph and heterotroph, oxidation and reduction.

Name the three main groups of photosynthetic pigments and state the function of each.

Describe the structure of the plant leaf and chloroplast. Define cuticle, epidermis, mesophyll, stomata, vascular bundle, grana, thylakoid, and stroma.

State the colors of light most effective in promoting photosynthesis, and explain why.

Write the overall reaction summary for photosynthesis.

Summarize the input and output for the four steps of photosynthesis: photochemical reactions, electron transport, chemiosmosis, carbon fixation (dark reaction), light reaction.

Describe the two photosystems, including chlorophyll a, P700, P680, antenna pigment, light trap, and reaction center.

Draw the two photosystems and show the energy flow relationships between them.

Explain the C3 cycle of carbon fixation, stating the importance of ribulose bisphosphate, RuBP carboxylase, and the number of turns of the cycle needed to produce a molecule of glucose.

Discuss how various environmental factors control the rate of photosynthesis.

Compare and contrast the C4 and C3 cycles and the relative benefits of each.

Describe the parts of the cell cycle and the three periods of interphase.

Describe the events in each of the stages of mitosis: prophase, metaphase, anaphase, telophase.

Define poles, centrioles, mitotic spindle, colchicine, cleavage furrow, and cell plate.

Describe how the kinetochore controls chromosome partitioning.

List the regulatory factors of the cell cycle and the function of each.

Describe the events in meiosis; include tetrad, synapsis, and separation of homologous chromosomes.

Distinguish between spermatogenesis and oogenesis.

Describe the significance of 'crossing over' in heredity.

Describe how the process of meiosis influences genetic variation.

Describe Mendel's experiments and give reasons why he was successful in discovering the laws governing the inheritance of genetic traits. State his three laws.

Define the terms genotype and phenotype, and their relationship to dominant and recessive.

Define parental (P1), first filial (F1), and second filial (F2) generations; homozygous, heterozygous, allele, monohybrid cross, dihybrid cross, homologous chromosomes, segregation, independent assortment, and linked genes.

Use the Punnett square to predict the results of monohybrid and dihybrid crosses, giving both genotype and phenotype ratios.

Describe the test cross and discuss its use as a genetic tool to distinguish between homozygous and heterozygous genotypes.

Describe how the discovery of linkage and the chromosome theory altered Mendel's original theory.

List and describe the mechanism of some non-Mendelian patterns of inheritance including incomplete dominance, multiple allelism and environmentally-influenced genes.

Describe the structure of the DNA molecule. Define purine, pyrimidine, complementary bases, double helix, antiparallel strands, 3' and 5' ends.

Describe how DNA is coiled and complexed with histones to form chromatin

Define mutation, list some kinds of mutations, and describe the importance of mutations.

Describe Griffith's experiment and how it was able to relate DNA to heredity.

Describe DNA replication, touching on DNA helicase, DNA polymerase, direction of replication, Okazaki fragments, DNA ligase, and replication bubbles.

Compare and contrast the structure of prokaryotic vs. eukaryotic DNA

List three differences between DNA and RNA.

State the "one-gene, one-enzyme" hypothesis.

Define what is meant by the genetic code.

Describe how the genetic code differs between DNA and RNA.

Describe the underlying principal of the Central Dogma.

Define what is meant by the transcription.

Describe the role of the promoter in transcription.

Describe the structure and origin of mRNA, tRNA and rRNA.

Describe the role of RNA polymerase and how it functions in transcription

Describe the structure of pre-mRNA

Describe the post-transcriptional processing of pre-mRNA

Define the terms start and termination signals, pre-mRNA, snRNAs, cap poly-A tail, introns, and exons.

Define what is meant by translation

Describe how the ribosome functions as the site for protein synthesis

Describe the basic structure of tRNA and its role in translation.

List the stages of translation and the processes that occur at each stage.

Define the terms, P site, A site and catalytic site

Describe what is meant by post-translational processing and its role in protein synthesis.

Describe the experimental basis of the lac operon theory.

Define the terms operator, repressor, and functional genes.

Define the role of CAP in transcriptional regulation.

Describe the structure of a typical eukaryotic gene and the DNA sequences involved in the regulation of that gene.

Describe how the altering of chromatin structure can be a regulatory mechanism.

Describe what is meant by 'flanking sequences' and what they do in gene regulation.

Identify some of the post-transcriptional and post-translational regulatory controls on gene expression.

Describe the characteristics of prokaryotic and karyotic genomes.

Define the term transposable element and describe its function.

List some of the uses that may be made of genomics.

Describe how Vg1 gene influences early embryonic development.

List the stages of fertilization and describe how each stage is regulated.

Describe how the zygotic genome is activated.

Define what is meant by the term 'Organizer'.

Describe the role of cell adhesion proteins in differentiation.

Define the process of induction and apoptosis.

Describe the function of bicoid and maternal effect genes in development.

Describe how the gap, pair-rule and segment polarity genes organize the embryo.

Explain how the differential expression of homeotic genes results in the formation of different structures from different body segments.

Contrast the processes of determination and differentiation.

Define evolution, gene pool, and natural selection.

Describe the 4 premises of evolution by natural selection.

Explain the LaMarck and the Darwin/Wallace theories of evolution.

Define homologous, analogous, and vestigial structures, adaptive radiation.

Explain the following evidence for the occurrence of evolution: artificial selection, fossil record, comparative anatomy, embryology, and biogeography. Give an example of each.

Explain why genetic diversity is essential in a species.

State the Hardy-Weinberg Law and use it to determine allele frequencies in a population.

State and explain the 5 situations in which the Hardy-Weinberg Law is invalid.

Describe evolution as deviation from the Hardy-Weinberg equilibrium through mutation, gene flow, genetic drift, founder effect, and natural selection.

Define what is meant by directional, stabilizing and disruptive selection and compare and contrast their respective mechanisms.

Define speciation and distinguish between allopatric and sympatric speciation.

List the different types of premating and postmating isolating mechanisms.

Describe the mechanisms of polyploidy and hybridization.

Describe the environment on earth, which led to the formation of the first living organisms.

Trace the steps by which life may have originated on earth from the formation of organic monomers to the rise of eukaryotic organisms.

Describe some of the techniques that are used to discover the evolution of Life.