LESSON-1ATOMS AND MOLECULES: MOLECULAR BASIS OF LIFE.

A. Objectives.1. List, know the chemical symbol, and explain the differences between major, minor,

and trace elements that make up the living matter; relate the elemental composition of the living matter to that of the earth’s crust. Discuss the chemical composition of food.

2. Explain the basic structure of an atom, location of protons, neutrons, and electrons. Discuss the distribution of electrons around the atom nucleus. Define atom number and atom mass; know differences between isotopes.

3. State the octet rule that governs chemical bonding. Explain the differences between covalent and ionic bonds and give examples. Know structure of molecular oxygen, hydrogen, and nitrogen gas, sodium chloride ...

B. Lecture outline.

1. ELEMENTAL COMPOSITION OF THE LIVING MATTER.a.Major elements: N, O, C, H.b. Minor elements:c.Trace elements.

2. STRUCTURE OF AN ATOM.Elements and atoms (SBM p27-31)

3. CHEMICAL BONDS.CHEMICAL BONDS (SMB P32-36)

a.ionic bonds and saltsb. covalent bonds

LESSON 2WATER AND BUFFERS.

C. Objectives.1. Give the chemical formula of water; list the biological properties of water ad explain

their importance. Specify: surface tension, water’s adhesive and cohesive properties. Explain: heat of vaporization, evaporative cooling, specific heat.

2. How does water dissolve sugar? Know the meaning of dipole, polar molecule, non-polar compounds, hydrophilic, hydrophobic, lipophilic, lipophobic compounds, hydration, hydrogen ion, proton, hydroxyl ion.

3. Explain {H+], pH, neutral, acidic, and basic pH. State the proton concentration at each pH value. Explain the properties of buffers, how they work, and their importance for the living material.

D. Lecture outline.

1. WATER

WATER (SBM P37-40).

a. Water is a dipole and hydrogen bonds form between water molecules.b. Water clings to polar (hydrophilic) molecules: hydration and water

organizes non-polar molecules.c.Water helps maintain a stable temperature.

2. ACIDS, BASES, AND BUFFERS.Acids, bases, and salts (SBM p40-42)

A. Water ionizes.b. pH measures proton concentration.c.Buffers minimize pH changes.

LESSONS - 3THE CHEMICAL BUILDING BLOCKS OF LIVING MATERIAL.

A. CARBOHYDRATES AND LIPIDS.

A. Objectives.

- Explain the nature of organic molecules; identify the carbon core and functional groups; give the chemical notation for hydroxyl-, carboxyl-, amino-, sulfhydryl-, and phosphate-groups, define and identify asymmetric carbon atoms, stereoisomers (geometric isomers), and enantiomers.

- Explain the nature of a macromolecule and polymeric molecule, how they can be formed and dismantled; explain graphically dehydration and hydrolysis.

- Give the general formula of a carbohydrate; relate the linear and ring structure of glucose; give examples of monosaccharides, disaccharides and polysaccharides; compare starch, amylose, amylopectin, pectins, glycogen, cellulose, mannan, chitin.

- Define triglyceride, glycerol, fatty acid; compare structurally and functionally saturated,unsaturated and polyunsaturated fatty acids; compare oils and fats and explain their properties at different temperatures; give a graphic picture of a phospholipid; compare the structure and properties of phospholipids and triglycerides; list examples of complex lipids.

B. Lecture outline.

1. ORGANIC MOLECULES,.

Read: Carbon atoms and molecules (SBM p46-50).

a. structure of organic molecules.b. polymers and macromolecules.c. building macromolecules: dehydration and hydrolysis.

2. CARBOHYDRATES

Read: Carbohydrates (SBM p50-55).

a. simple sugars.b. disaccharides.c. polysaccharides.

3. LIPIDS.

Read: Lipids (SBM p56-59).

a. triglycerides: fats and oils.b. phopholipids.c. complex lipids: cholesterol, prostaglandins and carotenoids.

LESSON- 4 and 5THE CHEMICAL BUILDING BLOCKS OF LIFE:

B. AMINO ACIDS AND PROTEINS.

A. Objectives.

- Give the basic structure of an amino acid; identify the amino group, carboxyl group and side chain.

- Explain why amino acids have different properties, what is special about the amino acids in each group and name some amino acids of each group.

- Explain and draw the peptide bond and how it relates amino acids to peptides and proteins.

- Explain in words and figure the relationship between the primary, secondary, tertiary and quaternary structure of proteins; describe the alpha helix and beta-pleated sheet; discuss how different amino acid sequences lead to different tertiary structures; discuss the nature and role of disulfide bonds in tertiary and quaternary structure; describe the quaternary structure of multimeric proteins.

- Discuss the differences between globular and fibrous proteins and relate these to their secondary and tertiary structure; what is protein conformation? protein denaturation? and chaperones?

B. Lecture outline.

1. AMINO ACIDS.

Read: Proteins (SBM p59-67).

a. structure of an amino acid:b. different classes of amino acids.

2. PEPTIDE BOND.

Read: Figure 3.18 (SBM p63).

3. PROTEIN STRUCTURE.

a. primary structure:b. secondary structure:

- alpha helix.- beta-pleated sheet.

b. tertiary structure: disulfide bonds.c. quaternary structure.d. denaturation, folding, and chaperones.

LESSON-6THE CHEMICAL BUILDING BLOCKS OF LIFE.

C. NUCLEIC ACIDS.

A. objectives.

— List and draw the structure of a nucleotide; number the carbons of the pentose from 1’ to 5’; identify the phosphodiester bond between nucleotides; list the structure of ATP, NAD and FAD; identify the high-energy bonds of ATP; why is ATP the’energy currency of life’?

— Give the essential structural characteristics of DNA; draw the molecule; list the major differences between purines and pyrimidines; discuss the direction of nucleic acid strands.

— Compare the structure of DNA and RNA.

B. Lecture outline.

Read: Nucleic acids (SBM p67=70)

1. THE BUILDING BLOCKS

a. five carbon sugar: ribose or deoxyribose.b. phosphate group.c. organic, cyclic, nitrogen base: purines and pyrimydines.

2. NUCLEOTIDES

Read: Figure 3.13 (R&J p47)

ATP Figure 7-5 (SBM p15)cAMP Figure 3-25 (SBM p70) and Figure 6-8 (SBM p143)NAD Figure 7-7 (SBM p160) FAD

3. DNA. Fig. 3.15 (R&J p48), 14.9c (R&J p286), 14.10a (R&J p287).

4. RNA. Fig. 3.16 (R&J p49).

LESSON - 7 and 8METABOLISM AND BIOLOGICAL CATALYSTS.

A. Objectives.

— Define: metabolism, anabolism and catabolism, endergonic and exergonic reactions, substrate, product, enzyme, active center, pH optimum, activator, inhibitor, allosteric effect, cofactor, coenzyme, prosthetic group or co—factor.

— Explain in word and figure activation energy; define the role of a catalyst; explain the function of an enzyme and relate the structure of an enzyme to its function; discuss why enzymes are substrate—specific; explain the statement: “a cell must possess almost as many different kinds of enzymes as it has reactions to catalyze.”

- Explain how an enzyme can be regulated and how it can be affected by its environment; what are allosteric effectors?, conformation of a protein?; discuss the concept of allosteric regulation;

- Give the structure of a generic biochemical pathway; predict the result when an enzyme of the pathway becomes inactivated, or activated; under which conditions do you expect regulation by negative feedback? positive feedback?

B. Lecture outline.

1. METABOLISM

Read: Energy and metabolism (SBM p155-157)

a. anabolism and catabolism.b. endergonic and exergonic reactions.

2. ACTIVATION ENERGY.

Read: Enzymes (SBM p160-167).

a. activation energy:b. catalysts, catalyzed reactions:

3. NATURE OF ENZYMES.

a. How enzymes work: active center.b. enzyme specificity.c. coenzymes, cofacors.

2. FACTORS AFFECTING ENZYME ACTIVITY: regulation.

a. Factors affecting enzyme activity: Temperature, pH, and salts

b. regulation of enzyme activity: Enzyme inhibition.

3. BIOCHEMICAL PATHWAYS.

LESSON - 9MEMBRANES.

A. MEMBRANE STRUCTURE.

A. Objectives.

- Describe and draw schematically a picture of a generic biological membrane; relate the structure to microscopic images of the membrane.Explain how Overton deduced the lipophilic nature of membranes; use Gorter and Grendel’s experiment to deduce that the lipid bilayer is the basis of the membrane streucture; explain the structure of phospholipids and how they form a lipid bilayer.Describe the permeability of a lipid bilayer for oxygen, water, lipids, large hydrophobic molecules, small hydrophobic molecules, ions, charged molecules, (large) polar molecules (e.g., size of amino acids, monosaccharides and up).

- Explain the relationship of proteins and carbohydrates with the membrane; note differences in the Danielli structure and the fluid mosaic model; relate the distribution of amino acids to the different functional domains of transmembrane proteins; explain the nature of glycoproteins.

- Discuss how the nature of membrane lipids (or fatty acid tails) determines the temperature sensitivity of the membrane; define: glycoprotein, glycolipid, spectrin, clathrins, cholesterol

B. Lecture outline.

1. THE LIPID FOUNDATION OF MEMBRANES.

Read: The structure of biological membranes (SBM p107-115).

a. Charles Overton (1895): the importance of lipids.b. Gorter and Grendel (1925): the lipid bilayer.c. Phospholipids.d. Bilayer sheets: permeability of lipid bilayer.

2. MEMBRANE STRUCTURE.

a. Davson—Danielli model (1935): a protein-lipid sandwich.b. Singer and Nicolson (1972): the fluid mosaic model.c. molecular organization of membrane: transmembrane proteins and glycoproteins

3. ADAPTATION OF MEMBRANES TO THE ENVIRONMENT.

LESSON - 11MEMBRANES.

B. MEMBRANE TRANSPORT.Diffusion and Osmosis.

A. Objective.

— List 4 functions of the membrane.— Define diffusion, osmosis, osmotic pressure, hydrostatic pressure, isotonic, hypotonic

and hypertonic medium, and contractile vacuole.— Apply the principles of osmosis to animal cells, plant cells, bacteria, fungi and

protozoa (amoebae, flagellates and ciliates) in fresh water and in sea water.— Use the principles of osmosis to prevent microbial growth in food products; explain

why an antibiotic that destroys the cell wall of bacteria can be used as a cure in human an animal infections.

B. Lecture outline.

1. DIFFUSION AND OSMOSIS.

Read: Diffusion and Osmosis (SBM p116-118).

a. diffusion.b. osmosis.c. isotonic, hypertonic and hypotonic medium.

note: Maintaining osmotic balance.

LESSON-12MEMBRANES

B. MEMBRMIE TRANSPORT.Bulk transport and selective transport of molecules.

A. Objective.

- Explain and draw schematically the principle of endocytosis; compare endocytosis, receptor—mediated endocytosis, phagocytosis, pinocytosis and exocytosis; contrast osmotrophs and phagotrophs structurally and functionally.

- Discuss the importance of the selective permeability of membranes.- Compare passive and active transport, transport by simple diffusion and facilitated

diffusion.- Explain the principle of active transport and apply to the sodium-potassium pump, and

coupled channel.

B. Lecture outline.

2. TRANSPORT OF BULK MATERIAL ACROSS THE MEMBRANE.

a. Endocytosis

Read: Exocytosis amd endocytosis (SBM p123-127).

2. SELECTIVE TRANSPORT OF MOLECULES..

Read: Passive transport (SBM p115-120).Read: Active transport (SBM p120-123).

a. passive transport- diffusion,— facilitated diffusion.

b. active transport— sodium-potassium pump.— co- and counter transport: coupled channels.

C. Study Questions.

See: Lesson 12.

LESSON - 13PROKARYOTIC CELL

A. Objectives

- Describe the structure of the bacterial cell, with its chromosome, ribosome and inclusions; discuss the site equivalent to the chloroplast and mitochondria of eukaryotes; compare the bacterial flagellum to the eukaryotic kinetochore.

- Describe and draw schematically the structure of peptidoglycan; compare concisely gram—positive and gram—negative bacteria.

- List differences between the prokaryotic and eukaryotic cell especially: size, presence of organelles, organization of genetic material, ribosomes, flagella and cell wall.

- Explain the origin of eukaryotes by symbiosis of prokaryotes and find evidence for this in the comparison of the structure and function of cell organelles and the structure of the prokaryotic cell.

B. Lecture outline

1. THE STRUCTURE OF THE PROKARYOTIC CELL.

Read: Prokaryotes (SBM p512-517)Prokaryotes and Eukaryotic cells (SBM p80-810

a. the protoplastb. the cell wall: peptidoglycanc. gram-positive and gram-negative bacteriad. appendages: flagella, pili or fimbriae

2. COMPARISON BETWEEN THE PROKARYOTIC AND EUKARYOTIC CELL.

3. SYMBIOSIS AND THE ORIGIN OF EUKARYOTES.

Read: Eukaryotic cells descended from prokaryotic cells (SBM p453-454).

LESSON - 14EUKARYOTIC CELL

THE NUCLEUS and GERL.

A. Objectives

- Explain and draw schematically the structure and function of plasma membrane, nucleus, nuclear envelope, nucleolus, chromosomes, cytoplasma, Golgi complex, endoplasmic reticulum and lysosomes; discuss the functional relationship of the membrane-bound organelles forming GERL and the nucleus and plasma membrane.

B. Lecture outline

1. PROPERTIES OF CELLS

Read: All organisms are composed of cells (R&J p78-85)

a. the cell theoryb. most cells are very small.c. prokaryotes and eukaryotes.

2. THE ORGANIZATION OF THE CYTOPLASM.

3. NUCLEUS

Read: The cell nucleus (SBM p84-87)

— nuclear envelope— nucleolus— chromosomes

4. GERLRead: Organelles in the cytoplasm (SBM p88-93)

a. Golgi complex.b. endoplasmic reticulum.c. lysosomes.d. secretory vesicles

LESSON - 15EUKARYOTIC CELL

RIBOSOMES, MITOCHONDRIA, CHLOROPLASTS,CENTRIOLE FLAGELLUM AND CYTOSKELETON

A. Objectives

— Explain and draw the structure of ribosomes, mitochondria, chloroplasts, centriole, kinetochore, cell wall and cytoskeleton; relate each cell structure and organelle to its function.

— Compare the structure of an animal and plant cell.

B. Lecture outline

1. RIBOSOMES

Read: Ribosomes manufacture proteins (SBM p89)

2. MITOCHONDRIA AND CHLOROPLASTS

Read: Mitochondria and chloroplasts produce energy (SBM p94-97).a. mitochondriab. chloroplastc.

3. CYTOSKELETON

a. actin filaments — actinb. microtubules - protofilaments - tubulind. intermediate filaments — vimentin, keratin

4. CENTRIOLE AND UNDULIPODIUM (flagellum and cilium) a. centriole b. undulipodia

LESSON - 17EUKARYOTIC CELL

C. THE EXTERIOR OP THE CELL.

A. Objectives

- Provide a general structure of a membrane receptor; explain the importance of receptors.

- Discuss why cells need identification markers; list specific examples of identification markers; predict under which circumstances the presence of identification markers on your cells becomes of practical importance.

- Discuss how many cells cooperate to form tissues; compare adhering, organizing and communicating junctions; define desmosomes, tight junctions and gap junctions.

- Discuss the role of the glycocalyx in the functions of the cells; describe the cell wall structure of plants.

B. Lecture outline

1. COMMUNICATION BETWEEN CELLS.

Read: Cell Junctions (SBM p127-130).

a. receptors.b. identification numbers.

c. junctions between cells: - anchoring junctions: desmosomes, hemidesmosomes, and adherens junctions - organizing junctions: tight junctions. - communicating junctions: gap junctions — connexins

2. CELL COAT OR GLYCOCALYX IN ANIMAL CELLS.

3. CELL WALL IN PLANT CELLS.

LESSON - 18 and 19EUKARYOTIC CELL

CELL-TO-CELL SIGNALLING.

A. Objectives

- Define the different types of cell signaling: direct contact, paracrine signaling, endocrine signaling, and synaptic signaling.

- Describe and give examples of cell signaling using intracellular and extracellular receptors. What reaction is catalyzed by the adenylyl cylase? guanylyl cyclase? What is the structure of cAMP? CGMP? What is No? Give the basic structure of steroids? How do steroid hormones function?

- Signaling transduction involves signal molecules, cell surface receptors, intracellular messengers, a protein kinase cascade, and transcription factors. Explain. Explain the function of chemically gated ion channel receptors, receptor tyrosirie kinases, and G— protein—linked receptors. Give an overview of the beta—adrenergic receptor.

- List various molecules that function as intracellular secondary messengers. Give the basic structure of cAMP and inositol triphosphate. Explain the origin of both messengers. What is the source of intracellular calcium? What is the role of calmodulin?

- What are protein kinases? Identify the amino acids to which phosphates are linked. Explain how a protein kinase cascade amplifies a signal. What is the role of phosphatases?

B. Lecture outline

1. TYPES OF CELL-TO-CELL SIGNALING.

Read: Sending signals (SBM p136-137)

2. LIPOPHYLIC SIGNALS USE INTRACELLULAR RECEPTORS.

Read: Intracellular receptors (SBM p138 Figure 6-4)

3. HYDROPHYLIC SIGNALS USE CELL SURFACE RECEPTORS.

Read: Reception (SBM p137-140)Signal transduction (SBM p140-145)Responses to signals (SBM p145-147)

a. Different types of cell surface receptor: gated ion channels, receptor tyrosine kinase, and G protein—linked receptors.

b. Intracellular, second messengers: cAMP, calcium, and inositol triphosphate.

c. Protein kinase cascade.

LESSON - 20ENERGY METABOLISM: INTRODUCTION

A. Objectives

- Explain what energy is; state the principal sources of energy of the living world; relate energy to uptake of nutrients.

- Explain the principles of oxidation, reduction, oxidation-reduction reactions; state the reduction of carbon dioxide and the oxidation of glucose; what are reduction potentials; give the spontaneous flow of electrons between different substances;

- Define intermediate electron carrier, electron tower, primary electron donor, terminal electron acceptor.

B. Lecture outline

1. WHAT IS ENERGY?

Read: Biological work (SBM p153-154)).

2. ENERGY SOURCES OF THE LIVING WORLD.

- phototrophs and chemotrophs- (chemo) organotrophs and (chemo) lithotrophs

3. CHEMICAL ENERGY IS PRODUCED BY OXIDATION

Read: Redox reactions (SBM p36)Energy transfer in redox reactions (SBM p159-160

a. oxidation—reductionb. reduction potentialsc. electron tower

LESSON - 21ENERGY METABOLISM: INTRODUCTION

A. Objectives

— Describe ATP and discuss its role as a universal energy currency; explain the ATP-ADP cycle; explain different ways by which ATP is generated and compare them; define substrate—level phosphorylation, and electron transport phosphorylation,

— Define electron carriers, intermediate electron carrier; describe NAD+, NADH+ and FAD and explain their roles in energy metabolism,

— Discuss the elements and organization of an electron transport system; define soluble and membrane—bound intermediate electron carriers (give examples of both); describe the general structure of a cytochrome; what is the cellular location of electron transport systems?; what is a proton motive force?; explain how a proton motive force is generated; give the basic structure of ATPase; explain how a proton motive force is used to synthesize ATP.

B. Lecture outline.

1. ATP: THE ENERGY CURRENCY.

Read: ATP: the energy currency of the cell (SBM p157-159)

:Modes of ATP production:- substrate-level phosphorylation— electron transport phosphorylation

2. NAD+, NADH+, AND FAD: SOLUBLE INTERMEDIATE ELECTRON CARRIERS.

Read: Enzyme cc factors (Figure 7-7. SBM p160)

3. ELECTRON TRANSPORT SYSTEM.

Read: The electron transport chain (SBM p179-183).

a. dissection of an electron transport system,b. generation of a proton motive force,c. electron transport synthesis of ATP

LESSON - 22ENERGY METABOLISM: THE CHEMOORGMTOTROPHS

THE OXIDATION OF GLUCOSE

A. Objectives

- Explain the oxidation of an organic molecule such as glucose to carbon dioxide and water by glycolysis and Krebs cycle; discuss the steps that result in ATP production by substrate-level phosphorylation; identify the oxidation steps; know the cost of ATP production in terms of coenzyme reduction; characterize the events occurring in each step of the two pathways; locate the site of glycolysis and citric acid cycle in the prokaryotic and eukaryotic cell.

B. Lecture outline

1. OXIDATION OF GLUCOSE: OVERVIEW.

Read: The four stages of aerobic respiration (SBM p173-185)

2. THE GLYCOLYSIS

Read: In glycolysis, glucose yields two pyruvate (SBM p174-178).

a.preparatory reactionsb.oxidation processC.summary

3. THE CITRIC ACID CYCLE, TRICARBOXYLIC ACID CYCLE OR KREBS CYCLE

Read: Pyruvate is converted to acetyl CoA (SBM p175-178)The citric acid cyclce oxidizes acetyl CoA (SBM p178-179)

a.introduction of pyruvate into the Krebs cycleb.Krebs cyclec.summary

4. BALANCE (Table 9.1 (R&J p199)]

Oxidation of 1 mole of glucose yielded 4 moles of ATP at a cost of 10 moles reduced NADH+H+ and 2 moles reduced FADH2.

LESSON - 23ENERGY METABOLISM: THE CHEMOORGANOTROPHS

RESPIRATION AND FERMENTATION

A. Objectives

— Explain the burden of energy production by chemoorganotrophs and suggest solutions.— Explain the essence of fermentation and its need for or sensitivity to air; state what

makes different fermentation pathways different; discuss the consequences of a fermentative metabolism; list some applications of fermentative pathways.

— Define respiration and compare to fermentation; explain the ATP production by electron transport phosphorylation; explain the proton motive force.

— Discuss energy yields of a fermenting and respiring organism; list advantages and disadvantages; give examples of fermenting and respiring organisms; locate the site of substrate-level and electron transport phosphorylation in the prokaryotic and eukaryotic cell.

B. Lecture outline

1. PROBLEM FACED BY CHEMOORGANOTROPHS

Read: The electron transport chain is coupled to ATP synthesis (SBM p179-185)

2. FERMENTATION

Read: Anaerobic respiration and fermentation (SBM p186-188)

a. fermentation pathway: generalb. variations on a themec. disadvantages, advantagesd. balance sheet

3. RESPIRATION

Read: Aerobic respiration of one glucose yields a maximum of 36 to 38 ATPs. (SBM p183-185)

a. mitochondrial electron towerb. generation of a proton motive forcec. ATP synthesisd. balance sheet

4. CARBOHYDRATE METABOLISM OF CHEMOHETEROTROPHS: C-heterotrophs

LESSON - 24ENERGY METABOLISM: THE PHOTOTROPHS

HASRVEST OP LIGHT ENERGY

A. Objectives

- Explain the two parts of photosynthesis; discuss the physical properties of light and the nature of light-harvesting pigments; explain what it means when chlorophyll or carotenoid “harvest” light energy.

- Explain the energy production of plants; discuss why the pathway is called the Z-scheme; identify the photosystems; trace the origin, flow and final destination of the electrons; write down a summary reaction of photophosphorylation

B. Lecture outline

1. PHOTOSYNTHESIS

2. CAPTURING LIGHT ENERGY

a. the physical nature of light

Read: Light (SBM p192-193)

b. light-harvesting pigments

Read: Chloroplasts (SBM p193-196)

a. chlorophyllsb. carotenoidsc. photophosphorylation

3. OXYGENIC PHOTOPHOSPHORYLATION OF PLANTS AND ALGAE: THE Z-SCHEME

Read: Overview of photosynthesis (SBM p196-197)The light-dependent reactions (SBM p198-201)

LESSON - 25ENERGY METABOLISM: THE PHOTOTROPHS

CARBON FIXATION: THE CALVIN CYCLE

A. Objectives

- State the energy problem of the phototroph; explain why phototrophs are C(carbon) -autotrophs;

- Give an overview of the Calvin cycle; tell what happens during a single turn of the Calvin cycle; explain the synthesis of glucose by the Calvin cycle; make a balance sheet of the synthesis of glucose by the Calvin cycle and note the origin of the substrates.

- List the balance sheet for photosynthesis; discuss short-comings of photosynthesis of plants; explain differences between C-3, C-4, and CAM plants.

B. Lecture outline

1. PROBLEMS OF PHOTOTROPHS: C-autotrophs

2. REDUCTION OF CARBON DIOXIDE: THE CALVIN CYCLE

Read: The carbon fixation reactions (SBMp202-204)

a. key reactions of the Calvin cycleb. synthesis of a 6-C sugarc. balance sheet

3. ENERGY METABOLISM OF PLANTS

a. structure and functional relationship of chloroplastsb. C3, C4, and CAM plants.

Read: Photorespiration reduces photosynthesis efficiency (SBM p204)The initial carbon fixation step differs in C4 and CAM plants (SBM p204-206)

- the problem of ribulose-l,5-diphosphate carboxylase,- photorespiration losses in C3 plants,— C4 plants concentrate carbon dioxide,— carbon fixation in succulents (CAM).

LESSON - 26THE BASIC STRUCTURE OF VIRUSES

A. Objectives

— Give a characterization of a virus; know the name of some viruses important to us; tell how viruses were discovered; relate the size of viruses to the size of cells and bacteria.

— Give a picture of the structure of a generalized (animal) virus and note the function of the different parts; explain what the origin of the envelope is; what determines the structure of the glycoproteins.

— Discuss the diversity of viruses; make a picture of a bacteriophage; explain a lysogenic and lytic cycle; define prophage.

— Discuss the differences between DNA and RNA viruses; give a review of the replication of an animal virus.

B. Lecture outline

Read: Viruses (SBM p501-510)

1. VIRUSES ARE INTRACELLULAR PARASITES.

2. VIRUSES ARE VERY SMALL.

3. VIRUSES HAVE A SIMPLE STRUCTURE

Read: The structure of viruses (R&J p676)

a. nucleocapsidb. envelope

4. DIVERSITY OF VIRUSES

a. bacteriophages: lytic and lysogenic cyclesRead: Figure24.2 and 24.3 (SBM p504)

b. animal viruses: DNA and RNA viruses

5. REPLICATION OF ANIMAL VIRUSES

— budding of enveloped viruses

LESSON - 27DNA: THE GENETIC MATERIAL.

A. Objectives

- Use the Hammerling, Griffith-Avery, Hershey-Chase, and FraenkelConrad experiments to argue that genetic material is present in the nucleus, is DNA (and 1RNA in RNA viruses); design analogous experiments to argue the same points; explain why Griffith and Avery did not conclude that RNA was the genetic material of bacteria.

- Draw and explain the structure of a nucleotide and nucleic acid strand; properly number the carbon atoms of the pentose; explain the direction of a nucleic acid strand.

- List, explain and use Chargaff’s rules of base pairing; tell what Franklin’s contribution was to unraveling the DNA structure; give an account of the structure of the DNA molecule; list alternative structures that fulfil Chargaff’s rule and discuss why they are not likely correct.

- Know who and when the structure of the DNA molecule was unraveled.

B. Lecture outline

1. DNA IS THE GENETIC MATERIAL

Read: Acetabularia and the control of cell activities (SBM p86-87)DNA is the transforming principle in bacteria (SBM p261-262)DNA is the genetic material in certain viruses SBM p263)

a. Genetic information is stored in the nucleus (J. Hammerling and J. Brachet, 1930)b. the Fred Griffith (1928)-Oswald Avery (1944) experiment: bacteriac. the Herschey—Chase experiment (1952): DNA virusesd. the Fraenkel—Conrad experiment (1954): RNA viruses

The Fraenkel-Conrat Experiment: Some Viruses Direct Their Heredity with RNA

One objection might still be raised about accepting the hypothesis that DNA was the genetic material. Some viruses contain no DNA and yet manage to reproduce themselves quite satisfactorily. What is the genetic material in this case?

In 1957 Heinz Fraenkel-Conrat and coworkers isolated tobacco mosaic virus (TMV) from tobacco leaves. From ribgrass (Plantago), a common weed, they isolated a second, rather similar kind of virus, Holmes ribgrass virus (HRV). In both TMV and HRV the viruses consist of a protein coat and a single strand of RNA. When they had isolated these viruses, the scientists chemically dissociated each of them, separating their protein from their RNA. By putting the protein component of one virus with the RNA of another, they were able to reconstitute hybrid virus particles.

The payoff of the experiment was in its next step. To choose between the alternative hypotheses “the genetic material of viruses is protein” and “the genetic material of viruses is RNA,” Fraenkel-Conrat now infected healthy tobacco plants with a hybrid virus composed of TMV protein capsules and HRV RNA, being careful not to include any nonhybrid virus particles (Figure 14-8). The tobacco leaves that were infected with the reconstituted hybrid virus particles developed the kinds of lesions that were characteristic of HRV and that normally formed on infected ribgrass. Clearly, the hereditary properties of the virus were determined by the nucleic acid in its core and not by the protein in its coat.(Raven and Johnson (1992). Biology 3th Edition. P286)

FIGURE 14-8Fraenkel-Conrat’s virus reconstitution experiment. Both TMV and HRV are plant RNA viruses that infect tobacco plants, causing lesions on the leaves. Because the two viruses produce different kinds of lesions, the source of any particular infection can be identified. In this experiment, TMV and HRV were both dissociated into protein and RNA and the protein and RNA were separated from one another. Then hybrid virus particles were produced by mixing the HRV RNA and the TMV protein and allowing virus particles to form from these ingredients. When the reconstituted virus particles were painted onto tobacco leaves, lesions developed of the HRV type. From these lesions, normal HRV virus particles could be isolated in great numbers; no TMV viruses could be isolated from the lesions. Thus the RNA (HRV) and not the protein (TMV) contains the information necessary to specify the production of the viruses.

LESSON - 28DNA: DISCOVERY OF THE STRUCTURE.

A. Objectives

- Draw and explain the structure of a nucleotide and nucleic acid strand; properly number the carbon atoms of the pentose; explain the direction of a nucleic acid strand.

- List, explain and use Chargaff’s rules of base pairing; tell what Franklin’s contribution was to unraveling the DNA structure; give an account of the structure of the DNA molecule; list alternative structures that fulfil Chargaff’s rule and discuss why they are not likely correct.

- Know who and when the structure of the DNA molecule was unraveled.

B. Lecture outline

2. THE STRUCTURE OF DNA

Read: The Structure of DNA (SBM p263-266)

a. nucleotides, nucleic acid revisited

b. the DNA molecule

- Chargaff’s rules (1948)

- X-ray crystallography (Rosalind Franklin, 1953) Two parallel strands (2 nm wide) Helical 10 nucleotides per turn (periodicity of 34 nm)

- the double helix (Watson and Crick, 1953)

LESSON - 29DNA REPLICATION IS SEMI-CONSERVATIVE

A. Objectives

- Explain the problem of DNA replication in light of its role as the bearer of genetic information; compare carefully the differences between the liberal, conservative and semi—conservative models.

- Explain the Meselson-Stahl experiment; define ‘heavy’ DNA, density separation; discuss each step of the experiment in light of the three models; apply a Meselson-Stahl experiment to an eukaryotic cell (see lesson 21)

B. Lecture outline

1. PROBLEM

Read: DNA REPLICATION (SBM p266-276)Figure 12-7 (SBM p268)

a. liberal modelb. conservative modelc. semi—conservative model

2. MESELSON AND STAHL EXPERIMENT

Read: Figure 12-8 (SBM p269)

a. making ‘heavy’ DNAb. separation of DNA by densityc. the experimentd. conclusion

3. HOW DNA COPIES ITSELF.

a. DNA of eukaryotesb. DNA of bacteria

LESSON - 230DNA REPLICATION MACHINERY

A. Objectives

- List enzymes involved in the replication of DNA; give limitations of DNA polymerase; What is the role of DNA helicases, topoisomerases, SSB proteins.

- Discuss the initiation of DNA replication; what is the role of the RNA primer? How is the primer synthesized? What is the nature of the primase?

- Discuss the replication of the continuous and discontinuous strands, the leading and lagging strands. What are Okazaki fragments? What is the role of the ligase?

- Discuss why DNA shortens during replication? What is the end of DNA that shortens during replication? What is the telomerase? What is the nature of a telomerase? What is the function of the telomerase?

B. Lecture outline

1. HOW DNA COPIES ITSELF

Read: DNA REPLICATION (SBM p266-276)Figure 12-12 (SBM p273)Figure 12-11 (SBM p272)

a. The DNA replication machinery.b. DNA polymerase is error-proof: proofreading.c. Telomeres and telomerase.

LESSON – 31THE EUKARYOTIC CHROMOSOME.

A. Objectives

— define haploid, diploid, centromere, chromatin, chromatid, chromosome, nucleus, nucleoslus, nucleosome, histones, mitosis, cytokinesis, binary fission, centromere, centriole, spindle figure, aster, spindle equator.

— explain the structure of chromosomes from nucleic acid strand to DNA, to chromatid and chromosome.

B. Lecture outline

READ: Eukaryotic chromosomes (SBM p212-215)

1. THE EUKARYOTIC CHROMOSOME

Read: Chromosomes are highly ordered structured (R&J p209-211)

a. historyb. human chromosomesc. structure

LESSON - 32CELL CYCLE AND MITOSIS

A. Objectives

— Define haploid, diploid, centromere, chromatin, chromatid, chromosome, nucleus, nucleoslus, nucleosome, histones, mitosis, cytokinesis, binary fission, centromere, centriole, spindle figure, aster, spindle equator.

- State the different phases of the eu]caryotic cell cycle and tell what happens during each phase; contrast division of the eukaryotic to that of the prokaryotic cell; compare cyokinesis of plant and animal cells.

- Describe the different phases of mitosis; relate mitosis to DNA duplication; make cartoon pictures of mitosis; explain the origin of the nuclear envelope, the shortening of the spindle fibers.

B. Lecture outline

READ: The cell cycle and mitosis (SBM p215-221

2. THE CELL CYCLE

3. MITOSIS

a. prophase: formation of mitotic apparatusb. metaphase: division of centromeresc. anaphase: separation of chromatidsd. telophase: reformation of nucleus

4. CYTOKINESIS

a. animal cellsb. plant cells.

5. CELL DIVISION IN PROKARYOTES

LESSON - 33CONTROL OF THE CELL CYCLE.

A. Objectives.

— Describe the general nature of cell cycle control; explain the goal of the G1, G2 and M check points; define cyclin, cyclindependent kinase, mitosis—proinoting factor, proteasome, ubiquitin and ubiquinated cyclin.

- Discuss the relationship between growth factors and the cell cycle; relate cell cycle control and cell-cell signaling.

B. Lecture outline.

READ: Regulation of the cell cycle (SBM p221-223)

1. General strategy of cell cycle control.

2. Molecular mechanisms of cell cycle control.- the G2 check point.- the G1 check point.- the M checkpoint

3. Controlling the cell cycle in multicellular eukaryotes.

4. Growth factors and the cell cycle.

LESSON - 34GENE EXPRESSED: TRANSCRIPTION.

A. Objectives

- State the problem of molecular biology. Compare transcription with translation— Describe the 3 species of RNA and discuss their role in gene expression; provide an

overview of protein synthesis; compare transcription with translation; describe synthesis of RNA; list the locations in the nucleus where the different species of RNA are produced.

— Explain the consequences of transcript processing; discuss where it happens; define exon, intron, endonuclease

B. Lecture outline

1. PROBLEM: FROM INFORMATION TO METABOLISM

Read: Information flow from DNA to Protein: an overview (SBM p282-283)

2. THERE ARE 3 TYPES OF RNA

a. messenger RNA (mRNA)b. ribosomal RNA (rRNA)c. transfer PNA (tRNA)

3. TRANSCRIPTION

Read: Transcription (SBM p285-288)

C. Study Questions.

LESSON - 35GENE EXPRESSED: RNA PROCESSING

A. Objectives

- Compare transcription in pro- and eukaryotes.- Discuss the processing of the RNA-transcript in mRNA. Explain the 5’ cap, the polyA-

tail, and removal of introns. Describe the role of the spliceosome.- Explain the role of RNA in regulating gene expression.- Explain information flow in retro viruses.

B. Lecture outline

1. COMPARE TRANSCRIPTION IN PRO- AND EUKARYOTES

Read: Variations in gene expression in different organisms (SBM p292-298)

2. PROCESSING OF THE PRIMARY RNA TRANSCRIPT

a. 5’ CAPb. 3’ polyA-tailc. Removal of Exons

3. Role of RNA in regulation of gene expression.

4. Information flow in retro viruses.

C. Study Questions.

LESSON - 36

GENE EXPRESSION: THE GENETIC CODE.

A. Objectives

- State the objective of protein translation; discuss the properties of the genetic code as discovered by Francis Crick;

- Discuss the work of Nienberg, Natthaei, and Khorana in cracking the genetic code; explain the genetic code; identify the molecule that carries codons;

- Explain the charging of tRNA molecules; discuss the minimal number of different tRNA molecules required; discuss the nature of ‘tRNAactivating’ enzymes (aminoacyl tRNA transferases), their specificity for amino acids and codons.

B. Lecture outline

1. CRACKING THE GENETIC CODE

Read: Biologists cracked the genetic code in the 1960s (SBM p283-285)

a. the triplet code (Crick, 1961)b. Marshall Nirenberg and Heinrich Matthaeic. H. Gobind Khorana

2. THE TRIPLET CODE

3. CHARGING OF tRNA

LESSON - 37GENE EXPRESSION: TRANSLATION.

A. Objectives

- Discuss the initiation of protein synthesis; identify where it happens, what cell organelles are involved; verbally and by picture state the 5 steps of protein chain elongation; discuss chain termination.

— Define codon, anti—codon, stop codon, activating enzyme, aminoacyl tRNA transferase.

B. Lecture outline

3. THE MECHANISM OF PROTEIS SYNTHESIS: TRANSLATION

Read: Translation (SBM p288-292)

a. chain initiation

b. 5 steps of chain elongation, including translocation

c. chain termination

LESSON - 38GENE REGULATION

TRANSCRIPTIONAL CONTROL IN PROKARYOTES.

A. Objectives.

— Describe the general structure of an operon; define promotor, operator, regulator, repressor, activator, structural gene;

- Explain how substrate availability regulates transcription of genes of catabolic enzymes and product accumulation regulates transcription of genes of anabolic enzymes

— Diferentiate between positive and negative regulation and between regulation by induction and repression of transcription; Explain 4 different types of regulation of transcription; Explain the two control mechanisms of the Lac operon.

B. Lecture Outline.

Read: Gene regulation in bacteria (SBM p306-312)

1. ORGANIZATION OF AN OPERON.

a. the promotor binds RNA polymerase.b. the operator binds the regulator: repressor or activator/inducerc. the transcription unit is transcribed:

2. EXAMPLES OF GENE EXPRESSION.

a. The lactose breakdown: substrate induces transcription of the genes of catabolic enzymes. [Figure 14-2 (SBM p307)]

b. The tryptophan synthesis: product represses transcription of genes of anabolic enzymes. [Figure 14-4 (SBM p310)]

3. GENERALIZATION.

a. positive and negative control.b. induction and repression.c. 4 different types of regulation of transcription.

— negative control with induction of transcription. — negative control with repression of transcription. — positive control with induction of transcription. — negative control with repression of enzyme control.

4. COMBINATION OF SWITCHES: THE Lac OPERON.Read: Figure 14-5 (SBM p311)

C. Study Questions.

LESSON - 39GENE REGULAUTION

EUKARYOTES

A. Objectives.

— Explain how eukaryotic gene expression is regulated at multiple levels; describe the structure of the eukaryotic operon, define its elements; explain how different transcription factors cooperate to regulate gene expression.

- Explain how proteins can bind to specific DNA sequences; define the major and minor groove of DNA; define helix—turn-helix, homeodomain, zinc finger and leucine zipper domains;

- Explain how gene function is controlled by RNA splicing, regulation of translation, degradation of proteins, and regulation of enzyme activity.

B. Lecture Outline.

1. MULTIPLE LEVELS REGULATION OF EUKARYOTIC GENE EXPRESSION.

READ: Gene regulation in eukaryotic cells (SBM p312-319)

2. TRANSCRIPTIONAL CONTROL OF THE EUKARYOTIC GENE

a. Core promotor: TATAAA—box.b. basal transcription factors allow PNA polymerase to bind to the core promotor.c. proximal control elements bind regulatory transcription factors.d. distal control elements:

— activators bind to enhancers. — repressors bind to silencers. — coactivators link enhancers to basal or regulatory transcription factors.

3. HOW TRANSCRIPTION FACTORS BIND SPECIFIC DNA SEQUENCES

a. the helix-turn-helix motif.b. the homeodomain motif.c. the zinc finger motif.d. the leucine zipper motif.

4. POST-TRANSCRIPTIONAL CONTROL IN EUKARYOTES.

a. RNA processing and RNA splicing.b. translational control: selecting which mRNAS are translated.c. posttranslational control: e.g., glycosylation, targetingd. ubiquitin-dependeflt protein degradatione. regulation of enzyme activity.