LESSON-1
ATOMS 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 salts
b.covalent bonds
LESSON 2
WATER 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, nonpolar 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 - 3
THE 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:
2.
a.
structure of organic molecules.
b.
c.
polymers and macromolecules.
building macromolecules: dehydration and hydrolysis.
CARBOHYDRATES
Read:
a.
b.
c.
3.
Carbon atoms and molecules (SBM p46-50).
Carbohydrates (SBM p50-55).
simple sugars.
disaccharides.
polysaccharides.
LIPIDS.
Read:
a.
b.
c.
Lipids (SBM p56-59).
triglycerides: fats and oils.
phopholipids.
complex lipids: cholesterol, prostaglandins and carotenoids.
LESSON- 4 and 5
THE 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:
3.
Figure 3.18 (SBM p63).
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-6
THE CHEMICAL BUILDING BLOCKS OF LIFE.
C. NUCLEIC ACIDS.
A. objectives.
—
—
—
B.
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.
Lecture outline.
Read:
1.
Nucleic acids (SBM p67=70)
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 8
METABOLISM 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:
a.
b.
2.
anabolism and catabolism.
endergonic and exergonic reactions.
ACTIVATION ENERGY.
Read:
a.
b.
3.
Energy and metabolism (SBM p155-157)
Enzymes (SBM p160-167).
activation energy:
catalysts, catalyzed reactions:
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 - 9
MEMBRANES.
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:
a.
b.
c.
d.
2.
The structure of biological membranes (SBM p107-115).
Charles Overton (1895): the importance of lipids.
Gorter and Grendel (1925): the lipid bilayer.
Phospholipids.
Bilayer sheets: permeability of lipid bilayer.
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 - 11
MEMBRANES.
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-12
MEMBRANES
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:
2.
Exocytosis amd endocytosis (SBM p123-127).
SELECTIVE TRANSPORT OF MOLECULES..
Read:
Read:
Passive transport (SBM p115-120).
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 - 13
PROKARYOTIC 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
the protoplast
b. the cell wall: peptidoglycan
c. gram-positive and gram-negative bacteria
d. appendages: flagella, pili or fimbriae
a.
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 - 14
EUKARYOTIC 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 theory
b. most cells are very small.
c. prokaryotes and eukaryotes.
2.
THE ORGANIZATION OF THE CYTOPLASM.
3.
NUCLEUS
Read:
—
—
—
4.
The cell nucleus (SBM p84-87)
nuclear envelope
nucleolus
chromosomes
GERL
Read:
a.
b.
c.
d.
Organelles in the cytoplasm (SBM p88-93)
Golgi complex.
endoplasmic reticulum.
lysosomes.
secretory vesicles
LESSON - 15
EUKARYOTIC 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
3.
Read: Mitochondria and chloroplasts produce energy (SBM p94-97).
a. mitochondria
b. chloroplast
c.
CYTOSKELETON
a. actin filaments actin
b. microtubules protofilaments tubulin
d. intermediate filaments vimentin, keratin
—
-
-
—
4.
CENTRIOLE AND UNDULIPODIUM (flagellum and cilium)
a.
centriole
b. undulipodia
LESSON - 17
EUKARYOTIC 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 19
EUKARYOTIC 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:
2.
LIPOPHYLIC SIGNALS USE INTRACELLULAR RECEPTORS.
Read:
3.
Sending signals (SBM p136-137)
Intracellular receptors (SBM p138 Figure 6-4)
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 - 20
ENERGY 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:
2.
Biological work (SBM p153-154)).
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—reduction
b. reduction potentials
c. electron tower
LESSON - 21
ENERGY METABOLISM: INTRODUCTION
A. Objectives
—
—
—
Describe ATP and discuss its role as a universal energy currency; explain the ATPADP 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:
3.
Enzyme cc factors (Figure 7-7. SBM p160)
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 - 22
ENERGY 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:
2.
The four stages of aerobic respiration (SBM p173-185)
THE GLYCOLYSIS
Read:
In glycolysis, glucose yields two pyruvate (SBM p174-178).
a. preparatory reactions
b.oxidation process
C.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 cycle
b.Krebs cycle
c. 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 - 23
ENERGY 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:
2.
The electron transport chain is coupled to ATP synthesis
(SBM p179-185)
FERMENTATION
Read:
Anaerobic respiration and fermentation (SBM p186-188)
a. fermentation pathway: general
b. variations on a theme
c. disadvantages, advantages
d. balance sheet
3.
RESPIRATION
Read:
Aerobic respiration of one glucose yields a maximum of 36 to 38 ATPs.
(SBM p183-185)
a. mitochondrial electron tower
b. generation of a proton motive force
c. ATP synthesis
d. balance sheet
4.
CARBOHYDRATE METABOLISM OF CHEMOHETEROTROPHS: C-heterotrophs
LESSON - 24
ENERGY 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 Zscheme; 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. chlorophylls
b. carotenoids
c. photophosphorylation
3.
OXYGENIC PHOTOPHOSPHORYLATION OF PLANTS AND ALGAE: THE ZSCHEME
Read:
Overview of photosynthesis (SBM p196-197)
The light-dependent reactions (SBM p198-201)
LESSON - 25
ENERGY 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 cycle
b. synthesis of a 6-C sugar
c. balance sheet
3.
ENERGY METABOLISM OF PLANTS
a. structure and functional relationship of chloroplasts
b. 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 - 26
THE BASIC STRUCTURE OF VIRUSES
A. Objectives
—
—
—
—
B.
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.
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. nucleocapsid
b. envelope
4.
DIVERSITY OF VIRUSES
a. bacteriophages: lytic and lysogenic cycles
Read: Figure24.2 and 24.3 (SBM p504)
b. animal viruses: DNA and RNA viruses
5.
REPLICATION OF ANIMAL VIRUSES
—
budding of enveloped viruses
LESSON - 27
DNA: 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:
a.
b.
c.
d.
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)
Genetic information is stored in the nucleus (J. Hammerling and J. Brachet, 1930)
the Fred Griffith (1928)-Oswald Avery (1944) experiment: bacteria
the Herschey—Chase experiment (1952): DNA viruses
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 14-8
Fraenkel-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 - 28
DNA: 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 - 29
DNA 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 model
b. conservative model
c. semi—conservative model
2.
MESELSON AND STAHL EXPERIMENT
Read:
a.
b.
c.
d.
3.
Figure 12-8 (SBM p269)
making ‘heavy’ DNA
separation of DNA by density
the experiment
conclusion
HOW DNA COPIES ITSELF.
a. DNA of eukaryotes
b. DNA of bacteria
LESSON - 230
DNA 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 – 31
THE EUKARYOTIC CHROMOSOME.
A.
Objectives
—
—
B.
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.
Lecture outline
READ: Eukaryotic chromosomes (SBM p212-215)
1.
THE EUKARYOTIC CHROMOSOME
Read:
Chromosomes are highly ordered structured (R&J p209-211)
a. history
b. human chromosomes
c. structure
LESSON - 32
CELL CYCLE AND MITOSIS
A.
Objectives
—
-
B.
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.
Lecture outline
READ: The cell cycle and mitosis (SBM p215-221
2.
THE CELL CYCLE
3.
MITOSIS
a.
b.
c.
d.
4.
prophase: formation of mitotic apparatus
metaphase: division of centromeres
anaphase: separation of chromatids
telophase: reformation of nucleus
CYTOKINESIS
a. animal cells
b. plant cells.
5.
CELL DIVISION IN PROKARYOTES
LESSON - 33
CONTROL 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 - 34
GENE 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:
2.
Information flow from DNA to Protein: an overview (SBM p282-283)
THERE ARE 3 TYPES OF RNA
a. messenger RNA (mRNA)
b. ribosomal RNA (rRNA)
c. transfer PNA (tRNA)
3.
TRANSCRIPTION
Read:
C. Study Questions.
Transcription (SBM p285-288)
LESSON - 35
GENE 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 polyAtail, 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:
2.
Variations in gene expression in different organisms (SBM p292-298)
PROCESSING OF THE PRIMARY RNA TRANSCRIPT
a. 5’ CAP
b. 3’ polyA-tail
c. 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 Matthaei
c. H. Gobind Khorana
2.
THE TRIPLET CODE
3.
CHARGING OF tRNA
LESSON - 37
GENE 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 - 38
GENE 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:
1.
ORGANIZATION OF AN OPERON.
a.
b.
c.
2.
the promotor binds RNA polymerase.
the operator binds the regulator: repressor or activator/inducer
the transcription unit is transcribed:
EXAMPLES OF GENE EXPRESSION.
a.
b.
3.
Gene regulation in bacteria (SBM p306-312)
The lactose breakdown: substrate induces transcription of the genes of catabolic
enzymes. [Figure 14-2 (SBM p307)]
The tryptophan synthesis: product represses transcription of genes of anabolic
enzymes. [Figure 14-4 (SBM p310)]
GENERALIZATION.
a.
b.
c.
positive and negative control.
induction and repression.
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 - 39
GENE 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.
b.
c.
d.
Core promotor: TATAAA—box.
basal transcription factors allow PNA polymerase to bind to the core promotor.
proximal control elements bind regulatory transcription factors.
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.
b.
c.
d.
4.
the helix-turn-helix motif.
the homeodomain motif.
the zinc finger motif.
the leucine zipper motif.
POST-TRANSCRIPTIONAL CONTROL IN EUKARYOTES.
a.
b.
c.
d.
e.
RNA processing and RNA splicing.
translational control: selecting which mRNAS are translated.
posttranslational control: e.g., glycosylation, targeting
ubiquitin-dependeflt protein degradation
regulation of enzyme activity.