CELLULAR ORGANIZATION I. Biological organization What is the hierarchy of life in terms of cells, organ systems, organisms, tissues, organs, chemicals, and subcellular organelles? II. Cellular metabolism How do anabolism and catabolism contribute to metabolism ? What are the roles of hydrophilic and hydrophobic substances in living things? Why are minerals important? What is the importance of carbohydrates, lipids, proteins (especially enzymes ) and nucleic acids? III. Cellular functions What is the evolutionary significance of the Cell Theory ? Are viruses cellular? IV. Plasma membrane (Fig. 5-6) Is every cell enclosed by a plasma membrane ? Why? Does every cell have a cell wall ? V. Cell size (Fig. 4-2) What are the consequences of a cell ? s surface-to-volume ratio ? How do we express the size of a cell or its subcellular constituents in SI units: meter ( m ); millimeter ( mm ), micrometer ( ì m ), and nanometer ( nm )? VI. Prokaryotes and eukaryotes How do the cells of prokaryotes and eukaryotes compare in terms of evolutionary history , size, and organization? VII. Research tools used by cell biologists A. Microscopy (Figs. 4-3, 4-4) How do light microscopy , transmission electron microscopy (TEM) , and scanning electron microscopy (SEM) compare in terms of methods and applications, effective magnification , resolution , and contrast ? Can vital stains be used in all types of microscopy? B. Cell fractionation (Fig. 4-5) What does it mean to lyse a cell? What is an ultracentrifuge ? What would you expect to find in the pellet ? the supernatant ? VIII. Organelles of eukaryotes (Table 4-1, Figs 4-7 and 4-8) What is the structure and function of each organelle ? What is the importance of internal membranous organelles? Are all organelles membranous? What is the lumen of an organelle? A. Nucleus What is/are chromatin , chromosomes , the nuclear envelope , and nuclear pores ? What is the relationship between the nucleolus and ribosomes ? B. Cytoplasm Are the cytoplasm and the cytosol the same? C. Endomembrane system What is the importance of vesicles in the endomembrane system ? 1. Nucleus (Fig. 4-11) Why is the nucleus considered part of the endomembrane system? In what ways is the nuclear area of a prokaryotic cell like a eukaryotic nucleus? How is it different? 2. Endoplasmic reticulum (Fig. 4-12) What are the functions of the rough endoplasmic reticulum and smooth endoplasmic reticulum ? 3. Golgi complex (Figs. 4-13, 4-14) Are all proteins processed by the Golgi complex ? 4. Plasma membrane What is exocytosis ? 5. Lysosomes (Fig. 4-15) What kinds of cells have lysosomes ? What happens in lysosomes? 6. Vacuoles What some of the things plant cells can accomplish by using their vacuoles ? D. Energy-converting organelles Why do cells need to carry out energy conversions? 1. Mitochondria (Fig. 4-19) What kinds of cells have mitochondria (sing. mitochondrion )? What happens in cellular respiration ? What is the significance of the mitochondrial cristae ? What is ATP ? 2. Plastids (Fig 4-20) What is a plastid ? What kinds of cells have chloroplasts ? What happens in photosynthesis ? E. Cytoskeleton (Fig. 4-21) What are the components of the cytoskeleton? Why is the existence of some purported cytoskeletal elements controversial? How do various cytoskeletal elements compare in diameter? in length? 1. Actin microfilaments (Fig. 4-26) In what way do actin monomers contribute to the structure of microfilaments ? What roles do microfilaments have in the cell? 2. Microtubules (Fig. 4-22; Fig. 4-23) In what way d o tubulin dimers contribute to the structure of microtubules ? How do cells use kinesin ? a. Cilia and flagella (Fig. 4-25) Why are cilia (sing. cilium) and flagella (sing. flagellum) called 9 + 2" structures ? What do microtubules contribute to the functioning of cilia and flagella? b. Basal bodies and centrioles (Fig. 4-24) Why are basal bodies and centrioles called 9 X 3" structures ? What kinds of cells possess centrioles? What is the relationship between basal bodies and centrioles? MITOTIC CELL DIVISION I. Chromosome structure (Figs. 10-2; 10-4) What is chromatin ? How do histones and DNA associate in nucleosomes ? II. Cell cycle (Fig. 10-5) What roles do the following play in the cell cycle : G 1 phase , S phase , G 2 phase , mitosis , and cytokinesis ? What is interphase ? III. Mitotic cell division A. Mitosis (Fig. 10-6) What is accomplished when a cell undergoes mitosis ? Is the term mitosis simply a synonym for cell division? * Specific example : Follow a cell that has 5 chromosomes through the stages of mitosis below. 1. Prophase Sketch a mitotic prophase chromosome and label sister chromatids , sister centromeres , and sister kinetochores . What do we mean when we refer to a duplicated chromosome? When do chromosomes become duplicated? * Specific example : How many total chromosomes are present? How many chromatids, centromeres, and kinetochores? 2. Metaphase (Figs. 10-7, 10-9) What is the metaphase plate ? How does the structure of a chromosome at mitotic metaphase compare with one at mitotic prophase? * Specific example : How many total chromosomes are present? How many chromatids, centromeres, and kinetochores? If a cell has centrioles , how many are there and how are they arranged during mitotic metaphase? What kinds of cells have centrioles? What kinds of cells have microtubule organizing centers (MTOCs) ? How can one distinguish among kinetochore microtubules , polar microtubules , and astral microtubules ? Are all three kinds found in all mitotic cells? 3. Anaphase How does the structure of a chromosome at mitotic anaphase compare with one at mitotic prophase? 4. Telophase How does the structure of a chromosome at mitotic telophase compare with one at mitotic prophase? mitotic metaphase? Mitotic anaphase? * Specific example : How many total chromosomes are present in a mitotic telophase nucleus? How many chromatids, centromeres, and kinetochores? Has the purpose of mitosis been accomplished? B. Cytokinesis (Fig. 10-10) Why do plant cells undergoing cytokinesis form a cell plate , whereas animal cells do not? C. Mechanism of chromosome movement What happens to kinetochore microtubules when the chromosomes move to the poles? IV. Preview of meiosis What are the roles of gametes and zygotes in a sexual life cycle? Do all cells contain homologous pairs of chromosomes? How does a haploid (n) cell differ from a diploid (2n) cell? How do we define the value of n. ? Specific example : What is the value of n in our example? Is the cell in our example haploid or diploid? Would you have been able to answer this question if the cell we started with had 10 chromosomes instead of 5? Does the ploidy of a cell change as it goes through the S phase? What is accomplished during meiosis ? Can a diploid cell undergo mitosis? meiosis? Can a haploid cell undergo mitosis? meiosis? ATOMS, MOLECULES, AND WATER Students are responsible for all of the material in Chapter 2 (review of the basics of high school chemistry), using this outline as a guide. If you are weak in chemistry, seek help right away! Only selected material will be actually covered in lecture. I. Atomic structure (Fig 2-1 - but do not try to memorize the periodic table!) What is an atomic mass unit (amu) ? What is a dalton ? How do electrons , neutrons , and protons compare in mass, charge, and atomic location? Do all atoms of the same element have the same atomic mass ? The same atomic number ? Why? What is the standard notation used to express these values? II. Isotopes and use of tracers in biology (Figs. 2-2 and 2-3) Why can isotopes of the same element generally substitute for each other? Why are radioactive tracers extraordinarily useful to biologists? How does the technique of autoradiography work? III. Ions How can an atom ionize, becoming a cation ? An anion ? How can a group of atoms become an anion or a cation (polyatomic ion)? IV. Some kinds of chemical bonds A. Covalent bonds (Fig. 2-5) How is the number of electrons in the valence shell of an atom related to the number of covalent bonds it can form? How many covalent bonds can be formed by each of the following: H, O, C, N, P, S? What is meant by electronegativity ? Which of the following are relatively electronegative atoms: H, O, C, N, P, S? What is a polar covalent bond ? Are all molecules that contain polar covalent bonds considered polar molecules ? B. Ionic bonds How can you predict that two atoms will form an ionic bond between them? C. Hydrogen bonds (Figs. 2-11, 2-13) How do hydrogen bonds form? How do hydrogen bonds and covalent bonds compare in strength? D. van der Waals interactions Under what conditions do van der Waals interactions occur? Are van der Waals interactions strong or weak forces? V. Properties of water In what ways do the physical properties of water depend on hydrogen bonding? Why are some substances hydrophilic , and others hydrophobic ? A. Cohesion and adhesion; capillary action (Fig. 2-14) Why is water cohesive? What kinds of substances does water adhere to? How do the cohesive and adhesive properties of water contribute to capillary action ? What is responsible for surface tension ? B. Specific heat Does water have high or low specific heat ? Why? What are the implications for living things? C. Heat of vaporization Does water have a high or low heat of vaporization ? Why? What is evaporative cooling ? D. Ice (Fig. 2-16) Why does ice float? What implications does this have for life on earth? VI. Acids and bases A. The pH scale (Table 2-2; Fig. 2-17) Why is the mole concept so useful? What is the significance of Avogadro ? s number ? What is an acid ? A base ? What is an acidic solution ? A basic solution ? A neutral solution ? How is pH calculated . .. if you know the hydrogen ion concentration? . . . if you know the hydroxide ion concentration? How do weak acids/bases compare with strong acids/bases? B. Buffers What kinds of substances are best suited to serve as buffers ? Why? Why is the concept of a dynamic equilibrium essential to understanding how a buffering system works? BIOLOGICAL MOLECULES I. Properties of hydrocarbons (Fig. 3-1) What properties of carbon make it so well-suited to serve as the central component of organic compounds? Are hydrocarbons hydrophilic or hydrophobic? Why? Draw the structural formulas of methane and ethane . What are some of the shapes that hydrocarbons can have? II. Functional groups (Table 3-1) What are the properties of each of the following functional groups : hydroxyl group , carbonyl group , carboxyl group , amino group , phosphate group , sulfhydryl group, and methyl group ? Why do they have these p roperties? III. Main classes of biological molecules What is a macromolecule ? What is a monomer ? How do macromolecules form? A. Carbohydrates What functional groups are found in every carbohydrate ? 1. Monosaccharides (Figs. 3-6; 3-7) What is the difference between an aldehyde sugar and a ketone sugar? Are sugars hydrophobic or hydrophilic? Why What happens when a monosaccharide undergoes a rearrangement to form a ring structure? Can a ring form in more than one way? 2. Disaccharides (Fig. 3-8) What is condensation synthesis ? What is hydrolysi s? How can two monosaccharides such as glucose and fructose be joined to form a disaccharide ( sucrose in this case)? 3. Polysaccharides What is a macromolecule ? What is a monomer ? How do macromolecules form? a . Storage polysaccharides (Fig. 3-9) What features relating to hydrogen bonding give a storage polysaccharides , such as starch and glycogen , the ability to form helical structures? b. Structural polysaccharides (Fig. 3-10) What features relating to hydrogen bonding give a structural polysaccharide , such as cellulose , the ability to provide strength through the interaction of adjacent fibers? B. Lipids Are lipids primarily hydrophobic or hydrophilic? Why? 1. Triacylglycerols (Fig. 3-12) How do 3 fatty acids and one glycerol react to form a triacylglycerol ? What is the main function of triacyglycerol in cells? 2. Properties of fatty acids a. Saturated fatty acids What is a saturated fatty acid saturated with? b. Unsaturated fatty acids What characterizes the hydrocarbon chain of an unsaturated fatty acid ? How does the fluidity of unsaturated fatty acids compare wi th the fluidity of saturated fatty acids? Why? What is the effect of van der Waals interactions? c. Monounsaturated fatty acids How many double bonds does a monounsaturated fatty acid have? d. Polyunsaturated fatty acids How many double bonds occur in a polyunsaturated fatty acid ? e . . Trans fatty acids Are trans fatty acids saturated or unsaturated? Are the physical properties of trans fatty acids more like those of saturated or unsaturated fatty acids? 3. Phospholipids (Fig. 3-13) How do 2 fatty acids, glycerol, a phosphate group, and a hydrophilic group such as choline, react to form a phospholipid ? How do the amphipathic properties of phospholipids enable them to form a lipid bilayer in the presence of water? 4. Steroids (Fig. 3-15) How can you recognize a steroid ? What is the function of cholesterol in cells? What are some other functions of steroids? C. Proteins 1. Amino acids (Fig. 3-16) Draw the structural formula of an amino acid . What distinguishes individual amino acids? How can polar amino acids , non-polar amino acids , acidic amino acids , and basic amino acids be recognized? 2. Protein structure a. Primary structure (Fig. 3-18, 3-19) What kind of chemical bond is a peptide bond , and how does it form? b. Secondary structure (Fig. 3-20) What part of a polypeptide chain is responsible for secondary structure ? What kinds of chemical bonds are responsible for secondary structure? How does an á helix differ from a ß pleated sheet? c. Tertiary structure (Fig. 3-21) What parts of a polypeptide chain are responsible for tertiary structure ? How do hydrogen bonds , ionic bonds , hydrophobic interactions , and disulfide bonds contribute to tertiary structure? d. Quaternary structure (Fig. 3-22) Can a single polypeptide chain have quaternary structure ? What kinds of bonds or interactions can contribute to quaternary structure? D. Nucleic acids (DNA and RNA) - to be discussed in genetics lectures MEMBRANES AND TRANSPORT I. Model of the plasma membrane (Fig. 5-6) What is meant by the term fluid-mosaic membrane model ? What components of a membrane have fluid properties? What components form the mosaic ? What molecules form the lipid bilayer ? Why are they able to do this? What are the characteristics of integral membrane proteins and peripheral membrane proteins ? Do they have similar functions? Where are membrane glycoproteins and membrane glycolipids found, and what some of their functions? II. Membrane transport What are the properties of a selectively permeable membrane ? A. Simple diffusion Why does simple diffusion predictably result in net movement down a concentration gradient ? What do we mean by passive transport ? What is the energy source for simple diffusion? 1. Diffusion of solutes (Fig. 5-11) 2. Osmosis (Table 5-1; Figs. 5-12, 5-13, 14) Why is osmosis considered a special case of diffusion? What is the osmotic pressure of a solution ? What happens if: . . . an animal cell is placed in a solution that is hypertonic ? hypotonic ? isotonic ? . . . a plant cell or other walled cell is placed in a solution that is hypertonic? hypotonic? isotonic? Is a typical plant cell healthiest when it is turgid , plasmolyzed , or flaccid ? How do aquaporins act to promote the rapid diffusion of water in some cells? B. Carrier-mediated transport Which of the following cannot easily pass through a lipid bilayer, and therefore require a membrane carrier protein? Gases? Ions? Large polar molecules such as sugar? Water? Hydrophobic substances? 1. Facilitated diffusion (Figs. 5-15, 5-16)) Does the law of simple diffusion (stated in part IIA above) also apply to facilitated diffusion? Can facilitated diffusion work against a concentration gradient? What is the energy source for facilitated diffusion? 2. Carrier-mediated active transport (Fig. 5-17) Do the laws of diffusion apply to carrier-mediated active transport ? Can carrier-mediated active transport work against a concentration gradient? Why are carriers that work by active transport called pumps ? What is the energy source for carrier-mediated active transport? B. Transport of particles and large molecules What are the energy sources for endocytosis and exocytosis ? What role does the plasma membrane play in these processes? 1. Exocytosis (Fig. 5-20) 2. Endocytosis a. Phagocytosis (Fig. 5-21) What kinds of materials are transported by phagocytosis ? b. Pinocytosis (Fig. 5-22) What is transported by pinocytosis ? c. Receptor-mediated endocytosis (Fig. 5-23) What are some of the advantages of receptor-mediated endocytosis ? ENZYMES AND ENERGETICS I. Biological work What is potential energy ? What is kinetic energy ? Can energy change form in a biological system? II. The laws of thermodynamics (Fig. 7-2) Do the laws of thermodynamics apply to an open system ? to a closed system ? What is the relationship between the first law of thermodynamics and the second law of thermodynamics ? What is the relationship between entropy and potential energy in a closed system? Can heat do work? Can heat energy do work? Can heat energy do work in a cell? III. Energy and chemical reactions (Fig. 7-3) In what sense is the free energy of a chemical system free ? A. Exergonic (spontaneous) reactions What happens to free energy in an exergonic reaction ? to entropy? Why is an exergonic reaction referred to as a downhill reaction ? Can an exergonic reaction occur in isolation in a closed system? B. Endergonic reactions What happens to free energy in an endergonic (spontaneous) reaction ? to entropy? Why is an endergonic reaction referred to as an uphill reaction ? Can an endergonic reaction occur in isolation in a closed system? What kinds of reactions are used in energy coupling to enable cells to drive endergonic reactions? IV. Enzymes as biological catalysts Is a catalyst consumed in a chemical reaction? A. Activation energy (Fig. 7-10) Compare the required activation energy of a reaction that is catalyzed vs. the same reaction uncatalyzed. Can an enzyme affect the free energy change of a reaction? B. The enzyme-substrate complex (Fig. 7-11) What is the function of the active site of an enzyme? How does the induced fit model explain the way the enzyme-substrate complex reduces the required activation energy of the reaction it catalyzes? C. Significance of biochemical pathways Why are most biochemical reactions reversible? Is the direction of a reaction determined by the enzyme catalyzing it? How does a biochemical pathway enable the cell to control the direction of a series of reactions? D. Factors that affect enzymatic reactions 1. Temperature What effect is predicted if you raise the temperature of an uncatalyzed reaction? A catalyzed reaction? 2. pH Why do most enzymes have a pH optimum? 3. Cofactors a. Inorganic cofactors Many inorganic cofactors are metal ions. Why? b. Organic cofactors (coenzymes) Is a coenzyme a protein? What do most coenzymes do? 4. Regulation: activation and inhibition a. Competitive inhibition (Fig. 7-17a) How is an enzyme ? s active site affected in competitive inhibition ? b. Non-competitive inhibition (Fig. 7-17b) How is an enzyme ? s active site affected in noncompetitive inhibition ? VI. Energy transfer by ATP A. Structure of ATP (Fig. 7-5) What happens when ATP (adenosine triphosphate) is converted to ADP (adensosine diphosphate) ? B. Central role of ATP in energy metabolism (Fig. 7-6) What roles do ATP and ADP play in endergonic and exergonic reactions? C. Mechanism of energy transfer by ATP How does ATP transfer energy? VII. Oxidation-reduction (redox) reactions What is transferred in a redox reaction ? How does this relate to energy? A. Reduction of NAD + to form NADH (Fig. 7-7) Which has more energy, NAD + or NADH ? B. Role of NADH in cellular metabolism CELLULAR RESPIRATION I. Overview of the oxidation of glucose What kinds of cells carry out aerobic cellular respiration ? Why do you breathe? Eat? II. Steps of aerobic respiration (Fig. 8-2) (Note: these reactions do not occur in separate cellular compartments in prokaryotes) A. Cytosol - Glycolysis (Fig. 8.3) Rank the following with respect to their energy value in metabolism: two pyruvates ; one glucose ; one fructose 1,6 bisphosphate , two glyceraldehyde 3-phosphates (G3P ) . In what forms is energy captured in glycolysis ? B. Mitochondrial reactions 1. Review of mitochondrial structure Sketch a mitochondrion, labeling the outer membrane , inner membrane , intermembrane space , cristae , and matrix . 2. Conversion of pyruvate to acetyl CoA (Fig. 8-5) What role does coenzyme A (CoA) play in metabolism? Is energy captured in the conversion of pyruvate to acetyl CoA? Is there any change in the number of carbons per molecule? 3. Citric acid cycle (also known as the Krebs cycle, tricarboxylic acid cycle, or TCA cycle) (Fig. 8-6) Give a summary of the citric acid cycle , including the roles of oxaloacetate , acetyl CoA, carbon dioxide, and citric acid. How many carbons does each of these have per molecule? In what forms is energy captured in the citric acid cycle? 4. Electron transport and chemiosmotic phosphorylation (oxidative phosphorylation) (Figs. 8-8, 8-9, 8-10) What is meant by oxidative phosphorylation ? What is the immediate electron source for the mitochondrial electron transport chain ? The terminal electron acceptor? What is the significance of a concentration gradient with respect to energy? How does ATP synthase function in chemiosmotic phosphorylation in mitochondria? 5. Energy yield of aerobic respiration (Fig. 8-11) Rank the following with respect to their energy value in metabolism: glucose, ATP, NADH, FADH 2 6. Fermentation (Fig. 8 - 13) What is an anaerobic process? What is the energy yield of alcohol fermentation ? Of lactic acid fermentation ? PHOTOSYNTHESIS I. Overview of photosynthesis What kinds of cells carry out photosynthesis ? Where does most of a tree ? s biomass come from? What is the ultimate source of the carbon in all those organic molecules in your body? II. Light-dependent reactions (in thylakoids) A. Absorption of light energy 1. Electromagnetic spectrum (Fig. 9-1) Why is visible light the part of the electromagnetic spectrum that is most important in biological processes that use electromagnetic energy? 2. Photosynthetic pigments a. Structure of chlorophyll (Fig. 9-5) What part of a chlorophyll molecule is involved in capture of light energy? What is the function of the hydrocarbon side chain? b. Comparison of absorption spectrum of chlorophyll and action spectrum for photosynthesis (Fig 9-6) Why do chorophyll a and chlorophyll b differ in their absorption spectra ? Does the action spectrum for photosynthesis perfectly match the combined absorption spectra of chlorophylls a and b? Why? Why are carotenoids referred to as accessory pigments ? 3. Structure of the chloroplast (Fig. 9-4) Make a simplified sketch a chloroplast, labeling the outer membrane, intermembrane space, inner membrane, stroma , thylakoid membrane , and thylakoid lumen . Which part(s) should be colored green? Which parts form the grana (sing. granum)? 4. Light-harvesting antenna complexes (Fig. 9-10) What is the function of the reaction center of a light harvesting antenna complex ? Why is a primary electron acceptor necessary? B. Electron transport by noncyclic electron flow (Fig. 9-11) What happens when Photosystem II absorbs light energy? What is the role of P680 ? Why is the term photolysis of water somewhat misleading? What happens when Photosystem I absorbs light energy? What is the role of P700 ? What is the electron source for noncyclic electron flow ? What is the terminal electron acceptor? C. Chemiosmotic phosphorylation (photophosphorylation) 1. Structure of the thylakoid membrane (Figs. 9-12, 9-13) How does ATP synthase function in chemiosmotic photophosphorylation in chloroplasts? 2. Comparison of chemiosmosis in mitochondria and chloroplasts III. The Calvin cycle and carbon fixation (in the stroma) (Fig. 9-14) What reaction does rubisco (ribulose bisphosphate carboxylase) catalyze in the initial carbon fixation reaction of the Calvin cycle ? How does the cellular function of NADPH differ from that of NADH? What is the importance of glyceraldehyde 3-phosphate (G3P) to carbohydrate synthesis?
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