Study Guide for Exam 2

BIOL 105

Fall 2010

Dr. Schroeder

A. Metabolism a. Metabolic pathways linked i. Catabolic pathways ii. Anabolic pathways b. Thermodynamics i. Conservation of energy (1st law) ii. Entropy of Universe increases (2nd law) iii. Living organisms are OPEN systems iv. Spontaneous Reactions 1. Occur without adding energy 2. May happen very slowly 3. G < 0 v. Free energy 1. G = H T S 2. Exergonic and endergonic reactions a. Which is spontaneous? b. Which requires energy input? vi. Equilibrium can a metabolic reaction every be in equilibrium? c. Enzymes are catalysts i. Not used up in the reaction ii. Lower activation energy iii. Do not change G

iv. Enzyme Inhibitors 1. Competitive inhibitors 2. Non-competitive inhibitors v. Regulation 1. Active Sites and Regulatory Sites 2. Allosteric regulation a. Increase or decrease enzyme activity b. Molecule binds somewhere OTHER THAN active site 3. Negative feedback (sometimes positive feedback) 4. Localization

vi. Enzyme Kinetics (Monkeys and Peanuts) 1. Monkeys are enzyme, peanuts are substrate 2. What happens when the amount of substrate changes? 3. What happens when the amount of enzyme changes? 4. How do you GRAPH the information? a. Use what you learned in lab B. Cellular Respiration a. Fuel + O2 CO2 + H2O + Energy i. What fuels are used? 1. How do fuels (other than glucose) fit into the scheme (generally) ii. What form is the energy? (there are two) iii. Series of Redox reactions 1. Reducing means the molecule GAINS an ea. Adding an e- REDUCES the + charge on the molecule 2. Oxidizing means the molecule LOSES an e3. Glucose is oxidized and O2 is reduced a. NAD+ is reduced to NADH when carrying electrons b. O2 is the final electron acceptor iv. Free Energy 1. Glucose: G = 686 kcal/mol 2. ATP: G = 7.3 kcal/mol b. Glycolysis i. Cytoplasm ii. Break glucose into pyruvate iii. Transfer electrons to NADH iv. Net gain of 2 ATP via substrate level phosphorylation 1. Invest 2 ATP and make 4 ATP

c. Citric Acid Cycle i. Mitochondrial matrix ii. Convert pyruvate to CO2 iii. Requires O2 iv. Transfer electrons to NADH and FADH2 v. Net gain of 2 ATP via substrate level phosphorylation

d. Oxidative Phosphorylation i. Inner mitochondrial membrane (imm) ii. Electron Transport Chain 1. Series of multi-protein complexes pass electrons in a series of redox reactions 2. Uses electrons carried by NADH and FADH2 3. Protons (H+) pumped into intermembrane space to create a gradient 4. NO ATP IS MADE iii. Chemiosmosis 1. Makes 90% of ATP 2. ATP Synthase (enzyme) uses energy of proton gradient to make ATP from ADP + inorganic phosphate (Pi)

e. Other Catabolic Pathways i. Fermentation 1. No electron transport chain 2. ATP made by substrate level phosphorylation a. How much less ATP per glucose? 3. Needs to regenerate NAD+ a. Lactic acid fermentation b. Ethanol fermentation

ii. Cellular respiration 1. Aerobic (above) 2. Anaerobic a. Electron transport chain but O2 is not the final electron acceptor b. Facultative Anaerobic cells can use cellular respiration when O2 is present, and fermentation when it is absent C. Photosynthesis a. Autotrophs vs. Heterotrophs i. Photoautotrophs b. Properties of light i. Waves and particles ii. Wavelengths ( ) compared to energy iii. Photons iv. Fluorescence 1. What causes it? 2. How is the energy of fluorescent light related to the light that excited the electron? c. Leaf structure i. Chloroplasts ii. Stomata d. Chlorophyll i. Why is it green? ii. What wavelengths of light are absorbed? Reflected or transmitted? iii. Porphyrin ring iv. Absorption spectrum vs. Action spectrum 1. Look at the lab, too 2. What was Engelmans s experiment? v. Pigments can only absorb photons of light with the exact energy needed to excite an electron to a higher orbital e. Photosynthesis is NOT the opposite of cellular respiration very different enzymes and reactions i. 6 CO2 + 12 H2O + Light energy p C6H12O6 + 6 O2 + 6 H2O ii. Water is split into H (goes into sugar and new water) and O (goes to O2) 1. How do we know that the O2 comes from water and not from CO2? iii. CO2 is fixed (C, O to sugar, O to new water) iv. Series of redox reactions f. Light Reactions i. Occurs in the Thylakoid membranes ii. Water to electrons + H+ + O2 iii. Makes ATP 1. Chemiosmosis

2. Photophosphorylation iv. Photosystems 1. Light harvesting complexes 2. Reaction center complex 3. PS II has P680, PS I has P700 a. What are P680 and P700? b. What do they do? c. Why do they have different names? 4. How does light travel from PS II to PS I? a. Electron transport chain b. Makes ATP c. How else can PS I get energy? 5. What happens in cyclic electron flow? v. Chemiosmosis 1. Compare and contrast in mitochondria and chloroplasts a. What is the same? b. What is different? c. Where does it occur in each organelle? THE LIGHT REACTIONS Summary

g. Calvin Cycle i. Occurs in the Stroma ii. Turns CO2 into sugar using the electrons and ATP made in light reactions iii. Why is calling this the dark reactions misleading? iv. Compare to citric acid cycle

v. 3 Steps 1. Carbon fixation a. Rubisco (enzyme) b. How many APT and NADPH per CO2 molecule at this step? c. Uses CO2 2. Reduction a. How many APT and NADPH per CO2 molecule at this step? b. What happens to the G3P made (per 3 turns of the cycle)? 3. Regeneration of CO2 acceptor a. How many APT and NADPH per CO2 molecule at this step? b. Why is this important? vi. Dealing with dehydration 1. Close stoma to keep water in, can t get rid of O2 or get CO2 2. Strategies a. C3 plants - photorespiration b. C4 plants PEP carboxylase instead of Rubisco c. CAM plants open stoma at night, store CO2 as organic acids PHOTOSYNTHESIS summary

D. Cell Communication and Signal Transduction (chapter 11) a. Direct communication pores between cells b. Cell recognition membrane proteins c. Secreted signals i. Paracrine ii. Synaptic iii. Endocrine d. 4 steps

i. Reception 1. Ligand binds receptor 2. Receptors on plasma membrane (or in cytoplasm) ii. Transduction 1. Relay molecules amplify signal 2. Signal transduction pathways iii. Response 1. Activate genes or proteins 2. Change activity of cell iv. Reset 1. Need to end the response AND the signal transduction pathways 2. Get ready for another signal to arrive e. Evolved long ago single celled organisms use same molecules as mammals f. Types of receptors i. G protein-coupled receptors ii. Tyrosine kinase receptors iii. Ion channel receptors iv. Steroid hormone receptors v. Know mechanisms for each class 1. How receptor is activated by ligand binding 2. What next steps are g. Phosphorylation i. Know the functions of kinases and phosphorylases ii. Know what a phosphorylation cascade is h. Second messengers i. cAMP, Ca++, and IP3 ii. interactions in second messenger cascades i. cellular responses i. activate or turn off gene ii. activate or inactivate a protein iii. induce cell division j. Fine tuning responses to multiple signals E. Cell Cycle and Mitosis (chapter 12) a. Binary fission b. Mitosis and Cytokinesis (what happens in each stage) i. Interphase 1. G1 2. S 3. G2 ii. Prophase iii. Prometaphase iv. Metaphase v. Anaphase vi. Telophase

vii. Cytokinesis 1. In animal cells 2. In plant cells c. Chromosomes and sister chromatids d. Mitotic spindle i. Centrosome ii. Kinetochore microtubules iii. Nonkinetochore microtubules iv. Aster e. Regulation of cell cycle i. Cytosolic molecules ii. Checkpoints iii. Cell cycle clock F. Meiosis (chapter 13) a. Alternation of generations i. Asexual reproduction ii. Sexual reproduction iii. Polyembryony b. haploid and diploid stages i. animals ii. plants iii. fungi c. meiosis - 1 round of replication 2 rounds of division i. Meiosis I separates homologous chromosomes ii. Meiosis II separates sister chromatids iii. Know the stages of both Meiosis I and Meiosis II iv. Know what stages are unique to Meiosis d. Karyotypes e. Know similarities and difference between Mitosis and Meiosis (Figure 13.9) f. Genetic Variation i. Mutations 1. Alleles 2. Locus (plural = loci) ii. Independent assortment (when does it occur?) iii. Crossing over (when does it occur?) iv. Random fertilization G. Mendelian Genetics (chapter 14) a. Blending theory compared to Particulate theory b. Monohybrid crosses, Dihybrid crosses i. Parental generation ii. F1 generation iii. F2 generation

c. d. e.

f.

iv. Punnett Squares v. Test crosses is an individual with dominant phenotype Homozygous or Heterozygous? 1. Genotype vs. Phenotype 2. Dominant vs. Recessive The Law of Segregation (monohybrid crosses) The Law of Independent Assortment (dihybrid crosses) The Laws of Probability i. Addition Rule ii. Multiplication Rule Complications i. Incomplete or codominance ii. Multiple alleles iii. Epistasis iv. Polygenic inheritance v. Environmental effects

H. Chromosomal Basis of Inheritance (chapter 15) a. Chromosomal theory of inheritance based on Mendel s particles b. Compare chromosomal inheritance to stages of Meiosis c. T.H. Morgan and flies i. Why study flies? ii. What was first mutation? iii. What was unusual about the F2 generation? iv. How is this related to the lab? d. Sex-linked traits i. Sex determination how does it vary? ii. Recessive sex-linked traits 1. How are traits (in humans) inherited? 2. Are they more common in males or females? iii. X and Y chromosomes 1. How are they similar? 2. How are they different? 3. How are they separated in meiosis? 4. Gene dosage compensation what is the Barr body? e. Linked genes i. Chromosome mapping ii. Genetic recombination 1. What is the physical basis? 2. When does it happen?