Pursuit of Excellence in Science Club: Biology Syllabus

Siddharth Trehan January 29, 2013

Contents
1 Foundations 1.1 Chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.3 Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Molecular Biology 2.1 Membrane Structure and 2.2 Metabolism . . . . . . . 2.3 Cell Communication . . 2.4 Cell Cycle . . . . . . . . 3 3 4 5 8 8 8 8 8 9 9 9 9 9 10 10 10 10 10 10 10 10 10 10 11 11 11 11 11

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3 Genetics 3.1 Molecular Genetics . . . . 3.2 Viruses and Biotechnology 3.3 Genomics . . . . . . . . . 3.4 Classical Genetics . . . . .

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4 Animal Physiology 4.1 Homeostasis . . . . . . . . . . . 4.2 Nervous and Endocrine Systems 4.3 Sensory and Motor Mechanisms 4.4 Circulation and Gas Exchange . 4.5 Thermoregulation . . . . . . . . 4.6 Osmoregulation and Excretion . 4.7 Nutrition . . . . . . . . . . . . . 4.8 Immunity . . . . . . . . . . . . 4.9 Reproduction and Development

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5 Plant Anatomy and Physiology 5.1 Organization of the Plant Body . . . 5.2 Soil and Nutrition . . . . . . . . . . . 5.3 Responses to Environmental Changes 5.4 Reproduction and Development . . .

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1.1
1.1.1

Foundations
Chemistry
Readings

1. Campbells chapters 2-4 2. Lehningers chapters 1-2 3. Alberts chapters 1-2 1.1.2 Objectives

1. Why is water the most important molecule in all biological systems? 2. How do acids and bases work, and how are they important as buer systems? What is the Henderson-Hasselbach equation? 3. What is chemical equilibrium, and what are some factors that govern it? What are rate laws, and do they aect equilibrium? 4. What is the Gibbs Free Energy equation? What is the meaning of the dierent variables? 5. What is oxidation and reduction? 6. Give some examples of how the aforementioned concepts are important in biology. 7. In what ways is carbon the central atom of biology? 8. Give the name, structure, functions, and examples of the important functional groups in biology. 9. How do most monomers polymerize? 10. Identify the dierent classes of macromolecules, their functions, and the functional groups associated with them. How can each be further classied? What are some important properties of the monomers that compose them? 1.1.3 Problems A B C Given that: [A]i is the initial amount of A, [B]i is the initial amount of B, [C]i is the initial amount of C, k1 is the rate constant for A B, and k2 is the rate constant for B C 3

1. Consider the following chemical equilibrium:

Find an equation for the concentration of A, B, and C after a time t. 2. The amino acid glycine is often used as the main ingredient of a buer in biochemical experiments. The amino group of glycine, which has a pKa of 9.6, can exist either in the protonated + form (N H3 ) or as the free base (N H2 ) because of the reversible equilibrium. (a) In what pH range can glycine be used as an eective buer due to its amino group? (b) In a 0.1 M solution of glycine at pH 9.0, what fraction of glycine has its amino group in + the N H3 form? (c) How much 5 M KOH must be added to 1.0 L of 0.1 M glycine at pH 9.0 to bring its pH to exactly 10.0?
+ (d) When 99% of the glycine is in its N H3 form, what is the numerical relation between the pH of the solution and the pKa of the amino group?

3. Consider the important enzyme complex ATP synthase. This enzyme is an example of a molecular motor: if it is provided with energy, it can change its conformation and perform work. In this case, when protons ow through it, it can use their kinetic energy to phosphorylate a molecule of ADP, converting it to ATP. Taking this into consideration: (a) perform stoichiometric calculations on the oxidation of n molecules of NADH or f molecules of FADH2 to phosphorylate ADP to ATP (hint: use reduction potential and Gibbs free energy). (b) devise a mechanism whereby the mitochondria can transfer the energy from a reduced molecule such as NADH or FADH2 to ADP, producing ATP as the end-product.

1.2
1.2.1

Cells
Readings

1. Campbells chapter 6 1.2.2 Objectives

1. What are some similarities and what are some dierences between prokaryotes and eukaryotes? What are the advantages of compartmentalization, and what adaptations have enabled the transition from prokaryotic to eukaryotic cells? 2. What is the role of the dierent classes of macromolecules in a cell? 3. What are some techniques that can be used to analyze dierent components of the cell? 4. What are the components of the endomembrane system and what is the function of the individual parts? How is the endomembrane system assembled? 5. What is the function of the organelles present outside of the endomembrane system? 6. What are the components of the cytoskeleton and what are their structure and function? 7. What is prokaryotic endosymbiosis? What evidence is there to support it? 4

1.2.3

Problems

1. The outer and inner membranes of the mitochondrion partition the cell into two compartments: the cytoplasm and the mitochondrial matrix. The enzyme pyruvate dehydrogenase is found only inside the mitochondrion and catalyzes the following reaction: pyruvate + NAD+ + CoA acetylCoA + NADH + H+ + CO2 Assume the following information about this reaction: (a) The Gibbs free energy change in the forward direction is -20 kJ/mol. (b) The activation energy for the reaction with and without pyruvate dehydrogenase, respectively, is 0.6 kJ/mol and 60 kJ/mol (c) The concentration of pyruvate outside the mitochondrion is 5 mM, and the concentration inside the mitochondrion is 20 mM. The volume of the cytoplasm is 40 nL and volume of the mitochndrion is 10 nL. The concentration of pyruvate in the mitochondrion and in the cytoplasm is constant over time. (d) Pyruvate is exported into the mitochondrion through passive, facilitated diusion. Answer the following three questions: (a) What is the equilibrium constant for the reaction in the cytoplasm and in the mitochondrion (hint: remember that in the cytosol, the reaction does not proceed along with the formation of ATP and NADH: excess energy is dissipated as heat)? (b) What is the rate of the forward and reverse reactions in the cytoplasm and in the mitochondrion? (c) Suppose cell X has a mutation such that pyruvate dehydrogenase is present in both the cytoplasm and in the mitochondrion. Consider the equilibrium constant you found for the mitochondrion in question (a). Is the overall equilibrium constant in cell X dierent from this old equilibrium constant? In other words, does compartmentalization change the equilibrium constant for a reaction? If not, then what is the evolutionary advantage of compartmentalization for metabolic pathways? 2. Fill in the following table with the cellular organelles in which each of the following processes occur, adding details on the process of synthesis, degradation, or modication: Beaker Synthesis Degradation Modication Carbohydrates Lipids Proteins Nucleic acids

3. Give reasons for why the organelles of the endomembrane system are not separated by membranes, but they are separated from the cytosol, the mitochondria, and the peroxisomes.

1.3
1.3.1

Evolution
Readings

1. Campbells chapters 22-23 2. Griths chapters 20, 22 5

1.3.2

Objectives

1. Dene the following terms: gene, allele, genome. What is the so-called central dogma of biology? Where is the genetic information of a cell contained, and where is it processed? 2. Dene genetic variation and identify its sources. What is the biological importance of sex? 3. What is Hardy-Weinberg equilibrium? What are its assumptions? 4. How does natural selection work? 5. What are other mechanisms of evolution other than natural selection? Give examples of cases in which each occurs. 6. What is sexual selection and why does it occur? 7. What is Hamiltons Rule? 8. What is the dierence between microevolution and macroevolution? 1.3.3 Problems

1. Given that: x {AA, Aa, aa}, p(n) and q(n) are allele frequencies of A and a at a given time (n is directly proportional to both time and number of generations), and the general expression for Hardy-Weinberg equilibrium with selection is uAA (n)p(n)2 + uAa (n)2p(n)q(n) + uaa (n)q(n)2 = 1 show that: (a) the coecients for Hardy-Weinberg equilibrium are of the form: n n n n ux (n) = (Wx )(WAA p(0)2 + WAa 2p(0)q(0) + Waa q(0)2 )1 (b) both underdominance and overdominance lead to populations with a xed allele frequency (c) gene ow may reverse the eect of natural selection 2. E coli, cells are rod-shaped, about 2 pm long and 0.8 pm in diameter. The molecular weight of an E. coli DNA molecule is about 3.1 x 10 g/mol. The average molecular weight of a nucleotide pair is 660 g/mol, and each nucleotide pair contributes 0.34 nm to the length of DNA. (a) Calculate the length of an E. cole DNA molecule. Compare the length of the DNA molecule with the cell dimensions. How does the DNA molecule t into the cell? (b) Assume that the average protein in E. coli consists of a chain of 400 amino acids. What is the maximum number of proteins that can be coded by an E. coli DNA molecule?

3. An unknown substance, X, was isolated from rabbit muscle. Its structure was determined from the following observations and experiments. Qualitative analysis showed that X was composed entirely of C, H, and O. A weighed sampleof X was completely oxidized, and the H2O and CO2 produced were measured; this quantitative analysis revealed that X contained 40.00% C, 6.710% H, and 53.29% O by weight. The molecular mass of X, determined by mass spectrometry, was 90.00 u. Infrared spectroscopy showed that X contained one double bond. X dissolved readily in water to give an acidic solution; the solution demonstrated optical activity when tested in a polarimeter. (a) Determine the empirical and molecular formula of X. (b) Draw the possible structures of X that t the molecular formula and contain one double bond. Consider linear or branched structures and disregard cyclic structures. Note that oxygen makes very poor bonds to itself. (c) What is the structural signicance of the observed optical activity? Which structures in (b) are consistent with the observation? (d) What is the structural signicance of the observation that a solution of X was acidic? Which structures in (b) are consistent with the observation? (e) What is the structure of X? Is more than one structure consistent with all the data?

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2.1 2.2 2.3 2.4

Molecular Biology
Membrane Structure and Function Metabolism Cell Communication Cell Cycle

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3.1 3.2 3.3 3.4

Genetics
Molecular Genetics Viruses and Biotechnology Genomics Classical Genetics

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4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 4.9

Animal Physiology
Homeostasis Nervous and Endocrine Systems Sensory and Motor Mechanisms Circulation and Gas Exchange Thermoregulation Osmoregulation and Excretion Nutrition Immunity Reproduction and Development

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5.1 5.2 5.3 5.4

Plant Anatomy and Physiology

Organization of the Plant Body Soil and Nutrition Responses to Environmental Changes Reproduction and Development

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