Class Preparation Assignment Questions

Biology I

Fall 2013

The purpose of class preparation assignment questions is to encourage students to read and think about the material of Biology I before covering it in class, to provide students with an idea of some topics that the instructor feels are important from each chapter, and to provide some feedback to students on how well they understand the chapter topics and concepts. Students may collaborate to figure out the answers for class preparation assignment questions, but each student in a study team must understand the questions and answers to have achieved the learning goals, so each student must submit separate assignments written in his/her own words. Students who turn in answers with wording very similar or identical to the text, internet sources, or another students work will receive NO CREDIT for the assignment, as plagiarism is unacceptable in college work. Consequences for academic dishonesty (see syllabus and SNC catalog) will be enforced for plagiarism. Answers may be handwritten (if legible) or typed. CPA assignments may be e-mailed (please include your name as part of the file name) or a hard copy handed in. Both e-mailed and hard copy CPAs are due at the beginning of the class period on the due date and will NOT be accepted later. Due dates are listed next to the assignment and on the running schedule of classes. Due dates may be postponed if the running schedule is modified, but will never be earlier than indicated on this page. Each CPA assignment is worth 15 points. The best 18 CPA scores will count toward a students grade. Thus, CPA assignments are worth 22.5% of the final grade for Biology I! Since there are 3 more CPA assignments possible than will count toward a students grade, students will NOT be allowed to turn in CPA for credit after the due date and time, even if an absence is excused. Students may turn in late CPAs for feedback, but not for credit.

CPA 1 Chapter 1: Principles of Life

Due Wednesday, August 21

1. What evidence exists that life on earth had a single origin, that is, all living things evolved from a common ancestor? 2. What are the three major branches of the tree of life? In which branch(es) do organisms have prokaryotic cells? In which branch(es) do organisms have eukaryotic cells? Which branch(es) contain plants, animals, and fungi? 3. What is homeostasis? Why is it important? 4. We can learn things about how living organisms work by studying them at various levels in a hierarchy of organization from individual molecules to the biosphere. Describe how things from lower levels are organized into sequentially higher levels of the hierarchy. You will find more on this at www.whfreeman.com/hillis1e in Chapter 1, Activity 1.2. 5. What are adaptations? How are they related to natural selection and evolution? 6. Describe the difference between a non-scientists definition of theory and a scientists definition of theory. How can these differences confuse the non-scientist about the reliability of information gained through scientific thinking?

Suzanne Gollery

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Class Preparation Assignment Questions

Biology I

Fall 2013 Due Monday, August 26

CPA 2 Chapter 2: Life, Chemistry, and Energy Part I

1. Silicon (Si) has an atomic number of 14. Draw the electron shell configuration of silicon. Use the octet rule to predict how many covalent bonds a silicon atom will make to fill its outer electron shell. (Hint: For help with questions 1 3, go to www.whfreeman.com/hillis1e/ , choose Chapter 2, and click on Animated Tutorial 2.1: Chemical Bond Formation. View the four parts of this tutorial to learn more about electron shells, the octet rule, and chemical bonds.) 2. What kind of chemical bonds will hold magnesium and chloride atoms together in a molecule of MgCl2? Justify your answer. (See Animated Tutorial 2.1) 3. Compare and contrast ionic bonds and hydrogen bonds. How are they similar? How are they different? 4. What does it mean when we say that molecules are hydrophilic or hydrophobic? Which of the following molecules are hydrophilic? Which are hydrophobic?

MgCl2

CH3CH2CH2CH3

5. Show where partial charges exist on this molecule:

CPA 3 Chapter 2: Life, Chemistry, and Energy Part II

Due Wednesday, August 28

1. Which functional group makes sugars so soluble in water? Explain why sugars dissolve in water. 2. The equation below shows a condensation (dehydration) reaction by which mannose and fructose will be joined to form a disaccharide. Circle the atoms that will be removed from the two simple sugars as they are joined. What molecule forms in addition to the disaccharide? (Hint: Also see Animated Tutorial 2.2, the subsection on carbohydrates for help with this question.)

+
3. Compare and contrast cellulose, starch, and glycogen. How are they similar? How are they different? 4. How are the structures of fats and oils different? How do their different structures affect their properties? (Hint: Also see Animated Tutorial 2.2, the subsection on lipids, for help with this question.)

(more CPA 3 questions on the next page)

Suzanne Gollery

pg. 2

Class Preparation Assignment Questions

Biology I

Fall 2013

5. Various representations of phospholipids are shown. For each, label the head and tails. Choose one phospholipid to show which part is polar, which part is nonpolar, and where the phosphate group is located.

6. Answer the Apply the Concept questions on page 31. (Hint: think about whether the reactions are anabolic or catabolic.) The energy changes that occur during one of these three chemical reactions will look like the diagram to the right. Which reaction has this energy diagram? (Hint: Figure 2.14 will help you understand changes in energy during chemical reactions.)

Reactants

Products Time course of reaction

CPA 4 Chapter 3: Peptide bonds, hierarchy of protein structure Due Wednesday, September 4

1. Which functional groups are present in all amino acids? Sketch these functional groups in their ionic forms, the forms usually present in cells. Why are these functional groups important to the primary structure of proteins? 2. How many amino acid side chains are there among amino acids normally found in proteins? The amino acids can be classified into four groups based on the chemical properties of their side chains. List the four groups and briefly describe their properties. Which amino acids belong in each group? (Dont worry, you wont need to memorize the structures and names of amino acids for an exam. I just want you to think about how their structures vary, because it will be important for understanding how proteins function.) 3. Describe the two types of protein secondary structure in your own words. What kinds of chemical bonds stabilize the secondary structures of proteins? 4. List and briefly describe the chemical bonds that stabilize protein tertiary structures. 5. Open your favorite web browser and search the images with the words protein structure. Identify proteins with and without quaternary structure from among the images. (Hint: often the distinct polypeptides of proteins with quaternary structure will be shaded with different colors in drawings, as in Hillis Figure 3.7E, so you can find proteins that have or lack quaternary structure by just viewing their images.) List four proteins that have quaternary structure. List four proteins that lack quaternary structure.

Suzanne Gollery

pg. 3

Class Preparation Assignment Questions CPA 5 Chapter 3: Enzymes

Biology I

Fall 2013 Due Monday, September 9

1. Explain the relationship between activation energy (Ea) and the rates of biochemical reactions.

2. On the free energy diagram to the right, label the reactants and products, activation energy (Ea), and change in free energy (G). Will this reaction proceed spontaneously? Why, or why not? Assume that this free energy curve represents the reaction in the absence of an enzyme. Draw another curve that shows energy changes with an enzyme present.

Time course of reaction

3. Describe three ways that enzymes interact with substrate(s) to catalyze biochemical reactions. 4. What are cofactors, coenzymes, and prosthetic groups? How are they involved in the functioning of enzymes? 5. Before answering this question, go to the Hillis website (www.whfreeman.com/hillis1e/ ) and watch Animated Tutorial 3.2: Enzyme Catalysis. Use the house-shaped button to return to the beginning of the tutorial. Click on each of the four choices (substrate, substrate + enzyme, substrate + enzyme + competitive inhibitor, or substrate + enzyme + noncompetitive inhibitor) in turn to see how the chemical reaction will proceed in each case. Enzymes illustrate a very important concept about protein structure: A proteins three-dimensional structure is important for its function. Explain this concept as it relates to enzymes. 6. List two factors besides inhibitors that affect enzyme activity. Why do these factors alter enzyme activity?

CPA 6 Chapter 3 & section 36.1: Protein concepts

Due Wednesday, September 11

1. Go to the Hillis website (www.whfreeman.com/hillis1e/ ) and watch Animated Tutorial 3.1 Macromolecules: Proteins in order to answer this question. One of the most important concepts in biology is that structure is important for function. A proteins three-dimensional structure is important for its function. What about collagens primary structure is important for its 3D structure? Describe collagens quaternary structure. How is collagen similar to rope? What is the function of collagen in animal tissues? How is its structure important for its function? 2. One important concept about proteins is that proteins bind to things (ligands) as they function. What binds to enzymes at the active site and how is this important for enzyme function? What binds to enzymes at the allosteric site and how is this important for enzyme function? 3. Another important concept about proteins is that proteins are often dynamic machines, that is, their shapes change as they function. Choose a protein and explain why movement (a change in shape) is important for its function. Suzanne Gollery

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Class Preparation Assignment Questions

Biology I

Fall 2013

4. Explain in one sentence how muscle cells get shorter as they contract. 5. This line drawing illustrates the interaction between a myosin head and the actin (thin) filament during muscle contraction. Describe what is happening in each step (A, B, C, and D). What will happen next (after step D)?

Submit exam 1 questions:

Due Monday, September 16, by 1 p.m.

Write exam 1 questions based on material from chapters 1-3 and section 36.1, plus materials used in class. Exam questions can be in multiple choice or short answer format. Use question stems (posted on Moodle) to help you write thoughtful questions. Students will receive 2 points extra credit for each of their exam questions used for the Exam 1 Review. Submitted exam questions might also appear on Exam 1, whether or not they were used on the Exam 1 Review.

CPA 7 Chapter 4: Cells 1. Briefly describe two ways that biologists study cells.

Due Monday, September 23

2. Compare and contrast prokaryotic and eukaryotic cells. How are they similar? How are they different? Which domains (major lineages of the tree of life) have prokaryotic cells? Which have eukaryotic cells?

Suzanne Gollery

pg. 5

Class Preparation Assignment Questions

Biology I

Fall 2013

3. Complete the table. The first structure has been done as an example. Students will also be responsible for identifying these structures on micrographs (photographs of cells taken with a microscope) such as Hillis Fig. 4.9, left, or illustrations of cells, such as those on pages 62 and 63 of the Hillis text. Subcellular structure Description and Function(s) Slimy carbohydrate layer surrounding cell walls of some bacteria that protect cells, help cells attach to surfaces, and keep cells from drying out Check if present in these cells Prokaryotes Plants Animals

Capsule

Cell wall

Centrioles

Chloroplasts

Cilia

Cytoplasm (in cytosol)

Cytoskeleton

Desmosomes

Extracellular matrix

Flagella

Gap junctions

Golgi apparatus

Intermediate filaments

Lysosomes

Suzanne Gollery

pg. 6

Class Preparation Assignment Questions Subcellular structure

Biology I

Fall 2013 Check if present in these cells Prokaryotes Plants Animals

Description and Function(s)

Microfilaments

Microtubules

Mitochondria

Nucleus

Peroxisomes

Plasma membrane

Plasmodesmata

Ribosomes

Rough ER

Smooth ER

Tight junctions

Vacuole

Vesicles

4. Which organelles from the table make up the endomembrane system? Describe the movement of proteins that have just been synthesized on the rough ER through the endomembrane system until they are secreted to the outside of the cell.

Suzanne Gollery

pg. 7

Class Preparation Assignment Questions

Biology I

Fall 2013 Due Monday, September 30

CPA 8 Chapter 5 through section 5.4: Cell membranes and Transport

1. Use the list of terms to label each structure with a leader line pointing to it. Briefly describe the function of each structure in cell membranes. (Hint: this is much like Activity 5.1 on the Hillis web site. This will be easier if you view the figure in color.) a. b. c. d. e. f. g. Carbohydrate Channel protein Cholesterol Cytoskeletal filament Glycolipid Glycoprotein Integral membrane (transmembrane) protein h. Lipid bilayer i. Peripheral membrane protein j. Phospholipid

2. Compare and contrast diffusion and osmosis. How are they similar? How are they different? 3. Compare and contrast facilitated diffusion (see Animated Tutorial 5.1) and active transport (see Animated Tutorial 5.2). How are they similar? How are they different? 4. Compare and contrast primary active transport and secondary active transport. How are they similar? How are they different? (See Animated Tutorial 5.2 for both.) 5. Compare and contrast endocytosis and exocytosis. How are they similar? How are they different? (See Animated Tutorial 5.3 for both.) CPA 9 Section 5.5: Cell Signaling Due Wednesday, October 2

1. Cells that respond to a particular chemical signal are called target cells. What makes a target cell different than a cell that does not respond to the particular chemical signal? 2. Two real situations involving chemical signaling are described below. Decide which exemplifies paracrine signaling and which exemplifies endocrine signaling (signaling involving a hormone). Explain your answers. a. When you are exposed to a stressful situation, your brain stimulates your adrenal glands to secrete epinephrine (also called adrenaline), a chemical signal that travels through your blood vessels to reach many targets and coordinate an appropriate response to the stressor. For example, epinephrine stimulates your liver to release glucose into your blood for increased energy, increases your heart rate and blood pressure to deliver more O2 and glucose to your brain and muscles so that you can think clearly and act effectively on any decisions, while also inhibiting digestion, so that your bodys resources can be used for the stress response, rather than digesting food. Suzanne Gollery

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Class Preparation Assignment Questions

Biology I

Fall 2013

b. When you get a cut and inflammatory response occurs. Damaged cells at the injury site secrete chemical signals that act on nearby blood vessels, causing smooth muscle in blood vessel walls to relax, so that more blood can flow to the site of injury, and making the capillaries more leaky, so that white blood cells can exit the blood to clean up debris and any bacteria that entered the broken skin. Other chemical signals released by damaged cells stimulate pain sensory receptors in the skin, so that your brain perceives pain and you are conscious of the injury and its location. 3. Briefly describe a signal transduction pathway that occurs when each of these types of signal receptor molecules are activated by a chemical signal. a. Ion channel receptor b. G protein-linked receptor (one example is described in Animated Tutorial 5.5 on the Hillis web site) c. Protein kinase receptor 4. Signal transduction pathways invariably involve many steps. Explain two reasons why having multiple steps in signal transduction is advantageous.

CPA 10 Section 6.1: Oxidation-reduction, electron carriers, and ATP Synthase

Due Monday, October 7

1. Watch this YouTube mini-lecture (by Heather Roberts at Stanford University) about how energy from ATP can be used to power exergonic biochemical reactions: http://www.youtube.com/watch?v=4O6DFv2p5js. Now do Activity 6.1 on the Hillis web site (the NEXT button is the green arrow in the upper left). Explain in your own words how potential energy to power cellular processes is stored in an ATP molecule. 2. ATP and NADH are both energy carrier molecules. In what form does NADH carry potential energy? 3. The reactions below are oxidation-reduction reactions. In each reaction, which molecule is oxidized (donates electrons)? Which is reduced (gains electrons)? Give the reaction equation if Cu transfers electrons to NAD+ instead of to Ag+.

4. Watch Animated Tutorial 6.1 on the Hillis web site and then answer the questions. a. What source of potential energy is used by ATP Synthase to power ATP synthesis? b. Why must ATP Synthase be located within a cell membrane, such as the inner mitochondrial membrane? c. Explain how ATP Synthase illustrates this important concept about protein function: proteins are often dynamic machines, that is, their shapes change as they function. (Hint: watch this DnaTube video to see the answer to this question: http://www.dnatube.com/video/104/ATP-synthase-structure-andmechanism)

Suzanne Gollery

pg. 9

Class Preparation Assignment Questions

Biology I

Fall 2013 Due Wednesday, October 9

CPA 11 Chapter 6, sections 6.5 & 6.6: Photosynthesis

1. Explain how the electron transport chain of the light reactions of photosynthesis is related to ATP synthesis. (Hint: see Animated Tutorial 6.3 on the Hillis web site.) You will NOT be expected to remember the names of the protein complexes that make up the ETC! 2. How is O2 generated during photosynthesis (see Animated Tutorial 6.4 on the Hillis web site)? Is O2 the most important product of photosynthesis (from the point of view of autotrophs)? Why, or why not? 3. Figure 6.19 is set up like a free energy diagram for the light reactions (compare to the free energy diagram in Figure 2.14 and to the right on this page). Is photosynthesis an exergonic or endergonic process? Is it an anabolic or catabolic process? Ultimately, where does the energy come from that is needed for photosynthesis to occur? How is the energy captured by photosynthesis stored for later use in a plant, alga, or bacterium? 4. Why is it important that both NADPH and ATP are generated by the light reactions? (Hint: what is the final product of photosynthesis?) 5. Show where each of the following things occur or are located on this diagram of a chloroplast. a. b. c. d. e. f. g. h. i. ATP is produced here ATP Synthase Calvin cycle Electron transport chain (ETC) High [H+] (high concentration of hydrogen ions) Low [H+] (low concentration of hydrogen ions) Stroma Thylakoid membrane Thylakoid space

CPA 12 Chapter 6, sections 6.2 6.4: Respiration and Fermentation

Due Monday, October 14

1. Figure 6.8 shows a free energy diagram for the process of cellular respiration. Study this figure while answering these questions: a. Is cellular respiration an exergonic or endergonic process overall? How can you tell? b. Some of the enzymes that catalyze the several small steps of cellular respiration are enzymes of the ETC. What mechanical process do these ETC enzymes couple to the stepwise oxidation of glucose or other food molecules? How is this, in turn, coupled to ATP Synthesis? (You will NOT be expected to remember the names of the protein complexes that make up the ETC!) c. Which of the initial reactants is oxidized in this process? Which is reduced? Suzanne Gollery

pg. 10

Class Preparation Assignment Questions

Biology I

Fall 2013

2. Show where each of the following things occur or are located on this diagram of a mitochondrion. a. b. c. d. e. f. g. h. i. j. k. l. m. ATP is synthesized here ATP Synthase Citric acid cycle Cytosol Electron transport chain (ETC) Fermentation in the absence of O2 Glycolysis High [H+] (high concentration of hydrogen ions) Inner mitochondrial membrane Intermembrane space Low [H+] (low concentration of hydrogen ions) Matrix Oxidation of pyruvate

3. Complete the table: Stage of cellular respiration Glycolysis Oxidation of pyruvate and citric acid cycle ETC and chemiosmosis Reactants that enter this stage Energy-rich products By products (waste products)

4. Why do animals and other heterotrophs that use oxidative cellular respiration require O2? Be specific, that is, explain exactly how O2 is used in oxidative respiration. 5. Compare and contrast fermentation and cellular respiration. How are they similar? How are they different? 6. We can get energy from our foods without eating any carbohydrates, because fats and proteins can also enter the metabolic pathways of cellular respiration to be oxidized in order to make ATP. At which points can fats and proteins enter respiratory pathways? (Hint: see Figure 6.14.)

Suzanne Gollery

pg. 11

Class Preparation Assignment Questions Submit exam 2 questions:

Biology I

Fall 2013 Due Wednesday, October 16, by 1 p.m.

Write exam 2 questions based on material from chapters 4 6, plus materials used in class. Exam questions can be in multiple choice or short answer format. Use question stems (posted on Moodle) to help you write thoughtful questions. Students will receive 2 points extra credit for each of their exam questions used for the Exam 2 Review. Submitted exam questions might also appear on Exam 2, whether or not they were used on the Exam 2 Review.

CPA 13 Chapter 7: Cell Cycle and Cell Division

Due Wednesday, October 23

1. What are the advantages and disadvantages of sexual reproduction? What are the advantages and disadvantages of asexual reproduction? Many organisms use both sexual and asexual reproduction (animals are rather unusual in that we often cant reproduce asexually). When are organisms likely to use asexual reproduction? When are organisms likely to use sexual reproduction? 2. Cell division is not only undertaken for the purposes of reproduction in multicellular organisms. Describe reasons for cell division in multicellular organisms in addition to reproduction. 3. What happens during each of these phases in the eukaryotic cell cycle? Why is regulation of the cell cycle important? a. G1 phase b. S phase c. G2 phase d. M phase 4. How is genetic variability among offspring generated during sexual reproduction in eukaryotes? Discuss three factors that contribute to genetic variability. 5. Compare and contrast mitosis and meiosis. How are they similar? How are they different? 6. What is apoptosis? Describe two reasons why apoptosis is important for multicellular organisms? CPA 14 Ch 8: Mendelian Inheritance and Punnett Squares 1. Distinguish between these pairs: a. b. c. d. e. f. Haploid and diploid F1 generation and F2 generation Gene and allele Dominant and recessive Homozygous and heterozygous Genotype and phenotype Due Monday, October 28

2. Write the genotypes of all possible gametes produced in a dihybrid cross by a parent with genotype AaBB? 3. Describe the relationships between genes, chromosomes, and alleles in a diploid organism. The last CPA 14 question is on the next page. Suzanne Gollery

pg. 12

Class Preparation Assignment Questions

Biology I

Fall 2013

4. The figure below illustrates a dihybrid cross. In geometroids, triangular heads are dominant to diamond heads and two eyes are dominant to one eye. A homozygous triangular geometroid with two eyes mates with a homozygous diamond geometroid with a single eye. Their offspring interbreed, producing the F2 generation summarized in the Punnett square. All phenotypes of the F2 generation are diagrammed. a. b. c. d. e. f. g. h. What are the genotypes of the parents? What are the phenotypes of the parents? How many distinct genotypes are present in the F2 generation? How many distinct phenotypes are present in the F2 generation? Why is the answer to question c a larger number than the answer to question d? What is the phenotype of an individual with the homozygous recessive genotype? What is the phenotype of an individual with the heterozygous genotype? What is the phenotypic ratio in the F2 generation?

HE

hE HhEE

He HHEe

he HhEe

P:
HHEE

x
hhee HhE

HE

HHEE

F1:
F2:

hE

HhEE

hhEE

HhEe

hhEe

He

HHEe

HhEe

HHee

Hhee

he

HhEe

hhEe

Hhee

hhee

CPA 15: Inheritance Problems These are posted on Moodle in a separate file.

Due Wednesday, October 30

Suzanne Gollery

pg. 13

Class Preparation Assignment Questions CPA 16 Sections 3.1 and 9.1: DNA structure in 3D

Biology I

Fall 2013 Due Monday, November 4

1. Compare and contrast DNA and RNA. How are they similar? How are they different? 2. The figure to the right shows a very short section of DNA double helix. a. Circle a single nucleotide, including the phosphate group, deoxyribose sugar, and nitrogenous base. b. Label the 5 and 3 ends of each strand. c. Identify the four bases indicated by the colored arrows (you will NOT need to identify specific bases from their structures or draw their structures on an exam). (Hint: view the figure in color.) d. What is the overall electrostatic charge of DNA? 3. What does it mean when we say that the two strands of the DNA double helix are complimentary?

CPA 17 Sections 9.2 and 9.3: DNA replication, repair, and mutations

Due Wednesday, November 6

1. What do we mean when we say that DNA replication is semiconservative? (Hint: See Animated Tutorial 9.2 on the Hillis website.) 2. Briefly state how each of the following are involved in DNA replication: (Hint: See Animated Tutorials 9.3: DNA Replication Part I and 9.4: DNA Replication Part II and your text.) a. b. c. d. e. f. g. DNA ligase (Text) DNA polymerase (Part II) DNA template strand (Part I) Okazaki fragments (Part II) Origins of replication (Part I) Primers (Part I) Telomeres (Text)

3. Which functional groups of nucleotides participate in the chemical reaction that joins a new nucleotide to a growing DNA strand? Use these terms in your answer: DNA strand, incoming nucleotide, and condensation reaction (also called dehydration reaction). (See Animated Tutorial 9.3: DNA Replication Part I) 4. Compare and contrast point mutations and chromosomal mutations. How are they similar? How are they different? 5. How do mutations occur? Are they always the result of mutagens? Explain. 6. Why are mutations important for evolution?

Suzanne Gollery

pg. 14

Class Preparation Assignment Questions

Biology I

Fall 2013 Due Monday, November 18

CPA 18 Sections 10.1 through 10.3: Transcription and the Genetic Code

1. What does it mean when we say that genes are expressed? Briefly describe the roles of DNA, RNA, and protein in determining the phenotype of an organism? 2. Compare and contrast DNA replication and transcription. How are they similar? How are they different? (Hint: View Animated Tutorials 9.3, 9.4, and 10.1) 3. The base sequence of a template DNA strand for a very short gene is shown below. a. Write the complimentary mRNA sequence beneath the template DNA. Label its 5 and 3 ends. b. Underline codons within the mRNA. (Remember that translation starts with a particular codon, which isnt at the very beginning of the mRNA.) c. Use the genetic code table on page 197 to translate the mRNA and write the primary protein structure encoded by this gene. 3 G T T A C C G A T T A G C A T G C A A T G C C C A C G G A A T C A 5

4. What would be the consequences of the following mutations on expression of a gene? (Hint: Interactive Tutorial 10.1 on the Hillis website will help with some of these.) a. A mutation that deletes the promoter of the gene b. A mutation that disrupts the consensus sequence for splicing at one end of an introns (Hint: See Animated Tutorial 10.2) c. A mutation in the center of an intron d. A mutation that alters a single nucleotide within an exon (Hint: there is more than one potential consequence in this case.) e. A mutation that changes the stop codon to another codon (for example, UGA changes to CGA) f. Insertion of nucleotide within an exon

CPA 19: Sections 10.4 and 10.5: Translation, protein processing, and comparison of prokaryotic and eukaryotic gene expression

Due Wednesday, November 20

1. Briefly state how each of the following are involved in translation. (See Animated Tutorial 10.4.) a. b. c. d. e. f. g. h. i. Aminoacyl-tRNA synthetases tRNAs Anticodon mRNA Ribosome A site E site P site Release factor

2. How does a eukaryotic cell know which proteins should be moved into which organelles once the proteins are translated? Suzanne Gollery

pg. 15

Class Preparation Assignment Questions

Biology I

Fall 2013

3. What protein modification is accomplished in each of these processes? Give a specific example in which a protein is modified each way. a. Glycosylation b. Phosphorylation c. Proteolysis 4. Compare and contrast gene expression in prokaryotic and eukaryotic cells. How is it similar? How is it different? (Hint: you will need to think about all of the information from Chapter 10 to answer this question well.)

CPA 20 Chapter 11: Repressor and Activator Proteins 1. Distinguish among these pairs: a. b. c. d. Constitutive gene and inducible gene Repressor protein and activator protein Operon and gene Promoter and operator

Due Monday, December 2

2. The Hillis text describes regulation of the lac and trp operons in E. coli as examples of inducible and repressible operons, respectively. What does it mean when we say that an operon is inducible? What does it mean when we say that an operon is repressible? Explain why it makes sense that lactose induces expression of the lac operon (see Animated Tutorial 11.1), whereas tryptophan represses expression of the trp operon (see Animated Tutorial 11.2). (Hint: think about what the cells do with lactose and tryptophan.) 3. Describe the interactions of general transcription factors, RNA polymerase, regulator proteins, and activators in coordinating transcription initiation in eukaryotic cells. (See Animated Tutorial 11.3.) 4. Why is it adaptive (why does it provide a selective advantage) for cells to be able to regulate gene expression?

CPA 21 Chapter 11: Post-transcriptional Regulation of Gene Expression and Epigenetic Changes

Due Wednesday, December 4

1. Explain how gene expression can be regulated after transcription in each of these ways. a. Alternative splicing of pre-mRNAs b. Repression of translation (this can happen by two different mechanisms, that is, in two different ways) c. Regulation of protein stability 2. Biologists were surprised to find only about 33,000 protein-coding genes in the human genome; they had estimated, prior to sequencing the human genome, that there would be more than 100,000 genes based on the number of distinct human proteins detected. Can you explain this discrepancy? 3. Compare and contrast mutation and epigenetic changes to chromosomes. How are they similar? How are they different? 4. Explain why identical twins (monozygotic twins) are not exactly identical. If the alleles in their genomes are the same, why do we observe phenotypic differences? Suzanne Gollery

pg. 16