BIOL 151L – Study Questions – Chapter 17 – From Gene to Protein – pp. 325-350

1. Explain briefly what Archibald Garrod meant in 1909 by an “inborn error of metabolism.” What was his idea about the connection between genes and enzymes in human?

2. Review the following, which your book calls the “molecular chain of command" (p. 328): DNARNAprotein (also called "The Central Dogma of Molecular Biology"). What is the process of transcription? Where in the cell does it take place? What is the product of transcription? What is translation, and where in the cell does it take place? Transcription and translation are said to be “coupled” in prokaryotes – what does that mean (see Fig. 17.3a)? Why are they not coupled in eukaryotes? Explain these last two sentences in terms of the differences in the structure of the prokaryotic versus the eukaryotic cell (and see Figure 17.3 in your text – very important). Be sure that you learn these two underlined (and in bold) vocabulary words above – they are some of the most important in molecular biology, and are easily confused, as well as used very often!

3. What is a codon in a messenger RNA (mRNA) molecule? How many nucleotides are in a codon that codes for one amino acid? How many possible codons are there, given that there are four different nucleotides? How many of these code for one of the twenty amino acids? What is the redundancy (p. 330) in the code? How many of the codons code for stop codons, and what are these? How many start codons are there? Explain what the reading frame of a messenger RNA is. How many reading frames are possible in a region of a messenger RNA? Finally, in the mRNA molecule given below, circle the codons and then use the "Dictionary of the Genetic Code" on page 330 to determine what amino acid each codes for: 5' A U G C C A G G A U C C U A A 3'

4. Taking a closer look at transcription, what enzyme synthesizes the mRNA molecule by making a complementary copy of one strand of the DNA? (Note that this mRNA molecule is complementary and antiparallel to the DNA template strand.) What is the signal sequence on the DNA template strand that tells the RNA-synthesizing enzyme where to start? To which end (5' or 3') of the growing RNA strand are nucleotides added? How does the RNA-synthesizing enzyme know when to stop copying the DNA into RNA?

5. In eukaryotes, but not prokaryotes, RNA is modified after transcription and before it leaves the nucleus for the cytoplasm, where the ribosomes are located. (Why doesn't this happen in a prokaryotic cell?) What modifications are made to each end of the eukaryotic mRNA, and what functions do these modifications serve?

6. What is RNA splicing? What are introns and exons?. What is the function of the spliceosome (its name helps here)? Notice that some RNAs that get spliced do it without protein enzymes, but rather through ribozymes (= RNA "enzymes"). In fact, the enzyme that is responsible for forming the peptide bonds between amino acids in the growing polypeptide chain on a ribosome is actually an RNA molecule within the ribosome!

7. Recall that the process of protein synthesis, translation, involves the "translation" from one language (that of nucleic acids = the mRNA) into another (the amino acids that make up a protein). The mRNA molecule is made up of codons that carry the message and get translated. What is the "interpreter" in this process? Note that individual transfer RNAs (tRNAs) bring individual amino acids to the ribosome, the site of protein synthesis. How do these tRNAs associate the amino acid that each carries with a particular codon on the mRNA? One analogy used is that a tRNA molecule is like a flashcard with a "nucleic acid word" (anticodon) on one side and a "protein word" (amino acid) on the other (attached to the 3’ end of the tRNA). Also, notice that the anticodon on the tRNA binds, using complementary base-pairing, to a codon on the mRNA (e.g. an AAA anticodon will pair with a UUU codon). Notice the structure of a tRNA – it is a small molecule of RNA that folds into a cloverleaf structure that is stabilized by base pairing within the molecule itself (similar to the way a protein has a globular, tertiary structure held together by H bonds, ionic bonds, etc.). (continued next page)

8. What enzyme is responsible for attaching an amino acid to its correct tRNA? What fits into the active site of this enzyme? How many different types of this enzyme are there in a cell? Why? What would be considered the product of this enzymatic reaction?

9. What are the two components that make up all ribosomes? The ribosome can be thought of as a docking platform where the mRNA and the tRNAs come together for the process of translation to take place. Given this, what are the three binding sites on the ribosome (what binds to each of them)? Study Figure 17-16 and note that a tRNA carrying the growing Polypeptide chain binds to the P site, while the incoming tRNA carrying the next Amino acid to be added binds to the A site . (Do note that the structure of prokaryotic versus eukaryotic ribosomes are very similar, yet different enough that there are drugs that paralyze prokaryotic but not eukaryotic ribosomes – i.e. tetracycline and streptomycin, which are taken by humans to combat bacterial infection.)

10. Note that in the process of initiation of translation (Fig. 17-17), the three types of RNA in a cell are brought together – the mRNA, which carries the instructions for making the protein, the initiator tRNA, which brings the first amino acid needed to build the protein, and the ribosomal RNAs (rRNAs), which are a main component of the ribosome (along with many proteins). Note what binds to what and where in this complex.

11. Go over the three stages of elongation (during translation) – study Figure 17-18. 1) Codon recognition -- An incoming tRNA carrying the next amino acid to be added to the growing polypeptide chain hydrogen bonds through its anticodon to the codon on the mRNA that is currently positioned in the A site of the ribosome. 2) A peptide bond is formed between the incoming amino acid and the end of the polypeptide chain on the tRNA in the P site. The polypeptide chain is transferred to the tRNA in the A site during this process. 3) Translocation – the ribosome moves one codon down the mRNA, positioning the next codon to be read into the A site, and moving the tRNA with the growing polypeptide chain into the P site. This step requires energy, obtained through the hydrolysis of GTP (an energy source similar to ATP).

12. What happens at the termination step of protein synthesis (Fig. 17-19)? What are the stop codons, and where do they have to be to bring about termination? What does a release factor do?

13. What is a polyribosome (see Figure 17-20)?

14. What kinds of things happen to a protein during posttranslational modification? Give an example.

15. What is a signal sequence found at the beginning of some proteins? What is its function? Note (see Fig. 17-21) how this targets both the protein, and the ribosome on which it is being made, to the surface of the endoplasmic reticulum, thus turning a free ribosome into a bound ribosome (remember those terms from studying cell structure?). Where does the newly made protein end up?

**16. What is a mutation? What is a point mutation? What is the genetic basis for sickle-cell disease (see Figure 17-22)? What is a base-pair substitution? In terms of a base-pair substitution, what is the difference between a silent mutation and a missense mutation? What is a nonsense mutation? How is it that insertions or deletions of one or two nucleotides change the reading frame of the genetic message = a frameshift mutation? Why is this such a serious mutation? Will an insertion of three nucleotides cause a frameshift mutation? Why? Note that there are many physical and chemical agents that interact with DNA to cause mutations -- these are called mutagens, and obviously can be very dangerous.

**17. In conclusion and in summary, study Figure 17-25 for an overview of transcription and translation in a eukaryotic cell.

**Do use the Summary of Key Concepts at the end of the chapter (p. 349-350) to help you review the information in this chapter – there's a lot of it, and it’s critically important!

BIOL 151L – Study Questions – Chapter 18 – Regulation of Gene Expression – pp. 351-380Part I

Friday, November 6 – Monday, November 9, 2009

1. Why is it important that bacteria be able to regulate their metabolism to match particular environments or circumstances? How can cells regulate the activity of an enzyme already present in a cell (see Fig. 18.2). What is feedback inhibition? Why is it also important that bacteria be able to regulate whether particular genes (i.e. a gene that encodes a particular enzyme) are “off” or “on” at particular times or under particular circumstances?

2. What is an operon? What are the three component parts (page 352 and Fig. 18.3), and what is the function of each? To which does RNA polymerase bind to begin transcription? To which does the repressor bind, and what is the consequence of that binding?

3. We will study the regulation of the trp operon and the lac operon as examples of gene regulation in bacteria. Study the structure of the trp operon (Fig. 18.3). What is the end product of the enzymes made from the genes of that operon? Notice that this is a product often needed by the cell, and as a result this operon is normally switched ON in the cell. However, there is a way to turn off the operon when there is enough of the end product already present in the cell. How does that happen? What is the corepressor, and how does it shut off the operon? Notice that because this operon is normally ON, but can be switched off, it is an example of a repressible operon.

4. On the other hand, the lac operon (see Fig. 18.4) is considered an inducible operon because it is normally switched OFF in the cell, but can be switched on under certain conditions. When the structural genes of the lac operon are expressed, they make enzymes that allow bacteria to break down and use the sugar lactose as an energy source. When lactose is not available, the lac operon is turned off (the genes are not transcribed by RNA polymerase) – how is this accomplished? What is the role of the repressor? When lactose is present, the genes are expressed – how is this accomplished? What is the inducer, and what is its role? How is the presence or absence of lactose monitored? Overall, this is an example of negative control, where the binding of a molecule (the repressor) switches off the operon.

5. The same operon provides an example of positive control, where the binding of a molecule turns on the operon. In this specific case, the system allows the operon to monitor whether an alternative energy source, glucose, is available. If so, it is "cheaper" for the bacterium to use glucose instead of lactose and, consequently, the lac operon should remain turned off. Describe how this positive regulation of the lac operon works (see Fig. 18.5). What molecule is it whose binding turns on the operon? How does the concentration of glucose in the cell affect this binding?

6. Your text talks about the two types of regulation of the lac operon as an on-off switch and a volume control (p. 355). Which is which?

BIOL 151L – Study Questions – Chapter 18 – Regulation of Gene Expression – pp. 351-380Part II

Monday-Wednesday, November 9-11, 2009

**This is a huge chapter, and we will only be able to cover selected parts (we’ll skip Concept 18.4). Please be sure to read through the Summary of Key Concepts at the end of the chapter – pp. 378-379 – to review the major concepts.

Concept 18.2 – Eukaryotic gene regulation: 1. Quick review -- during what part of the cell cycle are genes expressed (i.e. transcribed and translated into their products)? What is the purpose of cell differentiation in a multicellular organism? What percentage of the genes in a typical human cell are expressed at any given time? Overview -- What determines which of the genes in a cell are expressed?

2. Make use of Figure 18.6 to review the various stages in the expression of a eukaryotic gene. Note that regulation of the expression of genes can occur at all stages (although not all possible modes of regulation are used for every gene, of course).

3. How can the state of the chromatin (i.e. chromatin structure) in the vicinity of a gene control whether or not it is expressed (specifically, whether or not it is transcribed)? Are genes in heterochromatin (tightly packed DNA) or euchromatin (more loosely packed DNA), more likely to be expressed? In general, what is the role of histone modifications in gene transcription?

4. Use Figures 18.8 and 18.9 to review the typical organization of a eukaryotic gene and its regulatory (or control) regions. Be sure to review all of the following: promoter, introns and exons, 5' cap and 3' poly-A tail, transcription factors (very important!!! – what general class of molecule are these – carbohydrate, lipid, protein, or nucleic acid?) and enhancers (VERY IMPORTANT!! – what class of molecule are these?).

5. The control of gene expression can occur at many steps along the path from gene to functional protein. How is the process of transcription of a gene controlled in a eukaryote? Note the interaction of transcription factors, RNA polymerase, the promoter, and enhancer sequences. Which of these are proteins, which are DNA sequences? Note that enhancer sequences can be many thousands of nucleotides away from a gene. How then do they exert their influence on whether the gene is transcribed? (See Figures 18.9 and 18.10). How do regulatory proteins like activators recognize, and bind to, specific sequences in the DNA (see Fig. 18.10)? What is the importance of protein-protein interactions? What is “combinatorial control” and why is it important?

6. In a prokaryote, genes that need to function at the same time are often turned on and off as a unit by being part of the same operon (remember the trp and lac operons?). In eukaryotes, genes that need to be expressed at the same time are usually scattered over different chromosomes. How then are they turned on and off at the same time ( = coordinately controlled genes)?

7. Expanding on the previous question, explain how the sudden appearance of a steroid hormone in the cytoplasm of a cell can act to turn on a specific gene in the nucleus of that cell. How would a nonsteroid hormone (which is not lipid soluble and thus can not diffuse across the cell membrane) act to turn on a gene in the nucleus (a good review of concepts from Chapter 11)?

8. What kinds of post-transcriptional control can alter the expression of a particular gene? Give an example of how alternative splicing can affect the expression of a gene (and the particular gene product that comes from that gene).Give an example of a gene that is regulated by the extent of mRNA degradation.

9. What kinds of translational and post-translational control can affect the expression of a eukaryotic gene?

(continued on back)

Chapter 18 – Regulation of Gene Expression – Part II – page 2

Concept 18.3: Noncoding RNAs and their role in controlling gene expression:10. Remember that only about 1.5 % of the human genome codes for proteins. What exactly are “noncoding RNAs”?

11. What are microRNAs (miRNAs) and what do they do? Specifically, with what species of RNA do they interact in a cell, and how do they affect that other RNA molecule? (See Figure 18.13)

(Skip Concept 18.4)

Concept 18.5: Cancer: 12. ***This is important – make sure you work through and understand the following questions about the onset of cancer in relation to changes in gene expression. a) There are normal genes in cells that produce proteins that normally regulate cell growth, cell division, and cell adhesion; many of these turn on cell growth when needed. These normal, essential genes are called proto-oncogenes, because they have the potential to become oncogenes, or cancer-causing genes. Explain two ways by which a proto-oncogene can become an oncogene (your book gives three main categories of possibilities – see Figure18.20). b) There are also normal proteins in the cell that normally help inhibit cell division. These normal genes are called tumor-suppressor genes. How could a mutation in such a gene lead to cancer?

13. a) Give an example of how a mutation in the ras gene can lead to cancer (review Figure 18.21-a). In terms of the two types of cancer-causing genes discussed in question #12 above, what kind of a gene is the ras gene? b) Explain how a mutation in the p53 gene can lead to cancer (review Figure 18.21-b). In terms of the two types of cancer-causing genes discussed in question #13 above, what kind of a gene is the p53 gene? What functions does normal p53 (the “guardian angel of the genome”) perform in the cell?

14. Note (Fig. 18.22) that the development of colorectal cancer has many steps, including the accumulation of multiple gene mutations in oncogenes and tumor-suppressors. Because of the gradual development of this type of cancer, early detection and treatment are very promising.

15. Give an example of an inherited gene that could be involved in a genetic predisposition to cancer.

BIOL 151L – Study Questions – Chapter 19 – Viruses – pp. 381-395Wednesday, November 11, 2009

1. Are viruses living? What did researchers mean when they said that viruses lead “a kind of borrowed life”? Be sure you understand this – it captures the essence of a virus.

2. Why has the study of viruses been, and continues to be, useful?

3. Describe the discovery of viruses. What are their unique characteristics, which separate them from small organisms like bacteria?

4. What are the distinctive features of a virus? What is a virus?

5. What are the two component parts of a simple virus? What additional structures are found in some viruses? What is the origin of each of the component parts? What viruses have the most complex capsids?

6. What is the host range of a virus? Give an example of a virus with a broad host range, and of one with a narrow host range.

7. What does it mean that a virus is an “obligate intracellular parasite”? Describe what happens in a simplified viral life cycle (see Fig. 19.4). What necessary components does a virus get from the host cell in which it is reproducing?

8. How does an enveloped animal virus acquire its membrane (envelope), and how does the membrane help it infect a new cell (see Fig. 19.7)?

9. Review the life cycle of retroviruses (Figure 19.8). What does the enzyme reverse transcriptase do? What is a well-known example of a retrovirus, and what disease does it cause?

10. a) What is the relationship between vaccines and viral disease? Why don’t antibiotics work against viruses causing disease? What are “emerging viruses”? Give an example of an emerging virus that is causing great worry today. b) Of what importance are plant viruses? What are viroids, and why are they unique? What are prions, and why are they even more unique? What’s an example of a disease caused by a prion? What characteristics of prions make them “especially alarming”?

*** (See other side for Study Questions – Chapter 20 – Biotechnology – Part I)

BIOL 151L – Study Questions – Chapter 20 – Biotechnology– pp. 396-407Part I – DNA Cloning – Friday, November 13, 2009

1. Define each of the following terms: recombinant DNA, genetic engineering, biotechnology, According to the first sentence of this chapter, 1995 marked the sequencing of the first complete genome of an organism (what was it?). Less than 10 years later, the 3 billion nucleotides of the human genome had been sequenced. How was this accomplishment essential to the experiment shown in Figure 20.1?

2. What is gene cloning, and why is it done? Describe for yourself an overview of gene cloning with a bacterial plasmid, shown in Figure 20.2. What is a “clone” in the sense used here? What are the two basic purposes for which a cloned gene is useful?

3. What is a restriction enzyme, and what is a restriction enzyme recognition sequence (or restriction site)? What is a restriction fragment with sticky ends? Why are these sticky ends so useful in making recombinant DNA? What is the role of DNA ligase in making recombinant DNA (see Figure 20.3)?

4. What is a cloning vector and what is its function in genetic engineering? What are the five essential steps in using bacterial plasmids (as cloning vectors) to clone a human (or other eukaryotic) gene (see Figure 20.4)? What is the purpose of the host organism (in this example, the bacterial cell) in genetic engineering?

**5. Study Figure 20.4 and the accompanying text about cloning a human gene in a bacterial plasmid. Notice that the plasmid carries a gene for resistance to the drug ampicillin. ** How is this useful in finding bacteria that have been successfully transformed by the plasmid, versus those that have not picked up the plasmid? **How is the lacZ gene in the plasmid (which codes for ß-galactosidase – review the lac operon)) used to tell the difference between a bacterium carrying a plasmid only and a bacterium carrying a plasmid with a foreign gene inserted in it?

6. What is a genomic library (see Figure 20.5)?

7. What is nucleic acid hybridization (you will hear about this term in the lab about the PCR, next week)? What is a nucleic acid probe, and how can it be used to identify a bacterial cell that contains a plasmid carrying a particular cloned gene (see Figure 20.7)? Why is denaturation an essential part of this procedure?

8. If you want a particular cloned eukaryotic gene to be expressed as a protein product in a bacterial cell, what important signals must be provided in the cloning vector (an expression vector)?

9. What methods can be used for introducing DNA into cells? What is a useful method for a bacterial cell? an animal cell? a plant cell?

10. What is the polymerase chain reaction (PCR)? What are its important features (Fig. 20.8)? How is it used? (We’ll talk about this in the lab next week.)

11. What is gel electrophoresis (see Fig. 20.9), and what is its purpose? How can restriction fragment analysis distinguish between the normal and sickle-cell alleles of the β-globin gene (Fig. 20.10)?

12. Review the process of how a probe binds to DNA complementary to it in nucleic acid hybridization. Study how this technique plus gel electrophoresis of restriction fragments are used together in a technique called Southern blotting (see pages 405-407; Figure 20.11)? How can these techniques together be used to identify one individual from another (see Fig. 20-11)?

BIOL 151L – Study Questions – Chapter 20 – DNA Technology – pp. 409-425 Part II - 2008

13. What is a DNA microarray assay and what of interest can be done with it? Why is this new type of assay so useful?

14. How is the technique of RNA interference (RNAi) used to help determine the function of a new gene? How is in vitro mutagenesis used, and what is a “knock out” mutant?

15. When was the successful cloning of whole plants first accomplished? What does it mean for a cell to be “totipotent”? How is plant cloning used today in agriculture?

16. Describe how reproductive cloning of a mammal by nuclear transplantation is accomplished (Fig. 20.18; a review of Lab #1, so long ago now). What are some of the problems observed that are associated with animal cloning?

17. Review the differences between embryonic stem cells (and why they are special) versus adult stem cells. What does it mean for stem cells to be pluripotent? What is “therapeutic cloning”?

18. How is DNA technology (e.g. the PCR) being used in the diagnosis of infectious diseases? Give an example. How is it being used in the diagnosis of genetic diseases? Give an example, and be sure you understand how it would work. What ethical issues are being raised by the diagnosis of alleles involved in genetic disease?

19. How are RFLPs (“restriction fragment length polymorphisms” = “rif-lips’) useful in diagnosing genetic disorders (review Figure 20.10)?

20. Give an example of gene therapy that has been attempted and is aimed at somatic cells (illustrated in Fig. 20.22). What problem has arisen with this gene therapy, at first thought to be successful? What is the difference between this and gene therapy aimed at human germ cells? Why does this latter potential therapy raise important ethical questions? Do you think that there should be laws banning this? Why or why not?

21. Give several examples where DNA technology has been used to produce pharmaceutical products for humans. How is biotechnology being used to produce vaccines? Give several examples.

22. What are transgenic organisms and how are they made? What is one example of a transgenic animal used as a pharmaceutical factory? What are “pharm” plants?

23. What is a human’s genetic profile (now a preferable term to DNA fingerprint)? How are RFLPs and STRs (what are they?), or VNTRs (as in lab), being used in forensics? Study Fig. 20.24 to understand the importance of STR analysis.

24. Agrobacterium tumefaciens is a bacterium accused of having "trans-kingdom sex." What does this mean, and how is it being exploited in the development of transgenic plants? What is an example of a transgenic crop plant developed specifically to improve food quality for human consumption? What is an example of one engineered to resist destructive microbes and insects?

25. What are some important safety and ethical questions raised by DNA technology? State both some benefits as well as some concerns for several genetically-engineered products.

BIOL 151L – Study Questions – Chapter 22 – Descent with Modification: A Darwinian View of Life

**Be sure to read pp. 450-451 – a fascinating interview with Scott V. Edwards on his research on evolution in birds – from the evolution of songbirds to the evolution of genes involved in disease resistance in birds.

1. Take a look at the beetle in Figure 22.1 – what is it doing? How does this beetle illustrate three key observations about life – the striking suitability of organisms to their environment, the unity of life, and the rich diversity of life?

2. What is the definition of evolution introduced early in this chapter? Explain what is meant by the two related but different ways of viewing evolution – as a pattern, or as a process. Which of these is solidly supported by factual observations about the natural world?

3. Darwin's ideas on evolution were truly radical for his time. What was the prevailing Western world view that his ideas threatened? Briefly, what were some of the roots of the prevailing world view before Darwin?

4. How did observations coming from paleontology and geology influence Darwin's ideas? In particular, what two conclusions that followed from the observations of Hutton (the principle of gradualism) and Lyell (the principle of uniformitarianism) strongly influenced Darwin? Which of these was most essential to Darwin's theory of evolution?What parts of Lamarck's theory of evolution were visionary and close to Darwin's own? What major component of his theory was incorrect? Why? Give an example that illustrates this idea and the evidence that shows it is wrong.

5. What observations that Darwin made while on the voyage of the Beagle particularly helped him to develop his ideas on evolution and the origin of species?

6. Darwin's treatise, The Origin of Species, was published in 1859. One of his two main ideas was "descent with modification." What did Darwin mean by that? How did he relate his ideas to the metaphor of a tree?

7. Describe the logic of Darwin's theory of natural selection, his second main idea in The Origin of Species. What are the four observations of nature he presented and the two inferences he drew from them? Explain the theory of natural selection in your own words.

8. How did a 1798 essay on population growth by Thomas Malthus influence Darwin’s thinking? What was the main point of this essay? What evidence for this do we see around us?

9. What are the mechanisms of chance by which variation within a population arises (this is a review of previous chapters)? In contrast, natural selection does not occur by chance. Why? How does artificial selection help explain, and lend support to, Darwin's ideas?

10. Why can an individual not evolve? What is the smallest biological unit that can evolve over time?

11. Your textbook offers two examples of natural selection in action today – each illustrating natural selection as a mechanism of evolution in populations. Looking at the example of the evolution of drug-resistant HIV, a) explain the important distinction that underlies the statement that “natural selection is more a process of editing rather than a creative mechanism.” Also, explain why the following statement is in accurate : “Anti-HIV drugs have created drug resistance in the virus.” b) How does this example illustrate the principle that natural selection is situational, thus dependent on time and place?

12. Describe the evidence in support of the evolutionary view of life from each of the following areas of biology: a) anatomical homologies (including observations from comparative anatomy, comparative embryology, and vestigial organs; BTW, what does the term “homologous” mean?); b) molecular homologies; c) homologies and the evolutionary tree; d) biogeography; e) the fossil record. What is convergent evolution? How does Darwin’s theory account for both the similar mammalian forelimbs with different functions shown in Fig. 22.17, and the similar lifestyle of the two distantly related mammals shown in Fig. 22.20?

13. In the last section of this chapter, be sure you understand the increased weight of the word "theory" in a scientific sense as opposed to the general use of the word. Finally, don’t forget the closing thought in this chapter – that the diverse products of evolution are elegant and inspiring, and, as stated by Darwin in The Origin of Species, "There is grandeur in this view of life."

BIOL 151L – Study Questions – Chapters 23 –The Evolution of Populations

1. Read carefully the first page of this chapter -- about the finches in the Galapagos Islands. Be sure you understand, and can explain, whether it is the individual or the population that evolves over time. Review the concept of natural selection. What is microevolution? Give an example. What are the three main mechanisms that cause microevolution discussed in this chapter? Why/how is natural selection unique among them?

2. What is the difference between heritable and nonheritable genetic variation within a population? Give an example of each. Give an example of geographic variation between different populations of a species (and be sure you understand the difference between the terms “species” and “population”).

3. What are the two main sources of the genetic variation in populations that makes evolution possible (both of which we discussed earlier in this course)? One of these is particularly relevant to bacteria and viruses, the other more so to multicellular organisms. Which is which, and why? Be sure to review the three mechanisms that contribute to the shuffling of existing alleles during sexual reproduction.

4. What is a population? What is the population's gene pool?

5. State the Hardy-Weinberg principle. To discuss the Hardy-Weinberg theorem in relation to population genetics, please notice the structure of the simple population presented on pages 473-474 (and in Fig. 23-7). In this population, there are two alleles for flower color, red (CR) and white (CW), which show incomplete dominance. Pages 473-474 and Figures 23.6 and 23.7 show how to calculate the probability of each of the three genotypes (CRCR, CWCW, and CRCW) appearing in the next generation when you have a population where 80% of the alleles in the population as a whole are CR (or p = 0.8) and 20% are CW (and thus q = 0.2)---as shown in Fig. 23.6. Study and be sure you understand how the resulting genotypic ratios of the three are 64% (.64), 4% (.04), and 32% (.32), respectively, using the Hardy-Weinberg equation of p2 + 2 pq + q2 (shown in Fig. 23.7). What the Hardy-Weinberg theorem states is that, under certain well-defined conditions, the frequencies of both the alleles and the genotypes within this population will remain the same over successive generations – that is, under certain conditions you will have a nonevolving population. What are the five conditions that must be met for this "Hardy-Weinberg" equilibrium to be maintained in a population?

6. What are the three major factors that alter allele frequencies in a population and cause most evolutionary change?

7. Natural selection can cause evolution via differential reproductive success among varying members of a population. Explain how this might happen in our hypothetical population of wildflowers if white flowers were more visible than red or pink flowers to herbivorous insects that eat the flowers. What does the text mean by saying that, of the forces that can change a gene pool, only selection is likely to be adaptive?

8. What is genetic drift? Two situations that can lead to populations small enough for genetic drift to occur are the bottleneck effect and the founder effect. Explain each of these, and give an example you understand. What is the take-home message of the case study of the greater prairie chicken?

9. Explain how gene flow can change the genetic composition of a population. Does this increase or decrease genetic differences between populations? How does this relate to human evolution (Fig. 23.11)?

10. Describe the effects of the three differing types of selection on a varying characteristic within a population – stabilizing selection, directional selection, and disruptive selection.

11. How does diploidy (and "the heterozygote advantage") preserve genetic variation? How does this relate to the sickle-cell allele and malaria?

12. Be sure to review the end of the chapter and the reasons given for why natural selection cannot fashion perfect organisms.

BIOL 151L – Study Questions – Chapter 8 – An Introduction to Metabolism (pp. 142-145; 149-151)

1. What is energy? What must cells do in terms of energy in order to perform the operations of life?

2. What are the first and second laws of thermodynamics? How do those relate to life on the earth? Where does the energy come from, ultimately, that is necessary to continually create the order that is the essence of life on earth?

3. The immediate source of energy that powers cellular work is ATP. Review the structure of a molecule of ATP (Fig. 8.8). Where in this molecule is energy stored, and how can it be released? Review the ATP Cycle shown in Figure 8.12, noting how ATP couples the cell's energy-yielding processes to the energy-consuming ones.

Study Questions -- Chapter 9 – Cellular Respiration: Harvesting Chemical Energy (pp. 162-184)(for class periods Wednesday-Friday, December 2-4, 2009)

1. During chemical reactions, electrons are transferred from one molecule to another. This relocation of electrons releases the energy stored in food molecules, and this energy is used to synthesize ATP in cells. These electron transfers are called redox reactions, involving both oxidation and reduction. Define these two terms.

2. What does your textbook mean when it says that electrons "fall" from organic molecules to oxygen during cellular respiration? Oxygen is very electronegative, and as such it pulls electrons toward it (just as you learned in the polarity of the water molecule). As electrons are pulled toward an atom of oxygen, is energy released or required? Be sure you understand this – it is very important.

3. Electrons (e-) are often accompanied by protons (H+) as they move from one molecule to another, and by watching for the appearance, or disappearance, of H atoms, one can watch the reduction, and oxidation, respectively, of molecules. An important shuttle for electrons as they are moved from one place to another is the coenzyme NAD+, which toggles between its oxidized form (NAD+) and its reduced form (NADH). Notice the appearance of the H on the reduced form (NADH). The change in charge (NAD+ NADH) tells you that two electrons have been picked up by NAD+ in addition to the proton (H+). Another coenzyme involved in transferring electrons is FAD, which toggles back and forth between FAD and FADH2. Which is the reduced form? the oxidized form? In the overall equation for cellular respiration, C6H12O6 + O2 6 CO2 + 6 H2O, which molecule is oxidized and which is reduced? Remember to watch for the transfer of protons (H+), which accompany the transfer of electrons. (Hint, notice that C6H12O6 loses its H atoms (= electrons and protons) to become CO2 …….. etc.).

4. Glycolysis is the first step in the breakdown of glucose for the release of energy. Is oxygen required for this process? Where does this glycolysis take place in the cell? What are the net products at the end of the process?

5. If oxygen is present in the cell, the next step in respiration is the Krebs cycle. Where does this take place in the cell? What are the outputs from the Krebs cycle for each molecule of glucose originally split and fed into the Krebs cycle?

6. How is the energy that is stored in the molecules of NADH and FADH2 (which have been produced during glycolysis and the Krebs cycle) released in small increments in the electron transport chain? How is this energy used to create and maintain an H+ gradient across the inner mitochondrial membrane? How is this gradient (a source of potential energy) used by the enzyme ATP synthase to make ATP? What is chemiosmosis? This is the essence of oxidative phosphorylation – the creation of the ATP that powers all activities of the cell – be sure you understand it.

7. If there is no oxygen available, the cell can generate a small amount of ATP via fermentation. Give two examples of this process. **What is the important role of this process in terms of the coenzyme NAD+/NADH?

8. What is the energy output, in terms of molecules of ATP produced, for 1) glycolysis + fermentation versus 2) glycolysis + the Krebs cycle + electron transport?

9. Why was the appearance of oxygen on earth so important to the evolution of complex, multicellular life forms? (More on this in the next chapter….)

BIOL 151L – Study Questions – Chapter 10 – Photosynthesis – pages 185-205For classes Monday and Wednesday, December 7-9, 2009

1. Plants are autotrophs. What does that term mean? What nutrients do plants require? What does the term photoautotroph mean -- what is the source of energy used by plants?

2. What organelle in a plant is the site of photosynthesis? What is the green pigment that absorbs the light energy that drives photosynthesis? Take a good look at Figure 10-3 on page 187. In the "Leaf Cross Section," notice the stomata, small pores on the underside of a leaf, by which CO2 enters and O2 exits the leaf. Notice also the chloroplasts within the cells of the leaf in that same figure. Study the figure of the chloroplast in the lower right corner. Notice the stacks of thylakoid membranes, in which the chlorophyll is found. Where is the stroma?

3. What is the overall, simplified equation for photosynthesis? Be sure you show the energy in this equation. Note that the most important result of the shuffling of atoms during photosynthesis is the extraction of hydrogen from water and its incorporation into sugar (glucose) molecules. Notice too the important waste product of photosynthesis – oxygen. In your equation, which of the input molecules is reduced? Which is oxidized?

4. Stage one of photosynthesis is known as the light reactions. This is the "photo" part of photosynthesis, where light energy from the sun is converted to chemical energy. This involves the movement of electrons, and in this case the electrons are boosted to higher energy levels in the chlorophyll molecule by the incoming light energy. Your job is to now trace the path this electron takes from there during what is called "noncyclic electron flow." Trace the electron from its start in Photosystem II to the end of its journey when it (along with H+) is accepted by NADP+ to produce NADPH, one of the main products of Stage One of photosynthesis. Study both Figure 10-13 (from left to right) and Figure 10-14.

5. Where is ATP produced during Stage One? By what mechanism is it produced? Where have you seen this before? Be sure to review the Overview of the light reactions and chemiosmosis in Figure 10-17.

6. In summary, what are the two main products produced during Stage One? As importantly, where is oxygen produced during this process, and why?

7. Stage Two of photosynthesis is know as the Calvin cycle (the "synthesis" part of photosynthesis). This is sometimes called the "dark reactions," because these reactions are not dependent on light as are those of Stage One. Where do the reactions of Stage Two take place in the cell? During Stage Two, carbon enters the Calvin cycle in the form of CO2 entering the leaf through the stomata; the ATP produced during Stage One is used as an energy source; and the NADPH produced during Stage One provides the necessary reducing power (that is, the protons [(H+] and electrons). All of this together results in the carbon being "fixed" into molecules of glucose, the end product of photosynthesis. For starters, into what molecule is the incoming CO2

incorporated , and what enzyme is essential for doing this? Notice that this is probably the most abundant protein on Earth. That's a factlet you should remember.

8. Study the Calvin cycle in Figure 10-18. Notice where ATP is needed, where NADPH is needed, and where a sugar molecule is outputted. Is it glucose that is outputted from the Calvin cycle? If not, what? In this cycle, notice the regeneration of the CO2 acceptor, ribulose bisphosphate, or RuBP.

9. Go back to your main equation representing photosynthesis. Review where each reactant comes into the process, and where each product comes from.

**Do Self-Quiz problems #1, 2, 3, 5, and 7 on page 205.