Unless specific pages are indicated, I will test on the entire chapter. The material I tell you to concentrate on will be tested in the greatest detail and depth. For the other information, I am looking more for a general understanding or overview of the topic. Also - don't forget you are responsible for all of the material and the assigned pages presented in class.

I hope the study guide is helpful.

Chapter 8: Metabolism:Energy, Enzymes and Regulation

Concentrate on the roles of ATP, oxidation/reduction and enzymes in metabolism . Know the molecules of life present in ATP and enzymes. Understand how enzymes function as catalysts. Be able to distinguish holo- and apo- enzyme and prosthetic group and coenzyme. Understand what happens when enzymes are denatured.

Chapter 9: Energy Release and Conservation

In addition to the specific information provided in your class notes, a metabolism review handout is on our web page to help you understand the material.

Chapter 10: Metabolism:  The use of Energy in Biosynthesis

I will test on the Calvin Cycle. Chemoautotrophic organisms  use this cycle to fix carbon dioxide. I want you to have a basic understanding of this cycle. I will also test on anaplerotic reactions.

Chapter 11 - Genes: Structure, Replication, and Mutation

You are responsible for the whole chapter. I will concentrate on the following:

1. Know the difference (chemical and functional) between DNA and RNA.

2. DNA replication

a. understand the process

b. know the role of the various enzymes involved (helicases, primase (which is a DNA dependent  RNA polymerase), topoisomerases such as DNA gyrase, and ligase.

c. know why a primer is needed

d. know why there are leading and lagging strands and what Okasaki fragments are.

e. When I provide you with a replicating strand of DNA, you should be able to determine the leading and lagging strands

a. understand how the code is organized

b. understand the genetic code - types of codons (sense vs. nonsense or stop codons), what we mean when we use the terms codon, wobble and degeneracy.
 

a.  understand how a typical bacteial gene is organized (specifically understand the function of the following: cistron, promoter, leader sequence and coding region).

b.  understand that DNA contains genes for proteins as well as for tRNA and rRNA.  These RNAs are transcription products.
 

a.  Be sure to understand what a mutation is - a stable, heritable change in the DNA - how they occur - how mutagens can be classified according to their mechanism of of action (page 246,8 - another big hint) and how they are expressed.
 

b.  In class we discussed many terms used to describe mutations: forward, reverse, point, frameshift, transition, transversion, silent, neutral, missense and nonsense. Understand what these are.

c.  I will give you a strand of DNA and, as noted above, will have you transcribe it into mRNA and then translate it into protein. (Again - you should know how to use the codon chart). I will then indicate what changes occur to the original strand of DNA. You will have to make the change, then carry out transcription and translation. You will then tell me the type of mutation that occurred. We have already worked out similar problems in class.

d.  Understand how mutants are detected and isolated.

e.  Understand the Ames test and how it is used to detect potential carcinogens.

I did not assign the whole chapter on the syllabus - but don't forget we covered some of this material in class such as

1.  transcription
 

a. know what happens in this process (i.e., DNA--> RNA)

b. know the enzyme used by the cell (DNA dep. RNA polymerase)

c. be able to distinguish between procaryotic and eucaryotic transciption
 

a. know what happens in this process. (i.e., RNA --> protein)

b. know the role of each of the following in translation: mRNA, tRNA, rRNA, ribosomes,codons

d. when I provide you with a strand of DNA you should be able to transcribe and translate it (that is - I'll give you the DNA sequence - you give me the sequence of amino acids in the protein ultimately synthesized.
 
 

I will test on the entire chapter and will concentrate on the following:

1. Understand bacterial recombination and be able to define the following terms: exo- and endogenote (understand the possible fate of the exogenote in the recipient cell), merozygote.

2. Understand what plasmids are and that they can be eliminated from host cells by a process called curing. Know the different types of plasmids (for example the F (fertility) factor is a plasmid)  and how they integrate into bacterial chromosomes.

3. Know what transposons are and be able to distinguish between a composite transposon and an insertion sequence.

4. For conjugation, transformation and transduction know that genetic recombination is a potential outcome.

5. For conjugation know the outcome of all of the potential matings and understand what sexduction is.

6. Understand how conjugation can be used to map the genome.

7. Understand the mechanism of transformation.

8. To understand transduction you must first understand what happens in the lytic cycle and lysogeny (Figure 13.8).

9. For transduction be able to distinguish between generalized and specialized transduction - understand specifically what is happening in each of these processes.
 
 

Chapter 14: Recombinant DNA Technology

I will test on the entire chapter and will concentrate on the following:

1. Understand the role of plasmids and restriction endonucleases in recombinant DNA technology.

2. Understand  how to obtain double-stranded complementary DNA (cDNA) from mRNA.

3. Be able to recognize palindromic symmetry.

4. Understand how we use the Southern blotting technique to isolate a specific gene from a DNA mixture.

5. Understand how to isolate "foreign DNA"and how to introduce it into a cloning vector. Know how to introduce a recombinant plasmid containing foreign DNA (a chimera) into a bacteria cell and then how to detect the bacterial colonies (clones) that contain the recombinant plasmid. Understand how using plasmids with antibiotic resistances can be helpful when we try to select for those bacterial clones which have recombinant plasmids present.

6. Understand how to carry out PCR and why we use this technique.
 

Chapter 15: Microbial Genomics

1. Understand the kind of information genomics provides to scientists.

2. Understand how we carry out whole-genome shotgun sequencing and how this technique allows us to sequence a bacterial genome. Also know what we do with the sequence information, once obtained.

3. The other aspect of genomics that I discussed in class was the use of DNA microarrays to evaluate bacterial gene expression.  For that topic I assigned page 1018 and Figure 42.26 in the text.  Be sure you understand how gene expression is determined.

                                                                                                                                                                                                                        10/20/02