Spring 2012
Current Assignments
DNA replication - Thu, 4/12
Chapter 9 covers DNA replication and recombination. Because of time limitations, we will only cover the replication section. This chapter goes into more detail on the replication process than we have time for in this course, so you won't be responsible for all the material in this chapter. Sorting out the most important things from the less important details may be a little difficult. You don't need to read in depth your first time through-just get the overall picture. After lecture, you may want to return to the book and reread the sections that correspond most closely to the lecture notes. Just make sure you understand how replication produces identical copies of DNA and how this is related to what happens later in mitosis (or meiosis). You should also understand how replication is semiconservative, discontinuous, and bidirectional. Study carefully the diagrams that explain replication until you understand these concepts fully.
The assigned homework problems for this section are problems 10.07-10.10
Course Evaluation - EXTRA CREDIT - Deadline: 4/27
In order to get student input for the university and for each DSU instructor, Delta State asks that all students complete a course evaluation survey at the conclusion of each course they take. It will only take you a short amount of time to complete the evaluation, but the information you provide will be very useful to the instructor. Your responses on the evaluation will be kept confidential. You will not be asked to give your name. Dr. Tiftickjian will not see the results of this evaluation until after the semester has ended and all grades have been turned in.
All course evaluations are done online. You will receive an e-mail from from the DSU administration that will come to your okramail account with the instructions for completing the evaluation.
As an incentive for you to take the time to do the evaluation, you will receive 5 points of extra credit for completing the survey. TO RECEIVE YOUR EXTRA CREDIT, YOU MUST FOLLOW THE STEPS BELOW - DO NOT START THE SURVEY UNTIL YOU HAVE READ ALL OF THESE INSTRUCTIONS.
- Follow the link in the e-mail you receive or just go directly to deltastate.campuslabs.com/courseeval
- Login with your okramail username and password, then follow the instructions to complete the survey.
- As you near the end of the survey, make a note of the text of question number 32 (Note: this question comes near the end of the survey. It is the first one where you type in your own answer-not one of the multiple choice questions.).
- When you finish the survey, send an e-mail to Dr. T. at jdtift@gmail.com with the word "Evaluation" in the subject line and the first few words of question number 32 (the question, not your answer) in the body of the message.
- In order to receive your extra credit, Dr. T. must get your e-mail by Friday, 4/27/2012.
Transcription - Mon, 4/16 (during lab)
Chapter 10 deals with transcription, the process that produces RNA from DNA. This topic is covered much detail in the textbook-more detail than have have time for in lecture. You should read all of the textbook assignment, but focus mostly on just what is covered in lecture. The most important point here is to understand how the genetic code contained in the alleles of DNA are copied to form RNA, which in turn is "decoded" during translation to produce a protein. In the introduction to this material in lecture, we review the "one gene-one protein" concept. This is the foundations of molecular genetics. Make sure you understand why this is important and how the molecular definition of a gene is related to the traditional definition of a gene that we have used up to this point.
The assigned homework problems for this section are problems 11.01-11.06.
Translation - Tue, 4/17
We will cover most of chapter 11 which deals with translation, the process that assembles proteins using the code carried by a gene. As in the previous sections, this is a complex process that we can only cover the basics of here. Use the lecture outline and your notes as your primary guide, but read the appropriate parts of the text to support the information presented in lecture
The assigned homework problems for this section are problems 11.07-11.12
Gene regulation - Thu, 4/19
This chapter covers much of the details of the complex topic of gene regulation. We will just touch on a small part of this material, mainly covering the lac operon. Make sure you understand how this particular operon works. Most important in this section is the basic reason why gene regulation is necessary and how it is involved in inducible proteins and also in the broader aspect of developmental biology.
The assigned homework problem for this section is problem 11.13.
Population genetics - Tue, 4/24-Thu, 4/26
Chapter 17 introduces the basic concepts of population genetics. We will cover most of this chapter but in somewhat less detail than the text does. Be sure you learn how to calculate allele frequencies and understand the Hardy-Weinberg principle. You should also understand how various factors can cause allele frequencies (an thus genetic variation) to change over time.
The assigned homework problems for this section are those of problem set 12
Final Exam - Tue, 5/1 - 3:00 PM
The final exam is partly comprehensive and will cover major topics from the whole semester, but will concentrate on material covered since the third exam (molecular genetics and population genetics). Remember that we only covered parts of the chapters on these topics. Follow the page numbers in the reading assignments for the exact sections you are responsible for. Most of the exam that covers the new material will be problems similar to those assigned for topics covered since the previous exam. Those are problems 10.07-10.10, all of problem set 11, and all of problem set 12. The format of the exam will be similar to the other lecture exams - a few multiple choice questions, a couple of short written questions, and, of course, problems. There will be general questions on the older material, but no detailed problems. You will want to review the major principles from the previous chapters, but spend most of your study time on the new material-that will make up about 2/3 of the test.
For a more complete breakdown of the topics and problems to be covered by the final, check out the more detailed study guide.
Past Assignments
Welcome to genetics -
To returning students - welcome back to campus! To new students - welcome to Delta State! And - welcome to Genetics! I hope you will find this an enjoyable and useful course. Good luck in all your classes this term and especially in BIO 328.
During the first class meeting, we will discuss in detail everything you need to know about the workings of the course, but there are a few things you should know before the semester begins if you happen to see this message ahead of time. The most important thing is to make sure you meet the prerequisites for the course. Please read the following information carefully. If you have any questions before the semester begins, please ask. You can contact me by phone or email. My contact information is on the my home page.
BIO 328 is a required core course for all biology majors. In addition, it is often taken by other science majors, especially chemistry/pre-medical majors. As you should already be aware, The Division has a policy that science major must reach "full admission" status before taking upper-level courses in the major (courses numbered 200 or above). For BIOLOGY majors, full admission means that you have COMPLETED the following courses with no grades below C: BIO 100, BIO 101, CHE 101, CHE 102, CHE 103, CHE 104. This requirement also applies to ENVIRONMENTAL SCIENCE majors who elect to take this course. Nearly all chemistry majors who take genetics should also have had these prerequisites (although full admission for chemistry majors is slightly different than for biology majors).
All DSU science instructors are required to verify that students enrolled in upper-level courses have full admission status. Students who do not have full admission status will not be allowed to take this course unless they have specific permission from their advisors. If Division records indicate that you DO NOT have full admission, you will receive an email message stating this.
A few other things you might want to know in advance...
TEXTBOOK
The textbook you need to buy is: Benjamin Pierce, Genetics Essentials: Concepts and Connections, 2010, Freeman, ISBN: 978-1-4942-3040-7.
You don't have to buy the book before classes start, but you might want to if you don't plan to get it from the DSU bookstore. There are other sources you might want to check for the best price. Several online book sellers carry the book, both new and used. If you consider buying online, remember to consider shipping cost and how soon you will receive your book. You must have your copy no later than the end of the first week of classes.
WEBSITE
I maintain a website for the course. If you would like to check it out in advance, go to:
http://www.doctortee.com/genetics
If you visit the the site before the semester begins, it may not be completely ready for current semester; the information you see there may be from the last time the course was taught. But the course content is basically the same; there won't be many changes except for the schedule.
Again WELCOME! I am looking forward to a great semester.
What is Genetics? - Tue, 1/10-Thu, 1/12
Your first assignment of the semester is to read Chapter 1 of the textbook. This chapter is an introduction to the science of genetics and a brief review of some of the history of this fascinating branch of biology. All of the concepts introduced here will be expanded upon during the rest of the semester. You should try to get a feel for the differences among the three main branches of genetics: transmission genetics, molecular genetics, and population genetics. Pay particular attention to the list of fundamental concepts, which starts on page 11. Nearly all of these you should already be familiar with form your general biology courses. List list of main concepts is really a guide to this whole course. You should refer back to the list often as we expand on these ideas.
In the lecture outline, you will find, a listing some of the landmark discoveries in the history of genetics. You don’t need to memorize this list now, but you should refer back to this as we go through the semester. We will be covering most genetics concepts in the order in which they were discovered. You will want to remember who the major players in this story were. We won’t go into every historical detail, but we will talk about the major discoveries and their significance. The history of genetics is a very interesting story.
To comment on this entry, visit the blog.Mendelian Genetics and monohybrid crosses - Tue, 1/17
[NOTE: We will skip chapter 2 for now, but return to it later.] Start reading chapter 3. Follow the reading assignments in this chapter carefully by page number, because we do not cover it in sequential order. This is probably the most important chapter of the text. You won’t be able to understand the more advanced topics without a firm background in the fundamentals of Mendelian genetics. Be sure you understand how Mendel performed his experiments and how he interpreted his results. We will discuss this in depth in class. Be sure that you understand completely the manner in which Mendel performed his crosses. Remember that he worked with pea plants, so you need to understand that basic reproductive process in flowering plants. You learned this in general biology, but you might want to review the basic parts of a flower and remember how the gametes are transferred.
Lots of important terminology is introduced in the chapter. Pay attention to the terms in bold type. We will use these terms throughout the semester, so it pays to make them part of your familiar vocabulary right from the start.
The focus of the material at the beginning of the chapter is Mendel’s analysis of monohybrid crosses. These breeding experiments led to the Principle of Segregation which is the backbone of Mendelian genetics. Make sure you understand what segregation means.
Don't worry about the section on relating genetics to meiosis (pages 45-46). We will come back to that section after we have covered meiosis later.
We will be working through examples of monohybrid crosses in class. The assigned homework for this section is all of Problem set 1
Dihybrid crosses - Thu, 1/19
Read the section of chapter 3 that introduces dihybrid crosses. For now, just concentrate on understanding dihybrid crosses through Punnett square analysis (pages 52-53). We will return to this section again after discussing probability.
A dihybrid cross is one in which two separate traits are considered in a single cross, such as seed color and seed shape, or plant height and flower color. Dihybrid crosses are a bit more complicated than monohybrid crosses, but analyzing them involves that same kind of logic. Mendel’s study of dihybrid crosses led to the Principle of Independent Assortment. You should study carefully the cross described on page 58. Be sure you understand how to use the Punnett square to predict the phenotype ratio. In a cross like this, what is it that is sorting independently?
The section on pages 53-56 discusses using the branch diagram (also called the forked-line) method for predicting the outcome of a cross. You can skip this section on your first reading, but come back to it after we complete the probability section. You need to understand probability rules before the forked-line method will make sense.
We will be working through examples of dihybrid crosses in class. The assigned homework for this section is all of problem set 2
Probability - Tue, 1/24
The next section of the chapter we cover discusses some of the basic rules of probability. You may recall some of this material from a previous math or statistics course you have had. Probability is important to Mendelian genetics because it deals with how to predict how likely a random event is. Fertilization is a random process. If the male and/or female parents can produce more than one genetic kind of gamete, then which sperm fertilizes which egg is a random event. When you do a Punnett square to predict the genotype or phenotype outcome of a cross, you are actually calculating probabilities. In this section we will formalize this concept a bit more and learn some shortcuts for calculating the probability of a certain outcome of a particular cross. One of these shortcuts is the forked-line method. After we have covered this in lecture, go back to pages 53-56 for an example of how to apply the forked-line method to dihybrid crosses.
The assigned homework problems for this section are all of problem set 3
The chi-square test - Thu, 1/26
The next section of the chapter we cover discusses covers how to use a statistical “goodness of fit” test to compare the actual results of a cross with the predicted results. Here you will learn how to use the chi-square test. This is a valuable goodness of fit test commonly used in Mendelian and population genetics. Be sure to practice it enough so that it becomes a routine thing for you.
The assigned homework problems for this section are 4.01-4.05
Pedigree analysis - Tue, 1/31
The last section of Chapter 3 describes how to analyze pedigree charts. A pedigree chart is simply a “family tree” type diagram that shows which members of a family, for several generations, have a particular trait. From this information, you can often tell something about the inheritance of the trait, for example whether the allele for the trait is dominant or recessive. Once that has been determined, one can often determine genotypes and make predictions about future offspring of certain families
The assigned homework problems for this section are 4.06-4.08
First Exam - Tue 2/7
The first exam will include all covered material from chapters 1 and 3 of the textbook and associated lecture material. As with all the exams, there may be a few multiple choice and other objective questions, but most of the exam will be problems similar to those assigned as homework. Problems like those on sets 1 through 4 will be included in this exam. My best advice is to practice as many problems as possible. Remember that the answers to all assigned problems are available on the course web site so you can check your work. Additional problems from the textbook that you can use for practice are also given at the end of each problem set. If you are having difficulty with any problems, that should be a clue that you don't yet have a full understanding of some underlying concepts. Ask about any problems you are having trouble with during lecture, or come by during office hours.
For a breakdown of the topics and types of problems to be covered by this test, check out the online study guide.
Extensions of Mendelian Genetics - Thu, 2/2-Thu, 2/16
Chapter 4 covers inheritance patterns that are extensions of Mendel's basic principles of segregation and independent assortment. In this section we will discuss such things as incomplete dominance, multiple alleles, and multiple gene inheritance (epistasis). Pay close attention to the order of the reading assignments because we will not cover the topics in lecture in the same order that they are covered in the book. You should omit the sections on sex determination and sex-linkage (pages 70-82) at this time. We will return to those sections later in connection with chromosome theory.
Although some of this chapter may seem kind of complicated, especially epistasis, it is not that difficult if you remember Mendel's basic laws of segregation and independent assortment still apply. We really aren't changing the rules, just expanding on them. For the most part, problems can still be analyzed genotypically with a Punnett square or forked-line diagram. It's when you convert the genotypes to phenotypes that things get complex than we have covered up to this point.
This chapter also briefly covers cytoplasmic inheritance (also called maternal inheritance). This inheritance pattern differs from Mendelian inheritance because the genes for such traits are located outside the nucleus. Instead, these genes are contained in the chloroplasts and mitochondria. We will cover this only briefly in lecture, so be sure to read this section carefully so that you understand why inheritance of such traits does not follow Mendelian rules.
The assigned homework problems for this section is problem set 5.
Sex determination and sex-linked genes - Thu, 2/23
The sections of the chapter on sex determination and sex-linkage will serve as an introduction to our discussion of how genes are related to chromosomes. Prior to this point, we have not been concerned with what genes actually are or where they are located. We have just defined them as “particles” which somehow are passed from parents to offspring through the gametes. This is as far as Mendel could take it because in his day, the structure and behavior of chromosomes were not known. Now we are ready to start asking how the chromosomes in the nucleus of a cell actually carry the genes.
In this section we discuss several different mechanisms by which sex is determined. We will also cover a bit of the history of how T.H. Morgan and his colleagues discovered that chromosomes contain genes. This leads us to the concept of sex-linked traits. Morgan's discovery of sex-linkage provided a clue about genes being attached to chromosomes because the sex chromosomes in fruit flies are visibly different from other chromosomes.
The assigned homework problems for this section are those of problem set 6.
Chromosome structure and behavior - Thu, 2/23-Thu, 3/1
Chapter 2 introduces chromosomes and explains how the behavior of chromosomes during cell division (especially meiosis) is correlated with Mendel's laws of segregation and independent assortment. It may seem that we are going backwards because we are coming back to this chapter after covering chapters 3 and 4. One reason for going in this order is that one does not need to know about chromosomes to understand Mendel's basic laws (Mendel did not know about them). We are now ready to see how chromosomes are related to segregation and independent assortment.In this section, we will discuss the microscopic structure of chromosomes, and their behavior during mitosis and meiosis. An good understanding of meiosis is critical to understanding genetics. Meiosis is not that hard to learn if you spend enough time thinking about why chromosomes must do the things they do as related to an organism's life cycle and how it produces gametes. Be sure to spend plenty time with the diagrams that compare mitosis and meiosis (pages 23, 26-27, 31). Also discussed in this chapter are plant and animal life cycles and how they vary depending on at which stage meiosis takes place.The assigned homework problems for this section are those of problem set 7.
To comment on this entry, visit the blog.Chromosome variation - Tue, 3/6
We will cover the topic of chromosome variations in a fairly brief manner and not go into the amount of detail that the textbook does. Chapter 7 is the reference for this section, but the text goes into more somewhat more depth in this subject than we have time for. You should read this chapter as an overview of chromosome variation, but don't study it in detail. Use it mainly as a reference for looking up any of this material that you may not completely understand from lecture.
Here we will cover some of the kinds of chromosome changes that can occur when chromosomes break and when mitosis or meiosis does not function correctly. Be sure you understand the following chromosome changes: deletion, duplication, inversion, translocation, aneuploid, polyploid.The assigned homework problems for this section are those of problem set 8.
To comment on this entry, visit the blog.Second Exam - Thu, 3/8
The second exam will include all covered material from extensions of Mendelian genetics through meiosis and life cycles (chapters 5, 4, and 2). Most of the exam will be problems similar to those on problem sets 5 through 7.
The format of the exam will be similar to the first one - mostly problems with a couple of short written questions. The main topics to concentrate on are: modifications of Mendelian principles (such as incomplete dominance and multiple alleles, epistasis, quantitative inheritance) , sex determination, sex-linkage, chromosome structure, mitosis, and meiosis. Be sure to ask yourself questions like: how does the chromosome theory relate to Mendel's principles? How does the behavior of chromosomes explain segregation and independent assortment?
Remember too that the concepts in this section build on those covered on the first exam. If you had any difficulties on the first exam, be sure to review those topics again. You still need to understand things like Punnett squares, probability, forked-line method, and the chi-square test.
For a more complete breakdown of the topics and problems to be covered by this test, see the study guide.
Spring Break - Mon, 3/12 - Fri, 3/16
Have a great break!
Genetic Linkage - Tue, 3/20-Thu, 3/29
In the previous chapters, we learned that genes are not really individual particles, as Mendel thought, but are actually located on chromosomes. Each chromosome can contain thousands of genes. Chapter 5 delves into the question: how do we know where genes are located on chromosomes?
The chapter begins with a discussion of a some crosses in which independent assortment seems not to be valid. This is then explained by considering that fact that genes are located on chromosomes-an idea called linkage. Most of the chapter deals with how one does 2-point and 3-point test crosses designed to determine the positions of gene loci on chromosomes. This technique is called gene "mapping."
Although not covered in this chapter, we will also discuss the basics of tetrad analysis. This is an alternative method of gene mapping that can be done with certain organisms (fungi).
The problems you will be working in this section on linkage and gene mapping are some of the most involved of those you do all semester. Be sure to give yourself plenty of time to understand them fully, and practice as many extra problems as you have time for. Getting a complete understanding of how gene mapping works requires a good understanding of meiosis. Make sure all the aspects of meiosis are clear to you, especially segregation of homologous chromosomes, independent assortment (and when is does not happen), and the effects of crossing over.
The assigned homework problems for this section are those of problem set 9
To comment on this entry, visit the blog.DNA structure - Tue, 4/3-Thu, 4/5
Chapter 8 introduces molecular genetics. After recounting how DNA was discovered as the genetic material, this chapter covers the structure of the DNA molecule. This is a very important chapter because it lays the foundation for an understanding of how DNA carries out all the functions that genes must perform. In the chapters that follow, we will discuss those functions in detail.
The assigned homework problems for this section areproblems 10.01-10.06
Third Exam - Tue, 4/10
The third exam will include all the material we covered from Chapters 7, 5, and 8. Most of the exam will be problems similar to the homework assigned in this section. Those are: all problems from set 8, all the problems from set 9, and problems 1-6 from set 10. The format of the exam will be similar to the first two - a few multiple choice questions, a couple of short written questions, and, of course, problems. The main topics to concentrate on are: chromosome variations, linkage-what it means and how to tell that two genes are linked, gene mapping, 2-point and 3-point test crosses, tetrad analysis-what it can tell you and how you analyze ascospore data, how we know that genes are made of DNA (some of the history), basic structure of nucleotides and how they form DNA, base pairing rules, and the double helix. You are guaranteed to see a 3-point cross (which will count a significant number of points), so be sure to practice this well.
Remember too that concepts from the current chapters build on those from previous ones. If you had any difficulties on the last test (especially on meiosis), be sure to review those topics again. You still need to understand things like chromosomes, chromatids, bivalents, meiosis, independent assortment, crossing over, etc. There could even be a problem which would require a chi-square test or an understanding of probability, at least as it relates to recombination.
For a more complete breakdown of the topics and problems to be covered by this test, there is a more detailed study guide available.
Delta State University > Biological and Physical Sciences > Dr. Tiftickjian > BIO 328 > Assignments
