Syllabus 1

BIOLOGY 311: GENETICS

FALL, 2013

Mary Rose Lamb

Office: T-223B Office Phone 879-3301

Lab: T-220 Lab Phone 879-3341

e-mail: mrlamb@pugetsound.edu

Text: Genetics: A Conceptual Approach (4th

edition). Benjamin A. Pierce. W.H.

Freeman and Company. 2012.

Goal of the Course: Genetics is one of the core classes for Biology, Molecular and

Cellular Biology, and Biochemistry majors. It is also strongly recommended for people

who are planning on pursuing a career in the health professions. In this University, the

Genetics course covers three major areas: classical transmission genetics, the flow of

genetic information in the cell, and the molecular basis of gene function. In addition, the

course covers some of the modern methods of molecular genetics and you will have a

chance to use those techniques in the laboratory. When you finish the course you should

have a thorough grounding in:

-how genetic information is passed from one generation to the next in a variety of

organisms

-how genes are mapped using both classical and modern techniques

-how DNA is replicated in the cell

-how RNA is transcribed and modified

-how protein is synthesized

-the nature of the genetic code

-some of the ways that genes are regulated in prokaryotes and eukaryotes

-some of the ways in which genes in populations are studied.

In addition, the course will give you an opportunity to develop some new writing skills

and to participate in an experiment using the tools of modern molecular genetics. Those

exercises will help you learn:

-how to use the primary literature of genetics to write a review of a field of

interest to you

-how a geneticist can design screens to isolate mutants with particular phenotypes

-how you can use published and on-line information to find out more about the

gene you’re studying.

Lab: Genetics includes a formal lab that will introduce you to some of the principles

and techniques used in genetic research. If you are enrolled in the course, you must also

be registered for a lab. Unless you have a valid excuse and have checked with your lab

instructor, you must attend your assigned lab each week.

Problem Sets: Most genetics texts contain problem sets at the end of each chapter to

help you test your understanding of the material covered in that chapter. You will be

assigned problem sets each week. The purpose of the problem set is to help you

understand the material covered and to give you a chance to familiarize yourself with the

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sorts of problems that you might encounter on exams. Problems are often mini-

experiments or thought experiments in which you are asked to explain or predict results

for the proposed experiment.

You will also be assigned one problem set each week that will be worth 3 points.

Exams: Two “mid-term” exams will be given on the dates indicated in the schedule.

The first exam is worth about 120 points, the second about 150 points. The final exam is

also worth 150 points and includes 50 points of cumulative or review material.

The exams are designed to challenge you and stimulate your thinking about

genetics. However, many students feel pressured to finish the exam in 50 minutes. I

want to test how well you think, not how fast you think. For that reason, the mid-term

exams will be given on the evenings of the day indicated on the schedule, from 6:00-9:00

PM. If you cannot be present for two hours of that time, please contact me by the class

before the scheduled exam so that a time convenient to both student and teacher can be

arranged.

NO MAKE-UP EXAMS WILL BE GIVEN. However, the instructor of the course is

not always an ogre. If you are sick or have some other valid reason for missing the exam,

please contact the instructor. While make-up exams are not given, we may be able to

work something out.

The Papers: A short paper will be due at the end of September. One five to seven page

paper will be due in class on November 25, 2013. Further instructions for the paper are

given later in the syllabus and will also be given in class.

Grading: This class will be graded straight-scale, based on the percentage of the total

points that you accumulate from exams, papers, and labs. The scale is as follows:

97-100% = A+ 73-76% = C

93-96% = A 70-72% = C-

90-92% = A- 67-69% = D+

87-89% = B+ 63-66% = D

83-86% = B 60-62% = D-

80-82% = B- Below 60% = F

77-79% = C+

Late Assignments: Late papers, lab reports, etc. will be accepted. Late papers will be

penalized 3% per day late. The one exception to this is homework. Late homework is

not accepted.

Reserve Materials: Journals, exams, answers to problem sets, and articles pertinent to

the course may be placed on reserve in the Collins Library or posted on the Genetics

bulletin board in Thompson Hall. Please note that the theft of materials made available to

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the class in these ways is a violation of the Academic Honesty policy of this University.

This policy is set forth in the Academic Handbook and you are encouraged to review it.

Theft of reserve materials hurts everyone in the course except the thief. Therefore,

anyone caught stealing reserve materials from his or her classmates will fail the course

automatically.

Plagiarism and Cheating: Theft of another person’s words or ideas is the most serious

crime that can be committed in an academic community. While some of the assignments

in this course will allow you to work in groups, others must be completed individually.

Please know which is which and follow appropriate guidelines for the assignment.

Cheating on exams or plagiarism on papers or lab reports are also grounds for failing the

course.

If you need to refresh your memory about the nature of plagiarism, you may go

here:

http://www.pugetsound.edu/student-life/student-handbook/academic-

handbook/academic-integrity/

If you did not receive instruction on avoiding plagiarism in your freshman seminar

courses, please take some time to complete the course that the library has set up for you.

For that course, go here:

http://alacarte.pugetsound.edu/subject-guide/6-Academic-Integrity-Puget-Sound

If you are found to have committed plagiarism in this class you will lose 100

points or the value of the assignment that was plagiarized, whichever is greater.

Lecture Schedule

This class is divided into three major sections. The first section of the class is

devoted to transmission genetics (Mendelian genetics and gene mapping techniques) and

an introduction to population genetics. In the second section of the course, we consider

molecular genetics and the flow of information in the cell: replication, transcription and

translation. In the last portion of the class we examine gene function and come back to

populations. In each section, we will also look at modern applications of the concepts

and techniques covered. Rather than giving you a day-by-day list of readings and topics,

here is a list of topics and the text readings associated with them. Check the Moodle site

for the course for daily or weekly readings and assignments. You will also receive

additional reading assignments beyond your text.

Section 1: Transmission Genetics and the Chemistry of DNA

September 4-October 2, 2013

Topic Reading in Text

Review of Mendelian Genetics Chapter 3

Meiosis and Chromosomes Chapter 2

Sex Chromosomes Chapter 4

Advanced Mendel Chapter 5

Mapping genes ala Morgan Chapter 7

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Human Genetics

Pedigree Analysis Chapter 6

Karyotypes Chapter 6

Somatic Cell Genetics Chapter 6

Hardy-Weinberg and Gene Flow Chapter 25

Section 2: Molecular Genetics

October 4- November 6, 2013

Topic Reading in Text

Structure of DNA Chapter 10

DNA and Chromosomes Chapters 9 & 11

DNA Replication Chapter 12

Applications of DNA Replication Chapters 19 & 20

What is a Gene? Chapter 14

Transcription of RNA Chapter 13

Processing of RNA Chapter 14

Translation of Protein Chapter 15

Molecular Understanding of Mutation Chapter 18

Section 3: Gene Function and Modern Genetics

November 9 -December 11, 2013

Topic Reading in Text

Bacterial Genetics Chapter 8

Regulation of Genes in Bacteria Chapter 16

Regulation of Genes in Eukaryotes Chapter 17

Evolutionary Genetics Chapter 25

Important Dates in the Course

Sept. 18 Quiz on Mendelian Genetics (Take Home)

Oct. 2 First Short Paper Due

9 Exam I

14-16 “Reverse Genetics” Proposal Due in Lab

25 First Lab Report Due

Nov. 1 Review Paper Bibliography

13 Exam II

25 Review Paper Due

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Dec. 11 Final Lab Report due in lecture

18 Final Exam, 8-10 AM

Things the University Wants You To Know!

Classroom Emergency Response Guidance:

Please review university emergency preparedness and response procedures posted at

www.pugetsound.edu/emergency/. There is a link on the university home page.

Familiarize yourself with hall exit doors and the designated gathering area for your class

and laboratory buildings.

If building evacuation becomes necessary (e.g. earthquake), meet your instructor at the

designated gathering area so she/he can account for your presence. Then wait for further

instructions. Do not return to the building or classroom until advised by a university

emergency response representative.

If confronted by an act of violence, be prepared to make quick decisions to protect your

safety. Flee the area by running away from the source of danger if you can safely do so.

If this is not possible, shelter in place by securing classroom or lab doors and windows,

closing blinds, and turning off room lights. Stay low, away from doors and windows, and

as close to the interior hallway walls as possible. Wait for further instructions.

Accessibility and Accommodation:

If you have a physical, psychological, medical or learning disability that may impact your

course work, please contact Peggy Perno, Director of the Office of Accessibility and

Accommodations, 105 Howarth, 253.879.3395. She will determine with you what

accommodations are necessary and appropriate. All information and documentation is

confidential.

Student Bereavement Policy:

Upon approval from the Dean of Students’ Office, students who experience a death in the

family, including parent, grandparent, sibling, or persons living in the same household,

are allowed three consecutive weekdays of excused absences, as negotiated with the Dean

of Students’. For more information, please see the Academic Handbook.

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Biology 311: Genetics

Fall, 2013

Things I Will Assume You Know From Your Pre-requisite Courses

Biology 111 or the equivalent is a required pre-requisite for this course and Cell

Biology is strongly recommended. I will make the assumption that you remember the

parts of those courses relevant to genetics. That means that I will not cover those topics

in depth in this course. If you do not remember anything from those courses or you

transferred in to Puget Sound and are not sure that your courses were truly equivalent to

those given here, a detailed list of what I assume you already know is given below.

All of the topics and terms listed below are important to your further

understanding of genetics. You must master them if you are going to excel in this course.

To encourage you to do so, you will be quizzed on the Basic Mendelian Genetics in a

take-home exam that will be distributed on September 18. To prepare yourself for that

quiz, make sure that you understand Chapters 2 and 3 and pages 81-87 in your text. If

you find it difficult to do that on your own, I’ve posted links to videos on Moodle to help

you master the material.

As you review the material, try the “Helpful Problems” at the end of Chapters 2,

3, and 4. Pay attention to the vocabulary and make sure you can use the terms below as a

geneticist would use them.

Basic Mendelian Genetics (to be mastered no later than 9/18/13)

A. Terms You Should Know and Be Able to Define: When there is more than

one term on a line, in addition to making sure that you know what a geneticist means by

the following terms, ask yourself if you know how those things are similar and how they

are different.

true-breeding

homozygous heterozygous

phenotype genotype

gene allele

dominant recessive

reciprocal cross back cross test cross

parental generation first filial (F1) generation

hybrid

monohybrid cross dihybrid cross

Law of Segregation

Law of Independent Assortment

pedigree

sex linkage X-linkage Y-linkage

sex chromosome autosome

homogametic sex heterogametic sex gamete

hemizygous

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B. Concepts and Skills You Should Have Mastered: Make sure that you are

confident of your ability to solve the problems at the end of Chapters 2 and 3. There are

usually multiple examples of a particular concept. Keep going until you can do the

problems easily. A lot of doing well in genetics is learning to think like a geneticist and

then practicing until it’s natural to you. Some of it is skill, but most of it is effort.

If you need additional problems, note that there are a number of genetics books

available on-line through the National Library of Medicine:

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=iga.TOC

This is the address for the 1999 edition of Griffith’s Introduction to Genetic Analysis.

You can also reach the book by going to the Biology Research Gateway from the UPS

Library website. Click on PubMed. In the PubMed site, look at the toolbar at the top of

the page. Click on “Books”. Scroll down the list of books and click on the icon for

Introduction to Genetic Analysis.

Another part of genetics is learning to recognize patterns and then using those

patterns to figure out what is going on. For instance, if you are given the information that

two black mice are mated and they produce a total of 12 offspring: 9 black and 3 white;

based on that information you can tell the genotypes of the parents and the white

offspring as well as which trait is dominant and which is recessive. You can do that

because you know that a 3:1 phenotypic ratio in the offspring is characteristic of a

monohybrid cross, that is, a cross between two parents heterozygous for a single gene. If

you learn the patterns, you don’t have to struggle quite as hard doing the problems. You

will have a hypothesis about what is happening that you can test.

Here are a few patterns that you might want to recognize (all are phenotypic ratios

of offspring):

What type of cross gives you a 3:1 ratio?

What type of cross gives you a 9:3:3:1 ratio?

What types of crosses give you a 1:1 ratio?

What types of crosses give you a 4:0 ratio?

Where more than one type of cross can give you the same phenotypic ratio, what would

you do to figure out which of the possibilities you were dealing with?

In which type of cross do only male offspring exhibit the recessive trait while all

female offspring exhibit the dominant trait?

The following questions refer to using human pedigrees :

If you have a pedigree in which an affected child is born to two unaffected parents, what

is the most likely explanation for the trait?

If every affected child has one affected parent, what is the most likely explanation for the

trait?

If most of the affected offspring are male, what is the most likely explanation for

inheritance of the trait?

If most of the affected offspring are female, what is the most likely explanation for

inheritance of the trait?

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If all of the affected offspring are male, what is the most likely explanation for inheritance

of the trait?

Other skills that you should have include:

The ability to figure our genotypes from phenotypes and vice versa

The ability to figure out phenotypic and genotypic probabilities using the forked line

method

The ability to use raw numbers to figure out phenotypic ratios

C. Mitosis and Meiosis: You are responsible for knowing the phases of mitosis

and the significant events that occur in each phase. You should also be able to use the

following terms as a geneticist would:

chromosome chromatid

sister chromatids non-sister chromatids

centromere spindle

diploid haploid

homologous chromosomes homologs

synapsis

synaptonemal complex

chiasmata

crossing-over

equational division reduction division