Welcome to

Genetics!

BIOL 310Tricia Hardt Smith, PhD

Tricia Hardt Smith, PhD Email: hardtta@vcu.edu

Phone: 804-828-6058

Office: Trani Building, Room 220f

First door on the right when you enter room 220. Come on by!

Office Hours: TR 9-11 am or by appt.

Feel free to request an appt.

Dr. Tricia Hardt Smith BS: University of Florida (Gainesville, FL)

Zoology, emphasis on herpetology MS: Tulane University School of Medicine (New

Orleans, LA) Pharmacology (Drugs!): Snake and Toad

Venom PhD: Medical College of Virginia; Virginia

Commonwealth University Pharmacology: Drugs of Abuse,

Cannabinoids Postdoc: MCV VCU

Opioids, Morphine

Bibliography

My Methods Protein

purification, identification

Cell Culture Electrophysiology

What about you?

GeneticsBIOL 310; Fall 2013  Instructor: Tricia Hardt Smith, PhD Email: hardtta@vcu.eduOffice: Trani Building, Room 220f Phone: (804) 828-6058 Office Hours: MW 10-12, or by appointment. Lecture: MW 4:00 – 5:15 pm Trani Life Sciences Building 151 Welcome to Genetics, the science of heredity!! Genetics is less than 160 years old, but its fast pace of accomplishments has been astonishing. Genetics is a science that studies biological information and how all living organisms pass this information on to their progeny and how they use it in their life time. The development of genetic concepts and technologies and their applications have a profound impact on agriculture, medicine and the society in general. Thus, the study of Genetics, from the Mendel’s laws of transmission of the genetic material to the detailed study of gene function and genomes, are key and essential for any student in the Biological Sciences. We will explore Mendel’s work, evolution and population genetics. We also touch a bit of molecular genetics. I hope I can accomplish most of this broad objective through the semester. Enjoy the class!! SPECIFIC OBJECTIVES: At the end of the class I expect that you will Correlate meiosis and mitosis with Mendel principles.Make predictions of results for genetics crosses using Mendel principles and probability concepts.Use Mendel principles to explain different forms of inheritance: codominance, epistasis, quantitative traits.Describe the structure and function of nucleic acids.Understand control of gene expression and its role in different biological processes. Explain the inheritance of traits using classical and molecular genetic concepts. Describe the role of genes in the evolution of organisms. Understand the importance of genetics in today’s society and be a critical reader of genetic research news.  Prerequisites BIOL 218 and UNIV 200 or HONR 200 with minimum grades of C.. Textbook:- Sanders and Bowman. Genetic Analysis: An integrated approach. (2012). Pearson Education - Gonick L. and Wheels M. The Cartoon Guide to Genetics (updated edition, recommended)

READENTIRESYLLABUS!

GradingThe grade will be computed using the following criteria:Exams 80 % Quizzes 15%Homework 5 % You may calculate your grade at any time; here is how your grade is calculated:  Exams are 80% of your grade, quizzes are 15% and homework is 5%.  Each exam is worth 100 points (50 x 2), so there are total of 400 possible points for exams.  Your extra credit (up to 13 possible points; 10 for review sessions and 3 for Phylo), will be added to this portion of your grade.  Quiz 1 and 2 are worth 10 points, quiz 3-5 are worth 20 points, for a total of 80 possible points. Homework on Mastering Genetics will be worth a combined total of all points for those assignments, about 123 points.

Here's how you would calculate your grade if you got every single possible point, including all the extra credit:

80%(413/400) + 15%(80/80) + 5%(123/123) = 0.826 + 0.15 + 0.05 = 1.026 = 102.6% !  Final Grade Scale89.50-100% =A 79.50-89.49% =B 69.50-79.49% =C 59.50-69.49% =D Below 59.50% =F

GradingThe grade will be computed using the following criteria:Exams 80 % Quizzes 15%Homework 5 %  Final Grade Scale89.50-100% =A 79.50-89.49% =B 69.50-79.49% =C 59.50-69.49% =D Below 59.50% =F I DO NOT BEND ON THESE GRADE BARRIERS. Sorry, the line has to be somewhere.

The final course grading will be determined using a ten-point scale and will depend on your overall performance in all the tests and quizzes. Letter grades will be assigned at the end of the course. Please be aware that I do not curve any exam or final grades. Also I do not “round” grades. Only changes due to mathematical error will be granted.  Grades will be posted in Blackboard and you have one week to check them and get back to me with any question or concerns about them. No grades will be changed after the one-week period.  A grade of Incomplete (I) will be given only if an excused absence is granted for the final exam.

Blackboard – http://blackboard.vcu.eduInformation for our course will be posted on blackboard. I will administer quizzes and post announcements, the syllabus, handouts, grades, etc. You will need your VCU e-mail address and password to log in. Blackboard will give you instructions if this is your first time using it. Email and communicationElectronic mail or "e-mail" is considered an official method for communication at VCU because it delivers information in a convenient, timely, cost effective and environmentally aware manner. Students are expected to check their official VCU e-mail on a frequent and consistent basis in order to remain informed of university-related communications. The university recommends checking e-mail daily. Students are responsible for the consequences of not reading, in a timely fashion, university-related communications sent to their official VCU student e-mail account. This policy ensures that all students have access to this important form of communication. It ensures students can be reached through a standardized channel by faculty and other staff of the university as needed. Mail sent to the VCU e-mail address may include notification of university-related actions, including disciplinary action. Please read the policy in its entirety: http://www.ts.vcu.edu/kb/3407.html

I will use your vcu.edu account to send out class announcements. I will not answer emails that do not come from your vcu.edu account. In the email include your class in the subject area, please no ‘text messaging’ style messages, use the “reply with history” option and also be courteous and concise. I will also post announcements to the class on the Blackboard page.Please remember that this is a large class. If the preceptors can answer your questions about class content, please contact them first.

Do NOT reply to announcements sent out from Blackboard, your email will get lost and I will not respond.

I answer all emails; usually within 24 hours M-F

ExaminationsDue to the size of the class, all exams will be multiple choice. You will have four examinations given during scheduled class periods and a fourth exam during the final exam period. During exams you will be seated in allocated seats, your bags will be placed at the front of the room, no hats will be allowed to be worn, no phones will be allowed on your person. You will be required to show your ID when you turn in your answers and you will need your V number. Please make sure that you know exactly when the tests are, I will not give any test, including the Final, early or late under any circumstance. Also I will not give a test if you are 15 minutes late or a student has already finished and turned the exam.  

Absences from an exam: Due to the size of the class I DO NOT offer make-up exams. If you have a valid reason to miss an exam you must contact me within 24 hours of the exam (preferably before). Valid reasons include: funerals (must provide obituary), hospitalization (must provide hospital documentation), Serve illness (must provide an official doctors note stating that you are too sick to take the exam – please note VCU health services notes rarely state this); other reasons will be considered but official documentation must be provided. If no proof is provided you will receive a 0. In the event that I approve an absence I will discuss an appropriate alternative assessment based on the circumstances this could include a mix of multiple

choice, short answer and oral responses. All students must take the final exam during the final exam period – no make-ups will be allowed.

Academic Dishonesty All VCU students are presumed upon enrollment to have acquainted themselves with and have an understanding of the Honor System. Therefore, it is a student's responsibility to ask course instructors to clarify expectations for each assignment in order to be in compliance with the Honor System. The 2007 - 8 VCU Honor System policy statement and purpose is located at http://www.students.vcu.edu/rg/policies/honor.html . Cheating will be taken very seriously and will be reported.

DON’T CHEAT!!!!!!!!I will not hesitate to report you

Cheating is your problem too!! Cheating = Grade Inflation = Less respect for VCU degree!

Due to the size of this class seating in the exam is close. Please think about your body language. Keep your eyes down on your paper and your body within your space. I will be watching closely for wandering eyes.

Quizzes- PUT THESE 5 QUIZZES ON YOUR CALENDAR!I will post 5 quizzes online in-between each exam in the Mastering Genetics website. These will be done at home in your own time by a defined deadline (4 days after posting). The quizzes are based on a pool of questions so quizzes will not be the same between users. The dates for these quizzes are in the class schedule. Quizzes are intended to make you aware of what you do not know so that you can better prepare for the tests.  Homework- DUE EVERY FRIDAY!Homework will be posted in the Mastering Genetics website. Each homework assignment has a strict due date and time. No extensions or make-ups will be offered after the due date. Please be aware that you need an access code to be able to join Mastering Genetics. This code is included with purchase of a new book, may be purchased in conjunction with an eBook, or can be purchased directly from the Mastering Genetics website.

Mark Your Calendar!

Mastering Genetics• Required to complete your quizzes & homework

• 20% of your final grade.

• Requires an access code

• How to purchase an access code

• An access code comes with the purchase of a new textbook ($194.50)

• Purchas access code and eBook through VCU bookstore ($104)

• Purchase directly on the Mastering Genetics website ($60.50)

Homework is due at the end of each week!• Course ID: MGENSMITHSPRING2014• Homework for each week is due that Friday every week at 5:00 pm!

• 10 random question pulled from pool.

• First TWO homework assignments due JAN 22th! • First assignment is an introduction to the Mastering Genetics Program

and does NOT contain course material

-You will need to try hints

• Second assignment will cover chapter 1

• NEXT HOMEWORK DUE JAN 24th!

• Please try to do homework #1 ASAP to iron any technical details before assignments are really due!

Religious Holidays, Student Athletes, Active Duty Military Members and Students with DisabilitiesSection 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act of 1990 require Virginia Commonwealth University to provide an 'academic adjustment' and/or a 'reasonable accommodation' to any individual who advises us of a physical or mental disability. If you have a physical or mental limitation that requires an academic adjustment or an accommodation, please arrange a meeting with me at your earliest convenience. If you need time due to a religious holiday or you are a student athlete please contact me within the first two weeks of classes. If you are a member of the military and will be affected by deployment or training, please let me know within the first two weeks of class or when issued orders. September 6th is the last day to provide a written notification of intent to observe religious holidays

SCHEDULE The Add/Drop deadline is January 19th, 2014 Please note that March 21st, 2014 is the last day to withdraw for a course with a mark of “W” As this is a required course for many I urge you to meet with me if you are considered withdrawal so that we can see if there is any way to improve your performance in class.  January 24th, 2014 is the last day to provide a written notification to me that you are planning to observe a religious holiday. Students athletes, please provide your schedule to me at this time if your schedule will conflict with any assignments Please inform me as soon as possible of any scheduled absences for athletic or academic reasons. * Disclaimer: The schedule, the dates and content of tests and other aspects of this syllabus could change as a result of unplanned closings, inclement weather, and other uncontrollable factors. Therefore the dates in this syllabus are tentative. Material for quizzes and exams will be announced in class and will be posted in Blackboard.

A “W” looks bad too!

FINAL EXAM WILL BE HELD ON THE LAST DAY OF CLASS!

Please register your clicker!

TIPS & TRICKS: HOW TO DO WELL IN MY CLASS Go to review sessions from the very beginning. Build ‘insurance’. You might get flustered on an exam and not do your best one day. Have a cushion for that. Shop around the preceptor sessions to find a good ‘match’ You must participate while in review sessions. Preceptors have total control over attendance. Non participation or partial attendance at session will NOT result in extra credit. Extra credit at review sessions is a privilege, not a right. Keep your own records of the review session you attend! (Date, time, leader!) Do NOT miss review sessions or class due to your work schedule. Schedule your work around review sessions. If you receive $10 an hour, missing 10 review sessions will give you $100. Failing this class or receiving a low grade will cost you over $1000. Mark your calendar for all homeowork and quizzes! Do these assignments as soon as they are open! Do NOT wait until the last minute! I will not reopen homework or quizzes unless you have a medical excuse covering the entire period in which the assignment was open! Thus, you will get a zero for the assignment if you have a technical or life issue arise just before the assignment is due! 

What has worked for you in earlier courses may not work here. Be prepared to modify your study habits, another lesson you must learn. If you are spending a lot of time doing it one way and it’s not working, try something else. Try ‘lecturing’ in front of your computer. Draw the material. Color code the material. Watch videos repeatedly. Make flash cards. TALK WITH YOUR FRIENDS. Even try interpretive dance!  Do not multitask while studying. EAT before the exam. Your brain needs the glucose! SLEEP before the exam. DO NOT reply to class announcements for Blackboard! Start your own email chain or I will not respond! Deal with test anxiety. Take practice tests. Write questions to ‘get into the mind’ of a question writer. Take your time, read carefully and do not second guess yourself! #1 phrase heard in my office: ‘I just made a lot of stupid mistakes’ If your test anxiety is severe, Disability Support Services is an option. Disability Support Services is in Student Commons, Room 102. You may take the test there. It is your responsibility to set work with them ahead of the exam, schedule your own exam, and send me a reminder to deliver the exam. This is required for each exam. http://www.students.vcu.edu/dss/

COME TO CLASS AND KEEP UP WITH THE MATERIALCramming will not work for this class. DO the practice problems. ‘Overloaded’ students usually do not do well in this class. This class is a large time commitment. Do not spend all your time studying for another ‘hard’ class. This IS the hard class. There is no curve. There’s a lot of extra credit. Don’t expect your tests to be easy too. No practice tests, ‘crib sheets’, study guides, etc. will be provided. Please make them yourself; they will help you out. Do not reply directly to class announcements. Send me a new email if you have questions.

Review Sessions! Review the materials with your classmates! Small classroom envirnoment

Extra Credit! You can earn 5 extra points before exam 2 and 5 extra credit points after exam 2 10 points max total

Schedule to be posted to Blackboard soon!

Extra credit is a privildege:

Arrive on time

Stay the whole time

Participate

KEEP TRACK OF YOUR OWN ATTENDANCE!

Date & time

Session Leader

Preceptors!

Nathan Smith smithnw2@mymail.vcu.edu

Savanah Atkins atkinssg@vcu.edu

Jenna Pham phamj@vcu.edu

Ryan Johnson johnsonrm3@vcu.edu

Claudia Valenzuela valenzuelacs@vcu.edu

Rebecca Lambert lambertra2@vcu.edu

Zeeshan Qureshi qureshiza@vcu.edu

Fall 2013 Supplemental Instructor

TBA

How Else Can I Get Extra Credit?

CLICKER QUESTIONS! During normal lectures, a special extra credit multiple

choice question will announced. Not all clicker questions are extra credit!

Every 5 correct responses will earn you one point of extra credit! No partial credit.

Only one clicker per person or no extra credit at all & a trip to the VCU Honor Court!

Extra credit is added to the exam portion of your grade.

This question will cover LAST material’s lecture and will be difficult! You must keep up and study to earn these points!

Lectures by Kathleen FitzpatrickSimon Fraser University

Copyright © 2012 Pearson Education Inc. Mark F. Sanders John L. Bowman

G E N E T I CA N I N T E G R A T E D A P P R O A C H

A N A LY S I S Chapter 1The Molecular Basis of

Heredity, Variation, and Evolution

The Cartoon Guide to GeneticsBy Larry Gonick & Mark Wheelis

Amazon.com $13.95

Let’s Get Started!....

We will cover all of Chapter 1.

18 Things You Should Know About Genetics

http://www.youtube.com/watch?v=bVk0twJYL6Y

How is the study of genetics utilized? Basis of Disease

Gene Therapy

Research Tools: Genetically modified organisms

Pharmaceuticals: Drug production

Agriculture: Resistance to herbicides and disease

Industry: Commercial production

Priest in bird mask artificially pollinating plantsAssyrian relief (882-859 BCE)

Modern maize from domestication of wild ancestor teosinite

Humans have been aware of genetics, via selective breeding, for over 10,000 years

How do we propagate?• The first ideas…

– Ancient writings: Hindu and Talmud– Greeks

Pangenesis Inheritance of acquired

characteristics

• The middle ages…– Spontaneous generation

(supported by Leeuwenhoek)– Disproved by Redi & Spallanzani

experiments

• 17th Century…– Pre-formation → "Homunculus"– William Harvey (1598 – 1657) →

Epigenesis: Body organs develop de novo

• Blending theory of inheritance– Offspring are a blend, or mixture, of

parental traits

The First Century of Modern Genetics

• An amateur botanist named Gregor Mendel published an explanation of hereditary transmission in plants in 1866

• His work was independently rediscovered in 1900 by three botanists: Correns, de Vries, and von Tschermak

38

Genetics – Central to Modern Biology

• All life on Earth is based on the same structure of genetic material!

• All life on Earth shares a common origin, or progenote

• The three domains of life:

• Eukarya (true nucleus, multiple chromosomes)

• Bacteria (no true nucleus, single chromosomes)

• Archaea (no true nucleus, single chromosomes)

Mechanisms of Replication and Gene Expression Shared by Eukarya, Bacteria, and Archaea

• DNA replication precisely duplicates the DNA duplex prior to cell division

• In transcription, one DNA strand is used to direct RNA synthesis

• Messenger RNA, mRNA, undergoes translation to produce proteins at nucleoprotein structures called ribosomes

DNA Is the Hereditary Material

• Avery, MacLeod, and McCarty identified deoxyribonucleic acid (DNA) as the hereditary material (1944)

• This inaugurated the “molecular era” of the field of genetics, in the second half of the 20th century

• During the 1950s the structure and replication of DNA were elucidated

Rosalind Franklin

• Rosalind Franklin, a biophysicist, used x-ray diffraction to examine the crystal structure of DNA

• X-rays that pass through the crystalized structure are diffracted, creating a pattern collected on x-ray film

• Watson and Crick used Franklin’s x-ray diffraction data to deduce that DNA structure was a double helix

Recognize Rosalind Franklin!

http://www.youtube.com/watch?v=35FwmiPE9tI

DNA Is the Hereditary Material

• Deoxyribonucleic acid (DNA) is the hereditary material

• Ribonucleic acid (RNA) is used by some viruses

• DNA has a double-stranded structure, a DNA double helix, or DNA duplex

• DNA is converted to RNA to make proteins. It is thought that RNA is older than DNA, and that all life originated from RNA-based life forms!

• Genome: complete set of genetic information carried by a species

• Chromosome: single long molecule of double-stranded DNA

• Gene: Basic unit of heredity• Allele: One of two or more

alternative forms of a gene• Locus: Specific place on a

chromosome occupied by an allele

What is a Gene?

http://www.youtube.com/watch?v=5MQdXjRPHmQ

BASIC VOCABULARY

Erwin Chargaff

• Austrian scientist immigrated to US during the Nazi era.

• Chargaff discovered that for most organisms the percentage of adenine and thymine are equal, and the percentage of guanine and cytosine are equal

• This is known as Chargaff’s rule• Watson and Crick used Chargaff’s rule to

formulate the hypothesis that nucleotides are arranged as complementary base pairs (A with T and C with G)• He told Watson & Crick ‘all he knew’• Spoke out against molecular biology = no Nobel

Prize?

Complementary Base Pairing

• Complementary base pairing occurs between an A on one strand and a T on the other, or a G on one strand and a C on the other

• Hydrogen bonds form between the complementary base pairs

• The 5 and 3 designations of the phosphate and hydroxyl at the ends of the DNA strands establish polarity; the two strands are antiparallel

http://www.biologycorner.com/bio1/DNA.html

DNA Nucleotides• DNA nucleotides are composed of a deoxyribose (5-carbon) sugar, a

phosphate group, and one of four nitrogenous bases designated:

• Adenine (A)

• Guanine (G)

• Thymine (T)

• Cytosine (C)

http://science.howstuffworks.com

Source: http://www.dna-sequencing-service.com/dna-sequencing/dna-nucleotides

http://click4biology.info/c4b/3/chem3.3.htm

Nucleotides are linked together by a phosphodiester bond between the 5 phosphate group of one nucleotide and the 3 hydroxyl of another

Where is the genetic material located?

Where else?

Mitochondria and Chloroplasts

• Plant and animal cells contain mitochondria

• Plant cells contain chloroplasts

• These organelles contain their own DNA on single circular chromosomes

• These organelles can suffer from their own genetic diseases

Image: Miguelsierra

1.2 The Structure of DNA Suggests a Mechanism for Replication

• The molecular structure of DNA was key to understanding:

• How DNA could carry genetic information

• How the molecule replicated

• Meselson and Stahl demonstrated that DNA replication was semiconservative about 5 years after DNA structure was elucidated

• Semiconservative replication creates two new duplexes, each composed of one parental (original) strand and one newly made daughter strand

• Each parental DNA strand serves as a template for the synthesis of its daughter strand.

Semiconservative DNA Replication:Each parental DNA strand serves as a template for the synthesis of its daughter strand.

DNA polymerase syntheses daughter strand one nucleotide at a time, adding only to the 3’ end

DNA elongates 5’→3’

More in Ch. 7

1.3 Transcription and Translation Express Genes

• The central dogma of biology describes the flow of hereditary information; the original was proposed by Francis Crick

Updated Central Dogma

• Reverse transcription uses reverse transcriptase and an RNA template (from RNA-containing viruses) to produce complementary DNA

• Micro-RNAs are small RNA molecules with roles in regulation of gene expression in plants and animals

Types of RNA

• Several types of RNA are produced in a cell; messenger RNA (mRNA) is the only type that is translated

• Ribosomal RNA (rRNA) forms part of the ribosomes

• Transfer RNA (tRNA) carries amino acids to ribosomes, to be assembled into proteins

RNA

• RNA consists of ribose, a phosphate group, and one of four nucleotide bases; three of these – A, C, and G – are the same as DNA

• Uracil replaces thymine in RNA; U pairs with A in RNA:RNA complementary base pairing

• RNA polymerase is the enzyme that synthesizes RNA transcripts

Transcription

• Transcription uses one strand of DNA to direct synthesis of a single-stranded RNA transcript

• The DNA strand from which the RNA is synthesized is called the template strand

• The complementary partner of the template strand is called the coding strand

DNA → mRNA

Promoters help regulate the initiation of transcription, which begins near the promoter site at the start of transcriptionTranscription ends at the termination sequenceEukaryotic genes have exons, with coding information, and introns that are removed from the transcript prior to translation

Regulation of Transcription

Translation

• Translation converts the genetic message carried by mRNA into a sequence of amino acids joined together by covalent peptide bonds at the ribosome

• The resulting polypeptide, upon folding, makes up all or part of a protein

• Each amino acid is specified by a codon, three consecutive nucleotides on the mRNA

• Translation begins with the start codon

• The start codon AUG; from here, ribosomes move in the 5 to 3 direction

mRNA → Protein

The Process of Translation

• Amino acids are transported to ribosomes by tRNAs

• Complementary base pairing takes place between the mRNA codon and the anticodon of the tRNA, and allows for the correct amino acids to be added to the chain

• When a ribosome reaches one of three stop codons, translation ceases

www.boundless.com

The Genetic Code

• mRNA specifies an amino acid sequence using the genetic code

• There are 64 possible triplet codons, read in the 5 to 3 direction; each specifies one amino acid

• There are 20 common amino acids; some amino acids are specified by one codon and others by up to six different codons

Protein polypeptide chains resemble the coding strand of DNA. Which

molecule does RNA polymerase bind to and work on?

A. DNA coding strand

B. DNA template strand

C. mRNA

D. tRNA

E. Protein polypeptide

DNA coding st

rand

DNA template

stra

ndmRNA

tRNA

Protein polyp

eptide

20% 20%20%20%20%

Questions?

Theory of Evolution

• Since life originated, millions of species have come and gone; these changes occurred through evolution

• Evolution: the theory that all organisms are related by a common ancestry and have diversified over time primarily via natural selection

• The theory was independently proposed in the late 1850s by Charles Darwin and Alfred Wallace

1871

http://mthfr.net

Random genetic mutation

http://evolution.berkeley.edu

Natural Selection is NOT random. Evolution and environment go hand-in-hand

1.4 Evolution Has a Molecular Basis

• Life is not static or uniform; it evolves as DNA acquires mutational changes

• The biochemical processes that replicate DNA and express genetic information are universal

• Life on Earth most likely originated from a single source, 3.5 – 4.0 billion years ago; the earliest known fossils appear similar to bacteria that exist today

Natural Selection

• Natural selection works at the phenotypic level, but is based on underlying genetic variation

• As one morphological form is favored over another, the frequencies of alleles associated with each form are altered

• Darwin’s theory is now firmly established

Darwin’s Principles of Populations Are Supported by Biological Findings

• Phenotypic variation reflects genetic variation (allele variation)

• Organisms carrying certain allele variants have a reproductive advantage over those who do not

• Certain variant forms of traits give individuals that possess them a higher rate of survival and reproduction; these traits are passed to the next generation with higher frequency

http://www.nature.com/ng/journal/v43/n11/fig_tab/ng.986_F1.html

Evolution on a Small Scale

• Two different frog populations in two different environments may both evolve coloration patterns making them less visible to predators based on their unique environment

• Many genes are likely to be involved in producing a phenotype such as coloration

• Multiple alleles exist for each of these genes– Each individual

possessed two alleles of each gene

– More than two different alleles for each gene can exist within the population

۞Alleles will be selected based on their fit to the particular environment they evolve in!

Evolution at Its Smallest Scale

Four Processes That Lead to Changes in Allele Frequencies in a Population Over Time

• Natural selection: the differential reproductive success of members of a species, due to possession of different forms of adaptive characters; those forms that are best adapted will increase in a population

Four Processes That Lead to Changes in Allele Frequencies in a Population Over Time

• Migration: the movement of members of a species from one population to another can rapidly alter allele frequencies

Four Processes That Lead to Changes in Allele Frequencies in a Population Over Time

• Mutation: the slow addition of allelic variants that increase the diversity of a population and serve as “raw material” of evolutionary change

Four Processes That Lead to Changes in Allele Frequencies in a Population Over Time

• Random genetic drift: the random change of allele frequencies due to chance in rapidly mating populations

Tracing Evolutionary Relationships

• Evolutionary relationships among organisms can be depicted in a diagram called a phylogenetic tree

• The most commonly used approach is the cladistic approach, which sorts evolutionary relationships into groups called clades

• Members of a clade have shared derived characteristics, either morphological or molecular

Working with a Phylogenetic Tree

• The tree finches form a monophyletic group, which includes a common ancestor and all of its descendants

• Insect-eating finches form a paraphyletic group, one that includes a common ancestor and only some of its descendants.

83

Paraphyletic Group:Trait has evolved multiple times or been lost multiple times during evolution‘para’: above, beside, abnormal, resembling

Fig 1.13

Constructing Phylogenetic Trees Using Morphology and Anatomy

• To construct a phylogenetic tree, consider the common morphological features shared by groups of the organisms under consideration

• Find an outgroup; an organism lacking a feature shared by all of the others (the ingroup)

Constructing Phylogenetic Trees Using Molecules

• Phylogenetic trees based on molecular features are constructed based on DNA or protein sequences

• Parsimony: The simplest explanation for the known differences among groups has the greatest likelihood of being correct.

• The most closely related molecular sequences have the smallest number of differences between them

• Shared characteristics that evolved independently arise by convergent evolution or homoplasy (e.g., bird vs. bat wings)

• Shared features used to construct phylogenetic trees must not have evolved independently

Multiple Sequence Alignment Sequence alignment of three or more biological

sequences, generally protein, DNA or RNA

Generated by ClustalX

Are any of you Gamers?

A. Yes!B. I’ve dabbledC. No

Yes!

I’ve dabbled No

0%0%

100%

Do you like extra credit?

A.Yes!B.No!

Yes!No!

0%

100%

Phylo! http://phylo.cs.mcgill.ca

Play a video game for extra credit!

Be involved in real science that has resulted in publication in peer-reviewed journals!

http://www.youtube.com/watch?v=OdQuO0HY88Y

http://www.youtube.com/watch?v=OdQuO0HY88Y

How to Play Phylo For Extra Credit• Register to play at: http://phylo.cs.mcgill.ca• Once registered, you will join the exam to get

credit. Only puzzles completed in the exam will count towards credit.

• You will login & register to the exam using the event ID. You must provide the full name & email address

• Exam Event ID VCU+BIOL310• You will need to complete 20 puzzles• If you have problems registering or playing,

email/call/come see me right away.

• Step 1: Register on the main Phylo website.

• Step 2: Using your Phylo username and password, login as a student.

• http://phylo.cs.mcgill.ca/teaching/student/

• Step 3: Fill the form and use the event ID provided by your instructor to register to an event. All fields are mandatory.

• Step 4: Go to play Phylo! (Make sure that you are logged in when you play)

How to Play Phylo For Extra Credit

Modern Genetics Has Three Major Branches

• Transmission genetics (Mendelian genetics) is the study of the transmission of traits in successive generations

• Evolutionary genetics studies the origins of and genetic relationships between organisms, and evolution of genes and genomes

• Molecular genetics studies inheritance and variation of nucleic acids and proteins

WHY LEARN GENETICS?

WHAT EXCITING THINGS ARE HAPPENING NOW?

Gene Therapy Cures Cancer!

= B cell (bone)Cancer; when one of a body’s own cell mutates and grows out of control

Lymphoblastic leukemia: B cells of the immune system become malignant

CD19= T cell (thymus)White blood cells;lymphocytes

Gene TherapyRemove T cells and insert gene directing T cells to attack CD19

“Recognize & Attack CD19!”

Technical Issue: all B cell have CD19, so all B cells are killed. Patients received a bone marrow transplant to boost the immune system until the body was able to regenerate it’s own healthy B & T cells (months)

1 patient cured in 8 days, 4 in 8 weeks3 patients remission: 5 months – 2 years

Genetics Creates Synthetic Life!• Intro: http://www.youtube.com/watch?

v=L61bII-bMKU

• http://www.youtube.com/watch?v=HLP6x4h1tOM

• Craig Venter

• 2007:First entire human genome sequenced (his own).

• 2010: Synthesized Life

• synthesize a 1.08 million base pair Mycoplasma mycoides genome

• ‘Boots up’ genetic code in bacterial cell

Fig. 5 Images of M. mycoides JCVI-syn1.0 and WT M. mycoides.

D G Gibson et al. Science 2010;329:52-56

Published by AAAS

Artificial

Wild-type

Watermarks in the Artificial Genome

• watermark 1 an HTML script which reads to a browser as text congratulating the decoder with an email link (mroqstiz@jcvi.org) to click to prove the decoding.

• watermark 2 contains a list of authors and a quote from James Joyce: "To live to err, to fall, to triumph, to recreate life out of life".

• watermark 3 contains more authors and a quote from Robert Oppenheimer (uncredited): "See things not as they are, but as they might be".

• watermark 4 contains yet more authors and a quote from Richard Feynman: "What I cannot build, I cannot understand".

QUESTIONS?