1. Welcome to
Genetics!
BIOL 310
Tricia Hardt Smith, PhD

2. 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. 

3. Dr. Tricia Hardt Smith

BS: University of Florida (Gainesville, FL)


MS: Tulane University School of Medicine (New
Orleans, LA)


Pharmacology (Drugs!): Snake and Toad
Venom
PhD: Medical College of Virginia; Virginia
Commonwealth University


Zoology, emphasis on herpetology
Pharmacology: Drugs of Abuse,
Cannabinoids
Postdoc: MCV VCU

Opioids, Morphine

4. Bibliography

5. My Methods
 Protein
purification,
identification
 Cell
Culture
 Electrophysiology
60
40
V o lta g e
(m V )
20
0
-20
-40
-60
0
100
200
300
T im e ( m s )
400
500
S w e e p : 1 3 V is ib le : 1 o f 1 3

8. What about you?

9. Genetics
BIOL 310; Fall 2013
Instructor: Tricia Hardt Smith, PhD
Office:
Trani Building, Room 220f
Email: hardtta@vcu.edu
Phone: (804) 828-6058
Office Hours: MW 10-12, or by appointment.
Lecture: MW 4:00 – 5:15 pm Trani Life Sciences Building 151
READ
ENTIRE
SYLLABUS!
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)

10. Grading
The 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 Scale
89.50-100% =A
79.50-89.49% =B
59.50% =F
69.50-79.49% =C
59.50-69.49% =D
Below

11. Grading
The grade will be computed using the following criteria:
Exams
80 %
Quizzes
15%
Homework
5%
Final Grade Scale
89.50-100% =A
79.50-89.49% =B
59.50% =F
69.50-79.49% =C
59.50-69.49% =D
Below
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.

12. Blackboard – http://blackboard.vcu.edu
Information 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 communication
Electronic 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

13. Examinations
Due 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.
Due to the size of the
class I DO NOT offer make-up exams.
Absences from an exam:
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.

14. DON’T CHEAT!!!!!!!!
I will not hesitate to report you
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.
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.
Cheating is your problem too!!
Cheating = Grade Inflation = Less respect for VCU degree!

15. Mark Your Calendar!
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.

16. 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)

17. 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!

18. Religious Holidays, Student Athletes, Active Duty Military
Members and Students with Disabilities
Section 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

19. SCHEDULE
The Add/Drop deadline is January 19th, 2014
A “W” looks
bad too!
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.

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

22. Please
register
your
clicker! 

23. 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!

24. 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/

25. COME TO CLASS AND KEEP UP WITH THE MATERIAL
Cramming 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.

26. 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:


Stay the whole time


Arrive on time
Participate
KEEP TRACK OF YOUR OWN ATTENDANCE!

Date & time

Session Leader

27. 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

28. Fall 2013 Supplemental
Instructor

TBA

29. 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!


Only one clicker per person or no extra credit at all & a trip
to the VCU Honor Court!


No partial credit.
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!

30. GENETIC
AN INTEGRATED APPROACH
A N A LY S I S
Chapter 1
The Molecular Basis of
Heredity, Variation, and
Evolution
Lectures by Kathleen Fitzpatrick
Simon Fraser University
Mark F. Sanders
John L. Bowman
Copyright © 2012 Pearson Education Inc.

31. The Cartoon Guide to Genetics
By Larry Gonick & Mark Wheelis
Amazon.com $13.95

32. Let’s Get Started!....
We
will cover all of
Chapter 1.

33. 18 Things You Should Know
About Genetics
http://www.youtube.com/watch?
v=bVk0twJYL6Y

34. 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

35. Humans have been aware of genetics, via selective
breeding, for over 10,000 years
Priest in bird mask
artificially pollinating
plants
Assyrian relief (882-859 BCE)
Modern maize from
domestication of wild
ancestor teosinite

36. 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

37. • Blending theory of inheritance
– Offspring are a blend, or mixture, of
parental traits

38. 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

39. 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)

41. 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

42. 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

44. 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

45. Recognize Rosalind Franklin!

http://www.youtube.com/watch?v=35FwmiPE9tI

46. 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!

47. BASIC VOCABULARY
•
•
•
•
•
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.co
m/watch?
v=5MQdXjRPHmQ

48. 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?

50. 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

51. 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)
Source: http://www.dna-sequencingservice.com/dna-sequencing/dnanucleotides
http://science.howstuffworks.com

52. Nucleotides are linked
together by a
phosphodiester bond
between the 5′ phosphate
group of one nucleotide
and the 3′ hydroxyl of
another
http://click4biology.info/c4b/3/chem3.3.htm

54. Where is the genetic material located?
Where else?

55. 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

56. 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.

57. 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 

58. 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

59. 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

60. 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

61. 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

62. Transcription
DNA → mRNA
• 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

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

64. Translation
mRNA → Protein
• 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

65. 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
www.boundless.com
• When a ribosome
reaches one of three
stop codons,
translation ceases

67. 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

69. Protein polypeptide chains resemble
the coding strand of DNA. Which
molecule does RNA polymerase bind
to and work on?
e
po
lyp
ep
t id
m
RN
A
nd
tra
tR
NA
Pr
ot
ei
n
DN
A
te
m
pl
at
es
str
a
ng
co
di
DN
A
A. DNA coding strand
B. DNA template
strand
C. mRNA
D. tRNA
E. Protein
polypeptide
nd
20% 20% 20% 20% 20%

70. Questions?

71. 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

72. http://mthfr.net
Random genetic
mutation
Natural Selection
is NOT random.
Evolution and
environment go
hand-in-hand
http://evolution.berkeley.edu

73. 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

74. 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

75. 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

76. 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

77. Evolution at Its Smallest Scale
•
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!

78. 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

79. 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

80. 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

81. 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

82. 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

83. 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.
Paraphyletic Group:
Trait has evolved
multiple times or been
lost multiple times during
evolution
‘para’: above, beside, abnormal,
resembling
Fig 1.13

84. 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)

85. 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

86. Multiple Sequence Alignment

Sequence alignment of three or more biological
sequences, generally protein, DNA or RNA
Generated by ClustalX

89. Are any of you Gamers?
100%
d
bl
e
da
b
I’v
e
0%
No
0%
Ye
s!
Yes!
B. I’ve dabbled
C. No
A.

90. Do you like extra credit?
A. Yes!
100%
B. No!
No
!
Ye
s!
0%

91. 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

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

94. 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.

95. How to Play Phylo For Extra Credit
• 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)

96. 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

97. WHY LEARN GENETICS?
WHAT EXCITING THINGS ARE
HAPPENING NOW?

98. Gene Therapy
Cures Cancer!

99. = B cell (bone)
= T cell (thymus)
White blood cells;
lymphocytes
Cancer; when one of a body’s
own cell mutates and grows out
of control
CD19
Lymphoblastic leukemia: B cells
of the immune system become
malignant
Gene Therapy
Remove T cells and insert
gene directing T cells to
attack CD19
“Recognize &
Attack CD19!”
1 patient cured in 8 days, 4 in 8 weeks
3 patients remission: 5 months – 2 years
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)

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

101. Fig. 5 Images of M. mycoides JCVI-syn1.0 and WT M. mycoides.
Artificial
Wild-type
D G Gibson et al. Science 2010;329:52-56
Published by AAAS

102. 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".

103. QUESTIONS?