Transcript Genetics 321 - Western Washington University

Genetics 321
From Mendel to Genomes
10 Weeks
Jeff Young, Botanist
[email protected]
x3638
Office: BI412
Office Hours
M,W,F: 12:30 - 1:30 pm
…by appointment.
Arabidopsis thaliana
Genome-based study of plant
physiology and environmental
responses.
Class Business
• Bulletin Board outside of BI463,
– Answer Keys,
– etc.
• Graded exams and quizzes,
– outside of BI412,
• Online Materials...
http://fire.biol.wwu.edu/young/321g07.html
...via Biology Department Home Page -> Courses -> Jeff Young’s Courses -> Genetics.
Itinerary
• M W F, 10 - 11:20, 5 minute break (~10:45).
• M & F, Usually, questions and answers after break,
• W, (without exception) quiz 11:05 - 11:20,
• All midterms in class, 10:00 - 11:20,
– Final 10:30 - 12:30, Tuesday, December 11
Genetics 321
From Mendel to Genomes
10 Weeks
Essential Genetics: A
Genomics Perspective
by Hartl and Jones, 4th ed.
ISBN: 0-7637-3527-2
Text Assignments:
• Unless amended in class, all
reading assignments listed on the
syllabus are required,
• Additional reading assignments
will be made,
• You will be responsible for ‘in
class’ additions and changes made
to the syllabus.
Grades
 Three hourly exams plus final exam (450 pts),
 You will have the full session time to complete each exam,
 You will be allowed one 11” x 8.5” crib sheet, one side, for each exam,
 Exams - 150 points each, Final Exam cumulative.
 Quizzes will be given every Wednesday (total 100 pts),
 will cover the basics of the assigned reading
(including that day's assignment),
 quizzes 12.5 points each, ~15 minutes,
 quizzes may be taken in teams of two (except Q #1 and #2),
 No Make-up Quizzes, absolutely no exceptions,
 can drop two (2) lowest quiz scores (except Q #1 and #2).
 Total course points - 550
Extra Credit
• e-mail me a synopsis of a news story concerning
Genetics, in the body of the email, 1 per email,
• 1 point each for up to 15 points,
– maximum, 2 per week,
• journal, date, byline, who, where, what and the
significance,
• in English sentences,
– not an automatic point,
– must be well presented.
Extra Credit Sources
• paper newspapers,
• online newspapers,
– do not just cut and paste,
– I reserve the right to be the final judge and arbiter of valid extra
credit contributions,
• you will receive automatic notification(within 24 hours) that your
email got to me. This is not automatic approval.
• if I suspect that liberties are being taken, your extra credit account
will be tallied to zero permanently,
• I’ll let you know if I have a problem with your entry.
• no professional journals.
Geneticsville
Young Pass
Get behind
Don’t Listen
Map
Nature Lake
Hard Mountains
Don’t work problems
Don’t read material
Skip Class
You are here...
Unhappyham
Genetics
...the study of heredity and variation.
The most powerful tool in the biologists toolbox.
Not just for biologists,
- societal,
- personal.
Classical Genetics
eucaryotic
...the transmission of the primary hereditary material,
Genes
DNA
Chromosomes
Genomes
DNA Nucleotides
“Bases”
Chromosomes
Long Polymers
Phosphodiester Bonds
Backbone
Hydrogen Bonds
Double Helix
Genomes
... haploid chromosome
component of an organism,
•human (23), 3 Gb,
• fruit fly (4), 120 Mb,
• nematode (5), 100 Mb,
• mustard (5), 120 Mb,
• yeast (16), 12 Mb,
• bacteria, (1), ~5-15 Mb.
chromosome
~ 5 - 150 Mb long
Units of Heredity
Classical Genetics
Genome
chromosome:
DNA (Mb long)
proteins
gene
DNA (kb long)
promoter:
controls expression
structural:
codes for a protein
Transmission of Hereditary Materials
(meiosis/sex)
...Meiosis: the process of two consecutive cell
divisions in the diploid progenitors of sex
cells.
Meiosis
Cell Biology
Genetics
...the mechanism, timing and
steps of cell division,
…a major result of cell division
is the partitioning of DNA,
…how a cell divides,
…transmission of genomes,
…growth and repair.
…via the transmission of
chromosomes.
Chromosomes
…self-replicating genetic structures.
• two copies of each chromosome are present at some
stage of an eukaryotic organism’s life cycle,
– haploid: cells carrying one full set of chromosomes,
– diploid: cells carrying two full sets of chromosomes,
• n = number of haploid chromosomes.
• 2n = number of chromosomes in a diploid organism.
Haploid
n=2
(sex cells)
Chromosome I
2n = 4
Chromosome II
homologous
chromosomes
Diploid
(somatic cells)
homologous
chromosomes
Chromosome I
Chromosome II
Homologous Chromosomes
…a pair of chromosomes containing the same linear gene
sequence, each derived from one parent,
– homologous chromosomes carry the same complement of genes,
– the DNA sequence of the genes on homologous chromosomes may
differ,
• alleles: genes at the same location (locus) on homologous
chromosomes, but that have different DNA sequences.
Alleles
A-
Alternative forms
of the same gene.
aHeterozygous
B-
b-
C-
C-
Homozygous
Alleles occur at the same locations (loci) on homologous chromosomes.
Meiosis
S: synthesis of DNA,
chromosomes are replicated.
Haploid Cell
Diploid Cell
Synthesis
represents gene A,
from one parent.
A- -A
a- -a
B-
b-
-B
Homologous Chromosomes
-b
represents the
same gene from
the other parent,
codes for the
~same protein,
may have a
slightly different
DNA sequence.
Chromosome Structure
(cartoons)
sister chromatids
M phase
centromere: region of the
chromosome where
chromatids attach.
sister chromatids
Meiosis
S: synthesis of DNA,
chromosomes are replicated.
M: meiosis ( two
divisions) after one
synthesis.
Haploid Cell
Diploid Cell
Meiosis Prophase I
… Synapsis: the highly specific parallel
alignment of homologous chomosomes
during the first division of meiosis,
A A a a
…tetrad: the two homologous
chromosomes become attached
along their length in a structure
termed a tetrad.
B B b b
Chiasmata
Meiosis Prophase I
cont.
A a A a
B B b b
Crossing Over: rearranges the genes from each parent.
Meiosis Metaphase I -- Telophase I
A a Aa
B B b b
A a
A a
B B
b b
Meiosis Prophase II -- Telophase II
Aa
aA
BB
no DNA synthesis
bb
a
A
A
a
B
B
b
b
Meiosis is critical for sexual
reproduction in all diploid
organisms
...meiosis leads to the formation of gametes,
– gametes (one from each parent) conjugate to
form a zygote,
...meiosis is the basis for extensive variation
among members of a population.
Genetic Recombination I
Crossing over.
Genetic Recombination II
I-A
I-a
II-b
II-B
2n combinations of chromosomes,
n = haploid number of chromosomes.
I-A II-b
I-A
II-B
I-a
I-a
II-b
Random Assortment of Chromosomes.
II-B
2n combinations of chromosomes
n = number of chromosomes
•
•
•
•
•
•
•
•
n
n
n
n
= 1,
= 2,
= 3,
= 5,
2n = 2
2n = 4
2n = 8
2n = 32 Arabidopsis
n = 23, 2n = 8,388,608 H. sapiens
n = 39, 2n = yip! dog
Mendelian Genetics
• Gregor Mendel (1822-1884),
• Augustinian monk,
» Botanist,
• Pisum sativa,
• Garden pea,
» 1st “Model System”.
Model Systems
• Modern Biology depends largely on the ability to
study simple organisms, and then apply the
resulting principles to more complex systems,
– i.e., ask simple questions about immensely
complex processes,
– the answers are often simple, though not
obvious.
Model Organisms
• Ease of cultivation,
• Rapid Reproduction,
• Small size,
• Fecund (large brood size),
• Mutants are available and easy to identify,
• Broad literature and experimental background available.
Model Organisms
organism
aka
n
# genes
E. coli
S. cereviisae
C. elegans
Drosophila
Arabidopsis
M. musculus
bacteria
yeast
roundworm
fruit fly
dicot plant
mouse
NA
16
5
4
5
40
4,377
5,770
19,000
13 379
25,498
100,000 25,000- 40,000?
H. sapiens
human
23
100,000 25,000-40,000?
P. sativum
pea
7
~26,0
,000
20,000- 25,000?
General Cell Function
ECOCYC
Cell Cycle
Nature 405, pp. 830
~400 of 6022 Saccharomyces cerevisiae genes are active in
conjunction with the cell cycle.
Model Organisms
organism
aka
n
# DNA bases
E. coli
S. cereviisae
C. elegans
Drosophila
Arabidopsis
M. musculus
bacteria
yeast
roundworm
fruit fly
dicot plant
mouse
NA
16
5
4
5
40
4,639,675
12,495,682
100 Mb
100 Mb
120 Mb
120 Mb
H. sapiens
human
23
3 Gb
P. sativum
pea
7
? Mb
Genome Sizes
Genomics
DNA: Reagent for the 21st Century
“Biology is in the midst of an intellectual and
experimental sea change....
...essentially the discipline is moving from
being largely a data-poor science to becoming
a data-rich science. ”
Vukmirovic and Tilghman, Nature 405, 820-822 (2000)
 > 145 Gb (Aug, 2006)
 > 165,000 organisms
2007
Complete Genomic Sequences
DNA Sequence:Reagent for the 21st Century
2001
9 ARCHAEAL
36 BACTERIAL
6 EUKARYAL
2007
• 345 Eukaryotic Genome
Sequencing Projects
– Complete - 26,
– Assembly - 130,
– In Progress - 189
• 477 Complete Microbial
Genomes
2007: ~ 1,793 Viral Genomes, >547 Organelles, others…
Genomics
• The systematic study of genomes that begins with
large scale DNA sequencing (Structural Genomics),
– Functional genomics: how particular DNA sequences
facilitate biological functions,
– Comparative Genomics: differences between individuals,
differences between species, etc.
– Bioinformatics: computational discipline that has evolved
to handle modern biological data...
Post Genomics Era
Genetic Testing
Drug Discovery
Gene Therapy
More Genomics
Fundamental Research
-Baxter, IR, Young, JC, Armstrong, G, Fosters, N, Bogenschutz, N, Cordova, T, Peer, WA, Hazen, SP,
Murphy, A, Harper, JF. (2005) A plasma membrane H+-ATPase is required for the formation of
proanthocyanidins in the seed coat endothelium of Arabidopsis thaliana. PNAS, 102 (7): 2649–2654
- Robertson WR, Clark K, Young JC, Sussman MR. (2004) An Arabidopsis thaliana Plasma Membrane Proton
Pump Is Essential for Pollen Development. Genetics. 168(3):1677-87
Online Mendelian Inheritance In Man
OMIM
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
Bioinformatics
Post-Genomics Biology
“The new paradigm, now emerging, is that all genes will be
known (in the sense of being resident in databases available
electronically), and that the starting point of a biological
investigation will be theoretical.”
- Walter
Gilbert
Nobel Laureate, Chemistry
DNA Science
"I guess there's cool stuff about science," Watanabe continued, "like space
travel and bombs. But that stuff is so hard, it's honestly not even worth the
effort."
Friday
• Turn in take home quiz, beginning of class,
• Read Chapter 1, and review Chapter 3 if
you are shaky with meiosis.