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History
of Transmission Genetics
Early
Views
Grasping at straws
Spontaneous generation
Aristotle
form/substance
hot/cold form = male/female
Establishment of existence of sperm and eggs (17th century)
Preformationism
homunculi
Epigenesis
differentiation
Pangenesis (19th
century)
gemmules
Lamarckianism
or the Theory of Acquired Characteristics
Weismann
somatoplasm
germplasm
Twentieth
Century
Observation of chromosomes; mitosis and meiosis; haploid vs. diploid
Rediscovery
of Mendel's work - inheritance governed by a pair of units
Pairs of chromosomes related to Mendel's pairs of units??!!
1940's - DNA = genetic material
1950's - Structure of DNA
1960's - Genetic code understood
Review
Prokaryote
vs. eukaryote
Diploid vs. haploid
Sexually reproducing vs. asexual
Mitosis
and meiosis both involve the separation of chromosomes during some type of cell
division. Therefore we will start
with some background information on chromosomes.
Diploidy
Homologous
chromosomes or homologues
Diploid number; 2N
Humans: 2N = 46; 2 sets of 23 different
chromosomes
Culex pipiens:
2N = 6; 2 sets of 3 different chromosomes
Maternal
and paternal homologues
Gross morphology of chromosomes
Chromatids
- what we see: two strands of DNA per chromosome!
present ONLY when cell is dividing; DNA is duplicated; not normal
structure
Centromeres
- metacentric, telocentric, acrocentric chromosomes
Telomeres
Karyotype
MITOSIS
Normal
cell division; growth, somatic cell replacement, etc.
One
2N cell ---> two identical 2N cells
One
division
Cell
cycle: G1-->S-->G2-->mitosis-->G1-->
and so on.....
5
phases
(interphase)->prophase->metaphase->anaphase->telophase->(interphase)
know what the chromosomes
are doing at each stage!
MEIOSIS
Gamete
(or spore) production
only; oogenesis and spermatogenesis
One
2N cell ---> four genetically different 1N cells
Two
divisions
INT->PRO I->MET I->ANA I->TEL I->(PRO II)->MET
II->ANA II->TEL II
Prophase I
has 5 stages
leptonema, zygonema, pachynema, diplonema, diakinesis
**again,
know what the chromosomes are doing at each stage!**
New terms:
Chiasmata, tetrad,
disjunction, independent assortment, reductional division, equational division,
nondisjunction, gametogenesis
Check out:
http://www.biology.arizona.edu/cell_bio/activities/cell_cycle/cell_cycle.html
Requirements of the genetic
material:
1.
Stable
2. Able to reproduce
3.
Carries all information
4. Capable of variation
Major experiments indicating DNA
as the genetic material
1.
Griffiths - "transforming principle"
2. Avery, MacLeod, and
McCarty
3.
Hershey and Chase
4. Guthrie and Sinsheimer
Structure of DNA
- Watson, Crick, Franklin,
Wilkins
General
structure
Components
Deoxyribose
sugar - 5 carbon sugar, ring form
Phosphate
groups (PO4)
Nitrogenous
bases
Purines: adenine, guanine
Pyrimidines: thymine, cytosine, (uracil)
Structure
Nucleoside:
sugar with base attached to 1' carbon
Nucleotide:
sugar w/ base plus phosphate group attached to 5' carbon
Phosphodiester
bonds
One DNA molecule consists of two chains of nucleotides bound together by hydrogen bonds between bases on opposite chains - double helix
**Note
well:
DNA molecule is:
Polar
Complementary
Antiparallel
Forms
of DNA:
A-DNA
B-DNA
Z-DNA
Simple diagram
Viruses - anything goes
Bacteria - “naked” DNA
Super coiling
RNA and protein stabilized
Eukaryotes
Chromosome gross structure
DNA + histone proteins = chromatin
Nucleosomes
Euchromatin and heterochromatin
Centromeres and telomeres
Eukaryotic genomes
Repeated DNA sequences
Repetitive DNA
Satellite DNAs
Renaturation
kinetics
Repeated sequences
in the human genome
LINEs
SINEs
Alu sequences
Necessary
to copy chromosomes prior to cell division; insures each cell has a full
complement of genetic information. Now each chromosome consists of 2
chromatids.
Semi-conservative
replication
(as opposed to dispersive or conservative)
Each
strand is used as a template for a
new strand
Meselson and Stahl
Density-gradient centrifugation
Origins of replication
Bi-directional replication
Always
5' to 3'
Leading strand
Continuous
replication
Lagging strand
Discontinuous
replication
Okazaki
fragments
Enzymes
needed
To cut DNA
Nucleases
To unwind helix
Helicase
Topoisomerase (prokaryotes)
To make RNA primer
RNA primase
To polymerize new DNA
DNA polymerase III
To remove and replace RNA primers
DNA polymerase I
To seal Okazaki fragments
Ligase
Simple
Mendelian Genetics
Mendel's
Four Postulates
Unit factors in pairs
Dominance/recessiveness
Random segregation
Independent assortment
Mendel's
secret:
Observed one trait at a time
Quantitative approach (he counted things)
Monohybrid
crosses
Parental generation
F1 or first filial generation
F2 generation ratios: 3 to 1
Gene/allele/locus
Illustrates first three postulates
Remember, we're talking about pieces
of chromosomes - think meiosis!
Phenotype vs. genotype
homozygote vs. heterozygote
Punnett squares
Dihybrid crosses
Independent
assortment (remember meiosis!)
F2 phenotypic ratios:
9:3:3:1
Test cross or backcross
Reciprocal crosses
Trihybrid
crosses
The
forked-line or branch method
Predicting
outcomes of random events
Sum rule
One event; either of two or more
mutually exclusive outcomes
Product rule
More than one event; specific outcomes
for each
Binomial expansion (multiple, unordered events)
n!
P = ------- psqt
s!t!
Statistics
The Chi-square test for
goodness of fit
(observed - expected)2
c2
= S ------------------
expected
Expected vs. observed numbers
Degrees of freedom
Probability level
Pedigrees
Symbols
Generations
assigned Roman numerals
Individuals in a given generation assigned Arabic numerals
open circle
= female; closed circle = female
with the trait in question
open square
= male; closed square =
male with the trait in question
and more....
Assumptions
Everyone is telling the
truth!
Unless evidence to the contrary, assume individuals
marrying in to the pedigree are as normal as possible
Autosomal
recessive patterns
Autosomal
dominant patterns
Chromosomes,
Sex Determination, and Sex Linkage
Review
of Mendel’s Postulates in terms of chromosomal behavior in meiosis
Sex-linked
or X-linked Traits
Hemizygous males
Reciprocal crosses
Hemophilia
Characteristic patterns of recessive sex-linked traits
X-linked dominant traits
Y-linked traits
Sex
determination
Many modes of sex determination
Heterogamy; heterogametic sex vs. homogametic sex: XX XY, ZZ ZW
Humans:
just what's on that Y chromosome after all?
SRY region
ZFY region
XY females and XX males?
Two one-gene sexual disorders in
humans
Androgen Insensitivity Syndrome
Guevodoces
Dosage
compensation and X-inactivation
Barr bodies
Lyon hypothesis
Mosaicism; calico cats
Situations
where dominance/recessiveness does not hold or is complicated
Mechanisms of dominance
Incomplete dominance; example:
carnations
Co-dominance; example: MN blood group
Multiple alleles; example: ABO blood
group, coat color in rabbits
Lethal alleles
Cuenot's
mice
Mechanisms of lethality
Genic
interactions -
one trait controlled by more than one gene
Production of novel phenotypes; example: shape of comb in poultry
Mechanisms
Metabolic pathways
Eye color in Drosophila
Epistasis
- one gene masks another; example: coat color in mice
(Pleiotropy - more than one trait affected by one gene; example: PKU)
Modifier genes
Factors
affecting phenotype
Genetic factors
Incomplete penetrance/variable expressivity
Sex-limited
traits
Sex-influenced traits
Environmental factors
Phenocopies
Linkage,
Mapping, and Recombination
Linkage
Linked
genes = genes located on the same chromosome
Cis or coupling configuration
Trans or repulsion configuration
Test cross ratios
Recombination
or crossing-over
Parental vs. recombinant types
% Recombination
distance in map units (m.u.)
Double crossing over
Mapping
Three-point cross
Coefficient of coincidence
Interference
Advanced Mapping
Ordered tetrad mapping
Detection of linkage in humans through pedigree analysis
lod score
Somatic cell genetics
Cell
fusion
Gene mapping using chromosomal abnormalities
The Human Genome Project
Genetics
of Viruses and Prokaryotes
Bacteriophage
life cycle
Infection of host
Early phage proteins
Degradation of host chromosome
Replication of phage chromosome
Late phage proteins
Lysis
Genetic recombination in phages
Mixed
infections
Eukaryotic
viruses
DNA viruses
Retroviruses
Reverse transcriptase
HIV
Genetic
recombination in bacteria
Transformation
Competence
Exogenous DNA
Conjugation
F+
x F-
conjugation
F
factor
Plasmid
Donor
vs. recipient strains
Hfr
conjugation
Sexduction
Mapping
bacterial chromosomes
Interrupted mating techniques
Distances in minutes
Transduction
Virally
mediated
The Central Dogma of Molecular Biology
1. DNA may self-replicate (DNA synthesis; needed only when a cell divides)
2.
DNA -----------------> RNA ------------------> protein (normal
gene function)
transcription
translation
Connection between DNA and polypeptides
Garrod
- "inborn errors of metabolism"
Alkaptonuria
Presence or absence of enzymes inherited
Beadle and Tatum
Neurospora
"One gene - one enzyme"
Sickle
cell anemia
Alpha and beta hemoglobin
"One gene - one
polypeptide"
Basic structure of polypeptides
Amino
acids
Central carbon, amino group, carboxyl
group, R group
Peptide bonds
1o
structure - order of amino acids
2o structure - hydrogen bonds between amino groups
and carboxyl groups
3o structure – interactions (bonds) between R
groups
4o structure – interactions (bonds) between
polypeptides
Transcription
and RNA Processing
Differences between DNA and RNA
Ribose
sugar
Uracil
replaces thymine
Single stranded
Four types of RNAs
mRNA
tRNA
rRNA
hnRNA
One gene uses only one strand of
the DNA to carry information
Sense
or coding strand
Template vs. nontemplate strand
RNA
polymerase
RNA polymerase I
- rRNA
RNA polymerase II -
mRNA
RNA polymerase III - tRNA
Promoters
Consensus sequences
Prokaryotes
Pribnow
box or -10 box
-35 box
Eukaryotes
-25 box (TATA box)
-75 box (CAAT box)
Allow binding of RNA polymerase and localized
"melting" of DNA double strand
Elongation
5' to 3' direction
Complementarity
Termination
Prokaryotes
Inverted
repeats
Rho factor
Termination and
Post-transcriptional modification of RNA (eukaryotes)
Primary transcript
Methylguanine cap on 5' end
Poly-A tail on 3' end
Splicing
Introns
Exons
Heterogeneous nuclear RNA (hnRNA)
tRNA - translator molecule; “workers”
3-dimensional structure
Anticodon
Amino
acid
Charging;
Aminoacyl tRNA
Ribosome - "machinery"
Large and small subunits
Aminoacyl site
Peptidyl site
Exit site
Initiation
Prokaryotes: Shine-Dalgarno sequence
Eukaryotes: scanning hypothesis
Binding of first tRNA at aminoacyl site
(methionine or N-formyl
methionine)
Movement of complex; first tRNA enters
peptidyl site
Binding of second tRNA at aminoacyl site
Elongation
Formation of peptide bond between two
amino acids
Movement of complex; empty aminoacyl site
New tRNA binds at aminoacyl site
Repeat elongation steps until stop codon
enters aminoacyl site
Termination
Release factors (proteins) release
polypeptide, mRNA, ribosome
The Genetic Code
Triplet code - 3 bases make up one “codon”
Non-overlapping
Degenerate - 64 codons --> 20 amino acids
One start codon (AUG), three stop codons (UGA, UAA, UAG)
Universal (or close enough)
Techniques of
Molecular Genetics
Recombinant
DNA
Restriction endonucleases
Bacterial enzymes
Restriction sites (specific sequences cut)
Flush cuts
Staggered cuts -
"sticky ends"
Cloning
Vectors
Phages
Cosmids
YACs
BACs
Target genes
Genomic libraries
Electrophoresis
Restriction
Fragment Length Polymorphism (RFLP) analysis
DNA
fingerprinting
VNTRs
Southern blots
DNA
sequencing - Sanger or dideoxy method
Chain terminators: ddATP, ddCTP, ddGTP, ddTTP
DNA
amplification - PCR analysis
Chromosome
walks and jumps
Localization
of human genes
Huntington’s disease
Cystic fibrosis
Duchenne muscular dystrophy
The
Human Genome Project
Gene Therapy
Gene Regulation in Prokaryotes
Constitutive
enzymes
Adaptive
enzymes
Inducible
Repressible
lac
operon
Inducible
Jacob and Monod model
i = inhibitor gene
Inhibitor protein
p = promoter
o = operator
z = beta-galactosidase
y = permease
a = trans-acetylase
Structural
vs. regulatory genes
Polycistronic
mRNA
Effector molecule
Normal functioning of the operon
Allosteric protein
Catabolite repression of
the lac operon
Glucose vs. cAMP levels
Catabolite activator protein
cAMP-CAP complex
Increased
efficiency of the promoter
trp
operon
Repressible
r = repressor gene
aporepressor protein
p = promoter
o = operator
t = 5 genes ----> tryptophan synthetase
Normal functioning of the operon
Contrast to lac
Attenuation
of the trp operon
Leader/attenuator region
Mutually exclusive pairing
Transcription termination
signal
Gene
Regulation in Eukaryotes and The Genetics of Cancer
Transcriptional,
post-transcriptional, translational control possible
Operon-like
mechanisms
Familial hypercholesterolemia
Cell surface receptors
Low density lipoproteins
Feedback inhibition
Environmental
induction of transcriptional control
Heat shock proteins
Light and RBC
Hormones
Transcriptional
control
Transcription factors
Enhancer or silencer sequences
Zinc fingers
Leucine
zippers
Helix-turn-helix
Helix-loop-helix
Regulation
through chromosome organization
Lampbrush chromosomes
Polytene chromosomes
Euchromatin vs. heterochromatin
Genetic basis of cancer
Chromosomal changes and cancer
Burkitt's lymphoma
Philadelphia chromosome
The
cell cycle and cancer
Checkpoints: G1 - S; G2 - M
Important proteins:
cyclins and kinases
Retinoblastoma
2 mutations required in the RB gene to induce tumor formation
Gene product - pRB;
needed to stop cell cycle
Wilm's tumor
Proto-oncogenes and oncogenes
Somatic
vs. germinal mutations
Spontaneous
vs. induced
Generally:
random
reversible
not directed
Point mutations
Nonsense:
stop codon
Missense:
codon for a different amino acid
Neutral or silent:
synonymous codon
Frameshifts
Generally massive
missense or nonsense; loss of function of gene
Errors in replication
Tautomeric shifts
Deamination
Depurination
Environmental mutagens
Ultraviolet
radiation
Some well understood examples of chemical mutagens
Base
analogues
Substances that change base
structure
Acrydine
dyes
Ionizing radiation
Ames
test
Salmonella
his-
revertants to his+
Changes
in the numbers of chromosomes: Aneuploidy and Polyploidy
Polyploidy;
3N, 4N, etc.
Suffix:
-ploid or -ploidy
Haploidy or monoploidy; plants vs. animals
3N or more in animals
3N or more in plants
Allopolyploids vs. autopolyploids
Instant
speciation: Raphanobrassica
Polyteny and endomitosis
Aneuploidy;
2N + 1, 2N - 1, 2N + 2, etc.
Suffix:
-somic or -somy
Nondisjunction
Human aneuploids
Trisomy 21
47, XYY
Trisomy 18
47, XXX
Trisomy 13
Klinefelter syndrome
Turner syndrome
Changes in chromosome structure
Changes
in the number of genes on the chromosome
Deletions
Effects on
phenotype
Prader-Willi and
Angelman syndromes
Duplications
Evolutionary
effects: hemoglobins
NOR and Down
syndrome
Changes in the location of genes on the chromosome
Inversions; cross over
"suppressors"
Translocations
Reduction of
fertility
Cancers associated
with translocations
Transpositions
Transposable genetic elements
Prokaryotes
Insertion sequences
Terminal repeats
Transposase
Eukaryotes
Dissociation and activator in maize
P elements in Drosophila
Hybrid dysgenesis
Retrotransposons
Genetic
and evolutionary significance of transposable elements
Genetics
of mitochondria and chloroplasts
Maternal
inheritance
Actions of chloroplast genes
Actions of mitochondrial genes
mtDNA and human disease
Maternal imprinting
Fragile
X syndrome in humans
Chromosome 15 micro-deletion in humans
Basics
Populations
Biological species concept
Mendelian population or deme
Genetic
variability
Polymorphism vs. monomorphism
Allele
frequencies
p and q
p = percentage of one allele in population; q = percentage of alternate
allele
p + q = 1
The
Hardy-Weinberg equilibrium
Genotype frequencies:
AA
AB
BB
p2
2pq
q2
p2
+ 2pq + q2 = 1
Using Hardy-Weinberg to quantify changes in allele/genotype
frequencies
Testing
for equilibrium
Estimating
allele and genotype frequencies
Forces that may change allele/genotype frequencies
Migration
or gene flow
Results in convergence of populations
Dqr
= m(qm – qr)
qn = qn-1 + Dq
Non-random
mating
Typically results in a decrease in heterozygotes
Random
genetic drift (small
population size)
Totally random changes in allele frequencies
Founder principle
Mutation
Extremely slow change
Dq = mp - nq q1 = q0 + Dq
m
qeq= ----------
m + n
Selection
Fitness
Darwinian fitness
Relative fitness; w
Selection coefficient; s
w + s = 1
Mean population
fitness:
_
w
= p2(wAA) + 2pq(wAB) + q2(wBB)
Change in allele frequencies with selection:
p02(wAA)
+ p0q0(wAB)
p1 =
------------------------------------------------
p02(wAA)
+ 2p0q0(wAB) + q02(wBB)
Selection
equilibrium
s2
seq
= ----------
s1 + s2
Heterosis
Maintenance of variation
Fluctuation
in environment
Habitat choice
Frequency dependent selection
Continuous
vs. discontinuous variation
Normal curve vs. phenotypic classes
Continuous
traits
Much intra-genotypic
variation; no clear-cut divisions between phenotypes
e.g.,
height, weight, hair color, skin color, etc.
Polygenic
More
than one gene
Generally, genes have additive effects
1/4n
=
proportion of one of the extreme phenotypes, where n = the number of loci
involved
Multifactorial
Strongly influenced by the environment
Norm of reaction of a genotype
Thresholds
Discontinuous traits with polygenic,
multifactorial inheritance
Ways
to measure genetic influence versus environmental influence:
Heritability (narrow)
YO
- Y
h
= ------------------
YP
- Y
Concordance
Twin studies