There Can Be No Twisted Thought Without a Twisted Molecule

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• "There Can Be No Twisted Thought Without a
  Twisted Molecule"
• Ralph W. Gerard
• Neurophysiologist

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31241 Behavioral and Cognitive
NeuroscienceProfessor A.K. JohnsonFall
2009OutlineTopic 1 Genes and Behavior10/15
10/20

• I. Introduction
• A. Levels of Analysis of Neural Function and
  Psychological Processes
• B. Molecular and Cell Biology
• C. The Central Dogma of Molecular Genetics
• II. Genes and the "Realization" of Phenotypic
  Traits
• A. Mendelian Genetics and Genes as the Units of
  Heritability
• B. Phenotype Genotype
• C. Beadle and Tatum
• 1. One gene-one enzyme hypothesis
• 2. Inborn errors of metabolism
• III. Proteins and Proteomics
• A. Amino Acids
• B. Peptide Bond and Peptides
• C. Protein Structure
• D. Protein Function
• E. Proteins
• 1. What proteins do

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Topic 1 Genes and Behavior(Continued)

• V. Chromosomes and Genes A. Some Facts About
  the Human Genome B. Karyotyping of the Human
  Genome C. Sexual Reproduction 1. Benefits 2.
  Meiosis 3. Stirring the Genetic Pot D. The
  Human Genome Project
• VI. Sexual and Genetic Errors A. Alterations in
  Disomy B. DNA Mutations C. Phenylketonuria D. O
  MIM Online Mendelian Inheritance in
  Man E. Identifying Genes Causing Illness
• VII. Genetic Engineering A. Strategy and methods
  for manipulating genes B. Gene therapy

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Key Terms and Concepts
Peptides Phenotype Phenylketonuria
(PKU) Phosphorylation Point mutation Polymerase Po
lymers Polymorphisms Prokaryotes Proteinomics Prot
eins Ribosome Rough endoplasmic reticulum Silent
mutation Smooth endoplasmic reticulum Tertiary
structure Transcription Translation Trisomy tRNA U
racil Watson-Crick model Wild type
Allele Allosteric proteins Amino
acids Aneuploidy -ase as a suffix Autosome Barbara
McClintock Catalyst Central dogma of molecular
biology Centromere Chromatin Chromosome Codon Cros
sing over Cytokines Deletion Diploid Disomy DNA
(deoxyribonucleic acid) Endogenous Energy of
activation Enzyme Eukaryotes Exogenous
Exons Frame shift mutations Gene-environment
interaction Genes Genotype Haploid Introns Karyoty
pe Kinase Lysosomes Meiosis Metaphase Missense
mutation Mitosis Molecular weight Muscular
dystrophy Mutation Neuron Nucleosome Nucleotide Nu
cleus Nullisomy One gene-one enzyme
hypothesis Peptide bond
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Levels of Organization in the Nervous System
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The Central Dogma of Molecular Biology
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A 135 Year Time Line of Genetic Discovery
1866 Mandel "Genes" discovered 1871 Nucleic
acids (DNA is one) discovered 1901 Mandel
Rediscovered 1910s Chromosomal theory 1951
First protein sequenced (insulin) 1953
Structure of DNA discovered 1960s Better
understanding of genetic code 1975-79 First
human genes located 1977 DNA sequencing
begins 1986 DNA sequencing first
automated 1989 First disease gene located
cystic fibrosis 1995 First genome sequenced
(Hib, a bacteria that causes meningitis) 1999
First human chromosome sequenced 2000 Private
company maps human genome federal project
completes working draft 2001 Both working
drafts of human genome published
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The Seven Characteristics of Peas Studied by
Mendel
Gregor Mendel (1822-1884) The father of
genetics Mendel G. 1865, Versuche uber
Pflanzen-Hybriden, Verh. Naturforshung
43-47
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The Classic Genetic Analysis of Gregor Mendel
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Mendel's "Laws"
1. The genetic determinants are particulate they
don't blend. (He called the determinants
elementen only much later were the determinants
or elementen called genes.) 2. Each individual
(plant in Mendel's case) has two copies of the
heredity determinants (genes). 3. The genetic
determinants (genes) for a particular
characteristic (e.g., seed shapesphericals vs.
wrinkled) can exist in different forms. In
Mendel's peas, one allele was dominant and one
allele was recessive for each of the traits he
studied. These different forms of "genes" became
known as alleles. (Each particular gene type is
referred to as an allele when the two copies of
the alleles are the same they are called
homozygous and when they are different they are
called heterozygous.) The alleles remain
discrete and don't blend. 4. Although all somatic
cells (i.e., non-sex cells) have two copies of
each allele, only one allele is passed on to an
offspring from a female and one from a male in
the form of a gamete (sex cell i.e., egg or
sperm) in sexual reproduction. This is the law
of segregation.
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Examples of Inheritance That areControlled by a
Single Gene
Species Character (Phenotype) Mice Albin
o/normal coat, pale/normal ears Red
clover Red/white flowers Fruit flies Normal/vestig
ial wings Humans Blue/brown eyes, cystic
fibrosis, sickle cell anemia, phenylketonuria
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Increased Complexity of Mendelian GeneticsThe
Demonstration of IndependentAssortment of Genes
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Four Things That Mendel Did That Lead to His
Success in Establishing the Concept of Units of
Heredity
Chose a simple organism that normally
self-pollenated. Chose a "true breeding"
variety of garden pea because they
self-pollenate. He chose "characteristics"
(traits phenotypes) that could be determined
unambiguously. He studied large n's to come to
his conclusions.
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Complicating Issues Not Faced By Mendel
Codominance Lethal genes Gene linkage
More than just two alleles for each gene
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Thomas Hunt Morgan (1866-1945)
Columbia University Founder of modern
experimental genetics Chromosomal theory of
heredity Drosophila melanogaster 1933
Nobel Prize
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The Unification of Genetics and
BiochemistryOne Gene-One Enzyme Hypothesis
Archibald Garrod (1857-1936) British
physician 1909 recognized that the disease
alkaptonuria was caused by a rare recessive gene
mutation inherited according to Mendelian rules
Treatise on "Inborn Errors of Metabolism"
surmised the nature of the genetic defect. "We
may further conceive that the splitting of the
benzene ring in normal metabolism is the work of
a special enzyme, and that in congenital
alkaptonuria this enzyme is wanting." "Inborn
Errors of Metabolism" (1923) George W. Beadle
(1903-1989) and Edward L. Tatum (1909-1975)
1958 Nobel Prize Neurospora crassa (bread
mold) Normal spores require only water, sugar,
ammonium salt for nitrogen, and biotin 1 in
1000 required an enriched medium of a single
added substance such as a vitamin or amino acid
to restore growth They concluded that the
mutant cells carried a defect in a single gene
that impaired the production of an enzyme for a
single metabolic step (1941 "Genetic Control of
Biochemical Reactions in Neosporin") That is
one gene was responsible for one enzyme
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Schematic Illustration of Energy of Activation
inthe Absence and Presence of a Catalyst (Enzyme)
Enzyme Substrate Enzyme-Substrate
Enzyme-Substrate ? Enzyme Products E S
ES ? E P
? ?
? ?
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The Twenty Common Amino AcidsThat Are
Incorporated Into Proteins
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Three Dimensional Representations of Amino Acids
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Peptide Bonds, Polypeptides and Proteins
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Levels of Protein Structure
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Functional Roles of Peptides/Proteins
Enzyme Systems Signaling (e.g., First and
Second Messengers) Structural Motility
Transport and Storage Immune System
Functions Regulation of Transcription
Nutrition
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Allosteric Proteins Many Proteins Change Their
Confirmation Upon Binding a Ligand
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Phosphorylation by ATP Can Activate an Allosteric
Protein
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Neuronal Proteins Regulated by Phosphorylation
Regulated Protein Protein Kinase
Effect Enzymes involved in
neurotransmitter biosynthesis and degradation
Tyrosine hydroxylase PKA, PKC, CaM-KII Increase
in enzyme activity Tryptophan
hydroxylase CaM-KII Increase in enzyme
activity G protein-couple receptors
?-adrenergic receptor PKA, GRKII Receptor
desensitization Opioid receptors GRKII Receptor
desensitization Neurotransmitter-gated ion
channels GluR1 (AMPA subunit) PKA Increase in
response NMDAR1 (NMDA subunit) PKC, tyrosine
kinase Increase in response Ion channels
Voltage-gated Na channel PKA, PKC Decrease in
channel conductance Voltage-gated Ca2
channel PKA Increase in channel
conductance Enzymes and other proteins involved
in the regulation of second messengers
Phospholipase C? Tyrosine kinase Increase in
enzyme activity IP3 receptor PKA Increase in
Ca2 release Protein kinases PKA PKA Increase
in dissociation and activity CaM-K1 and
IV CaM-KK Increase in enzyme activity
Trk Trk Increase in signaling Protein
phosphatase inhibitors DARPP-32 PKA,
PKG Increase in inhibitory activity Inhibitor
1 PKA Increase in inhibitory activity Inhibitor
2 GSK3 Decrease in inhibitory activity Cytoskelet
al proteins MAP-2 PKA Promotion of microtubule
assembly Tau cdk-5 and others Increase in
aggregation Myosin light chain MLC-K Increase
in binding to actin Synaptic vesicle proteins
Synapsin PKA, CaM-KII Increase in
neurotransmitter release Transcription factors
CREB PKA, CaM-KIV, RSK Increase in
transactivation STAT proteins JAK Increase in
transactivation
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Components and Primary Structure of DNA
Deoxyribose and
Purines
PyrimidinesPhosphodiester Backbone
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DNA Base Paring
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The Watson-Crick Double Helix (The B DNA Model)
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Cell Division (Mitosis or M Phase)Requires DNA
Replication
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A Model for DNA ReplicationTemplate Strands
and Daughter Molecules
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RNA
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Basic Principle of TranscriptionThe Process of
Generating mRNA From DNA
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Protein Synthesis in Eucaryotes
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Transcription and RNA Splicing of Exons and
Alternative Splicing of Different Exons
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TranslationThe Process of Generating a
Peptide (Protein) From mRNA
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The Structure of a Typical tRNA
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The Genetic Code
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A Series of Ribosomes Simultaneously Translate
the Same RNA Molecule
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Control of Gene Expression
Inhibition by Nucleosomal Structure of
Chromatin Transcriptional Control
Cis-Regulatory Elements - Promotor Elements ?
Core Promotor ? Enhancer Elements ? Repressor
Elements Trans-Regulatory Elements -
Transcription Factors ? CREB Family (Cyclic
AMP Response Element Binding
Protein) TGACGTCA ? AP-1 Family Fos and
Jun Immediate Early Genes ? Steroid Hormone
Receptors
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The Packaging of Chromatin
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Removal of the Inhibition of Gene Expression
Produced by the Nucleosomal Structure of Chromatin
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Cis and Trans Regulatory ElementsAct to Regulate
Transcription Initiation
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Looping of DNA Allows Activator or Repressor
Proteins to Interact with Basal
Transcription/Polymerase II Complex
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Intracellular Pathways Underlyingthe Regulation
of Gene Expression
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Regulation of CREB Phosphorylation
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Regulatory Elements of the c-Fos Gene Can Be
Activated By Various First Messengers That Act
Through Different Second Messenger Cascades
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Different Fos-Like Proteins (or AKA
Fos-Related Antigens FRAs) Activated by Acute
Stimuli in Neurons HaveDifferent Latencies for
Induction and Different Time Courses
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Human Chromosomes, Genes, DNA and Proteins Some
Facts and Figures

• There are 23 pairs (diploid) of chromosomes
  22 pairs somatic and 1 pair of sex chromosomes.
• The length of unwound DNA in each somatic cell
  is 5? to 6?.
• The entire human genome contains about 3
  billion base pairs.
• The average chromosome contains about 150
  million base pairs.
• Only about 2-10 of chromosomal DNA contains
  protein-coding sequences of nucleotide bases.
• As recently as a few years ago, it was
  estimated that there are as many as 100,000 genes
  in the human genome.
• More recent estimates place the number of
  genes at 30,000. However as a result of
  alternative splicing of mRNA there are 5 times
  this number of proteins.
• Alternative base sequences in a given gene
  constitutes different alleles or polymorphisms.
• Alterations in genes (i.e., different alleles)
  may confer either adaptive advantages or
  disadvantages to organisms.
• Alterations in chromosome numbers are likely
  to be maladaptive.

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Genetic "Errors"

• Errors in meiosis
• Errors in the sequence of DNA bases in
  chromosomes

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Map of Normal Human Chromosomes at Metaphase
Karyotype Ideogram Autosomes Sex chromosomes
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The Sexual Reproduction Cycle Seen in Higher
Eucaryotes Involves an Alteration of a Haploid
Generation of Cells with a Diploid Generation of
Cells
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Comparison of Meiosis with Normal Cell Division
(Mitosis)
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Meiosis and Independent Assortment
ofNon-Homologous Chromosomes
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Errors of Sorting and Distributing Chromosomes

• Errors taking place in meiosis produce altered
  numbers of chromosomes
• - Diploidy normal number of chromosomes
• - Polyploidy deviation from diploidy of all
  chromosomes
• - Aneuploidy deviation of a single chromosome
• ? Nullisomy
• ? Monosomy
• ? Trisomy

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The Karyotype of an Individual with Down's
Syndrome
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Aneuploidies in Human Populations

• Chromosome ApproximateCondition
  Involved Frequency
• Involving Gain of an Autosomal Chromosome
• Edward's Syndrome 18 1 in
  5,000
• Pateau's Syndrome 13 1 in
  5,000
• Down's Syndrome 21 1 in
  750
• Sex Chromosome Aneuploidies
• Turner's Syndrome XO 1
  in 10,000
• Klinefelter's Syndrome XXY 1 in
  2,000
• Triple X Syndrome XXX
  1 in 2,000

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Sexual and Genetic Errors

• Mutations or "errors" in the ordering of the
  sequence of bases or the structure of DNA.
• - Gross rearrangement of DNA
• - Subtle changes in one or a few bases

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Barbara McClintock (1902-1992)
Cornell University 1983 Nobel Prize
Microscopic evidence for breakage and
rearrangements of chromosome segments Zea mays
(corn)
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Crossing Over During Meiotic Prophase I
(C)
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Gross Mutations Arising From Rearrangement of
Chromosome Segments During Meiotic Prophase I

• Deletions
• Insertions
• Rearrangements

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More Subtle Mutations of DNA

• DNA Polymorphisms
• ? Single nucleotide substitutions occur in 1 in
  300-1000 nucleotides in
• genomic DNA
• ? Point Mutations
• - Missense
• - Nonsense
• - Frame shift
• - CG dinucleotides are mutation hot spots
• CG to TG
• CG to CA
• ? Consequences of mutations
• - Loss of function
• - Gain of function
• - Promoter mutations
• - mRNA truncation
• - mRNA run on
• ? Trinucleotide repeat mutations

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Examples of the Consequences of Mutation

• ? Mutations affecting amino acid sequence, but
  not gene expression - beta-hemoglobinopathies e
  .g., sickle cell disease - loss of function
  metabolism
• ? Mutations affecting gene expression, deletions,
  insertions or other rearrangements that result in
  no gene expression e.g., beta-thalassemia
• ? Transcription mutations - promoter area
  mutations that result in reduced or increased
  gene expression
• ? RNA splicing mutations
• ? Translation mutations - initiation codon for
  protein synthesis altered
• ? Unstable protein mutants

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Examples of Human Genetic Defects

• Disease Frequency
• Sickle cell anemia 1/400 (US blacks)
• Defect in beta-chain of hemoglobin.
  Heterozygotes are common in
• resistant to malaria, but homozygotes are sick.
  First Africa
• molecular disease to be identified.
• Phenylketonuria 1/5,000
• Mental retardation due to lack of enzyme. Can
  be (W. Europe)
• detected in newborn babies by analysis of
  urine. rare elsewhere
• Special diet prevents symptoms.
• Adenosine deaminase deficiency Rare
• Enzyme defect causes immune deficiency.
• First defect approved for human gene therapy.
• Cystic fibrosis 1/2,000 (whites)
• Defective ion transport with indirect effects on
  mucus rare in Asians
• secretion in lungs.

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The Sequence of Amino Acids in ? and ? Chains of
Normal Hemoglobin and "Fingerprints" of Normal
and Sickle-Cell Hemoglobin
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Phenylketonuria (PKU) An Example of a "Simple"
Inborn Error of Metabolism

• Phenylalanine accumulates in the blood because
  of a block in conversion to tyrosine (lack of
  phenylalanine hydroxylase).
• If undetected and untreated, PKU leads to
  profound mental retardation.
• Affects 1 in 5,000 newborns in Western Europe.
• Autosomal recessive trait.
• The heterozygous trait is rather common (?2).
• Therefore 2 heterozygous parents have a 1 in 4
  chance of having a child with PKU.
• PKU can be detected at birth (Guthrie Test).
• Treatment is feeding diet low in phenylalanine
  and rich in tyrosine.
• Phenylalanine hydroxylase gene (PKU) mapped on
  human chromosome 12q24.1.

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Conversion of Phenylalanine to Tyrosine, Showing
the Phenylalanine Hydroxylase and
Dihydropteridine Reductase Reactions
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http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?dbO
MIM
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Strategies Used in Locating and Identifying Genes
and the Genetic Contribution to Diseases

• Examples of
• Strategy Application
  Comments Uses in Psychiatry
• Linkage Gene mapping May use extended pedigrees
  or relative pairs Bipolar affective disorder
• analysis
• Many statistical variants Schizophrenia
• Usually provides a gene location
  without Alcohol dependence
• specifically identifying the gene
• Family Identification Uses affected probands
  plus relatives Tourette's syndrome
• association of phenotypic (usually parents)
• effects of
• specific Several statistical
  variants Schizophrenia
• genes
• Identifies linkage disequilibrium of a gene
• with a phenotype, which does not
• necessarily identify the specific
• polymorphism responsible for the effect

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ADH, alcohol dehydrogenases ALDH, acetaldehyde
dehydrogenases
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The Basis of Classic Gene Mapping
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Linkage Analysis
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Modes of Inheritance of Single Gene
Disorders (i.e., Mendelian Inheritance) (a)
Autosomal Dominant, (b) Autosomal Recessive, and
(c) X-Linked
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The Benefits of Sexual Reproduction

• In multicellular animals the diploid phase is
  complex and long, the haploid phase is simple and
  fleeting.
• Sexual reproduction gives a competitive
  advantage to organisms in an unpredictably
  variable environment.
• New genes evolve by duplication and
  divergence.
• Sexual reproduction helps keep a diploid
  species diploid.
• A diploid species has a spare copy of each
  gene that can mutate to serve a new function.
• A diploid species can rapidly enrich its
  genome by adding new genes.

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All Mutations Are Not Necessarily Bad
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Francis Galton (1822-1911)
Hypothesized that intellectual abilities must
follow the rules of inheritance in the same way
as the physical traits of height and eye color.
Heredity Genius (published in 1889). Coined
the term "eugenics" First to use the
experimental approach of twin studies.
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Genetics Contribute to Determining
Behaviorand Behavior Contributes to
Determination ofFitness and the Process of
Natural Selection
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Genomics Insights from the Human Genome Project

• The human genome contains 3 billion chemical
  nucleotide bases (A, C, T, and G).
• The average gene consists of 3000 bases, but
  sizes vary greatly, with the largest known human
  gene being dystrophin at 2.4 million bases.
• Genes have been pinpointed and particular
  sequences in those genes associated with numerous
  diseases and disorders including breast cancer,
  muscle disease, deafness, and blindness.
• The functions are unknown for more than 50 of
  discovered genes.
• The human genome sequence is almost (99.9)
  exactly the same in all people.
• Genes appear to be concentrated in random
  areas along the genome, with vast expanses of
  noncoding DNA between.
• Repeat sequences that do not code for proteins
  make up at least 50 of the human genome.
• Repeat sequences are thought to have no direct
  functions, but they shed light on chromosome
  structure and dynamics.
• Over time, these repeats reshape the genome by
  rearranging it, thereby creating entirely new
  genes or modifying and reshuffling existing
  genes.
• The human genome has a much greater portion
  (50) of repeat sequences than the mustard weed
  (11), the worm (7), and the fly (3).
• Over 40 of the predicted human proteins share
  similarity with fruit-fly or worm proteins.
• Chromosome 1 (the largest human chromosome)
  has the most genes (2968), and the Y chromosome
  has the fewest (231).
• About 3 million locations have been identified
  where single-base DNA differences occur in
  humans. This information promises to
  revolutionize the processes of finding DNA
  sequences associated with such common diseases as
  cardiovascular disease, diabetes, arthritis, and
  cancers.
• Human Genome Program, U.S. Department of Energy

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Impact of Genetics on Biomedical Knowledge and
Treatment Over the Next 40 Years

• 2010
• Predictive genetic tests for 25 conditions.
• Gene therapy effective for a few conditions.
• Many primary care physicians begin to practice
  genetic medicine.
• Preimplantation diagnosis widely available, but
  use widely debated.
• Effective legislative solutions to genetic
  discrimination and privacy in place in the U.S.
• Access to genetic medicine inequitable,
  especially in developing world.
• 2020
• Gene-based designer drugs for decisions such as
  diabetes and hypertension available.
• Cancer therapy is precisely targeted.
• Dx/Rx pharmacogenomic approach is standard
  procedure for many drugs.
• The genetic cause(s) of mental illness is
  identified.
• Homologous recombination in the germ line is
  possible.
• 2030
• Genes involved in aging process fully
  catalogued.
• Clinical trials underway to extend lifespan.
• Full computer model of human cell replaces many
  laboratory experiments.
• Complete genetic sequence of individual is
  routine and costs less than 1,000.
• Major anti-technology movements active in U.S.
  and elsewhere.

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