Bi 341 Chapter 1 The Genetic Code of Genes and Genomes & Introduction - KB

BI 341 INTRODUCTION
Kim H. Brown, PhD

Welcome
• About me: Dr. Kim H. Brown
B.Sc. Biology, Northern Arizona University, 1993
M. Sc. Zoology, Washington State University, 2000
PhD Zoology Washington State University, 2004
Post Doctoral Fellow University of Idaho, 2004-2008
Post Doctoral Fellow Harvard Medical School/Brigham
and Women’s Hospital, 2008-20012
Assistant Professor, PSU 2012-Present
Office: SRTC 334
Email: kibr2@pdx.edu
Office hours: M-Th 1:00-2:00pm or By Appointment
Syllabus
The course syllabus can be
found on our D2L webpage.
It is your ultimate resources
for navigating this course
https://d2l.pdx.edu
Why study genetics?
• Why am I here?
• Who am I?
• Philosophy
• Religion
• Art
• Self help books
• SCIENCE
Science & the big questions
Bi 211-213 can answer “Why am I here”
Chemical evolution: Biological macromolecules
emerge from the primordial soup and build life, order
from chaos
“We’re what happens when two substances collide, and by
all accounts we really should have died.” -Andrew Bird
Science & the big questions
Who am I? We can find some
answers in genetics & Bi 341
Genes: The blueprints of
individuality
Heredity: Determines which
genes each individual will get
out of the gene pool
Evolution: The reason why our
genes are what they are
e.g. which genes are present in
the gene pool
Evolution and Natural Selection
• Evolution:
– It is a change in the characteristics of a population over
time
– It means that species are related to one another and can
change through time
• Natural selection explains how evolution occurs
http://science.discovery.com/tv-
shows/greatest-discoveries/videos/100-
greatest-discoveries-shorts-natural-
selection.htm
Genes & Traits
Any observable property of an
organism is a trait
– Actions of gene products
(proteins) produce
visible traits such as
eye color and hair color
Genes are contained on
chromosomes
– Chromosomes are found
in the nucleus of human
cells and other higher
organisms Image: dream designs / FreeDigitalPhotos.net
How Do Scientists Study Genes?
Karyotype: A complete set of
chromosomes from a cell that
has been photographed during
cell division and arranged by
size and shape in a standard
order
Cytogenetics: Study of the

organization and arrangement
of genes on a chromosome,
and study of chromosome
number and structure A karyotype arranges the
chromosomes in a standard
format so they can be
evaluated for abnormalities
How Do Scientists Study
Genes?
Molecular genetics
– The study of genetic events
at the molecular level
– Identification, isolation, and
analysis of specific genes
Population genetics
– The study of inherited
variation in populations of
individuals
– Forces, such as
environment, that result in
changing gene frequencies
over generations
How Do Scientists Study
Genes?
Transmission genetics
– Study inheritance
patterns and how traits
are passed from
generation to generation
Pedigree analysis
– Construction of family
trees used to follow A pedigree represents the
transmission of genetic inheritance of a trait through
traits in families several generations of a
(inheritance) family.
Genetics in Basic and Applied
Research
Recombinant DNA
technology
– Techniques whereby
DNA fragments are
linked to self-
replicating vectors,
which are replicated in
a host cell, often
bacteria Glowing Animals:
– Genetically modified http://dotsub.com/view/9
organisms: Carry and c05baba-72fe-4640-95af-
express genes from 2e14c6ecb85a
another species
Genetics in Basic and Applied
Research
Clone: Genetically identical molecules, cells, or organisms,
all derived from a single source or parent
Gene therapy: Normal genes are transplanted into
humans with defective copies to treat genetic diseases
– Intro to genetic engineering:

http://www.youtube.com/watch?v=HZmZ161nj
r8
Applied Biotechnologies
Medicine
– Vaccines
– Customized proteins
for treating disease
Agriculture
– Increased crop yields
– Lower fat content
– Disease-resistant Transgenic corn has been genetically modified
to be resistant to herbicides used to kill weeds.
crops
The Human Genome Project
• Begun in 1990 with the aim of determining the entire sequence of
the 3.2 billion nucleotides of the human genome
• Analysis of single nucleotide polymorphisms (changes) show
differences among individuals at the molecular level
• Genomes of many other organisms have been sequenced, too
Genetic Testing
• Genes associated with hundreds of genetic diseases
have been cloned and are used to develop genetic tests
– Cystic fibrosis
– Sickle cell anemia
– Muscular dystrophy
– Phenylketonuria (PKU)
How does applied genetics affect
society?
– New technologies permit the identification of and determination of
function of all 25,000 human genes
– Genes associated with hundreds of genetic diseases have been
cloned and used to develop genetics tests and new treatments
– In vitro fertilization and genetic testing help families make
informed decision concerning family planning
– Stem-cell research offers hope for treating many diseases
– The use of recombinant DNA technology or biotechnology allows
the production of novel plants and animals - GMOs
Eugenics and the misuse of
genetics has affected social policy
Eugenics: the attempt to improve the human species by
selective breeding
• Early to mid- 1900s: US attempted
to affect the make up of the
population by preventing
immigration and the introduction of
less desirable traits
• Laws restricting reproductive rights
and requiring certain individuals to
be sterilized were instituted
• Used by Nazis in Germany to
promote mass killings of individuals
believed to be genetically inferior
and ultimately genocide
ELSI
• Ethical, Legal, and Social Issues
• Part of Human Genome Project (1990)
• Research on genomics and society
– How should genomic information be used?
– How will it affect health care?
– How does it affect how we think about health,
disease, and personal responsibility?
– What is the effect on policy?
– Many resources and links here
What Choices Do We Make?
• With the completion of the Human
Genome Project, new methods of
genetic testing, and the ability to
transfer genes, we are faced with
many personal and social
decisions
• Ethical use of genetic information
and biotechnology requires
participation by a broad cross
section of society
• We can make informed personal
decisions and formulate public
policy only if we have a knowledge
of genetics and how genetics is
used in biotechnology.
PORTLAND STATE BI 341
CHAPTER 1: THE GENETIC CODE OF GENES
AND GENOMES
Radhika Reddy, PhD

Objectives
1. Review central concepts surrounding DNA
1. Road to the discovery of DNA as the molecule of heredity
1. Avery, McLeod, McCarty Experiment
2. The Hershey–Chase Experiment
2. Structure and function of DNA
1. Watson and Crick, the double helix
2. DNA replication: the introduction of mutations at this step and its
contribution to genetic diversity
3. The Central Dogma of Biology
1. Transcription
2. Translation
3. Gene function
1. Experiments surrounding one-gene-one-enzyme hypothesis: Beadle
and Tatum
2. The interaction between genes and environment to determine traits
3. Gene mutation and complementation groups
4. The contribution of gene mutation to evolution
DNA is the molecule of heredity
• Inherited traits are
determined by the elements
of heredity (genes), that are
transmitted from parents to
offspring in reproduction
• Genes are composed of the

chemical deoxyribonucleic
acid or DNA
Figure 01.06: Molecular structure

of a DNA double helix.
DNA is the molecule of heredity
• DNA was discovered by
Friedrich Miescher in 1869
• In 1920s microscopic
studies with special
stains showed that DNA
is present in
chromosomes
• In 1944 Avery, McLeod, and

McCarty provided the first
evidence that DNA is the
genetic material
1. Griffith Experiment
• Griffith showed that R
colonies can be
“transformed” into S
colonies
• Avery, McLeod and

McCarty identified the
chemical substance
responsible for changing
rough, non-virulent cells of
Streptococcus pneumoniae
(R) into smooth
encapsulated infectious
cells (S):
Griffith’s experiment demonstrating
bacterial transformation
Avery, McLeod, McCarty Experiment
• Transforming activity
was destroyed by
DNAse, but not by
RNAse or protease
• Conclusion:
transforming factor
that converts R cells
to S cells is DNA
The Hershey–Chase Experiment
• Hershey and Chase T2 virus
infection of the bacterium
Escherichia coli
1. Virus attaches to the cell and
injects its genes into the cell
2. These genes then direct
production of new virus
particles
• During infection, the protein coat,

or capsid, of the original parent
virus is left behind as a ghost
attached to the exterior of the cell
McGraw Hill Animation:
http://highered.mheducatio
n.com/olc/dl/120076/bio21
.swf
Hershey and Chase grew

the virus in the presence of
one of two radioactive
isotopes
• 32Por 35S
• Labeled viruses were
used to infect E. coli
cells
Hypothesis: If genes consist of
proteins
• Then only radioactive
protein found inside the cells
• No radioactive DNA found
inside the cells
Result:
• Radioactive protein found in
ghosts
• Radioactive DNA found in
the cells
• Thus DNA, not protein, is
the genetic material
Objectives
1. Transcription
2. Translation
3. Gene function
and Tatum
The Structure of DNA is a double helix
composed of two intertwined strands
• In 1953 Watson and Crick proposed the
three- dimensional structure of DNA
• DNA is a double-stranded helix
comprised of a linear sequence of
paired subunits: nucleotides
• Each nucleotide contains any one of
four bases: adenine (A), thymine (T),
guanine (G), and cytosine (C)
• A central feature of double-stranded
DNA is complementary base pairing: A
pairs only with T and G with C
(Chargaff’s Rule)
Base pairing in DNA and RNA
• Complementary base pairing specifies the linear
sequence of bases in RNA
• Adenine pairs with uracil; thymine pairs with
adenine; guanine pairs with cytosine
Which of the following is not consistent with Erwin
Chargaff's findings?
a) (A + G)  (C + T)
b) (A + C)  (G + T)
c) AT
d) (C + G)  (A + T)
e) (A + G) / (C + T)  1
Which of the following is not consistent with Erwin
Chargaff's findings?
d) (C + G)  (A + T)
Chargaff's findings were that in double-stranded DNA,

the percentages of A and T nucleotides are the same,
as well as the percentages of C and G nucleotides.
However, the G–C content does not have to be the
same as the A–T content, and it usually differs.
DNA is a double helix
• DNA backbone forms right-
handed helix
• Each DNA strand has polarity =

directionality
• The paired strands are oriented

in opposite directions =
antiparallel
DNA Replication
• Watson-Crick model of DNA
replication:
• The strands of the original
(parental) duplex separate
• Each parental strand serves as
a template for the production of
a complementary daughter
strand by means of A-T and G-
C base pairing
DNA replication review:

http://highered.mheducation.com/site
s/0072943696/student_view0/chapter
3/animation__dna_replication__quiz_
1_.html
Which of the following is not included in the
Watson-Crick model of DNA structure?
a) It is composed of two strands.

b) The two strands are held together by H bonds between
nitrogenous bases.
c) The strands run parallel.
d) The resultant helix is right-handed.
e) The helix has a constant diameter of 20 Å.
Which of the following is not included in the
Watson-Crick model of DNA structure?
c) The strands run parallel
Watson and Crick described the B form of DNA. In this

model, the two strands run in opposite directions, or
antiparallel. This means that for one strand, the 5'
carbon is on top, while for the other strand, the 3'
carbon is on top.
Objectives
1. Transcription
2. Translation
3. Gene function
and Tatum
Genes affect organisms through the
action of proteins
• The genetic information
contained in the
nucleotide sequence of
DNA specifies a
particular type of protein
Stated Clearly Video: What

is DNA
http://statedclearly.com/vide
os/what-is-dna/
Central Dogma
• Central Dogma of
molecular genetics:
• DNA  RNA  Protein
• DNA is the informational

molecule that does not
code for protein directly
but rather acts through an
RNA intermediate
• DNA codes for RNA =
transcription
• RNA codes for protein =
translation
Transcription
• Transcription: production of
messenger RNA strand that
is to DNA template
• RNA contains the base uracil

in place of thymine and the
sugar ribose instead of
deoxyribose
• RNA is synthesized from

template DNA following
strand separation of the
double helix
Translation
• The sequence of bases in
mRNA codes for the sequence
of amino acids in a polypeptide
• The mRNA is translated in a
non-overlapping group of three
bases = codons that specify the
sequence of amino acids in
proteins
• Each codon specifies one amino
acid
• Transfer RNAs (tRNA) contain
triplet base sequences =
anticodons, which are
complementary to codons in
mRNA
Code Redundancy
Translation
• Translation occurs ribosomes which
contain ribosomal RNA (rRNA)
• tRNAs carry amino acids and
position them on ribosomes
• Translation results in the synthesis
of a polypeptide chain composed of
a linear sequence of amino acids
whose order is specified by the
sequence of codons in mRNA
Review of transcription and translation PBS documentary: DNA, The secret of

life: http://www.youtube.com/watch?v=D3fOXt4MrOM
Mutations
• Mutation refers to any heritable
change in a gene
• The change may be:
substitution of one base pair in
DNA for a different base pair;
deletion or addition of base
pairs
• Any mutation that causes the
insertion of an incorrect amino
acid in a protein can impair its
function
Stated Clearly Video : How does new genetic information evolve

http://statedclearly.com/videos/how-does-new-genetic-information-evolve-part-1-
point-mutations/
Objectives
1. Transcription
2. Translation
3. Gene function
and Tatum
Genes affect organisms through the
action of proteins
• In 1908 Archibald Garrod proposed that enzyme defects
result in inborn errors of metabolism = hereditary diseases
• Garrod studied alkaptonuria and identified the abnormal
excreted substance = homogentisic acid
YouTube Video:
Alkaptonuria, a
patient experience
https://www.youtube
.com/watch?v=cSmv
QrSrmLk
Genes and Proteins
• Alkaptonuria: defect In
conversion of a substrate
molecule to a product
• Defective enzyme =
homogentisic acid 1,2
dioxygenase
• homogentisic acid cannot
be converted ti 4-
maleylacetoacetic acid
• This disease is hereditary,
indicating a relationship
between gene mutation and
protein production.
Genes and Proteins
• Another defective enzyme
in the same pathway,
phenylalanine hydroxylase
(PAH), leads to
phenylalanine accumulation
which causes the condition
known as phenylketonuria
(PKU)
• Incidence of PKU,
characterized by severe
mental retardation, is about
one in 8000 among
Caucasian births.
What Do Genes Do?
• Genes carry the instructions
for making and maintaining
an individual
• George Beadle and Edward
Tatum proposed the one
gene one enzyme
hypothesis
• Damage a gene by
creating a mutant
• Then observe the
resulting effect on the
mutant’s phenotype
The One-Gene, One-Enzyme Hypothesis
• Beadle and Tatum used an
experimental approach called
genetic analysis
• Damaged genes in the
bread mold Neurospora
crassa
• Observed that defects in
particular genes resulted in
the mold’s inability to
produce specific proteins
• The results of their experiments inspired their
one-gene, one-enzyme hypothesis
• Proposed that each gene contains the information needed
to make an enzyme
FIGURE 01.F11: BEADLE AND TATUM OBTAINED MUTANTS OF THE
FILAMENTOUS FUNGUS NEUROSPORA CRASSA BY EXPOSING ASEXUAL
SPORES TO X-RAYS OR ULTRAVIOLET LIGHT.
The results of their experiments inspired their one-gene, one-
enzyme hypothesis
• Proposed that each gene contains the information needed to
make an enzyme
METABOLIC PATHWAY
FOR ARGININE
BIOSYNTHESIS
INFERRED FROM
GENETIC ANALYSIS OF
NEUROSPORA
MUTANTS.
The mold used by Beadle and Tatum in
their series of experiments _____.
A) can normally produce all the enzymes it needs to grow on

minimal medium
B) grew on minimal medium after treatment with X-rays
C) were unable to produce any enzymes after treatment with
X-rays
D) all of the above
The mold used by Beadle and Tatum in
their series of experiments _____.
A) can normally produce all the enzymes it needs to grow

on minimal medium
B) grew on minimal medium after treatment with X-rays
C) were unable to produce any enzymes after treatment with
X-rays
D) all of the above
Since the X-ray treated mold was able to grow on media
enriched with metabolites C and D (but not A or B)of this
metabolic pathway:
1 2 3
A ------->B -------> C -------> D
where the numbers are enzymes and the letters are

metabolites, Beadle and Tatum concluded that the mold lacked
enzyme _____.
A) 1
B) 2
C) 3
Since the X-ray treated mold was able to grow on media
enriched with metabolites C and D (but not A or B)of this
metabolic pathway:
1 2 3
A ------->B -------> C -------> D
where the numbers are enzymes and the letters are

metabolites, Beadle and Tatum concluded that the mold
lacked enzyme _____.
A) 1
B) 2
C) 3
Objectives
1. Transcription
2. Translation
3. Gene function
and Tatum
Traits are determined by both genes and
environment
• One gene can affect more than one trait = pleiotropy
• Any trait can be affected by more than one gene as well as
environment
• Most complex traits are affected by multiple genetic and
environmental factors
• Often several genes are involved in genetic disorders and the
severity of a disease may depend upon genetic status and
environmental factors
https://www.23andme.com/gen101/
phenotype/
Complementation
• A mutant screen is a
large-scale, systematic
experiment designed to
isolate multiple new
mutations affecting a
particular trait
• Mutant screens
sometimes isolate
different mutations in the
same gene.
• A complementation test
brings two mutant genes
together in the same cell
or organism.
The Principal of Complementation
• If this cell or organism is
nonmutant, the mutations
are said to complement
one another and it means
that mutations are in the
different genes.
• If the cell or organism is

mutant, the mutations fail
to complement one
another, and it means that
mutations are in the same
gene.
Complementation
• A gene is defined
experimentally as a set of
mutant alleles that make up
one complementation group.
• Any pair of mutant alleles in
such a group fail to
complement one another and
result in an organism with a
mutant phenotype.
• Non complementing
mutations are in the same
complementation group
RESULTS OF COMPLEMENTATION TESTS. (B) AN
EXAMPLE SHOWING INTERPRETING THE RESULTS.
Objectives
1. Transcription
2. Translation
3. Gene function
and Tatum
Evolution: the result of selected mutations
• All creatures on Earth
share many features of the
genetic apparatus and
many aspects of
metabolism
• Groups of related
organisms descend from a
common ancestor
• Evolution occurs whenever
a population of organisms
with a common ancestry
gradually changes in
genetic composition over
time
Figure 01.24: Evolutionary relationships as
inferred from similarities in DNA sequence.
Evolution
• The totality of DNA in a single cell = genome
• The complete set of proteins encoded in the genome

= proteome
• Genes or proteins that derive from a common
ancestral sequence via gene duplication = paralogs
• Genes that share a common ancestral gene via
speciation = orthologs
• The molecular unity of life is seen in comparisons
among genomes and proteomes
Stated Clearly Evolution: Common structural features

http://statedclearly.com/videos/what-is-evolution/

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BI 341 INTRODUCTION

Kim H. Brown, PhD

Cytogenetics: Study of the

– Intro to genetic engineering:

Radhika Reddy, PhD

• Genes are composed of the

Figure 01.06: Molecular structure

• In 1944 Avery, McLeod, and

• Avery, McLeod and

• During infection, the protein coat,

Hershey and Chase grew

Chargaff's findings were that in double-stranded DNA,

• Each DNA strand has polarity =

• The paired strands are oriented

DNA replication review:

a) It is composed of two strands.

c) The strands run parallel

Watson and Crick described the B form of DNA. In this

Stated Clearly Video: What

• DNA is the informational

• RNA contains the base uracil

• RNA is synthesized from

Review of transcription and translation PBS documentary: DNA, The secret of

Stated Clearly Video : How does new genetic information evolve

A) can normally produce all the enzymes it needs to grow on

A) can normally produce all the enzymes it needs to grow

where the numbers are enzymes and the letters are

where the numbers are enzymes and the letters are

• If the cell or organism is

• The complete set of proteins encoded in the genome

Stated Clearly Evolution: Common structural features

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