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• Chapter 19
• Microbial Models: The
Genetics of Viruses and
Bacteria
Viral structure
• Virus: “poison” (Latin);
infectious particles
consisting of a nucleic
acid in a protein coat
• Capsid; (viral
envelopes); DNA or
RNA
• Bacteriophages
(phages)
Viral reproduction: Lytic Cycle
• Host range: infection of a
limited range of host cells
(receptor molecules on the
surface of cells)
• The lytic cycle:
1- attachment
2- injection
3- hydrolyzation
4- assembly
5- release
• Results in death of host cell
• Virulent virus (phage
reproduction only by the lytic
cycle)
Viral reproduction: Lysogenic Cycle
• Genome replicated w/o
destroying the host cell
• Genetic material of virus
becomes incorporated
into the host cell DNA
(prophage DNA)
• Temperate virus (phages
capable of using the lytic
and lysogenic cycles)
• May give rise to lytic cycle
RNA viruses
• Retroviruses: transcribe
DNA from an RNA
template (RNA--->DNA)
• Reverse transcriptase
(catalyzing enzyme)
• HIV--->AIDS
Viroids and Prions
• Viroids: tiny, naked
circular RNA that infect
plants; do not code for
proteins, but use cellular
enzymes to reproduce;
stunt plant growth
• Prions: “infectious
proteins”; “mad cow
disease”; trigger chain
reaction conversions; a
transmissible protein
Bacterial genetics
• Nucleoid:
region in bacterium
densely packed with DNA
(no membrane)
• Plasmids:
circles of DNA
small
• Reproduction:
binary fission (asexual)
Bacterial DNA-transfer processes
•
Transformation: genotype alteration by the
uptake of naked, foreign DNA from the
environment (Griffith expt.)
•
Transduction: phages that carry
bacterial genes from 1 host cell to another
•generalized - random transfer of host cell
chromosome
•specialized - incorporation of prophage
DNA into host chromosome
Conjugation

direct transfer of genetic material; cytoplasmic bridges; pili; sexual
Bacterial Plasmids
• Small, circular, self-replicating DNA separate from the bacterial
chromosome
• F (fertility) Plasmid: codes for the production of sex pili (F+ or F-)
• R (resistance) Plasmid: codes for antibiotic drug resistance
• Transposons: transposable genetic element; piece of DNA that can move
from one location to another in a cell’s genome (chromosome to plasmid,
plasmid to plasmid, etc.); “jumping genes”
Operons, I
•
•
•
•
•
•
Unit of genetic function consisting of coordinately
related clusters of genes with related functions
(transcription unit)
Repressible (trp operon):
tryptophan (a.a.) synthesis
promoter: RNA polymerase binding
site; begins transcription
operator: controls access of RNA
polymerase to genes
(tryptophan not present)
repressor: protein that binds to
operator and prevents attachment of
RNA polymerase - coded from a
regulatory gene (tryptophan present acts as a corepressor)
transcription is repressed
– when tryptophan binds to a
regulatory protein
Operons, II
• Inducible (lac operon):
- lactose metabolism
• lactose not present:
repressor active, operon off;
no transcription for lactose
enzymes
• lactose present:
repressor inactive, operon
on; inducer molecule
inactivates protein repressor
(allolactose)
•
Transcription is stimulated when
inducer binds to a regulatory
protein
Unit of genetic function consisting of
coordinately related clusters of genes with
related functions (transcription unit)
• Chapter 19
• The Organization and
Control of Eukaryotic
Genomes
Chromatin
• Def: complex of DNA and proteins
• DNA Packing
•histone protein (+ charged amino acids phosphates of DNA are - charged)
• Nucleosome
•”beads on a string”; basic unit of DNA
packing
• Heterochromatin
•highly condensed interphase DNA
(can not be transcribed)
• Euchromatin
•less compacted interphase DNA (can be
transcribed)
Molecular Biology of Cancer
•
•
•
•
Oncogene
•cancer-causing genes
Proto-oncogene
•normal cellular genes
How?
1movement of DNA; chromosome
fragments that have rejoined incorrectly
2-amplification; increases the number of
copies of proto-oncogenes
3-proto-oncogene point mutation; protein
product more active or more resistant to
degradation
Tumor-suppressor genes
•changes in genes that prevent
uncontrolled cell growth (cancer growth
stimulated by the absence of suppression)
• Chapter 20 and 21
BioTechnology
Genomics
&
O.J. Simpson capital murder case,1/95-9/95
•
•
Odds of blood in Ford Bronco not being R. Goldman’s:
• 6.5 billion to 1
• Odds of blood on socks in bedroom not being N. Brown-Simpson’s:
• 8.5 billion to 1
Odds of blood on glove not being from R. Goldman, N. Brown-Simpson, and O.J.
Simpson:
• 21.5 billion to 1
• Number of people on planet earth:
• 6.1 billion
• Odds of being struck by lightning in the U.S.:
• 2.8 million to 1
• Odds of winning the Illinois Big Game lottery:
• 76 million to 1
• Odds of getting killed driving to the gas station to buy a lottery ticket
• 4.5 million to 1
• Odds of seeing 3 albino deer at the same time:
• 85 million to 1
• Odds of having quintuplets:
• 85 million to 1
• Odds of being struck by a meteorite:
• 10 trillion to 1
Recombinant DNA
• Definition: DNA in which genes
from 2 different sources are linked
• Genetic engineering: direct
manipulation of genes for
practical purposes
• Biotechnology: manipulation of
organisms or their components to
perform practical tasks or provide
useful products
Bacterial plasmids in gene cloning
DNA Cloning
•
•
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Restriction enzymes (endonucleases):
in nature, these enzymes protect bacteria from
intruding DNA; they cut up the DNA (restriction);
very specific
Restriction site:
recognition sequence for a particular restriction
enzyme
Restriction fragments:
segments of DNA cut by restriction enzymes in a
reproducable way
Sticky end:
short extensions of restriction fragments
DNA ligase:
enzyme that can join the sticky ends of DNA
fragments
Cloning vector:
DNA molecule that can carry foreign DNA into a cell
and replicate there (usually bacterial plasmids)
Steps for eukaryotic gene cloning
•
•
•
•
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Isolation of cloning vector
(bacterial plasmid) & gene-source
DNA (gene of interest)
Insertion of gene-source DNA into
the cloning vector using the same
restriction enzyme; bind the
fragmented DNA with DNA ligase
Introduction of cloning vector into
cells (transformation by bacterial
cells)
Cloning of cells (and foreign genes)
Identification of cell clones
carrying the gene of interest
DNA Analysis & Genomics
• PCR (polymerase chain
reaction)
• Gel electrophoresis
• Restriction fragment
analysis (RFLPs)
• Southern blotting
• DNA sequencing
• Human genome project
Polymerase chain reaction (PCR)
• Amplification of any piece
of DNA without cells (in
vitro)
• Materials: heat, DNA
polymerase, nucleotides,
single-stranded DNA
primers
• Applications: fossils,
forensics, prenatal
diagnosis, etc.
DNA Analysis
• Gel electrophoresis: separates nucleic acids or proteins on the basis of
size or electrical charge creating DNA bands of the same length
Restriction fragment analysis
• Restriction fragment length polymorphisms (RFLPs)
• Southern blotting: process that reveals sequences and the
RFLPs in a DNA sequence
• DNA Fingerprinting
Southern Blotting
•
Southern blotting: process that reveals sequences and the RFLPs in a DNA sequence
•
Southern blotting is a laboratory technique used to detect a specific DNA sequence
in a blood or tissue sample. A restriction enzyme is used to cut a sample of DNA into
fragments that are separated using gel electrophoresis. The DNA fragments are
transferred out of the gel to the surface of a membrane. The membrane is exposed
to a DNA probe labeled with a radioactive or chemical tag. If the probe binds to the
membrane, then the probe sequence is present in the sample.
Southern Blotting
DNA Sequencing
• Determination of nucleotide
sequences (Sanger method,
sequencing machine)
• Genomics: the study of
genomes based on DNA
sequences
• Human Genome Project
Practical DNA Technology Uses
• Diagnosis of disease
• Human gene therapy
• Pharmaceutical products
(vaccines)
• Forensics
• Animal husbandry (transgenic
organisms)
• Genetic engineering in plants
• Ethical concerns?
GENOMICS
AP Biology Chap 21
• Genomes – set of genes and their interactions
• Bioinformatics – computational methods of gene
analysis
- NCBI National Center Biotechnology
Information – database of DNA
sequences and proteins (proteomes)
NCBI HomePage
• The most ambitious mapping project to date has
been the sequencing of the human genome
• Officially begun as the Human Genome Project
in 1990, the sequencing was largely completed
by 2003
• The project had three stages:
– Genetic (or linkage) mapping
– Physical mapping
– DNA sequencing
Fig. 21-2-4
Chromosome
bands
Cytogenetic map
Fluorescence In Situ
Hybridization
Genes located
by FISH
1
Linkage mapping
Genetic
markers
2
Physical mapping
Overlapping
fragments
3
DNA sequencing
• A linkage map (genetic map) maps the
location of several thousand genetic markers
on each chromosome
• A genetic marker is a gene or other
identifiable DNA sequence
• Recombination frequencies are used to
determine the order and relative distances
between genetic markers
Fig. 21-3-3
1 Cut the DNA
into overlapping
fragments short enough
for sequencing
2 Clone the fragments
in plasmid or phage
vectors.
3 Sequence each
fragment.
4 Order the
sequences into
one overall
sequence
with computer
• A complete haploid set of human chromosomes
consists of 3.2 billion base pairs
By summer 2007,
genomes had been
sequenced for 500
bacteria, 45
archaea, and 65
eukaryotes
including
vertebrates,
invertebrates, and
plants
What do we know?
• Humans have 20,488 genes
• With alternate gene splicing, we can make
75,000 polypeptides
• Genomes of most bacteria and archaea range
from 1 to 6 million base pairs (Mb); genomes
of eukaryotes are usually larger
• Free-living bacteria and archaea have
1,500 to 7,500 genes
• Unicellular fungi have from about 5,000
genes and multicellular eukaryotes from
40,000 genes
• Number of genes is not correlated to
genome size
• Humans and other mammals have the
lowest gene density, or number of genes,
in a given length of DNA
Table 21-1
About the human genome…
•
•
•
•
•
Only 1.5% codes for proteins, rRNA and tRNA
The rest is used for
regulatory sequences and introns 24%
pseudogenes (nonfunctioning genes) 15%
repetitive DNA 59%
Fig. 21-7
Exons (regions of genes coding for protein
or giving rise to rRNA or tRNA) (1.5%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
L1
sequences
(17%)
Introns and
regulatory
sequences
(24%)
Unique
noncoding
DNA (15%)
Repetitive
DNA
unrelated to
transposable
elements
(15%)
Alu elements
(10%)
Simple sequence
DNA (3%)
Large-segment
duplications (5–6%)
Repetitive DNA
• 44% transposable elements (jumping genes)
•
- Transposons - cut and paste (ex Alu in
primates)
•
- Most of these are retrotransposons –
cut, copy to RNA, RT to DNA, and
paste
(ex Line1 or L1)
• 15% – large segment and simple sequence DNA
•
- small ones STR - Short Tandem Repeats
often used in centromeres and telomeres
Fig. 21-9
Transposon
DNA of
genome
Transposon
is copied
New copy of
transposon
Insertion
Mobile transposon
(a) Transposon movement (“copy-and-paste” mechanism)
Retrotransposon
New copy of
retrotransposon
RNA
Insertion
Reverse
transcriptase
(b) Retrotransposon movement
Animation
Quiz 5 Transposons:
Shifting
Segments of
the Genome
“Jumping Genes”
• The first evidence for wandering DNA
segments came from geneticist Barbara
McClintock’s breeding experiments with
Indian corn
Fig. 21-8
Genes
• Many eukaryotic genes are present in one
copy per haploid set of chromosomes
• More than ½ occur in multigene families –
such as for RNA products and hemoglobin
Fig. 21-10
DNA
RNA transcripts
Nontranscribed
spacer
-Globin
Heme
Hemoglobin
Transcription unit
-Globin
DNA
18S
5.8S
28S
rRNA
-Globin gene family
-Globin gene family
Chromosome 16
Chromosome 11

     2 1  
2

G
A
1



5.8S
28S
18S
(a) Part of the ribosomal RNA gene family
Embryo
Fetus
and adult
Embryo
Fetus
(b) The human -globin and -globin gene families
Adult
Genomic Evolution
• Duplication of chromosome sets (polyploidy)
• Chromosome alteration – duplications,
inversions
• Exon shuffling
• Transposons
• Humans have 23 pairs of chromosomes,
while chimpanzees have 24 pairs
• Following the divergence of humans and
chimpanzees from a common ancestor, two
ancestral chromosomes fused in the human
line
Why we
Are
Smarter!
• The rate of duplications and inversions seems to
have accelerated about 100 million years ago
• This coincides with when large dinosaurs went
extinct and mammals diversified
How transposons affect genomes
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•
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Multiple copies may facilitate crossing-over
Insertion may block protein sequence
Insertion may affect promoters
Insertion may carry new genes to an area
May create new sites for alternative splicing in
RNA
Fig. 21-12
TransposableGene
element
Nonsister
chromatids
Crossover
Incorrect pairing
of two homologs
during meiosis
and
Comparing evolutionary
developmental processes
“evo-devo”
• Homeobox – 180 nucleotides that regulate
gene expression during development
• Found in many organisms, both inverts and
verts
• Called “hox genes” in mammals
• You should read “Our Inner Fish”!
Fig. 21-17
Adult
fruit fly
Fruit fly embryo
(10 hours)
Fly
chromosome
Mouse
chromosomes
Mouse embryo
(12 days)
Adult mouse
• Sometimes small changes in regulatory
sequences of certain genes lead to
major changes in body form.
• For example, variation in Hox gene
expression controls variation in legbearing segments of crustaceans and
insects
for example, flies with feet in place of
antennae.