• Chapter 19
• Microbial Models: The
Genetics of Viruses and
Bacteria

• Virus: “poison” (Latin); infectious particles consisting of a nucleic acid in a protein coat
• Capsid; (viral envelopes); DNA or
RNA
• Bacteriophages
(phages)

• 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)

• 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

• Retroviruses: transcribe
DNA from an RNA template (RNA--->DNA)
• Reverse transcriptase
(catalyzing enzyme)
• HIV--->AIDS

• 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

• Nucleoid: region in bacterium densely packed with DNA
(no membrane)
• Plasmids: circles of DNA small
• Reproduction: binary fission (asexual)

• 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

 direct transfer of genetic material; cytoplasmic bridges; pili; sexual

• 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”

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

• 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

• 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)

• Oncogene
•cancer-causing genes
• Proto-oncogene
•normal cellular genes
• How?
movement of DNA; chromosome
1fragments 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. BrownSimpson’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

• 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

• 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)

• 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

• PCR (polymerase chain reaction)
• Gel electrophoresis
• Restriction fragment analysis (RFLPs)
• Southern blotting
• DNA sequencing
• Human genome project

• 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.

• Gel electrophoresis: separates nucleic acids or proteins on the basis of size or electrical charge creating DNA bands of the same length

• Restriction fragment length polymorphisms (RFLPs)
• Southern blotting: process that reveals sequences and the
RFLPs in a DNA sequence
• DNA Fingerprinting

• 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.

• Determination of nucleotide sequences (Sanger method, sequencing machine)
• Genomics: the study of genomes based on DNA sequences
• Human Genome Project

• Diagnosis of disease
• Human gene therapy
• Pharmaceutical products
(vaccines)
• Forensics
• Animal husbandry (transgenic organisms)
• Genetic engineering in plants
• Ethical concerns?

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
Cytogenetic map
Fluorescence In Situ
Hybridization
Genes located by FISH
Chromosome bands
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 software.

• 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

• 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

• 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%)
Introns and regulatory sequences
(24%)
Unique noncoding
DNA (15%)
L1 sequences
(17%)
Alu elements
(10%)
Simple sequence
DNA (3%)
Repetitive
DNA unrelated to transposable elements
(15%)
Large-segment duplications (5–6%)

• 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
Reverse transcriptase
(b) Retrotransposon movement
Insertion
Animation
Quiz 5 -
Transposons:
Shifting
Segments of the Genome

• The first evidence for wandering DNA segments came from geneticist Barbara
McClintock’s breeding experiments with
Indian corn

Fig. 21-8

• 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 Transcription unit
DNA rRNA
18S
28S
5.8S
28S
5.8S
18S
(a) Part of the ribosomal RNA gene family
Heme

-Globin
Hemoglobin

-Globin


-Globin gene family
Chromosome 16




2


1

2

1




-Globin gene family
Chromosome 11
G

A
 

 
Embryo
Fetus and adult Embryo Fetus
(b) The human

-globin and

-globin gene families
Adult

• 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

• 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
Nonsister chromatids element
Crossover
Incorrect pairing of two homologs during meiosis and

• 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