18.1
I. Discovery of Viruses
A. In 1883, Adolf Mayer discovered he could transmit diseases between plants by rubbing
together sap extracted from diseased leaves onto healthy ones
B. He concluded that the disease must be caused by an extremely small bacterium not able to
see under a microscope
C. Dimitri Ivanovsky demonstrated that the sap was still infectious even after passing through a
filter designed to remove bacteria
D. Martinus Beijerinck ruled out the possibility that the disease was due to a toxin produced by
a bacterium by demonstrating that the infectious agent could reproduce
E. Beijerinck determined that the pathogen could reproduce only within the host
F. The sap could infect subsequent generations
G. In 1935, Wendell Stanley crystallized the pathogen, the tobacco mosaic virus (TMV)
II. Structure of a Virus
A. Smallest viruses are 20nm in diameter
B. Viruses can crystallize, showing they are not cells
C. They are particles consisting of nucleic acid polymers enclosed within proteins, and
sometimes a membrane-like envelope
1. These viral envelopes are derived from the membrane of the host cell
D. The genome of viruses may consist of double-stranded DNA, single-stranded DNA, doublestranded RNA, or single-stranded RNA, depending on the kind of virus
E. The viral genome is usually organized as a single linear or circular molecule of nucleic acid
F. The smallest viruses have only four genes, while the largest have several hundred
G. The capsid is the protein shell enclosing the viral genome
1. Capsids are built from protein subunits called capsomeres
H. Some viruses have accessory structures to help them infect their hosts
I. Some viruses have some host cell viral proteins and glycoproteins
J. The most complex capsids are found in viruses that infect bacteria, called bacteriophages or
phages
1. Referred to as T1, T2, T3, etc.
III.
Viral Reproduction
A. Viruses lack the enzymes for metabolism and the ribosomes for protein synthesis
B. Each type of virus can infect and parasitize only a limited range of host cells, called its host
range
C. Viruses identify host cells by a “lock and key” fit between proteins on the outside of the virus
and specific receptor molecules on the host’s surface
D. Most viruses of eukaryotes attack specific tissues
1. Ex. The AIDS virus binds only to certain white blood cells
E. Basic steps of viral reproduction
1. The genome of the virus enters the host cell
2. Once inside, the viral genome commandeers its host to copy the viral nucleic acids and
proteins
3. The host provides nucleotides, ribosomes, tRNAs, amino acids, ATP, and other
components for making the viral components dictated by viral genes
4. The nucleic acid molecules and capsomeres then self-assemble into viral particles and
exit the cell
5. The simplest type of viral reproductive cycle ends with the exit of many viruses from the
infected host cell, a process that usually damages or destroys the host cell
F. Lytic Cycle
1. Virulent phages reproduce only by a lytic cycle
2. Attachment- the virus finds a host cell and links to a specific region on the cell surface
3. Entry and degradation- the virus injects its DNA into the host cell; the DNA of the host
cell is inactivated
4. Synthesis- The viral DNA takes over making viral proteins and viral nucleic acid. Viral
coats of protein (capsids) are then assembled with the nucleic acids filling the cell with
new virus particles
5. Assembly- the nucleic acids and proteins made by the cell assemble into new virus
particles
6. Release- enzymes dissolve the host cell membrane from within. The cell then bursts
open (cell lysis) and the newly formed virus particles are released, free to infect other
bacterial cells
7. Restriction enzymes help break down foreign DNA to prevent extinction of bacteria
species
a. Chemical modifications to the bacteria’s own DNA prevent its destruction by
restriction nucleases
b. Natural selection also favors phage mutants that are resistant to restriction enzymes
G. Lysogenic cycle
1. Temperate phage- able to reproduce using both the lysogenic and lytic cycle
2. First, the phage attaches to the host cell and injects its DNA
3. Then, factors determine whether to proceed with the Lytic of lysogenic cycle
4. If the lysogenic cycle is chosen, then the phage DNA integrates into the bacterial
chromosomes becoming a prophage
5. As the bacteria reproduces, it makes daughter cells also containing the virus
6. Sometimes, the cell will switch back to the lytic cycle, then releasing all the viruses
within the host
IV. Animal Viruses
A. Viruses equipped with an outer envelope use the envelope to enter the host cell
1. Glycoproteins on the envelope bind to specific receptors on the host’s membrane
2. The envelope fuses with the host’s membrane, transporting the capsid and viral genome
inside
3. After the capsid and viral genome self-assemble, they bud from the host cell covered
with an envelope derived from the host’s plasma membrane, including viral glycoproteins
a. Some viruses have envelopes that are not derived from plasma membrane
i. The envelope of the herpesvirus is derived from the nuclear envelope of the host
B. RNA viruses
1. In some with single-stranded RNA (class IV), the genome acts as mRNA and is
translated directly
2. In others (class V), the RNA genome serves as a template for complementary RNA
strands, which function both as mRNA and as templates for the synthesis of additional
copies of genome RNA
3. All viruses that require RNA synthesis to make mRNA use a viral enzyme that is
packaged with the genome inside the capsid
4. Retroviruses (class VI) have the most complicated life cycles
a. These carry an enzyme called reverse transcriptase that transcribes DNA from an
RNA template
b. The newly made DNA is inserted as a provirus into a chromosome in the animal cell
c. The host’s RNA polymerase transcribes the viral DNA into more RNA molecules
d. These can function both as mRNA for the synthesis of viral proteins and as genomes
for new virus particles released from the cell
e. HIV is a retrovirus
i. Glycoproteins on the virus help it attach to white blood cells
ii. After HIV enters the host cell, reverse transcriptase molecules are released into
the cytoplasm and catalyze synthesis of viral DNA
iii. HIV is a provirus, meaning it remains in the host cell permanently
V. Viral Evolution
A. Viruses do not fit our definition of living organisms; an isolated virus is biologically inert
B. Likely evolved after the first cells appeared
C. Most molecular biologists favor the hypothesis that viruses originated from fragments of
cellular nucleic acids that could move from one cell to another via injured cell surfaces
D. A viral genome usually has more in common with the genome of its host than with those of
viruses infecting other hosts
E. Some viruses have genetic sequences that are quite similar to seemingly distantly related
viruses
F. The evolution of capsid genes may have facilitated the infection of undamaged cells
G. Candidates for the original sources of viral genomes include plasmids and transposable
elements
1. Plasmids are small, circular DNA molecules that are separate from chromosomes
2. Plasmids, found in bacteria and in eukaryote yeast, can replicate independently of the
rest of the cell and are occasionally transferred between cells
3. Transposable elements are DNA segments that can move from one location to another
within a cell’s genome
H. The ongoing evolutionary relationship between viruses and the genomes of their hosts is an
association that makes viruses very useful model systems in molecular biology
18.2
VI. Viruses and symptoms
A. Some viruses damage or kill cells by triggering the release of hydrolytic enzymes from
lysosomes
B. Some viruses cause the infected cell to produce toxins that lead to disease symptoms.
C. Others have molecular components, such as envelope proteins, that are toxic
D. Many of the temporary symptoms associated with a viral infection result from the body’s
own efforts at defending itself against infection
E. Most viral symptoms are easily recovered from (Ex. Flu), though others are permanent
(Ex. Polio)
VII. Prevention
A. Vaccines-harmless variants of the pathogenic microbes that stimulate the immune
system to mount defenses against the pathogen
B. Antibiotics are powerless against viruses
C. Most antiviral drugs resemble nucleosides and interfere with viral nucleic acid synthesis
D. Multidrug “cocktails” are the most effective treatment for HIV
VIII. Emerging Viruses
A. HIV (AIDS virus) seemed to appear suddenly in the early 1980s
B. The emergence of new viral diseases is due to three processes: mutation; spread between
species, and spread from an isolated population
1. RNA viruses tend to have high mutation rates because replication of their nucleic acid lacks
proofreading
2. It is estimated that about 75% of new human diseases originated in other animals
C. Changes in host behavior and environmental changes can increase the emergence of new viruses
IX. Plant Viruses
A. More than 2,000 types of viral diseases of plants are known
1. These diseases account for an annual loss of $15 billion worldwide
B. Plant viruses can stunt plant growth and diminish crop yields
C. Most are RNA viruses with rod-shaped or polyhedral capsids
D. In horizontal transmission, a plant is infected with the virus by an external source
1. Plants are more susceptible if their protective epidermis is damaged, perhaps by
wind, chilling, injury, or insects.
2. Insects are often carriers of viruses, transmitting disease from plant to plant.
E. In vertical transmission, a plant inherits a viral infection from a parent.
1. This may occur by asexual breeding or in sexual reproduction via infected seeds
F. Viruses spread between plant cells by the plasmodesmata
1. Proteins encoded by viral genes can alter the diameter of plasmodesmata to allow
passage of viral proteins or genomes
G. Agricultural scientists try to breed resistant plant varieties
X. Viroids and Prions
A. Another dwarf class of pathogens are known as viroids
1. they are long circular RNA molecules, only several hundred nucleotides long
2. They infect plants
3. Don’t encode proteins
4. Seem to cause errors in the regulatory systems that control plant growth
a. Symptoms include abnormal development and stunted growth
B. Infectious proteins are called prions
1. appear in a number of degenerative brain diseases
a. Ex. has plagued the European beef industry in recent years
b. Includes mad cow disease
2. Most likely transmitted by food
3. Very slow acting agents; the incubation period until symptoms appear is around ten
years
4. Virtually indestructible
a. Not deactivated by heating at cooking temperatures
5. Current hypothesis: a prion is a misfolded form of a protein normally present in brain
cells. When the prion gets into a cell containing the normal form of the protein, it
will convert it to the prion version.
a. Prions way trigger chain reactions increasing their numbers
b. first proposed in 1980
18.3
I. Bacterial genomes and replication
A. The best-studied bacterium is Escherichia coli
1. For E. coli, the chromosomal DNA consists of about 4.6 million nucleotide pairs with
about 4,400 genes
B. Mostly, the bacterial genome is one double-stranded, circular DNA molecule that is
associated with a small amount of proteins
C. Tight coiling of DNA results in a dense region of DNA, called the nucleoid, which is not
bound by a membrane
D. Many bacteria have plasmids, much smaller circles of DNA
1. Each plasmid has only a small number of genes, from just a few to several dozen
E. Bacterial cells divide by binary fission (asexual)
1. Their DNA replicates from one origin of replication
F. Bacteria proliferate very rapidly in a favorable natural or laboratory environment
1. Under optimal laboratory conditions, E. coli can divide every 20 minutes, producing a
colony of about 10^7 bacteria in as little as 12 hours
2. It grows slower in the human colon
II. Mutations
A. Through binary fission, most of the bacteria in a colony are genetically identical to the
parent cell
1. The probability of a spontaneous mutation occurring in E. Coli genes are about
1x10^-7 per cell division
2. About 9 million mutant E. coli are produced in the human gut each day
3. Natural selection chooses which mutations/traits are more beneficial
III.
Genetic recombination
A. Bacterial recombination occurs through three processes: transformation, transduction,
and conjugation
B. Researchers conducted an experiment with two strains of bacteria, one that could not
produce tryptophan but could produce arginine, and one that could produce arginine but
not tryptophan. They studied further generations to see that some had the ability to
produce both amino acids.
C. Transformation is the alteration of a bacterial cell’s genotype by the uptake of naked,
foreign DNA from the surrounding environment
1. For example, the harmful bacteria causing pneumonia could be mixed with the
healthy bacteria strain, and make it pathogenic
2. Occurs by crossing-over
D. Transduction occurs when a phage carries bacterial genes from one host cell to another
as a result of aberrations in the phage reproductive cycle
1. A virus may accidently take up some of its host’s DNA, and some of this DNA can
subsequently replace the homologous region of the second cell
2. Occurs by crossing-over
3. Transfers bacterial genes at random
4. Specialized transduction only transfers those genes near the prophage site on the
bacterial chromosome
E. Conjugation, sometimes known as bacterial “sex,” transfers genetic material between
two bacterial cells that are temporarily joined
1. A sex pilus from the male initially joins the two cells and creates a cytoplasmic
mating bridge between cells
2. “Maleness” is the ability to form a sex pilus and donate DNA, and results from an F
factor from a chromosome section or plasmid (Ex. F plasmid)
3. Episome- a genetic element that can replicate either as part of the bacterial
chromosome or independently
a. Episomes such as the F plasmid can undergo reversible incorporation into the
cell’s chromosome
b. Temperate viruses are also episomes
4. The F plasmid facilitates genetic recombination when environmental conditions no
longer favor existing strain
F. F plasmid in conjugation
1. The F plasmid/factor consists of about 25 genes, most required for the production of
sex pili
2. Cells with either the F factor or the F plasmid are called F+ and they pass this
condition to their offspring
3. Cells lacking either form of the F factor, are called F-, and they function as DNA
recipients
4. When an F+ and F- cell meet, the F+ cell passes a copy of the F plasmid to the Fcell, converting it
5. A cell with the F factor built into its chromosome is called an Hfr cell (for High
frequency of recombination).
a. Hfr cells function as males during conjugation
b. The Hfr cell initiates DNA replication at a point on the F factor DNA and begins to
transfer the DNA copy from that point to its F- partner
6. Random movements almost always disrupt conjugation long before an entire copy of
the Hfr chromosome can be passed to the F- cell
7. Newly acquired DNA aligns with the homologous region of the F- chromosome
IV. Antibiotics and R plasmid
1. In the 1950s, Japanese physicians began to notice that some bacterial strains had
evolved antibiotic resistance
2. Mutations may reduce the ability of the pathogen’s cell-surface proteins to transport
antibiotics into the bacterial cell
3. Some of these genes code for enzymes that specifically destroy certain antibiotics
4. The genes allowing resistance are carried by plasmids, specifically the R plasmid
a. When a bacterial population is exposed to an antibiotic, individuals with the R
plasmid will survive and increase in the overall population
b. Because R plasmids also have genes that encode for sex pili, they can be
transferred from one cell to another by conjugation
V. Transposition
A. The DNA of a single cell can also undergo recombination due to movement of
transposable genetic elements
B. Transposable elements never exist independently but are always part of chromosomal or
plasmid DNA
C. During transposition, the transposable element moves from one location to another in a
cell’s genome
1. The movement may be within the chromosome, from a plasmid to a chromosome, or
between plasmids
2. Transposable elements may move by a “copy and paste” mechanism
D. The simplest transposable elements, called insertion sequences, exist only in bacteria
1. An insertion sequence contains a single gene that codes for transposase, an enzyme
that catalyzes movement of the insertion sequence from one site to another within
the genome
2. The insertion sequence consists of the transposase gene, and is surrounded by a
pair of inverted repeat sequences
a. The transposase enzyme recognizes the inverted repeats as the edges of the
transposable element
b. Transposase cuts the transposable elements from its initial site and inserts it into
the target site
3. Insertion sequences cause mutations when they happen to land within the coding
sequence of a gene or within a DNA region that regulates gene expression
a. Insertion sequences account for 1.5% of the E. coli genome, but a mutation in a
particular gene by transposition is rare, occurring about once in every 10 million
generations
E. Transposons are moveable transposable elements longer and more complex than
insertion sequences
1. Transposons include extra genes that travel together, such as genes for antibiotic
resistance
2. In some bacterial transposons, the extra genes are sandwiched between two
insertion sequences
3. Transposons may help bacteria adapt to new environments.
4. Transposons can add a gene for antibiotic resistance to a plasmid already carrying
genes for resistance to other antibiotics
5. In an antibiotic-rich environment, natural selection factors bacterial clones that have
built up R plasmids with multiple antibiotic resistance through a series of
transpositions
6. Transposable elements are also important components of eukaryotic genomes.
18.4
VI. Environmental fluctuation
A. Mutations and gene transfer generate the genetic variation that makes natural selection
possible
B. An individual bacterium, locked into the genome that it has inherited, can cope with
environmental fluctuations by exerting metabolic control
1. Ex. E. coli cell living in the human colon needs tryptophan for survival
2. If the human’s diet is lacking in this amino acid, the bacterium activates a metabolic
pathway that makes tryptophan from another compound
3.
If the human begins to eat more tryptophan, the bacterium stops producing it
C. Cells can adjust the activity of enzymes already present
1. Fast response that depends on the sensitivity of many enzymes to chemical cues that
increase or decrease their catalytic activity
2. Ex: the first enzyme in the tryptophan synthesis pathway is inhibited by the pathway’s
end product, which is known as feedback inhibition
D. Cells can adjust the amount being made of certain enzymes; they can regulate the
expression of the genes encoding the enzymes
1. Ex: If the environment continues to provide enough tryptophan that the cell needs, the
cell stops making the enzymes that work in the tryptophan pathway
2. This control of enzyme production happens at transcription
VII.
Operons
A. The basic mechanism for this control of gene expression in bacteria, the operon model, was
discovered in 1961 by François Jacob and Jacques Monod
B. Operon- a functioning unit of genomic DNA containing a cluster of genes under the control
of a single regulatory promoter
C. E. Coli tryptophan pathway
1. E. coli synthesizes tryptophan from a precursor molecule in a series of steps, with each
reaction catalyzed by a specific enzyme
2. The five genes coding for these enzymes are clustered together on the bacterial
chromosome, served by a single promoter
3. Transcription gives rise to one long mRNA molecule that code for all five enzymes in the
tryptophan pathway
4. The mRNA is interrupted with start and stop codons that signal where the coding
sequence for each polypeptide begins and ends
D. A key advantage of grouping genes of related functions into one transcription unit is that a
single “on-off switch” can control a cluster of functionally related genes
1. The switch is a segment of DNA called an operator
a. The operator, located between the promoter and the enzyme-coding genes, controls
the access of RNA polymerase to the genes
E. By itself the trp (tryptophan) operon is turned on and the RNA polymerase can find to the
promoter and transcribe the genes of the operon
F. The trp repressor protein can turn off the operon
1. The repressor binds to the operator and blocks attachment of RNA polymerase to the
promoter, preventing transcription of the genes
2. A repressor protein is specific and recognizes and binds only to the operator of that
particular operon
3. The binding of repressors to operators is reversible
a. The number of active repressor molecules available determines the on or off mode of
the operator
4. Repressors contain allosteric sites that change shape depending on the binding of other
molecules (active vs. inactive)
5. When concentrations of tryptophan in the cell are high, some tryptophan molecules bind
as a corepressor to the repressor protein
6. At low levels of tryptophan, most of the repressors are inactive, and the operon is
transcribed
G. The trp repressor is the product of a regulatory gene called trpR, which is located some
distance away from the operon it controls and has its own promoter
1. Regulatory genes are expressed continuously, although at a low rate
H. A corepressor is a small molecule that cooperates with a repressor protein to switch an
operon off
VIII. Repressible and inducible operons
A. An operon is said to be repressible if its transcription is usually on, but can be inhibited when
a specific small molecule binds allosterically to a regulatory protein
a. Ex: The enzymes for tryptophan synthesis are referred to as repressible enzymes
b. Repressible enzymes generally function in anabolic pathways, which synthesize
essential end products from raw materials (precursors)
c.
By suspending production of an end product when it is already present in sufficient
quantity, the cell can allocate its organic precursors and energy for other uses
B. An operon is said to be an inducible operon if it is usually off but can be stimulated when a
specific small molecule interacts with a regulatory protein
1. The inducer inactivates the repressor
a. Ex. The lac (lactose) operon contains a series of genes that code for enzymes that
play a major role in the hydrolysis and metabolism of lactose
b.
In the absence of lactose, this operon is off, as an active repressor binds to the
operator and prevents transcription
c. Lactose metabolism begins with hydrolysis of lactose into glucose and galactose
d. This reaction is catalyzed by the enzyme ß-galactosidase. The gene for ßgalactosidase is part of the lac operon, which includes two other genes coding for
enzymes that function in lactose metabolism
e. The regulatory gene, lacI, located outside the operon, codes for an allosteric
repressor protein that can switch off the lac operon by binding to the operator
i.
f.
The lac repressor is active all by itself
When lactose is present in the cell, allolactose, an isomer of lactose, binds to the
repressor. This inactivates the repressor, and the lac operon can be transcribed
g. Inducible enzymes usually function in catabolic pathways, digesting nutrients to
simpler molecules
h. The way they work helps the cell avoid wasting energy and precursors making
proteins that are not needed
IX. Positive gene regulation (with the lac operon)
A. When a regulatory protein interacts directly with the genome to switch transcription on it is
said to be positive gene regulation
B. For the lactose-utilizing enzymes to be synthesized in appreciable quantity, it is not sufficient
for lactose to be present in the bacterial cell
C. The other requirement is that the simple sugar glucose be in short supply
1. E. coli preferentially uses glucose. The enzymes for glucose breakdown (glycolysis) are
continually present
D. Even if the lac operon is turned on by the presence of allolactose, the degree of transcription
depends on the concentrations of other substrates.
1. If glucose levels are low, then cyclic AMP (cAMP) accumulates.
2. The regulatory protein catabolite activator protein (CAP) is an activator of transcription
a. When cAMP binds to CAP, the regulatory protein (CAP) assumes its activate shape
and can bind to a specific site at the upstream end of the lac promoter
b. The attachment of CAP to the promoter directly stimulates gene expression
3. If the amount of glucose in the cell increases, the cAMP concentration falls, and without
it, CAP detaches from the operon
a. Because CAP is inactive, transcription of the lac operon proceeds at only a low level,
even in the presence of lactose
E. The lac operon is under dual control
1. Negative control by the lac repressor
a. The state of the lac repressor (with or without bound allolactose) determines
whether or not transcription of the lac operon’s genes occurs at all
2. Positive control by CAP
a. The state if CAP (with or without bound cAMP) controls the rate of transcription if
the operon is repressor-free
3. CAP helps regulate several other operons that encode enzymes used in catabolic
pathways
4. When glucose is plentiful and CAP is inactive, the synthesis of enzymes that catabolize
compounds other than glucose generally slows down
a. The cell’s ability to catabolize other compounds, such as lactose, enables a cell
deprived of glucose to survive
b.
The specific compounds present at the moment determine which operons are
switched on
These multiple contingency mechanisms su