Important
words and concepts from Chapter 18, Campbell & Reece, 2002 (1/29/2005):
by Stephen T. Abedon (abedon.1@osu.edu)
for Biology 113 at the Ohio State University
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Course-external links are
in brackets Click [index] to access site index Click here to
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(1) Chapter title: Microbial Models: The
Genetics of Viruses and Bacteria
(a)
[microbial models: the genetics
of viruses and bacteria, the genetics of viruses and
bacteria (Google Search)] [index]
(2) Relevance of
microorganisms
(a)
Microorganisms are the most important component of environmental health
(b)
Microorganisms cause diseases
(c)
Microorganisms can help heal as well as prevent disease
(d)
Microorganisms have numerous commercial/industrial applications
(e)
Mitochondria and chloroplasts are microorganisms
(f)
Microorganisms serve as model systems
(g)
Microorganisms are extremely abundant
(h)
Microorganisms are Fun!
(i)
See Figure 18.1, Comparing
the sizes of a virus, a bacterium, and a eukaryotic cell
(4)
(a)
Different kinds of microorganisms include
(i)
Bacteria
(ii)
Viruses
(iii)
Fungi
(iv)
Algae
(v)
Protozoa
(b)
This chapter will consider mostly the first two types on this list,
bacteria and viruses
(c)
[types of microorganisms
(Google Search)] [index]
VIRUSES
(5) Virus distinguishing features
(a)
Viruses are smaller than bacteria (typically, at least)
(b)
Viruses are obligate intracellular
parasites (some bacteria are also)
(c)
Viruses are structurally simpler than cellular organisms
(d)
Viruses possess a relative dearth of metabolic machinery
(e)
Many viruses have unusual genomes
(f)
There exists a relative dearth of antiviral "antibiotics"
(g)
Viruses go through an acellular stage
(h)
[virus distinguishing features
(Google Search)] [index]
(a)
Viruses tend to vary in terms of their
(i)
Genome type
(iii)
Host range
(iv)
Life cycles
(b)
[viral characteristics
(Google Search)] [index]
(a)
The genomes of viruses are typically much smaller
than the genomes of cellular organisms
(b)
Virus genomes are also not always composed dsDNA
(c)
Depending on virus, genomes can be
(i)
dsDNA
(ii)
ssDNA
(iii)
dsRNA
(iv)
ssRNA
(d)
Virus genomes can also take on a variety of configurations, depending
on the virus including
(i)
Linear
(ii)
Circular
(iii)
Segmented (more than one DNA molecule, each holding a different gene
or genes)
(iv)
Diploid (most viruses are haploid, though)
(e)
See Table 18.1, Classes of
animal viruses, grouped by type of nucleic acid
(f)
[virus genome types
(Google Search)] [index]
(a)
Defining characteristic of viruses is their
protected extracellular state
(b)
Protection is achieved via a capsid
(c)
In addition, an envelope may be present, surrounding the capsid
(d)
See Figure 18.2, viral
structure
(e)
[capsid, enveloped virus (Google Search)] [index]
(9)
Capsid (capsomers)
(a)
A capsid is a protein shell that surrounds and protects a virus genome
while the virus is in the extracellular state
(b)
The proteins that make up the capsid are called capsomers
(c)
Note that capsids can come in a variety of shapes and levels of
complexity
(i)
Helical
(ii)
Polyhedral
(iii)
Complex
(d)
See Figure 18.2, viral
structure
(e)
[capsid, capsomer OR capsomere
(Google Search)] [index]
(a)
Some viruses are additionally surrounded by an
envelope
(b)
An envelope is a lipid bilayer
located external to the capsid
(c)
Envelopes are derived from host-cell lipid bilayers
(d)
In addition to host membrane proteins, envelopes contain virus-coded
proteins
(e)
These virus proteins are involved in host-cell attachment and genome
uptake
(f)
In non-enveloped viruses,
the capsid proteins are responsible for facilitating host-cell attachment and
genome uptake
(g)
See Figure 18.2, viral
structure
(h)
[enveloped virus (Google Search)] [index]
(a)
All viruses are limited in the host cells they may
successfully infect
(b)
One term that describes this limit is host range
(c)
Many viruses are limited to only a single host species
(d)
Other viruses have broader host ranges, being capable of successfully
infecting more than one host species
(e)
Many viruses are additionally limited in the cell types they are able
to infect within a host
(f)
One determinant of the host range of a virus is the
"lock-and-key" fit between the virus capsid or envelope
proteins and virus receptors, the latter of which typically consist of
host-proteins (or carbohydrates) found on the surface of cells
(g)
[virus host range (Google Search)] [index]
(12)
Bacteriophage (phage)
(a)
Note that host range often plays a role in the
naming of viruses
(b)
One category, ones which infect only bacteria, are
called bacteriophages (a.k.a., phage or phages for short)
(c)
[bacteriophage or phage
(Google Search)] [bacteriophage ecology group
(MicroDude)] [index]
(a)
Viruses have varied life cycles, some of which
are very complex
(b)
A life cycle, in general, is a series of events that an organism goes
through from birth through reproduction
(c)
The simplified virus life cycle consists of
(i)
Adsorption to a host cell
(ii)
Uptake of the virus genome into the
cell
(iii)
Transcription
of virus genes
(iv)
Translation of the resulting virus mRNAs
(v)
Replication of the virus genome
(vi)
Packaging of the new virus genomes into capsids
(vii)
Progeny-virus release from the host cell
(d)
See Figure 18.3, A
simplified viral reproductive cycle
(e)
Life cycles we will consider in more detail include
(i)
The lytic life
cycle
(ii)
The lysogenic life
cycle
(iii)
The life cycle of an enveloped animal virus
(iv)
The life cycle of a retroviruses
(f)
[viurus life cycle, life cycle (Google Search)] [index]
(a)
A lytic life cycle requires the destruction of the host cell before
progeny release may occur
(b)
This host-cell destruction is called lysis
(c)
See Figure 18.4, The lytic
cycle of phage T4
(d)
[virus life cycle (Google Search)] [index]
(15)
Lysogenic life cycle (prophage, provirus, temperate virus)
(a)
In a lysogenic life cycle virus progeny are neither produced nor
released
(i)
Temperate virus = a virus capable of going through a lysogenic cycle
(ii)
Prophage = a bacteriophage whose
genome has integrated into its host's genome during lysogenic
growth
(iii)
Provirus = equivalent to prophage but more generally applicable (e.g., to animal
viruses)
(b)
Note that a temperate virus must have some alternative life cycle, one that results in progeny production and
release
(c)
Typically this alternative life cycle is a lytic one (e.g.,
phage lambda, a.k.a., l)
(d)
See Figure 18.5, the lysogenic
and lytic reproductive cycles of phage l, a temperate
virus
(e)
[lysogenic cycle, prophage, provirus, temperate virus (Google Search)] ["Lytic, Lysogenic,
Temperate, Chronic, Virulent, Quoi?" (Bacteriophage Ecology Group)] [index]
(a)
Prophages can carry bacterial virulence factors (genes that produce toxins, for example)
(b)
Often these factors are required for the bacteria to cause
disease
(c)
Examples include those bacteria responsible for shigatoxigenic E.
coli, diphtheria, botulism, and scarlet fever
(d)
[prophage and disease
(Google Search)] [index]
(a)
Certain animal viruses are capable of entering a
proviral state
(b)
This state allows the virus to remain within the host without inducing
a host anti-viral immune response
(c)
Such viruses include the herpesviruses and retroviruses
(d)
[provirus and disease
(Google Search)] [index]
(a)
Enveloped viruses do not go through a lytic cycle
(b)
Instead they produce and release progeny "chronically", i.e.,
without necessarily first destroying the host cell
(c)
Progeny release often occurs simultaneous with envelope acquisition
(d)
See Figure 18.6, The
reproductive cycle of an enveloped virus
(e)
[enveloped virus (Google Search)] [index]
(19)
Retroviruses (reverse transcriptase)
(a)
One type of enveloped animal virus is the
retrovirus
(b)
Retroviruses are named for their RNA genomes which are converted to DNA
in the course of the viral intracellular life cycle
(c)
The enzyme that accomplishes this feat is called
reverse transcriptase
(d)
Interestingly, once converted to DNA, the virus then makes new viral
genomes as well as mRNAs simultaneously, as the same molecule
(e)
An example of a retrovirus is human immunodeficiency virus (HIV)
(f)
See Figure 18.7, HIV, a
retrovirus
(g)
[retrovirus, reverse transcription,
reverse transcriptase
(Google Search)] [index]
BACTERIA GENETIC VARIATION
(a)
Evolutionary adaptation is dependent on genetic variation
(b)
Genetic variation comes from two sources (and ultimately only the
former)
(i)
Mutation
(ii)
Sex
(c)
[genetic variation (Google Search)] [index]
(a)
Bacteria display a higher per-gene
mutation rate compared with more-complex (larger-genomed) organisms
(b)
In short, per-genome mutation rates are fairly constant
across dsDNA-genomed organismal types, and bacteria simply have fewer genes
(and thus more mutations per gene per round of
replication)
(c)
Bacteria additionally replicate faster than do more complex organisms;
they thus not only have more mutations per gene per round of
replication, they also have more rounds of replication
(d)
Bacteria also take up very little space and require relatively few
resources per round of replication (ditto)
(e)
The bottom line is that a typical bacterial population can generate a
whole lot of mutational variation, very quickly
(f)
[bacteria mutation (Google Search)] [index]
(a)
Bacteria do not exist as diploids, do not
undergo meiosis, and do not tie together sex with
reproduction; consequently what a human might call sex and what a bacteria
might call sex are difficult to reconcile as similar processes
(b)
Nevertheless, sex at its basis involves recombination between DNAs sourced from different parents
(c)
Bacteria tend to be naturally adept at recombination (as mechanisms of
repair of DNA damage); the trick then is how DNA from different parents ends up
within a single cell
(d)
Various mechanisms allow this to occur
(i)
Transformation
(ii)
Transduction
(iii)
Conjugation
(e)
All three mechanisms have in common that the DNAs transferred from one
cell to another tend to be transferred only as small "snippets" of
DNA, rather than whole chromosomes
(f)
[bacteria sex (Google Search)] [index]
(a)
We already considered transformation in terms of Griffith's experiments with Streptococcus in mice
(b)
Transformation is the uptake of DNA directly from the environment by a
bacterial cell
(c)
Some bacteria are better at this than are others
(d)
Bacteria that are not good at this (e.g., E. coli) can be induced to pick up DNA as a laboratory artifact
(e)
Such induction is important to bioengineering
(f)
[transformation DNA
(Google Search)] [index]
(a)
Transduction involves the movement of snippets of DNA from one cell to
another as an accidental stowaway within a bacteriophage
(b)
Some bacteriophages are better at transducing than others
(c)
Transduction can be distinguished into two types
(d)
[DNA transduction (Google Search)] [index]
(a)
Specialized transduction involves temperate phages
(b)
Here when the temperate phages excise themselves from their host's genome they sometimes excise adjacent sections of their host's
genome
(c)
This is called specialized because there is a strong bias toward the
movement of specific pieces of DNA (i.e., those adjacent to the normal prophage insertion point)
(d)
See Figure 18.13,
Transduction
(e)
[specialized transduction
(Google Search)] [index]
(a)
Generalized transduction involves the packaging of host DNA independent
of phage DNA
(b)
Viruses thus-constructed are not capable of
infecting new cells (i.e., completing their life cycle) because they lack phage
genes
(c)
However, they are able to carry snippets of host DNA from one bacteria to another
(d)
See Figure 18.13,
Transduction
(e)
[generalized transduction
(Google Search)] [index]
(a)
In conjugation bacteria dock together and purposefully pass DNA,
usually from one (called the male) to a recipient (called female)
(b)
Typically it is plasmids that are passed rather than
chromosomal DNA
(c)
See Figure 18.14, Bacterial
mating
(d)
See Figure 18.15,
Conjugation and recombination in E. coli
(e)
[bacteria conjugation
(Google Search)] [index]
(a)
Some bacterial genes are not found on the bacterial chromosome
(b)
Instead, genes may be located on smaller pieces of DNA
called plasmids
(c)
Plasmids typically do not contain genes essential to host functioning
(d)
This is because plasmids may be accidentally lost from cells, along
with the genes they hold and any associated functions
(e)
[plasmid OR plasmids
(Google Search)] [index]
(a)
Plasmids can hold genes that are
useful under certain circumstances
(b)
One such circumstance is in the face of exposure to antibiotics
(c)
Plasmids holding anti-antibiotic genes are termed R plasmids
(d)
Bacteria can acquire R (and other) plasmids
fully formed via conjugation or transformation
(e)
Thus, resistance to antibiotics (etc.) need not develop de novo in a bacterial lineage by mutation, but instead may be acquired fully formed
(i.e., fully evolved)
(f)
As a consequence, bacteria are able to acquire resistance to
antibiotics much more easily and rapidly than they might were they limited
solely to chromosomal evolution
(g)
[R plasmids (Google Search)] [index]
BACERIA PHENOTYPIC VARIATION (ADAPTATION)
(a)
The term adaptation has at least two biological meanings
(i)
Genetic change resulting in greater evolutionary fitness (evolution)
(ii)
Physiological change resulting in more appropriate interaction with the
environment
(b)
In both cases what is occurring is some kind of organismal (population
or individual) change that occurs in response to environmental input
(c)
[physiological adaptation
bacteria (Google Search)] [index]
(a)
In this section we will first consider mechanisms of physiological
adaptation in bacteria
(b)
We will then consider mechanisms that input genetic variation into bacterial populations (genetic
variation being the first step toward any evolutionary change)
(c)
In all cases, what we will be considering is various aspects of the
field of molecular genetics
(d)
[molecular genetics
(Google Search)] [index]
(a)
Physiological adaptation is useful because it allows an organism to
fine tune its use of resources to better fit its environment
(b)
The idea is to avoid using cell resources to make products that are
readily available from the environment or otherwise not currently needed
(c)
It makes energetic sense to make or use proteins
responsible for certain metabolic processes only when those processes are
needed
(d)
See Figure 18.19, Regulation
of a metabolic pathway
(e)
Note that you have already leaned about one form of adaptation: feedback inhibition
(f)
Here we will consider control of gene function
(a)
Within bacteria many biochemical pathways are
catalyzed by a series of enzymes
(b)
These enzymes in turn are coded by genes
(c)
As a matter of both utility and control of gene expression, it is
fairly common (in bacteria) for groups of genes responsible for the expression
of a biochemical pathway to be simultaneously transcribed as a single mRNA
(d)
The DNA responsible for the transcription of this mRNA together with
certain transcriptional-control sequences is termed an operon
(e)
[operon model (Google Search)] [index]
(34)
Operon (cofactor)
(a)
An operon typically consists of the following components
(i)
One or more structural genes
(ii)
A promoter
(iii)
An operator
(b)
Additionally, there may be one or more regulatory genes
and associated proteins
(c)
Finally, there typically exist various smaller molecules that serve as cofactors in
gene regulation
(d)
The basic idea is to simultaneously turn on or turn off the expression
of a subset of metabolically related enzymes
(e)
[operon, operon cofactor (Google Search)] [index]
(a)
Genes within operons that
produce proteins are called structural genes
(b)
These are the genes whose expression is controlled by the operator
(c)
[structural gene (Google Search)] [index]
(a)
The promoter is the site of RNA polymerase binding
(b)
The promoter is found upstream of the first structural gene in
the polytranscript
(c)
[promoter transcription
(Google Search)] [index]
(a)
The operator is a DNA sequence upstream of the first structural
gene
(b)
Protein binding to the operator controls RNA polymerase activity
(c)
[operator DNA (Google Search)] [index]
(a)
The regulatory gene, itself, is not part of the operon proper
(b)
A regulatory gene produces a protein that binds to the operator
(c)
When bound, this protein may facilitate operon expression (positive
control)
(d)
Alternatively, the protein, when bound, may inhibit protein expression
(negative control)
(e)
[regulatory gene (Google Search)] [index]
(a)
A protein that binds the operator, thus
inhibiting operon expression, is termed a repressor
(b)
[repressor (Google Search)] [index]
(a)
A cofactor that activates a repressor is called a corepressor
(b)
That is, in this case the repressor is inactive (won't inhibit operon
expression) until the cofactor is present
(c)
[corepressor (Google Search)] [index]
(a)
An inducer is a cofactor that
inactivates a repressor
(b)
That is, in this case the repressor is active (will inhibit operon
expression) until the cofactor is present (after which the repressor no longer
inhibits operon expression)
(a)
It is important to keep in mind while discussing operons that
the various bindings that occur all do so reversibly
(b)
Specifically, repressors reversibly interact with operators
(c)
And corepressors reversibly interact with repressors
(d)
As a consequence, low concentrations of active repressor results in a
relative dearth of binding to operators (and thus of operon expression)
(e)
Similarly, low concentrations of corepressor results in a relative
dearth of cofactor-repressor binding and therefore little repressor activation
(f)
[reversible operon (Google Search)] [index]
(43)
Trp operon (corepressed operon)
(a)
The trp operon is an example of a corepressed operon
(b)
Corepression is a common means of controlling the synthesis of anabolic
pathways
(c)
The basic idea is that when tryptophan concentrations within a cell are
adequate, the cell stops making the enzymes required
for tryptophan synthesis
(d)
Here tryptophan within the cell serves as the corepressor
(e)
That is, excess trp binds the appropriate repressor which in
turn shuts off the trp operon
(f)
See Figure 18.20, The trp operon: regulated synthesis of
repressible enzymes
(g)
[inducible operon (Google Search)] [index]
(44)
Lac operon (inducible
operon)
(a)
The lac operon is an example of an inducible operon
(b)
Induction is a common means of controlling the synthesis of catabolic
pathways
(c)
In this case, when no lactose is available in a cell's environment, the
cell avoids making the large quantities of the enzymes necessary
to digest lactose
(d)
However, when lactose is present in reasonable quantities, a lactose
derivative serves as an inducer
(e)
That is, the binding of lactose (actually, its derivative) to the lac
operon repressor inactivates
the repressor, thus allowing expression of the lac operon genes
(f)
See Figure 18.21, The lac operon: regulated synthesis of
inducible enzymes
(g)
[lac operon (Google Search)] [index]
(a)
The lac and trp operons are two
examples of negative control of gene expression
(b)
That is, when the operator is bound, transcription is inhibited
(c)
[negative control, negative control transcription
(Google Search)] [index]
(a)
Positive control, in contrast, involves protein-DNA binding
that enhances promoter activity (rather than blocking RNA polymerase activity)
(b)
That is, with positive control, protein binding results in more gene
expression from the operon
(c)
[positive control, positive control transcription
(Google Search)] [index]
(47) CRP (cAMP receptor protein)
(a)
CRP stands for
(b)
When CRP binds cyclic AMP (a
derivative of ATP), CRP is activated
(c)
When activated, CRP can bind to a promoter and
positively modulate operon activity
(d)
Cyclic AMP (cAMP) is a signal produced, here, when
intracellular glucose concentrations are low
(e)
The idea is that a cell will preferentially employ glucose as a carbon and energy source
(f)
When glucose concentrations are high, cAMP is depleted, CRP is not
active, and CRP-controlled operons
(e.g., lac operon) display reduced expression
(g)
When glucose concentrations are depleted, cAMP is produced, CRP is
activated, and CRP-controlled operons display enhanced expression
(h)
See Figure 18.22, Positive control: cAMP receptor protein
(i)
[cAMP receptor protein,
catabolite activator protein
(Google Search)] [index]
(48)
Vocabulary [index]
(a)
Adaptation
(c)
Bacteria sex
(d)
Bacteriophage
(e)
CRP
(f)
Capsid
(h)
Capsomers
(j)
Cofactor
(k)
Conjugation
(m)
Corepressor
(n)
Envelope
(r)
Genome types
(s)
Host range
(t)
Inducer
(u)
Inducible operon
(v)
Lac operon
(w)
Life cycle
(y)
Lytic life
cycle
(aa)
Negative
control
(bb)
Operator
(cc)
Operon
(ee)
Phage
(ff)
Plasmids
(gg)
Positive
control
(hh)
Promoter
(ii)
Prophage
(jj)
Prophage and
disease
(kk)
Provirus
(ll)
Provirus and disease
(mm)
R plasmids
(nn)
Regulatory
gene
(oo)
Relevance
of microorganisms
(pp)
Repressor
(qq)
Retroviruses
(uu)
Structural
gene
(vv)
Temperate virus
(ww)
Transduction
(xx)
Transformation
(yy)
Trp operon
(aaa)
Viral characteristics
(bbb)
Virus distinguishing
features
(ccc) Why adapt?