Microbial Models: The Genetics of Viruses and Bacteria

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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(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]

INTRODUCTION TO MICROBIOLOGY

(2) Relevance of microorganisms (see also microorganism)

(a) Microorganisms are the most important component of environmental health

(b) Microorganisms cause diseases

(d) Microorganisms have numerous commercial/industrial applications

(e) Mitochondria and chloroplasts are microorganisms

(f) Microorganisms serve as model systems for understanding the basic molecular principles of life (e.g., the central dogma of molecular genetics)

(g) Microorganisms are extremely abundant

(h) Microorganisms are Fun!

(i) See Figure, Comparing the sizes of a virus, a bacterium, and a eukaryotic cell

(3) Types of microorganisms (see also microorganism)

(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

VIRUS TYPES

(4) Virus distinguishing features (see also virus and virus-caused diseases)

(a) Viruses are smaller than bacteria (typically, at least)

(b) Viruses are obligate intracellular parasites (some bacteria are also)

(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]

(5) Viral characteristics

(a) Viruses tend to vary in terms of their

(i) Genome type

(ii) Capsids and envelopes

(iii) Host range

(iv) Life cycles

(b) [viral characteristics (Google Search)] [index]

(6) Genome types (see also virus genomes)

(a) The genomes of viruses are typically much smaller than the genomes of cellular organisms

(b) Virus genomes are also not always composed dsDNA

(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]

(7) Capsids and envelopes (see also capsid and envelope)

(a) Defining characteristic of viruses is their protected extracellular state

(b) Protection is achieved via a capsid

(d) See Figure, viral structure

(e) [capsid, enveloped virus (Google Search)] [index]

(8) Capsid (capsomers) (see also capsid and capsomere)

(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

(i) Helical

(ii) Polyhedral

(iii) Complex

(d) See Figure, viral structure

(e) [capsid, capsomer OR capsomere (Google Search)] [index]

(9) Envelope (see also envelope)

(a) Some viruses are additionally surrounded by an envelope

(b) An envelope is a lipid bilayer located external to the capsid

(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, viral structure

(h) [enveloped virus (Google Search)] [index]

(10) Host range (see also host range)

(a) All viruses are limited in the host cells they may successfully infect

(b) One term that describes this limit is host range

(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]

(11) Bacteriophage (phage) (see also bacteriophage)

(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)

VIRAL LIFE CYCLES

(12) Life cycle (see also life cycle)

(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

(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, 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) [virus life cycle, life cycle (Google Search)] [index]

(13) Lytic life cycle (see also lytic cycle)

(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, The lytic cycle of phage T4

(d) [virus life cycle (Google Search)] [index]

(14) Lysogenic life cycle (prophage, provirus, temperate virus) (see also lysogenic cycle, prophage, provirus, and temperate(virology))

(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., as to animal viruses)

(b) Note that a temperate virus must have some alternative life cycle , one that results in progeny production and release

(d) See Figure, 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]

VIRUSES AND DISEASE (VERY BRIEF CONSIDERATION)

(15) Prophage and disease (see also lysogenic conversion)

(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

(d) [prophage and disease (Google Search)] [index]

(16) Provirus and disease

(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

(d) [provirus and disease (Google Search)] [index]

(17) Enveloped viruses (see also enveloped virus)

(a) By and large enveloped viruses are viruses of animals (though not all animal viruses are enveloped)

(b) Enveloped viruses do not go through a lytic cycle

(d) Progeny release often occurs simultaneous with envelope acquisition

(e) See Figure, The reproductive cycle of an enveloped virus

(f) [enveloped virus (Google Search)] [index]

(18) Retroviruses (reverse transcriptase) (see also retrovirus and 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

(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, HIV, a retrovirus

(g) [retrovirus, reverse transcription, reverse transcriptase (Google Search)] [index]

BACTERIA GENETIC VARIATION

(19) Genetic variation (see also 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

(20) Bacteria mutation

(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]

(21) Bacteria sex (see also bacterial sex)

(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]

(22) Transformation (see also transformation (genetic))

(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

(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]

(23) Transduction (see also transduction)

(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

(i) Specialized transduction

(ii) Generalized transduction

(d) [DNA transduction (Google Search)] [index]

(24) Specialized transduction (see also specialized transduction)

(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, Transduction

(e) [specialized transduction (Google Search)] [index]

(25) Generalized transduction (see also generalized transduction)

(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

(d) See Figure, Transduction

(e) [generalized transduction (Google Search)] [index]

(26) Conjugation (see also conjugation)

(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, Bacterial mating

(d) See Figure, Conjugation and recombination in E. coli

(e) [bacteria conjugation (Google Search)] [index]

(27) Plasmids (see also plasmid and conjugative plasmid)

(a) Some bacterial genes are not found on the bacterial chromosome

(b) Instead, genes may be located on smaller pieces of DNA called plasmids

(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]

(28) R plasmids (see also resistance plasmid)

(a) Plasmids can hold genes that are useful under certain circumstances

(b) One such circumstance is in the face of exposure to antibiotics

(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)

(29) Adaptation (see also 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

(30) Molecular genetics (see also molecular genetics)

(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)

(d) [molecular genetics (Google Search)] [index]

(31) Why adapt?

(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, Regulation of a metabolic pathway

(e) Note that you have already learned about one form of adaptation: feedback inhibition

(f) Here we will consider control of gene function

OPERON MODEL OF BACTERIAL CONTROL OF GENE EXPRESSION

(32) Operon model

(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]

(33) Operon (cofactor) (see also operon and 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

(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]

(34) Structural gene (see also structural gene)

(a) Genes within operons that produce proteins are called structural genes

(b) These are the genes whose expression is controlled by the operator

(35) Promoter (see also promoter)

(a) The promoter is the site of RNA polymerase binding

(b) The promoter is found upstream of the first structural gene in the polytranscript

(36) Operator (see also operator)

(a) The operator is a DNA sequence upstream of the first structural gene

(b) Protein binding to the operator controls RNA polymerase activity

(37) Regulatory gene (see also regulatory gene)

(a) The regulatory gene, itself, is not part of the operon proper

(b) A regulatory gene produces a protein that binds to the operator

(d) Alternatively, the protein, when bound, may inhibit protein expression (negative control)

(e) [regulatory gene (Google Search)] [index]

(38) Repressor (see also repressor)

(a) A protein that binds the operator, thus inhibiting operon expression, is termed a repressor

(b) [repressor (Google Search)] [index]

(39) Corepressor (see also corepressor)

(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

(40) Inducer (see also inducer)

(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)

(41) Reversible interactions

(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

(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]

CONTROL OF PROKARYOTE GENE EXPRESSION

(42) Trp operon (corepressed operon) (see also Trp operon and 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, The trp operon: regulated synthesis of repressible enzymes

(g) [inducible operon (Google Search)] [index]

(43) Lac operon (inducible operon) (see also Lac operon, inducible operon, and induction (genetic))

(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, The lac operon: regulated synthesis of inducible enzymes

(g) [lac operon (Google Search)] [index]

(44) Negative control (see also negative control of gene expression)

(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

(45) Positive control (see also positive control of gene expression)

(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

(46) CRP (cAMP receptor protein) CAP (catabolite activator protein) (see also catabolite repression, cAMP receptor protein, catabolite gene activator protein, and positive control of energy metabolism)

(a) CRP stands for cAMP Receptor Protein

(b) When CRP binds cyclic AMP (a derivative of ATP), CRP is activated

(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, Positive control: cAMP receptor protein

(i) [cAMP receptor protein, catabolite activator protein (Google Search)] [index]

VOCABULARY

(47) Vocabulary [index]

(a) Adaptation

(b) Bacteria mutation

(d) Bacteriophage

(e) CRP

(f) Capsid

(g) Capsids and envelopes

(h) Capsomers

(i) cAMP receptor protein

(j) Cofactor

(k) Conjugation

(l) Corepressed operon

(m) Corepressor

(n) Envelope

(o) Enveloped viruses

(p) Generalized transduction

(q) Genetic variation

(r) Genome types

(s) Host range

(t) Inducer

(u) Inducible operon

(v) Lac operon

(w) Life cycle

(x) Lysogenic life cycle

(y) Lytic life cycle

(z) Molecular genetics

(aa) Negative control

(bb) Operator

(cc) Operon

(dd) Operon model

(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

(rr) Reverse transcriptase

(ss) Reversible interactions

(tt) Specialized transduction

(uu) Structural gene

(vv) Temperate virus

(ww) Transduction

(xx) Transformation

(yy) Trp operon

(zz) Types of microorganisms

(aaa) Viral characteristics

(bbb) Virus distinguishing features

(ccc) Why adapt?

Chapter 18, Bio 113 questions:

(#) Name four ways that viral genomes may vary between viral types (other than in terms of length or nucleotide sequence). That is, name specific characteristics of viral genomes that are not universal to all viruses.

A: dsDNA, ssDNA, dsRNA, ssRNA, linear, circular, segmented

(#) The proteinaceous, protective outer coating which defines, along with the nucleic acid inside, a virus as a virus (and not, for example, a plasmid or a viroid) is called a(n) __________. In enveloped viruses a lipid bilayer surrounds this structure.

A: capsid

(#) Matching: (a) lytic cycle, (b) lysogenic cycle, (c) enveloped virus life cycle, (d) retrovirus life cycle. Each may be used more than once. Choose best answer (and choose the latter only if the answer is uniquely associated with retroviruses and not with any of the other choices).

(i) destruction of cell coincides with progeny release __________

(ii) progeny release does not coincide with cell destruction __________

(iii) RNA-dependent DNA polymerase _________

(iv) integration into host chromosome __________

(v) associated with specialized transduction __________

A: (i) a, (ii) c, (iii) d, (iv) b, (v) b.

(#) In terms of the transcription of the trp operon, repressor activation results in what?

A: a lack of transcription

(#) Differentiate the prokaryote structural gene and the prokaryote regulatory gene in terms of location relative to a chromosomal feature and the function of the protein products.

A: the structural gene is found within the operon whereas the regulatory gene is found elsewhere on the chromosome; the protein product of the regulatory gene is a protein which acts to regulate protein expression whereas the product of the structural gene is a protein whose synthesis a regulatory gene may be regulating

(#) Ribosomes are expensive to produce and therefore the number of ribosomes present in a cell tends to reflect the level of translation that is occurring within that cell. Assume that the ribosome genes are found as part of a single operon (there are a number of reasons for why this is not true, but bear with me) and that when ribosomes are in excess a small signaling molecule is also produced in excess (e.g., a polypeptide whose absolute concentration reflects the degree to which ribosomes are idle). Assume that this signaling molecule can serve as a cofactor to a repressor protein. Describe the interaction between repressor, cofactor, operator, and operon given an excess of ribosomes and a consequently induced inhibition of further ribosome production (i.e., in terms of repressor activity, operator binding, and operon transcription).

A: The cofactor interacts with the repressor, thus activating the repressor. Activated repressor binds the operator, thus inhibiting transcription from the operon.

(#) Sex is fundamentally a mechanism of recombination between DNAs sourced from different parents. Give the names of the three mechanisms by which the DNA from different bacterial parents may be collocated in a single cell, thus potentially allowing the occurrence of recombination, and thereby bacteria sex.

A: transformation, transduction, conjugation

(#) A defining component of a virus is the capsid that protects the virus genome during passage through the extracellular environment. What is the capsid's other function?

A: Targeting the virus genome to the cytoplasm of a host cell.

(#) Contrast a virus with a cellular organism by naming three viral features that are not (i.e., differ significantly from those) found in cellular organisms.

A: Viruses possess or are: an acellular stage, typically smaller, unusual genomes, dearth of metabolic machinery, few antivirals.

(#) The types of organisms (e.g. species) that a virus may successfully infect is known as a virus' __________.

A: Host range

(#) Lambda (l) virus is an example of a bacteriophage that, unlike bacteriophage T4, can exhibit a __________life cycle.

A: Lysogenic

(#) Name a disease that is caused by an enveloped animal virus.

A: AIDS (also herpes simplex, etc.)

(#) In bacteria, a stretch of DNA that includes transcriptional control sequences (promoter, operator) that are immediately upstream of a region that codes for an mRNA is called a/an __________.

A: operon.

(#) Define corepressor in a manner that unambiguously describes its role in the control of gene expression.

A: A corepressor binds a repressor molecule thereby inactivating the repressor molecule such that it may inhibit gene expression.

(#) Describe how allolactose (the lac operon negative-control cofactor) serves to induce the transcription of the lac operon.

A: Allolactose binds the lac repressor, inactivating it, which results in its diffusion away from the lac operator and subsequent binding of RNA polymerase to the promoter and initiation of transcription

(#) A form of bacterial sex that is mediated by bacteriophage is called __________.

A: transduction.

(#) What is an R plasmid? Be sure to define both "R" and "plasmid".

A: An R plasmid is a small, closed circular, extrachromosomal piece of bacterial DNA that contains genes which code for antibiotic resistance

(#) What is the cofactor employed in the regulation of the trp operon?

A: Trp

(#) What is the corepressor employed in the regulation of the trp operon?

A: Trp

(#) What is a capsid?

A: A capsid is the protective protein covering of a virus' genome during the virus' acellular stage

(#) A virus' __________ refers to the types of cellular species that the virus is capable of infecting.

A: Host range

(#) Infection by a virus with a __________ life cycle obligately ends with the destruction of the host cell.

A: Lytic

(#) What is a provirus?

A: A provirus is a virus genome that has integrated into the dsDNA genome of its host (e.g., phage lambda and HIV have proviral stages)

(#) What chemical reaction is catalyzed by reverse transcriptase? (note that you can be reasonably non-specific in your answer, i.e., I am not looking for all substrates and products, just the particularly important ones that distinguish this chemical reaction from those better-associated with the central dogma of molecular genetics)

A: RNA à DNA, i.e., RNA-templated DNA polymerization

(#) Which mutates at a faster rate, a bacterial gene or a eukaryotic gene?

A: Bacterial genes have a faster mutation rate than eukaryotic genes

(#) In Griffith's (1928) experiment, the technical term for the uptake of DNA by Streptococcus is __________.

A: Transformation

(#) What is conjugation?

A: Conjugation is the passage of DNA from one bacteria to a second bacteria to which the first bacteria is directly connected via a sex pili

(#) How do R plasmids differ from non-R plasmids?

A: R plasmids contain genes that code for resistance to something, e.g., to antibiotics

(#) All operons consist of three major components. Name them. Recall that an operon is basically just a sequence of DNA (i.e., there are no protein components).

A: Operator, promoter, structural genes

(#) What is a regulatory gene?

A: A regulatory gene codes for a protein that effects negative or positive control on an operon, typically by binding to promoter sequences and either inhibiting or enhancing RNA polymerase binding

(#) Matching: (a) allolactose (a lactose derivative), (b) cAMP (c) tryptophan.

(i) Corepressed operon: __________

(ii) Inducible operon: __________

(iii) Positive control: __________

A: (i) (c) tryptophan, (ii) (a) allolactose, (iii) (b) camp

(#) True or False, microorganisms primarily impact on the human condition as causers of human disease.

A: False

(#) The structurally (and metabolically) simplest microorganisms are the __________.

(i) Bacteria

(ii) Viruses

(iii) Fungi

(iv) Algae

(v) Protozoa

A: (ii) Viruses

(#) Contrast capsid and virus envelope in terms of location and molecular structure.

A: A capsid is made of protein and surrounds the nucleic acid; an envelope consists of a lipid bilayer (plus envelope proteins) and surrounds the capsid

(#) What is a phage?

A: A phage is a virus that infects bacteria

(#) True or False, temperate bacteriophages can display a lytic cycle to release progeny to the extracellular environment.

A: True

(#) Reverse transcriptase catalyzes what reaction?

A: The polymerization of DNA from an RNA template (conversion of ssRNA to dsDNA)

(#) Transformation, transduction, and conjugation are all mechanisms that accomplish what?

A: Transferring bacteria DNA from one bacterial cell to another in the course of bacteria sex

(#) The removal of bacterial DNA that is adjacent to normal prophage host-chromosome insertion points and the movement of that bacterial DNA to new bacteria cells together are called __________ transduction.

(i) Conjugative

(ii) Generalized

(iii) Insidious

(iv) Primary

(v) Specialized

A: Transferring bacteria DNA from one bacterial cell to another in the course of bacteria sex

(#) Describe the characteristics of an environment within which one might find bacteria containing R plasmids.

A: (v) Specialized

(#) Which is NOT a sequence of DNA?

(i) Origin of replication

(ii) Promoter

(iii) Operator

(iv) Gene

(v) Corepressor

A: For example, one that contains antibiotics

(#) Contrast corepressor and inducer.

A: (v) Corepressor

(#) There exists a great deal of variation among viruses in terms of genome type. In addition to segmented versus not segmented, circular versus linear, and haploid versus diploid, virus genomes can also be single-stranded DNA, double-stranded DNA, or __________.

A: A corepressor binds a repressor and thereby activates the repressor whereas an inducer binds a repressor and thereby inactivates the repressor

A: RNA (single or double stranded)

(#) Describe or draw the trp operon and associated factors and proteins in the configuration in which you would expect them to be found when the amino acid tryptophan is abundant in Escherichia coli's immediate environment.

A: Operon = promoter followed (more or less) by operator followed by structural genes; Repressor is protein bound to operator; tryptophan is bound to repressor

(#) What is an inducer?

A: An inducer is a cofactor that inactivates a repressor upon binding

(#) Name two ways that viruses differ from bacteria.

A: Viruses are acellular, they have other than dsDNA genomes, they tend to not have circular genomes, they typically are smaller than bacteria, etc.

(#) Which do viruses not possess?

(i) Capsid

(ii) Capsomer

(iii) Envelope

(iv) Plasma membrane

(v) ssRNA genome

A: (iv) Plasma membrane

(#) Besides envelope proteins, what sort of material do virus envelopes consist of?

A: Lipids, i.e., phospholipids

(#) Viruses whose host ranges are limited to bacteria are called __________.

A: Bacteriophages, phages

(#) The typical virus life cycle consists of following. What major component of the typical virus life cycle is missing from the list?

(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) Progeny-virus release from the host cell

A: Packaging of virus genome into capsid\

(#) True or False, retroviruses are an example of a non-enveloped animal virus that employs reverse transcriptase to convert RNA genomes into DNA.

A: False

(#) Transduction involves the acquisition of DNA via what method of DNA transport/uptake?

A: virus (phage)-mediated

(#) To engage in sex, a bacterium must not only be capable of undergoing recombination with foreign DNA, but that DNA must be able to find its way into a bacterium's cytoplasm. Three means by which this latter step may be accomplished includes via transformation, transduction, and __________.

A: Conjugation

(#) What is a plasmid?

A: A plasmid is a relatively small is circular dsDNA found in the bacteria cytoplasm

(#) What does the R in R plasmids stand for/mean about so designated plasmids?

A: Resistance, e.g., resistance to antibiotics

(#) An operon consists of an operator, structural genes, and _________.

A: A promoter

(#) Regulatory genes produce proteins that do what? ("regulate" or the equivalent is not good enough)

A: Bind to operators

(#) Distinguish repressor from corepressor from inducer.

A: The corepressor is a small molecule that binds to the repressor, activating it

(#) Explain how CRP modulates gene expression.

A: The binding of CRP positively modulates operon activity (by facilitating the binding of RNA polymerase); binding occurs only when cyclic AMP is plentiful, which occurs when energy supplies within the cell are low; thus, CRP facilitates the catabolism of non-glucose substrates when glucose supplies (etc.) are low

(#) The binding of the tryptophan to the trp __________ ultimately results in a shutting off of the trp operon.

A: Repressor

(#) The lac operon is an example of a(n) __________ operon (i.e., not a corepressed operon).

A: Inducible or negatively-controlled are both correct

(#) Distinguish positive from negative control of prokaryotic mRNA transcription.

A: Positive control means protein binding to DNA increases transcription while negative control means that protein binding to DNA decreases transcription

(#) Given a choice, a bacterial cell will preferentially employ __________ as an energy source.

(i) cAMP

(ii) Glucose

(iii) Lactose

(iv) Sucrose

(v) Tryptophan

A: (ii) Glucose

(#) Contrast repressor mediated control of the Lac and Trp operons. That is, how, specifically does the control of these two operons differ, besides that one senses tryptophan concentrations and the other lactose concentrations.

A: For the lac operon small-molecule binding (allolactose) inactivates the repressor while for the trp operon small-molecule binding (tryptophan) activates the repressor

(#) What is a corepressor?

A: A corepressor is a small molecule that binds to repressor, activating it

(#) Which generally is not part of an operon?

(i) Operator

(ii) Promoter

(iii) Regulatory gene

(iv) Repressor binding site

(v) Structural gene(s)

A: (iii) Regulatory gene

(#) Bacteria can acquire resistance to various antibiotics via the acquisition of an R __________ via transformation or conjugation.

A: Plasmid

(#) Contrast conjugation and transformation.

A: In conjugation two bacteria dock together with one bacteria sending a plasmid to the second; with transformation DNA instead is picked up from the extracellular environment

(#) To effect generalized transduction a virus or phage must carry bacterial DNA, but as a consequence lacks what?

A: Phage/virus genes/genome/DNA

(#) The excision of pieces of DNA adjacent to a prophage and the then carrying of that DNA to a new bacterium is called…

(i) Generalized conjugation

(ii) Generalized transduction

(iii) Generalized transformation

(iv) Specialized conjugation

(v) Specialized transduction

(vi) Specialized transformation

A: (v) Specialized transduction

(#) What are the three mechanisms employed by bacteria by which "snippets" of bacterial DNA is transported from one bacterium to another?

A: Conjugation, transformation, transduction

(#) In general terms, genetic variation comes from two sources, __________ and sex.

A: Mutation

(#) __________viruses (all one word) employ reverse transcriptase to convert RNA genomes into dsDNA genomes.

A: Retro

(#) Which is the odd term out:

(i) Lysogenic

(ii) Phage T4

(iii) Prophage

(iv) Provirus

(v) Temperate virus

A: (ii) Phage T4

(#) What is a provirus?

A: A provirus is a virus genome that has integrated into the genome of its host cell

(#) A virus envelope consists of what?

A: An envelope is a lipid bilayer, plus virus envelope proteins

(#) The morphology of what aspect of viruses can be described as helical, polyhedral, complex, etc.?

A: Capsid

(#) Name at least four ways that a virus genome can differ from that, for example, of a bacterium.

A: Smaller, RNA, single stranded, segmented, diploid

(#) Types of microorganisms include bacteria (both archaebacteria and eubacteria), viruses, algae, protozoa, and _________.

A: Fungi

(#) Distinguish positive control from negative control of RNA synthesis.

A: In positive control protein binding to DNA increases rates of transcription whereas in negative control protein binding to DNA decreases rates of transcription

(#) In the prokaryotic systems that we considered, protein-DNA binding that enhances promoter activity is described as __________ control.

A: Positive

(#) In the lac operon the presence of lactose up regulates the lac operon. Explain why this is not an example of positive control of operon transcription.

A: DNA binding of the lac repressor blocks transcription while for positive control protein-DNA binding instead up regulates rather than down regulates transcription

(#) Cyclic AMP binds to what in the course of up regulation of catabolic pathways such as an already induced lac operon?

A: CRP (cAMP receptor protein)

(#) The movement of DNA into bacterial cells via virus transport can come in two more or less distinct varieties described as specialized or generalized _________, which are the movement of bacterial genes linked to temperate phage genomes and the accidental packaging of bacterial DNA instead of phage DNA, respectively.

A: Transduction

(#) Retroviruses are enveloped viruses with ssRNA, diploid genomes, but may be differentiated from other kinds of viruses particularly in terms of what aspect of their nucleic-acid replication?

A: Reverse transcription of their RNA genomes into DNA

(#) Which of the following does is not a description associated with viral integration into the genome of a host cell?

(i) Lysogenic

(ii) Lytic

(iii) Prophage

(iv) Provirus

(v) Temperate

A: (ii) Lytic

(#) What is a viral capsid?

A: A protein shell surrounding a virus' genome

(#) What is a viral envelope?

A: An envelope is a lipid bilayer surrounding the capsid of an enveloped virus

(#) For certain kinds of various animal viruses, what is derived from host-cell lipid bilayers?

A: Envelopes

(#) The lock-and-key fit between viral proteins and the virus receptor proteins found on the surface of cells is an important determinant of viral __________.

A: Host range

(#) In a typical virus life cycle, what occurs immediately after virion adsorption to the host cell and immediately before transcription of viral genes?

A: Uptake of the virus genome into the cell

(#) What is the defining feature of a temperate virus that distinguishes it from a non-temperate virus?

A: Ability to display a lysogenic cycle

(#) What is generalized transduction?

A: Generalized transduction is the movement of DNA from bacterium to bacterium by defective bacteriophage that contain only bacterial DNA and not phage DNA

(#) The ability of a bacterium to replicate despite the presence of an Antibiotic can occur as a consequence of acquisition of a(n):

(vi) A plasmid

(vii) C plasmid

(viii) G plasmid

(ix) K plasmid

(x) R plasmid

A: (v) R plasmid

(#) What is an operon?

A: An operon is the template DNA for RNA transcription as well as the transcriptional control sequences

(#) Which of the following is not a DNA sequence:

(i) Operator

(ii) Promoter

(iii) Regulatory gene

(iv) Repressor

(v) Structural gene

A: (iv) Repressor

(#) Describe the induction process for a negatively controlled inducible operon.

A: Protein repressor bound to DNA prevents transcription and binding of inducer to repressor inactivates

(#) True or False, when glucose densities are low, cAMP Receptor Protein effects positive control over Lac operon expression.

A: True