Microbiology Test 2
Which of the following are viable methods of release of newly assembled viral particles?
budding or lysis of host cell
What structure can the viral genome take?
ds-DNA ss-DNA ds-RNA ss-RNA
mRNA
encodes polypeptides
Early proteins
enzymes needed for DNA replication and transcription
Circular permutation
feature of many virus genomes where same genes arranged in different orders
How many DNA polymerases does E. coli have?
five
Virus
genetic element that cannot replicate independently of a living (host) cell
Neuraminidases
-destroy glycoproteins and glycolipids -allows liberation of viruses from cell
Lysozyme
-makes hole in cell wall -lyses bacterial cell
Viral structural proteins and proteins involved in the release of new viral particles that are synthesized after genomic replication begins would be considered
-middle and late proteins
Negative control
A regulatory mechanism that stops transcription
What is the benefit for a bacteriophage to be a temperate (or lysogenic) virus?
A single infection event can produce millions of new viral particles instead of hundreds of viral particles.
Some viruses have plus sense RNA genomes. Which of the following could describe one of those viruses?
A virus that contains RNA with the same nucleotide sequence as the functional mRNA that its host cell will translate to produce viral products
What is the replication cycle of a bacterial virus
Attachment (absorption) of the vision Penetration (Entry injection) of the vision nucleic acid Synthesis of virus nucleic acid and protein by host cell metabolism as redirected by the virus Assembly of the capsids and packaging of viral genomes into new virions Release of mature virions from host cell
Open reading frame
Aug followed by a number of codons and a stop codon
What are the easiest viruses to grow
Bacterial viruses
Classes of viruses based on the host they infect
Bacterial viruses Archaeal viruses Animal viruses Plant viruses Other viruses
When determining the number of virus particles in a suspension, why is the number obtained always less than the actual viral titer?
Because all of the virus particles do not infect with 100% efficiency
The major site of protein binding in DNA is the major groove. Why is this a good site for binding?
Because the major groove is wider, it is more accessible to binding proteins.
Initiation
Begins at an AUG start codon
DNA synthesis in prokaryotes
Bidirectional because of the circular chromosome Two replication forks moving in opposite directions
How is virus repocatopm typically characterized
By a one-step growth curve
What kind of regions do eukaryotic genes have
Coding and noncoding
Exons
Coding sequences
Effectors
Collective term for inducers and repressors Typically small molecules Can be structural analogs of substrates/products
Supercoiling
Compacts DNA to accommodate the genome of linear DNA which is several hundred times longer than the cell
When a transposon is cut from one location in genome and pasted into a new location, it is called __________.
Conservative transposition
How do transcription and translation occur in prokaryotes
Coupled transcription and translation occur producing proteins at a maximal rate
Gene
Functional unit of genetic information
Which statement describes the difference between the normal neuron protein PrPC and the pathogenic version PrPSc?
The amino acid sequence is identical, but the three-dimensional conformation is different.
Two-component regulatory systems rely on a balance of phosphorylation and dephosphorylation of sensor kinases and response regulators. If the response regulator became permanently phosphorylated due to lack of phosphatase activity, which of the following would NOT happen?
The cell would become more sensitive to the environmental stimulus.
During conjugation, if an Hfr cell is mated with an F- cell, why will the F- cell remain F-?
The cells would not stay in contact long enough for the entire Hfr genome to be transferred.
Which of the following would result in a frameshift mutation?
The deletion of two nucleotides in a codon
What would be the most likely effect of a mutation in the operator of a lac operon?
The genes would be constitutively expressed.
Diauxic growth
Two exponential growth phases if two energy sources available Better energy source consumed first, growth stops After lag, growth resumes with second energy source
What kind of chromosomes do eukaryotes have
Two or more linear chromosomes
Stop codons
UAA, UAG, UGA
Which of the following examples is an example of lysogenic conversion?
Vibrio cholerae bacteria produce cholera toxin when infected with a phage.
What are the viral life cycles
Virulent Temperate
Virulent virus life cycle
Virus always lyses and kills host after infection
Obligate intercellular parasites
Viruses Need a host to reproduce
Retroviruses appear to be among the more ancient viruses evolutionarily. Which of the following additional lines of evidence do not agree with this finding?
Viruses evolved from escaped introns in eukaryotic cells.
Temperate virus life cycle
Viruses replicate their genomes in tandem with host genome and without killing the host
Frameshift mutations can be very severe. What is one reason why they are often so serious?
When a frameshift mutation occurs, it causes changes in many bases downstream and can affect many of the amino acids in the protein.
In Archaea, some regulatory proteins that control transcription can act as repressors, activators, or both. How is this possible?
When acting as a repressor, the regulatory protein binds to a different DNA sequence than when it is acting as an activator.
Which of the following examples describes a type of catabolite repression?
When glucose is present, the lac operon is inhibited.
One group of chemical mutagens includes the base analogs. How do these lead to mutations?
When replication occurs, complementary base pairing may fail because the base analog may not be treated the same way as the base that it replaced
Codon bias
multiple codons for the same amino acid are not used equally
Bacteriocins
proteins that inhibit or kill closely related species or different strains of the same species
Release factors
recognize stop codon and cleave polypeptide from tRNA
Global control systems
regulate expression of many different genes simultaneously
In certain circumstances, a single regulatory protein controls multiple operons. This situation would be called a(n) __________.
regulon
Viruses that contain an envelope, two identical copies of the RNA genome, and reverse transcriptase are called __________.
retroviruses
Transposable elements
segments of DNA that can move from one site to another site on the same or a different DNA molecule Inserted into other DNA molecules (Chromosomes, plasmids, viral genomes)
Terminally redundant
some DNA sequences duplicated on both ends
Icosahedral symmetry
spherical viruses; most efficient arrangement of subunits in a closed shell
A retrovirus has a genome that consists of __________.
ssRNA
What is the difference between an F+ and an Hfr bacterium?
the Hfr donor has an F factor integrated into its main chromosome, but the F+ donor does not
The appearance of an abundance of colonies close to the test disk after an Ames test would suggest __________.
the chemical tested is a mutagen
Size of e. coli genome
4.6 Mbp
How does replication always proceed
5' to 3'
What is the general structure of RNA
60 different tRNAs Mammalian cells have 100-110 different tRNAs Single stranded Extensive secondary structure Cloverleaf shape
The genetic code has many important characteristics. For example, a specific codon always means the same thing in a particular species. Codons mean the same thing in most species (even though there are some exceptions). In some cases, a particular amino acid can be specified by more than one codon (the genetic code is degenerate). Which of the following answers describes an example of the degenerate nature of the code?
AUU, AUC, and AUA all code for Ile
Capping
Addition of methylated guanine to 5' end of mRNA, needed to initiate translation
Where do allosteric repressors bind
After being activated they bind to region of DNA near promoter called the operator
Where do corepressors bind
Allosteric repressor proteins
Elongation
Amino acids brought to the ribosome and added to the growing polypeptide Occurs in the A and P sites of the ribosome
An organism that cannot synthesize methionine is an example of __________.
An auxotroph
Cells can regulate their metabolism by regulating enzyme activity or by regulating enzyme synthesis (i.e., by regulating whether they produce the enzyme that catalyzes a reaction). Which of the following examples would be the best form of regulation when an enzyme needs to be available very rapidly?
An enzyme is activated by the binding of a molecule to its allosteric site.
What toe of virus can be cultivated in tissue cultures
Animal viruses
tRNA
COnvert mRNA to amino acid sequence of protein
Penetration
Capsid left outside the cell Viral genome and viral proteins enter host cell
Virion structure
Capsomere Capsids
rRNA
Catalytic and structural ribosome components
Proteins that play a major role in cell function
Catalytic proteins Structural proteins Regulatory proteins
DNA polymerases
Catalyze polymerization of deoxynucleotides
Release
Cell lysis, budding, or extraction
Operon
Cluster of consecutive genes whose expression is under control of a single operator All genes transcribed as single mRNA Transcription physically blocked when repressor binds to operator
Central dogma
DNA -> RNA -> Protein
Replication
DNA is duplicated by DNA polymerase
What kind of genome do viruses have
DNA or RNA they can be linear or circular Single stranded or double stranded
Transcriptional units
DNA segments transcribed into 1 RNA molecule bounded by initiation and termination sites
What are the multiple outcomes after DNA binding
DNA-binding protein may catalyze a specific a specific reaction on the DNA molecule The binding event can block transcription The binding event can activate transcription
The plaque assay
Detecting and counting viruses Plaques are clear zones that develop on lawns of host cells where successful viral infection occurs
Plasmids
Double stranded DNA that replicate separately from chromosome Usually circular Generally beneficial for the cell (ANTI BIOTIC RESISTANCE NOt extracellular, unlike viruses Found in many bacteria and Archaea Genetic information encoded on plasmids not essential for cell function under all conditions May confer a selective growth advantage Some cells contain multiple plasmids
Why is DNA replication semiconservative
Each of the two resulting double helices has one parental strand and one new strand
What are the three parts that T4 genomes can be divided into
Early Middle Late
Latent period
Eclipse+ maturation
Viral genomes
Either DNA or RNA genomes Single stranded or double stranded Either linear or circular Usually smaller than those of cells
Some viruses, especially animal viruses, have an envelope surrounding their nucleocapsid. This envelope may have viral proteins embedded in it. Why are the viral proteins more readily recognized and targeted by the immune system than the envelope?
Enveloped viruses are often coated with animal cell membrane as they leave the cell. This membrane is a major component of the viral envelope. The viral proteins are more readily recognized by the immune system, as they are more distinct from the materials normally found in and on the cells. However, the envelope can contain several types of viral components as well.
Catabolite repression
Example of global control Controls use of carbon sources if more than one present Synthesis of unrelated catabolic enzymes is repressed if glucose is present in growth medium Also called glucose effect Ensures that the best carbon and energy source is used first
Where do RNAs have to go for translation in eukaryotes
Exported outside the nucleus
Transformation is a useful technique for making genetically modified bacteria in the laboratory. There have been efforts to transform Archaea, but it has been more difficult than transforming Bacteria. One reason that it has been difficult is that Archaea lack a peptidoglycan cell wall. Why does that affect the ability of researchers to develop techniques to transform them?
Genes for resistance to penicillin and related antibiotics can't be used as selectable markers.
The genome sequence of an organism can provide information about the organism's __________.
Genes, function, and evolutionary history
How is the T4 genome packaged
Genome is pumped into head under pressure using ATP Packaging occurs in three stages (pro heads assembly, packaging motor assembled at opening, double stranded linear genome pumped into pro head using ATP After head is filled with DNA, T4 tail tail fibers and other components are self assembled Late enzymes break membrane and peptidoglycan Lysis occurs and visions are released
Eclipse
Genome replicat4ed and proteins translated
7 fundamental groups of viral species
Group 1- Double stranded DNA viruses Group 2- Single stranded DNA viruses Group 3 Double stranded RNA viruses Group 4- Positive single stranded RNA viruses Group 5- Negative single stranded RNA viruses Group 6- RNA retroviruses Group 7- DNA pararetroviruses
Enveloped viruses
Have an outer layer consisting of a phospholipid bilayer and viral proteins
Enveloped viruses structure
Have lipoprotein membrane surrounding nucleocapsid RNA or DNA genomes Envelope proteins attach to and infect animal host cells Relatively few enveloped plant or bacterial viruses because of cell walls surrounding cell membrane Entire vision enters animal cell during infection Enveloped viruses exit more easily Usually lyse the cell
Naked viruses
Have no outer layers
Virus symmetry
Helical symmetry Icosagedral symmetry
Lysogenic infection
Host cell genetically altered because viral genome becomes part of the host genome Cell host does not die
One-step growth curve
Increase occurs when cells burst
Capsomere
Individual protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid making up the capsid
Transcription
Information from DNA is transferred to RNA by RNA polymerase
Translation
Information in RNA is used to build polypeptides
What is the repressors role
Inhibition so it is called negative control
Introns
Intervening noncoding sequences Rare in Archaea Found in tRNA and rRNA genes of Archaea
How are genes transcribed in Eukaryotes
Into single single mRNAs
What is the role of ribosomal RNA
Involved in ribosome subunit association and positioning tRNAs Catalyzes peptide bond formation Interacts with elongation factors
Wobble
Irregular base pairing allowed at third position of tRNA
Retroviruses become proviruses integrated into the host chromosome soon after infecting the host cell, and can remain there indefinitely. The provirus DNA can then be transcribed and translated by the host cell, making new retroviral RNA genomes, enzymes, and structural proteins. New retroviral virions can then assemble and bud through the host cell membrane continuously over long periods of time. What is one implication of this retroviral life cycle?
It is difficult to completely cure an animal host of the virus, since anti-retroviral drugs will only eliminate circulating virions, not proviruses.
The Ames test is commonly used to test whether a particular chemical is mutagenic. When you conduct an Ames test, you need two groups of plates. One group of plates contains bacteria that are exposed to the chemical of interest, while the other plates contain bacteria that are not exposed to the chemical. Why is the latter group needed if you are just interested in the rate of mutation caused by the chemical?
It is important to compare the rate of mutations with the chemical to the normal background mutation rate. Mutations occur spontaneously even without the presence of a mutagen
Helical symmetry
Length of virus determined by length of nucleic acid Width of virus determined by size and packaging of capsomere
Enymes inside virions
Lysozyme Neuraminidases Nucleic acid polymerases
Chromosomes
Main genetic element in prokaryotes
Attachment of viruses
Major factor in host specificity Requires complementary receptors on the surface of a susceptible host for its infecting virus Receptors include proteins, carbohydrates, glycoproteins, lipids, lipoproteins or other cell structures Receptors on host cell carry out normal functions for cell
Degenerate code
Multiple codons encode a single amino acid
How are genes transcribed in prokaryotes
Multiple genes may be transcribed in one mRNA
Inert
No movement or metabolism
Nucleocapsids
Nucleic acid + protein in enveloped viruses
What is the major difference between prokaryotic and eukaryotic viruses
Nucleic acid entry in prokaryotes and vision entry in eukaryotes
What ado information macromolecules include
Nucleic acids and proteins
Where do replication and transcription occur in Eukaryotes
Nucleus
Where does splicing occur in eukaryotes
Nucleus via the spliceosome
Titer
Number of infectious units per volume of fluid
Burst size
Number of virions released
Termination
Occurs when ribosome reaches a stop codon
Steps of supercoiling
One part of circle is laid over the other Helix makes contact in two places DNA gyrase makes double strand break Unbroken helix is passed through the break Double strand break resealed behind unbroken helix Following DNA gyrase activity, two negative supercoils result
Maturation
Packaging of nucleic acids in capsids
What are amino acids linked to form polypeptide
Peptide bonds
Explain why viroids can only infect and damage plant cells, but not animal cells.
Plant cells contain a RNA polymerase that can copy RNA can animal cells do not.
How are virulence factors encoded in several pathogenic bacteria
Plasmid genes
What kind of nucleotides are DNA and RNA
Polynucleotides
Repression
Preventing the synthesis of an enzyme in response to sufficient amounts of a product
Induction
Production of an enzyme in response to the presence of substrate Typically affects catabolic enzymes Ensures enzymes are synthesized only when needed
What are the polymers of amino acids
Proteins
Regulatory proteins
Proteins that regulate cell process
How is transcription carried out
RNA polymerase uses DNA as template RNA precursors are ATP, GTP, CTP, UTP Only one strand is transcribed No priming needed
Nucleic acid polymerases
RNA replicases Reverse transcriptase
Viruses rely on the host cell machinery to make new viruses, but they sometimes provide their own enzymes (such as reverse transcriptase, which is an RNA-dependent DNA polymerase). Which of the following types of enzymes would a virus need to provide in order to replicate within a cell? In other words, which of these enzymes would not normally be found in a cell unless a virus provided it?
RNA replicases (RNA-dependent RNA polymerases) for RNA viruses
Which of the following groups contains some representatives with genomes that are so small that they may have as few as two genes?
RNA viruses
Reverse transcriptase
RNA-dependent DNA polymerase in retroviruses
RNA replicases
RNA-dependent RNA polymerases
Positive contol
Regulator protein activates the binding of RNA polymerase to DNA
Splicing
Removing introns and joining exons
Virulent infection
Replicates and destroys host
Rho-dependent termination
Rho protein recognizes specific DNA sequences and causes a pause in the RNA and RNA polymerase
What kind of chromosomes do most bacteria and archaea have
Singular circular chromosomes carrying all/most genes
RIbosomes
Sites of protein synthesis
How do bacteriophages replicate their genomes
Small DNA viruses use cell's DNA polymerase More complex DNA viruses encode their own polymerases T4 also encodes primases, helicases, and 8-protein DNA replisome complex
What violates the central dogma
Some viruses
Where do activator proteins bind
Specifically to activator binding site
Inducer
Substance that induces enzyme synthesis
Corepressor
Substance that represses enzyme synthesis
Which of the following is an example of negative control using an inducible system?
The lac operon in E. coli is turned off when lactose is not present. A repressor binds to the operator and prevents RNA polymerase from binding to the promoter. When allolactose (closely related to lactose) is present, it binds to the repressor and prevents the repressor from binding. In this way, the presence of lactose allows the operon to be turned on to express the genes need to use lactose.
Plaque assays are often used to estimate the number of virions in a sample of a particular volume (the titer). The count is given as plaque-forming units. Which of the following is NOT generally a concern that must be considered in evaluating the results of plaque assays?
The largest problem is that single viruses may create multiple plaques, resulting in overestimates of the number of viruses present.
Functional analysis of the genome of a prokaryote shows that 20% of the genome is for metabolism, 1% for biosynthesis of amino acids, 8% for peptide ABC transporters, and 2% for replication. What can you determine about the environment this organism lives in?
The organism lives in an environment rich in organic material, particularly amino acids and proteins.
Capsid
The protein shell that surrounds the genome of a virus particle
Some bacteria have unusually high mutation rates. Is there an adaptive reason why they might have such high mutation rates?
These bacteria may be able to adapt rapidly to a new environment
In a culture of bacteria, there are some individuals that are unable to synthesize histidine. What is the best and most likely description of how these individuals differ from the other bacteria in the culture?
They differ in their genotype and in their phenotype.
Anticodon
Three bases on tRNA that recognize codon Three nucleic acids encoding its cognate amino acid
Polysomes
a complex formed by ribosomes simultaneously translating mRNA
The SOS DNA repair system is __________.
a last ditch effort to prevent cell death from large amounts of damage
A change in the nucleotide sequence of DNA that is passed on to daughter cells is referred to as __________.
a mutation
Which of the following could describe a virus?
a particle composed of a protein capsid surrounding single-stranded DNA
Genetic code
a triplet of nucleic acid bases (codon) encodes a single amino acid
Polyadenylation
addition of 100-200 adenylate residues to stabilize mRNA
Because the influenza virus is segmented, when two different strains infect the same cell, a major change in the virus can occur that is called __________.
antigenic shift
Why do some bacteriophages, like ΦX174, using rolling circle replication instead of the bidirectional replication?
because ΦX174 is a single-stranded DNA virus and it does not need to have copies of both strands of the intermediate made for viral assembly
Middle and late proteins
head and tail proteins and enzymes required to liberate mature phage particles
Positive supercoiling
helps prevent DNA melting at high temperatures
Lysogen
host cell that harbors prophage
Three major steps of protein synthesis
initiation, elongation, termination
Topoisomerases
insert and remove supercoils
DNA gyrase
introduces supercoils into DNA via double-strand breaks
There are several different types of mutations possible in the base sequence of DNA. If a GGC (glycine) codon were changed to UGC (cysteine), it would be termed a __________.
missense mutation
Transcription in a virus that has an RNA genome is more complex than in a DNA-based virus because __________.
the virus must make a DNA intermediate the viral genome must encode for RNA-dependent RNA polymerase the virus must carry its own RNA-dependent RNA polymerase
Which is a likely reason for viruses to have developed?
to increase genetic diversity in cells
One reason that regulation of gene expression is important is that it saves energy and materials from being used when they are not needed. Although most genes have more than one form of regulation acting upon them, at which point would regulation be most efficient in conserving energy and materials if the product of a gene is not needed?
transcriptional regulation (regulation of whether transcription occurs)
Start codon
translation begins with AUG
Reading frame
triplet code requires translation to begin at the correct nucleotide
Negative supercoiling
twisted in opposite sense relative to right-handed double helix; found in most cells
What does DNA helicase do
unwinds DNA
Virus particle
virion Extracellular form of a virus Exists outside host and facilitates transmission from one host cell to another
Replication fork
zone of unwound DNA where replication occurs