Virginia Tech BIOL 2604 Professor Seyler Exam 4

DNA

herpesvirus is (DNA/RNA) and enveloped

lysogeny

Lambda Phage Infection

if enough cII, cIII, and cI get made, these proteins can trigger _____________

lytic

Lambda Phage Infection

the Cl protein (lambda repressor) causes repression of lambda (lytic/lysogenic) events

Cos

Lambda Phage Infection

rolling circle DNA replication

- after replication, each Lambda virion receives 1 copy of the genome

- the site where the DNA is cut for each capsid is called the _______ site

c1 protein

Lytic Growth of Lambda After Induction

lack of what protein? favors the lytic cycle by allowing activation of PL and PR.

Excisionase

Lytic Growth of Lambda After Induction

Xis (__________________) and Int are produced, resulting in excision of the genome from the host chromosome

VII

hepadnaviruses are DNA, enveloped, and class ______

RNA

retroviruses are (DNA/RNA), enveloped, class VI

Lambda

double-stranded DNA temperate phage

class I (ds DNA)

what class does Lambda belong to?

the C1 (lambda repressor protein) and the Cro protein

Penetration of the Lambda Genome

- lambda DNA injects into the host and then circularizes

- expression of what 2 proteins? will determine which pathway (lytic or lysogenic) occurs

lytic

Lambda Phage Infection

when the Cro protein is the dominant regulatory molecule, what cycle, the lytic or the lysogenic, occurs?

PR, PL

Lambda Phage Infection

Cro being the dominant regulatory molecule → lytic cycle triggered → expression of transcripts from what 2 promoter?

RecA protease

Lambda Phage Infection

this destroys the Cl (Lambda repressor) protein, resulting in Cro activation and entry into lytic cycle

rolling circle DNA replication

Lambda Phage Infection

when lambda goes into the lytic pathway, it has to replicate its genome. By what mechanism does Lambda replicate its genome?

RNA

orthomyxoviruses (influenza viruses) are ss (DNA/RNA), segmented, & enveloped

RNA

rhabdoviruses are (DNA/RNA), enveloped

persistent infection

Consequences of Virus Infection in Animal Cells

type of infection with slow release of virus without cell death

latent infection

Consequences of Virus Infection in Animal Cells

type of infection where the virus is present but not causing harm to cell; later emerges in lytic infection, lying the host cell

nervous

Latent Infections

- examples: Herpes simplex virus, Varicella virus

- characteristics: primary acute infection, virus harbored in ___________ tissue, recurrent infections, recurrence with trauma or stress, no virus production during latent stage

antigenic SHIFT

Influenza Viruses (orthomyxoviruses)

rearrangement of genome segments to produce different viruses; some genes from one virus and one from another switch → different viruses; mixing and matching → different virus particles

antigenic DRIFT

Influenza Viruses (orthomyxoviruses)

minor antigenic changes due to genetic mutations; minor changes to coding sequences of genes of these proteins; if you change the protein a little, the antibodies are no longer going to recognize the new viruses

class I (ds DNA)

what class does T4 belong to?

class VI (ss RNA genome that replicates w/ DNA intermediate)

what class do retroviruses belong to?

class VI (ss RNA genome that replicates w/ DNA intermediate), class VII (ds DNA genome that replicates w/ RNA intermediate)

Which viral classes require the reverse transcriptase enzyme?

viral genome

which genome (host or viral) encodes the reverse transcriptase enzyme?

an RNA template

the reverse transcriptase enzyme purpose: produces DNA from what?

positive

(positive/negative) sense RNA viruses can use the nucleic acid directly as mRNA.

phage-encoded nucleases

A __________________ is an enzyme responsible for degrading the genome of the host cell.

reverse transcriptase

The Genome of Retroviruses

- class VI: ss RNA genome that replicates w/ DNA intermediate

- RNA enveloped

- contains __________ __________________ enzyme that copies the information from its RNA genome into DNA

DNA

retroviruses replicate through a ________ intermediate.

pol

Genome Map of Retroviruses

what gene encodes the reverse transcriptase enzyme?

provirus

Steps of Retrovirus Replication

(1) entrance into host

(2) uncoating

(3) reverse transcription from ss RNA to ds DNA

(4) integration into host DNA → _______________

(5) transcription to ss RNA (mRNA)

(6) encapsidation of 2 genomes and reverse transcriptase

(7) release by budding

HIV

name the prime example of a retrovirus

plants

viroids = small (~250-400 bases) circular ssRNA particles known to infect _________

regulatory RNA

Viroids

- naked nucleic acid (no capsid)

- do not encode proteins, completely dependent on host-encoded enzymes

- mechanism of action unknown but thought to function as a _______________ ________, disrupting normal expression of proteins

prions

infectious agents whose extracellular form consists entirely of protein (no nucleic acid)

PrPsc has a different conformation/folding from PrPc

How Prions Cause Disease

- the host cell encodes the prion (since the prion has no nucleic acid)

- the host contains the PrPc gene (native form of the prion)

- pathogenic form of the prion = PrPSc

- how is PrPsc different from PrPc?

- when the PrPSc form enters a host cell that is expressing PrPc, it promotes conversion of PrPc into the pathogenic form (a.k.a the pathogenic prion replicates by converting preexisting native prions into the pathogenic form)

- as the pathogenic prions accumulate and aggregate → disease

mad cow disease

name the example of a disease called by prions

point mutation

Molecular Basis of Mutation

this type of mutation results from a change in a single base pair and can lead to a single amino acid change in a polypeptide or to no change at all, depending on the particular codon involved

3 types: silent, missense, nonsense

silent mutation

Molecular Basis of Mutation

type of point mutation where the changed base does not affect the coded amino acid; change in base still codes for the same AA

missense mutation

Molecular Basis of Mutation

type of point mutation where the changed base changes the AA that is coded for

nonsense mutation

Molecular Basis of Mutation

type of point mutation where the changed base results in the coding for a stop codon

frameshift

Molecular Basis of Mutation

deletions and insertions cause more dramatic changes in the DNA, including _______________ mutations, and often result in complete loss of gene function

RecA

this protein has the main function in catalyzing DNA recombination, but also recognizes problems in DNA

recombination

homologous _________________ arises when closely related DNA sequences from two distinct genetic elements are combined in a single element

transformation, transduction, conjugation

what are the 3 methods that genetic material gets into bacterial cells?

transformation

3 Methods of Genetic Material Getting Into Bacterial Cells

(1) _________________: uptake of “naked” DNA directly from the environment; DNA is taken up by another cell

transduction

3 Methods of Genetic Material Getting Into Bacterial Cells

(2) _________________: phage-mediated transfer of DNA

conjugation

3 Methods of Genetic Material Getting Into Bacterial Cells

(3) _____________ = transfer via cell-to-cell contact; pilus mediated

capsule

Streptococcus pneumoniae becomes transformed

the ___________ is a virulence factor, allowing the cell to cause the pneumonia disease

mouse

How Transformation Was Discovered

- smooth cells (w/ capsule) → death in __________

- rough cell (no capsule) → no death

- heat-killed smooth cells → no death

- heat-killed smooth strain + live rough cells → death (live S and R strains isolated from dead mouse)

this experiment proved that the live rough cells transformed into smooth cells (because the DNA from the smooth cells was transferred into the rough cells)

transformation with DNA fragments, transformation with a plasmid

what are the 2 ways transformation can occur?

transducing particle

How Generalized Transduction Occurs

(1) phage DNA enters host

(2) destruction of host DNA

(3) phage DNA replicates & coat proteins synthesized

(4) virus capsid synthesis & virus assembly

(5) if by accident the bacterial DNA gets packaged instead of the phage DNA, the bacterial DNA packaged in the capsid = _____________ ________________

gene transfer

How Generalized Transduction Occurs

(6) lysis of cell → release of phage particles and subsequent infection of another cell

(6) bacterial DNA (from the transducing particle) can be injected into a new host and can be integrated into the host DNA → stable ________ ___________

specialized transduction

Temperate phage have alternate life cycles whereby they can replicate new virions (lytic cycle) or integrate its genome into the host, replicating with the bacterium (lysogenic cycle).

These viruses may undergo __________________ _____________________

virus genome

The Difference Between Generalized and Specialized Transduction

generalized: DNA derived from virtually any portion of the host genome is packaged inside the mature virion in place of the virus genome

specialized: DNA from a specific region of the host chromosome is integrated directly into the ______ _____________—usually replacing some of the virus genes

bacteriophage

Generalized transduction transfers any part of the bacterial DNA, while specialized transduction transfers specific regions of the bacterial DNA.

Generalized transduction occurs due to random errors during the packaging of the viral capsid, whereas specialized transduction occurs when the ______________________ genome integrates into and excises from the bacterial chromosome; need the prophage for specialized transduction

hosts

Specialized Transduction

When the new virus genomes enter new bacterial _______, they take with them the bacterial genes from the previous host. If these newly introduced bacterial genes become integrated into the genome of the new host, the specialized transduction is successful.

conjugation

the transfer of genes from one prokaryotic cell to another by a mechanism requiring cell-to-cell contact

2 F+ cells

Conjugation Steps

(1) F+ cell (donor) extends pilus to F- cell (recipient)

(2) cell pairs stabilize; F plasmid (in the F+ cell) nicked into 1 strand

(3) 1 strand is transferred from the F+ cell to the F- cell, F plasmid is simultaneously replicated in F+ cell

(4) complementary strand is synthesized in recipient cell

(5) DNA transfer and synthesis is completed, cells separate

what is the resulting cell types?

Hfr strain

Conjugation

another form of conjugation can occur when the F plasmid integrates into the bacterial host chromosome, resulting in a ______ __________

F+

a cell that has the F plasmid; F plasmid is separate from the bacterial host chromosome

F-

a cell that does not have an F plasmid; serves as the recipient in conjugation

Hfr, F- (recipient stays F-)

conjugation between an Hfr strain cell and a F- cell results in what cell types?

NTPs

Transcription Steps

________ = building blocks for building RNA, including ATP, GTP, UTP, CTP

single promoter that has multiple coding sequences; 2 or more genes transcribed into a single RNA and under the control of a single regulatory site

What constitutes a prokaryotic operon?

sugar operons

these operons are named based on their substrate; therefore, these operons will be turned on in the presence of their substrate and will be inhibited when the substrate is not present

example: lac operon

amino acid operon

these operons are named based on what the genes of the operon code for; therefore, these operons will be turned on when there is a lack of the substrate/when the proteins that the genes encode for are needed

example: arginine operon

-35 sequence, -10 sequence

What two specific consensus sequences are recognized by the RNA polymerase within the promoter?

polycistronic

Differences b/w Prokaryotic and Eukaryotic Transcription

PROKARYOTES

- single form of RNA polymerase

- introns are rare

- ___________________ messages

- little RNA processing (especially mRNA)

- few transcription initiation factors

- transcription is cytoplasmic

nucleus

Differences b/w Prokaryotic and Eukaryotic Transcription

EUKARYOTES

- multiple forms of RNA polymerase

- introns are common

- monocistronic messages

- extensive RNA processing

- multiple transcription initiation factors

- transcription is in ______________

polycistronic

characteristic of prokaryotic transcription where an mRNA has multiple genes whose expression is also controlled by a single promoter and a single terminator

sigma subunit

Which RNA polymerase subunit is responsible for recognizing the promoter?

at level of enzyme activity, at the level of transcription, at the level of translation

At what three levels can you control bacterial enzyme activity?

inactive

3 levels can you control bacterial enzyme activity

- at transcription level: no mRNA synthesis

- at translation level: no enzyme synthesis

- at enzyme activity level: enzyme is made, but is ___________

RNA polymerase, DNA template

Mechanisms of Regulating Gene Product Activity

transcriptional regulation can be implemented through molecules that bind what 2 things?

RNA polymerase

Mechanisms of Regulating Gene Product Activity

if you have something that binds to _____ ________________ to inhibit it, that will inhibit all genes

DNA template

Mechanisms of Regulating Gene Product Activity

if you have something that binds to the _____ ______________ to inhibit transcription, that would be specific to specific genes

efficiency

Why Regulation of Certain Genes at Certain Control Levels

relates to speed vs. ______________

- much more efficient way to regulate is at the level of transcription if you don’t need the protein product at all

- but if you need that protein at some point but not now, its better to regulate at the enzyme activity so that the protein can be turned on if it is needed quickly when it is needed

- conserve resources and energy if we don't need those products

protein domain

a functional part of the protein that does a specific job for the protein (DNA binding domain, domain that holds dimeric proteins together)

operator

sequence of DNA that is an inverted repeat that is recognized by a repressor protein

corepressor

Arginine Operon

- normal state: repressor NOT bound, transcription of arginine genes (to make arginine) occurs

- in the presence/excess of arginine, arginine acts as a _____________, binds to the repressor, allowing the repressor to bind to the operator and block transcription of more arginine

operator

Repressors bind to (operator/promoters)

inducer

A molecule that binds to a repressor to turn on expression of a gene is called a ______________

activator binding site

Activators bind to (operators/activator binding site)

inducer

A molecule that binds to an activator to turn on gene expression is termed a ________________

ß-galactosidase

Lac Operon

- the operon that allows for the creation of enzymes that are needed to use lactose as energy

- - relative low amount of lactose in the cell, but once lactose is added, the cells will transcribe the Lac operon to produce the enzyme ____________________ = needed to breakdown lactose

inducer

Lac Operon

- normal state: not a lot of lactose → repressor is bound to the operator on the Lac operon, transcription does not occur

- in the presence of lactose, lactose acts as an __________, binds to the repressor, inhibiting the repressor from binding to the operator → transcription of the Lac operon occurs to transcribe genes needed for the breakdown of lactose

inducer

Positive Control Induction at the Maltose Utilization Operon

- normal state: activator protein not bound to RNA polymerase, RNA polymerase not bound to promoter → no transcription

- in the presence of maltose, maltose acts as an _________ and binds to the activator protein, stabilizing the RNA polymerase at the promoter → transcription occurs

negative control

action of a repressor to inhibit transcription

low

Lac Operon Regulation & Catabolite Repression

the activator site is bound when the glucose levels are (high/low)

CAP (catabolite activator protein)

Lac Operon Regulation & Catabolite Repression

what is the activator protein for the lac operon?

cAMP

Lac Operon Regulation & Catabolite Repression

in the presence of glucose, adenylate cyclase does not convert ATP → _________ = inducer of CAP

lactose

Lac Operon Regulation & Catabolite Repression

in the absence of glucose, adenylate cyclase converts ATP → cAMP, which binds to CAP protein → CAP protein binds to operon, allowing Lac operon transcription to get enzymes to breakdown __________

CAP activator protein will bind when glucose levels are low

lac operon is both positively and negatively controlled

how is the lac operon positively controlled?

if lactose levels are low, the repressor protein binds to the operator and prevents transcription

lac operon is both positively and negatively controlled

how is the lac operon negatively controlled?

Diauxic

____________ growth, meaning double growth, is caused by the presence of two sugars on a culture growth media, one of which is easier for the target bacterium to metabolize.

lac operon

Diauxic Growth

if glucose and lactose are put in the medium, the cells would preferably use glucose first and use it until it is all gone → cells stop growing for a little → cells start to express other genes (the _____ ___________ starts to be expressed) to use lactose

low, low

In the presence of glucose, cAMP levels are (low/high), leading to (low/high) expression of the lac operon.