CH11 Flashcards
what kind of DNA does lambda virus have
dsDNA
it is a temperate phage
what is the pupose of cos sites in the lambda genome
they allow the linear DNA to circularize at the cos sites
what are concatemers
copies of the virus genome
what site does lambda bind to
maltose porin
what happenes if the cro promoter wins
if the cro protein wins then the virus replication leads to lysis of the cell
what happenes if the CI and CII promoter win
leads to lysogeny
CI: lambda repressor
what kind of virus is influenza A and what pandemics came from it
it is an RNA virus and it caused H1N1, H2N2, H3N2 AND H5N1
What does the H1N1 refer to on the influenza virus
the hemagglutinin (binding) and neuraminidase (releases virus particle from the cell)
What is the effect of H5N1
(bird flu) can infect humans and cause a 50% mortality rate
definition of antigenic shift
two different strains that mix
definition of antigenic drift
singular event (mutation)
how does reverse genetics go?
- CDNA
- Plasmids
- Host cell
- Analysis
Key: RNA polymerase 1
what needs to happen for the influenza virus to spread
the neuraminidase needs to remove the sialic acid
towards what direction does the dynein motor move on the microtubule
the negative end
towards what direction does the kinesin motor move on the microtubule
the positive end (used by influenza virus)
influenza replication video
https://www.youtube.com/watch?v=oXzwtGFyBik
what are lentiviruses
cause infections that progress slowly over many hears (HIV)
what are simple retroviruses
simple genomes that cause tumors and leukemia
how does HIV attach to the host cell?
binds to the CD4 receptor of lymphocytes.
note if you do not have CCR5 then you cannot get infected
how does HIV enter host cell
The envelope and host membrane fuse, and the HIV core directly enters the cytoplasm. HIV core then dissolves and releases its contents.
HIV replication video
https://www.youtube.com/watch?v=PlSvywlLuNw
what is a gene transfer vector
a DNA sequence that can express a recombinant gene in an animal or plant cell.
what kind of DNA does the Herpes virus have
double-stranded DNA
what kind of diseases can herpes cause?
chickenpox, shingles, lymphoma, and sarcoma
Herpes life cycle video
https://www.youtube.com/watch?v=fH1zS7hlW54
the herpes virus DNA exists in the latent form as what kind of virus?
episome
what is an episome
a genetic element inside some bacterial cells, especially the DNA of some bacteriophages, that can replicate independently of the host and also in association with a chromosome with which it becomes integrated.
definition of auxotrophic
The inability of an organism to synthesize a particular organic compound required for its growth
definition of prototrophs
Any microorganism that can synthesize its nutrients from inorganic material.
what does the Ames test measure
it uses bacteria to measure mutagenicity
note: there is a 95% correlation between carcinogenicity and mutagenicity
what does F+ and F- mean in bacteria
bacteria produce a sex pilus from fertility factor positive (donor) to fertility factor absent (F- recipient)
what is an hfr in conjugation
(high frequency recombinant) when the f plasmid is inserted into the bacterial chromosome
what does f’ mean in conjugation
f’ is an f+ that has picked up genes from hfr
video on bacterial cconjugation
https://www.youtube.com/watch?v=hm8SZaFmlWg
how long does it take for the plasmid in conjugation to pass on?
5 minutes
how long does it take for the chromosome in conjugation to pass on?
100 minutes
when does generalized transduction occur
occurs when random pieces of bacterial DNA are packaged into a phage. It happens when a phage is in the lytic stage
generalized transduction can transfer what kind of genes
they can transfer any genes but the number of phage particles containing a particular gene is limited
what is specialized transduction
the process by which a restricted set of bacterial genes are transferred to another bacterium
difference between generalized and specialized transduction
in generalized transduction, the bacteriophages can pick up any portion of the host’s genome. In contrast, with specialized transduction, the bacteriophages pick up only specific portions of the host’s DNA.
two kinds of mobile genetic elements
- insertion sequence (jumping)
- transposon codes for multiple antibiotic resistance
what are transposable elements
segments of DNA that can move from one location in the genome to a target sequence in another
transposition video
https://www.youtube.com/watch?v=kbOfT7LJ3R0
difference between conservative and replicative transposition
conservative: the transposable element is cut and pasted into host DNA
replicative: transposable element is ccopied to yeild two transposable elements, one in the original position and one in the target dna
what are restriction enzymes
cleave DNA molecules at or near a specific sequence of bases.
where does type 2 restriction enzyme cut
palindromic sites
it separates methylase and restriction endonuclease enzymes
what is CRISPR
a primitive microbial immune system
CRISPR video
https://www.youtube.com/watch?v=Aqw4DihmoQY
two types of DNA repair
- error-proof repair
- error-prone repair
error proof repair pathways
methyl mismatch repair, photoreactiviation, nucleotide exision repair, base excision repair, and recombinational repair
when does error-prone repair occur
when the damage is so severe that the cell has no other choice but to die
what kind of viruses have both RNA and DNA
Hepadnaviridae family
what are rescued bacteria
when the cell with antibiotic resistance lysis it covers the other cells with antibiotic resistance
when does insertional inactivation occur
when foreign DNA is made to insert into a restriction site inside a gene to resist antibiotics, hence causing the gene to turn non-functional or in an inactivated state.
can bacteria process introns
no
steps in PCR
- add dna
- add primers
- add dna polymerase
- heat and cool
how large are PCR primers
25 nucleotides
what is PCR used for
used to amplify, or copy, a specific DNA target from a mixture of DNA molecules.
what are introns
a segment of a DNA or RNA molecule which does not code for proteins and interrupts the sequence of genes
what is the TI plasmid
its a plasmid used for genetic modification in plants
table for types of DNA repaid
Powerpoint 9 slid 71
levels of gene expression control
Alteration of DNA sequence
Control of transcription
Control of mRNA stability
Translational control
Postranslational control
is DNA sequence control reversible?
least reversible, whereas control at the protein level is the most rapid and most reversible
to change their appearance microbes use what
gene regulation called phase variation
(provides immune avoidance)
two types of DNA rearrangement can be used to generate phase variations
Gene inversions and
Slipped-strand mispairing
can slipped-strand mispairing turn a gene on or off
yes
Two-component signal transduction systems sense the external environment:
- Sensor kinase in the cell membrane
- Response regulator in the cytoplasm
what is an operon
a unit made up of linked genes which is thought to regulate other genes responsible for protein synthesis.
what is a Gratuitous inducer
a gratuitous inducer is a molecule which is structurally similar to another molecule that induces transcription for a specific product
what does maximum expression of the lac operon require
the presence of cAMP and cAMP receptor protein (CRP).
what does the cAMP-CRP complex bind to
binds to the promoter, and interacts with RNA pol to increase the rate of transcription initiation.
what represses the lac Y operon
glucose
In catabolite repression, an operon enabling the catabolism of one nutrient is repressed by the presence of a more favorable nutrient. What nutrient is that
glucose
what is responsible for the breakdown of lactose into sugars for cellular metabolism in E. coli
the Lac operon
what is the lac operon repressor’s inducer molecule
lactose
what breaks down lactose into glucose and galactose?
beta galactosidase
video on the lac operon
https://www.youtube.com/watch?v=oBwtxdI1zvk
what lets lactos into the cell
permease
what is the definition of anabolism
the synthesis of complex molecules in living organisms from simpler ones together with the storage of energy; constructive metabolism.
how are anabolic pathways repressed
by inactive aporepressors
- these bind to the end product of the pathway, which is called the corepressor
what is the purpose of the trp operon
needed for the production of tryptophan
video on trp operon
https://www.youtube.com/watch?v=EvLy_1_Y3tk
where does RNA polymerase bind on the operon
the promoter
where does the repressor bond on the operon
the operator
what does an operon consist of
the promoter and operator that regulate for a set of genes upstream
what binds to the trp repressor to stop tryptophan synthesis
tryptophan as a feedback inhibition moleculte
video on transcriptional attenuation
https://www.youtube.com/watch?v=RQrdY07JkFU
when tryptophan levels are high what does the cell use to shut down the expression of tryptophan
negative regulation and attenuation
what codes for the aporepressor
the trpR gene
if the cell has excess tryptophan what does tryptophan do
it binds to the aporepressor to form the holorepressor wich blocks RNA polymerase
where does attenuation occur on the operon
the leader which lies between the operator and the first structural gene trpE
what regions on the (operon) leader base pair to form the anti-attenuator stem loop
regions 2 and 3
how is the attenuator stem-loop formed and what does it do
when regions 3 and 4 are pair on the leader operon which triggers transcription termination
attenuation is the result of a cells what
rate of protien synthesis
repression of tryptophan is a result of what
the external concentration of tryptophan
what is the stringent response
a way for bacteria to deal with starvation
the stringent response is triggered by
ppGpp which alters transcription
what is a regulon
a collection of operons that are regulated by a single regulatory protein
what are regulons controlled by
sigma factors which are used to regulate transcription
what is the purpose of sigma H
it is a heat-shock response
what is the purpose of a riboswitch
used for translational and transcriptional regulation
definition of chemotaxis
how bacteria respond in the presence of attractants in the enviroment
what causes the formation of biofilm
a signal molecule called cyclic di-GMP
what does quorum sensing refer to
the process where bacterial cells work together at high density
video on quorum sensing
https://www.youtube.com/watch?v=mQ43fuJJW7M
how do bacteria quorum sense
they sense that there are a bunch of bacteria around them when they each produce a bunch of autoinducers
what system of genes mediates the bacteria’s bioluminescence
the lux system of genes
what do the autoinducers bind to so they can create quorum sensing
the LuxR inducer
what produces autoinducers in quorum sensing
LuxI
how do bacteria sense bacterial density to form biofilms
they use autoinducers
