BIO 2200 Exam 3 Flashcards
What is gene expression?
transcription of gene into mRNA followed by translation of mRNA into protein
Why is regulation important?
It helps conserve energy and resources by making sure the right genes are turned on or turned off
What are the two major levels of regulation in the cell?
One controls the activity of preexisting enzymes, while the other controls the amount if an enzyme
What is the main site of protein binding on DNA?
the major groove; inverted repeat sequences are frequently binding sites for regulatory proteins
What are homodimeric proteins?
proteins composed of two identical polypeptides which interact with inverted repeats on DNA
Describe the helix-turn-helix domain of binding proteins.
First helix is the recognition helix and second helix is the stabilizing sequence. Examples are lac and tcp repressors of E. coli
Describe the zinc finger domain of protein.
A protein structure that binds to a zinc ion. Typically two or three zinc fingers on proteins that use them for DNA binding.
Describe the leucine zipper domain of protein.
Leucine residues are spaced every seven amino acids. It does not interact directly with DNA.
What are three outcomes of DNA-binding proteins?
DNA-binding proteins may catalyze a specific reaction on the DNA molecule (i.e., transcription by RNA polymerase). The binding event can block transcription (negative regulation) or activate transcription (positive regulation).
How is gene expression controlled in bacteria?
These systems are greatly influenced by environment in which the organism is growing. Presence or absence of specific small molecules can also control gene regulation. Interactions between small molecules and DNA-binding proteins result in control of transcription or translation.
What is negative control of transcription?
a regulatory mechanism that stops transcription
What is repression?
prevention of the synthesis of an enzyme in response to a signal; typically affects anabolic enzymes
What is induction?
production of an enzyme in response to a signal; typically affects catabolic enzymes
What is an inducer?
substance that induces enzyme synthesis; turns on expression
What is a corepressor?
substance that represses enzyme synthesis
What is an effector molecule?
collective term for inducers and repressors; can either turn on or off expression
What molecules do repressors bind to?
allosteric repressor protein, which becomes active and binds to regions of DNA near promoter called the operator
What is an operon?
cluster of genes arranged in a linear fashion whose expression is under control of a single operator (operator is located downstream of the promoter)
What is positive control of transcription?
regulator protein activates the binding of RNA polymerase to DNA
Give an example of positive control.
Maltose catabolism in E. coli;
Maltose activator protein cannot bind to DNA unless it first binds maltose
What is the site where activator proteins bind?
activator-binding site
What is a regulon?
Multiple operons controlled by the same regulatory protein are called a regulon; exist in both positive and negative control
What are global control systems?
regulate expression of many different genes simultaneously
What is catabolite repression?
example of global control; synthesis of unrelated catabolic enzymes is repressed if glucose is present in growth medium; lac operon is under control of catabolite repression; it ensures the “best” carbon and energy source is used first
What is diauxic growth?
two exponential growth phases; when glucose is available, the organisms uses that as energy, then stops, then breaks down lactose for energy
What is a key molecule in many metabolic control systems?
Cyclic AMP; it is a regulatory nucleotide
What happens during diauxic growth?
CRP is an activator protein; cAMP is an allosteric inducer for CRP; when glucose is present, there are low levels of cAMP, but when glucose is absent, there are high levels of cAMP; When cAMP is present, CRP is activated
What happens when lactose is absent during diauxic growth?
the lactose repressor is bound, even in the presence of cAMP, which blocks the RNA polymerase
What must happen in order to break down lactose?
you must have both absence of glucose and presence of lactose
What do Archaea use to control transcription?
Archaea use DNA-binding proteins to control transcription –> more closely resembles control by Bacteria than Eukarya.
What are the repressor proteins in Archaea?
NrpR is an example of an archaeal repressor protein from Methanococcus maripaludis –> Represses genes involved in nitrogen metabolism
What type of regulatory system do prokaryotes?
two-component regulatory system
What is signal transduction?
in prokaryotes, when external signal is detected by sensor and transmitted to regulatory machinery; most are two-component regulatory systems
Give an example of a modified two-component regulatory system.
Modified two-component system used in chemotaxis to sense temporal changes in attractants or repellents and regulate flagellar rotation.
What are the three main steps in chemotaxis?
1) Response to Signal: sensory proteins in cytoplasmic membrane sense attractants and repellents. Methyl-accepting chemotaxis proteins (MCPs) bind to attractant or repellent and initiate flagellar rotation.
2) Controlling Flagellar Rotation: controlled by CheY protein –> CheY results in counterclockwise rotation and runs and CheY-P results in clockwise rotation and tumbling.
3) Step 3: Adaptation: Feedback loop allows the system to reset itself to continue to sense the presence of a signal. This involves modification of MCPs
What does the Che protein do?
provides motility to flagella in the clockwise or counterclockwise rotation
What is quorum sensing and what does it do?
mechanism by which bacteria assess their population density; ensures sufficient number of cells are present before initiating a response that requires a certain cell density to have an effect (e.g., toxin production in pathogenic bacterium)
What do autoinducer molecules do? (3)
diffuses freely across the cell envelope,
reaches high concentrations inside cell only if many cells are near, and binds to specific activator protein and triggers transcription of specific genes
What was the first autoinducer discovered?
Acyl homoserine lactone
How was quorum sensing first discovered?
Quorum sensing was first discovered as mechanism regulating light production in bacteria including Aliivibrio fischeri.
What are two examples of quorum sensing?
P. aeruginosa switches from free living to growing as a biofilm; Virulence factors of Staphylococcus aureus
What is a stringent response? What is it triggered by?
global control mechanism triggered by amino acid starvation; triggered by (p)ppGpp
What happens during the stringent response?
Alarmones, produced by RelA, signal amino acid starvation –> rRNA and tRNA synthesis decreases –> amino acid synthesis increases
What is the heat shock response controlled by? What do heat shock proteins do?
largely controlled by alternative sigma factors; Heat shock proteins counteract damage of denatured proteins and help cell recover from temperature stress (very ancient proteins); Heat shock response also occurs in Archaea
What is endospore formation in bacillus triggered by?
Triggered by adverse external conditions (i.e., starvation or desiccation)
What is caulobacter differentiation? What is it controlled by?
when bacteria is in two different forms: Swarmer cells (dispersal role) and stalked cells (reproductive role); Controlled by three major regulatory proteins
What regulates mRNA? How is transcription of these enhanced?
Antisense RNA’s (small); transcription of antisense RNA is enhanced when its target genes need to be turned off
What are riboswitches? Where are they located? Where are they found? What type of control is riboswitch control analogous to?
RNA domains in an mRNA molecule that can bind small molecules to control translation of mRNA. Located at 5’ end of mRNA. Found in some bacteria, fungi, and plants. Riboswitch control is analogous to negative control.
What is attenuation? What was the first example?
Transcriptional control that functions by premature termination of mRNA synthesis. First example was the tryptophan operon in E. coli.
Where does translation-independent attenuation?
Gram-positive Bacteria, such as Bacillus
What is a virus?
genetic element that cannot replicate independently of a living (host) cell
What is the study of viruses called?
virology
What is a virion (virus particle)? What is it made of?
extracellular form of a virus; exists outside host and facilitates transmission from one host cell to another; contains nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material
What are two characteristics of viral genomes?
either DNA or RNA genome; some circular, but most linear
How can viruses be classified?
on the basis of the hosts they infect (bacterial viruses; arc heal viruses, animal viruses, plant viruses, etc)
What is the size of viruses?
most are smaller than prokaryotic cells (0.02 to 0.3 micrometers)
What is a capsid? What is it composed of?
the protein shell that surrounds the genome of a virus particle; composed of a number of protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid
What is a capsomere?
subunit of the capsid; smallest morphological unit visible with an electron microscope
What is a nucleocapsid?
complete complex of nucleic acid and protein packaged in the virion
What is an enveloped virus?
virus that contains additional layers around the nucleocapsid; envelope makes initial contact with the host cell
What is helical symmetry of viruses? What are the length and width determined by?
rod-shaped viruses (e.g. tobacco mosiac virus); length of virus determined by length of nucleic acid; width of virus determined by size and packaging of protein subunits
What is icosahedral symmetry?
spherical viruses (e.g. human papillomavirus); most efficient arrangement of subunits in a closed shell
What is a complex virus?
virions composed of several parts, each with separate shapes and symmetries; bacterial viruses contain complicated structures (icosahedral heads and helical tails)
What does the lysozyme do?
makes hole in cell wall and lyses bacterial cell
What are the enzymes critical to infection?
lysozyme, nucleic acid polymerases, and neuraminidases
What are neuraminidases?
enzymes that cleave glycosidic bonds and allow liberation of viruses from cell
What are the easiest viruses to grow? What are the hardest?
Bacterial viruses are the easiest to grow (serve as a model system to study viruses); Plant viruses are hardest to grow
What is a titer?
number of infectious units per volume of fluid
What is a plaque assay?
analogous to the bacterial colony; one way to measure virus infectivity
What are plaques?
clear zones that develop on lawns of host cells; each plaque results from infection by a single virus particle
What is a virus?
genetic element that cannot replicate independently of a living (host) cell
What is the study of viruses called?
virology
What is a virion (virus particle)? What is it made of?
extracellular form of a virus; exists outside host and facilitates transmission from one host cell to another; contains nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material
What are two characteristics of viral genomes?
either DNA or RNA genome; some circular, but most linear
How can viruses be classified?
on the basis of the hosts they infect (bacterial viruses; arc heal viruses, animal viruses, plant viruses, etc)
What is the size of viruses?
most are smaller than prokaryotic cells (0.02 to 0.3 micrometers)
What is a capsid? What is it composed of?
the protein shell that surrounds the genome of a virus particle; composed of a number of protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid
What is a capsomere?
subunit of the capsid; smallest morphological unit visible with an electron microscope
What is a nucleocapsid?
complete complex of nucleic acid and protein packaged in the virion
What is an enveloped virus?
virus that contains additional layers around the nucleocapsid; envelope makes initial contact with the host cell
What is helical symmetry of viruses? What are the length and width determined by?
rod-shaped viruses (e.g. tobacco mosiac virus); length of virus determined by length of nucleic acid; width of virus determined by size and packaging of protein subunits
What is icosahedral symmetry?
spherical viruses (e.g. human papillomavirus); most efficient arrangement of subunits in a closed shell
What is lysogen?
a bacterium containing a prophage
What does the lysozyme do?
makes hole in cell wall and lyses bacterial cell
What are the enzymes critical to infection?
lysozyme, nucleic acid polymerases, and neuraminidases
What are neuraminidases?
enzymes that cleave glycosidic bonds and allow liberation of viruses from cell
What are the easiest viruses to grow? What are the hardest?
Bacterial viruses are the easiest to grow (serve as a model system to study viruses); Plant viruses are hardest to grow
What is a titer?
number of infectious units per volume of fluid
What are satellite viruses?
defective viruses for which no intact version exists; rely on unrelated viruses as helpers
What are plaques?
clear zones that develop on lawns of host cells; each plaque results from infection by a single virus particle
What are the five steps of viral replication?
1) Attachment (adsorption) of the virus to a susceptible host cell
2) Entry (penetration) of the the vision or its nucleic acid
3) Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus
4) Assembly of capsids and packaging of viral genomes into new visions (maturation)
5) Release of mature virions from host cell
How is attachment of vision to host cell highly specific?
It requires complementary receptors on the surface of a susceptible host and its infecting virus. These receptors on host cell carry out normal functions for cell (e.g. uptake proteins, cell to cell interaction).
What is a permissive cell?
host cell that allows the complete replication cycle of a virus to occur
How does Bacteriophage T4 penetrate into its host cell?
The host cell is E. coli. Virions attach to cells via tail fibers that interact with polysaccharides on E. coli cell envelope. Tail fibers retract and tail core makes contact with E. coli cell wall. Lysozyme-like enzyme forms small pore in peptidoglycan. Tail sheath contracts and viral DNA passes into cytoplasm.
What are restriction modification systems?
It is a DNA destruction system. Only effective against double-stranded DNA viruses. Restriction enzymes (restriction endonucleases) cleave DNA at specific sequences. Modification of host’s own DNA at restriction enzyme recognition sites prevents cleavage of own DNA
What are two ways viruses evade bacterial restriction systems?
1) Chemical modification of viral DNA (glycosylation or methylation)
2) Production of proteins that inhibit host cell restriction system
What are the life cycles of viruses?
Virulent mode (viruses lyse host cells after infection) and temperate mode (viruses replicate their genomes in tandem with host genome without killing host [virus can also be lytic])
What type of dsDNA did the first studied viruses have? T4?
first studied dsDNA was linear; T4 has a dsDNA genome that is circularly permuted and terminally redundant, which both affect genome packaging.
What modified base does T4 DNA have?
5-hydroxymethylcytosine; this makes the DNA resistant to virtually al known restriction enzymes
What three parts can the T4 genome be divided into?
1) Early and middle proteins: enzymes needed for DNA replication and transcription
2) Late proteins: head and tail proteins and enzymes required to liberate mature phage particles
What are temperate viruses?
viruses that can undergo a stable genetic relationship within the hist, but can also kill cells through lytic cycle
What is lysogeny?
a state where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with the host chromosome
What is lysogen?
a bacterium containing a prophage
What are the five steps of viral replication?
1) Attachment (adsorption) of the virus to a susceptible host cell
2) Entry (penetration) of the the vision or its nucleic acid
3) Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus
4) Assembly of capsids and packaging of viral genomes into new visions (maturation)
5) Release of mature virions from host cell
How is attachment of vision to host cell highly specific?
It requires complementary receptors on the surface of a susceptible host and its infecting virus. These receptors on host cell carry out normal functions for cell (e.g. uptake proteins, cell to cell interaction).
What is a permissive cell?
host cell that allows the complete replication cycle of a virus to occur
How does Bacteriophage T4 penetrate into its host cell?
The host cell is E. coli. Virions attach to cells via tail fibers that interact with polysaccharides on E. coli cell envelope. Tail fibers retract and tail core makes contact with E. coli cell wall. Lysozyme-like enzyme forms small pore in peptidoglycan. Tail sheath contracts and viral DNA passes into cytoplasm.
What are restriction modification systems?
It is a DNA destruction system. Only effective against double-stranded DNA viruses. Restriction enzymes (restriction endonucleases) cleave DNA at specific sequences. Modification of host’s own DNA at restriction enzyme recognition sites prevents cleavage of own DNA
What are two ways viruses evade bacterial restriction systems?
1) Chemical modification of viral DNA (glycosylation or methylation)
2) Production of proteins that inhibit host cell restriction system
What are the life cycles of viruses?
Virulent mode (viruses lyse host cells after infection) and temperate mode (viruses replicate their genomes in tandem with host genome without killing host [virus can also be lytic])
What type of dsDNA did the first studied viruses have? T4?
first studied dsDNA was linear; T4 has a dsDNA genome that is circularly permuted and terminally redundant, which both affect genome packaging.
What modified base does T4 DNA have?
5-hydroxymethylcytosine; this makes the DNA resistant to virtually al known restriction enzymes
What three parts can the T4 genome be divided into?
1) Early and middle proteins: enzymes needed for DNA replication and transcription
2) Late proteins: head and tail proteins and enzymes required to liberate mature phage particles
What are temperate viruses?
viruses that can undergo a stable genetic relationship within the hist, but can also kill cells through lytic cycle
What is lysogeny?
a state where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with the host chromosome
What is lysogen?
a bacterium containing a prophage
What are the four consequences of virus infection in animal cells?
1) Persistent infections: release of virions from host cell does not result in cell lysis. Infected cell remains alive and continues to produce virus
2) Latent infections: delay between infection by the virus and lytic events
3) Transformation: conversion of normal cell into tumor cell
Cell fusion: two or more cells become one cell with many nuclei
What are retroviruses?
RNA viruses that replicate through a DNA intermediate.
How are the genomes in retroviruses unique?
It has two identical ssRNA molecules of the plus (+) orientation. Also, it contains specific genes: - gag: encode structural proteins - pol: encode reverse transcriptase and integrase - env: encode envelope proteins
What is the process of replication of a retrovirus?
1) Entrance into the cell
2) Removal of virion envelope at the membrane
3) Reverse transcription of one of the two RNA genomes
4) Integration of retroviral DNA into host genome
5) Transcription of retroviral DNA
6) Assembly and packaging of genomic RNA
7) Budding of enveloped virions; release from cell
What are defective viruses? What do the require to provide some function?
Viruses that are parasitic on other viruses. Require other virus (helper virus) to provide some function.
What are satellite viruses?
defective viruses for which no intact version exists; rely on unrelated viruses as helpers
What are viroids? Give 4 characteristics.
infectious RNA molecules that lack a protein coat; Smallest known pathogens (246–399 bp), cause a number of important plant diseases,
small, circular, ssRNA molecules, and do not encode proteins, instead they completely dependent on host-encoded enzymes
What are prions? Give 3 characteristics.
infectious proteins whose extracellular form contains no nucleic acid; Known to cause disease in animals (transmissible spongiform encephalopathies), host cell contains gene (PrnP) that encodes native form of prion protein that is found in healthy animals, and prion misfolding results in neurological symptoms of disease (e.g., resistance to proteases, insolubility, and aggregation)
What is infectious prion disease?
pathogenic form of prion protein is transmitted between animals or humans
What is sporadic prion disease?
random misfolding of a normal, healthy prion protein in an uninfected individual
What is inherited prion disease?
mutation in prion gene yields a protein that changes more often into disease-causing form
What is a mutation?
Heritable change in DNA sequence that can lead to a change in phenotype (observable properties of an organism)
What is a mutant?
A strain of any cell or virus differing from parental strain in genotype (nucleotide sequence of genome)
What is a wild-type strain?
Typically refers to strain isolated from nature
What are selectable mutations?
Those that give the mutant a growth advantage under certain conditions. These are useful in genetic research.
What are non selectable mutations? What does detection of such mutations require?
Those that usually have neither an advantage nor a disadvantage over the parent. Detection of such mutations requires examining a large number of colonies and looking for differences.(screening).
What is replica plating useful for?
Replica plating is useful for identification of cells with a nutritional requirement for growth (auxotroph).
What are induced mutations?
Those made environmentally or deliberately. They can result from exposure to natural radiation or oxygen radicals.
What are spontaneous mutations?
Those that occur without external intervention.
What are point mutations?
Mutations that change only one base pair.
Can lead to single amino acid change in a protein, an incomplete protein, or no change at all.
What is a silent mutation?
Does not affect amino acid sequence.
What is a missense mutation?
amino acid is changed; polypeptide altered
What is a nonsense mutation?
codon becomes stop codon; polypeptide is incomplete
What is a frame shift mutation?
Deletions or insertions that result in a shift in the reading frame. Often result in complete loss of gene function.
What is reversion?
alteration in DNA that reverses the effects of a prior mutation
What is a revertant? Same-site revertant? Second-site revertant?
A revertant is a strain in which original phenotype is restored. Same-site revertant is a mutation that is at the same site as original mutation. Second-site mutation is a mutation that is at a different site in the DNA.
What is site-directed mutagenesis?
Where genetic engineering allows for the introduction of specific mutations.
What are the mutation rates for DNA, DNA viruses, and RNA?
errors in DNA replication occur at a frequency of 10^-6 to10^-7 per kilo base; DNA viruses have error rates 100–1000x greater; The mutation rate in RNA genomes is 1000-fold higher than in DNA genomes because RNA repair mechanisms similar to DNA repair mechanisms do not exist
What are mutagens?
chemical, physical, or biological agents that increase mutation rates
What are the two categories of mutagenic electromagnetic radiation?
1) Non-ionizing (UV radiation); pyrimidine dimer is one effect of UV radiation
2) Ionizing (X-rays, cosmic rays, and gamma rays); ionize water and produce free radicals –> free radicals damage macromolecules in the cell
What are the three types of DNA repair systems?
1) Direct reversal: mutated base is still recognizable and can be repaired without referring to other strand
2) Repair of single strand damage: damaged DNA is removed and repaired using opposite strand as template
3) Repair of double strand damage: a break in the DNA (Requires more error-prone repair mechanisms )
When DNA damage is large scale, what repair system might the cell use?
SOS regulatory system
What is recombination?
physical exchange of DNA between genetic elements
What is homologous recombination?
process that results in genetic exchange between homologous DNA from two different sources
What is transformation? Who discovered it?
Genetic transfer process by which DNA is incorporated into a recipient cell and brings about genetic change. Fredrick Griffith worked with Streptococcus pneumoniae.
What are competent cells? What is electroporation?
cells capable of taking up DNA and being transformed; Electricity can be used to force cells to take up DNA (electroporation)
What is transfection?
Transformation of bacteria with DNA extracted from a bacterial virus
What is transduction?
Transfer of DNA from one cell to another by a bacteriophage
What are the two modes of transduction?
1) Generalized transduction: DNA from any portion of the host genome is packaged inside the vision
2) Specialized transduction: DNA from a specific region of the host chromosome is integrated directly into the virus genome
What is bacterial conjugation? Donor cell? Recipient cell?
mechanism of genetic transfer that involves cell-to-cell contact; donor cell: contains conjugative plasmid; recipient cell: does not contain plasmid
Give 4 characteristics of the F (fertility) Plasmid?
1) Circular DNA molecule; ~100 kbp
2) Contains genes that regulate DNA replication
3) Contains several transposable elements that allow the plasmid to integrate into the host chromosome
4) Contains tra genes that encode transfer functions
What does merodiploid mean?
Bacterial strain that carries two copies of any particular chromosomal segment
What is complementation?
Process by which a functional copy of a gene compensates for a defective copy
Why does genetic manipulation of Archaea lag behind Bacteria?
1) Archaea need to be grown in extreme conditions
2) Most antibiotics do not affect Archaea
3) No single species is a model organism for Archaea
What are transposable elements?
Discrete segments of DNA that move as a unit from one location to another within other DNA molecule
What are two main types of transposable elements and what do they do?
transposons and insertion sequences; both carry teens encoding transposase and both have inverted repeats at their ends
