Ch. 18 Microbial Models: The Genetics of Viruses and Bacteria & Ch. 20 DNA Technology and Genomics

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virus

parasite that can live only inside another cell; commandeers the host cell machinery to transcribe and translate all the proteins it needs to make copies of itself; consists of DNA/RNA enclosed in protein coat; gains entry into cell through special receptors, causing it to be limited to one specific cell type

capsid

protein coat that bacterial DNA or RNA is enclosed by

viral envelope

found in some viruses, it is derived from the membrane of host cells, and it cloaks the capsid and aids the virus in infecting the host

host range

the range of organisms that a cirus can attack; mutations in the virus can expand this

bacteriophages

the most complex and best understood virus is this one, which infects bacteria. It can reproduce with either the lytic cycle or lysogenic cycle

lytic cycle

cycle where phage enters host cell, takes control of the cell machinery, replicates itself, and then causes the cell to burst (EXPLOSION!!!!!), releasing a new generation of infectious phage viruses

lysogenic cycle

virus replicates without destroying the host cell. The phage virus remains dormant at specific site in the host DNA. As the host cell divides, the phage is replicated and infection spreads until an environmental trigger switches it to the other cycle's phase

prophage

the state in which the phage virus remains dormant at a specific site in the host DNA

lytic phase

environmental trigger causes prophage of lysogenic cycle to switch into this phase

temperate viruses

viruses capable of both modes of reproducing, lytic and lysogenic, within a bacterium

retroviruses

viruses that contain RNA instead of DNA and replicate in an unusual way. RNA serves as a template for synthesis of complementary DNA (cDNA); reverses flow of information from the usual DNA to RNA sequence using reverse transcription. Usually permanent prophage and can make multiple viral genome copies

reverse transcriptase

the enzyme involved in reverse transcription in retroviruses which reverse the flow of information from DNA to RNA

transduction

phae virsuses acquire bits of bacterial DNA as they infect one cell after another, leading to genetic recombination

generalized transduction

the moving of random pieces of bacterial DNA as the phage lyses one cell and infects another during the lytic cycle

specialized (restriced) transduction

transfer of specific pieces of DNA. During lysogenic cycle, phage integrates into host cell at certain site. When the phage later ruptures out of the host DNA, it might carry a piece of adjacent host DNA with it and insert host DNA into next host it infects

nucleoid

the bacterial chromosome that is a circular, double-stranded DNA molecule with no nuclear membrane

both; single point of origin; theta replication

Bacteria replicate in _______ directions and from ______________ by a process of _____________

conjugaton

primitive sexual method; not the main mode

binary fission

main mode of reproduction that is asexual; results in population with identical genes (with some mutations)

bacterial transformation

Griffith discovered with his experiments with R & S strains of bacteria. It is the process that provides a mechanism for the recombination of genetic information in some bacteria. A genetic change takes place in the cell where the extracellular DNA is taken up

plasmid

foreign, small, circular, self-replicating DNA that inhabits a bacterium; bacterium express the genes carries by this

pili

F plasmids contain genes for production of these cytoplasmic brdiges that connect to an adjacent cell and that allow DNA to move from one cell to another through conjugation

R plasmid

carry the genes for antibiotic resistance

operon

unit of DNA that controls the transcription (expression) of a gene: contains promoter, operator, structural genes, and regulatory genes

promoter

a region where RNA polymerase attaches, it is used in regulation of gene expression on the operon. It is a sequence of DNA to which the RNA polymerase attaches to begin transcription

operator region

region used in regulation of gene expression on the operon. It blocks the action of the RNA polymerase if this region is occupied by a repressor protein

structural genes

contain DNA sequences that code for several related enzymes that direct the production of some particular end product

regulatory gene

it lies outside the operon region, produces repressor proteins. They also make activator proteins.

repressor proteins

they are made by the regulatory gene and they occupy the operator region and block the binding of RNA polymerase

activator proteins

they are made by the regulatory gene and assist the attachment of RNA polymerase to the promoter region

inducible

Lac operon; one type of operon which is switched OFF until it's induced to turn on. 3 enzymes are coded for in this operon

repressible

trytophan operon; one type of operon that allows RNA polymerase to bind to the promoter and transcribe structual genes because it is always in ON position until not needed and thus becomes repressed by a corepressor. It has 5 structural genes that code for enzymes to make trytophan, the corepressor that binds with an inactive repressor which binds w/ the operator and stop RNA polymerase

noncompetitive inhibition

both substances compete for 2 active sites; exemplified by the relationship between RNA polyermerase and the repressor

allolactose

it is similar to lactose, making it an inducer or allosteric effector that can bind to the repressor and cause it to change shape and prevent the repressor from blocking RNA polymerase

trytophan

amino acid that acts as a corepressor and allosteric effector because it binds to the repressor which binds to the operator and stops RNA polymerase from binding to the promoter and making the structural genes

prions

not cells or viruses but are misfoldded proteins normally in the brain; they cause disease like mad cow disease or Creutzfeldt-Jakob disease for humans

transposons

discovered by Barbara McClintock, they are transposable genetic elements that are also called jumping genes. They jump in a cut-and-paste fashion from one part of the genome to another, creating either insertion sequences or complex ___________

insertion sequences

one type of transposon that have only one gene which codes for transposase

transposase

enzyme existing in insertion sequnces for moving the sequence from one place to another; can cause mutation if in DNA region that regulates gene expression

complex transposon

one type of transposon that is longer than insertion sequence and have extra genes for antibiotic resistance, seed color, etc.; discovered by McClintock who saw this in corn

junk

human DNA that doesnt code for protein product

regulatory sequences

noncoding DNA that control gene expression

introns

sequences of noncoding DNA that interrupt genes

repetitive sequences

noncoding DNA that never gets transcribed

tandem repeats

back-to-back repetitive sequences

polymorphic regions

highly variable noncoding regions of DNA

recombinant DNA

combination of DNA from 2 sources into one molecule; occurs in nature due to viral transduction, bacterial transformation, conjugation, and moving transposons

uses of cloned genes

-making protein product
-replacing nonfunctioning gene using gene therapy
-to make multiple copies of gene for analysis
-to engineer bacteria to clean up environment

vector

cell that faciliates the carrying of a gene

gene cloning procedure

1. isolate gene of interest
2. insert gene into plasmid
3. insert plasmid into vector that carries plasmid after making bacteria competent
4. clone gene (plasmid and selected gene are reproduced along with the bacteria that reproduce themselves during binary fission)
5.identify bacteria that had gene and harvest it from the culture

competent

condition of a bacterium that is able to take up a plasmid

restriction enzymes

basic biotechnology tool that is extracted from bacteria and then used to cut DNA at specific recognition sequences (sites) and leave sticky ends so it can connect with other sticky ends on other restriction fragments; examples are EcoRI, BamHI, HindIII; used in gene cloning

gel electrophoresis

separates large molecules of DNA on the basis of their rate of movement through agarose gel in an electric field; smaller molecule=faster run; flows from cathode (-) to anode (+); commonly used to separate proteins and amino acids or to prepare for sequencing DNA

DNA probe

radioactively labeled single strand of DNA can be used in gel electrophoresis to identify the location of a specific sequence within the DNA

polymerase chain reaction

cell-free, automated technique by which a piece of DNA is amplified by placing in Taq polymerase along with nucleotides and primers

restriction fragment length polymorphisms

junk of human DNA showed restriction fragment pattern is different in every individual, resulting in this; example is DNA fingerprint

cDNA

DNA produced using fully processed mRNA from cells and the enzyme reverse transcriptase to make DNA transcripts from the fully processed RNA (since only a gene without introns must be inserted)

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