nucleotides
Basic units of DNA molecule, composed of a sugar, a phosphate, and one of 4 DNA bases
Coupling proteins
facilitates communication between the Mpf and Dtr system
Determine which proteins get transferred to recipient
bound to channel proteins and activates relaxase by protein interaction
self transmissible plasmids
have all factors need for conjugation
including: Dtr componets like a mob site and tra genes encoding relaxase, primer and helicase
Mpf components like a sex pilus, channel protein and reseptors for pheromones
mobilizible plasmids
lack one or more tra fucntions but have a mob site and are smaller than self transmisible plasmids
inorder for conjugation to occur the tra genes must be on the chromosome or on a helper plasmid
genome
All the genetic information in an organism; all of an organism's chromosomes.
genetics
The scientific study of heredity
genes
DNA segments that serve as the key functional units in hereditary transmission.
base pairs
Any of the pairs formed between complimentary bases in the two nucleotide chains of DNA, such as A-T and C-G (DNA); A-U and C-G (RNA)
nucleoid
A dense region of DNA in a prokaryotic cell.
Chromosomes
A cellular structure carrying genetic material, found in the nucleus of eukaryotic cells. Each chromosome consists of one very long DNA molecule and associated proteins
histones
Globular protein that assist in DNA packaging in eukaryotes. Histones form octamers around which DNA is wound to form a nucleosome.
plasmids
self-replcating" extrachomosomal DNA in addition to the main bacterial chromosome. Can contain genes for antibiotic resistance, but is not essential for growth under all conditoins.
Are plasmids circular or linear?
They can be either. As well as cary in size
what is colicin?
a toxin that kills other closely realted bacteria
What are some examples of phenotypes conferred by plasmids?
R-factors: encodes resistance
F-factors: encodes fertility
ColE1 encodes colicin
Ti encodes tumors
what are some examples of useful phenotypes?
colony phenotypes
Auxotrophs
conditionally lethals
Resistance mutants
mutation rates vs. Frequencies
both predict the chance of a mutation occurring, are proportional to the "tatget size"
However, frequency can be used to predict the type of mutation
mutation rates
is the chance of mutation per cell division
mutation Frequencies
is the number of mutants / number of plated
Roberts rules to very frequent mutations
loss of plasmid -10^-2
loss of tandem duplication -10^-1
duplications -10^-3
Roberts rules for detectable mutations
spontaneous reversion -10^-6 to -10^-8
Precise excision of a transposon -10^-9
how to name plasmids? Example pBR322
p = plasmid
BR = Bolivar and Rodriguez (discoverers)
322 = 322nd derivate
capsid
the head of a bacteriophage which is made up of protein or glycoproteins
often icosohedral, sometimes fillamentous
why do cells have plasmids?
bacterial cells want to devide rapidly and to increase the cding capavty of the species by shearing DNA.
What are some types of plasmid structure?
circular and supercoiled
linear with telomeres and covalently joined ends
what is unidirectional plasmid replication?
when replication starts at the origin of replicatoin (oriV) and copies its
DNA in one direction
What is bidirectional plasmid replication
when replication starts at the origin of replicatoin (oriV) and copies its DNA in oppposit direction uses two DNA pimers
What is a plasmids host range?
many plasmids have norrow (can only live in one species) or broad (can live in a number of species)
what is a plasmid copy number?
the number of copies of a single plasmid in a cell (not total number of all types)
what is a low plasmid copy number?
1/cell
stringent plasmids are low copy and replication is tightly controlled
what is a medium plasmid copy number?
2~15/cell
what is a high plasmid copy number?
50 ~100/ cell
Relaxed plasmids are high copy and only stop replication when a certain number exist in the cell.
Randomly assorted to daughter cells
what is a cured cell?
A cell that has lost its plasmid
what does partitioning do?
pertitioning ensures that at least one copy of the plasmid segregates into each daughter cell. some plasmids use addiction systems to ensure cells without a plasmid copy is killed.
What is Incompatibility?
When more than one plasmid can not coexist in the host cell. incompatibility involes control of copy number or partitioning
what are ways to detect and isolate a plasmid?
Minipreps
CsCl- EtBr purification
What ar some desired features of a plasmid cloning vector
small (to accept larger insert DNA)
high copy number (easy to purify)
selectable marker (easy to isolate transformants)
Convenient REN cleavage site that cut only once
transformant
A bacterium that has been transformed
what is CsCl- EtBr purification?
ethidium bromide intercalates in DNA
EtBr will bind to nicked or linear DNA than to supercoild and makes DNA less dense
CsCl density gradient separates DNAs after centrifugation
nucleosomes
stacks of histones bound by DNA
chromatin fibers
formed by tightly packed nucleosomes
leading strand
The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.
lagging strand
A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.
methylation
A chemical modification of DNA that does not affect the nucleotide sequence of a gene but makes that gene less likely to be expressed.
genotype
An organism's genetic makeup, or allele combinations.
phenotype
An organism's physical appearance, or visible traits.
transcription
(genetics) the organic process whereby the DNA sequence in a gene is copied into mRNA
translation
(genetics) the process whereby genetic information coded in messenger RNA directs the formation of a specific protein at a ribosome in the cytoplasm
central dogma
theory that states that, in cells, information only flows from DNA to RNA to proteins
RNA primer
short segment of RNA used to initiate synthesis of a new strand of DNA during replication
Messenger RNA
RNA molecule that carries copies of instructions for the assembly of amino acids into proteins from DNA to the rest of the cell
Transfection
uptake of viral DNA or RNA
ribosomal RNA
type of RNA that combines with proteins to form ribosomes
transfer RNA
type of RNA molecule that transfers amino acids to ribosomes during protein synthesis
Regulatory RNA
some RNAs are used to regulate gene function
RNA Polymerase
Enzyme similar to DNA polymerase that binds to DNA and separates the DNA strands during transcription
promoters
regions of DNA that have specific base sequences
terminator
A special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene
introns
Noncoding segments of nucleic acid that lie between coding sequences.
exons
A coding region of a eukaryotic gene. Exons, which are expressed, are separated from each other by introns.
codons
A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.
anticodons
Three-base sequence in a transfer RNA molecule base that pairs with a complementary codon in mRNA
a site
holds the tRNA carrying the next amino acid to be added to the chain
p site
Peptidyl-tRNA site; the stie on a ribosome where the growing peptide (attached to a tRNA) is found during translation.
E site
One of a ribosome's three binding sites for tRNA during translation. The E site is the place where discharged tRNAs leave the ribosome. (E stands for exit.)
quorum sensing
Communicate and cooperate in the formation and function of biofilms
operon
A segment of DNA containing adjacent genes including structural genes and an operator gene and a regulatory gene
operator
Region of DNA that controls RNA polymerase's access to a set of genes with related functions.
inducible operons
gene expression normally "turned off" but can be turned on when repressor no longer binds to operator site
repressible operons
normally "turned on" and deactivate when repressor binds to the operator site
microRNAs
can bind to complementary sequences on mRNA molecules either degrading the target mRNA or blocking its translation
viron
a virus partcle
riboswitches
Folded RNAs that act as switches regulating protein synthesis in response to environmental conditions
Small interfering RNA
Similar to miRNA, but formed from longer, double stranded RNA molecules
mutation
A heretirary change in a gene or chromosome.
what are some seneral properties of mutations?
Lethal changes are not mutations as they cannot be inherited
some mutations revert to wild-type phenotype.
Reversion
restores the orighinal sequence of the affected DNA
Suppression
when a second mutation suppresses the effects of the first
may be inter- or intra-genic
inter: occurs when the second mutation is in a different gene than the first
intra: occurs when the second mutation is the same gene as the first
point mutations
chemical changes in just one base pair of a gene
include missense, nonsense, samesense and frameshift mutations
Frameshift mutation
A base change that changes all amino acids downstram.
almost always destroy protein function
polar because they disclose nonsense codons
revert ar detectable frequencies and can be suppressed by mutant tRNAs
slippage during DNA replication leads to frames
specialized transuction
...
generalized transduction
any region of the donor DNA can be transferred
deletion mutations
can arise by "looping out" during recombination, involving direct repeats.
generally inactivate protein function and DO NOT revert
may affect more than one gene, may fuse genes or operons and alter regulation or creat chimeric proteins
Named using delta i
Tandem duplication
occurs from recombination at the replication fork, and are highly unstable.
inactivates the dene product if internal to the gene
large duplications may have no phenotype
can fuse genes or alter regulation and are highly unstable
samesense mutations
change DNA sequence encoding an amino acid but not the amino acid in the protein product
Missense mutations
Most common, a base pair mutation in which the new codon makes sense in that it still codes for an amino acid but its not the wild-type.
most inactivate protein functions
some cause partial protein function therfore, leaky phenotype, or conditionally leth
Transition change
A base pair change from purine to purine or pyrimidine to pyrimidine
Transverion change
a base pair change from purine to pyrimidine or pyrimidine to purine
what are some ways a mutation can occur?
mispairing during replication
failure to repair DNA damage corretly
gross mutations
gain or loss of entire gene segments or inversions or transpositions of gene sequences. MAJOR change or non-functional cell
inversion mutation
result from recombination involving inverted repeats
unlike deletions, may revert by reinverting the affected sequence
may alter regulation or create fusion proteins
named using the letter "IN" preceeding the affected gene ie, IN(purB- trpA)3
silent mutations
neutral mutations
nonsense mutations
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.
may be polar depending on the location within a gene
may or may not have phenotypes and revet at dectable frequencies
what were other names for nonsense mutations?
amber (UAG), ochre (UAA) or opal (UGA)
mutagens
A chemical or physical agent that interacts with DNA and causes a mutation.
pyrimidine dimmers
What can happen when DNA that has been damaged by UV light exposure is used as template for replication
nucleotide analogs
fake nucleotides that are incorporated into the mRNA transcripts or genome of the viruses
light repair
repair enzymes are activated by visible light
dark repair
independent of light
base-excision repair
DNA repair that first excises modified bases and then replaces the entire nucleotide.
mismatch repair
The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides.
SOS response
Induced by UV, and during this response, cell division is inhibited. So cells exposed to UV radiation are longer because cells grow mostly in length, not in diameter.
mutants
a cell that does not successfully repair a hereditary mutation from wild-type
natural competence
both gram positive andd negative bacteria
usually occurs only late in exponential phase
not all cells (usually) become competent
best understood in Bacillus subtilus because a genetic system exists
What is Electroporation?
cells are highly concentrated
ions are removed
bufferis iso-osmotic but non-conductive
cells actually conduct cerrent
high voltage is used up to 10kV
transient pores allow entry of DNA
How does Haemophilus influenzae take up dsDNA?
through a tranformasome
DNA uptake in Bacillus subtilis
DNA is taken up by ComG and passes ComEA-ComEC
wild-type
Phenotype of Genotype (allele of a gene)that normally predominates in a natural population of organism (or strain of organism)
positive selection
process in which advantageous genetic variants quickly increase in frequency in a population
negative selection
Causing apoptosis in cells that are self-reactive.
Ames test
Test in which special stains of bacteria are used to evaluate the potential of chemicals to cause cancer
carcinogens
Cancer causing agents
horizontal gene transfer
The transfer of genes from one genome to another through mechanisms such as transposable elements, plasmid exchange, viral activity, and perhaps, fusions of different organisms.
donor cell
the cell from which the DNA is derived for transfotmation
recipient cell
the cell that takes up the DNA during transformation
recombiant
DNA that has been transformed artificially
transformation
Process in which one strain of bacteria is changed by a the uptake of naked DNA from the environment
competent cell
a "state" in which bacteria can take up DNA by transformation
bacteriophage
A virus that infects bacteria
phage
A virus that infects bacteria; also called a bacteriophage.
transduction
the transfer of DNA for one bacterial cell to a nother by a virus
transducing phages
Take up bacterial DNA that was similar to its own sized DN
Conjugation
A temporary union of two organisms for the purpose of DNA transfer.
F plasmid
The plasmid form of an F factor.
pilus
A contractile organ, made of only one protein (pilin) in a helical array
Many tra proteins involved in export and assembly
The sex pilus attaches F+ and F- bacteria during conjugation.
vary in shape and is highly antigenic
A phage binding site
Hfr cells
high frequency of recombination; sex factor gets incorporated into the bacterial genome so when conjugation bridge forms, the whole bacterial chromosome duplicates and attempts to transfer over, many times conjugation bridge breaks before all of it can ge
transposons
(jumping genes) short strands of DNA capable of moving from one location to another within a cell's genetic material
inverted repeats
The ends of a simple transposable element contain
transposition
movement of a gene on a chromosome
insertion sequences
Possess only genes encoding enzymes required for transposition; bounded by inverted repeat
genetic elements
any extrachromosomal genetic material
insertion mutations
caused by mobile genetic elements (MGEs) found in the genomes of almost all organisms.
almost always inactivate gene products
revert frequently
complex transposons
consist of 2 simple transposons with other genes in between them; when they move, they bring other genes with them (can travel from 1 organism to another of even to different species); spread genes (good or bad) to another species/more organisms