UF MCB 3020 Exam 3 – Flashcards

refers to the use of living organisms to create products that are useful to humans

DNA from two or more sources...allows for creation of DNA sequences not otherwise found in biological organisms

1. isolate plasmid DNA from bacterial cell 2. isolate DNA of interest 3. Insert the gene of interest into plasmid DNA...forms recombinant DNA 4. insert the recombinant DNA into a bacterium 5. culture and grow the bacteria

a type of endonuclease that cuts up DNA *normally leave "sticky ends" of DNA

short nucleotide sequences that are recognized by restriction enzymes as the place to cut DNA normally palindromes

cut DNA that is left with short, single stranded sequences on both sides of the fragments

seals the two strands of "sticky ended" DNA together by catalyzing phosphodiester bonds between the single-stranded breaks. **results in recombinant DNA

makes a cell competent to pick up DNA from the environment by applying an electrical shock to it, which increases membrane permeability.

competent cells are engineered to lack these proteins, which may try to otherwise destroy the inserted sequence or attempt to correct the recombinant DNA

turns single-stranded RNA into double-stranded DNA it is an RNA-dependednt DNA polymerase

the DNA produced by reverse transcriptase and the RNA template

1. apply s short poly-T primer to single-stranded RNA 2. add reverse transcriptase and 4 nucleotides 3. add RNaseH enzyme to cut up the RNA and regenerate the RNA primers 4. add DNA polymerase and DNA ligase to synthesize a new strand

provides a means for transferring a gene of interest to a host organism

an origin of replication a selectable marker unique restriction sites (polylinkers or multicloning sites)

*most common cloning vector* a self-replicating piece of extrachromosomal DNA found in prokaryotes -mid-sized range (20,000 base pairs or less) pBR322 and pUC19

virus that infects bacteria carry smaller fragments between 9,000-25,00 base pairs

a hybrid between a plasmid and a phage carry large fragments between 30,00 and 47,000

synthetic chromosomes that contain fragments of DNA integrated into a host chromosome 1. P1 artificial chromosomes (PACs) 2. Bacterial artificial chromosomes (BACs) 3. yeast artificial chromosomes (YACs) **carry up to 1 MILLION bp

used to determine the location of genes, differences in genes, and where and when genes are expressed Includes... 1. PCR 2. gel electrophorese 3. restriction fragment analysis 4. blotting techniques

quickly and easily makes copies of even a very small amount of DNA. targets the DNA with the following: 1. Primers 2. thermostable DNA polymerase (taq polymerase) 3.deoxyribonucleotide triphostates (dATP, dCTP, dGTP, dTTP) **the solution is heated to 90 to 50 to 70 and then again

a technique that separates nucleic acids and proteins on the basis of their size and electrical charge, using a gel that is a polymer then stained with ethidium bromide for DNA to be visible

a tool for genetic fingerprinting, genome mapping, localization of the genes, paternity testing, and microbial classification.

compares genomes based on the number of short tandem repeats

variation of RELP that compared ribosomal RNA

technique that combines electrophoresis and hybridization to detect specific DNA fragments

uses radioactive DNA hybridization probes and autoradiography to identify the presence or absence of a specific gene

method for detecting radioactively labeled molecules

a collection of an organism's entire genomic DNA, which is stored in a population of identical vectors, each of which has a fragment of the DNA

a technique to introduce a mutation in one or more of the genes in a genome (target sequence "swaps" for the complementary sequence that was introduced)

enzymes and other means are used to remove the cell walls of multiple cells, creating protoplasts. These are then fused together, which is a large scale method of change to the genome. **mainly with fungi**

the body's "antiviral" molecule genetic engineering has allowed for the creation of bacteria that specialize in producing alpha, beta, and gamma interferons

the treatment of disease by inserting "therapeutic DNA" into a patient's cells hope that specialized transduction can be used for this one day

essential for proper growth, development, and reproduction immediate removal of a primary metabolite will impact the microbe's ability to survive and reproduce

not directly involved in growth, development, or reproductions removal will not immediately impact the microbe's ability to survive and reproduce **exogenous even typically triggers the production of this

many spies of fungi and bacteria naturally produce antibiotics as a means of "chemical warfare", i.e. in the presence of another species of bacteria that is a strong competitor for resources.

a modified form of penicillin created in a lab that is more effective

scientists have found a way to take out the tumor-inducing genes and other non-essential regions, which allows the plasmid to be used as a cloning vector for DNA of interest. allows for GMO

naturally produced agents that kill pests. i.e. BT toxin

a bioreactor in which the volume is kept constant b continuously adding fresh medium which removing the culture liquid

mass culture of microorganisms

serve as gelling agents and modify the flow of liquids dextran and PHB

emulsifies and solubilizes another substance, such as oil

using organisms to remove pollutants from a contaminated site

a polymer that consists of only 6 carbon glucose molecultes

a polymer of both 6 carbon sugars and 5 carbon sugars

patented a bacterium that produces alcohol using both 5 carbon AND 6 carbon sugars

use of live organisms to facilitate a chemical reaction that converts a substance to a chemically modified form

uses microorganisms, enzymes, or organelles and a physical transducer to detect the presence of a substance.

the transmission of genetic information from parent to offspring in sexual or asexual reproduction

the transmission of genetic info between organisms in a manner other then traditional sexual/asexual reproduction

creation of new combinations of alleles through the exchange of genetic material

involves the transfer of genetic material between bacteria through direct contact

a bridgelike structure that is a part of the Type IV secretion system. allows for direct transfer of plasmid

a special piece of DNA that can exist either as a segment of DNA or as a plasmid, which gives the bacterial cell the ability to form a sex pilus and encode DNA

F+ cells

F- cells

it can simply be transferred from the F+ cell to the F- cell and the entire plasmid is transferred

rolling-circle replication happens and the recombination results in the integration of the Hfr genome into the acceptor cell genome. the sex pilus is fragile, so only part of the Hfr cell's bacterial chromosome is transferred

the male cell when the F factor is located in the actual chromosome

involves the direct uptake of genetic material from a bacterium's surroundings

when a bacterium dies and its pieces disassemble, bits of "naked DNA" are released into the surrounding and are able to be taken up through transformation

rare in nature but commonly used in the lab bacterium become more receptive to taking up genes from the environment when they undergo significant stress/environmental change

when cell is receptive to taking up DNA from the environment

sometimes a phage that is released after the lytic cycle carries with it pieces of its host's genome that were not originally part of the virus, when it infers another bacterium it will transduce that genetic info

involves the transfer of a restricted set of only a few, specific bacterial genes to another bacterium via a phage that has become a part of the host chromosome.

involves the transfer of any bacterial gene to a recipient bacterium using a phage

convey antibiotic resistance

are able to "jump" from plasmid to the bacterial chromosome and from the bacterial chromosome to the plasmid.

a virus that infects a bacterium

a type of page replication cycle resulting in the release of new phages by lysis (and death) of the host cell

a phage replication cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage and does not kill the host

the process in which the environmental cue causes the prophage to begin synthesizing new phage particles, which will eventually enter the lytic cycle

a phage that is capable of establishing lysogeny and integrating into the bacterial host

a bacterium that contains a virus **can actually help bacteria in some cases

an integrated phage that can stay integrated in the host's DNA for many generations

the study of the physical nature of genomes i.e. the Human Genome Project

the study of genome using computers

a computer process that determines where genes start and end, which allows them to locate genes on the genome

a long sequence of codons not interrupted by a stop codon. used in annotation

the study of how a genome works

open reading frames presumes to encode proteins

two genes that consist of similar sequences and are found in the same genome. they have a similar function usually arise due to gene duplication events

two genes that consist of similar sequences and are found in different organisms. they likely have the same function

short patterns of amino acids that are known to have a specific function

analysis carried out by a computer

allows scientists to observe the pattern of DNA expression for thousand of genes at a time

the study of the entire collections of proteins produced by an organism

the study of protein function that determines what actually occurs in the cell

the study of 3D structure of proteins

separates proteins based on charge and molecular mass

the study of metabolome, or the entire set of a small-molucules metabolites present which in the cell at a given time

the study of lipide, or the entire lipid profile of a cell

the study of the differences among genomes of different organisms. given researchers insights into what kind of vaccines or therapies may be useful to fight against virulent pathogens

the study of the metagenomes, or the genetic material recovered from environmental samples.

published a rough draft of the human proteome, or the complement of proteins produced by different organs throughout the body.

an obligate, intracellular parasite that is sub-microscopic and has a wide variety of hosts

an inert version of the host that exists outside the cell

Mandatory: Nucleic acid (single/double DNA/RNA) capsid Optional: envelope spike

the outer protein cover that protects the virus' genetic material and is made of capsomeres which automatically self-assemble about the nucleic acid **determines the shape, protects, interacts with receptors on host cell, ad facilitates the penetration

unique to viruses, a polyhedron with 20 triangular faces, 30 edges, and 12 vectors

composed of lipids and proteins that derive from the host cell's membranes. helps a virus enter host cell. it makes a virus easier to kill

protein found in the viral envelope that assist in the recognition and attachment to the host cell

allows scientist to count the number of viral plaques, or clear areas where the virus has killed cells due to lysis

positive-sense RNA that can be dirtily translated to viral proteins

negative-sense RNA that is complimentary to viral mRNA, so it has to be used to create a +RNA first

the ideal way to develop drugs or viruses that would stop the viral infection at the mucous membrane. drugs that convey mucosal immunity work by increasing antibody levels in the mucous secretions

programmed cell death

1. lysis 2. transforming the cell genome 3. altering the structure (making nucleus larger, making cell larger, causing cell membrane to be more elastic, forming syncitia) 4. altering gene expression 5. inhibiting RNA or protein synthesis 6. constructing new viruses rather than normal gene expression 7. apoptosis

"mega cells" a more efficient "virus production machine" single cell with multiple nuclei

1. attachment/absorption 2. penetration ( 2b. uncoating) 3. synthesis/replication 4. assembly (maturation or packaging) 5. release (this is where a viral envelope would come from)

family of viruses that replicates by converting its single-stranded RNA genome to a double-stranded DNA and integrating it into the host cell's genome

1. DNA-RNA hybrid is formed when RT creates a DNA strand complementary to the virus' single-stranded RNA 2. the RNA strand is removed 3. the newly synthesized DNA is used as a template for the synthesis of a complementary strand, making the final molecule

an enzyme that integrates the newly formed double-stranded DNA into the host's chromosome

Once integrated into the host's chromosome, the viral DNA is called this

HIV

involves something other than oral ingestion and passage of the virus through a mucous membrane i.e. an insect bite or trauma

respiratory tract

important immune system cells that fight infection in the alveoli

occurs when viruses are present in the blood stream

in pregnant women, viruses can pass from the mother to the fetus via the placenta

the many ways a virus can leave the body **point of exit does not always equal point of entry

"standard kind" acute infection virus infects the host, hijacks the cellular machinery to make copies and then destroys the host by lysis

when the virus is able to circumvent the host's defenses and use its cellular machinery to replicate

the virus is able to successfully complete the process of replication

the virus is unable to successfully complete the process of replication

the virus reproduces slowly and are released by the cell over a long period of time. chronic infection

the virus affects the host's genetic makeup, causing some kind of mutation in the host chromosome often at a point in the host's genome called an oncogene, which has the capacity to cause cancer **always a provirus

the virus remains in the host cell in a dormant state until a trigger activates it and causes it to make copies of itself **once the trigger is activated it become a lytic infection

refers specifically to the effects of a viral infection that can be visualized with a microscope. 1. viral plaque 2. enlargement of cell/nucleus/both 3.membrane changes 4. makes syncytia 5. leaky internal organs

exposing bacteria to viruses then diluting the sample enough that no additional host cells are infected by new viruses

after the virus binds to receptors on the host cell, the host cell membrane forms an endosome containing the virus

the virus produces compounds to lower the pH inside the endosome so that the virus can uncoat and fuse with the endosome

the virus disassembles after fusion with the endosome and are released into the cytoplasm. This means that there is technically no whole viruses

there are no detectable infections in the cell, although the virus is using the cell machinery to replicate

the number of observable viruses increase as the viruses assemble

the number remains high and eventually are released from the cell

collection of signs and symptoms

objective manifestation that can be detected by others

internal manifestation that is only detected by the individual

a group of cells that are removed from an organism and placed in a suitable environment, where they are allowed to grow

a layer of homogenized cells growing side by side but not on top of one another

cancer cells mixed with primary cells that can grow forever

chemicals that fight against diseases in humans and animals

chemicals that can be specifically used to kill microbes and thus fight against infectious diseases

the drug must kill or neutralize the microbe without killing or neutralizing the host cell

1. selective toxicity 2.must be able to reach the target at the right concentration 3.must be able to bind to and penetrate the cell, avoiding inactivation and extrusion

minimum drug level required for clinical treatment

minimum dose at which the drug produces side effects in patients

toxic dose/therapeutic dose

they attack only a small number of different pathogens

they attack a wide variety of pathogens

kill microbes

inhibit their growth

the lowest concentration of a drug that is effective in inhibiting the growth of the pathogen

antimicrobial agents that kill or neutralize bacteria discovered by Alexander Fleming (penicillin in the 1920s)

the standard method for determining the sensitivity of a bacterium to a particular antibiotic. think about what we did in lab

a "clear zone" were growth is inhibited due to a sensitivity to the antibiotic

prevents cells from proliferating by preventing the synthesis of cell walls **most important target **1 of three most successful

disturb the process of protein synthesis, often by targeting ribosomes **1 of three most successful

disrupt steps in key metabolic pathways **1 of three most successful

prevent synthesis of DNA or RNA

somehow impact the assembly or proper functioning of the cell

bacteriCIDAL group that inhibits the final step in bacterial wall synthesis (peptidoglycan synthesis), or transpeptidation

beta-lactam ring that consist of three carbons and one nitrogen. essential for their bioactivity

(penicillinase) an enzyme that destroys the beta-lactam ring and neutralizes the effect of penicillin

chemically modified penicillin, that typically has a broader range

bacteriCIDAL a natural form of penicillin that is particularly effective against G+ bacterium

bacteriCIDAL semisynthetic form of penicillin that is resistant to penicillinase but is less active the Penicillin G

bacteriCIDAL cell wall synthesis inhibitor antibiotics that are functionally and structurally similar to penicillin with beta-lactam rings. for those allergic to pcn

bacteriCIDAL cell wall synthesis inhibitor glycopeptide antibiotic that blocks transpeptidation during cell wall synthesis, during which the peptidoglycan layers are linked via peptide bridges. **at a different point then pcn

blocks the synthesis of the building blocks of the cell wall INSIDE the cell

blocks transportation of those building blocks outside the cell

bacteriCIDAL bind to the small (30S) ribosomal subunit, which disrupts the process of correctly reading the mRNA ex= Streptomycin very energetically costly to make

these four ringed structures with many side chains attached bind to and combine with the small (30S) subunit and prevent aminoacyl-tRNA molecules from binding to the ribosome's A site BROAD-spectrum and bacertioSTATIC **acne

bacertioSTATIC contains several carbon lactone rings linked to sugar ex= erythromycin which is BROAD and usually bacerioSTATIC and binds to the 23S unit of the large (50S) ribosomal subunit, inhibiting the elongation of the peptide chain

bacertioSTATIC extremely toxic with several side effects only used in life-threatening situations. it binds to the 23S unit of the large (50S) subunit, inhibiting elongation

drugs that block the function of the metabolic pathways through competitive inhibition of those metabolites of key enzymes **often structural analogs

structures similar to metabolites, but they do not function in the same way

a common pathway that is targeted by antibiotic antimetabolites. Humans cannot synthesize folic acid, unlike bacteria.

bacertioSTATIC disrupt the folic acid pathway by acting as a structural analog of p-aminibenzoic acid (PABA), which is a precursor

bacertioSTATIC a synthetic antimetabolite that interferes with folic acid production later in the pathway

two drugs work together to accomplish more than the additive effect of the two drugs working separately 2+2=5

trimethoprim and sulfa drugs are often prescribed together

combination of amoxicillin and clavulanate potassium

isoniazid and rifampin

BOTH inhibits lipid synthesis

inhibit DNA polymerase, DNA helicase, or other enzymes involved in making the DNA supercoil

inhibit RNA polymerase

bacteriCIDAL BROAD-spectrum, synthetic drugs that inhibit DNA gyrase and DNA topoisomerase, which makes DNA supercoil.

bacteriCIDAL inhibits RNA polymerase

bacteriCIDAL a quinolone used in 2001 for anthrax

bacteriCIDAL a drug that bings to the plasma membrane, disrupting its structure and permeability VERY toxic

the lowest concentration of a drug that is effective in controlling the growth of the pathogen

an organism's ability to eliminate or neutralize the effect of an antimicrobial drug Begins with a spontaneous mutation that then undergoes HGT

Natural selection favors bacteria with antibiotic resistance because they are more likely to survive and reproduce

once antibiotic resistance has evolved, it can be spread through HGT

1.preventing entrance of the drug 2.using efflux pumps to remove the drug before it can have effect 3. inactivating the drug 4. modifying the enzyme or organelle that the drug targets 5. using an alternative pathway or increasing the production of a target metabolite

they actively pump the antibiotic out of the cell before it can have effect think bailing out the water that is entering the boat, as long as you do it fast enough it won't sink

1. bacterial chromosomes 2. Resistance (R) plasmids 3. composite transposons

1. Dr. prescribe antibiotics in high enough concentrations and the correct combination to kill ALL bacteria 2. Dr. can prescribe fewer antibiotics 3. Researchers can develop new drugs and treatments

typically it is easier to achieve selective toxicity in antibiotics because they are prokaryotes

must have unique targets i.e. HIV reverse transcriptase HIV protease

protease inhibitors because they inhibit post-translation modification of viral proteins

antiviral; prevents the flu virus from penetrating and uncoating

antiviral; shortens the length of infection and helps prevent spreading

antiviral;prevents herpes from replicating

antiviral; inhibits the hepatitis virus

unique compound in fungi that acts like cholesterol and can be effective target of antifungals

antifungal: block the biosynthesis of ergosterol and inhibit cell membrane synthesis

anti fungal:cause leakage of cellular components when they bing to sterols in the cell membrane

an anti-parasite drug used to prevent malarial

essentially a ball of lipids that formed the precursor to the cell membrane

liposome engulfed a free-floating RNA molecule

an RNA molecule capable of catalyzing a biochemical reaction

the notion that self-replicating RNA molecules were the precursors to modern life

early eukaryotic cell engulfed a prokaryotic cell but did not digest them and allowed to prokaryotic cell to live within the host in a symbiotic relationship, eventually becoming chloroplasts and mitochondria

- both chloroplasts and mitochondria have their own circular chromosome, which replicates independently -both have bacteria-like ribosomes -both have their own, independent protein-synthesis mechanisms

consist of branched aliphatic chains linked together with ether linkages

members of Archaea thrive in extreme conditions such as high/low temperatures, no O2, extreme pH levels, or high salt **can also be found in more typical environments

live in extremely salty conditions, were the concentration levels are above 1.5M aerobic chemoheterotrophs

strictly anaerobic and produce methane as a byproduct of metabolism used in water treatment process found in rumen of cow, anaerobic sludge, and within anaerobic protozoans

live in extremely high temperatures sulfur metabolizing

live in extremely low pH conditions

live in extremely high pH conditions

the study of interaction of microbes with the biotic and abiotic environment in which they live

chemically and physically change nutrients from one form to another

a number of classes of microbes convert carbon from one form to another

nitrogen-fixing bacteria take the gaseous nitrogen in the atmosphere and turn it into a nitrogen that can be used by plants in the soil (i.e. think legumes)

converts NH3 to NO3- (ammonia to nitrate)

nitrate in the soil into gas **not good

decays plants and animal wastes into NH3 (ammonia)

reduces sulfur oxides into H2S

remember photosynthetic microbes release O2 as a byproduct

a waste management technique that uses biological agents to degrade environmental pollutants

involves physically removing solid organic materials the sludge is then transferred to a large tank where anaerobic methanogens degrade the organic molecules

involves the use of microbes to remove organic material from the liquid portion of the sewage

involves the removal of inorganic materials thru chemical means

disinfect the water to remove all microbes

a measure of the amount go dissolved O2 required by aerobic biological organisms in the H2O to break down the organic material the greater the BOD->the greater the stress on marine life

simply a holding tank for waste water, not a treatment system

1.water is stored in large reservoirs to settle sediments. Alum is added to precipitate particles to settle sediments 2. bacteria is removed by filtering H2O through sand and charcoal is added to remove toxic organic materials 3. water is chlorinated

looking for indicator organisms (that are normally GI pathogens found in fecal matter but not H2O) **normally coliforms

the process of decomposing organic matter and recycling as fertilizer reduces solid matter but 2/3 in a meter of months adding soil introduces microorganisms