Term
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Definition
| When a particular microorganism obtains the ability to resist the activity of a particular antimicrobial agent to which it was previously susceptible. This can result from the mutation of genes involved in normal physiological processes and cellular structures, from the acquisition of foreign resistance genes or from a combination of these two mechanisms |
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Term
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Definition
| This is the accumulation and adhesion of molecules, atoms, ions, or larger particles to a surface, but without actually penetrating the surface |
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Term
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Definition
| this is an abnormal or harmful effect to an organism caused by exposure to a chemical. It is indicated by some result such as death, a change in food or water consumption, altered body and organ weights, altered enzyme levels, or visible illness. An effect may be classed as adverse if it causes functional oranatomical damage, causes irreversible change in the homeostasis of the organism, or increases thesusceptibility of the organism to other chemical or biological stress. A non-adverse effect will usually bereversed when the organism is no longer being exposed to the chemical. |
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Term
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Definition
| This results when the binding of an activator molecule to an allosteric site causes a change in the active site that makes it capable of binding substrate. |
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Term
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Definition
| The place on an enzyme where a molecule that is not a substrate may bind, thus changing the shape of the enzyme and influencing its ability to be active. |
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Term
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Definition
| Antimicrobial drug that is used to treat a diseased caused by bacteria. |
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Term
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Definition
| Antimicrobial agent that is produced naturally by an organism |
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Term
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Definition
| Portion of the tRNA molecule that is complementary to a codon on mRNA |
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Term
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Definition
| Chemotherapeutic agent used to treat microbial infection |
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Term
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Definition
| The 2 DNA strands are said to be antiparallel. One goes 5’ to 3’, the other 3’ to 5’. |
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Term
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Definition
| Drug that interferes with the replication of virus. All antiviral drugs are chemically synthesized; none are antibiotics |
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Term
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Definition
| : In virology, fourth stage of the lytic replication cycle, in which new virions are assembled in the host cell. |
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Term
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Definition
| In virology, first stage of the lytic replication cycle, in which the virion attaches to the host cell. |
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Term
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Definition
| : Kills bacteria, as opposed to bacteriostatic; affects the vital count |
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Term
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Definition
| Capable of dissolution or destruction of bacteria; affects the turbidity |
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Term
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Definition
| Virus that infects and usually destroys bacterial cells |
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Term
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Definition
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Term
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Definition
| Molecule that binds with the hydrogen ions when dissolved in water. |
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Term
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Definition
| a complementary arrangement of nucleotides in a strand of DNA or RNA. For example, in both DNA and RNA, guanine and cytosine pair |
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Term
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Definition
| biological half-life refers to biological elimination from the body and effective half-life refers to the combined action of radioactive decay and biological elimination. |
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Term
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Definition
| Branch of microbiology in which microbes are manipulated to manufacture useful products |
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Term
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Definition
| Antimicrobial that works against many different kinds of pathogens. |
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Term
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Definition
| Test for determining the minimum inhibitory concentration in which a standardized amount of bacteria is added to serial dilutions of antimicrobial agents in tubes or wells containing brother |
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Term
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Definition
| Number of viruses released during the lytic phase. |
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Term
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Definition
| A protein coat surrounding the nucleic acid core of a virion |
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Term
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Definition
| A proteinaceous subunit of a capsid. |
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Term
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Definition
| DNA synthesized from an mRNA template using reverse transcriptase. |
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Term
| Central dogma of molecular biology |
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Definition
| In genetics, fundamental description of protein synthesis. (DNA=>RNA=>protein) |
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Term
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Definition
| Chemical used to treat disease. |
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Term
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Definition
| : Develops slowly, usually with less severe symptoms and is continual or recurrent. |
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Term
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Definition
| Triplet of mRNA nucleotides that codes for specific amino acids. |
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Term
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Definition
| A cell that is able to take in new DNA and transform its own DNA without any chemical help; can be natural or artificial (induced) |
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Term
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Definition
| Blocks enzyme activity by blocking active sites. |
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Term
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Definition
| The correspondence or similarity between nucleotides or strands of nucleotides of DNA and RNA molecules that allows precise pairing. |
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Term
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Definition
| Type of cell culture created from tumor cells. |
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Term
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Definition
| In genetics, method of horizontal gene transfer in which a bacterium containing a fertility plasmid forms a conjugation pilus that attaches and transfers plasmid genes to a recipient in reproduction of ciliates: coupling of mating cells. |
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Term
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Definition
| : enzymes produced by the cell under all physiological conditions |
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Term
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Definition
| cell-cell signaling that arrests growth when two or more cells come into contact with each other |
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Term
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Definition
| small ligand that binds to a repressor allowing the repressor to bind to the operator. |
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Term
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Definition
| Phenomenon in which resistance to one antimicrobial drug confers resistance to similar drugs |
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Term
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Definition
| structural changes in host cell resulting from viral infection. |
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Term
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Definition
| Mechanism by which enzymes cut damaged DNA sections from a molecule, creating a gap that is repaired by DNA polymerase and DNA ligase. |
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Term
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Definition
| more than one codon can code for the same amino acid |
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Term
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Definition
| Monosaccharide, pentose sugar found in DNA chains |
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Term
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Definition
| growth utilizing two different energy sources, i.e. glucose and lactose |
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Term
| Discontinuous replication: |
|
Definition
| method of replication on the lagging strand |
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Term
|
Definition
| Nucleic acid consisting of nucleotides made up of a phosphate, a deoxyribose pentose sugar, and an arrangement of the bases AGCT. |
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Term
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Definition
| Period of time between infection by a virus and the appearance of the mature virus within the cell. |
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Term
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Definition
| molecule that binds to a protein, altering its activity. |
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Term
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Definition
| Membrane surrounding the viral capsid. |
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Term
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Definition
| Eukaryotic equivalent to a prokaryotic plasmid. |
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Term
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Definition
| Coding sequence of mRNA. Exons are connected to produce a functional mRNA molecule. |
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Term
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Definition
| Method of controlling the action of enzymes in which the end product of a series of reactions inhibits an enzyme in an earlier part of the pathway. |
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Term
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Definition
| a rod-shaped phage, generally ssDNA |
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Term
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Definition
| Type of mutation in which nucleotide triplets subsequent to an insertion or deletion are displaced, creating new sequences of codons that result in vastly altered polypeptide sequences. |
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Term
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Definition
| A specific sequence of nucleotides that codes for a polypeptide or an RNA molecule. |
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Term
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Definition
| Collection of bacterial or phage clones, each of which carries a fragment of an organism’s genome. |
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Term
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Definition
| phage carries a random DNA segment from a donor host cell’s chromosome or plasmids to a recipient host cell |
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Term
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Definition
| The manipulation of genes via recombinant DNA technology for practical applications. |
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Term
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Definition
| The exchange of segments, typically genes, between two DNA molecules. |
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Term
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Definition
| The sum of all genetic material in a cell or virus. |
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Term
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Definition
| Actual set of genes in an organism's genome. |
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Term
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Definition
| High frequency of recombination cell containing an F plasmid that is integrated into the prokaryotic chromosome. |
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Term
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Definition
| Globular protein found in eukaryotic and archaeal chromosomes |
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Term
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Definition
| Process in which a donor cell contributes part of its genome to a recipient cell, which may be a different species or genus from the donor |
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Term
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Definition
| In symbiosis, member of a parasitic relationship that supports the parasite |
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Term
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Definition
| Type of operon that is not normally transcribed and must be activated by inducers. |
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Term
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Definition
| : In virology, excision of a prophage from the host chromosome, at which point the prophage re-enters the lytic phase. |
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Term
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Definition
| Noncoding sequence of mRNA, which is removed to make functional mRNA |
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Term
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Definition
| Resistance due to inherent characteristics of the microorganism |
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Term
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Definition
| Daughter strand of DNA synthesized in short segments that are later joined. Synthesis of the lagging strand always moves away from the replication fork, and lags behind synthesis of the leading strand |
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Term
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Definition
| In virology, process by which an animal virus, sometimes not incorporated into the chromosomes of the cell, remains inactive in the cell, possibly for years. |
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Term
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Definition
| Daughter strand of DNA synthesized continuously toward the replication fork as a single long chain of nucleotides. |
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Term
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Definition
| Enzyme that catalyzes the joining of two adjacent nucleotides |
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Term
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Definition
| Mechanism by which prokaryotic DNA photolyase breaks the bonds between adjoining pyrimidine nucleotides, restoring the original DNA sequences
. |
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Term
|
Definition
| Change in phenotype due to insertion of a lysogenic bacteriophage into a bacterial chromosome. |
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Term
|
Definition
| Bacteriophage that does not immediately kill its host cell |
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Term
|
Definition
| The fusion of the nucleic acid of a bacteriophage with that of a host bacterium so that the potential exists for the newly integrated genetic material to be transmitted to daughter cells at each subsequent cell division. |
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Term
|
Definition
| infection of a bacterium by a bacteriophage with subsequent production of more phage particles and lysis, or dissolution, of the cell. |
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Term
|
Definition
| The viral DNA exists as a separate molecule within the bacterial cell, and replicates separately from the host bacterial DNA. |
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Term
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Definition
| Collection of microscopic DNA spots attached to a solid surface, used to measure gene expression. |
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Term
| Minimal bactericidal concentration (MBC): |
|
Definition
| An extension of the MIC test in which samples taken from clear MIC tubes are transferred to plates containing a drug-free growth medium and monitored for bacterial replication. |
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Term
| Minimal inhibitory concentration (MIC): |
|
Definition
| The smallest concentration of an antimicrobial that will inhibit the growth of a microorganism. |
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Term
|
Definition
| A substitution in a nucleotide sequence resulting in a codon that specifies a different amino acid: what is transcribed makes sense, but not the right sense. |
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Term
|
Definition
| Messenger RNA, used during transcription. |
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Term
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Definition
| Physical or chemical agent that introduces a mutation |
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Term
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Definition
| In genetics, a permanent change in the nucleotide base sequence of a genome. |
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Term
|
Definition
| virus lacking an outer lipoprotein layer |
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Term
| Noncompetitive inhibitors |
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Definition
| : Inhibitory substance that blocks enzyme activity by binding to an allosteric site on the enzyme other than the active site. |
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Term
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Definition
| A substitution in a nucleotide sequence that causes an amino acid codon to be replaced by a stop codon. |
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Term
|
Definition
| A technique used to study gene expression by detection of RNA in a sample. |
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Term
|
Definition
| capsid with an enclosed nucleic acid |
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Term
|
Definition
| Monomer of a nucleic acid |
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Term
| Obligate intracellular parasite |
|
Definition
| parasite that cannot reproduce outside their host cell |
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Term
|
Definition
| Discontinuous DNA fragments from the lagging strand during DNA replication. |
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Term
|
Definition
| Genes that have the potential to cause cancer. Usually, cells that ought to die (apoptosis) end up proliferating. |
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Term
|
Definition
| Regulatory element in an operon where repressor protein binds to stop transcription. |
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Term
|
Definition
| A series of genes, a promoter and often an operator sequence controlled by one regulatory gene |
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Term
|
Definition
| Named typically with ori. This is the sequence in a genome in which replication is initiated. |
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Term
|
Definition
| A nucleic acid sequence that is read identically in both directions; sequences that restriction enzymes target. |
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Term
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Definition
| Polymerase chain reaction, technique of recombinant DNA technology that allows researchers to produce a large number of identical DNA molecules in-vitro. |
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Term
| Penicillin binding protein (PBP) |
|
Definition
| Involved in the final stages of the synthesis of peptidoglycan. |
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Term
| Plaque forming unit (pfu): |
|
Definition
| Measure of the number of particles capable of forming plaques per unit volume. (1000 pfu/microliter) |
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Term
|
Definition
| Virus that infects and usually destroys bacterial cells. |
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Term
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Definition
| The physical features and functional traits of an organism expressed by genes in its genotype. |
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Term
|
Definition
| In phage typing, the clear region within the bacterial lawn where growth is inhibited by bacteriophages. |
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Term
|
Definition
A small, circular molecule of DNA that replicates independently of the
chromosome. |
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Term
|
Definition
| A genetic mutation affecting only one or a few base pairs in a genome |
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Term
|
Definition
| : Enzymes that assist with the polymerizations of DNA or RNA against existing strands. |
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Term
|
Definition
| Process by which mutants are selected by eliminating wild-type phenotypes
. Ex: Searching for penicillin resistant E.coli, grow E.coli on a penicillin plate. |
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Term
|
Definition
| Nucleic acid molecule with a specific nucleotide sequence that has been labeled with a radioactive or fluorescent chemical so that its location can be deleted |
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Term
|
Definition
| a live microorganism, beneficial to the host |
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Term
|
Definition
| Region of the DNA where transcription begins. |
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Term
|
Definition
| An inactive bacteriophage, which is inserted into a host's chromosome |
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Term
|
Definition
| contribute to normal cell growth, inhibit cancerous growth |
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Term
|
Definition
| Inactive virus in an animal cell. |
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Term
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Definition
| Mutation in which adjacent pyrimidine bases covalently bond to one another caused by non-ionizing radiation in the form of ultraviolet light |
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Term
|
Definition
| DNA molecule resulting from genetic recombination between donated and recipient nucleotide sequences. |
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Term
|
Definition
| Cells or DNA molecules resulting from genetic recombination between donated and recipient nucleotide sequences. |
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Term
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Definition
| An administrative legislation that constitutes or constrains rights (obviously not a micro definition, great job). |
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Term
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Definition
| : A collection of genes or operons under the regulation by the same regulatory protein. |
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Term
|
Definition
| Literally looks like a fork. Formed by breaking the hydrogen bonds by helicase during DNA replication. |
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Term
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Definition
| A gene that researchers attach to a regulatory sequence of another gene of interest. |
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Term
|
Definition
| A DNA-binding protein that regulates the expression of one or more genes by binding the operator and blocking the attachment of RNA polymerase. |
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Term
|
Definition
| Type of operon that is continually transcribed until deactivated by repressors. |
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Term
|
Definition
| Enzyme that cuts DNA at specific nucleotide sequences and is used to produce recombinant DNA molecules. |
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Term
|
Definition
| Any ++ssRNA virus that uses the enzyme reverse transcriptase carried within its capsid to transcribe DNA from its RNA. |
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Term
|
Definition
| Enzyme that creates a flow of genetic information in the opposite direction of conventional transcription... Uses an RNA template to make a molecule of DNA called the cDNA (complementary DNA) |
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Term
|
Definition
| Rho factor binds to the transcription terminator pause site, an exposed region of RNA after the open reading frame at GC-rich sequences that lack obvious secondary structure. |
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Term
|
Definition
| Enzyme that synthesizes RNA by linking RNA nucleotides that are complementary to genomic sequences in DNA. |
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Term
|
Definition
| RNA molecule used by DNA polymerase or reverse transcriptase as a starting point for DNA synthesis. |
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Term
|
Definition
| A plasmid that encodes resistance to one or more antimicrobial drugs. |
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Term
|
Definition
| Form of ribonucleic acid which, together with polypeptides, makes up the structure of ribosomes. |
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Term
|
Definition
| when there’s a visual difference between microorganisms in a media |
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Term
|
Definition
| when you put a microorganism in a media that inhibits the growth of another microorganism |
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Term
|
Definition
| Principle by which an effective antimicrobial agent must be more toxic to a pathogen than to a pathogen's host. |
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Term
| Semiconservative replication |
|
Definition
| method of DNA replication where the progeny is a product of 1 new strand + 1 parental strand |
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Term
|
Definition
| Mutation produced by base-pair substitution that does not change the amino acid sequence, because of the redundancy of the genetic code
. |
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Term
|
Definition
| Technique used in recombinant DNA technology that allows researchers to stabilize specific DNA sequences from an electrophoresis gel and then localize them using DNA dyes or probes. |
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Term
|
Definition
| only certain host sequences are transferred with phage DNA - the sequences are not RANDOM like generalized transduction; property of lysogenic phage |
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Term
|
Definition
| The number of different kinds of pathogens a drugs acts against. |
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Term
|
Definition
| Type of mutation in which a nucleotide base pair is replaced. |
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Term
|
Definition
| Giant, multinucleated cell formed by fusion of virally infected cell to neighboring cells. |
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Term
|
Definition
| Interplay between drugs that results in efficacy that exceeds the efficacy of either drug alone |
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Term
|
Definition
| In virology, the production of new viral proteins and nucleic acids using the metabolic machinery of the host cell; fourth stage of lytic replication cycle. |
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Term
|
Definition
| Used in PCR. Not denatured at 94 degrees celsius so the machine doesn’t need to be replenished with DNA polymerase after each cycle |
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Term
|
Definition
| Bacteriophage that does not immediately kill its host cell. |
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Term
|
Definition
| : Region of DNA where transcription ends |
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Term
|
Definition
| A measure expressing the relative toxicity of a chemotherapeutic drug. It is the lowest dose toxic to the patient divided by the dose used for therapy. |
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Term
|
Definition
| Process in which the genetic code from DNA is copied as RNA nucleotide. |
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Term
|
Definition
| Method of horizontal gene transfer in which DNA is transferred from one cell to another via a replicating virus (phage). |
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Term
|
Definition
| Method of horizontal gene transfer in which the recipient cell takes up free DNA from the environment. |
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Term
|
Definition
| Plant or animal that has been genetically altered by the inclusion of genes from other organisms. |
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Term
|
Definition
| Process in which the sequence of the genetic information carried by mRNA is used by ribosomes to construct polypeptides with specific amino acid sequences. conversion of RNA to polypeptide chain |
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Term
|
Definition
| Mutation in which a genetic segment is transferred to a new position through the action of a DNA sequence called transposon. |
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Term
|
Definition
| (Transfer RNA) Form of ribonucleic acid that carries amino acids to the ribosome. |
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Term
|
Definition
| Segment of the DNA found in most prokaryotes, eukaryotes, and viruses that codes for the enzyme transposase and can move from one location in a DNA molecule to another location in the same or different molecule. “jumping genes” |
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Term
|
Definition
| cloudiness of a fluid caused by the presence of cells. Turbidity decreases (solution becomes clear) when cells are completely lysed |
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Term
|
Definition
| In animal viruses, the removal of a viral capsid within a host cell |
|
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Term
|
Definition
| In genetics and recombinant DNA technology, nucleic acid molecule such as a viral genome, transposon, or plasmid that is used to deliver a gene into a cell. |
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Term
|
Definition
| Estimation of the size of a microbial population based upon the number of colonies formed when diluted samples are plated onto agar media |
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Term
|
Definition
| A virus outside of a cell, consisting of a proteinaceous capsid surrounding a nucleic acid core. |
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Term
|
Definition
| extremely small, circular piece of RNA that is infectious and pathogenic in plants. |
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|
Term
| Western blot test: (Immunoblot) |
|
Definition
| Variation of an ELISA (Enzyme-Linked ImmunoSorbent Assays) test that can detect the presence of antibodies against multiple antigens; used to verify the presence of antibodies against HIV in the serum of individuals who have tested positive by ELISA. |
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Term
|
Definition
| In a diffusion susceptibility test, a clear area surrounding the drug-soaked disk where the microbe does not grow. |
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Term
|
Definition
| Antimicrobial agents that are produced naturally by an organism. |
|
|
Term
| What organisms make antibiotics? |
|
Definition
| Fungi (molds) and bacteria |
|
|
Term
| How are antibiotics made? How do they work? |
|
Definition
| By a process of fermentation, where the microorganisms (eg. penicillium mold) is grown in large quantities. |
|
|
Term
| How do antibiotics interact? |
|
Definition
Synergy - sum of activity of two antibiotics is greater than the action of each - Tuberculosis treatment
Additive
Antagonistic |
|
|
Term
| How do you measure their effectiveness? antibiotics |
|
Definition
1)determine the MIC by dilution of antibiotic in a culture to see which is the minimal concentration of antibiotic is effective for inhibiting growth
2) Determine the minimum bactericidal concentration (MBC)
3)Conventional disk diffusion method (Kirby-Bauer) |
|
|
Term
| What are the mechanisms by which antibiotics work? |
|
Definition
Inhibiting the translation of proteins
Disrupting cytoplasmic membranes
Inhibiting general metabolic pathways,
Inhibiting the replication of DNA,
Blocking the attachment of viruses to their hosts or by blocking a pathogens recognition of its host.
(inactivation of antibiotic - beta- lactamase breaks bond with C and N and make penicillin inactive) |
|
|
Term
| What are the biological targets? antibiotics |
|
Definition
Cell wall, cell membrane, DNA synthesis, RNA synthesis, Protein synthesis,
Metabolism, substrate concentration. |
|
|
Term
| Why are antibiotics chemically modified? |
|
Definition
| produce more effective and less toxic drugs |
|
|
Term
| How do antibiotics affect growth? |
|
Definition
Inhibition of cell wall synthesis
Bacterial Walls
Fungal Walls
Inhibition of protein synthesis
Disruption of cytoplasmic membranes
Inhibition of metabolic pathways
Inhibition of Nucleic Acid Synthesis |
|
|
Term
| Can you draw a growth curve that shows how a bacteriostatic antibiotic would work? |
|
Definition
| stop reproduction - flat line once antibiotic is added |
|
|
Term
| How about a Bactericidal one? Bacteriolytic? |
|
Definition
| bactericidal kills bacteria by inhibiting organelles and bacteriolytic kills bacteria by destroying the cell membrane - growth curve should decline immediately after addition of antibiotic |
|
|
Term
| How do you determine the MIC of an antibiotic? |
|
Definition
| minimum inhibitory concentration; determined by agar or broth dilution methods |
|
|
Term
| Why do some antibiotics work against some species and not others? |
|
Definition
|
|
Term
| How do organisms become resistant to antibiotics? |
|
Definition
repeated use in small doses
Extra DNA pieces called R-plasmids, the mutation of genes, by producing enzymes like b-lactamase, induce change in cell membrane to prevent entry of drug, alter drug’s target to prevent its binding, ect. |
|
|
Term
| What are the different mechanisms to become resistant to antibiotics? |
|
Definition
Inactivation of antibiotics
Change the target
Reduced Permeability
Efflux
Change the Pathway |
|
|
Term
| How are the DNA strands held together? |
|
Definition
|
|
Term
| Why is it important that DNA the strands are not covalently bound? |
|
Definition
| so they exist as double stranded and allows for replication - can unwind |
|
|
Term
| With arrows show how DNA will be replicated from the origin of replication. What goes on at the replication fork? |
|
Definition
| DNa helicase breaks the hydrogen bonds holding the DNA strands together. Single stranded binding protein stabilizes the single strands to prevent them from joining back together. |
|
|
Term
Show how DNA is replicated in the leading strand. Show how DNA is replicated in the lagging strand. What are the functions of each enzyme/protein in the reaction? Label 3' and 5' ends of both the template strands and the strand being synthesized.
Be able to explain what it means when we say that synthesis occurs from the 5' to 3' end. What is meant by semiconservative DNA replication? |
|
Definition
Leading strand-moves away from the origin of replication.
* Primase- enzyme that lays down RNA primer (provides 3’ end) so that DNA polymerase III can synthesize a new strand of DNA (DNA polymerase needs an RNA primer in order to synthesize the new DNA, it can’t function on the single strand of DNA present). Nucleotides are then added and H-bonded with the template strand. DNA Polymerase III acts as the proof-reader for errors. DNA Polymerase I, replaces RNA primer with DNA.
Once DNA polymerase removes the RNA primers as it is synthesizing the new DNA strand, ligase seals the nicks of the strands together
1) Primase lays down MULTIPLE RNA primers (1 every 1000-2000 base pairs)
2) Nucleotides pair with their complements
3) DNA Polymerase III joins the nucleotides and proof-reads (Creates okazaki fragments)
4) DNA Polymerase I replaces RNA primer
5) Ligase seals gap b/w Okazaki fragments |
|
|
Term
| Compare and contrast DNA replication in prokaryotes and eukaryotes |
|
Definition
Prokaryotes have 1 origin of replication, Eukaryotes can have multiple origins of replication
Eukaryotic replication:
- 4 different DNa polymerases
-eukaryotic okazaki fragments = shorter than prokaryotic okazaki fragments
-methylate cytosine exclusively |
|
|
Term
| Is there an advantage to having multiple origins of replication in eukaryotes? |
|
Definition
| Multiple origins of replication in eukaryotes allow the process of replication to occur quicker and more efficiently. This is necessary because the genome of a eukaryote is very large compared to the genome of a prokaryote. |
|
|
Term
| Compare and contrast the chromosome structure of eukaryotes and prokaryotes |
|
Definition
| eukaryotes have linear chromosomes, prokaryotes have circular chromosomes |
|
|
Term
How does information flow in a bacterial cell? Between generations of cells?
Between cells of the same generation? Within a cell? |
|
Definition
DNA is replicated.. Transcribed to RNA... Translated to Amino Acids
between cells of the same generation - horizontal gene transfer |
|
|
Term
| What is the cellular phenotype? How does it differ from the cellular genotype |
|
Definition
| genotype is the set of genes the cell carries and phenotype is the physical characteristics and functional trait of the organism |
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Term
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Definition
The DNA helix unwinds (via DNA helicase) and each strand serves as a template. DNA Polymerase III attaches the complementary nucleotide to the template strand. DNA Ligase links the nucleotides together.
Semiconservative - each of the 2 progeny double helices have 1 parental + 1 new strand |
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Term
| What is the template strand? |
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Definition
| the template strand is the original strand of DNA that codes for the complementary strand of DNA or RNA |
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Term
| What is the direction of synthesis? |
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Definition
| 5’ to 3’. New nucleotides are only added to the 3’ end. |
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Term
| What enzymes are involved? |
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Definition
| helicase, RNA primer (primase), DNA polymerase III, DNA polymerase I, Ligase |
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Term
| What is a replication fork? |
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Definition
| Y-shaped region of a piece of DNA associated with the site of replication. It is Y shaped because the double stranded DNA has unwound and become two single strands |
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Term
| What is the origin of replication? |
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Definition
| a particular sequence in a genome at which replication is initiated |
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Term
| What is needed to initiate replication? |
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Definition
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Term
| how does adding a nucleotide work |
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Definition
| nucleotides are added to the OH group on the 3’ end of the previous nucleotide |
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Term
| Which strand is synthesized continuously? |
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Definition
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Term
| What is meant by the term semi-conservative replication? |
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Definition
| in the newly synthesized DNA, there is one daughter strand and one parent strand |
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Term
| How often are mistakes in replication made? |
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Definition
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Term
| What do we call a mistake in replication? |
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Definition
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Term
| What is "proofreading" and how does this affect the number of mistakes in replication |
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Definition
| When a mistake is made in replication, Polymerase III has a proofreading function that is able to rewind and fix the mistake to limit the number of mistakes that are made in replication |
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Term
| What does transcription mean? |
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Definition
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Term
| How does RNA polymerase recognize a DNA sequence? |
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Definition
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Term
| What is the direction of RNA synthesis? |
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Definition
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Term
| How does RNA differ from DNA |
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Definition
| RNA has ribose, DNA has deoxyribose as the pentose sugar. RNA also uses Uracil instead of Thymine. RNA is single-stranded, and DNA is double-stranded. |
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Term
| How does mRNA of a prokaryote differ from a eukaryote? |
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Definition
| eukaryote has 5’ cap, exons, introns, and poly-A tail; prokaryotes have little editing, no introns |
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Term
| Is a primer required for transcription? Why or why not? |
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Definition
| no because you are using RNA polymerase (unlike when you used DNA polymerase in replication) |
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Term
| What effect do mistakes in transcription have on information flow? |
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Definition
| no mRNA synthesis. Could create the wrong sequence on mRNA, which will lead to the wrong translation of amino acids leading to a nonfunctional protein. |
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Term
| How is rRNA produced? What is the function of rRNA? Why is the rRNA of significance in phylogenetic studies? |
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Definition
rRNA molecules are formed in the nucleus particularly in the nucleoli.
eukaryotic ribosomes= 80S, prokaryotic ribosomes = 70S
smaller subunit of the ribosome is shaped to accommodate 3 codons at one time. A site, P site, Exit site. |
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Term
| Define a "gene". If you are studying the gene sequence for a genomics project, how would you detect a gene in the DNA? |
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Definition
| molecular unit of heredity of a living organism. |
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Term
| From looking at the DNA what can you predict about the protein? |
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Definition
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Term
| What is a promoter? (Use the word "sequence" in your answer) What role does the promoter play in transcription? |
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Definition
| sequence of DNA that serves as the initiation site of transcription, found at the 5’ end of genes |
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Term
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Definition
a subunit of RNA polymerase, necessary to recognize a promoter.
helps RNA polymerase recognize the promoter region in transcription |
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Term
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Definition
| mRNA is translated by ribosome to produce amino acid chain or polypeptide that will fold into a protein |
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Term
| What are start and stop codons? There are 64 codons. From where does that number come? |
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Definition
start codons indicate the beginning of a polypeptide sequence, stop codons indicate the end of a polypeptide sequence.
A code of 3 nucleotides could code for a maximum of 4^3 or 64 amino acids |
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Term
| here are only 20 amino acids but 64 combinations of nucleotides |
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Definition
| (multiple codons code for the same amino acid) and this is because of the wobble effect → basically, the nucleotide in the third position doesn’t matter (aka a lot of the codons are the same for an amino acid except the nucleotide in the third position) |
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Term
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Definition
| Mutations are permanent changes in the nucleotide base sequences of genomes. |
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Term
| What are the different types of mutations? |
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Definition
Point mutations are the most common form of mutations.
Frameshift mutations include insertions and deletions. Some substitution mutations can result in a silent mutation since the change in the base pair does not affect the amino acid sequence (due to redundancy). Missense mutations are when a point mutation causes at least one amino acid to change to a completely different amino acid. Nonsense mutations are when one base-pair substitution changes an amino acid codon into a stop codon resulting in a nonfunctional protein |
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Term
| Why are spontaneous mutations significant even though they occur relatively infrequently? |
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Definition
| They can completely destroy a protein so it is no longer functional. |
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Term
| Would you expect a substitution or frameshift mutation to be more harmful? Explain your answer. |
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Definition
| A frameshift mutation is more harmful because instead of just altering one amino acid, the shift causes every nucleotide after the insertion/deletion point to be changed. If the missense mutation is at a critical region, it causes the protein to become nonfunctional. Also through the shift, a stop codon can be formed, resulting in a nonsense mutation. Substitution mutations have a chance to be a silent mutation due to the redundancy in the genetic code. |
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Term
| How does the "wobble" effect protect organisms from simple substitution changes? |
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Definition
| Because many times, the nucleotide in the third position doesn’t matter. It could be any of the four nucleotides and still code for the same amino acid |
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Term
| Given a DNA sequence, could you determine the overall effect of a given mutation |
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Definition
1) Determine the sequence of amino acids that would be produced without the mutation
2) Determine the new sequence of amino acids that are produced with the mutation. If there is a difference in amino acid sequence, there is an overall effect of the given mutation. |
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Term
| Sometimes a single mutation does not change the phenotype. Why? |
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Definition
| A mutation in a single nucleotide may not change the phenotype because of the redundancy of the genetic code. For example, if UUC were mutated to become UUU, no phenotypic change would occur because they both code for the amino acid phenylalanine. |
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Term
| How do bacteria repair mutations? What are the different types of repair mechanisms? How do they differ? How are they similar? |
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Definition
Light repair = Repair of pyrmidine dimers. DNA photolyase an enzyme activated by visible light breaks pyrmidine dimers, reversing the mutation and restoring the original DNA sequence.
Dark repair = dark repair enzymes cut the damaged section of the molecule, creating a gap that is repaired by DNA polymerase I and DNA ligase (operates in the absence of light)
Base excision repair = Excise the erroneous base, then DNA polymerase I fills in the gap
Mismatch repair = mismatch repair enzymes scan the new DNA looking for mismatched bases, which they remove and replace. Distinguish between new DNA and old DNA because old strand is methylated.
SOS response = when damage to a DNA is so extreme that regular processes can’t fix it. Produce new DNA polymerases (IV and V). IV and V are really bad at copying, but it gives the chance that some of the offspring of bacteria can survive. |
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Term
| How do mutations contribute the antibiotic resistance? |
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Definition
| A random mutation that occurs in a bacteria could be advantageous for the bacteria and allow it to survive in the presence of antibiotics. By the process of natural selection, bacteria with this advantageous characteristic are more likely to survive, more likely to reproduce with one another, and more likely to create offspring with the same characteristic, provided by a random mutation. |
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Term
| Why is a ribosome a usual target for antibiotic resistance? |
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Definition
| damaging the ribosome will inhibit protein synthesis |
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Term
| How can bacteria acquire new DNA? What is lateral gene transfer? What are the processes? How are they similar? How are they different? |
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Definition
| Lateral gene transfer (horizantal) - donor cell contributes part of its genome to a recipient cell (can be of different species). Typically, recipient cell inserts part of the donor’s DNA into its own chromosome, becoming a recombinant cell. |
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Term
| What is the difference between a recipient and a donor cell in Conjugation? Transformation? Transduction? |
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Definition
Transformation - recipient cell takes up DNA from the environment
Transduction - transfer of DNA from one cell to another via a replicating virus
Conjugation - donor cell remains alive. Physical contact between donor and recipient cell via conjugation pilus. |
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Term
| How does conjugation with an F plasmid differ from conjugation with an Hfr? |
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Definition
A F plasmid has a gene that codes for the conjugation pili. F+ cells (those with the pili) are donors during conjugation. Recipient cells are F- cells.
A Hfr cell can conjugate with an F- cell, but the F plasmid doesn’t remain independent in the cytosol, but instead integrates at a specific DNA sequence in the cellular chromosome. |
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Term
| How do you select for a mutation? |
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Definition
Positive selection or Negative Selection.
Probes--which bind specifically and exclusively to their complementary nucleotide sequences and have either radioactive or fluorescent markers |
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Term
| What is transformation? How does natural transformation differ from artificial transformation. What is a competent cell? |
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Definition
Competent cell - cells that have the ability to take up DNA from their environment
Transformation: a recipient cell takes up DNA from the environment such as DNA released from a dead cell.
Artificial Transformation: Cells rarely are competent to take up DNA naturally so you can use techniques such as electroporation, to make the membrane porous and take up DNA. |
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Term
| Are all bacteria capable of taking up DNA? |
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Definition
| No. Only some bacteria are naturally competent: ex: bacillus, staphylococcus, etc. Scientists can manipulate bacteria to become artificially competent though by making alterations in the cell wall and cytoplasmic membrane that allow DNA to enter the cell. |
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Term
| Why can't all plasmids be transferred by conjugation? What are R factors? Why are they significant medically speaking? What is an F (fertility) plasmid? What is an episome? How is an Hfr cell formed? |
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Definition
| Not all bacterial cells have F plasmids that code for the sex pilus. The R factors or plasmids are resistance factors. The natural transfer of genes by conjugation among diverse organisms heightens some scientists’ concerns about the spread of the resistance plasmids among pathogens. |
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Term
| What structures are needed for Conjugation? |
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Definition
| Conjugation Pili coded by the F plasmid or in the HFR cell |
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Term
| What is a transposon? How do they contribute to evolution? |
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Definition
| Transposon - segments of DNA that move themselves from one location in a DNA molecule to another location in the same or different molecule. They can contribute to evolution by creating new polypeptide sequences (changing the DNA for the progeny) |
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Term
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Definition
| Transformation is when a recipient cell takes up DNA from its environment, |
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Term
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Definition
| cells that have the ability to take up DNA from their environment |
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Term
| Natural vs induced competence? |
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Definition
| natural - streptococcus haemophilus, neisseria, bacillus, staphylococcus, pseudomonas. Have alterations in the cell wall and cytoplasmic membrane that allow DNA to enter the cell. Induced competence: Escherichia, manipulate the temperature and salt content of the medium to allow competency. |
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Term
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Definition
| Transduction is the transfer of DNA from one cell to another via a replicating virus. |
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Term
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Definition
| Eukaryotic equivalent of bacterial plasmids |
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Term
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Definition
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Term
| Why are they significant medically speaking |
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Definition
| They code for antibiotic resistance |
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Term
| What is the role of a restriction enzyme? |
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Definition
| Restriction enzymes cut DNA molecules only at locations called restriction sites → specific nucleotide sequences, which are usually palindromes. |
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Term
| How does it generate distinct fragments of DNA? |
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Definition
| by cutting at restriction sites |
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Term
| What is the role of a vector? |
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Definition
| nucleic acid molecules such as viral genomes, transposons, and plasmids used to deliver a gene into a cell. |
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Term
| What are the essential features of a vector that allow it to work in Escherichia coli? |
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Definition
| Ability to survive inside the cell, a recognizable genetic marker |
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Term
| How do you select for the presence of the introduction of a plasmid in a bacterial population? |
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Definition
| By using the selectable marker... for example, also including a gene for penicillin resistance and growing the bacteria on a penicillin plate. Colonies that grow have taken up the plasmid |
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Term
| What is the role of DNA ligase in a cloning experiment? |
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Definition
| anneals fragments to produce a recombinant plasmid |
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Term
| What features are needed in a plasmid to allow for the expression of a human gene, whose DNA was generated from cDNA? |
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Definition
| reverse transcriptase because if there are introns or exons in the gene, then the E. coli will not be able to incorporate into its DNA |
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Term
| What is the difference between a plasmid and a vector? |
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Definition
| plasmid is an example of a vector |
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Term
| How does a Southern blot work? |
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Definition
| USed to transfer DNA from agarose gels to nitrocellulose membranes, which are less delicate. Denature the DNa with NAOH. Once the DNA has been separated by size, blot it out in the electrophoresis gel. DNA is transferred and bonded with heat to a nitrocellulose membrane. Radioactive probes expose photographic film revealing the DNA of interest. |
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Term
| How does a western blot work? |
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Definition
| same as southern blotting, except you are using proteins instead of DNA and instead of identifying probes you are looking for antibodies. |
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Term
| Why are viruses not considered to be cells? |
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Definition
| viruses can’t replicate on their own, they rely on their host for cell replication machinery |
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