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Module 13 in the Syllabus

The Molecular Biology Laboratory Images
Image gallery for study with links to larger teaching JPEGs for classroom presentation

Question Drill for The Molecular Biology Laboratory
Conceptual Vocabulary Self-Test

Basic Terms Crossword Puzzle

Basic Puzzle Solution

Conceptual Vocabulary
ChromatographyChromatography is the collective term for laboratory techniques which separate analytes dissolved in a mobile phase by passing them through a stationary phase.
Gel electrophoresisGel electrophoresis is a technique used for the separation of biological molecules using an electric field.
DNA electrophoresisDNA electrophoresis is an analytical technique used to separate DNA fragments by size though the use of an electric field which forces the fragments to migrate through a gel.
AgaroseAgarose is a material used to form a common type of electrophoresis gel which is derived from the cell membranes of some species of red algae or seaweed.
Capillary electrophoresisCapillary electrophoresis separates biological macromolecules based on their size to charge ratio in the interior of a very narrow tube filled with an electrolyte.
CentrifugationCentrifugation is a process that involves the use of the centripetal force for the separation of mixtures.
DNA sequencingThe term DNA sequencing encompasses biochemical methods for determining the order of the nucleotide bases in a DNA oligonucleotide.
Polymerase chain reactionThe polymerase chain reaction is a technique widely used in molecular biology to exponentially amplify a fragment of DNA by in vitro enzymatic replication.
Restriction enzymeA restriction enzyme is an enzyme that cuts double-stranded DNA in such a way that the fragments from different chromosomes or genes can be spliced together by ligases.
SDS-PAGESDS-PAGE, officially sodium dodecyl sulfate polyacrylamide gel electrophoresis, is a technique used to separate proteins according to their electrophoretic mobility.
Thin layer chromatographyThin layer chromatography is a chromatography technique involving a stationary phase consisting of a thin patina of adsorbent material immobilised on a flat, inert carrier sheet.
DialysisDialysis is the process of separating molecules in solution by the difference in their rates of diffusion through a semipermeable membrane.
SupernateSupernate refers to the liquid or clear fluid above a sediment or precipitate.
Cloning vectorA cloning vector is a small DNA vehicle that carries a foreign DNA fragment.
PlasmidA plasmid is a DNA molecule separate from chromosomal DNA which is capable of autonomous replication. It is typically circular and double-stranded.
ProphageA prophage is a phage genome inserted as part of the linear structure of the DNA chromosome of a bacterium.
ImmunostainingImmunostaining is a general term in biochemistry that applies to any use of an antibody-based method to detect a specific protein in a sample.
FractionationFractionation is a separation process in which a certain quantity of a mixture is divided up in a large number of smaller quantities in which the composition changes according to a gradient.
DideoxynucleotidesDideoxynucleotides are nucleotides lacking a three prime hydroxyl group on their deoxyribose sugar. After one is added by a DNA polymerase to a growing nucleotide chain, no further nucleotides can be added.
Shotgun sequencingIn shotgun sequencing, DNA is broken up randomly into numerous small segments, which are sequenced. The process is repeated until multiple overlapping reads for the target DNA are obtained
Edman degradationEdman degradation is a method of sequencing amino acids in a peptide in which the amino-terminal residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues.
Taq polymeraseTaq polymerase is a thermostable DNA polymerase named after the thermophilic bacterium Thermus aquaticus from which it was isolated. This enzyme is able to withstand the high temperature required during PCR.
Transgenic bacteriaTransgenic bacteria refers to bacteria which have been genetically engineered.
Molecular cloningMolecular cloning refers to the procedure of isolating a defined DNA sequence and obtaining multiple copies of it in vivo.
Fertility factorThe Fertility factor (also known as F factor or sex factor) is a bacterial DNA sequence that allows a bacterium to produce a sex pilus necessary for conjugation.
PilusA pilus is a hairlike appendage found on the surface of many bacteria.
TransformationTransformation is the genetic alteration of a cell resulting from the uptake and expression of foreign genetic material.
Hybridization probeA hybridization probe is a labeled fragment of DNA of variable length which is used to detect in DNA or RNA samples the presence of nucleotide sequences that are complementary to the sequence in the probe.
ELISAIn ELISA technique an unknown amount of antigen is affixed to a surface, and then a specific labeled antibody is washed over the surface so that it can bind the antigen.
Ion-exchange ChromatographyIon-exchange chromatography is a process that allows the separation of ions and polar molecules based on the charge properties of the molecules.
Affinity chromatographyAffinity chromatography is a chromatographic method of separating biochemical mixtures, based on a highly specific biologic interaction such as that between antigen and antibody or enzyme and substrate.
UltracentrifugeThe ultracentrifuge is a centrifuge optimized for spinning a rotor at very high speeds, capable of generating acceleration as high as 1,000,000 g.
Peptide mass fingerprintingIn peptide mass fingerprinting an unknown protein is cleaved into peptides by a protease such as Trypsin to form a collection of peptides serving as a unique identifier of the unknown protein.
Restriction digestA restriction digest is a procedure which uses a restriction enzyme to selectively cleave DNA strands into shorter segments, which are more suitable for analytical techniques such as chromatography.
AgrobacteriumAgrobacterium is a genus of Gram-negative bacteria that causes tumors in plants, well known for its ability to transfer DNA between itself and plants.
cDNA libraryA cDNA library is a collection of clones containing cDNAs. These are often intended to represent as many as possible of the mRNAs contained within a cell.
LibraryIn molecular biology, a library is a collection of molecules in a stable form that represents some aspect of an organism.
Northern blotThe Northern blot is a technique used in molecular biology research to study gene expression which analyzes RNA by electrophoresis, transfer to a membrane, and detection with a hybridization probe.
Southern blotThe Southern blot is a technique used in molecular biology research to study gene expression which analyzes DNA by electrophoresis, transfer to a membrane, and detection with a hybridization probe.
AutoradiographAn autoradiograph is an image produced on an x-ray film or nuclear emulsion by the pattern of decay emissions from a distribution of a radioactive substance.
Western blotThe Western blot is a technique used in molecular biology research which analyzes proteins by electrophoresis, transfer to a membrane, and detection with an antibody probe.
EluentThe eluent in chromatography is the liquid or gas entering a chromatographic bed.
High performance liquid chromatographyIn high-performance liquid chromatography (HPLC) a liquid mobile phase containing the analyte is pumped at high pressure through a column of the stationary phase.
Reversed-phase chromatographyReverse-phase chromatography includes any chromatographic method that uses a non-polar stationary phase.
Reverse transcription polymerase chain reactionReverse transcription polymerase chain reaction is a laboratory technique for amplifying a defined piece of a ribonucleic acid (RNA) molecule.
AmpliconsAmplicons are pieces of DNA formed as the products of natural or artificial amplification events.
AdapterAn adapter in genetics engineering is a short, chemically synthesized, double stranded DNA molecule which is used to link the ends of two other DNA molecules.
LysogenA lysogen is a phage that does not go into a lytic cycle but instead either integrates into the host bacteria's chromosome or lives as a stable plasmid within the host cell.
CompetenceCompetence is the ability of a cell to take up extracellular DNA from its environment.
In situ hybridizationIn situ hybridization is a technique that uses a labeled DNA or RNA probe to localize a specific DNA or RNA sequence in a portion or section of tissue.
DNA microarrayA DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is a collection of microscopic DNA spots arrayed on a solid surface by covalent attachment to a chemical matrix.
Advanced terms that may appear in context in MCAT passages
Protein microarrayA protein microarray is a piece of glass on which different molecules of protein have been affixed at separate locations in an ordered manner thus forming a microscopic array.
Ethidium bromideEthidium bromide is an intercalating agent commonly used as a nucleic acid stain in molecular biology laboratories for techniques such as agarose gel electrophoresis.
Secondary antibodyA secondary antibody is an antibody that binds to a primary antibody usually as part of a detection, purification or cell sorting application.
Silica gelSilica gel is a granular, porous form of silica which is often used in chromatography as a stationary phase.
Size exclusion chromatographySize exclusion chromatography is a chromatographic method in which particles are separated based on their size, or in more technical terms, their hydrodynamic volume.
Differential centrifugationDifferential centrifugation is a procedure in which a homogenate is subjected to repeated centrifugations in which, after each time, the pellet is removed and the centrifugal force is increased.
Nested polymerase chain reactionNested polymerase chain reaction is a modification of polymerase chain reaction intended to reduce the contaminations in products due to the amplification of unexpected primer binding sites.
Restriction modification systemThe restriction modification system based on sequence specific restriction enzymes is used by bacteria to protect themselves from foreign DNA, such as bacteriophages.
EndolysinEndolysin is a generic term describing an enzyme that lyses a bacterial membrane.
Hok/sok systemThe host killing/suppressor of killing system, also known as hok/sok system is a postsegregational killing system of the plasmid R1 of Escherichia coli.
Gene knockoutA gene knockout is a genetically engineered organism that carries one or more genes in its chromosomes that have been made inoperative.
Phage displayPhage display is a test to screen for protein interactions by integrating multiple genes from a gene bank into phage.
Southwestern blotSouthwestern blotting, based along the lines of Southern blotting, involves characterizing proteins that bind to DNA.
Van Deemter's equationVan Deemter's equation in chromatography relates the variance per unit length of a separation column to the linear mobile phase velocity by considering physical, kinetic, and thermodynamic properties of a separation.
Aqueous normal phase chromatographyAqueous normal phase chromatography is a chromatographic technique which encompasses the mobile phase region between reversed-phase chromatography and organic normal phase chromatography.
Multiplex Ligation-dependent Probe AmplificationMultiplex ligation-dependent probe amplification is a variation of the polymerase chain reaction that permits multiple targets to be amplified with only a single primer pair.
Hfr cellAn hfr cell is a bacterium with a conjugative plasmid integrated into its genomic DNA.
Bacterial artificial chromosomeA bacterial artificial chromosome is a DNA construct, based on a fertility plasmid, used for transforming and cloning in bacteria.
Yeast artificial chromosomeA yeast artificial chromosome (YAC) is a vector used to clone large DNA fragments which contains the telomeric, centromeric, and replication origin sequences needed for replication.
Multiple cloning siteA multiple cloning site, also called a polylinker, is a short segment of DNA which contains many, usually 20 or more, restriction sites - a standard feature of engineered plasmids.
Beta-lactamaseBeta-lactamases are enzymes produced by some bacteria and are responsible for their resistance to beta-lactam antibiotics like penicillins, cephalosporins, cephamycins and carbapenems.
Blue white screenThe blue-white screen is a molecular technique that allows for the detection of successful ligations in vector-based gene cloning.
X-galX-gal is a galactoside and indole used in gene cloning to indicate whether a bacterium expresses the beta-galactosidase enzyme, which is encoded by the lacZ gene.
Electrophoretic mobility shift assayAn electrophoretic mobility shift assay is a common technique used to study protein-DNA or protein-RNA interactions.
DNase footprinting assayA DNase footprinting assay is a technique from molecular biology that detects DNA-protein interaction using the fact that a protein bound to DNA will often protect that DNA from enzymatic cleavage.
SNP arrayAn SNP array is a type of DNA microarray which is used to detect polymorphisms within a population.
ChIP-on-chipChIP-on-chip is a technique that combines chromatin immunoprecipitation (ChIP) with microarray technology (chip).
PhagemidA phagemid or phasmid is a type of cloning vector developed as a co-infection of the M13 helper phage and plasmids to produce a smaller version of the virus.

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