BIOL 4004 exam 1

Detection

The ability to perceive an object

Resolution

The ability to discriminate between two objects that are close together

Limit of Resolution

The maximum amount of information that can be obtained from an image, determined by the lens numerical aperture (N.A.) and illumination wavelength

Numerical Aperture (N.A.)

A measure of the light gathering capability of a lens

Fixation

Use of a chemical to cross-link proteins in stable networks to preserve biological structure

Embeding

Introducing a medium (wax, resin, or gel) into a sample to support its normal three dimensional structure

Sectioning

Cutting a specimen into slices thin enough to be penetrated by the illumination to be used for imaging

Empty Magnification

Magnifying the image past the limit of optical resolution so that no new detail is revealed

Stains

Molecules which bind particular cellular components

Fluorophores

Molecules that absorb light at an excitation wavelength and release light at a longer emission wavelength

Contrast

Visual difference between two components, or a component and the background, so that the component can be identified

Dye

A colored stain

Transmission Electron Microscopy

Electrons pass through a specimen to form an image that resolves subcellular structures and complexes.

Fluorescence Resonance Energy Transfer (FRET)

Use of fluorescent protein fusions with overlapping spectra to visualize the proximity of the proteins (and thus any interaction) in live cells

EM Tomography

Many TEM micrographs taken up to 60˚ in either direction are combined into a 3D image of a sample

Confocal microscopy

Collects optical sections of a fluorescent sample as a z-stack or in a maximum intensity projection

GFP fusion protein

Placing the sequence of GFP in-frame with a gene of interest to produce a protein that contains GFP

Microtome

An instrument that creates very thin slices of a sample

Scanning Electron Microscopy

Electrons are scattered or emitted to create a three dimensional surface image of a sample

GFP reporter line

Using the promoter of a gene of interest to drive GFP expression in an organism

Wavelength

Distance between the wave peaks of the illumination

Fluorescence Recovery After Photobleaching (FRAP)

A technique where a patch of fluorescent molecules is photobleached and recovery of fluorescence is tracked to measure kinetics of a system, like a membrane

Hybridoma cell line

A fusion of a B lymphocyte and a tumor cell that produces unlimited quantities of a particular antibody

In vitro

Experiments carried out using cultured cells in a dish ("in glass")

Column chromatography

General term for a purification technique that separates proteins by passing over a matrix-filled column

Gel filtration chromatography

Use of this technique based on size

Affinity chromatography

Use of this technique based on a protein interaction

Ion exchange chromatography

Use of this technique based on charge

Restriction nuclease

An enzyme that cleaves double stranded DNA at a specific short palindromic nucleotide sequence

Probe

A short, labeled, single stranded nucleic acid sequence used to identify the location of its complementary sequence

Ligase

The enzyme that repairs the phosphodiester bond to covalently join two DNA fragments, creating recombinant DNA molecules

cDNA library

A library containing copies of all mRNAs expressed in a sample

Pluripotent stem cells

Cells with the potential to differentiate into any cell type

Monoclonal antibody

A single antibody produced by a particular B lymphocyte

Western blot

Technique where proteins are run on a gel, transferred to a membrane, and identified with a labeled antibody

Polymerase chain reaction (PCR)

Using sequence-specific primers to amplify a particular target DNA sequence through multiple cycles of heating (denaturing), cooling (annealing), and DNA synthesis

X-ray crystallography

The diffraction pattern of X-rays through a purified, crystalized protein is used to produce an atomic model

Reverse genetics

Engineering a mutation in a specific, known gene of interest in order to study the resulting protein's function

Multipotent stem cells

Cells with the potential to differentiate into many cell types

Immunoprecipitation

Technique where an antibody is used to purify a specific protein from a complex mixture

Forward genetics

Screening randomly generated mutants for phenotypes to identify genes important for a process

Chain terminators

The individual nucleotides that are labeled with a fluorescent tag in DNA sequencing

Immortalized cell line

An experimental cell line capable of unlimited cell divisions

Conditional mutation

A mutation that can be turned on or off, or that is revealed only in a certain cell type or at specific times

Nuclear magnetic resonance (NMR) spectroscopy

The spin of hydrogen nuclei in a magnetic field yields spectra that predict the 3D structure of a protein in solution

Polyclonal antibody

An antibody mixture produced from immunized animal serum

Gel electrophoresis

Separating DNA or protein through a matrix (such as agarose or polyacrylamide) using an electric field

Primary cell culture

Culturing cells isolated directly from an organism

In situ hybridization

Visualizes which cells express an mRNA within an organism

Genomic library

A library made from DNA fragments of the entire genome

Transformed cell line

A cell line derived from cancer cells

Hybridization

Annealing of complementary single stranded nucleic acids

Mass spectrometry

Ionized peptides are separated by mass-to-charge ratio

Expression vector

A vector with a strong promoter that drives transcription of any coding sequence inserted downstream

Membrane-anchored protein

Protein attached to membrane by a covalent lipid modification

Unsaturated fatty acid

A fatty acid with one or more carbon cis-double bonds

Micelles

A droplet of amphiphilic molecules (lipid or detergent) in water with polar, hydrophilic domains facing out and hydrophobic, non-polar domains packed together in the interior

Alpha helix

The structure formed by most membrane-spanning protein segments, made of ~20-30 hydrophobic amino acids

Hydrophillic

"Water loving," form hydrogen bonds and dissolve in water

Transmembrane protein

Proteins that extend through the lipid bilayer with mass on both faces, usually described by the number of times they cross or "pass" through the membrane

Saturated fatty acid

A fatty acid with only single bonds between its carbon atoms

Liposomes

Artificial spherical lipid bilayers that form spontaneously in solution, used to reconstitute membrane proteins

Beta barrel

The structure made by multiple transmembrane amino acid strands arranged as a sheet and rolled into a cylinder

Nanodiscs

Artificial lipid bilayer/protein patches stabilized by an HDL belt

Hydrophobic

"Water fearing," can't hydrogen bond with or dissolve in water

Glycosylation

The addition of sugar molecules to a lipid or protein

Single-particle tracking

A technique using video microscopy to record the path of an individual labeled membrane protein over time

Phospholipids

The most abundant membrane lipids, contain a polar head group and two hydrocarbon fatty acid tails

Membrane-associated proteins

Protein found at the membrane because of a non-covalent interaction with a membrane protein (the protein itself does not extend into the lipid bilayer)

Amphiphillic

A molecule with both hydrophobic and hydrophilic regions

Cholesterol

The major sterol found in animal cells that modulates the properties of the lipid bilayer by increasing phospholipid packing, leading to reduced permeability

Phase transition

When a membrane changes from a fluid to a gel-like state at a particular temperature

Flippase

The translocator that transfers specific phospholipids directionally between monolayers, creating the asymmetry of phospholipids within the membrane

Leaflet

A single monolayer of a lipid bilayer

Phosphoglycerides

The most prevalent lipid in animal cell membranes, it has a glycerol backbone

Cortical cytoskeleton

Cytoskeletal networks attached to proteins on the cytosolic face of the plasma membrane, can create mechanical barriers to lateral diffusion of membrane proteins within them

Glycocalyx

The carbohydrate coating of cells due in part to glycolipids and glycoproteins found only on the extracellular face of the membrane

Lipid rafts

Dynamic, specialized membrane domains concentrated with particular lipids and membrane proteins

Hydropathy plot

A calculation made across segments of a polypeptide that expresses the amount of free energy needed to transfer the amino acids into water; a measure of hydrophobicity

Passive transport

When a molecule moves across a membrane through a transporter or channel without the use of energy

Optogenetics

A technique using focused blue light to depolarize a specific neuron expressing a channelrhodopsin derivative

Membrane potential

The voltage difference across a membrane created by electrochemical gradients

Aquaporins

Channels that use a hydrogen bond relay mechanism to specifically pass water molecules (excluding ions)

Selectivity filter

Determines which ion(s) may pass through a channel based on size, charge, and amino acid contacts

Symporters

Transporters that move two solutes in the same direction across a membrane

Active transport

Using energy to move a solute across a membrane 'uphill' against the electrochemical gradient

Voltage-gated channels

Channels that open and close in response to changes in the electrochemical gradient across a membrane

Channel

Create a continuous hydrophilic pore across a membrane

Action potential

Rapid depolarization and repolarization of the plasma membrane due to the flow of ions through voltage-gated channels, the basis of neural transmission

Uniporter

Move a single type of molecule across a membrane

Gating

When a specific stimulus causes a conformational change within the channel pore to open or close it

Refractory period

When voltage-gated Na+ channels are inactivated and K+ channels restore the resting membrane potential

Mechanically-gated channels

Channels that open in response to force stimuli

Synapse

A junction where a nerve cell releases neurotransmitters to signal to another cell

Transporter

Pass individual molecules across a membrane through a conformational change, open on one side then the other

Depolarization

A rapid change in the charge across a membrane toward a positive value

Ligand-gated channels

Channels that open or close after binding of a specific molecule, like a neurotransmitter

Coupled transport

Using the energy stored in an electrochemical gradient to power the transport of another solute against its gradient

Presynaptic cell

The cell that releases neurotransmitters to turn an action potential into a chemical signal at a synapse

Patch clamp

Technique where the flow of current through individual ion channels is recorded from a membrane fragment held onto a micropipette by suction