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Molecular Biology of the Cell 4 Terms
mboc4 cell molecular biology
357
Biology
Graduate
11/16/2009

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Term
ATP-binding cassette (ABC) transporter proteins
Definition
Large superfamily of membrane transport proteins that use the energy of hydrolysis of ATP to transfer peptides and a variety of small molecules across membranes
Term
acetyl
Definition
Chemical group with R-C(=O)CH3. Important in metabolism and are added to some proteins as a posttranslational modification
Term
acetyl CoA
Definition
Small water-soluble molecule that carries acetyl groups in cells. Consists of an acetyl linked to coenzyme A by an easily hydrolyzable thioester bond
Term
(nicotinic) acetylcholine receptor
Definition
Transmitter-gated ion channel that opens in response to binding of acetylcholine, converting a chemical signal to an electrical one.
Term
acetylcholine
Definition
Neurotransmitter that functions with a special class of chemical synapses; the neurotransmitter of vertebrate neuromuscular junctions.
Term
acid hydrolase
Definition
Group of diverse lysosomal hydrolytic enzymes (e.g. proteases, nucleases) with optimal activity at acidic pH (~5.0)
Term
acrosomal vesicle
Definition
Region at the head of a sperm that contains a sac of hydrolytic enzymes that digests the zona pellucida of an egg
Term
acrosome reaction
Definition
Reaction that occurs when a sperm begins entry into an egg, releasing the contents of the acrosomal vesicle to help the sperm penetrate the zona pellucida
Term
action potential
Definition
Rapid, transient, self propagating electrical excitation in the PM of a cell; makes long distance nervous system signaling possible.
Term
activated carrier
Definition
General term for a small diffusible coenzyme that stores easily-exchangeable energy in the form of energy-rich covalent bonds, e.g. ATP, NADPH
Term
acyl group
Definition
Functional group derived from a carboxylic acid R-C(=O)OH group
Term
adaptin
Definition
Protein that binds clathrin to the plasma membrane cytoplasmic surface
Term

adenomatous polyposis coli (APC)

(protein)

Definition
Tumor suppressor that forms part of a complex (along with GSK3 and Axin) that recruits free cytoplasmic β-catenin and degrades it
Term
adherens junction
Definition
Cell junction that attaches actin filaments to the plasma membrane, e.g. adhesion belts linking adjacent epithelial cells and focal contacts on the bottom of cultured fibroblasts
Term
adhesion belt (zonula adherens)
Definition
Beltlike adherens junction that encircles the apical end of an epithelia cell and attaches it to adjacent cells.
Term
epinephrine (adrenaline)
Definition
Catecholamine hormone released by chromaffin cells in the adrenal gland or by some neurons in response to stress. Elicits responses such as increased heart rate and blood sugar
Term
primitive knot/node
Definition
The organizer for gastrulation in vertebrates
Term
affinity chromatography
Definition
Purification of a protein mixture by passing it over a matrix with ligands for specific protein(s) attached so the matrix retains desired proteins
Term
affinity constant (Ka)
Definition

Measure of the strength of binding of the components in a complex

 

For the reaction A + B ↔ AB:

      [AB]

Ka = -----------

      [A][B]

Term
affinity maturation
Definition
Progressive increase in the affinity of antibodies for an antigen with the passage of time after immunization
Term
aldehyde
Definition
Organic compound containing the group R-C(=O)H; Can be oxidized to an acid or reduced to an alcohol
Term
alkaloid
Definition
Small but complex nitrogen-containing metabolite produced by plants as a defense against herbivores, e.g. caffeine, morphine, colchicine
Term
alkyl group
Definition
General term for a group of covalently linked C and H atoms such as methyl and ethyl groups
Term
allele
Definition
One of a set of alternative forms of a gene, of which a diploid cell will have two occupying the same position on homologous chromosomes
Term
allelic exclusion
Definition
The expression of only one Ig chain or TCR chain gene from either homologous loci present for that gene in a lymphocyte
Term
allosteric protein
Definition

Protein that changes conformation when it binds another molecule or is covalently modified

 

The change alters the activity of the protein and can form the basis of directed movement

Term
amide
Definition
Molecule containing a carbonyl group (-C=O) linked to a N
Term
amine
Definition
Chemical group containing nitrogen and hydrogen; becomes (+) charged in water
Term
aminoacyl-tRNA synthetase
Definition
Enzyme that attaches/"charges" a tRNA molecule to its correct amino acid via an ester bond
Term
amino group
Definition
Weakly basic functional group derived from ammonia (NH3) in which at least one H is replaced by another atom. Can accept a proton and carry (+) charge in aqueous solution
Term
aminoacyl tRNA
Definition
Activated form of amino acid used in protein synthesis. Consists of a ester linkage of an amino acid's carboxyl to a tRNA's hydroxyl
Term
anaphase-promoting complex (APC)
Definition
Ubiquitin ligase that promotes the destruction of inhibitors of proteins that inhibits the degradation of cohesins that hold sister chromatids together
Term
animal pole
Definition
In yolky eggs, the yolk-free side that cleaves more rapidly than the other pole.
Term
ankyrin
Definition
Protein mainly responsible for attaching the spectrin cytoskeleton to the erythrocyte plasma membrane via integral proteins.
Term
antenna complex
Definition
Photosystem protein complexes bound to chlorophyll and other pigments and capture light energy and channel it to the photochemical reaction center.
Term
antigenic variation
Definition
Pathogenic microorganism ability to change antigens displayed on the cell surface, enabling them to evade immune system attack
Term
antigen-presenting cell
Definition
Cell that displays foreign antigens complexed with MHC molecules on its surface
Term
antiporter
Definition
Carrier protein that transports two different ions or small molecules across a membrane in opposite directions, either simultaneously or in sequence
Term
antisense RNA
Definition
RNA complementary to a specific mRNA that can hybridize to the targeted mRNA and inhibit its function
Term
ADP-ribosylation factor (ARF)
Definition
Monomeric GTPase responsible for regulating both COPI and clathrin coat assembly at Golgi membranes
Term
aster
Definition
Star-shaped system of microtubules emanating from a centrosome or from a mitotic spindle pole
Term
autocatalysis
Definition
Reaction catalyzed by one of its products, creating a positive feedback on its reaction rate
Term
avidity
Definition
Total binding strength of a polyvalent antibody with a polyvalent antigen
Term
axoneme
Definition
Bundle of microtubles and associated proteins that forms the core of a cilium or flagellum responsible for movement of an eukaryotic cell
Term
bacteriorhodopsin
Definition
Pigmented plasma membrane protein of a halophile bacterium that pumps protons out in response to light
Term
basal body
Definition
Short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium or flagellum which serves as a nucleation site for the axoneme's growth. Similar in structure to a centriole
Term
β-catenin
Definition
Multifunctional cytoplasmic protein involved in cell-cell adhesion by linking cadherins to the actin cytoskeleton. Can also act independently as a gene regulatory protein in the Wnt signaling pathway
Term
biotin
Definition
Low-mol. weight compound used as a coenzyme for transferring carbon dioxide groups. Useful technically as a covalent label for proteins, allowing them to be detected by strong binding to avidin
Term
bivalent (tetrad)
Definition
A duplicated chromosome paired with its homologous duplicated chromosome at the beginning of meiosis
Term
black membrane
Definition
Artificial planar lipid bilayer membrane
Term
blastomere
Definition
A cell formed by the cleavage of a fertilized egg
Term
blastula
Definition
Early stage of an animal embryo consisting of a hollow ball of cells before gastrulation
Term
bright-field microscope
Definition
Normal light microscope that obtains images by simple transmission of light through the viewed object
Term
brush border
Definition
Dense covering of microvilli on the apical surface of epithelia in the intestine and kidney that aids absorption by increasing cell surface area
Term
Ca2+-dependent protein kinase (CaM kinase)
Definition
Protein kinase regulated by the binding of activated calmodulin; indirectly mediates the effects of Ca2+ by phosphorylating other proteins
Term
cadherin
Definition
Family of proteins that mediates Ca2+-dependent cell-cell adhesion in animal tissues
Term
Ca2+ ATPase (calcium pump)
Definition
Transport protein of the sarcoplasmic reticulum that pumps Ca2+ out of the cytoplasm into the sarcoplasm using ATP
Term
Calvin/carbon-fixation cycle
Definition
Major metabolic pathway that incorporates CO2 into carbohydrates during the second stage of photosynthesis in plants
Term
CaM-kinase II
Definition
Multifunctional calmodulin-dependent protein kinase found in all animals that autophosphorylates upon activation. Especially abundant in the brain and thought to have roles in learning and memory in vertebrates.
Term
capacitation
Definition
Effect of the female reproductive tract that elicits a change in membrane composition of the acrosomal sperm head that results in an influx of Ca2+ and increased cAMP to hyperactivate sperm motility
Term
carboxyl group
Definition
Carbon atom with the configuration -(C=O)-OH. Molecules containing this group are weak acids
Term
carcinoma
Definition
Cancer of epithelial cells; most common form of human cancer
Term
carrier protein
Definition
Membrane transport protein that binds to a solute and transports it across the membrane by undergoing a series of conformational changes
Term
cartilage
Definition
Connective tissue composed of chondrocytes embedded in a matrix rich with type II collagen and chondroitin sulfate
Term
caveola
Definition
Invaginations at the cell surface that bud off internally to form pinocytotic vesicles. Thought to form from lipid rafts.
Term
CD28
Definition
Protein on T cells that binds to the costimulatory B7 protein on "pro" antigen-presenting cells, providing secondary signals required for naïve T cell activation
Term
CD4
Definition
Coreceptor found on T cells that bind to the outside of class II MHCs
Term
CD8
Definition
Coreceptor found on cytotoxic T cells that bind to the outside of class I MHCs
Term
Cdk inhibitor
Definition
Protein that binds to and inhibits cyclin-Cdk complexes; primarily involved in G1 and S phases
Term
cell cortex
Definition
Specialized layer of cytoplasm on the inner face of the plasma membrane. In animal cells it is an actin-rich layer responsible for cell surface movements.
Term
cell plate
Definition
Flattened membrane-enclosed structure that forms by fusion of cytoplasmic vesicles of a dividing plant cell to form the precursor of a new cell wall
Term
cell-mediated immune response
Definition
Adaptive immune response in which antigen-specific T cells are activated to do tasks such as killing infected cells and activating macrophages
Term
cellularization
Definition
The formation of cells around each nucleus in a multinucleate cytoplasm, transforming it into a multicellular structure
Term
central (primary) lymphoid organ
Definition
Organ in which lymphocytes develop; in adult mammals: the thymus and bone marrow
Term
centriole
Definition
Short cylindrical array of microtubules usually found at the center of a centrosome in animal cells
Term
centrosome cycle
Definition
Duplication of the centrosome (during interphase) and separation of the two new centrosomes at prophase to form the poles of the mitotic spindle
Term
CG island
Definition
Region of DNA with greater than average density of CG sequences; usually remain unmethylated
Term
channel protein
Definition
Membrane transport protein that forms an aqueous pore through which specific solutes (e.g. ions) can pass
Term
chemiosmotic coupling
Definition
Mechanism of using a gradient of protons across a membrane to drive an energy-requiring process such as ATP synthesis and bacterial flagella rotation
Term
chiasma (chiasmata)
Definition
X-shaped connection visible between paired homologous chromosomes in meiosis I and represents a site of crossing over
Term
chromaffin cell
Definition
Cell that stores adrenaline in vesicles and secretes it in response to stress signals from the nervous system
Term
cilium
Definition
Hairlike extension of a eukaryotic cell containing a core bundle of microtubules and capable of performing repeated beating movements. Found in large numbers on the surface of may cells, and are responsible for the swimming of many single-celled organisms.
Term
cis face
Definition
Face where material enters a Golgi stack.
Term
cis Golgi network (CGN)
Definition
Network of interconnected cisternae and tubules which receives vesicles from the ER and transfers material to the cis face of the Golgi apparatus
Term
cisterna
Definition
Flattened membrane-bounded compartment as found in the ER or Golgi
Term
citric acid cycle
Definition
Aerobic metabolic pathway that oxidizes acetyl groups from food into CO2 and H2O; occurs in the mitochondria
Term
class I MHC
Definition
Molecule present on almost all cell types and presents viral peptides on the surface of infected cells, where they are recognized by cytotoxic T cells
Term
class II MHC
Definition
Molecule present on professional antigen presenting cells and presents foreign peptides to helper T cells
Term
coated pit
Definition
Region of the plasma membrane coated with protein that continually form and bud off by endocytosis to form intracellular vesicles
Term
coenzyme
Definition
Small molecule tightly associated with an enzyme that participates in catalysis, often by binding covalently to the substrate, e.g. biotin, NAD+, CoA
Term
coenzyme A (CoA)
Definition
Small molecule used in the enzymatic transfer of acyl groups in the cell
Term
cofactor
Definition
Inorganic ion or coenzyme required for enzymatic activity
Term
cohesin
Definition
Complex of proteins that hold sister chromatids together along their length before separation triggered by separin
Term
collagen
Definition
Fibrous protein rich in Gly and Pro; major component of the ECM and connective tissues. Exists in many forms: type I, the most common, in skin/tendon/bone, type II in cartilage, type IV in basal laminae
Term
colony-stimulating factor (CSF)
Definition
General name for molecules that control hematopoietic differentiation
Term
combinatorial control
Definition
Describes the control of a cellular process step (e.g. initiation of transcription) by a combination of proteins rather than an individual one
Term
compartment
Definition
Embryo regions formed exclusively from the descendants of a few founder cells; no movement between these regions can occur once they are delimited
Term
complement system
Definition
System of serum proteins activated by antibody-antigen complexes or by microorganisms; eliminates pathogens by directly lysing them or promoting their phagocytosis
Term
complex oligosaccharide
Definition
Chain of sugars attached to a glycoprotein; generated by trimming the original oligosaccharide from the ER and adding sugars
Term
condensin
Definition
Protein complex involved in chromosome condensation prior to mitosis; target of the M-Cdk
Term
conditional mutation
Definition
Mutation that changes a protein or RNA so its function is altered only in some conditions, e.g. extreme temperatures
Term
confocal microscope
Definition
Light microscope that produces a clear image of a plane within a solid object using a laser as a pinpoint light source and scans across the plane to produce a 2D "optical section"
Term
connexon
Definition
Water-filled pore in a cell's PM formed by a protein hexamer; part of a gap junction that forms a continuous channel between two cells
Term
constitutive secretory pathway (default pathway)
Definition
Pathway present in all cells by which molecules are continually delivered to the PM from the Golgi in vesicles that fuse with the PM
Term
convergent extension
Definition
Cellular tissue rearrangement that causes it to extend in one dimension and shrink in another (e.g. skinnier but longer)
Term
cooperativity
Definition
Phenomenon of when binding of one ligand to a target promotes the binding of successive ligands; seen in the assembly of large complexes and enzymes or receptors composed of multiple allosteric subunits
Term
co-translational
Definition
Describes import of a protein into the ER before the polypeptide is completely synthesized
Term
cristae
Definition
One of the folds of the inner mitochondrial membrane
Term
critical concentration
Definition
Concentration at which a monomer is in equilibrium with the assembled form of a protein (e.g. G-actin<=>F-actin)
Term
cryptochrome
Definition
Riboflavin-containing protein responsive to blue light and found in both animals and plants; involved in animal circadian rhythms
Term
phosphodiesterase
Definition
Main inhibitors of cyclic nucleotide monophosphates by hydrolyzing cyclic bonds
Term
cyclic GMP
Definition
Soluble intracellular signaling molecule formed by guanylyl cyclase in response to retinal photoreceptor stimulation
Term

coenzyme Q:cytochrome c-oxidoreductase

(cytochrome bc1 complex)

Definition
Second of three electron-driven proton pumps in the oxidative phosphorylation chain; accepts electrons from ubiquinone (CoQ10)
Term
cytochrome oxidase complex
Definition
Third of three electron-driven proton pumps in oxidative phosphorylation; accepts electrons from cytochrome c uses oxygen as an electron acceptor to generate water
Term
cytochrome
Definition
Colored, heme-containing protein that transfers electrons during cellular respiration and photosynthesis
Term
default pathway
Definition
Automatic delivery of material from the Golgi to the plasma membrane if no sorting signals are present
Term
degenerate
Definition
Describes multiple states with the same result: e.g. multiple codons for the same amino acid
Term
dendritic cell
Definition
Cell derived from bone marrow and specialized for uptake of particulate material by phagocytosis and acts as a professional antigen-presenting cell
Term
desmosome
Definition
Type of anchoring cell-cell junction formed between two epithelial cells; characterized by dense protein plaques with inserted intermediate filaments
Term
diplotene
Definition
Fourth stage of meiosis I in which chiasmata are seen
Term
DNA affinity chromatography
Definition
Technique for purifying sequence-specific DNA-binding proteins by trapping them in a matrix covalently linked to DNA fragments
Term
DNA footprinting
Definition
Technique for determining the sequence to which a DNA-binding protein binds, as well as the binding affinity
Term
DNA helicase
Definition
Enzyme involved in opening the DNA double helix into single strands for DNA replication
Term
DNA primase
Definition
Enzyme which synthesizes a short strand of RNA on a DNA template, producing a primer for DNA synthesis
Term
dominant negative mutation
Definition
Mutation with a dominant phenotype elicited by interference of the function of normal gene products by the mutant products
Term
dynamic instability
Definition
Property of sudden conversion from growth↔shrinkage in a protein filament, e.g. microtubules or F-actin
Term
dynamin
Definition
Cytosolic GTPase that binds to the neck of clathrin-coated vesicles in the budding process and completes vesicle formation
Term
dynein
Definition
A family of large motor proteins that use ATP to move along microtubules. In cilia, this protein forms the side arms in the axoneme that cause microtubule doublet sliding
Term
dysplasia
Definition
Disordered cell growth and behavior in a tissue
Term
effector cell
Definition
Cell that carries out the final response/function of a process. e.g. activated lymphocytes in the immune system
Term
elastin
Definition
Amorphous hydrophobic protein that forms extracellular extensible fibers that makes tissue resilient
Term
endosome
Definition
Membrane-bounded organelle in animal cells that carries newly endocytosed materials and usually fuses with lysosomes for degradation
Term
endothelial cell
Definition
Flattened cell type that forms a sheet lining blood vessels
Term
enhancer
Definition
Regulatory DNA sequence to which proteins bind and influence the rate of transcription of a gene that can be thousands of base pairs away
Term
enveloped virus
Definition
Virus with a capsid surrounded by a lipid membrane derived from the host cell when the virus buds from the host
Term
ER resident protein
Definition
Protein that remains in the ER lumen or its membranes and functions there, as opposed to proteins that are in transit in the ER
Term
ER retention signal (KDEL)
Definition
Short amino acid sequence (Lys-Asp-Glu-Leu) that prevents a protein from moving out of the ER; found on ER resident proteins
Term
erythropoietin
Definition
Growth factor that stimulates the production of RBCs; produced by the kidney and acts on precursors in the bone marrow
Term
ester
Definition
Molecule formed by the condensation of a hydroxyl (-OH) with an acyl (-COOH), resulting in an R-(C=O)-O-R
Term
FADH2
Definition
Activated carrier molecule produced by the citric acid cycle that yields 1.5 or 2 ATP per molecule in oxidative phosphorylation
Term
Fas (protein)
Definition
Membrane receptor that initiates apoptosis in the receptive cell after binding to its ligand
Term
Fc receptor
Definition
Family of receptors specific for the invariant constant region of immunoglobulins with the exception of IgM and IgD
Term
fibrillar collagen
Definition
Type of collagen molecule that assembles into rope-like structures, which include type I, II, III, V, and XI.
Term
fibronectin
Definition
ECM protein involved in adhesion of cells to the matrix and guidance of migrating cells during embryogenesis. Integrins are receptors for this protein
Term
filopodium
Definition
Thin, spike-like protrusion with an actin filament core generated on the leading edge of a crawling animal cell
Term
fluorescein
Definition
Dye that fluoresces green when illuminated with blue or UV light
Term
focal adhesion kinase (FAK)
Definition
Cytoplasmic tyrosine kinase present at cell-matrix focal adhesions in association with the cytoplasmic tails of integrins
Term
free energy (G)
Definition
Energy that can be extracted from a system to drive reactions; takes into account changes in both energy and entropy
Term
γ-tubulin ring complex (TuRC)
Definition
Protein complex that mimics the (+) end of a microtubule and is an efficient nucleator of microtubules
Term
ganglion
Definition
Cluster of neurons and associated glia located outside the CNS
Term
ganglioside
Definition
Glycolipid having one or more sialic acid residues in its structure. Found in the PM of eukaryotic cells and abundant in nerve cells.
Term
gastrulation
Definition
Stage in animal embryogenesis during which an embryo is transformed from a blastula to a structure with a gut (gastrula)
Term
gene conversion
Definition
Process by which the sequence of one DNA helix can be transferred and alter the sequence of another DNA helix. It occasionally occurs during recombination
Term
genetic map
Definition
Map of a chromosome in which relative distance between genes is determined by the amount of recombination that occurs between them
Term
genomic imprinting
Definition
Parental influence on whether a gene is expressed in the embryo depending
Term
glial cell
Definition
Supporting cell of the nervous system, e.g. oligodendrocytes and astrocytes in the CNS and Schwann cells in the PNS.
Term
glutaraldehyde
Definition
Small reactive molecule (O=CHCH2CH2CH2CH=O) with two aldehyde groups often used as a cross-linking fixative
Term
glycerol
Definition
Small three-carbon molecule with one hydroxyl per carbon and is the parent compound of many small molecules including phospholipids
Term
glycocalyx (cell coat)
Definition
Carbohydrate-rich layer that forms the outer coat of eukaryotic cells. Composed of oligosaccharides linked to intrinsic PM glycoproteins and glycolipids, as well as secreted glycoproteins/proteoglycans reabsorbed on the cell surface
Term
glycosaminoglycan (GAG)
Definition
Long, linear, highly charged polysaccharide (e.g. chodroiton sulfate, hyaluronic acid, heparin) composed of a repeating pair of sugar, one of which is always an amino sugar. Mainly found covalently linked to a protein core in ECM proteoglycans.
Term
glycosylphosphatidylinositol anchor (GPI anchor)
Definition
Lipid linkage by which some membrane proteins are bound. Formed as the proteins travel through the ER
Term
Gq
Definition
G protein class that activates phospholipase C-β and begins the inositol phospholipid signaling cascade
Term
grana
Definition
Stacked chlorophyll-containing thylakoid discs in chloroplasts that are the site of light-trapping reactions of photosynthesis
Term
granulocyte
Definition
White blood cell distinguished by conspicuous cytoplasmic granules; includes neutrophils, basophils, and eosinophils
Term
gray crescent
Definition
Band of pale pigmentation that appears in some amphibian species opposite the site of sperm entry; caused by rotation of the egg cortex and associated pigment granules; marks the future dorsal side
Term
GTP
Definition
Nucleotide triphosphate with a special role in microtubule assembly, protein synthesis, and cell signaling.
Term
helix-loop-helix (HLH)
Definition
DNA-binding structural motif present in many gene regulatory proteins; should not be confused with helix-turn-helix
Term
helper T cell
Definition
Type of T cell that helps stimulate B cells to produce antibodies and activates macrophages to kill ingested microorganisms
Term
heme
Definition
Iron-containing cyclic organic molecule that carries O2 in hemoglobin and carries an electron in cytochromes
Term
hemopoiesis
Definition
Generation of blood cells mainly in the bone marrow
Term
heterocaryon
Definition
Cell with multiple genetically different nuclei; produced by the fusion of two or more different cells
Term
high-mannose oligosaccharide
Definition
Chain of sugars generated by a trimming of original mannose-rich oligosaccharide that leaves most of the mannose residues with no subsequent addition of sugars
Term
histidine-kinase-associated receptor
Definition
Transmembrane receptor found in bacteria, yeast, and plant cells; involved in sensing stimuli such as bacterial chemotaxis; associated with histidine protein kinase on its cytoplasmic side
Term
histone
Definition
Type of small abundant Arg and Lys-rich proteins which form nucleosomes in eucaryotic chromosomes
Term
heterogenous nuclear ribonuclear protein (hnRNP)
Definition
Proteins that assemble on newly synthesized RNA, compacting it and signals that the pre-mRNA is not fully processed and ready for export
Term
Holliday junction
Definition
X-shaped structure observed In DNA recombination in which two molecules are held together at the site of crossing over; also called a cross-strand exchange
Term
homeobox
Definition
Short 180bp conserved DNA sequence that encodes a DNA-binding protein motif found in genes that orchestrate development in a wide range of organisms
Term
homeodomain
Definition
DNA-binding domain that defines a class of gene regulatory proteins important in animal development
Term
homeotic gene
Definition
Gene that determines which body part a region of a body develops
Term
Hox cluster/complex
Definition
Tightly linked cluster of genes in animals that have a linear correspondence to the anterior-posterior segmentation of the body
Term
hydronium ion
Definition
H3O+, a water molecule associated with a proton
Term
inhibitor of apoptosis (IAP) family
Definition
Family of proteins that are intracellular inhibitors of apoptosis
Term
imaginal disc
Definition
Group of cells set aside in Drosophila embryos that are determined to develop into an adult structure (e.g. eye, leg, wing)
Term
induction [developmental bio.]
Definition
Change in the developmental fate of one tissue caused by interaction with another tissue
Term
inhibitory G protein (Gi)
Definition
G protein that can regulate ion channels and inhibit adenylyl cyclase
Term
inhibitory neurotransmitter
Definition
Type of neurotransmitter that opens transmitter-gated Cl- or K+ channels in the postsynaptic membrane of a nerve or muscle cell, inhibiting the generation of an action potential
Term
initiation factor
Definition
Protein that prmotes the proper association of ribosomes with mRNA and required for initiation of translation
Term
initiator tRNA
Definition
Special tRNA that initates translation. Always carries Met in eukaryotes, and fMet in some prokaryotes
Term
innate immune response
Definition
Immune response that involves pre-existing defenses of the body e.g. skin, mucosa, antimicrobial molecules, phagocytes. Non-specific toward pathogens
Term
inner nuclear membrane
Definition
Nuclear envelope membrane that contains binding sites for chromatin and the nuclear lamina
Term
inositol phospholipids (phosphoinositides)
Definition
Family of lipids containing phosphorylated inositol derivatives. Although minor components of the PM, they are important in signal transduction in eucaryotes
Term

insulator

[genetics]

Definition
DNA sequence that prevents a DNA-bound gene regulatory protein in the control region of a gene from influencing transcription of surrounding genes
Term
integrin
Definition
Large family of transmembrane heterodimers involved in adhesion of cells to the ECM and other cells
Term
intercalary regeneration
Definition
Regeneration that fills in missing tissue when two mismatched parts of a structure are grafted together (e.g. an upper leg and foot regenerating the middle segment)
Term
interferon-γ (IFNγ)
Definition
Cytokine secreted by TH1 cells to enhance cell-mediated immunity via anti-viral response and macrophage activation
Term
interleukin
Definition
Secreted protein that mainly mediates local interactions between leucocytes during inflammation/immune response
Term
ionophore
Definition
Small hydrophobic molecule that dissolves in lipid bilayers and increases their permeability to specific inorganic ions; can carry normally inpermeable molecules; can also disrupt ion concentration gradients
Term
iron-sulfur center
Definition
Electron-transporting groups consisting of 2 or 4 Fe atoms bound to an equal number of S atoms; found in a class of electron-transport proteins
Term
isoprenoid
Definition
Member of a large family of lipid molecules with a carbon skeleton based on multiple five carbon isoprene CH2=C(-CH3)-CH=CH2 units, e.g. retinal and dolichol
Term
Jak-STAT pathway
Definition
Rapid signaling pathway in which signals (e.g. interferon) activate gene expression, involves Janus kinases and signal transducers and activators of transcription
Term
joule
Definition
Standard unit of energy equal to approximately .24 calories
Term
potassium (K+) leak channel
Definition
K+ transporting ion channel that remains open even in a resting state
Term
ketone
Definition
Organic molecule containing a carbonyl (C=O) bound to two carbon groups (R3C-CO-CR3)
Term
kinesin
Definition
Type of motor protein that uses ATP hydrolysis to move along a microtubule; transports intracellular cargo along microtubule tracks
Term
kinetochore
Definition
Complex structure on mitotic chromosome centromeres which attaches to microtubules; plays an active part in movement of chromosomes to centrioles
Term
laminin
Definition
Heterotrimeric ECM protein found in basal laminae, where it forms sheetlike networks
Term
lampbrush chromosome
Definition
Paired chromosome in meiosis in immature amphibian eggs, in which chromatin forms large stiff loops extending out from the chromosome's central axis
Term
lectin
Definition
Protein that binds tightly to specific sugars; frequently isolated from plant seeds and used to purify glycoproteins or detect them on cell coats
Term
lepotene
Definition
First phase of meiosis I in which paired duplicated homologous chromosomes condense and become visible in light microscopy
Term
leucine zipper
Definition
Structural motif in many DNA-binding proteins consisting of two α-helices from separate proteins joined together in a coiled-coil (i.e. zipper-like)
Term
leucine-rich repeat (LRR) protein
Definition
Common type of receptor Ser/Thr kinase in plants. Characterized by Leu-rich extracellular sequences.
Term
linkage [biochemistry]
Definition
Mutual effect of the binding of one ligand on the binding of another; central feature of the behavior of all allosteric proteins
Term
lipase
Definition
Enzyme that catalyzes cleavage of fatty acids from the glycerol moiety of a triglyceride
Term
lipid raft
Definition
Plasma membrane subdomain enriched in sphingolipids and cholesterol
Term
local mediator
Definition
Secreted signal molecule that acts as a short range paracrine signal
Term
long-term potentiation
Definition
Long-lasting increase in the sensitivity of certain synapses in the hippocampus; induced by a short burst of repetitive firing by presynaptic neurons
Term
low-density lipoprotein
Definition
Large complex composed of a single protein molecule and many esterfied cholesterol molecules and other lipids. Form in which cholesterol is transported in the blood and absorbed by cells
Term
lysogeny
Definition
Bacterial state in which it carries the DNA of an inactive virus in its genome. The virus can be activated to replicate and lyse the cell
Term
mannose-6-phosphate (M6P)
Definition
Unique marker attached to oligosaccharides on some glycoproteins targeted toward lysosomes
Term
mitogen-activated protein kinase (MAP kinase)
Definition
Class of kinases that relays signals from the plasma membrane to the nucleus; turned on by a wide range of proliferation or differentiation-inducing signals
Term
mating-type locus (MAT locus)
Definition
Locus that determines the mating type (α or a) of a haploid budding yeast cell
Term
[mitochondrial] matrix space
Definition
Central subcomparment of a mitochondrion, bounded by the inner mitochondrial membrane; corresponds to the stroma in a chloroplast
Term
Mini Chromosome Maintenance (MCM) complex
Definition
Protein complex that binds to origin recognition complexes in eucaryotic DNA in early G1 and are involved in forming the pre-replicative complex
Term
megakaryocyte
Definition
Large myeloid cell with a multilobed nucleus; remains in the bone marrow when mature and generates platelets that bud off from long cytoplasmic processes
Term
meristem
Definition
Organized group of dividing cells whose progeny give rise to the tissues and organs of a flowering plant, e.g. the tips of shoots and roots
Term
mesenchyme
Definition
Immature, unspecialized form of connective tissue in animals consisting of cells embedded in thin ECM
Term
metaplasia
Definition
Replacement of a differentated type of cell with another differentiated type; usually caused by abnormal stimuli
Term
microsome
Definition
Small vesicle originating from fragmented ER produced from cell homogenates
Term
microtubule-associated protein (MAP)
Definition
Any protein that binds to microtubules and modifies their properties, e.g. dynein
Term
microvillus
Definition
Thin cylindrical membrane-covered projection on the surface of an animal cell containing a core bundle of actin filaments; present in large numbers on absorptive surfaces of epithelial cells
Term
midbody
Definition
Structure formed at the end of cleavage that can persist for some time as a tether between two daughter cells in animals
Term
minus end
Definition
Comparatively slower-growing end of a microtubule or microfilament
Term
mismatch repair
Definition
DNA repair process that corrects errors during DNA replication by removing a short stretch of newly synthesized DNA and replacing it with the correct sequence based on the template strand
Term
mitochondrial precursor protein
Definition
Mitochondrial protein encoded by a nuclear gene, synthesized in the cytosol, and transported into mitochondria
Term
monocyte
Definition
Type of white blood cell that leaves the bloodstream and matures into a macrophage in tissues
Term
mosaic [dev. bio.]
Definition
An organism made from a mixture of cells of different genotypes
Term
motor protein
Definition
Protein that uses energy derived from nucleotide triphosphate (NTP) hydrolysis to propel itself along a filament or another polymer
Term
myeloid cell
Definition
Any white blood cell other than lymphocytes e.g. baso/eosino/neutrophils
Term
myoepithelial cell
Definition
Type of unstriated muscle cell frequently found in glandular epithelia
Term
nicotine adenine dinucleotide (NAD+)
Definition
Activated carrier that participates in an oxidation(?) reaction by accepting a hydride (H-) ion from a donor molecule; the product is an important carrier of electrons for oxidative phosphorylation
Term
NADH dehydrogenase complex
Definition
First of the three electron-driven proton pumps in the mitochondrial respiratory chain. It accepts electrons from NADH
Term
nicotine adenine dinucleotide phosphte (NADP+)
Definition

Activated carrier used extensively in biosynthetic pathways

 

Contrast with the us of NAD+ in catabolic pathways

Term
natural killer cell
Definition
Cytotoxic cell of the innate immune system that can kill virus-infected cells; shares a common progenitor with T-cells and B-cells
Term
Nernst equation
Definition
Quantitative expression that relates the concentrations of an ion across a membrane to the voltage difference (E = RT/zF ln ([out]/[in]))
Term
neural cell adhesion molecule (N-CAM)
Definition
Cell adhesion molecule of the Ig superfamily, expressed by many cell types including most nerve cell and mediates cell-cell attachment independent of Ca2+
Term
neurite
Definition
General term for a process from a nerve cell in culture; does not specify if it is an axon or dendrite
Term
neutrophil
Definition
White blood cell that enters inflamed/infected tissues and uptakes particulate material by phagocytosis
Term
nitrogen fixation
Definition
Biochemical process by which certain bacteria reduce atmospheric nitrogen to ammonia
Term
N-linked oligosaccharide
Definition
Chain of sugars attached to a protein through the NH2 of an asparagine
Term
noncyclic phosphorylation
Definition
Photosynthetic process that produces both ATP and NADPH in plants and cyanobacteria
Term
nonsense mediated decay
Definition
Mechanism for removing aberrant mRNAs containing premature stop codons before they can be translated
Term
Notch
Definition
Receptor protein heavily involved in development determination, and is activated by cleavage in response to binding cell-surface ligands on other cells
Term
notochord
Definition
Stiff rod of mesoderm that runs along the dorsal side of all chordate embryos; becomes incorporated into the vetebral column in vertebrates
Term
NSF
Definition
Protein with ATPase activity that disassembles vSNARE and tSNARE complexes in vesicle fusion
Term
nuclear lamin
Definition
Subunit of the intermediate filaments of the nuclear lamina
Term
nuclear organizer
Definition
Region of a chromosome containing a cluster of rRNA genes that gives rise to a nucleolus
Term
nucleoporin
Definition
Any of a number of proteins that make up a nuclear pore complex
Term
nucleoside
Definition
Molecule composed of a purine/pyrimidine base linked to a sugar
Term
occluding junction
Definition
Cell junction that seals cells together in an epithelium, forming a barrier that even blocks small molecules
Term
oligodendrocyte
Definition
Glial cell that forms myelin sheaths around multiple axons
Term
O-linked glycosylation
Definition
Addition of an oligosaccharide chain to the OH group of a Ser or Thr side chain
Term
operon
Definition
A bacterial group of contiguous genes transcribed into a single mRNA molecule
Term
origin recognition complex (ORC)
Definition
Large protein complex bound to the DNA at origins of replication throughout the cell cycle in eucaryotes
Term
osteoclast
Definition
Macrophage-like cell that erodes bone, enabling it to be remodeled and allowing expansion/growth; contrast with osteoblasts, which secrete bone matrix
Term
outer nuclear membrane
Definition
Nuclear membrane continuous with the ER and studded with ribosomes
Term
overlap microtubule
Definition
Mitotic or meiotic spindle microtubule interwoven at the equator with microtubules from the other pole
Term
oxidative phosphorylation
Definition
Process in bacteria and mitochondria in which ATP formation is driven by transfer of electrons from food to molecular oxygen. Involves generation of an electrochemical gradient and chemiosmotic coupling
Term
pachytene
Definition
Third stage of meiosis I, in which synapsis is complete
Term
parthenogenesis
Definition
Production of a new individual from an unfertilized egg
Term
patch-clamp
Definition
Electrophysiological technique that attaches a tiny electrode tip to a patch of cell membrane to record the flow of current through individual ion channels
Term
peripheral/secondary lymphoid organ
Definition
Lymphoid organs in which T and B cells interact with foreign antigens, e.g. spleen, lymph nodes
Term
peroxisome
Definition
Small membrane-bound organelle that uses molecular oxygen to oxidize organic molecules
Term
phage display
Definition
Technique for detecting protein interactions by repeatedly screening a library of genetically modified phages against an affixed protein
Term
phase-contrast microscope
Definition
Light microscope that exploits interference effects; used to view living cells
Term
phosphatidylinositol 3-kinase (PI3K)
Definition
Kinase activated by cell surface receptors; involved in intracellular signaling pathways; phosphorylates phospholipids at the inositol ring
Term
phospholipase C-β
Definition

Cleaves membrane phospholipids to diacylglycerol (DAG) and inositol triphosphate (IP3)

 

Activated by Gq proteins

Term
phospholipase C-γ
Definition

Cleaves membrane phospholipids to diacylglycerol (DAG) and inositol triphosphate (IP3);

Activated by receptor tyrosine kinases

Term
photosynthetic electron-transfer
Definition
Light-driven photosynthesis reactions that move electrons along a transport chain in the thylakoid membrane, generating ATP and NADPH
Term
phragmoplast
Definition
Structure made of microtubules and actin filaments that forms in a prospective plane of division in a plant cell; guides formation of a cell plate
Term
plasmodesmata
Definition
Cell-cell junction in plants that connects the cytoplasm of adjacent cells
Term
pleckstrin homology domain (PHD)
Definition
Domain found in intracellular signaling proteins that binds to inositol phospholipids phosphorylated by PI3K
Term
plus end
Definition
The faster growing end of a microtubule or microfilament
Term
polymorphic
Definition
Describes a gene with many different alleles, none of which is predominant in the population
Term
polysome
Definition
mRNA molecule with a number of actively translating ribosomes attached
Term
positional value
Definition
A cell's internal record of its position in a multicellular organism
Term
prenylation
Definition
Covalent attachment of an isoprenoid CH2=(C-C)-CH=CH2 lipid group to a protein
Term
primordial germ cell
Definition
Cell set aside early in embryonic development that is a precursor to cells that will give rise to gametes
Term
primosome
Definition
Complex of DNA primase and DNA helicase formed on the lagging strand of a replication fork, thereby improving replication efficiency
Term
protein kinase C
Definition
Kinase activated by Ca2+ and diacylglycerol (DAG) and phosphorylates target proteins on specific Ser and Thr kinases
Term
proteoglycan
Definition
Molecule consisting of one or more glycosaminoglycan chains attached to a core protein
Term
pulse-chase
Definition
Technique for following the movement of a substance through a cellular pathway by briefly adding labeled substrate ("pulse") followed by unlabled substrate ("chase")
Term
quinone
Definition
Small, lipid soluble mobile electron carrier molecule found in the respiratory and photosynthetic transport chains
Term
Rab (protein)
Definition
Family of monomeric GTPases in the PM and organelle membranes involved in specificity of vesicle docking
Term
Ran (protein)
Definition
Monomeric GTPase present both in cytosol and nucleus required for the active transport of macromolecules in/out of the nuclear pore complex; hydrolysis of the GTP is thought to provide the energy for this transport
Term
Ras (protein)
Definition
Large family of GTP-binding proteins that help relay signals from cell surface receptors to the nucleus
Term
RecA (protein)
Definition
Procaryotic DNA repair protein thought to be the prototype for a class of DNA-binding proteins that catalyze synapsis of homologous DNA during genetic recombination
Term
recycling endosome
Definition
Large vesicle formed from a fragment of an endosome as an intermedite stage on the passge of recycled receptors back to the plasma membrane
Term
redox pair
Definition
Pair of molecules in which one acts as an electron donor and the other as an acceptor
Term
redox potential
Definition
Affinity of a redox pair for electrons, generally measured as the voltage difference between an equimolar mixture of the pair and a standard reference, e.g. NADH/NAD+ has low potential, O2/H2 has high potential
Term
respiration
Definition
General term for the oxidative breakdown of sugars or other organic molecules using O2 and producing CO2 and H2O as waste
Term
reverse genetics
Definition
Approach to discovering gene function by starting from a gene and protein and creating mutants to analyze its function
Term
rhodopsin
Definition
Light-sensitive GPCR in the rod photoreceptor cells in the retina
Term
RNA editing
Definition
Production of a functional mRNA by insertion or alteration of nucleotides in an RNA molecule after it is synthesized
Term
RNA pol II holoenzyme
Definition
Pre-assembled complex with most of the transcription factors required for functioning and the mediator protein complex
Term
RNA interference (RNAi)
Definition
Degradation of RNA intended to remove foreign RNAs e.g. viruses. Fragments cleaved from dsRNA direct degradation of similar RNA sequences
Term
rod photoreceptor
Definition
Photoreceptor cell in the retina responsible for noncolor vision in poor light
Term
sarcoma
Definition
Cancer of connective tissue
Term
sarcomere
Definition
Repeating unit of a myofibril in a muscle cell, composed of an array of overlapping myosin and actin filaments between two adjacent Z discs
Term
satellite DNA
Definition
Regions of highly repetitive eucaryotic DNA, usually identifiable by its unusual nucleotide composition; not transcribed and has no known function
Term
selectin
Definition
Family of cell surface sugar-binding proteins that mediate transient Ca2+-dependent cell-cell adhesion in the bloodstream, such as white blood cells rolling on the endothelium of blood vessels
Term
septate junction
Definition
Occluding cell junction in invertebrates; ladder structure is distinct from vertebrate tight junctions
Term
SH2 domain
Definition
Domain that binds short amino acid sequences containing phospho-Tyr
Term
SH3 domain
Definition
Domain that binds Pro-rich sequences
Term
signal peptidase
Definition
Enzyme that removes terminal signal sequences once protein sorting processes are complete
Term
signal-recognition particle (SRP)
Definition
Ribonucleoportein particle that binds an ER signal sequence in a partially synthesized polypeptide and delays translation and directs the polypeptide to the ER
Term
small nuclear RNA (snRNA)
Definition
Small RNA molcules complexed with proteins to form ribonucleoproteins involved in RNA splicing
Term
smooth endoplasmic reticulum
Definition
Region of the ER involved in lipid synthesis
Term
SNARE proteins
Definition
Family of transmembrane proteins present in organelle membranes and vesicles involved in guiding vesicles to correct destinations; they exist in pairs, a v-SNARE of a vesicle binds specifically to a complementary t-SNARE at the target membrane
Term
spectrin
Definition
Protein associated with the cytosolic side of the plasma membrane in erythrocytes, forming a rigid support network
Term
Spemann's organizer
Definition
Specialized tissue at the dorsal lip of the blastopore in an amphibian embryo that acts as a source of differentiation signals
Term
spindle-attachment checkpoint
Definition
Checkpoint during mitosis that occurs before anaphase
Term
spliceosome
Definition
Large assembly of snRNP ribonucleoproteins that performs pre-mRNA splicing
Term
Src family
Definition
Family of cytoplasmic tyrosine kinases that associate with the cytoplasmic domains of some enzyme-linked receptors (e.g. T cell receptors) that lack intrinsic Tyr-kinase activity
Term
standard free energy change
Definition
Free energy change of two reacting molecules at 25C and 1atm when all components are at a concentration of 1M/liter
Term
start-transfer signal
Definition
Short amino acid sequence that enables a polypeptide to start being translocated across the ER membrane; multipass membrane proteins have both N-terminal and multiple internal signals
Term
stereocilium
Definition
Large, rigid microvillus found on the apical surface of hair cells in the ear; arranged in "organ pipe" arrays and mechanically gated
Term
stimulatory G protein (Gs)
Definition
G protein that when activated, activates the enzyme adenylyl cyclase and stimulates production of cAMP
Term
stop-transfer signal
Definition
Hydrophobic amino acid sequence that halts translocation of a polypeptide through the ER membrane, anchoring the polypeptide in the membrane
Term
stroma [tissue]
Definition
Structural connective tissue in which glandular or epethilia are embedded; contrast with parenchyma, functional tissue
Term
structural gene
Definition
Region of DNA that codes for an actual transcriptional/translational product, rather than a region that regulates gene expression
Term
substratum
Definition
Solid surface to which a cell adheres
Term
sulfhydryl (thiol, SH)
Definition
Chemical group containing -SH; found in the amino acid Cys; two of these can form a disulfide bond
Term
synapsis
Definition
The initial formation of base pairs between complementary DNA strands in genetic recombination, OR the pairing of maternal/paternal chromosomes as they become attached along their length
Term
synaptonemal complex
Definition
Structure that holds paired chromosomes together during prophase I; promotes genetic recombination
Term
syncytium
Definition
Mass of cytoplasm containing multiple nuclei enclosed by a single membrane; typically the result of cell fusion or incomplete division cycles of just the nuclei but not the cytoplasm
Term
synteny
Definition
The presence of the same genes in the same order on chromosomes of different species
Term
TATA box
Definition
Consensus sequence in the promoter of eucaryotic genes that binds general transcription factors and specifies where transcription is initiated
Term
terminator
Definition
Signal in bacterial DNA that halts transcription
Term
thioester bond
Definition
High-energy bond formed by condensation between an acyl (acid) (-COR) group and an thiol group (-SH); e.g. those seen in acetyl CoA
Term
thylakoid
Definition
Flattened chloroplast membrane sac containing chlorophyll and pigments and carries out light-trapping reactions of photosynthesis. Stacks of these form grana.
Term
tight junction
Definition
Cell-cell junction that seals adjacent epithelial cells together, preventing the passage of most molecules past the epithelial sheet
Term
TIM/TOM complexes
Definition
Protein translocators in the mitochondrial membranes
Term
Toll-like receptor family (TLRs)
Definition
Family of mammalian pattern-recognition receptors abundant on macrophages, neutrophils, and gut epithelia; recognizes pathogen-associated molecules such as lipopolysaccharide and peptidoglycan
Term
trans face
Definition
Golgi face at which material leaves the Golgi for the surface or another rcell compartment
Term
transcription attenuation
Definition
Inhibition of bacterial gene expression by premature termination of transcription
Term
transcytosis
Definition
The uptake of material at one face of a cell, transfer across in vesicles, and discharge from another face
Term
transforming growth factor-beta superfamily
Definition
Family of secreted proteins that act as hormones and local mediators to control a wide range of functions, including development; e.g. activins, BMPs
Term

transition state

[biochemistry]

Definition
Transient structure in the course of a chemical reaction and has the highest free energy; formation of this state is a rate-limiting step
Term
translational control
Definition
Control of gene expression by selection of which mRNAs are translated
Term
trans-splicing
Definition
RNA splicing present in a few eucaryotes where two separate RNAs are joined to form one mRNA
Term
type III secretion system
Definition
Bacterial system for delivering toxic proteins into host cells
Term
unfolded protein response
Definition
Cellular response triggered by accumulation of misfolded proteins in the ER; involves increased ER chaperones and degradative enzymes
Term
uniporter
Definition
Carrier protein that transports a single solute from one side of a membrane to the other
Term
vegetal pole
Definition
Yolk-rich end of an animal egg
Term
X-inactivation center
Definition
Site in an X chromosome in which inactivation/packaging into heterochromatin is initiated and spread outwards
Term
Z disc/line
Definition
Platelike region of sarcomere to which the plus ends of actin filaments are attached
Term
zygotene
Definition
Second stage of meiosis I in which the synaptonemal complex begins to form between the sets of sister chromatids in each bivalent chromosome
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