Glossary
ABC transporters
ATP-binding cassette transporters. A large family of proteins which characterized by conserved ATP-binding domains and clusters of membrane spanning alpha-helices (i.e., integral membrane protein) believed to form a transmembrane pore. The individual members of the family display a wide spectrum of substrate (i.e., transport) specificity.
amino acid
The basic building block of proteins. Amino acids are joined together chemically into long linear polymers to form proteins and polypeptides.
apicoplast
A non-photosynthetic plastid found in Plasmodium and other apicomplexa. Plastids are cytoplasmic organelles bound by 2-4 membranes, contain their own DNA and often contain photosynthetic pigments. Chloroplasts of plants are examples of plastids. The apicoplast is characterized by three-to-four membranes, a 35 kb circular DNA and no pigments.
ATP
Adenosine triphosphate. The primary source of energy for cells. The third phosphate is hydrolyzed by enzymes called ATPases resulting in the formation of ADP (adenosine diphosphate) and phosphate. The energy stored in the hydrolyzed phosphate bond is captured and used to carry out a function associated with that particular ATPase.
actin filaments (microfilaments)
Filament formed by the polymerization of globular actin proteins. A major cytoskeletal element found in all eukaryotic cells. Actin filaments are also involved in the generation of contractile force through associations with myosin.
anabolism
Also referred to as 'constructive' metabolism. It is the process of converting simple molecules to more complex molecules. An example include the de novo synthesis of precursors, or building blocks, used for the synthesis of macromolecules such as proteins and nucleic acids. The assembly of the precursors into macromolecules would also be an example of anabolism. The antonym is catabolism.
archabacteria
Bacteria-like organisms that that exhibit many unique features as well as features typical of either prokaryotes or eukaryotes. Their rRNA sequences are distinctly different from both eubacteria and eukaryota (see 3-domain tree of life).
band 3
A multipass integral membrane protein which functions as an anion transporter. Band 3 also functions as an attachment site for the spectrin-actin submembrane cytoskeleton of erythrocytes.
catabolism
Also referred to as 'destructive' metabolism. It is the opposite of anabolism and involves breakdown of molecules into simpler components. For example, the breakdown and oxidation of glucose to carbon dioxide and the capture of the released energy in the form of ATP is a catabolic process. Catabolism also includes the breakdown of macromolecules into their monomeric units.
chromosome
Structure composed of DNA and proteins representing the basic hereditary unit. The long DNA molecule is packaged into compact structure found within the nucleus.
cytochrome
Heme proteins serving as electron carriers in electron transport chains involved in respiration. See also oxidative phosphorylation.
cytoskeleton
Filamentous structures which are responsible for cell shape. The three major cytoskeletal systems are actin filaments (also called microfilaments), microtubules and intermediate filaments (only found in multicellular organisms). Microfilaments and microtubules are also capable of generating force and movement through associated motor proteins.
cytostome
A subcellular structure found on the surface of many diverse protozoa that is involved in feeding via an endocytic pathway.
DNA
Deoxyribonucleic acid. DNA encodes all the information necessary for synthesizing proteins and can be duplicated by the cell, and therefore is the hereditary material of life (see Central Dogma).
endocytosis
Uptake of material into a cell by invagination of the plasma membrane and the formation of a membrane-bound vesicle. Pinocytosis is the uptake up external fluid material (i.e., 'cell drinking') and is distinguished from phagocytosis which involves taking up large particulate matter or other cells (i.e., 'cell eating'). The uptake of specific substances is accomplished through receptor-mediated endocytosis. Exocytosis is the opposite of endocytosis.
enzyme
A protein that catalyzes a biochemical reaction. Enzymes are often parts of metabolic pathways that involve the conversion a molecule into another molecule. [See diagrammatic example of metabolic pathways.]
epidermal growth factor (EGF)-like module
A small structural domain, or motif, within a protein. The EGF-like domain is characterized by spacing of cysteine residues which form disulfide bonds (see Protein Structure).
eukaryote
An organism in which the cells are compartmentalized. In particular, the cells have a distinct nucleus and cytoplasm. The eukaryotes, prokaryotes (= bacteria) and archaea make up the three major domains of life.
exocytosis
The export of substances from cells mediated by the fusion of secretory vesicles with the plasma membrane. The contents of vesicles are released following membrane fusion. Endocytosis is the opposite of exocytosis.
glutathione (GSH)
A tripeptide (g-L-glutamyl-L-cysteineylglycine) which participates in many redox reactions within cells. GSH functions in many metabolic processes as well as in detoxifying ROI.
glycophorins
Single pass integral membrane proteins exposed on the erythrocyte surface.
glycosylphosphatidylinositol (GPI) anchor
A complex glycolipid covalently attached to the C-terminal end of a protein. The fatty acid chains of the lipid are imbedded in the lipid bilayer of the membrane and anchor the protein to the membrane.
heme
A prosthetic group found associated with many proteins. Heme-containing proteins typically function in electron transfers (eg., cytochromes) or binding oxygen (eg., hemoglobin). Heme is composed of an iron atom and protoprophyrin IX.
hemoglobin
An abundant protein found in erythrocytes that functions in the transport of oxygen to the tissues and the removal of carbon dioxide from the tissues. Hemoglobin is a tetramer consisting of 2 alpha-globin chains and 2 beta-globin chains. A heme group is associated with each of the 4 globin chains.
hemozoin
A waste product formed by the malaria parasite as a byproduct of hemoglobin degradation. It is also known as the malaria pigment. Free heme groups are covalently linked through a carboxylic group and the iron into a dimer which is identical to b-hematin. These dimers form an insoluble substance through a biomineralization or biocrystallization process.
homolog
Genes with similar sequences due to common ancestory. Homologs can be classified as orthologs or paralogs. Genes with sequence similarities not due to common ancestory are analogs.
immunoglobulin (Ig) superfamily
Proteins which have one or more Ig-like domains. The domain is about 100 amino acids and exhibits a characteristic structure stabilized by a disulfide bond. Most members of the family mediate cell-cell recognition or antigen recognition in the immune system. Members outside of the immune system include other cell adhesion molecules and various growth factor receptors.
integral membrane protein
Proteins which pass through the lipid bilayer of the membrane. Integral membrane proteins can have a single transmembrane domain or multiple transmembrane domains.
ligand
Any molecule that binds to a specific site on a protein or other macromolecule. Most often used in the context of receptors.
lysosome
A subcellular organelle characterized by acidic pH and hydrolytic enzymes.
membrane
A double layer of lipid molecules and associated proteins (see Figure) which define subcellular compartments or enclose the cell. Types of proteins associated with membranes are: integral membrane proteins, peripheral membrane proteins and GPI-anchored proteins.
microtubules
Long cylindrical structures composed of proteins called tubulins. Microtubules function as cytoskeletal elements, a major component of cilia and flagella, and the mitotic spindle. Motor proteins are involved in microtubule based motility.
mitochondrion
A doubled-membrane organelle that carries out electron transport and oxidative phosphorylation and produces most of the ATP in eukaryotic cells. The inner membrane is often folded into numerous cristae.
motor proteins
Cytoskeletal proteins involved in the generation of force. Motor proteins function by converting the chemical energy released from the hydrolysis of ATP into mechanical energy. Myosin functions as an actin-filament associated motor protein and kinesin and dynein are microtubule associated motor proteins.
nucleus
Prominent membrane-bound organelle in eukaryotic cells containing the DNA organized into chromosomes.
organelle
A subcellular compartment which carries out a particular function(s).
ortholog
Homologous genes that perform the same functions in different species.
oxidative phosphorylation
The enzymatic phosphorylation of ADP to ATP coupled to electron transport in the mitochondria. Electrons derived from TCA cycle intermediates flow down a series of electron-carrier proteins (i.e., cytochromes) until finally being transferred to molecular oxygen. The available free energy derived from the electrons, as they move to successively lower energy levels, is captured in the phosphate bond of ATP.
paralog
Homologous genes that are the result of gene duplication within an evolutionary lineage (eg., species) which may or may not have similar functions.
peptide
also called polypeptide. A linear polymer of amino acids similar to a protein. Generally refers to a shorter polymer than a protein, which are either natural cellular products or products resulting from the degradation of proteins by proteases.
peripheral membrane protein
Proteins that associate with the outer surfaces of the membrane lipid bilayer through non-covalent interactions with integral membrane proteins or the polar groups of the lipids.
plasma membrane
The outermost membrane(s) of a cell.
prokaryote
Organisms with cells lacking a well-defined membrane enclosed nucleus as well as other membrane bound organelles. They include bacteria and cyanobacteria. See also eukaryote.
protease
An enzyme that hydrolyses the peptide bond between amino acids of a protein. Also called peptidase. Endopeptidases cleave within the polypeptide chain. The specificity of cleavage is determined by the amino acids near the scissile (i.e., hydrolyzed) bond. Exopeptidases remove amino acids either one or two at a time from the ends of the polypeptide chain. Exopeptidases are either amino-peptidases or carboxy-peptidases depending upon the specificity for either the N-terminus or the C-terminus, respectively. Proteases are grouped into 4 major classes depending on their mechanism: serine, cysteine (or thiol), aspartic (or acid), and metallo.
protein
The major macromolecular constituent of cells. Responsible for cellular structure and function. Composed of a linear polymer of amino acids folded into a unique 3-dimensional structure. See also peptide.
PVM
Parasitophorous vacuolar membrane. A membrane surrounding intracellular parasites. In the case of apicomplexa it is formed during parasite entry. See merozoite invasion for more information on the PVM and its formation.
receptor
A protein that binds a specific ligand. Cell-surface receptors are generally integral membrane proteins with a receptor-binding domain exposed on the extracellular side.
redox reactions
refer to oxidation-reduction reactions. Oxidation is the loss of electrons and reduction is the gain of electrons. Redox reactions proceed with the transfer of electrons from an electron donor (i.e., reducing agent) to an electron acceptor (i.e., oxidizing agent). Electron donors and acceptors function as conjugate reductant-oxidant pairs:
electron donor « e- + electron acceptor
After gaining an electron, the oxidant becomes the reductant and can be recycled by donating its electron and visa versa. Electrons will tend to flow from electronegative donors such as NADH to more electropositive acceptors such as cytochromes and ultimately oxygen. The transfer of electrons can also be mediated by a hydrogen atom in which case the dehydrogenation equals oxidation and hydrogenation equals reduction.
RNA
Ribonucleic acid. The primary function of RNA involves the decoding of information stored in DNA by directing the synthesis of proteins (see Central Dogma). The 3 types of RNA are: messenger (mRNA), ribosomal (rRNA), and transfer (tRNA). The mRNA is transcribed from DNA and encodes the information necessary for the synthesis of proteins. The rRNA are a component of ribosomes, the organelle responsible for translating mRNA into protein. The tRNA decodes the genetic code and transfers the appropriate amino acid to the growing polypeptide chain.
ROI
reactive oxygen intermediate. Highly reactive forms of oxygen (eg., hydrogen peroxide, super oxide, hydroxyl radical) capable of doing cellular damage.
secretory vesicle
A membrane-bound organelle in which molecules destined for export are stored prior to their release, or exocytosis.
selectins
Cell adhesion proteins that recognize specific carbohydrate groups. Some selectins mediate the initial binding of neutrophils (white blood cells) to endothelial cells during the inflammatory response.
spectrin-actin submembrane cytoskeleton
Cytoskeletal elements associated with the erythrocyte membrane as peripheral membrane proteins. Spectrin proteins and short actin filaments form a 2-dimensional network on the cytoplasmic side of the erythrocyte plasma membrane. Other proteins are involved in the attachment of this network to band 3 and glycophorin.
tricarboxylic acid (TCA) cycle
A biochemical pathway of respiration in which acetyl residues are oxidized to carbon dioxide and hydrogen atoms via a cyclical series of enzymatic reactions. The hydrogen atoms--or more precisely, their equivalent electrons--are utilized in electron transport and oxidative phosphorylation.
 

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