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Glossary of terms |
α-cellulose – the residue remaining after lignin and hemicellulose have been removed from a cell wall Arabidopsis – a small flowering plant related to cabbage and mustard. Arabidopsis thaliana (thale cress, mouse-eared cress) was the first plant to have its genome sequenced. Arabinose - a 5 carbon sugar (pentose, C5H10O5) present in grass hemicellulose. Arabinoxylan – a hemicellulose with a backbone of 1,4 β-D-xylosyl residues and side-chains composed of arabinosyl residues. A major hemicellulose in grass cell walls. Atomic force microscopy - a high-resolution form of scanning-probe microscope that provides information on a materials surface features.
Bacteria - unicellular microorganisms that do not contain a nucleus and typically have no membrane-bound organelles Bagasse - the biomass remaining after sugarcane stalks have been crushed and the juice extracted Bioenergy - energy generated from renewable biological sources Biofuel - solid, liquid, or gas fuel derived from biomass Biomass - living or recently dead biological material which can be used as fuel or for industrial production BTU - British thermal unit is a unit of energy used in the USA. Replaced by the SI unit of energy, the joule (J). 1 BTU = 1.054-1060 J
Carbohydrate – generic term that includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more terminal groups to carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom, an amino group, a thiol group or similar heteroatomic groups. Cell – the individual units, enclosed by a membrane or wall, that make up a living organism Cellulose – a polysaccharide composed of 1,4 linked β-D-glucosyl residues Cellulose microfibril - macromolecular fibers 3 to 6 nm in diameter. Contain up to 36 individual glucan chains hydroigen bonded to one another Cellulosome – a complex containing structural proteins and enzymes. Involved in binding to and hydrolyzing cellulose Consolidated bioprocessing - a process whereby biomass is converted to sugar and then fermented to a product by one or more microorganisms in a single reaction vessel Coumaric acid – 3-(4-hydroxyphenyl)-2-propenoic acid. A component of lignin
Deconstruct – to break into smaller parts DP – degree of polymerization. The number or monomer units in a polymer
Enzyme – a protein that catalyses a chemical reaction EROEI - Energy Returned on Energy Invested Ester – compounds of general form R1-C(=O)-O-R2 Esterase – a enzymes that hydrolyses etser bonds Ether – compounds of general formula R1-O-R2 Exon - region of DNA within a gene that is transcribed to messenger RNA
Ferulic acid - (E)-3-(4-hydroxy-3-methoxy-phenyl)prop-2-enoic acid. A component of lignin. Also found linked by a ester bond to hemicelluloses and some pectins Fourier transform infra-red spectroscopy – a technique for obtaining infra red spectra of a material FRA – a class of mutants identified in Arabidopsis that have fragile stems with irregular and abnormal xylem.
Galactose – a monosaccharide (C6H12O6). A component of pectins and hemicelluloses Galacturonic acid - galactose in which the C6 alcohol (CH2OH) has been oxidized to a carboxylic acid (COOH). Has the formula C6H10O7. A major component of pectins Gassification – a process for turning a solid material into a mixture of carbon monoxide and hydrogen (syngas) that can be converted into other chemicals or used to generate heat and electricity GATL – GAlactronic acid Transferase Like. A family of genes identified in Arabidopsis that share some sequence homology with the GAUT family of genes. GAUT – GAlactUronic acid Transferase. A family of genes identified in Arabidopsis that have homology to GAUT1, a homogalacturonan galacturonosyltransferase Gene - a region of genomic sequence that corresponds to a unit of inheritance Glucose – a monosaccharide (6-(hydroxymethyl)oxane-2,3,4,5-tetrol) C6H12O6. Starch and cellulose are polymers composed of glucose units linked together in different ways Glucomannan – family of polysaccharides composed of 1,4-linked β-D-mannosyl and glucosyl residues. Accounts for much of the hemicellulose in conifers. Also present in some plant tubers (e.g Konjac gum– Amorphophallus). Glucuronic acid – glucose in which the C6 alcohol (CH2OH) has been oxidized to a carboxylic acid (COOH). Has the formula C6H10O7 Glucuronoxylan – a family of hemicellulosic polysaccharides with a backbone composed of 1,4-linked β-D-xylosyl residues. Glucuronic acid and 4-O-methyl glucuronic acid are attached to O-2 of some of the xylosyl residues. Glycan hydrolase – a enzyme that cleaves glycosidic bonds by hydrolysis Glycan lyase - a enzyme that cleaves glycosidic bonds by a β-elimination reaction. Glycosyltransferase – a enzyme that transfers a glycosyl residue from a donor molecule to a acceptor molecule Golgi apparatus – a cellular organelle. Site of synthesis of pectin and hemicelluloses in plants. Grass – Poaceae, a group of monocotyledenous plants
Hemicellulose – A family of polysaccharides that contain 1,4-linked β-D-pyranosyl residues in which O-4 is equatorial (e.g. glucose, mannose, and xylose). In plant cell walls these polysaccharides interact non-covalently with cellulose. They are typically solubilized using aqueous alkali. Homogalacturonan – a pectic polysaccharide composed of 1,4-linked α-D-galactosyluronic acid residues
Intron - non-coding sections of DNA Ionic-liquid – a liquid that contains predominantly ions rather than molecular species. A salt in which the ions are poorly coordinated, which results in these solvents being liquid below 100°C, or at room temperature IRX – a class of mutants identified in Arabidopsis that have irregular and abnormal xylem
Joule - SI unit of energy. 1 joule = 0.239 calories
Kappa number – the yield obtained after kraft pulping Kraft pulping process - produces wood pulp which is almost pure cellulose fibers by using sodium hydroxide and sodium sulfide to extract the lignin.
Laccase - copper containing oxidase enzymes that are found in many plants, fungi and microorganisms. Involved in lignin formation in plants Lignin – a natural polymer composed of cross-linked polyphenolic compounds. A major component of biomass Lignocellulosic – a term often used to describe plant biomass. This biomass is composed predominantly of cellulose, hemicellulose and lignin
Mass spectrometry (MS) - an analytical tool used for measuring the molecular mass of a sample. Structural information can be obtained using tandem mass spectrometery (MSn). Miscanthus - a genus of 15 species of perennial grasses native to tropical and sub-tropical regions. Miscanthus x giganteus has potential as a energy crop. Methyl glucuronic acid – glucuronic acid that contains a methyl ether at C-4 Monolignol – the precursors for lignin formation Monosaccharide - polyhydroxy aldehydes H-[CHOH]n-CHO or polyhydroxy ketones H-[CHOH]n-CO-[CHOH]m-H with three or more carbon atoms. A single unit, without glycosidic connection to other such units.
Nuclear magnetic resonance spectroscopy (NMR) – a family of techniques that exploit nuclear magnetic resonance to study molecules. Nucleoside diphosphate sugars – Activated forms of sugars used by glycosyltransferases for the biosynthesis of complex carbohydrates. Some examples are uridine diphosphate glucose (UDP-Glc) and guanosine diphosphate mannose (GDP-Man)
Oligosaccharide - compounds in which monosaccharide units are joined by glycosidic linkages. The term 'oligosaccharide' is typically used to refer to a defined structure as opposed to a polymer of unspecified length. Oryza sativa – domesticated rice, a member of the Poaceae (true grasses). The first grass to have its genome sequenced
Pectin – A family of polysaccharides that contain 1,4-linked α-D-galactosyluronic acid residues. Peroxidase – a group of enzymes that catalyze oxidation-reduction reactions. Peroxidases reduce H2O2 to water while oxidizing a variety of substrates Phenolic - a class of chemical compounds consisting of a hydroxyl group (-O H) attached to an aromatic hydrocarbon group. Exist as low molecular weight compounds (e.g flavonoids) and as polymers (e.g lignin) Phloem – living tissue that transports organic nutrients, particularly sucrose, to all parts of the plant Plasma membrane – external membrane of a cell. Location of enzyme complexes (rosette terminal complexes) involved in cellulose synthesis in plants Polysaccharide - the name given to a macromolecule (glycan) consisting of a large number of monosaccharide (glycose) residues joined to each other by glycosidic linkages Populus trichocarpa – Black cottonwood. The first hardwood tree to have its genome sequenced. Has potential as a energy crop Pretreatment – a chemical process used to decrease the recalcitrance of biomass. May involve hot water or aqueous alkali Primary cell wall – the wall surrounding a growing plant cell
QTL - quantitative trait loci are stretches of DNA that are closely linked to the genes that underlie a particular trait. QTLs can be identified to help map regions of the genome that contain genes involved in specifying a particular quantitative trait
Recalcitrance – the resistance of biomass to conversion to fermentable sugar Rhamnogalacturonan I (RG-I) – a pectic polysaccharide with a backbone composed of the repeating disaccharide 2-α-L-Rhap(1,4)-α-D-GalpA-(1. Oligosaccharides containing arabinosyl, galactosyl, fucosyl, and glucuronosyl residues may be attached to C4 of the rhamnosyl residue. Rhamnogalacturonan II (RG-II) – A pectic polysaccharide with a backbone of 1,4-linked α-d-galactosyluronic acid residues. Four structurally complex oligosacchardies are attached to the backbone. In the primary wall RG-II exists as a dimer that is cross-linked together by a borate diol-diester
Secondary cell wall – the wall, typically lignified, that surrounds a plant cell that has ceased to grow Starch – a polysaccharide composed of 1,4 and1,4,6-linked α-D-glucosyl residues Sucrose - a disaccharide (α-D-glucopyranosyl-(1→2)-β-D-fructofuranose) with the molecular formula C12H22O11. Common name – table sugar. Sugar – a generic name for low molecular weight carbohydrate. Commonly used to describe glucose, fructose, and sucrose. Switchgrass (Panicum virgatum) – warm season grass. One of the dominant species of the central North American tallgrass prairie. Has potential as a energy crop.
Trichoderma – conidial-producing fungi, common in soil. Saprophytes that produce diverse enzymes. Trichoderma reesii is used commercially to produce cellulases and hemicellulases
UDP sugars – activated form of a sugar used in the biosynthesis of complex carbohydrates including cell wall polysaccharides. Examples include UDP-Glucose, UDP-xylose, UDP-arabinose, and UDP-galacturonic acid
Vascular tissue – tissues that transport water (xylem) and organic nutrients (phloem) through a plant
Wall – the polysaccharide-rich material that surrounds a plant cell Wood – the secondary xylem of a woody plant. Wood is composed of cellulose (40%–50%), hemicellulose (15%–25%) and lignin (15%–30%).
Xylan – a polysaccharide composed of 1,4-linked β-D-xylosyl residues Xylem – tissue in plants responsible for responsible for the transportation of water and mineral nutrients Xylose - a 5 carbon (pentose) sugar present in grass hemicellulose. Xyloglucan – a hemicellulosic polysaccharide with a backbone composed of 1,4-linked β-D-glucosyl residues. Oligosaccharides composed of xylosyl, galactosyl, arabinosyl, and fucosyl residues are linked to C6 of up to 75% of the glucosyl residues.
Yeast - eukaryotic microorganisms classified in the kingdom Fungi. Saccharomyces cerevisiae is used in baking and fermenting alcoholic beverages
Zea mays - cereal grain that was domesticated in Mesoamerica and then spread throughout the American continents. Currently used for much of the bioethanol production in the US
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