Biochemistry Terms

alginate — component of the cell walls of many rhodophytes and kelps. Alginates have an affinity for water, and so help to slow dessication when the algae are exposed to the air; they are commercially important in the production of paper, toothpaste, beer, and frozen foods.

amino acid — unit molecule from which proteins are constructed by polymerization.

ATP — “adenosine triphosphate”. A relatively stable, high energy molecule used to fuel chemical reactions within cells.

biochemistry — the study of those molecules used and manufactured by living things.

bioluminescence — the production of light by a chemical reaction within an organism. The process occurs in many bacteria and protists, as well as certain animals and fungi.

brevitoxin — neurotoxin produced by the dinoflagellate Ptychodiscus brevis.

calcite — A common crystalline form of natural calcium carbonate, CaCO3, that is the basic constituent of limestone, marble, and chalk. Also called calcspar.

calcium carbonate — n. A white compound, CaCO₃, that occurs naturally as marble, chalk, limestone, and calcite. It is used by many marine invertebrates, such as corals and echinoderms, and by protists, such as coccolithophorids, to construct their exoskeletons. Calcium carbonate, in the form of calcite, is also incorporated into the eggshells of amniotes, except for turtles whose eggs are composed of aragonite (CaCO₃ + magnesium).

carbohydrates — class of biochemical compounds which includes sugars, starch, chitin, and steroids.

cathodoluminescence — n. An analytical technique used in geology and paleontology to analyze the different minerals in a sample, or diagenetic history of a sample — how crystals grew, were deformed, and were replaced. A beam of electrons is fired at a sample to produce visible light, which can then be used to interpret the mineralogical and diagenetic history of the sample.

cellulose — carbohydrate polymer of the simple sugar glucose. It is found in the cell walls of plants and green algae, as well as dinoflagellates. Cellulose is the most abundant compound on earth that is manufactured by living things.

chitin — n. A carbohydrate polymer found in the cell walls of fungi and in the exoskeletons of arthropods, which provides strength for support and protection; chitinous– adj.

chlorophyll — n. The green-colored pigment that absorbs light during photosynthesis, often found in plants, algae, and some bacteria; it includes a porphyrin ring, and often has a long hydrophobic tail. More info?

collagen — long proteins whose structure is wound into a triple helix. The resulting fibers have a high tensile strength. Collagen is a primary component of mammalian hair.

dinosteranes/dinosteroids — chemicals found in dinoflagellates, which have been useful in documenting their existence early in the fossil record.

DNA — “deoxyribonucleic acid”. The nucleic acid which carries the genetic code of an organism. It is the primary component of chromosomes. MORE?

enzyme — complex protein which helps to speed biochemical reactions. Enzymes are important in the construction and degradation of other molecules.

flagellin — protein which is the primary component of prokaryotic flagella.

fucoxanthin — yellowish-brown pigment found in some members of the Chromista, including kelps and diatoms.

glucose — simple sugar, and the primary product of photosynthesis. It is polymerized to make cellulose and chitin.

glycoprotein — a membrane-bound protein which has attached branching carbohydrates. These may function in cell-cell recognition, such as in human blood groups and immune system response, as well as in resisting compression of cells.

hemoglobin — protein complex found in the blood of most chordates and the roots of certain legumes. It binds oxgen molecules, and in chordates serves as the means by which the oxygen is supplied to the cells of the body.

histones — proteins attached to the DNA of eukaryotes which allows it to be packaged into chromosomes.

hydrophilic — “water loving”. Hydrophilic compounds dissolve easily in water, and are usually polar.

hydrophobic — “water fearing”. Hydrophobic compounds do not dissolve easily in water, and are usually non-polar. Oils and other long hydrocarbons are hydrophobic.

integrin — adhesive protein of the extracellular matrix in animals.

ion — an atom or small molecule which carries a positive or negative charge.

isotopic analysis — n. The study of the geochemistry of stable isotopes in naturally occurring sediments and biological structures. Stable isotopes are atomic variations of elements that are stable over long periods of time, meaning they do not radioactively decay. Several elements, like oxygen and carbon, have several stable forms. Oxygen, for example, occurs in nature as ¹⁶O and ¹⁸O — these two forms are isotopes. They have different numbers of neutrons (¹⁶O has two more neutrons than ¹⁸O), and and is therefore heavier. Because the two isotopes have different masses, chemical and physical reactions like bonding, evaporation, and precipitation occur at different frequencies. The ratio of stable isotopes is preserved in chemical compounds like water, ice, and calcium carbonate and provides information on the environmental conditions at the time the compound formed. For example, the ratio of ¹⁸O/¹⁶O in an ice sample is linked to the water temperature of ancient oceans, which in turn reflects ancient climates.

laminarin — a beta-glucan polysaccharide produced by many chromists through photosynthesis.

lipids — a class of biochemical compounds which includes fats, oils, and waxes.

luciferase — enzyme which activates luciferin to produce bioluminescence.

luciferin — compound whose activated form emits light.

neurotoxin — poison which interferes with nerve function, usually by affecting the flow of ions through the cell membrane.

nucleic acid — class of biochemical compounds which includes DNA and RNA. They are among the largest molecules known.

nucleotide — unit from which nucleic acids are constructed by polymerization. It contains a sugar, a phosphate group, and an organic base. ATP is a nucleotide.

ossification — n. The process of bone formation. Special cells called osteoblasts secrete minerals that combine with a network of collagen fibers, forming the hard bone matrix.

peptidoglycan — carbohydrate polymer cross-linked by proteins. It is found in the cell wall of Gram positive bacteria, where it stains with the dye crystal-violet.

phosphate — an ion consisting of a phosphorus atom and four oxygen atoms. Among other things, it is used in the constuction of nucleic acids.

photosynthesis — biochemical process in which light energy is absorbed by chlorophyll, and is used to fuel the building of sugar molecules.

phycocyanin — blue, water-soluble pigment found in the cyanobacteria and the red algae.

phycoerythrin — red, water-soluble pigment found in the cyanobacteria and red algae.

pigment — any colorful compound, used by living things to absorb or block sunlight, and in sexual displays. More info?

polymer — a large molecule constructed from many smaller identical units. These include proteins, nucleic acids, and starches.

protein — class of biochemical compounds constructed from amino acids. Proteins may be structural, such as those that make up hair and cartilage, or they may be reactive, such as the enzymes.

proteinaceous — describes any structure which is composed of protein.

proteoglycan —

rbcL — a gene which is located in the chloroplast of photosynthetic organisms. It codes for the large subunit of the protein rubisco, and its sequence has been useful in plant phylogenies.

RNA — “ribonucleic acid”. The nucleic acid which carries the DNA message into parts of the cell where it is interpreted and used. The 18S ribosomal RNA sequence has been used in many groups of organisms to reconstruct phylogeny.

rubisco — protein which fixes carbon in photosynthetic organisms. It binds molecules of carbon dioxide to a five-carbon molcule. Rubisco is the most common protein on earth.

saxitoxin — neurotoxin found in a variety of dinoflagellates. If ingested, it may cause respiratory failure and cardiac arrest.

scanning electron microscope (SEM) — n. A special kind of microscope that scans samples with a high-energy beam of electrons to produce a high-resolution, detailed, three-dimensional image. An SEM can magnify a sample up to 250 times that of the best light microscopes.

silica — amorphous silicon dioxide (glass). It is a structural component in many organisms, such as diatoms and horsetails.

spongin — proteinacous compound of which the spicules in Demospongiae are composed.

starch — a complex polymer of glucose, used by plants and green algae to store surplus sugar for later use.

sugar — any of several small carbohydrates, such as glucose, which are “sweet” to the taste