adenosine

amines

Nitrogen is the key atom in amines. Alkyl (-CnH2n+1) or other groups are attached to the N through a carbon atom of the group. Amines are designated primary, secondary, and tertiary according to the number (1,2, or 3) of groups replacing the H atoms of an NH3 template molecule.

amino acids

Commonly called the 'building-blocks of proteins', amino acids comprise a carboxylic acid group (COOH), an attached side chain, and an amino group (NH2). The general structure of alpha amino acids is COOH-HCR-NH2, where R represents a side-chain specific to each amino acid, and the carboxyl and amino acids are attached to the same carbon atom.

Amino acids form peptide and protein polymers. metastream - amino acid : animation - peptide : image - primary structure protein : animation - protein : Over 90 amino acids are found in nature, while only 20 proteinogenic, standard amino acids are coded for by DNA. Of interest, 13 of the 21 amino acids found in cellular protein were generated in the Miller-Urey experiment, glycine being the commonest.

Several of the proteinogenic amino acids are termed ‘essential’ because they cannot be synthesized by the body’s metabolism and must be ingested in the diet. For adult humans isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine are essential, while children also require dietary histidine and arginine. Two other amino acids, selenocysteine and pyrrolysine, are sometimes incorporated during translation from RNA to protein.

In addition to their roles as substrates in peptide and protein synthesis, amino acids have other biologically important functions. Glycine, and glutamate, are both employed as neurotransmitters.

Non-standard amino acids are produced by post-translation modification, and some non-standard amino acids are produced only by plants and micro-organisms. Many amino acids are modified in the synthesis of other bio-active molecules: tryptophan is a precursor of the neurotransmitter serotonin, and glycine is one of the reactants in the synthesis of porphyrins such as heme. Numerous non-standard amino acids are also biologically important: GABA is another neurotransmitter, carnitine is employed in lipid transport within cells. Others non-standard amino acids include citrulline, homocysteine, hydroxyproline, hydroxylysine, ornithine, and sarcosine.

Virtual Cell Textbook - Biomolecules : Cell Textbook - Cell Biology : Main page of BioChemistry : Main page of Molecules : Main page of Pathways : Main page of Genes : Main page of Cell : Main page of Cell to Cell : Main page of Neuron: Main page of Brain:

amphipathic

An amphipathic, or amphiphilic molecule contains both nonpolar hydrophobic and polar hydrophilic groups.

The hydrophobic group can be a long carbon chain, of the form: CH3(CH2)n, where n is greater than 4 and less than 16. Biologically important amphoteric molecules are the phospholipids, one of the main constituents of biological membranes, which naturally form bilayers. The phospholipid cell membrane insulates the cells from the surrounding medium.

catecholamine

catalyst

chemical gradients

covalent bond

enzyme

MIT Biology Hypertextbook: Enzyme Mechanisms: "Not all proteins are enzymes, but most enzymes are proteins (the exception is catalytic RNA). A catalyst is a molecule which increases the rate of a reaction but is not the substrate or product of that reaction. A substrate (A) is a molecule upon which an enzyme acts to yield a product (B).

A ------> B
Enz

The free energy of this reaction is not changed by the presence of the enzyme, but, for a favored reaction (where delta G is negative), the enzyme can speed it up."

Enzymes couple with substrates in transitional states, effecting conformational changes (3D structure) that facilitates transition to products.

MIT Biology Hypertextbook on Enzyme Biochemistry : Chemical Energetics : Enzyme Mechanisms : Enzyme Kinetics : Feedback Inhibition

heterocyclic

Heterocyclic compounds contain a 5 or 6 atom ring structure such as found in benzene and aromatic hydrocarbons, but with other atoms substituting for ring carbons. Thus, atoms such as sulfur, oxygen or nitrogen comprise part of the ring. Examples are pyridine (C5H5N) and pyrimidine (C4H4N2), and the nucleic acids.

hydrophilic

Hydrophilic, meaning 'water loving', is the chemical property of dissolving in, or orienting toward ionic, charged, solutions (such as extra- and intracellular fluids). Hydrophilic molecules or hydrophilic groups on amphipathic molecules can transiently bond with water (H2O) through the hydrogen bond. Such bonding is thermodynamically favorable, rendering these molecules soluble in water and in other polar solvents. Hydrophilic molecules are also termed polar molecules, and hydrophobic molecules are termed nonpolar molecules.

Back to: Main page of BioChemistry : amphipathic : phospholipids : hydrophobic : Main page of Cell : ion channels : cell membrane :
Main page of Genes : Main page of Neuron:

http://en.wikipedia.org/wiki/Hydrophilic

hydrophobic

Hydrophobic, meaning 'water avoiding', molecules exhibit orientation toward, or solution in, uncharged media (such as oils). This condition is opposite to hydrophilic. A hydrophobic molecule, or the hydrophobic moiety of an amphipathic molecule is typically uncharged and is not capable of hydrogen bonding. Its lack of an electrical charge enables it to dissolve more readily in oil or other hydrophobic, nonpolar solvents than in water or polar media. Hydrophilic molecules are also termed polar molecules, and hydrophobic molecules are termed nonpolar molecules.

Back to: Main : ion channels :

hydrogen bond

A hydrogen bond results from an attractive intermolecular force between two partial electric charges of opposite polarity. Although stronger than most other intermolecular forces, a hydrogen bond is much weaker than either an ionic bond or a covalent bond.

Within macromolecules such as proteins and nucleic acids, hydrogen bonds can exist between two parts of the same molecule and constrain the molecules' 3D shape.

More at: Wikipedia

Back to : Main page of BioChemistry : hydrophilic : hydrophobic : proteins : peptides :
Main page of Cell : Main page of Genes :
Main page of Neuron: Main page of Brain:

ionic bond

lipid

lysosome

neurotransmitter

peptide bond

peroxisome

peptide

Peptides comprise linked amino acids in specific sequences. Peptides differ from proteins, which are chains of hundreds of amino acids, in being less than 50 amino acids in length. Three large classes of peptides are recognized: ribosomal peptides, nonribosomal peptides, and digested peptides.

Ribosomal peptides sequences are genetically coded, and they are synthesized at the endoplasmic reticulum by translation of mRNA. Often proteolysis generates the mature form. Ribosomal peptides function as hormones and signalling molecules.

Digested peptides are the result of nonspecific proteolysis as part of the digestive cycle.

Nonribosomal peptides are confined primarily to unicellular organisms, plants, and fungi. They are synthesized using a modular enzyme complex.

pH

phospholipid

Phospholipids are formed from four components: fatty acids, a negatively charged phosphate group, an alcohol and a backbone. Phospholipids with a glycerol backbone are known as glycerophospholipids or phosphoglycerides. There is only one type of phospholipid with a sphingosine backbone; sphingomyelin. Sphingomyelin is present in all eukaryotic cell membranes, but is mainly present in cells of the nervous system. Phospholipids, along with glycolipids and cholesterol, are a major component of all biological membranes.

protein

receptor

ribozyme

Ribozyme Enzymology: "Ribozymes are antisense RNA molecules that have catalytic activity. They function by binding to the target RNA moiety through Watson-Crick base pairing and inactivate it by cleaving the phosphodiester backbone at a specific cutting site.

Five classes of ribozymes have been described based on their unique characters in the sequences as well as three-dimensional structures (Bunnell,1997). They are denoted as (1) the Tetrahymena group I intron, (2) RNase P, (3) the hammerhead ribozyme, (4) the hairpin ribozyme, and (5) the hepatitis delta virus ribozyme. They may catalyze self-cleavage (intramolecular or 'in-cis' catalysis) as well as the cleavage of external substrates (intermolecular or 'in-trans' catalysis) (Ohkawa, 1995). "

Ribosomes are large intracellular aggregates attached to the endoplasmic reticulum. They comprise several RNAs and scores of proteins, and function as ribozymes.

thermochemistry

Thermochemistry refers to chemical thermodynamics -- the energetic principles that underly chemical reactions, phase changes, and solution formation. In essence, thermodynamically favourable reactions move naturally from reactants to products, and are accelerated in the presence of specific catalysts or enzymes.

Main page of BioChemistry : covalent bond : hydrogen bond : ionic bond : Main page of Cell : mitochondrion : Main page of Genes :
Main page of Neuron: