Friday, November 02, 2007

a biochemistry

Saturday, December 30, 2006



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:


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.
Thursday, December 28, 2006



chemical gradients

covalent bond

Tuesday, December 26, 2006


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

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
Saturday, December 23, 2006


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, 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:


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:
Friday, December 22, 2006

ionic bond

Tuesday, December 19, 2006



Sunday, December 17, 2006


Friday, December 15, 2006

peptide bond



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.



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.


Wednesday, December 13, 2006



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.
Monday, December 11, 2006


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:
Thursday, May 11, 2006


Monday, October 03, 2005

Spontaneous evolution of modularity and network motifs -- Kashtan and Alon 102 (39): 13773 -- Proceedings of the National Academy of Sciences

From the Cover: Spontaneous evolution of modularity and network motifs -- Kashtan and Alon 102 (39): 13773 -- Proceedings of the National Academy of Sciences: "Biological networks have an inherent simplicity: they are modular with a design that can be separated into units that perform almost independently. Furthermore, they show reuse of recurring patterns termed network motifs. Little is known about the evolutionary origin of these properties. Current models of biological evolution typically produce networks that are highly nonmodular and lack understandable motifs. Here, we suggest a possible explanation for the origin of modularity and network motifs in biology. We use standard evolutionary algorithms to evolve networks. A key feature in this study is evolution under an environment (evolutionary goal) that changes in a modular fashion. That is, we repeatedly switch between several goals, each made of a different combination of subgoals. We find that such 'modularly varying goals' lead to the spontaneous evolution of modular network structure and network motifs. The resulting networks rapidly evolve to satisfy each of the different goals. Such switching between related goals may represent biological evolution in a changing environment that requires different combinations of a set of basic biological functions. The present study may shed light on the evolutionary forces that promote structural simplicity in biological networks and offers ways to improve the evolutionary design of engineered systems."

Nadav Kashtan and Uri Alon
Spontaneous evolution of modularity and network motifs
Published online before print September 20, 2005, 10.1073/pnas.0503610102
PNAS | September 27, 2005 | vol. 102 | no. 39 | 13773-13778
Tuesday, September 27, 2005

Crystallin Proteins: A New View On The Evolution Of The Eye Lens

Insight Into Our Sight: A New View On The Evolution Of The Eye Lens: "Fish, frogs, birds and mammals all experience image-forming vision, thanks to the fact that their eyes all express crystallins and form a lens; however, the vertebrates' nearest invertebrate relatives, such as sea squirts, have only simple eyes that detect light but are incapable of forming an image. This has lead to the view that the lens evolved within the vertebrates early in vertebrate evolution, and it raises a long-standing question in evolutionary biology: How could a complex organ with such special physical properties have evolved?

In their new work, Shimeld and colleagues approached this question by examining the evolutionary origin of one crystallin protein family, known as the �?-crystallins. Focusing on sea squirts, invertebrate cousins of the vertebrate lineage, the researchers found that these creatures possess a single crystallin gene, which is expressed in its primitive light-sensing system. The identification of the sea squirt's crystallin strongly suggests that it is the single gene from which the vertebrate �?-crystallins evolved.

The researchers also found that, remarkably, expression of the sea squirt crystallin gene is controlled by genetic elements that also respond to the factors that control lens development in vertebrates: The researchers showed that when regulatory regions of the sea squirt gene are transferred to frog embryos, these regulatory elements drive gene expression in the tadpoles' own visual system, including the lens. This strongly suggests that prior to the evolution of the lens, there was a regulatory link between two tiers of genes: those that would later become responsible for controlling lens development, and those that would help give the lens its special physical properties. This combination of genes appears to have then been co-opted in an early vertebrate during the evolution of its visual system, giving rise to the lens."

Cell Press
Friday, January 28, 2005


Sunday, October 10, 2004

Item links


amino acid
amino acids


covalent bond
covalent bonds



hydrogen bond
hydrogen bonds
hydrogen bonding


ionic bond
ionic bonds
ionic bonding








receptor subunits


secretory vesicle
secretory vesicles

Monday, January 01, 1990

Blogroll of Atheist Sites

home image


companion sites

Companion Site Links

© The content of this blog is intended for personal or educational use. All rights are reserved for commercial use of contents. All images created by site author.