Cell Biology

... from active transport to vesicles

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 neurotransmitters 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 neurotransmitters, 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 :

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caspases

Apoptosis: Modified: Caspases (cysteinyl aspartate-specific proteases) are enzymes that cleave specific proteins at aspartate residues, and which contain cysteine residues at their active sites. Many caspase isoforms are promoters of apoptosis. Caspases can be activated by the death receptor pathway and the mitochondrial pathway.

At least 14 caspase isoforms have now been identified, and the isoforms are broadly categorised into initiators, effectors and inflammatory caspases. Initiator caspases such as caspase-8 and 9 cleave and activate effector caspases such as caspase-3. Effector caspases cleave specific proteins that ultimately leads to cell death by apoptosis. Caspase activity leads to a proteolytic cascade in which one caspase can activate other caspases, thus amplifying the apoptotic signalling pathway.

Cleavage of proteins by caspases can either activate them (other caspases, ICAD), or they can deactivate them (PKB/Akt, Raf-1, PARP-1). In general, proteins that promote apoptosis are activated, and proteins that promote survival are inactivated.

Tables  Apoptosis vs Necrosis  Apoptosis 

• A • adhesion • C • cell membranescellular adhesion moleculescellular signal transductioncentrioleschemotaxischloroplastcilia & flagellacommunicationconcentration gradientscytokine receptorscytoplasmcytoskeleton • E • energy transducersendoplasmic reticulumendosomesexosome • F • flagella & cilia • G • Golgi apparatusGPCRs • H • hormones • I • ion channels • L • lysosome • M • meiosismicrotubulesmitosismitochondrion • N • Nitric Oxideneurotransmissionneuronal interconnectionsnuclear membranenuclear pore • P • pinocytosisproteasomeprotein degradationpumps • R • receptor proteinsreceptor-mediated endocytosis • S • second messengerssignaling gradientssignal transductionspindlestructure • T • transporttwo-component systems • U • ubiquitin • V • vacuolevesicle

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proteins

Proteins are complex, macromolecules comprised of amino acids linked by peptide bonds into long chains. The sequence (primary structure) and properties of constituent amino acids generate the 3D conformational structure (tertiary and quaternary structure) that is vital to the biological function of proteins. image - primary structure protein : animation - protein :

Proteins are essential to the structure and biological viability of all living cells and viruses. The cellular proteome is the total cellular protein under a particular set of conditions, while the complete proteome is the sum of all potential proteomes of a cell. Proteomics has become the subject of much research in cell and molecular biology.

Proteins play a number of vital roles as:
a. Enzymes or subunits of enzymes – catalyzing cellular reactions.
b. Structural or mechanical roles – structural components of tissues, components of the cytoskeleton, centrioles, cilia and flagella, microtubules, molecular motors.
c. Intra- and intercellular signaling functions – ion channels, receptors, membrane pumps.
d. Regulatory proteins in genetic transcription, RNA processing, spliceosomes.
e. Products of immune response that aid in targetting of foreign substances and organisms
f. Storage and transport of various ligands.
g. The source of essential amino acids.

Almost all natural proteins are encoded by DNA, which is transcribed into pre-mRNA, then processed to yield mRNA, which then serves as a template for translation by ribosomes at the rough endoplasmic reticulum .

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