Carbon atoms can attach to carboxyl group and amino group {amino acid}|. The carbon atom also attaches to hydrogen atom and functional group {side chain, amino acid}. Cells can have 150 different amino acids.
asymmetry
Central carbon is asymmetric, because it has four different groups. It can rotate light clockwise (R) or counterclockwise (L).
groups
Amino acids have groups. Alkyl amino acids are glycine, alanine, valine, leucine, and isoleucine. Aromatic amino acids are phenylalanine, tryptophan, and tyrosine. Sulfur amino acids are cysteine, which is thiol, and methionine, which is thioether. Hydroxyl amino acids are the alcohols serine and threonine and the phenol tyrosine. Acidic amino acids have charge -1 in solution: aspartic acid and glutamic acid. Amide amino acids are asparagine and glutamine.
Lysine and arginine, which have amino group, are basic amino acids and have charge +1 in solution. Histidine is basic amino acid, is secondary amine, has aryl ring with two nitrogens, has charge +0.5 in solution, and has smaller charge in solution because it is weak base.
Imino acid is proline, which is secondary amine. Non-polar amino acids are alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, and proline.
polymerization
Amino acids can polymerize to make protein. Twenty different amino acids are in protein. Proteins have only L-amino acids, not R-amino acids. Amino acids that are fewest in proteins are methionine, then histidine, and then tryptophan. Methionine is first amino acid in protein chain. Free amino acid to dipeptide ratio is 10:1.
absorption
Intestine absorbs 92% of amino acids.
types
Delta-aminolevulinic acid comes from glycine and succinyl-CoA. Epinephrine comes from tyrosine. Melanin comes from tyrosine. Phenylalanine makes tyrosine. Serotonin comes from tryptophan. Amino acids can make folic acid, S-adenosylmethionine, thyroxine, histamine, sphingosine, and NAD+. Amino acids can lose amino group to become carboxylic acids in TCA cycle. Carboxylic acids in TCA cycle can gain amino group to become amino acids. Amino acids can break down to ammonia and urea.
Fibrinogen, thrombin, and blood-factor proteins participate in blood clotting {blood clotting}|.
Proteins {conjugated protein} can bind to other molecules.
Cysteine can bind to another cysteine {cystine} by disulfide bond.
Glutamic acid {glutamate, protein} builds purines and pyrimidines.
Cell proteins {heat-shock protein} can increase during stress. HSP40 carries newly folded amino-acid chains. HSP60 chaperone covers proteins as they fold, to prevent partly folded proteins from hitting others, and binds to misfolded intermediates to restart folding. HSP70 holds ATP, but when ATP leaves, it binds peptide and so aids protein conformation and assembly. HSP90, such as gp96, organizes proteins from other chaperones into receptors and other multiprotein structures. HSP70 and HSP90 carry antigens to antigen-presenting-cell CD91 receptors.
Small proteins {interferon}| can bind to plasma membranes and can protect against viruses that degrade mRNA and block protein-synthesis initiation. After viral-gene expression starts, interferon can stop all viral-gene expression {interferon response}. In humans, viruses that make long double-stranded RNAs trigger PKR enzyme production, which stops mRNA translation to protein. RNAse L breaks down mRNA. Interferon cytokine secreted by virus-infected cells enhances both these responses.
Alpha-keratin {keratin}| is in skin, hair, wool, horn, and nails. Alpha-keratin has three to seven amino acid chains in bundle, cross-linked by disulfide bonds, which then bundle again. Scales, claws, beaks, silk, and feathers have beta-keratin. Beta-keratin is mostly glycine, alanine, and serine.
Amino acids can link by peptide bonds {peptide}|. Peptides do not branch. Peptides are transmitters and hormones.
Proteins {protein hormone}, such as insulin, growth hormone, and adrenocorticotropin, can be hormones.
Protofibrils {protofibril} are soluble, have 4 to 30 misfolded proteins that clump together, and do not break down quickly enough in disease, later forming fibrils and {amyloid} plaque.
Urea processing uses the following steps {urea cycle}. Ammonia builds up in cells from various deaminations. Ammonia is toxic, because it blocks TCA cycle. In mitochondria, ammonia reacts with two ATP, carbon dioxide, and water molecule to make one carbamyl phosphate. In cytoplasm, carbamyl phosphate reacts with ornithine to make citrulline. Citrulline diffuses to cytosol and reacts with aspartic acid, which splits to give arginine and fumarate. Water reacts with arginine to make nitrogen compounds {urea}| {ornithine}. Urea is not toxic, can cross membranes, and excretes in urine.
Proteins, such as snake venoms, can be poisons {toxin}|. Bacteria make diphtheria toxin. Cobra venom and banded kait venom bind to acetylcholine receptor. Tetanus toxin and black-widow-spider toxin affect acetylcholine vesicle release. Tetanus toxin prevents glycine release. Benzodiazepines, phencyclidine, and strychnine are toxins. Poisons can stay inside cells {endotoxin} or secrete to outside {exotoxin}. LAL chemical, from horseshoe crab blood, tests for endotoxins in drugs and implants.
Botulinus toxin {botulism}| affects acetylcholine vesicle release.
Proteins {enzyme}| can be catalysts. Enzyme and ribozyme catalysts regulate biochemical reactions. Coenzymes can bind to or assist enzymes.
history
Schwann discovered pepsin [1825], which cuts proteins. Robiquet and Boutron discovered emulsin [1830]. Leuchs discovered ptyalin [1831]. Payen and Persoz discovered amylase [1833], which cuts starches. Corvisart discovered trypsin [1856], which cuts proteins. Kuhne invented the word enzyme [1878]. Bertrand discovered need for coenzymes [1897]. Arthur Harden and William John Young discovered coenzyme for zymase [1906]. Henri studied enzyme kinetics and proposed enzyme-substrate complex [1903]. Barger and Stedman discovered that physostigmine inhibited cholinesterase [1923], which metabolizes choline. Jones and Perkins discovered ribonuclease [1923], which cuts RNA. Enzymes are proteins [1925]. Briggs and Haldane used steady state for enzyme kinetics [1925]. Sumner discovered urease [1926], which metabolizes urea. Stedman discovered acetylcholinesterase [1932], which metabolizes acetylcholine. Aeschlimann discovered that neostigmine inhibited cholinesterase [1931]. Hellerman hypothesized need for thiol groups in enzymes, as did Bersin and Logemann [1933]. Hellerman hypothesized need for metal bridges in enzymes [1937]. Mann and Keilin discovered that sulfanilamide inhibited carbonic anhydrase [1940]. Sanger and Tuppy found insulin amino-acid sequence [1951]. Sutherland discovered cyclic AMP in animal cells [1956]. Koshland hypothesized enzyme conformation changes upon binding [1958]. Kendrew used x-ray crystallography on myoglobin [1958]. Merrifield developed solid-phase peptide synthesis and built insulin and ribonuclease [1963].
types
Chymotrypsin, cytochrome, diastase, flavin, lipase, lysozyme, nuclease, RNA polymerase, thermolysin, and DNA polymerase are enzymes.
transition states
About 100,000,000 transition-state shapes exist for enzymes.
In competitive inhibition, inhibitor shape can be similar to substrate shape, so inhibitor can bind to enzyme at substrate site {active site}.
In non-competitive inhibition, inhibitors can bind to enzymes at other sites {allosteric site} to alter active sites.
Molecules {coenzyme}| can bind to enzymes to activate them. Michaelis and Wollman discovered that free radicals formed from alpha-tocopherol [1950]. Lipmann isolated coenzyme A [1945]. Mitchell, Snell, and Williams isolated folic acid [1941]. O'Kane and Gunsalus isolated lipoic acid [1948]. Metals can be coenzymes [1930]. Jansen and Donath isolated thiamine [1926]. Fildes hypothesized that molecules similar to natural substrates or coenzymes compete and are therapeutic. Methotrexate treats leukemia (Farber) [1946].
Post-transcription, enzymes {proteolytic enzyme} can cleave terminal amino acids and break peptide chains into pieces: proteinase, peptidase, pepsin, trypsin, chymotrypsin, carboxypeptidase, amino peptidase, dipeptidase, endopeptidase, and exopeptidase.
Reagents {substrate} can bind to enzymes at active sites.
Enzyme precursors {zymogen} can split or react to create enzymes.
Molecules {inhibitor} can bind to enzyme to reduce reaction rate {enzyme inhibition}.
Inhibitor shape can be similar to substrate shape, so inhibitor can bind to enzyme at active site {competitive inhibition}.
Inhibitor can bind to enzyme at allosteric site to alter active site {non-competitive inhibition}.
Inhibitor can bind directly to enzyme-substrate complex to change activation energy {uncompetitive inhibition}.
Heat-shock proteins {foldase}, such as HSP60, envelope proteins as they fold to prevent partly folded proteins from hitting others.
Heat-shock proteins {chaperone} bind to misfolded intermediates to restart folding.
Molecules {ubiquitin, protein}| can bind misfolded proteins and go to proteosomes to break peptide bonds.
Proteins can be for protection {immunity}|. Antigen binding to beta-lymphocyte surface triggers process that creates plasma cells. Plasma cells specialize to make antibody to antigen.
Antigens can enter body. Immunoglobulin proteins {antibody}| bind antigens, so body can remove foreign molecules. Antibodies bind to antigens by hydrogen bonds, van der Waals forces, and ionic bonds. Antibody-connecting subunits can cross plasma membrane and bind to cells.
structure
Antibodies have three subunits. Two subunits can bind to one antigen each. One subunit connects two binding subunits to make Y-shaped structure. Antibodies have two light protein chains and two heavy protein chains, linked by disulfide bonds. Light chains are at Y tips. All antibodies have kappa or lambda light chain but different heavy-chain constant regions. Heavy chains are in arms and base of Y. Light and heavy chains have variable end and constant end. Several hundred genes code variable regions, making millions of different antibodies. About 100,000,000 different antibody shapes can exist.
precipitation
When one antibody binds to two antigens, complex becomes insoluble. Bound molecules precipitate from solution, and then cell phagocytes eat them.
Five proteins {immunoglobin}| affect immunity. IgA is in secretions. Immune system makes IgM first. IgG increases as IgM decreases. IgE is for allergies. IgD is another immunoglobin.
Large molecules {antigen}| can enter body from outside.
Antigens have regions {epitope}| where other molecules can bind.
Small molecules {hapten} can bind to epitope.
Protein groups {complement, protein} can lyse cells if antibodies bind to cells.
Genes {joint gene} {J gene} can code for connections between light and heavy chains.
5-Chemistry-Biochemistry-Protein
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Date Modified: 2022.0225