- is the application of chemistry to the study of biological processes at the cellular and molecular level. It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology, and biology to investigate the chemistry of living systems.
- Amino acids are organic compounds that contain amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, although other elements are found in the side chains of certain amino acids.
- literally means “the fear of water”
- hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water. In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, thus, prefer other neutral molecules and nonpolar solvents.
- A hydrophilic molecule or portion of a molecule is one whose interactions with water and other polar substances are more thermodynamically favorable than their interactions with oil or other hydrophobic solvents. They are typically charge-polarized and capable of hydrogen bonding.
- An Ionic Bond is a specific type of chemical bond formed between a “metal” and a “nonmetal.”
- The goal of forming chemical bonds is to have an octet. “Octet” means that an element has eight electrons.
- Tyrosine is an amino acid that is naturally produced in the body from another amino acid called phenylalanine. It’s found in many foods, especially in cheese, where it was first discovered. In fact, “tyros” means “cheese” in Greek
- Tryptophan is an α-amino acid that is used in the biosynthesis of proteins. Tryptophan contains an α-amino group, an α-carboxylic acid group, and a side chain indole, making it a non-polar aromatic amino acid. It is essential in humans, meaning the body cannot synthesize it; it must be obtained from the diet.
- Phenylalanine is an amino acid found in many foods and used by your body to produce proteins and other important molecules. It has been studied for its effects on depression, pain and skin disorders.
- Alanine is an important source of energy for muscles and central nervous system, strengthens the immune system, helps in the metabolism of sugars and organic acids, and displays a cholesterol-reducing effect in animals. ( NCI04) from NCIt. Alanine is an Amino Acid. The chemical classification of alanine is Amino Acids.
- Glycine is an amino acid that has a single hydrogen atom as its side chain. It is the simplest amino acid, with the chemical formula NH₂‐CH₂‐COOH. Glycine is one of the proteinogenic amino acids. It is encoded by all the codons starting with GG.
- Proline is a proteinogenic amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and a side chain pyrrolidine, classifying it as a nonpolar, aliphatic amino acid.
- Isoleucine is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and a hydrocarbon side chain with a branch. It is classified as a non-polar, uncharged, branched-chain, aliphatic amino acid.
- Leucine is an essential amino acid that is used in the biosynthesis of proteins. Leucine is an α-amino acid, meaning it contains an α-amino group, an α-carboxylic acid group, and a side chain isobutyl group, making it a non-polar aliphatic amino acid.
- Valine is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and a side chain isopropyl group, making it a non-polar aliphatic amino acid. It is essential in humans, meaning the body cannot synthesize it: it must be obtained from the diet.
- Methionine is an essential amino acid in humans. As the substrate for other amino acids such as cysteine and taurine, versatile compounds such as SAM-e, and the important antioxidant glutathione, methionine plays a critical role in the metabolism and health of many species, including humans.
- Aspartic Acid is a non-essential amino acid in humans, Aspartic Acid has an overall negative charge and plays an important role in the synthesis of other amino acids and in the citric acid and urea cycles. Asparagine, arginine, lysine, methionine, isoleucine, and some nucleotides are synthesized from aspartic acid.
- Glutamic acid is an α-amino acid that is used by almost all living beings in the biosynthesis of proteins. It is non-essential in humans, meaning the body can synthesize it. It is also an excitatory neurotransmitter, in fact the most abundant one, in the vertebrate nervous system.
- Serine is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, a carboxyl group, and a side chain consisting of a hydroxymethyl group, classifying it as a polar amino acid.
- Threonine is an amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, a carboxyl group, and a side chain containing a hydroxyl group, making it a polar, uncharged amino acid. It is essential in humans, meaning the body cannot synthesize it: it must be obtained from the diet.
- Cysteine is a semiessential proteinogenic amino acid with the formula HO₂CCHCH₂SH. The thiol side chain in cysteine often participates in enzymatic reactions, as a nucleophile. The thiol is susceptible to oxidation to give the disulfide derivative cystine, which serves an important structural role in many proteins.
- is the process by which an atom or a molecule acquires a negative or positive charge by gaining or losing electrons, often in conjunction with other chemical changes.
- A peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 of one alpha-amino “acid” and N2 of another along a peptide or protein chain.
- Polypeptides are chains of amino acids. Proteins are made up of one or more polypeptide molecules. The amino acids are linked covalently by peptide bonds. The graphic on the right shows how three amino acids are linked by peptide bonds into a tripeptide.
Fibrous and Filamentous Proteins
- Keratin– Keratin is one of a family of fibrous structural proteins. It is the key structural material making up hair, nails, feathers, horns, claws, hooves, and the outer layer of skin. Keratin is also the protein that protects epithelial cells from damage or stress.
- Collagen – Collagen is the main structural protein in the extracellular space in the various connective tissues in the body. As the main component of connective tissue, it is the most abundant protein in mammals, making 25% to 35% of the whole-body protein content.
- Fibroin- is an insoluble protein present in silk produced by the larvae of Bombyx mori, other moth genera such as Antheraea, Cricula, Samia and Gonometa, and numerous other insects.
- Elastin/Fibrillin- Fibrillin is a glycoprotein, which is essential for the formation of elastic fibers found in connective tissue. Fibrillin is secreted into the extracellular matrix by fibroblasts and becomes incorporated into the insoluble microfibrils, which appear to provide a scaffold for deposition of elastin.
- Lamin- Lamins, also known as nuclear lamins in type V intermediate filaments, are fibrous proteins providing structural function and transcriptional regulation in the cell nucleus. Nuclear lamins interact with inner nuclear membrane proteins to form the nuclear lamina on the interior of the nuclear envelope.
- Actin- Actin is a family of globular multi-functional proteins that form microfilaments. It is found in essentially all eukaryotic cells, where it may be present at a concentration of over 100 μM; its mass is roughly 42-kDa, with a diameter of 4 to 7 nm.
- Tubulin- Tubulin in molecular biology can refer either to the tubulin protein superfamily of globular proteins, or one of the member proteins of that superfamily. α- and β-tubulins polymerize into microtubules, a major component of the eukaryotic cytoskeleton.
- Actin is a family of globular multi-functional proteins that form microfilaments. It is found in essentially all eukaryotic cells, where it may be present at a concentration of over 100 μM; its mass is roughly 42-kDa, with a diameter of 4 to 7 nm.
- An antibody, also known as an immunoglobulin, is a large, Y-shaped protein produced mainly by plasma cells that is used by the immune system to neutralize pathogens such as pathogenic bacteria and viruses.
- Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as transfer RNA or small nuclear RNA genes, the product is a functional RNA.
- Catalysis is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst, which is not consumed in the catalyzed reaction and can continue to act repeatedly. Because of this, only very small amounts of catalyst are required to alter the reaction rate in principle.
- Hemoglobin or haemoglobin, abbreviated Hb or Hgb, is the iron-containing oxygen-transport metalloprotein in the red blood cells of almost all vertebrates as well as the tissues of some invertebrates. Hemoglobin in blood carries oxygen from the lungs or gills to the rest of the body.
- Myoglobin is an iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals. It is distantly related to hemoglobin which is the iron- and oxygen-binding protein in blood, specifically in the red blood cells.
- Carbohydrates are often classified according to the number of saccharide units they contain. A monosaccharide contains a single carbohydrate, over 200 different monosaccharides are known.
- Polysaccharides are polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages, and on hydrolysis give the constituent monosaccharides or oligosaccharides. They range in structure from linear to highly branched.
- Glyceraldehyde is a triose monosaccharide with chemical formula C₃H₆O₃. It is the simplest of all common aldoses. It is a sweet, colorless, crystalline solid that is an intermediate compound in carbohydrate metabolism.
- Glucose is a simple sugar with the molecular formula C₆H₁₂O₆. Glucose is the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and most algae during photosynthesis from water and carbon dioxide, using energy from sunlight.
- an epimer is one of a pair of stereoisomers. The two isomers differ in configuration at only one stereogenic center. All other stereocenters in the molecules are the same in each. Doxorubicin and epirubicin are two epimers that are used as drugs.
- A furanose is a collective term for carbohydrates that have a chemical structure that includes a five-membered ring system consisting of four carbon atoms and one oxygen atom. The name derives from its similarity to the oxygen heterocycle furan, but the furanose ring does not have double bonds.
- Pyranose is a collective term for saccharides that have a chemical structure that includes a six-membered ring consisting of five carbon atoms and one oxygen atom. There may be other carbons external to the ring.
- Glycosaminoglycans or mucopolysaccharides are long linear polysaccharides consisting of repeating disaccharide units. The repeating unit consists of an amino sugar along with a uronic sugar or galactose.
- Proteins attached to oligosaccharides or polysaccharides
- Glycoproteins are proteins which contain oligosaccharide chains covalently attached to amino acid side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as glycosylation. Secreted extracellular proteins are often glycosylated.
- Peptidoglycan is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall. The sugar component consists of alternating residues of β- linked N-acetylglucosamine and N-acetylmuramic acid.
- Proteoglycans are proteins that are heavily glycosylated. The basic proteoglycan unit consists of a “core protein” with one or more covalently attached glycosaminoglycan chain. The point of attachment is a serine residue to which the glycosaminoglycan is joined through a tetrasaccharide bridge.
- Proteins attached to glycosaminoglycan
- Lipids can be more formally defined as substances such as a fat, oil or wax that dissolves in alcohol but not in water. Lipids contain carbon, hydrogen and oxygen but have far less oxygen proportionally than carbohydrates. Lipids are an important part of living cells.
- a fatty acid is a carboxylic acid with a long aliphatic chain, which is either saturated or unsaturated. Most naturally occurring fatty acids have an unbranched chain of an even number of carbon atoms, from 4 to 28.
- Glycerolipids are a structurally heterogeneous group of lipids that play key structural and functional roles in bacterial, plant, and animal membranes. They all have at least one hydrophobic chain linked to a glycerol backbone in an ester or ether linkage.
- Glycerophospholipids or phosphoglycerides are glycerol-based phospholipids. They are the main component of biological membranes.
- Sphingolipids are a class of lipids containing a backbone of sphingoid bases, a set of aliphatic amino alcohols that includes sphingosine. They were discovered in brain extracts in the 1870s and were named after the mythological sphinx because of their enigmatic nature.
- are a large group of secondary metabolites which either contain alternating carbonyl and methylene groups (-CO-CH2-), or are derived from precursors which contain such alternating groups. Many polyketides have antimicrobial and immunosuppressive properties. Many mycotoxins produced by fungi are polyketides.
- any of a class of organic compounds composed of two or more units of hydrocarbons, with each unit consisting of five carbon atoms arranged in a specific pattern. Isoprenoids play widely varying roles in the physiological processes of plants and animals.
- Sterols, also known as steroid alcohols, are a subgroup of the steroids and an important class of organic molecules. They occur naturally in plants, animals, and fungi, and can be also produced by some bacteria (however likely with different functions).
- is a steroid that acts as a hormone. Steroid hormones can be grouped into two classes: corticosteroids and sex steroids. Within those two classes are five types according to the receptors to which they bind: glucocorticoids, mineralocorticoids, androgens, estrogens, and progestogens.
- Active in Immune System
- produced by the adrenal gland and known particularly for its anti-inflammatory and immunosuppressive actions. The adrenal gland is an organ situated on top of the kidney. It consists of an outer cortex (adrenal cortex) and an inner medulla (adrenal medulla).
- An androgen is any natural or synthetic steroid hormone that regulates the development and maintenance of male characteristics in vertebrates by binding to androgen receptors.
- Female Sex Hormones
- Estrogens are hormones that are important for sexual and reproductive development, mainly in women. They are also referred to as female sex hormones. The term “estrogen” refers to all of the chemically similar hormones in this group, which are estrone, estradiol (primary in women of reproductive age) and estriol.
- also sometimes written progestagens or gestagens, are a class of steroid hormones that bind to and activate the progesterone receptor (PR). Progesterone is the major and most important progestogen in the body.
- The prostaglandins (PG) are a group of physiologically active lipid compounds called eicosanoids having diverse hormone-like effects in animals. Prostaglandins have been found in almost every tissue in humans and other animals. They are derived enzymatically from the fatty acid arachidonic acid.
- Thromboxane is a member of the family of lipids known as eicosanoids. The two major thromboxanes are thromboxane A2 and thromboxane B2. The distinguishing feature of thromboxanes is a 6-membered ether-containing ring. Thromboxane is named for its role in clot formation.
- Leukotrienes are a family of eicosanoid inflammatory mediators produced in leukocytes by the oxidation of arachidonic acid and the essential fatty acid eicosapentaenoic acid by the enzyme arachidonate 5-lipoxygenase.
- Vitamin D is a group of fat-soluble secosteroids responsible for increasing intestinal absorption of calcium, magnesium, and phosphate, and multiple other biological effects. In humans, the most important compounds in this group are vitamin D₃ and vitamin D₂.
- Vitamin E is a group of eight fat soluble compounds that include four tocopherols and four tocotrienols. Vitamin E deficiency, which is rare and usually due to an underlying problem with digesting dietary fat rather than from a diet low in vitamin E, can cause nerve problems.
- Vitamin K is a group of structurally similar, fat-soluble vitamins found in foods and in dietary supplements. The human body requires vitamin K for complete synthesis of certain proteins that are needed for blood coagulation or for controlling binding of calcium in bones and other tissues.
- A prokaryote is a unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle. The word prokaryote Prokaryotes are divided into two domains, Archaea and Bacteria.
- It defines the boundary of cells/organelles
- The lipid bilayer is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells.
- Ion channels are protein molecules that span across the cell membrane allowing the passage of ions from one side of the membrane to the other. They have an aqueous pore, which becomes accessible to ions after a conformational change in the protein structure that causes the ion channel to open.
- An ionophore is a chemical species that reversibly binds ions. Many ionophores are lipid-soluble entities that transport ions across a cell membrane.
- A deoxyribonucleotide is the monomer, or single unit, of DNA, or deoxyribonucleic acid. Each deoxyribonucleotide comprises three parts: a nitrogenous base, a deoxyribose sugar, and one phosphate group.
- a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. The monomer itself from ribonucleotides forms the basic building blocks for RNA.
- The genetic code is the set of rules used by living cells to translate information encoded within genetic material into proteins.
- Ribosomes comprise a complex macromolecular machine, found within all living cells, that serves as the site of biological protein synthesis. Ribosomes link amino acids together in the order specified by messenger RNA molecules.
Gibbs Free Energy
- the Gibbs free energy is a thermodynamic potential that can be used to calculate the maximum of reversible work that may be performed by a thermodynamic system at a constant temperature and pressure.
- Metabolism is a term that is used to describe all chemical reactions involved in maintaining the living state of the cells and the organism. Metabolism can be conveniently divided into two categories:
- Catabolism – the breakdown of molecules to obtain energy
- Anabolism – the synthesis of all compounds needed by the cells
- Metabolism is closely linked to nutrition and the availability of nutrients. Bioenergetics is a term which describes the biochemical or metabolic pathways by which the cell ultimately obtains energy. Energy formation is one of the vital components of metabolism.
- A number of molecules can act as electron carriers in biological systems. In cellular respiration, there are two important electron carriers, nicotinamide adenine dinucleotide (abbreviated as NAD+ in its oxidized form) and flavin adenine dinucleotide (abbreviated as FAD in its oxidized form).
- Allosterism describes the change in the affinity for binding of a ligand or substrate that is caused by the binding of another ligand away from the active site (allosteric = other site)
- Phosphorylation is the chemical addition of a phosphoryl group (PO3-) to an organic molecule. The removal of a phosphoryl group is called dephosphorylation. Both phosphorylation and dephosphorylation are carried out by enzymes (e.g., kinases, phosphotransferases).
- Dephosphorylation is the removal of a phosphate (PO43−) group from an organic compound by hydrolysis. It is a reversible post-translational modification. Dephosphorylation and its counterpart, phosphorylation, activate and deactivate enzymes by detaching or attaching phosphoric esters and anhydrides.