Biochemistry Notes summary

« Biochimie 1.

Carbohydrates : - chemistry: monomers (monosaccharides) and polymers (polysaccharides) the chemical formula is approximately C (H O) n 2 n - biological functions of carbohydrates: source of energy, storage form of energy -> short term: glucose in blood; medium term: glycogen/starch (plants) structural function in plants (cellulose) and bacteria; in mammals: part of the extracellular matrix part of glycoproteins, glycolipids and nucleic acids (DNA and RNA) - classification of carbohydrates (based on chemical characteristics): monosaccharides: Aldoses: Ketoses: Pentoses: Ribose Ribulose Hexoses: Glucose Fructose Galactose Mannose 1.1 Monosaccharides: - aldehydes and ketones with multiple hydroxyl groups “carbon hydrate”, (C-H O) 2 n triose, tetrose, pentose, hexose, heptose… - structure of trioses : aldotrioses and ketotrioses are isomers the number of the C-atoms starts at the end carrying the aldehyde/keto group ex: glyceraldehyde has an asymmetric carbon -> 2 enantiomers are possible, the D-form and the L-form - isomers: compounds with the same chemical formula but different structural formula  Constitution isomers (structural isomers): same chemical formula, different structure (atoms bonded in a different way)  Stereoisomers: same structure, different arrangements of the substituents of bonds  Enantiomers: stereoisomers that behave like image and mirror-image (differences in all chiral centres)  Diastereomers: stereoisomers that don’t behave like image and mirror-image (e.g.: cis-trans-isomers at double bonds)  Epimers: pairs of diastereomers of a molecule with various chirality centres that differ only at one centre (e.g.: glucose, galactose)  Anomers (sugar chemistry): special case of epimers which differ at the first carbon atom (- and -form of a sugar) - D-aldoses containing 3, 4, 5 and 6 carbon atoms: the second last carbon atom determines if the sugar is in the D or L-form  D-erythrose: 1      D-ribose: D-xylose: D-glucose: D-mannose: D-galactose: - D-ketoses containing 3, 4,5 and 6 carbon atoms:  D-fructose: - pyranose formation: the open-chain form of glucose cyclizes when the C-5 hydroxyl group attacks the oxygen atom of the C-1 aldehyde group -> this forms an intramolecular hemiacetal 2 anomeric forms can result:  (36%) and  (64%) -> the change from one of those forms to the other is called a mutarotation schema: see worksheets - the six-membered pyranose-ring is not planar: its saturated carbon atoms have a tetrahedral geometry -> chair and boat form - glucose and its most important epimers: worksheets - fructose, a ketohexose: an intramolecular hemiketal is formed by the cyclization of the keto group and a hydroxyl group (analogous to the hemiacetal of aldoses) in the anomeric forms of D-fructofuranose, the -form is more abundant C-1 is bonded to 2 H-atoms and is not chiral - ring structure of fructose: it can form both five-membered furanose and six-membered pyranose rings -> in each case: both  and  anomers are possible - structure of important pentoses: see worksheets ketopentoses only occur as furanoses: they form hemiketals 1.2 Disaccharides: - they are formed of 2 monosaccharides - formation of the disaccharides lactose and sucrose: in any glycosidic linkage, the anomeric carbon of one sugar molecule (either the  or  conformation) is linked to a hydroxyl oxygen on another sugar molecule -> the linkages are named accordingly (e.g.: 14) - important disaccharides: see worksheets glucose + fructose -> sucrose galactose + glucose -> lactose glucose + glucose -> maltose - the anomeric C-atom with a free hydroxyl group is called the reducing end -> the carbonyl group can be oxidized to a carboxyl group (after opening of the ring) and therefore has a reducing effect - in sucrose: the anomeric carbons of both monosaccharide units are engaged in the -1,2linkage -> sucrose is not a reducing sugar 2 - glycosidic linkages: e.g.

the ribonucleoside guanosine, the gluconucleoside indican (precursor of the indigo dye) 1.3 Polysaccharides: - homopolysaccharides (only one type of monosaccharides) : unbranched or branched heteropolysaccharides: 2 monomer types unbranched or multiple monomer types branched - important homopolymers: glycogen (storage form of glucose in animal cells) starch (amylose and amylopectin, storage form of glucose in plants) cellulose a) Glycogen: - glycogen: storage form of glucose in muscle and liver -1,4-linked glucose residues, branches at every 10th residue are created by -1,6-glycosidic bonds regulation by hormones adjusts the glycogen metabolism - in the liver: glycogen synthesis and degradation are regulated to maintain blood-glucose levels as it is required to meet the needs of the whole organism in muscle, these processes are regulated to meet the energy needs of the muscle itself - branch point in glycogen: 2 chains of glucose molecules, joined by -1,4-glycosidic bonds, are linked by an -1,6-glycosidic bond -> this creates a branch point -> such an -1,6-glycosidic bond forms at approximately every 10 glucose units: thus glycogen is a highly branched molecule - to break up a glycosidic bond: a water molecule is required - “form follows function”: a glycogen particle is an optimized storage molecule easy access for degrading and synthetizing hormones tight package of glucose units - many free ends: enzymes can act on them -> speed of breakdown is very high b) Starch = amylose and amylopectin - more than half the carbohydrate ingested by human beings is starch - amylose: 20% long unbranched chains of D-glucose, connected by (14) linkages (as in maltose) approx.

200-300 glucose residues - amylopectin: 80% highly branched over 100 000 glucose residues 14 linked glucose residues branch points are 16 linkages, occurring every 24-30 residues c) Cellulose: - fibrous, tough, water-insoluble substance found in the cell wall of plants: e.g.

in stalks, stems, trunks and all the woody portions of the plant body -> it constitutes much of the mass of wood; cotton is almost pure cellulose 3 - linear, unbranched homopolysaccharide: it consists of 10 000 to 15 000 D-glucose units in -configuration - parallel cellulose chains form sheets with interchain hydrogen bonds stacks of these sheets are held together by hydrogen bonds and van der Waals interactions -> it is a highly cohesive structure: this gives cellulose fibres exceptional strength and makes them water insoluble (despite their hydrophilicity) - -1,4 linkages favour straight chains: these are optimal for structural purposes (e.g.

in cellulose) -1,4 linkages favour bent structures: theses are more suitable for storage (e.g.

in starch and glycogen) d) Chitin: - linear homopolysaccharide : it is composed of N-acetylglucosamine residues in (14) linkage the only chemical difference from cellulose is: the replacement of the hydroxyl group at C-2 with an acetylated amino group - chitin forms extended fibres, similar to those of cellulose like cellulose, it cannot be digested by vertebrates - it is the principle component of the hard exoskeletons of nearly a million species of arthropods (e.g.

insects, lobsters, crabs) - second most abundant polysaccharide in nature, next to cellulose (an estimated 1 billion tons of chitin are produced each year in the biosphere) 1.4 Modified monosaccharides - carbohydrates can be modified by the addition of substituents other than hydroxyl groups: such modified carbohydrates are often expressed on cell surfaces e.g.

-L-Fucose, -D-acetylgalactosamine, -D-acetylglucosamine, sialic acid (Nacetylneuraminate) a) Extracellular matrix: - mainly proteins (like collagen) and proteoglycans - proteoglycans: core protein, bound covalently to long unbranched polysaccharides bottlebrush model of the proteoglycan (like a branch of a pine tree) -> numerous core proteins are non-covalently linked to the central hyalyronate strand - glycosaminoglycans (GAG, or mucopolysaccharides): repetitive disaccharide units composed of an amino sugar (N-acetyl-glucosamine or Nactetyl-galactosamine) and typically a uronic acid sulphate groups are introduced after polymerisation -> high negative charge density - 4 main types of GAG:  Hyaluronic acid  Chondroitin and dermatan sulphate  Keratan sulphate  Heparan sulphate (heparin: no component of the connective tissue; occurs in the intracellular granules of mast cells) - repeating units in glycosaminoglycans: there is a great variety of modifications and linkages that are possible 4 - the general structure of glycosaminoglycans: e.g.

chondroitin sulphate 1 glucoronic acid linked to a N-acetylgalactosamin-6-sulphate (repetitive) - synthesis of the GAG at the core protein : the trisaccharide unit xylose, galactose and galactose links the repetitive disaccharides to the core protein - gels composed of GAG: the application of pressure on cartilage squeezes water away from the charged regions of its proteoglycans : until charge-charge repulsions prevent further compression -> high resilience - glycocalix: thick (up to 1 400 units) carbohydrate coat it consists of closely packed oligosaccharides attached to cell-surface proteins and lipids - glycosidic bonds between proteins and carbohydrates:  O-linked: linkage through an oxygen atom (Ser, Thr)  N-linked: linkage through an azote atom (Asn) 2.

Lipids a) Common characteristics: - hydrophobicity: lipids are not well soluble in water -> they are well soluble in organic solvents: chloroform, benzol, ether… Biological functions of lipids: - storage of energy, in particular in the adipose tissue - thermal insulation, pressure padding - main component of biological membranes - signalling molecules: hormones, second messengers - bile salts: solubilisation of lipophilic substances during digestion - electrical insulation: central and peripheral nervous system Classification based on chemical characteristics: - complex lipids (can be hydrolysed): .... »