Biochemistry Revision PDF - Top Edu Academy

Top Edu Academy Biochemistry Safa Albaba Revision Amino Acids - Amino acids are the building blocks of proteins - Amino acid structure is an alpha carbon attached to 4 groups: am...

Top Edu Academy Biochemistry Safa Albaba Revision Amino Acids - Amino acids are the building blocks of proteins - Amino acid structure is an alpha carbon attached to 4 groups: amino group (-NH2), carboxylic group (-COOH), hydrogen atom, and R-group (side chain). - The R-group is what makes each amino acid different than other amino acids. - Amino acids are classified according to 3 classifications: 1- Chemical classification Neutral Amino Acids Acidic Basic Aliphatic Hydroxy Aromatic Sulfur Heterocyclic AA AA Glycine Serine Phenylalanine Cysteine Histidine Aspartate Ornithine Alanine Threonine Tyrosine Cystine Tryptophan Glutamate Citrulline Valine Tyrosine Tryptophan Methionine Proline Arginine Leucine Hydroxyproline Hydroxyproline Lysine Isoleucine Hydroxylysine Hydroxylysine 2- Metabolic classification Glucogenic Mixed Ketogenic Lysine Isoleucine Rest of Amino Acids Tyrosine Leucine Tryptophan Phenyl alanine 3- Biological classification Valine Isoleucine Threonine Tryptophan Arginine Leucine Lysine Methionine Phenylalanine Histidine - VITTAL LyMPH are indispensable or essential amino acids. - Arginine and histidine are semi essential. - The rest are dispensable or nonessential. - Proline and hydroxyproline have imino group instead of amino groups. - All amino acids in the protein structure are α-amino acids, L-amino acids, and optically active. - The only optically inactive amino acid is glycine because its’ R-group is hydrogen. - The pH at which a protein carries no net electrical charge is called its isoelectric point. 1 Top Edu Academy Biochemistry Safa Albaba Proteins ‫الترتيب مهم‬ - Glutathione is a tripeptide formed of 3 amino acids: γ-glutamic acid, cysteine, and glycine. - Bonds that form protein structure are (strong and weak) and (primary and secondary) - Peptide bonds (primary strong) are formed by a reaction between an amino group of one amino acid and a carboxylic group of the next one. It yields H2O. C-N - Disulfide bonds (secondary strong) are formed between 2 cysteine (NOT cystine) residues. It connects 2 polypeptide chains together. - Hydrogen bonds (secondary weak) are formed between the hydrogen atom of –NH of one peptide chain and oxygen of CO- the adjacent peptide chain. O-H - Hydrophobic bonds (secondary weak) are formed by the non-polar side chains of neutral amino acids. - Electrostatic bonds (secondary weak) are salt bonds formed between oppositely charged groups in the side chains of amino acids. (also called ionic or salt bond) - The strongest bond is the peptide bond. - Protein Structure: Structure Description Bonds Structure Formed Primary Amino acid sequence Peptide bonds Polypeptide chain Hydrogen bonds Interaction between Alpha helices Secondary Ionic bonds close amino acids Beta pleated sheets Disulfide bonds Hydrophobic bonds Globular protein Interaction between Tertiary Electrostatic bonds Fibrous protein far amino acids Van der Waals forces (3D) Hydrophobic bonds Dimeric protein Quaternary Multiple polypeptides Electrostatic bonds Trimeric protein Van der Waals forces Multimeric protein - Primary structure is amino acids linked by peptide bonds forming a chain. Its determined by DNA. - Secondary structure is fine folding of that chain. - Tertiary structure is course folding and super folding forming native protein or domains. - Quaternary structure is multiple protein subunits: dimeric, trimeric, and multimeric. Ex. Hemoglobin and lactate dehydrogenase. - An example of a genetic disease related to primary protein structure is Sickle Cell Anemia where the normal glutamic acid at position 6 of the β-chains is replaced by valine. - Diseases caused by protein misfolding are called amyloid disease, Alzheimer is an example. - Protein denaturation results in the unfolding and disorganization of a protein’s higher structures without the hydrolysis of peptide bonds. Primary structure is not changed. - An application of denaturation is cooking and heat coagulation test. - Breaking down of a protein into amino acids is called hydrolysis, the primary structure is broken down. - Next page is about protein classification 2 Top Edu Academy Biochemistry Safa Albaba Classification Types Notes contain all the 10 essential amino acids Nutritional High Biological Value and are easily digestible Value Low Biological Value deficient in one or more of the essential amino acids or are indigestible Fibrous: water insoluble Keratin, collagen, myosin *** Axial Ratio Globular: water soluble albumin, globulin & myoglobin *** Albumins - Globulins - Histones - Simple: only give hair, nails, and superficial layer of skin, Keratins wool, horns amino acids on White fibers of connective tissues are Scleroproteins Collagens present in skin, bones, teeth, tendons, hydrolysis and blood vessels Or yellow fibers of connective tissues present Albuminoids Elastin in lungs, uterine walls, tendons, big arteries Composition Reticulines spleen, liver & lymph gland Phosphoproteins Casein or milk protein Lipoproteins Plasma lipoproteins (LDL, HDL) Glycoproteins Mucus, saliva Conjugated Metalloproteins Transferrin Chromoproteins Hemoglobin Nucleoproteins Chromosomes Catalytic Enzymes Structural collagen, elastin& keratin Contractile myosin, actin & flagellar proteins Function Transport hemoglobin, albumin & transferrin Regulatory insulin & growth hormone Genetic histones Protective immunoglobulins& clotting factor - Peptide is less than 50 amino acids while protein is more than 50 amino acids. 3 Top Edu Academy Biochemistry Safa Albaba Carbohydrates - Carbohydrates are the most abundant biomolecules. They are classified according to the number of sugar subunits they consist of monosaccharides (simple sugars), disaccharides (2), oligosaccharides (3-10), and polysaccharides (more than 10). - The asymmetric carbon (chiral carbon) gives monosaccharides 2 properties: optical activity and isomerism. - Isomers: 1- Enantiomers (D and L): mirror images. Ex. D-glucose and L-glucose. 2- Anomers (α and β): different distribution of H and OH group around the asymmetric anomeric carbon atom C1 in aldoses or C2 in ketoses after cyclization of the molecule, e.g., α- and β- glucose are anomers 3- Epimers: different distribution of H and OH groups around a single asymmetric carbon atom. Ribose is an epimer for each of arabinose and xylose. Glucose is an epimer for each mannose (C2) and galactose. - Monosaccharides: Classified according to the number of C atoms into trioses, tetroses, pentoses, & hexoses. Classified according to the type of carbonyl group into aldoses & ketoses. Aldotrioses Glyceraldehyde Ketotrioses Dihydroxyacetone Aldotetroses Erythrose & threose Ketotetroses Erythrulose Aldopentoses Ribose, arabinose, & xylose Ketopentoses Ribulose & xylulose Aldohexoses Glucose, galactose, & mannose ketohexoses Fructose - Glucose is blood sugar; it is called dextrose because it is dextrorotatory. - Fructose is found in fruits and honey, it is called levulose because it is levorotatory. - Dihydroxyacetone is the only carbohydrate which does not have any chiral carbon atoms. - RNA has ribose. - Monosaccharides reactions: Reaction yields reagent Example Strong reagent: bromine Aldonic acids water Glucose to gluconic acid Moderate reagent: diluted Uronic acids Oxidation Sugar acids HNO3 or H2O2 Glucose to glucuronic acid Strong reagent: concentrated Aldaric acids HNO3 Glucose to glucaric acid Glucose to sorbitol Sugar Fructose to mannitol and sorbitol Reduction - alcohols Galactose to dulcitol Ribose to ribitol Removing Deoxy Ribose to deoxyribose - oxygen sugars L-galactose to L-fucose Adding sugar Glucosamine - amines amines Hyaluronic acid 4 Top Edu Academy Biochemistry Safa Albaba - Disaccharides Maltose Reducing Isomaltose Disaccharides Lactose Non reducing Sucrose - Polysaccharides 5