Biochemistry 1 PDF

Introduction to By Prof. Moushira AbdelWahab The Basics of life: Chemistry ILOs: By the end of this lecture student should be able to Define Biochemistry Enumerate essential elements in the human body. Identify the major macromolecules in living cells. Describe structur...

Introduction to By Prof. Moushira AbdelWahab The Basics of life: Chemistry ILOs: By the end of this lecture student should be able to Define Biochemistry Enumerate essential elements in the human body. Identify the major macromolecules in living cells. Describe structure and properties of water. Define metabolism and recognize its types. Recognize the structure of ATP; the cellular energy currency. Recognize the function of ATP. Discuss the two levels for sources for ATP synthesis. What is Biochemistry? The chemistry of life Biochemistry: study of living organisms at the molecular level Molecules are Made of Atoms (Elements) The 13 essential elements for life C Carbon 6 Na Sodium 11 H Hydrogen 1 K Potassium 19 O Oxygen 8 Ca Calcium 20 N Nitrogen 7 Mg Magnesium 12 P Phosphorus 15 Cl Chlorine 17 S Sulfur 16 Fe Iron 26 I Iodine 53 Main elements of life C, H, O, N, P, S  Make up two important classes of molecules  Water: the most abundant compound in your body  Macromolecules: the structures of the giant molecules of biology.  These elements make up about 97.5% of body weight  Carbon is the central atom of organic chemistry and biochemistry Na, K, Ca, Mg, Cl, Fe, I  Usually form small, water-soluble molecules which tend to form ions in solution  Single atom of iron, copper, magnesium for some proteins  They make up almost 2.5% of the body weight  Macromolecules Living cells include very large molecules, called macromolecules. There are 4 main macromolecules in human body. 1. Proteins 2. Lipids 3. Carbohydrates 4. Nucleic acids These macromolecules are polymers; they are derived from monomers Polymers Monomers Carbohydrates Monosaccharide Proteins Amino acids Nucleic acids Nucleotides Lipids Fatty acids Common theme:  Monomers form polymers through condensations  Polymers are broken down through hydrolysis. Water: The Medium for Life  Water Water forms 50 to 95% of most organisms. Water molecule is composed of two atoms of hydrogen and one atom of oxygen (H2O). Each hydrogen atom is linked to oxygen by a single covalent bond.  Water molecules are dipoles The sharing of electrones in oxygen-hydrogen bond is + H unequal and result in 2- asymmetrical distribuation of O electrones (polar covalent bond) Oxygen is more electronegative than hydrogen H + H bonding between 1 water molecules 3 2 4 Properties of H2O Thermal Properties of H2O The maximum No of H bonds are 4 (ice), on warming to melting Temp ~ 15% of the H bonds break, on boiling water molecules are free from one anther and vaporize.  Thermal Properties of H2O Water is liquid over most of the range of temperature found on the earth’s surface, it melts at 0 ºC and boils at 100 ºC.  Solvent Properties of H2O The dipolar structure of water allows it to be the best solvent Ionic compounds (e.g., KCl) and polar covalent compound (e.g., C2H5OH) tend to dissolve in water The underlying principle is electrostatic attraction of unlike charges; the positive dipole of water for the negative dipole of another molecule, etc. Solvent Properties of H2O Hydrophilic: water-loving tend to dissolve in water Hydrophobic: water-fearing tend not to dissolve in water Amphipathic: molecules that have both hydrophobic and hydrophilic regions, e.g., sodium palmitate METABOLISM  metabolism is the term that involves all chemical reactions that occur to various foodstuffs inside the body. It includes processes of: 1. “Anabolism" or building up 2. “Catabolism" or breakdown ANABOLISM (Building Up) (Synthetic Pathway) Those biochemical processes (or metabolic pathways) that aim to build up molecules contributing to body structure & function. Anabolism and Catabolism Anabolism encompasses the biosynthetic and energy requiring reactions. In general, the reactions of anabolic pathways are reductive and consume reducing potential and (energy) (ATP) Catabolic reactions are energy producing, are oxidative and produce reducing cofactors. 1 33 Catabolism (degradation) (breakdown) Those biochemical processes (or metabolic pathways) that aim to: 1. Extract energy from the foodstuffs. 2. Protect the body from toxic & useless compounds NOTES Foodstuffs catabolism  Energy  ATP ATP hydrolysis  Energy  Covalent bond “Energy Currency”. ATP is a nucleoside triphosphate containing adenine, ribose, and three phosphate groups. High-Energy Phosphates Are Designated by ~P instead the usual Standard free energy of hydrolysis of some organophosphates of biochemical importance Compound ∆G (kcal/mol) Phosphoenolpyruvate −14.8 Carbamoyl phosphate −12.3 1,3-Bisphosphoglycerate (to 3-phosphoglycerate) −11.8 Creatine phosphate −10.3 ATP →ADP + Pi −7.3 ADP →AMP + Pi −6.6 Pyrophosphate −6.6 Glucose 1-phosphate −5.0 Fructose 6-phosphate −3.8 AMP −3.4 Glucose 6-phosphate −3.3 Glycerol 3-phosphate −2.2 ATP synthesis at two main levels: 1. Substrate level phosphorylation 2. Oxidative Phosphorylation Substrate level phosphorylation RP + ADP  ATP + R Substrate level phosphorylation Substrate level phosphorylation ATP synthesis at two main levels: 1. Substrate level phosphorylation 2. Oxidative Phosphorylation (respiratory chain) A. NADH  2.5 ATP B. FADH2  1.5 ATP  RESPIRATORY CHAIN (RC) AND OXIDATIVE PHOSPHORYLATION Definition: Mitochondrial system that couples respiration to the generation of high-energy intermediate, ATP. Oxygen oxidizes the reducing equivalents (NADH & FADH). This generates free energy  Used for phosphorylation of ADP to give ATP MITOCHONDRIA IS CALLED “HOUSE OF ENERGY” Site: The components of RC are located in the inner mitochondrial membrane, near the enzymes of TCA cycle & other oxidizing enzymes that generate reduced equivalents. What will happen? Oxidation Of Hydrogen & Phosphorylation Of ADP: Hydrogen + Oxygen  Water + energy Energy + ADP + Pi  ATP Resources: 1-Lectures 2-Text Books : Lippincott’s illustrated reviews,Biochemistry Harper’s illustrated Biochemistry