Dr. Madushani Silva (MBBS) North Colombo Teaching Hospital – Ragama

Biochemistry Chemistry of living organisms. The study of biology at the molecular level.

Biochemistry has become the foundation for understanding all biological processes. It has provided explanations for the causes of many diseases in humans, animals and plants 3

What is Biochemistry ? Biochemistry is the application of chemistry to the study of biological processes at the cellular and molecular level. A. Studying the structure and behavior of the complex molecules found in biological material and B. the ways these molecules interact to form cells, tissues and whole organism 4

Elements Make up all matter. 92 occur in nature. Identified by names or chemical symbols (abbreviations of modern or Latin names). Identified by number (based on structure of subunits or atoms). Described and organized in periodic table.

Periodic Table

Molecules and Compounds Molecules Formed when two or more atoms unite on the basis of their electron structures Can be made of like atoms or atoms of different elements Compounds Composed of two or more elements

8 Many Important Biomolecules are Polymers Biopolymers - macromolecules created by joining many smaller organic molecules (monomers) Condensation reactions join monomers (H 2 O is removed in the process)

9 Linking Monomers Cells link monomers by a process called dehydration synthesis (removing a molecule of water) This process joins two sugar monomers to make a double sugar Remove H Remove OH H 2 O Forms

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11 Breaking Down Polymers Cells break down macromolecules by a process called hydrolysis (adding a molecule of water) Water added to split a double sugar

Molecular Organisation of a cell 12

13 Water Water is used in most reactions in the body Water is called the universal solvent About percent of an organism is water

Biomolecules Carbohydrates Lipids Proteins Nucleic acid

15 Biomolecules – Structure Building block Simple sugar Amino acid Nucleotide Fatty acid Macromolecule Polysaccharide Protein (peptide) RNA or DNA Lipid Anabolic Catabolic

Sugars Carbohydrates most abundant organic molecule found in nature. Initially synthesized in plants from a complex series of reactions involving photosynthesis. Basic unit is monosaccharides. Monosaccharides can form larger molecules e.g. glycogen, plant starch or cellulose. 16

Functions Store energy in the form of starch (photosynthesis in plants) or glycogen (in animals and humans). Provide energy through metabolism pathways and cycles. Supply carbon for synthesis of other compounds. Form structural components in cells and tissues. Intercellular communications 17

Carbohydrates Composed of carbon, hydrogen, and oxygen. Sugars Monosaccharides Ex. Glucose Disaccharides Ex. Sucrose Polysaccharides Ex. Glycogen, Peptidoglycan

Carbohydrate - Glucose

Carbohydrate - Sucrose

21 Monosaccharides -Polysaccharides Glycosidic bonds connecting glucose residues are in red Glucose - Cellulose

Carbohydrate - Peptidoglycan

Carbohydrate - Glycogen

Fatty acids - Lipids Are monocarboxylic acid contains even number C atoms Two types: saturated (C-C sb) and unsaturated (C-C db) Fatty acids are components of several lipid molecules. E,g. of lipids are triacylglycerol, steriods (cholestrol, sex hormones), fat soluble vitamins. Functions Storage of energy in the form of fat Membrane structures Insulation (thermal blanket) Synthesis of hormones 24

Lipids Fatty Acids The building blocks of lipids. biology.clc.uc.edu courses.cm.utexas.edu

26 Triglyceride Glycerol Fatty Acid Chains

Lipids Examples are: Waxes Fats and oils Phospholipids Steroids Phospholipid Cell Membrane.

28 Structure of a biological membrane A lipid bilayer with associated proteins

29 Steroids The carbon skeleton of steroids is bent to form 4 fused rings Cholesterol is the “base steroid” from which your body produces other steroids Estrogen & testosterone are also steroids Cholesterol Testosterone Estrogen Synthetic Anabolic Steroids are variants of testosterone

Proteins Made up of polymers of amino acids. “beads on a string.” 20 primary amino acids exist. A polymer of 3 or more amino acids forms a polypeptide.

Amino acids - Proteins: Amino acids: Building blocks of proteins. R Group (side chains) determines the chemical properties of each amino acids. Also determines how the protein folds and its biological function. Functions as transport proteins, structural proteins, enzymes, antibodies, cell receptors. 31

Proteins Primary Structure Linear sequence of amino acids. Secondary Structure Form helices or sheets due to their structure. Tertiary Structure A folded protein. Quaternary Structure 2 or more polypeptide chains bonded together.

Protein Structure

34 Proteins as Enzymes Many proteins act as biological catalysts or enzymes Thousands of different enzymes exist in the body Enzymes control the rate of chemical reactions by weakening bonds, thus lowering the amount of activation energy needed for the reaction -> Catalysator -> No not interfere with the equilibrium of reaction -> Enzymes are reusable !!!!

Enzymes Are proteins. Are considered biological catalysts. Speed up a chemical reaction without being altered. Names often end in “- ase.” Ex. Lipase, carbohydrase. Act on a substrate. Proteins, including enzymes, can be denatured.

36 Enzymes: Active site - a cleft or groove in an enzyme that binds the substrates of a reaction Egg white lysozyme The nature and arrangement of amino acids in the active site make it specific for only one type of substrate. (accepts just one enaniomer)

Nucleic Acids DNA and RNA. (DNA - deoxyribonucleic acid, RNA - ribonucleic acid). Is the “hereditary molecule.” Contains genes that code for a certain product. DNA is translated into RNA which is used to produce a protein or other product.

Nucleic Acid Structure DNA nucleotides Building blocks of DNA. RNA nucleotides Building blocks of RNA.

Nucleic Acid Structure DNA Nitrogenous base Deoxyribose Phosphate group RNA Nitrogenous base Ribose Phosphate group

Nitrogenous Bases Adenine (A) Guanine (G) Cytosine (C) Thymine (T) – only DNA Uracil (U) – only RNA DNA and RNA

Nitrogenous Bases A and G Purines (double- ring structures) C, T, and U Pyrimidines (single-ring structures) hyperphysics.phy-astr.gsu.edu

DNA Structure Nucleotides bond between sugar and phosphate groups to form long polymers. Double-stranded DNA - The two nucleotide polymers bind at the nitrogenous bases. Bonding forces cause the double-stranded polymer to form a double helix.

DNA Structure James Watson (left) and Francis Crick (right) discovered the double-helix structure of DNA and its process of replication in the 1950s.

DNA Replication Occurs during cell division. Both strands of the double-helix unwind and replicate a complimentary strand. The parent strand and new daughter strand form a new double-helix. DNA polymerase is one enzyme used in replication process.

45 Macromolecules

46 Macromolecules

47 Life needs 3 things : (1) ENERGY, which it must know how to: Extract Transform Utilize

Glycolysis: the preferred way for the formation of ATP 48

49 Life needs (2) SIMPLE MOLECULES, which it must know how to: Convert Polymerize Degrade

50 Life needs (3) CHEMICAL MECHANISMS, to: Harness energy Drive sequential chemical reactions Synthesize & degrade macromolecules Maintain a dynamic steady state Self-assemble complex structures Replicate accurately & efficiently Maintain biochemical “order” vs outside

51 Trick : Life uses enzymes to speed up otherwise slow reactions

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Biochemical Reactions Metabolism: total sum of the chemical reaction happening in a living organism (highly coordinated and purposeful activity) a. Anabolism- energy requiring biosynthetic pathways b. Catabolism- degradation of fuel molecules and the production of energy for cellular function All reactions are catalyzed by enzymes The primary functions of metabolism are: a. acquisition & utilization of energy b. Synthesis of molecules needed for cell structure and functioning (i.e. proteins, nucleic acids, lipids, & CHO c. Removal of waste products 53

Even though thousands of pathways sound very large and complex in a tiny cell: The types of pathways are small Mechanisms of biochemical pathways are simple Reactions of central importance (for energy production & synthesis and degradation of major cell components) are relatively few in number 54

Energy for Cells Living cells are inherently unstable. Constant flow of energy prevents them from becoming disorganized. Cells obtains energy mainly by the oxidation of bio- molecules (e- transferred from 1 molecule to another and in doing so they lose energy) This energy captured by cells & used to maintain highly organized cellular structure and functions 55