Biochemistry of Life PDF

Introduction to Biochemistry The Macromolecules of Life __________ CASE – Biology Department  OBJECTIVES At the end of the lesson, you can: ❑ explain how chemistry enriches the understanding of the biological system; ❑ relate basic ideas on how molecules be...

Introduction to Biochemistry The Macromolecules of Life __________ CASE – Biology Department  OBJECTIVES At the end of the lesson, you can: ❑ explain how chemistry enriches the understanding of the biological system; ❑ relate basic ideas on how molecules behave to how the biological system functions; and, ❑ Define the major macromolecules that its importance in living organisms What is Bio & Chemistry Branch of Science CONCERNED WITH Chemistry Biology THE CHEMICAL AND identification of the PHYSICOCHEMICAL substances of which study of PROCESSES AND matter is composed SUBSTANCES THAT living things OCCUR WITHIN (interaction, combination and LIVING ORGANISMS change)  Biochemistry Life’s origin may be explained chemically. With the idea of the Big Bang, we had established the formation of elements and, later on, common gases like water, carbon dioxide, ammonia, methane, etc. These gases occupied the primitive Earth which were A series of chemical reactions would form the necessary believed to be the monomers of biomolecules from simple precursors. Image Source: Campbell & Farrell. Biochemistry, 7th ingredients needed to form Edition. p.7 biomolecules. Models of Atomic Structure Three Types of Bonding Covalent Bonds and Polarity Covalent bonds: – Form between atoms that share electrons rather than donating or receiving them – Single covalent bonds share a pair of electrons (H2) – Double covalent bonds share two pairs of electrons and are more rigid than single bonds (O2) Covalent Bonds and Polarity Polar molecule: – Results when a molecule is formed between two atoms that have different electronegativity, or ability to attract electrons Nonpolar molecule: – Molecules formed when atoms have similar electronegativity Ionic Bonds: Electron Transfer Ionic bonds: – Formed when electrons are transferred completely from one atom to another and are not shared Ionization: Formation of Charged Particles Ionization: – The formation of charged particles when a molecule formed by ionic bonds dissolves in a solvent ❖Cations: positively charged ions ❖Anions: negatively charged ions ❖Electrolytes: substances such as salts, acids, and bases that release ions when dissolved in water Ionization Hydrogen Bonding Hydrogen bonds: – Formed due to attractive forces between nearby atoms or molecules – A weak type of bond that forms between a hydrogen covalently bonded to one molecule and an oxygen or nitrogen atom on the same molecule or on a different molecule – This bond is temporary and easily disrupted van der Waals forces: – Weak attractions between molecules that show polarity – Neighboring groups with slight attractions will interact and remain associated Hydrogen Bonding in Water Chemical Reactions Synthesis reaction: – Reactants bond together in a manner that produces an entirely new molecule S + O 2 → SO 2 Decomposition reaction: – Bonds on a single reactant molecule are permanently broken to release two or more product molecules 2H 2O 2 → 2H 2O + O 2 Chemical Reactions Exchange reactions: – Reactants trade portions with each other and release products that are combinations of the two AB + XY ⇄ AX + BY Catalysts: – Substances that increase the rate of a reaction without being consumed in the process – Enzymes are catalysts in cells Solutions Hydrophilic: – Molecules such as salt or sugar that attract water to their surface Hydrophobic: – Nonpolar molecules such as benzene that repel water Amphipathic: – Molecules such as phospholipids that have both hydrophilic and hydrophobic properties Acidity, Alkalinity, and the pH Scale Hydrogen Ion and Hydroxide Ion Acidic solution: Concentrations at a Given pH – Occurs when a component dissolved in water releases excess hydrogen ions (H+) Basic solution: – Occurs when a component dissolved in water releases excess hydroxyl ions (OH−) The pH Scale The Chemistry of Carbon Inorganic chemicals: – Molecules that do not contain both carbon and hydrogen – NaCl – Mg3(PO4)2 – CaCO3 – CO2 Organic chemicals: – Molecules with a basic framework of the element of carbon bonded to other atoms – Simplest: CH4 – Complex: antibody molecules with a molecular weight of 1,000,000 The Chemistry of Carbon Carbon is the fundamental element of life: – Ideal atomic building block to form the backbone of organic molecules – Four electrons in outer orbital can be shared with four other atoms, including other carbons  Biochemistry: Chemical Foundations The Wonders of CARBON C C C C This Photo by Unknown Author is licensed under CC BY-SA  Representative Functional Groups and Functional Groups Classes of Organic Compounds Molecular groups or accessory molecules that bind to organic compounds – Help define the chemical class of organic compounds – Confer unique reactive properties on the whole molecule – Reactions of an organic compound can be predicted by knowing its functional group  Looking at the Biochemistry: logic of the living system Life observes levels of Atoms and molecules as organization. fundamental F1 building blocks Thi s Photo by Unknown Author i s l icensed under CC BY-ND Thi s Photo by Unknown Author i s l icensed under CC BY-SA Thi s Photo by Unknown Author i s l icensed under CC BY-SA-NC Thi s Photo by Unknown Author i s l icensed under CC BY  Looking at the Biochemistry: logic of the living system Life performs various Set of chemical metabolic processes. reactions F2 Gas exchange in the alveoli involves the formation and dissociation of the complex between hemoglobin and oxygen or carbon dioxide gases. This Photo by Unknown Author is licensed under CC BY-SA  Looking at the Biochemistry: logic of the living system Forms energized biomolecules: ATP & NADPH Life engages in energy F3 transformation. This Photo by Unknown Author is licensed under CC BY  Looking at the Biochemistry: logic of the living system Life has the capacity F4 for self-replication. DNA as the genetic material. This Photo by Unknown Author is licensed under CC BY-SA-NC This Photo by Unknown Author is licensed under CC BY-SA-NC Macromolecules Biochemistry: – Scientific field that explores the compounds of life Four main families of biochemicals: – Carbohydrates – Lipids – Proteins – Nucleic acids Macromolecules Functions of macromolecules: – Structural components – Molecular messengers – Energy sources – Enzymes (biochemical catalysts) – Nutrient stores – Sources of genetic information (1) Carbohydrates: Sugars and Polysaccharides Saccharide: a sugar Monosaccharide: a simple sugar containing three to seven carbons Disaccharide: combination of two monosaccharides Polysaccharide: polymer of five or more monosaccharides Monosaccharides and disaccharides are named with the suffix –ose – Hexose: composed of six carbons – Pentose: composed of five carbons Common Classes of Carbohydrates Macromolecules and Their Functions: Carbohydrates  Examples of Polysaccharides Cellulose: – Long, fibrous polymer – Gives strength and rigidity to plants and microscopic algae – One of the most common organic substances on earth – Digestible only by bacteria, fungi, and protozoa Agar: – Important in preparing solid culture media – Natural component of seaweed – Polymer of galactose and sulfur-containing carbohydrates  Examples of Polysaccharides Chitin: – Polymer of glucosamine – Found in the exoskeletons of certain fungi Peptidoglycan: – Polysaccharides are linked to peptide fragments – Provides the main source of structural support to bacterial cell walls Lipopolysaccharide: – Complex of lipid and polysaccharide found in the outer membrane of gram-negative bacteria – Responsible for symptoms of fever and shock  Examples of Polysaccharides Glycocalyx: – Composed of polysaccharides bounds in various ways to proteins – Functions in attachment to other cells or as a site for receptors Glucose polymers starch and glycogen: – Storage molecules in cells – Must be broken down by appropriate enzymes for use by the cell – Hydrolysis: digestion or breakdown of polysaccharides that requires the addition of water (2) Lipids: Fats, Phospholipids, and Waxes Lipid: – Operational term for substances that are not soluble in polar solvents such as water but are soluble in nonpolar solvents such as benzene and chloroform – Long or complex hydrocarbon chains that are hydrophobic Triglycerides Triglycerides: – Storage lipids – Fats and oils – Composed of a single molecule of glycerol bound to three fatty acids – Glycerol: 3-carbon alcohol with three OH groups that serve as binding sites – Fatty acids: long chain hydrocarbons with a carboxyl group at the end Synthesis and Structure of a Triglyceride Fatty Acids Saturated fatty acid: – All carbons in the fatty acid chain are single-bonded to two other carbons and two hydrogens Unsaturated fatty acid: – A fatty acid in which at least one double bond exists between carbon atoms Phospholipids Phospholipids: – Contain only two fatty acids attached to a glycerol – Third binding site holds a phosphate group bound to an alcohol – Have a hydrophilic region and a hydrophobic region – Allows the molecule to form bilayers and membranes Membrane Lipids Membrane formation in an aqueous solution: Polar heads of phospholipids attracted to the water phase Nonpolar tails repelled from the water phase Membranes and lipid bilayers: – Hydrophilic face orients itself toward the solution – Hydrophobic tails immerse themselves in the bilayer – These characteristics allow selective permeability and fluidity Steroids and Waxes Steroids: – Ringed compounds commonly found in cell membranes and animal hormones – Cholesterol: reinforces cell membranes in animal cells and cell- wall-deficient bacteria (mycoplasmas) – Ergosterol: found in the cell membranes of fungi Wax: – Ester formed between a long-chain alcohol and a fatty acid – Soft and pliable when warmed, water resistant when cold – Natural waterproofing of skin, fur, feathers, etc. – Bacteria that cause tuberculosis and leprosy produce a wax that repels ordinary laboratory stains and contributes to their damaging effects on the body Macromolecules and Their Functions: Lipids (3) Proteins: Shapers of Life Predominant organic macromolecule in cells – Determine structure, behavior, and unique qualities of organisms Amino acids: – Building blocks of proteins – Exist in 20 different naturally occurring forms – Linked by peptide bonds Basic Structure of Amino Acids α (alpha) carbon Amino group (NH2) Carboxyl group (COOH) Hydrogen atom (H) R group: imparts unique characteristics to the amino acid Peptides Peptide: – Molecule composed of short chains of amino acids Polypeptide: – Has more than 20 amino acids – Not all polypeptides are large enough to be considered proteins Protein Structure Primary (1°) structure: – The type, number, and order of amino acids Secondary (2°) structure: – Arises when functional groups on the outer surface of the molecule interact with each other ❖α helix ❖β pleated sheet Protein Structure Tertiary (3°) structure: – Torsion caused by interaction between functional groups – Covalent disulfide bonds Quaternary (4°) structure: – Large multiunit proteins formed by more than one polyprotein Enzymes and Antibodies Enzymes: – Catalysts for chemical reactions in cells – Specificity comes from the unique patterns in enzyme binding sites Antibodies: – Complex glycoproteins with specific attachment regions for bacteria, viruses, and other microorganisms (4) Nucleic Acids Deoxyribonucleic Acid (DNA): – Contains a special coded genetic program with detailed and specific instructions for each organism’s heredity Ribonucleic Acid (RNA): – Helper molecules responsible for translating and carrying out the instructions of DNA Nucleic Acid Structure DNA and RNA are composed of repeating nucleotide subunits Nitrogen base Pentose (5-carbon) sugar Phosphate Purines and Pyrimidines Purines: – Nitrogen bases composed of two rings – Adenine and Guanine Pyrimidines: – Nitrogen bases composed of one ring – Thymine, Cytosine, and Uracil DNA versus RNA DNA: – Contains all of the nitrogen bases except uracil – Nitrogen bases are covalently bonded to deoxyribose RNA: – Contains all of the nitrogen bases except thymine – Nitrogen bases are covalently bonded to ribose RNA: Protein Synthesis and Regulation Long, single strand of nucleotides Three major types of RNA: – mRNA: copy of a gene – tRNA: carrier that transports the correct amino acids to the ribosome for protein assembly – rRNA: major component of ribosome Macromolecules and Their Functions: Nucleic Acids ATP: Energy Molecule Adenosine Triphosphate (ATP): – Adenine – Ribose – Three phosphates Releases energy when the bond is broken between the second and third phosphates Thank You!