Lecture 2: Chapter 2 The Chemical Level of Organization Pages: 26- 61

Learning Objectives Describe an atom and compare the ways atoms combine to form molecules. Distinguish among the types of chemical reactions that are important to physiology. Describe the role of enzymes in metabolism. Distinguish between organic and inorganic compounds. Explain the importance of water, pH and buffers to living systems. Discuss the structures and functions of carbohydrates, lipids, proteins, nucleic acids and high energy compounds.

Atoms, Molecules and Bonds Atoms are the smallest stable units of matter Subatomic particles Protons = positive charge; weight of approximately 1 Dalton Neutrons = no charge; weight similar to protons Electrons = negative charge; weigh 1/1836th Dalton Protons and neutrons are found in the nucleus; electrons occupy electron cloud Atomic number = proton number; atomic mass = protons and neutrons Isotopes are elements with similar numbers of protons but different numbers of neutron

Hydrogen Atoms

Electrons occupy a series of energy levels or electron shells. The outermost electron shell determines the reactivity of the element.

Atoms and Energy Levels

Atoms combine through chemical reactions Molecule = a chemical structure consisting of molecules held together by covalent bonds Compound = a chemical substance composed of atoms of two or more elements There are three types of bond: Ionic, covalent, and hydrogen Ionic = attraction between positive cations and negative anions

Ionic Bonding Animation: Formation of Ions (see tutorial)

Covalent bonds exist between atoms that share electrons to form a molecule Double covalent bond Non-polar covalent bond Polar covalent bond

Hydrogen bonds are weak forces that affect the shape and properties of compounds Polar covalent bonds that occur when hydrogen covalently bonds with another element

Polar Covalent Bonds and the Structure of Water

Hydrogen Bonds

Matter and chemical notation Matter can exist as a solid, liquid or gas Depends on the interaction of the component atoms or molecules Molecular weight is the sum of the atomic weights of the component atoms Chemical notation Short-hand that describes chemical compounds and reactions See table 2.2 for examples of chemical notation

A chemical reaction occurs when reactants Chemical Reactions A chemical reaction occurs when reactants combine to generate one or more products All chemical reactions in the body constitutes metabolism Metabolism provides for the capture, storage and release of energy

Basic energy concepts Work = movement of an object or change in its physical structure Energy = the capacity to perform work Kinetic energy is energy of motion Potential energy is stored energy resulting from position or structure Conversions are not 100% efficient, resulting in release of heat

Metabolism Types of reaction Decomposition Synthesis Exchange Metabolism is the sum of all reactions Through catabolism cells gain energy (break down of complex molecules) Anabolism uses energy (synthesis of new molecules)

Reversible reactions All reactions are theoretically reversible At equilibrium the rates of two opposing reactions are in balance Anabolism = catabolism

Enzymes, energy and chemical reactions Activation energy is the amount of energy needed to begin a reaction Enzymes are catalysts Reduce energy of activation without being permanently changed or used up Promote chemical reactions

Enzymes and Activation Energy

Nutrients and Metabolites Inorganic Compounds Nutrients and Metabolites Nutrients are essential chemical compounds obtained from the diet Metabolites are molecules synthesized or broken down inside the body These can be classified as organic or inorganic compounds Organic compounds have carbon and hydrogen as their primary structural component Inorganic compounds are not primarily carbon and hydrogen

Water and its properties Water is the most important constituent of the body Solution is a uniform mixture of two or more substances Solvent is the medium in which molecules of solute are dispersed Water is the solvent in aqueous solutions

Water molecules and solutions

Electrolytes undergo ionization Compounds that interact readily with water are hydrophilic Compounds that do not interact with water are hydrophobic

pH is a measure of the concentration of hydrogen ions solution Neutral Acidic Basic

Acids and Bases Acids release hydrogen ions into solution Bases remove hydrogen ions from solution Strong acids and strong bases ionize completely Weak acids and weak bases do not ionize

pH and Hydrogen Ion Concentration

Salts and buffers Salt = an electrolyte whose cation is not hydrogen and whose anion is not hydroxide Buffers remove or replace hydrogen ions in solution Buffer systems maintain the pH of body fluids

Organic compounds Organic compounds generally include Carbon Hydrogen and sometimes Oxygen

Organic compounds Four major classes of organic compounds are Carbohydrates Lipids Proteins Nucleic acids High energy compounds are also organic compounds

Carbohydrates Important energy source for metabolism Monosaccharides, disaccharides and polysaccharides Di- and polysaccharides formed from monosaccharides by dehydration synthesis

The Formation and Breakdown of Complex Sugars Animation: The formation and breakdown of complex sugars (see tutorial)

The Structure of a Polysaccharide

Lipids include fats, oils, and waxes Five classes: Fatty acids Eicosanoids Glycerides Steroids Phospholipids Glycolipids

Fatty acids

Triglyceride Formation Triglycerides = three fatty acids attached by dehydration synthesis to one molecule of glycerol

Steroids Are involved in cell membrane structure Include sex hormones and hormones regulating metabolism Are important in lipid digestion

Steroids

Proteins perform many vital functions in the body Proteins perform many vital functions in the body. The six important types are: Structural proteins Contractile proteins Transport proteins Enzymes Buffering proteins Antibodies

Proteins are chains of amino acids Amino acids contain an amino group, a carboxylic group and a radical group Polypeptides are linear sequences of amino acids held together by peptide bonds

Amino Acids

Peptide Bonds

The four levels of protein structure are: Primary structure (amino acids sequence) Secondary structure (amino acid interactions) Tertiary structure (complex folding) Quaternary structure (protein complexes)

Protein Structure

Enzyme reactions Reactants (substrate) interact to yield a product by binding to the active site of the enzyme Cofactors must bond to the enzyme before substrate binding can occur Coenzymes are organic cofactors commonly derived from vitamins

Figure 2.21 A simplified view of enzyme structure and function Animation: Enzyme structure and function (see tutorial)

The shape of a protein determines its function Proteins pushed outside their optimal temperature and pH range become temporarily or permanently denatured and will cease to function

Nucleic acids Store and process information at the molecular level Made of purines and pyrimidines DNA and RNA

Purines and Pyrimidines

Nucleic Acids: RNA and DNA

Nucleic acids are chains of nucleotides Nucleotides are composed of a sugar, a phosphate and a nitrogenous base Sugar = deoxyribose (DNA) or ribose (RNA) DNA Bases = adenine, thymine, cytosine, guanine RNA bases = adenine, uracil, cytosine, guanine

High energy compounds store cellular energy in high energy bonds Adenosine triphosphate (ATP) Made by adding a phosphate group to adenosine diphosphate (ADP) Process referred to as phosphorylation

Biochemical compounds form functional units called cells Chemicals and Cells Biochemical compounds form functional units called cells Metabolic turnover allows cells to change and to adapt to changes in their environment

You should now be familiar with: Atoms and how they combine to form compounds. Chemical reactions and enzymes. Organic and inorganic compounds. Water, pH, and buffers. The structure and function of carbohydrates, lipids, proteins, nucleic acids and high energy compounds.