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Chapter 2

The Chemical Basis of LifeThe Chemical Basis of Life

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2.1 Basic Chemistry• Matter, Mass, and Weight

– Matter: anything that occupies space and has mass– Mass: the amount of matter in an object– Weight: the gravitational force acting on an object

of a given mass

• Elements and Atoms– Element: the simplest type of matter with unique

chemical properties; composed of atoms of only one kind

– Atom: smallest particle of an element that has chemical characteristics of that element

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Atomic Structure

• Atoms: composed of subatomic particles– Neutrons: no electrical

charge

– Protons: one positive charge

– Electrons: one negative charge

• Nucleus: formed by protons and neutrons

• Most of the volume of an atom occupied by electrons

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Atomic Number and Mass Number

• Atomic Number: equal to number of protons in each atom, which is equal to the number of electrons

• Mass Number: number of protons plus number of neutrons

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Isotopes and Atomic Mass• Isotopes: two or more forms of same element with same number

of protons and electrons but different neutron number– For example; there are three types of hydrogen– Denoted by using symbol of element preceded by mass number as 1H, 2H,

3H

• Atomic Mass: average mass of naturally occurring isotopes

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Radioactive Isotopes

• Forms of atoms that emit radioactivity such as gamma rays, which can then be measured

• Used clinically and in research

• Examples of uses– Tracking hormone uptake– Treating cancer– Sterilization of materials to be used in surgery

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The Mole and Molar Mass

• Avogadro’s Number: 6.022 x 1023

• Mole: Avogadro’s number of atoms, ions, molecules

• Molar mass: mass of one mole of a substance in grams, which is equal to its atomic mass units.– Avogadro’s number is to the chemist what a

dozen is to a baker.

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Electrons and Chemical Bonding• Intramolecular bonding occurs

when outermost electrons are either shared with or transferred to another atom– Ionic Bonding: atoms exchange

electrons – Covalent Bonding: two or

more atoms share electron pairs• Ion: an atom loses or gains

electrons and becomes charged– Cation: positively charged ion– Anion: negatively charged ion

• In an ionic bond, cations and anions are attracted to each other and remain close to each other

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Covalent BondsAtoms share one or more pairs

of electrons– Single covalent: two atoms

share one pair of electrons

– Double covalent: Two atoms share 4 electrons

– Nonpolar covalent: Electrons shared equally because nuclei attract the electrons equally

– Polar covalent: Electrons not shared equally because one nucleus attracts the electrons more than the other does

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Molecules and Compounds• Molecules: two or more atoms chemically

combine to form an independent unit– Example: a hydrogen molecule (H2)

• Compounds: a substance composed of two or more different types of atoms chemically combined– Example: water (H2O)

• Molecular Mass: determined by adding up atomic masses of its atoms or ions– Example: NaCl (22.99 + 35.45)

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Intermolecular Forces

• Forces between molecules

• Result from weak electrostatic attractions between oppositely charged parts or molecules, or between ions and molecules

• Weaker than forces producing chemical bonding

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Intermolecular Forces: Hydrogen Bonds

• Occur when the positively charged H of one molecule is attracted to the negatively charged O, N or F of another molecule – For example, in water the

positively charged hydrogen atoms of one water molecule bond with the negatively charged oxygen atoms of other water molecules

– Hydrogen bonds play an important role in determining the shape of complex molecules

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Intermolecular Forces:

Solubility and Dissociation

• Solubility: ability of one substance to dissolve in another– For example, sugar or salt

dissolves in water• Dissociation or Separation: in

ionic compounds, cations are attracted to negative end and anions attracted to positive end of water molecules; the ions separate and each becomes surrounded by water molecules

• Electrolyte: dissociation of an ionic compound in water

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Electrolytes and Nonelectrolytes

• Electrolytes: solutions made by the dissociation of cations (+) and anions (-) in water– Have the capacity to conduct an electric current– Currents can be detected by electrodes

• Nonelectrolytes: solutions made by molecules that dissolve in water, but do not dissociate; do not conduct electricity

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2.2 Chemical Reactions and Energy• Atoms, ions, molecules or compounds interact

to form or break chemical bonds– Reactants: substances that enter into a chemical

reaction.– Products: substances that result from the reaction

• Chemical bonds are made (synthesis; anabolism) and broken (decomposition; catabolism) during chemical reactions

• Metabolism: collective term used for the sum of all of the anabolic and catabolic reactions in the body

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Synthesis Reactions• Two or more reactants chemically combine to form a new and larger

product. Anabolism.– Chemical bonds made; energy stored in the bonds.

– Responsible for growth, maintenance and repair

– Dehydration: synthetic reaction where water is a product

– Produce chemicals characteristic of life: carbohydrates, proteins, lipids, and nucleic acids

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Decomposition Reactions• A large reactant is broken down to form smaller products.

Catabolism.– Chemical bonds broken; energy released. – Hydrolysis: water is split into two parts that contribute to the

formation of the products– Example: the breakdown of ATP to form ADP and inorganic

phosphate with a concomitant release of free energy

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Reversible Reactions

• Chemical reactions in which the reaction can proceed either from reactants to products or from products to reactants.

• Equilibrium: rate of product formation is equal to rate of reactant formation

• Example: CO2 and H+ formation in plasma

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Oxidation-Reduction Reactions

• Oxidation: loss of an electron by a substance• Reduction: gain of an electron by a substance• Oxidation-Reduction Reactions: the complete or

partial loss of an electron by one substance is accompanied by the gain of that electron by another substance– Synthetic/decomposition reactions can be oxidation -

reduction reactions

– Reactions can be described in more than one way

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Energy: the capacity to do work

• Potential Energy: energy stored in chemical bonds; energy that could do work if it were released. Breaking chemical bonds releases energy.

• Kinetic Energy: does work and moves matter• Mechanical Energy: energy resulting from the

position or movement of objects• Chemical Energy: form of potential energy in the

chemical bonds of a substance• Heat Energy: energy that flows between objects of

different temperatures

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ATP and Potential Energy

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Heat Energy

• When a chemical bond is broken and energy is released, only some of that energy is used to manufacture ATP.

• Energy that is released but not captured is released as heat.

• Heat is used by mammals to maintain body temperature.

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Speed of Chemical Reactions• Temperature affects rate of reaction.

– Increase in temperature means increase of kinetic energy. – Molecules move faster, collide harder and more frequently.

• Concentration of reactants. – As concentration of reactants increases, rate of reaction increases. – A decrease of O2 in cells can cause death as rate of aerobic chemical

reactions decreases.

• Catalysts: substances that increase the rate of chemical reactions without being permanently changed or depleted– Enzymes: proteinaceous catalysts that increase the rate of chemical

reactions by lowering the activation energy necessary for reaction to begin

• Activation Energy: minimum energy reactants must have to start a chemical reaction

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Activation Energy and Enzymes

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2.3 Inorganic Chemistry• Inorganic Chemistry: generally,

substances that do not contain carbon– Water, oxygen, calcium phosphate, metal ions

– Exceptions: CO, CO2, and HCO3-

• Organic Chemistry: study of carbon-containing substances. Those that are biologically active are called biochemicals.

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Water• Cohesion and adhesion properties• 50-60% of body, 92% of blood• High specific heat: large amount of heat required to

raise temperature of water– Stabilizes body temperature

• Protection– Lubricant, cushion

• Participates in chemical reactions– Many reactions take place in water– Dehydration and hydrolysis

• Serves as a mixing medium

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Mixing Medium (cont.)

• Mixture: substances physically but not chemically combined– Suspension: materials separate unless stirred. Sand and

water.– Colloid: dispersal of tiny particles through a medium. Milk.

• Solution: mixture of liquids, gasses, or solids that are uniformly distributed and chemically combined– Solvent: that which dissolves the solute– Solute: that which dissolves in the solvent

– *Blood is a mixture, solution, and colloid.

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Solution Concentrations• Concentration: measure of number of particles of

solute per volume of solution – Osmolality: reflects the number of particles

dissolved in one kilogram of water– One osmole is equal to Avogadro’s number of

particles in one kilogram of water.– Unit used by physiologists is milliosmoles because of the

low concentrations in the human body– Concentration of body fluids influences movement of fluid

into and out of cells.– 300 mOsm is average in the human body

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Acids and Bases; Salts and Buffers

• Acid: a proton donor or any substance that releases hydrogen ions

• Base: a proton acceptor or any substance that binds to or accepts hydrogen ions

• Salt: a compound consisting of a cation other than a hydrogen ion and an anion other than a hydroxide ion. Example: NaCl

• Buffer: a solution of a conjugate acid-base pair in which acid and base components occur in similar concentrations

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The pH Scale• Refers to the Hydrogen

ion concentration in a solution– Neutral: pH of 7 or equal

hydrogen and hydroxide ions

– Acidic: a greater concentration of hydrogen ions

– Alkaline or basic: a greater concentration of hydroxide ions

– Physiologic pH is 7.4

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Buffers

• Regulate pH

• Important biological buffers– Bicarbonate– Phosphates– Protein– Respiratory and renal mechanisms

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Oxygen and Carbon Dioxide

• Oxygen (O2): required in the final step in the series of reactions used to extract energy from food.

• Carbon dioxide (CO2): produced during the catabolism of organic compounds. – Metabolic waste product.– Combines with water in plasma and forms H+

thus affecting acid/base balance

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2.4 Organic Chemistry• Carbohydrates: composed of carbon, hydrogen,

oxygen. – Divided into monosaccharides, disaccharides, polysaccharides– Energy sources and structure

• Lipids: composed mostly of carbon, hydrogen, oxygen.– Relatively insoluble in water. – Functions: protection, insulation, physiological regulation,

component of cell membranes, energy source• Proteins: composed of carbon, hydrogen, oxygen,

nitrogen, sometimes iodine. – Functions: regulate processes, aid transport, protection, muscle

contraction, structure, energy• Nucleic Acids: composed of carbon, hydrogen, oxygen,

nitrogen, phosphorus. – Examples: ATP, DNA, RNA

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Carbohydrates: Monosaccharides• Simple sugars.

• Six-carbon sugars like glucose, fructose, and galactose are important in the diet as energy sources.

• Five-carbon sugars are components of ATP, DNA and RNA

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Carbohydrates: Disaccharides• Two simple sugars bound together by dehydration • Examples: sucrose, lactose, maltose

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Carbohydrates: Polysaccharides• Long chains of many monosaccharides.• Storage molecules for monosaccharides and form part of

cell surface markers • Glycogen formed by animals. • Starch and cellulose formed by plants

– Starch in food is used as a source of monosaccharides– Cellulose in food acts as fiber (bulk) in the diet

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Lipids: Fats• Ingested and broken down by hydrolysis

– Triglycerides: composed of glycerol and fatty acids– Functions: protection, insulation, energy source

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Lipids: Fats• Fatty acids may be saturated or unsaturated

– Saturated – contains all single bonds in the carbon chain, which produces a more rigid structure

– Unsaturated – contains one (mono) or more (poly) double bonds in the carbon chain, which produces a more relaxed structure

• Better because they do not stick to the inside of blood vessels.

– Trans fats – unsaturated fats that are artificially altered to be more saturated. Are the highest CV risk fat.

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Lipids: Phospholipids• Polar (hydrophilic) at one end; nonpolar (hydrophobic) at

the other. – Function: important structural component of cell membranes

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Lipids: Eicosanoids and Fat-soluble Vitamins

• Eicosanoids: Derived from fatty acids. – Function: Important regulatory molecules– Include thromboxanes, leukotrienes, and

prostaglandins

• Fat-soluble Vitamins: nonpolar molecules essential for normal functioning.

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Lipids: Steroids

• Cholesterol, bile salts, estrogen, testosterone. – Carbon atoms arranged in four rings

– Functions: physiological regulators and component of cell membranes

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Proteins• Amino acids: building blocks of protein• Peptide bonds: covalent bonds formed between amino

acids during protein synthesis

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Protein Structure

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Protein Structure

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Enzymes• Lower the activation energy necessary for a

reaction to occur; bring reactants into close proximity

• Three-dimensional shape contains an active site where reactants attach.

• Induced Fit Hypothesis: enzymes change shape to accommodate the shape of specific reactants

• Enzyme names usually end in –ase and often have the same word stem as the reactant; for example a lipid is a reactant for lipase.

• Cofactors: combine with active site and make nonfunctional enzymes functional– Organic cofactors called coenzymes

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Nucleic Acids – DNA and RNA

• Nucleotides– Composed of a five-carbon sugar, a nitrogenous base, and a phosphate

– Include the nucleic acids (DNA and RNA) and ATP

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DNA: Deoxyribonucleic acid

• Genetic material of cells copied from one generation to next

• Composed of 2 strands of nucleotides– Each nucleotide contains one of the organic bases of adenine or guanine (which

are purines) and thymine or cystosine (which are pyrimidines).

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RNA: Ribonucleic acid

• Similar to a single strand of DNA– Four different nucleotides make up organic

bases except thymine is replaced with uracil (pyrimidine)

• Responsible for interpreting the code within DNA into the primary structure of proteins.

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Adenosine Triphosphate (ATP)

• Energy currency of the body• Provides energy for other chemical reactions as anabolism

or drive cell processes as muscle contraction• All energy-requiring chemical reactions stop when there is

inadequate ATP