Chemistry Comes Alive Part A 2

The “stuff” of the universe Anything that has mass and takes up space Matter The “stuff” of the universe Anything that has mass and takes up space States of matter Solid – has definite shape and volume Liquid – has definite volume, changeable shape Gas – has changeable shape and volume

The capacity to do work (put matter into motion) Types of energy Kinetic – energy in action Potential – energy of position; stored (inactive) energy

Chemical – stored in the bonds of chemical substances Forms of Energy Chemical – stored in the bonds of chemical substances Electrical – results from the movement of charged particles Mechanical – directly involved in moving matter Radiant or electromagnetic – energy traveling in waves (i.e., visible light, ultraviolet light, and X rays)

Energy Form Conversions Energy is easily converted from one form to another During conversion, some energy is “lost” as heat

Atoms – more-or-less identical building blocks for each element Composition of Matter Elements – unique substances that cannot be broken down by ordinary chemical means Atoms – more-or-less identical building blocks for each element Atomic symbol – one- or two-letter chemical shorthand for each element

Properties of Elements Each element has unique physical and chemical properties Physical properties – those detected with our senses Chemical properties – pertain to the way atoms interact with one another

Major Elements of the Human Body Oxygen (O) Carbon (C) Hydrogen (H) Nitrogen (N) 96% of body matter

Lesser and Trace Elements of the Human Body Lesser elements make up 3.9% of the body and include: Calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), magnesium (Mg), iodine (I), and iron (Fe) Trace elements make up less than 0.01% of the body They are required in minute amounts, and are found as part of enzymes

The nucleus consists of neutrons and protons Atomic Structure The nucleus consists of neutrons and protons Neutrons – have no charge and a mass of one atomic mass unit (amu) Protons – have a positive charge and a mass of 1 amu Electrons are found orbiting the nucleus Electrons – have a negative charge and 1/2000 the mass of a proton (0 amu)

Models of the Atom Planetary Model – electrons move around the nucleus in fixed, circular orbits Orbital Model – regions around the nucleus in which electrons are most likely to be found

Models of the Atom Figure 2.1

Identification of Elements Atomic number – equal to the number of protons Mass number – equal to the mass of the protons and neutrons Atomic weight – average of the mass numbers of all isotopes Isotope – atoms with same number of protons but a different number of neutrons Radioisotopes – atoms that undergo spontaneous decay called radioactivity

Identification of Elements Figure 2.2

Identification of Elements Figure 2.3

Molecules and Compounds Molecule – two or more atoms held together by chemical bonds Compound – two or more different kinds of atoms chemically bonded together

Mixtures and Solutions Mixtures – two or more components physically intermixed (not chemically bonded) Solutions – homogeneous mixtures of components Solvent – substance present in greatest amount Solute – substance(s) present in smaller amounts

Concentration of Solutions Percent, or parts per 100 parts Molarity, or moles per liter (M) A mole of an element or compound is equal to its atomic or molecular weight (sum of atomic weights) in grams

Colloids and Suspensions Colloids, or emulsions, are heterogeneous mixtures whose solutes do not settle out Example: Jello and Cytosol Suspensions are heterogeneous mixtures with visible solutes that tend to settle out Example: Blood

Mixtures Compared with Compounds No chemical bonding takes place in mixtures Most mixtures can be separated by physical means Mixtures can be heterogeneous or homogeneous Compounds cannot be separated by physical means All compounds are homogeneous

Electron shells, or energy levels, surround the nucleus of an atom Chemical Bonds Electron shells, or energy levels, surround the nucleus of an atom Bonds are formed using the electrons in the outermost energy level Valence shell – outermost energy level containing chemically active electrons Octet rule – except for the first shell which is full with two electrons, atoms interact in a manner to have eight electrons in their valence shell

Chemically Inert Elements Inert elements have their outermost energy level fully occupied by electrons Figure 2.4a

Chemically Reactive Elements Reactive elements do not have their outermost energy level fully occupied by electrons Figure 2.4b

Types of Chemical Bonds Ionic Covalent Hydrogen

Ions are charged atoms resulting from the gain or loss of electrons Ionic Bonds Ions are charged atoms resulting from the gain or loss of electrons Anions have gained one or more electrons Cations have lost one or more electrons

Formation of an Ionic Bond Ionic bonds form between atoms by the transfer of one or more electrons Ionic compounds form crystals instead of individual molecules Example: NaCl (sodium chloride)

Formation of an Ionic Bond Figure 2.5a

Formation of an Ionic Bond Figure 2.5b

Covalent bonds are formed by the sharing of two or more electrons Electron sharing produces molecules

Single Covalent Bonds Figure 2.6a

Double Covalent Bonds Figure 2.6b

Triple Covalent Bonds Figure 2.6c

Polar and Nonpolar Molecules Electrons shared equally between atoms produce nonpolar molecules Unequal sharing of electrons produces polar molecules Atoms with six or seven valence shell electrons are electronegative Atoms with one or two valence shell electrons are electropositive

Comparison of Ionic, Polar Covalent, and Nonpolar Covalent Bonds Figure 2.8

Too weak to bind atoms together Common in dipoles such as water Hydrogen Bonds Too weak to bind atoms together Common in dipoles such as water Responsible for surface tension in water Important as intramolecular bonds, giving the molecule a three-dimensional shape

Hydrogen Bonds Figure 2.9

Occur when chemical bonds are formed, rearranged, or broken Chemical Reactions Occur when chemical bonds are formed, rearranged, or broken Are written in symbolic form using chemical equations Chemical equations contain: Number and type of reacting substances, and products produced Relative amounts of reactants and products

Examples of Chemical Reactions

Patterns of Chemical Reactions Combination reactions: Synthesis reactions which always involve bond formation A + B  AB Decomposition reactions: Molecules are broken down into smaller molecules AB  A + B Exchange reactions: Bonds are both made and broken AB + C  AC + B

Oxidation-Reduction (Redox) Reactions Reactants losing electrons are electron donors and are oxidized Reactants taking up electrons are electron acceptors and become reduced Therefore, both decomposition and electron exchange occur.

Energy Flow in Chemical Reactions Exergonic reactions – reactions that release energy Usually when a bond is broken. Endergonic reactions – reactions whose products contain more potential energy than did its reactants

Reversibility in Chemical Reactions All chemical reactions are theoretically reversible A + B  AB AB  A + B If neither a forward nor reverse reaction is dominant, chemical equilibrium is reached

Factors Influencing Rate of Chemical Reactions Temperature – chemical reactions proceed quicker at higher temperatures Particle size – the smaller the particle the faster the chemical reaction Concentration – higher reacting particle concentrations produce faster reactions Catalysts – increase the rate of a reaction without being chemically changed Enzymes – biological catalysts

Chemistry Comes Alive: Biochemistry Part B 2

Inorganic compounds Organic compounds Biochemistry Do not contain carbon Water, salts, and many acids and bases Organic compounds Contain carbon, are covalently bonded, and are often large

Inorganic: Water High heat capacity – absorbs and releases large amounts of heat before changing temperature High heat of vaporization – changing from a liquid to a gas requires large amounts of heat Polar solvent properties – dissolves ionic substances, forms hydration layers around large charged molecules, and serves as the body’s major transport medium

Inorganic: Water Reactivity – is an important part of hydrolysis and dehydration synthesis reactions Cushioning – resilient cushion around certain body organs

Contain cations other than H+ and anions other than OH– Inorganic: Salts Inorganic compounds Contain cations other than H+ and anions other than OH– Are electrolytes; they conduct electrical currents

Inorganic: Acids and Bases Acids release H+ and are therefore proton donors HCl  H+ + Cl – Bases release OH– and are proton acceptors NaOH  Na+ + OH–

Inorganic: Acid-Base Concentration (pH) Acidic solutions have higher H+ concentration and therefore a lower pH Alkaline solutions have lower H+ concentration and therefore a higher pH Neutral solutions have equal H+ and OH– concentrations

Inorganic: Acid-Base Concentration (pH) Acidic: pH 0–6.99 Basic: pH 7.01–14 Neutral: pH 7.00 Figure 2.12

Systems that resist abrupt and large swings in the pH of body fluids Inorganic: Buffers Systems that resist abrupt and large swings in the pH of body fluids Carbonic acid-bicarbonate system Carbonic acid dissociates, reversibly releasing bicarbonate ions and protons The chemical equilibrium between carbonic acid and bicarbonate resists pH changes in the blood

Organic Compounds Molecules unique to living systems contain carbon and hence are organic compounds They include: Carbohydrates Lipids Proteins Nucleic Acids

Organic: Carbohydrates Contain carbon, hydrogen, and oxygen Their major function is to supply a source of cellular food Examples: Monosaccharides or simple sugars Figure 2.13a

Organic: Carbohydrates Disaccharides or double sugars Figure 2.13b

Organic: Carbohydrates Polysaccharides or polymers of simple sugars Figure 2.13c

Organic: Lipids Contain C, H, and O, but the proportion of oxygen in lipids is less than in carbohydrates Examples: Neutral fats or triglycerides Phospholipids Steroids Eicosanoids

Organic: Neutral Fats (Triglycerides) Composed of three fatty acids bonded to a glycerol molecule Figure 2.14a

Organic: Other Lipids Phospholipids – modified triglycerides with two fatty acid groups and a phosphorus group Figure 2.14b

Organic: Other Lipids Steroids – flat molecules with four interlocking hydrocarbon rings Eicosanoids – 20-carbon fatty acids found in cell membranes Figure 2.14c

Organic: Representative Lipids Found in the Body Neutral fats – found in subcutaneous tissue and around organs Phospholipids – chief component of cell membranes Steroids – cholesterol, bile salts, vitamin D, sex hormones, and adrenal cortical hormones Fat-soluble vitamins – vitamins A, E, and K Eicosanoids – prostaglandins, leukotriens, and thromboxanes Lipoproteins – transport fatty acids and cholesterol in the bloodstream

Organic: Amino Acids Building blocks of protein, containing an amino group and a carboxyl group Amino acid structure

Organic: Amino Acids Figure 2.15a-c

Organic: Amino Acids Figure 2.15d, e

Organic: Protein Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.16

Organic: Structural Levels of Proteins Primary – amino acid sequence Secondary – alpha helices or beta pleated sheets

Organic: Structural Levels of Proteins Tertiary – superimposed folding of secondary structures Quaternary – polypeptide chains linked together in a specific manner

Organic: Structural Levels of Proteins Figure 2.17a-c

Organic: Structural Levels of Proteins Figure 2.17d, e

Organic: Fibrous and Globular Proteins Fibrous proteins Extended and strandlike proteins Examples: keratin, elastin, collagen, and certain contractile fibers Globular proteins Compact, spherical proteins with tertiary and quaternary structures Examples: antibodies, hormones, and enzymes

Organic: Protein Denuaturation Reversible unfolding of proteins due to drops in pH and/or increased temperature Figure 2.18a

Organic: Protein Denuaturation Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes Figure 2.18b

Organic: Molecular Chaperones (Chaperonins) Help other proteins to achieve their functional three-dimensional shape Maintain folding integrity Assist in translocation of proteins across membranes Promote the breakdown of damaged or denatured proteins

Organic: Characteristics of Enzymes Most are globular proteins that act as biological catalysts Holoenzymes consist of an apoenzyme (protein) and a cofactor (usually an ion) Enzymes are chemically specific Frequently named for the type of reaction they catalyze Enzyme names usually end in -ase Lower activation energy

Organic: Characteristics of Enzymes Figure 2.19

Organic: Mechanism of Enzyme Action Enzyme binds with substrate Product is formed at a lower activation energy Product is released

Organic: Mechanism of Enzyme Action Active site Amino acids 1 Enzyme (E) Substrates (s) Enzyme-substrate complex (E–S) H20 Free enzyme (E) 2 3 Peptide bond Internal rearrangements leading to catalysis Dipeptide product (P) Figure 2.20

Organic: Nucleic Acids Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus Their structural unit, the nucleotide, is composed of N-containing base, a pentose sugar, and a phosphate group Five nitrogen bases contribute to nucleotide structure – adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) Two major classes – DNA and RNA

Organic: Deoxyribonucleic Acid (DNA) Double-stranded helical molecule found in the nucleus of the cell Replicates itself before the cell divides, ensuring genetic continuity Provides instructions for protein synthesis

Organic: Structure of DNA Figure 2.21a

Organic: Structure of DNA Figure 2.21b

Organic: Ribonucleic Acid (RNA) Single-stranded molecule found in both the nucleus and the cytoplasm of a cell Uses the nitrogenous base uracil instead of thymine Three varieties of RNA: messenger RNA, transfer RNA, and ribosomal RNA

Organic: Adenosine Triphosphate (ATP) Source of immediately usable energy for the cell Adenine-containing RNA nucleotide with three phosphate groups

Organic: Adenosine Triphosphate (ATP) Figure 2.22

Organic: How ATP Drives Cellular Work Figure 2.23