Chapter 2 Chemistry of Life

Objectives Define the terms atom, element, molecule, and compound Describe the structure of an atom Compare and contrast ionic and covalent types of chemical bonding Distinguish between organic and inorganic chemical compounds

Objectives Discuss the chemical characteristics of water Explain the concept of pH Discuss the structure and function of the following types of organic molecules: carbohydrate, lipid, protein, and nucleic acid

Levels of Chemical Organization Atoms Nucleus—central core of atom Proton—positively charged particle in nucleus Neutron—uncharged particle in nucleus Atomic number—number of protons in nucleus Atomic mass—number of protons and neutrons combined What makes up an atom’s atomic mass? The number of protons and neutrons combined.

Levels of Chemical Organization Atoms Energy levels—orbital regions surrounding atomic nucleus that contain electrons Electron—negatively charged particle May contain up to 8 electrons in each level Energy level increases the farther away it is from the nucleus Describe an energy level. Energy levels (shells) are the limiting regions in which orbitals are arranged.

Models of the atom. The nucleus—protons (+) and uncharged neutrons—is at the core. Electrons inhabit outer regions called energy levels (A), which look more like a cloud because the electrons do not stay in one place (B). This is a carbon atom, a fact that is determined by the number of its protons. All carbon atoms (and only carbon atoms) have six protons.(One proton in the nucleus is not visible in this illustration.)

Levels of Chemical Organization Elements, molecules, and compounds Element—a pure substance; made up of only one kind of atom Molecule—a group of atoms bound together in a group Compound—substances whose molecules have more than one kind of atom

Chemical Bonding Chemical bonds form to make atoms more stable Atoms react with one another in ways that make their outermost energy level full Atoms may share electrons or donate or borrow them to become stable What is a chemical bond? The energy that holds two atoms together.

Chemical Bonding Ionic bonds Ions form when an atom gains or loses electrons in its outer energy level to become stable Positive ion—has lost electrons; indicated by superscript positive sign(s), as in Na+ or Ca++ Negative ion—has gained electrons; indicated by superscript negative sign(s), as in Cl– How is an ion formed? Ions form when an atom gains or loses an electron to become stable.

Chemical Bonding Ionic bonds Ionic bonds form when positive and negative (oppositely charged) ions attract each other Electrolyte—molecule that dissociates (breaks apart) in water to form individual ions; an ionic compound What is dissociation? Occurs when molecules dissolve in water because water molecules wedge between the ions and force them apart.

Ionic bonding. A, The sodium atom donates the single electron in its outer energy level to a chlorine atom having seven electrons in its outer level. Then both have eight electrons in their outer shells. Because the electron/proton ratio changes, the sodium atom becomes a positive sodium ion. The chlorine atom becomes a negative chloride ion. The positive-negative attraction between these oppositely charged ions is called an ionic bond. B, A cube-shaped crystal of sodium chloride (table salt).

Chemical Bonding Covalent bonds Covalent bonds form when atoms share their outer energy ions to complete the energy level and thus become stable Covalent bonds do not ordinarily easily dissociate in water Covalent bonding is used to form all of the major organic compounds found in the body What is covalent chemical bonding? Bonding that forms when atoms fill up their energy levels by sharing electrons rather than donating or receiving them.

Covalent bonding. Two hydrogen atoms move together, overlapping their energy levels. Although neither gains nor loses an electron, the atoms share the electrons, thereby forming a covalent bond.

Chemical Bonding Hydrogen bonds Hydrogen bonds do not create new molecules Hydrogen bonds weakly bond to neighboring molecules Hydrogen bonds are present in water, DNA, and proteins

Inorganic Chemistry Organic molecules contain carbon-carbon covalent bonds and/or carbon-hydrogen covalent bonds; inorganic molecules do not Organic molecules are generally larger and more complex than inorganic molecules Does the human body contain organic or inorganic molecules? The human body contains both kinds of compounds.

Inorganic Chemistry Water Water is an inorganic compound essential to life Water is a solvent (liquid into which solutes are dissolved), forming aqueous solutions in the body What is an aqueous solution? An aqueous solution is one in which water is the solvent for a mixture.

Inorganic Chemistry Water is involved in chemical reactions Dehydration synthesis—chemical reaction in which water is removed from small molecules so they can be strung together to form a larger molecule Hydrolysis—chemical reaction in which water is added to the subunits of a large molecule to break it apart into smaller molecules Chemical reactions always involve energy transfers, as when energy is used to build ATP molecules Chemical equations show how reactants interact to form products; arrows separate the reactants from the products

Water-based chemistry Water-based chemistry. Dehydration synthesis (on the left) is a reaction in which small molecules are assembled into large molecules by removing water (H and O atoms). Hydrolysis (on the right) operates in the reverse direction; H and O from water are added as large molecules are broken down into small molecules.

Inorganic Chemistry Acids, bases, and salts Water molecules dissociate to form equal amounts of H+ (hydrogen ion) and OH– (hydroxide ion) Acid—substance that shifts the H+/OH– balance in favor of H+; opposite of base Base—substance that shifts the H+/OH– balance against H+; also known as an alkaline; opposite of acid What solutions have an excess of hydrogen ions? Acids

Inorganic Chemistry Acids, bases, and salts pH—Mathematical expression of relative H+ concentration in an aqueous solution 7 is neutral (neither acid nor base) pH values above 7 are basic; pH values below 7 are acidic What is pH? pH—mathematical expression of relative H+ concentration in an aqueous solution

The pH scale. The H+ concentration is balanced with the OH− concentration at pH 7. At values above 7 (low H+), the scale tips in the basic direction. At values below 7 (high H+), the scale tips toward the acid side.

Inorganic Chemistry Acids, bases, and salts Neutralization occurs when acids and bases mix and form salts Buffers form chemical systems that absorb excess acids or bases and thus maintain a relatively stable pH

Organic Chemistry Carbohydrates—sugars and complex carbohydrates Contain carbon (C), hydrogen (H), oxygen (O) Monosaccharides— basic unit of carbohydrate molecules (e.g., glucose) Disaccharide—double sugar made up of two monosaccharide units (e.g., sucrose, lactose) What is the name of a substance in which many saccharides join together? Polysaccharide

Organic Chemistry Carbohydrates—sugars and complex carbohydrates Polysaccharide—complex carbohydrate made up of many monosaccharide units (e.g., glycogen; stored by the body) Function of carbohydrates is to store energy for later use

Carbohydrates. Monosaccharides are single carbohydrate units joined by dehydration synthesis to form disaccharides and polysaccharides. The detailed chemical structure of the monosaccharide glucose is shown in the inset.

Organic Chemistry Lipids—fats and oils Triglycerides Formed by a glycerol unit and joined to three fatty acids Store energy for later use What are the three main types of lipids in the body? Triglycerides, phospholipids, and cholesterol

Triglyceride. Each triglyceride is composed of three fatty acid units attached to a glycerol unit.

Organic Chemistry Lipids—fats and oils Phospholipids Similar to triglyceride structure, but have phosphorus-containing units—each with a head and two tails The head attracts water and the double tail does not, thus forming stable double layers (bilayers) in water Form membranes of cells

Phospholipids. A, Each phospholipid molecule has a phosphorus-containing “head” that attracts water and a lipid “tail” that repels water. B, Because the tails repel water, phospholipid molecules often arrange themselves so that their tails face away from water. The stable structure that results is a bilayer sheet forming a small bubble.

Organic Chemistry Lipids—fats and oils Cholesterol Molecules have a steroid structure made up of multiple rings Cholesterol stabilizes the phospholipid tails in cellular membranes and is also converted into steroid hormones by the body

Organic Chemistry Proteins Very large molecules made up of amino acids held together in long, folded chains by peptide bonds Structural proteins Form essential structures of the body Collagen is a fibrous protein that holds many tissues together Keratin forms tough, waterproof fibers in the outer layer of the skin

Protein. Protein molecules are large, complex molecules formed by one or more strands of amino acids. Each amino acid is connected to the next by a type of covalent bond called a peptide bond. Additional weak forces between atoms of the larger molecule then cause the strand to twist or fold into a secondary (second-level) protein structure. New relationships among the atoms then cause the molecule to fold again on itself to form a three-dimensional tertiary (third level) protein structure. Several tertiary proteins may join to form a quaternary (fourth-level) protein structure.

Organic Chemistry Proteins Functional proteins Participate in chemical processes of the body Examples include hormones, cell membrane channels and receptors, and enzymes Enzymes—chemical catalysts Help chemical reactions occur Enzyme action sometimes called lock-and-key model What is the lock-and-key model and how does it relate to enzymes? Each enzyme has a shape that “fits” with the specific molecules it works on, similar to the way a key fits specific locks.

Organic Chemistry Proteins Proteins can combine with other organic molecules to form “mixed” molecules such as glycoproteins or lipoproteins

Enzyme action. Enzymes are functional proteins whose molecular shape allows them to catalyze chemical reactions. Molecules A and B are brought together by the enzyme to form a larger molecule, AB.

Organic Chemistry Nucleic acids Made up of nucleotides A phosphate unit A sugar (ribose or deoxyribose) A nitrogen base (adenine, thymine or uracil, guanine, cytosine) What are the two forms of nucleic acid? The two forms are deoxyribonucleic acid [DNA] and ribonucleic acid (RNA).

Organic Chemistry Nucleic acids DNA (deoxyribonucleic acid) Used as the cell’s “master code” for assembling proteins Uses deoxyribose as the sugar and A, T (not U), C, and G as bases Forms a double helix shape What is the role of DNA in the body? It makes up the genetic code in the body.

DNA. Deoxyribonucleic acid (DNA), like all nucleic acids, is composed of units called nucleotides. Each nucleotide has a phosphate, a sugar, and a nitrogen base. In DNA, the nucleotides are arranged in a double helix formation.

Organic Chemistry Nucleic acids RNA (ribonucleic acid) Used as a temporary “working copy” of a gene (portion of the DNA code) Uses ribose as the sugar and A, U (not T), C, and G as bases

Organic Chemistry Nucleic acids By directing the formation of structural and functional proteins, nucleic acids ultimately direct overall body structure and function