Chapter 2: Chemistry of Life

Levels of Chemical Organization

Matter: Is anything that occupies space and has mass.

Atom: The smallest unit of matter and are used to build more complicated substances in the body.

Molecules: Are particles of matter that are composed of one or more atoms. The basic unit of matter.

Atoms

Observed using tunneling microscopes and atomic force microscopes (AFMs)

Atoms are composed of several kinds of subatomic particles

Protons: subatomic particle occurring in all atomic nuclei, with a positive electric charge equal in magnitude to that of an electron, but of opposite sign.

Neutrons: Neutrons have a neutral electric charge (neither negative nor positive) and have slightly more mass than positively charged protons.

Electrons: Negatively charged particles

Anion: negative charge

Cation: positive charge

The nucleus of an atom composed of positively charged protons and uncharged neutrons

Atomic Number: The number of protons in the nucleus

Atomic Mass: The number of protons and neutrons combined

Elements, Molecules, and Compounds

• Elements: Pure substances that consist of only one type of atom, characterized by their atomic number.

• Molecules: Combinations of two or more atoms bonded together, which can be of the same or different elements.

• Compounds: Substances formed when two or more different elements chemically bond in fixed ratios, resulting in unique properties.

• Chemical Bonds: Forces that hold atoms together in molecules and compounds, including ionic, covalent, and metallic bonds, which determine the properties and behaviors of the resulting substances. Make atoms more stable (full outermost shell is full).

• Isotopes: Two atoms that have the same atomic number but different atomic masses of the same element.

• Radioactive Isotope: Isotope that emits radiation

• Radiation can damage cells. Exposure to high levels of radiation may cause cells to develop into cancer cells.

Chemical Bonds

Ionic Bond: forms between an atom that has only one or two electrons in the outermost level (that would normally hold eight) and an atom that needs only one or two electrons to fill its outer level. The atom with one or two electrons simply “donates” its outer shell electrons to the one that needs one or two. Attraction of an anion to a cation.

Ionic compounds usually dissolve easily in water because water molecules are attracted to ions and wedge between the ions—thus forcing them apart.

Dissociate: To form free ions

Electrolytes: Compounds that form ions when dissolved in water

Important Ions in Human Body Fluids

Sodium: Na+

Chloride: Cl−

Potassium (Latin kalium): K+

Calcium: Ca++

Hydrogen: H+

Magnesium: Mg+

Hydroxide: OH−

Phosphate: PO4≡

Covalent Bond: When atoms share electrons to achieve a full outer shell, resulting in a stable molecule. These bonds are not easily broken and normally do not break apart in water.

Hydrogen Bond: A kind of weak attraction that helps to hold your body’s substance together. Slight electrical charges may develop in different regions of a molecule when tiny hydrogen atoms are not able to equally share their electrons in a covalent bond. Oppositely charged ends of various molecules then electrically attract one another. Helps hold proteins in complex folded shapes. Occurs between two different molecules.

Inorganic Chemistry

Organic compounds are composed of molecules that contain carbon-carbon (C–C) covalent bonds, carbon-hydrogen (C–H) covalent bonds, or both. Few inorganic compounds have carbon atoms in them, and none have C–C or C–H bonds. Organic molecules are generally larger and more complex than inorganic molecules.

Ex: Water is an inorganic compound and the most abundant compound in the body.

Solutions

Water is a solvent

Solute are dissolved

Aqueous Solution: Water is the solvent for a mixture (a blend of two or more kinds of molecules)

Dehydration Synthesis: A chemical reaction that involves the loss of water from the reacting molecules, allowing them to bond together and form larger molecules such as carbohydrates, proteins, and nucleic acids.

Hydrolysis: A chemical reaction that involves the addition of water to break down larger molecules into smaller units, such as the breakdown of carbohydrates into sugars or proteins into amino acids.

Adenosine Triphosphate (ATP): breaks apart in the muscle cells to yield the energy needed for muscle contraction.

Acids, Bases, and Salts

Acids: HCl dissociates into H⁺ and Cl⁻, it shifts this balance in favor of excess H⁺ ions. pH less than 7

Bases: Substances that accept hydrogen ions (H+) in solution, usually having a pH greater than 7.

Neutral: Pure Water pH 7

pH: The relative H+ concentration is a measure of how acidic or basic a solution is. The H+ concentration is usually expressed in units of pH. The formula used to calculate pH units gives a value of 7 to pure water. A higher pH value indicates a low relative concentration of H+—a base. A lower pH value indicates a higher H+ concentration—an acid. Scale 0-14

Salts: Salts: Compounds formed from the neutralization reaction between an acid and a base, which dissociate in water to produce ions. They play a crucial role in maintaining the balance of electrolytes in biological systems.

Normal body function can be maintained only within a narrow range of pH of about 7.35 to 7.45

Acidosis: Low blood pH

Alkalosis: High blood pH

The body can remove excess H+ ions by excreting them in the urine. Another way to remove acid is by increasing the loss of CO2 (an acid) by way of the respiratory system

Buffers: Chemicals in the blood that maintain pH

Organic Chemistry

Organic compounds are much more complex than inorganic compounds.

Major types of organic compound found in the body: carbohydrates, lipids (fats and oils), proteins, and nucleic acids.

Carbohydrate

The name carbohydrate literally means “carbon (C) and water (H2O),” signifying the types of atoms that form carbohydrate molecules.

Monosaccharide (glucose, galactose, fructose) Single monosaccharide unit Used as a source of energy; unit used to build other carbohydrates

Disaccharide (sucrose, lactose, maltose) Two monosaccharide units Can be broken into monosaccharides

Polysaccharide (glycogen, starch) Many monosaccharide units Used to store monosaccharides (thus to store energy)

Lipid

Lipids include a diverse group of molecules that do not usually dissolve in water.

Lipid molecules formed by a glycerol unit or “head” joined to three fatty acid “tails.” The fatty acid components can be classified as saturated or unsaturated. Saturated fatty acids tend to be solid at room temperature and are found in butter and lard. Unsaturated fatty acids tend to be liquids and are found in oils such as corn oil and olive oil.

Triglyceride One glycerol head, three fatty acid tails Stores energy; provides protective structural padding

Phospholipid One glycerol/phosphate head, two fatty acid tails Forms cell membranes

Steroid Four carbon rings at core Stabilizes cell membranes; category of hormones

Protein

In addition to containing carbon, hydrogen, and oxygen, all amino acids contain nitrogen (N)

Structural proteins Amino acids Form structures of the body (fibers)

Functional proteins (enzymes, hormones) Amino acids Facilitate chemical reactions; carry signals; regulate functions

HDL: High-Density Lipoprotein (HDL) - Often referred to as "good cholesterol," it helps transport cholesterol from the arteries to the liver for excretion. Carries cholesterol away from cells and to the liver for elimination from the body.

LDL: Low-Density Lipoproteins (LDLs) - The cholesterol in LDLs is often called “bad” cholesterol because high blood levels of LDL are associated with atherosclerosis, a life-threatening blockage of arteries.

Structural proteins are shaped in ways that allow them to form essential structures of the body. Collagen, a protein with a fiber shape, holds most of the body tissues together. Keratin, another structural protein, forms a network of waterproof fibers in the outer layer of the skin.

Functional proteins have shapes that enable them to participate in chemical processes of the body. Functional proteins include some of the hormones, growth factors, cell membrane channels and receptors, and enzymes.

Enzymes: Chemical Catalysts - help a chemical reaction to occur but are not reactants or products themselves.

Nucleic Acid

Deoxyribonucleic acid (DNA) Nucleotides (contain deoxyribose) Contains information (genetic code) for making proteins

Ribonucleic acid (RNA) Nucleotides (contain ribose) Serves as a copy of a portion of the genetic code during protein synthesis

Adenosine triphosphate (ATP) Modified nucleotide (ribose, adenine, and three phosphates) Transfers energy from nutrient molecules to power work in the cell

NUCLEOTIDE DNA RNA

Sugar Deoxyribose Ribose

Phosphate Phosphate Phosphate

Nitrogen base Cytosine Cytosine

Guanine Guanine

Adenine Adenine

Thymine Uracil

Double Helix: DNA molecule, nucleotides are arranged in a twisted, double strand

DNA double helix is the “master code”

Messenger RNA (mRNA) molecules have a sequence that forms a temporary “working copy” of a portion of the DNA code called a gene.

Modified Nucleotide called Adenosine Triphosphate (ATP) plays an important energy-transfer role in the body

When a phosphate breaks off of ATP—forming adenosine diphosphate (ADP)—the energy released is used to do work in cells.