Human Anatomy and Physiology I CHEMISTRY COMES ALIVE Chapter 2

Chapter 2 Outline Basic Chemistry Review of Matter, Energy, Atomic Structure, Elements, Molecules, and Chemical Bonds Biochemistry Inorganic Compounds Water, Salts, Acids and Bases Organic Compounds Carbohydrates, Lipids, Proteins, Nucleic Acids

Composition of Matter Elements Atoms Atomic symbol Cannot be broken down by ordinary chemical means Atoms Unique building blocks for each element Smallest unit of an element Atomic symbol One- or two-letter chemical shorthand for each element

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

Lesser Elements of the Human Body About 3.9% of body mass Calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), magnesium (Mg), iodine (I), and iron (Fe) < 0.01% of body mass Part of enzymes chromium (Cr), manganese (Mn), and zinc (Zn)

Atomic Structure Determined by numbers of subatomic particles Nucleus consists of neutrons and protons Neutrons No charge Mass = 1 atomic mass unit (amu) Protons Positive charge Mass = 1 amu

Atomic Structure Electrons Orbit nucleus Equal in number to protons in atom Negative charge 1/2000 the mass of a proton (0 amu)

Helium atom Helium atom Nucleus Nucleus 2 protons (p+) 2 neutrons (n0) 2 electrons (e–) 2 protons (p+) 2 neutrons (n0) 2 electrons (e–) (a) Planetary model (b) Orbital model Proton Neutron Electron Electron cloud

Proton Neutron Electron Hydrogen (H) (1p+; 0n0; 1e–) Helium (He) Lithium (Li) (3p+; 4n0; 3e–)

Identifying Elements Atomic number = number of protons in nucleus Mass number = mass of the protons and neutrons Atomic weight = average of mass numbers of all isotopes

Isotopes of Hydrogen Proton Neutron Electron Hydrogen (1H) (1p+; 0n0; 1e–) Deuterium (2H) (1p+; 1n0; 1e–) Tritium (3H) (1p+; 2n0; 1e–)

Radioisotopes Valuable tools for biological research and medicine Cause damage to living tissue Useful against localized cancers Radon from uranium decay causes lung cancer

Molecules and Compounds Most atoms combine chemically with other atoms to form molecules and compounds Molecule—two or more of the same type of atoms bonded together H2, O2 Compound—two or more different kinds of atoms bonded together C6H12O6

Chemical Bonds Electrons occupy up to seven electron shells (energy levels) around nucleus Octet rule Except for the first shell which is full with two electrons, atoms interact in a manner to have eight electrons in their outermost energy level (valence shell)

Chemically inert elements Outermost energy level (valence shell) complete 8e 2e 2e Helium (He) (2p+; 2n0; 2e–) Neon (Ne) (10p+; 10n0; 10e–)

Chemically Reactive Elements Outermost energy level not fully occupied by electrons Tend to gain, lose, or share electrons (form bonds) with other atoms to achieve stability

Chemically reactive elements Outermost energy level (valence shell) incomplete 4e 1e 2e Hydrogen (H) (1p+; 0n0; 1e–) Carbon (C) (6p+; 6n0; 6e–) 1e 6e 8e 2e 2e Oxygen (O) (8p+; 8n0; 8e–) Sodium (Na) (11p+; 12n0; 11e–)

Types of Chemical Bonds Ionic Covalent Hydrogen

Ionic Bonds Ions are formed by transfer of valence shell electrons between atoms Attraction of opposite charges results in an ionic bond Sodium atom (Na) (11p+; 12n0; 11e–) Chlorine atom (Cl) (17p+; 18n0; 17e–) Sodium ion (Na+) Chloride ion (Cl–) Sodium chloride (NaCl) + – (a) Sodium gains stability by losing one electron, and chlorine becomes stable by gaining one electron. (b) After electron transfer, the oppositely charged ions formed attract each other.

CI– Na+ (c) Large numbers of Na+ and Cl– ions associate to form salt (NaCl) crystals.

Covalent Bonds Formed by sharing of two or more valence shell electrons Allows each atom to fill its valence shell at least part of the time

Single Covalent Bonds Reacting atoms Resulting molecules or Structural + or Structural formula shows single bonds. Hydrogen atoms Carbon atom Molecule of methane gas (CH4) (a) Formation of four single covalent bonds: carbon shares four electron pairs with four hydrogen atoms.

Double Covalent Bonds Reacting atoms Resulting molecules or Structural + or Structural formula shows double bond. Oxygen atom Oxygen atom Molecule of oxygen gas (O2) (b) Formation of a double covalent bond: Two oxygen atoms share two electron pairs.

Triple Covalent Bonds Reacting atoms Resulting molecules or Structural + or Structural formula shows triple bond. Nitrogen atom Nitrogen atom Molecule of nitrogen gas (N2) (c) Formation of a triple covalent bond: Two nitrogen atoms share three electron pairs.

Hydrogen Bonds Attractive force between electropositive hydrogen of one molecule and an electronegative atom of another molecule

Hydrogen bond (indicated by dotted line) + – Hydrogen bond (indicated by dotted line) + + – – – + + + – The slightly positive ends (+) of the water molecules become aligned with the slightly negative ends (–) of other water molecules.

A water strider can walk on a pond because of the high surface tension of water, a result of the combined strength of its hydrogen bonds

What type of chemical bonds do we find in salt? Hydrogen Complex Covalent Ionic

Chemical Reactions Occur when chemical bonds are formed, rearranged, or broken Represented as chemical equations Chemical equations contain: Molecular formula for each reactant and product Relative amounts of reactants and products, which should balance 2H + O H2O

Synthesis reactions Smaller particles are bonded together to form larger, more complex molecules. Example Amino acids are joined together to form a protein molecule. Amino acid molecules Protein molecule

Decomposition reactions Bonds are broken in larger molecules, resulting in smaller, less complex molecules. Example Glycogen is broken down to release glucose units. Glycogen Glucose molecules

Exchange reactions Bonds are both made and broken (also called displacement reactions). Example ATP transfers its terminal phosphate group to glucose to form glucose-phosphate. + Glucose Adenosine triphosphate (ATP) + Glucose phosphate Adenosine diphosphate (ADP)

Rate of Chemical Reactions Rate of reaction is influenced by:  temperature   rate  particle size   rate  concentration of reactant   rate Catalysts:  rate without being chemically changed Enzymes are biological catalysts

Classes of Compounds Inorganic compounds Organic compounds Water, salts, and many acids and bases Do not contain carbon Organic compounds Carbohydrates, fats, proteins, and nucleic acids Contain carbon, usually large, and are covalently bonded

Water 60% – 80% of the volume of living cells Most important inorganic compound in living organisms because of its properties Involved in temperature regulation Body’s major transport medium Protects certain organs from physical trauma

How many electrons can the second valence shell hold? 8 2 10 7

Organic Compounds Contain carbon (except CO2 and CO, which are inorganic) Unique to living systems Include carbohydrates, lipids, proteins, and nucleic acids

Carbohydrates Sugars and starches Contain C, H, and O [(CH20)n] Three classes Monosaccharides Disaccharides Polysaccharides Major source of cellular fuel (e.g., glucose)

Lipids Contain C, H, O (less than in carbohydrates), and sometimes P Insoluble in water Main types Neutral fats or triglycerides – energy storage Phospholipids – cell membrane Steroids - Cholesterol, vitamin D, steroid hormones Eicosanoids - Prostaglandins

Proteins Polymers of amino acids (20 types) Joined by peptide bonds Contain C, H, O, N, and sometimes S and P Proteins have 4 levels of structure Primary, Secondary, Tertiary, Quaternary

Protein Synthesis + Dehydration synthesis: Hydrolysis: Peptide Amino acid Dipeptide Dehydration synthesis: The hydroxyl group of one amino acid is bonded to the amine group of the next, with loss of a water molecule. Hydrolysis: Peptide bonds linking amino acids together are broken when water is added to the bond. + Peptide bond

Protein Structure Amino acid (a) Primary structure The sequence of amino acids forms the polypeptide chain. Amino acid a-Helix: The primary chain is coiled to form a spiral structure, which is stabilized by hydrogen bonds. b-Sheet: The primary chain “zig-zags” back and forth forming a “pleated” sheet. Adjacent strands are held together by hydrogen bonds. (b) Secondary structure The primary chain forms spirals (a-helices) and sheets (b-sheets).

Tertiary structure of prealbumin (transthyretin), a protein that transports the thyroid hormone thyroxine in serum and cerebro- spinal fluid. (c) Tertiary structure Superimposed on secondary structure. a-Helices and/or b-sheets are folded up to form a compact globular molecule held together by intramolecular bonds.

Quaternary structure of a functional prealbumin molecule. Two identical prealbumin subunits join head to tail to form the dimer. (d) Quaternary structure Two or more polypeptide chains, each with its own tertiary structure, combine to form a functional protein.

Fibrous and Globular Proteins Fibrous (structural) proteins Strandlike, water insoluble, and stable Examples: keratin, elastin, collagen, and certain contractile fibers Globular (functional) proteins Compact, spherical, water-soluble and sensitive to environmental changes Specific functional regions (active sites) Examples: antibodies, hormones, molecular chaperones, and enzymes

Nucleic Acids DNA and RNA Contain C, O, H, N, and P Largest molecules in the body Contain C, O, H, N, and P Building block = nucleotide composed of N-containing base, a pentose sugar, and a phosphate group

Deoxyribonucleic Acid (DNA) Four bases adenine (A), guanine (G), cytosine (C), and thymine (T) Double-stranded helical molecule in the cell nucleus Provides instructions for protein synthesis Replicates before cell division, ensuring genetic continuity

Sugar: Deoxyribose Base: Adenine (A) Phosphate Thymine (T) Sugar Phosphate Adenine nucleotide Thymine nucleotide Hydrogen bond (a) Deoxyribose sugar Sugar-phosphate backbone Phosphate Adenine (A) Thymine (T) Cytosine (C) Guanine (G) (b) (c) Computer-generated image of a DNA molecule

Ribonucleic Acid (RNA) Four bases adenine (A), guanine (G), cytosine (C), and uracil (U) Single-stranded molecule mostly active outside the nucleus Three main types of RNA carry out the DNA orders for protein synthesis messenger RNA transfer RNA ribosomal RNA