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2 Basic Chemistry
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Composition of Matter Elements—fundamental units of matter
96 percent of the body is made from four elements Carbon (C) Oxygen (O) Hydrogen (H) Nitrogen (N) Atoms—building blocks of elements
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Subatomic Particles Nucleus Protons (p+) Neutrons (n0)
Orbiting the nucleus Electrons (e–) Number of protons equals numbers of electrons in an atom
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Figure 2.2
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Identifying Elements Atomic number— equal to the number of protons that the atom contains Atomic mass number—sum of the protons and neutrons
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Isotopes and Atomic Weight
Atoms of the same element with the same number of protons and the same atomic number Vary in number of neutrons
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Molecules and Compounds
Molecule—two or more atoms of the same elements combined chemically Compound—two or more atoms of different elements combined chemically
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Chemical Reactions Atoms are united by chemical bonds
Atoms dissociate from other atoms when chemical bonds are broken
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Chemical Bonds Ionic bonds
Atoms become stable through the transfer of electrons Form when electrons are completely transferred from one atom to another Ions Result from the loss or gain of electrons Anions are negative due to gain of electron(s) Cations are positive due to loss of electron(s)
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Figure 2.6
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Figure 2.6, step 1
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Figure 2.6, step 2
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Figure 2.6, step 3
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Chemical Bonds Covalent bonds
Atoms become stable through shared electrons Electrons are shared in pairs Single covalent bonds share one pair of electrons Double covalent bonds share two pairs of electrons
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Figure 2.8a
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Covalent Bonds Covalent bonds are either nonpolar or polar Polar
Electrons are not shared equally between the atoms of the molecule Have a positive and negative side or pole
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Figure 2.8b
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Chemical Bonds Hydrogen bonds Weak chemical bonds
Hydrogen is attracted to the negative portion of polar molecule Provides attraction between molecules
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Patterns of Chemical Reactions
Synthesis reaction (A + BAB) Atoms or molecules combine Energy is absorbed for bond formation Decomposition reaction (ABA + B) Molecule is broken down Chemical energy is released
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Figure 2.10a
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Figure 2.10b
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Patterns of Chemical Reactions
Exchange reaction (AB + CAC + B) Involves both synthesis and decomposition reactions Switch is made between molecule parts and different molecules are made
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Figure 2.10c
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Biochemistry: Essentials for Life
Organic compounds Contain carbon Most are covalently bonded Includes carbohydrates, lipids, proteins, nucleic acids Inorganic compounds Lack carbon Tend to be simpler compounds Includes water, salts, and some acids and bases
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Important Inorganic Compounds
Water Most abundant inorganic compound in the body Vital properties High heat capacity Polarity/solvent properties Chemical reactivity Cushioning
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Important Inorganic Compounds
Salts Easily dissociate into ions in the presence of water Vital to many body functions Include electrolytes which conduct electrical currents
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Chemical Reactions Dehydration synthesis—monomers or building blocks are joined to form polymers through the removal of water molecules
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Figure 2.13a
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Chemical Reactions Hydrolysis—polymers are broken down into monomers through the addition of water molecules
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Figure 2.13b
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Important Organic Compounds
Carbohydrates Contain carbon, hydrogen, and oxygen Include sugars and starches Classified according to size Monosaccharides—simple sugars Disaccharides—two simple sugars joined by dehydration synthesis Polysaccharides—long-branching chains of linked simple sugars
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Figure 2.14a–b
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Figure 2.14c
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Figure 2.14d
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Important Organic Compounds
Lipids Contain carbon, hydrogen, and oxygen Carbon and hydrogen outnumber oxygen Insoluble in water
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Lipids Common lipids in the human body Neutral fats (triglycerides)
Found in fat deposits Source of stored energy Composed of three fatty acids and one glycerol molecule Saturated fatty acids contain only single covalent bonds Unsaturated fatty acids contain one or more double covalent bonds
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Triglyceride, or neutral fat (a) Formation of a triglyceride
Glycerol 3 fatty acid chains Triglyceride, or neutral fat 3 water molecules (a) Formation of a triglyceride Figure 2.15a
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Figure 2.16a
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Figure 2.16b
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Lipids Common lipids in the human body (continued) Phospholipids
Contain two fatty acids rather than three Form cell membranes
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Phosphorus-containing (b) Phospholipid molecule (phosphatidylcholine)
Polar “head” Nonpolar “tail” Phosphorus-containing group (polar end) Glycerol backbone 2 fatty acid chains (nonpolar end) (b) Phospholipid molecule (phosphatidylcholine) Figure 2.15b
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Lipids Common lipids in the human body (continued) Steroids
Include cholesterol, bile salts, vitamin D, and some hormones Cholesterol is the basis for all steroids made in the body
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Figure 2.15c
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Important Organic Compounds
Proteins Account for over half of the body’s organic matter Provide for construction materials for body tissues Play a vital role in cell function Act as enzymes, hormones, and antibodies Contain carbon, oxygen, hydrogen, nitrogen, and sometimes sulfur Built from amino acids
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Proteins Amino acid structure Contain an amine group (NH2)
Contain an acid group (COOH) Vary only by R groups
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Amine group Acid group (a) Generalized structure of all amino acids
(b) Glycine (the simplest amino acid) (c) Aspartic acid (an acidic amino acid) (d) Lysine (a basic amino acid (e) Cysteine (a sulfur- containing amino acid) Figure 2.17a-e
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(a) Primary structure. A protein’s primary structure is the unique sequence of amino acids in the polypeptide chain. Amino acids Hydrogen bonds Amino acids (b) Secondary structure. Two types of secondary structure are named alpha-helix and beta- pleated sheet. Secondary structure is reinforced by hydrogen bonds. Dashed lines represent the hydrogen bonds in this figure. -pleated sheet Alpha- helix Figure 2.18a-b
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Figure 2.18c-d
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Proteins Fibrous proteins Also known as structural proteins
Appear in body structures Examples include collagen and keratin Stable
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Figure 2.19a
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Proteins Globular proteins Also known as functional proteins
Function as antibodies or enzymes Can be denatured
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(b) Hemoglobin molecule composed of the
Heme group Globin protein (b) Hemoglobin molecule composed of the protein globin and attached heme groups. (Globin is a globular or functional protein.) Figure 2.19b
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Enzymes Act as biological catalysts
Increase the rate of chemical reactions Bind to substrates at an active site
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Substrates bind to active 2 Structural changes Enzyme (E)
Product (P) e.g., dipeptide Substrates (S) e.g., amino acids Energy is absorbed; bond is formed. Water is released. Peptide bond + H2O Active site Enzyme-substrate complex (E-S) Enzyme (E) 1 Substrates bind to active 2 Structural changes Enzyme (E) site. Enzyme changes shape to hold substrates in proper position. occur, resulting in the product. 3 Product is released. Enzyme returns to original shape, ready to catalyze another reaction. Figure 2.20
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Important Organic Compounds
Nucleic Acids Built from nucleotides Pentose (5 carbon) sugar A phosphate group A nitrogenous base A = Adenine G = Guanine C = Cytosine T = Thymine U = Uracil.
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(a) Adenine nucleotide (Chemical structure)
Deoxyribose Phosphate sugar Adenine (A) (a) Adenine nucleotide (Chemical structure) KEY: Thymine (T) Cytosine (C) Adenine (A) Guanine (G) Figure 2.21a
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Nucleic Acids Deoxyribonucleic acid (DNA)
The genetic material found within the cell’s nucleus Provides instructions for every protein in the body Organized by complimentary bases to form a double-stranded helix Contains the sugar deoxyribose and the bases adenine, thymine, cytosine, and guanine Replicates before cell division
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(d) Diagram of a DNA molecule
Hydrogen bond Deoxyribose sugar Phosphate (d) Diagram of a DNA molecule KEY: Thymine (T) Cytosine (C) Adenine (A) Guanine (G) Figure 2.21c-d
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Nucleic Acids Ribonucleic acid (RNA)
Carries out DNA’s instructions for protein synthesis Created from a template of DNA Organized by complimentary bases to form a single-stranded helix Contains the sugar ribose and the bases adenine, uracil, cytosine, and guanine Three varieties are messenger, transfer, and ribosomal RNA
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Important Organic Compounds
Adenosine triphosphate (ATP) Composed of a nucleotide built from ribose sugar, adenine base, and three phosphate groups Chemical energy used by all cells Energy is released by breaking high energy phosphate bond ATP is replenished by oxidation of food fuels
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Adenine High energy bonds Ribose Phosphates (a) Adenosine triphosphate (ATP) Adenosine diphosphate (ADP) (b) Hydrolysis of ATP Figure 2.22a-b
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(a) Chemical work. ATP provides the
energy needed to drive energy- absorbing chemical reactions. Solute Membrane protein (b) Transport work. ATP drives the transport of certain solutes (amino acids, for example) across cell membranes. Relaxed smooth muscle cell Contracted smooth muscle cell (c) Mechanical work. ATP activates contractile proteins in muscle cells so that the cells can shorten and perform mechanical work. Figure 2.23a-c
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