The Chemical Level of Organization
Atoms, Molecules and Bonds
Atoms are the smallest stable units of matter
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Subatomic particles
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Protons = positive
charge; weight of approximately 1 Dalton
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Neutrons = no charge;
weight similar to protons
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Electrons = negative
charge; weigh 1/1836th Dalton
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Protons and neutrons are
found in the nucleus; electrons occupy electron cloud
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Atomic number = proton
number; atomic mass = protons and neutrons
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Isotopes are elements
with similar numbers of protons but different numbers of neutron
Electrons occupy a series of energy levels or electron shells.
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The outermost electron shell determines the reactivity
of the element.
Atoms combine through chemical
reactions
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Molecule = a chemical structure consisting of molecules
held together by covalent bonds
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Compound = a chemical substance composed of atoms of
two or more elements
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There are three types of bond: Ionic, covalent, and
hydrogen
Ionic Bonding
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Exchange
of electrons from one atom to another Ionic = attraction between
positive cations and negative anions
Covalent bonds exist between atoms that share electrons to form a
molecule
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Double covalent bond
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Non-polar covalent bond
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Polar covalent bond
Hydrogen bonds are weak forces that affect the shape and properties of
compounds
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Polar covalent bonds that occur when hydrogen
covalently bonds with another element
Matter and chemical notation
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Matter can exist as a solid, liquid or gas
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Depends on the interaction of the component atoms or
molecules
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Molecular weight is the sum of the atomic weights of
the component atoms
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Chemical notation
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Short-hand that describes chemical compounds and
reactions
Chemical Reactions
A chemical reaction occurs when reactants combine to generate one or more
products
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All chemical reactions in the body constitutes
metabolism
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Metabolism provides for the capture, storage and
release of energy
Basic energy concepts
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Work = movement of an object or change in its physical
structure
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Energy = the capacity to perform work
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Kinetic energy is energy of motion
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Potential energy is stored energy resulting from
position or structure
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Conversions are not 100% efficient, resulting in
release of heat
Metabolism
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Types of reaction
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Decomposition
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Synthesis
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Exchange
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Metabolism is the sum of all reactions
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Through catabolism cells gain energy (break down of
complex molecules)
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Anabolism uses energy (synthesis of new molecules)
Reversible reactions
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All reactions are theoretically reversible
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At equilibrium the rates of two opposing reactions are
in balance
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Anabolism = catabolism
Enzymes, energy and chemical reactions
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Activation energy is the amount of energy needed to
begin a reaction
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Enzymes are catalysts
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Reduce energy of activation without being permanently
changed or used up
Inorganic Compounds
Nutrients and Metabolites
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Nutrients are essential chemical compounds obtained
from the diet
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Metabolites are molecules synthesized or broken down
inside the body
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These can be classified as organic or inorganic
compounds
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Organic compounds have carbon and hydrogen as their
primary structural component
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Inorganic compounds are not primarily carbon and
hydrogen
Water and its properties
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Water is the most important constituent of the body
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Solution is a uniform mixture of two or more substances
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Solvent is the medium in which molecules of solute are
dispersed
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Water is the solvent in aqueous solutions
Electrolytes undergo ionization
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Compounds that interact readily with water are
hydrophilic
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Compounds that do not interact with water are
hydrophobic
pH is a measure of the concentration of hydrogen ions solution
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Neutral
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Acidic
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Basic
Acids and Bases
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Acids release hydrogen ions into solution
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Bases remove hydrogen ions from solution
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Strong acids and strong bases ionize completely
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Weak acids and weak bases do not ionize
Salts and buffers
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Salt = an electrolyte whose cation is not hydrogen and
whose anion is not hydroxide
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Buffers remove or replace hydrogen ions in solution
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Buffer systems maintain the pH of body fluids
Organic
Compounds
Organic compounds
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Organic compounds generally include
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Carbon
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Hydrogen
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and sometimes Oxygen
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Four major classes of organic compounds are
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Carbohydrates
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Lipids
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Proteins
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Nucleic acids
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High energy compounds are also organic compounds
Carbohydrates
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Important energy source for metabolism
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Monosaccharides, disaccharides and polysaccharides
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Di- and polysaccharides formed from monosaccharides by
dehydration synthesis
Lipids include fats, oils, and waxes
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Five classes:
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Fatty acids
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Eicosanoids
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Glycerides
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Steroids
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Phospholipids
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Glycolipids
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Triglycerides = three fatty acids attached by
dehydration synthesis to one molecule of glycerol
Steroids
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Are involved in cell membrane structure
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Include sex hormones and hormones regulating metabolism
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Are important in lipid digestion
Proteins perform many vital functions in the body. The six important types
are:
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Structural proteins
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Contractile proteins
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Transport proteins
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Enzymes
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Buffering proteins
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Antibodies
Proteins are chains of amino acids
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Amino acids contain an amino group, a carboxylic group
and a radical group
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Polypeptides are linear sequences of amino acids held
together by peptide bonds
The four levels of protein structure are:
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Primary structure (amino acids sequence)
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Secondary structure (amino acid interactions)
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Tertiary structure (complex folding)
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Quaternary structure (protein complexes)
Enzyme reactions
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Reactants (substrate) interact to yield a product by
binding to the active site of the enzyme
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Cofactors must bond to the enzyme before substrate
binding can occur
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Coenzymes are organic cofactors commonly derived from
vitamins
The shape of a protein determines its function
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Proteins pushed outside their optimal temperature and
pH range become temporarily or permanently denatured and will cease to function
Nucleic acids
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Store and process information at the molecular level
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Made of purines and pyrimidines
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DNA and RNA
Nucleic acids are chains of nucleotides
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Nucleotides are composed of a sugar, a phosphate and a
nitrogenous base
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Sugar = deoxyribose (DNA) or ribose (RNA)
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DNA Bases = adenine, thymine, cytosine, guanine
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RNA bases = adenine, uracil, cytosine, guanine
High energy compounds store cellular energy in high energy bonds
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Adenosine triphosphate (ATP)
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Made by adding a phosphate group to adenosine
diphosphate (ADP)
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Process referred to as phosphorylation
Chemicals and Cells
Biochemical compounds form functional units called cells
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Metabolic turnover allows cells to change and to adapt
to changes in their environment