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