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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

 

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

      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)

 

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

      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

      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:

      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:

      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