Basic Chemistry for Biology Honors Biology 2013-2014

Composition of Matter

• Matter - Everything in universe is composed of matter • Matter is anything that occupies space or

has mass

• Mass – quantity of matter an object has

• Weight – pull of gravity on an object

Elements • Pure substances that cannot be broken down

chemically into simpler kinds of matter

• More than 115 elements (92 naturally occurring)

Periodic Table

• Elements are arranged by their atomic number on the Periodic Table

• The horizontal rows are called Periods & tell the number of energy levels

• Vertical groups are called Families & tell the outermost number of electrons

• Over 90% of the mass of an organism is composed of 6 elements (carbon, hydrogen, nitrogen, oxygen, phosphorous and sulfur)-CHNOPS

• Each element has unique chemical symbol • Consists of 1-2 letters

• First letter is always capitalized

Atoms • The simplest particle of an element

that retains all the properties of that element

• Properties of atoms determine the structure and properties of the matter they compose

The Nucleus

• Nucleus (central core) consists of positive charged protons and neutral neutrons

• Positively charged

• Contains most of the mass of the atom

The Protons= positive charge

• All atoms of a given element have the same number of protons

• Number of protons called the Atomic Number (ex: Oxygen has an atomic number of 8 – has 8 protons in its nucleus

The Neutrons • Neutral Charge (no charge)

• The number can vary slightly among atoms of the same element

• Different number of neutrons produces isotopes of the same element

Atomic Mass

• The atomic mass of an atom is found by adding the number of protons & neutrons in an atom

• The electrons add a negligible mass to the atom

The Electrons • Have a negative charge

• High energy particles with little or no mass

• Travel at very high speeds randomly at various distances (energy levels) from the nucleus

• Involved with making chemical bonds

• Atoms have energy levels or “electron clouds” • The 1st level can only hold 2 electrons • The other levels can hold 8 electrons • Atoms “want” to have full outer shells

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Mass Number

• The mass number of an atom is the total number of protons and neutrons

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Isotopes.

• Different atoms of an element that have the same number of protons but different numbers of neutrons are called

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• Stable isotopes doe not change their nuclear structure over time.

• Certain isotopes called radioactive isotopes are unstable because their nuclei decay to form a simpler and thus more stable configuration.

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Radioactive isotopes

• can be used to study both the structure and function of particular tissues

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Compounds

• Most elements do not exist by themselves.

• Elements readily combine with other elements in a predictable fashion

• A compound is a pure substance made up of atoms of two or more elements • The proportion of atoms are

always fixed

• A Chemical formula shows the kind and proportion of atoms of each element that occurs in a particular compound

• H2O

• Molecules are the simplest part of a substance that retains all of the properties of the substance and exists in a free state

• Some molecules are large and complex

Compounds vs. Molecules • A molecule is formed when two or more atoms join together

chemically. A compound is a molecule that contains at least two different elements. All compounds are molecules but not all molecules are compounds.

• Molecular hydrogen (H2), molecular oxygen (O2) and molecular nitrogen(N2) are not compounds because each is composed of a single element.

FYI • Water (H2O), carbon dioxide (CO2) and methane (CH4) are

compounds because each is made from more than one element. The smallest bit of each of these substances would be referred to as a molecule. For example, a single molecule of molecular hydrogen is made from two atoms of hydrogen while a single molecule of water is made from two atoms of hydrogen and one atom of oxygen.

Chemical Formulas

• Subscript after a symbol tell the number of atoms of each element

• H20 has 2 atoms of hydrogen & 1 atom of oxygen

• Coefficients before a formula tell the number of molecules

• 3O2 represents 3 molecules of oxygen or (3x2) or 6 atoms of oxygen

• The tendency of elements to combine and form compounds depends on the number and arrangement of electrons in their outermost energy level

• Atoms are most stable when their outer most energy level is filled

• Most atoms are not stable in their natural state

• Tend to react (combine) with other atoms in order to become more stable (undergo chemical reactions)

• In chemical reactions bonds are broken; atoms rearranged and new chemical bonds are formed that store energy

Covalent Bonds

• Formed when two atoms share one or more pairs of electrons

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Covalent bonds

• may be nonpolar or polar.

• In a nonpolar covalent bond, atoms share the electrons equally;

• Polar one atom does not attract the shared electrons more strongly than the other atom

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In a polar covalent bond,

• the sharing of electrons between atoms is unequal; one atom attracts the shared electrons more strongly than the other .

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Ionic Bonds

• Some atoms become stable by losing or gaining electrons

• Atoms that lose electrons are called positive ions

• Atoms that gain electrons are called negative ions

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Hydrogen Bond

• In a hydrogen bond, two other atoms (usually oxygen or nitrogen) associate with a hydrogen atom

• Hydrogen bonds are weak and cannot bind atoms into molecules. They serve as links between molecules.

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Solutions • A solution is a mixture in

which 2 or more substances are uniformly distributed in another substance

• Solute is the substance dissolved in the solution • Particles may be ions, atoms,

or molecules

• Solvent is the substance in which the solute is dissolved

• Water is the universal solvent

• Dissociation of water • Breaking apart of the water molecule into two ions of opposite charge

• H2O H+ (hydrogen ion) + OH- (hydroxide ion)

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Acids and Bases

• One of the most important aspects of a living system is the degree of acidity or alkalinity

Acids / Acidity

• High concentration of H+ (hydrogen) ions in solution

• HCl H+ + Cl-

Bases / Basic / Alkalinity

• Less H+ ions in solution, more OH- (hydroxide) ions

• NaOH Na+ + OH-

pH Scale

• Logarithmic scale for comparing the relative concentrations of hydrogen ions in a solution

• Ranges from 0 to 14

Each pH is 10X stronger than next

e.g. ph 1 is 10 times stronger than ph 2

The Ph Scale

• 0-6.9= acid: more H+ ions

• 7 = neutral: equal amounts of H+ & OH- ions

• 7.1-14 = base: less H+ ions and more OH- ions

• the lower the pH the stronger the acid

• The more H+ ions the lower the pH and the stronger the acid

• the higher the pH the stronger the base

• The more OH- ions the higher the pH and the stronger the base

• pH 7.0 is neutral

• pH Scale Principle: H+ ion concentration and pH relate inversely. OH- ion concentration and pH relate directly.

Buffers

• Control of pH is very important • Most enzymes function only within a very narrow pH • Control of pH is accomplished with buffers made by

the body –Buffer the pH slayer!! • Buffers keep a neutral pH

• Buffers neutralize small amounts of either an acid or base added to a solution

• Complex buffering systems maintain the pH values of your body’s many fluids at normal and safe levels

Buffering Systems in the Body

Bicarbonate Buffer System Is a mixture of carbonic acid (H2CO3) and its salt, sodium bicarbonate (NaHCO3) • If strong acid is added:

Hydrogen ions released combine with the bicarbonate ions and form carbonic acid (a weak acid) The pH of the solution decreases only slightly

• If strong base is added: It reacts with the carbonic acid to form sodium bicarbonate (a weak base) The pH of the solution rises only slightly

Protein Buffer System • Plasma and intracellular proteins are the body’s most plentiful and powerful

buffers • Some amino acids of proteins have:

Free organic acid groups (weak acids) Groups that act as weak bases (e.g., amino groups)

• Amphoteric molecules are protein molecules that can function as both a weak acid and a weak base

Physiological Buffer Systems The respiratory system regulation of acid-base balance is a physiological buffering system There is a reversible equilibrium between:

Dissolved carbon dioxide and water Carbonic acid and the hydrogen and bicarbonate ions CO2 + H2O « H2CO3 « H+ + HCO3¯

• When hyperventilation or rising plasma H+ occurs: Deeper and more rapid breathing expels more carbon dioxide Hydrogen ion concentration is reduced

• Alkalosis causes slower, more shallow breathing, causing H+ to increase Respiratory system impairment causes acid-base imbalance (respiratory acidosis or respiratory alkalosis)

CHEMICAL REACTIONS • A chemical reaction occurs when new bonds are formed or old

bonds break between atoms

• The starting substances of a chemical reaction are known as reactants or.

• The ending substances of a chemical reaction are the products.

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• Many chemical reactions are very complex involving multistep sequences called biochemical pathways

• Most chemical reactions require energy to begin

• The amount of energy needed to start the reaction is called activation energy

• Certain chemical substances (catalysts) reduce the amount of activation energy required

• Biological catalysts are called enzymes