NOTES FOR BIOLOGY 1001

SECTION 005

Spring 2005

DR. STEVEN POMARICO, INSTRUCTOR

PART 1B

CHAPTER 2

CHEMICAL FOUNDATIONS FOR CELLS

>>>>>>>An understanding of chemistry is important because the interaction between atoms is one of the lowest levels of biological organization.

>>>>>The basic unit of all forms of matter is the atom

---atom is the smallest unit of matter that retains the physical and chemical properties of the element.

--element is a substance that can’t be broken down into other substances by chemical reactions.

                   -elements are composed of atoms

>>>>>>>Atoms are made up of subatomic particles. The 3 most stable subatomic particles are: neutrons, protons, and electrons (see fig 2.2)

---Protons are positively charged particles found at the core, or nucleus, of the atom.

---Neutrons are uncharged particles found at the core, or nucleus, of the atom.

---Electrons are light, negatively charged particles that orbit around the nucleus in electron shells

>>>The Atomic Nucleus

---atomic number is the number of protons in an atom of a particular element (see table 2-1)

                   -The atomic number is constant for a given element

The mass number or atomic weight of an element is the number of protons plus the number of neutrons

The atoms of a particular element may have different numbers of neutrons

         This difference results in isotopes

---Isotopes are atoms of the same element which have different atomic weights

—Radioisotopes are isotopes which are unstable and breakdown or decay by emitting energy and particles.

>>>The Electron Orbitals

---Electron orbitals are the three-dimensional space around the nucleus of an atom where an electron will be found 90% of the time. (See fig 2.6)

---The electron orbitals of an atom are arranged in electron shells based on their energy level.

Each electron shell occupies a specific distance from the nucleus. The further away, the higher the energy level. (See fig 2.7)

The chemical behavior of an atom is determined by the number of electrons in the outermost electron shell.

An atom with an incomplete (partially full) electron shell is reactive whereas an atom with a full electron shell is non-reactive or inert.

If an atom has a vacancy in the outer electron shell, it will try to fill that vacancy or get rid of the “extra” electrons so the outer shell is full.

CHEMICAL BONDS: JOINING ATOMS TO MAKE MOLECULES

>>>>>>>A reactive atom will try to fill the valence shell by interacting with other atoms. This interaction may result in two atoms forming a chemical bond.

---Chemical bond is an attraction that holds two atoms together.

---Molecule is two or more atoms held together by chemical bonds. The smallest unit that retains the physical and chemical properties of a compound.

         Similar atoms > (molecule) > element

         Different atoms > molecule > compound

---compound is composed of 2 or more elements in a fixed ratio

                   -example: table salt, NaCl

                   -compounds are composed of molecules

---Mixture is composed of 2 or more elements and/or compounds in proportions that can vary.

                   -example: our atmosphere, nitrogen, helium, carbon dioxide, etc.

>>>Formation of ions

If an atom has an almost empty or an almost full outer electron shell it is more likely to form an ion (See fig. 2.9)

---Ion is a charged atom or molecule

         ---Anion is a negatively charged atom or molecule

         ---Cation is a positively charged atom or molecule

---Ionic bond is formed by the attraction between oppositely charged ions after the completion of an electron transfer

         Ionic compounds are called salts and usually form crystals as a solid.

                   Ionic bonds are strong in crystals but break easily in water.

>>>Sharing Electrons

>>>>>>>Covalent bond is a bond formed when two atoms share electrons.

An atom may have to share only one pair of electrons to fill the outer shell. Some atoms may have to share two (or more) pairs of electrons or may have to share with more than one atom to fill the outer electron shell.

---Single covalent bond shares a single pair of electrons

---Double covalent bonds share two pairs of electrons

---Triple covalent bonds share three pairs of electrons

>>>Non-polar Covalent Bonds versus Polar Covalent Bonds

---Nonpolar covalent bond is a covalent bond in which the sharing of the electron pair is equal.

---Polar covalent bond is a covalent bond in which the sharing of the electron pair is unequal.

When polar covalent bonds form, the molecules which result may also be polar.

         -positive charge at one end negative charge at the other.

>>>Hydrogen bonds form between polar molecules

---Hydrogen bond is formed by the charge attraction when a hydrogen atom which is covalently bonded to one atom is attracted to a second atom. (See fig. 2.11a)

         A weak attractive force about 20 times easier to break than a covalent bond.

         A charge attraction between oppositely charged polar molecules.

Weak bonds are often as important as strong bonds in biological systems.

         Reversible binding

         Can form between molecules or within large molecules.

         Can help stabilize three-dimensional shape of large molecules.

>>>WATER AND LIFE

Cells are 70-95% water.

Water covers 70% of the surface of the earth.

Some of the most biologically important polar covalent bonds are the bonds in water molecules.

         Because of these polar covalent bonds, water is a polar molecule (See fig 2.12)

         This polarity along with the hydrogen bonding ability make water a very                    versatile solvent.

Polar and ionic substances which are hydrophilic are easily dissolved in water.

---Hydrophilic describes the property of having an affinity for water.

The polarity of water molecules makes water a poor solvent for molecules which do not have charged regions

Nonpolar substances are hydrophobic.

---Hydrophobic describes the property of not having an affinity for water.

         -hydrophobic molecules clump together in water because of hydrophobic                                        interaction 

>>>Water helps to moderate the effects of changes in temperature. 

---Temperature is a measure of the molecular motion in a element, compound or mixture

         Three properties of water help keep temperature stable:

                   1) High specific heat

                   2) High heat of vaporization

                   3) High heat of fusion

---Specific heat is the amount of energy that must be absorbed or lost for one gram of matter to change its temperature by one degree Celsius.

                   -specific heat of water 1 calorie/gram

                   -specific heat of alcohol 0.6 calorie/gram

                   -specific heat of table salt 0.2 calorie/gram

                   -specific heat of rock 0.02 calorie/gram

---Calorie (cal) is the amount of energy it takes to raise the temperature of one gram of water by one degree Celsius.

Water has a high heat of vaporization and cools surfaces as it evaporates.

---Vaporization (evaporation) is the transformation of matter from a liquid to a gas.

---Heat of vaporization is the quantity of heat a liquid must absorb for 1 gram to be converted to the gaseous state.

         -Leads to cooling of the surface of a liquid when during evaporation.

Water has a high heat of fusion and freezes much slower than other liquids.

         When water freezes, it forms an unusual solid, Ice

>>>Water Molecules Tend To Stick Together

         Water has cohesive behavior which is the result of hydrogen bonding between the water molecules and the other molecules and includes cohesion, and surface tension.

---Cohesion is the attraction of a molecule to the same kind of molecule.

                             This is the phenomenon that holds water together.

---Surface tension is the force that increases the ability of a surface of a liquid to stretch without breaking. (See fig. 2-11)

         Water has a greater surface tension than most liquids because of the arrangement of the hydrogen bonds at the surface.

         Causes water to bead

Water molecules can dissociate. That means that the hydrogen atom of one water molecule leaves its electron behind and forms a hydrogen ion (H⁺) and a hydroxide ion (OH^-).

                             H                                       

                                (                                                       

                                  O                                                              H⁺

                                ' =>                      _

                             H                                                           O

                                                                                                       '

                                                                                                    H

In pure water the number of H⁺ ions = the number of OH^- ions

If the solution is acidic, then the number of H⁺ ions is greater than the number of OH^- ions.

Conversely if the number of OH^- ions is greater than the number of H⁺ ions, then the solution is basic.

---Acid is a substance which increases the concentration of H⁺ in a solution.

---Base is a substance which reduces the concentration of H⁺ in a solution.

>>>The pH Scale

The degree of acidity is expressed on the pH scale.

---pH scale is a scale used to measure the acidity of solutions. The scale ranges from 0 to 14. (See fig. 2-10)

          For a neutral solution pH =7

         For an acidic solution pH =5

         For a basic solution pH = 9

Because the pH scale is a logarithmic scale, a change of one pH unit represents a tenfold change in the concentration of H⁺.

Most biological solutions are between pH 6 and pH 8

>>>Buffers Help Maintain A Constant pH

---Buffers are substances that prevent large sudden changes in pH.

         Buffers are combinations of H⁺ donor and H⁺ acceptors

Buffers function by accepting H⁺ ions from solution when they are in excess,          and donating H⁺ ions to the solution when the supply is depleted.

         Example: Bicarbonate buffer