Chapter 2 ESSENTIAL CHEMISTRY FOR BIOLOGY

 

I.            What is matter?

Matter –

 

Matter is composed of chemical elements – substances that cannot be broken down into other substances

 

A. Atoms

•        Each element consists of one kind of atom

•        An atom is the smallest unit of matter that still retains the properties of an element

Fig 2.5

 

 

Mass

Charge

Neutrons

1 unit of mass

Neutral

Protons

1 unit of mass

Positive

Electrons

Little mass

Negative

 

NOTE:

1. Atoms are electrically neutral,

 

 

2.   Electron cloud arranged in energy shells

 

See fig 2.7

•        Atoms of the four elements most abundant in life

 

 

Electron Shells

-         lowest energy shell is nearest the nucleus. It holds

 

-         highest energy shell further from nucleus. The second shell holds

 

 

If outer shell is full →

 

If outer shell not full →

 

Electrons may move between shells by gaining / losing energy  →  FLUORENCE! Glow-in-the-dark

 

B. Elements

1. Pure substance containing one type of atom.

2. Arranged in a Periodic Table

Fig 2.2

•        All the elements are listed in the periodic table

 

Atomic Number:

 

Element Symbol:

 

Mass Number:

 

 

Each element has its own unique atomic number, element symbol, and mass number in its naturally occurring state.

Protons and neutrons have nearly the same mass thus:

Mass of Proton = Mass of Neutron

We assign each proton and each neutron a mass of 1.

Electrons have almost no mass, so we assign them a mass of 0.

 

Fig 2.3

3.  Twenty-five elements are essential to life

–      Four of these make up about 96% of the weight of the human body

–      Trace elements occur in smaller amounts

 

KNOW:  element symbol for:

O = Oxygen

C = Carbon

N = Nitrogen

H = Hydrogen

These are the elements that make up 96% of your body (by weight)

C.  Isotopes

1. Alternate forms of an atom that:

-          

 

 

-         

 

2. Isotopes are unstable → radiation.

 

Table 2.1

 

 

 

3. Uses of Radiation:

- X-Rays

- Radiation therapy

- Food sterilization

- Research

- Date rocks and fossils

D. Compounds & Molecules

- Compounds

 

 

NaCl

- Molecules

 

 

 

 

H2        NaCl

1. Atoms must bond to form molecules molecular formula – indicates # and kind of atoms

C6H12O6 = glucose

1.   Ionic Bonds

Fig 2.8

•        When an atom transfers or gains electrons, it becomes electrically charged

•        Charged atoms are called ions. One is (+) positive and the other is (-) negative

•        Ionic bonds are formed between oppositely charged ions

3.  Covalent Bonds

•        A covalent bond forms when two atoms share one or more pairs of outer-shell electrons.

•        A stronger bond is formed

Ex: H2O

 

•        Can share 1, 2, or 3 electrons

O ═ O    − C ≡ C −

Fig 2.9

 

Element

 

# Electrons in outermost shell

# Electrons needed to fill outermost shell

 

# covalent bonds

Hydrogen

Atomic # = 1

1

(In 1st shell)

 

 

Carbon

Atomic # = 6

4

(in 2ns shell)

 

 

Nitrogen

Atomic # = 7

5

(in 2nd shell)

 

 

Oxygen

Atomic # =8

6

(in 2nd shell)

 

 

 

Fig 2.9

Look more closely at water

Oxygen > # protons than Hydrogen, so Oxygen has a greater “+” charge, it holds electrons closer than Hydrogen.

 

 

Fig 2.11a

Polar Covalent bonds form between O’s Negative and H’s Positive poles

Fig 2.11b

•        The polarity of water results in weak electrical attractions between neighboring water molecules

•        These interactions are called hydrogen bonds

 

4.  Chemical reactions

-         

 

-         

 

 

reactants     →      products

Ex: 2 H2 + O2       →      2 H2O

 

II.            Importance of Water (thanks to Hydrogen bonds)

-        Water’s cohesive nature

-        Water’s ability to moderate temperature

-        Floating ice

-        Versatility of water as a solvent

 

1. Water’s cohesive nature

 

 

This is called COHESION and is very strong between water molecules. Cohesion allows for water to travel up, against gravity, in plants. Surface tension is related to cohesion and lets water act like it had an invisible film. (p. 29)

2. Water’s ability to moderate temperature

 

 

 

 

 

3. Floating ice

 

 

 

 

4. Versatility of water as a solvent

A solution

 

 

The dissolving agent is the solvent.

The substance that is dissolved is the solute.

If water is the solvent = aqueous solution.

Water is the solvent inside all cells, in blood, and in plant sap. It is the medium for all chemical reactions to occur.

 

III. Acids and Bases

A.

H2O    →        H+    +    OH-

 

H+      =      hydrogen ion

ACID. A chemical compound that donates H+ ions to solutions

 

OH-  =      hydroxyl ion

BASE (alkaline).

A compound that accepts H+ ions and removes them from solution.

 

 

 

 

B. In pure water

1. H+ = OH-     NEUTRAL

 

2. If ↑ H+        ACID       ↓ OH-

 

3. If ↓ H+        BASE      ↑ OH-

 

Fig 2. 17

•        To describe the acidity of a solution, we use the pH scale

Neutral =

 

Acidic =

 

(high H+)

Basic =

 

(low H+)

Each pH unit represents a 10-fold change in H+ concentration.

Ex. Lemon juice at a pH of 2 has 100 times more H+ than an equal amount of tomato juice at pH 4.

C.  Human blood and cells have a pH of ~ 7.4. This pH MUST BE MAINTAINED!

D.  Buffers

-         Compounds that resist pH changes

- they accept H+ ions when they are in excess

- they donate H+ ions when they are depleted

- Buffering is not foolproof

- Example: acid precipitation (rain)