Chapter 3 – Chemistry of Life

How is Chemistry related to Biology?

Four elements – carbon (C), oxygen (O), hydrogen (H), and nitrogen (N) make up 96% of living matter.

Review of the Atom

Atoms – the basic smallest unit of all matter

Subatomic Particle Charge Location

Atoms are electrically neutral.

o # protons = # electrons

Protons + Center of atom (nucleus)

Neutrons 0 Center of atom (nucleus)

Electrons - “cloud” around the nucleus

Elements

Pure substance made of only one kind of atom

Each represented by a symbol

Differ in the number of protons

Simplest element, hydrogen

Contains 1 proton, 1 electron

Neutrons usually equal to number of protons

Atoms that have different #’s of neutrons are called isotopes

The Periodic Table

The Periodic Table

Atomic number = number of protons

Atomic mass = protons + neutrons

Atomic Number

Element

Atomic Mass

Bonding

Compounds and molecules form by the chemical combination of two or more elements.

The number of valence (outermost) electrons determines the chemical activity and bonding ability of an atom.

Atoms combine (bond) to fill these outermost shells.

First shell is full with 2 electrons.

The remaining shells are “full” with 8 electrons.

Covalent Bonds – share valence electrons

Non-polar Covalent Bonds – share electrons equally

Polar Covalent Bonds – share electrons unequally results in the two ends

(poles) having slight positive and negative charges.

Ionic Bonding

Ionic bonds form between atoms when there is a transfer of electrons between one another. When an atom gains an electron… becomes a (-) ion. When an atom loses an electron… becomes a (+) ion.

Opposite charges attract, forming the bond.

Sodium atom (Na) Chlorine atom (Cl) Sodium ion (Na+) Chloride ion (Cl-)

Protons +11 Electrons -11 Charge 0

Protons +17 Electrons -17 Charge 0

Protons +11 Electrons -10 Charge +1

Protons +17 Electrons -18 Charge -1

Transfer of electron

Hydrogen Bonding

Hydrogen Bond – a weak attraction between two polar molecules

The slight positive end of one polar molecule is attracted to the slight negative end of another polar molecule.

Example: WATER!!!

Water

Importance:

Living things are ~75% water.

Water can absorb and store large amounts of energy (good insulator)

Water allows organisms to control their temperature (homeostasis)

Main characteristics 1. High surface tension

(cohesion) 2. Capillary action

(adhesion) 3. High heat of

vaporization 4. Resists temperature

change 5. Expands when it

freezes 6. Universal solvent

Cohesion

Cohesion – the attraction of water to itself

Because water is a polar molecule, it easily attracts other water molecules.

Surface tension

Attraction of water molecules to one another causes it to act like a stretched film over the surface of the water.

Adhesion

Attraction of water to other substances

The clinging of one substance to another.

Capillary action – movement of water up thin tubes Example – plants and the movement of water against

gravity!

High Heat of Vaporization

It takes a lot of energy to make water evaporate.

Importance: evaporative cooling – as water evaporates, the surface of the liquid that remains behind cools down

When sweat evaporates from skin, it draws away the heat to help cool the body.

Homeostasis!

Resists Temperature Change

Water changes its temperature less when it absorbs or loses a given amount of heat.

Significance… Homeostasis -beneficial in helping to maintain body

temperature as well

Coastal areas – a large body of water can absorb and store a huge amount of heat from the sun in the daytime and during the summer. At night and during the winter, the gradually cooling water can warm up the air. Example: Chicago and Lake Michigan

Water Expands When it Freezes

Water is less dense as a solid than a liquid, so ice floats in liquid water.

When water freezes, it expands because the hydrogen bonds keep the molecules at “arm’s length” and create a crystalline structure.

Important in the fitness of the environment. If ice sank, bodies of water would freeze solid, making life impossible.

Universal Solvent

Solution – a mixture in which all of the components are evenly distributed. Solvent – dissolves the solute (water) Solute – the substance that is dissolved

“Likes dissolve Likes” Water can easily dissolve other polar substances. Nonpolar substances do not dissolve in water. Oil

and water.

Acids and Bases

Acids – form hydrogen ions (H+)when dissolved in water

Bases – form hydroxide ions (OH)when dissolved in water

pH scale is based on the concentration of hydrogen ions in solutions Values between 0-14

Pure water 7

Acids <7

Soda, orange juice, vinegar, tomatoes, lemon, lime

Bases >7

Antacids, glass cleaner, baking soda

3.3 Carbon Compounds

Large molecules that contain carbon and hydrogen atoms

4 carbon compounds in all living things…

1) Carbohydrates

2) Lipids

3) Proteins

4) Nucleic Acids

Making Macromolecules

Monomers – smaller units (subunits) that join together to make larger molecules

Polymers – a long molecule consisting of many similar or identical building blocks

Monomer 1

Monomer 2

Monomer 4

Monomer 3

Polymer

Carbohydrates Elements

Monomers/ Basic Units

Functions

Location in Cell

Examples

C, H, O (1:2:1)

sugars

Short-term energy for cells, structural support, cell recognition

•Simple sugars/ monosaccharides (glucose, fructose) •Polysaccharides (cellulose, starch, glycogen)

Mitochondria

Carbohydrates, cont.

In some organisms, polysaccharides function as storehouses of energy

Starch – made by plants

Glycogen – made by animals

Both made of hundreds of linked glucose molecules

Cellulose – provides structural support for plants

Humans cannot digest cellulose

You cannot digest wood, mostly cellulose

Lipids

Elements

Monomers/ Basic Units

Functions

Location in Cell

Examples

C, H

Glycerol & Fatty Acid

Long-term energy for cells Water-proofing

Insulation Make up membranes around cells

Fats, Oils, Waxes, Phosholipids

Biological Membranes

Fats comparison

S -All carbon atoms in the chain are bonded to two hydrogen atoms (except the carbon at the end)

U-Some of the carbon atoms are linked by a “double” covalent bond, each with only one hydrogen atom-Produces kinks in the chain

Nucleic Acids

Elements

Monomers/ Basic Units

Functions

Location in Cell

Examples

C, H, O, N, P

Nucleotides

Store and transmit hereditary info

DNA RNA

Nucleus

Nucleic Acids

Nucleotide has 3 parts: a sugar, a base, and a phosphate group

Phosphate

Sugar

Base

Proteins

Elements

Monomers/ Basic Units

Functions

Location in Cell

Examples

C, H, O, N

Amino acids

Control reaction rates, Regulate cell processes, Transport substances in cells, Energy carriers

Enzymes Make up parts of hair, nails, skin

In membranes and cytoplasm

Proteins

20 amino acids are found in proteins

Some are polar, some are nonpolar

Some electrically charged, some are not

Folds help to compact the shape

Some are enzymes that promote chemical reactions

Some have structural functions

Collagen

Skin, ligaments, tendons, bone

Antibodies – defend against infection

Hemoglobin – carries oxygen from lungs to body tissues

PROTEINS ARE EVERYWHERE AND IN EVERYTHING!!!!

Proteins, cont’d

Carbon Compounds

include

Which are made of

which contain

Which are made of Which are made of Which are made of

which contain which contain which contain

Section 2-3 Concept Map

Carbohydrates Lipids Nucleic acids Proteins

Simple sugars

Glycerol/3 fatty Acid Subunits

Nucleotides

Amino Acids

Carbon, hydrogen,

oxygen

Carbon, hydrogen,

Carbon,hydrogen, oxygen, nitrogen,

phosphorus

Carbon, hydrogen,oxygen,

nitrogen,

Section 4 – Energy and Chemical Reactions

Energy is the ability to move or change matter

Exists in many different forms

Light, heat, chemical energy, mechanical, energy, and electrical energy, to name a few

Can be converted from one form to another

Energy can be stored or released by chemical reactions

Chemical Reactions

A chemical reaction is a process that changes one set of chemicals into another set of chemicals. Involves the breaking of bonds in the reactants and

the formation of bonds in the products.

Reactants – the elements or compounds that enter the reaction

Products – the elements or compounds that are produced by the reaction.

Reactants ----------> Products

2H2 + O2 --------> 2H2O

Energy and Chemical Reactions

Energy releasing = exothermic

Energy absorbing = endothermic

Catalysts

A catalyst is a substance that speeds up the rate of a chemical reaction.

Catalysts work by lowering the activation energy of a chemical reaction. Activation energy – the

amount of energy required to get the reaction started (to break the bonds in the reactants)

Example: Enzymes are proteins that act as catalysts in cells.

Enzyme Specificity

Substrate – substance on which an enzyme acts during a chemical reactions

Enzymes act only on specific substrates

EX – amylase assists in the breakdown of starch to glucose

Starch → glucose by amalyse

• Starch is amalyse’s substrate

Shape determines activity

Enzyme is typically a large protein with one or more deep

folds called active sites

Enzyme only acts on a specific substance because only that substrate

fits into its active site.

Enzyme Action

Factors in Enzyme Activity

Operate most efficiently within a certain range of temperatures

Outside of range temperatures can break or strengthen some of the enzyme’s bonds, changing it shape

Operate best within a certain pH value

Can cause bonds in the enzyme to break, reducing the effectiveness

ATP

Adenosine triphosphate

Energy Molecule of the cell

Single nucleotide with two extra energy-storing phosphate groups

When food molecules break down, some of the energy is stored temporarily in ATP.