The Chemistry of Life

Chapter 2

Atoms, Ions, and Molecules

Section 1:

Objectives1. What three subatomic particles make up

atoms?

2. How are all the isotopes of an element similar?

3. What are the two types of chemical bonds?

The Big Idea• Life Depends on chemistry

• Chemical reactions keep you alive

Atom• Basic unit of matter

Democrites

DALTON’S ATOMIC THEORYDalton performed experiments, unlike Democritus, to test his theory on atomic structure.Theory included the following ideas:All elements are composed of submicroscopic indivisible particles called atoms.Atoms of the same element are identical.Atoms of different elements can physically mix together or chemically combine with one another in whole-number ratios to form compounds.Chemical reactions occur when atoms are separated, joined, or rearranged.

• Protons -

• Neutrons -

• Electrons -

Positively charged (+)

Not charged (neutral)

Negatively charged (-)

Subatomic particlesBind together to form the nucleus

Electrons Protons

Neutrons

Nucleus

What are the 3 major parts of an atom?• Proton

• Neutron

• Electron

Describe Proton• Protons are positively charged particles found in the

atomic nucleus. Protons were discovered by Ernest Rutherford..

• Experiments done in the late 1960's and early 1970's showed that protons are made from other particles called quarks. Protons are made from two 'up' quarks and one 'down' quark.

Describe Neutron• Neutrons are uncharged particles found in the atomic

nucleus. Neutrons were discovered by James Chadwick in 1932.

• Experiments done in the late 1960's and early 1970's showed that neutrons are made from other particles called quarks. Neutrons are made from one 'up' quark and two 'down' quarks.

Describe Electron• Electrons are negatively charged particles that

surround the atom's nucleus. Electrons were discovered by J. J. Thomson in 1897.

• Electrons determine properties of the atom. Chemical reactions involve sharing or exchanging electrons.

Describe nucleus• The nucleus is the central part of an atom. It

is composed of protons and neutrons.

• The nucleus contains most of an atom's mass.

• It was discovered by Ernest Rutherford in 1911.

Describe Quark• Believed to be one of the basic building blocks of matter. Quarks

were first discovered in experiments done in the late 1960's and early 1970's.

• Three families of quarks are known to exist. Each family contains two quarks. The first family consists of Up and Down quarks, the quarks that join together to form protons and neutrons.

• The second family consists of Strange and Charm quarks and only exist at high energies.

• The third family consists of Top and Bottom quarks and only exist at very high energies.

Describe isotope• Atoms that have the same number of

protons but different numbers of neutrons

What is the Electron Cloud Model?

• Model of the atom pictures the electrons moving around the nucleus in a region called an electron cloud.

• The electron cloud is a cloud of varying density surrounding the nucleus. The varying density shows where an electron is more or less likely to be. Atoms with electrons in higher energy levels have additional electron clouds of different shapes that also show where those electrons are likely to be.

For more information, click here:

http://regentsprep.org/Regents/physics/phys05/catomodel/cloud.htm

Element• A pure substance that consists of

just one type of atom

6

CCarbon12.011

Atomic number

An elements atomic number = number of protons

Nonradioactive carbon-12 Nonradioactive carbon-13 Radioactive carbon-14

6 electrons6 protons6 neutrons

6 electrons6 protons8 neutrons

6 electrons6 protons7 neutrons

6

CCarbon12.011 Mass number

The Sum of protons and neutrons in the nucleus of an atom is its mass number

• The weighted average of the masses of an elements isotope is called its atomic mass

Radioactive isotopes• Can be dangerous

• Can be used practically• Radioactive dating

• Treat cancer

• Kill bacteria

Compounds• A substance formed by the chemical

combination of two or more elements in definite proportions

• Ex) H2O, NaCl

Table Salt

Ionic Bonds• Formed when one or more electrons

are transferred from one atom to another

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

Transferof electron

Protons +11Electrons -11Charge 0

Protons +17Electrons -17Charge 0

Protons +11Electrons -10Charge +1

Protons +17Electrons -18Charge -1

• If an atom loses an electron it becomes positive

• If an atom gains an electron it becomes negative

Ions• Positively and negatively charged

atoms

Covalent Bonds• Forms when electrons are shared

between atoms

Molecule• The structure that results when atoms

are joined together by a covalent bond

• Smallest unit of most compounds

Van der Waals Forces• A slight attraction that develops

between the oppositely charged regions of nearby molecules due to unequal sharing of electrons

Homework

1. Describe the structure of an atom.2. Why do all isotopes of an element have the

same chemical properties?3. What is a covalent bond?4. What is a compound? How are they related

to molecules?5. How do Van der Waals forces hold

molecules together?6. How are ionic bonds and Van der Waals

forces similar? How are they different?

Properties of Water

Section 2:

Objectives1. Why are water molecules polar?

2. What are acidic solutions?

3. What are basic solutions?

The Big Idea

• Much of our planet is covered in water• Water is necessary for life to exist• If life exists on other planets, there most

likely is water present• Water has many properties that make

life possible

Polarity(-)

(+)

The oxygen atom has a stronger attraction for electrons

Hydrogen Bonds• Because of waters partial charges, they

can attract each other and create hydrogen bonds

• Not as strong as covalent or ionic bonds

• Waters ability to create multiple hydrogen bonds gives it many special properties

Cohesion• Attraction between molecules of the

same substance

Adhesion• Attraction molecules of different

substances

Mixture• Material composed of two or more

elements or compounds that are physically mixed but not chemically combined

• Ex.) salt & pepper, earths atmosphere

Solutions• Mixture of two or more substances in

which the molecules are evenly distributed

• Ex. salt water

• Settles out over time

Solutions

Cl-

Water

Cl-

Na+

Water

Na+

Solute• Substance that is dissolved

• Ex. salt

Solvent• The substance that does the dissolving

• Ex. Water

Suspensions• Mixture of water and non-dissolved

materials

• Ex. sugar solution, blood

• Separate into pieces so small, they never settle out

The pH scale• Indicated the concentration of hydrogen

ions in a solution

Neutral

Acid

Base

Acids• Any compound that forms H+

(hydrogen) ions in solution

Base• A compound that produces OH-

(hydroxide) ions in solution

Buffers• Weak acids or bases that can react with

strong acids or bases to prevent sharp, sudden pH changes

Homework

1. Use the structure of a water molecule to explain why its polar

2. Compare acidic and basic solutions in terms of their H+ ion and OH- ion concentrations

3. What is the difference between a solution and a suspension?

4. What does pH measure?

5. The strong acid hydrogen fluoride (HF) can be dissolved in pure water. Will the pH of the solution be greater or less than 7?

Carbon-Based Molecules

Section 3:

Objective1. What are the functions of each group

of organic compounds?

LIFE’S BACKBONE• Most of the compounds that make up living things contain

carbon. In fact, carbon makes up the basic structure, or “backbone,” of these compounds. Each atom of carbon has four electrons in its outer energy level, which makes it possible for each carbon atom to form four bonds with other atoms.

• As a result, carbon atoms can form long chains. A huge number of different carbon compounds exist. Each compound has a different structure. For example, carbon chains can be straight or branching. Also, other kinds of atoms can be attached to the carbon chain.

Section 2-3

Interest Grabber

Methane Acetylene Butadiene Benzene Isooctane

MACROMOLECULES “GIANT MOLECULES”

• Formed by a process called polymerization

Monomers• Smaller units

Polymers• Linked up monomers

Carbohydrates• Compounds made up of carbon,

hydrogen, and oxygen atoms usually in a ratio of 1:2:1

• Main source of energy

• The monomers of starch are sugars

• Single sugar molecules are called monosaccharides

• The large macromolecules formed from monosaccharides are known as polysaccharides

Starch

Glucose

Lipids• Made mostly from carbon and hydrogen

atoms

• Used to store energy

Lipid Glycerol

Fatty Acids

Proteins• Macromolecules that contain nitrogen

as well as carbon, hydrogen, and oxygen

• Proteins are polymers of molecules called amino acids

Amino Acids

General structure Alanine Serine

Carboxyl group

• More than 20 different amino acids, can join to any other amino acid

• The instructions for arranging amino acids into many different proteins are stored in DNA

• Each protein has a specific role

• The shape of proteins can be very important

Proteins

Amino Acids

Nucleic Acids• Macromolecules containing hydrogen,

oxygen, nitrogen, carbon, and phosphorus

Double Helix

Nucleotides• Consists of 3 parts: 5-carbon sugar,

phosphate group and nitrogen base

Nitrogen Base

5-Carbon Sugar

Phosphate group

2 kinds of nucleic acids• RNA (ribonucleic acids) – contains

sugar ribose

• DNA (deoxyribonucleic acid) – contains sugar deoxyribose

Homework

1. Name four groups of organic compounds found in living thing

2. Describe at least one function of each group of organic compounds

3. Compare the structures and functions of lipids and starches

Chemical Reactions and Enzymes

Section 4 & 5:

Objectives1. What happens to chemical bonds during

chemical reactions?

2. How do energy changes affect whether a chemical reaction will occur?

3. Why are enzymes important to living things?

The Big Idea• Living things are made up of chemical

compounds

• Everything that happens to an organism is based on chemical reactions

Chemical Reactions• A process that changes or transforms

one set of chemicals into another

Reactants• Elements or compounds that enter into

a reaction

Products

• Elements or compounds produced by a chemical reaction

Example Reaction: Getting rid of carbon dioxide• In the blood

• In the lungs

CO2 + H20 H2CO3 (carbonic acid)

H2CO3 CO2 + H2O

Released as you breathe

Energy in reactions Energy-Absorbing Reaction Energy-Releasing Reaction

Products

Products

Activation energy

Activation energy

Reactants

Reactants

Activation Energy• The energy that is needed to get a

reaction started

Enzymes• Some chemical reactions are too slow

or have activation energies that are too high to make them practical for living tissue

• These chemical reactions are made possible by catalysts

Catalyst• Substance that speeds up the rate of

chemical reactions

• Work by lowering a reactions activation energy

Enzyme• Biological catalysts

• Speed up reactions in cells

• Very specific

• Named for the reaction is catylzes

• Enzyme names always end in -ase

Reaction pathwaywithout enzyme Activation energy

without enzyme

Activationenergywith enzyme

Reaction pathwaywith enzyme

Reactants

Products

Substrates• The reactants of enzyme catalyzed

reactions

• The active site of the enzyme and the substrate have complementary shapes

• Fit like a lock and key

Enzyme Action

Enzyme – substrate complex

Glucose

Substrates

ATP

Substratesbind toenzyme

Substratesare convertedinto products

Enzyme-substratecomplex

Enzyme(hexokinase)ADP

Products

Glucose-6-phosphate

Productsare released

Active site

Regulation of Enzyme Activity• Enzymes are affected by any variable that

affects chemical reactions1. pH

2. Temperature

3. Concentration

of enzyme

Homework

1. What happens to chemical bonds during chemical reactions

2. Describe the role of energy in chemical reactions3. What are enzymes, and how are they important to

living things?4. Describe how enzymes work, including the role of

the enzyme substrate complex5. A change in pH can change the protein. How might

a change in pH affect the function of an enzyme such as hexokinase (hint: think about the analogy of the lock and key)