•Unit 3• The Chemistry of Life

• Unit Objective:• To identify the carbon-based organic molecules of life and understand the roles they play in life processes.

Only copy down underlined material.Everything else is there for support.

•What’s Important About the Nutrition Label?• What does the label tell you?

• Why is this important?

•What Are Organisms Made Of?• Every organism is different depending upon it’s role or

needs but there are basic molecules that are universal.

•The Basic Compounds of Life.• Regardless of the amount, most organisms use these

elements to form the macromolecules of life.1. Fats

2. Proteins

3. Sugars

4. Nucleic Acids.

• These are the fundamental molecules of life that you will be required to know.

• These carbon-based molecules are known as Organic Compounds.

• Another molecule you will learn about in this mini-unit is water.

•Objectives• To review/identify what makes up matter.• To know the elements that form most organic molecules.• To review/understand why atoms form bonds.• To understand how and why these bonds are essential for

life by forming the carbon-based organic molecules of life.• This information will help you soon be able to explain how

these molecules participate in important processes in living things.

•Essential Questions• How does hydrogen, carbon, and oxygen combine to form

molecules that participate in living systems?• What do these molecules do to support life?

•Vocabulary• Atoms• Element• Valence electrons• Compound• Molecule• Ion

•Before You Learn About the Organic Macromolecules…• You must understand that all bigger molecules are built of smaller pieces.

• Everything of atoms…• Sometimes arranged into basic molecules.

• These smaller pieces are called…

• These will sometimes be called…• OR

• What is a subunit?• Something that is combined with other subunits to build

something bigger.

•Atoms

• All matter is made of very small particles called atoms.

• An atom is the smallest unit of matter that cannot be broken down by chemical means.

• These are the most basic subunit of matter & life.

• Every living and nonliving thing is made of matter.

• Matter is anything that has mass and takes up space.

•Atoms• The atom is composed of three main types of smaller particles.

• Protons: positively charged particles.

• Neutrons: particles with no charge.

• Electrons: negatively charged particles.

•Atoms• The particles are in two specific areas:

• The nucleus.• The electron cloud.

• Protons and neutrons are in the nucleus.

• Electrons are in various energy levels contained in the electron cloud around the nucleus.

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C

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What are the parts of an atom?

•How Is an Atom Built?• Find carbon on the periodic table.• This is the information for the element CARBON• Notice its row and column.

• Every box represents a different element.• An element is any quantity of a substance that is 100%

the same type of atom.• Being the same type means they have the same # of

protons. • Ex: Diamonds are always the element carbon, regardless of the

size, because every atom has 6 protons.

ROW

COLUMN

• The six highlighted below are the most abundant elements in the bodies of most biological organisms.

• Mark these in your Periodic Table.

•CHNOPS: What are the Most Abundant Elements in Biology?

•Reading the Periodic Table• Atomic Number• Symbol• Name• Atomic Mass

•Atomic Numbers, Mass, Electrons…• The boxes give a lot of information.• How do you know how many protons, electrons, and neutrons an element has?

• It’s all based upon the atomic number found in the periodic table.

• Atomic # = # protons • # electrons = # protons• # neutrons = atomic mass (whole) - # protons.

•IONS: What Happens When an Atom Gains or loses an Electron.• Ions are atoms that gain or lose electrons.

• This results in unequal numbers of p+ & e-.• These particles are now considered charged, or

ions.• Why? Some elements steal electrons.

•Formation of Ions: Count the p+ & e- before & after the exchange…

Sodium Before After Chlorine Before After

Protons +11 +11 Protons +17 +17

Electrons -11 -10 Electrons -17 -18

Total 0 +1 Total 0 -1

Na+ Cl-

Cation:A positively charged ion.

Anion:A negatively charged ion.

•Special Circumstance: IsotopesElements• Recall, elements are all the same type of atom because

every atom has the same number of protons.• For example, every atom for any amount of the element carbon

has six protons.• There are several types of carbon though.

• Atoms of an element can have different numbers of neutrons.

• Isotopes are atoms of elements that have a different number of neutrons.

• Isotopes create challenges and benefits because bonds form differently and they are usually radioactive to various degrees.

•Isotopes• Because Isotope atoms have the same number of protons, and also electrons, isotopes have the same chemical properties.

• The extra neutrons makes the isotope radioactive.

•The Numbers Really Matter• The numbers represent an atom’s proton, neutron, and electron number when it is un-bounded and electrically neutral.

• Atoms are rarely like this, stable, in nature.• Mainly because the electrons are always flying around.

electron

•The Energy Levels• Atoms are usually represented as a nucleus surrounded by rings.

• The rings are energy levels.• The row (going from left to right) tells you how many rings the atom has.

• Hydrogen is in the 1st row = one ring• Nitrogen is in the 2nd row = two rings

• Shown to the right.

• These are the atom’s energy levels.

•The Outer Ring… The Valence Shell• The outer ring holds the valence shell electrons.

• For most groups of atoms, you can determine the # of valence shell electrons from the column it’s in.

• How many does this element have?• What element is it?

• Knowing the valence shell is important because in the valence shell bonding happens.

•Reading the Periodic Table• The Column tells you how many electrons in the outer shell (valence electrons).

• The Row tells you how many rings (Energy levels)

•Concept Check• On your handouts, complete the blank atom for the element carbon.

• Draw the:• Correct # of electrons• Correct # of electron in the valence shell• Correct # of protons• Correct # of neutrons

• Put them in the correct places.

•Try It Again…• Try Phosphorus

• Draw the:• Correct # of electrons• Correct # of electron in the valence shell• Correct # of protons• Correct # of neutrons

• Put them in the correct places.

•Chemical Bonds• Remember, electrons are orbiting the nucleus in the region

called the electron cloud... In different energy levels.• The outer most edges of this cloud is called the valence shell.• There is a strict rule for how many electrons are in this valence

shell & each group is slightly different.• It’s based upon the group the element is in.• Group 1A (hydrogen, etc.) has one valence electron.• Group 2A (beryllium, etc.) has two.

•Chemical Bonds• Remember, electrons in the outermost level, or shell, are called

valence electrons.• When more than one atom combines, a force called a chemical

bond holds them together in the valence shell.• There are three types of bonds that you need to know.

• Covalent bonds• Ionic bonds• Hydrogen bonds.

• The RULE OF BONDING = Atoms tend to combine with each other such that eight electrons will be in the valence shell.

• The reason is stability!

•Valence electrons:

•Chemical Bonds, continued• Every other element will bond with other elements to get to 8 valence electrons.

• Chemical bonds form between groups of atoms because atoms become stable when they have eight electrons in the valence shell.

• When atoms of different elements combine, a compound forms.

• A compound is a substance made of the bonded atoms of two or more elements.

•Common Compounds• Ammonia (NH3)

• Water (H2O)

• Methane (CH4)

• Glucose (C6H12O6)

• Salt (NaCl)

•Ionic CompoundsIonic Bonding• Atoms can sometimes achieve a stable valence level by

losing or gaining electrons.• When this happens, the charge of the atom changes

slightly and an ion is formed.• An ion is an atom or group of atoms that has an electric

charge because it has gained or lost electrons.

• Opposite charges attract.• The attractive force between oppositely charged ions is

an ionic bond.

•How Do You Know How Many Electrons Get Exchanged?• It is all based upon the number of valence electrons for the element in its basic form.

• The metals on the left usually give electrons because they are closer to 8 if they lose a few.

• The non-metals on the right usually gain electrons because they will achieve 8 if they gain just a few.

• What happens when the electron leaves sodium and goes to chlorine?

• The electrons no longer equal the protons and they form into oppositely charged ions, like mini-magnets.These opposite charges attract each other!

•Find These Elements on you Periodic Table

How close are these elements to achieving 8 in their valence shell?Is it faster to gain a few or lose a few?The numbers of e- gained/lost are variable & correspond to how many they need.What about carbon?

Gains e-

Loses e-

CarbonGains or Loses e-

•Try Drawing Example B1: Sodium & Chlorine

•Formation of Ions: Count the p+ & e- before & after the exchange…

Sodium Before After Chlorine Before After

Protons +11 +11 Protons +17 +17

Electrons -11 -10 Electrons -17 -18

Total 0 +1 Total 0 -1

Na+ Cl-

•How Do You Show the Bonds?• Ionic

Or…

Bohr Model

Lewis Structure

•Try Drawing Example B2: Magnesium & Iodine

I

I+2

-1

-1

Since Magnesium donated 2 electrons what should its charge be?

Since each chlorine received one electron what should each charge be?

When Magnesium loses its outer electrons it exposes its next lower energy level, which happens to have 8 electrons.

•Chemical Bonds, continuedCovalent Bonding• One way that atoms bond is by sharing valence

electrons to form a covalent bond.

• A molecule is a group of atoms held together by covalent bonds.

• A water molecule, H2O, forms when an oxygen atom forms covalent bonds with two hydrogen atoms.

•Poor Oxygen…• Ah, I’m sad because my valence shell isn’t filled.• If there was only some way to get more.• Wait. Hey Buddy. If we shared some electrons, then we could both have

8…kinda.• Now we both can have eight!• Sometimes… and that’s enough to form a covalent bond.

•How Do You Show the Bonds?• Covalent

Or…

Bohr Model

Lewis Structure

•Illustrate Ionic & Covalent Bonding• 2 minutes…• With Lewis Structures, complete C2.

•Polarity

• Polar Molecules result when the resulting molecule has partial charges on opposite ends because of electrons are not shared equally.

• In some covalent molecules, the electrons are shared equally between the atoms in the molecule.

• In some covalent bonds, the shared electrons are attracted more strongly to one atom than to the other.

• It’s due to electronegativity (something you don’t need to know right now).

• As a result, one end of the molecule has a partial negative charge, while the opposite end has a partial positive charge.

•Same Atoms sharing electrons equally Make it Non-Polar

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•Not Sharing Electrons Equally Results in Polar Molecules

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Partially +The electrons spend less time on this side of water

Partially –The electrons spend more time on this side of water.

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•Not Sharing Electrons Equally can sometimes be 2 atoms, sometimes more.

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Partially +

Partially -

•Hydrogen Bonding• A hydrogen bond is a

bond that forms between the positive hydrogen atom of one molecule and the negative pole of another molecule.

Represented as dashed lines.

We will see these again…

•Polarity, continuedHydrogen Bonds• When bonded to an oxygen, nitrogen, or fluorine atom, a

hydrogen atom has a partial positive charge nearly as great as a proton’s charge.

• It attracts the negative pole of other nearby molecules. • This attraction is stronger than attractions between other

molecules, but not as strong as covalent bonds.• However, hydrogen bonding plays an important role in

many of the molecules that make up living things.

•Polarity of Water• Water is a molecule that shares electrons unequally.

• Oxygen attracts the electrons more than hydrogen does.

• This causes the oxygen atom to be, on average, more negative than the hydrogen, which tend to be more positively charged.

δ+

δ+

2δ-

•Polar Molecules: Water

δ+δ+

2δ-

The polarity of water makes it able to form polar bonds with other water molecules, called hydrogen bonds, due to the negative oxygen and the positive hydrogen.

•Special Circumstance: Noble Gasses• Some atoms won’t bond with other elements because they already have 8 valence electrons.

• These are called Nobel Gasses.• These are group 8A (all the way on the right).

•Concept Review• What are the three subatomic particles?• Where are they located?• Do electrons go anywhere they want?• What is an isotope?• What is an ionic bond?• What is a covalent bond?• What makes a molecule polar?

•Why Bonding is Important?• The reason why we review bonding is because the ability of atoms to interact with each other allows for them to build larger molecules.

• Depending on the types of numbers of atoms an almost limitless number of molecules and compounds can be formed, each with its own unique properties.

• These build on one another to make life possible.

•Closure…• Questions?

• What did you learn today?• Reflect in your warm ups…

•Now• Get into your groups. • Together you will use your notes and books to complete the worksheet provided so I know you understand the basic concepts of bonding.

• Due next class period.

•Atomic Models• There are a variety of ways to represent an atom…• It really depends on why you are showing the atom that will determine how you show it.

• Electron-Dot Diagrams = show electrons & protons for ions & bonding

• Space filling models = show how the molecule looks in 3D

• Bohr’s model = shows all electrons to represent energy levels. WHAT YOU BUILT

• Lewis structures = shows valence electrons (only) for bonding

•Lots of Atoms

• Which one’s right?

•How to Represent an Atom.• Standard Electron Dot Diagram.• Space-filling (O2)

• Bohr’s Model• Lewis Structure

•Lewis Dot Structures

Shows only the electrons that participate in bonding.

•Bohr’s V. Rutherford’s

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Different OrbitsSame Orbit

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•Where electrons actually are…Schrödinger• Q: Can you

identify where the electron is?

• A: No! because the electrons never stop moving!

•Group Section Questions: Answer these questions together as a group. Answers only. You have 10 minutes. We will cover these answers together at the end of class.

1. A(n) _________ is the smallest unit of matter that cannot be broken down by chemical means.

2. Identify the 3 sub atomic particles of atoms and their locations in words or in an illustration.

3. A(n) _________ is a substance made of only one kind of atom that has the same number of protons.

4. Locate oxygen and tell me how many protons, neutrons, and electrons it has. (use your periodic table…the atomic number is extremely useful).

5. Atoms are most stable when they have 8 electrons in their ______ ______.6. How many protons, electrons, neutrons, energy levels, and valence electrons

does carbon have?7. Name two ways that atoms can form bonds (combine to become more stable).8. Describe polarity and a popular polar molecule.9. Explain how polarity can cause salt & sugar to dissolve in water.10. Water is an example of a compound that is held together by ________ bonds.11. Atoms gain or lose ___________ to form ions.12. The opposite ends of a polar molecule have ___________ charges.13. A(n) _______ ______ is a weak chemical attraction between polar molecules.

1. A(n) _________ is the smallest unit of matter that cannot be broken down by chemical means.

2. Identify the 3 sub atomic particles of atoms and their locations in words or in an illustration.

3. A(n) _________ is a substance made of only one kind of atom that has the same number of protons.

4. Locate oxygen and tell me how many protons, neutrons, and electrons it has. (use your periodic table…the atomic number is extremely useful).

5. Atoms are most stable when they have 8 electrons in their __________ _________.6. How many protons, electrons, neutrons, energy levels, and valence electrons

does carbon have?7. Name two ways that atoms can form bonds (combine to become more stable).8. Describe polarity and a popular polar molecule.9. Explain how polarity can cause salt & sugar to dissolve in water.10. Water is an example of a compound that is held together by ___________ bonds.11. Atoms gain or lose _______________ to form ions.12. The opposite ends of a polar molecule have ___________ charges.13. A(n) __________ _________ is a weak chemical attraction between polar molecules.

atom

p+, e-, n0… p+, n0 in nucleus, e- in electron cloudelement

8 8 8

shellvalence6 6 6 2 4

Ionic (swapping electrons), covalent (sharing electrons) When a molecule has a partial + & partial – charge. Water is polar and can dissolve the ions & polar molecules in sugar & salt

because of polarity.

covalent

electronsopposite

bondhydrogen

•Group Section Questions: Answer these questions together as a group. Answers only. You have 10 minutes. We will cover these answers together at the end of class.

•Homework

• Build a Phosphorus Atom1. Find the atom on the periodic table

2. Determine the number of protons, electrons, & neutrons.

3. Determine the energy levels.

4. Fill in the electrons, protons, & neutrons.

• Illustrate the Ionic Bond of NaCl• Show the electron swapping with an arrow.

• Illustrate the compound H2O• Show how it is a polar molecule.

• Show hydrogen bonding between 2 H2O molecules

•Homework

• Build a Phosphorus Atom1. Find the atom on the periodic table

2. Determine the number of protons, electrons, & neutrons.

3. Determine the energy levels.

4. Fill in the electrons, protons, & neutrons.

• Illustrate the Ionic Bond of NaCl• Show the electron swapping with an arrow.

• Illustrate the compound H2O• Show how it is a polar molecule.

• Show hydrogen bonding between 2 H2O molecules

•Homework

• Build a Phosphorus Atom1. Find the atom on the periodic table

2. Determine the number of protons, electrons, & neutrons.

3. Determine the energy levels.

4. Fill in the electrons, protons, & neutrons.

• Illustrate the Ionic Bond of NaCl• Show the electron swapping with an arrow.

• Illustrate the compound H2O• Show how it is a polar molecule.

• Show hydrogen bonding between 2 H2O molecules

•Homework

• Build a Phosphorus Atom1. Find the atom on the periodic table

2. Determine the number of protons, electrons, & neutrons.

3. Determine the energy levels.

4. Fill in the electrons, protons, & neutrons.

• Illustrate the Ionic Bond of NaCl• Show the electron swapping with an arrow.

• Illustrate the compound H2O• Show how it is a polar molecule.

• Show hydrogen bonding between 2 H2O molecules

•In-class Exercise: Check For Understanding

• To check that you’ve been paying attention and you understand

• Build a Phosphorus Atom1. Find the atom on the periodic table

2. Determine the number of protons, electrons, & neutrons.

3. Determine the energy levels.

4. Fill in the electrons, protons, & neutrons.

• Illustrate the Ionic Bond of NaCl• Illustrate the compound H2O• Show hydrogen bonding between 2 H2O molecules

n0 = 15p+ = 15

•Section Questions: Answer these questions in your notebooks. Write complete sentences for them all.

Section 2.11.A(n) _________ is the smallest unit of matter that cannot be broken down by chemical means.2.Identify the parts (particles) of atoms and their locations in words or in an illustration.3.A(n) _________ is a substance made of only one kind of atom that has the same number of protons.4.Name one element & how many protons, neutrons, and electrons it has. (use the back of the book for reference…the atomic number is extremely useful).5.Atoms are most stable when they have eight electrons in their _________ _________.6.How many protons, electrons, neutrons, energy levels, and valence electrons does carbon have?7.Name two ways that atoms can form bonds (combine to become more stable).8.Explain how charges cause salt & sugar to dissolve in water.9.Water is an example of a compound that is held together by _____ bonds.10.Atoms gain or lose ________________ to form ions.11.The opposite ends of a polar molecule have _____________ charges.12.A(n) ___________ ___________ is a weak chemical attraction between polar molecules.Section 2.2List & describe the 4 properties of water that make life on Earth possible.An example of a substance that heats more slowly than many other substances is ______.Why does water float?An attraction between particles of the same substance is called_______, while an attraction between particles of different substances is called ________.Differentiate between acids & bases.A solution that contains more hydronium ions than hydroxide ions is ____ and has a pH below _____.What is a buffer & what is it’s role in maintaining homeostasis?

•Summary• All matter is made up of atoms. An atom has a positively

charged nucleus surrounded by a negatively charged electron cloud.

• Chemical bonds form between groups of atoms because most atoms became stable when they have eight electrons in the valence shell.

• Polar attractions and hydrogen bonds are forces that play an important role in many of the molecules that make up living things.

http://www.flw.com/datatools/periodic/118.htm

•Atoms, continued• 99+% of the atom’s mass is made up

of the protons and neutrons found in the nucleus.

• The other <1% of the atom’s mass is found by adding up all the individual electrons.

• The nucleus takes up less than 1% of the atom’s physical space… its volume, however.

• 99+% of the atoms actual space is the electron cloud where the electrons are zooming around at nearly the speed of light.

• Technically, we are 99% empty space!

Electron Cloud

Nucleus

•Quick Facts. Put an atom into perspective.• If you used a stadium to model and atom…

• The Houston Astrodome (Home of the Houston Astros…a baseball team) seats 60,000 fans, covers 9 acres and the dome rises to a height of 200ft.

• If you could blow up an atom to the size of this stadium a basketball could represent the volume of an atom's nucleus.

• The rest of the open area is the volume of where the electrons, maybe the size of tiny BB’s, would be constantly flying around at speeds approaching the speed of light through the electron cloud in their orbitals.

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•Technically, We Are 99.9% Empty Space?

• Why do we appear solid?

•Why Do Things Feel Solid?

We actually feel very little that is solid.What we feel is the interpretation of what solid is because of the electron clouds pushing away from one another.Which segues into the next part of the lesson.