Honors Biology Chapter 2

Chemistry

DRY ERASE ATOM ATTITUDE

• Everyone gets a dry erase board, dry erase pen, and tissue for erasing.

• The teacher will ask you a question about atomic structure, you will write your answer and hold up your board.

Are you wondering why we are learning chemistry in biology class?• All of our cells are made of chemical

compounds.• All the activities of our bodies work on

chemical reactions.• All of our body’s reactions use water.

Such as neurotransmitters affecting neurons

MATTER

• Anything that occupies space (VOLUME) and has MASS

• Is air matter?• Yes

Match as energy (capacity to do work) or matter (occupies space

and has mass)

• Water• Electricity• Air• Helium• Sunlight• Iron• Carbon

• Matter• Energy• Matter• Matter• Energy• Matter• Matter

2.1 ELEMENTS, ATOMS, COMPOUNDS (are matter)

YOU NEED TO KNOW

• The Names (spelled correctly) and the Symbols (written correctly) on p. 18 (Table 2.1)

• “Elements in the Human Body”• 25 elements (includes trace

elements)• QUIZ on FRIDAY Sept. 27

ELEMENTS

• Substance that cannot be broken down to other substances by ordinary chemical means (heating, adding an acid…)

• YouTube - ?Tom Lehrer's

The Elements" animated??

****ASAP SCIENCE Periodic Table

In Order

OR YouTube - ?The Elements Animation??

Where can you find an element?

The Periodic Table of the Elements – see Appendix 2 and get your personal copy

ELEMENTS AND SYMBOLS:Ca, H, Li, O, C, Mg

• What rules apply to writing the symbols (abbreviations of the elements)?

• First letter capital, second letter is lower case

• What are the four most common elements in the human body? (see chart)

• CHON• What are trace elements?• Less than 0.01% of human body weight

Which are elements?

• Cu• C• CO• N• NO• WHY?• Cu C N only

one kind of matter Gold - Au

COMPOUNDS• Substance of two or more different atoms

chemically combined in a fixed ratio• EXAMPLES: CO2

• H2SO4

• H2O

• CO• How is a compound written differently than an

element?• More than one kind of element (more than

one capital letter).• NOTE: H2 is not a compound – its an element• (Only one kind of element)

Subscripts (tell how many atoms there are)

Formula• Formula is the abbreviation for a

compound. • CO2 H2SO4 H2O• Carbon dioxide sulfuric acid water• What rules seem to apply to writing a

formula?• Capital letters for elements• Subscript number behind and just

below the line of what element it represents

Which are compounds?

• Na N H2 NO2 H2O Why?

• NO2

• H2O• 2 or more different elements

chemically joined (2+ diff. capital letters)

Which are symbols?Abbreviations for elements

• C CO2 Mn CO Ni Why?

•C Mn Ni • Only one capital letter

What’s the difference?

• Co CO co

• Symbol formula nothing

Which are formulas?Abbreviation for a compound

• H2SO4 Cl2 H20 Al Why?

H2SO4 H20 abbreviations for compounds (2 or more different kinds of elements)

Can you figure out the difference between a mixture and a

compound?

• A mixture is two or more elements (or compounds) NOT chemically joined.

• A compound is two or more atoms chemically joined.

• Do Worksheet: Elements, Compounds, Mixtures

DO WORKSHEET: Elements, Compounds, Mixtures

• (back of Atomic Mass and Atomic Number Worksheet)

• Work in groups of three, then we’ll compare answers.

2.2 What are trace elements?• Needed in the body in only small

amounts• Like mg (milligrams)• WHY IMPORTANT IF WE DON’T

NEED SO MUCH?• Minerals act as catalysts (speed

up reactions) for many biological reactions

Trace Elements

Needed by some organisms but only in very small amountsLike iodine, we need only 0.15 mg per dayA deficiency will cause a goiter

Trace Elements

• Fluorine – in drinking water, toothpaste• (help dental decay) But too much can

cause fluorosis (white chalky build-up)

Trace Elements

• Iron Rich Foods• Most important

use is to carry

oxygen in the blood

2.3 Atoms: protons, neutrons, electrons

• Do you know what these particles are?

2.3 Atoms: protons, neutrons, electrons

• Do you know what these particles are?

Protons

Neutrons

Electrons

• Basic Atomic Structure Youtube (1:57)

Atom

• Smallest unit of matter that retains the properties of the element

Li

Na

Which shows one atom?

• C N N2 H20 Why?

• C and N • only one in number • Which are elements?• C N N2

Molecule

• Two or more atoms held together by chemical bonds

Which are molecules?

• Co CO CO2 O2

Why?

• CO CO2 O2 two or more atoms (alike or not alike, it doesn’t matter) bonded together

Where is each subatomic particle located?

• Proton in the• Neutron nucleus

• Electron-outside the nucleus

What is the charge of each subatomic particle?

• Proton Neutron Electron

• + O _• positive none negative

What is the relative size?

• Proton neutron electron• 1 amu 1 amu ~1/2000 amu• AMU = atomic mass unit = 1/12 CARBON ATOM

Neutral Atoms (no charge) (as seen on the periodic table)

• 39 Mass Number p + n K Symbol

• 19 Atomic Number p• (electrons = number of protons)• Neutral if negative charges = positive )

How can you tell the mass number and atomic number?

When looking on the periodic table…

• Atomic Number• In order• Identify element by

its number of protons

• Mass Number• A decimal (average

of masses of all isotopes of that element)

Isotopes of Carbon

• What is the mass number decimal?

• 12.011

• What would you round it to?

• 12

What is the atomic number of?

• Silicon fluorine sodium WHY?

• 14 9 11• Number in succession (not

a decimal)• Number of protons

What is the mass number of…?

• Carbon nitrogen hydrogen• WHY?

• 12 14 1• Decimal number on periodic

table• Not other number in succession• Number of p + n

How do you find the number of…?• Protons electrons neutronsAtomic atomic mass number number number minus atomic no.

(if neutral)

How many?

• Protons electrons neutrons• Carbon

6 6 6

• Chlorine• 17 17 18

What is the atomic number?Mass Number?

• Number of p?• Number of e-?• Number of n?

Do Atomic Mass and Atomic Number WORKSHEET

•Collaborate with your partner next to you, then we’ll see what’s right.

Isotopeisotope animation

• Atoms that differ in number of neutrons

• Also differ in mass number (since it is p+n)

• 41 Note more n K

• 19 Note same p

Isotope Examples

Which is the neutral Li?Which are the isotopes of Li?

Which is the neutral Li?Which are the isotopes of Li?

Neutral – see periodic table

Which are isotopes?• 16 20 38 128 12

O F K I C 8 9 19 53 6

WHY?

32 P 15

NOTE: you are looking for a different number of neutrons than the elements found on the periodic table.

Which are isotopes?• 16 20 38 128 12

O F K I C 8 9 19 53 6

WHY?

20 38 128 F K I 9 19 53

Which are isotopes?• 16 20 38 128 12

O F K I C 8 9 19 53 6

WHY?

20 38 128 F K I 9 19 53

2.4 Radioactive Isotopes

• An isotope that decays spontaneously to emit (give off) particles or energy

• Here a radioisotope is used to examine a thyroid gland

Uses of Radioisotopes• C-14 dating (can date living things up to

6,000 years old) Carbon Dating (2:00 mins) or • Nuclear Medicine: What to expect (2:46 mins)• Bozeman Biology Radioactive Dating (9 mins)• Carbon-14 Dating (2 mins)

Thyroid tumorHighlight parts of the body for diagnosis

PET SCAN: detect tumors, weak spots in arteries

Uses of Radioisotopes

• Iodine-131 PIB molecule to

treat thyroid cancer detect Alzheimers

PET scan

Negative Effects of Nuclear Radiation

• Chernobyl Nuclear Plant Accident

Negative Effects of Radon

• Radon, a radioactive gas, causes lung cancer

• Found in regions containing uranium

2.5-2.7 Chemical Bonds

Ion• Charged atom• Differs in number of electrons• 39 Same mass number

K+ means lost one electron• 19 Same atomic number

ION

• Charged atom• Na+ (has lost one electron)• O-2 (has gained two electrons)• Shown with superscript +/- and

number on upper right• (can omit number if a “1”)

Cation• Positive ion• Na+

• Mg+2

• Lost electrons

Anion• Negative ion• Cl-

• O-2

• gained electrons

If one electron is…

• Lost what charge will the ion have?

•+1

11p+11 e-

11p+10e-

Which are ions?

• Cl O-2 Na+1 N2

Why?

• O-2 Na+1 • Charged atoms (lost or

gained electrons)• show charges as superscripts

Valence Electrons

• Outer shell electrons• Bonding capacity of an atom

How do electrons arrange themselves in an atom…

• In the outer electron shells (energy levels)?

• They are full with 2, 8, 8• Fill inner shell first, then go to next shell out(Outermost shell has the greatest energy)

Click on animation, scroll down

Get kinda complicated beyond 2,8,8…so that’s all we’ll do for now!

Which electrons determine…

•The chemical properties of the atom?

• Outermost shell

If one electron is gained…

• What charge will the ion have?

•-1

• If 2 electrons are lost… What charge will the ion have?

•+2• If two electrons are gained…

What charge will the ion have?

•-2

Filled outer e- shells

How many e- fill the first shell (nearest the nucleus)?How many e- fill the next two shells?

nucleus

Gain 1 e- or lose 7 e-?

If gains 1 e-, then it becomes -1

Gain 7 e- or lose 1 e-?

If loses 1 e-, the it becomes +1.

Gain or Lose ?

If it could as easily lose or gain e-, then it will probably share them. It will form a covalent bond.

Tutorial 2.1 Chemical Bond Formation

Fill in the chart of e-

Element Number of e-

First shell Second Third Shell Shell

carbon 12

lithium 3

Sodium 11

Oxygen 16

Fill in the chart of e-

Element Number of e-

First shell Second Third Shell Shell

carbon 6 2 4

lithium 3 2 1

Sodium 11 2 8 1

Oxygen 8 2 6

How are ion charges determined?• Cation = positive (+) ion• Anion = negative (-) ion

How are ion charges determined?

• If lose 1 e- = +1 charge• If gain 1 e- = -1 charge• If lose 2 e- = +2 charge• If gain 2 e- = -2 charge

Periodic Table Hint:

• You can tell how many electrons are in an atom’s outermost shell by just looking at its position on the periodic table!!!!!

Note any pattern of valence electrons (outer shell) as they appear in the periodic table?

+1 +2

share -3 -2 -1 0

e- in outer shells

Ion formed

e- in outer shell

Full outer e- shells

H

8

How many electrons in each shell?(atomic number is given)

• Carbon oxygen fluorine sodium• 12 16 9 11

• 2,4 2,6 2,7 2,8,1

Now let’s do the Drawing Atoms Worksheet(and next 4 slides)

• How the electrons fill their shells (link)

• 1st shell – 1 pair• 2nd shell – e- space

far apart, singles, then pair

• 3rd shell – e- space far apart, singles, then pair

•

Bohr Diagrams

C

1) Draw a nucleus with the element symbol inside.

2) Carbon is in the 2nd

period, so it has two energy levels, or shells.

3) Draw the shells around the nucleus.

Bohr DiagramLet’s do carbon (6 electrons)

• 1. Draw a nucleus.• 2. Draw the number of

rings needed.• 3. Start in the first shell-

only 2 e-, paired (put next to each other)

C

Bohr Diagrams

1) Since you have 2 electrons already drawn, you need to add 4 more.

2) These go in the 2nd

shell.3) Add one at a time -

starting on the top and going counter clock-wise.

C

1

2

3

4

Bohr Diagrams

If you were to have more electrons, start pairing them in the same clockwise order.

1

2

3

4

5

6

1

2

3

4

5

6

Now do on the Atomic Structure Worksheet

See the trend of how electrons fill the valence shells

• Lewis dot structures• Octet Rule – electrons fill a shell until it’s

full with 8 electrons• Atoms are most stable with a filled outer

electron shell

What do we call the forces that…

• Hold atoms together in a molecule?

• Chemical bonds…not to be confused with James Bond

Why do atoms bond?

•To have filled outer electron shells!

•Atom Heaven

What is a chemical bond?

• Attraction between two or more atoms due to opposite charges

• YouTube - ?Ionic and covalent bonding animation??

Bonding

• Covalent• share

electrons

• Ionic• transfer of

electrons• (lose or gain)

IONIC BOND

• An atom may lose one or more electrons and become positive (+)

• An atom may gain one or more electrons and become negative (-)

• The (+) and (-) ions formed now attract each other and form an ionic bond.

Covalent BondsClick HERE:

Polar Covalent Bonding (3 animations)•Electrons are shared

•Usually if near the same number of e- in outer shells

Covalent bonding can be shown as:

• Bohr model

• Electron-dot

• Structural Formula

Covalent Bonding

• Even sharing Uneven sharing

Writing Bonds

• Each “–” is

equal to “: “ or “two electrons”

Single C – C or C:CDouble C = C or C::CTriple C= C or C:::C

Different Ways to Represent Four Common Molecules

butane

LET’S REVIEW: Which atoms combine…

•with other atoms?

• Ones that do not have filled outer electron shells

REVIEW: What is the driving force to make atoms join with

other atoms to form compounds?

• TO HAVE FILLED OUTER ELECTRON SHELLS!!!!!!!!!!!!!!!!!!!!!!!!

REVIEW: How does an atom…

• Get a filled outer electron shell?

• Gaining, losing, or sharing electrons

What do you notice about the ion charge and the subscripts?

Do the Flip-Flop

• So you can cancel out the (+) and (-)

If there is only one atom, you do not need to write a “1”

You can reduce the subscripts if they are the same:

Fe+2 O-2 Fe2O2 reduce to FeO

Electronegativity

• "power of an atom in a molecule to attract electrons to itself."

• Electronegativity only has meaning in a bond.

Electronegativity

Tendency of an atom to attract electrons towards itself and thusthe tendency to form negative ions.

Electronegativities

• H = 2.1 O=3.5 C=2.5• H-H = 0.0 bond pure covalent• O-H bond = 1.4 polar • (3.5-2.1)• covalent• NaCl = 2.1 ionic

Electronegativity• The more electronegative

atom pulls shared electrons toward its nucleus.

• NONPOLAR – equal sharing of electrons

• POLAR – unequal sharing

of electrons

IONIC BOND

• What makes up ionic bonds?

• IONS

• WHY?

• Opposite charged ions attract

Making ionic bond in NaCl

• YouTube - ?Ionic and covalent bonding example??

• YouTube - ?Reaction of Sodium & Chlorine (with subtitles)??

SALT =

• Synonym for an ionic compound• Not just NaCl

Iron SulfideCopper Sulfate

Sodium chloride

Covalent Bond

• What makes up covalent bonds?

• Atoms that are sharing electrons

Covalent Bonds

• Polar Covalent• Unequal sharing of e-

• Nonpolar Covalent• Equal sharing of e-

Valence Shells Only Shown

How can they be written?

• Single bond double bond triple bond

• C-C C=C C=C• C:C C::C C:::C• 2 e- 4 e- 6 e-

Contrast

• YouTube: Ionic and Covalent Bonding animation

Molecule

• A group of two or more atoms held together by covalent bonds

Comparing Bonds

IONIC BOND (gain or lose e-)

COVALENT BOND (sharing e-)

What’s the difference between Intramolecular and

Intermolecular Forces?

What’s the difference between Intramolecular and

Intermolecular Forces?

What’s the difference?• Intermolecular

attractions are between one molecule and a neighboring molecule

• (Van der Waals, hydrogen bonds)

• USUALLY WEAKER

• Intramolecular attractions are the forces which hold an individual molecule together (for example, the covalent bonds or ionic bonds).

• USUALLY STRONG

WHAT IS THE STRENGTH COMPARISON?

• STRONGEST BOND

• WEAKEST BOND

• Covalent

• Ionic

• Hydrogen

• Van der Waals

INTERMOLECULAR FORCES

• A. H-bonds

(in water and DNA)• B. van der Waals- “dispersion”• (in tertiary protein structures)• C. Disulfide bridges • (in tertiary protein structures)

INTERMOLECULAR FORCES

• A. H-bonds

(in water and DNA)• B. van der Waals- “dispersion”• (in tertiary protein structures)• C. Disulfide bridges • (in tertiary protein structures)

Hydrogen Bonds

• attractive force between the hydrogen (partial + charge) attached to an electronegative atom of a different (oxygen, nitrogen, or fluorine) (has a partial negative charge.

• Hydrogen Bond Animation

Hydrogen Bonds: Intermolecular between H and F, O, or N

Hydrogen Bonds

• In Water – between O- and H+• In DNA – between bases

van der Waals

Van der WaalsDispersion Forces• are momentary very weak

forces of attraction between nonpolar molecules as they approach each other (opposite charged ends) 

Like gecko feet on glass

Temporary dispersion of electrons make temporary charges

Where might you find van der Waals?

• Water would not condense from vapor into solid or liquid forms if its molecules didn't attract each other.

• Many properties of molecular compounds, including crystal structures (e. g. the shapes of snowflakes), melting points, boiling points, heats of fusion and vaporization, surface tension, and densities.

• Gigantic molecules like enzymes, proteins, and DNA into the shapes required for biological activity.

Disulfide Bonds:Protein Tertiary Structure

• Disulfide Bond in Tertiary Protein

Disulfide Bonds

• Disulfide bonds are formed between the side chains of cysteine by oxidation (loss of e-) of two thiol groups (SH) to form a disulfide bond (S-S), also sometimes called a disulfide bridge.

THEME OF EMERGENT PROPERTIES

• New properties that arise with each step upward in the hierarchy or life, owing to the arrangement and interactions of parts as complexity increases.

• WHOLE IS GREATER THAN THE PARTS

How is the emergent property idea apply to a compound and atoms?

• HINT:

2.9 Chemical Reactions

• The making and breaking of chemical bonds, leading to changes in the composition of matter.

Chemical Reactions

• Reactants on the left of the arrow• Products on the right of the arrow• IDENTIFY:• 2Mg(s)  +  O2(g)  →    2MgO(s)

• MgO(s)  +   H2O(l)  →    Mg(OH)2(s)

• N2(g)  +  3H2(g)  →    2NH3(g)

Same number of each element on left side as on the right side

• CH4 (g) + 2O2 (g) CO2 (g) + 2H2O (g)

Reactants Products

C = 1H = 4O = 4

C = 1H = 4O = 4

Signs of a Chemical Reaction

• Precipitate forms

• Color Change

• Gas Forms

• Temperature change

Chemical Reaction Example

• An iron bar rusts. The iron reacts with oxygen in the air to make rust.

4 Fe + 3 O2 2 Fe2O3