Chapter 2: The Cliff Notes to Chemistry CLIFFS ... - …faculty.northseattle.edu/hiverson/Bio101_Spring2006_pdf/Chapter2... · ¥H2O Chapter 2: The Cliff Notes to Chemistry CLIFFS

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CLIFFS NOTES

CHEMISTRY

Chapter 2: The Cliff Notes to

Chemistry

• What is Chemistry?

• Atoms

• Subatomic Particles

• Chemical Bonds

• H2O

Chapter 2: The Cliff Notes to

ChemistryCLIFFS NOTES

CHEMISTRY

•Every object around you is made up of mass.

•Mass is made up of matter.

•Matter is made up of little particles called atoms.

• Chemistry is the science that deals with matter

• Matter is anything that takes up space and has

mass

– Living or non-living

• Smallest stable units of mass are atomsCLIFFS NOTES

CHEMISTRY

Why is Chemistry Important to

Biology?

CARBON ATOM

All living things are made of atoms

CARBON ATOM

Another Example

DNA

A Cell

Cells

Nucleus within cell

Kidney Tissue

An organ: Frog Kidney

An organism: A frog

All living things are made of

atoms

DNA

A Cell

DNA is a large molecule, comprised of atoms!!

nucleus

CARBON

ATOM

Zoom in

on DNA

2

• Atoms are composed of subatomic particles

The Structure of Atoms

– A proton is positively charged

– A neutron is electrically neutral

– An electron is negatively charged ]

Packed

In the atomic

nucleus

Orbits the

nucleus

How many protons, neutrons and electrons does a carbon atom have?

CARBON ATOM


How many protons, neutrons and

electrons does a helium atom have?

HELIUM ATOM

http://www.purchon.com/chemistry/helium.htm


• OK, atoms are obviously very, very, small and theyprobably don’t ‘weigh’ very much, or have much mass

• But, believe it or not, atoms do have mass

• Atomic mass is determined by the # of protons andneutrons.

• What is the atomic mass of a carbon atom? A heliumatom?

• Electrons do not contribute (much) to the mass (weight)of an atom.

Atoms

• Atomic mass (# of protons plus the # of

neutrons)

• Atomic number (# of protons)

• What about the electrons?++

++

What do you think makes a carbon

atom a carbon atom, and not a helium

atom?

HELIUM ATOM CARBON ATOM

Who am I?

What makes me

me?

What is the

meaning of life?

I think,

therefore I

am…a

carbon atom

Elements– Atoms are classified into groups called

elements

– Elements are substances that cannot be

broken down into other substances

– There are 92 naturally occurring elements on

Earth

– You can find all of them on the periodic table

HeliumLead

3

groups

periods

Periodic Table

(of course you do not have to memorize this!)

(C) Carbongroups

periods

Periodic Table

(of course you do not have to memorize this!)

Just focus

on these

four

elements

Why these four elements?

– 25 elements are

essential for life

– Four of these

make up about

96% of the

weight of the

human body

– Trace elements

occur in smaller

amounts

1.

2.3.

4.

The Periodic Table contains lots of

useful information

What does this tell us?

What does this tell us?

Why do we care?

• In an atom of carbon, if the atomic numberis 6, how many protons are there?

• How many electrons are there??

• It’s the electrons that we really care about!

+++

+

Electrons Orbit the Atomic Nucleus

• If protons were the size of a

tennis ball, electrons would

be orbiting the nucleus at a

distance of 6 miles away!!

• Outer most electrons (or

the lack-thereof) determine

how one atom interacts with

another atom

•Atoms may interact and form bonds, generating

larger, more complex molecules (like DNA)

4

DNA is a molecule

Molecules are made of atomsElectron Arrangement

• Electrons (e-) are arranged around the

atomic nucleus in electron shells (orbitals).

• Electron shells closest to the nucleus have

the lowest energy, while electrons farther

from the nucleus have greater energy.

• The first electron shell holds only 2 electrons

• The next electron shell holds up to 8 electrons

• The four elements most abundant in living things

only have these two shells (phew!)

Electron Shells

In case you forgot those four elements,

they are:

HYDROGEN (only has the first shell)

CARBON

NITROGEN

OXYGEN

Electron Arrangement in a Carbon Atom

Firstelectron shell(can hold2 electrons)

Outermostelectron shell(can hold8 electrons)

Carbon (C)Atomic number = 6

Electron Arrangement in a Carbon Atom




Rules to figuring out electron

arrangement:

1. What is the atomic number?

2. The number of total electrons is

the SAME as the atomic number.

- For carbon, it is 6

3. Place two electrons in the ‘first’

inner shell

4. Place remaining electrons in the

outer shell.

***To understand how an atom will

interact with other atoms, look at

how many ‘open atom spots’

there are left in the outer shell!

What is the arrangement of outer

shell electrons in an oxygen atom?8

O16

5

Atoms of the four elements most

abundant in life

Electron




Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Hydrogen (H)Atomic number = 1

Outer shell

electrons?

Outer shell

electrons?Outer shell

electrons?

Outer shell

electrons?

Atoms ‘prefer’ to have their outer

shell FILLED with electrons!



I, HYDROGEN,

would strongly

prefer to have 2

electrons in my

outer shell, and

not just 1!

I, OXYGEN,

would strongly

prefer to have 8

electrons in my

outer shell, and

not just 6!

• The first electron shell holds only 2 electrons

• The next electron shell holds up to 8 electrons

• Atoms (with the exception of Hydrogen and

Helium) prefer to have 8 electrons in the outer

electron shell

• The octet rule.

Atoms can ‘fill’ their outer electron shells

by forming chemical bonds with other

atoms

• Atoms can steal electrons from other

atoms; atoms can lose electrons to other

atoms

– Ionic bonds

• Atoms can share electrons with another

atom or atoms

– Covalent bonds

Next up….Chemical Bonds

Oxygen (O)Atomic number = 8Hydrogen (H)

Atomic number = 1

…..OR, what

will happen

when an atom

of OXYGEN

‘sees’ an atom

of

‘HYDROGEN’?

..Two atoms of

HYDROGEN??

Elements with unfilled electron

shells are reactive

• Chemical bonds are formed

• Three types of chemical bonds

1. Ionic bonds

2. Covalent bonds

3. Hydrogen bonds



Hey there

hydrogen,

you wanna

bond??

6

Ionic bonds are formed between

ions

• Remember that the atoms we have

discussed so far are electrically neutral

• Because the number of protons (+) was

equal to the number of electrons (e-)

• An ion is a charged species

– Anions

– Cations

Anions and Cations

• If an atoms gains an electron (e-), what happens

to its electrical charge?

• If an atom loses an electron (e-) what happens

to its electrical charge?

Formation of a sodium ion, Na+

Ionic bonds are formed between

ions

Sodium metal Chlorine GasTable salt (NaCl)

+

Ionic Bonding

Reactant(s) Product(s)

In a CHEMICAL REACTION there are reactants and

products. Note that during chemical reactions no atoms

are gained or lost, they are just rearranged!

Na Cl

http://jchemed.chem.wisc.edu/JCESoft/CCA/CCA0/Movies/NACL1.html

Covalent bonds occur when

atoms share electrons

or H-H or H2H H

e- e-

http://www.visionlearning.com

Covalent Bonds

• Example from www.visionlearning.com

• For every pair of electrons shared

between two atoms, a single covalent

bond is formed.

– In H2 there is ONE covalent bond

• Some atoms can share multiple pairs of

electrons, forming multiple covalent bonds.

7

Methane is a simple compound, consisting of one

atom of carbon and 4 atoms of hydrogen

In methane, Carbon has four covalent bonds to 4

different hydrogen atoms

Covalent Bonds

C

H

H

H

H

Covalent Bonds

• Are strong because the shared electrons

hold the atoms together

• Typically, the atoms involved in covalent

bonds remain electrically neutral

• Found in most of the carbon-containing

structural components of living things

H H

e- e-

Scary Figure Polar Covalent Bonds

• Polar covalent bonds are a type of

covalent bond

• Characterized by an unequal sharing of

electrons

e- Unfair!

Polar Covalent Bonds

• Polar covalent bonds form because

some atoms have a stronger affinity

for electrons than do other atoms

• Electronegativity

e-

Strongly

electronegative

Polar covalent bonds can result

in polar molecules

• In a polar covalent bond, one atom ‘pulls’ onelectrons more tightly than the other atom.

• The more electronegative atom ‘hogs’ electrons

• Thus, electrons will spend more time (onaverage) around the electronegative atom

• A slight or partial negative charge results

• The ‘electronegative’ end of the molecule has aparital negative charge

8


in polar molecules

• Oxygen is an electron (e-) hog

– oxygen is a very electronegative atom

– Oxygen has a strong desire for electrons,and once it has them, it ‘pulls’ on them verytightly

• Oxygen forms polar covalent bonds withhydrogen atoms

• Water (H2O) is one oxygen bound to twohydrogens

• H2O is a polar molecule

Polar Covalent Bonds: H2O


Atomic number = 1

What will happen when an atom of OXYGEN

‘sees’ an atom of ‘HYDROGEN’?

..Two atoms of HYDROGEN??


Atomic number = 1

What will happen when an atom of OXYGEN

‘sees’ an atom of ‘HYDROGEN’?

..Two atoms of HYDROGEN??



e- e-


•www.visionlearning.com


in polar molecules

2!-

!+

!+


in polar molecules

2!-

!+

!+

Partial negative

charge

Partial

positive

charge

9

What happens when one water

molecule ‘sees’ another water

molecule?

H

O

H

H

O

H

Hydrogen bonding occurs

between water molecules

Which of the following orientations of two

H2O molecules is most likely to occur?

POP QUIZ

Which of these do you think is

correct?

2!-

A. B. C.

Opposites will attract!

2!-

A. B. C.

Opposite charges will

attract one anotherLike charges would repel one another

Hydrogen bonding occurs


2!-

A. B. C.

Hydrogen

Bonds!

Like charges would repel one another

Hydrogen bonding

• Weak but important forces

• Can exist between adjacent molecules

• Occur when (partial negative ) !- is attracted to

(partial positive ) !+ of a Hydrogen atom

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Hydrogen bonds are weak (but

biologically important) bonds

•Hydrogen bonding


is transient (fleeting)

•Hydrogen bonding

keeps water molecules

very tightly associated

with one another

Hydrogen bonding gives H2O many

unique properties

• Water as a good solvent

• Water molecules stick

together

– Cohesion and surface tension

• Water can resist

temperature change better

than other liquids

Water as a Solvent

Ion in solution

Salt crystal

• What happens, at the molecular level,

when water is mixed with an ionic

compound, like table salt (NaCl)?

Ion in solution

Salt crystal

• What happens, at the molecular level,

when water is mixed with an ionic

compound, like table salt (NaCl)?

Na+

Cl- Water molecules surround the

charged species, interact closely with

them, and disrupt the salt crystal.

Water as a Solvent

http://programs.northlandcollege.edu/biology/Biology1111/animations/dissolve.html

• Water moleculesstick together asa result ofhydrogenbonding

The Cohesion of Water

– This is called

cohesion

– Cohesion is vital

for water

transport in plants

Microscopic tubes

evaporation

H2O

The Cohesion of Water

11

• Surface tension is the measure of howdifficult it is to stretch or break the surface ofa liquid

– Hydrogen

bonds give

water an

unusually high

surface tension

Figure 2.13

What is heat?

Molecules are always moving

around randomly, they ‘jiggle’.

Heat is just a measure of ALL

of these molecular movements,

in a body of matter.

TEMPERATURE: the

average SPEED of this

movement….”JUST HOW

FAST IS THIS MATTER

MOVING?”

What happens when a

solution of methane is

heated?

What happens when water

is heated??What happens FIRST???

What happens NEXT??

Water accounts for 2/3rds of

total body weight• Water can dissolve many molecules

making a solution

• Water is needed for some chemical

reactions

• Water can absorb and retain heat

How might water interact with

uncharged, non-polar molecules?

• Olive oil, a lipid

• A generalized triglyceride structure….

Gly

cero

l

Long, non-polar (not charged) chains of

carbons and hydrogens

Do water and oil ‘mix’?

Water molecules tend to be attracted

more to each other than to a non-

polar region of a molecule.

This results in the

non-polar

molecules being

‘excluded’ by

water.

non-polar region

12

Hydrophilic and Hydrophobic

Compounds• Hydrophilic compounds react readily with

water molecules

• Hydrophobic molecules do not readily

react with water

Na+

Cl

-

Hydrophilic Hydrophobic

Ionic and covalent bonds form…

• Molecules: a chemical structure containing

two or more atoms that are held together by

covalent bonds

• Compounds: a chemical substance made of

atoms of 2 or more elements

Documents

Chapter 2: The Cliff Notes to Chemistry CLIFFS ... - …faculty.northseattle.edu/hiverson/Bio101_Spring2006_pdf/Chapter2... · ¥H2O Chapter 2: The Cliff Notes to Chemistry CLIFFS