Download Chapter 2: What Are Atoms?

Chapter 2:
Atoms, Molecules & Life
What Are Atoms?
• An atom are the smallest unit of
matter.
• Atoms are composed of
Electrons = negatively charged particles.
Neutrons = particles with no charge
(neutral).
Protons = positively charged particles.
• Protons and neutrons are found in the
nucleus of an atom
• Electrons orbit the nucleus.
An atom is neutral, the # of electrons = #
protons
Chapter 2: Atoms, Molecules & Life
An example of an atom:
Periodic Table of Elements:
Element = Substance that can’t be
broken down or converted to another,
simpler substance by ordinary chemical
means.
Atomic Number = Number of protons in
the nucleus
Since # of protons always equals the #
of electrons, why don’t we use the # of
electrons as the atomic number?
Remember that neutrons are neutral, so there can
be more of them than protons.
Atomic Mass
= Number of protons &
neutrons in nucleus
Chapter 2: Atoms, Molecules & Life
Periodic Table
Why is the mass number a decimal?
Isotope = The same element with a different
number of neutrons
• C14
• P32
• U235
1
Isotopes
Isotopes
• Some isotopes, but not all, are radioactive.
• Isotopes: Same element,
different number of neutrons.
Example: Carbon 14 (C14) is radioactive
Example: Hydrogen 2 (not radioactive) and hydrogen 3
(radiocative)
• Different number of neutrons
changes the atomic mass, but
NOT the atomic number.
• Isotopes are useful in research
Nuclear experiments involved heavy water (H2)
Radiolabelling
Atomic number remains
1 for hydrogen and its
isotopes
used to be H3, but now other isotopes are used.
Radiocarbon Dating:
Crucial elements in life
• Technique for determining the age of materials that contain
carbon based on C14 levels
• Carbon
All organic matter has carbon.
18.5% of the human body mass is carbon atoms.
C12O2
• Hydrogen
C14O2
All macromolecules have hydrogen as a component.
Half-life ~ 5730 years
9.5% of the human body mass is hydrogen atoms.
• Oxygen
All macromolecules have oxygen as a component.
65% of the human body mass is oxygen atoms. Why so much oxygen?
• Nitrogen
All proteins have nitrogen as a component
1 C14 for every
1,000,000,000,000 C12
Other important elements in life
•
Calcium
Component of bones.
•
Phosphorus
A component of all cells (phospholipids).
•
Potassium
An important electrolyte, also keeps cell alive via
sodium potassium pump.
•
Sulfur
A component of some protein molecules.
•
Sodium
Another important electrolyte, sodium ion pumps.
3.3% of the human body mass is nitrogen atoms (mainly in muscle and
other proteins)
Compounds vs. Molecules
• Compound: A substance made up of different
types of atoms.
Example: Table salt, NaCl.
• Molecule: a particle composed of one or more
atoms held together by chemical bonds.
Example: Table salt, NaCl
Also the smallest unit of a compound.
• Not all molecules are compounds.
H2, O2, and other diatomic gases are not molecules.
Why?
2
How are molecules formed?
• The number of electrons in the outermost electron
shell determine whether an atom is reactive or inert.
How are molecules formed?
• How many electrons are
needed to fill an electron
shell?
Depends on which shell.
• First shell only needs two
hydrogen, helium.
• Second shell needs eight.
Carbon: reactive.
4 electrons in outer shell,
needs 4 more to fill shell
Neon: inert
8 electrons in outer shell,
Does not need electrons to fill shell
Inert Atoms = Atoms with their outermost shell either
completely full or empty
Reactive Atoms = Atoms with their outermost shell only
partially filled
Hydrogen
Helium
Carbon
Neon
Oxygen
Argon
Chemical bonds
• Types of chemical bonds
• Third shell needs eight.
How are molecules formed?
• Reactive atoms want to lose or gain electrons to
stabilize their outer (valence) shell.
(Figure 2.3)
Covalent bonds: the strongest chemical bond
• Atoms share electrons in covalent bonds.
Covalent: the strongest of the three main types.
Ionic: weaker than covalent bonds.
Sharing of
electrons
Hydrogen bonds: the weakest chemical bond of the
three main types.
• Chemical bonds are crucial for chemical reactions
Chemical Reaction = making or breaking chemical
bonds.
Chemical reactions are essential for all life.
3
Examples of Covalent Bonds:
Covalent bonds: the strongest
Share one pair of electrons (H2)
• Single covalent bond
• Most biological molecules
utilize covalent bonds.
H-H
Proteins
Carbohydrates
Lipids
DNA
Share two pairs of electrons (O2)
• Double covalent bond
• Carbon atoms are always
linked by covalent bonds.
O=O
Share three pairs of electrons (N2)
• Triple covalent bond
N N
Bonding Patterns (Table 2.3):
Non-polar Covalent Bonds:
Equal sharing of electrons
Polar Covalent Bonds:
Unequal sharing of electrons
Carbon (C)
Molecule is electrically neutral, but
poles are charged due to differences
in nuclear attraction for electrons
(electronegativity)
Oxygen (O)
Ionic Bonds
• Attractive force between atoms that have lost or gained
electrons
Creates ions (negatively or positively charged atoms)
Example of ionic bonds
• Sodium chloride (table salt)
Sodium wants to lose one electron to stabilize its outer shell
Chloride needs to gain one electron to stabilize its outer shell.
Sodium Chloride (NaCl - Figure 2.3)
Transfer of
electrons
4
Ionic bonds typically occur between atoms that are
located on opposite sides of the periodic table.
Hydrogen Bonds
• Attractive force between water
molecules due to polar covalent
bonds.
Electrons are far more attracted to
oxygen than to hydrogen atoms.
hydrogen atoms have a slight
positive charge.
Oxygen atoms have a slight
negative charge.
(Figure 2.5)
• Makes water a very special
molecule.
Water = Good Stuff!
Life most likely arose in water
Living organisms 60 - 90% water
Why is Water so Important to Life?
Humans and water
• Human body is 65% water.
• The average human can
survive several months
without food.
But you can only survive
3 – 4 days without water.
All life depends on water
• Search for life on other planets often includes
the search for H2O
• Phoenix spacecraft will land in
one
of Martian ice caps in hopes of
finding water and microbial life.
Importance of Water:
1) Water is an excellent solvent:
• liquid capable of dissolving other substances in itself
Dissolving Ionic Bonds:
(Salt)
(Figure 2.6)
Polar nature of water
Landed May, 2008,
found ice on
July 31st, 2008.
Why is Water so Important to Life?
Solution = Fluid containing dissolved substances
5
Hydrophilic vs hydrophobic
Dissolving Polar Covalent Bonds:
(e.g. glucose)
Hydrophilic Molecules:
Water-loving
+
-
• Molecules electrically
attracted to water
• Ions, polar molecules
Hydrophobic Molecules:
Water-fearing
• Molecules electrically
neutral (fats / oils)
(Figure 2.7)
• Molecules tend to clump
together in water
Importance of Water:
Hydrophilic
Hydrophobic
Importance of Water:
2) Water molecules tend to stick together (cohesion):
• Surface Tension: Tendency for a water surface to
resist breaking
3) Water Can Form H+ and OH- Ions (ionization):
H+ + OH-
H2O
• Adhesion: Tendency for water to stick to walls of
surfaces
Pure water contains equal amounts of H+ and OHFlow against
gravity
HCl
Acidic
H+ = OH-
H+
Walk on
water
Acids & bases disrupt the equilibrium.
> OH-
Water
Basic
NaOH
H+ = OHH+ <
OH-
Water
The pH of a solution describes its degree of acidity:
Acid
A substance that increases the [H+]
in a solution
Base
A substance that decreases the
[H+] in a solution
(Figure 2.9)
6
Importance of pH to living systems
Buffers
Buffers - solutes that act to resist changes to
the pH of a solution when H+ or OH- is
added.
Changes in pH disrupt life chemistry
Example: Blood
usual pH = 7.4
Biological fluids use buffers to help maintain
correct pH.
pH 7.0 , 7.8 lethal
So how does blood maintain a healthy pH?
Buffers maintain a solution at relatively constant pH:
• Stable pH essential for normal function
Importance of Water:
4) Water Moderates Temperature Changes:
• Buffers either accept or release a H+ in response to
changes in pH
Example: Bicarbonate ion (HCO3
Background:
• Temperature = Speed of molecules
• Slow molecules = Cool temperatures
• Fast molecules = Warm temperatures
-)
Too acidic?
HCO3- + H+
Bicarbonate ion
H2CO3
Hydrogen ion
• Specific Heat = energy needed to heat 1 gram of
a substance 1°C
Carbonic Acid
Too basic?
H2CO3 +
Carbonic Acid
OHHydroxide ion
A) Water Heats Slowly
• Energy first initiates breaking of hydrogen bonds…
• Specific HeatWater = 1 cal
• Specific HeatAlcohol = 0.6 cal
• Specific HeatGranite = 0.02 cal
HCO3- + H20
Bicarbonate ion
Water
Importance of Water:
4) Water Moderates Temperature Changes:
A) Water heats slowly
B) Water is an effective coolant
• Heat of Vaporization: Heat needed to convert liquid
water to water vapor
• 529 calories/gram (very high!)
By evaporating 1 g of water,
539 grams of human body cools 1°C
C) Water freezes slowly
• Moderates the effects of low temperatures
D) Water forms ice (less dense than fluid water):
• Acts as an insulator for life below
Why does ice weigh less than liquid water?
• Water is the most dense
(0.9998 g/cm3) at 40 C.
• Below 4 degrees, the water
molecules form more hydrogen
bonds, forming lattice like
crystals.
• This characteristic is very
important for aquatic
organisms.
Why??
7
Because ice floats!
Any questions?
Next Class
• We will be starting Chapter 3: Biological
molecules
• Remember there are games to use as study tools
Especially useful for learning terminology.
8