Transcript Atoms

Chapter 2
The Chemistry of Life
Section 2-1
The Nature of Matter
Objectives
What three subatomic particles make up
atoms?
 How are all of the isotopes of an element
similar?
 What are the two main types of chemical
bonds?

Atoms
Submicroscopic units of matter
 Smallest unit of all physical material

Structure of Atoms
Atoms

Key Concept:
Atoms Are Made of Subatomic Particles
 Protons
 Positive
Charge
 Neutrons
 Neutral
Charge
 Electrons
 Negative
Charge
Protons
Positively Charged
 Found In The Nucleus
 Strongly Bound to Neutrons
 Have the Same Mass as a Neutron

Neutrons
Carry NO Charge – NEUTRAL Charge
 Found In The Nucleus
 Strongly Bound to Protons
 Have the Same Mass as a Proton

Electrons
Negative Charge
 1/1840 the Mass of a Proton
 Constantly Circling The Nucleus
 Each Atom has the Same Number of
Protons and Electrons

Electrons
Shells correspond to energy levels
 1st shell holds max of 2 electrons
 Every other shell holds up to 8 electrons

Elements that make up 95%
of living organisms (by weight)
C
H
N
O
P
S
Carbon
Hydrogen
Nitrogen
Oxygen
Phosphorus
Sulfur
Elements

Pure Substance Containing Only ONE
Type of Atom
Atomic Number =
Number of Protons
 Atomic Mass =
Number of Protons & Neutrons

Helium
Isotopes

Elements that contain more Neutrons
than Protons are Isotopes.

Identified by their Mass Numbers

Chemical Properties Remain Unchanged

Number of Electrons Don’t Change
Radioactive Isotopes
Nuclei are Unstable
 They Break Down at a Constant Rate
Over Time
 Can be used to calculate age

Isotopes of Carbon
Molecules and Compounds

Molecules form when two or more atoms
bond together (example: O2)

Compounds form when two or more
different elements bond together (H2O)
Chemical Compounds


A Substance Formed By The CHEMICAL
Combination of Two or More Elements
Radically Changes The Chemical Properties Of
The Elements Involved:
Na
Cl
NaCl
= Explosive, Water (Stored Under Oil)
= Poison Gas
= Salt – Required for life (you eat it daily)
Chemical Bonding

Ionic Bonding
One or More Electrons Transferred
 Changes The Atoms Charge
 NaCl

Ionic Bonds

One atom donates electron to other atom
NaCl as a Crystal
NaCl
NaCl in Solution
Na+
Cl
-
Chemical Bonding
 Covalent
 Shared
Bonding
Electrons
 Single, Double, Triple Bonds Possible
 May Cause A Shift of Electron Cloud
Resulting In Molecules That Are Polar
Water
Covalent Bonds


H2
Atoms share outer electrons
Covalent Bonding
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Electron Model
H
H
Structural
Formula
H
H
Molecular
Formula
H2
a. Hydrogengas
A
single covalent bond results from
sharing one pair of electrons.
Covalent Bonding
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O
O
O
O
O2
b. Oxygen gas
A
double covalent bond results from
sharing two pairs of electrons.
Water The POLAR Molecule
Positive Pole
Negative Pole
Polar Covalent Bonds
If the sharing between two atoms is
unequal, the covalent bond is described as
polar.
 Water is an example of a polar molecule

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Electron Model
Ball-and-stick Model
Space-filling Model
Oxygen attracts the shared
electrons and is partially negative.
–
O
O
O
H
H
H
H
104.5°
H
+
H
+
Hydrogens are partially positive.
a. W ater (H2O)
Van der Waals Forces

Polar Molecules Stick Together Like Little
Magnets

NOT Strong Like Ionic & Covalent Bonds
But Strong Enough For A Gecko
 ????

The Gecko’s Foot
The Water Molecule
 Neutral
All
Charge
Molecules Are Neutral
The Water Molecule

Polarity
 A water molecule is polar because
there is an uneven distribution of
electrons between the oxygen and
hydrogen atoms.
(—)
(+)
Hydrogen Bonds
Polar water molecules act like magnets
and attract each other
 Hydrogen Bonds
 The attraction of the Hydrogen end
(+) of one molecule for the Oxygen
end (-) of another water molecule.
 They are the strongest bonds that
can form between molecules

Hydrogen Bonds
Cohesion
The attraction between molecules of
the same substance (e.g. water).
 Allows some insects and spiders to
walk on water.

Adhesion
Attraction between molecules of
different substances
 Responsible for Capillary forces in
plants

Solutions & Suspensions
Water is usually part of a mixture.
 There are two types of mixtures:
 Solutions
 Suspensions

Solution
Ionic compounds disperse as ions in
water
 Evenly distributed
 SOLUTE
 Substance that is being dissolved
 SOLVENT
 Substance into which the solute
dissolves

Solution
Properties of Water

Water is a solvent.

A solution contains dissolved substances, which
are then called solutes.

Hydrophillic molecules attract water

Hydrophobic molecules do not attract water.
Suspensions
Substances that don’t dissolve but
separate into tiny pieces.
 Water keeps the pieces suspended so
they don’t settle out.

Properties of Water

Water has high heat capacity(heat needed
to raise or lower temperature)
•
A calorie is the amount of heat energy needed to
raise the temperature of 1g of water 1°C.
 Modulates temperature in living bodies

Keeps the temperatures on earth stable
Acids, Bases & pH

1 water molecule in 550 million naturally
dissociates into a Hydrogen Ion and a
Hydroxide Ion
H2O 
H+
Hydrogen Ion
Acid
+ OH
-
Hydroxide Ion
Base
The pH Scale
Indicates the concentration of H+ ions
 Ranges from 0 – 14
 pH of 7 is neutral
 pH 0 – 6.99 is acid
H+
 pH 7.01 – 14 is basic
OH Each pH unit represents a factor of 10
change in concentration

Acids

Strong Acid
= pH 1-3
H+
Bases

Strong Base
= pH 11 – 14
OH-
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pure water, tears
Buffers

Weak acids or bases that react with
strong acids or bases to prevent sharp,
sudden changes in pH.
Buffers and pH

A buffer is a chemical or combination of
chemicals that keep pH within normal
limits.

Bicarbonate ions (HCO3-) and carbonic
acid (H2CO3) found in human blood buffers
the pH to 7.4
Buffers and pH
H2O + CO2  H2CO3
H2CO3  H+ + HCO3H+ + HCO3-  H2CO3
Excess OH- combines with H+ to form H2O
Together these reactions keep the blood
at a pH between 7.3 and 7.5
Buffers and pH
Decline in pH can cause coma
 Rise in pH called alkalosis can also cause
coma
 7.8 can result in tetany – prolonged
muscle spasm

The Chemistry of Carbon
 Carbon
4
Valence Electrons
 Bonds with
Hydrogen, Oxygen, Phosphorus,
Sulfur, Nitrogen
Other Carbon Atoms
General Characteristics of
Biological Molecules
Carbon based
 Interact by means of functional groups
 Assembled or disassembled by adding
or removing water

The Chemistry of Carbon
Methane:
Single Bonds
Acetylene:
Triple Bonds
The Chemistry of Carbon
Butadiene:
Double Bonds
Benzene:
Ring Bonding
The Chemistry of Carbon
 Covalent
Bonds
 Single, Double, Triple
 But Always Four (4) Bonds
 No Other Element is so versatile.
 Millions
of Different Structures
Changing Molecules

Assembling molecules
Growth and repair
 Producing molecules essential for
chemical reactions to take place


Disassembling molecules
Digestion
 Providing molecules that can enter cells

Assembly: Dehydration Synthesis
Monomers =
one building
block
 Polymers =
two or more
monomers
linked by
covalent
bonds

Disassembly: Hydrolysis

Hydrolysis is opposite of dehydration

Covalent bonds broken with addition of H2O

Energy in bond is released
Macromolecules
 Means
“Giant Molecules”
 Each Macromolecule Is
Constructed of Thousands to
Hundreds of Thousands of Smaller
Molecules Called Monomers.
Macromolecules
 Monomers
Are The Basic Building
Block (Smallest Unit) of Any
Macromolecule
 Glucose
 Nucleotides
 Amino
Acids
 Monomers
Builds Cellulose
Builds DNA & RNA
Builds Proteins
Combine And Become
Polymers Through Polymerzation
Groups of Macromolecules
 Carbohydrates
 Lipids
 Nucleic
Acids
 Proteins
Carbohydrates
 C:H:O
in ratio of 1:2:1
 Main source of energy
 Sometimes structural molecules
 Cellulose
 Sugars, starches
 Mono & Polysaccharides
Carbohydrates
Key Concept:
1.
2.
Living Things Use Carbohydrates As Their
Main Source of Energy!
Plants and some Animals Use
Carbohydrates For Structural Purposes:
 e.g. Cellulose
Carbohydrates - Monosaccharides
Single Sugars
Glucose (Universal)
Galactose (Milk)
Fructose (Fruits)
Carbohydrates - Polysaccharides
Macromolecules from Monosaccharides
Glycogen (Animals)
Carbohydrates - Polysaccharides
Macromolecules from Monosaccharides
Starch (Plants)
Cellulose (Plants)
Carbohydrates - Disaccharides
Sucrose:
Maltose:
Lactose:
Some Carbohydrates are Used for
Structure
Cellulose – plant cell wall material
 Chitin – in insects, fungi

Lipids (fats)
Key Concept:
Lipids Can Be Used To Store
Energy. Some Lipids Are Important
Parts Of Biological Membranes And
Waterproof Coverings
Lipids (fats)
Made Mostly of Carbon & Hydrogen
 Not Water Soluble
 Catagories of Lipids Include:

Fats
 Oils
 Waxes
 Steroids

Fats



Non-polar & insoluble
• Two types of subunits
Long term energy storage
– Glycerol
More energy than equivalent
– Fatty acids
carbohydrates
Lipids (fats)

Formed from Glycerol & Fatty Acids
Lipids (fats)

Saturated
Each Carbon Atom In The Fatty Acid Chain
Is Joined To Another Carbon By A Single
Bond
 That Means The Macromolecule Contains
The Maximum Number of Hydrogens
 Solid At Room Temperature
 Butter, Margarine, Lard, Shortening, etc.

Triglycerides

Saturated – carries as many H as possible
Lipids (fats)

Unsaturated
One Or More Carbon to Carbon Bond(‘s)
Is/Are Multiply Bonded
 These Lipids Are Liquid At Room
Temperature
 Olive Oil, Peanut Oil, Other Cooking Oils

Triglycerides


Unsaturated – double bond replaces H
Polyunsaturated – more than 1 double bond
Differences in Fats & Oils

Polyunsaturated - liquid at
room temp



Plant oils
Fish oils
Saturated-solid at room
temp


Animal fats
Tend to raise blood
cholesterol
Phospholipids
Phosphate group replaces a fatty acid
 Key component of cell membrane

Steroids
Examples include cholesterol
and sex hormones
 Important for membranes

Nucleic Acids
Key Concept:
Nucleic Acids Store &
Transmit Hereditary or
Genetic Information
Every Life Form Uses The
Same Nucleic Acids
Nucleic Acids
 Macromolecules
with C, H, O, N; P
 Polymers of Nucleotides:
5 Carbon Sugar
+Phosphate Group
+ Nitrogen Base
5 Carbon Sugars
 RNA
 Ribonucleic
Acid
 DNA
 Deoxyribonucleic
Acid
Summary of DNA and RNA
structural differences


DNA



RNA

Sugar is deoxyribose
Bases include A, T, C
and G
Double stranded


Sugar is ribose
Bases include A, U, C
and G
Single stranded
Hydrogen bond
bases
Adenine (A)
Thymine (T)
(DNA only)
backbone
Guanine (G)
a. DNA structure with base pairs: A with T and G with C
Cytosine (C)
b. RNA structure with bases G, U, A, C
Uracil (U)
(RN only)
5 Carbon Sugars
DNA
Deoxyribose
Sugar
RNA
Ribose
Sugar
The Only
Difference
Proteins
Key Concept:
Some Proteins Control the rate of
reactions and Regulate Cellular
Processes. Some Form Bones &
Muscles. Others Transport Substances
In/Out of Cells or Help Fight disease
Proteins
Macromolecules with C, H, O, N
 Polymers of Amino Acids
 Compounds with an Amino Group
(NH2) and a Carboxyl Group (-COOH)
on the other end

 Allows
 20
bonding between any amino acid
AA’s in nature
Amino Acid “R” Groups
Each Amino Acid Is Different in the
R-Group
Amino Acid “R” Groups
 Some
Polar, some Non-Polar
 Some Acidic, some Basic
 Some contain Carbon Rings
Protein Levels of Structure
Primary structure = amino acid sequence
 Secondary structure = shape

Coils
 Folds

Tertiary structure = complex shape caused
by hydrogen bonds
 Quaternary structure= final structure
formed when two or more different
proteins bond together

Levels of Organization
1.
2.
3.
4.
Sequence of Amino Acids
Amino Acid Twists & Folds Within
Chain
Twists & Folds of Chain Itself
Multiple Protein Chains May Be
Necessary To Make An Active Protein
Protein Shape Is Critical To Function
Summary of the macromolecules
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Organic
molecules
Examples
Monomers
Functions
CH2OH
Monosaccharides,
disaccharides,
Carbohydrates Polysaccharides
(starch, glycogen,
cellulose, chitin)
O
H
OH
Immediate
energy
and stored
energy;
structural
molecules
H
H
HO
OH
H
OH
Glucose
H
Lipids
Fats, oils, wax,
phospholipids,
steroids
H
H
H
H
H
C C
C
C
C
C
H
H
H
H
H
O
H C OH
H C OH
HO
H C OH
R
Fatty acid
H
Glycerol
Proteins
Structural,
enzymatic,
carrier,
hormonal,
contractile
amino
group
H2N
H
C
acid
group
COOH
R
group
Long-term
energy
storage;
membrane
components
Support,
metabolic,
transport,
regulation,
motion
Amino acid
phosphate
P
Nucleic acids
DNA, RNA
base
C
O
S
Nucleotide
Storage of
genetic
information
Chemical Reaction
Key Concept:
Chemical Reactions Always involve
breaking bonds of Reactants and the
formation of new bonds to form in
products
Chemical Reaction

Process that changes one set of
chemicals into another set of
chemicals.
Reactants  Products
Transport of CO2

CO2 Is NOT Very Soluble In Water

When CO2 Enters Your Bloodstream It
Reacts With Water To Form Carbonic Acid
H2CO3
Which Increases Your Bloods Carrying
Capacity – Then, The Reverse Happens In
Your Lungs
Transport of CO2
Tissue to Blood
CO2 + H20  H2CO3
Blood to Lung
H2CO3  CO2 + H20
Energy In Reactions
 Energy
is released or absorbed
every time chemical bonds
form or break.
 Energy changes determine
whether a reaction will take
place.
Energy In Reactions
Key Concept:
 Reactions That Release Energy
Often occur spontaneously
 Chemical Reactions That
Absorb Energy Will Not Occur
Without A Source Of Energy
Energy Releasing Reaction
2H2 + O2

2H2O
Activation Energy

Energy needed to start a reaction
Activation Energy
Reactions That Absorb Energy
 Will
not occur without a source
of energy
e.g. Decomposition of water
2H2O
2H2 + O2
Enzymes
Key Concept:
Cells Use Enzymes To Speed Up
Chemical Reactions That Take Place
In Cells
 Often
act as Catalyst
Speed up the rate of reaction
 Lower activation energy
Enzyme Effects
Enzyme-Substrate Complex

Enzymes Provide A Site Where
Reactants Can Be Brought Together To
React.
Reduces The Energy Needed For The Reaction
 Reactants AKA Substrates
 Substrates bind to active site

 Lock
& Key, VERY specific
Regulation of Enzymes
 pH
 Temperature
 Cells
contain “switch” proteins