Chemistry Overview
 Atoms, Elements, and Bonding
 Basic Types of Reactions
 Water, pH, and Salts
 Important Organic Biomolecules
* Carbohydrates
* Lipids
* Proteins
* Nucleic Acids
 Metabolism: Catabolism Fuels Anabolism
* How enzymes break down and build up molecules in the cell
* Cellular Respiration
* Fermentation
The Elements Found in Living Things
Life is made mostly of “CHON”
Figure 2.3
Atoms Are the Apples in the Bins Called Elements
• Atoms (apples) are the individual items belonging to a specific element
(variety) in the Periodic Table.
• Atoms belonging to an element are very similar but not identical (they
have slightly different masses)
Three atoms (apples)
from the variety
(element) Golden
Delicious
24.2 g
Periodic Table of Apple Varieties
29.6 g
25.9 g
Isotopes are alternate atomic forms for
an element.
Three “isotopes” of Golden Delicious
24.2 g

29.6 g
25.9 g
Mass number is the average mass of the different isotopes found in nature, in atomic mass units
• Radioisotopes used in PET scans, 181I for thyroid scans, radium and cobalt used in cancer
irradiation
Radioactive Isotopes can be used to form images
Positron Emission Tomography (PET) scan looks for where radioactive
fluorine-sugar is being used in the brain (blue areas)
Ionization and Bonding
• Ionic Bonds
• Covalent Bonds
• Hydrogen Bonds
 Atoms form gain/lose electrons or make bonds in order to
complete their outer (valence) electron shells
Ionic Bonds Are Formed Between Two or More
Electrically Unbalanced Atoms (Ions)
Covalent Bonds Are Sharing Arrangements Between
Two Atoms
When A Molecule Becomes Polar
Hydrogen Bonds: Bonds Between Polar Molecules
Chemistry Overview
 Atoms, Elements, and Bonding
 Basic Types of Reactions
 Water, pH, and Salts
 Important Organic Biomolecules
* Carbohydrates
* Lipids
* Proteins
* Nucleic Acids
 Metabolism: Catabolism Fuels Anabolism
* How enzymes break down and build up molecules in the cell
* Cellular Respiration
* Fermentation
Patterns of Chemical Reactions
 Synthesis reaction
(A+BAB)
 Decomposition
reaction
(ABA+B)
 Exchange reaction
(ABAC+B)
Chemistry Overview
 Atoms, Elements, and Bonding
 Basic Types of Reactions
 Water, pH, and Salts
 Important Organic Biomolecules
* Carbohydrates
* Lipids
* Proteins
* Nucleic Acids
 Metabolism: Catabolism Fuels Anabolism
* How enzymes break down and build up molecules in the cell
* Cellular Respiration
* Fermentation
Water’s Life-Supporting Properties
• Cohesion
QuickTime™ and a
decompressor
are needed to see this picture.
• Adhesion
• Capillary action
• Surface tension
• Moderates temperature change
• Can act as a cushion (e.g. in joints
• Can act as a lubricant (e.g. in lung pleura)
• Universal solvent
Water Can Dissolve A Large Number Of Substances
∂+
∂+
∂+
∂+
∂+
∂-
∂-
∂+
∂+
∂∂+
∂-
∂+
∂-
∂+
∂- ∂+
∂+
∂- ∂+ ∂+ ∂
∂+
∂+
∂+
∂ ∂+
∂+
∂+
Table salt
(NaCl) in water
∂-
• Water surrounds ions and polar molecules, dissolving them.
• Substances that dissolve in water are called hydrophilic.
• Substances that do not dissolve in water are hydrophobic
• Since the majority of substances on earth are hydrophilic,
water is called the universal solvent.
Figure 2.16
Water Breaks Can Break Apart to Form Ions
H2O
water
H+
hydrogen ion
+
OHhydroxide ion
• When there is an equal number of hydrogen and
hydroxide ions (H+ = OH-), water is pure and neutral.
• Some substances, when added to water give off H+ and
create acidic conditions (H+ > OH-). These substances are
acids.
• Other substances when added to water give off OHand create alkaline or basic conditions (H+ < OH-).
These substances are called bases or alkalis.
• Organisms cannot survive in acidic or basic
conditions because their chemicals are broken apart
The pH Scale Is Used to Measure Acidity or Basicity
High pH
Buffers
• Substances called
buffers can inhibit pH
change when part of a
water solution
OH- > H+
• Buffers soak up added
H+ or OH- like chemical
sponges
H+ = OH-
• Humans have the
carbonic acid-bicarbonate
buffer system:
H+ > OH-
absorbs OH-
H2CO3
Low pH
HCO3- + H+
absorbs H+
Salts and Electrolytes
 Salt Dissociation and Electrolytes
H2O
Chemistry Overview
 Atoms, Elements, and Bonding
 Basic Types of Reactions
 Water, pH, and Salts
 Important Organic Biomolecules
* Carbohydrates
* Lipids
* Proteins
* Nucleic Acids
 Metabolism: Catabolism Fuels Anabolism
* How enzymes break down and build up molecules in the cell
* Cellular Respiration
* Fermentation
Giant Molecules from Smaller Building Blocks
• On a molecular scale, many of life’s
molecules are gigantic.
Biologists call them macromolecules.
Examples: DNA, carbohydrates
• Most macromolecules are polymers.
Polymers are made by stringing together many
smaller molecules called monomers.
Cells link monomers by dehydration reactions.
monomers
polymer
Important Organic Biomolecules
Carbohydrates
Simple sugars (monosaccharides)
e.g. glucose, fructose, galactose
- contains easily harvested energy
Two-part sugars (disaccharides)
e.g. sucrose, lactose
Complex sugars (polysaccharides)
e.g. glycogen, starch
- for long-term energy storage
- some polysac. used for structural
support
glucose
fructose
glu -------- gal
(lactose)
(sucrose)
Glycogen
(“branchier” than starch
Lipids (Fats, Oils, Sterols, etc.)
Built of the monomers called fatty acids and glycerol; very hydrophobic
Fat or Oil (triglyceride)
(energy storage, insulation, cushioning)
Phospholipid
(barriers, such as membranes)
Steroid/Sterol
e.g cholesterol, estrogen, testosterone
(membrane fluidity maintenance, chemical signaling)
Important Organic Biomolecules
Protein
Single units:
Amino acid
(peptides)
Long chains of units:
Polypeptides (proteins)
Some functions:
Transport
labeling
Signaling
Catalysis (enzymes)
Body defense
Storage
Reception
Movement
Gating
Sensing
Cell
Globular protein
Fibrous/structural protein
Enzymes are protein
molecular catalysts that speed
up reactions: efficient,
specific, and controllable
Nucleic Acids
Single units: nucleotides
(five kinds: A,C,T,G,U)
Polymers:
Ribonucleic acid (RNA)
- information transfer
- molecular shuttle
- scaffolding for protein
editing
DNA
Deoxyribonucleic acid
(DNA)
- master information
storage molecule
RNA
Chemistry Overview
 Atoms, Elements, and Bonding
 Basic Types of Reactions
 Water, pH, and Salts
 Important Organic Biomolecules
* Carbohydrates
* Lipids
* Proteins
* Nucleic Acids
 Metabolism: Catabolism Fuels Anabolism
* How enzymes break down and build up molecules in the cell
* Cellular Respiration
* Fermentation
Metabolism: Breakdown of Food Fuels Construction of Biomolecules
Food molecules (high energy)
Breakdown
(Catabolism)
Complex biomolecules (high energy)
Energy from chemical bonds  Usable cellular energy (ATP)
Waste molecules (low energy)
Construction/
Synthesis
(Anabolism)
Simple molecules (low energy)
The Energy Stored in ATP Can Be Used to Perform Work in the Cell
• The energy released by ATP breaking
down into ADP and P can power a variety
of needs in the cell
Energized ATP:
ADP
Discharged ATP:
ADP
Powering the synthesis of
molecule Z:
P
P
X
+
Y
Z
Chemical Reactions within a Cell
 Metabolism is the word that describes all the chemical
reactions within a cell
• Catabolism (catabolic reactions) are breakdown reactions
that liberate energy
• Anabolism (anabolic reactions) are buildup reactions that
absorb energy
Cellular Reactions Either Use or Liberate Energy
 Catabolic/Breakdown Reactions release energy
o Molecules become more disorganized or less structured
X
+
Y
+
Z
 Anabolic/Buildup Reactions absorb energy
o Molecules become more ordered and complex
o ATP needed to power endothermic reactions
A
+
B
+ ATP
C
Cellular Reactions Either Use or Liberate Energy
X + Y
Z
+
Energy Level
 Breakdown Reactions Release Energy
Activation
Z
Energy
X+Y
Time
 Buildup Reactions Absorb or Require Energy
C
+ ATP
C
Energy Level
A + B
Activation
A+ B
Time
Energy
Activation Energy
• Activation energy
 Necessary for a chemical reaction
to proceed
 Activation energy is needed even
for breakdown reaction to get them
going
Energy Level
 Energy needed to allow the
reactants to form products
Activation
Z
Energy
X+Y
Time
•
In the laboratory, we heat the reactants in order to provide
activation energy for a chemical reaction
•
Inside the cell, a different mechanism is required as heating up
the reactants is not possible
Lower the energy required for the reaction
Enzymes Lower Activation Energy and Speed Up Reactions
Figure 5.8
Enzymes Catalyze Chemical Reactions in Living Things
• Biomolecules call enzymes lower activation
energy
Enzymes are folded proteins
Enzymes act as coordinators in a chemical
reaction, thereby speeding them up
Enzymes are catalysts for reactions; they speed
them up
Other Aspects of Enzymes
• Each enzyme is very selective
It has a pocket called the active site where
reactants (substrates) bind for catalysis
Only substrates with certain shapes can bind to
the enzyme and be catalyzed
Any particular enzyme therefore catalyzes only a
specific reaction with specific substrates
How Enzyme Catalyzes the Breakdown of Sucrose Sugar
Energy Level
Energy Level
sucrose
glucose
glucose+ +
fructose
fructose
Time
glucose-fructose
How Enzymes Work
Cannot progress because
activation energy too
formidable
Limitations of Enzyme Catalyzed Reactions
• Three-dimensional structure of an enzyme is
key to its functionality
 Anything which disrupts the intricate 3-D structure
of the active site ruins its ability to catalyze a
reaction
 Substrates cannot bind to a distorted active site
• Environmental changes that will ruin enzyme
activity by causing denaturation (unfolding)
 Very high or very low pH
 Very high temperatures (low temps just slow things
down)
 The presence of inhibitory molecules
Enzymes Become Non-Functional at pH Extremes and High Temperatures
H
H
OH-
+
+
(products formed per second)
Enzymatic rate
+
H
+
H
H
+
H
+
OH-
+
= denatured, non-functional enzyme
Enzyme within
Enzyme from
Reaction
rate is slow
a body cell
OH
at cold temperatures
hot springs
because
molecules
bacterium
OH
encounter enzyme
less often
OHOH-
H
+
H
OH-
H
+
+
OH-
H
OH-
+
H H
+
+
H
OH-
+
0
= folded, functional enzyme
2
4
6
8 10
pH (in pH units)
(products formed per second)
H
Enzyme within
a body cell
12
Enzymatic rate
Stomach
enzyme
10
20
30 40 50 60
Temperature (oC)
70
Inhibitors That Mimic the Normal Substrate
A competitive
inhibitor
Inhibitors That Bind to Other Enzyme
Pockets
A non-competitive inhibitor
Chemistry Overview
 Atoms, Elements, and Bonding
 Basic Types of Reactions
 Water, pH, and Salts
 Important Organic Biomolecules
* Carbohydrates
* Lipids
* Proteins
* Nucleic Acids
 Metabolism: Catabolism Fuels Anabolism
* How enzymes break down and build up molecules in the cell
* Cellular Respiration
* Fermentation
Food Energy Drives Growth, Repair, Reproduction
Cellular Respiration Reactions (Catabolic)
C6H12O6 + O2
food
oxygen
CO2 +
carbon dioxide
O2 +
oxygen
ATP
usable energy
then…..
Construction and Synthesis Reactions (Anabolic)
ATP + Food Nutrients
Growth, Repair, Reproduction
Cellular Respiration: Converting Sugar to ATP
C6H12O6 + O2
sugar
oxygen
CO2 +
O2 + 36ATP
carbon dioxide oxygen
CO2
usable energy
glucose
Glycolysis
CO2
NAD
2 ATP
NADH
2 pyruvates
Cell membrane
mitochondrion
Electron
Transport
Chain and ATP Mill
Krebs Cycle
Acetyl CoA
O2
H 2O
CO2
Lots of ATP
ATP Mill
ATP fuels
construction/synthesis
reactions inside the cell
Fermentation: Surviving Without Oxygen
C6H12O6
sugar
C2H4O2 + 2 ATP
lactic acid
Glycolysis
energy
glucose
NAD
2 ATP
NADH
2 pyruvates
lactic acid
Glycolysis, Krebs Cycle
and Electron Transport
Chain stopped without
O2, NADH cannot be
recycled, no ATP made
Chemistry Overview
 Atoms, Elements, and Bonding
 Basic Types of Reactions
 Water, pH, and Salts
 Important Organic Biomolecules
* Carbohydrates
* Lipids
* Proteins
* Nucleic Acids
 Metabolism: Catabolism Fuels Anabolism
* How enzymes break down and build up molecules in the cell
* Cellular Respiration
* Fermentation