Chapter 2: The Molecules of Cells
TOPIC OUTLINE
► Thermodynamics
 First Law
 Second Law
 Steady State vs Equilibrium
► Chemistry





Atoms and molecules
Chemical Reactions
Water
Acids and Bases
Biological Molecules
Definitions
► Energy




Potential
Kinetic
Chemical
Matter and energy are interconvertible.
► Work
► spontaneous
change vs non-spontaneous
change
► Do characteristics of life require work?
Types of Energy in Biological Systems
• Kinetic energy - energy of motion, work
done
• Potential energy - stored energy, can be
released to do work
• Archer draws bowstring back - used
kinetic energy
• Tension now in bowstring represents
potential energy
• Release of bowstring converts potential
energy to kinetic energy
Energy (cont’d)
Thermodynamics
►
a system:
Some portion of the universe that you wish to
study
►
The surroundings:
The adjacent part of the universe outside the
system, i.e. everything but the system
Changes in a system are associated with the
transfer of energy
Natural systems tend toward states of minimum energy
1st Law of Thermodynamics
 Total Energy in Universe is Constant
 energy cannot be created or destroyed
 Energy can be converted from one form to
another
 The pathway of conversion is irrelevant, the
energy change between identical initial and final
states is equal
 When it comes to energy-You can’t get
ahead!
2nd Law of ThermodynamicsYou can’t break even, either!
► No
conversion is 100% efficient.
► Total useful energy in a closed system decreases
as conversions occur.
► Closed systems go from complex to simple.
► Entropy
 Measure of Disorder
 Closed systems tend to their highest state of disorder
 Entropy of the universe increases with every
conversion
2nd Law of Thermodynamics
Randomness is spontaneous in a closed system
Examples of Entropy
• Beaker on left has different colored marbles separated from each
other
• Highly ordered system
low entropy
high entropy
• Low entropy
• Beaker on right has different
colored marbles scattered amongst
each other
• Highly disordered system
• High entropy
Other examples?
SUMMARY-THERMODYNAMICS
►First
Law: Energy cannot be created or
destroyed, but it can be changed from
one form to another.
►Second Law: Energy cannot be
changed from one form to another
without loss of usable energy
GRADIENTS—A CASE STUDY
► What
is a gradient?
► Types
 Pressure
 Temperature
 Chemical
► What
does the 2nd Law say about
gradients?
Equilibriums--Closed systems go to
equilibrium
Universe-200 atoms
Hydrogen—182
Helium---18
All others<1/2
Human 200 atoms
Hydrogen---126
Oxygen---51
Carbon—19
Nitrogen—3
All others---1
What happens if you achieve equilibrium?
Equilibrium vs Steady State
► Living
things go from simple to complex.
Evolution goes from simple to complex.
How? Are biological systems not subject to
the 2nd Law?
Basic Chemistry
Matter
Elements.
Atoms
Compounds
Molecules
Model of an Atom
Model of an Atom
Periodic Table of Elements
ATOMS
Atomic symbol
Atomic number
Atomic mass (weight).
CHEMICAL REACTIONS
►Electron
shells
►Valence (outer)
shell
►Octet rule
►Ionic bonds
►Covalent bonds
Atoms will ‘strive’ to fill their
outer (valence) orbitals
► If
an atom has 1 valence e-,
it’s ‘happy’ to give it away
► Example: Sodium
1 valence e-
Atoms will ‘strive’ to fill their
outer (valence) orbitals
AND…If an atom has 7
valence e-, it’s ‘happy’ to
pick up one
Ex. Chlorine
7 valence e-
Ionic Bonds
Ions can have important biological
functions.
Covalent Bonding
Each pair of electrons
represents the formation
of a covalent bond.
C
Carbon (C)
4
H
Hydrogen (H)
1
H
H
C
H
H
Methane CH4
Aside from single covalent bonds, double,
or triple covalent bonds can form.
Review
► Ionic
bonds occur when e- are shared in a
+/- arrangement
► Covalent bonds exist when one atom shares
1 or more e- with another atom.
► One covalent bond means 2 e- are involved.
Always involves a pair of e-
Oxidation/Reduction
►Oxidation----loss
of electron
►Reduction----Gain of electron
►Examples?
Water and Life
► Water
is the most abundant molecule in
living things.
► Water has special traits that make it
important to life.
Water molecules: 2-H covalently bonded
to 1-O. Covalent=shared e-. But is
sharing equal?
Chemistry of Water
Amazing stuff!!!
Should not be a liquid
at room temp…
Highly Polar
molecule.
WATER
►Hydrogen
►Polarity
bonds
Hydrogen Bonding
Positively charged hydrogen end
Negatively charged oxygen end
Covalent bonds between hydrogen and oxygen
Hydrogen Bonds
Characteristics of water:
1.
2.
3.
4.
5.
6.
7.
8.
liquid at room temperature
universal solvent for polar molecules
water molecules are cohesive
water molecules are adhesive
temperature of water changes slowly
absorbs heat upon vaporization
releases heat upon freezing
frozen water is less dense
Water as a
Solvent –
How it
Works
Dissociation of Water Molecules
Water dissociates and releases hydrogen ions
(H+) and hydroxide ions (OH-).
ACIDS AND BASES
►Acids
- release hydrogen ions
+
(H ) in solution.
 HCl  H+ + Cl-
►Bases
- take up hydrogen ions
+
(H ) or give off hydroxide ions
(OH ) in solution.
 NaOH  Na+ + OH-
pH—a Measure of Acidity
If ph<7, acid
7=neutral
If pH>7, base
►Buffers
--substances that
help to resist change in pH.
►Why important?
Water—Final Notes
►Hydrophilic--polar
►Hydrophobic–
non-polar
►Amphipathic---contain
hydrophilic and hydrophobic
parts
Organic Molecules—carbon based
Organic molecules are found in living
things.
The chemistry of carbon accounts for
the chemistry of organic molecules.
Macromolecules (Polymers)
Organic Molecules
monomer
polymer
Macromolecules (polymers)
and monomers.
Polymer
carbohydrate
protein
nucleic acid
Monomer
monosaccharides
amino acid
nucleotide
Dehydration Synthesis or
Condensation Reactions
vs
Hydrolysis
Dehydration (condensation) builds. Hydrolysis breaks down.
covalent bonds
Condensation
A
OH
+
H
B
A
B
Hydrolysis
If the reaction is carried out multiple times you create a polymer!
+ H—O—H
or
H2O
+ H2O molecules
Proteins
What do they do?
Structure
Act as enzymes to speed reactions
Serve as carriers
Act as antibodies
Transporters and channels
Proteins --polymers of amino acids.
Peptide Bonds
Proteins--Levels of Organization.
TERTIARY (3º) STRUCTURE—3D
► 1º
structure and
environment
► Factors—R-groups




Hydrogen bonding
Hydrophobic interactions
Ionic (salt) bridges
Disulfide bonds
► Native
vs Denatured
► REMEMBER: A
PROTEIN’S FUNCTION
IS A RESULT OF ITS
FORM!!
Enzymes—Biological Catalysts
►Catalyst?
 Speeds up reaction
►Proteins
The Model:
E+S
ES
E=Enzyme
S=Substrate
P=Product
E+P
Classes of Enzymes
1.
2.
3.
4.
5.
6.
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases
Enzymes Lower Energy of
Activation
Enzymes-- lower the energy barrier
Enzyme
EA
barrier
Reactants
1
Figure 5.5A
Products
2
Enzyme-Substrate Complexes
► Every
reaction in a cell requires a specific
enzyme.
► Enzymes are named for their substrates:
► Substrate
Enzyme
► Lipid
Lipase
► Urea
Urease
► Maltose
Maltase
► Ribonucleic acid
Ribonuclease
ACTIVE SITE
► Where
does
enzyme bind
to substrate?
► How does
enzyme
recognize its
substrate?
Induced Fit Model
Induced fit model
Enzymatic reaction
Cell Chemistry
►Enzymes—involved
in almost all
chemical reactions.
►Anabolism—The building
reactions. EX. Protein synthesis
►Catabolism—The breakdown
reactions. EX. Protein digestion
►Metabolism—sum of all reactions
Factors Affecting Enzymatic Speed
► REMEMBER—FORM
FUNCTION!!!
► Factors
FOLLOWS
 Substrate concentration-to a point
 Environment
►Temperature
►pH
►Salt
concentration
►ANYTHING
THAT AFFECTS FORM
AFFECTS FUNCTION!!!
Temperature Optimum
pH Optimum
INHIBITION MODELS
► Inhibition----reduced
activity
► Competitive
 E + S+ I ↔ ES + EI ↔E + P or I or P2
► Non-competitive (allosteric)
 E + S +I ↔ no or reduced ES ↔E + no
product or reduced product
EX. Feedback Inhibition
Feedback Inhibition
►Non-competitive
(allosteric) inhibition
 Allosteric site vs Active site
Feedback Inhibition 2
Feedback Inhibition 3
PROBLEM
ETHANOL
ETHYLENE GLYCOL
Enzyme Cofactors
►Cofactors
---may be necessary for
some enzymes to carry out their
functions. Two types:
 Metal ions. EX copper (Cu+2) or iron
(Fe+2)
 Coenzymes Organic molecules,
must be present for other enzymes
to function. EX vitamins
Levels of Protein Structure—
Quaternary (4º) Structure
Multiple chains:
interactions of more
than one polypeptide
chain to form the
complete, functional
protein. Ex.
Hemoglobin and
antibodies
Carbohydrates
•
•
•
•
Generally, C:H:O in a 1:2:1 ratio
(CH2O)n
Functions
• quick energy and short-term energy
storage. EX glycogen, starch
• Structure. EX. Cellulose
Polymer=polysaccharides EX. Starch
Monomers= monosaccharides EX.
glucose
NOMENCLATURE
►Based
on number of carbons
►3C==triose
►4C==tetrose
►5C==pentose, etc
Structure of Glucose
Disaccharides
Polymerization of Carbohydrates
POLYSACCHARIDES
STARCH
GLYCOGEN
CELLULOSE
LIPIDS
► NON-POLAR
BIOLOGICAL MOLECULES
► FUNCTIONS






Energy storage: Fats and oils.
Waterproofing: Waxes and oils
Insulation: Fat layers (blubber)
Cushioning: Fat layers (soles of your feet)
Regulating metabolism: Steroids
Component of cell membranes: Phospholipids
Lipid structure (Triglyceride)
Glycerol backbone
► Fatty acid tails
► Fats vs oils
►
X3
Triglyceride formation
H
H-C—OH
H-C—OH
H-C—OH
H
GLYCEROL
H
O HHHHH
HO-C-C-C-C-C-C-H
HHHHH
O HHHHH
HO-C-C-C-C-C-C-H
HHHHH
O HHHHH
HO-C-C-C-C-C-C-H
HHHHH
O HHHHH
H-C—O-C-C-C-C-C-C-H + H20
HHHHH
O HHHHH
H-C—O -C-C-C-C-C-C-H + H20
HHHHH
O HHHHH
H-C—O -C-C-C-C-C-C-H + H20
HHHHH
H
FATTY ACIDS
TRIGLYCERIDE + 3 H20
What type of reaction forms a triglyceride?
Dehydration Synthesis
Saturated vs. Unsaturated Fats
Saturated vs. Unsaturated Fats
Fatty Acids: cis vs. trans
-linolenic
acid
Trans -linolenic acid
Phospholipids
The major
structural
component
of cell
membranes
Phospholipid Behavior
Phospholipids
Soaps and Emulsifiers
Steroids-Hormones and
Structure
Nucleic Acids
►Polymers:
DNA and RNA
►Monomers: nucleotides
►Functions
 Information storage and
transmission
 ATP is energy currency of cell
Nucleotide Structure
DNA vs RNA
The Double Helix of DNAComplementary base pairing
The Central Dogma
DNA-gene
ATGAGTAACGCG
TACTCATTGCGC
Replication--duplication of DNA using DNA as the template
ATGAGTAACGCG
TACTCATTGCGC
DNA
+
ATGAGTAACGCG
TACTCATTGCGC
Transcription--synthesis of RNA using DNA as the template
mRNA-message
RNA
Translation--synthesis of proteins using RNA as the template
AUGAGUAACGCG
MetSerAsnAla
Protein--end produ
Protein
Mutation-DNA Change
Adenosine Triphosphate-ATP
Adenosine triphosphate (ATP) is
the energy currency of cells
Review
► Thermodynamics
► Basic
Chemistry
 Atoms
 Isotopes
 Molecules and Compounds
► Chemical Bonding
 Ionic and Covalent
 Hydrogen
► Properties of Water
► Acids and Bases, pH
Review 2
►3
Reactions
 Oxidation/reduction
 Dehydration (condensation)
 Hydrolysis
► Organic vs Inorganic
► Macromolecules
 Proteins
 Carbohydrates
 Lipids
 Nucleic Acids