Download APChapter2-5_ Aug 30-

AP Bio Chapter 2
Weak bonds
intermolecular and
intramolecular
Hydrogen
Van
Bonds
der Waals
Hydrogen Bonds
When
a hydrogen atom bonded to one
molecule is attracted to the slightly
negative area (often N or O) of
another molecule.
Very
Can
weak individual bond.
be a “strong” force if there are
many H bonds.
Hydrogen Bonds
Molecular Shape
Determined
by the positions of
the atom’s orbitals.
Molecular Shape
Crucial
in Biology : determines
how most molecules of life
recognize and respond to one
another.
Chemical Reactions
The
making and breaking of
chemical bonds.
Reactions do not destroy
matter, they only rearrange it.
Chemical Equations
A
way to represent what is
happening in a chemical
reaction.
Ex: 2 H2 + O2
2 H2O
Parts of the Equation
Reactants:
- the starting materials.
Products:
- the ending materials.
Note
- all atoms of the reactants
must be accounted for in the
products.
2 H2 + O2
2 H2O
Chemical Equilibrium
When
the conversion of
reactants to products is
balanced to the reverse
reaction.
Ex:
3 H2 + N2
2 NH3
Summary
We
will now put elements
together to form molecules
and build the next level in the
hierarchy.
What is the chemical?
Dihydrogen
Otherwise
monoxide
known as H2O
Chapter 3
Water and the Fitness of
the Environment
Question?
What molecule Is the most
common In living Cells?
Water - most cells are 70 - 95%
water.
The Water Planet
Properties Of Water
Be
ready and able to discuss
several of the following
properties.
1. Liquid Water Is
Cohesive
Water
sticks to water.
Why?
Because the polarity of water
results in hydrogen bonding.
2. Liquid Water is
Adhesive
Water
sticks to other
molecules.
Why?
Hydrogen bonding.
Water transport in trees uses
Cohesion and Adhesion
3. Water Has A High
Surface Tension
The
surface of water is
difficult to stretch or break.
Why?
Hydrogen
bonding.
4. Water Has A High
Specific Heat
Specific
Heat - the amount of
heat needed to raise 1 g of
the substance 1 degree C.
Why?
Hydrogen bonding.
Celsius Scale
Will
be used for most of our
temperature measurements.
O oC - water freezes
100 oC - water boils
37 oC - human body
5. Water Stabilizes
Temperature
Water
can absorb and store a
huge amount of heat from the
sun.
Result - climate moderation
Result - organisms are able
to survive temperature
changes.
Water Has A High Heat
Of Vaporization
Heat
of Vaporization:
the quantity of heat a liquid
must absorb for 1g of it to
convert to a gaseous state.
Evaporative Cooling
Result:
Water
cools organisms from
excessive heat buildup.
Why?
Hydrogen bonding
Water Expands When
It Freezes
The
distance between water
molecules INCREASES from the
liquid to the solid form.
Ice floats
Why?
Hydrogen
bonding
Result
Aquatic
life can live under ice.
6. Water Is A Versatile
Solvent
Water
will form a solution
with many materials.
Why?
it is a polar molecule
Solution
Homogeneous
mixture of two
or more substances.
Solvent
The
dissolving agent.
Solute
The
substance that is
dissolved.
Hydrophilic Materials
Materials that
Hydro - water
philic
Have
dissolve in water.
- to like or love
ionic or polar regions (polar
covalent bonds) on their
molecules for H+ bonds.
Hydrophobic
Materials
that repel water.
Hydro - water
phobic - to fear
Have
non-polar covalent
bonds. Ex - lipids.
Without Water
Life Would Not Be
Possible!!
Solution Concentration
Usually
Molarity
based on Molarity.
- the number of
moles of solute per liter of
solution.
Moles:
The
molecular weight of a
substance in grams.
One
Avogadro’s number of
molecules.
6.02 X 1023
Sugar
Copper Sulfate
Sulfur
Mercury Oxide
Sodium Chloride
Copper
Molarity Problem
How
do you make a 10 %
molar solution of sucrose?
Comment
AP
Biology students should
be able to calculate solutions
in Molarity.
Dissociation of Water
Water
can sometimes split into
two ions.
In
pure water the concentration
of each ion is 10-7 M
.
Adding
certain solutes
disrupts the balance between
the two ions.
The two ions are very
reactive and can drastically
affect a cell.
Acids
A
Substance that increases
the H+ conc. Of a solution.
Example: HCl
HCl
H+ + Cl-
Acid Rain
Acid Rain
Bases
Substances
that reduce the H+
conc.
1. by disassociation
2. by removing H+ from solution
Example:
NaOH
NaOH
Na+ + OH-
Neutrals
Materials
that are neither
acids nor bases.
pH 7
pH Scale
A
logarithmic scale for
showing H+ concentration
pH = - log [H+]
0
to 14
pH
Scale
Example:
For a neutral solution:
[H+] is 10-7
or - log 10-7
or - (-7)
or 7
pH scale
Acids:
pH <7 etc.
Bases: pH >7 etc.
Each
in H+
pH unit is a 10x change
[H+]
[OH-] = 10-14
Therefore,
if you know the
concentration of one ion, you
can easily calculate the other.
Buffers
Substances
that minimize
changes in H+ and OH- in a
solution.
Cells --prevent damage.
Most biological pH around 0
Carbonic acid:
+
H2 CO3
HCO3 + H
Summary
Be
able to discuss the properties
of water.
Be able to measure solution
concentrations in Molarity.
Be able to work pH scale
questions.
Describe buffers in the human
body.
Chapter 4
Carbon and the
Molecular Diversity of
Life
Organic Chemistry
The
study of carbon
compounds.
Urea
Carbon’s versatility
Forms
4 covalent bonds.
Molecular shape is
tetrahedral.
Bonds
easily to itself.
The
electron configuration of
carbon gives it compatibility to form
covalent bonds with many different
elements.
The valences of carbon and its
partners can be viewed as the
building code that governs the
architecture of organic molecules.
Fig. 4.3
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
3. Variation in carbon skeletons
contributes to the diversity of
organic
molecules
Carbon
chains form the skeletons of
most organic molecules.
Skeletons
vary in length
may be straight, branched, or arranged in
closed rings.
May
also include double bonds.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 4.4
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Isomers
Compounds
with the same
molecular formula but have
different structures.
Result:
Different chemical
properties.
Which of these are
isomers?
No
Yes
Yes
No
Types Of Isomers
1.
2.
3.
Structural
Geometric
Enantiomers
Structural Isomers
Different
in covalent
arrangements of their atoms.
Butane
Isobutane
Geometric Isomers
Differ
in
spatial
arrangements.
Arise from the
inflexibility of
double bonds.
Enantiomers
Molecules
that are mirror
images of each other.
Usually
involve an
asymmetric carbon.
Enantiomers:
mirror images
Left-handed(L)and
right-handed(D)
versions.
Usually one is
biologically active,
the other inactive.
Enantiomers
:four different atoms or
groups of atoms bonded to a carbon
Fig. 4.6c
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Comment
Organisms
are sensitive to
even the most subtle
variations in molecular
architecture.
Example - Thalidomide
Cells
can distinguish
between two isomers.
One is an effective drug.
The other causes birth
defects.
emergent
One
properties/structure
enantiomer of the drug
thalidomide reduced morning
CHAPTER 4 CARBON AND THE
MOLECULAR DIVERSITY OF LIFE
Section B: Functional Groups
1. Functional groups contribute to the molecular diversity of life
2. The chemical elements of life: a review
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Functional Groups
A
group of atoms attached to
a carbon skeleton.
Involved in chem rx.
Hydrophyllic
The
basic structure of testosterone
(male hormone) and estradiol
(female hormone) is identical.
Both
are steroids with four fused carbon
rings, but they differ in the functional
groups attached to the rings.
These
then interact with different
targets in the body.
Fig. 4.8
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Importance of
Functional Groups
Table 4.1 Functional Groups of Organic
Compounds
1.Hydroxyl Group: -OH





A hydrogen atom bonded to an
oxygen atom.
-OH
Very polar
hydrophilic.
Forms alcohols. ethanol
2. Carbonyl Group
A
carbon atom joined to an
oxygen atom by a double
bond.
Ex. - C=O
Two types of Carbonyl Group
compounds:
Aldehydes—C=O
at end
Ketones C=O in middle
Aldehydes
A
carbonyl group at the end
of a carbon skeleton.
Ex. - C=O
|
H
Sometimes written as
- CHO
Ketones
A
carbonyl group in the
middle of a carbon chain.
Ex.
-C-C-C||
0
3. Carboxyl Group
Group
with a carbon double
bonded to an oxygen and to
a hydroxyl group.
Ex. - C=OH
|
H
Written as: -COOH
Also called Carboxylic Acids
4. Amino Group-NH2
Nitrogen
bonded to two hydrogens.
 Act as a base.
Part
of amino acid
5. Sulfhydryl Group
Sulfur
bonded to a hydrogen.
Ex. -SH
Forms compounds called
thiols.
Helps stabilize protein
structure.
6. Phosphate Group
Phosphorus
with four oxygens.
Ex. -PO4
Has a net -2 charge
Involved with energy transfers.
Summary
Be
able to recognize isomers.
Know/identify the 6
functional groups;
properties; where found.
2. The chemical elements of
life:
a
review
Living matter consists mainly of
carbon, oxygen, hydrogen, and
nitrogen, with smaller amounts of
sulfur and phosphorus.
These elements are linked by strong
covalent bonds.
Carbon with its four covalent bonds
is the basic building block in
molecular architecture.
The great diversity of organic
molecules with their special
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 4.7
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Enantiomers
Molecules
that are mirror
images of each other.
Usually
involve an
asymmetric carbon.
Comment
Organisms
are sensitive to
even the most subtle
variations in molecular
architecture.
Example - Thalidomide
Cells
can distinguish
between two isomers.
One is an effective drug.
The other causes birth
defects.
1. Functional groups contribute
to the molecular diversity of life
The
components of organic
molecules that are most commonly
involved in chemical reactions.
Functional
groups are attachments that
replace one or more hydrogen atoms to
the carbon skeleton of the hydrocarbon.
Each
functional groups behaves
consistently from one organic
molecule to another.
The number and arrangement of
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
The
basic structure of testosterone
(male hormone) and estradiol
(female hormone) is identical.
Both
are steroids with four fused carbon
rings, but they differ in the functional
groups attached to the rings.
These
then interact with different
targets in the body.
Fig. 4.8
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
There
are six functional groups that
are most important to the chemistry
of life: hydroxyl, carbonyl, carboxyl,
amino, sulfhydryl, and phosphate
groups.
All
are hydrophilic and increase the
solubility of organic compounds in
water.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
CHAPTER 4 CARBON AND THE
MOLECULAR DIVERSITY OF LIFE
Section B: Functional Groups
1. Functional groups contribute to the molecular diversity of life
2. The chemical elements of life: a review
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Functional Groups
A
group of atoms attached to
a carbon skeleton.
Have consistent properties.
Their number and kind give
properties to the molecule.
Importance of
Functional Groups
Table 4.1 Functional Groups of Organic
Compounds
Hydroxyl Group
A
hydrogen atom bonded to
an oxygen atom.
Ex. -OH
Very polar. Allow the material
to be hydrophilic.
Forms alcohols.
Carbonyl Group
A
carbon atom joined to an
oxygen atom by a double
bond.
Ex. - C=O
Two types of Carbonyl Group
compounds:
Aldehydes
Ketones
Aldehydes
A
carbonyl group at the end
of a carbon skeleton.
Ex. - C=O
|
H
Sometimes written as
- CHO
Ketones
A
carbonyl group in the
middle of a carbon chain.
Ex.
-C-C-C||
0
Carboxyl Group
Group
with a carbon double
bonded to an oxygen and to
a hydroxyl group.
Ex. - C=OH
|
H
Written as: -COOH
Also called Carboxylic Acids
Carboxylic Acids
H+ (acid).
Form many weak organic
acids.
Donate
Amino Group
Nitrogen
bonded to two
hydrogens.
Ex. – N-H
|
H
Forms compounds called
amines.
Act as a base.
Sulfhydryl Group
Sulfur
bonded to a hydrogen.
Ex. -SH
Forms compounds called
thiols.
Help with protein structure.
Phosphate Group
Phosphorus
with four oxygens.
Ex. -PO4
Has a net -2 charge.
Sometimes written as “Pi”.
Involved with energy transfers.
Summary
Be
able to recognize isomers.
Know the seven functional
groups and what properties
they give to molecules.
2. The chemical elements of
life:
a
review
Living matter consists mainly of
carbon, oxygen, hydrogen, and
nitrogen, with smaller amounts of
sulfur and phosphorus.
These elements are linked by strong
covalent bonds.
Carbon with its four covalent bonds
is the basic building block in
molecular architecture.
The great diversity of organic
molecules with their special
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Chapter 5
The Structure and
Function of
Macromolecules
CHAPTER 5 THE STRUCTURE AND
FUNCTION OF MACROMOLECULES
Section A: Polymer principles
1. Most macromolecules are polymers
2. An immense variety of polymers can be built from a small set of monomers
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Introduction
Cells
join smaller organic molecules
together to form larger molecules.
Macromolecules
The
four major classes:
carbohydrates, lipids, proteins, and
nucleic acids.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Most macromolecules are
polymers
Consist
of many similar or
identical building blocks linked
by covalent bonds.
The repeated units are small
molecules called monomer
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Monomer
A
building block of a polymer.
Condensation Synthesis
or Dehydration Synthesis
The
chemical reaction that
joins monomers into
polymers.
Covalent bonds are formed
by the removal of a water
molecule between the
monomers.
Building Polymers:
Fig. 5.2a
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Disassembling
Polymers:
via hydrolysis.
“to
break with water”
Hydrolysis reactions
dominate the
digestive process,
guided by specific
enzymes.
Fig. 5.2b
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Hydrolysis
Reverse
of condensation
synthesis.
Hydro- water
Lysis - to split
Breaks polymers into
monomers by adding water.
Four Main Types Of
Macromolecules
Carbohydrates
Lipids
Protein
Nucleic
acids
Carbohydrates
Used
for fuel, building
materials, and receptors.
Made of C,H,O
General formula is CH2O
C:O ratio is 1:1
Types Of
Carbohydrates
Monosaccharides
Disaccharides
Polysaccharides
Monosaccharides
Mono
- single
Saccharide - sugar
Simple sugars.
3 to 7 carbons.
Can be in linear or ring
forms.
functions
Fuel
for cells—esp. glucose
Build other macromolecules
(rearrangement)
Fig. 5.4
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Monosaccharides
Can
be “Aldoses” or
“Ketoses” depending on the
location of the carbonyl
group.
Examples
Glucose
Galactose
Ribose
(hexoses)
Fructose
(pentose)
- OSE
Word
ending common for
many carbohydrates.
Disaccharides
Formed
in a dehydration
reaction
Covalent
bond called a
“glycosidic linkage”
Examples
Maltose
= glucose + glucose
Lactose = glucose + galactose
Milk
sugar
Sucrose
Table
= glucose + fructose
sugar
Major transport form of sugar
in plants
Fig. 5.5a
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Polysaccharides
Many
joined simple sugars.
Used for storage or structure.
Examples:
Starch-storage
in plants
Cellulose-plant cell wall; structure
Glycogen-animals; energy reserve
Chitin-Nitrogen containing;structural;
arthropod shell; fungi cell wall;
Glucose
has 2 possible ring
structures.
Hydroxyl group, attached to the number
1, carbon may be fixed above (beta
glucose) or below (alpha glucose) the
ring plane.

Fig. 5.7a
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
a glucose and b glucose
Starch
of 1-4 linkages of a glucose.
Linkage makes the molecule form
a helix.
Fuel storage in plants.
Made
a glucose
Cellulose
of 1-4 linkages of b glucose.
Linkage makes the molecule form
a straight line.
Made
This
allows H atoms on one strand
to form hydrogen bonds with OH
groups on other strands.
Groups
of polymers form strong
strands, microfibrils, that are basic
building material for plants (and
humans).
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
b glucose
Comment
Most
organisms can digest starch
(1- 4 a linkage), but very few can
digest cellulose (1- 4 b linkage).
Another
example of the link
between structure and function.
Glycogen
“Animal
starch”
Similar to starch, but has
more 1-6 linkages or
branches.
Found in the liver and muscle
cells.
Starch
Glycogen
Chitin
Structural polysaccharide
 Exoskeletons of arthropods
(including insects, spiders, and
crustaceans). Also fungi cell wall.

Similar
to cellulose, but,contains a
nitrogen appendage.
Pure chitin is leathery, but the addition of
calcium carbonate hardens the chitin.
Fig. 5.9
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Lipids--Introduction
Not
polymers.
Hydrophobic molecules.
Structures
dominated by nonpolar
covalent bonds.
Made
of C,H,O
No general formula.
C:O ratio is very high in C.
Highly diverse in form and function.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
1. Fats
Syn.
From Glycerol + fatty acid(s)
Glycerol:
contains hydroxyl (-OH) group
Fatty Acid: A long carbon chain (12-18
C) with a -COOH (acid) on one end and
a -CH3 at the other.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Triglyceride/triaclyglycero
3
fatty acids
+glycerol
Fig. 5.10b
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
The 3 Fatty Acids in a FAT
can be the Same or Different
Variations:
Length
of chain (# of
carbons).
 # of double bonds
 Locations of
double bonds.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Saturated vs. Unsaturated
Fats
Saturated Fatty acids
No
double bonds (between
carbons).
Straight chains
Found in animals
Solid at room temp.
Factor in
atherosclerosis.
Unsaturated fatty acids
One
or more double bonds.
Structure has a kink
at double bond(s).
Plants, fish.
Liquid at room temp.
Commonly called “oil”
Fig. 5.11b
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fats
with saturated fatty acids are
saturated fats.
Most
animal fats are saturated.
Saturated fats are solid at room
temperature.
A diet rich in saturated fats may
contribute to cardiovascular disease
(atherosclerosis) through plaque
deposits.
Fats
with unsaturated fatty acids are
unsaturated fats.
Plant
and fish fats, known as oils, are
liquid are room temperature.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fat- Functions
1.
Long-term Energy storage, esp.
in animals- (9kcal/g) : twice as
much as carb.
It’s
more compact than starch or
glycogen
Cushions
Insylates
Acid
Fat
REVIEW: Saturated Fats
Unsaturated Fats
Saturated
- no double bonds.
Unsaturated - one or more
C=C bonds. Can accept more
Hydrogens.
Double bonds cause “kinks”
in the molecule’s shape.
Question ?
Which
has more energy, a kg
of fat or a kg of starch?
Fat - there are more C-H
bonds which provide more
energy per mass.
Which is which?
Properties?
2. Phospholipids
Similar
to fats, but have only
two fatty acids.
The third -OH of glycerol is
joined to a phosphate
containing molecule (has a
negative charge).
Be able to draw;labelpolar and nonpolar ends
The Result Is…
Phospholipids
have
a hydrophylic head
tail, but a
hydrophobic tail.
Self-assemble into
micelles or bilayers,
an important part of
cell membranes.
At
the surface of a cell
phospholipids are arranged as a
bilayer.
Again,
the hydrophilic heads are on
the outside in contact with the
aqueous solution and the hydrophobic
tails from the core.
The phospholipid bilayer forms a
barrier between the cell and the
external environment.
They
are the major component of
membranes.
Fig. 5.12b
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
3. Steroids
Lipids
with four fused rings.
Examples:
cholesterol
Steroid
(sex hormones)
Functions off
Cholesterol in animals
Only
in animals.
Component in animal cell
membranes-stability & insulation.
Precursor from which all other
steroids are synthesized.
Many
are hormones, including the
vertebrate sex hormones.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Misc. Fat Info
Hydrogenation
Trans
fats
Proteins-Introduction
Proteins
are instrumental in about
everything that an organism does.
Humans have tens of thousands of
different proteins, each with their own
structure and function.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Functions Of Proteins
Structure
Storage
Enzymes
Antibodies
Transport
Movement
Receptors
Hormones
Movie
Proteins
Half
the weight of a dry cell.
Made of C,H,O,N, and
sometimes S.
Polymer of amino acids
Proteins
Polypeptide
chains of Amino
Acids linked by peptide
bonds.
One or more polypeptides
folded and coiled into
specific conformations.
Amino Acids
All
have a Carbon with four
attachments:
-COOH (acid)
-NH2 (amine)
-H
-R (some other side group)
R groups
20
different kinds:
Nonpolar
Polar
-
-
Electrically
Charged
Determines the physical &
chemical properties of the amino
acid.
Amino Acids
Amino Acids
Polypeptides
Formed
by dehydration
synthesis between the
carboxyl group of one AA and
the amino group of the
second AA.
Produce a backbone of: (NC-C)X
Levels Of Protein
Structure
Organizing
the polypeptide
into its 3-D functional shape.
Primary
Secondary
Tertiary
Quaternary
Primary
Sequence
of amino
acids in the
polypeptide chain.
Secondary
H-
Bonds between H and O
of backbone
Two main secondary
structures:
a
helix
pleated sheets
Tertiary
Bonding
between the R groups.
Examples:
hydrophobic
interactions
ionic bonding
Some disulfide bridges
(covalent bond )
 s-s form
When
Quaternary
comprised of two or
more polypeptides.
Examples:
 hemoglobin
 enzymes
 ketatin
Is Protein Structure
Important?
Denaturing Of A
Protein
Loss of structure (and function).
Due to :
pH
shifts
high salt concentrations
Heat
Example: Egg white cooking
Denaturation
Nucleic Acids: DNA and
RNA
Polymers
of nucleotides
Contain phosphorous
Nucleotides have three parts:
nitrogenous
base
pentose sugar
phosphate
DNA
 Deoxyribonucleic Acid.
 Makes
up genes.
 Genetic information
source for life.
 Double stranded molecule.
 Double helix.
 Sides– covalent bonds
 Rungs—hydrogen bonds
RNA
Ribonucleic
3
Acid.
kinds
Structure and protein synthesis.
Genetic information for a few
viruses only.
Single-stranded molecule.
DNA and RNA
More
will be said about DNA
and RNA in future lessons.
Summary
For
each macromolecule,
know the following:
Sig.
elements and monomers
Structures
Functions
Examples given in class