AGENDA
Hand in Homework #1
 Hand in in-class work from last class
 Questions / Concerns?
 Lecture Quiz #2
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REMINDERS:
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Pre-lab #3 due at beginning of lab period
Lab quiz #2 during lab
1st four Microworlds due at end of lab today
Reminder: Exam next class!
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Weeks 1-3
Chapters 1-3, 10.1-10.5
Study Hints
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Study in several shorter sessions
Write down answers to the Course Objectives
for the chapters 1-3.
Answer them IN YOUR OWN WORDS using
Vital Vocab (to be posted)
Make flash cards for Vital Vocab
Review the powerpoints and highlight Vital
Vocab and definitions
Important Points from Lecture
#2
Atoms are made up of protons,
neutrons and electrons.
 The number of protons, neutrons and
electrons give atoms their properties.
 Molecules are made from atoms linked
together by bonds

Lecture 3 Summary

Three bond types:
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COVALENT - share electrons, strong
IONIC - transfer electrons, medium
HYDROGEN - form between partial
charges (polar molecules), weak
Lecture 3 Summary
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Properties of water:
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Polar (hydrophobic sand demo)
“Sticky” - surface tension, capillary action
Ice floats
High specific heat
Universal solvent
Importance in body
Polar and Nonpolar
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Polar = charged
regions
“Like dissolves like”

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polar wants to be near
polar
Non-polar wants to be
near non-polar
Organic Compounds
CARBON

HYDROGEN
Is stable with how
many bonds?
Structural
formula

Is stable with how
many bonds?
Ball-and-stick
model
Space-filling
model
Methane
The 4 single bonds of carbon point to the corners of a tetrahedron.
Organic Compounds
CARBON

Is stable with how
many bonds?
Ethane
Propane
Carbon skeletons vary in length.
Organic Compounds
CARBON

Is stable with how
many bonds?
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
Organic Compounds
CARBON

Is stable with how
many bonds?
Cyclohexane
Benzene
Skeletons may be arranged in rings.
Why is the structure of carbon
important?

Almost infinite variety of possible structures for
biological molecules
HYDROCARBONS – composed of only
hydrogen and carbon
12
Exact structure of molecules is
important

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Structure = Function
ANIMATION: Campbell Ch 4 – L_dopa_A
Functional Groups
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Groups of atoms
attached to the
carbon skeleton of
molecules
Determine the
properties of organic
compounds
Part of molecule that
participates in
chemical reactions
Functional Groups
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Five main functional groups in biology:
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Hydroxyl group
Carbonyl group
Carboxyl group
Amino group
Phosphate group
These groups are all polar and make
compounds containing them hydrophilic
WHAT ATOMS MAKE
UP FUNCTIONAL
GROUPS?
WHY IS EACH OF
THESE FUNCTIONAL
GROUPS POLAR?
Atoms in the Functional
Groups

Stable with how many bonds?
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OXYGEN
NITROGEN
PHOSPHOROUS (atomic # 15)
Chemical Building Blocks of
Living Systems

Organic compounds
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Contain at least one CARBON atom
Hydrocarbon + functional group
Small molecules combine to form large
molecules (macromolecules)
Organic Macromolecule
Small
Molecule
Small
Molecule
Small
Molecule
Small
Molecule
Monomers vs Polymers
Monomer
Monomer
Monomer
Monomer
•Monomer (1 small molecule) usually has 1
functional group
•Polymer has many functional groups:
•Can interact with many other things
•Can perform a more complicated
function
Connecting and Unconnecting
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Dehydration synthesis
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Hydrolysis
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removal of a water molecule
Connects two monomers
Forms COVALENT BOND
addition of a water molecule
Disconnects two monomers
http://science.nhmccd.edu/biol/dehydrat/dehy
drat.html
Connecting
Short polymer
Unlinked monomer
Dehydration
reaction
Longer polymer
New COVALENT bond
Un-connecting
Hydrolysis
Broken COVALENT
bond
Four major classes of organic
macromolecules
Carbohydrates
 Nucleic acids
 Proteins
 Fatty Acids (lipids)

Carbohydrates
Monomer =
monosaccharide
 Structure
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carbon, hydrogen,
oxygen
(C1H2O1)n
Contains hydroxyl
and carbonyl
groups
Carbohydrates
Structural
formula
Abbreviated
structure
Simplified
structure
Carbohydrates

Functions
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Store and release energy (glucose, starch)
Structural support (cellulose)
Examples = glucose, sucrose, lactose
Carbohydrates
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MONOSACCHARIDE = one monomer of a
carbohydrate
DISACCHARIDE = two monomers
TRISACCHARIDE = three monomers
POLYSACCHARIDE = many monomers
Connected by WHAT kind of bond?
ANIMATION: Campbell
Ch 3 - Disaccharides
Polymer = Polysaccharides
Cellulose: Structure
•Polysaccharides
connected to form
strands with hydrogen
bonds
Starch: Energy storage
•Glucose connected together
to form a long chain
Structure = Function

Sweetness of sugars
depends on the
structure of the
polysaccharide
Polarity
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Are these sugars
polar or non-polar?
What do sugars do
in water?
Lipids

VARIOUS TYPES
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Triglycerides
Phospholipids
Waxes
Steroids
Lipids - Triglycerides
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Monomer = 3 fatty
acids + glycerol
Structure:
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Fatty Acids: Long
hydrocarbon chains
Glycerol: hydrocarbons
with hydroxyl (OH)
groups
Lipids - Triglycerides

Function: Stores
energy long-term
Polarity
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Is a lipid polar or
non-polar?
Does fat dissolve in
water?
Saturated vs Unsaturated
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Maximum number of
hydrogensattached to
carbons
No double bonds
between carbons
More flexible
Straight
Packs tightly
More solid at room
temperature
Saturated vs Unsaturated
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Some carbons
connected via double
bonds
Fewer than maximum
number of hydrogens
Less flexible (double
bonds are stiffer)
Kinked
Does not pack tightly
Less solid at room
temperature
Saturated vs Unsaturated
ANIMATION: Campbell
Ch 3 - Fats
Trans fats

Unsaturated fat made
by partially
hydrogenating an oil
Trans fats
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
Which will pack more
tightly, a “cis”
unsaturated fat or a
“trans” unsaturated fat?
Which will be more
solid at room temp?
“cis” unsaturated fat
“trans” unsaturated fat
Trans Fats - why are they bad?

Enzyme in the body
that digests fats is less
effective on trans
unsaturated fats
Lipids - Phospholipids

Structure – Glycerol connected to TWO
fatty acids and a phosphate group
POLAR OR NONPOLAR?
Phospholipid structure
Lipids - Phospholipids

Lipid bilayer:
Function: Makes up
membranes in cells
(phosphoplipids)
Membrane structure
Lipids - Waxes
–
–
STRUCTURE:
Consist of a single
fatty acid linked to an
alcohol
FUNCTION: Form
waterproof coatings
Lipids - Steroids
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STRUCTURE: Have
backbones bent into
rings
FUNCTION: Are often
hormones or the
basis of hormones
EXAMPLE:
Cholesterol
Lipids - Steroids
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Naturally found in
living things
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Testosterone
Estrogen
Progesterone
Corticosteroids
(regulate metabolism)
Found in other
organisms - Insects
have them
Lipids - Steroids
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Anabolic Steroids –
natural and synthetic
versions of
testosterone
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Build up bone and
muscle mass
Lipids - Steroids

Anabolic Steroids –
natural and synthetic
versions of
testosterone
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Build up bone and
muscle mass
Can cause serious
health problems
Proteins
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Monomer = amino
acids
There are 20
different amino acids
Protein structure is
determined by order
of amino acids
Leucine (Leu)
Hydrophobic
Serine (Ser)
Aspartic acid (Asp)
Hydrophilic
Amino Acid Structure
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Structure:
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Central C
Amino Acid Structure
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Structure:
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Central C
Amino group
Amino Acid Structure
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Structure:
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Central C
Amino group
Carboxyl Group
Amino Acid Structure
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Structure:
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Central C
Amino group
Carboxyl Group
R group
Amino Acid Structure
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Structure of R group
determines the
properties of each
amino acid
Hydrophobic or
hydrophilic
Charged or
uncharged
Small or large
Amino Acid Structure
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Hydrophilic or Hydrophobic?
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Polar or
Non-polar?
Amino Acid Structure
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Hydrophilic or Hydrophobic?

Polar or
Non-polar?
Amino Acid Structure

Hydrophilic or Hydrophobic?
Amino Acid Structure

Hydrophilic or Hydrophobic?
Protein Structure
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How are amino acids connected together?
DEHYDRATION SYNTHESIS
PEPTIDE BOND =
What type of bond?
Protein Structure
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Very complicated
Described as four levels:
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Primary
Secondary
Tertiary
Quaternary
Protein Primary Structure
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The unique sequence of amino acids forming
the polypeptide
Amino acids connected by peptide (covalent)
bonds
ANIMATION: Campbell
Ch 3 – Primary Structure
Protein Secondary Structure

The coiling or folding
of the chain,
stabilized by
hydrogen bonding
between O and H of
backbone
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Alpha helix
Beta pleated sheet
Levels of Protein Structure
Amino acids
Hydrogen
bond
Alpha helix
Pleated sheet
Alpha Helixes
Beta Pleated Sheets
ANIMATION: Campbell
Ch 3 – Secondary
Structure
Protein Tertiary Structure
Levels of Protein Structure

The overall threedimensional (globular)
shape of the
polypeptide
Amino acids
Hydrogen
bond
Alpha helix
Polypeptide
(single subunit
of transthyretin)
Pleated sheet
Protein Tertiary
Structure
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Determined by:
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Hydrogen Bonds
Ionic Bonds
Hydrophobic / hydrophilic
interactions
Disulfide bonds – covalent
bonds between S atoms
ANIMATION: Campbell
Ch 3 – Tertiary Structure
Protein Quaternary Structure
Levels of Protein Structure
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The association of
two or more
polypeptide chains
Not found in all
proteins
ANIMATION: Campbell
Ch 3 – Quaternary
Structure
Amino acids
Hydrogen
bond
Alpha helix
Polypeptide
(single subunit
of transthyretin)
Transthyretin, with
four identical
polypeptide subunits
Pleated sheet
Proteins: 3D Structure
Protein Structures
Insulin
Snake Venom
Protein Structures
DNA Binding protein
Bacterial protein of
undetermined function
R groups and interactions
determine structure

“World’s largest protein”
Specific Shape Determines
Function
1.
ENZYMES:
perform chemical
reactions
Metabolic
Pathways
Specific Shape Determines
Function
2.
Structural: hair,
cartilage,
muscle, cell
cytoskeleton
TUBULIN
Specific Shape Determines
Function
3.
Contractile:
producers of
movement in
muscle and other
cells
ACTIN / MYOSIN in muscles
Specific Shape Determines
Function
4.
Immune system:
marker proteins
identify self vs
other; antibodies
ANTIBODY
Specific Shape Determines
Function
5.
Transport: carry
other molecules
CHANNEL PROTEIN
Specific Shape Determines
Function
6.
Signaling: hormones, membrane
proteins
Specific Shape Determines
Function
7.
Gene
Regulatory:
control whether a
gene is active or
not
Proteins: 3D Structure

DENATURATION: chemical or physical
changes that can cause proteins to lose their
shape and thus their specific function
ANIMATION:
Cain Ch 4 –
Ch04a06
Nucleic Acids
Monomer = nucleotides
 Structure = three parts: sugar,
phosphate, and nitrogen-containing
base

Functions
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Nucleotide monomers can be used as
“energy currency”
Examples = ATP / ADP
Functions

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Stores genetic
information (traits and
inheritance)
Examples= DNA,
RNA
Nucleotide Structure

Nucleotides – the
building blocks of
nucleic acids

Made of:
Phosphate
Sugar
Nitrogenous Base
1.
2.
3.
Sugar-Phosphate Backbone
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
Nucleotides
connected together
with what type of
bond?
Alternating sugars
and phosphates
Nitrogenous Bases

Four bases:
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Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
Base Pairing

Bases form hydrogen
bonds with each other


A with T
C with G
PURINE with?
PYRIMIDINE with?
DNA Structure

DNA nucleotides are
linked together by
covalent bonds into a
single strand


phosphates are
bonded to sugars
sugars are bonded to
N Bases
DNA Structure

DNA bases are
bonded together with
hydrogen bonds to
form a double
stranded molecule
3-D DNA Structure

Based on the angle of
the bonds (remember
what a C with 4 bonds
looks like), DNA
forms a DOUBLE
HELIX
DNA Structure
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Hydrogen Bonds
occur between
Nucleotide Bases
the bonds between
which 2 bases are
stronger?
thousands of bases,
thousands of bonds,
thousands of big
twists
Polarity

Is DNA polar or nonpolar?
Determining that DNA is the
Genetic Material
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GRIFFITH: 1928
"Transforming
factor”
Determining that DNA is the
Genetic Material
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HERSHEY –
CHASE: 1952
Determined that the
heredity material
was DNA not protein
Studied the
bacteriophage T2
Head
DNA
Tail
Tail fiber
300,000

Determining that DNA is the
Genetic Material
Phage
Bacterium
Radioactive
protein
DNA
Batch 1
Radioactive
protein
Mix radioactively
labeled phages with
bacteria. The phages
infect the bacterial cells.
Batch 2
Radioactive
DNA
Empty
protein shell
Phage
DNA
Radioactivity
in liquid
Centrifuge
Agitate in a blender to
separate phages outside
the bacteria from the
cells and their contents.
Pellet
Centrifuge the mixture Measure the
so bacteria form a
radioactivity in
pellet at the bottom of the pellet and
the test tube.
the liquid.
Radioactive
DNA
Centrifuge
Pellet
Radioactivity
in pellet
Determining the Structure of
DNA
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CHARGOFF: 1949
Different species
have different
amounts of A, T, C, G
A always equals T
C always equals G
Determining the Structure of
DNA
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FRANKLIN and
WILKINS: 1950’s
X-ray crystalographic
determination that
DNA is a double helix
Determining the Structure of
DNA
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WATSON and
CRICK: 1953
Double helix structure
of DNA
Determining the Structure of
DNA
Determining the Structure of
DNA
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http://www.pbs.org/wgbh/nova/photo51/