Chemistry
Big Idea 2: Biological systems utilize
free energy and molecular building
blocks to grow, to reproduce, and to
maintain dynamic homeostasis
P.S. In Biology we talk mainly about Organic
Chemistry: The chemistry of molecules containing
Carbon.
Chemistry Joke of the Day
a Poem….
• Susan was in chemistry.
– Susan is no more,
• for what she thought was H2O
– was really H2SO4.
Essential knowledge 2.A.3: Organisms must
exchange matter with the environment to grow,
reproduce and maintain organization.
a. Molecules and atoms from the environment are
necessary to build new molecules
• Carbon moves from the
environment to organisms
where it is used to build
carbohydrates, proteins,
lipids, or nucleic acids.
Carbon is used in storage
compounds and cell
formation in all organisms.
.
• Nitrogen moves from the
environment to organisms
where it is used in building
proteins and nucleic acids.
Phosphorus moves from the
environment to organisms
where it is used in nucleic
acids and certain lipids.
Living systems depend on properties of
water that result from its polarity and
hydrogen bonding.
• Cohesion
• Adhesion
• High specific heat
capacity
• Universal solvent to
support reactions
• Heat of vaporization
• Heat of fusion (exo
vs.endo)
• Water’s thermal
conductivity.
Review of Chemistry
Review of Chem
Review of Water
Trans fats
Essential knowledge 4.a.1: the
subcomponents of biological molecules and
their sequence determine the properties of
that molecule.
a. Structure and function of polymers are derived from
the way their monomers are assembled.
• Lipids are nonpolar; however
phospholipids exhibit structural
properties, with polar regions
that interact with other polar
molecules such as water, and
with nonpolar regions where
differences in saturation
determine the structure and
function of lipids.
.
• Carbohydrates are composed
of sugar monomers whose
structures and bonding with
each other by dehydration
synthesis determine the
properties and functions of the
molecules. Cellulose vs. Starch.
Why does one dissolve?
Lipids
Is this a carbohydrate or a lipid? How can your tell?
Is this a carbohydrate or a lipid? How can you tell?
What is the difference between Linear vs. branched
polysaccharides?
slow release
starch
(plant)
energy
storage
glycogen
(animal)
fast release
What does
branching do?
Cow
can digest cellulose well;
no need to eat other sugars
Gorilla
can’t digest cellulose well; must
add another sugar source, like
fruit to diet
How do animals break down cellulose?
• How can herbivores digest cellulose so well?
– Mutualism
– BACTERIA live in their digestive systems & help digest celluloserich (grass) meals
Tell me about
the rabbits,
again, George!
Coprophage
I eat
Ruminants
WHAT!
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
a. Structure and function of polymers are derived from
the way their monomers are assembled.
• In nucleic acids, biological
information is encoded in
sequences of nucleotide
monomers. Each nucleotide
has structural components: a
five-carbon sugar (deoxyribose
or ribose), a phosphate and a
nitrogen base (A,T,C,G,U). DNA
and RNA differ in function and
differ slightly in structure, and
these structural differences
account for the differing
functions.
• In proteins, the specific order
of amino acids in a
polypeptide (primary
structure) interacts with the
environment to determine the
overall shape of the protein,
which also involves secondary
tertiary and quaternary
structure and, thus, its
function. The R group of an
amino acid can be categorized
by chemical properties
(Hydrophobic/philic, ionic),
and the interactions of these R
groups determine structure
and function of that region of
the protein.
What are the three
parts of Nucleotides?
– nitrogen base (C-N ring)
– pentose sugar (5C)
• ribose in RNA
• deoxyribose in DNA
– phosphate (PO4) group
Are nucleic acids
charged molecules?
Nitrogen base
I’m the
A,T,C,G or U
part!
How are Proteins
structured?
Because everybody needs a
Chaperonin!
– monomer = amino acids
• 20 different amino acids
– polymer = polypeptide
• protein can be one or more
polypeptide chains folded &
bonded together
• large & complex molecules
• complex 3-D shape
hemoglobin
RuBisCO can’t do
photosynthesis without it!
H2O
Sickle cell anaemia
I’m
hydrophilic!
Just 1
out of 146
amino acids!
But I’m
hydrophobic!
Isomers
• Molecules with same molecular formula
but different structures (shapes)
– different chemical properties
– different biological functions
6 carbons
6 carbons
6 carbons
Form affects function
• Structural differences create important
functional significance
– amino acid alanine
• L-alanine used in proteins
• but not D-alanine
– medicines
• L-version active
• but not D-version
– sometimes with
tragic results…
stereoisomers
Form affects function
• Thalidomide
– prescribed to pregnant women in 50s & 60s
– reduced morning sickness, but…
– stereoisomer caused severe birth defects
b. Directionality influences structure
and function of the polymer.
• Nucleic acids have
ends, defined by
the 3’ and 5’
carbons of the
sugar in the
nucleotide, that
determine the
direction in which
complementary
nucleotides are
added during DNA
synthesis and the
direction in which
transcription occurs
(from 5’ to 3’)
• Proteins have an
amino (NH2) end
and a carboxyl
(COOH) end, and
consist of a linear
sequence of amino
acids connected by
the formation of
peptide bonds by
dehydration
synthesis between
the amino and
carboxyl groups of
adjacent
monomers.
The nature of the
bonding between
carbohydrate subunits
determines their
relative orientation in
the carbohydrate,
which then determines
the secondary structure
of the carbohydrate.
Learning Objectives:
• LO 4.1: The student is
able to explain the
connection between
the sequence and the
subcomponents of a
biological polymer and
its properties.
• LO 4.2: The student is
able to refine
representations and
models to explain how
the subcomponents of a
biological polymer and
their sequence
determine the
properties of that
polymer
A Review for You!
Chemistry of Carbon
Building Blocks of Life
2007-2008
Why study Carbon?
• All of life is built on carbon
• Cells
– ~72% H2O
– ~25% carbon compounds
•
•
•
•
carbohydrates
lipids
proteins
nucleic acids
– ~3% salts
• Na, Cl, K…
Chemistry of Life
• Organic chemistry is the study of carbon
compounds
• C atoms are versatile building blocks
– bonding properties
– 4 stable covalent bonds
H
H
C
H
H
Diversity of molecules
• Substitute other atoms or groups around
the carbon
– ethane vs. ethanol
• H replaced by an hydroxyl group (–OH)
• nonpolar vs. polar
• gas vs. liquid
• biological effects!
ethane (C2H6)
ethanol (C2H5OH)
Functional groups
• Parts of organic molecules that are involved
in chemical reactions
– give organic molecules distinctive properties
hydroxyl
 carbonyl
 carboxyl

amino
 sulfhydryl
 phosphate

• Affect reactivity
– makes hydrocarbons hydrophilic
– increase solubility in water
Viva la difference!
• Basic structure of male & female hormones is
identical
– identical carbon skeleton
– attachment of different functional groups
– interact with different targets in the body
• different effects
Hydroxyl
• –OH
– organic compounds with OH = alcohols
– names typically end in -ol
• ethanol
Carbonyl
• C=O
– O double bonded to C
• if C=O at end molecule = aldehyde
• if C=O in middle of molecule = ketone
Carboxyl
• –COOH
– C double bonded to O & single bonded to OH
group
• compounds with COOH = acids
– fatty acids
– amino acids
Amino
• -NH2
– N attached to 2 H
• compounds with NH2 = amines
– amino acids
• NH2 acts as base
– ammonia picks up H+ from solution
Sulfhydryl
• –SH
– S bonded to H
• compounds with SH = thiols
• SH groups stabilize the structure of proteins
Phosphate
• –PO4
– P bound to 4 O
• connects to C through an O
• lots of O = lots of negative charge
– highly reactive
• transfers energy between organic molecules
– ATP, GTP, etc.
Macromolecules
Building Blocks
of Life
2007-2008
Macromolecules
• Smaller organic molecules join together to
form larger molecules
– macromolecules
• 4 major classes of
macromolecules:
– carbohydrates
– lipids
– proteins
– nucleic acids
– And a minor one: ATP
Polymers
• Long molecules built by linking repeating
building blocks in a chain
– monomers
• building blocks
• repeated small units
H2O
– covalent bonds
Dehydration
Synthesis
http://sciencestage
.com/v/621/chemis
try-experimentsciencedehydrationsugar.html
HO
H
HO
HO
H
H
How to build a polymer
You gotta
be open to
“bonding!
• Synthesis
– joins monomers by “taking” H2O out
• one monomer donates OH–
• other monomer donates H+
• together these form H2O
H2O
– requires energy & enzymes
HO
H
Dehydration synthesis
HO
H
enzyme
Condensation reaction
HO
H
How to break down a polymer
Breaking up
is hard to do!
• Digestion
– use H2O to breakdown polymers
• reverse of dehydration synthesis
• cleave off one monomer at a time
• H2O is split into H+ and OH–
– H+ & OH– attach to ends
– requires enzymes
– releases energy
HO
H2O
enzyme
H
Hydrolysis
Digestion
HO
H
HO
H
Any Questions??
And now on to Acids and Bases
2007-2008
Ph Scale Fig 2.9, pg. 43
potential hydrogen
• Measured on grams of Hydrogen (H+)
– pH of 1= .1g of H+, pH of 2= .01g of H+
• Acid: form hydronium ions (H+)
– pH of less than 7 ( 1 to 6.9)
• Base: form hydroxide ions (OH-)
– pH of more than 7 (7.1 to 14)
• Acid + Base: salt & water, the solution is
neutral with a pH of 7.
– NaOH + HCl = H2O + NaCl with a pH of 7
pH Scale
What is a Buffer?
• Chemical substances that neutralizes small
amounts of an acid or base added to a
solution.
• Why are these important to your body?
– Think Blood pH 7.45
What is a Buffer?
• three main buffers in the body:
– bicarbonate buffer system: in the blood and
stomach to neutralize acids
– protein buffer system: inter and extra cellular
buffering used with hemoglobin and blood
– phosphate buffer system: used in the urinary
system to remove H+ ions and make urine acidic
Enzymes (most are Proteins)
pg. 21 Barron’s
• Catalysts: Lower activation energy needed to
start a chemical reaction. See fig 2.22, pg.54
• Nonspecific Inhibitors: Temperature, pH, radiation,
electricity:
• Terms: substrate, active site, product
• Can be denatured
• Induced fit
Enzymes continued…
• Characteristics:
– Globular proteins
(tertiary structure)
– Substrate specific
– Not destroyed /reused
– Named after substrate
with “ase” ending
– Catalyze in both
directions
• Catalyze with help
– Cofactor: inorganic
– Coenzyme: vitamin
• Control of Enzyme
Activity
– Competitive Inhibition:
competes for the space
with the substrate
– Noncompetitive
Inhibition/ Allosteric:
secondary site stops
enzyme from functioning
• PFK too much ATP
• Cooperativity: amplifies the
response of an enzyme to
its substrate. Hemoglobin,
more oxygen it has….