Biochemistry
AP BIOLOGY - SUMMER 2013
WEEK 1
INTRO QUIZ
Every week we’ll have a short quiz to review last week’s
material and check our understanding. This week, I just
want to know a couple things about you for my own
information.
1.
2.
3.
4.
5.
What grade are you in?
Are you taking AP Bio in the next school year?
Are you taking the AP Bio exam next May?
Have you taken a (high school) biology class before?
What is your favorite school subject?
Atomic Basics
 An atom is a tiny piece of
matter made of protons,
neutrons, and electrons.
 Two atoms with the same
number of protons behave the
same—we say they are the
same element.
 Elements are organized in the
periodic table, with an
abbreviation of 1 or 2 letters.
(e.g. Oxygen is O, Carbon is C,
Potassium is K, Iron is Fe)
Atomic Details
 The number of protons determines the element—
that’s what makes it carbon or radium.
 The number of electrons determines a charge.
More electrons than protons means that it is a
negative ion. Fewer electrons than protons means
that it is a positive ion.
 The number of neutrons determines the isotope.
NOTE: In experiments,
scientists will use a
weird isotope to label
certain atoms and track
them in a reaction.
Bonds Make Molecules
 Protons and neutrons are stuck
in the center, or nucleus of the
atom—they don’t change.
carbon dioxide
 Electrons are on the outside, so
CO2
they move around. Atoms make
bonds with other atoms when
they share or trade electrons.
 Atoms that are bonded together
are called molecules, and we
write the abbreviations for the
atoms right next to each other,
with little subscripts for how
many of each atom.
H2O
dihydrogen
monoxide
Do You Buy Organic?
ORGANIC MOLECULES
 Organic molecules are associated
with life and life processes
 Organic molecules involve
carbon, which is covalently
bonded.(A covalent bond is a
strong bond.)
 Some people define organic
molecules as having C-H bonds.
 Examples of organic molecules:
methane
benzene
INORGANIC MOLECULES
 Inorganic molecules are not always
associated with life, but they may be
important for life anyway.
 Many inorganic molecules have no
carbon.
 Sometimes inorganic molecules do
have carbon, but it doesn’t make the
characteristic C-H bonds that are
present in organics molecules.
 Examples of inorganic molecules.
sulfur hexafluoride
carbon dioxide
 Unequal charge makes water form
WATER:
the magic molecule!
weak hydrogen bonds with other
water molecules.
 These bonds make water “sticky”
The water molecule is very
important to life chemistry.
The electrons in water are
shared unevenly: the oxygen
hogs the electrons, while the
hydrogens become more
positive.
This is called being polar.
and give it special properties.
 Water is not the only molecule that
makes hydrogen bonds! They are
important in DNA and other large
molecules too.
 Adhesion: sticks to things
WATER:
the magic molecule!
REMEMBER!
Water molecules are polar
due to unequal electron
sharing.
They form weak hydrogen
bonds with other water
molecules.
 Cohesion: sticks to itself

Surface tension is caused by cohesion and
adhesion. This pulls water up the stems of
plants by capillary action
 Heat capacity: stores heat

Water helps animals stabilize their body
temperatures
 Solvent: dissolves stuff

Water pulls apart polar molecules like salt and
makes them into solutions
Making Bigger Molecules
 Some molecules are tiny, but the
molecules we need for life need to
be bigger and more complex.
Polymer
 A single unit or piece is called a
monomer.
“mono-” means “one”
 A larger molecule is made up of
many repeated monomers bonded
together: this is called a polymer.
“poly-” means “many”
 When we stick monomers together,
we are polymerizing them—and
water comes out! When we break
polymers apart, we put in water to
hydrolyze them.

(Remember, one of water’s skills is acting
as a solvent and breaking things apart.)
Monomer
Chemical Reactions
 We “read” a chemical reaction from left to right.


On the left are the reactants, that go in.
On the right are the products, that come out.
 There are the same number of C’s, H’s, and O’s on the left
and the right: the equation is balanced.

Atoms are only being rearranged, not created or destroyed
 The little marker “light” is not necessary, but it shows that
in this reaction energy is going in, or being stored.
Catalysts Speed Up Chemical Reactions
 Catalysts are molecules
that speed up, or catalyze,
chemical reactions.
 Every reaction has an
activation energy: a little
“you must be this tall”
energy requirement before
the reaction can go.
 Catalysts lower the
activation energy, so more
reactants can turn into
products more quickly.
(the ONLY Chemical Reaction Biologists Care About)
 Photosynthesis goes this way 
 Plants take carbon dioxide from the atmosphere
 They mix it with water from the ground, using the energy of
sunlight to power the reaction.
 Out comes glucose (a sugar) and waste oxygen
 Cellular respiration goes this way 
 Living things (animals and plants) take oxygen from the air
 They break down glucose and other foods into water (which is
useful) and carbon dioxide (which is waste)
Which of the following best characterizes the reaction
represented below?
A + B + energy → AB
(A) Hydrolysis
(B) Catabolism
(C) Oxidation-reduction
(D) Exergonic reaction
(E) Polymerization
Which of the following best characterizes the reaction
represented below?
A + B + energy → AB
(A) Hydrolysis
(B) Catabolism
(C) Oxidation-reduction
(D) Exergonic reaction
(E) Polymerization
The 4 Macromolecules of Life
1. CARBOHYDRATES
2. LIPIDS
The 4 Macromolecules of Life
1. CARBOHYDRATES
2. LIPIDS
 Monomer: simple sugars like the
 Monomer: carboxyl (C and H)
glucose molecule
 Polymer: starches like cellulose
and glycogen
 Starches are used to store energy
in plants (cellulose) and animals
(glygocen)
 Polymer: fatty acid chains
 Lipids are non-polar; they
share electrons equally and
don’t dissolve in water.
The 4 Macromolecules of Life
3. PROTEINS
4. NUCLEIC ACIDS
The 4 Macromolecules of Life
3. PROTEINS
4. NUCLEIC ACIDS
 Monomer: amino acid
 There are 20 amino acids.
 Monomer: nucleotide
 Each nucleotide is made of a
 Polymer: peptide bonds
link amino acids into proteins
 Note that proteins have
nitrogen, unlike
carbohydrates and lipids.
phosphate, sugar, and base.
 Polymer: DNA or RNA
 DNA has a double helix
structure caused by hydrogen
bonds between the bases.
Protein
Structure
Proteins are complex
molecules with 4 levels of
structure
(1) Primary structure
the order of amino acids in
the polymer
(2) Secondary structure
weak hydrogen bonds bend
the chain into a helix or
pleated sheet
(3) Tertiary structure
the 3D shape of the protein
(polypeptide) chain
(4) Quaternary structure
a collection of separate
polypeptide chains linked
together.
Enzymes are Protein Catalysts
 Enzymes are proteins that serve as
catalysts. When something catalyzes
a reaction, it speeds the reaction up.
 Enzymes have a complicated protein
structure with an active site. The
reactants in a reaction bind here—they
are called the substrate.
•
Enzymes work best in an
environment with a specific
temperature and pH (acidity).
High temperatures or very
acidic environments can
denature a protein—
destroying its structure and
making it useless.
Which of the following can be used to determine the rate
of enzyme-catalyzed reactions?
(A) rate of disappearance of the enzyme
(B) rate of disappearance of the substrate
(C) rate of disappearance of the product
(D) change in volume of the solution
(E) increase in activation energy
Which of the following can be used to determine the rate
of enzyme-catalyzed reactions?
(A) rate of disappearance of the enzyme
(B) rate of disappearance of the substrate
(C) rate of disappearance of the product
(D) change in volume of the solution
(E) increase in activation energy
CNOPS
 Keep in mind which elements were in those molecules!
They are very important for living things.
 Lots of CARBON {C} in all of the macromolecules.
 Plenty of OXYGEN {O} in there too!
 NITROGEN {N} in proteins and nucleic acids.
 PHOSPHORUS {P} in nucleic acids especially!
 Many amino acids also contain SULFUR {S}
 Living organisms have to get these atoms from
somewhere—eating, pulling them from the air, or from
the soil. Cycles of these atoms are important in nature.
How Life Began…?
 As we saw, the macromolecules of life
are large, complicated polymers
composed of many monomers linked
together with bonds.
 It is difficult to make these large
molecules without the complicated
machinery of a living cell to coordinate
their creation.
 But where did the first cells get their
molecules from?
 The primordial soup hypothesis suggests
that atoms and molecules were exposed to
energy (from sunlight, lightning, etc) and
catalysts (minerals on rocks, etc).
 This formed the basic organic monomers:
amino acids, nucleotides, and
monosaccharides.
 Eventually, chemical reactions polymerized
the monomers and made polymer chains.
2) A feature of amino acids not found in
carbohydrates is the presence of
a) Phosphorus
b) Nitrogen
c) Hydrogen
d) Oxygen
e) Carbon
2) A feature of amino acids not found in
carbohydrates is the presence of
a) Phosphorus
b) Nitrogen
c) Hydrogen
d) Oxygen
e) Carbon
For questions 3-6, match a letter to each description. A single letter may
be used once, twice, or not at all.
a)
b)
c)
d)
e)
Glycogen
Cellulose
Triglyceride
Polypeptide
Nucleic Acid
3) A name for a polymer of amino acids.
4) The stored form of sugar in humans
5) A lipid that consists of three fatty acids covalently bonded to
glycerol.
6) A substance which humans cannot digest.
For questions 3-6, match a letter to each description. A single letter may
be used once, twice, or not at all.
a)
b)
c)
d)
e)
Glycogen
Cellulose
Triglyceride
Polypeptide
Nucleic Acid
3) A name for a polymer of amino acids. D
4) The stored form of sugar in humans. A
5) A lipid that consists of three fatty acids covalently bonded to
glycerol. C
6) A substance which humans cannot digest. B
Questions 114 - 115 refer to an experiment in polypeptide hydrolysis.
Polypeptides are placed into warm watery solutions in separate beakers, each
containing a different substance that has been isolated from pancreatic juice or
intestinal tissue. After two hours, the contents of the individual beakers are
analyzed. The results are below.
Incubated with:
Peptides present:
Mucus
Polypeptides
Trypsin
Dipeptides; tripeptides
Chymotrypsin
Dipeptides; tripeptides
Carboxypeptidase
Amino acids, dipeptides,
tripeptides
Aminopeptidase
Amino acids, dipeptides
8. It appears that the only substance that has no enzymatic activity is:
A. mucus.
B. trypsin.
C. chymotrypsin.
D. carboxypeptidase.
E. aminopeptidase.
Questions 114 - 115 refer to an experiment in polypeptide hydrolysis.
Polypeptides are placed into warm watery solutions in separate beakers, each
containing a different substance that has been isolated from pancreatic juice or
intestinal tissue. After two hours, the contents of the individual beakers are
analyzed. The results are below.
Incubated with:
Peptides present:
Mucus
Polypeptides
Trypsin
Dipeptides; tripeptides
Chymotrypsin
Dipeptides; tripeptides
Carboxypeptidase
Amino acids, dipeptides,
tripeptides
Aminopeptidase
Amino acids, dipeptides
8. It appears that the only substance that has no enzymatic activity is:
A. mucus.
B. trypsin.
C. chymotrypsin.
D. carboxypeptidase.
E. aminopeptidase.
Questions 114 - 115 refer to an experiment in polypeptide hydrolysis.
Polypeptides are placed into warm watery solutions in separate beakers, each
containing a different substance that has been isolated from pancreatic juice or
intestinal tissue. After two hours, the contents of the individual beakers are
analyzed. The results are below.
Incubated with:
Peptides present:
Mucus
Polypeptides
Trypsin
Dipeptides; tripeptides
Chymotrypsin
Dipeptides; tripeptides
Carboxypeptidase
Amino acids, dipeptides,
tripeptides
Aminopeptidase
Amino acids, dipeptides
9. The only substances that act on the terminal residues of the polypeptide are
A. carboxypeptidase and chymotrypsin.
B. mucus and trypsin.
C. trypsin and chymotrypsin.
D. carboxypeptidase and aminopeptidase.
E. polypeptides and aminopeptidase.
Questions 114 - 115 refer to an experiment in polypeptide hydrolysis.
Polypeptides are placed into warm watery solutions in separate beakers, each
containing a different substance that has been isolated from pancreatic juice or
intestinal tissue. After two hours, the contents of the individual beakers are
analyzed. The results are below.
Incubated with:
Peptides present:
Mucus
Polypeptides
Trypsin
Dipeptides; tripeptides
Chymotrypsin
Dipeptides; tripeptides
Carboxypeptidase
Amino acids, dipeptides,
tripeptides
Aminopeptidase
Amino acids, dipeptides
9. The only substances that act on the terminal residues of the polypeptide are
A. carboxypeptidase and chymotrypsin.
B. mucus and trypsin.
C. trypsin and chymotrypsin.
D. carboxypeptidase and aminopeptidase.
E. polypeptides and aminopeptidase.
 Don’t leave any questions blank. The
Grade yourself
(on the AP curve)
AP exams have removed the
guessing penalty completely.
 Try to eliminate answers that you
6 out of 9 = grade of 5
5 out of 9 = grade of 4
4 out of 9 = grade of 3
3 out of 9 = grade of 2
2 out of 9 = grade of 1
know are wrong before guessing .
 Look for word roots like “glyco-”,
“mono-”, “poly-”, “-ose” to give you
hints for unknown vocabulary. Break
words down into pieces
 Don’t be disheartened by how tricky
these questions are! Luckily, you
only have to get about 65% to score a
5 on the AP Bio exam
The Free Response Section
 The new AP Biology exam has two types of free
response questions—long free response, and short
free response.
 A long free response question might ask you to draw
drafts or diagrams, and answer many different subquestions labelled (a)-(e)
 Think of these more like short response questions
than essays: it is ok to write a short paragraph for
each letter.
Free Response Tips
 Always label the question parts (a), (b), (c)…
 Be clear and direct: you don’t have to be literary.
 However, you do have to write in sentences. Bullet
points or outlines are ignored.
 Graders will be looking for key words: you can make a
vocabulary list before you start writing
 Don’t do extra work—if a question asks for 3 examples,
and you give 4, they will ignore the 4th one. They won’t
pick out the correct ones for you.
 You may draw diagrams to illustrate your answer, but
the diagram must be labelled and you must write a few
sentence explaining it/referring to it.
HW: Free Response Question
(1996) The unique properties (characteristics) of
water make life possible on Earth. Select three
properties of water and:
a) for each property, identify and define the property
and explain it in terms of the physical/chemical
nature of water.
b) for each property, describe one example of how
the property affects the functioning of living
organisms.