AP Biology Notes for Biochemistry and Properties of Water

1. Chapter 2-3
Biochemistry
AP Biology

2. Why do atoms bond?
• Atoms bond because of a difference
in their electronegativity.
• Electronegativity is the ability of an
atom to attract electrons.
• Electrons determine chemical and
physical properties of atoms.

3. Nucleus

4. Types of Bonds
• Ionic bonds form when the atoms
electronegativity’s are very different
and one has a much stronger pull.
• This generally occurs with metals
and nonmetals.
• Covalent bonds happen when both
atoms are similar and results in
electron sharing.
• This generally occurs with non-
metals.

6. • Covalent bonds come in two forms.
• Nonpolar covalent bonds are when
electrons are shared equally.
• Polar covalent bonds form when
electrons are shared unequally.
• Some electrons spend more time
around the more electronegative
atom and a partial charge results.
• Water is an example of a polar
molecule.

8. • Hydrogen bonds generally occur
between molecules and with
hydrogen atoms and other atoms.
• Positively charged hydrogen atoms
weakly bond with the negatively
charged area of another atom.

9. hydrogen
oxygen

11. Watch water bend!

13. Water
• Water has 5 important properties.
• 1. Water is an excellent solvent.
• 2. Water has a high specific heat
capacity.
• 3. Solid phase is less dense than
liquid phase.

14. • 4. Water has strong cohesion and
high surface tension.
• 5. Water has strong adhesion and
capillary action.

15. Water is an excellent
solvent.
• Ionic substances are soluble
(dissolve) in water because of the
polar water molecules act upon the
compounds and separate them into
their ions.
• Substances with polar covalent
bonds are also affected because
they possess a charged pole also.

16. • Hydrophilic molecules dissolve readily in
water.
• Nonpolar covalent molecules do not
dissolve in water or are hydrophobic
because they lack charged poles.

18. • Because so many molecules
dissolve in water, it is considered the
universal solvent.
• A solute is any substance that
dissolves in a solvent.
• When the solvent is water, the
solution is said to be aqueous.

20. Water has a high
specific heat capacity.
• Specific heat is the degree to which
1 gram of a substance changes
temperature in response to a gain or
loss of heat.
• Since water has a high specific heat,
it responds very slowly to
temperature changes.

21. • STOP
• Mini-Lab
• What will the graph for water look
like when ice is heated until it boils?

22. • Heat of fusion-energy required to
change water from a solid to a liquid.
• Heat of vaporization-energy required
to change water from liquid to gas
• It is important to note that in phase
change graphs, the line does not
change in two places. Why?

23. Density of Water is
Special!

24. • Water is one of the only
substances on Earth in which the
solid phase is less dense than the
liquid phase!
• Because of this, life can exist in
many places.

25. When winter comes, the ice
floats and keeps fish safe.
ICE
Ouch!

26. If ice was actually
denser than
water…….
I wish I could
get to safer
water below!

27. • Most substances contract when it
converts to its solid form.
• Since water expands when it
freezes, it becomes less dense
allowing it to float.
• This ability has a profound effect on
life on Earth, especially in its
beginning stages.

28. Water has strong
cohesion and surface
tension.
• Cohesion occurs when like
molecules stick together.
• This occurs because of hydrogen
bonding.

30. Cohesion creates surface
tension.
Water is very
sticky!

32. Water has strong
adhesion and capillary
action.
• This results from the attraction of the
poles of water molecules to other
polar substances.

33. • This is when molecules that are
not alike are attracted, example,
water to walls of a test tube, or
plant walls
• When you see adhesion, think
adhesive, sticky.

35. Capillarity
• This is when
water goes up
a small, narrow
tube like a
plant stem or
paper towel.
• Adhesion
makes this
possible.

36. Temperature Moderation
• Water must gain or lose a
relatively large amount of energy
for its temperature to change.
• When water is heated, most of the
thermal energy that the water
initially absorbs breaks the
hydrogen bonds between the
molecules.

37. • When the bonds are broken,
the thermal energy is released
and increases the motion of
the molecules.
• Water’s ability to absorb large
amounts of energy helps keep
cells at an even temperature
despite temperature changes
in the environment.

38. solid liquid
gas
Break
bonds
Break
bonds
Make
bonds

39. stop

40. Organic Compounds
• Organic molecules contain carbon.
• A carbon atom has 4 electrons in its outer
level which means it can create 4 bonds
with any other atoms including itself.
• This makes carbon an excellent backbone
for many organic molecules.
• Carbon can even form rings and double
and triple bonds!

42. • Large organic molecules are called
macromolecules.
• Most macromolecules are polymers.
• Polymers are made of single units
called monomers that are repeated
many times.
• An organic molecule’s properties are
determined by their functional
groups.

43. Functional Groups
• A functional group is a group of atoms that
have specific characteristics.
• For example an alcohol is a functional
group that has oxygen and hydrogen
attached.

44. • Drunk Bear
• Drunk Squirrel

46. How are polymers made
and broken?
• Monomers link together in a
condensation (dehydration)
reaction.
• When two monomers combine,
water is released.

47. • When polymers are broken, it
is called a hydrolysis reaction.
• Water is broken into two parts
and breaks the bonds that
holds the monomers together.

52. Energy Currency
• Life processes require energy.
• This energy is available to life in the
form of a compound called ATP.
• ATP has three phosphates on the
molecule and when one phosphate is
broken off, energy is released.

55. Carbohydrates
• A monomer of a carbohydrate is
called monosaccharide.
• A monosaccharide is a simple
sugar.
• Two forms of glucose alpha and
beta differ simply by the reversal
of the H and OH groups.

58. • Two monosaccharides form a
disaccharide.
• A disaccharide is made by
glycosidic linkage.
• During this process, a water
molecule is lost.

60. • A polysaccharide is a complex
molecule composed of three or more
monosaccharides formed by
glycosidic linkage.
• What are some carbs?

61. Cellulose is an unbranched polymer
of glucose with linkages that are
chemically very stable. Glycogen and starch are polymers of
glucose, with branching at carbon 6
(see Figure 2.9).

63. Important Carbohydrates
• Starch (alpha-glucose) is the
principal energy storage molecule in
plant cells.
• Glycogen (alpha-glucose) is the
major energy storage molecule in
animal cells.
• Cellulose (Beta-glucose) serves as
a structural molecule in the walls of
plant cells and is a major component
of wood.

64. • Chitin (Beta-glucose) is a polymer similar
to cellulose.
• Chitin serves as a structural molecule in
the walls of fungus cells and in the
exoskeletons of insects, other arthropods
and mollusks.
• It is important to note that alpha-glucose
linkages are easily digested by humans
and other animals but only specialized
organisms can digest Beta-glucose
linkages.

66. Layers of cellulose fibrils, as
seen
in this scanning electron micro-
graph, give plant cell walls great
strength.
Within these potato cells, starch
deposits (colored purple in this
scanning electron micrograph)
have a granular shape.
The dark clumps in this electron
micrograph are glycogen
deposits in a monkey liver cell.

67. stop

68. Lipids
• Lipids are large, non- polar molecules
that are nearly insoluble in water but
highly soluble in nonpolar substances
like ether or chloroform.
• There are 3 major classes of lipids.

69. Types of Lipids
• A triglyceride is composed of three
molecules of fatty acids joined to an
alcohol called glycerol.
• Fatty acids are unbranched carbon chains
that make up most lipids.

70. Glycerol
(an alcohol)
3
3
Fatty acid
molecules
Triglyceride

71. Triglycerides
• Fatty acids vary in structure with the number of
carbons and placement of single and double covalent
bonds.
• Single bonds in fatty acids mean all the available
spaces are taken up by hydrogen atoms so they are
called saturated fatty acids.
• As a result, saturated fatty acids pack together more
tightly, have higher melting temperatures, and are
usually solid at room temperature.

72. Palmitic acid
Carbon
Oxygen
Hydrogen

73. • The double bond in a fatty acid
creates a bend at the bond slightly
spreading the triglyceride apart.
• This means there are available
bonds so this is called unsaturated
fatty acids.
• Monounsaturated fats have one
double bond while polyunsaturated
fats have two or more double bonds.

74. • Unsaturated fatty acids are looser
because of the space the double
bond gives so they have lower
melting temperatures and are usually
liquid at room temperature.

75. Linoleic acid

76. Phospholipids
• Phospholipids are made from two
fatty acids connected to the glycerol
backbone and a phosphate group.
• The two fatty acid “tails” are
hydrophobic and the “head” is
hydrophilic and oriented to the
outside.
• These form the basis for all cell
membrane structures.

77. Choline
Phosphate
Glycerol
Hydrocarbon
chains
Hydrophilic
head
Hydrophobic
tail

79. • Hydrophilic-water-loving,
molecules dissolve in water
• Hydrophobic-water-fearing,
molecules do not dissolve in
water

82. Steroids
• Steroids are characterized by a
backbone of four linked carbon
rings.
• Examples of steroids include
cholesterol (a component of cell
membranes) and certain hormones,
including testosterone and estrogen.

84. stop

85. Proteins
• Proteins are organic compounds
made from monomers called amino
acids.
• There are 20 different amino acids.
• The differences between the amino
acids are their R groups.

87. • Two amino acids bond to form a dipeptide.
• In a condensation reaction, two amino
acids form a covalent bond called a
peptide bond.
• Long chains of amino acids are called
polypeptides.
• What are some proteins?

89. • Proteins can be grouped according to
their functions.
• Structural Proteins-keratin, collagen, silk
• Storage Proteins-casein, ovalbumin, zein
• Transport Proteins-hemoglobin, facilitated
transport
• Defensive Proteins-antibodies
• Enzymes

91. Protein Structure
• The primary structure of a protein
describes the order of amino acids.
• The secondary structure of a protein
is a 3 dimensional shape that results
from hydrogen bonding.
• This produces spirals or a folded
plane like a pleated sheet. (fibrous
proteins)

95. • The tertiary structure includes
additional three-dimensional
shaping and often dominates the
structure of globular proteins.
• The shaping is increased by
additional hydrogen bonding, ionic
bonding, the hydrophobic effect and
disulfide bonds.

97. • The quaternary structure describes
a protein that is assembled from two
or more separate peptide chains.
• Hemoglobin for example consists of
four peptide chains that are held
together by hydrogen bonding.

101. • Under normal cellular conditions, the
primary structure of a protein
determines how it folds into its
particular three-dimensional shape.
• Structure also depends on physical
and chemical conditions of the
environment.
• Adverse conditions can weaken the
bonding and is known as
denaturation.

104. stop

105. Enzymes are a special kind
of protein.
• In order for a chemical reaction to take place, the
reacting molecules must first collide with sufficient
energy to trigger the formation of new bonds. (Activation
energy)
• Many reactions require the presence of a catalyst to
accelerate the rate of reaction so it occurs within an
appropriate span of time.
• Enzymes are a protein that acts as a catalyst by lowering
the activation energy required for a reaction to take
place.

107. • Chemical reactions that occur in biological
systems are referred to as metabolism.
• Breakdown of substances is called
catabolism.
• Formation of new products is called
anabolism or synthesis.
• Enzymes work to accelerate either
catabolism or anabolism by acting upon a
specific substrate.

110. Types of Reactions
• Exergonic reactions release energy
when complete.
• Endergonic reactions absorb energy
when complete.
• Many metabolic processes use
coupling which pairs both reactions
together.

114. • Enzymes are substrate specific and
can only act upon one specific item
under the correct conditions.
• An enzyme remains unchanged
during the chemical reaction and
doesn’t take actual part in the
process. It is not used up.
• Enzymes can catalyze a reaction in
both the forward and reverse
directions.

115. • Most enzymes are named after their
substrate and the ending is changed
to –ase.
• The induced-fit model describes
how enzymes work.

117. Induced-Fit Model
• Within the enzyme there is an active
site in which the substrate readily
reacts because of its shape.
• The interaction of the substrate and
the enzyme causes the enzyme to
change shape.
• The new position places the
substrate molecules into a position
favorable to their reaction.

122. Effects on Enzymes
• Temperature-raising or lowering
temperature can cause an enzyme to
malfunction
• Most enzymes are particularly adapted to
the temperature conditions of the
organism it works in.
• A change in pH can decrease the ability of
an enzyme to function.

125. • A foreign chemical or metal can decrease the ability
of an enzyme to function.
• The presence of co-factors (non-protein helpers)
influence enzymes by donating or accepting
electrons. (vitamins)
• Some metals increase an enzyme’s function (Iron,
magnesium)
• The amount of ATP present in the system affects
enzyme function.
• ATP is made via phosphorylation and broken via
hydrolysis.

128. Enzyme Regulation
• Enzymes have two binding sites-one
active and one allosteric.
• Allosteric sites are for allosteric
factors.
• An allosteric activator binds to the
enzyme and induces the active
form.
• An allosteric inhibitor binds to the
enzyme and induces the inactive
form.

130. Inhibition
• In feedback inhibition, the end
product of the reactions acts as an
allosteric inhibitor, shutting down the
enzyme.
• In competitive inhibition, the
substance mimics the substrate and
occupies the active site displacing
the real enzyme and not allowing the
reaction to occur.

133. • In noncompetitive inhibition, a substance binds
to the allosteric site and changes the shape of
the enzyme, stopping its ability to work.
• Many toxins and antibiotics are this type of
inhibitor.
• Cooperativity is different in which the enzyme
becomes more receptive to additional substrate
molecules after one substrate attaches to the
active site.
• This is common with enzymes with quaternary
structure like hemoglobin.

138. • How does aspirin work?
• Use what we’ve learned about
enzymes to fully explain your
answer.
• Include important vocabulary terms
and a diagram if necessary.
• Include specific information, do not
be general!

141. stop

142. Nucleic Acids
• Nucleic acids are large and complex
organic molecules that store important
information in the cell.
• RNA stores and transfers information to
make proteins.
• DNA contains information that is essential
for cell activities.

143. • Both RNA and DNA are composed of
monomers called nucleotides.
• A nucleotide has 3 components: a
phosphate group, a sugar and a
nitrogen base.

150. What are some of the
differences between
DNA and RNA?