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BIOCHEMISTRY
WATER
THE AMAZING MOLECULE
H2O
• Composed of 2 hydrogen atoms and 1 oxygen
•
•
•
atom, ________ bonded.
Higher _____________ of oxygen results in
the molecule being polar.
This polar arrangement is responsible for the
formation of hydrogen bonds.
The hydrogen bonds are the basis for the
unique properties of water….
H2O
• Composed of 2 hydrogen atoms and 1 oxygen
•
•
•
atom, covalently bonded.
Higher electronegativity of oxygen results in
the molecule being polar.
This polar arrangement is responsible for the
formation of hydrogen bonds.
The hydrogen bonds are the basis for the
unique properties of water….
This includes:
• high specific heat
• high melting and boiling points
• high heat of vaporization
• a solid that is less dense than the liquid
• high degree of cohesion, adhesion, and
surface tension
Water is also an excellent solvent.
Many chemicals, including acids and bases readily
dissolve in water. What are they called?
Acids, you may recall, are substances that increase
[H+] hydrogen ion concentration when placed into
solution. pH range is between _______
Bases, on the other hand, reduce [H+]. This is
because they generally accept H+ ions directly or
indirectly. pH range is between 7 and 14.
OH-
H+
Water is also an excellent solvent.
Many chemicals, including acids and bases readily
dissolve in water. What are they called?
solutes
Acids, you may recall, are substances that increase
[H+] hydrogen ion concentration when placed into
solution. pH range is between _______
0 and 7
Bases, on the other hand, reduce [H+]. This is
because they generally accept H+ ions directly or
indirectly. pH range is between 7 and 14.
OH-
H+
The numbers of the pH scale were not selected
arbitrarily. They represent the inverse logarithm
of the [H+].
In an aqueous solution, the product of the H+ and
OH- is constant at 10-14.
Water has a pH of 7. Why is this said to be
neutral?
Explain your answer on the basis of ion
concentration.
The concentration of H+ ions is cancelled
out by the equal concentration of OH- ions.
Buffers
• substances that minimize changes in the
concentrations of +/- ions in a solution.
• Ability to donate/receive H+ ions easily.
• Important for maintaining homeostasis
within an organism.
Example: blood (contains both CO2 and H2O)
CO2 + H2O  H2CO3   H+ + HCO3- 
H2O + HCO3-   H2CO3 + OH_
Click here to see more on buffers
Buffers
• substances that minimize changes in the
concentrations of +/- ions in a solution.
• Ability to donate/receive H+ ions easily.
• Important for maintaining homeostasis
within an organism. PBW organisms maintain stability
Example: blood (contains both CO2 and H2O)
CO2 + H2O  H2CO3   H+ + HCO3- 
H2O + HCO3-   H2CO3 + OH_
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Organic Compounds

Compounds which contain carbon Many are recognized by the presence of functional groups Functional
Group
Structural Formula
Methyl
-CH3
Hydroxyl
-OH
Carboxyl
-COOH
Amino
-NH2
Phosphate
-PO3
Carbonyl
-C=O
Types of Compounds they
can be found in
Organic Compounds

Compounds which contain carbon Many are recognized by the presence of functional groups Functional
Group
Structural Formula
Types of Compounds they
can be found in
Methyl
-CH3
Hydrocarbons
Hydroxyl
-OH
Alcohols
Carboxyl
-COOH
Carboxylic Acid
Amino
-NH2
Amines
Phosphate
-PO3
Organic
Phosphates
Carbonyl
-C=O
Ketones (middle)
Aldehydes (end)
Functional groups help to give molecules
their properties.
Methyl
Hydrocarbons
Hydroxyl
Alcohols
Carboxyl
Carboxylic Acid
Amino
Amines
Phosphate
Organic phosphates
Carbonyl
Ketones
aldehydes
Functional groups help to give molecules
their properties.
Methyl
Hydrocarbons
Nonpolar, hydrophobic
Hydroxyl
Alcohols
Polar, hydrophilic
Carboxyl
Carboxylic Acid
Polar, hydrophilic, weak acid
Amino
Amines
Polar, hydrophilic, weak base
Phosphate
Organic phosphates
Polar, hydrophilic, weak base
Carbonyl
Ketones
aldehydes
Polar, hydrophilic
 These
functional groups, along with other
combinations of atoms, form the basis of
larger molecules…..
Macromolecules
Basic
monomers
composition
Carbohydrates C, H2O
Lipids
C, H>O
Protein
C,H, O, N,S
Nucleic
acids
C,H,O,N,P
polymers
Macromolecules
Basic
monomers
composition
Carbohydrates C, H2O
Lipids
Protein
Nucleic
acids
polymers
Monosaccharide
C, H>O
Fatty acid,
glycerol
C,H, O, N,S Amino acid
Di-,polysaccharide
triglyceride
C,H,O,N,P
DNA,RNA
nucleotide
polypeptide
Carbohydrates -Energy
Monosaccharides – glucose, fructose,
galactose (C6H12O6) {
}
 Disaccharides – maltose (glu+glu)
sucrose (glu+fru)
 Polysaccharides – includes starch amylose,
glycogen (1-4 α linkage)  storage molecules
chitin (nitrogen group attached),
4
α
cellulose
(1-4 β linkage)

structural molecules
H
1
OH
OH
β
H
Carbohydrates -Energy
Monosaccharides – glucose, fructose,
Same formula, different structures is }
galactose (C6H12O6) { Isomers
an example of…
Look up
 Disaccharides – maltose (glu+glu)
sucrose (glu+fru) glycosidic linkage
 Polysaccharides – includes starch amylose,
glycogen (1-4 α linkage)  storage molecules
H
chitin (nitrogen group attached),
4
1
α
cellulose
OH
Structurally
(1-4 β linkage) difficult to

structural molecules
break bonds of
the β linkage.
More on this when
we cover enzymes.
OH
β
H
Lipids – Energy Storage
 All
are hydrophobic
 Composed of 2 monomers –
3 fatty acids (carboxyl w/hydrocarbon chain) and
glycerol {C3H5(OH)3} held together by
ester bond. (not in textbook, similar to glycosidic bond)
Fatty acids vary in length, #, bonds
 Saturated fats – carbon is “saturated” w/H.
 Unsaturated fats – one or more double
carbon bonds.
Lipids
Saturated
Unsaturated
Lipids
Saturated
Unsaturated
Solid at room temp.
Liquid at room temp.
Mostly in animals
Mostly in plants
No double carbon bonds Double bonds found
between carbon
Lipids
– related to fats; have 2
fatty acids, but also have phosphate
molecule. Hydrophilic at one end,
hydrophobic at the other end.
Major component of cell membrane.
 Steroids – have a carbon skeleton of
4-fused rings. Ex. Cholesterol, hormones
 Phospholipids
Use your textbook and find out what
this molecule is.
Proteins
 Functions
include structure, storage,
transport, messengers, contractile
movement, immune defense, aid to
chemical reactions (enzymes).
 Make up 50% of most cells’ dry weight.
 Amino acid monomers form polypeptides.
 20 amino acids joined in a variety of #’s
and orders via peptide bonds.
Proteins

There are 4 levels of protein structure:
primary – unique amino acid sequence held
together by peptide bonds.
secondary – coiling of polypeptide into
specific patterns (α helix and β pleated
sheet are basic forms) See txtbk pg. 76
tertiary – folding back of molecule on itself
via disulfide bridges and H bonds.
quaternary – interaction of 2 or more
polypeptides.
Proteins
 Using
pipe cleaners to represent chains of
amino acids, demonstrate the secondary,
tertiary, and quaternary structures of
protein.
Primary
Secondary
Tertiary
Quaternary
Proteins
 Physical
and chemical conditions can alter
the secondary through quaternary
conformations. This alteration is called
denaturation. This can render a molecule
biologically active or inactive.
 For example changes in temperature and
pH. (Temp) Changes that occur to egg
white as it is cooked. (pH) Milk curdles
when vinegar acid is added.
Proteins
Explain hair curling in terms of
your knowledge of proteins.
Enzymes and Chemical Reactions
The
chemical reactions that occur within a
biological system are called metabolism. These
reactions include both the buildup (anabolism) and
breakdown (catabolism) of substances.
 Chemical reactions will only occur if there is
sufficient energy to initiate the formation of new
bonds. This energy is known as activation
energy.

Enzymes are catalysts which lower the
activation energy.
Enzymes and Chemical Reactions

Enzymes act upon substrates, either activating
or accelerating the reaction by placing the
substrate into a position that allows the reaction
to occur. This lowers the activation energy.
 Enzymes are substrate-specific, much like a key
is specific to one lock.
 A substrate binds to an enzyme at its active site,
an area that has a complementary shape or
polarity to the substrate.
Enzymes and Chemical Reactions

This arrangement of enzyme-substrate is known
as the Induced-Fit Model.
 Once a reaction occurs, enzymes release the
substrate.
 Unchanged by the interaction, the enzyme is
ready to interact with another substrate
molecule.
 Most enzymes are recognizable by the suffix
ending –ase.
Enzymes and Chemical Reactions

Denaturation, due to changes in temperature
and pH, will cause changes in the enzyme’s
shape, thus altering the active site. An enzyme
may be activated or inactivated in this fashion,
therefore the chemical reactions with the
substrates are affected by these shape changes.
ex. Pepsinogen (stomach enzyme that digests
protein) changes into the activated shape
(pepsin) at a very low pH provided by HCl. It can
only digest protein when active.
Enzymes and Chemical Reactions
 Some
enzymes may also be affected by
chemicals, other than the substrate,
binding to them.
 Certain substances (regulators or
effectors) can bind to an alternate part of
an enzyme (allosteric site), altering its
shape.
 Cofactors (nonprotein), binding to a
portion of the active site, may hold the
enzyme in the correct shape, or serve to
attract the substrate. ex. Many vitamins
The Negatives….
When a substance mimics a substrate, it may bind
to the active site in place of the substrate. Such
a situation is called competitive inhibition.
 Regulators binding to an allosteric site,
preventing the enzyme from working, are
considered “negative” and result in
noncompetitive inhibition.
 If a substance, in either of these cases, is an
end product of the reactions brought on by the
enzyme, than feedback inhibition occurs, a selfregulating system that stops the reaction when
enough product has been created.
…and The Positives
 Allosteric
enzymes may also “turn on” if
the regulator or effector molecule brings
the enzyme into the correct shape for the
substrate. This would be
positive regulation.
 Cooperativity is a situation that occurs
when an enzyme becomes more receptive
to receiving substrates once it is initially
bound by the first substrate.
OK, enough of enzymes!
Nucleic Acids
 Information
molecule.
 Two types – DNA and RNA
 Composed of repeating nucleotides.
 Nucleotide is made of a sugar, phosphate,
and nitrogen base.
 Sugar differs between DNA and RNA.


DNA  deoxyribose
RNA  ribose
 Structure


differs between DNA and RNA.
DNA is arranged in a double helix.
RNA is single stranded.
Nucleic Acids

Two families of nitrogen bases

Pyrimidines -hexagonal ring –
• cytosine, thymine*, uracil**
• * DNA only
• ** RNA only


Purines – two fused rings (6-5) –
• adenine, guanine
Much more on these molecules when Genetics
is studied.