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Topic 2
Biochemistry
I. Biologically Important Compounds
• A. Organic and Inorganic Compounds
▫ 1. organic compounds – contain the
element carbon – also contain hydrogen
 Examples:
▫ 2. inorganic compounds – any compound
that is not organic
 Examples:
II. Carbohydrates and Lipids
• A. Carbohydrates – compounds of
carbon, hydrogen, and oxygen – have a
ratio of 2 hydrogen to 1 oxygen
▫ 1. monosaccharides – simple sugars –
glucose is the most common simple sugar –
other simple sugars include galactose and
fructose
Glucose
▫ 2. disaccharides – sugars
whose molecules are made up
of two monosaccharide
molecules bonded together –
maltose and sucrose are two
examples
Disaccharide
 3.
polysaccharides – complex
carbohydrates made up of chains of
monosaccharides – starch, cellulose
and glycogen are examples – starch
is a food storage compound in
plants, cellulose makes up the cell
walls of plants, glycogen is a food
storage compound in animals
Polysaccharide
• B. Dehydration Synthesis – chemical
process by which simple molecules are
joined to form larger molecules with the
removal of water
• C. Hydrolysis – chemical process by
which larger molecules are broken down
by the addition of water – opposite of
dehydration synthesis
• D. Lipids – serve mainly as sources of
energy and structures for cell membranes
– include fats(solids from animals),
oils(liquids from plants), and waxes – the
ratio of hydrogens to oxygens is greater
than 2 : 1 and varies from one lipid to
another – made from one glycerol
molecule and three fatty acids by
dehydration synthesis
Lipids – one glycerol and three
fatty acids
One lipid
E. Lipids also include steroids and
cholesterol
- see steroid below
III. Nucleic Acids and Proteins
• A. Nucleic Acids - long chains of repeating
units that carry hereditary or genetic
information and control the life processes
of cells
▫ 1. DNA – deoxyribonucleic acid – genetic
material
▫ 2. RNA – ribonucleic acid – controls
production of proteins
• B. Nucleic acids are made of chains of repeating
units called nucleotides – nucleotides have three
parts:
▫ 1. a 5 carbon sugar – DNA has deoxyribose and
RNA has ribose
▫ 2. a phosphate group
▫ 3. a nitrogenous base – DNA has adenine,
thymine, guanine and cytosine – RNA has
adenine, uracil, guanine, and cytosine
Parts of nucleic acids
• C. Proteins - contain carbon, hydrogen,
oxygen, and nitrogen - may also contain
sulfur - used to make cell structures,
enzymes, hormones, and hemoglobin
▫ 1. chemical structure - made up of amino
acids - has an amino group, carboxyl
group, central carbon, hydrogen and an R
group
▫ 2. polypeptide - chains of amino acids formed by dehydration synthesis – forms
peptide bonds
Structure of an amino acid:
Amino Acids:
Amino Acids:
Dehydration Synthesis of a dipeptide
Peptide bond
D. Levels of Structure in Proteins
• 1. The primary
structure of a
protein is its unique
sequence of amino
acids.
• 2. The secondary
structure of a protein
results from hydrogen
bonds at regular intervals
along the polypeptide
backbone.
▫ Typical shapes
that develop from
secondary structure
are coils (an alpha
helix) or folds
(beta pleated
sheets).
Levels of Structure in Proteins
• 3. Tertiary structure is
determined by a variety of
interactions among R groups
and between R groups and the
polypeptide backbone.
▫ These interactions
include hydrogen
bonds among polar
and/or charged
areas and ionic bonds
between charged
R groups
Levels of Structure in Proteins
• 4. Quarternary
structure results
from the aggregation
of two or more
polypeptide subunits.
IV. Enzymes – a type of protein
A. importance of enzymes - control
chemical reactions - can be used over and
over again because they are not changed
by the reaction - catalysts
• B. structure and function of enzymes
▫ 1. Chemical nature - all enzymes are
proteins - may need a coenzyme to help
them (usually a vitamin)
▫ 2. Active site - the small region on
the enzyme that is involved in the
chemical action
▫ 3. Enzyme-substrate complex substrates are the materials that
are acted on by the enzyme - when
the enzyme and substrate combine
they form an enzyme-substrate
complex
▫ 4. Lock-and-key model - the
shape of the active site fits only
one specific substrate
▫ 5. induced fit model – the
shape of the active site changes
slightly to fit the shape of the
substrate
▫ 6. Replacement of enzymes - even though
enzymes can be used again they will
eventually wear out and new enzymes must
be made
▫ 7. Names of enzymes - end in ase and are
often named after the substrate they work
on - example: maltase breaks down
maltose
• C. Factors affecting enzyme action
▫ 1. Temperature - enzyme action is
generally low at low temp. - as
temp. rises so does rate of action however at some point the enzyme
becomes denatured and no longer
works
Enzymes and temperature
▫ 2. Enzyme and substrate
concentration - will
increase to a point then
level off
▫ 3. pH - different enzymes
work best at different pH
levels
Enzymes and pH
V. Water
Water – An important inorganic
compound
▫ 1. cohesion – property of water that allows
the water molecules to “stick” to each other
▫ 2. adhesion – property of water that allows
the water molecules to “stick” to other
substances
▫ 3. capillary action – property of water that
allows water to travel upwards against
gravity through tiny spaces
VI. Functional Groups
• The components of organic molecules that are
most commonly involved in chemical reactions
are known as functional groups.
▫ Functional groups are attachments that replace
one or more hydrogen atoms to the carbon
skeleton of the hydrocarbon.
• A. In a hydroxyl group (-OH), a hydrogen atom
forms a polar covalent bond with an oxygen which
forms a polar covalent bond to the carbon skeleton.
▫ Because of these polar covalent bonds hydroxyl
groups improve the solubility of organic
molecules.
▫ Organic compounds with hydroxyl groups are
alcohols and their names typically end in –ol --- also found in carbohydrates
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• B. A carbonyl group (=CO) consists of an
oxygen atom joined to the carbon skeleton by a
double bond.
▫ If the carbonyl group is on the end of the
skeleton, the compound is an aldelhyde.
▫ If not, then the compound is a ketone.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• C. A carboxyl group (-COOH) consists of a carbon atom
with a double bond with an oxygen atom and a single bond
to a hydroxyl group.
▫ Compounds with carboxyl groups are carboxylic
acids.
▫ A carboxyl group acts as an acid because the
combined electronegativities of the two adjacent
oxygen atoms increase the dissociation of hydrogen
as an ion (H+).
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• D. An amino group (-NH2) consists of a nitrogen
atom attached to two hydrogen atoms and the
carbon skeleton.
▫ Organic compounds with amino groups are
amines.
▫ Amino acids, the building blocks of proteins, have
amino and carboxyl groups.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• E. A sulfhydryl group (-SH) consists of a sulfur
atom bonded to a hydrogen atom and to the
backbone.
▫ Organic molecules with sulfhydryl groups are
thiols.
▫ Sulfhydryl groups help stabilize the structure of
proteins.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• F. A phosphate group (-OPO32-) consists of
phosphorus bound to four oxygen atoms (three
with single bonds and one with a double bond).
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings