Topic 3.2
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Do you think we are what we eat?
How does what we eat determine who we are?
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Organic compounds
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Almost all the molecules a cell makes are
compounds of carbon atoms bonded to one another
and to atoms of other elements.
Carbon has 4 outer electrons and completes its outer
shell by sharing electrons with other atoms in four
covalent bonds.
Hydrocarbons
• Compounds only composed of carbon and hydrogen
• They are all nonpolar molecules
• Example:methane
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More organic…
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Carbon skeleton
 Carbon atoms can bond together in chains or various
lengths. Ex. Ethane and propane
 Can be unbranched (butane) or branched (isobutane)
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Isomers
 Some compounds have the same molecular formula
but different structures (1-Butene and 2-Butene)
 This will result in unique properties.
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Organic compound properties are influenced
by:
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Size and shape of its carbon skeleton
Atoms attached to skeleton (Functional Group)
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Functional group
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Groups of atoms that usually participate in chemical
reactions
Functional groups of organic compounds are polar
 Oxygen or nitrogen atoms exert a strong pull on shared
electrons.
 Makes the compounds hydrophilic (water-loving) and
therefore soluble in water
 Sets for necessary conditions for their roles in waterbased life. Female and male sex hormones differ mainly
in functional groups help produce contrasting male
and female features
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Hydroxyl group
Hydrogen atom bonded to an oxygen atom, bonded to the carbon
skeleton of a molecule
– Ex. ethanol
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Carbonyl group
Carbon atom linked by a double bond to an oxygen atom.
If carbon atom of carbonyl group is at the end of a carbon skeleton,
the compound is an aldehyde.
– If carbonyl group is within a carbon chain, the compound is a
ketone.
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Carboxyl group
Carbon double bonded to an oxygen and also bonded to a
hydroxyl group.
• Acts as an acid by contributing an H+ to a solution and becoming
ionized.
• Carboxylic acid
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Amino group
Composed of nitrogen atom bonded to two
hydrogen atoms.
• Amine
• Amino acids contain both a carboxyl group and
amino group
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Phosphate group
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Phosphorous atom bonded to four oxygen atoms
Usually ionized and attached to the carbon skeleton
by one of its oxygen atoms.
ATP
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On a molecular scale, these molecules are
gigantic
Four main classes:
Carbohydrates
 Lipids
 Proteins
 Nucleic acids
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Polymers
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Large molecules consisting of many identical or similar
molecular units strung together.
For proteins, there are bout a trillion different kinds in
nature
Monomers
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Units that serve as building blocks of polymers
A cell makes all of its diverse macromolecules with
about 40 to 50 common monomers.
DNA is made from 4 monomers (nucleotides)
Only 20 amino acids, in different sequences, that make
up all of your proteins
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Dehydration Reaction
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A reaction that removes a molecule of water.
Cells link monomers together to form polymers
One monomer loses a hydroxyl group and the other
loses a hydrogen atom and forms a new covalent
bond.
Require the help of enzymes
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Hydrolysis
Breaks down polymers into monomers with water.
 Hydrogen joins to one monomer, and a hydroxyl
group joins to the adjacent monomer.
 Require the help of enzymes
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Ranges from small sugar molecules to large
polysaccharides
Three types:
Monosaccharides
 Disaccharides
 Polysaccharides
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Carbohydrate monomers (single-unit sugars)
Examples: Glucose and fructose
Molecular formula is usually a multiple of
CH20; formula for glucose is C6H12O6.
Two trademarks of a sugar:
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A number Hydroxyl groups (make it an alcohol)
A carbonyl group (depending on location, make it an
aldehyde or ketone
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Glucose and fructose are isomers
Same chemical formula, different placement of
carbonyl groups
 Different properties: fructose is sweeter than glucose
In aqueous solutions, usually form rings
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Other types of sugars: pentose, hexose
Main fuel molecules for cellular work, and raw
materials for making amino acids
Mono’s not used immediately are usually
incorporated into di’s and poly’s
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Form via a dehydration reaction between two
monosaccharides.
Most common example: sucrose
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Made from glucose and fructose
Found in plant sap, stems of sugar cane (table sugar)
Example: maltose
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Made from two glucose molecules
Used in germinating seeds, beer, malted milk shakes,
and malted milk ball candy
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Polymers of monosaccharides linked together by
dehydration reactions
Some are storage molecules, which cells break
down as needed to obtain sugar
Example: starch
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Found in roots and other tissues of plants, consists
entirely of glucose monomers.
Potatoes and grains are made of starch
 Hydrolyze it within digestive system and break down to
glucose monomers.
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Example: glycogen
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Form animals store excess sugar
More highly branched than starch
Stored as granules in our liver and muscle cells,
which hydrolyze the glycogen to release glucose
when it is needed.
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Example: Cellulose
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Most abundant organic compound on Earth, forms
cable-like fibrils in the tough walls that enclose plant
cells.
Resembles starch and glycogen in being a polymer of
glucose, but form unbranched rod:
 Joined by hydrogen bonds arranged parallel to each
other makes strong fibrils in trees
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Can’t be hydrolyzed by most animals
 Not a nutrient for humans, but helps keep out digestive
system healthy: Most fresh fruits, vegetables, and grains
are rich in fiber
 Cows and termites can digest celluse via microorganism
in their Digestive Tract
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Types: Fats, Phospholipids, waves, and
steroids
Consist mainly of carbon and hydrogen atoms
linked by nonpolar covalent bonds.
Not attracted to water molecules: hydrophobic
(water-fearing)
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Salad dressing: oil (lipid) separates from vinegar
(mostly water)
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Fat- a large lipid made from two kids of
smaller molecules
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Gyclerol- 1
 Alcohol with 3 carbons, each bearing a hydroxyl group
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Fatty acids- 3
 Consists of a carboxyl group and a hydrocarbon chain
with about 15 carbon atoms
 Carbon in the chains are linked to each other and hydrogen
atoms by nonpolar covalent bonds make hydrocarbon
chain hydrophobic
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Main function is energy storage
A gram of fat stores more than twice as much
energy as a gram of polysaccharide such as
starch.
Triglyceride
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1 glycerol and 3 fatty acids link together via
dehydration synthesis.
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Unsaturated
Fatty acids and fats with double bonds
 Kinks prevent the molecule from packing tightly
together and solidifying at room temperature
 Mostly plant fats: Corn oil, olive oil, and other
vegetable oils.
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Saturated
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Fats with the maximum number of hydrogens.
Mostly animal fats: butter and lard are solid at room
temp.
May cause atherosclerosis
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Major component of cell membranes
Structurally similar to fats, but contain
phosphorous and have only two fatty acids
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Consist of one fatty acid linked to an alcohol.
More hydrophobic than fats
Effective natural coatings for fruits such as
apples and pears.
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Lipids whose carbon skeleton is bent to form
fused rings
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Three six-sided rings and one five-sided ring.
Example cholesterol
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Common in animal cell membranes
Used as a starting material for making other steroids,
including male and female hormones
Too much may atherosclerosis
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Polymer constructed from amino acid
monomers.
Each of the thousands of different proteins has
a unique three-dimensional shape that
corresponds to a specific function.
Important to cell structure and the function of
organisms.
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Defensive proteins
 Antibodies in your immune system
Signal proteins
 Hormones and other messengers
Hemoglobin
 Delivers 02 to working muscles
Transport proteins
 Move sugar molecules into cells for energy (insulin)
Storage proteins
 Ovalbumin (found in egg white) used as a source of amino acid
for developing embryos
Most important roles is as enzymes
 Chemical catalysts that speed and regulate virtually all
chemical reactions in cells
 Example, lactase
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Based on the differing arrangements of a
common set of just 20 amino acids.
Amino acids: have an amino group and a
carboxyl group
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Both of the functional groups are covalently bonded
to a central atom, called the alpha carbon
Also bonded to the alpha carbon is a hydrogen atom
and a chemical group symbolized by the letter R.
 R group is the variable part of an amino acid.
 R group structure determines the specific properties of
each of the 20 amino acids in proteins.
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Two main types
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Hydrophobic
 Example: Leucine
 R group is nonpolar and hydrophobic
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Hydrophilic
 Polar and charged a.a.’s help proteins dissolve in
aqueous solutions inside cells.
 Example: Serine
 R group is a hydroxl group
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Cells join amino acids together in a
dehydration reaction:
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Links the carboxyl group of one amino acid to the
amino group of the next amino acid as a water
molecule is removed.
Form a covalent linkage called a peptide bond
making a polypeptide
only 20 amino acids, but make 1,000s of proteins
 Most polypeptides are at least 100 a.a. in length; some
are thousands
 A functioning protein is one or more polypeptide
chains twisted, folded, and coiled into a 3-d shape
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Most enzymes are globular in shape
Structural proteins are typically long and thin.
Shape is what determines function
All proteins must recognize and bind to some
other molecule in order to function.
Denaturation
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Polypeptide chains unravel, losing their specific
shape, and function.
Examples: changes in salt concentration, pH, or
temperature
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Primary structure
Secondary structure
Tertiary structure
Quaternary structure
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Unique sequence of amino acids
For any protein to perform its specific function,
it must have the correct collection of amino
acids arranged in a precise order.
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Example: a single amino acid change in hemoglobin
causes sickle-cell disease
Determined by inherited genetic information.
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Parts of the polypeptide coil or fold into local
patterns.
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Patterns are maintained by regularly spaced
hydrogen bonds between the hydrogens of the
amino group and the oxygen of the carboxyl groups.
Coiling results in an alpha helix.
Folding leads to a pleated sheet.
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Many fibrous proteins have the alpha structure
over most of their length
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Example: structural protein of hair
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Make up the core of many globular proteins
Dominate some fibrous proteins, including the
silk proteins of a spider’s web
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Overall, three-dimensional shape of a
polypeptide.
Roughly describe as either globular or fibrous
Generally results from interactions among the
R groups of amino acids making up the
polypeptide.
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Results from association of subunits between
two or more polypeptide chains.
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DNA and RNA
Deoxyribonucleic Acid (DNA)
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Monomers made up of nucleotides:
 Nucleotides consist of:
 A five carbon sugar, deoxyribose
 Phosphate group
 Nitrogenous base (Adenine, Guanine, Cytosine, Thymine)
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Double helix consists of:
 Sugar-phosphate backbone held by covalent bonds
 Nitrogen bases are hydrogen bonded together; A pairs
with T and C pairs with G
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Genetic material that organisms inherit from their
parents.
Genes
 Specific stretches of DNA that program amino acid
sequences of proteins.
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Ribonucleic Acid (RNA)
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Intermediary for making proteins
Also made up of monomers of nucleotides
 Nucleotide of RNA:
 Sugar is ribose (not deoxyribose)
 Phosphate group
 Nitrogen bases (Adenine, Uracil (instead of Thymine,
Guanine, and Cytosine)
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RNA consists of a single polynucleotide strand
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FYI…The structural significance will make sense we
talk about protein synthesis later on this year…