Download Intro to Organic Chem

INTRODUCTION TO ORGANIC
COMPOUNDS
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Organic Compounds
– Carbon-based molecules are called organic
compounds
– By sharing electrons, carbon can bond to four other
atoms
– By doing so, it can branch in up to four directions
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Structural
formula
Ball-and-stick
model
Space-filling
model
Methane
The four single bonds of carbon point to the corners
of a tetrahedron.
• Methane and other compounds composed of only
carbon and hydrogen are called hydrocarbons
– Carbon, with attached hydrogen, can bond together
in chains of various lengths
Ethane
Propane
Length. Carbon skeletons vary in length.
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Butane
Isobutane
Branching. Skeletons may be unbranched or branched.
1-Butene
Double bonds.
2-Butene
Skeletons may have double bonds,
which can vary in location.
Cyclohexane
Rings.
Benzene
Skeletons may be arranged in rings.
• An organic compound has unique properties that depend
upon
– The size and shape of the molecule
– The groups of atoms (functional groups) attached to it
• A functional group affects a biological molecule’s
function in a characteristic way
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• Compounds containing functional groups are
hydrophilic (water-loving)
–This means that they are soluble in water,
which is a necessary prerequisite for their
roles in water-based life
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Functional Groups
• Hydroxyl group—
consists of a hydrogen
bonded to an oxygen
• Carbonyl group—a
carbon linked by a double
bond to an oxygen atom
• Carboxyl group—
consists of a carbon doublebonded to both an oxygen
and a hydroxyl group
Functional Groups (Cont’d)
• Amino group—composed of a
nitrogen bonded to two hydrogen
atoms and the carbon skeleton
• Phosphate group—consists of
a phosphorus atom bonded to
four oxygen atoms
• Methyl group- consists of a
carbon bonded to three hydrogen
Estradiol
Female lion
Testosterone
Male lion
• Four classes of biological molecules:
–Carbohydrates
–Proteins
–Lipids
–Nucleic acids
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• The four classes of biological molecules contain very large
molecules
– macromolecules
– Polymers -made from identical building blocks(monomers) strung
together
– monomers -building blocks
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• A cell makes a large number of polymers from a small group of
monomers
– Proteins are made from only 20 different amino acids, and DNA is
built from just four kinds of nucleotides
• The monomers used to make polymers are universal
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• dehydration reactions- remove water and link monomers to
form polymers
• hydrolysis- addition of water, breaks apart polymers
• All biological reactions of this sort are mediated by enzymes,
which speed up chemical reactions in cells
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Short polymer
Unlinked
monomer
Short polymer
Dehydration
reaction
Longer polymer
Unlinked
monomer
Hydrolysis
CARBOHYDRATES
Monosaccharides, disaccharides and polysaccharides
1:2:1 ratio of C:H:O
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Monosaccharides
– Monosaccharides-Sugar monomers
– -such as glucose, galactose and fructose
- bond together to form the polysaccharides
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Monosaccharides
•
carbon skeletons - three to seven carbon atoms
– Glucose and fructose are six carbons long
– main fuels for cellular work
– used as raw materials to manufacture other organic molecules
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Glucose
(an aldose)
Fructose
(a ketose)
Structural
formula
Abbreviated
structure
Simplified
structure
• Disaccharide-Two monosaccharides (monomers) bonded in a
dehydration synthesis reaction
– An example is a glucose monomer bonding to a fructose monomer
to form sucrose, a common disaccharide
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• Disaccharide-Two monosaccharides bonded in a dehydration
synthesis reaction
– Glucose + fructose  sucrose + water
– Glucose + galactose  lactose + water
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Glucose
Glucose
Glucose
Glucose
Maltose
• Polysaccharides are polymers of monosaccharides
– They can function in the cell as a storage molecule or as a structural
compound
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Polysaccharides
• Starch is a storage polysaccharide composed of glucose
monomers and found in plants
• Glycogen is a storage polysaccharide composed of glucose,
which is hydrolyzed by animals when glucose is needed
• Cellulose is a polymer of glucose that forms plant cell walls
• Chitin is a polysaccharide used by insects and crustaceans to
build an exoskeleton and used in fungi cell walls
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Starch granules in
potato tuber cells
Glycogen
granules
in muscle
tissue
STARCH
Glucose
monomer
GLYCOGEN
CELLULOSE
Cellulose fibrils in
a plant cell wall
Hydrogen bonds
Cellulose
molecules
Starch granules in
potato tuber cells
STARCH
Glucose
monomer
Glycogen
granules
in muscle
tissue
GLYCOGEN
CELLULOSE
Cellulose fibrils in
a plant cell wall
Hydrogen bonds
Cellulose
molecules
LIPIDS
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• Lipids-water insoluble (hydrophobic) compounds
energy storage
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-
Triglycerides
• Fatty acids link to glycerol by a dehydration reaction
• Glycerol-alcohol with 3 carbons, each with hydroxyl group
• Fatty Acid- carboxyl group and hydrocarbon chain of 16-18
carbons in length
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Glycerol
Fatty acid
Figure 2.15a
• Some fatty acids contain double bonds
– This causes kinks or bends in the carbon chain because the
maximum number of hydrogen atoms cannot bond to the carbons at
the double bond
– unsaturated fats -have fewer than the maximum number of
hydrogens
– saturated fats- Fats with the maximum number of hydrogens
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• Phospholipids
• - structurally similar to triglycerides
• -important component of all cells
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Chemical Nature of Phospholipids
head
tails
Hydrophilic
heads
Water
Hydrophobic
tails
Water
• Steroids are lipids composed of fused ring structures
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Four Ring Structure of Steroids
PROTEINS
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Proteins
• A protein is a polymer built from various combinations of 20
amino acid monomers
– Structures directly related to functions
– Enzymes-proteins that serve as metabolic catalysts, regulate the
chemical reactions within cells
– “-ase”
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Proteins
• Structural
•
•
•
•
•
contractile
Defensive
Signal
Receptor
transport
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Proteins
• Amino acids-building blocks of proteins
• Central carbon
• have an amino group and a carboxyl group
– Also bonded to the central carbon is a hydrogen atom and some
other chemical group symbolized by R
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Amino
group
Carboxyl
group
• Amino acids are classified as hydrophobic or hydrophilic
nonpolar R group and are hydrophobic
polar R group and are hydrophilic
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Leucine (Leu)
Hydrophobic
Serine (Ser)
Aspartic acid (Asp)
Hydrophilic
Carboxyl
group
Amino acid
Amino
group
Amino acid
Carboxyl
group
Amino acid
Amino
group
Amino acid
Peptide
bond
Dehydration
reaction
Dipeptide
• A polypeptide chain – 100’s or 1000’s of amino acids linked by
peptide bonds
– The shape of a protein determines its specific function
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• If for some reason a protein’s shape is altered, it can no longer
function
– Denaturation
– changes in salt concentration and pH, temperature
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• A protein can have four levels of structure
–
–
–
–
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
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• The primary structure- unique amino acid sequence
– The correct amino acid sequence is determined by the cell’s
genetic information
– The slightest change in this sequence affects the protein’s ability
to function
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Amino acids
Primary structure
Four Levels of Protein Structure
Primary structure
Amino acids
• secondary structure-coiling or folding of the polypeptide
– Coiling results in a helical structure called an alpha helix
– Folding may lead to a structure called a pleated sheet
– Hydrogen bonds
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Amino acids
Hydrogen
bond
Alpha helix
Secondary structure
Pleated sheet
Four Levels of Protein Structure
Primary structure
Amino acids
Hydrogen
bond
Secondary structure
Alpha helix
Pleated sheet
• tertiary structure-three-dimensional shape of a protein
– results from interactions between the R groups of the various amino
acids
– Disulfide bridges are covalent bonds that further strengthen the
protein’s shape
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Four Levels of Protein Structure
Primary structure
Amino acids
Hydrogen
bond
Secondary structure
Alpha helix
Tertiary structure
Polypeptide
(single subunit
of transthyretin)
Pleated sheet
Polypeptide
(single subunit
of transthyretin)
Tertiary structure
• quaternary structure-two or more polypeptide chains
(subunits) associate
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Transthyretin, with
four identical
polypeptide subunits
Quaternary structure
Four Levels of Protein Structure
Primary structure
Amino acids
Hydrogen
bond
Secondary structure
Alpha helix
Tertiary structure
Quaternary structure
Pleated sheet
Polypeptide
(single subunit
of transthyretin)
Transthyretin, with
four identical
polypeptide subunits
HOW ENZYMES FUNCTION
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• Energy is the capacity to do work and cause change
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– There are two kinds of energy
– Kinetic energy is the energy of motion
– Potential energy is energy that an object possesses as a
result of its location, stored energy
Energy is converted from one form to another.
• Chemical energy -potential energy
• it is the energy stored in chemical bonds, energy available for
release in a chemical reaction
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Chemical Reactions
• Release or store energy
• Exergonic reaction- releases energy
– reaction releases the energy in covalent bonds of the reactants
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Potential energy of molecules
Reactants
Amount of
energy
released
Energy released
Products
Chemical Reactions
• Endergonic reaction-requires an input of energy
• yields products rich in potential energy
– energy is absorbed and stored in covalent bonds of the products
– Building macromolecules
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Potential energy of molecules
Products
Energy required
Reactants
Amount of
energy
required
– Metabolism- all of the exergonic and endergonic reactions that
occur in an organism
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Activation Energy
– The start up energy
– Energy that must be absorbed by the reactants in any chemical
reaction in order to be break bonds
– Energy must be available to break bonds and form new ones
– This energy is called energy of activation
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Catalysts
A Catalyst is a substance that can change the rate of a
chemical reaction. It does this by decreasing the activation
energy that is needed to start a chemical reaction.
A Catalyst is NOT reactant or product. It is not changed or
used up during a reaction.
Enzymes are catalysts for chemical reactions in living things.
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Reaction
without
enzyme
EA without
enzyme
EA with
enzyme
Reactants
Net
change
in energy
(the same)
Reaction with
enzyme
Products
Progress of the reaction
Enzymes
• Proteins- have unique three-dimensional shapes
– Shape critical for function
– Substrates- the specific reactants that an enzyme acts on
-- the enzyme has an active site where the enzyme interacts with
the enzyme’s substrate
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1 Enzyme available
with empty active
site
Active site
Enzyme
(sucrase)
1 Enzyme available
with empty active
site
Active site
Enzyme
(sucrase)
Substrate
(sucrose)
2 Substrate binds
to enzyme with
induced fit
1 Enzyme available
with empty active
site
Active site
Substrate
(sucrose)
2 Substrate binds
to enzyme with
induced fit
Enzyme
(sucrase)
3 Substrate is
converted to
products
1 Enzyme available
with empty active
site
Active site
Glucose
Substrate
(sucrose)
2 Substrate binds
to enzyme with
induced fit
Enzyme
(sucrase)
Fructose
4 Products are
released
3 Substrate is
converted to
products
• Some enzymes require nonprotein helpers
– Cofactors are inorganic, such as zinc, iron, or copper
– Coenzymes are organic molecules and are often vitamins
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• Inhibitors are chemicals that inhibit an enzyme’s activity
– One group inhibits because they compete for the enzyme’s active
site and thus block substrates from entering the active site
– These are called competitive inhibitors
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Substrate
Active site
Enzyme
Normal binding of substrate
Competitive
inhibitor
Noncompetitive
inhibitor
Enzyme inhibition
• Other inhibitors do not act directly with the active site
– These bind somewhere else and change the shape of the enzyme so
that the substrate will no longer fit the active site
– These are called noncompetitive inhibitors
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• Enzyme inhibitors are important in regulating cell metabolism
– Often the product of a metabolic pathway can serve as an inhibitor
of one enzyme in the pathway, a mechanism called feedback
inhibition
– The more product formed, the greater the inhibition, and in this
way, regulation of the pathway is accomplished
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NUCLEIC ACIDS
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• DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)
• composed of monomers called nucleotides
– Nucleotides have three parts
– A five-carbon sugar
– called ribose in RNA and deoxyribose in DNA
– A phosphate group
– A nitrogenous base
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Nitrogenous
base
(adenine)
Phosphate
group
Sugar
• DNA nitrogenous bases- adenine (A), thymine (T), cytosine (C),
and guanine (G)
– RNA - A, C, and G, but instead of T, it has uracil (U)
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• A nucleic acid polymer, a polynucleotide, forms from the
nucleotide monomers when the phosphate of one nucleotide
bonds to the sugar of the next nucleotide
– The result is a repeating sugar-phosphate backbone with protruding
nitrogenous bases
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Nucleotide
Sugar-phosphate
backbone
• DNA
• double helix- 2 polynucleotide strands
• Bases of each strand hydrogen bond to each other
• A pairs with T, and C pairs with G, producing base pairs
• RNA is usually a single polynucleotide strand
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Base
pair
• A particular nucleotide sequence that can instruct the formation
of a polypeptide is called a gene
– Most DNA molecules consist of millions of base pairs and,
consequently, many genes
– These genes, many of which are unique to the species, determine
the structure of proteins and, thus, life’s structures and functions
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Adenosine Triphosphate (ATP)
• Temporary molecular storage of energy
• Consists of 3 phosphate
groups attached to
adenine & 5-carbon
sugar (ribose)
Figure 2.23