Organic Molecules

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Organic Molecules
Molecules unique to living systems contain carbon
and are referred to as organic molecules
Carbon, needing 4 more valence electrons, forms
covalent bonds (either polar or non-polar)
readily with

• Carbon
• Hydrogen
• Oxygen
• Nitrogen

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Carbon in Organic Molecules
Covalently bound carbon atoms form

• functional groups
• CH3
• COOH

• rings
• long chains

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Macromolecules
Most of the anatomy and physiology of the body is
provided by 4 different classes of organic
molecules

• Carbohydrates
• Lipids
• Proteins
• Nucleic acids

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• Each of these classes of macromolecules are made
  as 2 or more smaller molecular subunits called
  monomers (one unit) are covalently bonded to one
  another (synthesis reaction)

• results in a new molecule that is larger and
  structurally more complex

• as more and more monomers are bound to one
  another the molecule gets progressively larger
  resulting in a polymer (many units)

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Monomers of Macromolecules

• Monomers

• smallest subunits of macromolecules that exhibit
  chemical properties of the macromolecule

• Carbohydrate monosaccharide
• Lipids fatty acid
• Proteins amino acid
• Nucleic acids nucleotide

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• These large macromolecules can be broken back
  down to the individual monomers by breaking the
  covalent bond between monomers through a
  decomposition reaction

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Biochemical Reactions
The functioning of the body (physiology) occurs
as the organic molecules of the body react with
one another

• Written in symbolic form using chemical equations

• Chemical equations contain

• relative amounts of reactants (starting
  chemicals) and products (finishing chemicals)

• number and type of reacting substances, and
  products produced

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• Chemical reactions occur when covalent bonds in a
  molecule are formed or broken

the formation of a covalent bond uses energy
the breaking of a covalent bond releases energy
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Energy Sources

• Chemical

• stored in the covalent bonds of energy-rich
  molecules

• Electrical

-the movement of charged substances
(ions)

• Heat

• causes molecules to move

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• Mechanical

-moving molecules collide with one another which
transfers energy between the two molecules

• Energy sources can be converted from one form to
  another
• Energy is never lost! Simply transferred!

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Types of Chemical Reactions
1.Synthesis reactions
involve bond formation (creating larger molecules)
molecule A molecule B ? molecule AB
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Dehydration Synthesis

• Monomers bond together to form a polymer
  (synthesis), with the removal of a water molecule
  (dehydration)
• the 2 monomers react with each other through
  functional groups (example below shows 2 hydroxyl
  groups interacting)

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2.Decomposition Reactions

• Large complex molecules are broken down into
  smaller simpler ones
• AB ? A B

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Hydrolysis

• Splitting a polymer (lysis) by the addition of a
  water molecule (hydro)

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3. Exchange Reactions

• Two molecules collide and exchange atoms or group
  of atoms
• ABCD ? ABCD ? AC BD

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4. Oxidation-Reduction (Redox) Reactions

• Involves the transfer of electrons from one
  atom/molecule to another
• eg. formation of an ionic bond

• Reactants losing electrons become oxidized (Loss
  Electron(s) Oxidation LEO)

• Reactants gaining electrons become reduced (Gain
  Electron(s) Reduction GER)

OIL RIG Oxidation is loss, Reduction is gain
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• Na Cl ? Na Cl-
• Na is oxidized and Cl is reduced

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Energy Flow in Chemical Reactions
Exergonic reactions (exothermic)

• reactions that release energy (due to the
  breaking of bonds) typically in the form of HEAT
  into the environment of the reaction

-the reactants contain more energy than the
products

• Endergonic reactions (endothermic)

• reactions that remove energy (HEAT) from the
  environment of the reaction (required to form
  bonds)

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• the products contain more energy than the
  reactants

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Energy Flow in an Exergonic Reaction
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Metabolism

• All of the collective biochemical reactions of
  the body are grouped into two general classes

• Catabolic reactions
• energy releasing (exergonic) decomposition
  reactions

• Anabolic reactions
• energy absorbing (endergonic) synthesis reactions

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Reversibility in Chemical Reactions

• All chemical reactions are theoretically
  reversible
• A B ? AB

When neither the forward nor reverse reaction is
dominant, a chemical equilibrium (balance) is
reached
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Reaction Rates
-The rate of chemical reactions are determined by
molecular motion and collisions between chemicals

• The speed at which a chemical reaction proceeds
  is affected by

• the concentration of reactants
• more concentrated more collisions faster rate

• the temperature
• higher temperature faster molecular movement
  more collisions faster rate

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• the presence of catalysts
• molecular matchmakers
• bring reactants together faster
• biological catalysts are enzymes

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Carbohydrates

• hydrated (H2O) carbon
• Contain carbon, hydrogen, and oxygen
• Their major function is to supply a source of
  cellular fuel for energy

• Examples
• simple sugars (glucose) and complex sugars
  (starch)

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• Many carbohydrate names end in the suffix -ose
• glucose, maltose, amylose, fructose, sucrose

• CarbonHydrogenOxygen in a 121 atomic ratio
• (CH2O)n , n number of carbon atoms
• glucose C6H12O6

• Because they contain oxygen, they are polar
  molecules (hydrophilic or lipophobic)

• The monomer of carbohydrates is the
  monosaccharide (one sugar) of which there are a
  number of types

-glucose is the most biologically important
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Monosaccharides

• Simplest carbohydrates
• General formula is C6H12O6
• structural isomers
• same molecular formula, but different molecular
  structure

• Three major monosaccharides
• glucose, galactose and fructose
• mainly produced by hydrolysis of dietary complex
  carbohydrates during the process of digestion
  (polysaccharides)

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Disaccharides

• Pairs of monosaccharides covalently bonded via
  dehydration synthesis
• Three major disaccharides
• sucrose
• glucose fructose
• lactose
• glucose galactose
• maltose
• glucose glucose

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Polysaccharides

• Long chains of glucose form polysaccharides
• Starch
• the storage form of sugar produced by plants
• the source of dietary carbohydrates for the body
• hydrolyzed to glucose in the digestive tract and
  then moved into the blood and delivered to all
  cells of the body to be used as a fuel for energy
  production

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Polysaccharides

• Glycogen is an energy storage polysaccharide
  produced by animals
• Excess glucose in the blood following the
  digestion of a meal is taken up by the liver
  which synthesizes glycogen
• the liver gradually hydrolyzes glycogen is
  between meals and releases the glucose into the
  blood to ensure that all cells of the body have a
  sufficient supply of glucose to produce energy
• When glucose levels drop below its setpoint, you
  become hungry and eat to replenish the glucose

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Lipids (Fats, Oils, Waxes)

• Nonpolar organic molecules made mostly of carbon
  and hydrogen

-Contains much less oxygen than carbohydrates
-Energy rich molecules that can be used for
energy production
-typically occurs when there is an absence
of glucose in the body. (After the
carbohydrates are depleted.)
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• 4 primary types
• fatty acids
• triglycerides
• phospholipids
• steroids

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Fatty Acids

• Hydrocarbon chains of 4 to 24 carbon atoms
• always an even number of carbons
• Has more energy per molecule than glucose
• 2 different functional groups are at each end
• carboxylic acid group
• provides acidic properties to the molecule
• methyl group
• 2 different types exist
• Saturated
• solid at room or body temperature (RT/BT)
• Unsaturated
• some are solid but most are liquid at RT/BT

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Fatty Acids

• Saturated fatty acid
• each carbon in the hydrocarbon chain is saturated
  with hydrogen
• no double bonds between carbons (CC)
• Unsaturated fatty acid
• each carbon in the hydrocarbon chain is not
  saturated with hydrogen
• contains at least one CC or triple bond

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Monounsaturated contains only one triple or
double bond
Polyunsaturated contains many double or triple
bonds
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Triglycerides

• Three fatty acids bonded to one glycerol through
  the process of dehydration synthesis

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Triglycerides
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• Functions
• energy storage in adipose (fat) tissue

• each fatty acid of a triglyceride contains
  approximately 4 times more energy than a single
  molecule of a monosaccharide (glucose)

• insulation
• prevents excessive heat loss from the body

• protection
• provides shock absorption for organs that are
  surrounded by adipose tissue

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Phospholipids

• Similar in structure to a triglyceride consisting
  of
• 1 glycerol
• 2 fatty acids
• 1 phosphate group (PO4-)

• Amphiphilic (both loving) molecule
• has BOTH polar and nonpolar portions
• Hydrophobic tails consist of two fatty acids
• Hydrophilic head consists of a negatively
  charged phosphate group

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-Found in a liquid state at body temperature
-Predominant molecule in cellular membranes
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Phospholipid Structure
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Cholesterol

• Hydrocarbons are arranged in a 4 ringed backbone
• Used to make steroids including
• cortisol
• progesterone
• estrogen
• testosterone
• Found in cellular membranes

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Proteins

• Polymer of amino acids which are bonded together
  through covalent bonds that are called peptide
  bonds created by dehydration synthesis and broken
  by hydrolysis

• Proteins vary greatly in size
• some are as small as 9 amino acids in length
• some are as large as 4650 amino acids in length

Protein Functions

• PERFORM EVERY FUNCTION IN THE BODY
• Each protein is structurally and functionally
  unique

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• Catalysts
• enzymes speed up biochemical reactions

• Structural
• hold the parts of the body together

• Communication
• act as signaling molecules between body areas

• Cell Membrane Transport
• allow substances to enter/exit cells

• Recognition
• monitor any/all changes in the body

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• Movement
• muscle contraction

Characteristics of Enzymes

• Enzymes are chemically specific for a particular
  substrate (chemical on which an enzyme acts upon)
• each enzyme can only act upon one substrate

-Enzymes are unchanged by reactions that they
catalyze and are able to repeat the process many
times over

• Enzymes increase the rate of a chemical reaction
  by lowering the activation energy of the reaction
  
• amount of energy required to initiate a chemical
  reaction

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-Enzymes are frequently named for the type of
reaction they catalyze or by their substrate
-Enzyme names usually end in the suffix -ase
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Enzymes and Activation Energy
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Enzyme Structure and Action

• The region of an enzyme that recognizes a
  substrate is called the active site
• recognizes the specific molecular structure of a
  substrate

• An enzyme temporarily binds its substrate(s) and
  allows the appropriate chemical reaction proceed
• Synthesis
• Decomposition
• Exchange
• RedOx

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Enzyme action may occur different means
For example
1. Lock and key model - where substrate fits
exactly into enzyme like one key and one lock
Therefore one enzyme for every substrate
2. Induced fit - where enzyme changes shape
slightly to fit around substrate
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Enzymatic Catalysis of a Biochemical Reaction
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Amino Acids

• 20 different amino acids exist
• Each amino acid unique due to the functional
  group located at the R position on the molecule
• The chemical nature of each amino acid is
  determined by the chemistry of the R group
• possibilities are
• polar
• nonpolar

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Bonding of Amino Acids
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Humans utilize 20 different amino acids to make
proteins.
Of the 20 aa, approximately 12 are able to be
obtained from the re-arrangement of the R group,
these are called NON ESSENTIAL AA
i.e. one amino acid can be changed into
another one
The remaining 8 aa can not be obtained by this
method, they MUST obtained in the diet. These are
called ESSENTIAL Amino Acids.
In order to make proteins, all of the amino acids
must be present.
Foods that contain all of the essential AA are
complete.
Some foods contain some of the essential AA but
not all.
All of the essential AA may be obtained by eating
complimentary foods
i.e. one food contains some essential AA while
another contains the rest
Such as Rice and Beans or Peanut Butter, Jelly
and Bread
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Protein Structure

• Primary structure
• the amino acid sequence of the protein

• Secondary structure
• simple shapes that segments of amino acids make
  within the protien

• a helix (coiled), ß-pleated sheet (folded) shapes
  are held together by intramolecular hydrogen
  bonds between nearby amino acids

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• Tertiary structure
• the overall 3 dimensional shape of the protein

-determined by polar and nonpolar
interactions between the amino acids
of the protein and the surrounding water
stabilized by more intramolecular hydrogen bonds
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Protein Conformation and Denaturation

• Conformation
• overall 3 dimensional shape (tertiary/quaternary)
  that is required for function (activity)

-the function of some proteins requires an
ability to change their conformation (induced fit)

• Denaturation
• drastic conformational change in a protein caused
  by the breaking of hydrogen bonds within a protein

• increases in temperature
• increases or decreases in pH

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• can be partial or complete

• when a protein is partially denatured, its
  function is impaired
• when a protein is completely denatured, its
  function is lost

Nucleic Acids
-Molecules of instruction and heredity

• Largest molecules in the body

• Two major classes

• deoxyribonucleic acid (DNA)
• ribonucleic acid (RNA)

-The monomers of nucleic acids are nucleotides
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Nucleotides
-5 different nucleotides are used to make nucleic
acids

• single ringed nucleotides are called pyrimidines
• cytosine (C), thymine (T) and uracil (U)

• double ringed nucleotides are called purines
• adenine (A) and guanine (G)

• Nucleotides are covalently bound to one another
  between the sugar of one nucleotide and the
  phosphate of another nucleotide to make long
  molecules referred to as nucleic acid strands

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Nucleotides
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DNA

• Double-stranded helical molecule

• looks like a ladder that has been twisted

• each strand is between 100 million to 1 billion
  nucleotides in length

• 2 strands are held together by H-bonds between
  complimentary nucleotides on opposite strands

• H-bonds can only be made between a purine on one
  strand and a pyramidine on the other strand
• A can only bind with T
• G can only bind with C
• U is NOT part of DNA (only found in RNA)

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• The sequence of nucleotides in one of the strands
  contains the genetic code

• the amino acid sequence of all proteins

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Structure of DNA
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RNA
-Single-stranded molecule

• made from the nucleotides A, U, G and C

-Note T has been replaced with U

• Three varieties of RNA
• messenger mRNA
• transfer tRNA
• ribosomal rRNA

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Adenosine Triphosphate (ATP)
-Source of immediately usable energy for the cell
-Nucleotide derivative bound to 3 phosphate groups

• second and third phosphate groups are attached by
  high energy covalent bonds

• phosphate groups are negatively charged and
  naturally repel each other

• When Enzymes hydrolyze the high energy bond of
  ATP chemical energy is released

ATP ? ADP P energy

• the body can convert the ADP and P back into ATP
  using the energy stored in the covalent bonds of
  carbohydrates and lipids as a fuel

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ATP