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					    Sugar and Sugar Derivitives
Equal and Nutrasweet   Aspartame (aspartic acid, phenylalanine, and
                       methanol)
                       Dextrose with Maltodextrin
                       (used to increase bulk, carbohydrates)
Sweet and Low          Saccharin
                       Dextrose (used to increase bulk, carb., these carbs
                       can be significant for people with diabetes!!)



Splenda                Sucralose + Dextrose and Maltodextrin

Sugar (white)          Sulfur dioxide bleaching process

Sugar (brown)          Molasses is added to white sugar

Sugar (raw)            100% pure sugar cane
Equal and Nutrasweet Aspartame
Aspartic acid in free form raises levels of aspartate and glutamate in blood  excess glutamate and
   aspartate able to cross blood brain barrier  neuron degredation  chronic illnesses (MS,
   Epilepsy, Alzheimer‟s, brain lesions, nausea…)
    http://aspartame.mercola.com/

Sweet and Low Saccharin
Was listed as a potential carcinogen from 1977-2000. Warning labels have since been removed from
   packaging. Bladder tumors found in rats were the original reason for listing as a carcinogen.
(www.medicinenet.com)

Splenda Sucralose
Discovered while trying to develop new insecticide. “Although sucralose has a structure like sugar‟s
     and a sugar-like taste, it is not natural." (www.splenda.com)
“After you eat SPLENDA® Brand Sweetener, it passes through the body without being broken down for
     energy, so the body does not recognize it as a carbohydrate.” (www.splenda.com)
“Sucralose is made by replacing three hydrogen-oxygen groups on the sugar molecule with three
     chlorine atoms” (www.splenda.com).
“The presence of chlorine is thought to be the most dangerous component of sucralose. Chlorine is
     considered a carcinogen and has been used in poisonous gas, disinfectants, pesticides, and
     plastics.” (www.medicinenet.com)
No long-term studies have been done on humans. Studies in animals found that, “The alleged
     symptoms associated with sucralose are gastrointestinal problems (bloating, gas, diarrhea,
     nausea), skin irritations (rash, hives, redness, itching, swelling), wheezing, cough, runny nose,
     chest pains, palpitations, anxiety, anger, moods swings, depression, and itchy eyes.”
     (www.medicinenet.com)
EXAM II– March 15, 2011


  Will cover weeks 4, 5 and 6
WEEK 4 Continued

     Carbs
     Lipids
   (Chapter 3)
Though this is what we tend to think about, steroids are very important molecules
in the human body for proper function of cells !!
Types of Steroids
                   Cholesterol
• Is a steroid (therefore is a lipid)
• Provides stability in plasma membrane and structural
  support
• Too much cholesterol inhibits mobility of the plasma
  membrane  rigidity!
   – Rigid blood vessels increases blood pressure
   – Diets high in saturated fats and cholesterol can cause
     circulatory disorders
              Testosterone
•   Is a steroid and is therefore a lipid
•   Produced in the testes in males
•   Is the male sex hormone
•   Responsible for the development of male
    secondary sex characteristics
                  Estrogen
•   Is a steroid and is therefore a lipid
•   Produced in the ovaries in females
•   Is the female sex hormone
•   Responsible for the development of
    female secondary sex characteristics
Testosterone and Estrogen differ only by the
 functional groups attached to each
 molecule



                 The fabulous Ru Paul




Methyl and                              Hydroxyl/Alcohol
Carbonyl group                          group
              Lipids Cont.‟d
1) Fats- saturated fatty acids

2) Oils- unsaturated fatty acids

3) Phospholipids- plasma membrane

4) Steroids

5) Waxes
              V. WAXES
• Are lipids
• Are long chains of Fatty Acids




• High melting point, waterproof, resists
  degredation
   - Ex. Candle wax
              Uses of Wax
• Plants- waxes provide a protective
  coating to reduce loss of H2O

• Humans- wax protects outer ear canal
  – Ear wax contains „Cerumin‟ which repels
    insects and traps dust and dirt


• Bees- Wax used to make honey comb
  cells to store honey
          WEEK 5
Proteins
Enzymes and Metabolic Pathways
Nucleic Acids
ATP
CELLS
      - The Cell Theory
      - Cell size and composition
      - Prokaryotic/Eukaryotic Cells
      - Cellular Evolution
                   Proteins
A protein is a polymer of amino acid monomers

Protein synthesis occurs via dehydration synthesis
  (removal of water)
  -The bond between two amino acids is a peptide
  bond

Protein degredation occurs via hydrolysis (addition
  of water)
                     Proteins
• Over 100,000 proteins have been identified

• Proteins are essential for:
   – Metabolism- Enzymes speed up reactions in cells
   – Support- ex. Keratin in hair and nails, Collagen in
     ligaments and tendons
   – Transport- Hemoglobin, transport of oxygen
   – Defense- Antibodies
   – Regulation- Hormones, ex. Insulin regulates glucose
     in blood and in cells
   – Motion- Contractile proteins actin and myosin

   A PROTEIN consists of 1 or more polypeptides
               Peptides

• A peptide is two or more amino acids
  bonded together
• A POLYPEPTIDE is a chain of amino
  acids joined by peptide bonds

** A PROTEIN may contain more than one
  Polypeptide chain
         Hemoglobin




Hemoglobin is a protein made up of 4 polypeptide chains
            Peptide Bond
• A covalent bond between two amino acids
  is a peptide bond
• The bond is formed via dehydration
  synthesis
• The reaction occurs between the carboxyl
  group of one amino acid and the amino
  group of another

Draw
               Amino Acids
• There are 20 amino acids found in the human
  body
• Amino acid refers to the amino group (NH2) and
  the acid group (COOH) of the molecule
• The central Carbon in an amino acid is
  bonded to:
1- A Hydrogen
2- An Amino Group
3- A Carboxylic Acid
     Group
4- An R Group
     The Diversity of Proteins
• How is it possible that with only 20 amino
  acids in the human body there are over
  100,000 different kinds of proteins?

• The diversity of the R group determines
  the type of amino acid
• Combinations of different amino acids in
  different sequences leads to a diversity of
  proteins
             The R Group
• R groups range in complexity
  – Some are simple, ex. A Hydrogen R group
  – Some are complex, ex. A Carbon Ring R
    group
                 Cysteine
Cysteine is an amino acid
The R Group in cysteine ends with a –SH group
This –SH group often serves to connect one amino
  acid chain to another by a DISULFIDE BOND
            Disulfide Bond




The DISULFIDE bond occurs between the two Sulfur Atoms
The 20 Amino Acids

Depending on the R group
the Amino Acid will either
be:

NON POLAR, hydrophobic

POLAR, hydrophilic

IONIZED, acidic/basic
                      Proteins
• Every protein has a particular shape and
  structure
• The shape and structure is dependent upon the
  sequence of amino acids
EX.
 Protein 1 aa seq=

 Phenylalanine   Valine   Arginine   Lysine

 Protein 2 aa seq=

 Valine   Histidine   Leucine   Threonine
Protein 1 aa seq=

Phenylalanine   Valine   Arginine   Lysine




Protein 2 aa seq=

Valine   Histidine   Leucine   Threonine
PROTEIN 1




PROTEIN 2
           Shape of Proteins
A protein can have up to 4 levels of structure
**Not all proteins exhibit all 4 levels

The 4 structural levels of proteins:
1- Primary - amino acid sequence
2- Secondary - H bonds between amino acids
  cause a polypeptide to form an alpha helix or a
  pleated sheet
3- Tertiary - Due to covalent bonds between R
  groups, the polypeptide folds and twists
4- Quaternary – Occurs when two or more
  polypeptides join to form a single protein
Primary Structure
           Secondary Structure




THE STRUCTURES ARE HELD TOGETHER BY HYDROGEN BONDS
Ex. of proteins of this type are KERATIN (hair and spider webs)- they ONLY
have a secondary structure
             Tertiary Structure




Proteins with a tertiary structure are called “GLOBULAR” Proteins
-The structure is held together by Hydrogen, Ionic and Covalent bonds
between the R groups
-ENZYMES are globular proteins
-When protein loses its shape it becomes, “DENATURED”
Quaternary Structure
      Protein-Folding Diseases
• Proteins must fold into their correct shape to
  work properly

• CHAPERONE PROTEINS:
   – Located in the cell
   – Help new proteins fold into their shape

• If folding does not occur correctly, diseases can
  result:
   – Cystic Fibrosis
   – Alzheimer disease
          NUCLEIC ACIDS
Nucleic Acid- A polymer of nucleotides

Two types:

1- DNA- Deoxyribonucleic Acid

2- RNA- Ribonucleic Acid
              Nucleotide
Consists of three molecules:
1- Phosphate (phosphoric acid)
2- Pentose sugar
3- Nitrogen-containing base
            Pentose Sugars
In DNA the pentose sugar is:

DEOXYRIBOSE

In RNA the pentose sugar is:

RIBOSE

Both are 5-Carbon sugars, but deoxyribose lacks
  an Oxygen atom that is present in ribose
DNA- 4 Types of Nucleotides
                  • Adenine

                  • Guanine

                  • Cytosine

                  • Thymine
  RNA- 4 Types of Nucleotides
• Adenine

• Guanine

• Cytosine

• Uracil
     Purines and Pyrimidines
PURINES- double rings
 - Adenine
 - Guanine

PYRIMIDINES- single rings
 - Cytosine
 - Thymine (in DNA)
 - Uracil (in RNA)
          Nucleotide Bases
• A Purine or Pyrimidine is the “base” of a
  nucleotide
• They are called bases because they raise
  the pH of a solution
• Nucleotide bases exhibit complementary
  base pairing by hydrogen bonding in a
  DNA molecule
                      DNA
• DNA is a polymer of nucleotides

• The nucleotide bases of DNA are adenine,
  guanine, cytosine or thymine (A, G, C, T)

• Nucleotides join in a particular sequence via
  dehydration synthesis reactions

• The phosphate group joins with the sugar group
  to form the “backbone” of DNA while the
  nucleotide bases form hydrogen bonds causing
  the formation of an ALPHA HELIX
                       DNA




A always binds to T by forming a double bond (A 2 T)
C always binds to G by forming a triple bond (Ceee to G)

**A Purine bonds to a Pyrimidine

THIS IS KNOWN AS COMPLEMENTARY BASE PAIRING
                   RNA
• RNA is a polymer of nucleotides

• The nucleotide bases of RNA are adenine,
  guanine, cytosine or thymine (A, G, C, U)

• Nucleotides join in a particular sequence
  via dehydration synthesis reactions

• The phosphate groups join with the sugar
  group to form the “backbone” of RNA,
  however, RNA IS SINGLE STRANDED!
RNA
                DNA v RNA
Table 3.3

                  DNA         RNA
Sugar       Deoxyribose       Ribose
Bases       A, T, C, G        A, U, C, G
Strands     Double Stranded   Single stranded
Helix       YES               NO
   Adenosine Triphosphate (ATP)

ATP is a nucleotide

The base of the nucleotide is adenine
The sugar of the nucleotide is ribose
Tri refers to the 3 phosphate groups attached to
  the ribose sugar
  - The last two Phosphate bonds are
  UNSTABLE, easily broken
  - In cells, the end phosphate is hydrolyzed to
  release energy which results in ADP, adenosine
  diphosphate and a Phosphate molecule
                     ATP  ADP
The energy that is released by the hydrolysis of the terminal
 phosphate group is essential for cell function ex.:
  – Synthesis of macromolecules (carbs and proteins)
  – ATP supplies energy to muscles for contraction
                         Energy
  • Cells need a constant supply of ENERGY
  • Energy comes in 2 forms:
      – 1- Potential- Stored energy
         • Food is potential energy known as CHEMICAL
           energy (food= Carbs, proteins, fats= chemicals)
      – 2- Kinetic- The energy of motion
         • Walking is a type of kinetic energy known as
           mechanical energy
         • To walk you must convert chemical energy into
           mechanical energy

TEXT page 104
 Two Laws of Thermodynamics
First Law of Thermodynamics:
The law of conservation of energy states
  that energy cannot be created or
  destroyed, but it can be changed from one
  form to another.
Ex. A leaf cell uses solar energy to form
  carbohydrates during photosynthesis. Not
  all of the solar energy is used, the rest of
  the energy is dissipated in the form of
  HEAT (a type of energy)
            Second Law of
           Thermodynamics
The second law of thermodynamics states
 that energy cannot be changed from one
 form to another without the loss of usable
 energy. (page 105 top)

Ex. Muscles use carbohydrates as an energy
  source, once they contract and use energy, heat
  is given off. When heat is dissipated, it is no
  longer usable energy. Nothing is 100% efficient
  in terms of use of energy.
There is a universal tendency for things to
  become disordered (a fundamental law of
  physics- 2nd law of thermodynamics)
In the universe, the degree of disorder can
  only increase
The amount of disorder in a system can be
  quantified
The quantity used to measure disorder is
  called the entropy of the system
The greater the disorder, the greater the
  entropy
     2nd law/Entropy continued
SYSTEMS WILL CHANGE SPONTANEOUSLY
 TOWARD ARRANGEMENTS WITH GREATER
 ENTROPY (disorder)- Energy conversions result
 in HEAT, therefore the entropy of the universe is
 always increasing

Cells are highly organized, however when they use
 energy, heat is released causing disorder in the
 cell‟s environment.

Therefore, the cell‟s entropy INCREASES
As cells use energy to create molecules, heat is dissipated causing
Increased disorder in the cell‟s surroundings and increased order within
the cell.

Image from „The molecular Biology of the Cell- 4th ed., Fig. 2-38
          Breakout Session
• Why is the entropy of the universe always
  increasing?

• Think about your body. Why is our
  temperature exactly 98.6 degrees F/ 37
  degrees C?

Write down your answers. Up to an extra 5
 points. You may work in groups, 10
 minutes.
                  Enzymes
An enzyme is a protein molecule that functions as
  an organic catalyst to speed a chemical reaction
  without itself being affected by the reaction.

Enzymes are a part of metabolic pathways which
  are a series of linked reactions.

The cell has hundreds of metabolic pathways with
  many different types of enzymes working to
  speed up reactions
               Ribozyme
• A ribozyme works like an enzyme, but it is
  not a protein

• A ribozyme is made up of RNA, a polymer
  of nucleic acids with a ribose sugar

• Ribozymes sythesize proteins and RNA
                        Metabolic Pathways
                              4      Enzyme
           2
                                        4
               Enzyme
                  2
Enzyme
   1                        Enzyme            5
                               3

                        3
   1

molecule


   Products from the previous reaction
   Become the reactants of the next
   reaction !

   Ex. Molecule 2 is a product from
   The reaction between enzyme 1 and
   Molecule 1, but it is also the reactant        Every dot in the figure represents
   For the next step in the pathway               a molecule
                                                  Fig. 2-35 from “The Molecular Biology of the Cell-4th Ed.”
     Two Types of Metabolic
           Pathways
1- Catabolic
     Food molecules are the source of
  substrates. Food molecules contain large
  amounts of stored energy in their chemical
  bonds

2- Anabolic
    Molecules the form the cell. These
  molecules are broken down during
  metabolism and re-formed.
                 Metabolism
How a set of enzymes catalyze reactions
   generates a metabolic pathway.
Is the sum of all the biochemical reactions in a cell
-Living things create and maintain order.

-To create order, living things must perform
  chemical reactions.
  Ex. Amino acids, sugars, nucleotides, lipids are
  broken down and modified to supply the cell with
  energy
    Why speed up a reaction?
Molecules do not always react with one another
Sometimes they need help in the form of heat or
  other energy source

The amount of energy required for molecules to
  react with one another is called the ENERGY OF
  ACTIVATION

Enzymes help to speed up a reaction by
  DECREASING the ENERGY OF ACTIVATION
      The Enzyme-Substrate
            Complex
Enzymes function by binding to a substrate
 to help catalyze a reaction thereby
 producing a new product.
Remember, an enzyme does not change
 and is not affected during this process

      E      +      S  ES  E + P


    Enzyme       Substrate   Enzyme-Substrate   Enzyme   Product
                                 Complex
                  Enzyme Active Site
     In general only the “active site” of the
       enzyme binds to the substrate
I.                          II.                            III.




                                  A slight change at the
           Active Site of         active site allows
            the Enzyme            for the attachment of
                                  the substrate
 The INDUCED FIT MODEL
                          Free Energy or G is the amount of energy
                                          do work after Enzyme is
                          that is free to Because the a chemical reaction
Enzyme                                 induced by the substrate to
                          This Product now becomes the substrate for
                                       undergo a change at the
                          The next reaction and has a certain amount of
                                       active site, this kind of
                          Free energy
                                       SUBSTRATE-
                                       ENZYME model is known a
                          Some reactions are EXERGONIC and haveas
                          NEGATIVE free energy.
                                        “The Induced Fit a
                            Some reactions are ENDERGONIC and have
                                        Model”
                   SubstratePOSITIVE free energy.

                          Products usually have more energy than the
                                       The with an input of energy!
                          Reactants, but onlyactive site returns to
         New Product is
           released                    its original state after the
                                       product is released
        Exergonic v Endergonic
Exergonic Rxns.               Endergonic Rxns.

Spontaneous                   Require input of
                              energy to occur
Do not require input of
Energy                        Ex. Muscle Contraction

Release Energy or heat

Exergonic reactions can be used to drive endergonic
reactions which require energy!
   Factors that affect enzymatic
              speed
1- Substrate Concentration
        The more substrate in a solution, the larger the number
   of collisions between substrate and enzyme
2- pH
        Each enzyme has an optimal pH to function properly
3- Temperature
        As temps. Rise, enzyme activity increases, but too high
   and enzyme will denature
4- Enzyme Cofactors
        Cofactors are small inorganic ions or nonprotein organic
   molecules present at the active site in order to activate the
   enzyme.
        Non protein organic molecules are called coenzymes
       Why is this important?
Cells need energy to carry out metabolic
 processes
This energy is in the form of ATP

ATP is an energy carrier

When the terminal Phosphate group is
Hydrolyzed, ENERGY IS RELEASED!
   Adenosine Triphosphate (ATP)

ATP is a nucleotide

The base of the nucleotide is adenine
The sugar of the nucleotide is ribose
Tri refers to the 3 phosphate groups attached to
  the ribose sugar
  - The last two Phosphate bonds are
  UNSTABLE, easily broken
  - In cells, the end phosphate is hydrolyzed to
  release energy which results in ADP, adenosine
  diphosphate and a Phosphate molecule
ATP and the Electron Transport
            Chain
ATP is produced via the electron transport chain
  (ETC)
Chloroplasts in plant cells use solar energy to
  generate ATP using ETC
Mitochondria in animal cells use glucose to
  generate ATP using ETC

The ETC is a series of transfers of electrons
  whereby high energy electrons are transported
  through a series of steps to release energy for
  the synthesis of ATP
Energy comes from the transfer of electrons
       THIS WEEK IN LAB

Biologically Important Molecules
Proteins
Nucleic Acids
Enzymatic purification of DNA
Dische’s Test
              HOMEWORK

VIRUSES, BACTERIA and ARCHAEA
(Chapter 20)

The Eukaryotic Cell (pg. 68-84)

Membranes and Transport (pg. 85-100)

				
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