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					Textbook Chapter 3
1.   Introduction to Chemistry (a review)
2.   Acids, Bases, pH (review)
3.   Properties of Water
4.   Carbohydrates
5.   Lipids
6.   Proteins
7.   Enzymes
8.   Nucleic Acids
9.   ATP energy molecule
Key Vocabulary: Elements, Atoms, Ions, Ionic Compounds,
Molecular Compounds, Covalent Bonds, Ionic Bonds, Polar
Molecules, Non-Polar Molecules, pH, Acid, Base
Atomic Structure (Bohr Model)
Element Composition
Elements are types of atoms
 Each element is identified by the number of
  protons (atomic number).
 Living things contain mostly carbon(C-12),
  hydrogen(H-1), oxygen(O-16), and
  nitrogen(N-14)
 Others present in smaller percentages include
  sulfur (S), phosphorus(P), magnesium(Mg),
  iron(Fe), iodine(I), calcium(Ca),
  sodium(Na), chlorine(Cl) and potassium(K).
Chemical compounds
  Compounds are chemical combination of two or more
   elements (H2O)
  Atoms combine to form compounds either by
   transferring electrons from one atom to another, or by
   sharing electrons between them.
Organic means Carbon containing
 Organic Molecules contain Carbon.
 Organic Acids contain a special combination of atoms,
  COOH
 Organic Catalysts are enzymes that speed up chemical
  reactions and they too are made of Carbon
Atoms are neutral



 Atoms have a balance of protons
 and electrons, so they balance
 positive charges and negative
 charges
Molecular Compounds
 Formed from a combination of C,H,O, or N
  usually.
 Electrons are shared in these compounds,
  the process is called covalent bonding.
 Molecules include C6H12O6 O2 H2O CO2
Ionic Compounds:
 Ions are atoms that have lost or gained electrons
  and become positive (+) or negative (-)
 Ionic Compounds are made of metal ions and non-
  metal ions. Ex NaCl or KCl or NaF or KI
 Ionic substances do NOT usually contain “H”
 When electrons are transferred, the atoms acquire
  an electric charge and become ions. This process is
 called ionic bonding, and the compound forms an
 ionic crystal.
Formulas
  The composition of the compound can be
   shown by a formula.
  A formula shows the symbols of the
   elements in the compound, followed by a
   small subscript numbers showing the
   ratio of the atoms in the compound.
  A molecular formula tells you the number
   and type of atoms in the compound
Understanding Chemical Formulas
Subscript Notation
                         H2O


            subscrip
            t

              CA Science Standards #1 Atomic and
 7/8/2011     Molecular Structure                  14
Understanding Chemical Formulas
Subscript Notation
                       H2O




            CA Science Standards #1 Atomic and
 7/8/2011   Molecular Structure                  15
Understanding Chemical Formulas
Subscript Notation
                           H2O


            2 Hydrogens



                CA Science Standards #1 Atomic and
 7/8/2011       Molecular Structure                  16
Understanding Chemical Formulas
Subscript Notation
                       H2O                       Chemists don’t
                                                  write 1’s in a
                                                    formula
                             1 Oxygen



            CA Science Standards #1 Atomic and
 7/8/2011   Molecular Structure                                17
Understanding Chemical Formulas
Coefficients

                         3 H2O                         3x2 (math class)


            coefficien               coefficien
            t                        t



                  CA Science Standards #1 Atomic and
 7/8/2011         Molecular Structure                                 18
Understanding Chemical Formulas
Coefficients
                   3 H2O
The 3 can mean there are 3 molecules of
water.
                                                 Total of 9 atoms
3 x 2 = 6 hydrogen atoms
3 x 1 = 3 oxygen atoms


            CA Science Standards #1 Atomic and
 7/8/2011   Molecular Structure                                19
Practice:
How many atoms are there in…
CH4           CH4 = 5

NH3           NH3= 4

C6H12O6       C6H12O6= 24
Structural formula
A structural
formula shows how
atoms are joined by
covalent bonds to
form a molecule of
the compound.
Empirical Formula vs Molecular Formula
(Honors)
  Empirical Formula = smallest whole number ratio of
   atoms in a compound
  Molecular Formula = some multiple (x 1, x 2, x 3, etc) of
   the empirical formula that has the correct total
   number of atoms in the compound

            Empirical             Molecular
               H2O                  H2O
              CH2O                C6H12O6
             C2H4Cl                C4H8Cl2
 Acids donate      H +

Hydrochloric Acid
HCl(aq)      + H2O(l)     H3O+(aq) + Cl-(aq)

Acetic Acid (organic acid, -COOH)
CH3COOH(aq) + H2O(l) H3O+(aq) + CH3COO-(aq)
Water + Proton  Hydronium Ion




 water       proton
hydronium ion
Bases accept H+ or make OH-
BASES are substances that dissociate in
water and form [OH-] hydroxide ions...
    NaOH(s)     Na+(aq) +      OH- (aq)

Also… BASES accepts H+ ions

(ammonia) :NH3   + H+  [NH4+]
ammonium
Nitrogen Bases (:N)
The “N” has an extra pair of electrons
(:N) that is negative and attracts the
proton (H+) +
    :NH3 + H      [NH4] ammonium ion
                          +
Nitrogen Bases (:N)
Hydrogen Bonds
 Hydrogen is attracted to the elements:
    Nitrogen (N)
    Oxygen (O)
    Fluorine (F)
 This hydrogen bonding has effects in protein structure
 (helix and pleated sheet), nucleic acid structure(DNA
 helix), and lipid “head” interactions (lipid bilayer
 formation)
Equal Acids and Bases Neutralize

Acid     Base            Water
  H+(aq) + OH-(aq) HOH H2O(l)
                - Or -
H3O+(aq) + OH-(aq) 2HOH 2H2O(l)
Buffers
Buffers are substances that
stabilize the pH to a particular
amount and resist changes
from additional acid or base

Ex: PeptoBismol, Alkaselzer,
Mylanta
pH scale
pH scale: a measure of the hydrogen ion
concentration in a solution.

The pH scale has a range of 0 – 14.
if the pH is <7 the solution is acidic
if the pH is >7 the solution is basic
if the pH is = 7 the solution is neutral
..Ph LAB Results
  Substance         Color    Acid or Base
HCl           Red           Acid
dH2O          Purple        Neutral
NaOH          Green         Base
Windex
Vinegar
Soda
Lime
Lemon
Cascade
Oil
Water molecule? Or…
PROPERTIES OF WATER
             1. Polarity:
                 Positive side & Negative
                 side of the molecule
             2. Hydrogen Bonding: surface
                 tension,
                 cohesion,
                 adhesion,
                 capillarity,
                 high boiling point,
                 dissolves with other polar
                 compounds, attracted to
                 elements N,O,F
Polarity means separation of
positive(+) & negative(-) charges
              The electrons spend more
               time around the OXYGEN
               than they do around the
               HYDROGENS.


              OXYGEN is ( - )
              HYDROGENS are (+)
Because of it’s polarity… water is
a great solvent and dissolves
many substances!

                  Sugars
                  Proteins
                  Ionic
                   compounds
                   ex. Table salt(NaCl)
Water surrounds Ions and causes
dissolving!
HYDROGEN BONDING
            Holds water
             molecules together.
            Bond is between the
             + hydrogen atom in
            one molecule and a -
            oxygen atom in
            another molecule.
COHESION water-water bonds.



   Jesus lizard        Water Strider



       The surface tension of water
       allows for these two miracles.
                                    Adhesion
ADHESION attractive force between    of water
unlike substances                   molecules
                                      to the
                                      xylem
                                     in these
                                       Giant
                                     Sequoia
                                    trees lets
                                      it rise
                                    275 ft.by
                                     capillary
                                      action.
Capillarity or capillary action
is the rising of water up the tree from roots to leaves.
WATER IS A GREAT TEMPERATURE
MODERATOR
 Water is kept as a liquid because of hydrogen bonds.
 It takes a lot of energy to break these bonds to cause
  water to boil or evaporate.
 Water absorbs a lot of heat energy.
WATER BOILS AT A HIGHER
TEMPERATURE THAN ALCOHOL.
WHY?




               Water is MORE
               polar & has more
               hydrogen bonds.
Enzyme animations
 http://science.nhmccd.edu/BioL/dehydrat/dehydrat.h
  tml
 http://highered.mcgraw-
  hill.com/sites/0072507470/student_view0/chapter25/a
  nimation__enzyme_action_and_the_hydrolysis_of_su
  crose.html
 http://www.tvdsb.on.ca/Westmin/science/sbioac/bioc
  hem/condense.htm
Key Vocabulary: Monosaccharides, Dissacharides,
Polysaccharides, Glucose, Maltose, Cellulose, Starch, Glycogen
Monomers & Polymers
             MONOMERS are
              simple molecules
              used to construct
              larger carbon
              compounds called
              POLYMERS.


             BOX CAR = monomer
             TRAIN = polymer
How do we build polymers from
monomers?
Dehydration Synthesis

How do we break down
polymers into monomers?
Hydrolysis
Dehydration Synthesis
HYDROLYSIS splitting of a polymer by
adding a water molecule.
  Chemical          Macro-
building block      molecule
 (monomer)         (polymer)
simple sugars    carbohydrates
(ex. glucose)

Amino acids        proteins
 (20 types)

 Fatty Acids,        lipids
  Non-polar
hydrocarbons
 Nucleotides     nucleic acids
  (A,T,G,C)      (DNA, RNA)
CARBOHYDRATES
•Monomer = monosaccharide
Ex. glucose, fructose, galactose
•Polymer = polysaccharide
Ex. glycogen, starch, cellulose
Glucose
 The corners of the
  glucose hexagon have
  Carbon
 This is how organic
  structural formulas are
  drawn.

C6H12O6
Maltose, a dissacharide
 Polysaccharides: Starch, cellulose,
 glycogen(stored in liver)


                        STARCH




Liver stores glycogen            CELLULOSE
CARBOHYDRATES
 Made of C, H, & O.
 Ratio is 2 hydrogens:1 oxygen
 The number of carbons varies.
 Can exist as monomers or polymers.
     1. Monosaccharide (single sugar)
     2. Disaccharide (double sugar)
     3. Polysaccharide   (3 or more)
ISOMERS (honors only)
are molecules with the same molecular formula
but different shapes.
                         C 6H 12O6
                         Glucose (used for cell
                          energy)
                         Fructose (fruit sugar)
                         Galactose (milk
                          sugar)
LIPIDS
•Monomer = fatty acid
Ex. Palmitic acid, linoleic acid
•Polymer = complex combo
Ex. Triglyceride, phospholipid, wax & steroids
 FATTY ACIDS
Water              2 SIDES:
fearing            An unbranched carbon chain (12-
                     28 carbons) at one end
                   That is HYDROPHOBIC
                   water fearing

                   And a -COOH carboxyl group at
                    the other end
                   That is HYDROPHILLIC
                   water loving
          Water
          loving
LIPIDS (fats) long-term light weight
energy storage & structure
phospholipid




                      phospholipid bilayer
Phospholipid Bilayer
Other Phospholipid Arrangements
                      Heads are polar
                      Tails are
                       nonpolar
                      Heads come
                       together and
                       tails come
                       together.
PHOSPHOLIPIDS
Two fatty acids joined
 by a molecule of
 glycerol.
A double layer of
 phospholipids
 provide a stable and
 effective barrier for
 cells.
WAXES
Long fatty acid joined
  to a long alcohol
  chain.
Highly waterproof
Protective coating in
  plants and animals.
LIPIDS large, nonpolar, organic molecules that
don’t dissolve in water.


                            C,H, O but with a
                             higher ratio of
                             carbons & hydrogen
                             than carbohydrates.
                            Carbon-Hydrogen
                             bonds store energy.
  saturated vs.
  unsaturated
Saturated means each carbon is “full of hydrogens”.
BAD FOR YOUR HEALTH
(beware of hydrogenated products like margarine,
  shortening and CRISCO)

Unsaturated means the carbons have some double
 bonding and fewer hydrogens.
Best = polyunsaturated fats
These may lower your cholesterol!!! GOOD FOR YOU
COMPLEX LIPIDS
         TRIGLYCERIDE
         3 fatty acids + 1 glycerol
         Saturated ones have a high melting
            points & solid at room temperature-
            shortening.
         Unsaturated ones have lower melting
            points, are liquid at room temp and
            are found in plant seeds and fruits.
Key Vocab: Amino Acid, Peptide Bond, Primary Structure/linear
sequence, Amino, Carboxyl, Denature, Enzyme
STEROIDS
            Four fused carbon rings
             with various functional
             groups attached.
            Not made of fatty acids.
            Many animal hormones
             are steroids.
            Ex. Cholesterol,
             testosterone,
             progesterone etc.
Made from only the finest amino acids1
  PROTEINS
•Monomer = amino acid
Ex. Glycine, Alanine, Arginine,
Tryptophan
Wednesday, October 20, 2010
 Warmup today: Draw an amino Acid and label the
  parts!!
 Lecture: Protein Structure and Enzymes (oh yes, there
  is waaaay more stuff to know!) :-P
 Nucleic Acids
 Done and Done
Amino Acids are like Barbie® Dolls,
Same body, different clothes
Amino Acids make proteins
             4 Parts:
              hydrogen -H
              carboxyl (acid) -COOH
              amino group (base) -NH2

              R group, changes like the
              “clothes” (20 types for 20
              essential amino acids)
Dipeptide formation
Amino acids form peptide bonds




                     and HOH
STRUCTURE OF PROTEINS
is due to interactions of the R groups.
                                    PRIMARY
                                      chain
                                   SECONDARY
                                    Loop, sheet
                                    TERTIARY
                                    3-D clump
                                  QUATERNARY
                                  Two or more 3D
                                      proteins.
  Protein Structure
 Primary = amino acid chain
 Secondary = alpha(a)helix
  or beta(b)pleated sheet
 Tertiary = same strand, with
  alphas and betas twisting
  around each other
 Quaternary = separate
  strands connecting
  (Hb,hemoglobin
  made of 2a, 2b)
a-Helix and b-sheet
Oragami:
an example
of
structure
and
function
O2
LIGH
T
Hemoglobin
Peptides, Polypeptides, Protein
 Peptides are short (2-15) amino acids in length
 Polypeptides or proteins are made of several amino
  acids (16+) amino acids
    Insulin(hormone)
   Actin(muscle protein)
   Myosin(muscle protein)
   Fibrin(clotting fibers)
   Melanin(protects DNA from UV radiation)
   Enzymes (too many to list!!)
Insulin
Antibodies
     Antibodies Labeled with red-orange–
fluorescent Alexa Fluor® attaching to neuronal
         proteins, identifying proteins
Fibrin – making a blood clot

Red Blood Cells
trapped by fibrin
 Carboxyl and Amino Chemistry

 Carboxyl Group
 loses H+ (acid)

 Amino Group
 grabs H+ (base)
Amino Acids make proteins
               Ex. Skin, muscles, hair,
                enzymes, and some
                hormones.
               20 “essential” amino acids
                  hydrogen -H
                  carboxyl (acid) -COOH
                  amino group (base) -NH2
                  R group (20 types)
Proteins can be affected by
temperature
Proteins are affected by pH
Proteins , temperature and pH
 Proteins work at an optimal
  Temperature & pH. Some proteins
  work over a small range of
  temperatures and a small range of pH.
 If you go too far with temperature, or
  pH, the proteins become
  DE-NATURED, like a cooked egg
Fight Club..the lye scene…
 Base hydrolyzing
 protein on skin
Key Vocabulary: Enzyme, Catalyst, Active Site, Denaturing,
Inhibition*, Effect of pH, Effect of Temperature, Effect of
Substrate concentration
Enzymes = organic catalysts
1. Organic, meaning Carbon-based
2. Catalyst, any substance that speeds up a
   chemical reaction
3. Enzymes are made of Protein
4. Named with –ase ending
  1. Ex: Maltase, Protease, Lipase
5. Enzymes are recycled and react over and
  over
Enzymes react with Substrates




Substrates can be monomers,
disaccharides, proteins, DNA, anything
that attaches to an enzyme.
ENZYME:
Lock ‘n Key

               LOCK & KEY Model
               If the shape is not
               correct, no reaction
               will occur
Enzyme: Induced Fit

Enzyme flexes,
bends to fit the
substrate

                   Enzyme
Enzyme Topics (Honors)
 Co-enzymes
 Inhibitors
 Enzyme Kinetics
Coenzymes: the vitamins
             Molecules that work with
              enzymes to make chemical
              reactions happen
             Not made of protein
             Example Vitamin B12 is a
              water soluble vitamin with
              a key role in the normal
              functioning of the brain
              and nervous system.
 Coenzymes
Substrat
e
           Enzyme




  Coenzyme
Enzymes , temperature and pH

 Enzymes work at an optimal
  Temperature & pH. Usually enzymes
  work over a small range of
  temperatures and a small range of pH.
 If you go too far with temperature, or
  pH, the enzyme stops working, they
  become DE-NATURED
 Enzymes Continued
 Enzymes work on a specific substrate
  (chemical like water, glucose, fatty acids,
  proteins, amino acids, nucleic acids etc..)
 Enzymes are RECYCLED, they are used again
  and again.
 But if you give the enzyme too much substrate,
  then you fill all the active sites and the
  enzyme cannot process more substrate
Enzymes saturation w/ substrate
Non-competitive Inhibitor
Competitive Inhibition
 Neurotoxins, atropine
http://faculty.washington.edu/chudler/weap.h
tml Normal         Inhibitor      Atropine
                (nerve agent)    injection
DIGESTIVE ENZYMES
              Amylase- breaks
               carbs to sugar
              Peptidase- breaks
               peptide bonds…
               breaks proteins down
               into amino acids.
              Lipase- breaks lipids
               apart.
Key Vocabulary: Hydrogen Bonds, Nucleotide, DNA, RNA
NUCLEIC ACIDS
•Monomer = nucleotide
Ex. Adenine, Thymine, Cytosine, Guanine, Uracil
•Polymer = double strand or single strand
Ex. DNA or rRNA, mRNA, tRNA
DNA… twisted ladder, spiral
staircase, double helix
                  THE sugars and
                   phosphates make the
                   “uprights” of the ladder.
                 (covalent bonds)
                  The nitrogenous bases
                   make the “rungs” of the
                   ladder.
                 (hydrogen bonds)
                  STORES information
                   used in the manufacture
                   of proteins.
NUCLEOTIDES are the basic
building block
           All contain a sugar (ribose or
             deoxyribose) and a phosphate… the
             nitrogen containing base can differ
           - Adenine
           - Cytosine
           - Guanine
           - Thymine

           DNA’s sugar is DEOXYRIBOSE
           RNA’s sugar is RIBOSE
                DNA
NUCLEIC ACIDS   mRNA
                tRNA
                rRNA
ATP adenosine tri-phosphate
                Energy molecule


                Energy is stored in
                 the bonds between
                 the phosphate
                 groups.
ATP
ATP ADP +Pi +Energy
ATPase
22 September 2008
 Warmup (15): Finish water lab
 Collect Chapter 2 Cornell Notes
 Objectives: familiarize yourself with molecular
 structure, and molecular formulas of organic
 molecules
Friday, July 08, 2011
 Journal Question 4:
    What are some examples of polysaccharides?
    What foods are rich in polysaccharides?
    Why does alcohol cause you to gain weight (2 reasons)
 Topic: Lipids, Proteins, Enzymes (part 1)
 LAB: Potato Peroxidase lab
 HW: Read Marathon Runners Journal start at the
  beginning “FAT”and answer questions (1-20)
Friday, July 08, 2011
 Journal Question:
    What places does pH play an important role?
    What is a peptide bond?
    What is a dipeptide?
 Topic: Lipids, Proteins, Enzymes (part 1)
 HW: Read Marathon Runners Journal start at the
  beginning “FAT”and answer questions (1-20)
Monday, October 18, 2010
 Warmup = What are 3 types of polysaccharides?
 What is a triglyceride made of?
 What does the biuret test for?
 What does Benedict solution test for?
 Today = Protein Structure!
 HW = Marathon Runner Article
Friday, October 22, 2010
 Warm up: What is an enzyme made of?
 What is denaturing?
 What is the structure of a peptide bond?
 Topic: Enzymes
 Lab: Enymes
 HW: Rewrite Lab in composition book and outline
 notes (Cornell style for Chapter 3)
Nutrient Lab 1
 Purpose: To test different foods for nutrients: proteins,
  carbs, lipids, etc…
1 October 2008
 Hand in homework – Lab Write up Liver Enzyme lab
 Movie: Chemistry at work
 Notes: Biochemistry
 Homework: Chapter 3 Notes Cornell style, and answer
 p 62 #1-20, write out questions and answers
Monday, October 12, 2009
 Warmup: What are some examples of polysaccharides?
  Which one is stored in animals? What part of the
  amino acid is acidic?
 Silent Sustained Reading (SSR), Article: Marathon
  Runner, do Questions 1-33
\Lecture: Proteins and Enzymes
 Homework, Finish Article and put all questions in
  comp book!!
Tuesday, October 19, 2010
 Warmup:
    What kind of molecules do cells use FIRST for energy
     (fat or sugar)?
    What does anaerobic respiration refer to?
    What is glycogen?
 Today! Notes on Carbs and Lipids
 HW: Finish the Marathon Runner article.

				
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