Water and Biological Molecules by wuxiangyu


									    Chapter 3:
Water and Biological
       3.1 The Importance of Water

• Human use
  –   Drink it
  –   Cook in it
  –   Bathe in it
  –   Harness it for power
  –   Use it to dispose of wastes
  –   Swim in it
• 71% of the Earth’s surface is water
• 66% of body weight in humans
What is a Major player in Many of Life’s Processes
• Aqueous solution
• Water is the solvent breaks down the solute
  that has been put into it
• Fig. 3.1 solute NaCl + Solvent H2O
  – NaCl attracted to the polar water molecule
  – NaCl ion separate from each and become surrounded
    with water molecules
  – Na+O and Cl+H
 Effect of water molecule on NaCl

• Water
  – Surrounds the ions in order to keep them from
    getting back together
  – Keeps the ions evenly dispersed=solution
 Water structure gives it many unusual
1. Ice floats because it is less dense then water
• The cooling of water makes the water
   molecules slow their motion.
• When their motion is slowed they are able to
   form the maximum number of hydrogen bonds
   with each other.
• Result water molecules are spaced further
   apart when frozen.
2. Water has a great capacity to absorb and store
• Water is a great insulator frozen, liquid, or gas
• Due to
    –     Specific heat the amount of energy required to raise the
          substance by 1 degree Celsius.
•       Water has a high specific heat
    –     What does this mean?
          •   It takes a lot more energy to raise the temperature of water by 1
              degree Celsius.
•       Water VS Ethyl Alcohol
•       Water takes twice as much energy to raise the
        temperature by one degree.
•       As a result water releases heat only when the
        environment surrounding it is cooler.
• How is this accomplished?
  – Hydrogen bonds
     • Weak but have a huge effect when they occur in large
     • The large amount of molecules makes it harder to break
       these chemical bonds
     • These bonds give water molecules another unique
        – The ability of the water molecules to stay together.

• During plant transpiration water is brought from
  the roots to the leaves where evaporation occurs
  by the Cohesive ability of water.
3. Water’s cohesion gives it
        surface tension
•       Surface tension (water
        meets air) water molecules
        below the surface are equally
        attracted to in all direction to
        other water molecules.
    –     At the surface where water meets
          air it has no attraction to air
    –     The latter cause the “beading” of
          water droplets and allows small
          organisms to move across the
          surface w/out sinking.
What water cannot do
• There are molecules that do not
  dissolve in water nonpolar
  covalent molecules
  – Polar covalent molecule
    molecules made up of Hydrogens
    and carbons (H+C)
     • CH4 Methane, Petroleum,…
• Oils are not dissolved by water
  because it doesn’t have a
  charge for the water molecule
  to bond with
Two Important terms: Hydrophobic and
• Hydrophilic (“water-loving”) Cpds that will
  interact with water
• Hydrophobic (“water-fearing”)Cpds that do
  not interact with water
• Very important helps form cell barrier cell
3.3 Carbon is the central element in Life

• Carbon is the starting ingredient for life
• Life is based on Carbon
   – Just like baking the starting point is always flour
• Why is carbon used as a starting ingredient for life?
   – Has only 4 e- in the outter shell but needs a total of eight for
     maximum stability.
   – Obtains maximum stability by creating covalent (sharing e-)
• Organic Chemistry a branch of chemistry devoted
  to the study of cpds. That have carbon as their cnetral
   How does carbon link up with itself and
              other carbons?
Straight Chain Carbons
• Methane CH4
• PropaneC3H8
  – Carbons link together forming
    a straight chain carbon
• ButaneC4H10
  – Fuel found in cigarette lighters
  – Can have two forms
     • Isomers molecules that are the
       same in their chemical formula,
       but differ in the spatial
       arrangement of their elements
Carbon Rings
• Benzene C6H6
    –   Found in petroleum products
    –   Note the three sets of double bonds the
        atoms involved are sharing two pairs of
•   Glucose C6H12O6
    –   Blood Sugar
                    3.4 Functional Groups
• Carbons can become specialized with the addition of certain atoms
    – Functional groups a group of atoms that confers a special property on a carbon
      based molecule
    – Analogy Wrench
        • Socket wrench vs. an Allen wrench
• Ethane
    – Flammable gas
• Remove a H and add a functional group  hydroxyl
  -OH= ethyl alcohol
• Any –OH that is added to a hydrocarbon group (C-H) an alcohol is formed
• Not only has the molecular function changed but also the polarity
• The strong electronegativity of the oxygen in the –OH (hydroxyl group)
  ethyl alcohol is now polar and can bond with other charged or polar
                              •Nonpolar                                                 alcohol
                              •Flammable                                                •Polar

                   Remove a H and replace with a functional group –OH
                  3.5 Carbohydrates
• Four groups of Organic cpds
  1.   Carbohydrates
  2.   Lipids
  3.   Proteins
  4.   Nucleic Acids
• All made up of smaller subunits
  1. Carbohydrates
       • Simplest subunit glucose (monosaccharide)
       • Many monosaccharides starch (polysaccharide)
       • Monomer glucose a small molecule that can be combined
         with other similar or identical molecules to make a polymer
       • Polymer a large molecule made up of many simpler or
         identical subunits
  Carbohydrates: From Simple Sugars to

• Always contain
  – Hydrogen, Carbon, and
• Contain twice as many
  hydrogen atoms as oxygen
  – Glucose C6H12O6
  Building Blocks of Carbohydrates
• Monosaccharide simple sugars glucose
   – Glucose can bind to other monosaccharides to form complex
• Fig. 3.10
   – Maltose
   – Formed by two monomers of glucose
   – The link between the monomers is a single oxygen atom
   – The formation of Maltose requires for the removal of two
     hydrogens and 1 oxygen from two glucose molecules=Maltose
   – Note:
       • This is a reversible process
       • Functional group –OH is present
      Kinds of Simple Carbohydrates

• Monosaccharide
  – Glucose
  – Fructose
  – Deoxyribose
• Disaccharide
  – Sucrose
  – Lactose
  – Maltose
• -ose sugar
   Complex Carbohydrates are Made Up
    of Chains of Simple Carbohydrates
Polysaccharide polymers of
    –   Poly Many
    –   Saccharide sugar
    –   http://pslc.ws/macrog/kidsmac/tooncell
1. Cellulose cell wall
    –   Most abundant carb in the world
    –   Trees, cotton, leaves, and grasses
    –   In humans
         •   major source of insoluble fiber
         •   (whole grain and fresh fruits)
         •   Helps food move through the
             digestive tract
2. Chitin Arthropods, Crustaceans and
    •   Structural support
    •   Strength and shape for organisms
3. Starch Plants use for storage
    –   Potatoes, rice, carrots, and corn
4. Glycogen Animals use for storage
    – Stored in muscle cells
                                    3.6 Lipids
• Lipids
   – Insoluble in water
   – Made up of H, O, and C
        • Have more hydrogen then Carbohydrates
        • Glycerol
• Exist as;
   –   Oils
   –   Fats
   –   Cholesterols
   –   Hormones (testosterone and estrogen)
• Not a polymer
• No single structural unit is common to all lipids
• Due to their insolubility they can
   – Serve as internal containers
   – Store energy
   – Provide information
     One Class of Lipids is the Glycerides
• Glyceride:
  – Most common lipid
  – Two parts
     • Head
        – alcohol (glycerol)
     • Tail
        – fatty acida molecule found in many lipids that is composed of a hydrocarbon
          chain bonded to a carboxyl group
        – 4 22 Carbons
• Stearic Acid
  – Fatty acid found in animal fats
  – Long Fatty Acid tail
  – Head Functional Carboxyl Group COOH-
         Glycerol Triglyceride
• Triglyceride lipid molecule formed from three fatty
  acids and a glycerol
• -OH (alcohol) part of Glycerol combines with COOH-
  (carboxyl) part of fatty acid chain.= one glyceride
• Glycerol has 3 –OH+ (3 COOH + Fatty
• R=Hydrocarbon Chains (C-H)
              Triglyceride Tristearin
• 1 Glycerol +3 Stearic fatty acids= Tristearin
   – An exception to the rule
   – Normally, 1 Glycerol may have
      • 3 different types of fatty acids attached to it to form a triglyceride
      • 2 Fatty acids diglyceride
      • 1 Fatty acid monoglyceride
• Butter is composed of several fatty acids
     Saturated and
    Unsaturated Fatty
Three different types of fatty
• Palmitic
   – Saturated
   – No double bonds
• Oleic
   – Monounsaturated
   – One double bond
• Linoleic
   – Polyunsaturated
   – More then one double bond
   * Double bonds creates “kinks” in
     the molecules.
     Fatty Acids from Solids to Liquids
• Saturated (in Fatty Acids) with
   – Oils are turned into Saturated fats by adding
     Hydrogens (hydrogenation) this process
     enabled the liquid oils to be used as a solid
   – Saturated fats has been linked with heart
      • Increase the amount of cholesterol in body
      • Cholesterol lodges in the arteries of the heart
• Saturated Fatty Acid
   – No double bonds between Carbons of the
     hydrocarbon chain
• Monounsaturated Fatty acid
   – One double bond between carbon atoms
• Polyunsaturated Fatty Acid
   – Two or more double bonds between carbon
 Energy Use and
 Storage in Lipids
• Storage
   – Triglyceride
• Energy
   – Broken down to
     glycerol and Fatty
VS Carbohydrates
• Storage
   – Glycogen
• Energy
   – Glucose
    A second class of lipids is the steroids
• Steroids lipid
  molecule that has a
  central element in
  their structure, four
  carbon rings
   – Different steroids have
     different side chains
     attached to it no
 A Third Class of Lipid is the Phospholipid
• Phospholipid ( a charged
  lipid molecule composed
  – Glycerol + Phosphate
    group+ 2 Fatty acid tails
     • Phosphate group 1
       phosphorus atom surrounded
       by 4 Oxygen atoms
• Phospholipid dual nature
  – Hydrophilic head
    Phosphate (Charged=polar)
  – Hydrophobic tail  Fatty
• Phospholipids make up the
  membranes of cells
Importance of Proteins
• Almost every chemical                3.7 Proteins
  reaction that takes place in
  living things in enabled by a
  particular kind of protein
  called an enzyme
    – Each Enzyme has a particular
    – An animal cell may contain
      up to 4,000 different types of
• Other functions of proteins:
    –   Form tissues
    –   Transport molecules
    –   Allow muscles to contract
    –   Cells to move
    –   Some hormone are made
        from proteins
• If you remove water from
  the cell about half of the
  weight of a cell is
  accounted for by proteins
Proteins are made from Chains of Amino Acids
• Amino Acids Monomers of
   – Composed of 
       •   Carboxyl COOH (acid)
       •   Amine group NH2
       •   A central Carbon
       •   A side chain
   – The side chain (R) makes each amino acid
   – There are only 20 Amino Acids that make
     up all protein
       • The order of amino acids in a polypeptide
         chain makes different proteins
• Polypeptides Chain
   – 1030 Amino Acids
   – Can fold up in a specific three dimensional
     manner to form a
       • Protein
             – Made up of hundreds of amino acids strung
               up together and folded
             – Two or more peptide chains can make up
               one protein
         Shape is critical to functioning of all
    Proteins fold up in a specific way
    – Chemical forces between the Amino acids determine the three dimensional shape of a
    – Protein conformation, extremely crucial
• Insulin
    –   Released by the pancreas
    –   Moves through the bloodstream
    –   “Latches onto” to muscle cells
    –   Its presence allows glucose to get into the muscle and provide energy
    –   Able to latch onto cell by protein receptor
         • If both insulin and receptor (proteins) do not have the proper shape Glucose is not taken up
           by the muscle cell.
         • Insulin is used medically to treat some forms of diabetes mellitus.
         • Patients with type 1 diabetes mellitus depend on external insulin (most commonly injected
           subcutaneously) for their survival because of an absolute deficiency of the hormone.
         • Patients with type 2 diabetes mellitus have insulin resistance, relatively low insulin
           production, or both; some type 2 diabetics eventually require insulin when other medications
           become insufficient in controlling blood glucose levels.
          Four Levels of Protein Structures
• Primary Structure simply it
  sequence of amino acids
   – Electrochemical bonding and repulsion
     forces act on this structure and the result is a
     folded up protein
• Secondary structure once the forces
  begin to operate on the Amino Acid
   – Alpha helix corkscrew shape
   – Beta pleated sheet accordion shape
       • Silk
   – Protein can be made of one or the other or
• Tertiary structure Three
  dimensional shape
• Quaternary structure two or more
  polypeptide chains
    Proteins Can Become Undone

• PH
  – Alcohol
  – Works great as a disinfectant alters the shape of
    protein in bacteria
• Temperature
  – Raw VS cooked
  – Egg or meat
            Lipoproteins and Glycoproteins
•   Lipoproteins
    –   Combination of lipids and proteins
    –   Transport protein  fats
    –   Type depends on amount of lipid content
    –   Lipid is less dense then protein
1. High Density Lipoprotein (HDL)
    –   Carry cholesterol away from the outlying
        cells to the liver
2. Low Density Lipoprotein more
   lipids then protein
    –   Carries cholesterol to the outer lying tissues
    –   Bring about heart attacks
•   Glycoproteins
    –   Combination of proteins and carbohydrates
    –   Receptors
        •   in cells just like the insulin one
        •   Hormones
        •   Proteins released from the cell
     3.8 Nucleotides and Nucleic Acids
• Nucleic Acids
   – Information Storage devices of cells
   – Long polymers of Nucleotides
       • Each is composed of a three carbon sugar+
         nitrogenous containing base + phosphate group
• Two Types of Nucleic Acids
   – DNA Deoxyribose nucleic acid
   – RNA Ribonucleic Acid
   – Ribose sugar where 4/5 Carbons bond to a
     hydroxyl group (-OH)
   – DNA, Hdroxyl group is replaced with a hydrogen
   – RNA uses nucleotides Adenine, Uracil, Cytosine,
     and Guanine
   – DNA uses nucleotides Adenine, Thymine,
     Cytosine, and Guanine
   – RNA is a single strand of nucleotides
   – DNA consist of two nucleotide strands wound
     around each other in a double helix
•   Essays
•   Acid Rain: When Water is Trouble
•   From Trans Fats to Omega 3’s: Fats and

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