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					            Fields of Chemistry


   Inorganic                       Organic

• All molecules in organic chemistry must contain
  carbon – in an organified manner – which
  basically says you need some hydrogens- thus
  organic chemistry is a “Hydrocarbon” chemistry

• CO2 contains carbon – but since it does not
  contain hydrogen – it is inorganic
               Biochemistry


   Animal                               Plant


Human Other Animals

Since our focus is on human biochemistry – we
  will discuss the major biochemical molecules
carbohydrates, lipids, proteins and nucleic acids
   The Carbohydrates, Lipids, Nucleic
  Acids have two main commonalities

(1) a monomer to polymer relationship
(2) Interaction of Water into the chemical
  reactions

Organic Chemistry is a covalently bonded
 chemistry – thus all the chemical bonds
 joining monomers are covalent bonds
Monomer to Polymer Relationship
• A monomer is as individual unit capable of
  repeat
• The individual unit is a molecule itself
• The monomers chemically bond together to
  form “polymers” – the repeated unit
• Monomer of carbohydrate is termed a
  monosaccharide (glucose is an example)
• Monomer                     Chemical Bond
•           Polymer
•
  Interaction (Insertion) of Water into the
             chemical reactions
                                  H HO

• H20 Inserted -- result water molecule splits and
  one molecule gets the H and other the OH

• If a molecule of water is introduced into the chemical
  bond it will split it apart (hydration decomposition or
  hydrolysis decomposition)
    Interaction (Removal) of Water into the
               chemical reactions
                                H HO

•                  result        H20 removed

• -- result water molecule reformed and chemical
  bond reformed between the monomers. This is
  called dehydration (remove water) synthesis
  (anabolic process)
                 Carbohydrates
• Carbon, hydrogen, and oxygen are in 1:2:1 ratio.
• Most important as source of energy.
• Monosaccharide – simple sugar. 3-7 carbon atoms.
  – Triose – 3 carbons
  – Tetrose – 4 carbons
  – Pentose – 5 carbons
  – Hexose – 6 carbons
  – Heptose – 7 carbons
• Glucose is a hexose
                   Glucose
• May form straight chain or a ring structure.
• Ring is more common in human body.
          Carbon – Why for life?
• Carbon has an atomic number of 6 – with 4
  electrons in is outer energy level – thus it
  needs four more electrons. Carbon can
  combine covalently with 4 atoms to give it its
  4 electrons. The fact that one carbon atom
  can combine with so many atoms – gives it
  tremendous diversity – thus the basis of life
  on this planet.      x2
•                  x 1 C x3
•                      x4
     Carbon likes to bond to Carbon
           Carbon Backbone
• Though carbon can bond to 4 different atoms
  – it generally likes to bond to itself forming a
  “carbon backbone”

                C C C C C C
When I quickly draw a ring structure – the corners
always mean carbon unless I put some other atom
                     there.
 Nomenclature Naming of Organic Compounds
• In an organic chemistry course this subject would be,
  in detail, discussed – but it is beyond the scope of
  this course.
• Just for example
• How many carbons? Prefix - meth 1 eth 2 prop 3 but
  4 pent 5 hex 6
• Do you have double covalent bonds present in the
  molecule? Suffix – ane if no double bonds, ene if
  double bonds
• C C C                 versus C C         C
• Propane                         Propene
                    Isomers
• Molecules with the same molecular formula but a
  change in structural formula

• C6H12O6 is the formula for glucose, fructose and
  galactose – the atoms are arranged differently in
  3 –D space for each of those molecules

• Just like in our large world – shape makes a
  difference – so is the case in the molecular world
  – the arrangement of atoms in 3 –D space defines
  the molecule – switch the atoms around in the
  molecule and you form a new molecule
                 ISOMERS
• The body usually treats different isomers as
  distinct (different) molecules.
• Simple sugars such as glucose and fructose are
  isomers.
• Fructose is a hexose found in most fruits and
  in secretions of the male reproductive tract.
• So, separate enzymes and reaction sequences
  control its breakdown and synthesis.
          Types of Isomers

• Structural Isomers
• Geometric Isomers (Cis-Trans)
• Optical Isomers
            Monosaccharide
• The monomer (individual molecule capable of
  repeat) of a carbohydrate is termed a
  “Monosaccharide”
• Its empirical formula is CH2O
• The most notable monosaccharides
  glyceraldehyde (3-carbon carbohydrate),
  ribose and deoxyribose (5-carbon
  carbohydrate, glucose, galactose and fructose
  (6-carbon carbohydrate)
  Bonding Carbohydrate monomers together
• Monosaccharides bond together by the
  removal of a water molecule (dehydration
  synthesis) to form a covalent bond between
  the two monosaccharides known as a
  “glycosidic bond”
• When bond two monosaccharides together
  termed a disaccharide, when join 3 – 10
  together termed an Oligosaccharide – more
  than 10 together – termed a polysaccharide
           Common Disaccharides
• Sucrose – table sugar (glucose alpha 1,2 to
  fructose)
• Maltose – in beer (glucose alpha 1,4 to glucose)
• Lactose – in milk (galactose beta 1, 4 to glucose)
              Disaccharides
• Most foods contain disaccharides, but all
  carbohydrates except simple sugars must be
  broken down by hydrolysis before they can
  provide useful energy.
• Most commonly used in junk foods and
  candies, sodas.
                  Oligosaccharides
• Carbohydrates with 3 – 10 monosaccharides bonded
  together

• Oligosaccharides are often found as a component of
  glycoproteins or glycolipids and as such are often
  used as chemical markers, often for cell recognition.

• An example is ABO blood type specificity. A and B
  blood types have two different oligosaccharide
  glycolipids embedded in the cell membranes of the
  red blood cells, AB-type blood has both, while O
  blood type has neither.
             Polysaccharides
• Carbohydrates consisting of greater than 10
  monosaccharides bonded together
• Food wise some are termed the “starches”
  and one is termed “fiber”
• Their purposes are either for
  (1) Storage of energy (glycogen, amylose,
  amylopectin) or
  (2) Structure (Cellulose, chitin)
            Polysaccharides
• Can be straight chained or highly branched.
• Starches are glucose-based polysaccharides.
• Most starches manufactured by plants.
• Most starches can be broken down by human
  digestive tract.
• Cellulose is a polysaccharide that humans
  cannot break down.
• Provide bulk for digestive purposes.
STARCH
                 Glycogen
• Animal starch
• Branched polysaccharide composed of
  interconnected glucose molecules.
• Does not dissolve in water.
• Liver and muscles manufacture and store
  glycogen.
                     Lipids
• Contain carbon, hydrogen, and oxygen, but not in
  same ratio as carbohydrates.
• In general, contains much less oxygen.
• May also contain phosphorous, nitrogen, or
  sulfur.
• Most lipids are insoluble in water, so there are
  special transport mechanisms to carry them in
  the blood.
                    Lipids
• Form structural components of all cells.
• Important as energy reserves.
• Lipids provide twice the energy gram for gram
  as carbohydrates.
• Fat: 1 gram = 9 calories
• Carbohydrates: 1 gram = 4 calories
                   Lipids
• Account for 10 – 12 percent of body weight
  (normal or average),
• We will consider 5 types of lipids:
• 1. fatty acids
• 2. eicosanoids
• 3. glycerides
• 4. steroids
• 5. phospholipids and glycolipids
Unsaturated Fat
Solid Fat versus Liquid Fat at Room Temperature
                Fatty acids
• Long carbon chains with hydrogens attached.
• One end of the chain ALWAYS has a carboxylic
  acid group attached to it.
Typical fatty acids. Note the carboxylic acid end.
Carboxylic acid: CO2H
                Fatty acids
• The name carboxyl should help you remember
  that a carbon and hydoxyl (-OH) group are in
  it.
• The end opposite the carboxylic acid end is
  the hydrocarbon “tail”.
• When a fatty acid is placed in solution, only
  the hydrophilic carboxyl end associates with
  water molecules.
• The rest of the chain is hydrophobic.
                Fatty acids
• Saturated – each carbon atom has four single
  covalent bonds.
• Unsaturated – Some of the carbon – carbon
  bonds are double bonds, thus reducing the
  number of hydrogens.
• Monounsaturated – one double bond in the
  molecule.
• Polyunsaturated – numerous double bonds in
  the molecule.
         Fatty acids and Health
• Both saturated and unsaturated fats can be
  broken down for energy.
• Large amounts of saturated fats increases risk
  of heart disease.
• Current research suggests monounsaturated
  fats may be more effective than
  polyunsaturated fats in lowering risk of heart
  disease.
        Fatty acids and Health
• When margarine and vegetable shortening
  (CRISCO) are manufactured from
  polyunsaturated fats.
• Hydrogen is added to break double bonds to
  make the fat more solid (for baking,
  palatability, etc.), trans fatty acids are
  produced, which increase risk of heart
  disease.
         Fatty acids and Health
• A carbon in a fatty acid molecule is numbered
  beginning at the carboxylic acid end.
• The last carbon in the chain is called the
  “omega” carbon.
• So, if you have a double bond three carbons
  before the omega carbon, you have an
  “Omega-3 fatty acid”
Cis versus Trans Fatty Acids
                 Eicosanoids
• Lipids derived from arichidonic acid.
• Arachidonic acid cannot be synthesized by the
  body, so we have to get it through diet.
• Two major classes of eicosanoids:
  – Prostaglandins
  – Leukotrienes

  Virtually all tissues synthesize and respond to
    prostaglandins, so lekotrienes will be talked about
    later.
              Prostaglandins
• Short chained fatty acids that have 5 of their
  carbon atoms arranged in rings.
• Coordinate and direct cell activities.
• Powerful and effective in small quantities.
• Examples: released by damaged tissue to
  stimulate pain receptors.
• Start uterine contractions in birthing process.
Prostaglandins
              Prostaglandins
• Usually do not travel through circulatory
  system to reach target cell.
• So prostaglandins are called local hormones.
                 Glycerides
• Individual fatty acids cannot be strung
  together in a chain like the simple sugars.
• They can be attached to another compound
  called glycerol.
• The result is a lipid call a glyceride.
• A dehydration synthesis can produce a
  monoglyceride which is glycerol plus one fatty
  acid.
                  Glycerides
• Each additional reaction can produce a
  diglyceride (glycerol plus two fatty acids) or a
  triglyceride (glycerol plus three fatty acids).
               Triglycerides
• Known as neutral fats.
• Have 3 important functions:
         Triglyceride function 1
• Fatty deposits in body are energy reserves.
• In times of need, the triglycerides are
  disassembled to yield fatty acids that can be
  broken down to form energy.
         Triglyceride function 2
• Fat deposits under skin serve as insulation.
• Heat loss through a layer of lipids is about
  one-third that of other tissues.
        Triglyceride function 3
• Fat deposits around organs provide cushioning
  and protection.
                Triglycerides
• Stored in body as lipid droplets within cells.
• These absorb and accumulate lipid-soluble
  drugs, vitamins, or toxins.
• Good and bad: Store vitamins A, D, E and K
• Store pesticides such as DDT.
• Marijuana Is A Fat Soluble Substance
  Function of Cholesterol and other Steroids
1. Cholesterol is required to build and maintain cell
   membranes.
2. Within the cell membrane, cholesterol also
   functions in intracellular transport, cell signalling
   and nerve conduction.
3. Cholesterol is an important precursor molecule
   for the synthesis of Vitamin D and the steroid
   hormones, including the adrenal gland
   hormones cortisol and aldosterone as well as
   the sex hormones progesterone, estrogens, and
   testosterone and their derivatives.
                 Cholesterol Structure
Cholesterol is a sterol type steroid - are also known as
steroid alcohol. When a steroid has an OH (hydroxyl)
 group at the 3-position of the A-ring – it is termed a
                          sterol.
Cholesterol
   Where does cholesterol come
             from?
• Obtained from 2 sources:
  – Absorption from animal products in diet.
  – Synthesis within the body.

  There is a strong link between high cholesterol
    intake and heart disease.
  Sice body makes cholesterol, it is sometimes difficult
    to lower cholesterol levels only with diet.
          Types of cholesterol
• There are two types of cholesterol: "good"
  and "bad." It's important to understand the
  difference, and to know the levels of "good"
  and "bad" cholesterol in your blood. Too much
  of one type — or not enough of another —
  can put you at risk for coronary heart disease,
  heart attack or stroke.
          Types of cholesterol
• HDL is the "good" cholesterol which helps
  keep the LDL (bad) cholesterol from getting
  lodged into your artery walls. A healthy level
  of HDL may also protect against heart attack
  and stroke, while low levels of HDL (less than
  40 mg/dL for men and less than 50 mg/dL for
  women) have been shown to increase the risk
  of heart disease.
           Types of cholesterol
• The 4-ring region of cholesterol is the
  signature of all steroid hormones (such as
  testosterone and estrogen). All steroids are
  made from cholesterol.
• The combination of the steroid ring structure
  and the hydroxyl (alcohol) group classifies
  cholesterol as a "sterol." Cholesterol is the
  animal sterol. Plants only make trace amounts
  of cholesterol, but make other sterols in larger
  amounts.
          Types of cholesterol
• Because cholesterol contains both a water-
  soluble region and a fat-soluble region, it is
  called amphipathic.
• Cholesterol, however, is not water-soluble
  enough to dissolve in the blood. Along with
  fats and fat-soluble nutrients, therefore, it
  travels in the blood through lipoproteins such
  as LDL and HDL.
          Types of cholesterol
• HDL and LDL stand for "high-density
  lipoprotein" and "low-density lipoprotein."
  VLDL stands for "very low-density
  lipoprotein," IDL stands for "intermediate-
  density lipoprotein" and Lp(a) stands for
  "lipoprotein (a)."
                      LDL
• LDL that does not get taken up into cells tends
  to oxidize. The polyunsaturated fatty acids
  (PUFA) in its membrane get damaged by free
  radicals, and then they proceed to damage the
  protein in the surface, and finally the fatty
  acids and cholesterol in the core.
• Once LDL oxidizes, it can invade the arterial
  wall in areas that experience disturbed blood
  flow, like the points were arteries curve or
  branch.
                     LDL
• These areas, especially in people who do not
  exercise enough, are permeable to large
  molecules. Oxidized lipids cause them to
  attract white blood cells and initiate an
  inflammatory cascade that produces arterial
  plaque.
                      HDL
• HDL particles can extract free cholesterol from
  cell membranes and attach it to fatty acids,
  producing cholesterol esters. They generally
  pass this off to LDL and other apoB-containing
  proteins in exchange for fats, also called
  triglycerides, and fat-soluble vitamins such as
  vitamin E. The result is that, over time, HDL
  tends to be rich in fats and vitamin E, while
  the other lipoproteins, especially LDL, are rich
  in cholesterol.
                      HDL
• HDL delivers vitamin E to the endothelial cells
  that line the blood vessel wall.
• Both HDL and isolated Vitamin E suppress the
  ability of these cells to oxidize LDL with free
  radical-generating enzymes and also suppress
  their production of inflammatory molecules
  that attract the white blood cells that invade
  the arterial wall to form arterial plaques.
                  Steroids
• Large lipid molecules that share a common,
  distinctive carbon framework.
            Steroid functions
• Regulation of sexual function. Testosterone
  and Estrogen.
• Regulation of tissue metabolism and mineral
  balance. Adrenal cortex hormones
  corticosteroids and calcitrol.
• Derivatives called bile salts required for
  normal processing and breakdown of dietary
  fats. Produced in liver and store/secreted by
  gall bladder.
    Phospholipids and glycolipids
• Structurally related.
• Body can produce both of them.
• Phospholipid – phosphate group links a
  diglyceride to a nonlipid group.
• Glycolipid – carbohydrate is linked to a
  glyceride.
GLYCOLIPID
                  Protein
• A Protein is a polymer made up of monomers
  termed “amino acids”
             Protein functions
1. Support: structural proteins create a three-
   dimensional framework for the body and
   cells.
2. Movement: contractile proteins responsible
   for muscle contraction. Related proteins
   responsible for movement of individual cells.
3. Transport: lipids, respiratory gases, minerals,
   and hormones are bound to transport
   proteins.
            Protein functions
4. Buffering: prevent dangerous changes in pH.
5. Metabolic regulation: Enzymes accelerate
    chemical reactions in living cells. Enzymes
    are very sensitive to environmental
    conditions such as pH and temperature.
    Control pace and direction of metabolic
    pathways.
6. Coordination and control: Influence
    metabolic activities of every cell in body. Can
    affect a specific function of specific organs or
    organ systems.
7. Defense: Waterproof proteins of skin, hair,
    and nails.
     •   Antibodies- protect from disease
     •   Clotting proteins – restrict bleeding
Proteins are made-up of monomers called “amino
 acids. There 20 naturally occurring amino acids.
            Structure of proteins
•   Long chains of amino acids.
•   Typical protein has about 1000 amino acids.
•   Largest proteins may have 100,000 or more.
•   Each amino acid composed of a central carbon
    atom to which four groups are attached:
    – Hydrogen atom
    – Amino group (-NH2)
    – Carboxylic acid group (-COOH)
    – Variable group known as R or side chain.
         Structure of proteins
• Different R groups distinguish one amino acid
  from another, giving each its unique chemical
  properties.
• The name amino acid refers to the presence of
  the amino group and the carboxylic acid
  group.
• AAs are relatively small, water soluble
  molecules.
POLYPEPTIDES
Amino acids join together by performing
        dehydration synthesis




                                          Figure 2.17
              Peptide bonds
• Two amino acids can be linked together by
  dehydration synthesis.
• This creates a covalent bond between the
  carboxylic acid group of one amino acid and
  the amino group of another.
• This bond is known as a peptide bond.
• Two amino acids joined together would be a
  dipeptide.
                    Peptides
•   2 AA = dipeptide
•   3 AA = tripeptide
•   Tripeptides and larger are called polypeptides
•   If have more than 100 AA, it is called a
    protein.
          Charge of a protein
• At pH of body, carboxylic acid groups of AA
  give up their hydrogens.
• When the carboxylic acid group changes from
  –COOH to –COO- , they become negatively
  charged.
• So an entire protein always has a negative
  charge and is sometimes abbreviated as Pr-
R group still free
             Structure of proteins
• The primary structure of proteins:
   – the order of the amino acids joined together to
     make the protein.
   – Using three letter abbreviations, a bit of a protein
     chain might be represented by, for example:
• gly-gly-ser-ala is the primary structure for a polypeptide
  composed of , glycine, glycine, serine, and alanine, in that
  order, from the N-terminal amino acid (glycine) to the C-
  terminal amino acid (alanine).
           Structure of proteins
• The secondary structure of proteins:
• Within the long protein chains there are regions in
  which the chains are organized into regular
  structures known as alpha-helices (alpha-helixes) and
  beta-pleated sheets. These are the secondary
  structures in proteins.
• These secondary structures are held together by
  hydrogen bonds. These form as shown in the
  diagram between one of the lone pairs on an oxygen
  atom and the hydrogen attached to a nitrogen atom:
          Structure of proteins
• The tertiary structure of proteins
  – The tertiary structure of a protein is a description
    of the way the whole chain (including the
    secondary structures) folds itself into its final 3-
    dimensional shape.
  – The tertiary structure of a protein is held together
    by interactions between the the side chains - the
    "R" groups.
          Structure of proteins
• Quaternary Structure:
  – refers to the regular association of two or more
    polypeptide chains to form a complex.
  – Multimeric proteins contain two or more
    polypeptide chains, or subunits, held together by
    noncovalent bonds. Quaternary structure
    describes the number (stoichiometry) and relative
    positions of the subunits in a multimeric protein.
  – There are two major categories of proteins with
    quaternary structure - fibrous and globular.
            Fibrous Proteins:
• fibrous proteins such as the keratins in wool
  and hair are composed of coiled alpha helical
  protein chains with other various coils
  analogous to those found in a rope.
           Globular Proteins:

• globular proteins may have a combination of
  the above types of structures and are mostly
  clumped into a shape of a ball. Major
  examples include insulin, hemoglobin, and
  most enzymes.
Primary Structure – linear sequence of Amino
 Acids (the only thing DNA codes for directly)
Secondary Structure – does the Polypeptide or protein
  have repeating regions (alpha helix or beta pleated
   sheet). Secondary structuring is held together by
                 hydrogen bonds
   Tertiary Structure – describe the 3-D fold of the
single stranded Polypeptide or Protein (held together
 by different types of chemical bonds depending on
                   location and AA
 Quaternary structure – if the protein is made-up of
   more than one polypeptide chain (strand) – the
quaternary structure is the shape of the entire protein
              (inclusive of all its strands)
Fibrous Protein (L) Globular Protein (R)
          Shape and Function
• The shape of a protein determines its
  functional properties.
• Then shape is determined by the sequence of
  the amino acids.
• If one amino acid is changed in a protein
  consisting of 10,000 or more AA , the shape
  and function are altered.
           Shape and Function
• Several cancers and sickle cell anemia are the
  result of a sigle change in the AA sequence of
  a protein.
• Tertiary and quaternary structures depend on
  the amino acid sequence and also the local
  environment characteristics.
• If temperature or pH of the surroundings
  change, it can affect the function of a protein.
           Shape and Function
• Protein shape can also be affected by
  hydrogen bonding to other molecules in
  solution.
• This is significant especially when considering
  the functions of the proteins called enzymes.
                      Enzymes
                (a Biologic catalyst)
• A catalyst is a chemical additive that accelerates a
  chemical reaction without itself being consumed
  in the reaction.
• By the catalyst not being consumed in the
  chemical reaction – it is capable on working over-
  and-over again on several reactions of the same
  kind
• An enzyme is a biologic catalyst- thus it is a
  biochemical additive that accelerates a
  biochemical reaction without itself being
  consumed in the reaction
      What does an enzyme do to the energy of
                      activation?
• It lowers the energy of activation
• Key issue: An enzyme lowers the energy of
  reaction – but it in no way donates any energy to
  the reaction.
• If an enzyme donated energy to a reaction – it
  would slowly but surely become consumed in
  the reaction - REMEMBER THE DEFINITION
An enzyme lowers the
energy of activation




                       Figure 2.20
   How does an enzyme lower the energy of
                activation?
• Before an enzyme can function as a catalyst,
  the substrates in the reaction must bind to a
  specific region of the enzyme called the active
  site.
• The tertiary or quaternary structure
  determines the shape of the active site,
  typically a groove or pocket where the
  substrates can nestle.
• There are two active site shape models –
  – Lock and Key
  – Induced Fit
Lock and Key model
            Lock and Key model
• In this model, the amino acids that make up
  an enzyme's active site in the unbound state
  are said to form a shape that exactly matches
  the shape of the substrate. Thus, the substrate
  fits into this active site, just as a key fits into a
  lock whose shape is designed to match the
  key.
               Lock and Key
• However, the active sites of many enzymes do
  not have a shape in the unbound form that
  exactly matches the shape of the substrate.
  The shape of the active site changes when the
  substrate binds to the enzyme, creating a
  shape into which the substrate fits.
• This is known as induced fit model.
Induced fit model
    All enzymes share three basic
            characteristics
• 1. Specificity – each enzyme catalyzes only
  one type of reaction and can accommodate
  only one type of substrate molecule.
• 2. Saturation limits – the rate of reaction is
  directly proportional to the concentration of
  substrate and enzymes. When substrate
  molecules are high enough in concentration
  that all enzymes are being used, further
  increases in substrate concentration will not
  increase the reaction rate.
         Enzyme characteristics
• Saturation limit cont. – the substrate
  concentration required for the maximum
  reaction rate is called the saturation limit.
• An enzyme reaching the saturation limit is
  saturated.
         Enzyme characteristics
• Regulation – a variety of factors can turn
  enzymes off or on in a cell in order to control
  reaction rates.
• One example is the presence of cofactors.
• Every cell has lots of enzymes, so inactivation
  and activation of these enzymes is important
  for control of cellular activities.
• The activation/deactivation is immediate.
                 Cofactors
• Ions or molecules that must bind to the
  enzyme before the enzyme can bind the
  substrate.
• Calcium, magnesium are examples
               Coenzymes
• Non-protein organic molecules.
• Vitamins are common cofactors.
  Apoenzymes and Holoenzymes
• Apoenzyme- An enzyme that requires a
  cofactor but does not have one bound. An
  apoenzyme is an inactive enzyme, activation
  of the enzyme occurs upon binding of an
  organic or inorganic cofactor.
• Holoenzyme- An apoenzyme together with its
  cofactor. A holoenzyme is complete and
  catalytically active.
                 The Imposters
              What are the inhibitors?
• Enzyme inhibitors are molecules that bind to
  enzymes and decrease their activity (slow down the
  reaction).
• The imposter (inhibitor) molecule has a shape
  similar to the real substrate - remember in the
  induced fit model -the active site does not exactly
  fit the substrates – like in the old Lock and Key
  model – thus look-alike imposters could enter the
  active site
• Enzyme inhibitors can be bad – like taking a
  poison
• Enzyme inhibitors can be good – for example
  some of the antibiotics – they block a vitally
  needed enzyme in the pathogen’s
  biochemistry – but we don’t have the same
  enzyme -so it kills the pathogen but does not
  bother us.
           Types of Inhibitors
Competitive (attached to the active site)
• Reversible (transiently attaches to AS)
• Non-reversible (permanently attaches to AS)

Non-competitive (Attaches to other sites on
                   the enzyme)
Competitive Inhibition
Non-reversible (Irreversible) Inhibition

             Note how the irreversible inhibitor locks on
             by strong covalent bonding.
          Non-competitive Inhibition

 Substrate
                              Active Site




Allosteric site where
Non-competitive
Inhibitor binds
                   Enzyme Involvement in Disease
Virtually every chemical step of metabolism is catalyzed by an enzyme.
Disorders of these enzymes that result from abnormalities in their genes are
known as inborn errors of metabolism.

Phenylketonuria (PKU) is the most common disorder of amino acid metabolism,
and it is a paradigm for effective newborn screening. Phenylalanine is an
essential amino acid (meaning that it cannot be synthesized but must be taken
in through the diet). The first step to its breakdown is the phenylalanine
hydroxylase reaction, which converts phenylalanine to another amino acid,
tyrosine. A genetic defect in the phenylalanine hydroxylase enzyme is the basis
for classical PKU. Untreated PKU results in severe mental retardation, but PKU
can be detected by screening newborn blood spots, and the classical form can
be very effectively treated by using medical formulas that are limited in their
phenylalanine content.
          Enzymes and disease
• Alkaptonuria is a disorder of tyrosine
  breakdown. The intermediate that
  accumulates, called homogentisic acid, can
  polymerize to form pigment that binds to
  cartilage and causes progressive arthritis and
  bone disease and that also is excreted to
  darken the urine.
         Enzymes and disease
• Tay-Sachs disease is due to a defect in the
  beta-hexosaminidase A enzyme, which
  removes a sugar from certain lipids called
  gangliosides, which build up in the lysosome.
  The disease causes neurological symptoms, an
  enlarged head, and death in early childhood.
         Enzyme denaturation
• Every enzyme works best at a narrow pH and
  temp. range.
• If temp. increases, proteins change shape and
  function deteriorates.
• Body temp. above 110 degrees F causes death
  because proteins denature (permanent
  change in tertiary or quaternary structure).
• Denatured proteins are non-functional.
         Enzyme denaturation
• Enzymes also sensitive to pH changes:
  – Pepsin breaks down proteins in stomach and
    works at pH of 2.0
  – Trypsin also breaks down proteins in small
    intestine but works at pH of 7.7
 The Nucleic Acids (DNA and RNA)
• DNA is a polymer and is our genetic material
• RNA is a polymer and assists our genetic
  material
              Nucleic acids
• Large organic molecules composed of carbon,
  hydrogen, oxygen, nitrogen, and phosphorous.
• DNA = deoxyribonucleic acid
• RNA = ribonucleic acid
                    DNA
• Determines inherited characteristics
• Encodes information to make all proteins
  needed by body
                    RNA
• Cooperate to make proteins using information
  from DNA.
       Structure of nucleic acids
• Nucleic acid is series of nucleotides linked
  through dehydration synthesis.
• Nucleotide has three basic components
  – Sugar (ribose or deoxyribose)
  – Phosphate group
  – Nitrogenous base (adenine, guanine, cytosisne,
    thymine, uracil)
 Fig. 5-27c-1

                           Nitrogenous bases
Each nucleotide
                               Pyrimidines
contains one of
these 5 NBs!



                  Cytosine (C) Thymine (T, in DNA)   Uracil (U, in RNA)

                                         RNA has cytosine , adenine, guanine
DNA has                          Purines and uracil (RNA has no thymine)
cytosine ,
adenine,
guanine
and thymine
(DNA has no
uracil)
                          Adenine (A)           Guanine (G)

                       (c) Nucleoside components: nitrogenous bases
Fig. 5-27c-2

               A nucleotide has one of these two sugars – in DNA the nucleotide
               contains Deoxyribose as the sugar ( thus Deoxyribonucleic acid )
               and in RNA the nucleotide contains ribose
               (thus Ribonucleic Acid)

                                          Sugars




                   Deoxyribose (in DNA)            Ribose (in RNA)

                (c) Nucleoside components: sugars



                      Ribose has a oxygen at the second carbon and
                      Deoxyribose does not – thus deoxy
Fig. 5-27


        5 end
                                                                                        Nitrogenous bases
                                                                                            Pyrimidines
  5C

  3C

                                                       Nucleoside

                                                        Nitrogenous
                                                            base        Cytosine (C)   Thymine (T, in DNA) Uracil (U, in RNA)


                                                                                             Purines




                                        Phosphate
                                          group        Sugar
  5C                                                (pentose)
                                                                              Adenine (A)               Guanine (G)
 3C                                (b) Nucleotide

                                                                                               Sugars
        3 end
  (a) Polynucleotide, or nucleic acid



 The third component of the nucleotide is
 the phosphate group                                                    Deoxyribose (in DNA)              Ribose (in RNA)

                                                                      (c) Nucleoside components: sugars
         Nucleic Acid Structure
• Adenine and Guanine are double ring
  structures and called purines.
• Others are single ring and called pyrimidines.
• Uracil found only in RNA, thymine only in
  DNA.
• Easy to remember that uracil “replaces”
  thymine in RNA.
         Nucleic Acid Structure
• The nucleic acids are very large molecules that
  have two main parts. The backbone of a
  nucleic acid is made of alternating sugar and
  phosphate molecules bonded together.
• When a nitrogenous base attaches to a
  pentose (ribose or deoxyribose) sugar, a
  nucleoside is formed. Nucleoside is named
  after the nitrogenous base.
                Nucleotide
• When a nucleoside combines with a
  phosphate group.
• To make a nucleic acid, dehydration synthesis
  attaches the phosphate group of one
  nucleotide to the sugar of another.
• The “backbone” of a nucleic acid is a linear
  sugar to phosphate to sugar sequence with
  the nitrogenous bases projecting to one side.
        Single Strand Design of Nucleic Acid
        Design


                  Nitrogenous Base
Sugar
Phosphate group
                   Nitrogenous Base
Fig. 5-27ab
                     5' end


               5'C

              3'C

                                                                         Nucleoside

                                                                          Nitrogenous
                                                                              base


                                                                 5'C




                                                    Phosphate    3'C
                                                      group              Sugar
              5'C                                                      (pentose)

              3'C                               (b) Nucleotide


                     3' end
              (a) Polynucleotide, or nucleic acid
  DNA Special Bonding of Nitrogenous Bases

• The DNA code (Chargaff’s rule) a purine on
  one side hydrogen bonds to a pyrimidine on
  the other side
• More specifically if Adenine is on one side it
  will hydrogen bond to Thymine on the other
  side
• If Cytosine is on one side it will hydrogen bond
  to Guanine on the other side - so
                    A           T
                    G           C
Figure 2.22a, b
Figure 2.22a
                     RNA
• Single strand of nucleotides
• Three types:
  – Messenger (mRNA)
  – Transfer (tRNA)
  – Ribosomal (rRNA)


• Each has different shape and function, but all
  3 required for protein synthesis.
                      DNA
• Double strand of nucleotide chains.
• Complementary base pairing:
  – Purine bonds with opposing pyrimidine
  – Adenine:Thymine
  – Guanine:Cytosine
                     DNA
• The two strands of DNA are anti-parallel
• If one strand is in the 3’  5’ direction – the
  other side is in the 5’ 3’ direction
       High energy compounds
• Energy in cells obtained from enzymatic
  catabolism of organic substrates.
• The energy somehow has to be “captured” so
  it can be transferred from one molecule to
  another or from one part of the cell to
  another.
• Usual method of transfer involves creation of
  high-energy bonds.
       High energy compounds
• High-energy bond – covalent bond. When
  broken down releases energy that can be used
  by the cell.
• Humans: phosphate group connected to an
  organic molecule.
       High energy compounds
• Phosphorylation – attachment of phosphate
  group to another molecule.
• High-energy compound requires:
  – Phosphate group
  – Appropriate enzymes
  – Suitable organic substrates
       High energy compounds
• Most important substrate is adenosine.
• Adenosine monophosphate (AMP) is
  phosphorylated to Adenosine diphosphate
  (ADP). This requires significant energy
  expenditure.
• Adenosine diphosphate (ADP) is then
  phosphorylate to Adenosine triphosphate
  (ATP). More energy required at this stage
  also.
      Energy conversion in cells
• ADP converted to ATP and then reverted to
  ADP.
  – ADP + phosphate group + energy ↔ ATP + H2O
• Human cells are constantly using this energy
  for metabolism, protein synthesis, and
  contraction of muscles.
• ATP is most abundant energy source in body.
         Other energy sources
• Guanosine triphosphate (GTP)
• Uridine triphosphate (UTP)
• Used in specific enzyme reactions.
                     Quiz
• 1. Carbohydrates, lipids, and proteins are
  formed from their basic building blocks by the:
• A. removal of a water molecule between the
  building blocks
• B. addition of a water molecule between the
  building blocks
• C. addition of carbon to each molecule
• D. addition of oxygen to each molecule
                       2.
•   Complementary base pairing in DNA includes
•   A. adenine-uracil; cytosine-guanine
•   B. adenine-thymine; cytosine-guanine
•   C. adenine-guanine; cytosine-thymine
•   D. guanine-uracil; cytosine-thymine
                       3
• What is the role of enzymes in chemical
  reactions?
                        4
• List three important functions of triglycerides
  in the human body.
                      5
• List seven major functions performed by
  proteins.
                    Review
• P. 67: 21 – 31
• P. 68: 6 and 7

• When finished, continue with tissue and cell
  slides. Look at them many times so you can
  recognize the different cell and tissue types.

				
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