Macromolecules

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Macromolecules
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Macromolecules

• Large molecules greater than 100,000 daltons
• Polymers consist of many identical or similar
  building blocks
• Building blocks monomers with molecular weight
  500 daltons.
• Belong to 1 of 4 classes carbohydrates, lipids,
  proteins, nucleic acids.
• All classes of polymers assembled in same
  fundamental way

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MacromoleculesCarbohydrates

• Example Subunit, function and example
• Starch alpha glucose energy storage in plants
  found in grains, potatoes, corn
• Glycogen alpha glucose energy storage in
  animals liver and muscle
• Cellulose beta glucose structural carb. Found
  in cell walls paper, wood
• Chitin modified beta glucose structural
  support, arthropod exoskeleton

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Storage Carbohydrates
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MacromoleculesLipids

• Example subunit, function, example
• Fats glycerol and 3 fatty acids, energy storage
  butter, lard, seeds
• Phospholipids glycerol and 2 fatty acids and a
  phosphate group cell membranes, lecithin.
• Steroids 4 fused carbon rings, hormones
  estrogen, testosterone
• Prostaglandins ring structure and 2 fatty acids
  cause muscle contractions in labor and delivery.

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Macromolecules Proteins

• General types subunit function example
• Globular 20 amino acids catalysis, transport
  hemoglobin, myoglobin, protease
• Structural 20 amino acids support keratin
  (hair/nails), collagen (connective tissue).

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MacromoleculesNucleic Acids

• Types subunits function examples
• Deoxyribose Nucleic Acid (DNA) 4 nucleotides
  Adenine, Thymine,Cytosine,Guanine encode genes,
  chromosomes.
• Ribonucleic Acid (RNA) 4 nucleotides Adenine,
  Uracil, Cytosine, Guanine needed for gene
  expression messenger RNA, ribosomal RNA,
  transfer RNA

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Polymers
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General Principles

• All Living Organisms have the same kind of
  monomeric subunits.
• All macromolecules are assembled the same
  fundamental way
• A. Form covalent bonds between 2 subunit
  molecules
• B. An OH group is removed from 1 subunit
  and
• C. A -H atom is removed from the other
• Monomer to a polymer requires energy process is
  called dehydration synthesis or condensation
  anabolic chemical reaction.

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General Principles continued

• All macromolecules are disassembled into
  constituent subunits the same way
• A. Molecule of water is added
• Polymer changed to monomer with a release of
  energy. Name of reaction Hydrolysis catabolic
  reaction.

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Carbohydrates

• Most abundant molecules on earth e.g. cellulose
  which is a product of photosynthesis in plants
  and in algae.
• Hydrates of Carbon e.g. glucose
• C6H12O6 C6 (H2O)6
• C-H bonds yield energy when broken so ideal for
  energy storage.
• Simplest are simple sugars single sugars fuel
• a) Monosaccharides as little as 3
  carbon atoms to as many as 7 atoms 6 common. 3
  triose 5 pentose 6 hexose. Either ketone or
  aldehyde.

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Monosaccharides Simple Sugars
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Sugar in water

• In water solutions glucose and most other
  sugars form rings (1 Carbon bonds to O of 5
  Carbon) major nutrient of cells.
• e.g. glucose, fructose, galactose (fuel), ribose,
  deoxyribose (nucleic acids).

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Glucose Linear and Ring forms
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Disaccharides 2 monosaccharides joined by
glycosidic linkage

• Disaccharides are used for transport
• e.g.
• Glucose glucose maltose
• Glucose galactose lactose
• Glucose fructose sucrose

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Dissacharide Formation
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Storage Polysaccharides
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2. Storage in animals glycogen

• Glucose monomers highly branched largely
  insoluble in water greater chain length and more
  branched than starch.

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3. Structural Polysaccharides

• Cellulose most abundant organic compound on
  earth major component of cell wall.
• Found in plants confers rigidity and
  strength.
• Most animals cannot digest because of B
  glucose. Animals that can digest cellulose
  contain bacteria or protists that break B
  glycosidic linkage. E.g. termites and ruminants.

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Cellulose microfibrils
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Chitin exoskeleton of arthropods modified
cellulose (amino sugar)
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Lipids

1. Contain even more C-H bonds than carbohydrates.
2. C-H bonds are non-polar and cannot form hydrogen
   bonds with water.
3. Hydrophobically excluded by water molecules so
   they cluster together insoluble and can be
   deposited at specific locations within the
   organisms.

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(Neutral) Fat Structure

• Made up of 2 kinds of subunits
• glycerol (backbone of a fat molecule) 3 carbon
  alcohol.
• b) Fatty acids long hydrocarbon chains ending in
  a carboxyl group. O
• CH3-(CH2)n-C
• OH
• Generalized formula for a fatty acid memorize!

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Fatty Acids

• Fatty acids are also called triglycerides or
• triacylglycerol.
• Consider saturated (no double bonds) and
  unsaturated fatty acids (presence of double
  bonds).

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Saturated and Unsaturated Fatty Acids
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Fats as storage molecules

• More energy/gram
• Insoluble in water
• Take up less space
• Excellent for long term storage
• Also used for insulation and buoyancy

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Phospholipids

• Composed of glycerol, 2 fatty acids and a
  phosphate group.
• Polar head and Nonpolar tails.
• Major lipid in lipid bilayer of plasma membrane.
  
• In water, phospholipids self-assemble into
  micelle. Hydrophilic head on outside.
  Hydrophobic tail on inside.

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Phospholipids
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Phospholipid organization
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Steroid 4 fused rings e.g. Cholesterol
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• Glycerol fatty acid water glyceride
• Glyceride water Glycerol fatty acid

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1. Types Of Proteins

• Class Enzymes Function metabolism
• e.g. amylase, a digestive enzyme
  (Globular)
• polymerases, produce nucleic acids
• Class Globins Transport through body
• e.g. hemoglobin carries oxygen in blood
• myoglobin carries oxygen in muscle
  (Globular)
• Class Structural support (fibers)
• e.g. Keratin (hair, nails), collagen
  (cartilage), fibrin (blood clots). (Fibrous)
• Class Hormones regulation of body function
• e.g. Insulin (controls blood glucose
  levels) oxytocin (stimulates uterine
  contractions) Glob.

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More types of proteins

1. Movement Muscle proteins e.g. actin and myosin
   for contraction of muscle fibers. (Fibrous).
2. Storage Ion binding e.g. ferritin which stores
   iron especially in spleen casein which stores
   ions in milk. (Globular)
3. Defense Immunoglobins and toxin e.g.
   antibodies which mark foreign proteins for
   elimination and snake venom which blocks nerve
   function.(Globular)

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Structure polymers made up of 20 amino acids

• Amino acid molecule with an amino group and a
  carboxyl group R atom or atoms which make up
  the variable group. Specific to each of the 20
  amino acids.
• H R O
• N C C
• H H OH
  memorize

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Chemical classes of amino acids based on R

1. Non-polar R -CH3 folded into interior of
   protein by hydrophobic exclusion. Perfect for
   the outside of proteins that have to fit in a
   membrane (membrane channels and pumps).
2. Polar uncharged R groups with O hydrophilic.
   Perfect for outside of enzymes or to line
   tunnels for polar/ionic molecules placed in
   membranes.
3. Polar charged (Ionizable) R groups contain acids
   or bases. Hydrophilic.

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Nonpolar amino acids
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Polar Amino Acids
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Peptide Bond

• Bond between amino acids formed from dehydration
  synthesis
• or condensation reaction. Called peptide
  bond.
• Note repetitive polypeptide backbone
• N-C-C-N-C-C-N

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• Amino acid amino acid water dipeptide
• Dipeptide amino acid water polypeptide
• Polypeptide water dipeptide amino acid

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Lysozyme Ribbon and Space filled models
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Protein Structure

• 1st elucidated was myoglobin (Linus Pauling), 2nd
  was hemoglobin
• Primary structure unique sequence of amino
  acids determined by inherited information DNA
  RNA Protein

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Primary Structure of Lysozyme, 129 amino acid
sequence
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Red Blood Cells Normal and Sickled hemoglobin
valine replaces glutamic acid at 6
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Secondary Structure

• Refers to the local conformation of some part of
  the polypeptide.
• Result of hydrogen bonds
• Get folding
• Two very stable secondary structures occur widely
  in proteins
• 1. The alpha helix (coil) 2. beta pleated sheet.
  Bonds between 2 chains linking the amino acids
  in one chain to those in the other in the same
  protein.

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Secondary Structures of Proteins
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Secondary Structure

• Definition The folding of the amino acid chain
  by hydrogen bonding into these characteristic
  coils and pleats is called a proteins secondary
  structure.
• Supersecondary structure Motifs. Beta Alpha
  Beta motif creates a fold or crease.
• Beta Barrel a beta sheet folded around to
  form a tube.
• Alpha turn Alpha many proteins uses it to
  bind to the DNA double helix.

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Tertiary Structure

• Final folded shape of a protein which positions
  the various motifs and folds nonpolar side groups
  into the interior. Nonpolar groups fit together
  snugly, leaving no holes. Small changes in amino
  acids can greatly change the 3-D nature of a
  protein.
• A protein is driven into its tertiary structure
  by hydrophobic interactions with water.
• Also important are strong covalent bonds called
  disulfide bridge which form when 2 cysteine
  monomers are brought close together by the
  folding of the protein (use sulfhydryl groups).

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Tertiary Structure of a Protein
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Quarternary Structure

• A proteins subunit arrangement (not all proteins
  have a quarternary structure). Occurs when 2 or
  more polypeptide chains form a functional
  protein.
• E.g. hemoglobin is a protein composed of two
  alpha-chain subunits and two beta-chain subunits.
  Quarternary structure can bind prosthetic groups
  such as iron.
• This kind of protein is a conjugated protein

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Quarternary Structure of Protein with Prosthetic
Group (hb)
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Factors affecting protein structure

1. Physical and chemical conditions such as pH, salt
   concentration, temperature. Can cause the
   unraveling of protein denaturation (think egg
   white cooked). Proteins loss of its 3-D
   structure.
2. Presence of chaperone proteins normal cells
   contain more than 17 different kinds of proteins
   that act as molecular chaperonesthey seem to
   rescue proteins that are misfolded.

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Summary of Protein Structure
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Protein Denaturation Loss of 3-D structures
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Chaperonin Chaperone proteins to assure proper
folding of proteins
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Nucleic Acids

• Function to store and transmit hereditary
  information.
• Types DNA deoxyribonucleic acid hereditary
  material
• RNA ribonucleic acid reads
  the cells DNA-encoded information and directs
  the synthesis of proteins

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Nucleotide components of DNA and RNA
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Structure of DNA

• Long polymers of repeating subunits called
  nucleotides
• Nucleotides a) a five-carbon sugar (pentose)
  either deoxyribose or ribose (memorize the ring
  structure of ribose).
• b) a phosphate group
• c) an organic nitrogen-containing base
  (nitrogenous base) 2 families of bases
  pyrimidine (6-membered ring) and purine (6-member
  ring fused to 5-member ring).
• DNA Cytosine, Thymine (pyrimidines)
  Adenine and Guanine (purines)
• RNA thymine is replaced by Uracil
• Bond phosphodiester covalent bond between the
  phosphate of one nucleotide and the sugar of the
  next monomer. (Formed through dehydration-synthes
  is and removal of a water).
• Backbone of polymer sugar-phosphate-sugar-phosph
  ate

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DNA Molecule

• Double helix (Watson and Crick, 1953). 2 chains
  of nucleotides with sugar and phosphate on the
  outside (hydrophilic) and nitrogenous bases on
  the inside (hydrophobic).
• Precise pairing of bases such that A T and C
  G. Chains held together with hydrogen bonds.
  Each strand is the template of the other strand.
• Strands run anti-parallel to one another.

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DNA Double Helix
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Watson and Crick
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Rosalind Franklin
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Chitin Monomer modified B glucose
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Cellulose digestion as the result of gut bacteria
in rumen
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1. Be able to identify
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2. List 3 examples of

• Compound Example
• Monosaccharide
• Glucose, Galactose, Fructose
• Disaccharide
• Maltose, Sucrose, lactose
• Polysaccharide
• Starch, Cellulose, glycogen

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3. Functions of Carbs in Animals

• Glucose carried by blood to transport energy to
  cells throughout body.
• Lactose sugar in milk, provides energy to young
  mammals until weaned
• Glycogen short-term energy storage in liver and
  in muscles.

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3. Functions of carbs in plants

• Fructose used to make fruit sweet-tasting,
  attracting animals to disperse seeds in fruit.
• Sucrose Plants transport energy to cells
  throughout plant in phloem. (From sugar source
  to sugar sink.)
• Cellulose Basic structural unit of the plant
  cell wall used to make strong fibers.

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4. Functions of Lipids

• Energy Storage fat in humans, oils in plants
• Building membranes phospholipids and
  cholesterol form membrane structure
• Heat insulation layer of fat under the skin
  reduces heat losses
• Buoyancy lipids less dense than water so help
  animals float

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5. Compare the use of carbohydrates and lipids
in energy storage

• Carbohydrates
• More easily digested providing rapid energy
  release
• Water soluble so easy to transport and store

• Lipids
• More energy per gram
• Lighter storage method for same amount of energy.
• Insoluble in water.

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6. Outline the role of condensation and
hydrolysis in the relationships between

• Condensation Reactions
• 2 Amino Acids ? Dipeptide Water
• Many amino acids ? Polypeptide Water
• Monosaccharides ? Di or Polysaccharides Water
• Fatty acids Glycerol ? Glycerides water
• Hydrolysis Reactions
• Polypeptides Water ? Dipeptides or AAs
• Polysaccharides Water ?
• Di or monosaccharides
• - Glycerides water ? Fatty acids Glycerol

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7. Structure of proteins
Primary Structure sequence of amino acids
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Quarternary Structure
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8. Fibrous vs. Globular proteins

• Shape fibrous long, narrow
• globular rounded
• Solubility in water fibrous insoluble
• globular soluble
• Function fibrous structural
• globular enzymes, transport,
• defense
• Examples fibrous collagen, keratin, myosin
• globular catalase, hemoglobin,
  insulin

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9. Significance of Non polar and polar amino
acids
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Polar and Non-polar amino acids in proteins

• Outside membranes
• 1. Polar aa on surface water soluble
• 2. Nonpolar aa on inside stabilize structure.
• 3. Superoxide dismutase directs substrate to
  active site.
• 4. Lipase active site is non-polar/ outside is
  polar

• Inside membranes
• 1. Polar aa when in contact with water (cytoplasm
  extracellular matrix) to create channel for
  hydrophilic substances.
• 2. Non-polar aa cause proteins to remain
  embedded in membranes.

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10. State 4 Functions of proteins with example
of each

• Enzymes
• Structural
• Transport
• Movement
• Hormones
• Defense

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11. 12. Outline DNA nucleotide structure (RNA?)

• Nucleotides a) a five-carbon sugar (pentose)
  either deoxyribose or ribose (memorize the ring
  structure of ribose).
• b) a phosphate group
• c) an organic nitrogen-containing base
  (nitrogenous base) 2 families of bases
  pyrimidine (6-membered ring) and purine (6-member
  ring fused to 5-member ring).
• DNA Cytosine, Thymine (pyrimidines)
  Adenine and Guanine (purines)
• RNA thymine is replaced by Uracil

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13. Outline how DNA nucleotides are linked
together by covalent bonds

• Bond phosphodiester covalent bond between the
  phosphate of one nucleotide and the sugar of the
  next monomer. (Formed through dehydration-synthes
  is and removal of a water).
• Backbone of polymer sugar-phosphate-sugar-phosph
  ate

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14. Explain how a DNA double helix is formed
using complementary base pairing and hydrogen
bonds. 15. Draw and label.

• Precise pairing of bases such that A T and C
  G. Chains held together with hydrogen bonds.
  Each strand is the template of the other strand.
• 2 H bonds between A and T 3 between C and G

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15. Draw and label

• Include these labels
• Phosphate group
• Deoxyribose sugar
• Nitrogenous base
• Purine, Pyrimidine
• Adenine, Thymine, Guanine, Cytosine
• H bond
• Nucleotide
• Phosphodiester Bond
• Antiparallel strands
• 3 end 5 end

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7.6.1 Characteristics of Metabolic Pathways

• Sequence of chemical reactions
• Could be chains eg.
• Glycolysis synthesis of amino acids synthesis
  of DNA
• Could be cycles where substrate continually
  regenerated by the cycle eg.
• Krebs and Calvin

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7.6.2 Models of Enzyme-Substrate Specificity

• Lock and Key
• Fit between the shape and chemistry of its
  active site and the shape of the substrate
  described as lock (enzyme) and key (substrate).
• Implies rigidity. Shape is not flexible.
• Each enzyme only binds to one substrate.

• Induced Fit more like a handshake. Active site
  is rigid as substrate enters the active site,
  it is induced to change shape by the substrate.
  Result active site fits even more snugly around
  the substrate. An enzyme might bind gt1
  substrate. Accounts for the broad specificity of
  some enzymes.

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Advantage of Induced Fit

• Induced fit brings chemical groups of the active
  site into positions that enhance their ability to
  work on the substrate and catalyze the chemical
  reactions.

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7.6.3 Explain how enzymes catalyze chemical
reactions
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7.6.4. Types of Inhibitors with Examples

• Chemicals other than intended reactant bonded to
  the active site or changing the shape of the
  active site.
• Two general types Competitive and
  Noncompetitive

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Competitive vs. Non-competitive inhibition
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Eg. Competitive Inhibitors

• An inhibiting molecule structurally similar to
  the substrate molecule binds to the active site,
  preventing substrate binding. Eg. Inhibition of
  folic acid synthesis in bacteria by the
  sulfonamide (antibiotic) Prontosil. E.g. Carbon
  monoxide binds to the active site of hemoglobin
  and is a competitive inhibitor that binds
  irreversibly.
• See page 86 in new textbook
• See page 70 in review guide

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Competitive Inhibitor

• Always give 1) Inhibitor 2) Enzyme it inhibits
  
• Malonate inhibits Succinate dehydrogenase which
  should bind succinate and turn it into fumarate
  in Krebs Cycle
• Antibiotic, Prontosil (sulfur drug), inhibits
  Folic Acid synthesis enzyme (dihydropteroate
  synthetase) in bacteria. Usually binds to PABA

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Non-competitive Inhibitor

• Always give Inhibitor and what it interferes with
• E.g. Opioids (morphine) are inhibitors of the
  enzyme nitric oxide synthase which should bind
  arginine.
• Nitric oxide is a signalling molecule.
• E.g. Eg. Metal ions disrupting disulfide bridges
  in many enzymes including cytochrome oxidase
  (enzyme in electron transport chain). Hg2, Ag,
  Cu2 bind to SH groups, breaking S-S- linkages
  changes shape of the active site.

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7.6.5 Explain the control of Metabolic pathways.
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7.6.5 Explain the control of metabolic pathways.

• E.g. End-product inhibition. Name the enzyme,
  the end-product that turns it off.
• Phosphofructokinase turned off by ATP one of the
  first enzymes active in glycoslysis.
• Binding site On-off switch
• Allosteric site
• Advantage
• Do not accumulate unneeded intermediates.
• An example of
• Negative feedback

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E.g. Threonine to isoleucine

• Isoleucine turns off the enzyme threonine
  dehydratase which catalyzes the first chemical
  reaction in the conversion of threonine to
  isoleucine.