biochemistry. all matter is composed of atoms the structure of the atom electrons: negative...
TRANSCRIPT
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Biochemistry
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All Matter is composed of
Atoms
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The Structure of the AtomElectrons: Negative electrical charge
Protons: Positive electrical charge
Neutrons: No net electrical charge
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Molecules
• Two or more atoms held together by
Chemical bonds
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Chemical Bonds
• form because of the interactions between the electrons of the atoms
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The atom’s ELECTRONEGATIVITY
(ability to attract electrons)
• Determines the type and strength of the Chemical bond
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Ions• Ions are atoms that have either a
positive or negative
electrical charge because the
electron number is NOT equal to
the proton number
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IONIC BONDS
• Form between atoms when electrons are TRANSFERED
from one atom to another forming ions of opposite
electronic charges• http://www.dac.neu.edu/physics/b.maheswaran/phy1121/data/ch09/
anim/anim0904.htm
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Covalent Bonds• Form when atoms share
electrons• Occur when the
electronegativities between the atoms are similiar
• http://www.dac.neu.edu/physics/b.maheswaran/phy1121/data/ch09/anim/anim0904.htm
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• Some molecules have Single Covalent Bonds… which means
the atoms share one pair (a single pair) of electrons
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• Some molecules have Double Covalent Bonds… which means
the atoms share two pairs of electrons
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• Some molecules have Triple Covalent Bonds… which means the atoms share Three pairs of
electrons
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Nonpolar Covalent Bonds
• Occur when the electronegativities of both atoms are identical and the
electrons are shared equally
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Polar Covalent Bonds
• Occur when the electronegativities of both atoms are Different and the
electrons are shared unequally
Negative Pole
Positive Pole
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Hydrogen Bonds
• Hydrogen bonds are weak bonds which form between molecules
Hydrogen Bond
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Bond Strengths• Ionic Bonds are weak and are easily
broken in water
• Covalent Bonds are generally strong
• Hydrogen Bonds are very weak
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The Properties of Water
• 1. Water is the UniversalUniversal Solvent.
• Ionic compounds and Polar covalent molecules readily
dissolve in water
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Hydrophilic Molecules (water-loving)
• Are substances that dissolve in water…. Salts,
sugars, etc….
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Hydrophobic Molecules (water-fearing)
• Are substances that do not dissolve in water… oils,
waxes, etc…
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Water Has A High Specific HeatCapacity…. The capacity of a
substance to change temperature in response to a gain or loss of heat… water changes temperatures very
slowly• Specific Heat - the amount of heat needed to
raise 1 g of the substance 1 degree C.
• Why? ……… Hydrogen bonding.
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Water Has A High Heat Of Vaporization
• Heat of Vaporization: the quantity of heat a liquid must absorb for 1g of it
to convert to a gaseous state.
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Liquid Water Is Cohesive
• Water sticks to water.
• Why?
Because the polarity of water results in hydrogen bonding.
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Liquid Water is Adhesive
• Water sticks to other molecules.
• Why?
Hydrogen bonding.
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Water transport in trees uses Cohesion and Adhesion
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Water Has A High Surface Tension• The surface
of water is difficult to stretch or
break.
• Why?
• Hydrogen bonding.
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Water Stabilizes Temperature
• Water can absorb and store a huge amount of heat from the sun.
• Result - climate moderation
• Result - organisms are able to survive temperature changes.
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Evaporative Cooling
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Result:• Water cools organisms from
excessive heat buildup.
• Why?
As water evaporates it takes the heat with it.
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Water Expands and becomes less dense when It Freezes….so
it floats
• The distance between water molecules INCREASES from the liquid to the solid form.
• Why?
• Hydrogen bonding
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Water Benzene
Floats Sinks
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Result
• Ice floats and forms an blanket of insulation during the
winter……….Aquatic life
can live under ice.
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Water is used to make Solutions
• A Solution is a Homogeneous mixture of two or more
substances.
• Solvent + Solute Solution
• Sugar water, Saltwater, Pepsi
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Solvent
• The dissolving agent
• Present in a greater proportion
Examples:
• Water
• Methane
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Solute
• The substance that is dissolved.
• Present in smaller quantity
Examples:• Salt in saltwater
• Sugar in sugar water
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Solution Concentration
• Usually based on Molarity
• Molarity - the number of moles of solute per liter of solution.
• A mole is = 6.021x1023
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One Mole of each
Sulfur
Sugar
Copper Sulfate
Mercury Oxide
Copper
Sodium Chloride
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Dissociation of Water
• Water can sometimes split into two ions.
• In pure water the concentration of each ion is 10-7 M
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• Adding certain solutes disrupts the balance between the two
ions.
• The two ions are very reactive and can drastically affect a cell.
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Acids• Materials that can release H+
Example: HCl HCl H+ + Cl-
Hydrochloric acid, vinegar, etc…
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Effects of Acid Rain
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Bases
• Materials that can absorb H+
• Often reduce H+ by producing OH-
Example: NaOH NaOH Na+ + OH-
Drano, Soaps, etc…….
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pH Scale
• A logarithmic scale for showing H+ concentration in a solution.
pH = - log [H+]
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pH Scale
Acids: pH < 7Acids: pH < 7Neutral: pH 7Neutral: pH 7Bases: pH >7Bases: pH >7
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• Acids: pH <7 etc.
• Bases: pH >7 etc.
Each pH unit is a 10x change in H+
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Buffers• Materials that have both acid
and base properties.• Resist pH shifts.• Cells and other biological
solutions often contain buffers to prevent damage.
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Organic Molecules
• Contain carbon atoms, exceptions are carbon monoxide and carbon dioxide
• Carbon has 4 electrons available to form 4 chemical bonds….therefore large molecules
are easily formed using carbon as the backbone.
• Large carbon based molecules are usually found as long chains or rings.
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Macromolecules
• Most macromolecules are “polymers”“polymers” ….molecules that consist of a single unit (monomermonomer) repeated many times.
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Functional Groups
• Many organic molecules share similar properties because they have similar clusters of atoms, called the….. Function GroupsFunction Groups
• Each Functional Group gives the Each Functional Group gives the molecules a particular property, molecules a particular property,
such as acidity or polarity.such as acidity or polarity.
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Functional Groups
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Four Main Types Of Macromolecules
• CarbohydratesCarbohydrates
• LipidsLipids
• ProteinProtein
• Nucleic acidsNucleic acids
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Carbohydrates
• Used for fuel, building materials, and receptors.
• Made of C,H,O
• General formula is CH2O
• C:O ratio is 1:1
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Types Of Carbohydrates
• Monosaccharides
• Disaccharides
• Polysaccharides
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Monosaccharides• Mono - single• Saccharide - sugar• Simple sugars.• Can be in linear or
ring forms.• Glucose, Fructose,
Galactose…. all with the chemical formula C6H12O6….. Same chemical formula, different shapes.
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• Most words ending with the letters OSE are carbohydrates.
Glucose, Fructose, Galactose
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Disaccharides
• Sugar formed by joining two monosaccharides together thru the process of Dehydration
Synthesis….(removing water)…aka…. Condensation Synthesis.
• all with the chemical formula C12H22O11
• glucose + fructose = sucrose (table sugar) + H2O
• glucose + galactose = lactose ( the sugar in milk) + H2O
• glucose + glucose = maltose + H2O
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Condensation Synthesis or
Dehydration Synthesis • The chemical
reaction that joins monomers into polymers.
• Covalent bonds are formed by the removal of a water molecule between the monomers.
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Hydrolysis
• Reverse of condensation
synthesis.• Using water (Hydro),
to split (Lysis)• Breaks polymers
into monomers by adding water
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Examples of Disaccharides produced through Dehydration Synthesis
• Maltose = glucose + glucose
• Lactose = glucose + galactose
• Sucrose = glucose + fructose
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Polysaccharidesall with the chemical formula (CH2O)n
• Many joined simple sugars.• Used for storage or structure.
• Examples: Starch - a polymer of -glucose molecules, principle
energy storage molecules in plants Glycogen - a polymer of -glucose molecules, principle
energy storage molecules in animals, stored in the liver and muscles cells
Cellulose - a polymer of -glucose molecules, principle structural molecules in plant cell walls…. Major component of wood
Chitin - a polymer of -glucose molecules, each modified with a nitrogen group, principle structural molecule in the cell walls of fungi and the exoskeletons of the arthropods.
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Lipids (Fats)
• Diverse hydrophobic molecules which are insoluble in water (and other polar molecules) and
soluble in non-polar molecules like ether and chloroform
• Made of C,H,O• No general formula.
• C:O ratio is very high in C
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Types of Lipids (Fats)
• Triglycerides
• Phospholipids
• Steroids
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Triglycerides
• Three fatty acids joined to one glycerol.
• Joined by an “ester” linkage between the -COOH of the fatty acid and the -OH
of the alcohol.
• Differ in which fatty acids are used.
• Used for energy storage, cushions for organs, insulation.
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Acid Fat
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Fats and Oils
• Fats - solid at room temperature.
• Oils - liquid at room temperature.
• Saturated - solid at room temperature.
• Unsaturated - liquid at room temperature.
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Saturated Fats
• Saturated - no double bonds.
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Unsaturated Fats• Unsaturated - one or more C=C
bonds. Can accept more Hydrogens.
• Double bonds cause “kinks” in the molecule’s shape.
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Question ?
• Which has more energy, a kg of fat or a kg of starch? …. (Hint) in Fats there are more C-H bonds which provide more energy per mass.
• Answer… carbohydrates (starch) have 4 calories per gram, lipids have 9 calories per gram
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Phospholipids
• Similar to fats, but have only two fatty acids.
• The third -OH of the glycerol is joined to a phosphate group replacing a fatty acid
• Major component of the Plasma
Membrane of all cells
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Result
• Phospholipids are amphipathic which means they have a nonpolar, hydrophobic tail, but a polar, hydrophilic head.
• Self-assembles into bilayers, an important part of cell membranes.
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Steroids
• Characterized by a backbone of four fused carbon rings.
• Differ in the functional groups attached to the rings.
• Examples:
–cholesterol
–sex hormones
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Proteins
• Made of C,H,O,N, and sometimes S.
• No general formula
• Polymers of amino acids
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Uses Of Proteins
• Structural Proteins: used to make skin, hair, muscles, etc…
• Enzymes: Control Metabolism• Antibodies: Provide protection
against foreign substances• Transport Proteins: Transport
molecules across membranes• Storage: such as ovalbumin in
eggs
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Proteins
Proteins are Polypeptide chains of Amino Acids
linked by peptide bonds.
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Amino AcidsAmino Acids• All have a Carbon
with four attachments:
-COOH (acid)
-NH2 (amine) -R group• 20 different kinds
of amino acids because there are 20 different kinds of R groups
Amino GroupCarboxyl Group AKA: Acid Group
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Amino Acids
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Amino Acids
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R groups
The properties of the R groups
determine the
properties of the protein.
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Polypeptide Chains
• Formed by dehydration synthesis between the carboxyl group of one
amino acid and the amino group of the second Amino Acid.
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Levels Of Protein Structure
• Organizing the polypeptide into its 3-D functional shape.– Primary– Secondary– Tertiary– Quaternary
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Primary Structure
• Order of amino acids in the
polypeptide chain.
• Many different sequences are possible with
20 AAs.
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Secondary Structure• 3-D structure
formed by hydrogen bonding between the R groups.
• Two main secondary structures:
helix
- pleated sheets
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Tertiary• 3D shape as bonding
occurs between the R groups.
• Examples:
– Hydrophobic interactions
– Ionic bonding
– Disulfide bridges– Hydrogen Bonding
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Quaternary• When two or more polypeptides
unite to form a functional protein.
• Example: hemoglobin
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Is Protein Structure Important?
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Denaturing Of A Protein
• Events that cause a protein to lose structure (and function).
• Example:
–pH shifts
–high salt concentrations
–heat
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Nucleic Acids
• Stores the genetic Information
• Polymers of nucleotides
• Made of C,H,O,N and P
• No general formula
• Examples: DNA and RNA
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Nucleotides of DNA and RNANucleotides have three parts:
– Nitrogenous Base
– Pentose sugar (Deoxyribose in DNA and Ribose in RNA)
– Phosphate Group
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Nitrogenous Bases• Rings of C and N
• Two types:– Pyrimidines (single ring) Thymine, Cytosine– Purines (double rings) Adenine, Guanine
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Pentose Sugar• 5-C sugar
• Ribose - RNA
• Deoxyribose – DNA
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DNA: Deoxyribonucleic Acid• Double Helix Structure• The two strands of DNA
are antiparallel, oriented in opposite directions… one strand is arranged in the 3’ – 5’ direction while the other is arranged in the 5’ – 3’ direction (5’ means the phosphate group is attached to the 5th carbon on the Deoxyribose molecule.
• Makes up genes.
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RNA: Ribonucleic Acid
• Important molecule in protein synthesis.
• Genetic information for a few viruses only.
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Differences between DNA and RNA
• RNA is a single strand
• DNA has Deoxyribose, RNA has ribose
• Thymine is replaced by Uracil
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Chemical Reactions in Metabolic ProcessesChemical Reactions in Metabolic Processes
• In order for chemical reactions to occur, the reacting molecules must first collide and then have enough energy (Activation energy) to trigger the formation of new bonds.
• Some reactions require catalysts. Catalysts are molecules which trigger or accelerate chemical reactions without being chemically altered themselves.
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Metabolism• Chemical reactions which occur within
living organisms are called Metabolic reactions…..
• Two types of Metabolic Reactions:
*Anabolic Reactions:
Build molecules and store energy
*Catabolic Reactions:
Breakdown Molecules and release energy
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Chemical Equilibrium
• The net direction of metabolic reactions, forward or reverse, is determined by the concentration of the reactants and the products.
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Enzymes: Globular proteins which catalyze metabolic reactions.
• Enzyme: Catalyzes the Reaction
• Substrate: molecule acted upon
• Products: Resulting molecules• Enzyme + Substrate Enzyme – Substrate Complex Enzyme + Products
• Maltase + Maltose Maltase + Maltose Complex Maltase + glucose + glucose
Active Site
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Enzymes
• Most Enzymes end with the letters - ASE
• Enzymes are substrate specific….. Examples:
• Maltase can only breakdown Maltose
• Sucrase can only breakdown Sucrose
• Amylase can only breakdown Amylose
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EnzymesThe efficiency of Enzymes
is affected by:
- pH shifts: pepsinogen is only activated when stomach acids
lower the pH
- Heat: denatures enzymes
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Cofactors• Are nonprotein molecules that
assist enzymes… since they are nonproteins they are used up in the reactions.
• A holoenzyme is the union of a cofactor and enzyme.
• The enzyme is called an Apoenzyme when it’s part of a holoenzyme
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Inorganic Cofactors
Are usually metals, like Iron (Fe+2), Magnesium (Mg+2)
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CoEnzymes
Are organic molecules which aid in enzyme reactions…….
Some vitamins are coenzymes. Since they are nonproteins they
are also used up in the reactions.
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ATPAdenosine TriPhosphate
Source of Activation energy for Metabolic Reactions
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Allosteric Enzymes• Have two types of binding sites….
One for the substrate and one for the allosteric effector.
• Two types of Allosteric Effectors:
• 1. Allosteric Activator – binds to the enzyme and changes its shape to induces a reaction
• 2. Allosteric Inhibitor – binds to the enzyme and induces inactivity
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Allosteric Enzymes
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Competitive Inhibition
Is when an enzyme mimic occupies
the active site preventing a
reaction.
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Noncompetitor InhibitorNoncompetitor Inhibitor
Prevents enzyme reactions by binding to the substrate at locations other than the active or allosteric site.
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Cooperativity
• Occurs when an enzyme becomes receptive to additional substrate molecules after one substrate molecule attaches to an active site.
• Example: Hemoglobin…… its binding capacity to additional oxygen molecules increases after the first oxygen fills the active site.
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Cooperativity