the basics of chemistry for biology
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The Basics of Chemistry for Biology. Atoms: The units of elements Bonding: Covalent vs. Ionic Water: Water ‘ s unique properties. The Chemistry of Life. Matter (anything that takes up space) Composed of atoms Atom - PowerPoint PPT PresentationTRANSCRIPT
The Basics of Chemistry for Biology
• Atoms: The units of elements
• Bonding:Covalent vs. Ionic
• Water:Water‘s unique properties
The Chemistry of Life
• Matter – (anything that takes up space)– Composed of atoms
• Atom– Smallest unit of an element that
has the properties of the element– 2 regions
• Nucleus• Electron cloud
Inside the Atom: Subatomic Particles
• Protons: positive charged particles found in the nucleus (p+)
• Neutrons: neutral particles found in the nucleus (nº)
• Electrons: negative particles found in the electron cloud (e-) – Move around the nucleus in energy levels
Energy Levels of the Electron Cloud
The number of electrons on each level is given by the formula 2n2
where n is the level number
Number/Name # of e- it can hold
1-K 2
2-L 8
3-M 18
4-N 32
5-O 50
6-P 72
7-Q 98
Info from the Periodic Table
• Symbol • Atomic Number
(Z)– = Number of p+
• Mass Number (A)– = p+ + nº
Nuclides
A
Z XCopper
Oxygen
Practice SetSymbol/
NameAtomic Number
Atomic Mass
Nuclide Protons Neutrons Electrons
OOxygen
AuGold
NaSodium
KPotassium
ClChlorine
FFluorine
CaCalcium
Let’s Draw an Atom
1. Write the nuclide.2. Draw the Energy levels.3. Write the number of protons and
neutrons in the nucleus.4. Place the correct number of electrons on
each energy level.5. Leave unused energy levels empty.
Practice Drawing
Ions
• For a neutral atom, protons = electrons• Ion: an atom with more or fewer
electrons than it should normally have, causing a charge– Loss of electrons forms a positive ion
• Cation– Gain of electrons forms a negative ion
• Anion
Isotopes
• Isotopes: atoms of the same element with different masses due to different # of neutrons
• radioactive isotopes: unstable nuclei breakdown over time (nuclear decay)
Summary ChartSubatomic
particle number to be changed
How changed Atom is now a __ of the original
atom
Electron
Gained
Lost
Anion (negative ion)
Cation (positive ion)
Neutron Gained or Lost Isotope
Bonding and Compounds
• Compound: two or more atoms bonded together due to electron exchange (give & take) or electron sharing
Metals
• Metals are found mainly in columns I to III
• They give away electrons to bond– This forms positive ions: cations
Non-metals
• Non-metals are found mainly in columns III to VIII– They can take in electrons from a metal to
bond and form negative ions: anions– They can share electrons with another non-
metal and form molecules
Ionic Bonding
• Ionic Bonding: involves the giving of electrons by metals and the taking of electrons by non-metals– Examples
• Sodium chloride• Calcium chloride• Sodium oxide
– Forms IONS
Ionic bonding
Covalent Bonding
• Covalent Bonding: the sharing of electrons between two non-metals– Carbon dioxide– Methane– Nitrogen dioxide– Diphosphorus pentoxide
– Forms MOLECULES
Covalent Bonding
Polarity
• Polar: electrons are not shared equally between the two non-metals in a covalent bond
• Non-polar: electrons are shared equally between the two non-metals in a covalent bond
Polar covalent bond
Polar/nonpolar bonds
• van der Waals forces: forces of attraction between molecules– Weak forces
van der Waals forces
van der Waals interactions• Weak interactions between molecules or
parts of molecules that are brought about by localized change fluctuations
• Due to the fact that electrons are constantly in motion and at any given instant, ever-changing “hot spots” of negative or positive charge may develop
Hydrogen bonds• Hydrogen atom
covalently bonded to one atom is also attracted to another atom (oxygen or nitrogen) on another molecule– Strong– Water is best example
Cohesion
• Cohesion: attraction of molecules of the same substance to each other– Example water molecules to other
molecules in a glass
Water’s Properties• Polar~ opposite ends, opposite charges• Cohesion~ H+ bonds holding molecules
together (same substance, water to water)• Adhesion~ H+ bonds holding molecules to
another substance• Surface tension~ measurement of the
difficulty to break or stretch the surface of a liquid
• Specific heat~ amount of heat absorbed or lost to change temperature by 1oC
• Heat of vaporization~ quantity of heat required to convert 1g from liquid to gas states
• Density……….
Density• Less dense as solid
than liquid1. Due to hydrogen
bonding2. Crystalline lattice
keeps molecules at a distance
Mixtures• Combination of 2
or more elements physically but not CHEMICALLY (not bonded together)
Wet MixturesSoution All components are
distributed evenly Parts1. Solute: is dissolved2. Solvent: does the
dissolving
Example: Kool-aid dissolved in water
Suspension Components are distributed
unevenly, just mixed together
Parts1. Supernant: liquid2. Precipitate: solid
Example: snowglobe
Acid/Base & pH• Dissociation (breaking apart)
of water into a hydrogen ion and a hydroxide ion
• Acid: increases the hydrogen concentration of a solution
• Base: reduces the hydrogen ion concentration of a solution
• pH: “power of hydrogen”• Buffers: weak acids or bases
that react with strong acids or bases to prevent changes in pH
pH Scale
Acid Neutral Base
0 1 2 3 4 5 6 7 8 9 10 1112 13 14
Stronger Weaker WeakerStronger
Human body prefers pH of 6.5 to 7.5
Acids vs. BasesAcid• “Acidic”• More H+ than OH-
• Tastes sour• Turns litmus paper red• Found in coffee, tea, soft
drinks, and fruit juices
Base• “Alkaline”• More OH- than H+
• Tastes bitter• Turns litmus paper blue• Found in cleaners and
soaps
NeutralizationWhen Acids and Bases are mixed
chemically, they produce salt and water. This reaction is called neutralization because the end products are not acidic nor alkaline, they are neutral!
2006-2007
The Chemistry of Life
What are living creatures made of?
Why do we have to eat?
• 96% of living organisms is made of: carbon (C) oxygen (O) hydrogen (H) nitrogen (N)
Elements of Life
Molecules of Life• Put C, H, O, N together in different
ways to build living organisms• What are bodies made of?
– carbohydrates • sugars & starches
– proteins– fats (lipids)– nucleic acids
• DNA, RNA
Why do we eat?• We eat to take in more of these chemicals
– Food for building materials• to make more of us (cells)• for growth• for repair
– Food to make energy• calories• to make ATP
ATP
What do we need to eat?• Foods to give you more building blocks &
more energy• for building & running bodies
– carbohydrates– proteins– fats– nucleic acids– vitamins– minerals, salts– water
• Water– 65% of your body is H2O– water is inorganic
• doesn’t contain carbon
• Rest of you is made of carbon molecules– organic molecules
• carbohydrates• proteins• fats• nucleic acids
Don’t forget water
2006-2007
How do we make these molecules?
We build them!
How do we make these molecules?
We build them!
How to take large molecules apart• Digestion
– taking big molecules apart– getting raw materials
• for synthesis & growth– making energy (ATP)
• for synthesis, growth & everyday functions
+
ATP
Example of digestion
starch glucose
ATP
ATP
ATP
ATP
ATP
ATPATP
• Starch is digested to glucose
Building large molecules of life• Chain together smaller molecules
– building block molecules = monomers
• Big molecules built from little molecules– polymers
• Small molecules = building blocks
• Bond them together = polymers
Building large organic molecules
Building important polymers
sugar – sugar – sugar – sugar – sugar – sugar
nucleotide – nucleotide – nucleotide – nucleotide
Carbohydrates = built from sugars
Proteins = built from amino acids
Nucleic acids (DNA) = built from nucleotides
aminoacid
aminoacid–
aminoacid–
aminoacid–
aminoacid–
aminoacid–
How to build large molecules• Synthesis
– building bigger molecules from smaller molecules
– building cells & bodies• repair• growth• reproduction
+
ATP
How to take large molecules apart• Digestion
– taking big molecules apart– getting raw materials
• for synthesis & growth– making energy (ATP)
• for synthesis, growth & everyday functions
+
ATP
Example of digestion
starch glucose
ATP
ATP
ATP
ATP
ATP
ATPATP
• Starch is digested to glucose
Example of synthesis
amino acids protein
amino acids = building blockprotein = polymer
Proteins are synthesized by bonding amino acids
Old Food Pyramid
New Food Pyramid
The Chemistry of Life
Carbon, the Backbone
Carbon is special in the world of elements because it is able to bond to 4 other atoms at the same time!
Carbon, the BackboneSince Carbon can form so many bonds, it is considered the “backbone” of many compounds, that is Carbon is what the other atoms are all attached to
Special Covalent Bonds1. Single bond: one pair of electrons is
shared between two atoms2. Double bond: two pair of electrons
are shared between two atoms3. Triple bond: three pair of electrons
are shared between two atoms
Who can do these special cases?
C, N, O, and S can all form double bonds.
Only C and N can form triple bonds!
Carbon’s ShapesWhen Carbon bonds to other Carbon atoms, the resulting bond can take one of the following shapes:
1.Straight chain (in a straight line)2.Branched chains (like the straight chain,
but with a fork in the road3.Ring structures
Carbohydrates
Biochemical molecules that are used as both sources of energy and as short term energy storage• commonly called sugars and starches
Glucose
C6H12O6
Carbohydrates, I
Monosaccharides CH2O formula; simple sugars multiple hydroxyl (-OH) groups and 1 carbonyl (C=O) group: aldehyde (aldoses) ketone (ketoses) raw material for amino acids and fatty acids
Carbohydrates, II
Disaccharides glycosidic linkage (covalent bond) between 2 monosaccharides; covalent bond by dehydration reaction
Sucrose (table sugar) most common disaccharide
Carbohydrates, III• Polysaccharides
(Storage) Starch~ glucose monomers Plants: plastids Animals: glycogen
• Polysaccharides (Structural)Cellulose ~ most abundant
organic compound; Chitin ~ exoskeletons; cell
walls of fungi; surgical thread
Monomers and Polymers
• -mer: building blocks • Monomer: one building block
• Polymer: many building blocks
Proteins• Importance:
instrumental in nearly everything organisms do; 50% dry weight of cells; most structurally sophisticated molecules known
• Monomer: amino acids (there are 20) ~ carboxyl (-COOH) group, amino group (NH2), H atom, variable group (R)….
• Variable group characteristics: polar (hydrophilic), nonpolar (hydrophobic), acid or base
• Three-dimensional shape (conformation)• Polypeptides (dehydration reaction):
peptide bonds~ covalent bond; carboxyl group to amino group (polar)
Primary Structure• Conformation:
Linear structure
• Molecular Biology: each type of protein has a unique primary structure of amino acids
• Ex: lysozyme
• Amino acid substitution:hemoglobin; sickle-cell anemia
Secondary Structure
• Conformation: coils & folds (hydrogen bonds)
• Alpha Helix: coiling; keratin• Pleated Sheet: parallel;
silk
Tertiary Structure
Conformation: irregular contortions from R group bonding
hydrophobicdisulfide bridgeshydrogen bonds ionic bonds
Quaternary Structure
• Conformation: 2 or more polypeptide chains aggregated into 1 macromoleculecollagen (connective tissue)hemoglobin
Lipids• No polymers; glycerol and fatty acid• Fats, phospholipids, steroids• Hydrophobic; H bonds in water exclude fats• Carboxyl group = fatty acid• Non-polar C-H bonds in fatty acid ‘tails’• Ester linkage: 3 fatty acids to 1 glycerol
(dehydration formation)• Triacyglycerol (triglyceride)• Saturated vs. unsaturated fats; single vs.
double bonds
Lipids, II
Phospholipids
• 2 fatty acids instead of 3 (phosphate group)
• ‘Tails’ hydrophobic (water fearing); ‘heads’ hydrophilic (water loving)
• Micelle (phospholipid droplet in water)
• Bilayer (double layer);cell membranes
Steroids
• Lipids with 4 fused carbon rings• Ex: cholesterol:
cell membranes;precursor for other steroids (sex hormones); atherosclerosis
Nucleic Acids, I• Deoxyribonucleic acid (DNA)• Ribonucleic acid (RNA)• DNA->RNA->protein• Polymers of nucleotides
(polynucleotide):nitrogenous basepentose sugarphosphate group
• Nitrogenous bases: pyrimidines~cytosine, thymine, uracilpurines~adenine, guanine
Nucleic Acids, II
• Pentoses:√ribose (RNA)√deoxyribose (DNA)√nucleoside (base + sugar)
• Polynucleotide:phosphodiester linkages (covalent); phosphate + sugar
Nucleic Acids, III
• Inheritance based on DNA replication
• Double helix (Watson & Crick - 1953) H bonds~ between paired bases van der Waals~ between stacked bases
• A to T; C to G pairing• Complementary
Give the complimentary DNA strand:
A G T C T G C A
Give the complimentary RNA strand:
A G T C T G C A
Biochemical Type
Carbohydrates Lipids Proteins Nucleic Acids
Monomers Monosaccharides
Sugars
Fatty acids and glycerol
Amino acids nucleotides
Polymers Polysaccharides
Starches
NONE Polypeptides, aka proteins
polynucleotide
Forces holding together
Glycosidic linkages Ester linkages
Peptide bonds Bonds and van der Waals
phosphodiester linkages
Uses Energy storage and structural
support
Energy storage,
hormones, membranes
Structural building
materials
Genetic information
transfer
Biochemical Test
Carbohydrates Lipids Proteins Nucleic Acids
Biuret's Reagent
Blue turns violet in
proteins, and pink with
short-chain polypeptides
Benedict’s Solution
Simple sugars heated with
Benedict’s turns from blue to red
Iodine Starches turn dark purple or black
Brown Bag Test/ Sudan III
stain
Leaves spot on brown bag/ turns
fats red
Conformation Test Lab
Lab Information
In the laboratory investigation you will perform known tests using known reagents in order to obtain positive results for comparison with an unknown. Be sure to follow your lab directions exactly!
IDENTIFYING MACROMOLECULES
IN FOODLAB
Introduction
Carbohydrates, proteins, and fats are all essential nutrients.
We cannot manufacture these nutrients so we must obtain them from our environment.
Introduction In this lab, with the use of indicators as
chemical detection tools, you will analyze a variety of foods for the presence of nutrients.
Detection is based upon observing a chemical change that takes place most often a change in color.
Objective
Identify the presence of major nutrients such as simple carbohydrates (glucose), complex carbohydrates (starch), protein and fat in
common foods.
What is an indicator?
• Indicators are chemical compounds used to detect the presence of other compounds.
Background InformationINDICATOR MACRO-
MOLECULENEGATIVE
TESTPOSITIVE
TEST
Benedict’s solution
simple carbohydrate
blue orange
IKI solution complex carbohydrate
dark red black
Biuret solution
protein blue violet, black
Sudan IV lipid dark red reddish- orange
What is a Standard?
• An acknowledged measure of comparison for quantitative or qualitative value; a criterion.
Test for Simple CarbohydratesBenedict’s solution
• Benedict's solution is a chemical indicator for simple sugars such as glucose: C6H12O6.
• Aqua blue: negative test; yellow/green/brick red, etc.: positive test
Test for Simple CarbohydratesBenedict’s solution
• Unlike some other indicators, Benedict’s solution does not work at room temperature - it must be heated first.
Test for Complex CarbohydratesIKI solution
• IKI solution (Iodine Potassium Iodine) color change = blue to black
Test for Complex CarbohydratesIKI solution
• Iodine solution is an indicator for a molecule called starch.
• Starch is a huge molecule made up of hundreds of simple sugar molecules (such as glucose) connected to each other.
Test for Protein (amino acids)Biuret solution
• Biuret solution dark violet blue to pinkish purple
Test for Fats (lipids)Sudan IV
• Like lipids, the chemical Sudan IV is not soluble in water; it is, however, soluble in lipids.
• In this test dark red Sudan IV is added to a solution along with ethanol to dissolve any possible lipids.
Test for Fats (lipids)Sudan IV
• If lipids are present the Sudan IV will stain them reddish-orange (positive test).
QuestionWhy didn’t the test tube containing sucrose
change colors?
QuestionWhy didn’t the test tube containing starch
change colors?
ProcedureSimple carbohydrate
1. Add 5ml distilled H2O using pipette to test tube
2. Add 1ml of food sample to test tube3. Add 20 drops of Benedict solution4. Place test tube in a hot water
bath for 10 minutes.
ProcedureComplex carbohydrate
1. Add 5ml distilled H2O using pipette to test tube
2. Add 1ml of food sample to test tube3. Add 20 drops of IKI solution
ProcedureProtein (amino acids)
1. Add 5ml distilled H2O using pipette to test tube
2. Add 1ml of food sample to test tube3. Add 20 drops of Biuret solution
ProcedureFats (lipids)
• Add 5ml distilled H2O using pipette to test tube
• Add 1ml of food sample to test tube• Add 20 drops of Sudan IV
LAB SAFETY and CLEAN UP
WEAR safety goggles and apron
at all times
THOROUGHLY CLEAN lab area and
equipment
NO EDIBLE products in lab
Enzymes
Enzymes & Their Function
Reactions (Chemical Changes)
• Bonds are made or broken• Energy is used or released• Starting material: Reactant• Ending material: Product
Enzymes
Catalytic proteins: change the rate of reactions w/o being consumed
Free E of activation (activation E): the E required to break bonds
Substrate: enzyme reactant
Active site: pocket or groove on enzyme that binds to substrate
Induced fit model
EnzymesLearning objective: to examine what enzymes are anddescribe how they work.
Enzymes
What are they?
Why do we need them?
Name some examples ?
EnzymesGlobular proteins that catalyse chemical reactions in living organisms
Properties
Enzymes
Properties
Specific
Enzymes
Properties
Specific
Increase rate of the reaction
Enzymes
PropertiesSpecific
Increase rate of the reaction
Unchanged at the end of the reaction
EnzymesGlobular proteins that catalyse chemical reactions in living organisms
PropertiesSpecific
Increase rate of the reactionUnchanged at the end of the reaction
Need them
EnzymesGlobular proteins that catalyse chemical reactions in living organisms
PropertiesSpecific
Increase rate of the reactionUnchanged at the end of the reaction
Need them Reactions too slow to maintain lifeCan’t increase temperatures/pressure in cells (fatal)
Enzymes Are ProteinsThe enzyme binds to the substrates by its active site
The active site is a pocket formed by the folding of the protein where the substrates bind.
Enzymes Are ProteinsThe enzyme binds to the substrates by its active site
The active site is a pocket formed by the folding of the proteinwhere the substrates bind.
Active site
The active site involves a small number of key residues that actually bind the substratesThe rest of the protein structure is needed to maintain these residues in position
How do enzymes work?
An Example
An Example
Sucrose + H2O
Glucose + Fructose
An Example
Sucrose + H2O
Glucose + Fructose
Substrates
Products
For a reaction to occur the sucroseand water would have to collide with
enough energy to break and form bonds
For a reaction to occur the sucroseand water would have to collide with
enough energy to break and form bonds
This is the activation energy
Sucrose + H2O Glucose + Fructose
++
Substrates Products
Energy
Progress of reaction
Energy
Progress of reaction
Substrates
Energy
Progress of reaction
Substrates Products
Energy
Progress of reaction
Substrates Products
High energy intermediate
Energy
Progress of reaction
Substrates Products
High energy intermediate
Activation energy
The minimum amount of energy needed to start the reaction, leading to the formation of a high energy intermediate
= The Activation energy
Energy
Progress of reaction
Substrates Products
High energy intermediate
Activation energy
Enzymes reduce the height of the energy
barrier
“Activation Energy”
In a ‘natural’ reaction the product has a lower energy than the substrate so equilibrium will take it in the direction of the product.
However there is an energy ‘barrier’ to be overcome
Enzymes lower the activation energy required to bring about a reaction.
Ex. catalase reduces the activation energy for the reduction of H202 86-fold
Enzyme ActionWhat are the different models for enzyme action and which factors which control the rate of an enzyme reaction?
Lock and Key
Lock and Key
However certain substances can bind to the enzyme at sites other than the Active site and modify its activity (inhibitors/co-factors)
Idea that the enzyme is flexible
E
S
E
S
E
P P
Induced Fit
How do enzymes work?
• Reaction Mechanism
– In any chemical reaction a substrate is converted into a product.
– In an enzyme catalysed reaction the substrate first binds to the active site of the enzyme to form the enzyme-substrate complex
Molecule Geometry
• Substrate molecule fits into the enzyme like a lock & key.
• Enzyme shape distorts or it changes other factors to make the reaction happen
Enzyme reactions
enzyme + substrate enzyme-substrate complex
Enzyme reactions
enzyme + substrate enzyme-substrate complex
E +S ES
Synthesis reaction since you are forming ONE product
Synthesis Reaction
Active site
es
Synthesis reaction
Glucose-1-phosphate
Starch
Enzyme reactions
enzyme + productenzyme-substrate complex
E +PES
enzyme + substrate enzyme-substrate complex
E +S ES
Decomposition reaction since you are breaking down one thing into parts
Degradation reactions
animation
Degradation reactions
Starch
Maltose
Catalase
The enzyme catalase breaks down the waste substance hydrogen peroxide into water and oxygen.
Hydrogen peroxide oxygen + water
(enzyme)
catalase
(substrate) (products)
Degradation reaction
Substrate
Enzyme
Product
Hydrogen peroxide
Catalase
Oxygen and water
Starch Amylase MaltoseMaltose Maltase GlucoseProtein Pepsin PeptidesPeptides Proteas
eAmino acids
Fats Lipase Fatty Acids and Glycerol
Enzyme activity
How fast an enzyme is workingRate of Reaction
Enzyme activity
How fast an enzyme is workingRate of Reaction
Rate of Reaction = Amount of substrate changed (or amount product formed) in a given period of time.
Rat
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Enzyme activity
Variable you are looking at
Enzyme activity
Four Variables
Enzyme activity
Four Variables
Temperature
pH
Enzyme Concentration
Substrate Concentration
Effects on Enzyme Activity
TemperaturepHCofactors:inorganic, nonprotein helpers; ex.: zinc, iron, copperCoenzymes:organic helpers; ex.: vitamins
Reaction rate factors• Substrate
concentration– Initially rate
increases with substrate concentration
Reaction rate factors• Substrate
concentration– Initially rate
increases with substrate concentration
Enzyme activity
Temperature and pH affect the activity of an enzyme.
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Temperature
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Temperature
0 20 30 5010 40 60
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Temperature
0 20 30 5010 40 60
40oC - denatures
5- 40oC Increase in Activity
<5oC - inactive
Effect of heat on enzyme activtyIf you heat the protein above its optimal temperature
bonds break meaning the protein loses it secondary and tertiary structure
Effect of heat on enzyme activty
Denaturing the protein
Effect of heat on enzyme activty
Denaturing the proteinACTIVE SITE CHANGES SHAPE
SO SUBSTRATE NO LONGER FITS
Even if temperature lowered – enzyme can’t regain its correct shape
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pH
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pH
1 3 42 5 6 7 8 9
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pH
1 3 42 5 6 7 8 9
Narrow pH optima
WHY?
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1 3 42 5 6 7 8 9
Narrow pH optima
Disrupt Ionic bonds - Structure
Effect charged residues at activesite
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Enzyme Concentration
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Enzyme Concentration
Enzyme Concentration
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Substrate Concentration
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Substrate Concentration
Substrate Concentration
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Substrate Concentration
Substrate Concentration
Active sites full- maximum turnover
ENZYME INHIBITORSIrreversible (covalent); reversible (weak bonds)Competitive: competes for active site (reversible); mimics the substrateNoncompetitive: bind to another part of enzyme (allosteric site) altering its conformation (shape); poisons, antibiotics
S
S
P P
Shape of the active
site changes
Optimum Condition
Enzymes function best or are most active in specific conditions known as optimum
conditions.
• Enzymes:-– Are defined as a BIOLOGICAL catalyst i.e. something that speeds up
a reaction. Up to 1012 fold– Usually end in ‘…ase’. – Discovered in 1900 in yeasts. Some 40,000 in human cells– Control almost every metabolic reaction in living organisms– Are globular proteins coiled into a very precise 3-dimentional shape
with hydrophilic side chains making them soluble– Possess an active site such as a cleft in the molecule onto which
other substrate molecules can bind to form an enzyme-substrate complex
– Once the substrate has been either synthesised or split, enzymes can be re-used.
– Do not ‘create’ reactions– Widely used in industrial cleaning– Often require co-factors (co-enzymes) to function – metal ions, or
vitamin derivatives
Amylase + starch substrate