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Biochemistry. Atoms - tiny and compose all matter. Niles Bohr created idea that all atoms had an outer cloud of tiny subatomic particles called electrons that have a neg. charge. At centre is a nucleus composed of protons and neutrons.

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atoms tiny and compose all matter
Atoms - tiny and compose all matter
  • Niles Bohr created idea that all atoms had an outer cloud of tiny subatomic particles called electrons that have a neg. charge. At centre is a nucleus composed of protons and neutrons.
  • Each proton carries a positive charge and the number of them equates to the atomic #, whereas neutrons have no charge but when weight added to protons gives atomic mass
electrons and ions
Electrons and Ions
  • positive charges of nucleus balanced with neg. charges of electrons
  • electrons are difficult to pinpoint and as such are said to be in orbitals (an area where the electron may be found) and each orbital can hold only two electrons (p.11).
  • atoms in which the number of electrons do not equal the number of protons is an ion (charged)
  • can gain or lose, Na will lose (Na+) and Cl will gain (Cl-)
electrons and ions1
Electrons and Ions
  • Energy
  • electrons have energy related to their proximity to the nucleus (potential)
  • moving an electron out requires energy and moving one in releases energy
  • shells closest have least energy and ones furthest away have most
  • lose electron = oxidation, gain electron = reduction (redox reactions)
water
Water
  • only molecule of the most common ones that exists as liquid at earth's surface temp
  • allowed movement of other molecules without having to be covalently or ionically bound when earth was first being created (evolutionary important).
polarity of water
Polarity of Water
  • water has ability to form hydrogen bonds = weak bonds with 5 to 10% of strength of covalent bonds which derives from its structure and is responsible for living chemistry
  • one oxygen and two hydrogens off to the side, no unpaired electrons and no full charge due to electron attracting power of oxygen (electronegativity) it has a slight negative charge and the hydrogen ends therein have a slight positive charge (formation of intermolecular bonds)
  • positive end of one polar molecule will interact with the negative end of another polar molecule creating the hydrogen bond
solvency of water
Solvency of Water
  • water molecules gather around any molecule that exhibits a charge, full or partial
  • salt dissolves quickly due to double charge that is picked up by the double charge of the water molecule (hydrogen with chlorine and oxygen with sodium) ~ p. 18
    • miscible = liquid that dissolves in another liquid (ethanol and ethylene glycol)
    • immiscible = liquid that does not dissolve in another liquid
      • Gasoline and oil are immiscible in water, but miscible with each other.
organelles
Organelles
  • Nucleus – nuclear pores, chromatin and nucleolus

Ribosome

Endoplasmic Reticulum

Golgi Apparatus

Mitochondrion

Lysosome

Peroxisome

Centrosome

Vacuole

Cytoskeleton

Plastids

Cell membrane

Cell wall

Flagella/Cilia

understanding the cell membrane
Understanding the Cell Membrane
  • Via electron microscopy the cell membrane was discovered to have two layers (a bilayer)
  • Via chemical analysis the bilayer was found to be a phospholipid (two fatty acids and one phosphorous group attached to a glycerol)

Allows for a polar “head” and a non-polar “tail”

Creates a phospholipidbilayer

cell membrane structure
Cell Membrane Structure
  • Membrane Activities
    • Transport raw materials into cell
    • Transport products and wastes out
    • Prevent entry of unwanted material
    • Prevent escape of desired material
  • All of this needs to be done by each and every cell in our bodies
understanding the cell membrane1
Understanding the Cell Membrane
  • The Fluid-Mosaic Membrane Model
    • Mosaic of components throughout the membrane like raisins in raisin bread
  • Components that comprise the membrane:
    • Proteins – integral and peripheral
    • Carbohydrates – glycolipid, glycoprotein
    • PhospholipidBilayer
  • Cholesterol can incorporate itself in cell membranes
    • It makes the membrane less permeable to most biological molecules
cell membrane transport
Cell Membrane Transport
  • Homeostasis – near constant conditions that our bodies stay in. It is facilitated by a number of passive and active processes
  • Brownian Motion – random movement of molecules
    • Temperature Dependent?
  • Passive transport
  • Diffusion occurs across a concentration gradient (high to low)
  • Cell size limits diffusion
    • If cell is large, substances will need to diffuse too far so this process is not favorable
cell membrane transport1
Cell Membrane Transport
  • Osmosis – the diffusion of water across a selectively permeable membrane
    • Water in the extracellular fluid (ECF) and the cytoplasm is free to move across the cell membrane.
    • The water molecules move from an area of high water concentration to an area of lower water concentration across a semi-permeable membrane
cell membrane transport2
Cell Membrane Transport
  • Isotonic solutions – water concentration inside the cell equals that outside
  • Hypotonicsolutions – water concentration outside the cell is greater then inside (water moves into cell)
    • Can cause lysis
  • Hypertonic solutions – water concentration inside the cell is greater then outside (water moves out of cell)
    • Can cause plasmolysis
cell membrane transport3
Cell Membrane Transport
  • Facilitated Diffusion
    • A carrier protein facilitates the movement of large particles (glucose) from a region of high to low concentration
    • Depends on 3D shape of protein and molecule to complete process
    • Due to the fact this is driven by a concentration gradient is it considered diffusion

Channel Proteins – work the same way however they transport ions. Channel has to have a different charge than ion being moved.

cell membrane transport4
Cell Membrane Transport
  • Active Transport
    • The cell expends energy to move substances in or out
    • Often involves moving substances against a concentration gradient
    • A resting person uses up to 40% of their energy on active transport

The system that allows this to occur is an integral protein called a pump

cell membrane transport5
Cell Membrane Transport
  • Endocytosis – process by which larger molcules are accepted into the cell
    • Pinocytosis – small droplets of ECF are accepted into the cell
    • Phagocytosis – large droplets of ECF are accepted into the cell
    • Receptor-assisted endocytosis – membrane receptors attach to special materials in the ECF and accept them into the cell
  • Exocytosis – reverse of endocytosis
chemical basis of life

Chemical Basis of Life

Chemical Fundamentals (p. 24 - 55)

carbon
Carbon
  • Carbon atoms can form straight and branched chains as well as ring structures of various sizes and complexity. These act as backbones for biological molecules.
  • hydrogen, oxygen, sulfur and phosphorous can attach to the carbon backbone to form reactive clusters known as functional groups (p. 25).
  • Bonding capacity is the number of covalent bonds an atom can form with a neighbouring atom (p. 26).
chemical building blocks
Chemical Building Blocks
  • molecules formed by living organisms contain carbon and are called organic molecules and have carbons at centre and functional groups extending out (-OH is hydroxyl, -COOH is carboxyl).
  • most chemical rxns in body are transferring functional groups or breaking carbon bonds
  • some molecules are simple and others are quite complex and play a structural role or store information for the organism and are called macromolecules
  • there are 4 main types which are made up of smaller subunits: carbohydrates, lipids, proteins, nucleic acids
creation and destruction of macromolecules fig 5 p 28
Creation and Destruction of Macromolecules(fig. 5 p. 28)
  • The four macromolecules that exist all are put together in the same way.
    • Hydroxyl from one subunit and hydrogen is removed from the other (dehydration synthesis or condensation). Absorption of energy occurs. Referred to as anabolic reactions because large molecules are being made from smaller ones.
      • requires the correct chemical bonds being broken and is facilitated by catalysts which are special proteins called enzymes
creation and destruction of macromolecules fig 5 p 281
Creation and Destruction of Macromolecules (fig. 5 p. 28)
  • breaking substances down is just as important and it involves the addition of water (hydrolysis reaction) to an area where a covalent bond has been broken ~ essentially the undoing of a condensation reaction.
    • Referred to as catabolic as macromolecules are broken down into smaller subunits which usually occur during digestion.
carbohydrates
Carbohydrates
  • molecules that contain C:H:O in a 1:2:1 ratio
  • good for energy storage because they contain many C-H bonds which are most often broken by organisms to obtain energy
  • energy source; building materials; cell surface markers
sugars
Sugars
  • simplest are monosaccharides (taste sweet) and the most important of which is created by plants (C6H12O6)
  • can exist in straight form but when in water solution, almost always form rings
  • primary energy store in living organisms is glucose with 6 carbons
  • monosaccharides have an aldehyde (end) or ketone (middle) functional group attached to their carbon backbone (p.29)
sugars1
Sugars
  • ISOMERS = molecules with the same chemical formula but a different arrangement of atoms (glucose, galactose, fructose)
  • disaccharides or trisaccharides (oligosaccharides) are formed to allow easier transport throughout the body
    • sucrose (table sugar) is glucose + fructose
  • polysaccharides are several hundred monosaccharides linked together
    • serve as energy storage (starch and glycogen) and structural support (cellulose and chitin)
starches
Starches
  • storage of glucose as an insoluble form by joining them together into long polymers called polysaccharides (if side chains off the main, even less soluble)
  • starches are polysaccharides formed from glucose
    • examples are amylose, amylopectin and glycogen (animals) which is formed if there are too many glucose molecules within our bodies
cellulose
Cellulose
  • as compared to starch, in which all chains are attached to one side of the main chain, cellulose has the subunits of glucose switching back and forth making a more linear arrangement
  • because cellulose is not easily broken down, it works well as a biological structural material and occurs widely in this role in plants
  • good source of energy if you can break it down but not many organisms can. Cows break it down using bacteria in their stomachs and human need it to assist digestion
  • structural material in insects, fungi and other organisms is called chitin (adds nitrogen) = very difficult to digest as it is tough, resistant surface (p.34).
lipids
Lipids
  • insoluble in water (hydrophobic), but soluble in oil
  • contain fewer polar O-H bonds but more non-polar C-H bonds in comparison to carbohydrates
    • storage of energy, insulation, building membranes and chemical signaling molecules.
    • Fats, phospholipids, steroids, waxes
lipids fats
Lipids - Fats
  • long term insoluble storage molecules that contain more C-H bonds then normal carbohydrates
  • starches are insoluble due to long polymers but fats are insoluble because they are non-polar therein fat molecules will cluster together and are not soluble in water
  • 1 gram of fat = 38kJ of chemical energy
  • 1 gram of carbohydrate or protein = 17kJ of chemical energy
  • SI units = 1 cal (on food labels) equates to 4.18kJ
lipids fats1
Lipids - Fats
  • Fat molecules are built from two different kinds of subunits:

1. Glycerol - 3 carbon alcohol with each carbon bearing a hydroxyl (OH) group, backbone to which three fatty acids are attached

2. Fatty Acids - long hydrocarbons ending in carboxyl (COOH)

slide32

if there are three fatty acids attached to the backbone the resulting structure is a triglyceride

  • they vary in length between 14 and 20 carbons and if all carbons are all single bonds they are called saturated, if double bonds there is fewer then maximum number of hydrogen atoms and are called unsaturated
  • saturated fatty acids fit together closely and utilize van der Waals forces which increase the attraction between molecules and allow these molecules to be solids at room temperature.
slide33

if a fat has more than one double bond it is said to be polyunsaturated and have low melting points due to the fat molecules not being closely aligned

  • a liquid fat is called an oil but can be converted to solid by adding hydrogen (p.b.)
  • fats are much more efficient at storing energy and will yield twice as much chemical energy as carbos
  • esterification = glycerol is linked to fatty acids creating ester linkages (p. 37).
lipids phospholipids
Lipids - Phospholipids
  • - glycerol, two fatty acids and a highly polar phosphate group (polar) (p.38)
sterols steroids
Sterols (Steroids)
  • hydrophobic molecules containing four fused hydrocarbon rings and different functional groups.
  • cholesterol is a type of lipid called a steroid which when too much is ingested causes
    • plaques (atherosclerosis) to form which block blood vessels which may lead to blockage, high blood pressure, stroke or heart attack.
  • cells convert cholesterol into a number of compounds (vitamin
    • D, bile salts)
  • sex hormones for males and females are also steroids
    • membranes of cells are phospholipids, terpenes make up photosynthetic pigment carotene and light absorbing pigment carotene retinol found in your eyes
lipids waxes
Lipids - Waxes
  • lipids with long-chain fatty acids linked to alcohols or carbon rings
  • hydrophobic with a firm, pliable consistency = good for waterproofing (i.ecutin on plants or feathers of birds)
proteins
Proteins
  • most important proteins are enzymes which allow rxns to occur more quickly but remain unaffected or unaltered themselves (catalysts)
  • cartilage, bones, tendons, keratin, peptides (brain) all are made up of proteins
  • all are a long polymer chain of amino acid subunits linked end to end
  • structural building blocks and functional molecules which are what our DNA codes for
amino acids
Amino Acids
  • contain an amino group (-H2N) a carboxyl group (-COOH) a hydrogen atom and a functional group (R), all bonded to a central carbon atom (fig. 28, p. 41)
  • identity of each AA is linked to R group, 20 different R groups so 20 different AAs (p.49)
  • grouped into 5 chemical classes based on chemical nature of side groups
  • AA are amphiprotic which means they possess acidic (carboxyl) and basic (amino) R groups.
  • when ionized a positive amino (NH3+) at one end and a negative carboxyl (COO-) at the other which can allow a covalent bond to form between two amino acids called a peptide bond
  • 8 essential AA (must be obtained from food) and 12 we can create ourselves
polypeptides fig 30 p 43 fig 31 p 44
Polypeptides (fig. 30, p. 43 & fig.31, p. 44)
  • name given to long chain of amino acids linked end to end using peptide bonds
    • each protein has a sequence of steps that it goes through in its formation (occurring in cytoplasm):
  • Primary Structure
  • simple linking of AA together in a linear chain (peptide bond)
    • amino terminus (A-terminus) & carboxyl terminus (C-terminus)
    • completed by protein synthesis, one altered base pair could render protein useless
slide40

Secondary Structure

  • - each AA interacts with neighbors due to R chains and H bonds are created that allow B-pleated sheets and helices to be formed
slide41

Tertiary Structure

  • - depends a great deal on the secondary structure but is a folding back upon itself of the chain and
  • sheets and helices due to whether the R groups are polar or non-polar.
    • h-bonds, ionic bonds and van der Waals forces keep the polypeptide folded in its shape
    • cysteine has S in its R group and when near each other will form a disulfide bridge
slide42

Quaternary Structure

  • two polypeptides associate to form a functional unit, do not all need to be identical to come together (protein hemoglobin: 2 of type A polypeptide, 2 of type B polypeptide)
types of proteins
Types of Proteins
  • Globular Proteins
  • = carry out chemical reactions, antibodies (infection) are also globular
  • = composed of one or more polypeptide chains and are round
  • Structural Proteins
  • = keratin in hair, actin and myosin in muscles, most abundant (collagen)
denaturing
Denaturing
  • environment matters (pH, temperature, ionic concentration, chemicals)
  • usually return to normal when agent is removed provided polypeptide is still intact
    • Gastrin = enzyme in stomach works at a pH of 2, once in small intestine the pH is 10 so it denatures
  • Chaperone proteins = aid the growing polypeptide to fold into its tertiary structure
nucleic acids
Nucleic Acids
  • are long information storage polymers made up of repeating subunits called nucleotides
  • nucleotides are each made up of 3 smaller building blocks (fig. 42, p. 53):
  • 5-carbon (pentose) sugar
  • phosphate group (PO4-)
  • organic nitrogenous base
  • sugars are linked together in line by the phosphate groups creating a phosphodiester bond in which the phosphate group of one sugar binds to the hydroxyl group of the next sugar.
nucleic acids1
Nucleic Acids
  • the nitrogenous bases protrude out from the sugar and can be of 4 different types when dealing with DNA sequencing (guanine = cytosine, adenine = thymine)
  • DNA is a double chain (strand) of these nucleotides wrapped in a helix held with hydrogen bonds. The two strands are said to run antiparallel.
nucleic acids2
Nucleic Acids
  • - order codes genetic information and more directly the order and type of proteins that are going to be created and therein the distinctive traits in the body
  • DNA is also the unit that permits the transmission of hereditary information to offspring, master copy, but also RNA (ribonucleic acid) that is a temporary copy of sections of DNA that allows the aforementioned proteins to be created
slide48

Nitrogenous bases broken down into purines and pyrimidines (fig. 42, p.53)

    • Pyrimidines = small single rings  cytosine, thymine (DNA), uracil (RNA)
    • Purines = large double ring compounds  guanine, adenine
  • Nucleotides are also important intermediaries in a cell’s energy transformations
    • ATP = adenosine triphosphate ~ drives all of cell’s energy reactions
    • NAD+ = nicotinamide adenine dinucleotide ~ nucleotide derivative used in making ATP
    • NADP+ = nucleotide similar to NAD+ is used as a coenzyme in photosynthesis
chemical basis of life1

Chemical Basis of Life

Metabolism (p. 58 - 67)

energy and metabolism
Energy and Metabolism
  • if you stopped eating you would eventually die as your body would be deprived of its source of energy (the ability to do work).
    • life is a constant flow of energy, ingesting it, storing it and using it
  • living chemistry, all reactions that an organism performs is called metabolism (sum of all anabolic and catabolic processes).
energy
Energy
  • ability to bring about change or to do work
    • exists in two states: energy actively engaged in doing work (kinetic) and not actively doing work but has the capacity to do so (potential) (fig 1, p. 59)
  • work performed by living organisms involves the transfer of potential energy to kinetic energy
    • unit of kcal which is a unit of heat (all energy can be transferred to heat so it is used)

=1 cal is heat required to raise the temp of 1 gram of water 1 degree

thermodynamics
Thermodynamics
  • First Law of Thermodynamics - energy can change forms and can transform from potential to kinetic but it can be neither created nor destroyed. Total amount of energy in universe is constant.
  • potential energy in nut that a squirrel eats is then transferred to squirrel as potential energy (fat) and kinetic energy (running) and almost half is dissipated to the environment as heat where it speeds up the random motions of molecules (not lost, just not useful)
thermodynamics1
Thermodynamics
  • bond energy is a form of potential energy. It is the measure of the stability of a covalent bond, measured in kJ and is equal to the minimum energy required to break one mole of bonds between two types of atoms (table 1, p.59).
  • first law states that the universe is a closed system and no energy comes in or out but the earth itself is not a closed system as we are consistently receiving energy from the sun (photosynthesis transfers light energy to chemical energy which we and all animals use)
activation energy
Activation Energy
  • Potential energy diagram shows changes in potential energy that take place during a chemical reaction (fig. 2, p. 60)
    • energy that is required to start a reaction whether exothermic (energy released) or endothermic (energy required)
  • The change in energy is called the enthalpy of the reaction (ΔH).
  • ΔH is positive for endothermic reactions and negative for exothermic reactions.
  • The speed of the reaction does not depend on how much energy is going to be released (exothermic) but how much activation energy is initially put in
  • Catalysts are substances that lower the activation energy therein allowing reactions to occur more readily
entropy
Entropy
  • - a measure of the disorder of a system. Entropy increases when disorder increases.
  • - as energy transfers from potential to kinetic some is lost therefore the amount of useful energy available to do work decreases as progressively more energy is degraded to heat.
  • - when universe was formed 14 bya it had all the potential energy it was going to have and, favouring randomness, eventually all energy will be in a random and unusable form (100 by)
free energy gibbs free energy
Free Energy (Gibbs Free Energy)
  • energy that can do useful work.
  • A relationship between energy change, entropy change and the temperature of a reaction and allows us to predict if a reaction will occur spontaneously or not.
    • ΔG is the change in Gibbs free energy.
  • If ΔG is negative the changes are spontaneous (exergonic). If ΔG is positive that number is the amount of free energy required to drive the reaction and it is not spontaneous (endergonic).
  • Also, a change with a negative ΔG in one direction has an equivalent positive ΔG in the reverse direction.
thermodynamics2
Thermodynamics
  • Second Law of Thermodynamics - disorder (entropy) in universe is constantly increasing and that energy will spontaneously convert to less organized forms
    • disorder is more likely than order (a stack of six soda cans will tumble over then will six soda cans spontaneously leap and form a stack)
  • Think about this…organisms facilitate organization (molecules, nests, webs, homes) which seems in contrast to the second law of thermodynamics however, the apparent order created by anabolic processes is accompanied and counteracted by disorder causing catabolic reactions.
  • Cellular Respiration  ΔG = -2870kJ/mol C6H12O6 used
  • Photosynthesis  ΔG = +2870kJ/mol C6H12O6 formed
atp energy
ATP = ENERGY
  • adenosine triphosphate drives almost every energy requiring process that cells can perform (active transport, power movement, provide activation energy and to grow)
  • each ATP molecule is composed of three subunits (fig 8a, p. 65)

1. 5 carbon sugar = backbone to which other two are attached

2. Adenine = two carbon-nitrogen rings

    • each N in the ring has a pair of unshared electrons that weakly attract hydrogen ions therefore acts as a chemical base and is often referred to as a Nitrogenous Base
atp energy1
ATP = ENERGY

3. Triphosphate group = three phosphates linked together in a chain via high energy covalent bonds (linkage occurs due to a process called phosphorylation).

      • referred to as a high energy potential because bonds have low activation energy and are broken easily
      • outermost will break off easiest creating ADP
  • ATP is used to drive endergonic reactions and as such when the terminal P is hydrolyzed off there is a release of 31kJ/mol (ΔG = -31kJ/mol). It is noteworthy that in a living cell this amount of energy release is 54kJ/mol.
types of reactions there are four hydrolysis condensation neutralization redox
Types of Reactions – there are four (hydrolysis, condensation, neutralization, redox)
  • Hydrolysis
neutralization
Neutralization
  • Acids, Bases & Buffers
  • water molecules can react with each other
    • H20 + H2O  H3O+ + OH-
    • Hydronium & Hydroxide
  • Pure water
    • covalent bonds of water sometimes break, protons in hydrogen atom dissociates (H+)
    • remaining water retains shared electron but has one less proton so (OH-)
  • Acids = HCl(g) + H2O(l) H3O+(aq) + Cl-(aq)
  • Bases = NaOH(s) Na+(aq) + OH-(aq)
  • Neutralization Reaction
    • Acid + Base  Water + Salt
redox reactions
Redox Reactions
  • chemical reactions transfer one or more electrons from one reactant to another.
  • LEO says GER= Loss of Electrons is Oxidation and Gain of Electrons is Reduction
  • the substance that provides the electron is called the reducing agent
  • the substance that takes the electron is called the oxidizing agent

Na + Cl Na+ + Cl-

  • Loses electron Gains electron
  • Reducing agent Oxidizing agent sodium chloride
redox reactions1
Redox Reactions
  • energy can be stored in atoms if the energy added can boost an electron up an energy level and chemical energy can be released later by dropping the electron back to its original energy level
  • energy in chemical bonds can be transferred to new bonds and may involve electron transfer from one atom or molecule to another and these are oxidation/reduction reactions which are critical for life on earth
  • Redox is a key role in energy flow because as electrons pass form one atom to another they carry their own potential energy (they maintain their distance from the nucleus)
redox reactions2
Redox Reactions
  • Photosynthesis excites an electron and this is passed along as is the potential energy that goes with that until the electron returns to its original lower energy level.
  • in biological systems electrons do not travel around alone but will travel with a proton to make up H
    • therefore removal of H is oxidation and addition of H is reduction
redox reactions3
Redox Reactions
  • Photosynthesis
    • H transferred from H2O to CO2, reducing the CO2 to form C6H12O6
    • in this reaction electrons move to higher energy levels
    • CO2 to C6H12O6 stores 686 kcal of energy in the chemical bonds of the glucose
    • conversely cellular respiration is the reverse reaction in which glucose gets oxidized, H atoms are lost by glucose and gained by oxygen and this releases 686 kcal of energy
chemical basis of life2

Chemical Basis of Life

Enzymes (pg. 69-78)

chemical change
Chemical Change
  • Takes place when bonds between reactant molecules are broken and the rearrangement of atoms causes bonds to form between product molecules.
  • For bonds between reactant molecules to break, molecules must collide with enough force and the correct geometric orientation. Also, all reactions have an activation energy barrier that must be met. When these conditions are met, the transition state is reached and product molecules are formed.
  • The rate of reaction can be increased by increasing the heat or by adding a catalyst.
    • Which of these would be better suited to increase the rate of reactions occurring in a living organism?
catalysts
Catalysts
  • A substance that speeds up a chemical reaction: reactants are converted to products at a faster rate
    • How does a catalyst speed up the chemical reaction?
  • Catalysts are not consumed in a chemical reaction. Throughout the reaction they remain intact and at the completion of the reaction they are able to be used immediately to catalyze the same reaction again.
  • Catalysts can only speed up reactions that would occur anyways
    • They speed up both the forward and reverse reactions equally, thus they cannot change the position of equilibrium, only how fast that equilibrium is reached.
catalysts1
Catalysts
  • CO2 + H2O ↔ H2CO3
  • In the presence of carbonic anhydrase (enzyme), 600 000 molecules of product are formed every second
  • No enzyme 200 molecules of product/hour  increased by 10 million times
substrates and enzymes
Substrates and Enzymes
  • The substrate is the reactant that an enzyme acts on when it catalyzes a reaction
  • Substrates bind to a location on the enzyme referred to as the active site
    • Enzymes are specific for a particular substrate and usually will not bind an isomer of the substrate
  • Enzymes are protein catalysts, and they usually end in the suffix -ase
    • What property do proteins possess that would make them ideal enzymes (ie- specific for a substrate)?
enzyme substrate interaction induced fit model
Enzyme – Substrate Interaction (Induced Fit Model)
  • As the substrate enters the active site on the enzyme, its functional groups come into close contact with the functional groups on the amino acids
    • This interaction causes the protein (enzyme) to change shape to better accommodate the substrate
      • This is where the name “induced fit” comes from
  • The attachment of the substrate to the enzyme’s active site creates the enzyme-substrate complex
factors affecting the rate of enzyme activity
Factors Affecting the Rate of Enzyme Activity
  • Temperature
    • Increase the heat, increase the speed of reaction
      • Heat from the cell’s internal environment helps bring the substrate molecule to transition state
    • Every enzyme has an optimal temperature – above or below this temperature the enzyme does not work as well.
      • High temperatures disrupt protein structure resulting in denaturation and loss of enzyme function
      • Low temperatures result in bonds that are too rigid to allow induced fit
    • At what temperature would you expect most human enzymes to work optimally?
factors affecting the rate of enzyme activity1
Factors Affecting the Rate of Enzyme Activity
  • pH
    • Enzymes have an optimal pH at which they work best
      • Digestive enzyme pepsin works optimally at pH 2
      • Digestive enzyme trypsin works optimally ay pH 8
    • The active site, via the presence of acidic R groups, may provide an acidic environment in an otherwise neutral part of the cell thus allowing certain reactions to proceed more rapidly.
factors affecting the rate of enzyme activity2
Factors Affecting the Rate of Enzyme Activity
  • Saturation
    • Enzymes can become saturated with substrate; at this point adding more substrate will not increase the rate of reaction, because the enzymes are saturated with substrate
  • Enzyme requirements
    • Some enzymes require non-protein cofactors or organic coenzymesbefore they can work properly.
        • These molecules may bind to the active site with covalent bonds or bind weakly with the substrate
      • Cofactors include zinc (Zn2+) and magnesium (Mg2+) ions which become locked into active sites and help draw electrons from substrate molecules
      • Coenzymes include derivatives of many vitamins (NAD+, a derivative of vitamin B3)
        • NAD+ acts as an electron carrier in cellular respiration
        • NADP+ performs a similar role in photosynthesis
enzyme inhibition
Enzyme Inhibition
  • A variety of substances inhibit enzyme activity, but they do so in different ways
  • A competitive inhibitor is so similar to the actual substrate that it is able to enter the active site and block the normal substrate from binding (fig 6, p. 73)
    • This process is reversible!
    • What can we do to combat a competitive inhibitor?
enzyme inhibition1
Enzyme Inhibition
  • A non-competitive inhibitor does not bind to the enzymes active site. Instead, it attaches itself to another site on the enzyme – this binding causes a change in the conformation of the enzyme such that the enzyme loses its affinity for the substrate, or the binding may result in a loss of enzyme activity
    • Why is it that people who smoke are more likely to be short of breath during exercise than their non-smoking counterparts?
allosteric regulation
Allosteric Regulation
  • A way of allowing cells to control enzyme activity though the use of an allosteric site
    • Works by either restricting the production of a particular enzyme or by inhibiting the action of a particular enzyme that has already been produced.
    • Allosteric regulators attach to their sites using weak bonds
  • The allosteric site is usually located a fair distance away from the active site
allosteric regulation1
Allosteric Regulation
  • Substances that bind to the allosteric site may be either activators (stabilizes the protein keeping all active sites open) or inhibitors (stabilize the inactive form of the enzyme)
  • The binding of an activator or inhibitor to one allosteric site will affect the activity of ALL active sites on an enzyme.
feedback inhibition
Feedback Inhibition
  • Is a method used by cells to control metabolic processes involving a sequence of reactions, each catalyzed by a particular enzyme
  • A product formed later in the sequence of reactions will then act to allosterically inhibit an enzyme that catalyzes a reaction occurring earlier in the sequence (fig. 8, p. 74).
    • As the product is used up, there is less of it present in the cell to allosterically inhibit the enzyme; this causes the enzyme to be in its active form more often, thus catalyzing the earlier reaction in the sequence to drive the process to produce more product.
    • Your household thermostat also works via feedback inhibition!
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Feedback Inhibition
  • LOCATION of enzymes is also important
    • Cellular respiration enzymes  some are in cytoplasm and others are in the inner matrix of the mitochondria.
commercial and industrial uses of enzymes
Commercial and Industrial Uses of Enzymes
  • Starch Industry
    • Uses enzymatic hydrolysis to convert starch to glucose syrups (used as a sweetener in foods such as candies, jams, jellies, and pharmaceuticals such as cough syrups)
    • In a common process, amylase, produced by the bacterium Bacillus licheniformis, hydrolyzes starch to maltose. Then the enzyme glucoamylase, produced by moulds such as Aspergillusand Rhizopus, is added to hydrolyze maltose into individual glucose molecules.
commercial and industrial uses of enzymes1
Commercial and Industrial Uses of Enzymes
  • Dairy Industry
    • Uses protein hydrolyzing enzymes (proteases) to coagulate milk for the manufacture of cheese
    • Uses fat hydrolyzing enzymes (lipases)to develop characteristic cheeses (strong flavored cheese such as Romano)
  • Cleaning Industry
    • Uses proteases and amylases to remove stains such as blood, grass, milk, and perspiration from clothing
    • Dirt commonly found on clothing contains proteins, starch and lipids. Enzymes allow stains to be removed from clothing at a lower temperature and with less agitation