Biochemistry

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An introduction to biochemistry in bringing back your knowledge from your inorganic and organic chemistry subjects.

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Biochemistry

  1. 1. BIOCHEMISTRYBIOCHEMISTRY
  2. 2. CHEMISTRY OF LIFECHEMISTRY OF LIFE • ElementsElements: simplest form of a: simplest form of a substance - cannot be broken downsubstance - cannot be broken down any further without changing what it isany further without changing what it is • AtomAtom: the actual basic unit -: the actual basic unit - composed of protons, neutrons, andcomposed of protons, neutrons, and electronselectrons
  3. 3. THE ATOMTHE ATOM • Just like cells are the basic unit of life, theJust like cells are the basic unit of life, the ATOMATOM is the basic unit of matter.is the basic unit of matter. • They are very small. If placed side by sideThey are very small. If placed side by side one million would stretch a distance of 1cm.one million would stretch a distance of 1cm. • The atom is made up ofThe atom is made up of 33 particles.particles. ParticleParticle ChargeCharge PROTONPROTON ++ NEUTRONNEUTRON NEUTRALNEUTRAL ELECTRONELECTRON --
  4. 4. • Electrons are not present within the atom,Electrons are not present within the atom, insteadinstead THEY REVOLVE AROUND THETHEY REVOLVE AROUND THE NUCELUS OF THE ATOM & FORM THENUCELUS OF THE ATOM & FORM THE ELECTRON CLOUDELECTRON CLOUD • Draw a helium atom. Indicate where theDraw a helium atom. Indicate where the protons, neutrons and electrons are.protons, neutrons and electrons are. + + - - PROTONS NEUTRONS ELECTRONS ATOMIC # = 2 (PROTONS) ATOMIC MASS = 4 (PROTONS & NEUTRONS)
  5. 5. ISOTOPESISOTOPES • atoms of the same element thatatoms of the same element that HAVE AHAVE A DIFFERENT NUMBER OF NEUTRONSDIFFERENT NUMBER OF NEUTRONS • Some isotopes are radioactive. This meansSome isotopes are radioactive. This means that their nuclei is unstable and will breakthat their nuclei is unstable and will break down at adown at a CONSTANT RATECONSTANT RATE over time.over time. • There are several practical uses forThere are several practical uses for radioactive isotopes:radioactive isotopes: 1.1. CARBON DATINGCARBON DATING 2.2. TRACERSTRACERS 3.3. KILL BACTERIA / CANCER CELLSKILL BACTERIA / CANCER CELLS
  6. 6. COMPOUNDSCOMPOUNDS • a substance formed by the chemicala substance formed by the chemical combination ofcombination of 2 or more elements2 or more elements in definitein definite proportionsproportions – Ex: water, salt, glucose, carbon dioxideEx: water, salt, glucose, carbon dioxide
  7. 7. • The cell is aThe cell is a COMPLEX CHEMICALCOMPLEX CHEMICAL FACTORYFACTORY containing some of the samecontaining some of the same elements found in the nonlivingelements found in the nonliving environment.environment. • carbon (C), hydrogen (H), oxygen (O), andcarbon (C), hydrogen (H), oxygen (O), and nitrogen (N) are present in the greatestnitrogen (N) are present in the greatest percentagespercentages
  8. 8. TWO TYPES OFTWO TYPES OF COMPOUNDSCOMPOUNDS • Organic - Contain C, H, and O in someOrganic - Contain C, H, and O in some ratio (usually referred to as chemicals ofratio (usually referred to as chemicals of life)life) – Carbohydrates, Proteins, Lipids, Nucleic AcidsCarbohydrates, Proteins, Lipids, Nucleic Acids • Inorganic - usually "support" life - noInorganic - usually "support" life - no specific ratio of C, H, and Ospecific ratio of C, H, and O – Water (H2O), Carbon Dioxide (CO2)Water (H2O), Carbon Dioxide (CO2)
  9. 9. CHEMICAL BONDSCHEMICAL BONDS • Chemical bonds hold the atoms in aChemical bonds hold the atoms in a molecule together.molecule together. • There are 2 types of chemical bondsThere are 2 types of chemical bonds IONICIONIC andand COVALENTCOVALENT
  10. 10. IONIC BONDSIONIC BONDS • Occur when 1 or more electrons areOccur when 1 or more electrons are TRANSFERREDTRANSFERRED from one atom to another.from one atom to another. • When an atom loses an electron it is aWhen an atom loses an electron it is a POSITIVEPOSITIVE charge.charge. • When an atom gains an electron it is aWhen an atom gains an electron it is a NEGATIVENEGATIVE chargecharge • These newly charged atoms are now calledThese newly charged atoms are now called IONSIONS – Example: NaCl (SALT)Example: NaCl (SALT)
  11. 11. COVALENT BONDSCOVALENT BONDS • Occur when electrons areOccur when electrons are SHAREDSHARED by atoms.by atoms. • These new structures that result from covalentThese new structures that result from covalent bonds are calledbonds are called MOLECULESMOLECULES • ** In general, the more chemical bonds a** In general, the more chemical bonds a molecule has the more energy it containsmolecule has the more energy it contains SHARING IS CARING!SHARING IS CARING!
  12. 12. MIXTURESMIXTURES • Water is not always pure. It is often found asWater is not always pure. It is often found as part of a mixture.part of a mixture. • A mixture is a material composed ofA mixture is a material composed of TWO ORTWO OR MORE ELEMENTS OR COMPOUNDS THATMORE ELEMENTS OR COMPOUNDS THAT ARE PHYSICALLY MIXEDARE PHYSICALLY MIXED – Ex: salt & pepper mixed, sugar and sand –Ex: salt & pepper mixed, sugar and sand – can becan be easily separatedeasily separated
  13. 13. SOLUTIONSOLUTION Two parts:Two parts: • SOLUTE –SOLUTE – SUBSTANCE THAT IS BEINGSUBSTANCE THAT IS BEING DISSOLVED (SUGAR / SALT)DISSOLVED (SUGAR / SALT) • SOLVENTSOLVENT - the substance in which the solute- the substance in which the solute dissolvesdissolves • Materials that do not dissolve are known asMaterials that do not dissolve are known as SUSPENSIONSSUSPENSIONS.. – Blood is the most common example of aBlood is the most common example of a suspension.suspension. – Cells & other particles remain in suspension.Cells & other particles remain in suspension.
  14. 14. FORMULAFORMULA • The chemical symbols and numbers thatThe chemical symbols and numbers that compose a compound ("compose a compound ("reciperecipe")") • Structural FormulaStructural Formula – Line drawings of the– Line drawings of the compound that shows the elements incompound that shows the elements in proportion and how they are bondedproportion and how they are bonded • Molecular FormulaMolecular Formula – the ACTUAL– the ACTUAL formula for a compoundformula for a compound CC22HH66OO
  15. 15. ACIDS & BASESACIDS & BASES • Acids: always (almost) begin with "H" becauseAcids: always (almost) begin with "H" because of the excess of H+ ions (hydrogen)of the excess of H+ ions (hydrogen) – Ex: lemon juice (6), stomach acid (1.5), acid rainEx: lemon juice (6), stomach acid (1.5), acid rain (4.5), normal rain (6)(4.5), normal rain (6) Facts about AcidsFacts about Acids • Acids turn litmus paperAcids turn litmus paper BLUEBLUE and usuallyand usually tastetaste SOURSOUR.. • You eat acids daily (coffee, vinegar, soda,You eat acids daily (coffee, vinegar, soda, spicy foods, etc…)spicy foods, etc…)
  16. 16. ACIDS & BASESACIDS & BASES • Bases: always (almost) end with -OH becauseBases: always (almost) end with -OH because of the excess of hydroxide ions (Oxygen &of the excess of hydroxide ions (Oxygen & Hydrogen)Hydrogen) – EX: oven cleaner, bleach, ammonia, sea water,EX: oven cleaner, bleach, ammonia, sea water, blood, pure waterblood, pure water Facts about BasesFacts about Bases • Bases turn litmusBases turn litmus BLUEBLUE.. • Bases usually feelBases usually feel SLIPPERYSLIPPERY to touch andto touch and tastetaste BITTERBITTER..
  17. 17. Neutralization ReactionsNeutralization Reactions • When an acid reacts with a base to produce aWhen an acid reacts with a base to produce a salt and water.salt and water.
  18. 18. pH SCALEpH SCALE • measures degree ofmeasures degree of substance alkalinity orsubstance alkalinity or acidityacidity • Ranges fromRanges from 0 to 140 to 14 • 0 – 5 strong acid0 – 5 strong acid • 6-7 neutral6-7 neutral • 8-14 strong base8-14 strong base
  19. 19. • The goal of the body is to maintainThe goal of the body is to maintain HOMEOSTASIS (neutrality)HOMEOSTASIS (neutrality) – to do this when– to do this when pH is concerned, we add weak acids & bases topH is concerned, we add weak acids & bases to prevent sharp changes in pH.prevent sharp changes in pH. • These are calledThese are called BUFFERSBUFFERS
  20. 20. And now for theAnd now for the Biochemistry portion ofBiochemistry portion of things….things….
  21. 21. CARBOHYDRATESCARBOHYDRATES • Living things use carbohydrates as a key sourceLiving things use carbohydrates as a key source ofof ENERGYENERGY!! • Plants use carbohydrates for structurePlants use carbohydrates for structure ((CELLULOSECELLULOSE)) – include sugars and complex carbohydratesinclude sugars and complex carbohydrates (starches)(starches) – contain the elements carbon, hydrogen, and oxygencontain the elements carbon, hydrogen, and oxygen (the hydrogen is in a 2:1 ratio to oxygen)(the hydrogen is in a 2:1 ratio to oxygen)
  22. 22. Monosaccharides (simple sugars)Monosaccharides (simple sugars) • all have the formula C6 H12 O6all have the formula C6 H12 O6 • all have a single ring structureall have a single ring structure – (glucose is an example)(glucose is an example)
  23. 23. Disaccharides (double sugars)Disaccharides (double sugars) • all have the formula C12 H22 O11all have the formula C12 H22 O11 • sucrose (table sugar) is an examplesucrose (table sugar) is an example
  24. 24. PolysaccharidesPolysaccharides • Formed of three or more simple sugar unitsFormed of three or more simple sugar units • Glycogen - animal starch stored in liver & musclesGlycogen - animal starch stored in liver & muscles • Cellulose - indigestible in humans - forms cell wallsCellulose - indigestible in humans - forms cell walls • Starches - used as energy storageStarches - used as energy storage
  25. 25. How are complexHow are complex carbohydrates formedcarbohydrates formed and broken down?and broken down?
  26. 26. Dehydration SynthesisDehydration Synthesis • Combining simple molecules to form a moreCombining simple molecules to form a more complex one with thecomplex one with the removal of waterremoval of water – ex. monosaccharide + monosaccharide ---->ex. monosaccharide + monosaccharide ----> disaccharide + waterdisaccharide + water – (C6H12O6 + C6H12O6 ----> C12H22O11 + H2O(C6H12O6 + C6H12O6 ----> C12H22O11 + H2O • Polysaccharides are formed from repeatedPolysaccharides are formed from repeated dehydration syntheses of waterdehydration syntheses of water – They are the stored extra sugars known as starchThey are the stored extra sugars known as starch
  27. 27. HydrolysisHydrolysis • Addition ofAddition of WATERWATER to a compound toto a compound to SPLITSPLIT it into smaller subunitsit into smaller subunits – (also called chemical digestion)(also called chemical digestion) – ex. disaccharide + H2O --->ex. disaccharide + H2O ---> monosaccharide + monosaccharidemonosaccharide + monosaccharide C12 H22 O11 + H2 O ---> C6 H12 O6 + C6 H12 O6C12 H22 O11 + H2 O ---> C6 H12 O6 + C6 H12 O6
  28. 28. Lipids (Fats)Lipids (Fats) • Fats, oils, waxes, steroidsFats, oils, waxes, steroids • Chiefly function inChiefly function in energy storage, protection,energy storage, protection, and insulationand insulation • Contain carbon, hydrogen, and oxygen but theContain carbon, hydrogen, and oxygen but the H:O is not in a 2:1 ratioH:O is not in a 2:1 ratio • Tend to beTend to be largelarge molecules -- an example of amolecules -- an example of a neutral lipid is belowneutral lipid is below
  29. 29. • Neutral lipids are formed from the union ofNeutral lipids are formed from the union of oneone glycerol molecule and 3 fatty acidsglycerol molecule and 3 fatty acids • 3 fatty acids + glycerol ----> neutral fat (lipid)3 fatty acids + glycerol ----> neutral fat (lipid) • Fats -- found chiefly inFats -- found chiefly in animalsanimals • Oils and waxes -- found chiefly inOils and waxes -- found chiefly in plantsplants • Oils are liquid at room temperature, waxes areOils are liquid at room temperature, waxes are solidssolids • Lipids along with proteins are key components ofLipids along with proteins are key components of cell membranescell membranes • Steroids are special lipids used to build manySteroids are special lipids used to build many reproductive hormones and cholesterolreproductive hormones and cholesterol
  30. 30. PROTEINSPROTEINS • contain the elements carbon, hydrogen, oxygen,contain the elements carbon, hydrogen, oxygen, and nitrogenand nitrogen • composed of MANY amino acid subunitscomposed of MANY amino acid subunits • It is the arrangement of the amino acid thatIt is the arrangement of the amino acid that forms the primary structure of proteins.forms the primary structure of proteins. • The basic amino acid form has aThe basic amino acid form has a carboxylcarboxyl groupgroup on one end, aon one end, a methyl groupmethyl group that onlythat only has one hydrogen in the middle, and ahas one hydrogen in the middle, and a aminoamino groupgroup on the other end.on the other end. • Attached to the methyl group is aAttached to the methyl group is a RR groupgroup..
  31. 31. AN R GROUP IS ANY GROUPAN R GROUP IS ANY GROUP OF ATOMS – THIS CHANGESOF ATOMS – THIS CHANGES THE PROPERTIES OF THETHE PROPERTIES OF THE PROTEIN!PROTEIN!
  32. 32. FUNCTIONAL GROUPSFUNCTIONAL GROUPS • There are certain groups of atoms that areThere are certain groups of atoms that are frequently attached to the organic molecules wefrequently attached to the organic molecules we will be studying, and these are calledwill be studying, and these are called functionalfunctional groupsgroups.. • These are things likeThese are things like hydroxyl groupshydroxyl groups whichwhich formform alcoholsalcohols,, carbonyl groupscarbonyl groups which formwhich form aldehydesaldehydes oror ketonesketones,, carboxyl groupscarboxyl groups whichwhich formform carboxylic acidscarboxylic acids, and, and amino groupsamino groups which formwhich form aminesamines..
  33. 33. Major Protein FunctionsMajor Protein Functions • Growth and repairGrowth and repair • EnergyEnergy • Buffer -- helps keep body pH constantBuffer -- helps keep body pH constant
  34. 34. DipeptideDipeptide • formed from two amino acid subunitsformed from two amino acid subunits • Formed by the process ofFormed by the process of Dehydration SynthesisDehydration Synthesis • amino acid + amino acid ----- dipeptide + wateramino acid + amino acid ----- dipeptide + water
  35. 35. Hydrolysis of a dipeptideHydrolysis of a dipeptide • Breaking down of a dipeptide into amino acidsBreaking down of a dipeptide into amino acids • dipeptide + H2O ---> aminoacid + amino aciddipeptide + H2O ---> aminoacid + amino acid
  36. 36. Polypeptide (protein)Polypeptide (protein) • composed ofcomposed of three or morethree or more amino acids linkedamino acids linked by synthesis reactionsby synthesis reactions • Examples of proteins includeExamples of proteins include insulin,insulin, hemoglobin, and enzymes.hemoglobin, and enzymes. • ** There are an extremely large number of** There are an extremely large number of different proteins.different proteins. • The bases for variability include differences inThe bases for variability include differences in the number, kinds and sequences of aminothe number, kinds and sequences of amino acids in the proteinsacids in the proteins
  37. 37. NUCLEIC ACIDSNUCLEIC ACIDS • in all cellsin all cells • composed ofcomposed of NUCLEOTIDESNUCLEOTIDES • store & transmitstore & transmit heredity/geneticheredity/genetic informationinformation • Nucleotides consist of 3 parts:Nucleotides consist of 3 parts: • 1.1. 5-Carbon Sugar5-Carbon Sugar • 2.2. Phosphate GroupPhosphate Group • 3.3. Nitrogenous BaseNitrogenous Base
  38. 38. DNA (deoxyribonucleic acid)DNA (deoxyribonucleic acid) • contains the genetic code of instructions that direct acontains the genetic code of instructions that direct a cell's behavior through the synthesis of proteinscell's behavior through the synthesis of proteins • found in the chromosomes of the nucleus (and a fewfound in the chromosomes of the nucleus (and a few other organelles)other organelles)
  39. 39. RNA (ribonucleic acid)RNA (ribonucleic acid) • directs cellular protein synthesisdirects cellular protein synthesis • found in ribosomes & nucleolifound in ribosomes & nucleoli
  40. 40. CHEMICAL REACTIONSCHEMICAL REACTIONS • a process thata process that changeschanges one set of chemicals intoone set of chemicals into another set of chemicalsanother set of chemicals • REACTANTSREACTANTS – elements or compounds that– elements or compounds that enter into a chemical reactionenter into a chemical reaction • PRODUCTSPRODUCTS – elements or compounds that are– elements or compounds that are produced in a chemical reactionproduced in a chemical reaction • Chemical reactions always involve theChemical reactions always involve the breaking ofbreaking of bonds in reactantsbonds in reactants and theand the formation of newformation of new bonds in products.bonds in products.
  41. 41. • In a reaction, energy is either TAKEN INIn a reaction, energy is either TAKEN IN ((ENDOTHERMICENDOTHERMIC) or GIVEN OFF) or GIVEN OFF ((EXOTHERMICEXOTHERMIC)) • Can you think of an everyday example ofCan you think of an everyday example of each type of reaction?each type of reaction?
  42. 42. Enzymes and Enzyme ActionEnzymes and Enzyme Action • catalystcatalyst: inorganic or organic substance which: inorganic or organic substance which speeds up the ratespeeds up the rate of a chemical reaction withoutof a chemical reaction without entering the reaction itselfentering the reaction itself • enzymesenzymes: organic catalysts made of protein: organic catalysts made of protein • most enzyme names end in -asemost enzyme names end in -ase • enzymes lower the energy needed to start aenzymes lower the energy needed to start a chemical reaction. (chemical reaction. (activation energyactivation energy)) • begin to be destroyed above 45øC. (above thisbegin to be destroyed above 45øC. (above this temperature all proteins begin to be destroyed)temperature all proteins begin to be destroyed)
  43. 43. It is thought that, in order for an enzyme to affect the rate of aIt is thought that, in order for an enzyme to affect the rate of a reaction, the following events must take place.reaction, the following events must take place. 1.1. The enzyme must form aThe enzyme must form a temporary associationtemporary association with thewith the substance or substances whose reaction rate it affects.substance or substances whose reaction rate it affects. These substances are known asThese substances are known as substratessubstrates.. 2.2. The association between enzyme and substrate is thought toThe association between enzyme and substrate is thought to form aform a close physical associationclose physical association between the molecules andbetween the molecules and is called theis called the enzyme-substrate complexenzyme-substrate complex.. 3.3. While the enzyme-substrate complex is formed, enzymeWhile the enzyme-substrate complex is formed, enzyme action takes place.action takes place. 4.4. Upon completion of the reaction, the enzyme and product(s)Upon completion of the reaction, the enzyme and product(s) separateseparate. The enzyme molecule is now available to form. The enzyme molecule is now available to form additional complexes.additional complexes.
  44. 44. How do enzymes work?How do enzymes work? • substratesubstrate: molecules upon which an enzyme acts: molecules upon which an enzyme acts • the enzyme is shaped so that it can only lock upthe enzyme is shaped so that it can only lock up with awith a specific substratespecific substrate moleculemolecule enzymeenzyme substrate -------------> productsubstrate -------------> product
  45. 45. "Lock and Key Theory" • each enzyme is specific foreach enzyme is specific for one and ONLY oneone and ONLY one substratesubstrate (one lock - one key)(one lock - one key) • this theory has many weaknesses, but itthis theory has many weaknesses, but it explains some basic things about enzymeexplains some basic things about enzyme functionfunction
  46. 46. Factors Influencing Rate ofFactors Influencing Rate of Enzyme ActionEnzyme Action 1.1. pHpH - the optimum (best) in most living things is- the optimum (best) in most living things is close to 7 (neutral)close to 7 (neutral) • high or low pH levels usually slow enzyme activityhigh or low pH levels usually slow enzyme activity • A few enzymes (such as gastric protease) workA few enzymes (such as gastric protease) work best at a pH of about 2.0best at a pH of about 2.0
  47. 47. 2.2. TemperatureTemperature - strongly influences enzyme- strongly influences enzyme activityactivity • optimum temperature for maximum enzymeoptimum temperature for maximum enzyme function is usually about 35-40 C.function is usually about 35-40 C. • reactions proceed slowly below optimalreactions proceed slowly below optimal temperaturestemperatures • above 45 C most enzymes are denaturedabove 45 C most enzymes are denatured (change in their shape so the enzyme active site(change in their shape so the enzyme active site no longer fits with the substrate and the enzymeno longer fits with the substrate and the enzyme can't function)can't function)
  48. 48. 3.3. ConcentrationsConcentrations of Enzyme and Substrateof Enzyme and Substrate • ** When there is a fixed amount of enzyme and** When there is a fixed amount of enzyme and an excess of substrate molecules -- the rate ofan excess of substrate molecules -- the rate of reaction will increase to a point and then levelreaction will increase to a point and then level off.off.

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