Chemistry 3

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Chemistry 3

  1. 1.  Overview: The Molecules of Life  Another level in the hierarchy of biological organization is reached when small organic molecules are joined together Macromolecules  Are large molecules composed of smaller molecules  Are complex in their structures  Include proteins, carboydrates, lipids, and nucleic acids like DNA
  2. 2. Three of the classes of life’s organic molecules are polymers  Carbohydrates  Proteins  Nucleic acidsA polymer  Is a long molecule consisting of many similar building blocks called monomers
  3. 3.  Monomers form larger molecules by condensation reactions also called dehydration reactions Short polymer Unlinked monomer HO 1 2 3 OH HO HDehydration removes a watermolecule, forming a new bond H2O HO 1 2 3 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer
  4. 4.  Polymers can disassemble by  Hydrolysis (also called digestion) HO 1 2 3 4 HHydrolysis adds a water H2Omolecule, breaking a bond HO 1 2 3 OH HO H(b) Hydrolysis of a polymer
  5. 5.  Each class of polymer  Is formed from a specific set of monomers All living organisms are composed of the same types of polymers made up of the same monomer types – proteins, carbohydrates and nucleic acids. However, each organism is composed of many unique polymers (unique proteins, carbohydrates and nucleic acids) based on the arrangement of monomers An immense variety of polymers can be built from a small set of monomers
  6. 6.  Carbohydrates  Include both simple sugars and their polymers Monosaccharides (simple sugars)  Are the simplest sugars  Can be used for fuel - glucose  Can be converted into other organic molecules  Nucleotides include a 5 carbon sugar, ribose or deoxyribose  Can be combined into polymers
  7. 7.  Examples of monosaccharides Triose sugars Pentose sugars Hexose sugars (C3H6O3) (C5H10O5) (C6H12O6) H O H O H O H O C C C C H C OH H C OH H C OH H C OH Aldoses H C OH H C OH HO C H HO C H H H C OH H C OH HO C H H C OH H C OH H C OH Glyceraldehyde H H C OH H C OH Ribose H H Glucose Galactose H H H H C OH H C OH H C OH C O C O C O Ketoses H C OH H C OH HO C H H H C OH H C OH Dihydroxyacetone H C OH H C OH H H C OH Ribulose H Fructose
  8. 8.  Monosaccharides Notice the carbons  May be linear are numbered and  Can form rings this numbering system remains when they form a ring in water. H C O 6CH OH 1 6CH OH 2 2 CH2OH H 2C OH 5C H 5C O O 6 H H H H H O HO 3C H 5 H 4C H 1C 4C H 1C H OH OH 4 OH 1 4 H H H C OH O HO 3 2 OH 5 OH 2C OH 3C 2C OH H C OH 3 C H OH 6 H OH H OH H C OH H (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5.
  9. 9. (a) Dehydration reaction in the synthesis of maltose. The bonding CH2OH CH2OH CH2OH CH2OH of two glucose units O O O O forms maltose. The H H H H H H 1–4 H H H H H 1 glycosidic 4 H glycosidic link joins OH H OH H OH H linkage OH H the number 1 carbon OH HO OHOH of one glucose to the HO HO O OH number 4 carbon of the second glucose. H OH H OH H OH H OH Joining the glucose H2O monomers in a Glucose Maltose Glucose different way would result in a different disaccharide. CH2OH CH2OH CH2OH CH2OH H O O H O H 1–2 O H H H H H 1 glycosidic 2(b) Dehydration reaction OH H H HO OH H linkage H HO OH HO in the synthesis of HO CH2OH HO O CH2OH sucrose. Sucrose is a disaccharide formed H OH OH H H OH OH H from glucose and fructose. Notice that fructose, H2O though a hexose like Glucose Fructose Sucrose glucose, forms a five-sided ring. In living systems, these reactions Notice that the chemical are always done by enzymes. reactions take place at Cellular enzymes are controlled the functional groups
  10. 10.  Polysaccharides  Are polymers of sugars  Serve many roles in organisms  Storage  Starch is a polymer of glucose only  Glycogen is also a polymer of glucose  Cell wall - structure  Cellulose is a polymer of glucose  Chitin
  11. 11. Chloroplast Starch Is the major storage form of glucose in plants 1 m Amylose Amylopectin (a) Starch: a plant polysaccharide
  12. 12.  Glycogen  Consists of glucose monomers  Is the major storage form of glucose in animals Mitochondria Glycogen granules 0.5 m Glycogen (b) Glycogen: an animal polysaccharide
  13. 13. H O CH2O C CH2O H H O H C OH H O OH H H H H 4 OH H HO C H 4 1 OH H HO OH HO H H C OHWhich type of bond H OH H C OH H OH glucose H C OH glucosedepends on the (a) and glucose ring structuresenzyme CH2O CH2O CH2O CH2O H H H H O O O Owhich is controlled by OH 1 O 4 OH 1 O 4 OH 1 O 4 OH 1 O HOthe cell. OH OH OH OH (b) Starch: 1– 4 linkage of glucose monomers CH2O CH2O OH OH H H O O O OH O OH OH 1 4 O OH HO OH O O CH2O CH2O OH OH H H (c) Cellulose: 1– 4 linkage of glucose monomers
  14. 14.  Is a major component of the tough walls that enclose plant cells About 80 cellulose molecules associate to form a microfibril, the Cellulose microfibrils main architectural unit in a plant cell wall Microfibril the plant cell wall. of Cell walls 0.5 m Plant cells CH2OH OH CH2OH OH O O O O OH OH OH OH O O O O O O CH OH OH CH2OH H 2 Cellulose CH2OH OH CH2OH OH molecules O O O O OH OH OH OH Parallel cellulose molecules are O O O O O O CH OH OH CH2OH held together by hydrogen H 2 bonds between hydroxyl CH2OH OH CH2OH OH O O O O groups attached to carbon OH OH O OH O O OH O atoms 3 and 6. O CH OH O A cellulose molecule OH CH2OH H 2 is an unbranchedFigure 5.8 Glucose glucose polymer. monomer
  15. 15.  Cellulose is difficult to digest  Cows have microbes in their stomachs to facilitate this processWhat do these microbeshave that will allow them tobreak down cellulose?
  16. 16.  Chitin, another important structural polysaccharide  Is found in the exoskeleton of arthropods  Can be used as surgical thread CH2O H H O OH H OH H OH H H NH C O CH3 (a) The structure of the (b) Chitin forms the exoskeleton (c) Chitin is used to make a chitin monomer. of arthropods. This cicada strong and flexible surgical is molting, shedding its old thread that decomposes after exoskeleton and emerging the wound or incision heals. in adult form.
  17. 17.  Lipids  Are the one class of large biological molecules that do not consist of polymers  Share the common trait of being hydrophobic  Include  Fats  Phospholipids  steroids
  18. 18. H H H H H H H H O H H H H H H H HH C OH C C C C C C C C H C C C C C C C C HO H H H H H H H H H H H H H H HH C OH Fatty acidH C OH (palmitic acid) H Again, notice where the Glycerol (a) Dehydration reaction in the synthesis of a fat chemical reaction takes Ester linkage place. H O H H H H H H H H H H H H H H HH C O C C C C C C C C H C C C C C C C C H H H H H H H H H H H H H H H O H H H H H H H H H H H H H H HH C O C C C C C C C C H C C C C C C C C H H H H H H H H H H H H H H H O H H H H H H H H H H H H H H HH C O C C C C C C C C H C C C C C C C C H H H H H H H H H H H H H H H H (b) Fat molecule (triacylglycerol)
  19. 19. Saturated fatty acids Have the maximum number of hydrogen atoms possible (saturated with hydrogen) Have no double bonds Stearic acid (a) Saturated fat and fatty acid Oleic acid •Unsaturated fatty acids --Have one or more double(b) Unsaturated fat and fatty acid cis double bond bonds causes bending
  20. 20. A single bond allowsrotation, is longer andnot a strong as adouble bondA double bond isstronger, shorter, andmore rigid.Bonds help todetermine the 3-Dshape of a molecule.
  21. 21.  Consists of a hydrophilic “head” and hydrophobic “tails” CH2 + ) N(CH 3 3 Choline CH2 O O P O– Phosphate O CH2 CH CH2 Glycerol O O C O C O Fatty acids Hydrophilic head Hydrophobic tails (c) Phospholipid (a) Structural formula (b) Space-filling model symbol
  22. 22.  The structure of phospholipids  Results in a bilayer arrangement found in cell membranes WATER Hydrophilic head WATER Hydrophobic tail
  23. 23.  One steroid, cholesterol  Is found in cell membranes  Is a precursor for some hormones H3C CH3When written as a CH3ring, all points are CH3carbon unless CH3written inotherwise. Is this molecule polar or nonpolar? HO
  24. 24. Cholesterol fills in the spaces left by the kinks; stiffens the bilayer andmakes it less fluid and less permeable. How do you think bacteria,Do concept which do not use cholesterol,check 5.3 adjust the fluidity of their cell membrane?
  25. 25. Both saturated and trans fats correlate with heart problems and high levels or blood cholesterol. AtherosclerosisAnimal fats found in meat, butter, and cream are usuallysaturated, and solid at room temperature.Plant oils like corn oil contain more unsaturated fattyacids.Peanut and olive oil contain monounsaturated fattyacids.
  26. 26.  Enzymes  Are often a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for 2 Substrate binds to a molecule of substrate, the enzyme. Substrate reactant on which the enzyme acts. (sucrose)Is this part of theprotein polar ornonpolar? Glucose Enzyme OH (sucrase) H2O FructoseEnzyme remains H Ounchanged, readyto work again. 4 Products are released. 3 Substrate is converted to products.
  27. 27.  Polypeptides  Are polymers of amino acids A protein  Can consist of only one large polypeptide  Can consists of more than one polypeptides (subunits) bound together by non-covalent interactions  Hemoglobin  Some very small polypeptides are referred to as peptides Amino acids  Are organic molecules possessing both carboxyl and amino groups  Differ in their properties due to differing side chains, called R groups
  28. 28. Proteins are composed of amino acid building blocks and are diverse in structure (shape) and function. Amino acids have an amino group and an acid group bound to a central carbon. This central carbon forms 4Amino single bonds. One with the Acid groupgroup amino group, one with the carboxylic acid, one with hydrogen, and the last with a variety of different chemical groups (R group).
  29. 29.  20 different amino acids make up proteins CH3 CH3 CH3 CH3 CH3 CH CH2 H CH3 CH3 CH2 H3C CH O O O O O H3N+ C C H3N+ C C H3N+ C C H3N+ C C H3N+ C C O– O– O– O– O– H H H H H Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)Nonpolar CH3 CH2 S H2C CH2 NH O CH2 H2 N C C CH2 O CH2 CH2 O– O O H H3N+ C C H3N+ C C H3N+ C C O– O– O– H H H Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro) Know the structure of an amino acid, not all the R groups.
  30. 30. OH NH2 O NH2 O C OH SH C CH2 Polar OH CH3 CH2 CH CH2 CH2 CH2 O CH2 O O O O O H3N+ C C H3N+ C C H3N+ C C H3 N+ C C H3N+ C C H3 N+ C C O– O– O– O– O– O– H H H H H H Cysteine Tyrosine Asparagine Glutamine Serine (Ser) Threonine (Thr) (Gln) (Cys) (Tyr) (Asn) Acidic Basic NH3+ NH2 NH+ –O O O– O C C CH2 C NH2+ NH Electrically CH2 CH2 O CH2 CH2 CH2 charged O H3N+ C C CH2 CH2 CH2 H3 N+ C C O O– CH2 O– H3N+ C C O CH2 H H O– H H3N+ C C CH2 O O– H H3N+ C C O– H Aspartic acid Glutamic acid Lysine (Lys) Arginine (Arg) Histidine (His) (Asp) (Glu)Know both the name and abbreviation of all amino acids alongwith their chemical nature – polar, nonpolar, charged, acidic, . . .
  31. 31. The formation of a peptide bonds in a tetrapeptide
  32. 32.  Amino acids  Are linked by peptide bonds between the amino group of one amino acid and the acid group of the other amino acid OH Peptide bond OH SH Each peptide CH2 CH2 CH 2 bond is in a H H HThe chemical H N C C N C C OH H N C C OH plane. Thisreaction again takes H O H O contributes to H O DESMOSOMESplace at the (a) HO 2 the shape offunctional groups! OH the protein. DESMOSOMES DESMOSOMES Side OH SH Peptide chains CH2 CH2 bond CH2 H H H H N C C N C C N C C OH Backbone H O H O H O Amino end Carboxyl end (b) (N-terminus) (C-terminus)
  33. 33.  Two models of protein conformation Groove (a) A ribbon model A protein’s specific conformation (shape and chemical nature) Groove determines how it functions. (b) A space-filling model
  34. 34.  Primary structure  Is the unique sequence of amino acids in a polypeptide + HN 3 Gly ProThr Gly Thr Gly Amino acid Amino LeuPro Cys LysSeu Glu subunits end Met Val Covalent bonds Lys Val Leu Asp AlaVal Arg Gly Ser Pro Ala Peptide backbone imposes some Glu Lle Asp Thr Lys restrictions on the Gly lle Leu Ala Lys Trp Tyr Ser folding of a protein. Ser ProPhe His Glu His Ala Glu Val Ala Thr PheVal Why? Asn lle Thr Asp Tyr Ala Arg Ser Arg Ala Gly Pro Leu Leu Ser Pro SerTyr Tyr ThrSer Thr Ala Val o Val LysGlu c Thr AsnPro o– Carboxyl end
  35. 35.  Secondary structure  Is the folding or coiling of the polypeptide into a repeating configuration  Includes the helix and the pleated sheet pleated sheet O H H O H H O H H O H H R R RAmino acid C C N C C N C C N C C N C N C C N C C N C C N C C subunits R R R R H O H H OH H OH H O R R R R O C O O C O H C H H H C H C N HC H H C N HC N N C NH C N C N HC N helix C H O C H O C H O C H O C R R R R H R H C C H N O C N H N H O C All based on hydrogen N HO C H C R H C O C H C R H C R bonds between the R N H O C N H O C peptide bonds of O C N H O C N H R C H R C H different amino acids
  36. 36.  Tertiary structure  Is the overall three-dimensional shape of a polypeptide after it “folds” into a stable form.  Results from interactions between amino acids and R groups Hydrophobic interactions and van der WaalsWhat are CH CH22 CH interactions H3C CH3these? Hydrogen O H H3C CH3 Polypeptide bond O CH backbone HO C CH2 CH2 S S CH2 Disulfide bridge O CH2 NH3+ -O C CH2 Ionic bond
  37. 37. The distribution of polar and nonpolar amino acids is importantin how a protein folds. The nonpolar side chains tend tocluster in the interior of a molecule, avoiding contact withwater, while the polar side chains arrange themselves near theoutside.
  38. 38. Hydrophobic areas also tend to be found spanning the lipid bilayer of membranes like the plasma membrane.Transmembrane proteins often cross the membrane in an alphahelix because the peptide bond itself is hydrophic unless allpartial charges are equalized in an alpha helix or beta sheet.
  39. 39. Is the overall proteinstructure that resultsfrom the aggregationof two or morepolypeptide subunits
  40. 40. Hemoglobin contains two alpha globin subunits and two beta globin subunits. There are many Heme is the large site where multi- oxygen is subunit carried proteins in cells.
  41. 41. Larger protein molecules may contain more than onepolypeptide chain or subunit. The region that interacts withanother molecule through noncovalent bonds is the binding site.
  42. 42. Normal β Sickle-cell β Primary hemoglobin Primary Val hemoglobin Glu . . . Val His Leu Thr Pro Glul Glu . . . His Leu Thr Pro Val Exposed structure 1 2 3 4 5 6 7 structure 1 2 3 4 5 6 7 hydrophobic region Secondary Secondary and tertiary subunit and tertiary subunit structures structures Quaternary Hemoglobin A Quaternary structure structure Hemoglobin S Function Molecules interact with Function Molecules do one another to not associate crystallize into a with one fiber, capacity to another, each carry oxygen is carries oxygen. 10 m 10 m greatly reduced. Red blood Normal cells are Red blood cell shape full of individual cell shape hemoglobin Fibers of abnormal molecules, each hemoglobin carrying oxygen deform cell intoFigure 5.21 sickle shape. The sickle-cell hemoglobin does not fold into the proper shape because the amino acid sequence (Primary structure) is incorrect.
  43. 43.  20 different amino acids make up proteins CH3 CH3 CH3 CH3 CH3 CH CH2 H CH3 CH3 CH2 H3C CH O O O O O H3N+ C C H3N+ C C H3N+ C C H3N+ C C H3N+ C C O– O– O– O– O– H H H H H Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)Nonpolar CH3 CH2 S H2C CH2 NH O CH2 H2 N C C CH2 O CH2 CH2 O– O O H H3N+ C C H3N+ C C H3N+ C C O– O– O– H H H Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro) Know the structure of an amino acid, not all the R groups.
  44. 44. OH NH2 O NH2 O C OH SH C CH2 Polar OH CH3 CH2 CH CH2 CH2 CH2 O CH2 O O O O O H3N+ C C H3N+ C C H3N+ C C H3 N+ C C H3N+ C C H3 N+ C C O– O– O– O– O– O– H H H H H H Cysteine Tyrosine Asparagine Glutamine Serine (Ser) Threonine (Thr) (Gln) (Cys) (Tyr) (Asn) Acidic Basic NH3+ NH2 NH+ –O O O– O C C CH2 C NH2+ NH Electrically CH2 CH2 O CH2 CH2 CH2 charged O H3N+ C C CH2 CH2 CH2 H3 N+ C C O O– CH2 O– H3N+ C C O CH2 H H O– H H3N+ C C CH2 O O– H H3N+ C C O– H Aspartic acid Glutamic acid Lysine (Lys) Arginine (Arg) Histidine (His) (Asp) (Glu)Know both the name and abbreviation of all amino acids alongwith their chemical nature – polar, nonpolar, charged, acidic, . . .
  45. 45.  Depends on  the sequence of amino acid side chains (with R groups) and  the physical and chemical conditions of the protein’s environment  Denaturation is when a protein unravels and loses its native conformation Increased temperature Denaturation Change in pHWhat kinds of bonds are Organic solvent (hydrophobic)broken here? Normal protein Denatured protein What kinds of bonds are not Renaturation broken here?
  46. 46.  Most proteins  Probably go through several intermediate states on their way to a stable conformation.  Many proteins are being made in the cell all of the time. How do the fold correctly, how do they interact with their subunits correctly?
  47. 47.  Chaperonins  Are protein molecules that assist in the proper folding of other proteins Correctly folded Polypeptide protein CapHollowcylinder Chaperonin Steps of Chaperonin 2 The cap attaches, causing 3 The cap comes (fully assembled) Action: the cylinder to change shape in off, and the properly 1 An unfolded poly- such a way that it creates a folded protein is peptide enters the hydrophilic environment for the released. cylinder from one end. folding of the polypeptide.
  48. 48.  X-ray crystallography  Is used to determine a protein’s three-dimensional structure X-ray diffraction pattern Photographic film Diffracted X-rays X-ray X-ray source beam Crystal Nucleic acid ProteinDo conceptcheck 5.4 Figure 5.24 (a) X-ray diffraction pattern (b) 3D computer model
  49. 49.  Genes  Are the units of inheritance  Code for the amino acid sequence of polypeptides  Are made of nucleic acids There are two types of nucleic acids  Deoxyribonucleic acid (DNA)  Ribonucleic acid (RNA)
  50. 50.  Stores information for the synthesis of specific proteins – DNA DNA is the “ genetic material” inherited from parents 1 Directs RNA synthesis Synthesis of mRNA in the nucleus mRNA Directs protein synthesis indirectly NUCLEUS through messenger RNA CYTOPLASM 2 Movement of mRNA mRNA into cytoplasm via nuclear pore Ribosome 3 Synthesis of protein Amino Polypeptide acids
  51. 51.  Nucleic acids 5’ end  Exist as polymers called polynucleotides  Each polynucleotide 5’C O  Consists of monomers called3’C nucleotides O Nucleoside O Nitrogenous base O 5’C5’C O P O CH2 O O O3’C Phosphate 3’ end group 3’C Pentose OH sugar (a) Polynucleotide, or nucleic acid (b) Nucleotide
  52. 52.  Are made up of nucleosides and phosphate groups pyrimidines Nitrogenous bases Pyrimidines NH2 O O C C CH3 C N CH HN C HN CH C CH C CH C CH O N O N O N H H H Cytosine Thymine (in DNA) Uracil (in RNA) Uracil (in RNA) Nucleoside C T U U Nitrogenous Purines base NH2 O N CC N C C N NH HC HC O 5’C N C CH N C NH2 N N H H O P O CH2 Adenine Guanine O A G O Phosphate Pentose sugars 3’C 5” 5” group Pentose HOCH2 O OH HOCH2 O OH sugar 4’ H H 1’ H H 1’ 4’ H 3’ 2’ H H H 3’ 2’(b) Nucleotide OH H OH OH Deoxyribose (in DNA) Ribose (in RNA) Figure 5.26 (c) Nucleoside components
  53. 53. Nucleotide polymersare made up ofnucleotides linkedby the–OH groupon the 3´ carbon ofone nucleotide andthe phosphate onthe 5´ carbon onthe nextSo they “grow” atthe 3’ end.
  54. 54.  The sequence of bases along a nucleotide polymer  Is unique for each gene
  55. 55. The DNA Double Helix Anti-parallel complementary
  56. 56. Complementary base pairsDo conceptcheck 5.5
  57. 57.  Molecular comparisons  Help biologists sort out the evolutionary connections among species  Ribosomal RNA gene sequence is conserved.  Look for differences.

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