Biology 180 Chapter 5

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Biology 180 Chapter 5
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Chapter 5 Notes
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  1. Macromolecules
    • Most are large complex polymers of organic molecules

    • The molecule is a repetative string of a small organic molecule (a monomer)

    • • Examples
    • – Complex Carbohydrates- polymers of monosaccharides

    • – Proteins- polymers of amino acids
    • – Lipids- not a polymer
    • – Nucleic acids- polymers of nucleotides
  2. Making a polymer
    • Condensation (also called dehydration)

    – New bond is formed

    – Results in the removal of one water molecule per addition•

    The monomer provides the –OH and the growing polymer provides the -H

    – Requires energy

    – Requires enzymes to bring the reactants together in the proper way (catalysis)

    • Enzymes are a type of protein
  3. Dehydration reaction in the synthesis of a polymer
    Dehydration reaction: synthesizing a polymer

  4. Breaking down a polymer
    • Hydrolysis

    – Results in the addition of one water molecule per reaction

         • Monomer provides –H forms on the polymer end and –OH forms on the monomer that is released

    – Releases energy

    • – Requires enzymes for catalysis in vivo
    •    • in vivo= in life

    – Occur in vitro with heat and/or with acids andbases
  5. Hydrolysis of a polymer
  6. HHydrolysis: breaking down a polymer
  7. Protein Functions
    • • 50% of dry mass of cells
    • • Include
    •         – Enzymes, structural support, storage, transport,cellular communication, movement, immune response

    • See Table 5.15 for an overview on p. 78
  8. Enzyme Catalysis
    • Biological catalysts that specifically aid in particular reactions

        – Anabolism- Work by binding the reactants,bringing them together, and stressing appropriate bonds to allow new bond formation

        – Catabolism- Work by stressing a molecule to break an existing bond. 

    • • Enzymes are not used up during this process
    •      – Catalyze again and again
  9. The catalytic cycle of an enzyme
    Enzymatic proteins

    Function: selective acceleration of chemical reactions

    Example: digestive enzymes catalyze the hydrolysis of bonds in food molecules
  10. Protein structure
    • Monomer= amino acid

         – 20 different kinds

    • Polymer= polypeptide

    •protein= one or more polypeptides

    • Biologically active in the L configuration
  11. Amino Acids structure
    • • Alpha-carbon has four different groups on it
    •       – Amino group
    •       – Carboxyl group
    •       – Hydrogen– R group

    • • R-group
    •     – Side chain that defines the 20+ amino acids

    • • Properties of side chains
    •    – Nonpolar, Polar, and Electrically charged
  12. Nonpolar R-groups
    • • Glycine (Gly)
    • • Alanine (Ala)
    • • Valine (Val)
    • • Leucine (Leu)
    • • Isoleucine (Ile)
    • • Methionine (Met)
    • • Phenylalanine(Phe)
    • • Tryptophan (Trp)
    • • Proline (Pro)

    Nonpolar amino acids are hydrophobic
  13. Nonpolar amino acids of proteins
  14. Polar amino acids
    • • Serine (Ser)
    • • Threonine (Thr)
    • • Cysteine (Cys)
    • • Tyrosine (Tyr)
    • •Asparagine (Asn)
    • • Glutamine (Gln)

    Polar amino acids are hydrophilic
  15. Polar amino acids of proteins
  16. Electrically charged amino acids
    • (Acidic Amino Acids)
    • • Aspartic acid (Asp)
    • • Glutamic acid (Glu)

    • (Basic Amino Acids)
    • • Lysine (Lys)
    • • Arginine (Arg)
    • • Histidine (His)

    Electrically charged amino acids are hydrophilic
  17. Electrically charged amino acids
  18. Polypeptides
    • Amino acids linked by dehydration synthesis

    • Covalent bond between the amino acids is apeptide bond

    – Backbone= N-C-C(peptide bond)-N-C-C- etc.

    – Backbone formed is stiff and not free to rotate

    – Facilitated by ribosomes

    • Proteins are produced by the process of translation

       – mRNA is translated by ribosomes

    • Proteins fold during their formation into a specific shape
  19. Protein shape
    • • Depends on its sequence of amino acids
    •      – Primary structure
    • • Depends on the location of the protein when it isfolding
    •     – Proteins folded in vitro may fold differently than thosein vivo (example cooking and egg)
    •      – Chaperones aid in folding
    • • Two overall shapes of proteins
    •      – Globular- roughly spherical
    •      – Fibrous – long and skinny
  20. Lysozyme
    is a globular protein

  21. Four Levels of protein structure
    • • Primary structure
    • • Secondary structure
    • • Tertiary structure
    • • Quaternary structure
  22. Primary structure of protein
    • • Sequence of amino acids
    •      – Determined by DNA

    • All polypeptides have an amino end and a carboxyl end

  23. Secondary structure of protein
    • Coils and folds

    • Occur by hydrogen bonds between the amino acids

    • Usually forms in regions throughout a protein

    • Some regions have secondary structure, others do not

    • • 2 forms
    • – alpha-helix
    • – beta-pleated sheet
  24. Alpha-helix secondary structure
    • Coiled structure
    • Hydrogen bonds form every 4th amino acid

  25. Beta-pleated sheet secondary structure
    2 parallel chains connected by hydrogen bonds

  26. Tertiary structure of protein
    • Folding of the polypeptide into an overall shape

    • Occurs by interactions between R groups

  27. Types of interactions between R-groups
    • • Hydrophobic interactions
    •    – Non-polar R-groups avoid water by clustering together on the interior of the protein
    • • Van der Waals interactions
    •    – Hold the R-groups together if they get close enough
    • • Hydrogen bonds
    •     – Form between polar side groups
    • • Ionic bonds
    •     – Form between acidic (negative) and basic (positive) side groups
    • • Disulfide bridges
    •      – Between cysteine R-groups– Covalent bonds between the sulfur atoms
  28. Quaternary structure
    • Forms when a protein is composed of one or more polypeptides

    • Each polypeptide in the protein is a subunit
    •    – Dimer= composed of 2 subunits
    •     -Trimer= composed of 3 subunits

  29. Hemoglobin
  30. All levels of structure depend on the primary structure
    • DNA determines amino acid sequence

    • Amino acid sequence determines protein shape

    • Protein shape determines protein function
  31. Protein Denaturation
    • • The unfolding of a protein
    • • Denaturing conditions
    •    – Change in pH
    •    – Change in salt concentration
    •    – Change in temperature
    •    – Presence of organic solvent
    •    – Presence of reducing agents
    • • Denatured proteins are biologically inactive
    • • Denatured proteins do not always refold correctly after denaturing conditions are reversed.
  32. Denaturation and renaturation of a protein
  33. Chaperonins
    • • Proteins that assist in folding of proteins
    • • Form a shield around the protein
    •      – Allows protein to fold in the absence of  potentially negative environmental conditions


  34. Types of carbohydrates
    • • Sugars and sugar polymers
    • • Monosaccharide
    •     – One sugar monomer
    • • Disaccharide
    •     – 2 sugar monomers attached with a glycosidicl inkage
    • • Polysaccharides
    •    – Long polymers of sugar
  35. Structure of Monosaccharides
    • Contain carbon, hydrogen, and oxygen in aratio of 1:2:1.

    • – (CH2O)n n=#carbons
    • • 3 to 7 carbons long

    • • Examples
    • – Glucose (a hexose sugar=C6H12O6)
    • – Glyceraldehyde (a triose sugar= C3H6O3)
    • – Deoxyribose (a pentose sugar= C5H10O5)
    • – Biologically active sugars are in the “D” form
    •   • Right-handed sugars
  36. Structure of monosaccharides
    • • Contains a carbonyl group
    •     – Ketose sugar- if it has a ketone functional group
    •     – Aldose sugar- if it has an aldehyde functional group

    • • Contains many hydroxyl groups on carbon skeleton
    • • Forms rings in solution
    •   – Equilibrium between the linear and the ringed form
  37. Triose sugars
  38. Pentose sugars
  39. Hexose sugars
    Glucose, Galactose Aldose (Aldehyde Sugar)  


    Fructose (Ketone Sugar)
  40. Linear and ringed forms of glucose
    To form the ring carbon 1 bonds to the oxygen attached to carbon 5The two forms are in equilibrium
  41. Structure of disaccharides
    • Two sugars bonded together by a glycosidic linkage.

         – By dehydration

    • Examples

    • – Glucose + glucose = maltose
    • – Glucose + galactose = lactose
    • – Glucose + fructose = sucrose
  42. Dehydration reaction in the synthesis of maltose
    The number 1 carbon of glucose is bound to the number 4carbon of the second glucose Makes a 1-4 glycosidic linkage

  43. Dehydration reaction in the synthesis of sucrose
    The number 1 carbon of glucose isbound to the number 2carbon of the fructose Makes a 1-2 glycosidic linkage


  44. Polysaccharides
    • Multiple sugars bonded together

    • Properties of the polysaccharide are determined by

        – The linkage between the sugar units

    • alpha vs. beta form of glucose

    – How branched the polysaccharide is
  45. alpha-glucose vs. beta glucose
  46. Storage polysaccharides
    • • Polysaccharide that store energy
    •      – If organism needs energy, it hydrolyzes the glucose from the polymer
    •      – The energy in the glucose is converted to ATP

    • • Examples of energy storage polysaccharides
    •     – Plants- starch (amylose and amylopectin)
    •     – Animals- glycogen

    • Linkages are of the alpha form of glucose
  47. Starch: A plant polysaccharide
    • Polymer of glucose inplants

    • 1-4 linkage of alpha-glucose monomers

    • Stored in chloroplasts

    • • Two kinds
    • –Amylose- unbranchedstarch

    – Amylopectin- branchedstarch (each branch has an alpha 1-6 linkage)
  48. Glycogen: an animal polysaccharide
    • Polymer of glucose in animals

    • 1-4 linkage of alpha-glucose monomers

    • Stored in liver and muscle cells

    • More branched than amylopectin
  49. Structural polysaccharides
    • • Polysaccharides that give strength to cell walls or organisms
    •     – They form strong and insoluble fibers
    •     – They cannot be used for energy because the glucose cannot hydrolyze due to different linkage

    • • Examples of structural polysaccharides
    • – Cellulose-In plant cell walls
    • – Chitin-In arthropod exoskeletons
    • – Chitin-In fungal cell walls
  50. Cellulose
    • Structural polysaccharide in plant cell walls

    • Most abundant organic compound (1011 tons/year)

    • Unbranched Beta-Glucose polymer with Beta 1-4 linkages

    • Hydrogen bonding between chains allows for microfibril formation
  51. Chitin
    • • Polymer of glucose
    • • Has an amino containing group on carbon #2

    • Beta- 1-4 linkage

    • Part of arthropod exoskeletons

    • Found in fungal cell walls

    a structural polysaccharide
  52. Types of lipid
    • • Properties
    • – All or mostly hydrophobic
    •     • Non polar
    • – Contain mostly hydrocarbon chains

    • • 3 main types
    • – Fats and oils (triglycerides)
    • – Phospholipids
    • – Steroids
  53. Fat (triglyceride) structure
    • • Not polymers
    • • One Glycerol + Three Fatty acid chains
    • • Form by dehydration synthesis
  54. Formation of triglycerides
    • • Form by dehydration reaction
    •    – H20 is formed
    •    – -OH of carboxyl group of fatty acid and the -H of glycerol

    • • Linkage formed is an ester linkage
    • • A triglyceride (fat or oil) has fatty acids (each connected to glycerol by ester linkage)
  55. Fat molecule
    • • Glycerol- a three carbon alcohol
    • • Fatty acid- 16 or 18 carbon long hydrocarbon

    • – Has carboxyl group at end (so an acid)
    • – hydrophobic

    ester linkage
  56. Saturated fat and fatty acid
    • • No double bonds between carbons in fatty acid
    • • Tails pack tightly
    • • Usually solid at RT
    • • Include mostly animal fats
    •     – Butter, lard, bacon fat
  57. Unsaturated fat and fatty acid
    • • One of more double bonds between carbons of fatty acids
    • • Tail kinks at each double bond
    • • Do not pack closely
    • • Usually liquid at RT
    • • Mostly plant oils
    •   – Corn, olive, peanut oil
  58. Fats as food
    • • Yield 9 kilocalories/g
    •   – Food labels use substitute Cal for kcal…go figure!
    • • Animal fats are saturated (except fish oil)
    • • Plant fats are unsaturated (except palm oil and coconut oil)
    • • Margarine is partially hydrogenated oil so that it will solidify at room temperature
    •     – Artificial hydrogenation causes trans bonds rather than the natural cis bonds to form
    •     – Just as bad for you as butter
    •     – Fats contribute to atherosclerosis (fatty plaques that block blood flow)
  59. Phospholipid
    • • Structure
    •   – Not polymers
    •   – Glycerol + 2 Fatty acid chains + phosphate + additional charged/polar group
    •    – Form by dehydration synthesis
    •    – Have dual solubility= amphipathic
    •         • Glycerol “head” is hydrophilic
    •         • Fatty acid “tails” are hydrophobic
    • • Function
    •    – Major component of biological membranes
    •    – Phospholipid arrange as bilayers
  60. Phospholipid bilayer forms in an aqueous environment
  61. Steroid structure
    • • 4 fused carbon rings with various functional groups attached
    •     – Short hydrocarbon tail
    •     – -OH group on the ring

    • Includes cholesterol and various hormones

  62. Nucleic Acid Function
    • • Direct its own replication
    • • Directs RNA synthesis
    • • Controls protein synthesis

    (All occur by protein whose sequences is determined by DNA)
  63. DNA structure
    • • Monomer= nucleotide
    • • Polymer= polynucleotide (nucleic acid)

    • • A polynucleotide can be
    • – Deoxyribonucleic acid (DNA)
    • – Ribonucleic acid (RNA)
  64. Components of a nucleotide
    • • Pentose sugar
    • • Nitrogenous base
    • • Phosphate group

  65. Nucleotide components -Pentose sugar
    • • Can be Ribose sugar= RNA
    • • Can be Deoxyribose sugar=DNA
    • • Chemical difference is the presence orabsence of a hydroxyl group at the #2carbon

    • – Each carbon is numbered 1’ – 5’
    • – Deoxyribose sugar the 2’ carbon has an H
    • – Ribose sugar the 2’ carbon has an -OH
  66. Deoxyribose vs. Ribose sugar
  67. Nucleotide components nitrogenous base
    • • DNA
    • – Thymine (T), Adenine (A), Guanine (G), Cytosine (C)

    – Purines are A and G (Large, double ring molecules)

    – Pyrimidines are C and T (Small single ring molecules)

    • • RNA
    • – Uracil (U), A, G, and C
    • – Purines are A and G
    • – Pyrimidines are C and U
  68. Nitrogenous bases
    • • Pyrimidine
    •    – 6 membered ring of carbon and nitrogen
    •    – Numbered 1-6

    • • Purine
    •     – 6 membered ring + 5membered ring of carbon and nitrogen fused
    •    – Numbered 1-9
  69. Nucleotide components phosphate group
    • Located on the 5’carbon of the pentose sugar

    • If the structure lacks a phosphate it is called a nucleoside (rather than a nucleotide)
  70. Nucleic Acid
    • A string of polymerized nucleotides

    • • Nucleotides connected by phosphodiester bonds
    •      – form between the 3’ OH of one nucleotide and the 5’phosphate of another nucleotide

    • • Nucleic acid directionality
    •    – There is a chemical difference on the two ends
    •    – 5’ end- free phosphate group off of the #5 carbon onsugar
    •    – 3’end- free hydroxyl group off of the #3 carbon on sugar
  71. DNA double helix structure
    • • DNA “backbone”
    •      – Refers to the alternating phosphate and deoxyribose sugar

    • • DNA “rungs”
    •    – Refer to the Nitrogenous-bases

    • Strands are held together by hydrogen bonding between complementary base pairs on opposing strands

    – Guanine can form 3 Hydrogen bonds with Cytosine

    – Adenine can form 2 Hydrogen bonds with Thymine
  72. DNA denaturation
    • The separating of the two strands of the DNA double helix

    • • Denaturing conditions
    • – Change in pH
    • – Change in salt concentration
    • – Change in temperature
    • • The phosphate backbone is NOT affected
    • • Renaturation
    •   – Complementary bases on opposite strands find each other and the helix is reformed
  73. Melting temperature of DNA
    Tm

    • Tm= Temperature where DNA is ½denatured

    What affects Tm

    •     – % AT vs. GC base pairs
    •        • More energy is required to break GC than AT

    • – % mismatches between nucleotides
    •      • More energy is required to break helices with many complementary bases
  74. RNA Structure
    • Usually composed of a single stranded nucleic acid

    •  • RNA can form extensive secondary structure
    •    – It can form double helices WITHIN the molecule

    • • RNA has a sugar phosphate backbone
    •   – Pentose sugar is ribose
    • • RNA has 4 nitrogenous bases
    •    – Adenine, Uracil, Guanine, and Cytosine
  75. RNA function
    • Involved in transcription (mRNA)

    • Involved in with translation (rRNA, tRNA)

    Can be enzymatic

    • Can affect gene expression

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