GoConqr has a new look! Let us know what you think.

Sign up free

Flashcards

FC 5D- Biological Molecules

Victoria Whitfield Complete English 63 cards

FC 5D- Biological Molecules

Cards in this deck (63)

  1. 1PyrophosphateVERY high E molecule formed from 2 orthophosphates linking via phosphate anhydride bonds (stores E of ATP); P-O-PPyrophosphate
  2. 2NucleotidesSugar (ribose/deoxyribose) binds to base (purine/pyrimidine) at C1' binds and binds to phosphates (1, 2, or 3 groups) at C5' through PHOSPHODIESTER BONDS
  3. 3Amino Acid Absolute Configuration at the α PositionL-amino acids are the more common in nature, and are the type found in proteinsAmino Acid Absolute Configuration at the α Position
  4. 4GlyceraldehydeL-Glyceraldehyde: building block of ALL amino acids
    D+Glyceraldehyde: building block of ALL carbohydrates    Glyceraldehyde
  5. 5Chiral Center ClassificationD-sugars have R configuration at penultimate (2nd to last) C
    L-AA's have S configuration at penultimate C
    ***EXCEPTION: cysteine because the R group has higher priority and is R configuration    Chiral Center Classification
  6. 6Aspartic AcidPolar, Acidic
  7. 7Dipolar IonsAt low pH, AA's exist in the CATIONIC form.
    At high pH, AA's exist in the ANIONIC form.
    At pH = pI, AA's exist in the ZWITTERION form, which is overall neutral.
  8. 8Amino Acid ClassificationIf the R group contains carboxylic acid, then it's ACIDIC.
    -> Aspartic acid & glutamic acid
    If the R group contains an amine group, then it's BASIC.
    -> Lysine, arginine, and histidine
    HYDROPHILIC/POLAR/NEUTRAL if the R group contains acids, bases, amines or alcohols; if not then HYDROPHOBIC/NONPOLAR
  9. 9Amino Acid SynthesisSTRECKER SYNTHESIS
    starting material: R-aldehyde
    reagents: cyanide (KCN) & ammonium (NH4Cl) salts
    product: *racemic* AA with the -R group originally on the aldehyde
    GABRIEL SYNTHESIS
    starting material: R-halide
    reagents: 1. phthalimide, 2. NH2-NH2
    product: amino acid with the -R group originally on the halide
  10. 10HistidineContains R group with pKa so close to physiological pH that at pH 7.4 it can either be protonated or deprotonated acting as a proton acceptor(:B) or donor(A+)
    "His goes both ways"
  11. 11CysteineSince the R group is a thiol (-SH) there is a disulfide bridge formation when in an oxidizing environment.
    -CYSTINE: extracellular space oxidizes
    -CYSTEINE: intracellular space reduces
  12. 12ProlineHas a secondary α amino group, 2 N-C covalent bonds in the ring which causes kinks and is a α-helix breaker
  13. 13GlycineNo chiral αC due to H as R group meaning it's not optically active and has more conformational stability
  14. 148 Essential Amino AcidsIsoleucine
    Leucine
    Lysine
    Methionine
    Phenylalanine
    Threonine
    Tryptophan
    Valine
  15. 15Amino Acid Breakdown1) ACID HYDROLYSIS: when you add strong acid + heat; non-specific
    2) PROTEOLYSIS: when you add protease; highly specific
  16. 16Strecker Synthetic Synthesis-Starting Material: R-aldehyde
    -Reagents: cyanide (KCN), ammonium (NH4Cl)
    -Product: AA with the -R group originally on the aldehyde
    *Racemic product since only naturally-occurring AA are stereochemically pure L
  17. 17Gabriel Synthetic Synthesis-Starting Material: R-halide
    -Reagents: 1. phthalimide, 2. NH2-NH2
    -Product: AA with the -R group originally on the halide
  18. 18CysteineA side-chain that has a thiol group that forms a disulfide bond between 2 of them to create a cystine
  19. 19Peptide/Amide BondFormed by the amine group attacking the carbonyl carbon through dehydration to link AA's; very difficult to hydrolyze requiring a strong base, or a biological enzyme.Peptide/Amide Bond
  20. 20Protein Structure-PRIMARY STRUCTURE: sequence; *peptide bonds
    -SECONDARY STRUCTURE: backbone interactions; N-H & C=O *hydrogen bonds
    -TERTIARY STRUCTURE: electrostatic side chain-side chain interactions within AA; *hydrogen bonds, van der waahls, hydrophobic interactions, disulfide
    -QUATERNARY STRUCTURE: separate chains/subunits joining together by covalent disulfide bonding; *hydrogen bonds, van der waahls, hydrophobic interactions, disulfide
  21. 21Isoelectric PointpH at which the molecule is neutral (basic amine and acidic carboxylic acid)
    ACIDIC AA's/proteins with lots of acidic side chains have have a lower isoelectric point
    BASIC AA's/proteins with lots of basic side chains have a higher isoelectric point
    ZWITTERION is a neutral A+/:B hybrid
  22. 22Acid/Base StrengthStrongest acid/base has the weakest conjugate acid/base in order to resist deprotonation/protonation
    pH > pKa is the DEPROTONATED form
    pH < pKa is the PROTONATED form
    pka = ph + log([HA]/[A-])
  23. 23Denaturing-TEMPERATURE: affects all but primary
    -pH: affects all but primary & secondary because it breaks ionic bonds
    -CHEMICAL: affects all but primary
    -ENZYME: affects all
  24. 24LipidsEster groups make 1 & 2 VERY hydolyzable (chemical breakdown when H2O is added).
    1) Phospholipid bilayer
    2) Triglyceride (fat) energy storage
    3) Cholesterol; building block for the hydrophobic steroid hormones
  25. 25Fatty Acids-Synthesized 2C at a time from acetate.
    -Carboxyl group is exposed to polar environment 2/2 - and tails go inside 2/2 hydrophobic interactions.    Fatty Acids
  26. 26TriacylglycerolsThe storage form of fatty acids as E source; efficient 2/2 packing & E content.
    Formed: acid-catalyzed esterification of glycerol + 3 FA's into triacylglycerol
    Broken Down: base-catalyzed saponification of triacylglyceride into glycerol + 3 FA's    Triacylglycerols
  27. 27PhospholipidsMembrane fluidity is increased and melting point is decreased via...
    1) Unsaturation
    2) Decreased length
    3) The steroid cholesterol at low T (reverse occurs at high T)
  28. 28SteroidsTetracyclic ring system based on polycyclic amphipathic cholesterol structure.
    Obtained in diet, synthesized in liver, and carried in the blood packaged with fats/proteins into lipoproteins (plaque).
    Highly hydrophobic so steroid hormones diffuse through membrane thus receptors are INSIDE the cell    Steroids
  29. 29TerpenesSqualene (triterpene made of 6 isoprenes) is biosynthetically used to make steroids.
    TERPENOIDS are functionalized terpenes that are an isoprene skeleton + other elements.
    ex: Vitamin A
  30. 30SphingolipidFA derivatives of sphingosine (amino alcohol) that occur in the cell membranes of the brain & nervous tissue; concentrated in myelin to allow for insulation.
  31. 31WaxesAn ester with 2 long C-H chains on either side to make it VERY HYDROPHOBIC
  32. 32Non-Hydrolyzable LipidsSignaling molecules.
    -PROSTAGLANDINS: help signal inflammation, lower BP, lower gastric secretions, inhibit platelet aggregation (ex: NSAIDs)
    -STEROIDS: (ex: testosterone)
    -FAT SOLUBLE VITAMINS: co-factors that help an enzyme perform a function;
    *A- retinol; needed for light sensitivity & healthy mucous membranes
    *D- regulate P+ & Ca+ metabolism
    *E- antioxidant helps protect neurological function
    *K- regulates synthesis of prothrombin
  33. 33CarbohydratesCnH2nOn with at least 3C backbone that begins with either aldehyde or ketone and at least 2 -OH; in presence of strong acid hydrolyzes to monosaccharides.
    -D/L: absolute configuration assigned based on the chirality of the C furthest from the carbonyl group.
    -α/β: anomeric configuration.
    -Pyranose: 6 membered ring structure
    -Furanose: 5 membered ring structure    Carbohydrates
  34. 34Anomeric Configuration of Carbohydrates-OH that are L on Fischer are Up on Haworth; BETA.
    -OH that are D on Fischer are Down on Haworth; ALPHA.
    *CH2OH group on the absolute configuration C points up for D, and down for L.    Anomeric Configuration of Carbohydrates
  35. 35Cyclic Conformations of Carbohydrates-PLANAR: everything is eclipsed.
    -CHAIR: everything is staggered.
    *conformations in between are partially eclipsed.
    -BOAT: Flagpole interactions because axial groups attached to the head and tail of the boat clash.
    -TWIST BOAT: lessens these Flagpole interactions in addition to reducing the number of eclipsed interactions.    Cyclic Conformations of Carbohydrates
  36. 36Epimers/Anomers-EPIMERS: special type of diastereomers, different configuration in just 1 chiral C.
    -ANOMERS: special type of epimers, different configuration in the chiral, anomeric carbon when the molecule is in the cyclic form.
    *α/β forms are anomers
    *The anomeric C is always the carbonyl C
  37. 37Hydrolysis of Glycosidic LinkageLinkage involving the hydroxyl group of the anomeric C
    (sugar/base in nucleotides).
    in starch & glycogen.
    Hydrolysis of the glycosidic bond (covalent bond between 2 sugar molecules) has the same mechanism as hydrolysis of the acetal bond.
    glycoside + H2O + catalyst → hydrolysis.
    CATALYSTS: Amylase for starch & glycosylase for nucleotide.    Hydrolysis of Glycosidic Linkage
  38. 38Keto-Enol Tautomerism of Monosaccharides-Enol (alkene/alc) has the alcohol
    -Keto has the ketone and is MORE STABLE
    *in presence of H2O or H3O+    Keto-Enol Tautomerism of Monosaccharides
  39. 39Ketone/Aldehyde Physical PropertiesDipole-dipole interactions give these molecules higher boiling points than their corresponding alkanes, but not as high as the corresponding alcohols or carboxylic acids.
    *C=O polarity
  40. 40Acetal/HemiacetalNucleophilic Addition at C=O.
    Aldehyde/ketones react with 1 equivalent of alcohols to make hemiacetals & 2 equivalent to make acetals    Acetal/Hemiacetal
  41. 41ImineNucleophilic Addition at C=O.
    Primary amine (RNH2) + aldehyde/ketone = imine.
    Catalyzed in a weak acid    Imine
  42. 42EnamineNucleophilic Addition at C=O.
    Secondary amine (R2NH) + aldehyde/ketone = enamine.    Enamine
  43. 43CyanohydrinFormation heavily favors productCyanohydrin
  44. 44Oxidation of AldehydesOxidation of Aldehydes
  45. 45Aldol Condensation2 acetaldehyde -> aldo.
    *For carbonyl compounds w/ acidic α p+ in presence of strong :B    Aldol Condensation
  46. 46Retro-Aldol ReactionWhen treated with strong :B, deprotonation of the free hydroxyl group may induce the reverse of the aldol-rxn
  47. 47Kinetic vs. Thermodynamic EnolateWhen asymmetric ketones with more than 1 set of α p+ are treated with :B, 2 different enolates are possible
  48. 48EnolateEnolate
  49. 49C=O ReactivityBulky groups on either side of C=O blocks access to the electrophilic C, so reactivity goes down.
  50. 50α p+ AcidityAlpha proton is acidic because the resulting carbanion is stabilized by resonance.α p+ Acidity
  51. 51Alcohol Properties-Hydrogen bonding.
    -Higher boiling point than the same compound without the alcohol group.
    -Water soluble as long as molecule does not contain a long hydrophobic region.
  52. 52Alcohol Oxidation-KMnO4/CrO3 will oxidize primary alcohols to carboxylic acids, but PCC/other weak oxidizing agents will only oxidize a primary alcohol to aldehyde.
    -Secondary alcohols always oxidize to ketone.
    -Tertiary alcohols do not oxidize.    Alcohol Oxidation
  53. 53Alcohol DegreesAlcohol Degrees
  54. 54SN1-Stable carbocation, tertiary carbon center, protic solvent.
    -Need a good leaving group.
    -Unimolecular reaction, intermediate carbocation formed.    SN1
  55. 55SN2-Unstable carbocation, primary carbon center, aprotic (but polar) solvent.
    -Need a good leaving group.
    -Bimolecular reaction, passes through transition state.    SN2
  56. 56Alcohol ProtectionThe best protecting group for alcohol is the trimethylsilyl group.
    To protect, add Cl-SiMe3 to R-OH so the alcohol can get "capped" into R-O-SiMe3.
    To deprotect, add F-.
  57. 57Mesylates & TosylatesSulfonates R-SO3- are good leaving groups.
    R= methane -> methanesulfonate
    Toluene -> tosylate
    Trifluoromethane -> triflate
    MESYLATE can be prepared by reacting alcohol + mesyl chloride (MsCl).
    TOSYLATE can be prepared by reacting an alcohol + tosyl chloride (TsCl).    Mesylates &amp; Tosylates
  58. 58Carboxylic Acid Nomenclature & Physical PropertiesNOMENCLATURE: -oic acid, -dioic acid
    -High boiling point due to hydrogen bonding.
    -Soluble in water.
    -Electron withdrawing groups attached to positions close to the COOH helps to distribute the charge of the COO- and stabilize it and makes a stronger acid.
  59. 59Carboxylic Acid ReductionLiAlH4: COOH -> alcohol.Carboxylic Acid Reduction
  60. 60Carboxylic Acid DecarboxylationOccurs for beta-keto acidsCarboxylic Acid Decarboxylation
  61. 61Acid Derivative ReactivityACIDITY: Acid chloride > Anhydride > Esters > Amides
    -Acid halides are the most reactive derivatives because halides are very good leaving groups.
    -Amides are the most stable derivatives because NR2- is a terrible leaving group. Also, the C-N bond has a partial double bond characteristic. Proteins are made of peptide bonds, and they are very stable.
  62. 62Acid Derivative Steric & Electronic Effects-Bulky groups around the C=O group helps protect C center from Nu+ attack.
    -Groups that can redistribute & stabilize negative charges are good leaving groups.
    ex: anhydride has a good leaving group - the carboxylate ion - because the COO- can redistribute the negative charge to both oxygens via resonance.
  63. 63Acid Derivative Strain-Amide C=N bond can not rotate and thus have higher ring strain since they can't rotate to achieve the most stable conformation
    ex: beta-lactam, 4 membered ring + amide

Information

Description
Complete Flashcards on FC 5D- Biological Molecules, created by Victoria Whitfield on 15/05/2017.
Views
4
Rating

Feedback

What is it about?

What do you think of the new look?

How do you like it?