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McGill University
Biology (Sci)
BIOL 200

Lecture 1 Chemical Foundationslife occurs in a watery environmentobiomolecules can be classified as hydrophilic sugars hydrophobic fat and amphipathic phospholipidscovalent bonds strong bonds small distance between atomsocarbon most important atom can form 4 covalent bondsoie methane tetrahedral formaldehydenoncovalent interactions weaker larger distancecommon functional groups biomolecules hydroxyl acyl carbony carboxyl sulfhydryl amino phosphate pyrophosphatecommon linkages ester ether amidepolar bonds OH CO NH PO bc of electric dipole momentin water covalent bondsnoncovalent interactions cc bonds are especially stronga single noncovalent interaction is unstable at biological temperatures however in a biomolecule it is additive and very stablethe hydrolysis of ATP phosphoanhydride bond is 73 kcal which is stronger than some covalent bonds but less than CC bondsLecture 2Noncovalent interactions ionic interactions hydrogen bonds van dar walls interactionsoIonic interactions NaCl has strong interaction dissolve happily in water because it forms HYDRATION SHELL for close contact proteinprotein water needs to be excludedoIonchannel proteinTetrameric channel mediates transport of K from inside to outside of cell transmembrane protein hydration shell give selectivity of ion K channels because potassium ion is bigger than Na ion There are amino acid residues that come in contact with the ion with polar oxygen atoms that are spaced like a hydration shelloHydrogen bonds in liquid water dynamic network of hydrogen bonds solubility in water depends on its ability to form hydrogen bonds ie methanol methylamine peptide group ester groupoVan der waals interactions weak result from transient dipoles occur in all types of molecules form only when atoms are very closeoHydrophobic effect aggregated state of hydrophobic molecules hydrophobic surface area exposed to water is reduced water population less ordered higher entropy energetically more favorableoSpecificity of association between biological macromolecules is based on multiple noncovalent interactions precisely spatially organizedBuilding MacromoleculesMonomers to polymers amino acidspolypeptide peptide bond for protein nucleotide nucleic acid phosphodiester bond monosaccharidepolysaccharide glycosidic bond in each case when addition of monomer molecule of water is released all covalent bondsLarge structures based on noncovalent bonds cytoskeletonoActin filament microtubule Noncovalent bonds are easy to form and undo thus the polymers are very dynamicoLipid membrane hydrophobic environment in the leaf inside hydrogen bondsionic interactions at exterior of membraneBuilding blocks amino acidsoBaseacidamphotericoAlpha carbon atom that makes 4 covalent bondsoHydrogen bondoCarboxy group COO and amino group NH3 make up backbone of protein peptide bond with each otheroR side chain R group 20 different amino acids so 20 different R group governs what kind of noncovalent interactions the proteins participate inoHydrophobic amino acids R groups with no polar bonds except for tyrosine and tryptophan alanine Ala or A valine Val or V Isoleucine Ile or I Leucine Leu or L Methionine Met or M Phenylalanine Phe or F Tyrosine Tyr or Y Tryptophan Trp or WAromatic rings are free to rotateHydroxyl group of tyrosine can be modified by phosphorylation altered to phosphate group highly charged activates or inactivates proteinoHydrophilic amino acidsBasic lysine Lys or K moderate arginine Arg or R strong Histidine His or H weakAcidic Aspartate Asp or D Glutamate Glu or EPolar amino acids with uncharged R groups Serine Ser or S Threonine Thr or T Asparagine Asn or N Glutamine Gln or Qospecial amino acids cysteine Cys or C SH linkage and can form covalent interactions w other cysteine residues with disulfate bridge important in conferring 2ndary structure glycine Gly or G small and fits into tight spaces proline Pro or P side chain links also to amino group in backbone so they kink polypeptide group because of rigid bond fixed angleLecture 3Cysteine can disulfide bridge covalent bond in extracellular space ie plasma oxidizing ambient in cytoplasm not bonded so reducing ambientBuilding blocks sugars from carbohydrate monomers some multiple of CH2OoChemical groups many OHaldehyde or ketone
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