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Biological Sciences
Shelley A.Brunt

lec03 primary structure of proteins 1. amino acids a. hydrophobic b. hydrophilic c. ionize d. salt bridges basic structure of amino acid 2. side chain a. r group 3. alpha carbon a. carboxyl group b. alpha amino group 4. three potential places of dissociation a. amino acid b. carboxyl group c. r group i. beta carbon on r group nomenclature with the r,s system 1. nomenclature based on priority sequence to the four groups attached a. lowest atomic weight is assigned the lowest number (number 4) b. if atoms are identical, then atom with lowest amount of bonds is the lowest priority 2. all l-amino acids are s configuration except for cysteine mirror image pairs of amino acids 1. cannot be superimposed a. L and D serine cannot be superimposed b. left and right hand cannot be superimposed amino acids side chains 2. chemical classes a. aliphatic i. do not contain any aromatic rings 1. may contain ali-cyclic rings b. aromatic i. containing aromatic rings c. sulfur containing d. alcohols e. bases f. acids g. amides 3. subclasses a. nonpolar i. hydrophobic 1. five amino acids b. polar i. ionized ii. neutral pH (hydrophilic) 1. seven amino acids 4. property of side chain alters 3d shape a. hydrophobic side chains must be folded in such a way that it is away from water i. e.g. hydrophobic side chains of a water soluble protein fold into the interior of the protein 1. globular protein aliphatic amino acids (5) 1. shortest to longest a. glycine  alanine  valine  leucine  isoleucine i. longer the chain the more hydrophobic it is stereoisomers of isoleucine 2. four isomers since there are two chiral carbons aliphatic amino acids (4) 3. alanine / valine / leucine / isoleucine a. hydrophobic i. cluster away from water ii. important in establishing and maintaining 3d structure 1. critical in the folding of the protein that predict the active site for substrate proline 1. because of ring structure a. proline can only occur in certain places in proteins b. restrict folding structure c. never found in alpha helices i. but may be found at ends of alpha helices d. significantly less hydrophobic than the branched aliphatic amino acids 2. considered secondary amino group a. imine (imino amino acid) i. containing a C=N double bond 3. ring restricts protein geometry and often introduces changes in direction of the peptide chain folding aromatic r group amino acids 4. hydrophobic characteristics a. but both tyrosine and tryptophan also have hydrophlic properties because of OH and NH groups b. absorb at a particular UV light range i. ~260 phenylalanine (DNA / RNA also appear at 260) ii. ~280 for tyrosine and tryptophan 5. phenylalanine (F) a. Phe b. 260 nm c. contains benzyl side chain 6. tyrosine (Y) a. Tyr b. 280 nm c. contains phenol side chain i. OH group 7. tryptophan (W) a. Trp b. 280 nm c. contains bicyclic indole side chain i. benzene ring fused with 5 membered nitrogen containing pyrrole ring 1. NH group sulfur containing r groups 8. cysteine (C) a. critical in forming disulfide bridges b. important for stability of secreted proteins i. more resistant to degradation c. side chains are slightly hydrophobic d. during oxidation reaction i. capable in forming disulfide bonds 9. methionine (M) a. nonpolar thioether group i. ether group except sulfur is in the place of oxygen 1. thio for sulfur b. always first amino acid forming a protein i. not always present in the final protein product 1. gets cleaved off c. codon for ribosome i. low abundant amino acid in most protein formation of cystine from two oxidized cysteine molecules during protein hydrolysis 1. two cysteine molecules oxidize to form one cystine molecule via a disulfide bond a. slightly alkaline pH b. when disulfide bonds form i. they need to be in close proximity in 3d space (not necessarily close in primary structure) 2. intracellular proteins often do not contain disulfide bonds since oxidation is not favored inside the cell a. why? i. to form a disulfide bond, you need to oxidize the sulfhydryl groups  means you have to lose a proton ii. inside the cell, it is aqueous and you have an abundance of H+ which keeps the sulfhydryl groups in a stable protonated state iii. therefore if you have free H+ that can protonate the sulfhydryl groups, then oxidation will not be favored b. disulfide bonds present in many secreted proteins 3. disulfide bonds work to stabilize 3d structure side chains with alcohol groups: aliphatic side groups 4. serine (S) a. ser 5. threonine (T) a. thr 6. serine and threonine a. uncharged polar side chains contain beta-hydroxyl groups i. hydrophilic character to the aliphatic side groups ii. hydroxyl group on beta carbon b. but won't ionize in aqueous solutions i. weak ionization properties c. can be phosphorylated i. amino acid kinases acid vs basic r groups in functioning cells (pH ~7.4) 1. pH of acids are low 2. pH of bases are high 3. if you have a pH of 7.4, then a. acids will become deprotonated (loss of hydrogen  becomes negative) b. bases will become protonated (gain of hydrogen  becomes positive) basic r groups: nitrogenous bases that have positive (to?) charge at neutral pH 1. amino acid a. arginine (R) i. most basic (pH) amino acid ii. hard to deprotonate 1. always protonated iii. guanidinium ion b. lysine (K) i. alkylammonium ion c. histidine (H) i. imidazole rine  imidazolium ion when protonated 2. r groups strongly hydrophilic a. water loving 3. ability to form ionic base pairing function of protein 4. effect of one amino acid substitution a. specific function in protein i. substitution of amino acid 1. lycine to arginine a. protein will still carry out function, but it is harder because arginine is much more basic 2. lycine to proline a. loss of function, does not have similar characteristic (basicity) acid (carboxylate) r groups and amine derivatives 1. amino acids a. aspartate (D) b. glutamate (E) i. present in MSG c. asparagine (N) d. glutamine (Q) 2. in functioning cells a. carry an asparatate and glutamate i. net negative charge 1. due to dicarboxylic side groups 2. ionizable at neutral pH 3. hydrophilic side chains ii. ability to do similar things 1. active sites a. glutamate  aspartate (shorter) i. side chain is shortened 1. function is conserved, but ability to function may be compromised because of distance the substrate has to travel iii. at neutral pH 1. aspartate and glutamate form a. NOT aspartic acid NOR glutamic acid b. aspargine and glutamine i. normally found on surfaces of amino acids 1. interact with water and other polar amino acids through H bonds ii. amides 1. uncharged 2. highly polar 3. for exams a. visualize what side groups look like b. need to know 1 and 3 letter abbreviations i. particularly one letter abbreviation 1. slide 16 a. alanine i. A - ala b. arginine i. R - arg c. asparagine i. N - asn d. aspartic acid i. D - asp e. cysteine i. C - cys f. glutamine i. Q - gln g. glutamic acid i. E - glu h. glycine i. G - gly i. histidine i. H - his j. isoleucine i. I - ile k. leucine i. L - leu l. lysine i. K -lys m. methionine i. M - met n. phenylalanine i. F - phe o. proline i. P - pro p. serine i. S - ser q. threonine i. T - thr r. tryptophan i. W - trp s. tyrosine i. Y - tyr t. valine i. V - val u. asparagine or aspartic acid i. B - asx v. glutamine or glutamic acid i. Z - glx characteristics of amino acids 1. frequency in terms of percentages a. cysteine and tryptophan and histidine i. relatively low percentages 2. molecular weight of amino acid a. ~100 i. if you have 1000 amino acids in protein 1. then you have 100,000 in terms of MW for protein 3. pKa values of acidic and basic constituents a. carboxyl groups i. <3 b. amino acids i. >9 c. side chains (ctaglah) i. cysteine ii. tyrosine iii. aspartic acid iv. glutamic acid v. lysine vi. arginine vii. histidine d. pI of most amino acids i. add carboxyl group and amino acid group and divide by 2 e. pI of amino acids with 3 ionizable groups is different i. use two pKas surrounding the zwitterionic form 1. where pH is neutral other amino acids and derivatives 1. greater than 200 amino acids in living organisms a. but only 20 are used to make protein 2. other L-forms used as precursors to standard amino acids or intermediates in other biohemical pathways a. ... b. fungi and bacteria make d-amino acids that are used in cell walls and antibiotic synthesis c. biologically relevant amines i. glutamate  GABA (inhibitory neurotransmitter in brain) ii. histidine  histamine (controls blood vessel constriction and HCl constriction) d. precursors of hormones 3. amino acids are modified after incorporation into polypeptides such as proline to hydroproline a. implications in scurvy i. collagen and hydroproline b. can be modified by glycosylation i. addition of carbohydrate c. can be modified by phosphorylation d. bacterial amino acid
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