Fundamentals I: 11:00 - 12:00 Scribe: Christopher Bannon

Tuesday, August 11 5, 2009 Proof: Name Here

Dr. Miller Amino Acid Chemistry Page 3 of 5

AA – Amino Acid, PP – Polypeptide, grp – group, Know AA abbreviations as they are used extensively, ECM – Extra Cellular Matrix,

I. Amino Acids: The Building Blocks of Proteins [S1]:

II. AA used in Living Organisms – General Considerations [S2]

a. 21 AA’s incorporated directly into proteins, many more derived through post translational modifications

b. All have tetrahedral carbon atoms & polymerize via peptide bond formation

III. AA – Building Blocks of Proteins [S3]

a. Tetrahedral carbon bound to

i. R-group

ii. H atom

iii. Amine group (involved in peptide bond)

iv. Carboxyl group (involved n peptide bond)

b. Tetrahedral arrangement is chiral (except for Gly)

i. Bend plane of polarized light

IV. AA can Join via Peptide Bonds [S4]

a. Reaction of COO- & protonated amineè lost of H2O and attachment of N atom to C of COO-

i. 1 oxygen of carboxyl leaves with water

V. 20 AA in Proteins [S5]

a. Know names; structures; R-groups; 3 Letter, and 1 Letter abbreviations of all AA’s

b. Know how R-groups affect functionality of protein

VI. Non-polar Amino Acids [S6]

a. Proteins have hydrophobic bonding capabilities largely due to these 4 & next 4 AA’s

b. Leucine = branched hydrocarbon side chainè

i. very hydrophobic, very little reactivity except for hydrophobic bonding.

ii. Bulbous model provides a better view of functioning of AA in proteins; shows spatial arrangement,

1. 3-D area that the molecule takes up, that is not shown in ball and stick model.

c. Proline has a dense ring with a very tiny hole in the center of the ring

i. 3 hydrocarbon R-grp with delta carbon linked back onto amine of alpha carbonè forms a ring;

ii. alpha and beta carbon are inexorably linked by the ring

iii. No rotation by the side chain unless the whole AA shifts in conformationè

1. Incorporation of Pro into a PP chain adds region of rigidity,

2. Prevents free rotation of R-grp.

3. If lots of Pro exist in primary structureè takes on a 2o structure called a poly-proline helix, found in collagen helices

d. Alanine = simplest of all AA’s; R-group = CH3

e. Valine behaves very similarly to Ala, R-grp = isopropyl grp.

VII. Nonpolar Amino Acids Cont’d [S7]

a. Methionine: Has a sulfur in its side chain, (thio-ether side chain)

b. Tryptophan (W) = most hydrophobic of all side chains,

i. The least used AA of all.

ii. R-grp = “indole” group, contains 2 ring structures.

c. Phenylalanine has a benzene ring on it and has a very small opening in the center of the ring

d. Isoleucine is a structural isomer of Leu, difference = methyl has moved to the beta-carbon.

e. These 8 AA’s are the only hydrophobic AA’s.

f. There is no straight chain hydrocarbon for side chains, except in proline but even that is bent and covalently attached to amino grp

i. No straight chain involved in formation of AA in proteins

VIII. Polar & Uncharged Amino Acids [S8]

a. Glycine: neither polar and is uncharged,

i. not hydrophobic (grouped in this category by default)

ii. non-chiral

b. Serine: many times phosphorous is esterified on side chain of Ser

i. Can be glycosilated on side chain, as well as undergo other modifications

c. Glutamine = 1sts cousin of Glu. Has amine grp substituted for carboxylate

i. Not a primary amine, but is and AMIDE grp with NO acid-base potential

ii. Can provide hydrophilicity to PP’s

d. Asparagine = 1st cousin of Asp

i. Like Glu, no acid-base potential

ii. Used to provide hydrophilicity to proteins

I. Polar& Uncharged Amino Acids Cont’d [S9

a. Threonine: hydroxyl grp in side chain

b. Cysteine: sulfhydryl/ mercapto grp

i. Useful in cross-linking proteins;

ii. Similar to serine with OH replaced with SH

iii. AA exists = seleno-cysteine, has SeH instead of SH or OH in side chain

1. Has own tRNA

2. Incorporated into proteins like other AA’s

3. 21st AA

4. Shown that knockout mouse, lacking tRNA for seleno-cysteineè mouse = nonviable

c. Tyrosine (Phe with OH para beta-carbon)

i. Incorporated into PP chains readily

d. Histidine has protonated imidazole ring

i. Functions as a weak acid and has pKa from 6.5-7.

ii. Considered polar but largely uncharged AA b/c of pH environment in which it exists

iii. 10% ionized b/c pH of 7.4 = 1 pH unit above pKa of His = 6.5-7

II. Polar, Charged Amino Acids (negative)[S10]

a. Aspartic Acid: 1 methylene & 1 carboxyl grp in side chain

b. Glutamic Acid: 2 methylene & 2 carboxyl grp in side chain

c. Both = negatively charged as pKa’s ~4 while physiological pH = 7.4

III. Polar, Charged Amino Acids (positive) [S11]

a. Histidine

i. Some will be + charged, 90% will remain uncharged at physiological pH

b. Lysine: has primary amine group at end of 4 hydrocarbon side chain

i. Totally protonated at physiological conditions

c. Arginine: R-group has 3 carbons with delta C bonded to N

i. Nitrogen = bonded to C which is doubled bonded to NH2+ was well as single bonded to NH2

ii. pKa~12

IV. Several AA Occur in Proteins as a Result of Posttranslational Modifications [S12]

a. Hydroxylysine: in collagen

b. Hydroxylproline: in collagen

c. Hydroxyglutamate: in eye proteins (rhodopsin in cone cells)

d. Phosphorylated AA = signaling devices

V. Modified Amino Acids [S13]

a. Hydroxylysine: delta carbon = hydroxylated

b. Hydroxylproline: 4th carbon atom = hydrdoxylated

c. Both allow collagen chains to cross-link b/c of ability to H-bond due to OH on R-grp

i. Without these, can’t be sufficiently stabilized in triple helical formation

ii. Cross-linking provides structural rigidity

iii. Entered in evolution with arise of multicellular organisms

1. Need ECM for cells to live in

VI. Modified Amino Acids Cont’d [S14]

a. Phospho-serine: Phosphorous esterified to serine

b. Thyroxin: thyroid gland hormone

i. Knowledge of AA’s and their modifications allow understanding of hormones & functions of cells of body

1. Epinephrine = derivative of tyrosine

2. Histamine = decarboxylated Histidine (replaced with H on alpha-carbon)

3. Serotonin = decarboxylated Trp (replace COOH of alpha-Carbon with H) & with Trp’s 6 member ring hydroxylated

a. “feel good” molecule

b. Parent of melatonin (sleep hormone)

i. Derived through acylating amino grp of serotonin & etherifying another grp

VII. Acid-Base Properties of Amino Acids [S15]

a. All AA’s = weak polyprotic acids

VIII. pKa Values of Amino Acids [S16]

a. Alpha COOH grp of AA = pK ~2 (strong acid)

i. Competing/ adjacent to positive charged amine grp

1. Electrostatic repulsion of protons on amino grp

ii. pK = 4 of gamma carboxyl grp of Glu

1. no adjacent positive charge to encourage proton dissociation

iii. pK ~9 of amino grp on alpha-carbon

IX. Environment Dependence of Amino Acid Charge [S17]

a. During titration, AA changes charge

i. pH =1 has “+1” charge as carboxyl grp on alpha-carbon will not give up H (pKa ~2)

ii. pH = 7 has a neutral charge called “zwitter ion” b/c carboxyl releases proton (pKa ~4)

iii. pH = 13 has charge “-1” amine grp will give up H (pKa ~ 9)

iv. Local pH environments affect charge as well

1. Placing Glu near Arg in a pH solution of 7 for example

X. pKa Values of the Amino Acid R-Groups [S18]

a. Carboxyl in R-grp have pKa ~4

i. Asp pK=3.9

ii. Glu pK = 4.3

b. Histidine in R-grp ~ 6.5-7

c. Cysteine pK 8.3

d. Amino in R-grp pKa ~10-12

i. Lys pKa 10.5

ii. Arg pKa12

XI. pKa Values of the Amino Acid R-Groups Cont’d [S19]

a. OH in R-Grp

i. Ser pKa 13

ii. Thr pKa 13

iii. Tyr pKa 10.1

iv. Reason is that O is extremely electronegative and does not want to give up H to solution

1. Must have very high pH for dissociation to occur (pH> 13; not viable pH in physiologic environment)

XII. Glycine Titration Curve and Charge Dependence [S20]

a. AA will have 2 titration points,

i. 1 equivalent added to titrate carboxyl (pK ~2-3)

ii. 1 equivalent added to titrate amino grp (pK ~10)

b. Most biochemistry occurs in isoelectric point

i. No overall charge in free AA = isoelectric point

XIII. Glutamic Acid Titration Curve and Charge Dependence [S21]

a. 3 titration points for Glu

i. Carboxyl on alpha-carbon

ii. Amine on alpha-carbon

iii. Carboxyl on R-grp

XIV. A Sample Calculation [S22]

a. Find pH when ion = ¼ dissociated on alpha-carboxyl grp for Glu

i. pH = pKa + log ([A-]/[HA])

ii. pH = 2 log (1/3)

iii. pH = 1.523

XV. Lysine Titration [S23]

a. pK1 = titration of carboxyl grp

b. pK2 = titration of side chain amino group (R-grp)

c. pK3 = titration of primary alpha amino grp

XVI. Another Sample Calculation [S24]-à Stop HEre

a. pH of Lys solution if R-group is ¾ dissociated

i. pH = pKa + log ([A-]/[HA])

ii. pH = 10.5 log (3/1)

iii. pH = 10.977

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