Amino Acids and Peptides I Andy Howard Introductory Biochemistry Fall 2009, IIT

Amino Acids and Peptides IAmino Acids and Peptides I

Andy Howard

Introductory BiochemistryFall 2009, IIT

01/28/08 Biochemistry: Amino Acids

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Acids, bases, amino acidsAcids, bases, amino acids

We begin looking at specific categories of small molecules by examining acid-base equilibrium, both in general and in amino acids

These simple molecules are inherently important, and they help illustrate some general principles


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PlansPlans

iClicker stuffAcid-base equilibriumAmino acid structuresChiralityAcid/base chemistry


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iClicker quiz!iClicker quiz!

1. The correct form of the free energy equation is generally given as:– (a) H = G - TS– (b) PV = nRT– (c) G = H - TS– (d) S = H - G– (e) none of the above

(20 seconds for this one)


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iClicker quiz, problem 2iClicker quiz, problem 2

2. Suppose a reaction is at equilibrium with H = -6 kJ mol-1 andS = -0.02 kJ mol-1K-1.Calculate the temperature.– (a) 250K– (b) 280K– (c) 300K– (d) 310K– (e) 340K

45 seconds for this one


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iClicker quiz, problem 3iClicker quiz, problem 3

3. Suppose the reaction AB is endergonic with Go = 37 kJ/mol. What would be a suitable exergonic reaction to couple this reaction to in order to drive it to the right?– (a) hydrolysis of ATP to AMP + PPi

– (b) hydrolysis of glucose-1-phosphate– (c) hydrolysis of pyrophosphate– (d) none of the above

30 seconds for this one


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Acid-Base EquilibriumAcid-Base Equilibrium

In aqueous solution, the concentration of hydronium and hydroxide ions is nonzero

Define:– pH -log10[H+]– pOH -log10[OH-]

Product [H+][OH-] = 10-14 M2 (+/-) So pH + pOH = 14 Neutral pH: [H+] = [OH-] = 10-7M:

pH = pOH = 7.


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So what’s the equilibrium So what’s the equilibrium constant for this reaction?constant for this reaction?

Note that the equation isH2O H+ + OH-

Therefore keq = [H+][OH-] / [H2O]But we just said that

[H+] = [OH-] = 10-7MWe also know that [H2O] = 55.5M

(= (1000 g / L )/(18 g/mole))So keq = (10-7M)2/55.5M = 1.8 * 10-16M


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Alternative approachAlternative approach

Assume the protonated species is H3O+ rather than H+

Then the reaction is2 H2O H3O+ + OH-

keq = [H3O+][OH-] / ([H2O]2)At pH=7, [H3O+] = [OH-] = 10-7MDilute solution: [H2O] = 55.5M, so

keq = 10-14 M2/ [(55.5)2 M2] = 3.24*10-18


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Henderson-Hasselbalch Henderson-Hasselbalch EquationEquation

If ionizable solutes are present, their ionization will depend on pH

Assume a weak acid HA H+ + A-

such that the ionization equilibrium constant is Ka = [A-][H+] / [HA]

Define pKa -log10Ka

Then pH = pKa + log10([A-]/[HA])


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The Derivation is Trivial!The Derivation is Trivial!

Ho hum:pKa = -log([A-][H+]/[HA])

= -log([A-]/[HA]) - log([H+])= -log([A-]/[HA]) + pH

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

Often writtenpH = pKa + log([base]/[acid])


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How do we use this?How do we use this?

Often we’re interested in calculating [base]/[acid] for a dilute solute

Clearly if we can calculate log([base]/[acid]) = pH - pKa

then you can determine[base]/[acid] = 10(pH - pKa)

A lot of amino acid properties are expressed in these terms

It’s relevant to other biological acids and bases too, like lactate and oleate


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Reading recommendationsReading recommendations

If the material on ionization of weak acids isn’t pure review for you, I strongly encourage you to read the relevant sections in Garrett & Grisham

We won’t go over this material in detail in class because it should be review, but you do need to know it!


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So: let’s look at amino acidsSo: let’s look at amino acids

The building blocks of proteins are of the form H3N+-CHR-COO-;these are -amino acids.

But there are others,e.g. beta-alanine:H3N+-CH2-CH2-COO-


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These are zwitterionsThese are zwitterions

Over a broad range of pH:– the amino end is protonated and is therefore

positively charged– the carboxyl end is not protonated and is

therefore negatively charged

Therefore both ends are charged Free -amino acids are therefore highly

soluble, even if the side chain is apolar


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At low and high pH:At low and high pH:

At low pH, the carboxyl end is protonated

At high pH, the amino end is deprotonated

These are molecules with net charges


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Identities of the R groupsIdentities of the R groups

Nineteen of the twenty ribosomally encoded amino acids fit this form

The only variation is in the identity of the R group (the side chain extending off the alpha carbon)

Complexity ranging from glycine (R=H) to tryptophan (R=-CH2-indole)

Note that we sometimes care about-amino acids that aren’t ribosomal—like ornithine ornithine


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Let’s learn the Let’s learn the ribosomal amino acids.ribosomal amino acids.

We’ll walk through the list of 20, one or two at a time

We’ll begin with proline because it’s weird

Then we’ll go through them sequentiallyYou do need to memorize these, both

actively and passively


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Special case: prolineSpecial case: proline

Proline isn’t an amino acid: it’s an imino acid

Hindered rotation around bond between amine N and alpha carbon is important to its properties

Tends to abolish helicity because of that hindered rotation


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The simplest amino acidsThe simplest amino acids

Glycine

AlanineCN+HHHHCCOO-HHH

CN+HHHHCOO-H

methyl


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CN+HHHHCCOO-CCHHHHCHHHHH

CN+HHHHCCOO-CHCHHHHCHHHH

Branched-chain aliphatic aasBranched-chain aliphatic aas

Valine

Isoleucine

Leucine

CN+HHHHCCOO-CCHHHHHHH

isopropyl


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Hydroxylated, polar amino acidsHydroxylated, polar amino acids

Serine Threonine

CN+HHHHCCOO-OHHH

CN+HHHHCCOO-OCHHHHH

hydroxyl


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Amino acids with carboxylate Amino acids with carboxylate side chainsside chains

Aspartate Glutamate

CN+HHHHCCOO-CHHO-O

CN+HHHHCCOO-HHCHHCO-O

carboxylate

methylene


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Amino Acids with amide side Amino Acids with amide side chainschains

asparagine glutamineCN+HHHHCCOO-HHCHHCNOHH

CN+HHHHCCOO-HHCNOHH

Note: these are uncharged! Don’t fall into the trap!

amide


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Sulfur-containing amino acidsSulfur-containing amino acids

Cysteine Methionine

CN+HHHHCCOO-HHSH

CN+HHHHCCOO-HHSCCHHHHH

sulfhydryl


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Positively charged side chainsPositively charged side chains

Lysine Arginine

CN+HHHHCCOO-HHCCCHHHHHHN+HHH CN+HHHHCCOO-HHCNCHHHHHCNN+HHHH

Guani-dinium


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Aromatic Amino AcidsAromatic Amino Acids

Phenylalanine TyrosineCN+HHHHCCOO-HHCCCCCCHHHHH

CN+HHHHCCOO-HHCCCCCCHHHHOH

phenyl


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Histidine: a special caseHistidine: a special case

Histidine

imidazole


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Tryptophan: the biggest of allTryptophan: the biggest of all

TryptophanCN+HHHHCCOO-HHCCCNCCHHCCHHHH

indole

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Amino Acids and Peptides I Andy Howard Introductory Biochemistry Fall 2009, IIT