aa lecture 1

7/29/2019 Aa Lecture 1

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Amino acid

Dr Maryjane


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Amino Acid

Contents Introduction

Structure

Classification

Properties

Optical

Spectroscopic Acid/Base

Importance

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INTRODUCTION


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Amino Acid

Small and simple molecules

More than 300 are described in nature

Only 20 are commonly found as constituents of

mammalian proteinsThe only amino acids coded for by DNA

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Introduction


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DNA sequence codes for amino acid sequence of a protein


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STRUCTURE


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Structure

Two functional groups

#Amine NH2

#Carboxyl -COOH.

General formula H2NCHRCOOH

#Exception :Proline-Secondary amine Imine

#R Side chain

#Various alpha amino acids differ in side

chain (R group)


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Structure
http://upload.wikimedia.org/wikipedia/commons/c/ce/AminoAcidball.svg


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Structure

Common structural features: Central carbon ( carbon)-Assymetric carbon atom

Amino group

Carboxylic group

Unique side chain( = R group)

Hydrogen

20 standard amino acids in our body-All have Asymmetric carbon atom

EXCEPT- Glycine where R=H

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Structure


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At pH 7.4 (physiological pH), amino acids exist

in zwitterionic form (positive NH3+

andnegative COO- charges).


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CLASSIFICATION


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Amino acid are classified on the basis :

Structure

Side chain Characteristics

Metabolic fate

Nutritional requirement

Classification of amino acid


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ACCORDING TO STRUCTURE

Group I- Alkyl Chain Amino acids /Aliphatic side chain


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Group II-Hydroxyl (OH) group in the side chain

Group III-Sulfur (S) group in the side chain


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Group IV-Acidic group in the side chain

Group V-Basic group in the side chain


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Group VI-Aromatic group in the side chain

Group VII- Imino acid


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Classification of amino acid-nutritionalRequirement

20 standard amino acids in our body

10-Essential ,Remaining 10 -Non Essential

Essential amino acids

Not synthesized by our body.

Supplied in the diet

Essential for growth

Arg,His,Ile,Leu,Thr,Lys,Met,Phe,Trp,Val

Semi essential Arg -Essential only during the period of growth or

positive nitrogen Balance.

Any help in learning these little molecules prove truly valuable.


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Classification of Amino Acids

Nature of the side chain that ultimately dictates the role an amino acid

plays in the protein.

Useful to classify the amino acids according to the properties of their

side-chains.

Based on the properties of their side chains

Amino acids with non-polar side-chains

Amino acids with polar side-chains

Amino acids with uncharged polar side-chains

Amino acids with charged polar side-chains

Amino acids with acidic side-chains

Amino acids with basic side-chains

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hydrophobic


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Involved in hydrophobic interactions

Do not ionize nor participate in hydrogen bonds

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As part of proteins in aqueous solutions:

Amino acids with non-polar side-chains tend to cluster

together in the interior of the protein help give the

protein its 3-dimensional shape

As part of proteins located in hydrophobic environment (e.g.

membrane)

Amino acids with non-polar side chains are found on the

surface of the protein, interacting with the lipid environment

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Proline


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Zero net charge at neutral pH

Participate in hydrogen-

bonding (H-bonding)

Serine, threonine with

hydroxyl group

Asparagine and glutamine

with a carbonyl group and

an amide group

Amino acids with polar uncharged R side

chains


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Serine, threonine, tyrosine with hydroxyl group


Asparagine and glutamine with a carbonyl group and an

amide group


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Serve as attachments for other compounds

Attachment for phosphate group to hydroxyl group of serine,

threonine, tyrosine


Attachment of oligosaccharides in glycoproteins to:

Amide group of asparagine

Hydroxyl group of serine, threonine


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Two Cysteine residues can form disulfide bond



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Amino acids with acidic side-chains

Contain an extra carboxylic group in the side-chains

Carboxyl dissociates in acidic range of the pH scale (pH


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Amino acids with basic side-chains

Contain extra Amino group in the Side-chains

Amino group dissociates in the basic range of the

pH scale (pH>7)

Protons acceptor Basic amino acid-Arginine and lysine positively

charged at physiologic pH

Amino acids with charged side-chains

d kl b


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Is an almost neutral amino acid (6.5-7) which at physiologic pH is

positively charged

When incorporated with protein, side chain can either be positivelycharged or neutral

Depends on the ionic environment provided by the polypeptide chains of

the protein

An important property that contributes to its role in the functioning ofproteins (e.g. myoglobin)

Histidineweakly basic


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Amino Acids Abbreviations


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Optical Property

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M i f i


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1. D or L

Can occur in compounds with four different groups arranged around a

carbon atom (chiral carbon)

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Maintype of stereoisomers :

A i id ( t l i ) i t


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Amino acids (except glycine) can exist

in either the D or the L form

D and L forms of amino acids

Are mirror images of each other-Cannot be

superimposed

Are termed stereoisomers or enantiomers

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The carbon of each amino acid is a chiral carbon (a


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The carbon of each amino acid is a chiral carbon (a

carbon with 4 different groups attached to it)

O l L i id ll i h i


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Only L- -amino acids occur naturally in human proteins

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D- -amino acids occur in antibiotics,plant and bacterial cell wall


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Exhibited by the amino acids having the same molecular formula but

differ in optical activity Beam of plane polarised light is made to pass thru the solution of a

compound

Dextrorotatory behaviour ( d ) ( +)

Clockwise rotation of plane-polarized light

Levorotatory behaviour ( l ) ( - )

Counterclockwise rotation of plane-polarized light

Equimolar concentration of optical isomers-Racemic mixtureNo net

rotation

Optical Activity


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Optical Activity-the ability to rotate plane-polarizedlight


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Chiral molecules have optical activity

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Achiral molecules have no optical activity


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The common human amino acids are in the L-enantiomer form

Not all L-amino acids are levorotatory

L(+)-Alanine = L-enantiomer is dextrorotatory

L(-)-Serine = L-enantiomer is levorotatory

9 of the 19 L-amino acids commonly found in proteins are

dextrorotatory.

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Optical Activity


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ACID BASE PROPERTY


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Henderson-Hasselbalch equation

Describes the quantitative relation between the concentration of

a weak acid ( HA ) and its conjugate base ( A- )

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C id h l f b k id


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Consider the release of a proton by a weak acid

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By definition, the dissociation constant of the acid ( Ka ) is

Solving for H+ :

Taking the negative logarithm of each side:

HA H+ + A-

Weak acid proton Conjugate base

Ka =H+A-

HA

* The larger the Ka,

the stronger the acid

Ka A-

HAH+ =

- Log Ka - log A-

HA- Log H+ =


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-Log Ka - log

A

-

HA - Log H+ =

-Log H+ = pH

-Log Ka = pKa

pH = pKa - log A-

HA

A-

HA - log = + log

A-

HA

Henderson-Hasselbalch

equation

H d H lb l h ti


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Henderson-Hasselbalch equation

When A- = HA

pH = pKa + log 1

pH = pKa + 0

pH = pKa

pKa = pH at which the weak acid is 50% dissociatedhalf is in acid

form; half is in base form - expresses the strength of weak acids

pH = pKa + logH A

A-


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Applications of the Henderson-Hasselbalch equation

Preparing buffers

Buffermaximum buffering capacity occurs at a pH = pKa

created by mixing equal concentrations of a weak acid and its conjugate

base

A conjugate acid/base pair can serve as an effective buffer when the pH of

a solution is within approximately 1 pH unit of the pKa of the weak acid

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A li i f h H d H lb l h i


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Preparing buffers

Buffer

A solution that resists a change in pH following the addition of acid or base

Can be produced by mixing equal concentration of a weak acid with its

conjugate base

A conjugate acid/base pair can serve as an effective buffer when the pH of a

solution is within approximately 1 pH unit of the pKa of the weak acid

If an acid is added: the resulting H+ (from the added acid) combines with

the conjugate base A- to produce HA

If a base is added: the resulting H+ ( because combined with the added

base) will be replaced by the dissociation of the weak acid HA to H+ and A-

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Adding an alkali to an amino acid solution


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Adding an alkali to an amino acid solution

If the pH of a solution of amino acid is

increased by adding hydroxide ions

Adding an acid to an amino acid solution

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Hydrogen is removed

from NH3+

If the pH of a solution of amino acid is

decreased by adding an acid

COO- picks up a

hydrogen ion

When in aqueous solution, amino acids can act as both acids andbases (amphoteric)

Blood Buffers


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Blood Buffers

Bicarbonate

Hydrogen phosphate

Proteins



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HOOC

O-CO-CH3

-OOC

O-CO-CH3

+ H+

pKa = 3.5

Aspirin (neutral)Aspirin (anion)

Isoelectric point ( pI )


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pH at which the net charge on the molecules in solution is zero

Average of the 2 pK values on either side of the isoelectric molecule

Because there is no net charge at the isoelectric point, amino acids are least

soluble at this pH-

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pI = = 5.7( 2.3 + 9.1)

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General relationship between charge properties


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If pH < pI, then the amino acid will have a net

positive charge

If pH > pI, then the amino acid will have a netnegative charge

If pH = pI,then the amino acid will have no net charge.

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General relationship between charge properties

of amino acids and pH:

Amino acids without ionizable side chains have 2 pKa


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pKa for-carboxyl group

pKa for-amino group

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Example : alanine

pK1 = 2.3

R-COOH R-COO- + H+

pK2 = 9.1

R-NH3 R-NH2 + H+

pK1 = 2.3 pK2 = 9.1

Amino acids without ionizable side chains have 2pKa


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P ti f i id t it I l t i H


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Both the functional groups are ionized

Equal and opposite charges

No net charge

Properties of amino acidsat its Isoelectric pH

Titration of histidine


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Titration of histidine

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Histidine


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Histidine

pKafor-carboxyl group = 1.8

pKa

for-amino group = 9.2

pKafor the R-group = 6

has 3 pKas:

pI = = 7.6( 6.0 + 9.2)

2

+2 +1 0 -1

Glutamic Acid


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pI = pK1

+ pKR

/ 2

= (2.19 + 4.25) / 2

= 3.22


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IMPORTANCE


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Serve as monomeric units from whichproteins are

constructed-Proteins are the most abundant

macromolecules

Derivatives participate in :

Nerve transmission

Regulation of cell growth

Biosynthesis of porphyrins, purines, pyrimidines, urea

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Importance

Tyrosine


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y

Tyrosine is involved in the synthesis of:

Dopamine

Catecholamines-Epinephrine,nor epinephrine,dopamineChemical messengers-Transmit impulses across the

neurons in the brain and onward to the muscles

Control muscle movement

Tyrosine


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TyrosineNor Epinephrine

Tyrosine


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TyrosineMelanin

Tyrosinase-Deficiency-Albinism

Phenylalanine


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Epinephrine

Phenylalanine

Tryptophan Serotonin


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yp p

Tryptophan is involved in the synthesis of:

Melatonin

Serotonin

Niacin


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Test yourself

1. given the conjugate base is 100, weak acid

is 1, pK is 6. what is the pH?

2. given the conjugated base is 1000, the weak

acid is 1000, the pH is 7.4. what is the pK


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Test Yourself!

You have just admitted a male infant with a congenital

deficiency for pyruvate dehydrogenase and you suspect

lactic acidosis. The laboratory reports that the urine

contains 0.01 mM lactic acid and 1.0 mM lactate ions.

What is the pH of the urine? (Lactic acid, pK = 3.9)

A. 3.9

B. 4.9

C. 5.9D. 6.9

E. 7.9


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Which of the following describes the side chain of valine?

A. contains sulfur

B. contains a branched chain hydrocarbon

C. contains an aromatic ring

D. cyclic

E. unbranched with primary amine

TEST Yourself!

1) What general roles do amino acids serve in cells? Building blocks for proteins

2) What are the structural features of an amino acid? Amino group carboxyl group


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2) What are the structural features of an amino acid? Amino group, carboxyl group

and side chain.

3) Which part dictates the role of that amino acid is a protein? Side chain

4) What are the major types of amino acid side chains? Hydrophobic, polar non-

charged and polar charged.

5) Which are basic? (Arg, Lys and His), acidic? (Glu and Asp), polar but not

charged? (Thr, Ser,Tyr, Asn ,Gln and cys) hydrophobic? (Leu, Ile, Met, Phe, Ala,

Pro, Val,Trp)?

6) Be able to recognize those amino acids that are stipulated. Cys has -SH and Gly

has no side chain

7) Be able to associate the three-letter name with the full name. (Do not need to

know the one letter code, although it is used extensively)

8) What is the source of optical activity in amino acids? Presenceof chiral carbon

9) Which configuration of amino acids is found in proteins? L configuration

10) Meaning of stereoisomers (isomers of configuration), optical isomers (D and L),

enantiomers (two different isomers differing in configuring at one carbon only,chiral molecules (four different substituents on one carbon atom).

11) What are acids and bases? Acids donate proton and bases accept proton.

13) Which groups in amino acids are acidicprotonated carboxyl and protonated amino group.

basic? unprotonated carboxyl and unprotonated amino group.


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p y p g p

14) Be able to predict which forms of an amino acid exist at pH 1, 7 and 13. (group is protonated if

the pH is below the pKa of the group, and conversely) (Remember that the carboxyl group is

negatively charged when unprotonated and neutral if protonated. The amino group is positively

charged if protonated and neutral if unprotonated)

15) What is the value of Henderson Hasselbalch equation? Relates the pH, pKa and the amounts ofthe protonated and unprotonated forms of an ionized group.

16) What is the meaning of pKa? pKa is the pH at which an ionizible group is 50% protonated and

50% unprotonated.

17) What is a buffer? (a solution that resists changes in pH) How are buffers constructed? (Mixing

the protonated and unprotonated forms of an ionizable substance. Alternatively one can add acid

to the unprotonated form or NaOH to the protonated form.)

18) What are the requirements of a good buffer? Must have enough of the buffering substance to

absorb the expected amount of added base or acid and stay in the pH range required and the pH

must be within about 1 pH unit of the pKa.

19) What is isoelectric point? pH at which the molecule has no net charge Be able to find the

isoelectric point and the pKa of and ionizable group on a titration curve of a simple amino acid.

(see titration curves)

20) Know the approximate pKa values of an amino group and a carboxyl group in an amino acid. (2or 3 for carboxyl group and 9 or 10 for an amino group)

21) Be able to predict the protonation state of an ionizable group from the pKa and the pH. See

above

22) What are the major blood buffers? Bicarbonate, proteins and phosphate

aa lecture 1

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