Amino Acids and Amino Acids and ProteinsProteins

Larry SchefflerLarry SchefflerLincoln High Lincoln High SchoolSchoolPortland ORPortland OR

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Amino AcidsAmino Acids

Amino acids have both Amino acids have both a carboxyl group a carboxyl group

-COOH-COOH an amino group an amino group

-NH-NH22

in the same in the same molecule.. molecule..  2

Amino Acid Amino Acid StructureStructure

The general formula of an amino acid The general formula of an amino acid is shown hereis shown here

The group designated by The group designated by RR is usually is usually a carbon chain but other a carbon chain but other

structures are also structures are also

possiblepossible

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Amino Acid StructureAmino Acid StructureAmino acids may be Amino acids may be characterized as characterized as , , , , or or amino acids amino acids depending on the depending on the location of the amino location of the amino group in the carbon group in the carbon chain. chain.

are on the carbon are on the carbon adjacent to the adjacent to the carboxyl group. carboxyl group.

are on the 2are on the 2ndnd carbon carbon

on the 3on the 3rdrd carbon carbon from the carboxyl from the carboxyl groupgroup

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Amino Acids - Amino Acids - ProteinsProteins

Amino acids are the building Amino acids are the building blocks of proteins. Proteins are blocks of proteins. Proteins are natural polymers of successive natural polymers of successive amino acidsamino acids

There are 20 different amino There are 20 different amino acids that make up human acids that make up human proteinsproteins

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amino acidsamino acids

Amino acids found Amino acids found in proteins are in proteins are amino acidsamino acids. . The amino group The amino group is always found on is always found on the carbon the carbon adjacent to the adjacent to the carboxyl groupcarboxyl group

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Amino Acid Amino Acid FunctionsFunctions

1.1. Amino acids are the building blocks Amino acids are the building blocks

of proteinsof proteins

2.2. Some amino acids and their Some amino acids and their derivatives function as derivatives function as neurotransmitters and other neurotransmitters and other regulatorsregulators

Examples IncludeExamples Include

L-dopamineL-dopamine

EpinephrineEpinephrine

ThyroxineThyroxine

HistidineHistidine7

Amino Acids and ProteinsAmino Acids and Proteins

Amino acids Amino acids

forming forming proteins may proteins may be be characterized characterized as Acidic, as Acidic, Basic, or Basic, or neutral neutral depending on depending on the character the character of the side of the side chain chain attached.attached. 8

Acidic Amino AcidsAcidic Amino Acids

There are There are two acidic two acidic amino amino acids.acids.

There are There are two two carboxyl carboxyl groups and groups and only one only one amino amino group per group per molecule molecule

(asp)

(glu)

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Basic Amino Acids IBasic Amino Acids I

These amino These amino acids are acids are basic. They basic. They have more have more amino amino groups than groups than carboxyl carboxyl groups groups

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Basic Amino Acids IIBasic Amino Acids II

These amino These amino

acids are acids are also basic. also basic. They have They have more amino more amino groups than groups than carboxyl carboxyl groups groups

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Neutral Amino Acids Neutral Amino Acids II

These amino These amino Acids are Acids are considered considered neutral. There neutral. There is one is one carboxyl carboxyl group per group per amino group amino group

(ala)

(gly)

((leu)

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Neutral Amino Acids Neutral Amino Acids IIII

(Tyr)

(Trp)

(Cys)

(Ser)

(Val)

(Met) 13

Neutral Amino Acids Neutral Amino Acids IIIIII

(Ile)

(Asp)

(Gln)

(Thr)

(Phe)

(Pro)14

Amino Acids and Amino Acids and Optical IsomersOptical Isomers

Except for glycine, all amino acids Except for glycine, all amino acids have a have a chiral carbon atomchiral carbon atom. Therefore . Therefore they can have they can have optical isomersoptical isomers

The amino acids found in The amino acids found in proteins proteins are are all all levarotatory or L formslevarotatory or L forms..

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Amino Acids are Amino Acids are AmphotericAmphoteric

Amino acids are Amino acids are amphoteric.amphoteric. They are capable of They are capable of behaving as both an acid and a base, since they have behaving as both an acid and a base, since they have both a proton donor group and a proton acceptor both a proton donor group and a proton acceptor group. group.

In neutral aqueous solutions the proton typically In neutral aqueous solutions the proton typically migrates from the carboxyl group to the amino group, migrates from the carboxyl group to the amino group, leaving an ion with both a (leaving an ion with both a (++) and a (-) charge. ) and a (-) charge. 16

The ZwitterionThe Zwitterion

This dipolar ion form is known as a This dipolar ion form is known as a Zwitterion.Zwitterion.

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Essential Amino AcidsEssential Amino Acids

Of the 20 amino acids that make Of the 20 amino acids that make up proteins 10 of them can be up proteins 10 of them can be synthesized by the human bodysynthesized by the human body

The other 10 amino acids must be The other 10 amino acids must be acquired from food sources. acquired from food sources. These amino acids are known as These amino acids are known as essential amino acidsessential amino acids

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Essential Amino AcidsEssential Amino AcidsEssential amino Essential amino

acidsacids Arginine Arginine Histidine Histidine Isoleucine Isoleucine Leucine Leucine Lysine Lysine Methionine Methionine Phenylalanine Phenylalanine Threonine Threonine Tryptophan Tryptophan Valine Valine

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Non-Essential amino acidsNon-Essential amino acids Alanine Alanine (from pyruvic acid)(from pyruvic acid) Asparagine Asparagine (from aspartic acid) (from aspartic acid)

Aspartic Acid Aspartic Acid (from oxaloacetic acid)(from oxaloacetic acid) Cysteine Cysteine Glutamic Acid Glutamic Acid (from oxoglutaric acid) (from oxoglutaric acid)

Glutamine (from Glutamine (from glutamic acid) glutamic acid)

Glycine (Glycine (from serine and threonine) from serine and threonine)

Proline Proline (from glutamic acid) (from glutamic acid)

Serine Serine (from glucose)(from glucose) Tyrosine Tyrosine (from phenylalanine)(from phenylalanine)

Essential Amino AcidsEssential Amino Acids

Complete proteinComplete protein Contains all 10 Contains all 10

essential amino acidsessential amino acids Proteins derived from Proteins derived from

animal sources are animal sources are complete proteinscomplete proteins

Beans contain some Beans contain some complete protein as complete protein as wellwell

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Incomplete protein Incomplete protein Lack one of more of the Lack one of more of the

essential amino acidsessential amino acids Most vegetable proteins Most vegetable proteins

are incomplete proteinsare incomplete proteins Beans are an exception Beans are an exception

to this generalizationsto this generalizations

Peptide BondPeptide Bond

When two amino acids combine, When two amino acids combine,

there is a formation of an amide there is a formation of an amide and a loss of a water molecule and a loss of a water molecule

+ H2O

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Proteins- Levels of Proteins- Levels of StructureStructure

Amino acids can undergo condensation Amino acids can undergo condensation

reactions in any order, thus making it reactions in any order, thus making it possible to form large numbers of possible to form large numbers of proteins. proteins.

Structurally, proteins can be described in Structurally, proteins can be described in four ways. four ways.

1. Primary 2. Secondary3. Tertiary4. Quaternary structure.

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Primary StructurePrimary Structure

The primary structure of a protein is The primary structure of a protein is defined by the sequence of amino acids, defined by the sequence of amino acids, which form the protein. This sequence is which form the protein. This sequence is determined by the base pair sequence in determined by the base pair sequence in the DNA used to create it. The sequence for the DNA used to create it. The sequence for bovine insulin is shown belowbovine insulin is shown below

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Secondary StructureSecondary Structure The secondary structure describes the way The secondary structure describes the way

that the chain of amino acids folds itself due that the chain of amino acids folds itself due to intramolecular hydrogen bondingto intramolecular hydrogen bonding

Two common secondary structures are the Helix

and the sheet

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Tertiary StructureTertiary Structure

The tertiary structure The tertiary structure maintains the three maintains the three dimensional shape of dimensional shape of the protein. the protein.

The amino acid chain The amino acid chain (in the helical, pleated (in the helical, pleated or random coil form) or random coil form) links itself in places to links itself in places to form the unique twisted form the unique twisted or folded shape of the or folded shape of the protein. protein.

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Tertiary StructureTertiary Structure

There are four ways in which parts of the amino acid There are four ways in which parts of the amino acid chains interact to stabilize its tertiary shape.. They include:chains interact to stabilize its tertiary shape.. They include:

I.I.-- -- Covalent bondingCovalent bonding, for , for example disulfide bridges example disulfide bridges formed when two cysteine formed when two cysteine molecules combine in which molecules combine in which the –SH groups are oxidized:the –SH groups are oxidized:

II.II.-- -- Hydrogen bondingHydrogen bonding between between polar groups on the side chain.polar groups on the side chain.

III.III.-- -- Salt bridgesSalt bridges (ionic bonds) (ionic bonds) formed between –NHformed between –NH

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COOH groups COOH groups

IV.IV.---- Hydrophobic Hydrophobic interactions.interactions.26

Quaternary Quaternary StructureStructure

Many proteins are not single strandsMany proteins are not single strands

The diagram below shows the quaternary The diagram below shows the quaternary structure of an enzyme having four interwoven structure of an enzyme having four interwoven amino acid strandsamino acid strands

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The natural or native structures of The natural or native structures of

proteins may be altered, and their proteins may be altered, and their biological activity changed or biological activity changed or destroyed by treatment that does destroyed by treatment that does not disrupt the primary structure. not disrupt the primary structure.

Following denaturation, some Following denaturation, some proteins will return to their native proteins will return to their native structures under proper conditions; structures under proper conditions; but extreme conditions, such as but extreme conditions, such as strong heating, usually cause strong heating, usually cause irreversible change. irreversible change.

Denaturing ProteinsDenaturing Proteins

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Heat Heat

Ultraviolet Ultraviolet Radiation Radiation

Strong Acids Strong Acids or Bases or Bases

Urea Urea

Some Organic Some Organic SolventsSolvents

AgitationAgitation

Denaturing ProteinsDenaturing Proteinshydrogen bonds are broken by increased translational and vibrational energy.(coagulation of egg white albumin on frying.)

Similar to heat(sunburn)

salt formation; disruption of hydrogen bonds.(skin blisters and burns, protein precipitation.)

competition for hydrogen bonds.(precipitation of soluble proteins.)

(e.g. ethanol & acetone) change in dielectric constant and hydration of ionic groups.(disinfectant action and precipitation of protein.)

shearing of hydrogen bonds.(beating egg white albumin into a meringue.)

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A small change A small change

in the sequence in the sequence of the primary of the primary structure can structure can have a significant have a significant impact on impact on protein structureprotein structure

In sickle cell In sickle cell anemia a anemia a glutamic acid is glutamic acid is replaced by a replaced by a valine in the valine in the amino acid amino acid sequencesequence

Sickle Cell AnemiaSickle Cell Anemia

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Ninhydrin ReactionNinhydrin Reaction Triketohydrindene hydrate, commonly Triketohydrindene hydrate, commonly

known as known as ninhydrinninhydrin, , reacts with amino acids reacts with amino acids to form a purple colored imino derivative, to form a purple colored imino derivative, This derivative forms a useful test for amino This derivative forms a useful test for amino acids, most of which are colorless.acids, most of which are colorless.

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Protein Tests: BiuretProtein Tests: Biuret Biuret reagent is a light blue Biuret reagent is a light blue

solution containing Cusolution containing Cu2+2+ ion ion in an alkaline solution. in an alkaline solution. Biuret turns purple when Biuret turns purple when mixed with a solution mixed with a solution containing protein. The containing protein. The purple color is formed when purple color is formed when copper ions in the biuret copper ions in the biuret reagent react with the reagent react with the peptide bonds of the peptide bonds of the polypeptide chains to form a polypeptide chains to form a complex.complex.

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Xanthroprotic TestXanthroprotic Test

Concentrated Nitric acid will form a yellow Concentrated Nitric acid will form a yellow complex with tryptophan and Tyrosine side complex with tryptophan and Tyrosine side chains in proteinschains in proteins

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Disulfide Bridge TestDisulfide Bridge Test Disulfide bridges will react with Disulfide bridges will react with

PbPb2+2+ ion from lead acetate in an ion from lead acetate in an acidfied solution. A black acidfied solution. A black precipitate indicates the presence precipitate indicates the presence of disulfide-bonded cysteine in of disulfide-bonded cysteine in proteins. proteins.

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