Amino Acid Peptide Protein 2010

7/30/2019 Amino Acid Peptide Protein 2010

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Amino Acid, Peptide,

ProteinHarliansyah, Ph.D

Head Dept of Biochemistry,FKUY2010

Email : [email protected]


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A. Physical Properties

1. Solubility- soluble in water and insoluble inorganic solvents

2. Melting Points- melt at higher temperatures >

often 200C3. Taste

sweet (Gly, Ala, Val)

tasteless (Leu)bitter (Arg, Ile)Sodium Glutamate

salt of Glutamic Acid flavoring agent


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4. Optical Properties

- Assymetrica carbon atom isattached to 4different groups

exhibiting optical isomerism


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All AA except Glycine possessoptical isomers due toasymmetric -carbon atom

Some AA (Isoleucine, Threonine) 2nd asymmetric carbon


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D- and L- forms of AA based on

the structure of glyceraldehyde


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5. Amino acids as ampholytes

can donate a proton or accept a

proton

AA contain both acidic (-COOH)and basic (-NH2) groups


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Zwitterion or dipolar ion:

Zwitter from German word means

hybrid

Zwitter ion (or dipolar ion) a hybrid molecule containing (+) and (-) ionic

groups


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AA rarely exist in a neutral form with free carboxylic (-COOH) and

free Amino (-NH2) groups

Strongly acidic pH (low pH) AA (+)charged (cation)

Strongly alkaline pH (high pH) AA (-)charged (anion)

Each AA has a characteristic pH (e.g. Leucine, pH 6.0), at which

it carries both (+) and (-) charges and exist as zwitterion


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Chemical PropertiesGeneral Reactionsmostly due to the 2

functional groups

Reactions due to - COOH group

1. AA from salts (-COONa) with bases

and esters (-COOR) with alcohols

2. Decarboxylation- AA undergo decarboxylation to produce corresponding amines

3. Reaction with Ammonia

- the carboxyl group of dicarboxylic AA reacts with NH3 to form amide

Asparatic Acid + NH3 Asparagine

Glutamic Acid + NH3 Glutamine


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Reactions due to -NH2 group

4. The Amino groups behave as bases and

combine with acids (e.g. HCl) to form

salts (-NH3 + Cl)

5. Reaction with NINHYDRIN (Ruhemanns blue purple)


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6. Colour reactions of Amino Acids- AA can be identified by specific colour reactions

Color Reactions of proteins / AA

Reaction Specific group or AA

1. Biuret Reaction Two peptide linkages

2. Ninhydrin Reaction -Amino acids

3. Hopkins Cole Reaction Indole ring of aromatic AA (Trp)

4. Millions reaction Phenolic Group (Tyr)

5. Xanthoprotein Reaction Aromatic ring (Phen, Tyr,Trp)


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Millons Test


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6. Sakaguchi Reaction Guanidino Group (Arg)7. Nitroprusside Reaction Sulfhydryl groups (Cys)8. Paulys test Imidazole ring (His)

9. Sulfur test Sulfhydryl groups (Cys)10. Folin Coicalteaus Phenolic groups test (Tyr)

Fohls Reaction


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7. Transamination- important reaction in AA metabolism

- transfer of an amino group from an amino acid to a keto acid to form a new

AA

8. Oxidative deamination- AA undergo oxidative deamination to liberate free ammonia


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Characteristics of Peptide Bonds

1. Rigid

2. Planar

3. Partial double bond in character4. Generally exists in transconfiguration

5. Both _C = O and _NH2 groups of peptide

bonds are polar6. Involved in hydrogen bond formation


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Writing of Peptide Structures

The peptide chains are written with the freeAmino end (Nterminal residue) at the left,and the free carboxyl end (Cterminal residue)

at the right.

The AA sequence is read from Nterminal endto Cterminal end

Incidentally the protein biosynthesis also startsfrom the Nterminal Acid.


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Naming of Peptides

For naming peptides, the AA suffixes

ine(glycine), - an (tryptophan) ate (glutamate) arechanged toyl with the exception of C

terminal AA.

A tripeptide composed of an N

terminalglutamate, a cysteine and a Cterminal glycineis called:

glutamylcysteinyl - glycine

P l id Ch i


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Polypeptide Chains

- The linking together of many AA by peptide

bonds produces polypeptide chains.

a.Residues - AA, when in polypeptide

chains, are customarily referred to asresidues.

b.Large peptide chains - proteinpolypeptide chains are typically morethan 100 AA residues long. The

backbone of the chain is a recurring


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Bovine Insulin: the first sequenced protein


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Human: Thr-Ser-Ile

Cow: Ala-Ser-Val

Pig: Thr-Ser-Ile

Chiken: His-Asn-Thr


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The role of side chain in the

shape of proteinsWhere is water?

Hydrophobic

Hydrophilic


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Amino acid substitution in proteins from different species

Conservative Substitution of an amino acid by anotheramino acid of similar polarity(Val for Ile in position 10 of insulin)

Non conservativeSubstitution involving replacement

of an amino acid by another of

different polarity(sickle cell anemia, 6th position of hemoglobin

replace from a glutamic acid to a valine induceprecipitation of hemoglobin in red blood cells)

Invariant residues Amino acid found at the same position in

different species

(critical for for the sructure or function of the protein)


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Biuret Reaction


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Stabilized by hydrogen bonds H- bonds are betweenCO andNH

groups of peptide backbone

H-bonds are either intra- or inter-molecular

3 types : a-helix, b-sheet and triple-helix


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Two type ofbSheet structures

An anti paralellelb sheet

A paralellelb sheet


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Triple helix of Collagen


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Peptides of Physiologic Importance

1. Glutamine (Glutathione)

- a tripeptide composedof 3 AA

- gamma

glutamyl

cysteinyl glycine

- wildly distributed innature

- exists in reduced oroxidized states


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Functions:

a) As a coenzyme for certain enzymes asprostaglandin PGE2 synthaseglycoxylase

b) Prevents the oxidation of sulfhydryl groups of several proteins to

disulfide groupsc) In association with glutathione reductase participates in theformation of correct disulfide bonds in several protiens

d) In erythrocytes- maintains RBC membrane structure and

integrity- protects hemoglobin from getting oxidized by agents such

as H2O2


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e) Involved in the transport of AA in theintestine and kidney tubules via delta

glutamyl cycle or Meister cycle

f) Involved in the detoxification process

g) Toxic amounts of peroxidases and free

radicals produced in the cells are scavangedby glutathione peroxidase ( a seleniumcontaining enzyme).


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2. Thyrotropin Releasing Hormone (TRH)

- a tripeptide secreted by hypothalamus

Function:

Stimulate pituitary gland to release thyrotropic hormone

3. Oxytocin

- contains 9 AA (nonapeptide)

- hormone secreted by posteriorpituitary gland

Function:

Stimulate contraction of the uterus muscle during delivery

Stimulate contraction of muscle in breasts for milk ejection


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Oxytocin and vasopressin are two peptide hormones withvery similar structure, but with very different biologicalactivities.

Interestingly, their structures only differ by one amino acidresidue (the hydrophobic LEU number 8 in oxytocin is replaced

by a hydrophilic ARG residue in vasopressin).

Oxytocin is a potent stimulator of uterine smooth muscle, andalso stimulates lactation.

Vasopressin, also know as antidiuretic hormone (ADH), hasno effect on uterine smooth muscle, but causes reabsorbtionof water by the kidney, thus increasing blood pressure.


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4. Vasopressin (ADHantidiuretic hormone)- also a nonapeptide- produced by posterior pituitary gland

Function:Stimulates kidneys to retain water and thus

increases the blood pressure

5. Angiotensins- Angiotensin 1a decapeptide (10AA) which is

converted to angiotensin II (8AA)Function:

For the release of aldosterone from adrenal gland


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6. Methionine Enkephalin

- a pentapeptide found in the brain and has opiate

like function.Function:

It inhibits the sense of a pain.

7. Bradykinin and Kallidin

- nona and decapeptides respectively

- produced from plasma proteins by

snake venom enzymesFunction:

Powerful vasodilators


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8. Peptide Antibiotics- Antibiotics such as Gramicidin, Bacitracin,

tyrocidin and Actinomysin

peptide in nature

9. Dipeptide aspartame

- Consists of aspartate and phenylalanine- acts as Sweetener ~ used by diabetic patients

10. Gastrointestinal Hormones

- Gastrin, Secretin & etc.- gastrointestinal peptides serving ashormones


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- they differ in their

physicochemical properties

which ultimately determinethe characteristics of proteins


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The Proteins speak:

We are the basis of structure

and function of life;

Composed of twenty amino acids,

the building blocks;

Organized into primary, secondary, tertiary

and quaternary structure;

Classified as simple, conjugated

and derived proteins.


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- 4 different forces stabilize the tertiary structure of globular protein

i. Hydrogen bonding between R groups of residues in

adjacent loops of the chain

ii. Ionic attraction between oppositely charged R groups

iii. Hydrophobic interactions

iv. Covalent cross-linkages (via intrachain cystein residues)

F i f i


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Function of proteins

Proteins

are the most

important buffers in

the body.

Enzymatic catalysis

Transport and storage (the protein hemoglobin,albumins)

Coordinated motion (actin and myosin).

Mechanical support (collagen).

Immune protection (antibodies)

Generation and transmission of nerve impulses

- some amino acids act as neurotransmitters,

receptors for neurotransmitters, drugs, etc. are

protein in nature. (the acetylcholine receptor),

Control of growth and differentiation -

transcription factors

Hormones

growth factors ( insulin or thyroid stimulating

hormone)

Why?(a) Protein molecules

possess basic and

acidic groups which act

as H+ acceptors or

donors respectively if

H+ is added or removed.


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(a) Proteins are the most important buffers in the body. They are mainly

intracellular and include haemoglobin.

(b) The plasma proteins are buffers but the absolute amount is small compared

to intracellular protein.

(c) Protein molecules possess basic and acidic groups which act as H+

acceptors or donors respectively if H+ is added or removed.

Many proteins (thousands!) present in blood plasma

Proteins contain weakly acidic (glutamate, aspartate) and basic(lysine, arginine, histidine) side chains (or R groups)

At neutral pH, only histidine residues (containing imidazole Rgroup with pKa ~ 6.0) in proteins can act as a buffer component

Haemoglobin with 38 histidine/tetramer is a good buffer N-terminal groups of proteins (pKa ~ 8.0) can also act as a buffer

component


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Cl f i


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Classes of protein

1 - Structural protein : Keratin, Collagen (give support to cells)2 - Dynamic protein : Hormone, enzyme (for catalytic purpose)

- Based on the structure, protein can be divided to :

* Fibrin : Blood clotting* Fibrous : Myosin (from muscle)

* Globular : Half sphere form/structure eg. Enzyme

- Size : Varied - depending on functions

- 1 amino acid = 110 Daltons

- Most protein are highly folded


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Fibrous and Globular Proteins


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- There are also protein which its polypeptide chains are tightly

folded into a spherical or globular shape

Example of globular protein :

Lysozyme molecule with its tightly

bound polysaccharide substrate

(color)


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Enzyme Catalysis

T d


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Transport and storage - small molecules are often carried by proteins in the physiological setting(for example, the protein hemoglobin is responsible for the transport of oxygen to tissues). Many drugmolecules are partially bound to serum albumins in the plasma.

3-dimensional structure of hemoglobin.The four subunits are shown in red andyellow, and the heme groups in green.

The binding of oxygen is affected by molecules such as carbonmonoxide (CO) (for example from tobacco smoking, cars andfurnaces).

CO competes with oxygen at the heme binding site. Hemoglobinbinding affinity for CO is 200 times greater than its affinity foroxygen, meaning that small amounts of CO dramatically reduceshemoglobin's ability to transport oxygen. When hemoglobincombines with CO, it forms a very bright red compound called

carboxyhemoglobin.

When inspired air contains CO levels as low as 0.02%, headacheand nausea occur; if the CO concentration is increased to 0.1%,unconsciousness will follow. In heavy smokers, up to 20% of theoxygen-active sites can be blocked by CO.

Coordinated motion muscle is mostly protein and muscle contraction is mediated by the sliding


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Coordinated motion - muscle is mostly protein, and muscle contraction is mediated by the slidingmotion of two protein filaments, actin and myosin.

Platelet before activation Activated plateletActivated platelet

at a later stage than C)

Platelet activation is a controlled

sequence of actin filament:

Severing

Uncapping

Elongating

Cross linking

That creates a dramatic shape changein the platelet

M h i l t


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Mechanical support - skin and bone are strengthened by the protein collagen.

Abnormal collagen synthesis or

structure causes dysfunction of

cardiovascular organs,

bone, skin,

joints

eyes

Refer to Devlin

Clinical correlation 3.4 p121


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Immune protection - antibodies are protein structures that are responsible for reacting with specificforeign substances in the body.


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Generation and transmission of nerve impulses -

Some amino acids act as neurotransmitters, which transmit electrical signals from one nerve cell to another. Inaddition, receptors for neurotransmitters, drugs, etc. are protein in nature.

An example of this is the acetylcholine receptor, which is a protein structure that is embedded in postsynapticneurons.

GABA:

gamma Amino butyric acid

Synthesised from glutamate

GABA acts at inhibitory synapses in thebrain. GABA acts by binding to specificreceptors in the plasma membrane of bothpre- and postsynaptic neurons.Neurotransmetter


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Membrane transport proteins


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Protein degradation:


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Protein degradation:

Disease and protein folding:


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Disease

Example:

Neurodegenerative

diseases

Disease and protein folding:


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Digestion of Proteins

1. Mouth - food is chewed2. Stomach:

Gastrin - triggers chief cells to release HCl andpepsinogen

3. Small intestines:

Secretin-stim. release of pancreatic juices

Activation of proteolytic enzymes:

Trypsinogen trypsinChymotrypsinogen chymotrypsin

Proelastase elastase

Endo & exopeptidases activated

Products of enzyme action = amino acids


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Products of enzyme action = amino acids

Dipeptides & small peptides AA

Greater amount of AA in portal blood is in the form of

alanine

STOMACH

Protein digestion starts in the stomach

dietary proteins become denatured by gastric acid important for protein digestion because proteins arepoor substrates for proteases

ACID ENVIRONMENT is required for action of pepsin


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PEPSIN

A protease that works optimally at pH 2 a carboxyl protease

acts mostly as endopeptidase

does not cleave at random prefers peptide bonds formed by amino group of

aromatic AA

major breakdown products are not free AA but a

mixture of oligopeptides known as peptones


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INTESTINE

As acidic stomach contents reach duodenumrapidly neutralized by HCO3 in pancreatic secretions.

Proteolytic enzymes from pancreas include:

1. Trypsin

a serine protease

endopeptidase

specific for CO side of basic AA


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2. Chymotrypsin

a serine protease endopeptidase

specific for CO side of hydrophobic AA

1 & 2 = degrade peptones to smaller peptides

3. Carboxypeptidase A:

hydrophobic AA at C terminal

4. Carboxypeptidase B

basic AA at C terminus

Amino Acid Peptide Protein 2010

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