amino acid peptide protein 2010
TRANSCRIPT
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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