2- protein chemistry
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PROTEIN CHEMISTRY
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Proteins
Proteins are complex organicnitrogenous compounds of highmolecular weight
Proteins are the most complexmaterials produced in nature
They are consisting largely orentirely of -amino acids linkedtogether by peptide linkages
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Proteins The name protein is derived from the
Greekwordproteios of prime importance this is because proteins are the basis ofthe cytoplasm of cells and are present in all
living organisms Without proteins life would NOT bepossible
Proteins are the most abundantmacromolecules in living cells andconstitute 50 % or more of their dry
weight
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Proteins Proteins are polymers of-Amino Acids.
Proteins are synthesized from only 20 aminoacids, known asthe common amino acids
Amino acids are formed mainly of carbon,
hydrogen, oxygen and nitrogen
Nitrogen is a characteristic component of
proteins forming about 16% of their weight i.e.100 g of protein contains 16 g of nitrogen
Proteins perform many essential functions
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BIOLOGICAL IMPORTANCEOF PROTEINS
1- Plasma membrane proteins (channel,carrier, pump proteins) regulate thetransfer of various substances across
the cell membrane 2- All receptorsare protein in nature
3- All enzymes are proteins in nature 4- All antibodies (Immunogobulins) are
proteins in nature
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BIOLOGICAL IMPORTANCE
OF PROTEINS
5- Some hormones are proteins in nature e.g.
Insulin, Glucagon, Growth hormone, FSH,LH. 6- Some proteins are protective e.g. Keratins
(skin, hair, nails) make the skin resistant tochemicals 7- Some proteins have supportive functions
e.g. Collagen; the most abundant protein in
animals. 8- Hemoglobin is a protein carries O2 in the
blood
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BIOLOGICAL IMPORTANCEOF PROTEINS
9- Actin and Myosin are contractileproteins found in muscle cells and areresponsible for muscular contraction
10- Amino acids are converted to othernitrogenous substances of great
physiologic importance e.g. Creatine,Histamine, Serotonin, Heme, Purines,Pyrimidines.
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AMINO ACIDS
- Amino acids are the building unitsof proteins.
Each - amino acid consists of an
amino group (-NH2), a carboxylic acidgroup ( -COOH ), a hydrogen atom
(-H ) and a side chain group (-R), allconnected to a carbon atom called -carbon atom.
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AMINO ACIDS
The -carbon is the first carbonadjacent to the COOH group.
The side chain group ( R ) is specific
and unique for each amino acid. The R may be a hydrogen, a straight
or branched- chain aliphatic group, anaromatic ring or a heterocyclic ring.
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AMINO ACID
Representation of Amino Acid
NH2
H
R C
carboxylicgroup
amino group
side chainradicle
- carbonatom
COOH
Hydrogen atom
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Basic Amino Acid Structure -Carbon is chiralin all amino acids
except for glycine.
At pH 7.0 aminoacids have both
+ve and-ve chargesso called dipolar ionor zwitterions
Amino acids havea tetrahedralstructure (3Dshape).
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Natural Amino Acid are inthe L-configuration
L and D forms are called Optical isomers (=Stereoisomers = Enantiomers)
Biological system in all organisms synthesize and use
only L-amino-acids
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The R group determines the amino acid
Basic (+ve)
Charged polar
Lysine-CH2CH2CH2CH2NH2
Acidic (-ve)
Charged polar
Aspartic acid- CH2COOH
Uncharged polarCysteine- CH2SH
Uncharged polarSerine- CH2OH
Non-polarAlanine- CH3
Non-polarGlycine- H
Side chainAmino acidR group
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VValValineIIleIsoleucine
YTyrTyrosineHHisHistidine
WTrpTryptophanEGluGlutamic acid
TThrThreonineQGlnGlutamine
SSerSerineGGlyGlycine
PProProlineCCysCysteine
FPhePhenylalanineDAspAspartic acid
MMetMethionineNAsnAsparagine
KLysLysineRArgArginine
LLeuLeucineAAlaAlanine
One letterThree
letter
One letterThree
letter
AbbreviationAmino AcidAbbreviationAmino Acid
Table: Abbreviations for the 20 Amino Acids
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CHEMICAL CLASSIFICATION
The 20 amino acids are classified according to thechemical structure of the side chain ( R ) into:
1. Aliphatic
2. Hydroxy3. Sulfur containing
4. Aromatic
5. Acidic
6. Basic
7. Imino acids
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All aliphatic AA are nonpolar (Hydrophobic)
Valine, Leucine and Isoleucine are branched-chain AA
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Hydroxy Amino Acids
Hydroxy AA (Serine and Threonine) are Polar(Hydrophilic)
They Can form hydrogen bonds with their OH groups
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Sulfur Containing Amino Acids
Cysteine: Important in disulfide linkages
polar, Can form hydrogen bonds
Methionine: Methyl donor
Non-polar (hydrophobic)
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Aromatic Amino Acids
Phenylalanine and Tryptophan are nonpolar(hydrophobic)
Tyrosine is polar (hydrophilic): H-Bonding with its
(OH).
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Aspartate and glutamate are polar and negativelycharged (-ve) at physiologic pH
Asparagine and glutamine are polar but non charged
Acidic Amino Acids and their
amides
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Basic Amino Acids
Arginine, Lysine and Histidine are polar andpositively charged (+ve) at physiologic pH
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Imino Acids
Proline is imino acid because it contains imino group
(-NH) not amino group (-NH2)
Proline is heterocyclic and non-polar AA.
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NUTRITIONALCLASSIFICATION of AA
(B)- NON-ESSENTIAL AMINO ACIDS: Can be synthesized inside the body, so they must
not be taken in the diet. They include the other
10 amino acids N.B. The essential amino acids are not more
important to our body than the non-essential
amino acids. Both (all 20 AA) are equally needed and equally
essential for the normal growth and good health
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Table: Nutritionally Essential and
non-Essential Amino Acids
10- Tyrosine10- Valine
9- Serine9- Tryptophan
8- Proline8- Threonine
7- Glycine7- Phenylalanine
6- Glutamic acid6- Methionine
5- Glutamine5- Lysine
4- Cysteine4- Leucine
3- Aspartic acid3- Isoleucine
2- Asparagine2- Histidine
1- Alanine1- Arginine
Non-Essential Amino AcidsEssential Amino Acids
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Amino Acid deficiency in Selected
Vegetables and Grains
Low in MethionineSoy
Lysine, TryptophanAlmonds, Walnuts
MethioninePeas
Methionine, TryptophanBeans
Lysine, TryptophanCornLysineWheat, Rice, Oats
NoneEggs, Milk, Meat, Fish, Poultry
Amino Acid MissingFood Source
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PROPERTIES OF AMINOACIDS
All amino acids are optically activeexcept Glycine, this is because all
AA contain asymmetric carbonatom but in Glycinethe R group isa hydrogen atom so it has noasymmetric carbon atom
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Amino acids are linked together by condensationreaction between carboxylic and amino groupsfrom two different amino acids (with eliminationof water). The amide bond formed is called
peptide bond The product is called a peptide, and namedaccording to the number of amino acids involved:e.g. dipeptide (2), tripeptide (3), decapeptide
(10)
Big peptides (> 50 amino acids) are calledpolypeptides
Linking of amino acids: Peptide
Bond Formation
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PROTEIN
STRUCTURE
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PROTEIN STRUCTURE
A protein molecule may consist of one or
more polypeptide chains, which are usuallyfolded in regular manner that gives themolecule a specific shape
A polypeptide chain is formed of L--amino acids linked together by peptidebonds
At one end of the polypeptide chain thereis a free -amino group, the N-terminalamino acid residue
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PROTEIN STRUCTURE
At the other end there is a free -
carboxyl group, the C- terminal amino acidresidue
The peptide structure are written with
the N-terminal residue at the left andwith the C-terminal residue at the right
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Protein structure:
conformation and assembly
Primary Structure: The order of aminoacids: Amino acid sequence
Secondary Structure: H-bonding between
amino acids: twisting and folding Tertiary Structure Ionic-covalent- bonds:
Overall folding: spherical OR fibrous shape Quaternary Structure Organization ofmultiple protein units together
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Secondary StructuresSecondary StructuresAAsAAs areare arranged to minimize collision and to form Harranged to minimize collision and to form H--bondsbonds
Alpha Helix
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Alpha Helix
Pleated Sheets
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Pleated Sheets
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Intermolecular Forces in ProteinsIntermolecular Forces in ProteinsIntermolecular Forces in ProteinsIntermolecular Forces in Proteins
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Intermolecular Forces in ProteinsIntermolecular Forces in ProteinsIntermolecular Forces in ProteinsIntermolecular Forces in Proteins
Hydrogen bonding
Ionic bonds
Disulfide linkages Dispersion forces
Q SQ t St t
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rganization of multiple proteins (units) together
Quaternary StructuresQuaternary Structures
Example: hemoglobin: 2 units - 2 units.
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DENATURATION OF PROTEINS
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DENATURATION OF PROTEINS
It is the destruction of the
organization (internal structure) ofthe protein molecule (2ry, 3ry and 4rystructures) but the primary structure
remains intact So the polypeptide chains become
unfolded and irregularly arranged
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DENATURATION OF PROTEINS
CAUSES:
a- Physical agents: Heat, UV rays, X-ray, ultrasound
wave, high pressure or excessiveshaking
b- Chemical Agents:
acids, alkalis or urea
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Effects of Denaturation
Denaturation destroys the biologicactivity of a protein, there is loss ofhormonal, enzymatic and antibody
activity. The biologic activity of a protein
depends on their native conformation.
Denaturation destroys the nativeconformation of protein.
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Applications of protein denaturing
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Applications of protein denaturing
1- Boiling eggs: Change in albumin shape andsolubility.
2- Cooking meat: Easily chewable,digestible.
3- swabbing skin with alcohol (disinfectant):
Denatures/kills bacteria and viruses.
4- HCl in our stomach: denatures proteins,
making it easily digestible by enzymesSo, eating cooked eggs, meat and liver is more useful tohumans than eating them raw