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7/29/2019 FP-Bio-2 biochemistry 2
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Proteins are the most abundant and functionally divers
molecules in living systems. Every life process depends onthis class of molecules.
Amino Acids and Proteins
1. Enzymes - increase rate of reaction x 1 billion2. Carriers hemoglobin, transferrin
3. Receptors hormones, cytokines
4. Transport membrane channels
5. Structure collagen, elastin
6. Protective - immunoglobulins
7. Contractile - muscle, cytoskeleton
8. Regulatory (Hormones) govern metabolic pathway
Types and functions of Proteins
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Structure of Proteins
-The linear sequence of amino acids contain the necessary information to
generate protein molecule with a unique three-dimensional structure. Theprotein structure is describe by the following structural levels of
Primary
Secondary
Tertiary
Quaternary
Primary Structure of Proteins
-The amino acids sequence of in protein. Amino acids are covalently joined bypeptide bonds between -carboxyl group of one amino acid and -amino group
with other amino acid.
- many genetic disease results from abnormal amino acid sequence.
-There are different techniques for protein sequencing.
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4 Levels of Protein Structure
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The Peptide Bond
Amide bond formed by the COOH of an amino acid and the NH2 of the next amino acid
peptide bond
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Secondary Structure of Proteins-The polypeptide backbone dose not assume a random
three-dimensional structure but forms regular
arrangements of amino acids that located near to each
other in linear sequence called Secondary Structure
-helix
-Sheet
-turns
Weak Noncovalent Interactions
-helix:- It is spiral structure, consisting of tightly packed,
coiled polypeptide backbone core
-The amino acid side chains are extending outward from
central axis avoid interfering steriecally with each
other.- a very divers group of proteins contains -helix;
Keratins and fibrous proteins
- Stabilized by hydrogen bonding between peptide bond
Oxygen and amide hydrogen. H-bonds individually are
weak by collectively can stabilize the helix.
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*Some amino acids disrupt the -helix eg.
Proline: bec of its imino group is not
geometrically compatible with spiral structure of
-helix , its inserts a Kink in the chain.
Large no. of charged amino acids (glutamate,aspartate, histideine, lysine arginine) forming
ionic bonds or electrostatic repulsion
amino acids with bulky side chains (tryptophan)
amino acids with branched side chain like Valine
and isolucine.
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-Sheet:-Another form of the secondary structure in which all of the
peptide bond components are involved in H-bonding
- The surface of -Sheet appear pleated called -pleated
sheet
- The backbone of polypeptide chain is extended into Zigzag
rather than helical structure
- are usually represented by broad arrows
- are composed of two or more peptide chains (-strands) or
segments of polypeptide chains that are fully extended.
- The hydrogen bonds are perpendicular to the polypeptide
backbone.
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Tertiary structure- The structure of globular protein in aqueous solution is compact
-Hydrophobic side chains are buried in the interior while hydrophilic groups are
generally found on the surface- Hydrophilic a.a and peptide bond component that found in the interior of the
protein are occupied by H-bonding so cannot form H-bonds with water
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Interaction stabilizing the tertiary structure-Amino acid sequence determines the unique three-dimensional
structure of each polypeptide
- Interactions between amino acid side chains guide the folding
pathway of a polypeptide into a compact structure.
-The cooperation of four types of interactions stabilizes the tertiary
structure of a protein
1-Disulfide bonds:
Two cysteine resides are oxidized into cystine with S-S linkage
The folding of polypeptide can bring the cysteine residues in
proximity and permit covalent bonding
the disulfide bond is covalent and strong bond and stabilizes the
proteins
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2-Hydrophobic interaction: Amino acids with non-polar side chain located in the interior of
the polypeptide molecule and can associate with other hydrophobic
amino acids. Amino acids with polar or charged side chains tend to be located on
the surface of the molecule.
3-Hydrogen interaction:Amino acid side chain containing oxygen or nitrogen-bound hydrogen asserine, or threonine can form H-bonds with electron rich atoms as
carbonyl oxygen of the peptide bonds.
4-Ionic interaction:Negatively charged group in the side chain of aspartate or glutamate
can interact with positively charged groups as the amino group(-NH3)
in the side chain of lysine
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Quaternary Structure of Proteins:
-Monomeric proteins: consist of a single polypeptide chain.
Other proteins consist of two or more polypeptide chains that maybe structurally identical or totally unrelated.
two subunit protein is called dimeric protein, three subunit is called
trimeric . Multimeric protein has several subunit
The arrangement of these subunit is called Quaternary structure Subunits are associated together by non-covalent interactions
(hydrophobic, hydrogen interactions) or covalent interactions like
disulfide linkage
Subunit may either function independently or may workcooperatively
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The Four Levels of Protein Structure
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Protein Classification
Simple composed only of amino acid residues
Conjugated contain prosthetic groups
(metal ions, co-factors, lipids, carbohydrates)
Example: Hemoglobin Heme
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Protein Classification
One polypeptide chain - monomeric protein More than one - multimeric protein
Homomultimer - one kind of chain
Heteromultimer - two or more differentchains
(e.g. Hemoglobin is a heterotetramer. It hastwo alpha chains and two beta chains.)
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Protein ClassificationFibrous1) polypeptides arranged in long strands or
sheets2) water insoluble (lots of hydrophobic AAs)3) strong but flexible
4) Structural (keratin, collagen)
Globular
1) polypeptide chains folded into spherical orglobular form2) water soluble3) contain several types of secondary structure4) diverse functions (enzymes, regulatory
proteins)
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Protein Function
Catalysis enzymes
Structural keratin
Transport hemoglobin
Trans-membrane transport Na+/K+ ATPases Toxins rattle snake venom, ricin
Contractile function actin, myosin
Hormones insulin
Storage Proteins seeds and eggs Defensive proteins antibodies