Protein Chemistry PDF 2023-2024

# Protein Chemistry ## The Genius in Biochemistry Dr. Mohamed Agha 2023 - 2024 ## Contents - Introduction - 2 - Classification of Amino Acids - 5 - Amino acid in protein but not primary - 7 - Non protein Amino Acids - 7 - Properties of Amino Acids - 8 - Peptides - 9 - Proteins - 10 - Protein str...

# Protein Chemistry ## The Genius in Biochemistry Dr. Mohamed Agha 2023 - 2024 ## Contents - Introduction - 2 - Classification of Amino Acids - 5 - Amino acid in protein but not primary - 7 - Non protein Amino Acids - 7 - Properties of Amino Acids - 8 - Peptides - 9 - Proteins - 10 - Protein structure - 10 - The conformation of proteins - 11 - Denaturation of proteins - 12 - Classification of proteins - 13 - Collagen - 15 ## Protein Chemistry - Proteins are organic nitrogenous substances composed of C, H, O and N. - Enzymes and Hormones → Regulate Metabolism. - Contractile Proteins in muscles permits movement. - Collagen in bone forms framework for Ca-P crystals deposition. - Hemoglobin and Albumin transport essential molecules. - Immunoglobulins fight against bacteria and viruses. - They are composed of naturally occurring 20 Primary (Common) amino acids. - An amino acid is an organic Acid in which one H atom is replaced by an amino group (NH2), which is usually attached to the α carbon (next to COOH). - The side chain group “R” is distinctive for each amino acid. - Each amino acid has its specific tRNA & specific codon in DNA genetic code. ### Classification of Amino Acids | Name | Symbol | Structural formula | |:---------------|:-------|:---------------------------------------| | Glycine | Gly (G) | $H_2N-C-C-OH$ | | | | $H$ | | | | $H$ | | Alanine | Ala (A) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_3$ | | Valine | Val (V) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH(CH_3)_2$ | | Leucine | Leu (L) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2CH(CH_3)_2$ | | Isoleucine | Ile | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH(CH_3)CH_2CH_3$ | | Serine | Ser (S) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2OH$ | | Threonine | Thr (T) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH(OH)CH_3$ | | Cysteine | Cys (C) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2SH$ | | Methionine | Met (M) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2CH_2SCH_3$ | | Aspartic acid | Asp (D) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2COOH$ | | Asparagine | Asn (N) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2CONH_2$ | | Glutamic acid | Glu (E) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2CH_2COOH$ | | Glutamine | Gin (Q) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2CH_2CONH_2$ | | Arginine | Arg (R) | $H_2N-C-C-OH$ | | | | $H$ | | | | $(CH_2)_3NH-C(NH_2)-NH_2$ | | Lysine | Lys (K) | $H_2N-C-C-OH$ | | | | $H$ | | | | $(CH_2)_4NH_2$ | | Phenylalanine | Phe (F) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2C_6H_5$ | | Tyrosine | Tyr (Y) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2C_6H_4OH$ | | Histidine | His (H) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2-C_3H_3N_2$ | | Imino acid Proline | Pro (P) | $HN-C-C(=O)-CH_2CH_2CH_2$ | | | | $COOH$ | | Tryptophan | Trp (W) | $H_2N-C-C-OH$ | | | | $H$ | | | | $CH_2-C_8H_6N$ | ## According to structure 1. Aliphatic amino acids →having no ring structure. - Neutral: - Glycine, Alanine. - **Branched**: Valine, Leucine, Isoleucine. - Hydroxy containing: Serine, Threonine. - Sulfur containing: Cysteine, Methionine. - Acidic → Mono amino - Di carboxylic - Aspartic Acid, Glutamic Acid. - Basic Di amino - Mono carboxylic - Arginine, Lysine. - With side chains containing Amide group: - Asparagine, Glutamine. 2. Aromatic amino acids→Contain aromatic ring (benzene or phenol). - Tryptophan, Phenylalanine, Tyrosine. 3. Heterocyclic amino acids: - Tryptophan, Histidine, Proline. 4. Imino acids (NH): - Proline. - **(N.B)** - Basic amino acids → Arginine, Lysine & Histidine. - Hydroxy containing amino acids → Serine, Threonine, Tyrosine. - Arginine contains Guanidine group. - Proline & Tryptophan contain Pyrrole ring. - Tryptophan contains Indole ring. ## According to optical Activity (Isomerism):- - All amino acids are optically active and show isomers as they contain asymmetric C atom in a position Except Glycine. - a. D-amino acids: $NH_2$ to the right of the Asymmetric C atom. - b. L-amino acids: $NH_2$ to the left of the Asymmetric C atom. - c. Non - optically active: glycine - All amino acids in human proteins are L-a- amino acids. - Most sugars in the Body are D-sugars. - D & L isomers = stereo isomers = Optical isomers = Enantiomers. ## According to Polarity of R group:- - Polar amino acids include: - Amino acids containing OH → Serine, Threonine, Tyrosine. (Neutral) - Amino acids containing SH group → Cysteine. (Neutral) - Amino acids with Amide group → Asparagine, Glutamine. (Neutral) - Basic amino acids → Arginine, Histidine, lysine. - Acidic amino acids → Aspartic Acid, Glutamic Acid. - Non-Polar amino acids have non polar side chains that can't gain participate in hydrogen or ionic bonds (Oily – Lipid Like) → hydrophobic interactions. - Non-Polar amino acids face outside in hydrophobic environment and face inside in aqueous environment. - **Sickle Cell Anemia**: RBCs disease → Sickle RBCs rather than Disc shaped → due to replacement of polar Glutamate with non-polar Valine at 6th position of ẞ Chain of Hemoglobin A. ## According to the Nutritional value (Biological value):- - **A. Essential amino acids:** - Can't be synthesized by human body, so must be taken in diet. - They are: Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Lysine, Methionine, Arginine, Histidine and Threonine. - Proteins that contain all essential amino acids are of high biological value as meat, milk and egg proteins. - Proteins that are deficient in one or more of the essential amino acids are of low biological value as: - Collagen and Elastin are deficient in Tryptophan. - Zein in maize is deficient in Tryptophan & Lysine. - **B. Non – Essential amino acids:** - These are amino acids that can be synthesized in the body. - They include: - Glycine, Alanine, Proline. - Aspartic, Asparagine, Glutamic, Glutamine. - Serine, Tyrosine, Cysteine. - **(N.B)** - Arginine and Histidine are called Semi-Essential because they are formed in the body at a rate enough for adults, but not enough for growing individuals. ## Amino acids found in proteins But are not primary:- - After synthesis of proteins, some amino acids are modified in Post Translational processing, so they are called derived or modified amino acids (have no genetic code – No codon) 1. **4-Hydroxy Proline**: - Imino Acid found in collagen. - Formed by hydroxylation of Proline. 2. **5-Hydroxy Lysine**: - Found in collagen. - Formed by hydroxylation of Lysine. 3. **Cystine**: - Formed by conjugation of 2 Cysteine after oxidation. ## Non protein amino acids:- - These are amino acids that don't occur in proteins & have no genetic code but they perform other functions in human metabolism. - **1) β- Alanine**: - Component of CoA, Carnosine. - It is a catabolic product of some pyrimidine Bases. - **2) y-Amino Butyric Acid (GABA):** (from Glutamic Acid) - Inhibitory neurotransmitter of Nerve impulse in Brain & Nerve tissues. - **3) DOPA:** (from Phenyl Alanine) - Precursor of Melanin, Epinephrine and Norepinephrine. - **4) 3 - Mono Iodo Tyrosine.** - **5) 3,5 - Di Iodo Tyrosine.** - They are precursors for Thyroid Hormones (T3 & T4). ## Properties of amino acids:- ### Amphoteric properties:- - In solutions amino acids behave as acids & Alkalis due to presence of acidic group (COOH) & Basic group (NH2). - This is the amphoteric property of amino acids → they can react with Acids & Bases. | | | |:-------------|:----------------------| | Cation | $NH_3^+$ - R-C-COOH $H^+$ | | | $H$ | | | PH 1 (Acidic) | | | low pH | | Zwitterion | $NH_3^+$ - R-C-COO$^-$$H^+$ | | | $H$ | | | PH = 7 | | Anion | $NH_2$ - R-C-COO$^-$$H^+$ | | | $H$ | | | PH 11 (Alkaline) | | | high pH | - **Iso Electric Point (IEP) = Point of Isoelectricity (PI):**- - The PH at which an amino acid carries equal +ve & -ve charges. (Electrically neutral). - **Zwitterion:-** - It is the dipolar ion of amino acid at its IEP in an aqueous medium. (Non-charged). - If an electric current is passed in a medium where an amino acid occurs at its IEP, its ions will not migrate towards any of the electrodes. ### Formation of Peptide Bonds:- - Peptide bond is formed between amino group of one amino acid & carboxylic group of another amino acid with the removal of H2O (Dehydration Reaction). ### Peptides :- - A Peptide consists of 2 or more amino acids linked peptide bonds. - 2 amino acids → Dipeptide. - 3 amino acids → Tripeptide. - 100 ≥ amino acids >10 → Polypeptides. - Amino acids > 100 → Proteins. - Peptide chain is unbranched chain having a direction starting by an amino group to the left (N-terminus) and ends by carboxylic group the right (C-terminus). ### Examples of physiologically active peptides :- 1. Many hormones as insulin (51), glucagon (29), Angiotensin I (10), Angiotensin II (8) and gastrin (17) are peptides. 2. **L-Carnosine:-** - Naturally occurring dipeptide made by chemical combination between β- Alanine + L- Histidine. - Dietary sources: Meat, fish and poultry. - Biosynthesis: from its components ẞ -alanine +L-Histidine by Carnosine Synthetase in brain and muscle. - **Biological functions :** - Buffering action. - Antioxidant. 3. **Glutathione:-** - N-terminal Glutamic Acid + Cysteine + C- terminal Glycine. - It is Tripeptide & important Reducing agent. - It is present in reduced (G-SH) and oxidized (G-S-S-G) forms. ## Proteins - Proteins are formed of > 100 amino acids linked by peptide bonds. - Each protein has a unique amino acid number and sequence. - Alteration in amino acids sequence → abnormal function & disease (sickle cell disease). ### Protein Structure #### I-Covalent Bonds:- 1. **Peptide Bonds (Amide Bonds):**- - COOH of one amino acid combines with NH₂ of another amino acid with the removal of one molecule of H2O. - It is a rigid, strong bond, so it stabilizes protein structure. - Peptide bonds are not broken in denaturation of proteins. - They can be broken by: - Enzymatic action. - Strong acid at elevated temperature. - Strong base at elevated temperature. 2. **Disulfide bonds (S – S):**- - Occur between 2 cysteine in the same or different polypeptide chains. - It is a very stable bond that resists denaturation. - Present in Albumin, Insulin and Immunoglobulin. #### II-Non - covalent bonds:- - These are weak bonds, can be separated easily. - However the large number of these bonds in protein helps protein folding. 1. **Hydrogen bonds:-** - Formed by sharing of hydrogen atom between N and carbonyl oxygen of different peptide bonds. - It may be formed between Polar Uncharged (Neutral) R groups as (OH SH Amide group) with each other or with water. 2. **Hydrophobic interactions:-** - The Non-polar amino acids tend to be introduced to the inside of protein molecule exposed to water. - They are not true bonds but interactions that help to stabilize the protein molecule structure. - Polar amino acids tend to be located on surface. - Reverse occurs in Lipid environment. 3. **Electro static bonds (Ionic interaction) = (Salt bridge):**- - These bonds occur between the Polar charged groups of amino acids (NH3+ of basic amino acids & COO of acidic amino acids). - They are Either: - Repulsive: if the interactions between side chains of the same sign = both are (+) or both are (-). - Attractive: if the interactions between side chains of different charges = one is (+) and the other (-). #### The conformation of proteins (Orders of Protein structure) 1. **Primary structure of Proteins:-** - It refers to the number and sequence of amino acids in the polypeptide chain(s) linked by Peptide bonds. - It is important because many genetic diseases result with abnormal amino acid sequences. - The amino acid sequence is read from N-terminal (amino acid number 1) to C-terminal ends of the peptide. 2. **Secondary structure of Proteins:-** (Hydrogen Bonds) - Coiling, Folding, or Bending of the polypeptide chain leading to specific structure kept by interactions between amino acids close to each other. - The 2 main forms of secondary structure (α- helix ， ẞ– pleated sheets). 3. **Tertiary structure of Proteins:-** - It is the three dimensional structure of each polypeptide chain. - There are two main forms of tertiary structure (fibrous or globular). - **Protein Folding**: Formation of 3D structure of protein. - Protein folding is aided by proteins called Molecular Chaperones. - Mis-folded protein leads to diseases such as Alzheimer's disease. #### Domains:- - The functional and structural three dimensional units of a polypeptide. - Polypeptides > 200 amino acids generally consist of two or more domains. - Interactions stabilizing tertiary structure: Disulfide bonds, Hydrogen bonds, Hydrophobic interactions & Ionic interactions. (All bonds except Peptide) #### Quaternary structure of Proteins:- - The three dimensional structure of polypeptide chainS. - Proteins possess quaternary structure if they consist of 2 or more polypeptide chains. - These chains may be structurally identical or to totally unrelated united by Non-Covalent bonds (Hydrogen, Hydrophobic, Ionic). - Such proteins are termed Oligomers. - The individual polypeptide chain is termed Monomer or Subunit. - This protein will lose its function when subunits are dissociated. - e.g.: Haemoglobin (Hb) → has 2 a chains and 2 ẞ chains. ### Denaturation of proteins:- - It is the loss of native structure (natural conformation) of protein. - By many physical or chemical Agents. - Leading to changes in secondary, tertiary and quaternary structure of proteins. - Due to rupture of Non-Covalent bonds (Hydrogen, Hydrophobic, Electrostatic) and may be Disulphide, but not peptide Bonds. - With loss of Biological activity. - Denaturation disrupts all orders of protein structure except primary structure, since there is no hydrolysis of peptide bonds. - Denaturation may be reversible, but in most cases it is irreversible. #### Cause of Denaturation - **1. Physical Agents:** - Heating above 70°c. - Vigorous shaking & stirring. - X-rays. - Repeated freezing & thawing. - Exposure to high pressure. - Ultraviolet rays. - **2. Chemical Agents:** - Ions of heavy metals as $Mg^{+2}$ and $Pb^{+2}$. - ẞ-Mercapto ethanol destroys S-S bond by reduction. - Strong Acids and Bases (Extreme PH) - Urea. - Alcohol. ### Effects of Denaturation - **1. Biological changes:** - Loss of Biological activity of enzymes and protein hormones. - Changes of Antigenic property of proteins. - Easily digested at unfolding of the peptide chains. - Decreased solubility of protein so it precipitates. ## Classification of Proteins ### According to Shape:- - On the basis of axial ratios of proteins (ratios of length to breadth) 1. **Globular (spheroidal ) Proteins:** - They have an axial ratio of less than 10 (usually 3 or 4). - As plasma albumin, globulins & enzymes. 2. **Fibrous proteins:** - They have an axial ratio more than 10. - As keratin, myosin, fibrin, and collagen. ### Classification of Proteins according to Structure | | | | |:----------------------|:------------------------------------------------------------|:----------------------------------------------------------| | **Simple Proteins** | **Amino acids only** | **Conjugated (Compound) Proteins** | | | | **Amino acids + Prosthetic group** | | | | **(حاجة تانية)** | | | | **Derived Proteins** | | | | **Hydrolytic products of proteins as a result of acids, alkalis or enzymes.** | #### I-Simple Proteins:- - **a. Protamines & Histones:** - Water soluble Basic proteins rich in Histidine, Arginine & Lysine. - They are present in nucleoproteins. - Protamines are present in fish & histones are present in plants and animals. - Globin: protein part of Hb & myoglobin is considered a histone. - **b. Albumins (water soluble) & Globulins (soluble in dilutes salt solution):**- - These are heat coagulable, globular proteins of high biological value. - Globulins have larger molecular weight compared to Albumins. - They are present mainly in Blood plasma, egg white and milk. - **c. Scleroproteins = CT proteins = Albuminoids:-** - These are fibrous structural proteins, insoluble in most protein solvents. - **1. Keratins (Epidermal Protein):**- - Rich in sulphur containing amino acids (Cysteine). - They are proteins of outer surface of skin, hair and nails. - It is an a- helical polypeptide chain. - **2. Elastin:-** - Found in yellow Elastic tissue. - **3. Ossein:**- - The main protein of Bone and Teeth. - **4. Collagen.** #### II-Conjugated (Compound) Proteins:- - Amino Acids + Prosthetic group. - According to the prosthetic group, they are classified into: - **a. Phosphoproteins:-** - The prosthetic group (Phosphoric Acid) conjugated to OH of Serine or Threonine. - They are of animal origin as Caseinogen of milk & Vitellin of egg yolk. - Caseinogen - $Renin$ Soluble Casein + Ca → Precipitated as Ca-Caseinate (Cheese). - **b. Glycoproteins:-** - They have carbohydrates (glycan) covalently attached to polypeptide back bones. It is present in mucus. - **c. Lipoproteins:-** - Combination of proteins + lipids → in cell membranes & plasma lipoproteins. - **d. Nucleoproteins:-** - They contain nucleic acids (DNA&RNA) as prosthetic groups attached to protamines or histones. - They are found in cell nuclei and also in cytoplasm. - **e. Chromoproteins:-** - They contain Colored prosthetic group. - Haemoglobin = Haem (Red) + globin. - Myoglobin = similar to Hb, but present in skeletal muscles. - Cytochromes, Catalase, Peroxidase = Haem + specific proteins. - **f. Metalloproteins:-** - Contain Metal prosthetic group. - Hb & ferritin → Iron. - Ceruloplasmin → copper. ### III- Derived Proteins:- - Hydrolytic products of proteins as a result of acids, alkalis or enzymes. - Gelatin (hydrolytic product of Collagen) is an example. - It is poor in Essential amino acids. - Used as a supplementary protein as it is easily digested. #### Collagen - Collagens make up about 25% of the total proteins in mammals. - Long rod-like shape of collagen provides rigidity and strength to support organs and make connective tissue. #### Structure of collagens:- - Collagen is present as Triple helix (Tropo-collagen) made up of three polypeptide chains linked by Hydrogen bonds. - In Each chain the triplet X – Y – Glycine is repeated in the sequence. - One Third (33%) of the amino acids are Glycine. - Every third amino acid is Glycine & (X) often Proline & (Y) Hydroxy Proline, also Hydroxy Lysine occurs. (formed by post translational modification & are characteristic components of collagen). - Hydroxy Proline forms H-bonds between chains which: - Stabilize Triple helix. - Give collagen strength. - OH of Hydroxy Lysine - Glycosylated with Disaccharide (Glc – Gal). - Help linking Tropo-collagen molecules together. - Numerous Tropo-collagens aggregate Extracellular → Cylindrical fibrils. - Assembly of collagen fibril after protein is secreted from the cell → Collagen Fibers which covalently cross link to each other. ### Deficiency of Vitamin C: - Leads to a disease termed (Scurvy) as vitamin C is co-factor for Prolyl hydroxylase for formation of Hydroxy Proline. - Impaired collagen production leads to weak capillary wall which is characterized by: - Loosening of teeth and bleeding gums. - Formation of red spots around hair follicles and under finger nails (hemorrhage). - Defect in Bone and Teeth formation.