Medical Biochemistry PDF 2024

‫مكتب الدقة‬ ‫للخدمات المكتبية واالعمال االدارية‬ ‫‪Medical biochemistry‬‬ ‫السعر ‪ 5‬د‬ ‫التاري خ ‪0202 / 11 / 30‬‬ ‫طبق – كلية الطب ر‬ ‫البشي‬ ‫ج امعة ر‬ ‫بايو للسنة أوىل موديول الدفعة ‪11‬‬ ‫ر‬ ‫محاضة...

‫مكتب الدقة‬ ‫للخدمات المكتبية واالعمال االدارية‬ ‫‪Medical biochemistry‬‬ ‫السعر ‪ 5‬د‬ ‫التاري خ ‪0202 / 11 / 30‬‬ ‫طبق – كلية الطب ر‬ ‫البشي‬ ‫ج امعة ر‬ ‫بايو للسنة أوىل موديول الدفعة ‪11‬‬ ‫ر‬ ‫محاضة االول (بلوك اجلنرال)‬ ‫ال‬ ‫للدكتور ‪ :‬عوض الحسنوني‬ ‫العنوان ‪ :‬ح الحرية مقابل كلية الطب ر‬ ‫البشي‬ ‫‪EDITION 2024‬‬ ‫‪1‬‬  Medical biochemistry Introduction Objectives Know what biochemistry is and its principle. Know the major types of bio-molecules. Understand different types of chemical reactions involved in maintaining high degree of internal order. What is Biochemistry ? Biochemistry is the application of chemistry to the study of biological processes at the cellular and molecular level. It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology and biology to investigate the chemistry of living systems by: A. Studying the structure and behavior of the complex molecules found in biological material B. the ways these molecules interact to form cells, tissues and whole organism. Biochemical Reactions Metabolism: total sum of the chemical reaction happening in a living organism (highly coordinated and purposeful activity) a. Anabolism- energy requiring biosynthetic pathways b. Catabolism- degradation of fuel molecules and the production of energy for cellular function , All reactions are catalyzed by enzymes The primary functions of metabolism are: a. acquisition & utilization of energy b. Synthesis of molecules needed for cell structure and functioning (i.e. proteins, nucleic acids, lipids, & CHO c. Removal of waste products : are made of carbon, hydrogen, and oxygen atoms, always Carbohydrates in a ratio of 1:2:1., Carbohydrates are the key source of energy used by living things. The building blocks of carbohydrates are sugars, such as glucose and fructose. Basic unit is monosaccharides. mono-, di-, oligo-, and poly Each of these roots can be added to the word saccharide to describe the type of carbohydrate, Monosaccharides can form larger molecules e.g. glycogen. Proteins: Amino acids building blocks of proteins Contains amino.03 group and carboxyl group function groups (behavioral properties) ,R Group (side chains) determines the chemical properties of each amino acids. Also determines how the protein folds and its biological 2 function. Individual amino acids in protein connected by peptide bond. Protein Structure Level Primary Secondary Tertiary Quaternary Description The amino acid sequence Helices and Sheets Disulfide bridges Multiple polypeptides connect. Lipids: The molecular structure of a lipid consists primarily of hydrocarbons, organic molecules composed only of hydrogen and carbon atoms, Lipids are generally made up of triglycerides (glycerol molecule with 3 fatty acid tails attached). Two types of fatty acids saturated and unsaturated. Nucleic acids: Nucleic acids are polymers made up of nucleotide monomers, They contain the elements carbon, hydrogen, oxygen, phosphorus and nitrogen. Each nucleotide contains a phosphate group a 5 carbon sugar and a nitrogenous base. Two of the most common nucleic acids known are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). 0  Protein Structure and Function Proteins are very important molecules in cells. Proteins are the most abundant and functionally diverse molecules in living systems, Virtually every life process depends on this class of molecules. For example, enzymes and polypeptide hormones direct and regulate metabolism in the body, whereas contractile proteins in muscle permit movement. In bone, the protein collagen forms a framework for the deposition of Calcium phosphate crystals, in the bloodstream, proteins, such as hemoglobin and plasma albumin, all are constructed from one set of 20 amino acids, amino acids are the building blocks of protein. Proteins are linear polymers formed by linking the α-carboxyl group of one amino acid to the α-amino group of another amino acid with a peptide bond (also called an amide bond). An organic molecule composed of carbon, hydrogen, oxygen, and nitrogen. Function of Protein: 1-Structural Function (Fibrous Protein) is a protein with an elongated shape. Fibrous proteins provide structural support for cells and tissues. There are special types of helices present in three fibrous proteins α- keratin, collagen and elastin. These proteins form long fibers that serve a structural role in the human body, fibrous proteins have low solubility in water compared with high solubility in water of globular proteins. Collagen is the most abundant protein in the animal kingdom. It is found in many diverse organisms and organs, it is found in bone, cartilage, tendons and ligaments for tensile strength. Keratin is the protein that protects epithelial cells from damage. It is mainly involved in the formation of hair, nails, skin, hooves and horns. Elastin is found in connective tissues throughout the body. Whereas elastin provides elasticity, collagen provides rigidity to connective tissue. Elastin fibers are present in virtually all vertebrate tissues such as arteries some ligaments, and the lung. 4 2- Dynamic Function (Globular Protein) are carrier proteins that move molecules from one place to another around the body. Examples include hemoglobin, Transferrin and Ceruloplasmin. Hemoglobin transports oxygen through the blood via red blood cells. 3- Enzymes - are proteins that facilitate biochemical reactions. They are often referred to as catalysts because they speed up chemical reactions. Examples include the enzymes pepsin. Pepsin is a digestive enzyme that works in the stomach to break down proteins in food. 4- Hormonal Proteins - are messenger proteins, which help to coordinate certain bodily activities. Examples include insulin and oxytocin. Insulin regulates glucose metabolism by controlling the blood-sugar concentration. Oxytocin stimulates contractions in females during childbirth. 5- Antibodies - are specialized proteins involved in defending the body from antigens (foreign invaders). They can travel through the bloodstream and are utilized by the immune system to identify and defend against bacteria, viruses, and other foreign intruders. 6- Contractile Proteins - are responsible for movement. Examples include actin and myosin. These proteins are involved in muscle contraction and movement. 7- Clotting proteins-Blood clotting proteins generate thrombin, an enzyme that converts fibrinogen to fibrin, and a reaction that leads to the formation of a fibrin clot. 5  Amino Acids Structure Generally, amino acids have the following structural properties: -A carbon (the alpha carbon) -A hydrogen atom (H) -A Carboxyl group (-COOH) -An Amino group (-NH2) -A "variable" group or "R" group Although more than 300 different amino acids have been described in nature, only 20 are commonly found a constituents of mammalian proteins.[Note: These are the only amino acids that are coded for by DNA, the genetic material in the cell.] Each amino acid (except for proline, which has a secondary amino group) has a carboxyl group, a primary amino group, and a distinctive side chain (“R-group”) bonded to the α-carbon atom. At physiologic pH (approximately pH 7.4), the carboxyl group is dissociated, forming the negatively charged carboxylate ion (–COO–), and the amino group is protonated (–NH3+). In proteins, almost all of these carboxyl and amino groups are combined through peptide linkage and, in general, are not available for chemical reaction except for hydrogen bond formation. Thus, the nature of the side chains ultimately dictates the role an amino acid plays in a protein. It is, therefore, useful to classify the amino acids according to the properties of their side chains (Figure 1). 1 (Figure 1) Structural features of amino acids 7 Optical properties of amino acids: The α-carbon of an amino acid is attached to four different chemical groups and is, therefore, a chiral or optically active carbon atom. Glycine is the exception because its α-carbon has two hydrogen substituents and, therefore, is optically inactive. Amino acids that have an asymmetric center at the α-carbon can exist in two forms, designated D and L that are mirror images of each other (Figure 2). The two forms in each pair are termed stereoisomers, optical isomers, or enantiomers. All amino acids found in proteins are of the L-configuration. However, D-amino acids are found in some antibiotics and in plant and bacterial cell walls. )Figure 2) D and L forms of alanine are mirror images. 8 zwitterion In chemistry, a zwitterion meaning formerly called a dipolar ion, is a neutral molecule with both positive and negative electrical charges. (In some cases multiple positive and negative charges may be present.) Zwitterions are distinct from molecules that have dipoles at different locations within the molecule. (Figure 3) An amino acid contains both acidic (carboxylic acid fragment) and basic (amine fragment) centres. The isomer on the right is a zwitter ion. Net charge of amino acids at neutral pH: At physiologic pH amino acids have a negatively charged group (– COO–) and a positively charged group (– NH3+), both attached to the α-carbon. Substances, such as amino acids, that can act either as an acid or a base are defined as amphoteric, and are reffered to as ampholytes (amphoteric electrolytes). 9  Classification of amino acids 1. According to their nutritional importance: a- Essential amino acids: - is an amino acid that cannot be synthesized de novo by the organism, and thus must be supplied in its diet, Adults need to eat foods that contain the following eight amino acids: methionine, valine, tryptophan, isoleucine, leucine, lysine, threonine and phenylalanine. (Histidine and Arginine) semi-essential amino acid Made in small quantities within the human body, their supply in our diet may be necessary in some development stages or when a person suffers from certain diseases. b- Non-essential amino acids: do not have to be supplied by out diet. The human body may synthesize them of other amino acids or other chemical compounds like keton acids. alanine, , asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, and tyrosine. 2- According to their Metabolic:- Amino acids can be classified as glucogenic, ketogenic, or both based on which of the seven intermediates are produced during their catabolism. (see Figure 4). a. Glucogenic amino acids: - Amino acids whose catabolism yields pyruvate or one of the intermediates of the citric acid cycle are termed glucogenic. b. Ketogenic amino acids:- Amino acids whose catabolism yields either acetoacetate or one of its precursors (acetyl CoA or aceto acetyl CoA) are termed ketogenic. 13 (Figure 4) Amino acid metabolism shown as a part of the central pathways of energy metabolism. 11 3. According to the charge and polarity: a- acidic side chains:- The amino acids aspartic and glutamic acid are proton donors. At physiologic pH, the side chains of these amino acids are fully ionized containing a negatively charged carboxylate group (–COO–). They are, therefore, called aspartate or glutamate. aspartic acid glutamic acid 12 b- Basic side chains:- The side chains of the basic amino acids accept protons. At physiologic pH, the side chains of lysine and arginine (guanidino group) are fully ionized and positively charged. In contrast, histidine contains an imidazole ring side chain is weakly basic, and the free amino acid is largely unchanged at physiologic pH. However, when histidine is incorporated into a protein, its side chain can be either positively Charged or neutral, depending on the ionic environment provided by the Polypeptide Chains of the protein. This is an important property of histidine that contributes to the role it plays in the functioning of proteins such as hemoglobin. 10 c- Neutral (uncharged ) side chains 1- Amino acids with polar side chains :- These amino acids have zero net charge at neutral pH, Serine, threonine, and tyrosine each contain a polar hydroxyl group that can participate in hydrogen bond formation, They hydroxyl is also can form covalent bonds to other substituents that may modify the protein struture such as the oligosaccharide of glycoproteins and the phosphate of regulated enzymes. The side chains of asparagine and glutamine each contain a carbonyl group and an amide group, can serve as a site of attachment for oligosaccharide chains in glycoproteins UNCHARGED POLAR SIDE CHAINS Disulfide bond: The side chain of cysteine contains a sulf hydryl group (– SH), which is an important component of the active site of many enzymes. In proteins, the –SH groups of two cysteines can become oxidized to form a dimer, cystine, which contains a covalent cross-link called a disulfide bond (–S–S–). and are the strongest type of bond. 14 2- Amino acids with nonpolar side chains :- Each of these amino acids has a nonpolar side chain that does not gain or lose protons or participate in hydrogen or ionic bonds. The side chains of the nonpolar amino acids tend to cluster together in the interior of the protein. This phenomenon, known as the hydrophobic effect, is the result of the hydrophobicity of the nonpolar R-groups, which act much like droplets of oil that coalesce in an aqueous environment. The nonpolar R- groups thus fill up the interior of the folded protein and help give it its three- dimensional shape. However, for proteins that are located in a hydrophobic environment, such as a membrane, the nonpolar R-groups are found on the outside surface of the protein, interacting with the lipid environment.The importance of these hydrophobic in stabilizing protein structure. Proline: Proline differs from other amino acids in that proline’s side chain and α-amino N form a rigid, five-membered ring structure). Proline has a secondary (rather than a primary) amino group. It is frequently referred to as an imino acid. The unique geometry of proline contributes to the formation of the fibrous structure of collagen, and often interrupts the α-helices found in globular proteins. 15 NONPOLAR SIDE CHAINS 11 17  Classification of proteins Proteins ate divided into three main classes : 1. Simple protons 2. Conjugated proteins 3. Derived proteins SIMPLE PROTEINS 1-The simple proteins are those which are made of amino acid units only, joined by peptide bond. Upon hydrolysis they yield mixture of amino acids and nothing else Examples: Human plasma proteins. Plasma proteins are divided into two categories, albumin and globulin. 2- CONJUGATED PROTEINS Conjugated proteins are composed of simple proteins combined with a non- proteinous substance. The non-protein part is linked to protein through covalent bond, non-covalent bond and hydrophobic interaction. The non-proteinous substance is called prosthetic group or cofactor. Examples: phospho-proteins: casein in milk: in which prosthetic group is phosphoric acid and hemo-proteins: haemoglobin in which prosthetic group is heme. 3-DERIVED PROTEINS These are not naturally occurring proteins and are obtained from simple proteins by the action of enzymes and chemical agents. There are two classes of derived proteins. Primary derived proteins: These are derivatives of protein in which the size of protein molecules not altered materially Example: Coagulated proteins like cooked-egg albumin. Secondary derived proteins: These are derivatives of proteins in which the hydrolysis has certainly occurred, The molecules are smaller than the original proteins Example: Prolonged hydrolysis of natural proteins yields peptides. 18  PEPTIDE BOND In proteins, amino acids are joined covalently by peptide bonds, which are amide linkages between the α-carboxyl group of one amino acid and the α- amino group of another. For example, valine and alanine can form the dipeptide valylalanine through the formation of a peptide bond, A peptide bond is a covalent bond accompanied by loss of one water molecule. peptide is named starting with N-terminal amino acid and usually the N- terminal is located on the left hand side. Peptide bonds are not broken by conditions that denature proteins, such as heating or high concentrations of urea. Prolonged exposure to a strong acid or base at elevated temperatures is required to hydrolyze these bonds non enzymically. Peptide bond formation and hydrolysis 19 Characteristics of the peptide bond: The peptide bond has a partial double-bond character, that is, it is shorter than a single bond, and is rigid and planar (Figure 2.2B). This prevents free rotation around the bond between the carbonyl carbon and the nitrogen of the peptide bond. However, the bonds between the α-carbons and the α- amino or α-carboxyl groups can be freely rotated (although they are limited by the size and character of the R-groups). This allows the polypeptide chain to assume a variety of possible configurations. The peptide bond is generally a trans bond (instead of cis), in large part because of steric interference of the R- groups when in the cis position,and it is uncharged but polar. Naming the peptide: Linkage of many amino acids through peptide bonds results in an unbranched chain called a polypeptide. Each component amino acid in a polypeptide is called a “residue” because it is the portion of the amino acid remaining after the atoms of water are lost in the formation of the peptide bond. When a polypeptide is named, all amino acid residues have their suffixes (-ine, -an, -ic, or -ate) changed to -yl, with the exception of the C-terminal amino acid. For example, a tripeptide composed of an N- terminal valine, a glycine and a C-terminal leucine is called valylglycylleucine. Dipeptides- consist of two amino acid residues and one peptide bond. For example, Aspartame: consist of aspartate and phenylalanine (Aspartyl phenylalanine). It is present in African berry. Tripeptides- A tripeptide consist of three amino acid residues and two peptide bonds. For example, Glutathione (GSH) It is a tripeptide with a gamma peptide linkage between the carboxyl group of the glutamate side chain and the amine group of cysteine, and the carboxyl group of cysteine is attached by normal peptide linkage to a glycine. is an important antioxidant in plants, animals, fungi, and some bacteria. Glutathione is capable of preventing damage to important cellular components caused by reactive oxygen species such as free radicals, peroxides. 23 Chemical structure of Glutathione (GSH) Polypeptides- A polypeptide is a long, continuous, and unbranched peptide chain. For example Insulin: hormone secreted from pancreas. The human insulin protein is composed of 51 amino acids. 21  Structure of Proteins The 20 amino acids commonly found in proteins are joined together by peptide bonds. The linear sequence of the linked amino acids contains the information necessary to generate a protein molecule with a unique three-dimensional shape. The complexity of protein structure is best analyzed by considering the molecule in terms of four organizational levels, namely, primary, secondary, tertiary, and quaternary. PRIMARY STRUCTURE OF PROTEINS:- By definition, the primary structure of a protein is the linear sequence of amino acids. Together, this linear sequence is referred to as a polypeptide chain. The amino acids in the primary structure are held together by covalent bonds, which are made during the process of protein synthesis (translation). Understanding the primary structure of proteins is important because many genetic diseases result in proteins with abnormal amino acid sequences, which cause improper folding and loss or impairment of normal function. If the primary structures of the normal and the mutated proteins are known, this information may be used to diagnose or study the disease. SECONDARY STRUCTURE OF PROTEINS:- forms regular arrangements of amino acids that are located near to each other in the linear sequence. These arrangements are termed the secondary structure of the polypeptide. The α-helix, β- sheet, and β-bend (β-turn) are examples of secondary structures frequently encountered in proteins. -α-Helix It is a spiral structure, consisting of a tightly packed, coiled polypeptide backbone core, with the side chains of the component amino acids extending outward from the central axis to avoid interfering sterically with each other. 22  α-helix contain 3.6 amino acid residues per turn. The R-group of amino acids project outwards of the helix (Fig. 9).The α-helix is stabilized by intra chain hydrogen bonds formed between –N–H groups and –C=O groups that are four residues back. Each peptide bond participates in the hydrogen bonding. This gives maximum stability to α-helix. - β-Sheet The β-sheet is another form of secondary structure in which all of the peptide bond components are involved in hydrogen bonding. The surfaces of β-sheets appear pleated called “β-pleated sheets.”. Note also that in β-sheets the hydrogen bonds are perpendicular to the polypeptide backbone. Parallel and antiparallel sheets: A β-sheet can be formed from two or more separate polypeptide chains or segments of polypeptide chains that are arranged either antiparallel to each other (with the N-terminal and C-terminal ends of the β-strands alternating), or parallel to each other (with all the N-termini of the β-strands together. When the hydrogen bonds are formed between the polypeptide backbones of separate polypeptide chains, they are termed interchain bonds. A β-sheet can also be formed by a single polypeptide chain folding back on itself. In this case, the hydrogen bonds are intrachain bonds. -β-Bends (β-hairpin) A very simple structural motif involving β-sheets is the β-hairpin. β-Bends were given this name because they often connect successive strands of antiparallel β-sheets. β-Bends are generally composed of four amino acids, one of which may be glycine the other is proline that causes a “kink” in the polypeptide chain, β-Bends are stabilized by the formation of hydrogen and ionic bonds. -Supersecondary structures (motifs) Globular proteins are constructed by combining secondary structural elements (α-helices, β-sheets) Supersecondary structures are usually produced by packing side chains from 20 adjacent secondary structura elements close to each other. They are connected by loop regions (for example, β-bends). 24 25 TERTIARY STRUCTURE OF PROTEINS:- Three-dimensional folding of polypeptide chain is called as tertiary structure. It consists of regions of α-helices, β-pleated sheet, β-turns, motifs and random coil conformations. Interrelationships between these structures are also a part of tertiary structure. The unique three-dimensional structure of each polypeptide is determined by its amino acid sequence. Interactions between the amino acid side chains guide the folding of the polypeptide to form a compact structure. The following four types of interactions cooperate in stabilizing the tertiary structures of proteins. Disulfide bonds: A disulfide bond is a covalent linkage formed from the sulfhydryl group (–SH) of each of two cysteine residues, to produce a cystine residue. Hydrophobic interactions: Amino acids with nonpolar side chains tend to be located in the interior of the polypeptide molecule, where they associate with other hydrophobic amino acids. In contrast, amino acids with polar or charged side chains tend to be located on the surface of the molecule in contact with the polar solvent. 21 Hydrogen bonds: Amino acid side chains containing oxygen- or nitrogen-bound hydrogen, such as in the alcohol groups of serine and threonine, can form hydrogen bonds with electron-rich atoms, such as the oxygen of a carboxyl group or carbonyl group of a peptide bond. Ionic interactions: Negatively charged groups, such as the carboxylate group (– COO–) in the side chain of aspartate or glutamate, can interact with positively charged groups, such as the amino group (– NH3 +) in the side chain of lysine. Quaternary Structure Many proteins are made up of multiple polypeptide chains, often referred to as protein subunits. These subunits may be the same (as in a homodimer) or different (as in a heterodimer). The quaternary structure refers to how these protein subunits interact with each other and arrange themselves to form a larger aggregate protein complex. The final shape of the protein complex is once again stabilized by various interactions, including hydrogen bonds, ionic bonds, and hydrophobic interactions. 27 Protein folding:- Interactions between the side chains of amino acids determine how a long polypeptide chain folds into the intricate three- dimensional shape of the functional protein. Protein folding, which occurs within the cell in seconds to minutes, employs a shortcut through the maze of all folding possibilities. As a peptide folds, its amino acid side chains are attracted and repulsed according to their chemical properties. For example, positively and negatively charged side chains attract each other. Conversely, similarly charged side chains repel each other. In addition, interactions involving hydrogen bonds, hydrophobic interactions, and disulfide bonds all exert an influence on the folding process. Stages of Protein Folding:- 1- Domains formation: α-helical, β-pleated sheet, β-bend containing domains are formed in the initial step of folding of polypeptide chain. 2- Molten globule: partially folded proteins that have some characteristics of both folded (or ‘native’) and unfolded proteins. Like a native protein, the classic molten globule is compact and has native secondary structure, such as α helices and β-sheets; like an unfolded protein, it lacks specific native tertiary interactions. 3- Native conformation: native conformation develops from molten globule state after several minor conformational changes and rearrangements. Chaperones:- a specialized group of proteins, named “chaperones,” are required for the proper folding of many species of proteins. The chaperones also known as “heat shock” proteins interact with the polypeptide at various stages during the folding process. Some chaperones are important in keeping the protein unfolded until its synthesis is finished, or act as catalysts by increasing the rates of the final stages in the folding process. 28 Denaturation of proteins:- Denaturation may be defined as the disruption of the secondary, tertiary and quarternary structure of the native protein. Protein denaturation results in the unfolding and disorganization of the protein s secondary and tertiary structures, which are not accompanied by hydrolysis of peptide bonds, If the denaturation is severe, the protein molecules become insoluble and precipitation results as well as the changes in the properties of the proteins are permanent and “irreversible”. In case of mild denaturation, there is “reversible denaturation” leading to the slight changes in the 29 properties of the protein which can be restored to the native state after suitable treatment Denaturing agents include Physical (heat, UV and X-rays) and Chemical (Acidic, Basic, Urea and Heavy metal e.g Lead and mercury). 03  HEMEPROTEINS Hemeproteins are a group of specialized proteins that contain heme as a tightly bound prosthetic group. In hemoglobin and myoglobin, the two most abundant heme - proteins in humans, the heme group serves to reversibly bind oxygen. Structure of heme:- Heme is a complex of protoporphyrin IX and ferrous iron (Fe2+) The iron is held in the center of the heme molecule by bonds to the four nitrogens of the porphyrin ring. The heme Fe2+ can form two additional bonds, one on each side of the planar porphyrin ring. In myoglobin and hemoglobin, one of these positions is coordinated to the side chain of a histidine residue of the globin molecule, whereas the other position is available to bind oxygen 01 Myoglobin:- Myoglobin, a hemeprotein present in heart and skeletal muscle, functions both as a reservoir for oxygen, and as an oxygen carrier that increases the rate of transport of oxygen within the muscle cell. Myoglobin is a compact molecule, with approximately 80% of its polypeptide chain folded into eight stretches of α-helix. These α-helical regions, labeled A to H, are terminated either by the presence of proline, whose five-membered ring cannot be accommodated in an α-helix, or by β-bends and loops stabilized by hydrogen bonds and ionic bonds. The interior of the myoglobin molecule is composed almost entirely of nonpolar amino acids. They are packed closely together, forming a structure stabilized by hydrophobic interactions between these clustered residues. In contrast, 02 charged amino acids are located almost exclusively on the surface of the molecule where they can form hydrogen bonds, both with each other and with water. The heme group of myoglobin sits in a crevice in the molecule, which is lined with nonpolar amino acids. Notable exceptions are two histidine residues. One, the proximal histidine (F8) binds directly to the iron of heme. The second, or distal histidine (E7), does not directly interact with the heme group, but helps stabilize the binding of oxygen to the ferrous iron. Hemoglobin:- Hemoglobin is found exclusively in red blood cells (RBCs), where its main function is to transport oxygen (O2) from the lungs to the capillaries of the tissues. Hemoglobin A, the major hemoglobin in adults, is composed of four polypeptide chains two α chains and two β chains held together by noncovalent interactions. Each subunit has stretches of α-helical structure, and a heme- binding pocket similar to that described for myoglobin. a. T form: The deoxy form of hemoglobin is called the “T,” or taut (tense) form. In the T form, the two αβ dimers interact through a network of ionic bonds and hydrogen bonds that constrain the movement of the polypeptide chains. The T form is the low oxygen affinity form of hemoglobin. b. R form: The binding of oxygen to hemoglobin causes the rupture of some of the ionic bonds and hydrogen bonds between the αβ dimers. This leads to a structure called the “R,” or relaxed form, in which the polypeptide chains have more freedom of movement. The R form is the high oxygen affinity form of hemoglobin. 00 Type of hemoglobin 1-Hemoglobin A, the major hemoglobin which is 95-98% of hemoglobin found in adults, is composed of four polypeptide chains two α chains and two β chains—held together by noncovalent interactions. The tetrameric hemoglobin molecule is structurally and functionally more complex than myoglobin. 2- Hemoglobin A2 (Hb A2): Hb A2 is a minor component of normal adult hemoglobin, first appearing shortly before birth and, ultimately, constituting about 2% of the total hemoglobin. It is composed of two α-globin chains and two δ-globin chains (α2δ2). 3- Fetal hemoglobin (Hb F): Hb F is a tetramer consisting of two α chains identical to those found in Hb A, plus two γ chains (α2γ2). Hb F is replaced by hemoglobin A in the first weeks after birth. Under physiologic conditions, Hb F has a higher affinity for oxygen than does Hb A. 4- Hemoglobin A1c (HbA1c): Under physiologic conditions, Hb A is slowly and nonenzymically glycosylated, the extent of glycosylation being dependent on the plasma concentration of a particular hexose. The most abundant form of glycosylated hemoglobin is Hb A1c. It has glucose residues attached predominantly to the NH2 groups of the N-terminal valines of the β-globin chains. Increased amounts of Hb A1c are found in RBCs of patients with diabetes mellitus, because their Hb A has contact with higher glucose concentrations during the 120-day lifetime of these cells. 04 05 Binding of Mb and Hb to oxygen:- The degree of oxygen saturation (Y) of Mb and Hb ranges from zero to 100%. oxygen dissociation curve represent the measurement of Y at different partial pressure of oxygen (pO2). The graph shows an Important difference between Mb and Hb binding. The graph shows that Mb has higher binding affinity to oxygen than Hb. Mb The oxygen dissociation curve for myoglobin is hyperbolic shape. This reflects the fact that Mb reversibly binds a single oxygen molecules. Thus, the oxygenated (MbO2) and deoxygenated Mb exist in a simple equilibrium. Mb + O2 MbO2 The equilibrium is shifted to the right or the left as oxygen is added or removed from the protein. Mb binds to oxygen released from Hb at low pO2 found in th muscle. Mb provide oxygen to the muscle in response to oxygen need. Hb: The oxygen dissociation curve for Hb is sigmoid in shape, indicating that the subunits cooperate in the oxygen binding. This means that the binding of one molecule of oxygen to one heme subunit increase the oxygen binding affinity of the remaining heme groups in the same Hb molecule ( cooperative binding of oxygen). 01 07  HEMOGLOBINO PATHIES family of genetic disorders caused by production of a structurally abnormal hemoglobin molecule, synthesis of insufficient quantities of normal hemoglobin, or, rarely, both. A- Sickle cell anemia (hemoglobin S disease):- Sickle cell anemia, the most common of the red cell sickling diseases, is a genetic disorder of the blood caused by a single nucleotide alteration (a point mutation) in the gene for β-globin in which glutamate at position six has been replaced with valine. Sickle cell anemia is a homozygous, recessive disorder. The mutant β-globin chain is designated βS, and the resulting hemoglobin, α2βS 2, is referred to as Hb S. Sickle cell anemia is characterized by lifelong episodes of pain (“crises”), chronic hemolytic anemia with associated hyperbilirubinemia, stroke, splenic and renal dysfunction, erythrocyte in sickle cell anemia is less than 20 days. Therapy involves analgesics, Intermittent transfusions with packed red cells reduce the risk of stroke, the cumulative effect of the transfusions is iron overload (a syndrome known as hemosiderosis), Hydroxyurea, an antitumor drug. B- Thalassemias:- The thalassemias are hereditary hemolytic diseases in which an imbalance occurs in the synthesis of either the α- or the β-globin chains. Each thalassemia can be classified as either a disorder in which no globin chains are produced (αo- or βo-thal assemia), or one in which some chains are synthesized, but at a reduced level (α+- or β+-thalassemia). 1. β-Thalassemias: In these disorders, synthesis of β-globin chains 08 is decreased or absent, Increase in α2γ2 (Hb F) and α2δ2 (Hb A2) also occurs. There are only two copies of the β-globin gene in each cell (one on each chromosome 11). Therefore, individuals with β-globin gene defects have either β-thalassemia trait (β-thalassemia minor) if they have only one defective β-globin gene, or β-thalassemia major if both genes are defective. Because the β-globin gene is not expressed until late in fetal gestation, the physical manifestations of β-thalassemias appear only several months after birth, These patients require regular transfusions of blood. Bone marrow transplantation is the most appropriate treatment. 2. α-Thalassemias: These are defects in which the synthesis of α-globin chains is decreased or absent, typically as a result of deletional mutations. Because each individual’s genome contains four copies of the α-globin gene (two on each chromosome 16), If one of the four genes is defective, the individual is termed a silent carrier of α-thalassemia, because no physical manifestations of the disease occur. If two α-globin genes are defective, the individual is designated as having α -thalassemia trait. If three α- globin genes are defective, the individual has Hb H (β4) disease—a mildly to moderately severe hemolytic anemia. If all four α globin genes are defective, Hb Bart (γ4) disease with hydrops fetalis and fetal death results. 09  Fibrous Proteins Collagen and elastin are examples of common, well-characterized fibrous proteins of the extracellular matrix that serve structural functions in the body. For example, collagen and elastin are found as components of skin, connective tissue, blood vessel walls, and sclera and cornea of the eye. COLLAGEN:- Collagen is the most abundant protein in the human body. A typical collagen molecule is a long, rigid structure in which three polypeptides (referred to as “α chains”) are around one another in a rope-like triple helix. The three polypeptide α chains are held together by hydrogen bonds between the chains. Variations in the amino acid sequence of the α chains result in structural components that are about the same size (approximately 1,000 amino acids long), but with slightly different Properties, the most common collagen, type I, contains two chains called α1 and one chain called α2 (α12α2). Amino acid sequence: Collagen is rich in proline and glycine Glycine, the smalles tamino acid, is found in every third position of the polypeptide chain. It fits into the restricted spaces where the three chains of the helix come together. (–Gly–X–Y–)333, where X is frequently proline and Y is often hydroxyproline but can be hydroxylysine. Biosynthesis of collagen: the newly synthesized polypeptide precursors of α chains (prepro-α chains) contain a special amino acid sequence at their N-terminal ends. prepro-α chains → pro-α chain→Hydroxylation→Glycosylation→ → procollagen→tropocollagen molecules→collagen fibrils. 43 41 42 Hydroxylation: The pro-α chains are processed by a number of enzymic steps within the lumen of the RER while the polypeptides are still being synthesized. Proline and lysine residues found in the Y-position of the –Gly–X–Y– sequence can be hydroxylated to form hydroxyproline and hydroxylysine residues. These hydroxylation reactions require molecular oxygen, Fe2+, and the reducing agent vitamin C without which the hydroxylating enzymes, prolyl hydroxylase and lysyl hydroxylase, are unable to function. In the case of ascorbic acid deficiency (and, therefore, a lack of prolyl and lysyl hydroxylation), interchain H-bond formation is impaired, as is formation of a stable triple helix. Additionally, collagen fibrils cannot be cross-linked greatly decreasing the tensile strength of the assembled fiber. The resulting deficiency disease is known as scurvy. Glycosylation: Some hydroxylysine residues are modified by glycosylation with glucose or glucosyl-galactose. Collagen diseases: Collagenopathies Defects in any one of the many steps in collagen fiber synthesis can result in a genetic disease involving an inability of collagen to form fibers properly and, thus, provide tissues with the needed tensile strength normally provided by collagen. 1. Ehlers-Danlos syndrome (EDS):- can result from a deficiency of collagen-processing enzymes (for example, lysyl hydroxylas), or from mutations in the amino acid sequences of collagen. Collagen containing mutant chains is not secreted, and is either degraded or accumulated to high levels in intracellular compartments. Because collagen type III is an important component of the arteries, potentially lethal vascular problems occur. patients with EDS also show, defects in collagen type I fibrils. This results in fragile, stretchy skin and loose joints. 2. Osteogenesis imperfecta (OI):- This disease, known as brittle bone syndrome, is also a heterogeneous group of inherited disorders distinguished by bones that easily bend and fracture. 40 Type I OI is called osteogenesis imperfecta tarda. The disease is the consequence of decreased production of α1 and α2 chains. It presents in early infancy with fractures secondary to minor trauma. Type II OI is called osteogenesis imperfecta congenita, and is the most severe. Patients die of pulmonary hypoplasia in utero or during the neonatal period. Most patients with severe OI have mutations in the gene for either the pro-α1 or pro-α2 chains of type I collagen. The most common mutations cause the replacement of glycine residues (in –Gly–X–Y–) by amino acids with bulky side chains. The resultant structurally abnormal pro-α chains prevent the formation of the required triple-helical conformation. ELASTIN:- elastin is a connective tissue protein with rubber-like properties. Elastic fibers composed of elastin and glycoprotein microfibrils are found in the lungs, the walls of large arteries, and elastic ligaments. Elastin is an insoluble protein polymer synthesized from a precursor, tropoelastin, which is a linear polypeptide composed of about 700 amino acids that are primarily small and nonpolar (for example, glycine, alanine, and valine). Elastin is also rich in proline and lysine, but contains only a little hydroxyproline and hydroxylysine. Desmosine:- Desmosine is special amino acid formed by condensation of four molecules of lysine into a pyridinium ring. Elastin molecules aggregate in the extracellular space where they are crosslinked by stable desmosine bridges. Desmosine found only in elastin, allows elastin to stretch reversibly in all directions. Elastin disorders:- Elastic fibres are present in lung structures including alveoli, alveolar ducts, airways, vasculature and pleura. The rate of lung elastin synthesis is greatest during fetal and neonatal development, and is minimal in the healthy adult. 44 molecular structure of desmosine Role of α1-antitrypsin in elastin degradation:- Blood and other body fluids contain a protein, α1-antitrypsin that inhibits a number of proteolytic enzymes that hydrolyze and destroy proteins. Neutrophil elastase that is released into the extracellular space, and degrades elastin of alveolar walls, as well as other structural proteins in a variety of tissues, In the normal lung, the alveoli are chronically exposed to low levels of neutrophil elastase released from activated and degenerating neutrophils. This proteolytic activity can destroy the elastin in alveolar walls if unopposed by the action of α1-AT, the most important inhibitor of neutrophil elastase. Because lung tissue cannot regenerate, emphysema results from the destruction of the connective tissue of alveolar walls. The deficiency of elastase inhibitor can be reversed by augmentation therapy—weekly intravenous administration of α1-AT. The α1-AT diffuses from the blood into the lung. 45  Keratin:- They are about 30 types of keratins, Two major types of keratins are α- and β-keratins. α-keratin is arranged as α-Helix. α-keratin consist of right handed α-helix as basic unit. Three such α-helices get cross linked by disulfide bonds ( rich in cysteine) and form super secondary structure. Insoluble ( high content of hydrophobic amino acids). β-keratin, which is present in silk fibroin and spider web is arranged in β-pleated sheet.. β-keratin contains anti parallel β-pleated sheet. 41 47