Proteins: Structure, Types & Function PDF

Proteins: Structure, Types & Function Biochemistry I- for Dental Students Lecturer: Dr. Husam Abazid  Introduction Human body composed of many substances: Protein, Carbohydrates, Lipids, Water, Minerals etc. Proteins are the most abundant and fu...

Proteins: Structure, Types & Function Biochemistry I- for Dental Students Lecturer: Dr. Husam Abazid  Introduction Human body composed of many substances: Protein, Carbohydrates, Lipids, Water, Minerals etc. 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, acting like the steel cables in reinforced concrete. ❑ In the bloodstream, proteins, such as hemoglobin and plasma albumin, shuttle molecules essential to life, whereas immunoglobulins fight infectious bacteria and viruses.  Biological Functions of Proteins Enzymes: catalysts for reactions Transport molecules: hemoglobin; lipoproteins, channel proteins Contractile/motion: myosin; actin Structural: collagen; keratin, actin Defense: antibodies Signaling: hormones, receptors Toxins: diphtheria; enterotoxins  Protein Structure Peptides and proteins are polymers of amino acids More than 300 different amino acids have been described in nature, only twenty are commonly found as constituents of proteins ❖ These are the only amino acids that are coded for by DNA, the genetic material in the cell Amino acids are categorized according to different sources: Essential / nonessential Polar / nonpolar Charged / uncharged Basic / acid  Essential / nonessential Nonessential amino acids can be synthesized in sufficient amounts from the intermediates of metabolism or, as in the case of cysteine and tyrosine, from essential amino acids. In contrast, the essential amino acids cannot be synthesized (or produced in sufficient amounts) by the body and, therefore,must be obtained from the diet in order for normal protein synthesis to occur.  Amino Acid Structure Each amino acid has α-carbon atom bounded with: -Carboxyl group (COOH) -Amino group (NH2) > Except for proline which has an imino group (NH). - (H ): determines the direction of aa either D (dextro: right) or L (levetro: left) -Distinctive side chain (R-group) * Note: α-carbon is that carbon bound to Carboxyl group directly Amino acids are bound together by peptide bonds between amino and carboxyl groups  Polar/nonpolar amino acid: 1. Nonpolar Amino acids with nonpolar side chains does not gain or lose protons or participate in hydrogen or ionic bonds. The side chains of these amino acids can be thought of as “oily” or lipid-like, a property that promotes hydrophobic interactions Nonpolar Proline Glycine Alanine Phenylalanine Valine Leucine Isoleucine Tryptophan Methionine  Nonpolar aa Location of nonpolar amino acids in proteins: Nonpolar amino acids in proteins are found in aqueous solutions–– a polar environment–– the side chains of the nonpolar amino acids tend to cluster together in the interior of the protein like droplets of oil that coalesce in an aqueous environment. This phenomenon, known as the hydrophobic effect, is the result of the hydrophobicity of the nonpolar R-groups, which act much 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.  Nonpolar aa :1. 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, then, has a secondary (rather than a primary) amino group. referred 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 Nonpolar, non aromatic and nonessential. Proline, interrupts alpha helices by introducing bends because of its side chain being too rigid to be accommodated in the helix. Found in high concentration in collagen. Proline amino acid acts as a precursor of glutamic acid.  Nonpolar aa :2. Glycine Non-polar, nonessential. Collagen is 33% glycine. It can dissolve in both water and other organic solvents as it is having both hydrophobic and hydrophilic properties Is the precursor of heme, precursor of the purine ring An inhibitory neurotransmitter in the CNS. Improve the absorption of drug in the stomach..  Nonpolar aa :3. Alanine ▪ Nonpolar, nonessential ▪ Released from muscle during starvation, exercise, or after high carb meal.  Nonpolar aa :4. Phenylalanine Nonpolar, aromatic and essential precursor for: tyrosine, dopamine, norepinephrine, epinephrine, thyroxine and melanin. Phenylalanine is used to cure depression, hyperactivity disorder, Parkinson's decease. Phenylalanine is converted to tyrosine which in turn is converted to L-DOPA. L-DOPA is further converted to dopamine, noradrenaline and finally to adrenaline.  Nonpolar aa :5. Valine Nonpolar, essential. Its deficiency may affect the nerve myelin sheath. L-Valine involves in improvement of insomnia, nervousness, in disorders of the muscles, mental and emotional upsets and also effective as an appetite suppressant.  Nonpolar aa :6. Leucine Branched chain, essential, nonpolar,. High conc. in globulins and albumins (hemoglobin). Leucine acts as a major component for astacin, ferritin, and other 'buffer' proteins. Leucine is quite similar to valine, has only one additional methylene group in its side chain. Because of hydrophobic nature leucine is generally buried in folded proteins.  Nonpolar aa :7. Isoleucine Nonpolar Essential Isomer of leucine  Nonpolar aa :8. Tryptophan Nonpolar, aromatic, essential. Precursor for – Serotonin which regulates mood, behavior, body temperature & appetite). – Melatonin (bio clock, antioxidant) – Niacin (vitamin B3, nicotinic acid) The deficiency of tryptophan may cause the characteristic symptoms of protein deficiency like anxiety, depression and low mood, weight loss, impaired growth in infants and children and insomnia.  Nonpolar aa :9. Methionine Nonpolar, essential, s-containing. Precursor for: – Cysteine, which further produces Glutathione, involves in liver detoxification. It is also a powerful antioxidant which combats free radicals in the body. Methionine also involves in management of depression, arthritis pain, chronic liver disease and memory problems  2. Amino acids with uncharged 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. The side chains of asparagine and glutamine each contain a carbonyl group and an amide group, both of which can also participate in hydrogen bonds. Serine, Threonine, Tyrosine Asparagine, Glutamine , Cysteine 2. Amino acids with uncharged polar side chains  Amino acids with uncharged polar side chains: 1. Serine Polar, nonessential. Important in active site of enzymes. Able to H-bond. Plays an important role in cell growth and development.  Amino acids with uncharged polar side chains: 2. Threonine Essential Supports central nervous, cardiovascular, liver, and immune system functioning Threonine treatment also helps alleviate symptoms of Multiple Sclerosis - another disease affecting nerves and muscles. Besides, Threonine is recognized as an immunostimulant promoting the growth of thymus gland. Aiding the digestive and intestinal tracts to function more smoothly,  Amino acids with uncharged polar side chains: 3. Tyrosine Polar, nonessential, aromatic. Precursor for: – Thyroid hormones T3 – Thyroxine T4 – monoamines: catecholamines: (dopamine, norepinephrine, epinephrine) It is also acts as an antioxidant and used to suppress appetite, stress reduction, to combat anxiety, depression, allergies, and headaches. Tyrosine is able to increase energy and enhance libido which show a positive effect on several health conditions, like Parkinson's disease and Alzheimer's. Amino acids with uncharged polar side chains: 3. Tyrosine  Amino acids with uncharged polar side chains: 4. Asparagine Polar , nonessential. Found at beginning and end of α-helix because of H- bonding in R group. Forms acrylamide with sugar at high temp. The amide group of asparagine can be easily hydrolyzed to carboxyl group and form aspartic acid. It also acts as a common site for the bonding of carbohydrates in glycoproteins.  Amino acids with uncharged polar side chains: 5. Glutamine Polar, nonessential, most abundant free amino acids in the body. The amide group of glutamine is used in the production of the vitamins: NAD and NADP, CTP from UTP, purine nucleotides and asparagine and carbamyl phosphate which further used in the production of pyrimidine. Glutamine involves in the synthesis of other amino acids also like glutamate In the presence of two important enzymes, glutamate dehydrogenase and glutamine synthetase, both glutamine and glutamic acid involve in the production urea, GABA, amino sugars, nucleotides and polyamines.  Amino acids with uncharged polar side chains: 6. Cysteine Polar, nonessential. Sulfhydryl (-SH). Disulfide bond cross linking proteins which provides stability and folding to protein structure. A covalent disulfide bond between two cysteine to produce a Cystine residue. Many extracellular proteins are stabilized by disulfide bonds. Albumin, a blood protein that functions as a transporter for a variety of molecules, is an example  Amino acids with acidic side chains The amino acids aspartic and glutamic acid are proton donors. At physiologic pH, the side chains has a negatively charged carboxylate group (–COO-). They are, therefore, called aspartate or glutamate to emphasize that these amino acids are negatively charged at physiologic pH  Amino acids with acidic side chains 1. Aspartate Acidic, nonessential important for transporting e- in electron transport chain. Acts as an excitatory neurotransmitter in the central nervous system. The aspartic acid plays a very vital role in the Krebs cycle (citric acid cycle), in which it involve in the formation of other biochemical and amino acids like asparagine, methionine, isoleucine and arginine, threonine, lysine, are synthesized.  Amino acids with acidic side chains 2. Glutamate Acidic , nonessential, excites neuron. precursor for GABA (quiets excited neurons) Excitatory neurotransmitter (via NMDA receptors)  3. Amino acids with basic side chains The side chains of the basic amino acids accept protons. At physiologic pH the side chains of lysine and arginine are fully ionized and positively charged. In contrast, histidine is weakly basic, and the free amino acid is largely uncharged 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.  Amino acids with basic side chains 1.Histidine Basic , essential. It is a precursor for histamine which is synthesized within our body by the decarboxylation of histidine by histidine decarboxylase. Important in hemoglobin and myoglobin 3. Amino acids with basic side chains 2. Lysine Basic , essential. Important in collagen formation. Precursor for carnitine, carries long-chain fatty acids to mitochondria for use. It also affects the production of hormone, enzyme and antibodies.  3. Amino acids with basic side chains 3. Arginine Basic, nonessential. Precursor for nitric oxide (vasodilator). L-arginine acts as a precursor for vasopressin (ADH) Abbreviations and symbols for commonly occurring amino acids  Optical Properties of Amino Acids The α-carbon of each amino acid except glycine (optically inactive) is an optically active carbon atom (or asymmetric center), 19 of the 20 amino acids can exist as enantiomers D (Dextro) & L (levo) that are mirror images of each other. D-amino acids are found in some antibiotics and in plant and bacterial cell walls. All amino acids found in proteins are of the L-configuration.  Acidic and basic properties of amino acids Amino acids in aqueous solution contain weakly acidic α- carboxyl groups and weakly basic α-amino groups. In addition, each of the acidic and basic amino acids contains an ionizable group in its side chain. Thus, both free amino acids and some amino acids combined in peptide linkages can act as buffers. The quantitative relationship between the PH of the solution and concentration of a weak acid (HA) and its conjugate base (A ̅) is described by the Henderson-Hasselbalch equation.  Buffers A buffer is a solution that resists change in pH following the addition of an acid or base. A buffer can be created by mixing a weak acid (HA) with its conjugate base (A-). If an acid such as HCl is then added to such a solution, A- can neutralize it, in the process being converted to HA. If a base is added, HA can neutralize it, in the process being converted to A-. Maximum buffering capacity occurs at a pH equal to the pKa, but a conjugate acid/base pair can still serve as an effective buffer when the pH of a solution is within approximately ±1 pH unit of the pKa.  pH * PH is the concentration of protons in aqueous fluids * pKa is that pH which the protonated and unprotonated species are in equal concentration *Henderson-Hasselbalch equation can be used to calculate the quantitative relationship between the concentration of a weak acid and its conjugate base  A drug passes through membranes more readily if it is uncharged. Thus, for a weak acid such as aspirin, the uncharged HA can permeate through membranes and A- cannot. For a weak base, such as morphine, the uncharged form, B, penetrates through the cell membrane and BH⁺ does not. Therefore, the effective concentration of the permeable form of each drug at its absorption site is determined by the relative concentrations of the charged and uncharged forms. The ratio between the two forms is determined by the pH at the site of absorption, and by the strength of the weak acid or base, which is represented by the pKa of the ionizable group. The Henderson-Hasselbalch equation is useful in determining how much drug is found on either side of a membrane that separates two compartments that differ in pH, for example, the stomach (pH 1.0–1.5) and blood plasma (pH 7.4). Protein Structure & Function  OVERVIEW The 20 amino acids commonly found in proteins are joined together by peptide bonds. 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, Secondary and Tertiary are composed of one polypeptide but varies in the interaction between aa.  1 - Primary Structure of Proteins: – Primary protein structure refers to the sequence of amino acids, which is determined by only peptide bonds within one peptide chain. – amino acids are bounded by amide bonds called peptide bonds. – peptides bonds are formed by the free amino group (of the N-terminal amino acid) on the left and the free carboxyl group (of the C-terminal amino acid) on the right. – Direction of the polypeptide is N terminus-C- terminus.  Peptide bonds Peptide bonds are broken by: – Physical conditions: prolonged exposure to a strong acid or base at elevated temperatures – Enzymes Not broken by conditions that denature proteins, such as heating or high concentration of urea… Peptide bond are uncharged, and neither accept or release protons over the pH range of 2–12.  Determination of the amino acid composition of a polypeptide A purified sample of the polypeptide to be analyzed is first hydrolyzed by strong acid at 110°C for 24 hours. This treatment cleaves the peptide bonds and releases the individual amino acids, which can be separated by cation- exchange chromatography. Each amino acid is released from the chromatography column by eluting with solutions of increasing ionic strength and pH. The separated amino acids are quantitated by heating them with ninhydrin The amount of each amino acid is determined spectrophotometrically by measuring the amount of light absorbed by the ninhydrin derivative.  Sequencing of the peptide from its N-terminal end Sequencing is aprocess of identifying the specific amino acid at each position in the peptide chain, beginning at the N- terminal end. Phenylisothiocyanate, known as Edman reagent, is used to label the amino-terminal residue under mildly alkaline conditions. The resulting phenylthiohydantoin (PTH) derivative introduces an instability in the N-terminal peptide bond that can be selectively hydrolyzed without cleaving the other peptide bonds.  2 - Secondary Structure of Proteins: The polypeptide backbone forms regular arrangements of amino acids that are located near to each other in the linear sequence. The hydrogen bond between aa fold the polypeptide into various shapes, such as alpha helixes and beta pleated sheet. (α-Helix, β-Pleated Sheet or β-Bend )  Secondary structure : α-Helix α-Helix is the most common helices are found in nature, It is spiral structure, consisting of tightly packed, coiled polypeptide backbone core The side chains of component amino acids extending outward from the central axis. α-Helix is found as hair, skin,…, stabilized by hydrogen bonds Each hydrogen is attached to an amide nitrogen bonded to a carbonyl oxygen of four amino acids away. The α-helix is a right-handed helix. Each turn of the helix contains 3.6 amino acids.  Secondary structure : β- Sheet or β-Pleated Sheet The polypeptide backbone is extended in a zigzag structure resembling a series of pleats. It is composed of two or more polypeptide chains that are arranged either anti-parallel to each other, or parallel to each other. β-Bends reverse the direction of a polypeptide chain, often contain proline. β-Bends are generally composed of four amino acids, one of which may be proline—the amino acid that causes a “kink” in the polypeptide chain and Glycine Beta pleated sheet  Nonrepetitive secondary structure Approximately one half of an average globular protein is organized into repetitive structures, such as the α-helix and/or β-sheet. The remainder is nonrepetitive secondary structures having a loop or coil conformation. These are not “random,” but rather simply have a less regular structure than those described above.  Supersecondary structure (motifs): Globular proteins are constructed by combining secondary structural elements (α-helices, β-sheets, nonrepetitive sequences). These form primarily the core region- that is the interior of the molecule. They are connected by loop regions at the surface of protein.  3 - Tertiary Structure of Globular Proteins: The primary structure of a polypeptide chain determines its tertiary structure. “Tertiary” refers both to the folding of domains and to the final arrangement of domains in the polypeptide. Hydrophobic side chains are buried in the interior, whereas hydro philic groups are generally found on the surface of the molecule. Tertiary structure refers to the three-dimensional arrangement of all the atoms in the protein. The stabilizing interactions in a protein include disulfied bonds, hydrogen bonds, electrostatic (ionic) interactions (interactions between opposite charges), and hydrophobic (van-der Waals) interactions.  Domains Domains are the fundamental functional and three- dimensional structural units of polypeptides. Polypeptide chains that are greater than 200 amino acids in length generally consist of two or more domains. The core of a domain is built from combinations of supersecondary structural elements (motifs).  Bonds in Tertiary structure 1. 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  Bonds in Tertiary structure 2. 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  Bonds in Tertiary structure 3. 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. The two cysteines may be separated from each other by many amino acids in the primary sequence of a polypeptide or may even be located on two different polypeptide chains; A disulfide bond contributes to the stability of the three-dimensional shape of the protein molecule, and prevents it from becoming denatured in the extracellular environment..  Bonds in Tertiary structure 4. 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  4. Quaternary Structure of Globular Proteins: Proteins that have more than one peptide chain are called oligomers. The individual chains are called subunits. A protein according to number of subunits is called as: - Monomer (one) - Dimer (two) - Trimer (three) - Tetramer (four) The arrangement of oligomer subunits is called the quaternary structure of the protein.  4. Quaternary Structure of Globular Proteins: Subunits are held together by non-covalent interactions (Hydrogen bounds, ionic bond, and hydrophobic interactions). Subunits may either function independently of each other or work cooperatively, as in hemoglobin, in which the binding of oxygen to one subunit of the tetramer increases the affinity of the other subunit for oxygen. Hemoglobin is an example of a tetramer. It has two different kinds of subunits and two of each kind (2 α + 2 β)  Denaturation of proteins Protein denaturation results in the unfolding and disorganization of the protein’s secondary and tertiary structures, It is not accompanied by hydrolysis of peptide bonds. Denaturing agents include heat, organic solvents, mechanical mixing, strong acids or bases, detergents, and ions of heavy metals such as lead and mercury. Denaturation may, under ideal conditions, be – Reversible, in which case the protein refolds into its original native structure when the denaturing agent is removed. – Remain permanently disordered. Denatured proteins are often insoluble and, therefore, precipitate from solution.  Protein Denaturation Destroying the highly organized secondary and tertiary structure of a protein by breaking the bonds maintaining the three-dimensional shape of the protein (because these bonds are week) without accompanying by hydrolysis of peptide bonds is called denaturation.  Denaturation and renaturation of ribonuclease A. Treatment of native ribonuclease A (top) with urea in the presence of 2-mercaptoethanol unfolds the protein and disrupts disulfide bonds to produce reduced, reversibly denatured ribonuclease A  Protein Folding. Assessed by chaperone proteins Hydrolysis of several ATP molecules is required for chaperones function.  Diseases caused by protein abnormality 1. Amyloid disease Due to Misfolding of proteins o May occur spontaneously, or be o Caused by a mutation in a particular gene, or o After abnormal proteolytic cleavage, Formation of long, fibrillar protein assemblies consisting of β-pleated sheets. Amyloids are accumulation of these insoluble, spontaneously aggregating proteins, called Has been implicated in many degenerative diseases—particularly in the age-related neurodegenerative disorder, Alzheimer disease.  Diseases caused by protein abnormality 2. Prion disease The prion protein (PrP) has been strongly implicated as the causative agent of transmissible spongiform encephalopathies (TSEs), including: ❖ Creutzfeldt-Jakob disease in humans ❖ Scrape in sheep ❖ Mad cow disease in cattle This infectious protein is highly resistant to proteolytic degradation. Cause: number of α-helices present in noninfectious are replaced by β-sheets in the infectious form  Structures of Proteins 1-Primary structure: the linear sequence of amino acid residues in a protein. (peptide bonds only) 2-Secondary structure: regularities in local conformations, maintained by H- bonds. – α helix – β strands (only H- bonds added). 3-Tertiary structure: The completely folded polypeptide. Several distinct globular units linked by a short stretch of amino acid residues (domain). Stabilized by interactions of amino acid side chains in non-\neighboring region of the polypeptide. (many non-covalent bonds) 4- Quaternary structure: involves the association of two or more polypeptide into multi-subunit, Types of proteins 1. Globular 2. Fibrous Native conformation of a protein  1. Globular Proteins Globular proteins such as Albumins, Globulins, Enzymes, tend to have roughly spherical shapes o They are soluble in water ( as Hemoglobin). o The following part examines the relationship between structure and function for the clinically important globular hemeproteins. o  Structure of heme Heme is a complex of protoporphyrin IX and ferrous iron (Fe+2). The iron is held in the center of the heme molecule by bonds to the four nitrogens of the porphyrin ring. The heme Fe+2 can form two additional bonds, one each side of the planar porphyrin ring with histidine  Examples of heme groups and their function The heme group of a cytochrome functions as an electron carrier that is alternately oxidized and reduced. In contrast, the heme group of the enzyme catalase is part in the active side of the enzyme that catalyses the breakdown of hydrogen peroxide. In hemoglobin and myoglobin, the two most abundant heme- proteins in humans, the heme group serves to reversibly bind oxygen.  Myoglobin Myoglobin, a hemeprotein present in the heart and skeletal muscle , functions both as reservoir for oxygen , and as oxygen carrier that increases the rate of transport of oxygen within the muscle cell. Myoglobin consists of a single polypeptide chain that is structurally similar to the individual subunit polypeptide chain of the hemoglobin molecule.  α-Helical content: 80% of its polypeptide chain folded into 8 stretches of α-helix. These α-Helical regions, labeled A to H.  Structure and function of 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. However, the tetrameric hemoglobin molecule is structurally and functionally more complex than myoglobin. For example, hemoglobin can transport H+ and CO2 from the tissues to the lungs and can carry four molecules of O2 from the lungs to the cells of the body. Furthermore, the oxygen-binding properties of hemoglobin are regulated by interaction with allosteric effectors.  The two peptide chains within each dimers are held tightly together, primarily by hydrophobic interactions. Each subunit has stretches of α-helical structure, and a heme-binding pocket.  The Hb tetramer can be envisioned as being composed of two identical dimers, (αβ)1 and (αβ)2, in which the numbers refer to dimers one and two. Composition of each polypeptide differs form the other and is controlled by different genes  - (T Form): - (R Form): The deoxy form of Hb is called the The oxyginated form of Hb is called “T”, or Taut (tense) form. the “R”, or Relaxed form The two αβ dimers interact The binding of oxygen to Hb causes through a network of ionic and the rupture of some of the ionic and hydrogen bonds that constrain the hydrogen bonds between the αβ movement of the polypeptide dimers. chains. The T form is the low-oxygen- The R form is the high-oxygen- affinity form of Hb. affinity form of Hb.  Allosteric effects of Hemoglobin The ability of hemoglobin to reversibly bind oxygen is affected by the: 1- pO2 (through heme-heme interactions). 2- The pH of the environment 3- The partial pressure of carbon dioxide (pCO2) 4- The availability of 2,3- bisphosphoglycerate  Cooperative binding Means that the binding of an oxygen molecule at one heme group increases the oxygen affinity of the remaining heme groups in the same hemoglobin molecule.  Loading and unloading oxygen In the lung, the concentration of oxygen is high, and hemoglobin becomes virtually saturated (or loaded) with oxygen. In contrast, in peripheral tissues, oxyhemoglobin releases (or unloads) much of its oxygen.  Bohr effect : pH vs oxygen affinity When CO2 concentration increased, this will decrease pH and as a result, this will decrease oxygen affinity of hemoglobin which means increase the release of oxygen , and vice versa. The binding of CO2 stabilizes the T (taut) or deoxy form of hemoglobin, resulting in a decrease in its affinity for oxygen and a right shift in the oxygen dissociation. In the lungs, CO2 dissociates from the hemoglobin, and is released in the breath.  Source of the protons that lower the pH: [CO2 ] And [H+] in the capillaries of the tissue is higher that capillaries of the lungs. In the tissues CO2 is converted by carbonic anhydras to carbonic acid: CO2+H2O H2CO3 which spontaneously loses a proton, becoming bicarbonate (the major blood buffer) H2CO3 HCO3‾ + H+ The H+ produced by this pair of reactions contributes to the lowering of pH. This differential pH gradient (lungs having a higher pH, tissues a lower pH) favors the unloading of oxygen in the peripheral tissues, and the loading of oxygen in the lung.  Effect of 2,3-bisphosphoglycerate on oxygen affinity 2,3-BPG is an important regulator of the binding of oxygen to hemoglobin. 2,3-BPG decreases the oxygen affinity of hemoglobin by binding to deoxyhemoglobin but not to oxyhemoglobin. HbO2 + 2,3-BPG Hb-2,3-BPG + O2 Oxyhemoglobin deoxyhemoglobin This reduced affinity enables hemoglobin to release oxygen.  Response of 2,3-BPG levels to chronic hypoxia or anemia The concentration of 2,3-BPG in the RBC increases in response to – Chronic hypoxia, such as that observed in chronic obstructive pulmonary disease (COPD) like emphysema, – High altitudes, where circulating hemoglobin may have difficulty receiving sufficient oxygen. – Chronic anemia, in which fewer than normal RBCs are available to supply the body’s oxygen needs. Elevated 2,3-BPG levels lower the oxygen affinity of hemo- globin, permitting greater unloading of oxygen in the capillaries of the tissues  HB- CO Binding Carbon monoxide (CO) binds tightly (but reversibly) to the hemoglobin iron, forming carbon monoxyhemoglobin HbCO. When CO binds to one or more of the four heme sites, hemoglobin shifts to the relaxed conformation, causing the remaining heme sites to bind oxygen with high affinity and hemoglobin become unable to release oxygen to the tissues. The affinity of hemoglobin for CO is 220 times greater than for oxygen. Carbon monoxide poisoning is treated with 100% oxygen at high pressure, which facilitates the dissociation of CO from the hemoglobin.  Types of HB Minor hemoglobins – Hb A Hemoglobineopathies ❑ HbS – Hb A2 ❑ HbC – Hb A1c ❑ Hb CS – Hb F ❑ HbM ❑ Thalassemia  Minor hemoglobins - Hb A is the normal human hemoglobin, it is tetramer, composed of tow α-globin polypeptides and tow β-globin polypeptides. - Hb A2, normal, in adult, but at low levels compared with Hb A, composed of (α2δ2). - Hb F, synthesized only during fetal development, consisting of two α chains and two γ chains (α2γ2). - Hb A1C: glycosylated hemoglobin, under physiologic conditions, Hb A is slowly and nonenzymatically glycosylated. – It has glucose residues attached to the NH2 groups of the β-globin chains. – Increased amounts of HbA1C are found in RBCs of patients with higher glucoses  Hemoglobineopathies A- Sickle Cell Anemia (Hemoglobin S disease): – It is a genetic disorder of the blood caused by a single nucleotide alteration (mutation) in the gene for β-globin. – A molecule of Hb S contains two normal α-globin chains and two mutant β-globin chains, in which glutamate at position six has been replaced with the nonpolar valine, producing rigid, mis-shapen erythrocytes. – Treatment: Therapy involves adequate hydration, analgesics, and transfusions in patients at high risk for fatal occlusion of blood vessels. A molecule of Hb S contains tow normal α-globin chains and two mutant β-globin chains, in which glutamate at position six has been replaced with the nonpolar valine, producing rigid, misshapen erythrocytes. Such sickled cells frequently block the flow of blood in the narrow capillaries. This interruption in the supply of oxygen leads to localized anoxia (oxygen deprivation) in the tissue, causing pain and eventually death of cells in the vicinity of the blockage. Treatment: Therapy involves adequate hydration, analgesics, aggressive antibiotic therapy if infection is present, and transfusions in patients at high risk for fatal occlusion of blood vessels. Dactylitis%2B(SCD,%2Bprobable%2Bsalmonella)  Hemoglobineopathies B- Hemoglobin C disease: Lysine is substituted for the glutamate in the sixth position of the β-globin chain. C- Hemoglobin SC disease (Hb SC): Some β-globin chains have the sickle cell mutation, whereas other β-globin chains carry the mutation found in Hb C disease.  D- Methemoglobinemias (Hb M): Oxidation of the heme component of hemoglobin to the ferric (Fe+3) state forms methemoglobin, which cannot bind oxygen. This oxidation may be caused by ❖The action of certain drugs, such as nitrates, or endogenous products, such as reactive oxygen intermediates. ❖ Inherited defects, for example, certain mutations in the α- or β- globin chain promote the formation of methemoglobin (Hb M). The methemoglobinemias are characterized by “chocolate cyanosis” and chocolate-colored blood.  E- THALASSEMIAS: Thalassemias are hereditary hemolytic diseases in which an imbalance occurs in the synthesis of globin chains. As a group, they are the most common single gene disorders in humans. In the thalassemias, the synthesis of either the α- or the β-globin chain is defective. Thalassemia can be caused by a variety of mutations, including o Entire gene deletions, o Substitutions o Deletions of one-to-many nucleotides in the DNA. Two types: ❑ α-Thalassemias ❑ β-Thalassemias α-Thalassemias: - In these disorders, synthesis of α- globin chains is decreased or absent. - There are several levels of α-globin chain deficiencies. - Hb H (β4) disease- a mildly to moderately severe hemolytic anemia. - If all four globin genes are defective, Hb Bart (γ4) disease with hydrops fetalis and fetal death results β-Thalassemias: In these disorders, synthesis of β-globin chains is decreased, or absent, α-globin chain synthesis is normal. α-globin chains can not form stable tetramers and therefore, precipitate, causing the premature death of cells initially destined to become mature RBCs. Infants born with β-Thalassemia major are seemingly healthy at birth, but become severely anemic, usually during the first or second year of life, require regular transfusions of blood. Iron overload cause the death between 15-25 years.  Hb/Mb Oxygen dissociation curve: This graph illustrates that myoglobin has a higher oxygen affinity at all pO2 values than does hemoglobin. The higher the oxygen affinity, the lower the P50. Quarternary structure Fibrous Proteins  Fibrous proteins: Consisted of three long chains of polypeptides. Are insoluble in water (collagen). Keratin, myosin, collagen, fibrin are examples of Fibrous proteins,  COLLAGEN Collagen is the most abundant protein in the human body. A typical collagen molecule is a long, rigid structure in which three polypeptides (α-chains) are around one another in a rope- like triple helix.  Collagen and Elastin are examples of common, well- characterized fibrous proteins that serve structural functions in the body. They are found as components of skin, connective tissue, blood vessel walls, sclera and cornea of the eye. Each fibrous protein exhibits special mechanical properties, resulting from its unique structure, which are obtained by combining specific amino acids into regular, secondary structure elements.  Although these molecules are found throughout the body, their types and organization are dictated by the structural role collagen plays in a particular organ: ❖ In some tissues, collagen may be dispersed as a gel that gives support to the structure, as in the vitreous humor of the eye. ❖ In other tissues, collagen may be bundled in tight, parallel fibers that provide great strength, as in tendons. ❖ Collagen of bone occurs as fibers arranged at an angle to each other so as to resist mechanical shear from any direction.  Types of Collagen The super family of proteins includes more than 25 collagen types. 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 the same size (approximately 1,000 amino acids long), but with slightly different properties. These α-chains are combined to form various types of collagen.  Structure of Collagen I- Amino acid sequence: Collagen is rich in Proline and Glycine, both of which are important in the formation of the triple-helix (its ring structure, the smallest amino acid, respectively). – The Glycine residues are part of the repeating sequence, (-Gly-X-Y-), where X is frequently Proline and Y is often Hydroxyproline (Hyp) or Hydroxylysine (Hyl). – Thus, the α-chain can be regarded as a polypeptide whose sequence can be represented as (-Gly-X-Y-)333.  II- Triple-helical structure: Collagen has an elongated, triple-helical structure that places many of its amino acid side chains on the surface of the molecule. III- Hydroxyproline (Hyp) & Hydroxylysine (Hyl): Collagen contains Hyp and Hyl, which result from the hydroxylation of some of the Proline and Lysine residues after their incorporation into polypeptide chains. Hyp is important in stabilizing the triple-helical structure of collagen because it maximizes inter-chain hydrogen bond formation.  IV- Glycosylation: The hydroxyl group of Hyl residues of collagen may be enzymatically glycosylated. Most commonly, glucose and galactose are sequentially attached to the polypeptide chain prior to triple-helix formation.  Scurvy disease Scurvy is a disease caused by a dietary deficiency of ascorbic acid (vitamin C) Deficiency of vitamin C prevents proline hydroxylation. The defective pro-α chains fail to form a stable triple helix and are immediately degraded within the cell. Blood vessels become extremely fragile, and teeth become loose in their sockets.  Collagen diseases: image095 1-Ehlers-Danlos syndrome (EDS) or Marfan҆ s: This disorder is a heterogeneous group of generalized connective tissue disorders that result from inheritable defects in the metabolism of fibrillar collagen molecules. EDS can result from a deficiency of collagen-processing untitled1wk3 enzymes (for example, lysyl hydroxylase or procollagen peptidase), or from mutations in the amino acid sequences of collagen types I, III, or V. Because collagen type III is an important component of the arteries, potentially lethal vascular problems occur. The most clinically important mutations are found in the gene for type III 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.  Collagen diseases: Marfan%2520(9) 2- Osteogenesis imperfecta - Most patients with severe disease have mutations in the gene for type 1 collagen. - The structurally abnormal chains prevent folding of the protein into a triple- helical conformation  Structure of Elastin Elastin is an insoluble protein polymer which is a linear polypeptide, composed of about – 700 amino acids, that are primarily small & nonpolar – Rich in proline & lysine – Contains only a little hydroxyproline, & no hydroxylysine – In contrast to collagen, elastin is a connective tissue protein with rubber-like properties. – Elastin fibers composed of elastin and glycoprotein microfibrils – Found in the lungs, and large arteries walls. They can be stretched to several times their normal length, but recoil to their original shape when the stretching force is relaxed. Globular proteins vs Fibrous proteins 1. Compact protein structure Extended protein structure 2. Soluble in water (or in lipid Insoluble in water (or in lipid bilayers) bilayers) 3. Secondary structure is а complex Secondary structure is simple with a mixture of a-helix, b-sheet with predominant one type only and loop structures 4. Quaternary structure is held Quaternary structure is usually together by noncovalent forces held together by covalent bridges 5. Functions in all aspects of Structural function metabolism (enzymes, transport, (tendons, bones, muscle, immune protection, hormones, etc). ligaments, hair, skin)