Cell and Protein Structure (MGD) PDF

3/2/2024 1 Molecules, Genes, and Disease (MGD) Cell and Protein structure Dr. Ahmed Edan...

3/2/2024 1 Molecules, Genes, and Disease (MGD) Cell and Protein structure Dr. Ahmed Edan Assoc. Professor Wasit University March 4th, 2024 The living matter is composed of mainly carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur. These elements together constitute about 90% of the dry weight of the human body. Several other functionally important elements are also found in the cells. These include Ca, K, Na, Cl, Mg, Fe, Cu, Co, I, Zn, F, Mo, and Se. MGD/ Spring 2024/ AD 2 1  3/2/2024 Chemical composition of the human body: The chemical composition of a normal man, weighing 65 kg. Water is the solvent of life and contributes to more than 60% of the weight. This is followed by protein mostly in muscle) and lipid (mostly in adipose tissue). The carbohydrate content is rather low which is in the form of glycogen. 3 Major Classes of Compounds in the Human Body Water: Water is the most abundant chemical compound in living human cells, accounting for 65. percent to 90 percent of each cell. It's also present between cells. For example, blood and cerebrospinal fluid are mostly water. Fat: The percentage of fat varies from person to person, but even an obese person has more water than fat. Protein: In a lean male, the percentages of protein and water are comparable. It's about 16 percent by mass. Muscles, including the heart, contain a lot of muscle. Hair and fingernails are protein. Skin contains a large amount of protein, too. Minerals: Minerals account for about 6 percent of the body. They include salts and metals. Common minerals include sodium, chlorine, calcium, potassium, and iron. Carbohydrates: Although humans use sugar glucose as an energy source, there isn't that much of it free in the bloodstream at any given time. Sugar and other carbohydrates only account for about 1% of body mass. MGD/ Spring 2024/ AD 4 2  3/2/2024 Carbon: a unique element of life Carbon is the most predominant and versatile element of life. It possesses a unique property to form infinite number of compounds. This is attributed to the ability of carbon to form stable covalent bonds and C-C chains of unlimited length. It is estimated that about 90% of compounds found in living system invariably contain carbon 5 Most of the elements are found within compounds. Water and minerals are inorganic compounds. Organic compounds include fat, protein, carbohydrates, and nucleic acids. MGD/ Spring 2024/ AD 6 https://quizlet.com/221919890/unit-3-cell-structure-diagram/ 3  3/2/2024 Proteins Proteins are the most versatile macromolecules in living systems and serve crucial functions in essentially all biological processes. They function as catalysts, transport and store other molecules such as oxygen, provide mechanical support and immune protection, generate movement, transmit nerve impulses, and control growth and differentiation. Origin of the word ‘protein’ The term protein is derived from a Greek word proteios, meaning holding the first place. Berzelius (Swedish chemist) suggested the name proteins to the group of organic compounds that are the most important to life. Mulder (Dutch chemist) in 1838 used the term proteins for the high molecular weight nitrogen-rich and most abundant substances present in animals and plants. MGD/ Spring 2024/ AD 7 Functions of proteins Proteins perform a great variety of specialized and essential functions in living cells. These functions may be broadly grouped as static (structural) and dynamic Structural functions: Certain proteins perform brick-and-mortar roles and are primarily responsible for the structure and strength of the body. These include collagen and elastin found in bone matrix, vascular system, and other organs and ɑ-keratin present in epidermal tissues. Dynamic functions: The dynamic functions of proteins are more diversified in nature. These include proteins acting as enzymes, hormones, blood clotting factors, immunoglobulins, membrane receptors, and storage proteins, besides their function in genetic control, muscle contraction, respiration etc. Proteins performing dynamic functions are appropriately regarded as the working horses of a cell. 8 4  3/2/2024 Besides the above, proteins may also contain other elements such as P Fe, Cu I Mg, Mn Zn etc. MGD/ Spring 2024/ AD 9 Proteins are polymers of amino acids Proteins on complete hydrolysis (with concentrated HCl form several hours) yield L-ɑ- amino acids. This is a common property of all the proteins. Therefore, proteins are the polymers of L-ɑ-amino acids. Standard amino acids As many as 300 amino acids occur in nature— Of these, only 20—known as standard amino acids are repeatedly found in the structure of proteins, isolated from different forms of life (animal, plant and microbial). This is because of the universal nature of the genetic code available for the incorporation of only 20 amino acids when the proteins are synthesized in the cells. The process in turn is controlled by DNA, the genetic material of the cell. After the synthesis of proteins, some of the incorporated amino acids undergo modifications to form their derivatives. 10 5  3/2/2024 Central Dogma It is the process by which the instructions in DNA are converted into a functional product. It was first proposed in 1958 by Francis Crick, discoverer of the structure of DNA The central dogma of molecular biology explains the flow of genetic information, from DNA to RNA, to make a functional product, a protein. The central dogma suggests that DNA contains the information needed to make all of our proteins, and that RNA is a messenger that carries this information to the ribosomes The central dogma states that the pattern of information that occurs most frequently in our cells is:  From existing DNA to make new DNA (DNA replication)  From DNA to make new RNA (transcription)  From RNA to make new proteins (translation). https://www.yourgenome.org/ 11 Amino acids Amino acids are a group of organic compounds containing two functional groups— amino and carboxyl. The amino group (—NH2) is basic while the carboxyl group (— COOH) is acidic in nature. General structure of amino acids The amino acids are termed as ɑ-amino acids, if both the carboxyl and amino groups are attached to the same carbon atom, as depicted below The ɑ-carbon atom binds to a side chain represented by R which is different for each of the 20 amino acids found in proteins. The amino acids mostly exist in the ionized form in the biological system MGD/ Spring 2024/ AD 12 6  3/2/2024 Amino acids 13 Optical isomers of amino acids If a carbon atom is attached to four different groups, it is asymmetric and therefore exhibits optical isomerism. The amino acids (except glycine) possess four distinct groups (R, H, COO–, NH3+) held by ɑ-carbon. Thus, all the amino acids (except glycine where R = H) have optical isomers. The structures of L- and D-amino acids are written based on the configuration of L- and D-glyceraldehyde as shown in Fig.4.1. The L (Levorotatory) ; D (dextrorotatory) proteins are composed of L-ɑ-amino acids. MGD/ Spring 2024/ AD 14 7  3/2/2024 What is the basis for the preference for L amino acids? The answer is not known, but evidence shows that L amino acids are slightly more soluble than is a racemic mixture of D and L amino acids, which tend to form crystals. This small solubility difference could have been amplified over time so that the L isomer became dominant in solution. Although there are many ways to classify amino acids, we will assort these molecules into four groups, on the basis of the general chemical characteristics of their R groups: 15 Amino acids Non- Polar polar No charge + charge - charge MGD/ Spring 2024/ AD 16 8  3/2/2024 Classification of amino acids based on polarity Amino acids are classified into 4 groups based on their polarity. Polarity is important for protein structure. 1. Non-polar amino acids : These amino acids are also referred to as hydrophobic (water hating). They have no charge on the ‘R’ group. The amino acids included in this group are ( alanine, leucine, isoleucine, valine, methionine, phenylalanine, tryptophan and proline). 2. Polar amino acids with no charge on ‘R’ group : These amino acids, as such, carry no charge on the ‘R’ group. They however possess groups such as hydroxyl, sulfhydryl and amide and participate in hydrogen bonding of protein structure. The simple amino acid glycine (where R = H) is also considered in this category. The amino acids in this group are (glycine, serine, threonine, cysteine, glutamine, asparagine and tyrosine). 3. Polar amino acids with positive ‘R’ group : The three amino acids lysine, arginine and histidine are included in this group. 4. Polar amino acids with negative ‘R’ group : The dicarboxylic monoamino acids— aspartic acid and glutamic acid are considered in this group 17 Nutritional classification of amino acids The 20 amino acids are required for the synthesis of variety proteins, besides other biological functions. However, all these 20 amino acids need not be taken in the diet. Based on the nutritional requirements, amino acids are grouped into two classes— essential and nonessential. 1. Essential or indispensable amino acids : The amino acids which cannot be synthesized by the body and, therefore, need to be supplied through the diet are called essential amino acids. They are required for proper growth and maintenance of the individual. The ten amino acids listed below are essential for humans (and also rats) : Arginine, Valine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan. [The code A.V. HILL, MP., T. T. (first letter of each amino acid) may be memorized to recall essential amino acids. 18 9  3/2/2024 Nutritional classification of amino acids Other useful codes are H. VITTAL, LMP; PH. VILLMA, TT; PVT TIM HALL and MATTVILPhLy. The two amino acids namely arginine and histidine can be synthesized by adults and not by growing children, hence these are considered as semi–essential amino acids (remember Ah, to recall). Thus, 8 amino acids are absolutely essential while 2 are semi-essential. 2. Non-essential or dispensable amino acids : The body can synthesize about 10 amino acids to meet the biological needs, hence they need not be consumed in the diet. These are—glycine, alanine, serine, cysteine, aspartate, asparagine, glutamate, glutamine, tyrosine and proline. 19 Physical properties of amino acids 1. Solubility : Most of the amino acids are usually soluble in water and insoluble in organic solvents. 2. Melting points : Amino acids generally melt at higher temperatures, often above 200°C. 3. Taste : Amino acids may be sweet (Gly, Ala, Val), tasteless (Leu) or bitter (Arg, Ile). Monosodium glutamate (MSG; Ajinomoto) is used as a flavoring agent in food industry, and Chinese foods to increase taste and flavor. In some individuals intolerant to MSG, Chinese restaurant syndrome (brief and reversible flulike symptoms) is observed. MGD/ Spring 2024/ AD 20 10  3/2/2024 Aspartame Aspartame is an artificial non-saccharide sweetener 200 times sweeter than sucrose and is commonly used as a sugar substitute in foods and beverages. It is a methyl ester of the aspartic acid/phenylalanine dipeptide with the trade names NutraSweet, Equal, and Canderel. At room temperature, Aspartame is most stable at pH 4.3, where its half-life is nearly 300 days. Aspartame has been deemed safe for human consumption by over 100 regulatory agencies in their respective countries, including the FDA. 21 Chemical properties of amino acids The general reactions of amino acids are mostly due to the presence of two functional groups namely carboxyl ( COOH) group and amino ( NH2) group 1- Decarboxylation : Amino acids undergo decarboxylation to produce corresponding amines. This reaction assumes significance in the living cells due to the formation of many biologically important amines. For example, histamine forms form histidine 2- Reaction with ammonia : The carboxyl group of dicarboxylic amino acids reacts with NH3 to form amide MGD/ Spring 2024/ AD 22 11  3/2/2024 Amino acids as ampholytes : Amino acids contain both acidic ( COOH) and basic ( NH2) groups. They can donate a proton or accept a proton; hence amino acids are regarded as ampholytes. Zwitterion or dipolar ion : The name zwitter is derived from the German word which means hybrid. Zwitter ion (or dipolar ion) is a hybrid molecule containing positive and negative ionic groups. The amino acids rarely exist in a neutral form with free carboxylic ( COOH) and free amino ( NH2) groups. In strongly acidic pH (low pH), the amino acid is positively charged (cation) while in strongly alkaline pH (high pH), it is negatively charged (anion). Each amino acid has a characteristic pH (e.g. leucine, pH 6.0) at which it carries both positive and negative charges and exists as zwitterion Isoelectric point (symbol pI) is defined as the pH at which a molecule exists as a zwitterion or dipolar ion and carries no net charge. Thus, the molecule is electrically neutral. Berg, 7th ed. And Saty.&Chak, 4th ed. Isoelectric point (pI) The titration curve for alanine in the following figure demonstrates this relationship. At a pH lower than 2, both the carboxylate and amine functions are protonated, so the alanine molecule has a net positive charge. At a pH greater than 10, the amine exists as a neutral base and the carboxyl as its conjugate base, so the alanine molecule has a net negative charge. At intermediate pH's the zwitterion concentration increases, and at a characteristic pH, called the isoelectric point (pI). The negatively and positively charged molecular species are present in equal concentrations. This behavior is general for simple (difunctional) amino acids. Starting from a fully protonated state, the pKa's of the acidic functions range from 1.8 to 2.4 for -CO2H, and 8.8 to 9.7 for -NH3(+). The isoelectric points range from 5.5 to 6.2. Titration curves show the neutralization of these acids by added base, and the change in pH during the titration. MGD/ Spring 2024/ AD Berg, 7th ed. And Saty.&Chak, 4th ed. 12  3/2/2024 Berg, 7th ed. And Saty.&Chak, 4th ed. The pI is given by the average of the pKas that involve the zwitterion, i.e. that give the boundaries to its existence. There are 3 cases to consider.... 1-Neutral side chains These amino acids are characterized by two pKas : pKa1 and pKa2 for the carboxylic acid and the amine respectively. The isoelectronic point will be halfway between, or the average of, these two pKas, i.e. pI = 1/2 (pKa1 + pKa2). This is most readily appreciated when you realise that at very acidic pH (below pKa1) the amino acid will have an overall +ve charge and at very basic pH (above pKa2 ) the amino acid will have an overall -ve charge. For the simplest amino acid, glycine, pKa1= 2.34 and pKa2 = 9.6, pI = 5.97. Berg, 7th ed. And Saty.&Chak, 4th ed. 13  3/2/2024 2-Acidic side chains The pI will be at a lower pH because the acidic side chain introduces an "extra" negative charge. So the neutral form exists under more acidic conditions when the extra -ve has been neutralised. For example, for aspartic acid shown below, the neutral form is dominant between pH 1.88 and 3.65, pI is halfway between these two values, i.e. pI = 1/2 (pKa1 + pKa3), so pI = 2.77. https://www.chem.ucalgary.ca/courses/351/Carey5th/Ch27/ch27-1-4.html 3-basic side chains The pI will be at a higher pH because the basic side chain introduces an "extra" positive charge. So the neutral form exists under more basic conditions when the extra +ve has been neutralized. For example, for histidine, which was discussed on the previous page, the neutral form is dominant between pH 6.00 and 9.17, pI is halfway between these two values, i.e. pI = 1/2 (pKa2 + pKa3), so pI = 7.59. Arg pKa1=2.17 pKa2=9.04 pKa3=12.48 MGD/ Spring 2024/ AD 14  3/2/2024 The distribution of charged species in a sample can be shown experimentally by observing the movement of solute molecules in an electric field, using the technique of electrophoresis (Figure). For such experiments an ionic buffer solution is incorporated in a solid matrix layer, composed of paper or a crosslinked gelatin-like substance. A small amount of the amino acid, peptide or protein sample is placed near the center of the matrix strip and an electric potential is applied at the ends of the strip, as shown in the following diagram. The solid structure of the matrix retards the diffusion of the solute molecules, which will remain where they are inserted, unless acted upon by the electrostatic potential. 15  3/2/2024 The amino acids are held together in a protein by covalent Peptide bond peptide bonds or linkages. These bonds are rather strong and serve as the cementing material between the individual amino acids (considered as bricks). Formation of a peptide bond : When the amino group of an amino acid combines with the carboxyl group of another amino acid, a peptide bond is formed (Fig.4.5). Note that a dipeptide will have two amino acids and one peptide (not two) bond. Peptides containing more than 10 amino acids (decapeptide) are referred to as polypeptides. Characteristics of peptide bonds : The peptide bond is rigid. It generally exists in trans configuration. Both -C= O and -NH groups of peptide bonds are polar and are involved in hydrogen bond formation. Berg, 7th ed. And Saty.&Chak, 4th ed. Writing of peptide structures : Conventionally, the peptide chains are written with the free amino end (N-terminal residue) at the left, and the free carboxyl end (C-terminal residue) at the right. The amino acid sequence is read from the N-terminal end to the C-terminal end. Incidentally, the protein biosynthesis also starts from the N-terminal amino acid. Shorthand to read peptides : The amino acids in a peptide or protein are represented by the 3-letter or one letter abbreviation. This is the chemical shorthand to write proteins. Naming of peptides : For naming peptides, the amino acid suffixes -ine (glycine), -an (tryptophan), -ate (glutamate) are changed to -yl with the exception of C-terminal amino acid. Thus a tripeptide composed of an N terminal glutamate, a cysteine and a C-terminal glycine is called glutamyl-cysteinyl-glycine Berg, 7th ed. And Saty.&Chak, 4th ed. 16  3/2/2024 Protein structrue MGD/ Spring 2024/ AD Berg, 7th ed. And Saty.&Chak, 4th ed. SECONDARY STRUCTURE OF PROTEIN The conformation of polypeptide chain by twisting or folding is referred to as secondary structure. The amino acids are located close to each other in their sequence. Two types of secondary structures, ɑ-helix and β-sheet, are mainly identified. ɑ-Helix is the most common spiral structure of protein. It has a rigid arrangement of polypeptide chain. D-Helical structure was proposed by Pauling and Corey (1951) which is regarded as one of the milestones in the biochemistry research. The salient features of ɑ-helix (Fig.4.9) are given Berg, 7th ed. And Saty.&Chak, 4th ed. 17  3/2/2024 1. The ɑ-helix is a tightly packed coiled structure with amino acid side chains extending outward from the central axis. 2. The ɑ-helix is stabilized by extensive hydrogen bonding. It is formed between H atom attached to peptide N, and O atom attached to peptide C. The hydrogen bonds are individually weak but collectively, they are strong enough to stabilize the helix. 3. All the peptide bonds, except the first and last in a polypeptide chain, participate in hydrogen bonding. 4. Each turn of ɑ-helix contains 3.6 amino acids and travels a distance of 0.54 nm. The spacing of each amino acid is 0.15 nm. 5. ɑ-Helix is a stable conformation formed spontaneously with the lowest energy. 6. The right handed ɑ-helix is more stable than left handed helix (a right handed helix turns in the direction that the fingers of right hand curl when its thumb points in the direction the helix rises). Berg, 7th ed. And Saty.&Chak, 4th ed. β -sheet β sheets are composed of two or more segments of fully extended peptide chains (Fig.4.10). In the β -sheets, the hydrogen bonds are formed between the neighboring segments of polypeptide chain(s). Parallel and anti-parallel β -sheets The polypeptide chains in the β-sheets may be arranged either in parallel (the same direction) or anti-parallel (opposite direction). This is illustrated in Fig.4.10. β sheet may be formed either by separate polypeptide chains (H-bonds are interchain) or a single polypeptide chain folding back on to itself (H-bonds are intrachain). MGD/ Spring 2024/ AD Berg, 7th ed. And Saty.&Chak, 4th ed. 18  3/2/2024 TERTIARY STRUCTURE OF PROTEIN The three-dimensional arrangement of protein structure is referred to as tertiary structure. It is a compact structure with hydrophobic side chains held interior while the hydrophilic groups are on the surface of the protein molecule. This type of arrangement ensures stability of the molecule. Bonds of tertiary structure : Besides the hydrogen bonds, Three-dimensional structure of myoglobin. (A) A ribbon diagram shows that the protein consists disulfide bonds ( S-S), ionic interactions (electrostatic largely of a helices. (B) A space-filling model in the same orientation shows how tightly packed the bonds), hydrophobic interactions and van der Waals forces folded protein is. Notice that the heme group is also contribute to the tertiary structure of proteins. nestled into a crevice in the compact protein with only an edge exposed. One helix is blue to allow Domains : The term domain is used to represent the basic comparison of the two structural depictions. [Drawn from 1A6N.pdb.] units of protein structure (tertiary) and function. Berg, 7th ed. And Saty.&Chak, 4th ed. QUATERNARY STRUCTURE OF PROTEIN A great majority of the proteins are composed of single polypeptide chains. Some of the proteins, however, consist of two or more polypeptides which may be identical or unrelated. Such proteins are termed oligomers and possess quaternary structures. The individual polypeptide chains are known as monomers or subunits. A dimer consists of two polypeptides while a tetramer has four. Bonds in quaternary structure : The monomeric subunits are held Quaternary structure. The Cro protein of together by nonconvalent bonds namely hydrogen bonds, bacteriophage l is a dimer of identical subunits. [Drawn from hydrophobic interactions and ionic bonds. 5CRO.pdb.] Importance of oligomeric proteins : These proteins play a significant role in the regulation of metabolism and cellular function (e.g. Hemoglobin and lactate dehydrogenase.) Berg, 7th ed. And Saty.&Chak, 4th ed. 19