...altering/introducing a specific property 2 Course Outline Unit 1 – Introduction (9 hrs) Unit 2 – Protein Sequences and Properties (9 hrs) Unit 3 – Conformation of Proteins (9 hrs) Unit 4 – Principles and Approach (9 hrs) Unit 5 – Probing Structure for Molecular Recognition (9 hrs) 3 Unit 1 Introduction (9 hrs) Amino acid structure and properties Detection of the size of proteins Covalent structures in proteins Overview of chemical and biosynthesis of proteins Topogenesis Post-translational covalent modification of polypeptide chains 4 Amino Acids Amino acids are molecules containing an amine group, a carboxylic acid group, and a side-chain that is specific to each amino acid The amino group is attached to the carbon atom immediately adjacent to the carboxylate group (the α– carbon ) In some amino acids, the amino group is attached to a different carbon atom; for example, in gamma-amino acids (such as gamma-amino-butyric acid) the carbon atom to which the amino group attaches is separated from the carboxylate group by two other carbon atoms The various alpha-amino acids differ in their side-chains (Rgroup) that is attached to their alpha carbon,...
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...Alanine It is one of the most significant among the 20 common amino acids. It offers energy to your system. It releases into the blood stream during exercise time and induces carbohydrate-consuming effect to the health system. It promotes enhancement in the area of protein synthesis and nitrogen balance. Arginine Synthesized normally in the body, arginine is known to be a semi-essential amino acid. Sometimes more is required than normal production. Deficiencies may include poor wound healing, weakness in muscles, hair loss, irritations in skin, and constipation. Asparagine It is one of the 20 common amino acids. It is needed to maintain homeostatic balance in the nervous system. Amino acid transformation and ammonia synthesis are largely dependent on asparagine. Aspartic Acid Aspartic acid is one of two acidic amino acids belonging to the group of 20 common amino acids. It promotes enzyme activity, maintenance of solubility in the body, as well as homeostasis in ionic characters of proteins. Cysteine It is present only at the rate of 2.8% into proteins but it provides the 3-dimensional stability of the protein molecule. It also plays a crucial role in the metabolic process of many important enzymes. Glutamic Acid It is one of the important amino acid among all 20 common amino acids. It is responsible for transportation of glutamate and other amino acids to the blood barrier. Glutamine Glutamine is able to eliminate excess ammonia...
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...Amino acids Abstract Amino acids have a variety of chemically reactive groups. Protein, one of the essential constituents and is considered the most abundant organic molecules present in each cell, is comprised of polymers of amino acids. Casein, a globular protein found in milk in the form of Calcium caseinate, is isolated at its isoelectric pH of 4.6 through the process known as isoelectric precipitation. The isolated protein is separated into two, one of which remains the same, while the other is hydrolyzed using 4M NaOH in a hard glass test tube. To successfully characterize the isolated and confirmed that the isolated protein was casein. Introduction Amino acids have several reactive sides, and the reactions occurring for side chains, α-carboxyl, and α-amino groups are used to characterize the amino acid components and the protein itself. Proteins are organic compounds made of amino acids joined together by peptide linkages. These polymers of amino acids play an important role in all biochemical and physiological body processes; they act as hormones, receptors, enzymes, antibodies, and are considered a prerequisite for the structural integrity of the cells. Casein is a globular protein found in milk in the form of calcium salt, calcium caseinate, and has an isoelectric pH of 4.6. Color reactions were done to both intact and base hydrolyzed casein to qualitatively assess its characteristics as a protein. The following tests were done: * Biuret...
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...Amino Acids Amino acids are the building blocks of proteins. They band together in chains to form the stuff from which life is born. This is a two-step process: first, they get together and form peptides or polypeptides, and it is from these groupings that proteins are made. A total of 20 different kinds of amino acids form proteins, with the types involved determining the shape of the proteins formed. Commonly recognized ones include glutamine, glycine, phenylalanine, tryptophan, and valine. Three of those — phenylalanine, tryptophan, and valine — are essential amino acids for humans; the others are isoleucine, leucine, lysine,methionine, and threonine. This type cannot be synthesized by the body, so they must be ingested through food. One of the best-known essential amino acids is tryptophan, which performs several critical functions for people. It helps induce normal sleep; helps reduce anxiety, depression, and artery spasm risk; and helps produce a stronger immune system. Tryptophan is perhaps most well-known for its role in producing serotonin, which is what gets all the press at Thanksgiving time for putting people to sleep after the big holiday feast. Amino acids make up 75% of the human body. They are essential to nearly every bodily function, and every chemical reaction that takes place in the body depends on them and the proteins that they build. The essential amino acids must be ingested every day. Failure to get enough of even one of them can result in...
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...Identification of Unknown Amino Acid Elizabeth Amundson Lab Partner: Mary Witucki Introduction: The goal of this lab was to determine which two amino acids where contained within an unknown mixture by comparing the results of a primary amine test, an amide test, a benzene ring test, a thiol test, and paper chromatography to that of amino acids with known compositions. I hypothesize that alanine and lysine will test positive for primary amines because they are the only amino acids being tested in this reaction that contain a primary amine (-NH2). I hypothesize that glutamine will test positive for amides because it is the only amino acid being tested in this reaction that has an amide, or (R1-N-R2). I hypothesize that tryptophan will test positive for benzene rings because it is the only amino acid being tested that contains a benzene ring. I hypothesize that cysteine will test positive for thiols because it is the only amino acid being tested with a thiol, or (R-S-H). I also hypothesize that the hydrophilic amino acids will have smaller Rf values than the hydrophobic amino acids because the chromatography paper is more hydrophilic than the solvent being used, so they will have a higher affinity for the paper and will not travel very far with the solvent. It is important to be able to identify unknown amino acids so that it can be determined which amino acids are found in cells and proteins. Methods: Paper Chromatography 1. Pick either unknown A, B, or C. ...
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...Amino Acids and Athletics Ana-Merrie Selves SCI 241 Science of Nutrition December 10, 2010 Glenn Johnson Many athletes mistakenly believe that consuming protein will augment performance, and some even believe consuming additional of particular amino acids will further the effect of building muscle as well as amplify performance. However, research cannot support these beliefs, and specifically the intake of certain amino acid supplements has no connection to fitness. In fact, a paper by the American Dietetic Association stated an inordinate amount has not shown to improve performance (Stockton, 1988). The amount of protein optimal is arguable when talking to nutritionists and athletic doctors. The amount of protein recommended for adults is approximately two ounces a day for a 180-pound male, although research suggests young athletes may break down muscle protein for energy. A 1987 paper by the dietary association admitted the recommended daily amount could be low for exceedingly active adults, increasing the proposed daily amount be increased by nearly 25% (Stockton, 1988). North Americans are noted to eat double the protein necessary, whether active in sports or not, and essentially people are unlikely to consume too little protein. Consuming more protein previously was thought to achieve nothing, but also not harmful; simply expelling the excess (Stockton, 1988). Evidence now indicates that excessive protein or amino acid supplements may be damaging; kidney and digestion...
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...It is important to have amino acids and proteins in your body with any diet. Essential amino acids are those supplied by the diet, since the human body either cannot make them at all or cannot make them in sufficient quantity to meet its needs.Because your body needs amino acids for healthy nerve and brain functions and also for remolding muscles and bone tissues to function properly. If you don’t get enough amino acids it will result in degradation of the body’s proteins your body will pull it from your muscles and so on. Your body also does not store any amino acids for excess uses later; you must get it from foods. You will not get any amino acids from carbohydrates because they are mainly made of sugars and starches not protein which make amino acids. All amino acids have a similar chemical structure—each contains an amino group, an acid group, a hydrogen atom, and a distinctive side group that makes proteins more complex than carbohydrates The reason we need to have proteins in our diets is to give our body’s energy and also help our bodies grow. It also helps regulate the balancing of water and nutrients in our body. Proteins are what makes amino acids for our body and help it function and to keep everything healthy. Proteins maintain fluid balance and acid and base balance. They also transport substances such as oxygen, vitamins, and minerals to target cells throughout the body. Carbohydrates give your body energy also but when the body does not need that energy...
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...The popularity of increasing the “performance-enhancing” supplements, Protein and amino acids, has flourished among all athletes. This increase is attributed to the belief by many of the athletes that it provides endurance, strength and speed enhancement. Amino Acids (AA) enhanced physical feats, improved energy and recovery sooner from fatigue. The three vital Amino Acids which were given a high focal point among athletes are leucine, isoleucine, and valine referred to as BCAA’s or branched-chain amino acids, which are generally given as a supplement to athletes. Those same BCAA’s are essential amino acids that can be employed in skeletal muscles as a source of energy (Nemet & Eliakim, 2007). It was shown in studies, while exercising, there was a larger breaking down of proteins to meet the increasing energy needs of the skeletal muscles. With long-lasting exercise the BCAA’s in the blood decline promoting tryptophan’s uptake across the blood-brain barrier which could increase serotonin formation. This might cause a sedated feeling in the brain, which would cause fatigue in the athlete. It was also suggested that Amino Acids supplements would increase the athlete’s stamina as the breakdown of the proteins and BCAA’s decline during exercise are slowed down (Nemet & Eliakim, 2007). The AA supplementation was found to improve recovery. Forms of muscle damage have been caused by exercise which indicators include increases in creatine kinase (CK) and Lactate Dehydrogenase...
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...According to Henderson-Hasselbach equation, if pH of a solution is less than pKa, then the amino acid consists of primarily of next most protenated form, where as when the pH of the solution is greater than the pKa, then the amino acids consists of primarily of next most deprotenated form. If the pH of the solution equals that of a pKa, then the amino acid consists of 50% of next most protenated and 50% of next most deprotenated form. The ionization of the amino acid wholly depends on the pH of the solution that they are dissolved in. Suppose the pH of solution was low (pH=1.0), then the amino acid is completely protenated and it has obtained a cationic form. As the pH increases, the carboxylic acid group ionizes first. When the pH equals pKa, the amino acids exist as a combination of protenated and the next most deprotenated form. This trend continues until all of the ionizable groups has been deprotenated. As the pH increases further, the amino group will lose a proton and ultimately, at a high pH (pH=12.0), the anionic form is the predominant form in solution. In certain amino acids, the R group ionizes depending on their polarity and the pKa value. In most cases, R group ionizes second after carboxyl group performs its complete ionization. In this experiment, a titration was performed for glycine and...
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...Amino Acids and How They Relate to Athletics SCI/241~Nutrition July 8, 2010 Amino acids serve in many different ways in an athlete body. Typically amino acids were prescribed many years ago known as a “branched-chain amino acids (BCAA)” (Weider, 2003), characterized as supplement for body building. Muscles are generally made up of amino acids, athletes are encouraged to supplement with the loss. Another characteristic of BCAA is to generate energy. Amino acids taken before a workout will strengthen the athlete muscles. The intake of protein is encouraged before a workout also. Boost in the brain of an athlete mental capacity is consumed with the amino acids before a work out. However, an athlete must mentally stable their mind to do a tedious workout. Your immune system must functions at a healthy status at all times, in order to be an athlete. This is why amino acids help promote the building of a strong immune system. Sometimes the lack of a nutrient in the body can have an effect on the brain. Taking precautions is recommended to insure that supplemental intake of BCAA may not cause any problems to the brain; one should consult a physician before taking BCAA. Source: Rowley, Brian. “The ABCs if BCAAs: what every bodybuilder must know about these three powerful aminos. (Nutrition).” Joe Weider’s Muscle & Fitness June 2003:166+. General OneFile . Web. 8 July 2010....
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...biological reactions | ß-galactosidase | Transport and Storage | Hemoglobin | Movement | Actin And Myosin in muscles | Immune Protection | Immunoglobulins (antibodies) | Regulatory Function within cells | Transeription Factors | Hormones | Insulin Estrogen | Structural | Collagen | How does one group of molecules perform such a diverse set of functions? The answer is found in the wide variety of possible structures for proteins. In the English language, there are an enormous number of words with varied meaning that can be formed using only 26 letters as building blocks. A similar situation exists for proteins where an incredible variety of proteins can be formed using 20 different building blocks called amino acids. Each of these amino acid building blocks has a different chemical structure and different properties (Figure...
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...intact protein in wheat flour which is Gluten through hydrolysis and chromatography. Gluten was isolated then hydrolyzed by proteolytic enzyme and was subjected to different qualitative tests. Paper Chromatography was also performed to analyze the different amino acid components of gluten. Tests showed that Gluten has several amino acid components. INTRODUCTION Proteins are a class of organic compounds which are present in and vital to every living cell. In the form of skin, hair, callus, cartilage, muscles, tendons and ligaments, proteins hold together, protect, and provide structure to the body of a multi-celled organism. In the form of enzymes, hormones, antibodies, and globulins, they catalyze, regulate, and protect the body chemistry. In the form of hemoglobin, myoglobin and various lipoproteins, they affect the transport of oxygen and other substances within an organism. It is also known as polypeptides, are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer are joined together by covalent bonds called peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The physical and chemical properties unique to each amino acid are the result...
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...Bovine Spongiform Encephalopathy: A look at the molecular level COMPETENCY 208.5.2: AMINO ACIDS AND PEPTIDE BONDS, PROTEIN STRUCTURE BY: MELANIE MANGER Bovine Spongiform Encephalopathy Commonly know as Mad Cow Disease Although the United States has strict standards when it comes to food, BSE is absolutely an international issue A cow will ingest a food (usually a protein) that is contaminated, we as humans then in turn become infected when we eat food products made up from that particular cow Prions are an infectious agent that cause a protein in the body to fold abnormally form. Those proteins then replicate within the body and lead to brain degeneration and ultimately will cause the death of the infected individual BSE: The Molecular Level DNA makes RNA RNA makes amino acids chains of amino acids make proteins Amino acids have an amine group on one end and a carboxyl group on the other, with a Hydrogen and an R group (1 of 20 amino acids) attached to the Carbon. The amine (or amino) end of the peptide chain is known as the N-terminal, and the end with the carboxyl group is the C-terminal. Amino Acids (March 31, 2013). Retrieved July 16, 2014 from http://biochemanics.wordpress.com/2013/03/31/amino-acids/ BSE: The Molecular Level Peptide bonds are what link 2 amino acids together at the carboxyl group of one and the amine group of another Peptide bonds are created through dehydration synthesis and broken down through a process known as hydrolysis...
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...asddsaProteins (/ˈproʊˌtiːnz/ or /ˈproʊti.ɨnz/) are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within living organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine and—in certain archaea—pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by posttranslational modification, which alters the physical and chemical properties, folding, stability, activity...
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...The Nonsynonymous/Synonymous Substitution Rate Ratio versus the Radical/ Conservative Replacement Rate Ratio in the Evolution of Mammalian Genes Kousuke Hanada,* Shin-Han Shiu, and Wen-Hsiung Li* *Department of Ecology and Evolution, University of Chicago; and Department of Plant Biology, Michigan State University There are 2 ways to infer selection pressures in the evolution of protein-coding genes, the nonsynonymous and synonymous substitution rate ratio (KA/KS) and the radical and conservative amino acid replacement rate ratio (KR/KC). Because the KR/KC ratio depends on the definition of radical and conservative changes in the classification of amino acids, we develop an amino acid classification that maximizes the correlation between KA/KS and KR/KC. An analysis of 3,375 orthologous gene groups among 5 mammalian species shows that our classification gives a significantly higher correlation coefficient between the 2 ratios than those of existing classifications. However, there are many orthologous gene groups with a low KA/KS but a high KR/KC ratio. Examining the functions of these genes, we found an overrepresentation of functional categories related to development. To determine if the overrepresentation is stage specific, we examined the expression patterns of these genes at different developmental stages of the mouse. Interestingly, these genes are highly expressed in the early middle stage of development (blastocyst to amnion). It is commonly thought that developmental genes...
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