Proteins

10 Key excerpts on "Proteins"

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  eBook - PDF

  Methods in Molecular Biophysics

  Structure, Dynamics, Function

  • Igor N. Serdyuk, Nathan R. Zaccai, Joseph Zaccai(Authors)
  • 2007(Publication Date)
  • Cambridge University Press

    (Publisher)

   Biological macromolecules, although they are made up of a concatenation of subunits, have evolved to fulfil specific functions and have specific properties that are very dif- ferent from those of classical polymers.  All the molecules in a living organism either are Proteins or can be considered as products of protein action.  Proteins are made up of properly folded polypeptides of amino acid residues, and may include prosthetic groups with specific properties (such as the haem group, which binds oxygen). 62 A Biological macromolecules and physical tools  Colour in Proteins (e.g. the red in haemoglobin, or green in chlorophyll binding Proteins) is always due to a prosthetic group, because amino acids absorb in the UV region.  There are 20 main amino acids in natural Proteins, with a variety of chemical characteristics: acid and base, polar and non-polar, aliphatic and aromatic.  Primary structure is the subunit sequence in the macromolecule; secondary structures are favoured local chain conformations arising from chemical and steric constraints; tertiary structure is the three-dimensional conformation of the macromolecular chain (given by the coordinates of the constituent atoms); quaternary structure is the organi- sation of different or similar chains in a macromolecular complex.  The secondary structures of Proteins can be expressed on a Ramachandran plot in terms of angles of rotation of the peptide planes in the chain around the so-called alpha-carbons, to which the amino acid side-chains are bound.  α-helices and β -sheets are the main secondary structures found in Proteins.  The tertiary structure results from weak (non-covalent, except for the disulphide bond between two cysteines) interactions between the amino acids in the polypeptide chain.  Protein domains with distinct features have been identified in the solved tertiary struc- tures.

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  Introduction to Organic Chemistry

  • William H. Brown, Thomas Poon(Authors)
  • 2016(Publication Date)
  • Wiley

    (Publisher)

  595 WE BEGIN THIS CHAPTER with a study of amino acids, the building blocks of the biological macromolecules known as Proteins, and compounds whose chemistry is built on two familiar classes of compounds, the amines (Chapter 10) and carboxylic acids (Chapter 13). We will learn that the physical and acid–base properties of amino acids are crucial in deter- mining the structures of Proteins, which in turn determine their many functions in living organisms. 18.1 What Are the Many Functions of Proteins? Proteins are among the most important of all biological compounds. Among the functions performed by these vital molecules are the following: ● Structure —Structural Proteins such as collagen and keratin are the chief constituents of skin, bones, hair, and nails. ● Catalysis —Virtually all reactions that take place in living systems are catalyzed by a spe- cial group of Proteins called enzymes. Without enzymes, these many reactions would take place so slowly as to be useless. 18 Amino Acids and Proteins K E Y Q U E S T I O N S 18.1 What Are the Many Functions of Proteins? 18.2 What Are Amino Acids? 18.3 What Are the Acid–Base Properties of Amino Acids? 18.4 What Are Polypeptides and Proteins? 18.5 What Is the Primary Structure of a Polypeptide or Protein? 18.6 What Are the Three‐Dimensional Shapes of Polypeptides and Proteins? H O W TO 18.1 Approximate the Charge of an Amino Acid at Any Given pH C H E M I C A L C O N N E C T I O N S 18A Spider Silk: A Chemical and Engineering Wonder of Nature 18 © gabrielaschaufelberger/iStockphoto Spider silk is a fibrous protein that exhibits unmatched strength and toughness. Inset: Models of D‐alanine and glycine, the major components of the fibrous protein of silk. 596 C H A P T E R 1 8 Amino Acids and Proteins ● Movement —Muscle expansion and contraction are involved in every movement we make. Muscle fibers are made of Proteins called myosin and actin. ● Transport —A large number of Proteins perform transport duties.

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  Waves in Biomechanics

  THz Vibrations and Modal Analysis in Proteins and Macromolecular Structures

  • Domenico Scaramozzino, Giuseppe Lacidogna, Alberto Carpinteri(Authors)
  • 2022(Publication Date)
  • Springer

    (Publisher)

  7 C H A P T E R 2 Proteins: The Basis of Biological Mechanisms Proteins are one of the most important building blocks for the achievement of the numerous biological reactions that occur every day in our body. The oxygen that we introduce into our lungs while we are breathing is successfully delivered to tissues and organs by the relentless job of hemoglobin, a protein contained in our red blood cells. The biochemical process which allows our eyes to interpret the images of the real world is mediated by Proteins in charge of facilitating the conversion of photons into electrochemical signals which are then sent to the brain for final interpretation. Other Proteins, such as collagen, are extremely important to provide specific parts of our body adequate levels of stiffness and mechanical resistance. Proteins like kinesin are essential for the transportation of nutrients throughout the cell environment. The function of transmembrane Proteins, which are embedded within the cellular membrane, is crucial for regulating the movement of ions, nutrients and small molecules to and from the cell. Proteins also act as enzymes, catalyzing biochemical reactions and improving the reaction rate by lowering the activation energy. Other classes of Proteins, the antibodies, are extremely important to fight against and neutralize viruses and bacteria. As can be seen from the examples reported above, the role of Proteins can be very diverse. All these activities contribute to the correct functioning of our body as a whole.

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  Protein Biology & Proteomics (Concepts and Applications)

  • (Author)
  • 2014(Publication Date)
  • College Publishing House

    (Publisher)

  One of the most distinguishing features of polypeptides is their ability to fold into a globular state, or structure. The extent to which Proteins fold into a defined structure varies widely. Some Proteins fold into a highly rigid structure with small fluctuations and are therefore considered to be single structure. Other Proteins undergo large rearrange-ments from one conformation to another. This conformational change is often associated with a signaling event. Thus, the structure of a protein serves as a medium through which to regulate either the function of a protein or activity of an enzyme. Not all Proteins requiring a folding process in order to function, as some function in an unfolded state. Like other biological macromolecules such as polysaccharides and nucleic acids, Proteins are essential parts of organisms and participate in virtually every process within cells. Many Proteins are enzymes that catalyze biochemical reactions and are vital to meta-bolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the Proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other Proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since ani-mals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism. Proteins were first described by the Dutch chemist Gerhardus Johannes Mulder and named by the Swedish chemist Jöns Jakob Berzelius in 1838. Early nutritional scientists such as the German Carl von Voit believed that protein was the most important nutrient for maintaining the structure of the body, because it was generally believed that flesh makes flesh.

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  Concepts and Techniques of Molecular Biology

  • (Author)
  • 2014(Publication Date)
  • College Publishing House

    (Publisher)

  The extent to which Proteins fold into a defined structure varies widely. ______________________________ WORLD TECHNOLOGIES ______________________________ Some Proteins fold into a highly rigid structure with small fluctuations and are therefore considered to be single structure. Other Proteins undergo large rearrangements from one con-formation to another. This conformational change is often associated with a signaling event. Thus, the structure of a protein serves as a medium through which to regulate either the function of a protein or activity of an enzyme. Not all Proteins require a folding process in order to function, as some function in an unfolded state. Like other biological macromolecules such as polysaccharides and nucleic acids, Proteins are essential parts of organisms and participate in virtually every process within cells. Many Proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the Proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other Proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism. Proteins were first described by the Dutch chemist Gerhardus Johannes Mulder and named by the Swedish chemist Jöns Jakob Berzelius in 1838. Early nutritional scientists such as the German Carl von Voit believed that protein was the most important nutrient for maintaining the structure of the body, because it was generally believed that flesh makes flesh. The central role of Proteins as enzymes in living organisms was however not fully appreciated until 1926, when James B.

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  Biochemistry

  An Integrative Approach

  • John T. Tansey(Author)
  • 2019(Publication Date)
  • Wiley

    (Publisher)

  nanantachoke/ShutterStock Just as these building materials are used in constructing office buildings, amino acids are the building blocks of Proteins. CHAPTER 3 Proteins I An Introduction to Protein Structure and Function Proteins in Context Throughout history advances in materials have changed tools and how we make them. Ancient civilizations may have used clay pots or made weapons of bronze or iron. In modern times refined alloys of aluminum have been used in applications ranging from cans to aircraft. Perhaps people in the future will mark our current era by the use of plastics or silicon microchips. In biochemistry, we consider Proteins to be a wonder material used in thousands of applications. Proteins are polymers of amino acids which have evolved to have numerous distinct functions: they can be structural or catalytic, transmit information, help protect an organism by binding to foreign molecules, provide motility, store amino acids, or transport molecules within the cell or the organism. This chapter begins by discussing amino acids, the building blocks of Proteins, then moves on to the basics of protein structure and a brief description of how these macromolecules fold into their specific confor- mations. The chapter ends by examining several different examples of different Proteins. These aspects of protein chemistry are discussed in Dynamic Figure 3.1. CHAPTER OUTLINE 3.1 Amino Acid Chemistry 3.2 Proteins Are Polymers of Amino Acids 3.3 Proteins Are Molecules of Defined Shape and Structure 3.4 Examples of Protein Structures and Functions 67 68 CHAPTER 3 Proteins I COMMON THEMES Evolution’s outcomes are conserved. • Mutations to DNA sequences may result in alterations to a protein’s amino acid sequence. The new protein may function normally, have a new and slightly altered function, or be completely nonfunctional. • The amino acid sequence of Proteins can help establish the evolutionary relationship between organisms.

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  Textbook on Food Science and Human Nutrition

  • Sharma, Dipiti(Authors)
  • 2021(Publication Date)
  • Daya Publishing House

    (Publisher)

  5 Proteins 5.0 Introduction Jons J.Berzelius, in 1838 named a group of chemical substances as Proteins meaning of the first rank. The term protein was coined by dutch chemist G.T. Mulder in 1839 on the suggestion of Jons. J. Berzelius. The word protein was derived from the Greek word “proteios” which means “principal” or prime. These are the principal components of all living cells (of both plant and animal body) and are important in practically all aspects of cell structure and functions. The term protein signifies first or foremost and Proteins are the most abundant macromolecules in cells and constitute over 50 per cent of dry weight of most of the organisms. Next to water, protein is the most abundant component of the body. It accounts for about 1/6th of the live body weight. Out of which a third of it is found in the muscles, a fifth in the bones and cartilage, a tenth in the skin and the remainder is in other tissues and body fluid. Proteins are large, complex molecules that play many critical roles in the body. These macromolecules are characterized by their nitrogen content. The nitrogen in Proteins is in a specialform that can be readily used by our bodies for vital functions. In addition, some Proteins contain small quantities of sulphur, phosphorus and minerals. Plants have the ability to synthesize Proteins from inorganic nitrogen sources such as ammonia, nitrate and nitrite. Animals unlike plants cannot synthesize Proteins in this manner. Thus all animal life, either directly or This ebook is exclusively for this university only. Cannot be resold/distributed. indirectly, depends on plants to satisfy its daily protein requirement. Proteins are the instruments by which genetic information is expressed. They do most of the work in cells and are required for the structure, function, and regulation of the body’s tissues and organs. Proteins are crucial to the regulation and maintenance of essential body functions.

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  Man and His World/Terres des hommes

  The Noranda Lectures, Expo 67/Les Conferences Noranda/L'Expo 67

  • The Noranda Lectures/ Expo 67(Author)
  • 2019(Publication Date)
  • University of Toronto Press

    (Publisher)

  I was fascinated by the complexity of living organisms and the intri-cate ways in which they perform so many functions. I tried to understand these func-tions in a somewhat deeper way than is re-quired of a student, but I soon realized that I would first have to study chemistry, physics, and mathematics before trying to grapple with these complicated processes. I thus spent many years in the study of the exact sciences. When I felt that I had mastered, at least to a certain extent, some of the vast areas of these sciences, I returned to the study of life pro-cesses. Here I was fascinated by the large molecules, by the macromolecules of the cell which play a most important role in determin-ing life processes. Proteins and nucleic acids are among the most important materials in the living organ-ism. The protein myosin forms our muscles, collagen -our skin, keratin -our hair. Fibrin determines the process of blood clotting. Se-rum albumin and haemoglobin abound in our blood. Some of the Proteins are hormones, such as insulin, and others act as antibodies protecting us from micro-organisms. Last, but not least, all enzymes, i.e. the entire complex variety of catalysts of a living cell, are pro-teins. As for the nucleic acids, they store all the information of the cell. They actually keep the secrets of life in the best sense of the word. They direct the functions of the cell. They are responsible for all hereditary properties and govern protein biosynthesis. While considering Proteins and nucleic acids, I could not help wondering why nature chose large molecules for the essential pro-cesses of the cell. Could nature not carry out these reactions with small molecules and make the life of a chemist and a physicist so much simpler? But I soon realized that the special quality of a large molecule is a structure which is essentially linear, made up of many hundreds of thousands of atoms in one long chain that can be folded into a large variety

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  Biological Ultrastructure

  • Arne Engström, J. B. Finean(Authors)
  • 2013(Publication Date)
  • Academic Press

    (Publisher)

  C H A P T E R IV The Role of Proteins The Proteins, as the name impHes, are of first importance in the structure of fiving matter. No Hving cell is without them, and any discussion of biological ultrastructure must inevitably start with a consideration of the structure of the Proteins. They form the foundation upon which the com-plex systems which constitute living material are built. The Proteins provide some of the largest molecules, and are capable of the widest variation in size, shape, and constitution. They may occur in nature as pure protein systems, or in combination with substances such as lipids, carbohydrates, nucleic acids, and other organic molecules, as well as with a variety of inorganic ions. The combination may be loose, or it may be through stable chemical bonds, the number and variety of these providing endless possibilities for the stability of the general association. But these complex associations will be developed in all possible detail in later chapters, the purpose of the present chapter being, as it were, to iso-late the protein itself and to extract its structural characteristics. This process has been going on for a long time, and despite the significant ad-vances of the past few years, the first complete solution still lies ahead of us, although perhaps it may be close enough to consider the possibility of being able to add it in the proof of this volume. The tasks of identification, isolation, and physical and chemical characterization, have occupied biol-ogist, chemist, and physicist for over a hundred years, although neither the intensity of the study nor the method of attack has pursued a steady course. It is therefore perhaps as well to forget the chronological approach and to start from the fundamental structural units.

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  Advanced Nutrition

  Macronutrients, Micronutrients, and Metabolism, Second Edition

  • Carolyn D. Berdanier, Lynnette A. Berdanier(Authors)
  • 2015(Publication Date)
  • CRC Press

    (Publisher)

  153 8 Protein After the energy need is met, protein is the next most important macronutrient need. Food Proteins provide the amino acids that are needed to synthesize Proteins in the body. On the average, Americans consume about 100 g of protein per day. This is far more than what is actually needed. Protein, in its many forms, is an essential and universal constituent of all living things. As much as one-half of the dry weight of the cell is protein. The human body is, on the average, 18% protein. Besides being plenti-ful, Proteins serve a variety of functions. They serve as structural components, as biocatalysts (in the form of enzymes), as antibodies, as lubricants, as messengers (in the form of hormones and cytokines), as receptors, and as carriers or transporters. The building blocks of all Proteins are the amino acids. In this chapter, the chemistry and physiology of the Proteins are discussed. AMINO ACIDS C HEMISTRY Amino acids consist of carbon, hydrogen, oxygen, nitrogen, and occasionally sulfur. All amino acids with the exception of proline have a terminal carboxyl group C OH O and an unsubstituted amino (−NH 2 ) group attached to the α -carbon. Proline has a substituted amino group and a carboxyl group. Also attached to the α -carbon is a functional group identified as R; R differs for each amino acid (Table 8.1). The general structure of amino acids can be represented as COOH NH 2 H C R While it is convenient to represent amino acids in this manner, in reality, amino acids exist as the dipolar ion H R C COO – NH 3 + in the range of pH values (5.0–8.0) found within the body. In learning the structures of the essential amino acids, the student will find it useful to remember the basic structure of alanine. All of the other amino acids have R groups that replace the terminal methyl group in alanine. For example, in valine, the methyl group is replaced with an isopropyl group; in phenylalanine, it is replaced with a phenyl group.

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