Berg • Tymoczko • Stryer. Biochemistry. Seventh Edition. CHAPTER Protein Turnover &. Amino Acid Catabolism. The primary use of amino acids provided. Tymoczko, Lubert Stryer 7th Edition. by Jeremy Mark Berg (Author) › Visit Amazon's Jeremy Mark. Berg Page. Biochemistry Stryer 7th lesforgesdessalles.info | lesforgesdessalles.info . Tymoczko Lubert Stryer SEVENTH EDITION Biochemistry Jeremy M. Berg John L . from lesforgesdessalles.info MB, Biochemistry 5th Edition - Lubert lesforgesdessalles.info
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Results 1 - 12 of 21 28 Nov Biochemistry by Berg JM,Tymoczko JL, and Stryer L, published by W.H. Freeman and Company.. john l tymoczko lubert stryer. SEVENTH EDITION Biochemistry Jeremy M. Berg John L. Tymoczko Lubert Stryer LUBERT STRYER is Winzer Professor of Cell Biology, Emeritus, in the. Lubert Stryer – Biochemistry 5th Edi - majkf Biochemistry Stryer 5th ed - lesforgesdessalles.info Supplements Supporting Biochemistry, Fifth Edition.
In addition to many traditional problems that test bio- chemical knowledge and the ability to use this knowl- edge, we have three categories of problems to address specific problem-solving skills. Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains 33 Proteins have unique amino acid sequences specified by genes 35 Polypeptide chains are flexible yet conformationally restricted 36 xvi Contents 2. Indeed, the sequence of bases along DNA strands is how genetic information is stored. Even processes that appear to be quite distinct often have common features at the biochemical level. This diversity extends further when we descend into the microscopic world.
Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains 33 Proteins have unique amino acid sequences specified by genes 35 Polypeptide chains are flexible yet conformationally restricted 36 xvi Contents 2.
Polypeptide Chains Can Fold into Regular Structures Such As the Alpha Helix, the Beta Sheet, and Turns and Loops 38 The alpha helix is a coiled structure stabilized by intrachain hydrogen bonds 38 Beta sheets are stabilized by hydrogen bonding between polypeptide strands 40 Polypeptide chains can change direction by making reverse turns and loops 42 Fibrous proteins provide structural support for cells and tissues 43 2.
Visualizing Molecular Structures II: Proteins 60 Chapter 3 Exploring Proteins and Proteomes 65 The proteome is the functional representation of the genome 66 3. How do we recognize the protein that we are looking for? Portrait of a Protein in Action 1 95 7. The Bohr Effect 7. Basic Concepts and Kinetics 8. Phosphorylation Cascades Are Central to Many Signal-Transduction Processes 41 1 The insulin receptor is a dimer that closes around a bound insulin molecule Insulin binding results in the cross -phosphorylation and activation of the insulin receptor The activated insulin-receptor kinase initiates a kinase cascade Insulin signaling is terminated by the action of phosphatases Basic Concepts and Design Triose phosphate isomerase salvages a three-carbon fragment The oxidation of an aldehyde to an acid powers the formation of a compound with high phosphoryl-transfer potential Mechanism: The synthesis of acetyl coenzyme a from pyruvate requires three enzymes and five coenzymes Flexible linkages allow lipoamide to move between different active sites The mechanism of citrate synthase prevents undesirable reactions Citrate is isomerized into isocitrate Isocitrate is oxidized and decarboxylated to alpha-ketoglutarate Succinyl coenzyme A is formed by the oxidative decarboxylation of alpha-ketoglutarate A compound with high phosphoryl-transfer potential is generated from succinyl coenzyme A Mechanism: Succinyl coenzyme A synthetase transforms types of biochemical energy Oxaloacetate is regenerated by the oxidation of succinate The citric acid cycle produces high-transfer-potential electrons, ATP, and CO 2 Three Proton Pumps and a Physical Link to the Citric Acid Cycle The high-potential electrons of NADH enter the respiratory chain at NADH-Qoxidoreductase Ubiquinol is the entry point for electrons from FADH 2 of flavoproteins Electrons flow from ubiquinol to cytochrome c through Q-cytochrome c oxidoreductase The Q cycle funnels electrons from a two -electron carrier to a one-electron carrier and pumps protons Cytochrome c oxidase catalyzes the reduction of molecular oxygen to water T oxic derivatives of molecular oxygen such as superoxide radical are scavenged by protective enzymes Electrons can be transferred between groups that are not in contact The conformation of cytochrome c has remained essentially constant for more than a billion years Catalytic imperfection Hexose phosphates are made from phosphoglycerate, and ribulose 1,5-bisphosphate is regenerated Three ATP and two NADPH molecules are used to bring carbon dioxide to the level of a hexose Starch and sucrose are the major carbohydrate stores in plants Transketolase and transaldolase stabilize carbanionic intermediates by different mechanisms The Calvin cycle and the pentose phosphate pathway are mirror images Pyridoxal phosphate participates in the phosphorolytic cleavage of glycogen A debranching enzyme also is needed for the breakdown of glycogen Phosphoglucomutase converts glucose 1 -phosphate into glucose 6-phosphate The liver contains glucose 6-phosphatase, a hydrolytic enzyme absent from muscle Contents xxv Methylmalonyl CoA mutase catalyzes a rearrangement to form succinyl CoA Fatty acids are also oxidized in peroxisomes Ketone bodies are formed from acetyl CoA when fat breakdown predominates Ketone bodies are a major fuel in some tissues Animals cannot convert fatty acids into glucose Pyridoxal phosphate forms Schiff-base intermediates in aminotransferases Aspartate aminotransferase is an archetypal pyridoxal-dependent transaminase Pyridoxal phosphate enzymes catalyze a wide array of reactions Serine and threonine can be directly deaminated Peripheral tissues transport nitrogen to the liver Microorganisms Use ATP and a Powerful Reductant to Reduce Atmospheric Nitrogen to Ammonia The iron— molybdenum cofactor of nitrogenase binds and reduces atmospheric nitrogen Ammonium ion is assimilated into an amino acid through glutamate and glutamine A tyrosyl radical is critical to the action of ribonucleotide reductase Stable radicals other than tyrosyl radical are employed by other ribonucleotide reductases Thymidylate is formed by the methylation of deoxyuridylate Dihydrofolate reductase catalyzes the regeneration of tetrahydrofolate, a one-carbon carrier Several valuable anticancer drugs block the synthesis of thymidylate Initiation, elongation, and termination Human activities require energy.
The interconversion of different forms of energy requires large biochemical machines comprising many thousands of atoms such as the complex shown above. Yet, the functions of these elaborate assemblies depend on simple chemical processes such as the protonation and deprotonation of the carboxylic acid groups shown on the right.
Since the dis- covery that biological molecules such as urea could be synthesized from nonliving components in , scientists have explored the chemistry of life with great intensity. Through these investigations, many of the most funda- mental mysteries of how living things function at a biochemical level have now been solved. However, much remains to be investigated. As is often the case, each discovery raises at least as many new questions as it answers.
Furthermore, we are now in an age of unprecedented opportunity for the application of our tremendous knowledge of biochemistry to problems in medicine, dentistry, agriculture, forensics, anthropology, environmental sciences, and many other fields. We begin our journey into biochemistry with one of the most startling discoveries of the past century: The animal kingdom is rich with species ranging from nearly microscopic insects to elephants and whales.
This diversity extends further when we descend into the microscopic world. Single-celled organ- isms such as protozoa, yeast, and bacteria are present with great diversity in water, in soil, and on or within larger organisms. Some organisms can survive and even thrive in seemingly hostile environments such as hot springs and glaciers.
The development of the microscope revealed a key unifying feature that underlies this diversity. Large organisms are built up of cells, resembling, to some extent, single-celled microscopic organisms.
The construction of ani- mals, plants, and microorganisms from cells suggested that these diverse organisms might have more in common than is apparent from their outward appearance. With the development of biochemistry, this suggestion has been tremendously supported and expanded.
At the biochemical level, all organisms have many common features Figure 1. As mentioned earlier, biochemistry is the study of the chemistry of life processes. These processes entail the interplay of two different classes of mol- ecules: Members of both these classes of molecules are com- mon, with minor variations, to all living things.
For example, deoxyribonucleic acid DNA stores genetic information in all cellular organisms. Proteins, the macromolecules that are key participants in most biological processes, are built from the same set of 20 building blocks in all organisms.
Furthermore, proteins that play similar roles in different organisms often have very similar three-dimensional structures see Figure 1. Figure 1. The shape of a key molecule in gene regulation the TATA-box-binding protein is similar in three very different organisms that are separated from one another by billions of years of evolution.
Selected key events are indicated. Note that life on Earth began approximately 3. For example, the set of chemical transformations that converts glucose and oxy- gen into carbon dioxide and water is essentially identical in simple bacteria such as Escherichia coli E.
Even processes that appear to be quite distinct often have common features at the biochemical level. Remarkably, the biochemical processes by which plants capture light energy and convert it into more-useful forms are strikingly similar to steps used in animals to capture energy released from the breakdown of glucose. These observations overwhelmingly suggest that all living things on Earth have a common ancestor and that modern organisms have evolved from this ancestor into their present forms.
Geological and biochemical findings support a time line for this evolutionary path Figure 1. On the basis of their biochemical characteristics, the diverse organisms of the modern world can be divided into three fundamental groups called domains: Eukarya eukaryotes , Bacteria, and Archaea.
Domain Eukarya comprises all multicellular organisms, including human beings as well as many microscopic unicellular organisms such as yeast. The defining char- acteristic of eukaryotes is the presence of a well-defined nucleus within each cell. Unicellular organisms such as bacteria, which lack a nucleus, are referred to as prokaryotes. These organisms, now recognized as having diverged from bacteria early in evolution, are the archaea. Evolutionary paths from a common ancestor to modern organisms can be deduced on the basis of biochemical information.
One such path is shown in Figure 1. Much of this book will explore the chemical reactions and the associated biological macromolecules and metab- olites that are found in biological processes common to all organisms. The unity of life at the biochemical level makes this approach possible.
At the same time, different organisms have specific needs, depending on the particu- lar biological niche in which they evolved and live. By comparing and contrasting details of particular biochemi- cal pathways in different organisms, we can learn how biological challenges are solved at the biochemical level.
In most cases, these challenges are addressed by the adap- tation of existing macromolecules to new roles rather than by the evolution of entirely new ones. A possible evolutionary path from a common ancestor approximately 3.
We begin our exploration of the interplay between structure and function with the genetic material, DNA. The discovery that DNA plays this central role was first made in studies of bacteria in the s. This discovery was followed by the elucidation of the three-dimensional struc- ture of DNA in , an event that set the stage for many of the advances in biochemistry and many other fields, extending to the present. The structure of DNA powerfully illustrates a basic principle common to all biological macromolecules: The remarkable properties of this chemical substance allow it to function as a very efficient and robust vehicle for storing information.
We start with an examination of the covalent structure of DNA and its exten- sion into three dimensions. DNA is constructed from four building blocks DNA is a linear polymer made up of four different types of monomers.
It has a fixed backbone from which protrude variable substituents Figure 1. The backbone is built of repeating sugar-phosphate units. The sugars are molecules of deoxyribose from which DNA receives its name. Each sugar is connected to two phosphate groups through different linkages. Moreover, each sugar is ori- ented in the same way, and so each DNA strand has directionality, with one end distinguishable from the other. Joined to each deoxyribose is one of four possi- ble bases: These bases are connected to the sugar components in the DNA back- bone through the bonds shown in black in Figure 1.
All four bases are pla- nar but differ significantly in other respects. Thus, each monomer of DNA consists of a sugar-phosphate unit and one of four bases attached to the sugar. These bases can be arranged in any order along a strand of DNA.
Each unit of the polymeric structure is composed of a sugar deoxyribose , a phosphate, and a variable base that protrudes from the sugar-phosphate backbone. Sugar Phosphate Figure 1. The sugar-phosphate backbones of the two chains are shown in red and blue, and the bases are shown in green, purple, orange, and yellow. The two strands are antiparallel, running in opposite directions with respect to the axis of the double helix, as indicated by the arrows.
In , James Watson and Francis Crick deduced the arrangement of these strands and proposed a three-dimensional structure for DNA molecules.
This structure is a double helix composed of two intertwined strands arranged such that the sugar-phosphate backbone lies on the outside and the bases on the inside. The key to this structure is that the bases form specific base pairs bp held together by hydrogen bonds Section 1. Hydrogen bonds are much weaker than covalent bonds such as the carbon-carbon or carbon-nitrogen bonds that define the struc- tures of the bases themselves.
Such weak bonds are crucial to biochemical systems; they are weak enough to be reversibly broken in biochemical pro- cesses, yet they are strong enough, when many form simultaneously, to help stabilize specific structures such as the double helix.
DNA structure explains heredity and the storage of information The structure proposed by Watson and Crick has two properties of central importance to the role of DNA as the hereditary material. First, the struc- ture is compatible with any sequence of bases.
The base pairs have essen- tially the same shape see Figure 1. Without any constraints, the sequence of bases along a DNA strand can act as an efficient means of storing information. Indeed, the sequence of bases along DNA strands is how genetic information is stored. The DNA sequence determines the sequences of the ribonucleic acid RNA and protein molecules that carry out most of the activities within cells.
Second, because of base-pairing, the sequence of bases along one strand completely determines the sequence along the other strand. As Watson and Crick so coyly wrote: Adenine pairs with thymine A-T , and guanine with cytosine G-C. The dashed green lines represent hydrogen bonds. An Evolving Science Figure 1. If a DNA molecule is separated into two strands, each strand can act as the template for the generation of its partner strand. The three- dimensional structure of DNA beautifully illustrates the close connection between molecular form and function.
To lay the groundwork for the rest of the book, we begin our study of biochemistry by examining selected concepts from chemistry and showing how these concepts apply to biological systems. The concepts include the types of chemical bonds; the structure of water, the solvent in which most biochemical processes take place; the First and Second Laws of Thermodynamics; and the principles of acid-base chemistry. We will use these concepts to examine an archetypical biochemical process — namely, the formation of a DNA double helix from its two component strands.
The process is but one of many examples that could have been chosen to illus- trate these topics. Keep in mind that, although the specific discussion is about DNA and double-helix formation, the concepts considered are quite general and will apply to many other classes of molecules and processes that will be discussed in the remainder of the book.
The double helix can form from its component strands The discovery that DNA from natural sources exists in a double-helical form with Watson-Crick base pairs suggested, but did not prove, that such double helices would form spontaneously outside biological systems.
Suppose that two short strands of DNA were chemically synthesized to have complementary sequences so that they could, in principle, form a double helix with Watson-Crick base pairs. Subscribe to view the full document. I cannot even describe how much Course Hero helped me this summer. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.
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