Mathews - Biochemistry (Mathews 3rd Ed).pdf - Free ebook download as PDF File .pdf), Text File .txt) or read book online for free. Thomas M. Devlin, Ph.D. This book was set in ITC Garamond Light by BiComp Incorporated Textbook of Biochemistry BIOCHEMISTRY, GENETICS. and biochemistry, it is fitting that a web site accompanies this important When you're not on-line you can continue your study of biochemistry by using the.
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you will be happy that at this time biochemistry mathews pdf is available at our online library. biochemistry by mathews van holde and kevin g athern iii edition . Welcome to the Companion Web Site that accompanies the third edition of Biochemistry by Mathews,van Holde, and Ahern. At a time Amino acid/ Polypeptides (Figure )Biochemistry as a Biological Science Download. PDF | Imma Ponte and others published Bioquímica. C. K. Mathews, K. E. Van Holde. biochemistry by Mathews and van Holde, both Distinguished.
Nicotinate and Nicotinamide Metabolism Acetaldehyde Acetaldehyde is a two carbon compound participating in the reactions below: 1.
Amino acids broken down through pyruvate include alanine, cysteine, glycine, serine, threonine, and tryptophan. With the exception of the enzymes shown in red on the right hand side of the figure, the enzymes of gluconeogenesis and glycolysis are the same.
One starting point for gluconeogenesis is two molecules of pyruvate and the process ends with formation of one glucose molecule. Enzymes of Gluconeogenesis Eleven reactions are catalyzed in glucoenogenesis.
The enzymes involved and the reactions they catalyze are listed below. Glycolysis uses many of the same enzymes as gluconeogenesis, but with reversal of reaction direction. Normally the concentration of G6P is considerably lower than the KM of the enzyme. Glucosephosphatase is an important enzyme for making glucose from G6P in tissues, such as liver and kidney, that supply glucose to other tissues via the bloodstream.
The enzyme is not made appreciably in muscles, which obtain glucose for use in glycolysis either from the bloodstream or as G6P from glucosephosphate produced during glycogen catabolism.
The enzyme has been implicated in von Gierke's disease, a glycogen storage disorder see here. G6P is an intermediate in glycolysis, gluconeogenesis, the pentose phosphate pathway, the Calvin Cycle, glycogen biosynthesis, glycogen breakdown, and sugar interconversion.
The latter three pathways indirectly involve G6P via the enzyme phosphoglucomutase. It operates exclusively in the cytosol. Be aware that in contrast to pathways, such as glycolysis with a linear sequence of reactions or the citric acid cycle with a circular sequence of reactions , the pentose phosphate pathway has several possible "branches" that can be taken to allow it to supply the cell with different products as needed.
The primary products of the pathway include NADPH from the oxidative reactions , pentoses used in nucleotide synthesis , and miscellaneous other sugar phosphates.
A variation of the pentose phosphate pathway called the Calvin cycle is used by plants to fix CO2 in photosynthesis. In fact, the dark reactions are stimulated by light, but do not directly use the energy of light to function.
The dark reactions occur in the stroma of the chloroplast and are shown schematically in Figure The cycle can be viewed as occurring in two stages. In stage I, carbon dioxide is trapped as a carboxylate and reduced to the aldehyde-ketone level found in sugars. In stage II, the molecule that accepts CO2 is regenerated. Note with each turn of the cycle in Figure Thus, the end products of the Calvin cycle are hexoses and a regenerated acceptor molecule.
This reaction is catalyzed by the enzyme ribulose1,5-bisphosphate carboxylase, more commonly known as rubisco. The end product of this reaction is two molecules of 3-phosphoglycerate, a gluconeogenesis and glycolysis intermediate. Next, 3-phosphoglycerate is converted to 1,3 bisphosphoglycerate BPG and then to glyceraldehydephosphate G3P by the enzymes phosphoglycerate kinase and glyceradehydephosphate dehydrogenase, respectively.
These two reactions are similar to the analogous ones that occur in gluconeogenesis. Two of these are used to make one glucose-phosphate compound via gluconeogenesis and the other 10 are used to regenerate the 6 molecules of RuBP that are necessary to bind to 6 CO2 molecules. Of the 10 G3Ps involved in regeneration of RuBP, 4 go through part of the gluconeogenesis cycle and form 2 molecules of fructose-6phosphate F6P.
Stage II: Many of the reactions of the Calvin cycle also occur in the pentose phosphate pathway. As shown in Figure These intermediates include 4-xylulosephosphates and 2 ribulosephosphates. Conversion of the 4 xylulosephosphates to 4 ribulose-5phosphates occurs and the 6 ribulosephosphates are phosphorylated by kinases to regenerate the 6 RuBPs.
The overall equation for the Calvin cycle is shown in here. CO2 Fixation in Bacteria 2. CO2 Fixation in Plants Figure It contains two important activities. The enzyme also has an unusual oxygenase actvity, shown below: 2. This process is referred to as photorespiration and it occurs under conditions where the oxygen concentration is high.
The C4 cycle, which occurs in so-called C4 plants, bypasses some of the inefficiency of photosynthesis arising from photorespiration. See also: Calvin Cycle, Photorespiration, The C4 Cycle 3-Phosphoglycerate 3-Phosphoglycerate is an intermediate in the glycolysis, gluconeogenesis, and Calvin cycle pathways and in metabolism of serine, cysteine, and glycine.
See also: 2,3-Bisphosphoglycerate, 2-Phosphoglycerate Unnumbered Item Serine Serine is an amino acid found in proteins. In mammals, serine is a nonessential amino acid, meaning it does not need to be present in the diet. Serine's alcohol chain is a site of phosphorylation of many proteins. The hydroxy and sulfur-containing amino acids are generally more hydrophilic than their aliphatic analogs. Molecular Wt. L-Amino acids are the building blocks of proteins.
They are frequently grouped according to the chemical nature of their side chains. Figure 5. Table 5. The genetic code for each of the 20 amino acids above is shown here. Amino acids not found in proteins are shown here. Modified amino acids are sometimes found in proteins. Virtually all amino acids in proteins are in the L configuration. During times of starvation or low food supply, some amino acids called glucogenic can serve as precursors of glucose via gluconeogenesis.
Dietary amino acids are classified as being essential must be in the diet or non-essential can be synthesized by the organism. In mammals, glycine is a non-essential amino acid, meaning it does not need to be present in the diet. Glycine has the smallest functional group hydrogen of any of the amino acids. See also - Table 5. The amide nitrogen of glutamate is used for the synthesis of several amino acids, purine and pyrimidine nucleotides, and amino sugars, so glutamine synthetase plays a central role in nitrogen metabolism.
In animals, the enzyme is a key participant in detoxifying ammonia, particularly in the brain, and in ammonia excretion in the kidney. Accumulation of glutamate and glutamine depletes -ketoglutarate, which would interfere with the citric acid cycle. As a result, glutamine synthetase is tightly regulated. Mechanisms controlling the activity of glutamine synthetase include the following: Cumulative feedback Inhibition - Eight specific feedback inhibitors, which are either metabolic end products of glutamine tryptophan, histidine, glucosaminephosphate, carbamoyl phosphate, CTP, or AMP or indicators of the general status of amino acid metabolism alanine or glycine , can bind to any of the subunits of the enzyme and at least partially inhibit it.
The more inhibitors that bind, the greater the inhibition. Covalent modification adenylylation - A specific tyrosine residue in glutamine synthetase can react with ATP to form a phosphate ester with AMP see here.
Adenylylation renders the catalytic site of the enzyme inactive. Adenylylation and deadenylylation involve a complex series of regulatory cascades. Both processes are catalyzed by the same enzyme-a complex of adenylyl transferase AT and a regulatory protein, PII. The enzyme uridylyl transferase catalyzes uridylylation of PII, whereas deuridylylation is catalyzed by a different enzyme.
Uridylyl transferase is allosterically regulated, with ATP and -ketoglutarate activating it and glutamine inhibits it.
In mammals, glutamic acid is a non-essential amino acid, meaning it does not need to be present in the diet.
Glutamic acid surprise! In animals, vitamin K2 carboxylates glutamate residues in certain proteins, to give carboxyglutamate. This modification allows the protein to bind calcium, an essential event in the blood clotting cascade. Carboxylation of glutamate residues occurs in other proteins that are active in the mobilization or transport of calcium.
Glutamic acid is very important in transamination reactions in the body and as a precursor of other amino acids.
One Letter Code E Reactions involving glutamate: 1.
Mathews - Biochemistry (Mathews 3rd Ed).pdf
Glutamate Metabolism 2. Urea Cycle and Metabolism of Amino Groups Vitamin K In animals, vitamin K2 carboxylates glutamate residues in certain proteins, to give carboxyglutamate. Vitamin K is found in plants as phylloquinone vitamin K1 and in animals as menaquinone vitamin K2.
Vitamin K2 is essential for the carboxylation of glutamate residues in certain proteins, to give carboxyglutamate. Carboxylation of glutamate is also important in other proteins involved in the mobilization or transport of calcium. Although one of these, Vitamin D, is ultimately derived from cholesterol, the other three are not. Vitamin A - also called all-trans-retinol, is an isoprenoid alcohol that plays a key role in vision and a role in controlling animal growth.
Vitamin A must either be present in the diet, or derived from -carotene, an isoprenoid compound prominent in carrots.
See Figure Dehydrogenation of retinol yields the aldehyde, retinal, which has a role in vision. Another derivative of retinol is retinoic acid, which can be made by the oxidation of retinal.
Retinoids derivatives of retinol act like steroid hormones and interact with specific receptor proteins in the cell nucleus.
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The ligand-receptor complexes bind to specific DNA sequences, where they control the transcription of particular genes. Vitamin D - the most abundant form is D3, also called cholecalciferol. Vitamin D is not technically a vitamin, because it is not required in the diet. It arises from UV-photolysis of 7-dehydrocholesterol, an intermediate in cholesterol biosynthesis see here. Vitamin D regulates calcium and phosphorus metabolism, particularly the synthesis of the inorganic matrix of bone, which consists largely of calcium phosphate.
D3 undergoes two successive hydroxylations catalyzed by mixed-function oxidases. The first occurs at carbon 25 in liver. When calcium levels are low, hydroxylation occurs at carbon 1, yielding the active form, 1,25 OH D3, which stimulates osteoblasts to take up calcium.
In the intestine, 1,25 OH D3 stimulates transcription of a protein that stimulates calcium absorption into the bloodstream. When calcium levels are adequate, hydroxylation occurs instead at carbon 24, yielding the inactive 24,25 OH D3 form.
Vitamin E - also called -tocopherol. Vitamin E is an antioxidant. It is particularly effective in preventing the attack of peroxides on unsatured fatty acids in membrane lipids.
Deficiency of vitamin E also leads to other symptoms, however, so vitamin E probably plays other roles as yet undiscovered. Vitamin K - found in plants as phylloquinone vitamin K1 and in animals as menaquinone vitamin K2. Vitamin K2 is essential for the carboxylation of glutamate residues in certain proteins, to give -carboxyglutamate. Retinol Metabolism 2. The alcohol form of vitamin A, retinol, is the storage form in the body.
The aldehyde form, retinal, has a role in vision. The acid form, retinoic acid, functions in embryonic development. Vitamin A acts to some extent in the body as an antioxidant, protecting against oxidative damage.
Rod Photoreceptor All-trans-Retinal All-trans-retinal is a derivative of vitamin A involved in vision. In the eye, specialized photoreceptor cells of the retina, called rod cells are primarily responsible for lowlight vision, with relatively little color detection.
Rod cell outer segments contain lamellar protein disks rich in the protein opsin Figure Oxidation and isomerization of all-trans-retinol yields an intermediate, cis retinal, which is important in photoreception.
The chemistry of photoreception is shown in Figure Absorption of light by the retinal portion of the complex isomerizes the cis-bond in 11cis retinal to a trans-bond, forming an all-trans compound called bathorhodopsin. Release of a proton yields metarhodopsin II 4. Hydrolysis yields opsin and all-trans retinal.
Retinal isomerase converts all-trans retinal to cis retinal. At step 3 above, bathorhodopsin activated form of rhodopsin can activate transducin so that it binds GTP. This, in turn, stimulates a cascade of events that generates a visual signal to the brain. Rhodopsin Rhodopsin is the name of the complex between the protein opsin and cis retinal in the visual process Figure Absorption of light by the retinal portion of the complex isomerizes the cis-bond in cis retinal to a trans-bond, forming an all-trans compound called bathorhodopsin.
Bathorhodopsin activated form of rhodopsin can activate transducin so that it binds GTP. Rod Photoreceptor Unnumbered Item Transducin Transducin is a protein in the visual process that binds GTP after activation by a form of rhodopsin called bathorhodopsin Figure GTP is produced by substrate level phosphorylation in the citric acid cycle reaction catalyzed by succinyl-CoA synthetase.
Though several different types of RNA polymerase are known, all catalyze the following basic reaction, using the rules of complementarity A-T, G-C, C-G, and U-A, where the bases of ribonucleosides are listed first in each pair and the bases of deoxyribonucleosides are listed second. This was shown in experiments with rifampicin Figure The enzymes differ in their sensitivity to inhibition by -amanitin Figure Other transcriptional inhibitors - Cordycepin 3'-deoxyadenosine Figure The nucleotide of cordycepin is incorporated into growing chains, confirming that transcriptional chain growth occurs in a 5' to 3' direction.
Another important transcriptional inhibitor is actinomycin D Figure The tricyclic ring system phenoxazone intercalates between adjacent G-C base pairs, and the cyclic polypeptide arms fill the nearby narrow groove. DNA polymerase vs. RNA polymerase - Vmax see here for the DNA polymerase III holoenzyme, at about to nucleotides per second, is much higher than the chain growth rate for bacterial transcription nucleotides per second, which is the same as Vmax for purified RNA polymerase.
Replicative DNA chain growth is rapid but occurs at few sites, whereas transcription is much slower, but occurs at many sites. Once transcription of a gene has been initiated, RNA polymerase rarely, if ever, dissociates from the template until the specific signal to terminate has been reached.
Accuracy of template copying - Another important difference between DNA and RNA polymerases is the accuracy with which a template is copied.
With an error rate of about , RNA polymerase is far less accurate than replicative DNA polymerase holoenzymes, although RNA polymerase is much more accurate than would be predicted from Watson-Crick base pairing see here alone.
Recent observations suggest the existence of error-correction mechanisms. These processes may be akin to 3' exonucleolytic proofreading by DNA polymerases.
The following, however, are important differences: 1. Cleavage of 3' ends of RNA molecules usually removes oligonucleotides, rather than single nucleotides, and 2. The mechanism of transcriptional error correction is still an open question and the subject of ongoing research efforts.
The "message" in mRNA is carried in groups of three nucleotides called codons. Each codon specifies one amino acid in a protein according to the rules of the genetic code. The nucleoside monophosphates in RNA are called ribonucleoside monophosphates, however, because they contain the sugar ribose instead of 2deoxyribose, as is found in DNA. These are the same bases as DNA except that the base uracil is used in place of thymine T. Instead, RNA exists as a single-stranded entity, though extensive regions of many RNAs may form double helices within themselves by the base pairing rules.
The three predominant forms of RNA are all involved in translating the genetic information in the sequence of bases in DNA to a sequence of amino acids in proteins. One codon specifies the incorporation of a specific amino acid into a protein. One end of the tRNA contains a three nucleotide sequence called the anticodon loop that is complementary to the codon of the mRNA.
The other end of the tRNA is covalently attached to a specific amino acid. Because the amino acid carried by a tRNA is specific for each anticodon and each anticodon is complementary to the codons in mRNA, the tRNA provide the link between nucleic acid sequence and amino acid sequence for a protein during translation.
This process, which occurs on ribosomes, sequentially incorporates amino acids corresponding to the order of codons in the mRNA. Examples include pseudouridine, ribothymidine, and dihydrouridine See Figure Many eukaryotic RNAs have portions of them removed by a process called splicing.
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It is this process in which the snRNAs participate. The RNA World 2. DNA is a component of the chromosomes proteins are the other component. DNA is one of two types of nucleic acid. The word "triacylglycerol" is sometimes used synonymously with "triglyceride". In these compounds, the three hydroxyl groups of glycerol are each esterified, typically by different fatty acids. Because they function as an energy store, these lipids comprise the bulk of storage fat in animal tissues.
The hydrolysis of the ester bonds of triglycerides and the release of glycerol and fatty acids from adipose tissue are the initial steps in metabolizing fat. Examples of structures in this category are the digalactosyldiacylglycerols found in plant membranes  and seminolipid from mammalian sperm cells. In addition to serving as a primary component of cellular membranes and binding sites for intra- and intercellular proteins, some glycerophospholipids in eukaryotic cells, such as phosphatidylinositols and phosphatidic acids are either precursors of or, themselves, membrane-derived second messengers.
The major sphingoid base of mammals is commonly referred to as sphingosine. Ceramides N-acyl-sphingoid bases are a major subclass of sphingoid base derivatives with an amide -linked fatty acid.
The fatty acids are typically saturated or mono-unsaturated with chain lengths from 16 to 26 carbon atoms. Examples of these are the simple and complex glycosphingolipids such as cerebrosides and gangliosides.
Sterol lipids[ edit ] Sterol lipids, such as cholesterol and its derivatives, are an important component of membrane lipids,  along with the glycerophospholipids and sphingomyelins. The steroids , all derived from the same fused four-ring core structure, have different biological roles as hormones and signaling molecules. The eighteen-carbon C18 steroids include the estrogen family whereas the C19 steroids comprise the androgens such as testosterone and androsterone.
The C21 subclass includes the progestogens as well as the glucocorticoids and mineralocorticoids. Structures containing greater than 40 carbons are known as polyterpenes. Carotenoids are important simple isoprenoids that function as antioxidants and as precursors of vitamin A. Prokaryotes synthesize polyprenols called bactoprenols in which the terminal isoprenoid unit attached to oxygen remains unsaturated, whereas in animal polyprenols dolichols the terminal isoprenoid is reduced.
Saccharolipids describe compounds in which fatty acids are linked directly to a sugar backbone, forming structures that are compatible with membrane bilayers. In the saccharolipids, a monosaccharide substitutes for the glycerol backbone present in glycerolipids and glycerophospholipids. The minimal lipopolysaccharide required for growth in E. They comprise a large number of secondary metabolites and natural products from animal, plant, bacterial, fungal and marine sources, and have great structural diversity.
Many commonly used anti-microbial , anti-parasitic , and anti-cancer agents are polyketides or polyketide derivatives, such as erythromycins , tetracyclines , avermectins , and antitumor epothilones. The glycerophospholipids are the main structural component of biological membranes , as the cellular plasma membrane and the intracellular membranes of organelles ; in animal cells, the plasma membrane physically separates the intracellular components from the extracellular environment.
A biological membrane is a form of lamellar phase lipid bilayer.
The formation of lipid bilayers is an energetically preferred process when the glycerophospholipids described above are in an aqueous environment. In an aqueous system, the polar heads of lipids align towards the polar, aqueous environment, while the hydrophobic tails minimize their contact with water and tend to cluster together, forming a vesicle ; depending on the concentration of the lipid, this biophysical interaction may result in the formation of micelles , liposomes , or lipid bilayers.
Other aggregations are also observed and form part of the polymorphism of amphiphile lipid behavior. Phase behavior is an area of study within biophysics and is the subject of current[ when? So in an aqueous environment, the water molecules form an ordered " clathrate " cage around the dissolved lipophilic molecule.
They are a major source of energy because carbohydrates are fully reduced structures. In comparison to glycogen which would contribute only half of the energy per its pure mass, triglyceride carbons are all bonded to hydrogens, unlike in carbohydrates. Migratory birds that must fly long distances without eating use stored energy of triglycerides to fuel their flights.
They accomplish this by being exposed to the extracellular face of the cell membrane after the inactivation of flippases which place them exclusively on the cytosolic side and the activation of scramblases, which scramble the orientation of the phospholipids. After this occurs, other cells recognize the phosphatidylserines and phagocytosize the cells or cell fragments exposing them.
Acyl-carnitines are involved in the transport and metabolism of fatty acids in and out of mitochondria, where they undergo beta oxidation.Proteins are not made directly from DNA, however. In the intestine, 1,25 OH D3 stimulates transcription of a protein that stimulates calcium absorption into the bloodstream. Lactose is formed from UDP-Gal plus glucose by lactose synthase, in the presence of the protein lactalbumin.
In plants, adenosine-5'-phosphosulfate is the substrate. Glycine has the smallest functional group hydrogen of any of the amino acids. ATP is produced in the cell from ADP as a result of three types of phosphorylations - substrate-level phosphorylations, oxidative phosphorylation, and, in plants, photosynthetic phosphorylation.
Retinoids derivatives of retinol act like steroid hormones and interact with specific receptor proteins in the cell nucleus. These processes may be akin to 3' exonucleolytic proofreading by DNA polymerases. Note that the enzyme is named for the reverse reaction. Complex II, like complex I, contains iron-sulfur proteins, which participate in electron transfer.