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Cover Biochemistry and Molecular Biology

An alternative pathway of glucose oxidation: the pentose phosphate pathway  

This chapter examines the pentose phosphate pathway, which is a pathway of glucose oxidation which does not generate adenosine triphosphate (ATP) nor oxidize a molecule of glucose completely. The chapter considers the pentose phosphate pathway as a versatile pathway that produces ribose-5-phosphate for nucleotide synthesis, supplies nicotinamide adenine dinucleotide phosphate hydrogen (NADPH) for fat synthesis and other reductive systems, and provides a route for the metabolism of surplus pentose sugars coming from the diet. The pathway has an oxidative section converting glucose-6-phosphate into ribose-5-phosphate and it produces NADPH. The chapter explores how the nonoxidative section manipulates ribose-5-phosphate according to the needs of the cell. If a cell requires equal amounts of ribose-5-phosphate and NADPH, only the oxidative section is required.

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The basic molecular themes of life  

This chapter talks about living cells. These obey the laws of physics and chemistry. Energy is derived in cells from the breaking down of food molecules and released in a form that can drive chemical and physical work. The chapter considers adenosine triphosphate (ATP) as the universal energy currency in life. Energy from food breakdown is used to synthesize ATP from adenosine diphosphate (ADP) and phosphate. ATP breakdown can then be coupled to carry out biochemical work. The chapter analyses biological molecules which are based on the carbon atom bonded mainly to hydrogen, oxygen, nitrogen, and other carbon atoms. Noncovalent bonds are weak in comparison with covalent bonds but important in allowing interactions between molecules.

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Biochemical techniques  

This chapter reviews the different biochemical techniques. The experimental procedures by which biochemical information is obtained include molecular biological, immunological, biochemical, and biophysical techniques. Molecular biology techniques involve the analysis and manipulation of DNA, RNA, and protein. They include cloning genes/complementary DNAs; genomics/genome sequencing; gene therapy; and genetically modified (GM) crops. The chapter then looks at protein purification and analysis. It also considers immunological techniques, which exploit the high specificity and affinity of antibodies for their cognate antigen. They can be used simply to analyse the presence of a protein, examine post-translational modifications, probe protein–protein interactions, and interactions of protein with other macromolecules. Finally, the chapter studies biophysical techniques, which allow analysis of the structure and physical properties of biochemical macromolecules.

Book

Cover Biochemistry and Molecular Biology

Despo Papachristodoulou, Alison Snape, William H. Elliott, and Daphne C. Elliott

Biochemistry and Molecular Biology is made up of six parts. Part 1 covers the basic concepts of life. Part 2 is about the structure and function of proteins and membranes. The third part looks at metabolism and nutrition. The fourth part of the book covers information storage and utilization. The fifth part looks at cells and tissues. Finally, the sixth part is about protective mechanisms against disease such as blood clotting, xenobiotic metabolism, reactive oxygen, and the immune system.

Chapter

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Blood clotting, xenobiotic metabolism, and reactive oxygen species  

This chapter describes a number of processes in the body which are essential protective devices against different hazards. It mentions blood clotting. This involves two separate pathways of proteolytic enzymes, which converge at active factor X. This process activates prothrombin to thrombin, a proteolytic enzyme that converts fibrinogen to fibrin. Fibrin is a fibrous complex that entraps blood cells into a soft clot, which is then stabilized by cross-link formation between the strands. The chapter looks at the pathway that is triggered by a wound exposing an abnormal surface, such as collagen. The shorter extrinsic pathway results from the release of a factor from damaged cells.

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The cell cycle, cell division, cell death, and cancer  

This chapter looks at the eukaryotic cell cycle. This is divided into several phases: the first gap phase (G1), the DNA synthesis phase (S), the second gap phase (G2), and the mitotic or cell division phase (M). The chapter reviews progression through the phases. This depends on the synthesis of cyclin proteins specific for different phases. At the end of each phase the cyclins are destroyed by proteolysis. The cyclins are required to activate different cyclin-dependent protein kinases (Cdks) and determine which substrates a given kinase works on in each phase of the cycle. The chapter refers to the cyclin synthesis in G1, stating that it requires the receipt by the cell of a mitogenic signal from a growth factor or cytokine. After entering M phase, a further check is made to establish that all of the chromosomes are correctly placed on the mitotic spindle.

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The cell membrane and membrane proteins  

This chapter talks about biological membranes that have a lipid bilayer structure made up of a variety of different lipids held together by noncovalent bonds. It shows that lipids are arranged with their hydrophobic tails pointing to the middle of the bilayer and their hydrophilic sections to the outside. Lipid bilayers are two-dimensional fluids that can self-seal. They permit endocytosis, a process by which cells take in material, and enable cells to eject molecules in a reverse process called exocytosis. The chapter mentions fatty acid components and shows how these may be saturated or unsaturated in a cis configuration, which are essential for maintaining the bilayer in a fluid condition. Trans unsaturated fatty acids resemble saturated fatty acids in that they are straight chain, not kinked.

Chapter

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Cell signalling  

This chapter discusses the receptors of cells which receive signals from other cells. This is limited in scope in unicellular organisms, such as yeast and bacteria. However, in animal cells, such as mammalian ones, the number of signals needed to coordinate their activities is large. The chapter clarifies how signals control the most fundamental aspects of gene-control, cell survival, programmed cell death, and cell division. Cancer usually involves the malfunction of signalling pathways. The chapter analyzes signals that are variously proteins, peptides, steroids, and other lipid-related molecules, and nitric oxide. The signalling molecules bind to specific receptors of target cells and activate signalling pathways, which result in gene-control events in the nucleus and more direct effects on metabolism.

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Cells and viruses  

This chapter offers a broad survey of the structures and properties of cells and viruses, providing a biological background for the more detailed mechanisms of cell biology, biochemistry, and molecular biology. It explains that cells are the units of living systems, wherein each cell is surrounded by a lipid membrane and has a DNA genome. The two main classes of cellular organism are prokaryotes and eukaryotes, including archaea that are a third class of organism that can live in unusual environments. The chapter examines the large numbers of ribosomes in both prokaryotic and eukaryotic cells, which are large complex structures of RNA and proteins found in the cytosol. The cytoplasm of eukaryotic cells can be defined as the content of the cell excluding the nucleus, while the cytosol refers to the soluble constituents of the cytoplasm from which membrane-bounded organelles have been removed.

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Cellular components  

This chapter examines cellular components, starting with membranes. Membranes are made up of lipid, protein, and carbohydrate, and form a hydrophobic barrier to allow compartmentalization. The plasma membrane separates the contents of a cell from its environment. The chapter then looks at the cytoskeleton and the nucleoskeleton. The cytoskeleton is composed of networks of different types of filaments which are present throughout the cell. They serve as communication lines for cellular traffic, to allow cell movement, to stabilize cell structure, and to protect from physical stress. Meanwhile, the nucleoskeleton is the structure underlying the organization of genomic DNA within the nucleus. The chapter also considers the cytosol, which is the aqueous material remaining after extraction of insoluble components by ultracentrifugation, as well as organelles.

Chapter

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Control of gene expression  

This chapter explains how gene expression can be regulated at each stage of protein synthesis, but the majority of regulation is of transcription. The chapter covers E. coli , wherein groups of genes called operons often occur and are transcribed together, forming polycistronic messengers. In the lac operon, comprising three genes, a repressor protein effects control by blocking an operator region at the initiation site of transcription. The chapter considers the repressor as an allosteric protein that detaches and allows transcription of genes required to form enzymes needed to utilize the sugar in the presence of lactose. Transcription factors (TFs) are the keys to eukaryotic gene-control.

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DNA synthesis, repair, and recombination  

This chapter considers DNA synthesis as semiconservative as it is catalysed by DNA polymerases, which require the four deoxyribonucleoside triphosphates, a template or parental strand to copy, and a primer. The chapter refers to the primer of prokaryotes which is synthesized by the primase enzyme and is a short RNA copy of part of the parental strand. Synthesis starts at a site of origin on the chromosome where strand separation occurs. The chapter notes that E. coli has a single site of origin while eukaryotic chromosomes have hundreds. The chapter clarifies how a helicase separates parental strands that produces supercoiling ahead of it, noting that supercoils are removed by topoisomerases. The problem of maintaining the 5′→3′ direction of synthesis of both strands is solved by continuous synthesis of the leading strand and discontinuous synthesis of the lagging strand.

Chapter

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Energy considerations in biochemistrya  

This chapter looks at energy which changes during chemical reactions. Looking at this energy provides a reliable guide to the biochemistry of cells. The chapter describes free energy change (ΔG) as the most useful value as it expresses the amount of energy change in a reaction available to perform useful work. The ΔG value can be used to determine the equilibrium constant of a reaction. It also shows whether the reaction is likely to be reversible in cells. The chapter mentions free energy made available from food breakdown. This energy is used to synthesize adenosine triphosphate (ATP), the universal energy carrier of life. Catabolism or breakdown of food molecules drives anabolism or synthesis of molecules with ATP being the energy-carrying go-between.

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Energy release from fat  

This chapter shows the way that energy is released from fat involving the oxidation of fatty acids released from triacylglycerols. These are first converted into fatty acyl-Coenzyme As (CoAs). Then the acyl groups are transported into the mitochondria. The chapter emphasizes that fatty acyl-CoA cannot enter the mitochondrion, but an enzyme of the outer membrane transfers it to carnitine and a transport system transfers the acylcarnitine into the matrix where another enzyme transfers the acyl group back to CoA. In the matrix, the fatty acyl-CoA is converted into acetyl-CoA by a process called β-oxidation in which carbon atoms are released two at a time in the form of acetyl-CoA. The chapter describes the fatty acid chain of acyl-CoAs, which is dehydrogenated by a series of enzymes that produce β-ketoacyl-CoAs. Acetyl units are split off by the enzyme ketoacyl-CoA thiolase, which attaches each to CoASH and releases acetyl-CoA.

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Enzymes  

This chapter defines an enzyme as a catalyst which brings about a specific reaction by increasing the rate of reaction while remaining unchanged in the process. Also, the enzyme here cannot affect the equilibrium of a reaction. The chapter points out that an enzyme is a protein that binds substrates and lowers the activation energy of the reaction it catalyses, as the active site binding the substrate is perfectly complementary to the transition state. An enzyme aligns substrates and provides a catalytic site, which is a small region of the protein that contains chemical groupings essential for the catalysis. The chapter discusses enzyme kinetics. This explores enzymes by measuring reaction rates and the Michaelis-Menten equation which explains the kinetics of many enzyme-catalysed reactions in terms of the substrate binding to the enzyme and the enzyme-substrate complex breaking down to liberate products. An enzyme displaying Michaelis-Menten kinetics gives a hyperbolic curve. This happens when the initial reaction velocity is plotted against increasing substrate concentration.

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Enzymes  

This chapter focuses on enzymes, which are highly specific biological catalysts. Most are proteins, though some RNAs can act enzymatically. The chapter then looks at enzyme kinetics, enzyme inhibition, enzyme mechanisms, and enzyme regulation. An enzyme inhibitor is a substance that binds to an enzyme and interferes with its activity; inhibition may be reversible or irreversible. Most enzymes carry out relatively simple chemical transformations. Complex transformations involve a number of simple steps which together constitute a biochemical pathway. A subset of amino acid side chains of the enzyme frequently acts as acid/base catalysts or nucleophiles, and/or hydrogen bond to the transition state to stabilize it. Certain cofactors (such as metal ions or vitamin derivatives) confer additional chemical versatility on enzyme active sites. Finally, the chapter considers some multienzyme complexes.

Chapter

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Food digestion, absorption, and distribution to the tissues  

This chapter looks at digestion, wherein the polysaccharides and proteins of food are hydrolysed into their monomer subunits or simple sugars and amino acids in order to be absorbed by the intestinal epithelial cells in the bloodstream. The chapter looks at triacylglycerols or fats (TAGs) which are hydrolysed into fatty acids and monoacylglycerol, the process which is aided by bile salts that emulsify the fats to give a large surface area for the enzyme lipase to attack. The storage of fat is primarily in the adipocytes or fat cells of adipose tissue, where it occurs in large amounts as TAG. The chapter describes insulin, which is released in response to high glucose levels and stimulates fat and glycogen storage. Glucagon, released from the pancreas when blood glucose is low, stimulates release of glucose from the liver and of fatty acids from fat cells.

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Gene transcription  

This chapter discusses how a gene is expressed by one strand of DNA, a template strand. It is then copied into single-stranded RNA and protein-coding genes, wherein the mRNA is translated to form protein. The chapter refers to transcription and notes that this is catalysed by RNA polymerase using ATP, CTP, GTP, and UTP as building blocks. Prokaryotes have a single RNA polymerase, while eukaryotes have three: Pol I, Pol II, and Pol III. The chapter explains Pol II and shows that it transcribes protein-coding genes to make mRNA, while Pol I transcribes a large rRNA precursor, and Pol III transcribes small RNAs. The coding region of a prokaryotic gene is a continuous stretch of DNA, so that the primary transcript is a messenger RNA (mRNA) and can be translated immediately, while in eukaryotes the primary transcript.

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General principles of nutrition  

This chapter shows that nutrition is the science of food and the substances contained in it. The chapter notes that the main components of diet are macronutrients, which provide the bulk of the diet, and micronutrients, which include essential vitamins and minerals. The chapter explains that protein is needed to supply essential amino acids and fat is needed to supply essential fatty acids and provide sufficient energy in the diet. Most diets provide 10-15% of the energy in the form of protein and the remainder is made up of carbohydrate and fat. The chapter talks about the consumption of saturated fat, which is one of the risk factors for cardiovascular disease and some cancers, whereas consumption of polyunsaturated fat is considered healthy. A high consumption of sucrose can lead to dental caries.

Chapter

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The genome  

This chapter looks at DNA, which is a polynucleotide consisting of strands of deoxynucleotides linked by 5′→3′ phosphodiester links between the sugar residues. The chapter covers the four bases of DNA, which are A, T, G, and C. The DNA double helix consists of two antiparallel strands held together by complementary base pairing by hydrogen bonding between A and T, and G and C. The chapter discusses the bases in a double helix point to the inside of the molecule and the phosphate-sugar backbone to the outside, with the edges of the bases visible in the two grooves of the double helix. The bases themselves have flat hydrophobic faces and are stacked on one another.