2 Lecture - Chapters 2, 3 Chapter 2 Water accounts for about 70% of a cells weight & most intracellular reactions occur in an aqueous environment life on earth began in the ocean In each water molecule the 2 H atoms are linked to the O atom by covalent bonds the 2 bonds are highly polar bc the O is strongly attractive for electrons, whereas the H is only weakly attractive when a positively charged region of one molecule (H) approaches a negatively charged region (O) of a second water molecule, the electrical attraction between them can result in a weak bond called a hydrogen bond these bonds are much weaker than covalent bonds and are easily broken by the random thermal motions due to the heat and energy of the molecules it is only because of the hydrogen bonds that link water molecules together that water is a liquid at room temperature, with a high boiling point and high surface tension, rather than a gas molecules carrying plus or minus charges (ions) likewise interact favorably w water and are hydrophilic hydrophobic molecules, by contrast, are uncharged and form few or no hydrogen bonds, and so do not dissolve in water in hydrocarbons, the H atoms are covalently linked to C atoms by a largely nonpolar bond; because the H atoms have almost no net positive charge, they cannot form effective hydrogen bonds to other molecules All organic molecules are synthesized from and are broken down into the same set of simple compounds cells contain 4 major families of small organic molecules: the sugars, the fatty acids, the amino acids, and the nucleotides o
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Glucose = C6H12O6 the way that sugars are linked together to form polymers illustrates some common features of biochemical bond formation a bond is formed between an OH group on one sugar & an OH group on another by a condensation reaction, in which a molecule of water is expelled as the bond is formed the bonds created by all of these condensation reactions can be broken by the reverse process of hydrolysis, in which a molecule of water is consumed because each monosaccharide has several free hydroxyl groups that can form a link to another monosaccharide, sugar polymers can be branched, and the number of possible polysaccharide structures is extremely large the monosaccharide glucose is a key energy source for cells in a series of reactions, it is broken down to smaller molecules, releasing energy that the cell can harness to do useful work cells use simple polysaccharides composed only of glucose units principally glycogen in animals & starch in plants as energy stores
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A fatty acid molecule has 2 chemically distinct regions one is a long hydrocarbon chain, which is hydrophobic and not very reactive chemically the other is a carboxyl (-COOH) group, which behaves as an acid almost all fatty acid molecules in a cell are covalently linked to other molecules by their carboxylic acid group Fatty acids are stored in the cytoplasm of many cells in the form of droplets of triacylglycerol molecules, which consist of 3 fatty acid chains joined to a glycerol molecule when required to provide energy, the fatty acid chains are released from triacylglycerols and broken down into 2-carbon units these 2-carbon units are identical to those derived from the breakdown of glucose and they enter the same energyyielding reaction pathways fatty acids & their derivatives such as triacylglycerols are examples of lipids lipids comprise a loosely defined collection of biological molecules that are insoluble in water, while being soluble in fat & organic solvents such as benzene and typically contain either long hydrocarbon chains, as in the fatty acids and isoprenes, or multiple linked rings, as in steroids Most important function of fatty acids in cells is in the construction of cell membranes these thin sheets enclose all cells & surround their internal organelles and are composed largely of phospholipids, which are small molecules that, like triacylglycerols, are constructed mainly from fatty acids and glycerol in phospholipids, the glycerol is joined to 2 fatty acid chains, however, rather than to 3 as in triacylglycerols the 3rd site on the glycerol is linked to a hydrophilic phosphate group, which is in turn attached to a small hydrophilic compound each phospholipid molecule, therefore, has a hydrophobic tail composed of the 2 fatty acid chains & a hydrophilic head, where the phosphate is located molecules such as phospholipids, w both hydrophobic & hydrophilic regions are termed amphipathic (or amphiphilic) the membrane-forming property of phospholipids results from their amphipathic nature phospholipids will spread over the surface of water to form a monolayer of phospholipid molecules, w the hydrophobic tails facing the air & the hydrophilic heads in contact w the water 2 such molecular layers can readily combine tail-to-tail in water to make a phospholipid sandwich, or lipid bilayer structural basis of all cell membranes
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Amino acids one defining property is that they all possess a carboxylic acid group & an amino group, both linked to a single carbon atom called the alpha-carbon the importance of amino acids to the cell comes from their role in making proteins, which are polymers of amino acids joined head-to-tail in a long chain that is then folded into a 3-D structure unique to each type of protein covalent linkage b/w 2 adjacent amino acids in a protein chain forms an amide and it is called a peptide bond the chain of amino acids is also known as a polypeptide Nucleotide molecule made up of a nitrogen-containing ring compound linked to a five-carbon sugar, which in turn carries one or more phosphate groups nucleotides can act as short-term carriers of chemical energy adenosine triphosphate, or ATP, transfers energy in hundreds of different cell reactions ATP is formed through reactions that are driven by the energy released by the oxidative breakdown of foodstuffs the three phosphates are linked in series by 2 phosphoanhydride bonds, whose rupture releases large amounts of useful energy the terminal phosphate group in particular is frequently split off by hydrolysis, often transferring a phosphate to other molecules & releasing energy that drives energyrequiring biosynthetic reactions o
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Most fundamental role of nucleotides in the cell is in the storage & retrieval of biological information nucleotides serve as building blocks for the construction of nucleic acids long polymers in which nucleotide subunits are covalently linked by the formation of a phosphodiester bond between the phosphate group attached to the sugar of one nucleotide & a hydroxyl group on the sugar of the next nucleotide nucleic acid chains are synthesized from energy-rich nucleoside triphosphates by a condensation reaction that releases inorganic pyrophosphate during phosphodiester bond formation DNA & RNA are 2 main types of polynucleotide chains Macromolecules most abundant carbon-containing molecules in a living cell principal building blocks from which a cell is constructed & also the components that confer the most distinctive properties of living things o
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Most of the covalent bonds in a macromolecule allow rotation of the atoms they join, giving the polymer chain great flexibility & allows a macromolecule to adopt an almost unlimited number of shapes, or conformations, as random thermal energy causes the polymer chain to writhe & rotate however, the shapes of most biological macromolecules are highly constrained because of the many weak noncovalent bonds that form between different parts of the same molecule if these noncovalent bonds are formed in sufficient numbers, the polymer chain can strongly prefer one particular conformation, determined by the linear sequence of monomers in its chain most protein molecules & many of the small RNA molecules found inc ells fold tightly one into highly preferred conformation in this way noncovalent interactions also allow macromolecules to be used as building blocks for the formation of larger structures in cells, macromolecules often bind together into large complexes, thereby forming intricate machines w multiple moving parts that perform such complex tasks as DNA replication & protein synthesis
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Long linear reaction pathways are linked to one another, forming a maze of interconnected reactions that enable the cell to survive, grow, & reproduce - ~500 metabolic pathways & interconnections 2 opposing streams of chemical reactions occur in cells 1) catabolic pathways break down foodstuffs into smaller molecules, thereby generating both a useful form of energy for the cell & some of the small molecules that the cell needs as building blocks; 2) anabolic pathways use the energy harnessed by catabolism to drive the synthesis of the many other molecules that form the cell 2 set s of reactions constitute the metabolism of the cell o
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Second law of thermodynamics states that in the universe, or in any isolated system, the degree of disorder only increases o o G= Go+0.616ln[B]/[A] G:
Positive--no Negative--yes
Chapter 3 Protein molecule made from long chain of amino acids, each linked to its neighbor through a covalent peptide bond known as polypeptides repeating sequence of atoms along core of polypeptide chain is the polypeptide backbone attached to this repetitive chain are portions of the amino acids that are no involved in making a peptide bond & that give each amino acid its unique properties the 20 different amino acid side chains some of these side chains are nonpolar & hydrophobic, others are negatively or positively charged, some readily form covalent bonds o
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Folding of a protein chain is further constrained by many different sets of weak noncovalent bonds that form between one part of the chain and another these involve atoms in the polypeptide backbone, as well as atoms in the amino acid side chains 3 types of weak bonds: hydrogen bonds, electrostatic attractions, and van der Waals attractions individual noncovalent bonds are 30-300 times weaker than the typical covalent bonds that create biological molecules but many weak bonds acting in parallel can hold 2 regions of a polypeptide chain tightly together combined strength of large numbers of noncovalent bonds determines the stability of each folded shape
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An important factor governing the folding of any protein is the distribution of its polar & nonpolar amino aicds hydrophobic molecules, including the nonpolar side chains of particular amino acids, tend to be forced together in an aqueous environment in order to minimize their disruptive effect on the hydrogenbonded network of water molecules nonpolar (hydrophobic) side chains in a protein tend to cluster in the interior of the molecule while polar groups tend to arrange themselves near the outside of the molecule, where they can form hydrogen bonds w water & w other polar molecules o
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helix generated when a single polypeptide chain twists around on itself to form a rigid cylinder hydrogen bond forms between every 4th peptide bond, linked the C=O of one peptide bond to the N-H of another, giving rise to a regular helix
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sheet can form either from neighboring polypeptide chains that run in the same orientation (parallel chains) or from a polypeptide chain that folds back & forth upon itself, w each section of the chain running the direction opposite to that of its immediate neighbors (antiparallel chains) both types of sheets produce a very rigid structure, held together by hydrogen bonds that connect the peptide bonds in neighboring chains o
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Coiled-coil in other proteins, helices wrap around each other to form a particularly stable structure known as a coiled-coil can form when the 2 helices have most of their nonpolar (hydrophobic) side chains on one side, so that they can twist around each other w these side chains facing inward long rodlike coiled-coils provide the structural framework for many elongated proteins
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4 levels of organization of a protein amino acid sequence = primary structure stretches of polypeptide chain that form helices and beta sheets constitute proteins secondary structure full 3-D organization of a polypeptide chain is the tertiary structure & if a particular protein molecule is formed as a complex of more than one polypeptide chain, the complete structure is the quaternary structure protein domain substructure produced by any part of a polypeptide chain that can fold independently into a compact, stable structure a domain usually contains between 40 and 350 amino acids & it is the modular unit from which many larger proteins are constructed different domains of a protein are often associated w different functions (figure) the Src protein kinase, which functions in signaling pathways inside vertebrate cells, is considered to have 3 domains: the SH2 & SH3 domains have regulatory roles, while the C-terminal domain is responsible for the kinase catalytic activity the smallest protein molecules contain only a single domain, whereas larger proteins can contain as many as several dozen domains, often connected to each other by short, relatively unstructured lengths of polypeptide chain o
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Noncovalent bonds allow proteins to bind to each other to produce larger structures in the cell any region of a proteins surface that can interact w another molecule through sets of noncovalent bonds is called a binding site if a binding site recognizes the surface of a second protein, the tight binding of 2 folded polypeptide chains at this site creates a larger protein molecule w a precisely defined geometry each polypeptide chain in such a protein is called a protein subunit in the simplest case, 2 identical
folded polypeptide chains bind to each other in a head-to-head arrangement, forming a symmetric complex of 2 protein subunits (a dimer) held together by interactions between 2 identical binding sites o
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Cells contain many other types of symmetric protein complexes, formed from multiple copies of a single polypeptide chain the enzyme neuraminidase consists of 4 identical protein subunits each bound to the next in a head to tail arrangement that forms a closed ring o
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Hemoglobin contains 2 identical and 2 identical Beta-globin subunits, symmetrically arranged o
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Some protein molecules can assemble to form filaments that may span the entire length of a cell most simply, a long chain of identical protein molecules can be constructed if each molecule has a binding site complementary to another region of the surface of the same molecule an actin filament is a long
helical structure produced from many molecules of the protein actin actin constitutes one of the major filament systems of the cytoskeleton o
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Information for forming many of the complex assemblies of macromolecules in cells must be contained in the subunits themselves, because purified subunits can spontaneously assembly into the final structure under the appropriate conditions first large macromolecular aggregate shown to be capable of selfassembly from its component parts was tobacco mosaic virus (TMV) long rod in which a cylinder of protein is arranged around a helical RNA core if the dissociated RNA & protein subunits are mixed together in solution, they recombine to form fully active viral particles another complex macromolecular aggregate that can reassemble from its component parts is the bacterial ribosome this structure is composed of about 55 different protein molecules & 3 different rRNA molecules incubating the individual components under appropriate conditions in a test tube causes them to spontaneously reform the original structure most importantly, such reconstituted ribosomes are able to catalyze protein synthesis o
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