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Doug Thomson

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Chapter 2: Cell Chemistry and Biosynthesis THE CHEMICAL COMPONENTS OF A CELL An atom often behaves as if it has a fixed radius  Space-filling models give us a more accurate representation of molecular structure  A solid envelope represents the radium of the electron cloud at which strong repulsive forces prevent a closer approach of any second, non-bonded atom – the so-called van der Waals radius for an atom  At slightly greater distances, any two atoms will experience a weak attractive force, known as a van der Waals attraction  There is a distance at which repulsive and attractive forces precisely balance to produce an energy min in each atom’s interaction with an atom of a second, non-bonded element Water is the most abundant substance in cells  Water accounts for 70% of a cell’s weight  Hydrogen bond: the electrical attraction when a + charged region of one water approaches a – charged region of a second water; weaker than covalent bonds and are easily broken by the random thermal motion due to the heat energy of the molecules so each bond lasts only a short time  Explains why water is a liquid at room temp, with a high bp and high surface tension  Molecules that contain polar bonds can form H bonds with water dissolve readily in water  Ions likewise interact favourably with water  Such molecules are hydrophilic (water loving)  Hydrophobic (water hating) are uncharged and form few or no H bonds, and so go not dissolve in water Some polar molecular are acids and bases  Proton ( ): a molecule that had largely given up its electron to the companion atom  When water molecules surround the polar molecule, the proton is attracted to the partial negative charge on the O atom of an adjacent water molecule and can dissociate from its original partner to associate instead with the oxygen atoms of the water to generate a hydronium ion ( )  Acids: substances that release protons to form when they dissolve in water  Base: accepts protons to lower the concentration of ions, and thereby raise the concentration of  [ [  The concentration of is expressed using a log scale called the pH scale  The interior of a cell is kept close to neutrality, and it is buffered by the presence of many chemical groups that can take up and release protons near pH 7 Four types of noncovalent attractions help bring molecules together in cells  In aqueous solutions, covalent bonds are 10-100x stronger than the other attractive forces between atoms  Much of biology depends on the specific binding which is mediated by a group of noncovalent attractions that are individually quite weak, but whose energies can sum to create an effective force between two separate molecules 1. Electrostatic attractions a. Result from the attractive forces between oppositely charged atoms b. Quite strong in the absence of water c. Readily form between permanent dipoles but are greatest when the 2 atoms involves are fully charged d. Water cluster around both full charged ions and polar molecules, greatly reducing the attractiveness of these charged species for each other in most biological settings 2. Hydrogen bonds a. Represents a special form of polar interaction in which an electropositive H atom is partially shared by 2 electronegative atoms b. H can be viewed as a proton that has partially dissociated from a donor atom, allowing it to be shared by a second acceptor atom c. Highly directional – being strongest when a straight line can be drawn between all 3 of the involved atoms d. Water weakens these bonds by forming competing H-bond interactions 3. Van der Waals attraction a. Electron cloud around any nonpolar atom will fluctuate, producing a flickering dipole which will transiently induce an oppositely polarize flickering dipole in a nearby atom b. Generates a very weak attraction c. Water does not weaken these attractions  Fourth effect is not a bond at all, strictly speaking  A very important hydrophobic force is caused by a pushing of nonpolar surfaces out of the H-bonded water network  Brining any 2 nonpolar surfaces together reduces their contact with water; the force is nonspecific A cell is formed from carbon compounds  Because C is small and 4 e and 4 vacancies, nearly all the molecules in a cell are based on C  High stable covalent C-C bonds form chains and rings and hence generate large and complex molecules  Certain combination of atoms occur repeatedly in organic molecules; these chemical groups have distinct physical and chemical properties that influence the behaviour of the molecule in which the group occurs Cells contain 4 major families of small organic molecules  Some organic molecules are used as monomer subunits to construct macromolecules – proteins, nucleic acids, and large polysaccharides - of the cell  Small organic molecules are much less abundant that the organic macromolecules  3 major families: sugars, fatty acids, the amino acids, and the nucleotides Sugars provide an energy source for cells and are the subunits of polysaccharides  The simplest sugars – monosaccharides – are compounds with the general formula , where n is usually 3, 4, 5, 6, 7, or 8  Called carbohydrates because of this simple formula  The formula, however, does not fully define the molecule; same set of C, H and O can be joined together by covalent bonds in a variety of ways  Eg. Glucose can be converted into a different sugar simply by switching the orientation of specific OH groups  Each of these sugars can exist in either of 2 forms, D-form and L-form, which are mirror images of each other  Isomers: same chemical formula but different structures  Optical isomers: mirror-image pairs  In their open chain forms of sugars, they contain a number of OH groups and a carbonyl group  The carbonyl group can react with a OH group in the same molecule to convert the molecule into a ring  Once the ring is formed, this same C can become further linked, via O, to one of the C bearing a OH on another sugar, creating a disaccharide  Larder sugar polymers range from oligosaccharides up to giant polysaccharides  A bond is formed between an –OH group on one sugar and an-OH group on another by a condensation reaction, in which a molecule of water is expelled as the bond is formed  The covalent bond between two sugar molecules are known as a glycosidic bond  The bonds created can be broken by the reverse process of hydrolysis, in which water is consumed  Glucose is a key energy source for cells; in a series of reaction, it is broken down to smaller molecules, releasing energy  Cells use simple polysaccharides composed only of glucose: starch in plants and glycogen in animals  Sugars can also be used to mechanical supports; eg. Cellulose and chitin  Other polysaccharides are components of slime, mucus and gristle  Smaller oligosaccharides can be covalently linked to proteins to form glycoproteins and to lips to form glycolipids, which are recognized selectively by other cells through their side chains Fatty acids are components of cell membranes, as well as a source of energy  Have two chemically distinct regions: a long hydrocarbon chain (hydrophobic and not reactive) and carboxyl group (behaves as an acid, ionized in solution, hydrophilic and chemically reactive)  Almost all fatty acids in a cell are covalently linked to other molecules by their carboxylic acid group  saturated: no double bonds between C atoms and contains the max possible # of H  Unsaturated: one or more double bonds along their length, creating kinks and interfering with their ability to pack together in a solid mass  Are stored in the cytoplasm in the form of droplets of triacylglycerol molecules, which consist of 3 fatty acid chains joined to a glycerol molecule (the animal fats found in meat, butter and cream)  When required to provide energy, the fatty acid chains are released from triacylglycerols and broken down into 2-C units which are identical to those derived from the breakdown of glucose  Triacylglycerols serve as a concentrated food reserve in cells because they can produce about 6x energy than glu  Lipids: loosely defined collection of biological molecules that are insoluble in water, while being soluble in fat and organic solvents  Either long HC chains, or multiple linked rings (steroids)  Function: construction of cell membranes which enclose all cells and surround their internal organelles  Composed largely of phospholipids: Hydrophobic tail composed of the 2 fatty acid chains and a hydrophilic head, where the phosphate is located  Amphiphilic: molecules with both hydrophobic and hydrophilic regions  Phospholipids will spread over the surface of water to form a monolayer, with the hydrophobic tails facing the air and the hydrophobic heads in contact with water  Two such layers combine tail-to-tail in water -> lipid bilayer Amino acids are the subunits of Proteins  All possess a carboxylic acid group and an amino group, both linked to a single C called the α-C  Chemical variety comes from the side chain linked to α-C  Proteins: polymers of amino acids joined head-to-tail in a long chain folded into 3D structure  Peptide bond: the covalent linkage between 2 adjacent aa in a protein chain to form an amide  Polypeptide: chain of amino acids  Has an amino group at one end (N-terminus) and a carboxyl group as its other end (C-terminus)  Each of the 20 amino acids has a different side chain  All aa, except glycine, exist as optical isomers; only L-forms are ever found in proteins  D-forms occur in bacterial cell walls and in some antibiotics  Side chains: can form ions, uncharged, polar and hydrophilic, nonpolar and hydrophobic Nucleotides are the subunits of DNA and RNA  Molecule made up of a N-containing ring compound linked to a 5-C sugar (ribose or deoxyribose), which in turn carries one or more phosphate groups  N-containing rings are generally referred to as bases: under acidic conditions, they can each bind a proton  C, T, U are pyrimidines because they all derive from a 6-membered pyrimidine ring  G and A are purine: they have a second, 5-membered ring fused to a 6-membered ring  Nucleotides can act as short-term carriers of chemical energy  Adenosine triphosphate, the ribonucleotide, 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  Its three phosphates are linked in series by two phosphoanhydride bonds (rupture releases large amount of E)  Terminal P group is frequently split off by hydrolysis, often transferring a P to other molecules and releasing energy that drives energy-requiring biosynthetic reactions  Most fundamental role of nucleotides: storage and retrieval of biological information  Serve as building blocks of nucleic acids: long polymers in which nucleotide subunits are covalently linked by the formation of a phosphodiester bond between P group attached to the sugar of on nucleotide and a OH 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  Two main types of nucleic acids: ribonucleic acids (RNA) and deoxyribonucleic acid (DNA)  T is chemically similar to U, merely adding the methyl group on the pyrimidine ring  RNA usually occurs in cells as a single polynucleotide chain  DNA is virtually always a double stranded molecule composed of 2 chains running antiparallel held together by H-bonding between the bases of the two chains The chemistry of cells is dominated by macromolecules with remarkable properties  Proteins are abundant and versatile, performing thousands of distinct functions  Enzymes: the catalysts that direct the many covalent bond-making and bond-breaking reactions that the cell needs  Structural components: tubulin – a protein that self-assembles to make the cell’s long microtubules, or histones, proteins that compact the DNA in chromosomes  Molecular motors to produce force and movement: myosin in muscle  Each polymer grows by the addiction of a monomer onto the end of a growing polymer chain in a condensation reaction Noncovalent bonds specify both the precise shape of a macromolecule and its binding to other molecules  Most of the covalent bonds in a macromolecule allow rotation of the atoms they join, giving the polymer chain great flexibility and allowing a macromolecule to adopt an almost unlimited conformations as random thermal energy causes the polymer to writhe and rotate  However, the shapes are highly constrained because of the many weak noncovalent bonds that form between different parts of the same molecule  Most protein fold tightly into one highly preferred conformation  Although individually weak, the four types of noncovalent interactions cooperate to fold biological macromolecules into unique shapes  They can also add up to create a strong attraction between two different molecules when these molecules fit together very closely  Because the strength of the binding depends on the number of noncovalent bonds that are formed, interactions of almost any affinity are possible – allowing rapid dissociation when necessary Chapter 3 – Proteins  Constitute most of a cell’s dry mass  Building blocks and execute nearly all the cell’s functions  Proteins embedded in the plasma membrane form channels and pumps that control the passage of small molecules into and out of the cell  Other proteins carry messages from one cell to another or act as signal integrators that relay sets of signals inward from the plasma membrane to the cell nucleus THE SHAPE AND STRUCTURE OF PROTEINS The shape of a protein is specified by its amino acid sequence  Protein: made from a long chain of amino acids, each linked to its neighbour through a covalent peptide bond  Each type of protein has a unique sequence of amino acids  Polypeptide backbone: the repeating sequence of atoms along the core of the polypeptide chain  Side chains: attached to the polypeptide backbone and is not involved in making a peptide bond; gives each aa its unique properties  A sequence is always present in the N-to-C direction, reading from left to right  Nonpolar side chains tend to cluster in the interior of the molecule  Polar groups tend to arrange themselves near the outside of the molecule, where they can form H bonds  Polar aa buried within the protein are usually H-bonded to other polar aa or to the polypeptide backbone  Rotation can occur about the -C bond, whose angle of rotation is called psi, and about the N-bond, whose angle of rotation is called phi Proteins fold into a conformation of lowest energy  Most proteins have a single particular 3D structure determined by the order of the aa in its chain  Final folded structure, or conformation, of any polypeptide chain is generally the one that minimizes its free E  Treatment with certain solvents, which disrupt the noncovalent interactions holding the folded chain together, denatures a protein  Coverts it into a flexible polypeptide chain that has
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