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Chapter 2

Chapter 2 of Molecular Biology of the Cell

15 Pages
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Department
Biology
Course Code
BIO130H1
Professor
Kenneth Yip

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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 atoms interaction with an atom of a second, non-bonded element Water is the most abundant substance in cells Water accounts for 70% of a cells 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)
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