Chapter 2

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Biological Sciences
David Harrison

Cell Biology – The Chemical Basis of Life Chapter 2 2.1 Covalent Bonds The atoms that make up a molecule are joined by covalent bonds, pairs of electrons are shared between pairs of atoms. Atom is most stable when its outermost electron shell is filled. Two atoms can become joined by bonds in which more than one pair of electrons are shared. Double bonds can function as energy capturing centers, is used in vital processes such as respiration and photosynthesis. Positively charged nucleus of one atom exerts a greater attractive force on the outer electrons than the other. The more Electronegative the atom (greater attractive force) the more close the atoms are located to the atoms. Polar and Nonpolar Molecules Water attracts more electrons, so water is said to be polarized, meaning one atom has a negative charge and the other a partial positive charge. Molecules such as water that have an asymmetric distribution of charge (dipole) are polar molecules, they contain one or more electronegative atoms, O N and S. Molecules that lack electro negativity are strongly polarized, they are non polar. Large nonpolar molecules, such as waxes and fats are relatively inert. Ionization Some atoms are so strongly electronegative that they can capture electrons from other atoms during a chemical reaction. When there is an extra electron added to the atom, it has a negative charge and is an anion. When there is one less electron the atom is positive or cation. Na and Cl are stable because the have filled outer shells. A different arrangement can produce highly reactive species called a free radical. 2.2 Noncovalent Bonds Covalent bonds are strong bonds between atoms. Interactions between molecules, weaker linkages called Noncovalent bonds. Noncovalent bonds depend on shared electrons. Individual Noncovalent bonds are weak. Individual Noncovalent bonds are weak, when large numbers of them act together they become strong and stable. Ionic Bonds: Attractions Between Charged Atoms Tabel salt has an ionic bond, an attraction between fully charged components. The strength of ionic bonds in a cell is generally weak, due to the presence of water but deep within the core of a protein where water is often excluded such bonds can be influenced. Hydrogen Bonds When a hydrogen atom is covalently bonded to an electronegative atom, particularly an oxygen or nitrogen atom, the single pair of shared electrons is greatly displaced toward the nucleus of the electronegative atom, leaving the hydrogen atom with a partial positive charge. Nucleus of the hydrogen atom can approach near enough to an unshared pair of outer electrons of a second electronegative atom to form attractive interaction called hydrogen bond. Occurs between most polar molecules, large number of hydrogen bonds in DNA make it stable. Hydrophobic Interactions and van der Waals Forces Polar molecules are said to be hydrophilic (water loving). Nonpolar are hydrophobic (hate water). Hydrophobic interactions are not classified as true bonds because they do not result from an attraction between hydrophobic molecules. Polar molecules associate because they contain permanent asymmetric charge distributions within their structure. Distribution of electrons around an atom is any given instant is a statistical matter, and varies from one instant to the next, given time electron density may happen to b greater on one side of an atom. These transient asymmetries in electron distribution result in momentary separations of charge. If two molecules with transitory dipoles are very close to one another and oriented in the appropriate manner, they experience a weak attractive force called van der Walls force, that bonds them together. A single van der Waals force is very weak, and very sensitive, but some atoms need a weak bond so they can interact in the body and thus makes it important. Life Supporting Properties of Water Life on earth is dependent on water. 1. Water is a highly asymmetric molecules with O atom at one end and the two H atoms at the opposite end. 2. Each of the two covalent bonds in the molecule is highly polarized. 3. All three atoms in a water molecule are adept at forming hydrogen bonds. Each molecule of water can form hydrogen bonds with four other water molecules, producing a highly interconnected network of molecules. Each hydrogen bond is formed when the partially positively charged hydrogen of one water molecule becomes aligned next to a partially negative charged oxygen atom of another water molecule. Water molecules have an unusually strong tendency to adhere to one another. Evaporation from liquid to gas require water molecules to break hydrogen bonds, which is why it takes so much energy to get steam. Water is able to dissolve more types of substances than any other solvent. Water also determines the structure of biological molecules and they types of interactions in which they can engage. Water is fluid matrix around which insoluble fabric of cell is constructed. It is also medium through which materials move from one compartment of the cell to another. Able to form weak noncovalent bonds with water, polar molecules are soluble within water. 2.4 The Nature of Biological Molecules Bulk of an organism is water. Most of the remaining dry weight consists of molecules containing atoms of carbon. The compounds produced by living organisms are called biochemicals. A carbon atom can bond with up to four other atoms. Each carbon atom is able to bond with other carbon atoms. They can be linear, branched or cyclic. Functional Groups Hydrocarbons do not occur in significant amounts within most living cells, they constitute the bulk of the fossil fuels formed from remains of ancient living things. Functional Groups are particular groups of atoms that often behave as a unit and give organic molecules their physical properties, chemical reactivity and solubility in aqueous solution. Most common ones include ester bonds which form between carboxylic acids and alcohols, and amide bonds which form between carboxylic acids and amines. Electronegative atoms N P O and S make organic molecules more polar, more water soluble and more reactive. Functional groups can ionize and become positively or negatively charged. A Classification of biological molecules by function Organic molecules commonly found within cells can be divided into different categories based on role in metabolism. 1. Macromolecules – Molecules that form the structure and carry out the activities of cells are huge; highly organized molecules. Contain dozens to millions of carbon atoms. They perform complex tasks with precision and efficiency. Presence of macromolecules endows organisms with properties of life. Can be divided into four categories, proteins, nucleic acids, polysaccharides, and certain lipids. First three are polymers, consisting of a lot of monomers. Are monomers that are constructed from polymerization. Basic structure of each type of macromolecule are similar in all organisms. 2. Building Blocks of macromolecules. – Most macromolecules have a short lifetime, compared to cell itself, with exception of cell’s DNA, they are continually broken down and replaced. Most cells contain a supply of low molecular weight precursors ready to be incorporated into macromolecules. These include sugars (polysaccharides), amino acids (proteins), nucleotides (nucleic acids), and fatty acids (lipids). 3. Metabolic intermediates (metabolites)-Each series of chemical reactions is termed a metabolic pathway. Cell starts with Compound A converts it to B then to C, etc. The compounds formed along the pathways leading to the end products might have no function per se and are called metabolic intermediates. 4. Molecules of miscellaneous function- The vast bulk of the dry weight of a cell is made up of macromolecules and their direct precursors. Molecules of miscellaneous function include vitamins (primarily adjuncts to proteins), certain steroid or amino acid hormones, molecules involved in energy storage (ATP), regulatory molecules such as cyclic AMP and metabolic waste such as urea. 2.5 Four Types of Biological Molecules Four types: Carbohydrates, lipids proteins and nucleic acids. Carbohydrates Carbohydrates include simple sugars (monosaccharide’s) and larger molecules of sugar building blocks. Carbohydrates function primarily as stores of chemical energy and as durable building materials for biological construction. Most sugars are (CH O) Important sugars range from n values of 3 to 7. Sugars 2 n containing three carbons are trioses, four tetroses, five pentoses, hexoses, heptoses. Structure of Simple Sugars – Each sugar molecule consists of a backbone of carbon atoms linked together in a linear array by a single bond. Each of the carbons linked to a single hydroxyl group, except one bears a carbonyl. If carbonyl group is located at an internal position (ketone) its a ketose, carbonyls at the end of the sugar (aldehyde group) makes the sugar an aldose. Sugars with five or more carbon atoms undergo a self reaction that converts them into a closed or ring containing molecule. Rings are usually depicted as flat structures. Sugar ring is not a planar structure, but is a three dimensional conformation resembling a chair. Stereoisomers or enantiomers are two molecules that have essentially the same chemical reactivity, but their structures are mirror images. The molecule is D- if hydroxyl group is on right and L for left because it acts as a site of stereoisomerism, carbon 2 is referred to as an asymmetric carbon atom. If the hydroxyl group of this carbon projects to the right aldose is a D sugar if on left is an L-sugar. Molecule is alpha pyranose when OH group of the first carbon is below the plane of the ring, and beta pyranose when its upward. Linking Sugars together Sugars can be joined to one another by covalent glycosidic bonds. They form by a reaction between carbon atom C1 of one sugar and the hydroxyl group of another sugar, -C—O—C- linkage. Disaccharides (two sugar unites) serve primarily as readily available energy stores. Sucrose (sugar) is a major component of plant sap that carries chemical energy from one part to another. Lactose supplies newborn mammals with fuel for growth and development. Sugars can be linked to make olgiosaccharides (more then two sugars linked). They are found covalently attached to lipids and proteins, converting them into glycolipids and glycoproteins, especially in the plasma membrane. These carbohydrates can play an informational rule, they help distinguish one type of cell from another and help mediate specific interactions. Polysaccharides Liver tissues, contain an insoluble polymer of glucose called glycogen. As the body needed sugar, glycogen in the liver was transformed to glucose, which was released in the bloodstream to satisfy depleted tissues. Glycogen and Starch: Nutritional Polysaccharides - Glycogen is a branched monomer: glucose. Most of the sugar units are joined by alpha glycosidic bonds. Glycogen serves as a storehouse of surplus chemical energy in most animals. Glycogen is highly concentrated when stored in cells and appears as a dark staining. Plants bank their surplus chemical energy in form of starch, a polymer of glucose. Starch is a mixture of two different polymers, amylase and amylopectin. Starch is stored as densely packed granules, starch grains, which are enclosed in membrane bound or ganelles within the plant cell. Cellulose, Chitin, and glycosaminoglycans: Structural Polysaccharides – Cotton and linen have cellulose, which is the major component of plant cell walls. Cellulose consists solely of glucose monomers, the glucose units are joined by beta linkages. Chitin is an unbranched polymer of the sugar N- acetylglucosamine, which is similar in structure to glucose. Chitin is a tough, resilient, yet flexible material unlike certain plastics. Glycosaminoglycans (GAGs) their structure –A—B—A—B—where A and B represent two different sugars. Most GAGs are found in spaces that surround cells. Lipids Lipids are all nonpolar molecules with the ability to dissolve in organic solvents, and they are known for their inability to dissolve in water. Lipids include fats, steroids, and phospholipids. Fats Fats consist of a glycerol molecule linked by ester bonds to three fatty acids, the composite is triacylglycerol. Fatty acids are long, unbranched hydrocarbon chains with a single carboxyl group at one end. The hydrocarbon chain is hydrophobic, whereas the carboxyl group (--COOH) is hydrophilic. Molecules that have both phobic and philic regions are amphipathic. Fatty acids differ from one another in length of hydrocarbon chain and presence or absence of double bonds. Fatty acids lack double bonds, they are saturated but if they have double bonds they are saturated. The more double bonds the less effective these long chains can be packed together. This lowers the temperature at which fatty acid lipid melts. Fats that are liquid at room temperature are oils. Solid shortenings, are formed form unsaturated vegetable oils by chemically reducing double bonds. (hydrogenation
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