Chapter 2 - Cell Bio - The Chemical Basis of Life.docx

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University of Toronto Scarborough
Biological Sciences
Rene Harrison

The Chemical Basis of Life o Atoms that make up a molecule are joined together by a covalent bonds in which pairs of electrons are shared between pairs of atoms Fundamental principle that an atom is most stable when its outermost electron shell is filled. The number of bonds an atom can form depends on the number of electrons needed to fill its outer shell Water, for example, has the oxygen atom that is linked to each hydrogen atom by a single covalent bond. H:O or HO The formation of covalent bonds is accompanied by the release of energy; energy required to split CH, CC, CO covalent bonds is quite large between 80 to 100 (kcal/mol) of molecules Two atoms can be joined by bonds in which more than one pair of electron is shared. If two electron pairs are shared, as occurs in molecular oxygen, the covalent bonds are said to be double bonds, and if three pairs of electrons are shared as in molecular nitrogen, it is a triple bond. Quadruple bonds are not known to occur Atoms joined by a single bond are able to rotate relative to one another, whereas atoms of double or triple bonds lack this ability. Double bonds function as energy capturing centers, driving such vital processes as respiration and photosynthesis When atoms of the same element bond to one another, as in H2, the electron pairs of the outer shell are equally shared between the two bonded atoms When two unlike atoms are covalently bonded, however, the positively charged nucleus of one atom exerts a greater attractive force on the outer electrons than the other thus the most electronegative atom atom with most attractive force Nitrogen and oxygen are strongly electronegative atoms o Waters single oxygen atom attracts electrons much more forcefully than do either of its hydrogen atoms OH bonds of a water molecule are said to be polarized such that one of the atoms has a partial negative charge while other has partial positive charge Molecules such as water, that have an asymmetric distribution of charge or dipole are referred to as polar molecules Polar molecules contain one or more electronegative atoms, usually an O, N, and/or S. Molecules that consist entirely of carbon and hydrogen atoms are said to be nonpolar. Large nonpolar molecules, such as waxes and fats, are relatively inert Proteins and phospholipids contain both polar and nonpolar regions, which behave very differently o Some atoms are so strongly electronegative that they can capture electrons from other atoms during a chemical reaction. Example: Sodium and chlorine (NaCl) are mixed, the single electron in the outer shell of each sodium atom migrates to the electron-deficient chlorine atom as a result, these two atoms are transformed into charged ions Because the chloride ion has an extra electron, it has a negative charge it is referred to as an anion Since the sodium atom, which has lost its electron, has an extra positive charge, it is termed a cation o Covalent bonds are strong bonds between the atoms that make up a molecule Interactions between molecules are governed by a variety of weaker linkages called noncovalent bonds Noncolavent bonds do not depend on shared electrons but rather on attractive forces between atoms having an opposite charge. Individual noncovalent bonds are weak and are thus readily broken and reformed Even though individual noncovalent bonds are weak, when large numbers of them act in concert, as between the two strands of a DNA molecule or between different parts of a large protein, their attractive forces are addictive o A crystal table salt is held together by an electrostatic attraction between positively charge Na and negative charged Cl. This type of attraction between fully charged components is called ionic bond (or a salt bridge) Since cells within body are composed primarily of water, bonds between free ions are of little importance. In contrast, weak ionic bonds between oppositely charged groups of large biological molecules are of considerable importance. Example: when charged phosphate atoms in DNA molecule are closely associated with positively charged groups on the surface of a protein, ionic bonds between them help hold the complex together. Strength of ionic bonds in a cell is generally weak (about 3 kcal/mol) due to the presence of water, but within core of protein where little water, bonds can be much stronger o Hydrogen atoms are 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 This weak attractive interaction is called a hydrogen bond Hydrogen bonds occur between most polar molecules and are particularly important in determining the structure and properties of water. Hydrogen bonds also form between two polar groups present in large biological molecules, as occurs between two strands of a DNA molecule Since their strength is additive, the large number of hydrogen bonds makes DNA structure stable Individual hydrogen bonds are weak (2-5 kcal/mol) two strands can be partially separated to allow enzymes access to individual strands of the DNA molecule o Because of their ability to interact with water, polar molecules, such as sugars and amino acids, are said to by hydrophilic which means water loving Nonpolar molecules, such as steroid or fat molecules, are essentially insoluble in water because they lack the charged regions that would attract them to the poles of water molecules. When nonpolar compounds are mixed with water, the nonpolar, hydrophobic which is the water fearing molecules are forced to aggregates, which minimizes their exposure to the polar surrounding This association of nonpolar molecules is called a hydrophobic interaction
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