Chapter 2.1 Chemical Basis of Life PDF

CHAPTER 2 The Chemical Basis of Life and Required reading: Karp Chapter 2 The organic chemistry in this slide deck is largely review but is critical for our understanding of the major classes of macromolecules in the cell Remember that there is a glossary on-line for each chap...

CHAPTER 2 The Chemical Basis of Life and Required reading: Karp Chapter 2 The organic chemistry in this slide deck is largely review but is critical for our understanding of the major classes of macromolecules in the cell Remember that there is a glossary on-line for each chapter and you should always be clear on the meaning of a word Remember to use the all the on-line resources; the glossary, flashcards quizzes, practice questions (under assignments) and review the following animation – “Atoms and Chemical Bonds” 2.1-1  Distribution of some elements Note which elements are abundant in humans Red = most abundant (99%) Blue = 0.9% Green = required in trace amounts Yellow = undetermined if essential Remember that elements in vertical columns must gain or lose the same number of electrons to fill their outer shells and behave similarly in bond formation 2.1-2  2.1 | Covalent Bonds covalent bonds = pairs of electrons are shared between pairs of atoms. An atom is most stable when its outermost electron shell is filled, and the number of bonds an atom can form depends on the number of electrons needed to fill its outer shell 2.1-3  2.1 | Covalent Bonds The chemistry of living organisms is organized around carbon Carbon accounts for over half the dry weight of a cell Carbon atoms share electron pairs with each other and most commonly with hydrogen oxygen nitrogen sulfur Single bond = a single pair of electrons is shared and free rotation around the bond axis Double bond = two pairs of electrons are shared and no free rotation around the bond axis Triple bond = three pairs of electrons are shared and no free rotation around the bond axis 2.1-4 2.1 | Covalent Bonds Nonpolar and Polar Molecules Nonpolar Covalent = Equal sharing of electrons Polar Covalent = Uneven sharing of electrons: water’s oxygen atom attracts electrons better than does hydrogen The O-H bonds are polarized, one atom with a partial negative charge and the other atom a partial positive charge Generally (but not always) a single covalent bond between two atoms results in an unequal sharing of electrons electronegativity: an indication of an atom’s ability to attract an electron (they The high electronegativity value are electron deficient) of oxygen allows it to function as the final electron acceptor in the the more electronegative (or the stronger electron transfer chain which the electronegativity) the greater the then ultimately results in ability of an atom to attract an electron 2.1-5 production of ATP 2.3 | Noncovalent Bonds Hydrogen Bonds How many covalent bonds can an atom of hydrogen participate in? ONE What happens when hydrogen is covalently bound to a different electronegative atom? The electronegative atom “owns” they hydrogen electron creating an electropositive hydrogen Can the hydrogen still form an additional bond ? YES! With an electronegative atom 2.1-6 2.3 | Noncovalent Bonds Hydrogen Bonds Hydrogen Bond: weak attractive interaction between an electronegative atom and a hydrogen atom that is covalently linked to a second electronegative atom weak, but VERY important interactions in cells Hydrogen bears a partial positive charge when covalently bonded to an electronegative atom This hydrogen atom can approach a second electronegative atom to form an interaction called a hydrogen bond Hydrogen bonds (1 kcal/mol) are easily broken and occur between most polar molecules Since their strength is additive, the large number of hydrogen bonds between the strands makes the DNA duplex a stable structure 2.1-7  Water: H2O Water accounts for around 75-85% of a cell’s weight Most intracellular reactions occur in an aqueous environment Extracellular fluid usually aqueous In each water molecule: two H atoms are linked to the O atom by covalent bonds these are very polar covalent bonds because the oxygen “owns” the electrons hydrogen has a positive charge oxygen has a negative charge What happens when a positively charged region of one water molecule (hydrogen) approaches a negatively charged region (oxygen) of another water molecule? 2.1-8 Water: H2O the extensive hydrogen bonding between water molecules accounts for many of the properties of water 2.1-9  2.3 | Noncovalent Bonds The Life-Supporting Properties of Water The cell contains a complex mixture of dissolved substances, or solutes Water is able to dissolve more types of substances than any other solvent and helps determines the structure of molecules and their types of interactions Water is the fluid matrix around which the insoluble fabric of the cell is constructed and the medium through which materials move between compartments It is a reactant or product in many cellular reactions; and it protects the cell in many ways—from excessive heat, cold, or Hydrogen bond formation between neighboring water molecules damaging radiation 2.1-10  2.3 | Noncovalent Bonds The Life-Supporting Properties of Water The structure of water is suitable for sustaining life: 1) It is asymmetric, both H atoms are on one side 2) Both covalent O–H bonds are highly polarize 3) All three atoms readily form H-bonds. Evaporation requires that water molecules break their hydrogen bonds, taking energy to convert water to steam Mammals take advantage of this when they sweat because the heat required to evaporate the water is absorbed from the body, which thus becomes cooler 2.1-11  How many Hydrogen bonds is a water molecule capable of? A water molecule can form up to four hydrogen bonds simultaneously The oxygen atom of a water molecule is the hydrogen bond At 37o C ~ 15% of water acceptor for two hydrogen atoms molecules are joined to Each O-H group serves as a four others hydrogen bond donor When every water molecule forms the maximum of four hydrogen bonds creating a regular crystal lattice = ice 2.1-12 2.3 | Noncovalent Bonds Ionic bonds: Attraction between charged atoms A NaCl crystal is held together by an electrostatic attraction between Na+ and Cl− ions, called an ionic bond Ionic bonds within a crystal may be quite strong, but in water, these ions becomes surrounded by water molecules This inhibits oppositely charged ions from approaching one another closely enough to form ionic bonds. The dissolution of a salt crystal. Weak ionic bonds between oppositely charged groups of large biological molecules are of considerable importance Ionic bonds in a cell are weak (3 kcal/mol) due to water, but deep within the core of a protein, where water is often excluded, bonds can be much stronger 2.1-13  Water as solvent In the absence of water, electrostatic forces are very strong Hydrophilic = water loving Hydrophobic = water hating Ions dissolve readily in water Molecules that contain polar bonds and that can form hydrogen bonds with water dissolve readily in water includes sugars, DNA, RNA, and most proteins 2.1-14 Water as solvent water forms spheres of hydration that neutralize the attraction of + and 2.1-15 - ions  Covalent bonds are stronger and more stable than noncovalent bonds/interactions More energy is required to break covalent bonds than noncovalent More electrons are shared in double bonds so more energy is required to break a double bond than a single bond Noncovalent interactions are weak enough that they are continually formed and reformed at room temperature (and together, multiple noncovalent interactions can make one very strong interaction between molecules or parts of molecules) 2.1-16 The energy required to break the bonds varies Note that visible light is lower in energy than carbon-carbon bonds What would the consequences be if this were not the case? Think about the consequences of UV light (too much sun exposure) 2.1-17 Hydrophilic Molecules 2.1-18  2.3 | Noncovalent Bonds Hydrophobic “Interaction” and Van der Waals Forces Polar molecules associate with water and are hydrophilic Nonpolar molecules lack the charged regions that would attract them to water molecules and are hydrophobic They are forced into aggregates to reduce exposure to water, called a hydrophobic “interaction” (hydrophobic EFFECT) Not true bonds because they result from an energetic drive to exclude Hydrophobic interactions reduce water away from the hydrophobic exposure to hydrophilic molecules surfaces 2.1-19  Nonpolar molecules and nonpolar portions Hydrophobic molecules of molecules tend to aggregate in water = Hydrophobic Effect Water cannot form hydrogen bonds with nonpolar substances Water will form hydrogen bonds with other water molecules and surround a nonpolar molecule The less hydrophobic surface, the more energetically favorable it is for water to surround nonpolar molecules How is this accomplished? By nonpolar molecules being forced to aggregate C-C and C-H bonds are the most common nonpolar bonds in biological systems 2.1-20 Hydrophobic Effect Hydrophobic effect is NOT an attraction between particles but is instead an avoidance of an energetically unfavorable state 2.1-21 Hydrophobic Effect 2.1-22 2.5 | The Nature of Biological Molecules Major components of cell membranes Lipids Proteins Carbohydrates 2.1-23  2.5 | The Nature of Biological Molecules Compounds produced by living organisms are called biochemicals Most of the dry weight of an organisms consists of molecules containing atoms of carbon. The chemistry of life centers around the chemistry of the carbon atom Having four outer-shell electrons, a carbon atom can bond with up to four other atoms. Each carbon atom is able to bond with other carbon atoms so as to construct molecules with backbones containing long chains of carbon atoms, which may be linear, branched, or cyclic 2.1-24 2.5 | The Nature of Biological Molecules The size and electronic structure of carbon make it uniquely suited for generating over several hundred thousand molecules The simplest group of organic molecules, the hydrocarbons, are chains or rings that contain only carbon and hydrogen atoms Hydrocarbons do not occur in significant amounts within most living cells They are economically important, because petroleum products, including gasoline and natural gas, are hydrocarbons In biology, they are of limited importance because they are not soluble in water 2.1-25 2.5 | The Nature of Biological Molecules Functional Groups As more carbons are added, the skeletons of organic molecules increase in length and their structure becomes more complex Many important organic molecules in biology contain chains of carbon atoms, with certain hydrogen atoms are replaced by various functional groups Functional groups often behave as a unit and give organic molecules their physical properties, chemical reactivity, and solubility in aqueous solution The most common linkages between functional groups are ester bonds, which form between carboxylic acids and alcohols, and amide bonds, which form between carboxylic acids and amines 2.1-26  Learning objectives for chapter 2 Chemistry Review Understand covalent, noncovalent, polar covalent and nonpolar covalent bonds Understand the relationship between breaking bonds and types of bonds Understand hydrogen bonding Understand how water acts as a solvent Understand the hydrophobic effect