Bio5A Topics 2-3: Water & Carbon
Bio5A Topics 2-3: Water & Carbon Biol 5A
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This 5 page Class Notes was uploaded by Akash Patel on Monday March 28, 2016. The Class Notes belongs to Biol 5A at University of California Riverside taught by Sean Cutler in Winter 2016. Since its upload, it has received 8 views. For similar materials see Intro: Cell and Molecular Biology in Biology at University of California Riverside.
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Date Created: 03/28/16
TOPIC TWO: WATER ● Water forms a network of hydrogen bonds ○ H and O in water are joined by a polar covalent bond: the electrons in a water molecule spend more time near the oxygen ○ Water is a polar molecule with a partial negative charge near the oxygen and partial positive charge near the hydrogens ○ In its liquid state, water molecules can form four hydrogen bonds with other water molecules ○ The polar nature of water gives it several important properties ● Cohesion: when hydrogen bonds hold water molecules together ○ cohesion allows water to be transported in plants against the force of gravity ○ Water evaporates out of leaves and cohesion helps pull water up from the roots ○ contributes to surface tension ● Adhesion: when water interacts with other molecules ○ In a tree, it will form hydrogen bonds with the cell walls, helps it travel against the force of gravity ● Water is a polar solvent and will react with other polar molecules, called hydrophilic ● Hydrocarbon chains (regions involving C and H) are highly nonpolar and hydrophobic ● Water has a high specific heat capacity ○ Because of the many hydrogen bonds water molecules can form with each other in liquid, water requires a large amount of energy to change its temperature by even small amounts. ○ The specific heat of a substance is the amount of heat that must be added to increase 1g of the substance by 1 degree C ○ Specific heat of water: 4.18 J/g(degree C) ○ High specific heat allows it to absorb a large amount of energy without changing temperature much ● Water has a high heat of vaporization ○ hard to moderate the climate on earth ○ cooling effect of evaporating water keeps plant and animal life cool at higher temperatures ● Water is less dense when it is frozen ○ in liquid water, molecules are closer hydrogen bonds are breaking and reforming. ○ in ice, a regular array of water molecules forms, with stable hydrogen bonds ○ This property is important for life in earth’s bodies of water because if ice was denser than water, lakes and ponds would freeze from the bottom ● In liquid, sometimes a hydrogen nucleus transfers to another water molecule to produce a hydronium ion (H3O+) and a hydroxide ion (OH) ● Hydrogen has no neutron in its atomic nucleus ○ a hydrogen ion (H+) is the same thing as a proton ● The concentrations of H+ and OH are both 10^7 moles per L ○ When acids or bases are added, the relative concentration of the ions can be changed ○ Acids increase the concentration of H+ ions ○ Bases decrease the amount of H+ ions by accepting a proton or by producing OH ions ○ pH = log10[H+] ○ [H+][OH] = 10^14 ○ pH + pOH = 14 ○ in neutral water [H+]=10^7 so pH= log(10^7)= (7) = 7 ○ Acids have a pH < 7 ○ Bases have a pH > 7 ● A buffer is a substance that can minimize changes in H+ and OH in a solution by combining with excess H+ ions or donating them ○ As the pH rises, the equilibrium shifts to the right ○ As the pH falls, it shifts to the left ○ buffers allow biological systems to resist changes in pH so that biomolecules can stay in their optimum pH range TOPIC 3: CARBON ● Life on earth is carbonbased because of the properties of the carbon atom ○ Carbon has 4 valence electrons, allowing it to form covalent bonds with up to four different atoms ○ able to give rise to many complex compounds and polymers ○ Carbon Skeleton: interconnected carbons where various functional groups are attached ■ can be linear, branched, or in rings ■ usually involving single or double bonds ● The simplest carbon skeletons are hydrocarbons ○ molecules consisting only of carbon and hydrogen ○ Simple hydrocarbons containing no rings and only single bonds are alkanes ■ only have CH and CC bonds ○ named for the number of carbons in the longest chain ○ When carbon in a molecule has only single bonds, and all are available bonds are with hydrogen, it is saturated ○ Hydrocarbons with at least one double bond with 2 carbons, are called alkenes ○ Double bonds result in unsaturated molecules ■ unsaturated molecules are less flexible ○ Hydrocarbons involve only nonpolar bonds, hydrocarbons are hydrophobic ○ store a large amount of chemical energy ○ when completely oxidized, they generate CO2 and H2O and energy ○ Pure hydrocarbons are not generally found in cells but molecules with hydrocarbon portions ● Organic chemists draw carbon skeletons using a simplified notation ○ straight line is a single bond ○ double line is a double bond ○ end of a line or the place where two lines meet, is a carbon atom ○ atoms other than carbon are indicated by their chemical symbol ○ implied that all remaining bonds possible with a carbon are with hydrogens ● Two compounds are isomers if they share the same chemical formula but have different structures ○ creates different chemical properties ○ Structural isomers: differ in the arrangement of bonds ○ cistrans isomers: isomers that differ in arrangement of atoms around a C=C double bond ■ important in the properties of dietary fats and fatty acids in membranes ○ Enantiomers: isomers involving at least one asymmetric carbon ■ asymmetric carbon: one carbon joined to four different atoms or groups of atoms ■ 2 enantiomers are mirror images of each other and are named either L or D ■ In living systems, the L enantiomer is the most common form of amino acids ● There are 7 major functional groups ○ ○ Hydroxl, carbonyl, carboxyl, and amino contain oxygen or nitrogen and can participate in hydrogen bonding ● Hydroxl group ○ Turns hydrocarbon into an alcohol ○ found in carbohydrates ○ can interact with water ● Carbonyl group: ○ double bonded oxygen ○ if it is present in the middle of a carbon skeleton, the compound is called a ketone ○ if it is at the end, it is called an aldehyde ● Carboxyl group: ○ carbonyl group attached to a carbon that is also attached to a hydroxyl ○ highly polar, in solution ionizes to release a proton ○ also called carboxylic acid (COO) ● Amino group: ○ forms amine compounds ○ in solution, the lone pair of electrons on the nitrogen can interact with a proton and will function as a base ■ NH3+ ● Sulfhydryl group: ○ polar ○ consists of sulfur and hydrogen ○ amino acid cysteine contains this ● Phosphate group: ○ phosphate atom bonded to four oxygen atoms ○ if at the end of the molecule, it has a net charge of 2 ○ if in the middle of the molecule, it has a net charge of 1 ○ important in the structure of nucleotides ○ addition or removal of phosphates is also important for regulating the functions of proteins in cells ● Methyl group: ○ small hydrocarbon group ○ hydrophobic, unlike the other groups ○ important in DNA structure and gene regulation ○ in thymine but not uracil ● The major molecules in life systems are carbohydrates, lipids, proteins, and nucleic acids ○ Carbohydrates, lipids, and proteins can become large because their monomers form long polymers ● Long polymers are built up by adding monomers together ○ the OH of one monomer joins with the H of another monomer to form a net covalent bond and releases water ○ dehydration: a water molecule is removed from the two monomers, joining the monomers together ○ Nucleic acid polymers are used to store or convey genetic information ○ Proteins are products of genes ○ For lipids and carbohydrates, building of long polymers is a way to store energy or build cell structures ● To break down polymers, the covalent bond holding two monomers together is broken ○ To each part, a H or OH is added in a reversal of dehydration ○ Hydrolysis: breakdown of polymers into smaller pieces using water ○ For proteins and nucleic acids, hydrolysis is used primarily to recycle monomers ○ For lipids and carbohydrates, hydrolysis will start the process of collecting stored energy