Bio Week 2 Notes
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This 7 page Class Notes was uploaded by Mary Notetaker on Thursday September 8, 2016. The Class Notes belongs to BIO 101 at University of South Carolina taught by Mihaly Czako in Fall 2016. Since its upload, it has received 2 views.
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Date Created: 09/08/16
Chapter 2: The Chemical Context of Life Iodine is a trace element required by organisms in minute quantities by humans and other vertebrates but not bacteria/plants Chemical connection to biology o Biology is study of life o Living organisms and their environments are subject to basic laws of physics and chemistry Ex: use of formic acid by ants to protect themselves against predators and microbial parasites o Organisms are composed of matter – anything that takes up space and has mass Elements and compounds o Matter is made of elements Element – substance that cannot be broken down to toher substance by a chemical reaction Compound – substance consisting of two or more elements in a fixed ratio Different characteristiics than elements 2025% of 92 elements are essential C, H, O, N make up 96% of living matter Last 4% is Ca, Phosphorus, K, S Trace elements are required by organisms in minute quantities Some elements are poisonous Atoms o Composed of subatomic particles Protons, neutrons, electrons o P and N form atomic nucleus o E form cloud around nucleus o Neutron mass and proton mass are almost identical and measured in daltons o 1.66x10^27 Atomic nimber and atomic mass o Atoms of various elements differ in number of subatomic particles o Atomic # number of protons in nucleus o Mass # sum of protons and neutrons in nucleus o Atomic mass – atom’s total mass, approximated by mass # o Isotopes – atoms of same element w different number of neutrons Radioactive tracers o Radioactive isotopes used in diagnostic tools in medicine o Radioactive tracers used to track atoms through metabolism Radiometric dating o Parent isotope decays into its daughter isotope at a fixed rate, expressed as half life o Scientists measure the ratio of different isotopes and calculate how many half lives have passed since the fossil or rock was formed o Varies in time Energy levels of electrons o Energy is capacity to cause change o Potential energy is the energy matter has because of its location or structure o Electrons of an atom differ in amounts of potential energy o Electron’s state of potential energy is called its energy level or electron shell o E Distribution and Chemical properties o Chemical behavior of an atom is determined by the distribution of e in electron shells o PT shows e distribution for each element o Valence e in outermost shell o Chemical behavior of an atom is mostly determined by valence e o Electron orbitals – three dimensional space where electrons usually are o Each e shell has a specific number of orbitals o Elements w a full valence shell are chemically inert Formation and Function of molecules depend on chemical bonding of atoms o Atoms with full valence shells can share or transfer those electrons with other atoms Interactions usually result in attractions called chemical bonds o Covalent bond – sharing of a pair of valence e by two atoms, strongest bond Shared e count as part of each atom’s valence shell o Molecule – two or more atoms held together by covalent bonds o Single bond – single covalent, sharing of one pair of valence e o Double bond – double covalent, sharing of two pairs of valence e o Structural formula – notations that represents atoms and bonding Ex: HH Abbreviated further with molecular formula Ex: H2 o Covalent bonds form between atoms of same or different elements o Compound – combination of two or more elements o Valence – atom’s bonding capacity o Atoms in a molecule attract electrons to varying degrees o Electronegativity – atom’s attraction for the electrons in a covalent bond o More eneg, stronger pull of e o Nonpolar covalent bond – electrons shared equally o Polar covalent bond – one atom more EN, don’t share equally Unequal sharing of e causes partial pos or neg charge for each atom or molecule Ionic Bonds o Atoms sometimes take e from bonding partners Ex: e transfer from NA to Cl After transfer, both atoms have charges o Ion – charged atom or molecule o Cation – positively charged ion o Anion – negatively charged ion o Ionic bond 0 electrostatic attraction between an anion and a cation Compounds formed by ionic bond – ionic compounds/salts Often found as crystals in nature Weak Chemical Bonds o Most of strong bonds in organisms are covalent that form a cell’s molecules o Weak chemical bonds are also important Large biological molecules often held in functional form by weak bond Reversibility of weak bonds can be an advantage Gecko’s toe hairs to wall surface Hydrogen Bonds o Forms when a hydrogen atom covalently bonded to one EN atom is attracted to another EN atom In living cells – the EN partners are usually O or N atoms Van der Waals Interactions o If e distributed asymmetrically, may accumulate in one part of atom or molecule o VDW – attractions between molecules that are close together as a result of these charges Hydrophilic and hydrophobic o Hydrophilic – groups attracted to water o Hydrophobic – association/effect is result of thermodynamic favorability to place hydrophilic on the outside towards water and the HPs together on the inside Molecular shape and Function o Molecule’s shape – important to function Shape determined by positions of atom’s orbitals In covalent bond, s and p may hybridize, making specific shapes Shape crucial in biology because it determines how biological molecules recognize and respond to one another Opiates, like morphine, have similar effects because similar shapes and bind same receptors in brain Chemical reactions make and break chemical bonds o Chemical reactions – making and breaking of chemical bonds o Reactants – starting molecules of a chemical reaction o Products – final molecules of a chemical reaction o Photosynthesis – impt chemical reaction Sunlight is energy for conversion of CO2 and H2O to glucose and O2 o All chemical reactions are reversible o Chemical equilibrium – reached when forward and reverse reactions occur at the same rate o At equilibrium – relative concentrations of reactants and products don’t change Chapter 3: Molecule that supports all of life o water is the biological medium on Earth only common substance to exist in the natural environment in three physical states of matter structure of water molecule allows it to interact with other molecules – hydrogen bonds unique properties make it suitable for life Polar covalent bonds in water molecules = hydrogen bonding o Electrons of the polar covalent bonds spend more time near O than H because it is more EN o Water molecule is therefore polar, unevenly distributed charge o Polarity allows water to form hydrogen bonds 4 emergent properties of water contribute to earth’s stability ofr life o 4 properties facilitate healthy environment cohesive behavior collectively hydrogen bonds hold water together through cohesion cohesion helps transport water against gravity in plants adhesion is an attraction between different substances o ex: between water and plant cell walls surface tension is a measure of how hard it is to break the surface of a liquid water has unusually high surface tension due to hydrogen bonding between the water molecules at the airwater interface and to the water below ability to moderate temperature water absorbs heat from warmer air and releases stored heat to cooler air water can absorb or release a large amount of heat with only a slight change in its own temperature Temperature and Heat o Kinetic energy – energy of motion Associated with random motion of atoms or molecules is called thermal energy Temperature is a measure of energy that represents the average kinetic energy of the molecules in a body of matter Thermal energy in transfer from one body of matter to another is defined as heat o Caolore – amount of heat require to raise the temperature of 1g of water by 1 degree C Calories on food are kilocalories where 1 kcal = 1,000 calories Joule is unite of energy, 1 J = .239 cal or 1 cal = 4.184 J o Water has high specific heat Specific heat of a substance is the amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1 degree C Water resists changing its temperature because of its high specific heat This can be traced to hydrogen bonding Heat is absorbed when H bonds break Heat is released when H bonds form High specific heat of water minimizes temperature fluctuations to within limits that permit life o Evaporative cooling Evaporation – transformation of a substance from liquid to gas Heat of vaporization – heat a liquid must absorb for 1g to be converted to gas As liquid evaporates, its remaining surface cools, a process called evaporative cooling this helps stabilize temperatures in organisms and bodies of water expansion upon freezing ice floats in liquid water because hydrogen bonds in ice are more ordered, making ice less dense than water o water reaches its greatest density at 4 degrees C (39.2 F) o if ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth o scientists worry that global warming, caused by CO2 and other greenhouse gases is having a profound effect on icy environments around the globe rate at which glaciers and arctic sea are disappearing is posing an extreme challenge to animals that depend on ice for their survival versatility as a solvent solvent of life solution – liquid that is a completely homogeneous mixture of substances solvent – dissolving agent of a solution solute – substance that is dissolved aqueous solution – solution in which water is the solvent water is a versatile solvent due to its polarity when an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell water can also dissolve compounds made of nonionic polar molecules even large polar molecules like proteins can dissolve in water if they have ionic polar regions o Hydrophilic and Hydrophobic Substances Hydrophilic – substance that has an affinity for water Hydrophobic – substance that does not have an affinity for water Oil molecules are hydrophobic because they have relatively nonpolar bonds Hydrophobic molecules related to oils are the major ingredients of cell membranes, so is cholesterol Hydrophilic groups of atoms are attracted to water o Solute Concentration in aqueous solutions Most chemical reactions in organisms involve solutes dissolved in water When carrying out experiments, we use mass to calculate the number of solute molecules in an aqueous solution Molecular mass – sum of all masses of all atoms in a molecule Numbers of molecules are usually measured in moles, 1 = 6.02 * 10^23 molecules Avogadro’s number and the unit Dalton were defined so 6.02 * 10^23 Daltons = 1g Molarity – number of moles of solute per liter of solution o Possible evolution of life on other planets Biologists seeking life on other planets have concentrated their search on planets with water To date, more than 200 planets have been found outside our solar system, evidence that some have water vapor Mars has water o Acidic and basic conditions affect living organisms Hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other The hydrogen atom leaves its electron behind and is transferred as a proton, or hydrogen ion Molecule that lost the proton is now a hydroxide ion Molecule with an extra proton is now hydronium ion Water is in a state of dynamic equilibrium in which water molecules dissociate at the same rate at which they are formed Dissociation is rare changes in concentration of H+ and OH, can affect chemistry of a cell concentrations of H+ and OH are equal in pure water o adding certain solutes, acids and bases, effects concentration o biologists use pH scale to describe acidity or basicity of a solution o Acids and Bases Acid – any substance that increases the H+ of a solution Base – any substance that reduces the H+ concentration of a solution Strong acids and bases dissociate completely in water Weak acids and bases reversibly release and accept back hydrogen ions but can still shift H+ and OH away from neutrality o pH scale in any aqueous solution at 25C, product of H+ and OH concentration is constant and [H+][OH] = 10^14 pH = log[H+] acid < 7, base > 7 most biological fluids have pH between 6 and 8 o Buffers Internal pH of most living cells must remain close to pH 7 Buffers are substances that minimize changes in concentrations of H+ and OH in a solution Most buffers contain a weak acid and its corresponding base which combine reversibly with hydrogen ions o Acidification: A Threat to Water Quality Human activities such as burning fossil fuels threaten water quality CO2 is the main product of fossil fuel combustion About 25% of humangenerated CO2 is absorbed by the oceans CO2 dissolved in sea water forms carbonic acid, process called ocean acidification As seawater acidifies, H+ ions combine with carbonate ions to produce bicarbonate Carbonate is required for calcification (production of calcium carbonate) by many marine organisms, including reef –building corals Much progress made in learning about the delicate chemical balances in oceans, lakes, and rivers
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