CAMPBELL BIOLOGY IN FOCUS URRY CAIN WASSERMAN MINORSKY
CAMPBELL BIOLOGY IN FOCUS URRY CAIN WASSERMAN MINORSKY REECE 2 The Chemical Context of Life Lecture Presentations by Kathleen Fitzpatrick and Nicole Tunbridge, Simon Fraser University 2016 Pearson Education, Inc. SECOND EDITION Overview: A Chemical Connection to Biology Biology is a multidisciplinary science Living organisms are subject to basic laws
of physics and chemistry 2016 Pearson Education, Inc. Concept 2.1: Matter consists of chemical elements in pure form and in combinations called compounds Chemistry: study of matter Matter: anything that takes up space and has weight or mass; Made up of elements Elements: pure substances that can not be broken down further 92 naturally occurring elements Listed in Periodic Table of Elements C, Na, Ca 25 elements required for life 96% of life made of COHN 2016 Pearson Education, Inc.
Compound: a substance consisting of two or more elements in a fixed ratio It has emergent properties: characteristics different from those of its elements Sodium 2016 Pearson Education, Inc. Chlorine Sodium chloride The Elements of Life Trace elements: required in only tiny quantities E.g. In vertebrates, iodine (I) is required for normal activity of the thyroid gland In humans, an iodine deficiency can cause goiter
2016 Pearson Education, Inc. Table 2.1 2016 Pearson Education, Inc. ATOMS Elements are made up of tiny units called atoms the smallest complete unit of an element Atoms contain 3 smaller units called subatomic particles Subatomic particle symbol charge Proton p+ +1 each 1d Neutron n
0 1d Electron e- -1 each mass location nucleus nucleus 0 orbiting
Mass of 1dalton = 1d = 1.67 x 10-24 g NOTE: in an electrically neutral atom, the # of p + = # of e- Figure 2.3 Electrons Cloud of negative charge (2 electrons) Nucleus (a) 2016 Pearson Education, Inc. (b)
CHARACTERISTICS OF AN ATOM Atomic number: equal to the # p+ 6 C; shown top/top left of symbol in an electrically neutral atom, #p+ = # eidentity of element (never changes) Periodic Table is organized by atomic number Atomic mass: combined weights of p+ and n 12.01 C; shown bottom/bottom left of symbol mass = # p + # n n = mass atomic number NOTE: mass can vary, because number of n can vary Isotopes: atoms of same element with different masses same atom; different #n 12C, 13C, 14C CARBON ATOM
Atomic # = ? Atomic mass = ? #n=? Radioactive isotopes: are unstable and give off particles and energy as radioactivity Some applications of radioactive isotopes in biological research are: Dating fossils Tracing atoms through metabolic processes Diagnosing medical disorders 2016 Pearson Education, Inc. e- orbit nucleus in regions called orbitals
ORBITALS AND SHELLS 7 energy levels or electron shells Corresponds to 7 periods of Periodic Table Figure 2.5 (a) A ball bouncing down a flight of stairs can come to rest only on each step, not between steps. Third shell (highest energy level in this model) Second shell (higher energy level) First shell (lowest energy level)
(b) 2016 Pearson Education, Inc. Atomic nucleus Energy absorbed Energy lost ENERGY LEVELS (SHELLS) OF ELECTRONS There are 7 known energy levels or electrons shells Correspond to 7 periods in the Periodic Table of Elements 7 horizontal rows = 7 energy levels = 7 electron
shells 1st Energy Level: holds a maximum of 2 e 2nd Energy Level: holds a maximum of 8 more e 3rd Energy Level: holds a maximum of 8 more e The first 18 elements are in order by atomic number in the first 3 periods/e- shells Organized by atomic number into 7 periods or energy shells PERIODIC TABLE 1st shell: max 2 e-; 2nd & 3rd shells: max 8 e- each Figure 2.6 Hydrogen 1H Atomic mass
First shell 2 He 4.003 Atomic number Helium 2He Element symbol Electron distribution diagram Lithium
15P Sulfur 16S Chlorine 17Cl Argon 18Ar Second shell Third shell 2016 Pearson Education, Inc.
Elements in a row (period) are in the same outermost energy level READING THE PERIODIC TABLE Valence shell = outermost energy level Valence electrons are those that occupy the valence shell
All elements in 2nd energy level have 3 to 10 e- each; but dont forget that 1st shell has 2 e- Elements in a column are called a group. Same # e- in outermost/valence shell PERIODIC TABLE Noble elements He (2e-) Ne (10e-) Ar (18e-) All inert; Valence shells are filled; happy QUICK CHECK
Atoms can combine to form molecules linked by chemical bonds. CHEMICAL BONDS Molecule: A substance made up of 2 or more atoms Chemical bond: attractions when atoms fill each others valence shell What determines chemical bonding? e- in valence shell (outermost) Atoms try to complete each others valence shells 3 Types of Chemical Bonds:
Covalent: polar and nonpolar Hydrogen Ionic Covalent Bonds Formed by sharing 1 or more pairs of valence electrons; Very strong bond
Tends to be groups closer to the middle of the Periodic Table Valence: bonding capacity of an atom; number of covalent bonds needed to complete outer valence shell; # of holes H-H Structural formula H2 Molecular Valence for H = 1, O = 2; N = 3; C = 4 Atoms try to complete each others valence shells (fill it
to max) 1st shell = 2e2nd shell = 8 more e3rd shell = 8 more e In a structural formula, a single bond, the sharing of one pair of electrons, is indicated by a single line between the atoms For example, HH A double bond, the sharing of two pairs of electrons, is indicated by a double line between atoms For example, O=O 2016 Pearson Education, Inc. Figure 2.8 Name and Molecular Formula Electron Distribution Diagram
(a) Hydrogen (H2) H H (b) Oxygen (O2) O O (c) Water (H2O) H O H (d) Methane (CH4)
H H C H 2016 Pearson Education, Inc. H Structural Formula Space-Filling Model Electronegativity
Atoms in a molecule attract electrons to varying degrees Electronegativity : an atoms ability to attract and hold shared electrons The more electronegative an atom, the more strongly it pulls shared electrons toward itself O >>>H..think H2O (water) O>>>C..think CO2 (carbon dioxide) N>>>H..think NH3 (ammonia) C = Hthink CH4 (methane) 2016 Pearson Education, Inc. NONPOLAR COVALENT BOND Nonpolar Covalent Bonds: formed by equal sharing of electrons nonpolar = nonpulling
Both atoms are equally electronegative Molecule has no charge H2, O2, Cl2, CH4 Gasoline, fat, grease, butter POLAR COVALENT BONDS Polar Covalent Bonds: formed by large differences in electronegativity Unequal sharing (polar = pulling) Creates partial + and - changes Bonds inside of H O NH CO 2 3, 2
H2O O H 2016 Pearson Education, Inc. H Examples of Polar and Nonpolar Covalent Bonds IONIC BONDS Ionic Bonds: transferring electrons When 2 atoms are very different in electronegativities Groups closest to the right or left side of Periodic Table
Ion: charged atom # p+ does not equal #e Result is a positively charged atom (cation) and a negatively charged atom (anion) Cation (e- donor).hint: remember ca+ion Positively charged atom Has more p+ than e Na+, Mg+, K+, Ca+2 Anion (e-acceptor) Negatively charged atom Has more e- than p+ Cl-, Br-, F Figure 2.10-s1 Na
Cl Na Sodium atom Cl Chlorine atom The attraction between the two ions of opposite charges is the ionic bond; called salts; they are fairly strong bonds as crystals but fragile in water 2016 Pearson Education, Inc. Figure 2.10-s2 Na
Cl Na Cl Na Sodium atom Cl Chlorine atom Na Sodium ion (a cation) Cl Chloride ion
(an anion) Sodium chloride (NaCl) 2016 Pearson Education, Inc. Figure 2.11 Na Cl 2016 Pearson Education, Inc. Hydrogen Bonds A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom In living cells, the electronegative partners are
usually oxygen or nitrogen atoms 2016 Pearson Education, Inc. Figure 2.12 H O Water (H2O) H Hydrogen bond
Ammonia (NH3) N H H 2016 Pearson Education, Inc. H Hydrogen Bonds HYDROGEN BONDS
Weak attractions that help stabilize biological molecules Between H2O molecules, between strands of DNA, between polar molecules Molecular Shape and Function A molecules shape is key to its function in the cell Molecular shape determines how biological molecules recognize and respond to one another Biological molecules recognize and interact with each other with a specificity based on molecular shape Molecules with similar shapes can have similar biological effects 2016 Pearson Education, Inc. Figure 2.13
Space-Filling Model Ball-and-Stick Model O H 104.5 H Water (H2O) H H
C H H Methane (CH4) 2016 Pearson Education, Inc. Figure 2.14 Key Natural endorphin Carbon Hydrogen Nitrogen Sulfur Oxygen
Morphine (a) Structures of endorphin and morphine Natural endorphin Brain cell Morphine Endorphin receptors (b) Binding to endorphin receptors 2016 Pearson Education, Inc. Concept 2.4: Chemical reactions make and break
chemical bonds Chemical reactions are the making and breaking of chemical bonds The starting molecules of a chemical reaction are called reactants The final molecules of a chemical reaction are called products All chemical reactions are reversible: Products of the forward reaction become reactants for the reverse reaction Chemical equilibrium is reached when the forward and reverse reaction rates are equal 2016 Pearson Education, Inc. Figure 2.UN02 O2
2 H2 Reactants 2016 Pearson Education, Inc. 2 H2 O Reaction Products Concept 2.5: Hydrogen bonding gives water properties that help make life possible on Earth All organisms are made mostly of water and live in an environment dominated by water Water molecules are polar molecules, with the oxygen region having a partial negative charge () and the hydrogen region a slight positive charge ()
Two water molecules are held together by a hydrogen bond 2016 Pearson Education, Inc. WATER CHEMISTRY Water is abundant and essential for life. Life evolved in water Cells 70-95% Covers 75% of Earth Polar molecule Good solvent Figure 2.16
Hydrogen bond H O H 2016 Pearson Education, Inc.
Polar covalent bonds Hydrogen Bonding Hydrogen bonding between water molecules is basis for all of waters unusual properties Cohesion (high surface tension) High specific heat (resists changes in temperature) High heat of vaporization Water expands when it freezes Water is a versatile solvent Hydrophilic: water loving compounds
Dissolve in water Polar Ionic Hydrophobic: water fearing compounds Do not dissolve in water (separate) Nonpolar Oil, gasoline, butter, CH4 HYDROGEN BONDING IN WATER Water is characterized by extensive hydrogen bonding (LIQUID AND SOLID) H bonds close together H bonds farther apart & lock Figure 2.17
H2O Two types of waterconducting cells Adhesion Cohesion Direction of water movement H2O 2016 Pearson Education, Inc. 300 m
H2O Temperature and Heat Kinetic energy is the energy of motion Thermal energy is a measure of the total amount of kinetic energy due to molecular motion Temperature represents the average kinetic energy of molecules Thermal energy in transfer from one body of matter to another is defined as heat 2016 Pearson Education, Inc. A calorie (cal) is the amount of heat required to raise the temperature of 1 g of water by 1C The calories on food packages are actually kilocalories (kcal), where 1 kcal 1,000 cal The joule (J) is another unit of energy, where
1 J 0.239 cal, or 1 cal 4.184 J 2016 Pearson Education, Inc. Waters High Specific Heat The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1C The specific heat of water is 1 cal/(g C) Water resists changing its temperature because of its high specific heat 2016 Pearson Education, Inc. Waters high specific heat can be traced to hydrogen bonding Heat is absorbed when hydrogen bonds break Heat is released when hydrogen bonds form
The high specific heat of water keeps temperature fluctuations within limits that permit life 2016 Pearson Education, Inc. Figure 2.19 Burbank Santa Barbara 73 Los Angeles 90 (Airport) 75 70s (F) 80s
90s 100s 2016 Pearson Education, Inc. San Bernardino 100 Riverside 96 Santa Ana Palm Springs 84 106 Pacific Ocean 68 San Diego 72 40 miles
Evaporative Cooling Evaporation (vaporization) is transformation of a substance from liquid to gas Heat of vaporization is the heat a liquid must absorb for 1 g to be converted to gas As a liquid evaporates, its remaining surface cools, a process called evaporative cooling Evaporative cooling of water helps stabilize temperatures in bodies or water and organisms 2016 Pearson Education, Inc. Floating of Ice on Liquid Water Ice floats in liquid water because hydrogen bonds in ice are more ordered, making ice less dense Water reaches its greatest density at 4C If ice sank, all bodies of water would eventually
freeze solid, making life impossible on Earth 2016 Pearson Education, Inc. Figure 2.20 Hydrogen bond Liquid water: Hydrogen bonds break and re-form Ice: Hydrogen bonds are stable 2016 Pearson Education, Inc. Water: The Solvent of Life
A solution is a liquid that is a homogeneous mixture of substances A solvent is the dissolving agent of a solution The solute is the substance that is dissolved An aqueous solution is one in which water is the solvent Water is a versatile solvent due to its polarity, which allows it to form hydrogen bonds easily When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell 2016 Pearson Education, Inc. Figure 2.21 Na
Na Cl 2016 Pearson Education, Inc. Cl Acids and Bases Sometimes a hydrogen ion (H) is transferred from one water molecule to another, leaving behind a hydroxide ion (OH) The proton (H) binds to the other water molecule, forming a hydronium ion (H3O) By convention, H is used to represent the hydronium ion 2016 Pearson Education, Inc.
Figure 2.UN03 H O H H O H 2 H2 O 2016 Pearson Education, Inc. H
O H H Hydronium ion (H3O) O H Hydroxide ion (OH) Though water dissociation is rare and reversible, it is important in the chemistry of life H and OH are very reactive Solutes called acids and bases disrupt the balance
between H and OH in pure water Acids: increase the H concentration in water Bases reduce the concentration of H 2016 Pearson Education, Inc. Figure 2.23-1 OH OH H OH
OH OH OH H OH H H OH OH OH H H H Basic solution
Neutral solution OH OH 2016 Pearson Education, Inc.
H H H OH H OH H H H Acidic solution
H A strong acid like hydrochloric acid, HCl, dissociates completely into H and Cl in water: HCl H Cl Ammonia, NH3, acts as a relatively weak base when it attracts a hydrogen ion from the solution and forms ammonium, NH4 This is a reversible reaction, as shown by the double arrows: 2016 Pearson Education, Inc. Sodium hydroxide, NaOH, acts as a strong base indirectly by dissociating completely to form hydroxide ions: NaOH Na OH The hydroxide ions then combine with hydrogen
ions to form water 2016 Pearson Education, Inc. Weak acids act reversibly and accept back hydrogen ions Carbonic acid, H2CO3, acts as a weak acid: 2016 Pearson Education, Inc. The pH Scale In any aqueous solution at 25C, the product of H and OH is constant and can be written as [H][OH] = 1014 The pH of a solution is defined as the negative logarithm of H concentration, written as pH = log [H] For a neutral aqueous solution, [H] is 107 M, so
log [H] (7) 7 2016 Pearson Education, Inc. Figure 2.UN08 0 Acidic [H] [OH] Acids donate H in aqueous solutions; pH < 7. Neutral [H] [OH] Basic [H] [OH] 2016 Pearson Education, Inc. 7
Most biological fluids have pH values in the range of 6 to 8 Bases donate OH or accept H in aqueous solutions pH > 7 14 Figure 2.23 pH Scale 0 H H OH
OH H H H H H Acidic solution OH OH H H OH
OH OH H H H Neutral solution OH OH OH H OH
OH OH OH H Basic solution 2016 Pearson Education, Inc. Battery acid 2 Gastric juice, lemon juice 3 Vinegar, wine, cola Neutral _
[H] [OH ] Increasingly Basic _ [H] [OH ] H Increasingly Acidic _ [H] [OH ] 1 4 Tomato juice Beer 5 Black coffee
Rainwater 6 Urine Saliva 7 Pure water Human blood, tears 8 Seawater Inside of small intestine 9 10 Milk of magnesia 11 Household ammonia 12 Household 13 bleach Oven cleaner
14 Buffers The 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 buffer solutions contain a weak acid and its corresponding base, which combine reversibly with H 2016 Pearson Education, Inc. Carbonic acid is a buffer that contributes to pH stability in human blood: Response to a rise in PH H+ donor Response to H+ acceptor Hydrogen
(acid) a drop in pH (base) ion 2016 Pearson Education, Inc. Acidification: A Threat to Our Oceans Human activities such as burning fossil fuels threaten water quality CO2 is a product of fossil fuel combustion About 25% of human-generated CO2 is absorbed by the oceans CO2 dissolved in seawater forms carbonic acid; this causes ocean acidification 2016 Pearson Education, Inc. As seawater acidifies, hydrogen ions combine with carbonate ions to form bicarbonate ions (HCO3) It is predicted that carbonate ion concentrations
will decline by 40% by the year 2100 This is a concern because organisms that build coral reefs or shells require carbonate ions 2016 Pearson Education, Inc. Figure 2.24 CO2 CO2 H2O H2CO3 H2CO3 H HCO3 H CO32
220 240 260 280 [CO32] (mol/kg of seawater) Data from C. Langdon et al., Effect of calcium carbonate saturation state on the calcification rate of an experimental coral reef, Global Biogeochemical Cycles 14:639654 (2000). 2016 Pearson Education, Inc.
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