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INQUIRY: What creates “devil’s gardens” in the rain forest? BIOCHEMISTRY The Chemical Context of Life • Devil's gardens are large stands of trees in the Amazonian rainforest that consist almost entirely of a single species. • Which ant? Myrmelachista schumanni INQUIRY: Care to formulate a hypothesis, or two, or three? INQUIRY: Care to test a hypothesis, or two? Working under Deborah Gordon and with Michael Greene, graduate student Megan Frederickson sought the cause of “devil’s gardens”. Field experiments were performed in Peru. EXPERIMENT Cedrela sapling Insect barrier Duroia tree Inside, unprotected Which tree? Duroia hirsuta Devil’s garden Who tends this garden? Outside, protected Inside, protected Outside, unprotected 2 INQUIRY: Care to test a hypothesis, or two? Two saplings of a local nonhost tree species, Cedrela odorata, were planted inside each of 10 devil’s gardens. • At the base of one, a sticky insect barrier was applied. INQUIRY: Care to test a hypothesis, or two? INQUIRY: Care to collect some data?! Next, two more Cedrela saplings were introduced about 50 meters outside each garden, one with and one without the sticky insect barriers. The researchers observed ant activity on the Cedrela leaves and measured areas of dead leaf tissue after one day. They also chemically analyzed contents of the ants’ poison glands. INQUIRY: What do we conclude? ! Ants of the species Myrmelachista schumanni kill nonhost trees by injecting the leaves with formic acid, thus creating hospitable habitats (Devi's gardens) for the ant colony. • The other was left unprotected. WHY? EXPERIMENT Cedrela sapling Duroia tree Inside, unprotected EXPERIMENT Cedrela sapling Insect barrier Duroia tree Outside, protected Inside, unprotected Inside, protected Devil’s garden Devil’s garden Outside, unprotected EXPERIMENT Cedrela sapling Insect barrier Inside, unprotected Inside, protected Outside, protected Inside, protected Devil’s garden Outside, unprotected INQUIRY: Care to analyze some data?! INQUIRY: Care to analyze some data?! Insect barrier Duroia tree Outside, protected Outside, unprotected Matter consists of chemical elements in pure form and in combinations called compounds. INQUIRY: The formal conclusion from the authors of the study. RESULTS RESULTS Dead leaf tissue (cm2) after one day The ants made the injections from the tips of their abdomen into leaves of unprotected saplings in their gardens. Within one day, these leaves developed dead areas (examine the graph again!). • Element: a substance that cannot be broken down into other substances by chemical reactions. • There are 92 naturally occurring elements "Here we show that the ant, Myrmelachista schumanni, which nests in D. hirsuta stems, creates devil's gardens by poisoning all plants except its hosts with formic acid. 16 12 8 4 0 Inside, Outside, Inside, unprotected protected unprotected Outside, protected By killing other plants, M. schumanni provides its colonies with abundant nest sites—a long-lasting benefit, as colonies can live for 800 years." Cedrela saplings, inside and outside devil’s gardens 12 Matter consists of chemical elements in pure form and in combinations called compounds. An element’s properties depend on the structure of its atoms The Elements of Life C. HOPKINS CaFe • Compound: consists of 2 or more different elements combined in a fixed ratio. • A compound has characteristics different from its element. • Na (soft metal, explodes in water) + Cl (poisonous gas) NaCl (a seasoning we sprinkle on food without fear!) 13 • About 20–25% of the 92 elements are essential to life • Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter • Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur • Trace elements are those required by an organism in minute quantities • An atom is the smallest unit of matter that still retains the properties of an element. • Atoms are composed of subatomic particles • Relevant subatomic particles include – – – – – 14 15 Neutrons (no electrical charge) Protons (positive charge) Electrons (negative charge) p+ and n0 reside in a very dense nucleus e− reside in the electron cloud 16 One of these diagrams is fraught with danger! Cloud of negative charge (2 electrons) Atomic Number and Atomic Mass • Atoms of the various elements differ in number of subatomic particles • An element’s atomic number is the number of protons in its nucleus • An element’s mass number is the sum of protons + neutrons in the nucleus • Atomic mass, the atom’s total mass, can be approximated by the mass number but is actually represented by an AVERAGE molecular mass based on the abundance of various isotopes. Electrons Nucleus (a) (b) Speaking of Isotopes… More annoying Atomic Structure Vocabulary Question 1 • All atoms of an element have the same number of protons but may differ in number of neutrons • Isotopes are two atoms of an element that differ in number of neutrons • Radioactive isotopes decay spontaneously, giving off particles and energy • Some applications of radioactive isotopes in biological research are Why might scientists be interested in the "atomic mass" of an atom? • The Energy Levels of Electrons A. It tells how it will behave in a chemical reaction. B. It lets us know the valence of the atom if we know the atomic number. C. If we know the atomic number, we can determine the number of neutrons. D. We can use it to know if the atom is radioactive or not. • Energy is the capacity to cause change, perhaps by doing work. • Potential energy is the energy that matter has because of its location or structure, there are many kinds…not just gravitational PE! • The electrons of an atom differ in their amounts of potential energy • An electron’s state of potential energy is called its energy level, or electron shell* Number of protons Number of neutrons Atomic mass number All of the above 19 Energy must be absorbed in order to promote an electron to a higher E-level Electrons farther from the nucleus have more potential energy On to the electron cloud… A. B. C. D. – Dating fossils (C-14) – Tracing atoms through metabolic processes (I-131) – Diagnosing medical disorders 18 Question 2 Which of the following is the criterion upon which the modern periodic table is organized? • A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons, because the ball can come to rest only on each step, not between steps. • It’s a quantized event! * “Shell” is fraught with misconception—but biologists often use this description. “Energy level” is a much better phrase since the region is not “hard” like a shell. 24 This diagram focuses on the “shells” which can be misleading! What’s the big deal? Hydrogen 1H Electron Distribution and Chemical Properties Mass number First shell • The chemical behavior of an atom is determined by the distribution of electrons in electron energy levels and sublevels • The periodic table of the elements shows the electron distribution for each element—think of it as a giant BINGO card 2 He 4.00 Atomic number Helium 2He Element symbol Beryllium 4Be Boron 5B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Second shell Whether an atom will be able to interact with other atoms can be determined by A. Looking at the ratio of protons to neutrons in the nucleus. • Valence electrons are those in the outermost energy level (or sublevel) , or valence sublevel • The chemical behavior of an atom is mostly determined by the valence electrons • Elements with a full valence shell are chemically inert First shell Neon, with two filled Shells (10 electrons) Second shell (a) Electron distribution diagram Sodium Magnesium Aluminum 11Na 12Mg 13Al Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18Ar Third shell 27 Question 3 26 Out with the old model… Stuff you probably already know! Electron distribution diagram Lithium 3Li 25 29 28 …in with a better one—electron orbitals Heard of s, p, d and f? First E-level • An orbital is the three-dimensional space where an electron is found 90+% of the time • Each electron energy level consists of a specific number of orbitals Second E-level y x 1s, 2s, and 2p orbitals B. Whether it has an even or odd number of electrons. C. Determining the stability of the electrons in their valence orbitals around the nucleus. 1s orbital 2s orbital z Three 2p orbitals (c) Superimposed electron orbitals D. Identifying the atom as a metal or non-metal. (b) Separate electron orbitals 33 35 The formation and function of molecules depend on chemical bonding between atoms • Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms • These interactions usually result in atoms staying close together, held by attractions called chemical bonds Covalent Bonds Hydrogen atoms (2 H) Hydrogen atoms (2 H) • A covalent bond is the sharing of a pair of valence electrons by two atoms • In a covalent bond, the shared electrons count as part of each atom’s valence shell • A covalent bond is formed between shared pairs of electrons: 1 pair—a single bond 2 pairs—a double bond 3 pairs—a triple bond 36 37 Covalent Bonds: To share or not to share, that is the question! Hydrogen atoms (2 H) Name and Molecular Formula Electron Distribution Diagram Lewis Dot Structure and Structural Formula Electronegativity SpaceFilling Model (a) Hydrogen (H2) • The notation used to represent atoms and bonding is called a structural formula • Atoms in a molecule attract electrons to varying degrees • Electronegativity is an atom’s attraction for the electrons in a covalent bond • The more electronegative an atom, the more strongly it pulls shared electrons toward itself (b) Oxygen (O2) – For example, H—H • This can be abbreviated further with a molecular formula (c) Water (H2O) – For example, H2 (d) Methane (CH4) Hydrogen molecule (H2) 41 Not all sharing is created EQUAL! Not all sharing is created EQUAL! • In a nonpolar covalent bond, the atoms share the electron equally • In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally • In a nonpolar covalent bond, the atoms share the electron equally δ– O δ+ H H δ+ H2O • Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule • In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electrons equally Not all molecules with polar bonds are polar! Net dipole moment δ– O δ+ H H δ+ H2O • Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule 44 Question 5 For a covalent bond to be polar, the two atoms that form the bond must have A. B. C. D. 43 different atomic weights. the same number of electrons. different electronegativities. similar electronegativities. 49 Question 4 • In a nonpolar covalent bond, the atoms share the electron equally Which of the following statements best describes the difference between an element and a molecule? • In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electrons equally A. An element is composed of atoms; a molecule is not. B. An element is composed of only one kind of atom; molecules can be composed of more than one kind of atom. C. Elements always have lower atomic weights than molecules. D. Elements exist in nature only as parts of molecules. • Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule 45 46 47 Ionic Bonds: A case study involving greed! Ionic Bonds: A case study involving greed! Question 6 • Atoms sometimes strip electrons from their bonding partners • An example is the transfer of an electron from sodium to chlorine • After the transfer of an electron, both atoms have charges • A charged atom (or molecule) is called an ion • A cation is a positively charged ion • An anion is a negatively charged ion • An ionic bond is an attraction between an anion and a cation • Compounds formed by ionic bonds are called ionic compounds, or salts • Salts, such as sodium chloride (table salt), are often found in nature as crystals Why are covalent bonds more prevalent among biological molecules than ionic bonds? A. Ionic bonds only occur between metals and non-metals, and therefore aren't usually present in biological systems. B. You can have double covalent bonds, but not double ionic bonds, so covalent bonds provide more variety consistent with the structural demands required in biological systems. C. Biological conditions are often aqueous, and the water would cause ionic bonds to dissociate. D. Ions only form under extreme conditions not compatible with the cell's environment. 51 52 Here’s where the trouble starts… Here’s where the trouble continues… • There is a rift between biology and chemistry text books. • The biology book often speaks of “weak bonds” when they really mean intermolecular forces (forces of electrostatic attraction “between molecules”) which are not at all the same as sharing a pair of electrons within a molecule • IMFs are intermolecular whereas chemical bonds are intramolecular • Inter—means between molecules (think interstate highway, one between states, connecting states) • Intra—means within the molecule (actual chemical bonds) • Furthermore, the biology books often speak of van der Waals interactions which “lumps” all of the different IMFs together • Older chemistry books spoke of van der Waals but specifically meant London Dispersion forces. “Peer pressure” London dispersion forces (LDFs)—every molecule has these since every molecule has moving valence electrons. Essentially the electrons are in constant motion and not always evenly distributed (think traffic jam). If the electrons pile up on one portion of the three dimensional molecule, then we get a temporary concentration of negating charge, creating a temporary negative pole, if you will, since the electrons are not dispersed evenly we now refer to the molecule as a temporary dipole. More on that coming up… 55 LDFs increase with increasing numbers of electrons on a given molecule There are many types of IMFs 56 The larger the molecule, the more likely this will happen since the valence electrons are farther from the mother nucleus, thus less tightly held! What wasn’t polar at all is now “sort of” polar, thus +/- attractions now exist. 57 Induced Dipole- Induced Dipole IMFs a.k.a. LDFs, or Dispersion Forces What’s the big deal? • Molecules that were not originally attracted to one another, now find each other quite attractive, thus more energy is required to separate them! • In other words, molecules become “sticky” or adhere to one another. • Collectively, such interactions can be strong, as between the molecules of a gecko’s toe hairs and the surface of a wall. He’s not really defying gravity! • In Dipole-Induced Dipole, there is a permanent dipole (electronegativity difference is enough to make a permanent (+) and (-) end of the molecule) that induces a nonpolar molecule to become a dipole. • Now the two are more attracted to each other than they were before the induction occurred. • Ever induced behavior in another human? Got siblings?? The dotted lines represent attractive forces. This is also happening in all THREE DIMENSIONS! 60 Hydrogen Bonding: A Special Case of Dipole-Dipole IMFs Dipole – Dipole IMFs • A hydrogen bond is not the same as a bonded hydrogen! • It’s a special case of DipoleDipole IMFs • A bonded hydrogen is within a water molecule • A hydrogen bond is between molecules! • In Dipole-induced dipole, there is a permanent dipole (electronegativity difference is enough to make a permanent (+) and (-) end of the molecule that induces a nonpolar molecule to become a dipole. • Now the two are more attracted to each other than they were before the induction occurred. Bonded Hydrogens 63 C) I and III only D) I, II and III 67 • Hydrogen bonding occurs when the H of one molecule is attracted to a highly electronegative molecule on an adjacent molecule. • THE CATCH: For an H to be a candidate for hydrogen bonding, it must itself be attached to a highly electronegative element such as F, O or N (think “phone”…call me!) 62 Hydrogen Bonding: A Special Case of Dipole-Dipole IMFs Bonded Hydrogens (actual chemical bonds consisting of a shared pair of electrons) Hydrogen “bonds” (IMFs) 64 • Hydrogen bonding is an IMF that makes molecules more attracted to each other, thus more tightly held to each other, thus more energy is required to separate them! • Higher MP, BP, heat of vaporization, etc. occur as a result. • Also, enhanced solubility of substances such as ammonia. 65 66 Step 1: 1-s and 3-p atomic orbitals blend to make 4 sp3 molecular orbitals Why is Linus Pauling famous?? • He developed the electronegativity scale. • A molecule’s shape is very important to its function • A molecule’s shape is determined by the positions of its atoms’ valence orbitals • In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes Which of the following is true? I. Hydrogen bonds are a special case of dipole-dipole IMFs. II. Ionic substances dissolve in water. III. Polar substances dissolve in water. A) I only B) III only Hydrogen bonds (IMFs) Time to think in 3-D! Question 7 61 Hydrogen Bonding: A Special Case of Dipole-Dipole IMFs (actual chemical bonds consisting of a shared pair of electrons) 58 Dipole - Induced Dipole IMFs • Induced-Dipole, Induced-Dipole is just another name for what we just described as LDFs. (Don’t you just love grown-ups that can’t agree on terminology??) • A spontaneous traffic jam of electrons created a slight (-) charge on the end of the molecule with the most electrons leaving the other end slightly (+) 59 Temporary Dipole has formed • In the 1930’s Linus Pauling introduced the concept of hybridization to explain chemical bond formation. Hybridization is the mixing of atomic orbitals in an atom to generate a set of new atomic orbitals called hybrid orbitals. • Mixing an s orbital with one of the p orbitals generates two equivalent sp hybrid orbitals. Note that the number of hybrid orbitals is equal to the number of atomic orbitals that are hybridized. The set of two sp hybrid orbitals has a linear arrangement. The angle between the orbitals is 180˚. 69 70 71 Water & Methane are both sp3 hybridized The puzzle pieces have to fit! Question 8 • Biological molecules recognize and interact with each other with a specificity based on molecular shape Consider the Lewis structures shown below. Explain why each is or is not a valid structure. • Molecules with similar shapes can have similar biological effects • Long ago you accepted that the 4 DNA bases pair A-T and G-C, but WHY?? • Why can’t the A pair with the C? 73 72 The puzzle pieces have to fit! The boxed regions are shaped similarly! Ever heard of “a runner’s high”? • Why does a molecule have shape in the first place? • That has to do with IMFs holding things in “place” defining its 3-D shape. The big people word for “shape” is “conformation”. • In the case of A-T vs. G-C, it’s all about lining up that IMF called “hydrogen bonding”; 2 sites for A-T and 3 for G-C 75 • Our body manufactures endorphins which are made by the pituitary gland and bind to the receptors in the brain that relieve pain and produce euphoria during times of stress, such as intense exercise. Carbon Hydrogen Natural endorphin Pain killer! • The brain receptors “bind” with either with similar results. Nitrogen Sulfur Oxygen Morphine Natural endorphin • Opiates such as morphine and heroin are structured similarly, thus can bind with the receptors . These “bindings” are actually those electrostatic attractions we call IMFs. Brain cell Morphine Endorphin receptors (a) Structures of endorphin and morphine (b) Binding to endorphin receptors 77 Chemical Reactions Make and/or Break Chemical Bonds Chemical Reactions Make and/or Break Chemical Bonds Chemical Reactions Make and/or Break Chemical Bonds • Chemical reactions are the making and breaking of chemical bonds Lets get two things straight before going further… 1. Energy must be added to a system to BREAK a chemical bond. • The final molecules of a chemical reaction are called products 80 81 Chemical Equilibrium • All chemical reactions are reversible: products of the forward reaction become reactants for the reverse reaction • Chemical equilibrium is reached when the rate of the forward reactions is equal to the rate of the reverse reaction • Chemical equilibrium does NOT mean “equal” amounts of reactants and products are present, but rather that their concentrations have stabilized in a constant ratio! 84 Photosynthesis is a mighty important chemical reaction! • 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 • The starting molecules of a chemical reaction are called reactants 2. Energy is released when chemical bonds are MADE. 79 Created by: René McCormick National Math and Science Dallas, TX 82 • Photosynthesis is an important chemical reaction • Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen 6 CO2 + 6 H2O → C6H12O6 + 6 O2 83