Chemical Basis of Life

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Chemical Basis of Life

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1. Chemical Basis of Life Chapter 2

2. Thomas Eisner pioneered chemical ecology the study of the chemical language of nature He studies how insects communicate via chemical messages Thomas Eisner and the Chemical Language of Nature

3. Rattlebox moths release a chemical that spiders don’t like

4. Everything an organism is and does depends on chemistry Chemistry is in turn dependent on the arrangement of atoms in molecules In order to understand the whole, biologists study the parts (reductionism) 2.1 The emergence of biological function starts at the chemical level

5. Molecules and ecosystems are at opposite ends of the biological hierarchy

6. A biological hierarchy

7. A chemical element is a substance that cannot be broken down to other substances by ordinary chemical means About 25 different chemical elements are essential to life 2.2 Life requires about 25 chemical elements

8. Carbon, hydrogen, oxygen, and nitrogen make up the bulk of living matter, but there are other elements necessary for life

9. Goiters are caused by iodine deficiency (occurs when the thyroid gland is not able to produce enough thyroid hormone to meet the body's needs. The thyroid gland makes up for this lack by enlarging, which usually overcomes mild deficiencies of thyroid hormone).

10. Chemical elements combine in fixed ratios to form compounds Example: sodium + chlorine ? sodium chloride Properties of sodium and chlorine are VERY different from the properties of sodium chloride (emergent properties) 2.3 Elements can combine to form compounds

11. Salt (sodium chloride) crystals

12. The smallest particle of an element is an atom Different elements have different types of atoms An atom is made up of protons and neutrons located in a central nucleus 2.4 Atoms consist of protons, neutrons, and electrons

13. The Atomic Nucleus

14. Each atom is held together by attractions between the positively charged protons and negatively charged electrons

15. Atoms of each element are distinguished by a specific number of protons

16. Radioactive isotopes can be useful tracers for studying biological processes PET scanners use radioactive isotopes to create anatomical images 2.5 Connection: Radioactive isotopes can help or harm us

17. Electrons are arranged in shells The outermost shell determines the chemical properties of an atom These electrons are called valence electrons In most atoms, a full outer shell holds eight electrons 2.6 Electron arrangement determines the chemical properties of an atom

18. Atoms whose shells are not full tend to interact with other atoms and gain, lose, or share electrons

19. When atoms gain or lose electrons, charged atoms called ions are created An electrical attraction between ions with opposite charges results in an ionic bond 2.7 Ionic bonds are attractions between ions of opposite charge

20. Sodium and chloride ions bond to form sodium chloride, common table salt

21. Some atoms share outer shell electrons with other atoms, forming covalent bonds Atoms joined together by covalent bonds form molecules 2.8 Covalent bonds, the sharing of electrons, join atoms into molecules

22. Molecules can be represented in many ways

23. Atoms in a covalently bonded molecule may share electrons equally, creating a nonpolar molecule If electrons are shared unequally, a polar molecule is created Water is an example of a polar molecule 2.9 Water is a polar molecule

24. In a water molecule, oxygen exerts a stronger pull on the shared electrons than hydrogen

25. The charged regions on water molecules are attracted to the oppositely charged regions on nearby molecules This attraction forms weak bonds called hydrogen bonds Hydrogen bonds happen between water molecules (within water molecules you have polar, covalent bonds) van der Waals forces are similar attractive forces between molecules that have slight regions of polarization 2.10 Overview: Water’s polarity leads to hydrogen bonding and other unusual properties

26. Water, molecular model

27. Like no other common substance, water exists in nature in all three physical states:

28. Due to hydrogen bonding, water molecules can move from a plant’s roots to its leaves Insects can walk on water due to surface tension created by cohesive water molecules (because of hydrogen bonds) 2.11 Hydrogen bonds make liquid water cohesive

29. It takes a lot of energy to disrupt hydrogen bonds Therefore water is able to absorb a great deal of heat energy without a large increase in temperature It has a very high specific heat (1 cal/g-K) As water cools, a slight drop in temperature releases a large amount of heat 2.12 Water’s hydrogen bonds moderate temperature

30. HEAT = amount of energy associated with the movement of atoms/molecules Heat is the total amount of kinetic energy due to molecular motion in a body of matter. Heat is energy in its most random form TEMPERATURE = intensity of heat (i.e., average speed of molecules rather than the total amount of heat energy) A swimmer in the ocean: ocean is at a lower temperature than the human but the ocean has a lot more heat than the human A water molecule takes a large amount of energy with it when it evaporates This leads to evaporative cooling Evaporation is comparable to having the fastest runner leave a team and thus lower the average speed of the team Affected by humidity of air (amount of water in air) Heat, Temperature, & Evaporation

31. Molecules in ice are farther apart than those in liquid water 2.13 Ice is less dense than liquid water

32. Ice is therefore less dense than liquid water, which causes it to float If ice sank, it would seldom have a chance to thaw Ponds, lakes, and oceans would eventually freeze solid Frozen water floats (left) and frozen benzene sinks (right) Ice is less dense than liquid water

33. Solution is made up of a solvent (the substance that its dissolved into) and a solute (the substance that’s dissolved) Aqueous solutions have water as their solvent Solutes whose charges or polarity allow them to stick to water molecules dissolve in water They form aqueous solutions 2.14 Water is a versatile solvent

34. A compound that releases H+ ions in solution is an acid, and one that accepts H+ ions in solution is a base. This is the Brønsted-Lowry definition Arrhenius acid is same but Arrhenius base is an OH- donator A Lewis acid is an electron-pair acceptor and a Lewis base is an electron-pair donor Acidic solutions have high H+ concentrations; bases have high OH- (hydroxide ion) concentrations In aqueous solutions, the H+ actually combines with H2O to give a hydronium ion, H3O+ Acidity is measured on the pH (potential of Hydrogen) scale: 0-6.9 is acidic 7.1-14 is basic Pure water and solutions that are neither basic nor acidic are neutral, with a pH of 7.0 2.15 The chemistry of life is sensitive to acidic and basic conditions

35. pH levels of common substances The pH scale

36. Cells are kept close to pH 7.4 by buffers Buffers are substances that resist pH change They accept H+ ions when they are in excess and donate H+ ions when they are depleted Buffers are not foolproof If pH drops to 7 or increases to 7.8, it can cause death within a few minutes Cells and pH

37. Some ecosystems are threatened by acid precipitation (rain, snow, or fog) Acid precipitation is formed when air pollutants (sulfur oxide or nitrogen oxide) from burning fossil fuels combine with water vapor in the air to form sulfuric and nitric acids The acids cause damage to everything they contact 2.16 Connection: Acid precipitation threatens the environment

38. These acids can kill fish, damage buildings, and injure trees Regulations, new technology, and energy conservation may help us reduce acid precipitation German statue shows damage over 60 years or so Acid Damage

39. Acid precipitation damage to trees Acid Damage to natural forests

40. In a chemical reaction: reactants interact atoms rearrange products result 2.17 Chemical reactions rearrange matter

41. Living cells carry out thousands of chemical reactions that rearrange matter in significant ways Beta carotene splits in two to form two Vitamin A molecules Vitamin A is essential for sight 11-cis-retinal is derived from Vitamin A and is combined with scotopsin to yield rhodopsin Reactions in cells

42. External Setae Lab… Read quickly for an overview Don’t get caught up in equations or explanations or technical words Ask yourself many questions along the way! E.g., answer these questions: Do the authors ever say a hypothesis is proven? Why or why not? What hypotheses do they talk about along the way? What’s a gecko? What are setae? What is the van der Waals force? What were your hypotheses? Explain your conclusions (in your own words) Answer all the questions at the end

43. Where does chemical energy come from? If chemicals are bound, then breaking the bonds does not release energy. It requires external energy. This energy can come from the formation of stronger bonds between the atoms, such as when you burn some sort of fuel. The fuel bonds break, but stronger bonds are formed with oxygen for a net release of energy. It can also come from the thermal energy of its surroundings, such as when you break the ionic bonds in salt by dissolving it in water Those are sources of net energy change, however. At the site of the bond itself, this energy comes from the electromagnetic force (although there is some KE of the electrons in addition to the electrical PE). The charges (electrons and the nuclei) in chemicals are not perfectly evenly distributed, causing net electrostatic fields. When bonds are broken or formed, this motion of charges in the fields (which exert a force on the charges) either absorbs or releases energy because the charges are being pulled or pushed by the electric fields of all the other charges present. If you want to think of it as an exchange of something, think of it as an exchange of photons (leave virtual photons out of this, that's for much faster processes involved in particle physics), which carry the electromagnetic force.

44. How about nuclear energy source? The nucleus has its own forces, AND the electromagnetic force. Typical nuclear reactions are dictated by the strong force, which holds the nucleus together. The weak nuclear force predominantly causes beta decays. But the queston is about the force between the parts of a nucleus, what holds it together, and that is the strong force. The exact form of the strong nuclear force is still a mystery. We have what we believe to be relatively exact models for the other 3 forces (electromagnetism, the weak force, and gravitation), although there's some debate about the extent of the knowledge we have about those. But the exact nature of the strong nuclear force remains unknown. It results from the exchange of a zoo of virtual particles (gluons and mesons), and it depends on too many things (such as the spins of the protons and neutrons which are bound together in the nucleus) to go into here. But it's just another force like gravitation and electromagnetism. The reason you don't feel it personally is that it's very short-range, it essentiall ends at the boundaries of the nucleus itself. Electromagnetic forces (like what holds magnets on your refrigerator) and gravitation are long-range, so we're more familiar with them because they do operate on objects which are of lengths that we can see and touch. So, just like gravity pulls a rock towards the center of the Earth and makes it take energy to roll uphill (or pick up energy as it rolls downhill), adding nucleons (protons and neutrons) to or removing them from a nucleus requires energy. Think of the nucleus as a pit into which nucleons fall, pulled down by a strange type of gravity that suddenly gets really strong right next to and inside the hole. Now if you add a nucleon to a nucleus, it will generally just scatter unless there's some way to convert this strong force into energy that can be released. This can be in several forms, such as photons (gamma-rays are photons emmited by such processes which have very high energies) or other particles with high energies (say a proton fuses with a nucleus and a neutron is ejected). If the incoming nucleon has enough energy, that energy can be converted into new (generally unstable) particles. The nucleus is a complex place, so there's no single answer to that aspect of your question.

45. Final Nuclear Notes Mostly the energy released is in the form of kinetic energy of the products of the reaction. For example, in the proton-proton chain that powers the sun: proton + proton -> deuteron + positron + neutrino + KE of products The mass of the deuteron + positron + neutrino is less than the mass of the two protons; this excess mass was converted to energy, in the form of kinetic energy of the deuteron, positron, and neutrino. Usually, if there is electromagnetic radiation involved, it is listed explicitly (as a gamma ray), as in the next step in that chain: proton + deuteron -> helium-3 + gamma + KE of products So you get both electromagnetic radiation (the gamma ray) and energy, in the form of kinetic energy of the helium-3 nucleus and the gamma ray. Similarly, in fission reactions, the excess energy is in the form of kinetic energy of the nuclear fragments. In the following figure, this energy is referred to as "heat energy"; however, heat energy on an atomic scale is just kinetic energy

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