Chemistry of Life

1. Chemistry of Life

2. General Definitions • Most of the Universe consists of matter and energy. • Energy is the capacity to do work • All matter is composed of basic elements that cannot be broken down to substances with different chemical or physical properties. • Elements are substances consisting of one type ofatom • Atoms are the smallest particle into which an element can be divided.

3. 2.2 Life requires about 25 chemical elements • About 25 different chemical elements are essential to life

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

5. 2.3 Elements can combine to form compounds • Chemical elements combine in fixed ratios to form compounds • Example: sodium + chlorine  sodium chloride

6. General Definitions • Subatomic particles • The proton is located in the center (or nucleus) of an atom, each atom has at least one proton. • Protons have a charge of +1 • The neutron also is located in the atomic nucleus (except in Hydrogen). • The neutron has no charge • The electron is a very small particle located outside the nucleus. It determines the chemical behavior of an atom. • The charge on an electronis -1 • The number of protons in the atomic nucleus gives the atomic number.(H has 1, C has 6)

7. The nucleus is surrounded by electrons • An atom is made up of protons and neutrons located in a central nucleus 2 Protons Nucleus 2 Neutrons 2 Electrons A. Helium atom

8. Neutrons are electrically neutral • Each atom is held together by attractions between the positively charged protons and negatively charged electrons 6 Protons Nucleus 6 Neutrons 6 Electrons B. Carbon atom Figure 2.4B

9. The number of neutrons may vary • Variant forms of an element are called isotopes • Some isotopes are radioactive • Atoms of each element are distinguished by a specific number of protons Table 2.4

10. Nuclear Decay • If a nucleus has too few or too many neutrons it may be unstable, and will decay after some period of time. • For example, nitrogen-16 atoms (7 protons, 9 neutrons) beta decay to oxygen-16 atoms (8 protons, 8 neutrons) within a few seconds of being created. • In this decay a neutron in the nitrogen nucleus is turned into a proton and an electron by the weak nuclear force. The element of the atom changes because while it previously had seven protons (which makes it nitrogen) it now has eight (which makes it oxygen). Many elements have multiple isotopes which are stable for weeks, years, or even billions of years.

11. Radioactive isotopes can help or harm us • Radioactive isotopes can be useful tracers for studying biological processes • PET scanners use radioactive isotopes to create anatomical images

12. PET SCAN • Positron emission tomography, also called PET imaging or a PET scan, is a diagnostic examination that involves the acquisition of physiologic images based on the detection of radiation from the emission of positrons. • Positrons are tiny particles emitted from a radioactive substance administered to the patient. The positron is the antiparticle or the antimatter counterpart of the electron. The positron has an electric charge of +1, a spin of 1/2, and the same mass as an electron.

13. Positron Emission • Positron emission is a type of beta decay, sometimes referred to as "beta plus" (β+). In beta plus decay, a proton is converted, via the weak force, to a neutron, a beta plus particle (a positron) and a neutrino. Isotopes which emit positrons include Carbon-11, Nitrogen-13, Oxygen-15 and Fluorine-18; • for example: these isotopes are used in positron emission tomography, a technique used for medical imaging. http://en.wikipedia.org/wiki/Nuclear_decay

14. Electron-positron Collision Image of the "annihilation" process known in elementary physics. It shows how a positron (e+) is emitted from the atomic nucleus together with a neutrino (v). The positron moves then randomly through the surrounding matter where it hits several different electrons (e-) until it finally loses enough energy that it interacts with a single electron. This process is called an "annihilation" and results in two diametrically emitted photons with a typical energy of 511 keV each. http://en.wikipedia.org/wiki/Electron-positron_annihilation

15. How the procedure work? • A radioactive substance is produced in a machine called a cyclotron and attached, or tagged, to a natural body compound, most commonly glucose, but sometimes water or ammonia. • Once this substance is administered to the patient, the radioactivity localizes in the appropriate areas of the body and is detected by the PET scanner.

16. PET SCAN EQUIPMENT • PET scanner has a hole in the middle and looks like a large doughnut. • Within this machine are multiple rings of detectors that record the emission of energy from the radioactive substance in the body and permit an image to be obtained.

17. Inside the PET scanner During the annihilation process two photons are emitted in diametrically opposing directions. These photons are registered by the PET as soon as they arrive at the detector ring. After the registration, the data is forwarded to a processing unit http://en.wikipedia.org/wiki/Annihilation

18. How to separate healthy tissue from cancerous? • Different colors or degrees of brightness on a PET image represent different levels of tissue or organ function. • For example, because healthy tissue uses glucose for energy, it accumulates some of the tagged glucose, which will show up on the PET images. However, cancerous tissue, which uses more glucose than normal tissue, will accumulate more of the substance and appear brighter than normal tissue on the PET images.

19. Computed Tomography + PET Image fusion readily localized tumor location in the spleen (arrow) in this patient with lymphoma(green arrowheads indicate normal physiologic activity in the bowel and kidney).

20. Unified Image

21. 2.6 Electron arrangement determines the chemical properties of an atom • Electrons are arranged in shells • The outermost shell determines the chemical properties of an atom • In most atoms, a full outer shell holds eight electrons

22. Electrons and energy From: Life: The Science of Biology, 4th Edition, by Sinauer Associates

23. Atoms whose shells are not full tend to interact with other atoms and gain, lose, or share electrons Outermost electron shell (can hold 8 electrons) Electron First electron shell (can hold 2 electrons) HYDROGEN (H) Atomic number = 1 CARBON (C) Atomic number = 6 NITROGEN (N) Atomic number = 7 OXYGEN (O) Atomic number = 8 Figure 2.6

24. Where does table salt come from? • Supermarket? • Please pass the NaCl…

25. Ionic bonds are attractions between ions of opposite charge • 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 – + Na Cl Na Cl Na Sodium atom Cl Chlorine atom Na+ Sodium ion Cl– Chloride ion Figure 2.7A Sodium chloride (NaCl)

26. Sodium and chloride ions bond to form sodium chloride, common table salt (cubic structure) Na+ Cl– Figure 2.7B

27. Halite (NaCl) • Halite, sodium chloride, is found naturally in huge geologic deposits of salt minerals left over from the slow evaporation of ancient seawater. "Na" stands for "natrium," the Latin word for sodium. http://www.science-education.org/classroom_activities/chlorine_compound/nacl.html

28. Halophytes • True halophytes are plants that thrive when given water having greater than 0.5% NaCl. • They are salt-resistant! Sabal palmetto shows remarkable tolerance of salt, even being able to grow where washed by sea water at high tide

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

30. Formation of covalent bonds Methane CH4 From: Life: The Science of Biology, 4th Edition, by Sinauer Associates

31. Molecules can be represented in many ways Table 2.8

32. Bonds

33. Molecules • http://www.accessexcellence.org/RC/VL/GG/garland_PDFs/Panel_2.01a.pdf • http://www.accessexcellence.org/RC/VL/GG/garland_PDFs/Panel_2.01b.pdf

34. THE PROPERTIES OF WATER Water is a polar molecule • Atoms in a covalently bonded molecule may share electrons equally, creating a nonpolar molecule • If electrons are shared unequally, a polar molecule is created

35. This makes the oxygen end of the molecule slightly negatively charged • The hydrogen end of the molecule is slightly positively charged • Water is therefore a polar molecule • In a water molecule, oxygen exerts a stronger pull on the shared electrons than hydrogen (–) (–) O H H (+) (+) Figure 2.9

36. Water

37. Water

38. Water’s polarity leads to hydrogen bonding and other unusual properties • 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 bond

39. Hydrogen bonds make liquid water cohesive • 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

40. Water’s hydrogen bonds moderate temperature • 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 • As water cools, a slight drop in temperature releases a large amount of heat

41. Ice is less dense than liquid water • Molecules in ice are farther apart than those in liquid water Hydrogen bond ICE Hydrogen bonds are stable LIQUID WATER Hydrogen bonds constantly break and re-form

42. If ice sank, it would seldom have a chance to thaw • Ponds, lakes, and oceans would eventually freeze solid • Ice is therefore less dense than liquid water, which causes it to float

43. Water is a versatile solvent • Solutes whose charges or polarity allow them to stick to water molecules dissolve in water • They form aqueous solutions Na+ – – Na+ + + Cl– Cl– – – + + – Ions in solution Salt crystal Figure 2.14

44. http://www.accessexcellence.org/RC/VL/GG/garland_PDFs/Panel_2.02b.pdfhttp://www.accessexcellence.org/RC/VL/GG/garland_PDFs/Panel_2.02b.pdf

48. The chemistry of life is sensitive to acidic and basic conditions • A compound that releases H+ ions in solution is an acid, and one that accepts H+ ions in solution is a base • Acidity is measured on the pH scale: • 0-7 is acidic • 8-14 is basic • Pure water and solutions that are neither basic nor acidic are neutral, with a pH of 7

49. pH scale H+ OH– Lemon juice; gastric juice Increasingly ACIDIC (Higher concentration of H+) Grapefruit juice • The pH scale Acidic solution Tomato juice Urine NEUTRAL [H+] = [OH–] PURE WATER Human blood Seawater Neutral solution Increasingly BASIC (Lower concentration of H+) Milk of magnesia Household ammonia Household bleach Oven cleaner Basic solution Figure 2.15

50. 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 • Cells are kept close to pH 7 by buffers