CHAPTER 2 The Chemical Basis of Life

CHAPTER 2The Chemical Basis of Life Modules 2.1 – 2.8

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

The silkworm is the larva of Bombyx mori, the domesticated silkmoth. It is very important economically as the producer of silk. It is entirely dependent on humans for its reproduction and no longer occurs in the wild if it ever did so; silk culture has been practiced for at least 5,000 years in China (Goldsmith et al. 2004). Bombykol is a silkworm pheromone produced by the female to attract the male.

Rattlebox moths release a chemical that spiders don’t like • This spider caught a rattlebox moth and then let it go

ATOMS AND MOLECULES The Reductionist Approach---- The emergence of biological function starts at the chemical level • 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)

Molecules and ecosystems are at opposite ends of the biological hierarchy • Each level of organization in the biological hierarchy builds on the one below it • At each level, new properties emerge

D. Organ: Flight muscle of a moth Rattlebox moth • A biological hierarchy • The Reductionist Approach to the study of biology—studying the parts to understand the whole. C. Cell and tissue: Muscle cell within muscle tissue Myofibril (organelle) B. Organelle: Myofibril (found only in muscle cells) Actin Myosin Atom Figure 2.1 A. Molecule: Actin

The Reductionist studies the parts--- Life requires about 25 chemical elements • 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 • 4 elements make up 96% of the human body by weight. Which ones are they? • Bones compose about 18% of human body mass.

Carbon, hydrogen, oxygen, and nitrogen make up the bulk of living matter, but there are other elements necessary for life . Trace elements are essential (<0.01% wet weight). • Flouride is in our water and iodine is in our salt. Iron is in our red blood cells and is found in the heme group of the hemoglobin molecule. Table 2.2

Goiters are caused by iodine deficiency • The thyroid gland requires .15mg I/day for normal function. Iodine is essential in the formation of thyroid hormone. Figure 2.2

Iron is important in human biochemistry • In the human body, iron is present in all cells and has several vital functions—as a carrier of oxygen to the tissues from the lungs in the form of hemoglobin, as a transport medium for electrons within the cells in the form of cytochromes, and as an integral part of enzyme reactions in various tissues. Too little iron can interfere with these vital functions and lead to morbidity.

Get a laptop and …… • Choose a trace element and find out why it is essential to a healthy body. Discuss how the element functions and the diseases caused by too much and/or too little of the element.

2.3 Elements can combine to form compounds • Chemical elements combine in fixed ratios to form compounds • A compound is a substance composed of two or more elements • Example: Vitamin A is a compound as is table salt. • sodium + chlorine  sodium chloride

Elements and compounds important in biology • February 22, 2008) Scientists at the Queensland University of Technology (Australia) have applied for the limited release of genetically modified Cavendish bananas that possess more provitamin A, vitamin E and iron than conventional varieties. • In the bananas, the expression of iron has been enhanced by the inclusion of an iron-storage gene from wild soybeans and vitamin E has been enhanced by the use of genes from rice and rock cress. For the augmented expression of provitamin A, genes from maize, rock cress and the Erwinia bacterium have been employed. • If approved by the national Office of the Gene Technology Regulator, the release of as many as 1,290 banana lines would take place in North Australia. Goal of the research is the nutritional improvement of banana varieties in Uganda and other regions of Africa

GMO’s and Compounds Essential to Life • Are there other genetically modified organisms that confer nutritional compounds to humans? Research this. • Do all nations of the world encourage GMO research? • If not, who and why are they against this type of research?

The nucleus is surrounded by electrons. The nucleus represents the fly on the pitchers mound at Yankee Stadium and the gnats flying all over the stadium represent the electrons. • An atom is made up of protons and neutrons located in a central nucleus. • The repulsion between positively charged protons in the nucleus is overcome by the strong nuclear force. 2 Protons Nucleus 2 Neutrons 2 Electrons Figure 2.4A A. Helium atom

Neutrons are electrically neutral • The 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

The number of neutrons may vary • Variant forms of an element are called isotopes • Some isotopes are radioactive • The atomic mass of Carbon is 12.01. This is the average mass of the various isotopes of carbon found in nature. C-14 is radioactive. • Atoms of each element are distinguished by a specific number of protons. The number of protons is equal to the number of electrons. % in nature 98.89 C12 1.11 C13 Trace C14 Table 2.4

Atoms consist of protons, neutrons, and electrons • The smallest particle of an element is an atom • About 100 million atoms side by side = 1 cm • Different elements have different types of atoms

Radioactive isotopes can help or harm us • Radioactive isotopes can be useful tracers for studying biological processes. Living cells do not know the difference between isotopes. • Every organ in our bodies acts differently from a chemical point of view. Doctors and chemists have identified a number of chemicals which are absorbed by specific organs. The thyroid, for example, takes up iodine, the brain consumes quantities of glucose, and so on. With this knowledge, radiopharmacists are able to attach various radioisotopes to biologically active substances. Once a radioactive form of one of these substances enters the body, it is incorporated into the normal biological processes and excreted in the usual ways. • http://www.uic.com.au/nip26.htm

Radioactive isotopes can help or harm us • PET scanners use radioactive isotopes to create anatomical images • http://en.wikipedia.org/wiki/Positron_emission_tomography • A substance that emits positrons is injected into the patient. The positrons collide with electrons in tissues that are metabolically active. The energy released by these collisions is registered as “hot spots”. Figure 2.5A Figure 2.5B

PET • A very small dose of a radioactive chemical, called a radiotracer, is injected into the vein of your arm. The tracer travels through the body and is absorbed by the organs and tissues being studied. Next, you will be asked to lie down on a flat examination table that is moved into the center of a PET scanner—a doughnut-like shaped machine. This machine detects and records the energy given off by the tracer substance and, with the aid of a computer, this energy is converted into three-dimensional pictures. A physician can then look at cross-sectional images of the body organ from any angle in order to detect any functional problems

Isotopes Used in Medicine • Molybdenum-99 Used as the “parent” to produce technetium-99m the most widely used isotope in nuclear medicine. • Technetium-99m Most widely used to image the skeleton and heart muscle. Technetium-99m decays by a process called "isomeric"; which emits gamma rays and low energy electrons. Since there is no high energy beta emission the radiation dose to the patient is low. • Chromium-51 Used to label rbc’s and gastro intestinal protein loss • Cobalt-60 Used for radiotherapy • Dysprosium-165 Used in the synovectomy treatment of arthritis • Ytterbium-169 Cerebrospinal studies of the brain • Iodine-125 Used in prostate and brain cancer therapy. Used to diagnose deep vein thrombosis. Used to assay for hormones present in minute quantities • Iodine 131 Treating thyroid cancer and imaging the thyroid. Used in diagnosis of liver function, kidney blood flow and urinary tract obstruction. A strong gamma emitter, but is used for beta therapy.

X-ray • The basic production of X-rays is by accelerating electrons in order to collide with a metal target. (In medical applications, this is usually tungsten or a more crack-resistant alloy of rhenium (5%) and tungsten (95%), but sometimes molybdeym for more specialized applications, such as when soft X-rays are needed as in mammography. • In the X-ray tube the electrons suddenly decelerate upon colliding with the metal target and if the electron has enough energy it can knock out an electron from the inner shell of the metal atom and as a result electrons from higher energy levels then fill up the vacancy and X-ray photons are emitted.

CAT Scan • CAT SCAN A computerized axial tomography scan is more commonly known by its abbreviated name, CT scan or CAT scan. It is an x-ray procedure which combines many x-ray images with the aid of a computer to generate cross-sectional views and, if needed, three-dimensional images of the internal organs and structures of the body.

MRI • Unlike x-rays and computed tomographic (CT) scans, which use radiation, MRI uses powerful magnets and radio waves. The MRI scanner contains the magnet. The magnetic field produced by an MRI is about 10 thousand times greater than the earth's. • The magnetic field forces hydrogen atoms in the body to line up in a certain way (similar to how the needle on a compass moves when you hold it near a magnet). When radio waves are sent toward the lined-up hydrogen atoms, they bounce back, and a computer records the signal. Different types of tissues send back different signals. For example, healthy tissue sends back a slightly different signal than cancerous tissue.

Carbon Dating • Research Carbon Dating. • Discover the theory, the advantages and the drawbacks of the technique. • Complete a 1 page essay on the use of Carbon Dating

Carbon Dating • Because the half-life of carbon-14 is 5,700 years, it is only reliable for dating objects up to about 60,000 years old. However, the principle of carbon-14 dating applies to other isotopes as well. Potassium-40 is another radioactive element naturally found in your body and has a half-life of 1.3 billion years. Other useful radioisotopes for radioactive dating include Uranium -235 (half-life = 704 million years), Uranium -238 (half-life = 4.5 billion years), Thorium-232 (half-life = 14 billion years) and Rubidium-87 (half-life = 49 billion years).

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. A happy atom!!!!!!

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

2.7 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)

Na+ • Sodium and chloride ions bond to form sodium chloride, common table salt Cl– Figure 2.7B

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

Because of the nature of ionic and covalent bonds, the materials produced by those bonds tend to have quite different macroscopic properties. The atoms of covalent materials are bound tightly to each other in stable molecules, but those molecules are generally not very strongly attracted to other molecules in the material. On the other hand, the atoms (ions) in ionic materials show strong attractions to other ions in their vicinity. This generally leads to low melting points for covalent solids, and high melting points for ionic solids. For example, the molecule carbon tetrachloride is a non-polar covalent molecule, CCl4. It's melting point is -23°C. By contrast, the ionic solid NaCl has a melting point of 800°C. Furthermore, ionic bonds themselves tend to be weaker than covalent bonds, but this is a topic for a more advanced chemistry course as it is a generalization.

Test yourself………………. • Draw a model of the type of bond between potassium and chlorine. • Draw a model of the type of bond between hydrogen and fluorine. • Biologists love water!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Is it ionic or covalent?

H2O is a polar covalent molecule

CHAPTER 2 The Chemical Basis of Life