8/13/2009. Chemistry. Why study Chemistry? Definitions and the Basics. Elements in nature. Matter is anything that takes up spass and have mass.
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1 hemistry BioSci 105 Lecture 2 Reading: hapter 2 (Pages 14-25) utline I. Why study hemistry II. Elements Atoms Isotopes Periodic Table Electrons Bonding III. Bonds ovalent bonds Polarity Ionic bonds ydrogen bonding IV. Water V. Acids and Bases Why study hemistry? Definitions and the Basics hemistry is the basis for studying much of biology Matter is anything that takes up spass and have mass. The biology of the human body follows the rules of physics and chemistry. You need to understand enough about chemistry to know what kind of things will cross a membrane, and what are biological compounds make up cells. What is a protein? Atoms are units of matter that cannot be broken down into simpler substances. An element is a pure form of matter containing only one kind of atom. Elements in nature Text page 22 1
2 Atom Table 2.1 Review of Subatomic Particles We used to think that an atom could not be divided, now we know they are composed of parts (particles): Protons carry a positive charge Neutrons have no charge (neutral) Electrons carry a negative charge The Atom ont. Protons and neutrons are in the center of the atom Electrons orbit around the outer edge in orbitals In each atom the # electrons = # protons hemistry and Biology Shell Model of Electrons Electrons can be visualized as residing in shells around the nucleus. The first shell can have up to two electrons The second shell can have up to eight electrons The third, fourth shells can have up to eight electrons Figure 2.1c 2
3 Periodic Table of Elements Figure 2.2 Particle Mass Proton = 1 amu Neutron = 1 amu Electron = negligible The atomic number = the # of protons in an atom Atoms have equal numbers of protons and electrons. Isotopes Isotopes of ydrogen Atoms with the same number of protons but different numbers of neutrons are called isotopes 3
4 Radioactive Isotopes Radioactive Isotopes In 1896, enri Becquerel placed a rock on unexposed photographic plates inside a drawer. The rock contained uranium. The isotopes of uranium emit energy. After a few days the plate had an image of the rock. A co-worker, Marie urie, named this radioactivity. This is known as a radioisotope Radioisotopes are isotopes that are unstable, and become more stable by emitting energy and particles In contrast, most isotopes are stable Radioisotopes in Medicine Isotopes in medicine PET scans (Positron-Emission Tomography) Patient is injected with a compound that is labeled with an unstable isotope ancer cells are growing faster and take up more of the compound than normal cells Abnormal tissue takes up less of the compounds Figure 2.4 Atomic number Atomic weight The atomic weight = an average of the isotopes Mass number = round the atomic weight Mass Number = (Number of Protons) + (Number of Neutrons) For any element: Number of Protons = Atomic Number Number of Electrons = # Protons = Atomic Number Number of Neutrons = Mass Number - Atomic Number Number of Neutrons = Mass number - # of Protons 4
5 hemical Bonds For Be: Number of Protons = Atomic Number = 4 Number of Electrons = # of Protons = 4 Number of Neutrons = Mass Number - Atomic Number = 9-4 = 5 hemical bonds are unions between electron structure from different atoms Molecules are when two or more atoms join together. They can be the same element ( 2 ) or different elements ( 2 ) When different elements join the molecule is referred to as a compound molecule Electrons and Bonding hemistry and Biology If the outer shell is full, then it is non-reactive and stable = does not form chemical bonds. Incompletely filled outer orbital, then atom reactive and will form chemical bonds. ow many bonds it can form depends on how many empty spots in outer shell Figure 2.8 hemical Bonds ovalent bonds ovalent bonds Ionic ydrogen ovalent bonds The strongest bonds They form when two or more atoms share the electrons in their outer shells 5
6 ow many bonds can form? Each atom wants their outer shell filled. ydrogen only has one electron in its shell wants two, so it can form one bond. arbon has four electrons in outer shell, wants eight, so it can form four bonds. Double Bond Types of ovalent Bonds ovalent bonds Polar Nonpolar 1. ovalent Bonding ovalent Bonding When two atoms with unpaired electrons in the outer most shell come together and share electrons Each atom has an attractive force for the other atoms unshared electrons, but not enough to take it completely away ovalent bonds can be polar or nonpolar Nonpolar bonds the atoms have same pull on the shared electrons ( 2 ) Polar bonds the atoms don t equally share the electrons ( 2 ) 6
7 Polar ovalent Bond Figure 2.11a Polarity Polarity on t Some atoms have a greater pull on shared electron than other atoms The measure of this pull is electronegativity When a bond is made between atoms with different electronegativities it is a polar bond The greater the pull the more electronegative (remember that electrons are negative) Polar ovalent Bonding occurs with strong electrophiles (electronegative): atoms with nuclei that have a strong pull on electrons. ommon examples in biological molecules include: xygen Nitrogen Sulfur Polarity Water Alcohol The oxygen side of water is slightly negative and the hydrogen sides are slightly positive Ketone Aldehyde ydrocarbons
8 N S Polar Groups 3 3 xygen containing: arboxyl = - ydroxyl (alcohol) = - Phosphates = -P 4 arbonyl Ketone = - Aldehyde = - Nitrogen containing: Amino (-N 2 ) Sulfur containing: -S Nonpolar compounds arboxyl Alcohol 322 ydrocarbons lots of carbons and hydrogens bonded together Ketone Aldehyde Ether ydrocarbons 323 Terminology hemical formulas ydrophilic (water-loving) polar molecules that are attracted to water ydrophobic (water-fearing) nonpolar molecules that are pushed aside by water When we write compounds, we often write them as a formula that tells how atoms many of each element are present, but not the way the molecule is put together. You often can determine the way the molecule is put together by knowing how many bonds each element can form. 8
9 Examples Examples ow would you draw this compound? 2 ow would you draw this compound? 4 10 Examples Examples ow would you draw this compound? 4 8 ow would you draw this compound? 2 Examples 2. ydrogen Bonding ow would you draw this compound? 2 4 Weak attraction between a hydrogen atom with a partial positive charge and another atom with a partial negative charge (electronegative atom such as oxygen, nitrogen, or sulfur). 9
10 2. ydrogen Bonding 2. ydrogen bonds Individually weak, but many together can be strong. Determines shapes of many biological molecules including proteins and DNA Figure 2.11b 3. Ionic Bonds 3. Ionic bond Ion = atom that has gained or lost electrons, It no longer has a balance between protons and electrons, it is positive or negative charge Ionic bond is an association between ions of opposite charge Figure 2.10 hemical bonds Table
11 Water The Life Giving Molecule Water s Abundance Why are we so interested in finding evidence of water on Mars? What would it mean if we did not find evidence of water? r if we find evidence? Does it matter what form the water is? Life exists here because water is abundant 71% of Earth s surface is water 97.5% of the water is salt water Freshwater only accounts for 2.5% of water nly 0.53% is available to us to drink (rivers, lakes, ground water) 66% of the human body is water by weight 75-85% of a cell s weight is water Water Water is polar and forms hydrogen bonds ydrogen bonding Water is a great example of hydrogen bonding, itis the hydrogen bonds that give water much of its unique characteristics Exists in Three Forms Water exists in three forms Solid - Ice Liquid Vapor Ice As water approaches 0, freezing temperature, the molecules slow down. Water forms more hydrogen-bonds at lower temperature and forms a lattice structure The ice is less dense due to the lattice structure and to the fact that there are less molecules present than in the same volume of liquid 11
12 Ice caps The floating property of ice allows the Artic cean s ice cap to exist This is the habitat for polar bear and young seals, as well as many other species. These ice caps are melting, as they melt the habitat for these species shrinks. Properties of Water 1. Water is an excellent polar solvent So what do all this mean? The polarity and ability to form hydrogen bond give water its properties There are four properties of water Because water is polar and forms hydrogen bonds, it acts as a solvent for polar molecules Like dissolves in like, so polar molecules dissolve in water Water is considered the best polar solvent due in great part to its ability to form hydrogen bonds with other molecules 12
13 Why is this property important? Blood is approx 55% water so the fact that water is a good solvent makes blood a good way to transport things around. ells are made up of mainly water, the water keeps salts in your cells, blood and tissues in solution. 2. Water has ohesion 2. Water has ohesion Due to the hydrogen bonding, water has cohesion (the water molecules cling together) ohesion is the capacity to resist breaking under tension What allows bugs to walk on water? ydrogen-bonds create surface tension At the surface of water, where water meets air, the water molecules are being pulled down with a much greater force than they are being pulled up towards the air Why is this property important? 3. Water has igh heat capacity The cohesion of water allows blood move easier in the blood vessels. Also is responsible for moving water in plants It takes a great deal of energy to raise the temperature. When you increase the temperature of something, the molecule in it move faster, hydrogen bonds keep the water molecules in place so it takes lots of energy to break the bonds and heat the water 13
14 Why is this property important? 4. Water has igh heat of Vaporization Water in our bodies keep us at a constant temp. It takes a great deal of energy to make water evaporate (change water from a liquid to a gas). ydrogen bonds must be broken in order to change water from liquid to vapor Why is this property important? Acids and Bases Sweat is mainly water, when we sweat the body uses its heat to vaporize the water cooling us off. We are already familiar with acids and bases ommon acids: Lemon juice Sodas Vinegar ommon bases: Ammonia Many household cleaners Bleach Acids and Bases Ph Scale Acids Substances that donates hydrogen ions when in solution l + + l - Bases Substances that accept hydrogen ions when in solution Na Na In solution: + + l - + Na Nal The strength of acids and bases is measured using the p scale. p = -log 10 [ + ] [ + ] = conc in moles per liter It is inverse relationship: igher the p the lower the concentration of + Logarithmic: Each point increase in p represents a ten-fold decrease in + concentration. 14
15 Ph Scale Acids and Bases Scale from is the most acidic 14 is the most basic 7 is neutral (pure water) Table 2.3 Biological Fluids Blood p 7.35 hanges in p of ± 0.1 can damage cells, p of 7.8 can be lethal Biological fluids have buffers to keep the p stable. Most biological fluids are between 6 8 Stomach fluid p of under 2 15
16 Buffers Buffers Buffers resist p changes because they are chemicals that can take up excess + or - ur body wants to keep its fluids at an even p. Blood contains buffers that are weak acids that can dissociate into ions. For example when 2 enters the blood it combines with 2 to form carbonic acid ( 2 3 ). This weak acid dissociates to form + and bicarbonate ion ( 3- ) Acids in the Environment Acid Rain Read the section on page 25 The two main sources of acid rain are 2 S 4 and N 3 Most of 2 S 4 pollution comes from electric power plants Most of N 3 pollution comes from cars, buses etc Effects of Acid Rain Important oncepts Acid rain acidifies lakes and streams More acidic water leaches more heavy metals from the soil than normal water. Declining frog and fish populations may be due more to increased metal concentrations in the water than due to the acidic water itself Reading for next lecture: hapter 2 (pages 25 36) What are the three particles of an atom, where are they located, what is their charge, and mass. Be able to determine how many bonds each element can form. Be able to recognize if a molecule is drawn correctly. 16
17 Important oncepts Be able to read the periodic table to determine the number of protons, neutrons and electrons in the atoms of all the biologically important elements. What are the three most common elements in the human body Be able to draw the atom of any biologically important element, with the correct number of protons, neutrons, and electrons. Be able to draw the electrons in their correct shell. Important oncepts Be able to describe the types of chemical bonds Be able to draw a water molecule and hydrogen bonding between water molecules Be able to describe the four properties of water and their importance in living organisms. Understand the p scale Be able to identify polar and nonpolar molecules Important oncepts Understand the causes and effects of acid rain, know the chemicals that cause acid, the effects on the environment, and the human health effects associated with acid rain (see page 25) What are three electronegative elements found in biological molecules Definitions Matter, Atom, Element, Isotopes, Radioisotopes, hemical bonds, single bond, double bond, Molecules, ompound Molecules, Ion, Ionic bond, ovalent bond, Nonpolar bonds, Polar bonds, electronegativity, ydrogen bond, ydrophilic, ydrophobic, ohesion, acid, base, buffers, logarithmic, inverse, p, solvent, solute, solution 17
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