Chemistry 8/27/2013. Outline. Why study chemistry? Chemistry is the basis for studying much of biology.

Transcription

1 Chemistry Biology 105 Lecture 2 Reading: Chapter 2 (pages 20-29) Outline Why study chemistry??? Elements Atoms Isotopes Periodic Table Electrons Bonding Bonds Covalent bonds Polarity Ionic bonds ydrogen bonding Water Acids and Bases Why study chemistry? Chemistry is the basis for studying much of biology. The biology of the human body follows the rules of physics and chemistry. You need to understand enough about chemistry to know what kinds of things will cross a membrane, and what the biological compounds are that make-up cells. What is a protein? 1

2 Definitions and the Basics Matter is anything that takes up space and has mass. 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 The Atom We used to think that an atom could not be divided, but now we know atoms are composed of parts (particles): Protons carry a positive charge Neutrons have no charge (neutral) Electrons carry a negative charge 2

3 Table 2.1 Review of Subatomic Particles The Atom Protons and neutrons are in the center of the atom. Electrons orbit around the outer edge in orbitals. In each atom the # electrons = # protons. 3

4 Chemistry and Biology Figure 2.1c 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 canhaveuptoeight eight electrons. The third, fourth shells can have up to eight electrons. Protons are found in the 1. Nucleus 2. Orbital shells 50% 50% Nucleus Orbital shells 4

5 ow many electrons can be in the 1 st shell? 1. One 2. Two 3. Four 4. Eight 25% 25% 25% 25% One Two Four Eight ow many electrons can be in the 2nd shell? 1. One 2. Two 3. Four 4. Eight 25% 25% 25% 25% One Two Four Eight Periodic Table of Elements Figure 2.2 5

6 The atomic number = the # of protons in an atom Atoms have equal numbers of protons and electrons. Particle Mass Proton = 1 amu Neutron = 1 amu Electron = negligible 6

7 ow many electrons does Be have? 25% 25% 25% 25% Isotopes Atoms with the same number of protons but different numbers of neutrons are called isotopes. Isotopes of ydrogen: 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 Curie, named this radioactivity. This is known as a radioisotope. 7

8 Radioactive Isotopes Radioisotopes are isotopes that are unstable, and become more stable by emitting energy and particles. In contrast, most isotopes are stable. Radioisotopes in Medicine PET scans (Positron-Emission Tomography) Patient is injected with a compound that is labeled with an unstable isotope Cancer cells are growing faster and take up more of the compound than normal cells Abnormal tissue takes up less of the compounds Isotopes in Medicine Figure 2.4 8

9 Isotopes are atoms of the same element that differ in their number of 1. Protons 2. Electrons 3. Neutrons 4. None of the above 25% 25% 25% 25% Protons Electrons Neutrons None of the above Carbon has 6 protons, 6 electrons and 6 neutrons. Its atomic number is. 1. Six 2. Eight 3. Twelve 4. Twenty-four 25% 25% 25% 25% Six Eight Twelve Twenty-four Carbon has 6 protons, 6 electrons and 6 neutrons. Its atomic weight is. 1. Six 2. Eight 3. Twelve 4. Twenty-four 25% 25% 25% 25% Six Eight Twelve Twenty-four 9

10 Atomic number Atomic weight Atomic Weight = an average of the isotopes Mass Number = round the atomic weight Mass Number = (Number of Protons) + (Number of Neutrons) Number of Neutrons = (Mass Number) (Number of Protons) For any element: Number of Protons = Atomic Number Number of Electrons = Number of Protons = Atomic Number Number of Neutrons = Mass Number -Atomic Number For Be: Number of Protons = Atomic Number = 4 Number of Electrons = Number of Protons = 4 Number of Neutrons = Mass Number - Atomic Number = 9-4 = 5 10

11 Chemical Bonds Chemical bonds are unions between electron structures from different atoms. Molecules are when two or more atoms join together. The atoms can be the same element ( 2 ) or different elements ( 2 O). When different elements join, the molecule is referred to as a compound molecule. Electrons and Bonding If the outer shell is full, then it is non-reactive and stable = does not form chemical bonds. Incompletely filled outer orbital, then atom is reactive and will form chemical bonds. ow many bonds it can form depends on how many empty spots in outer shell. ow many neutrons does Li have? 25% 25% 25% 25%

12 Chemistry and Biology Figure 2.8 Chemical Bonds Covalent bonds Ionic bonds ydrogen bonds Covalent Bonds Covalent bonds: The strongest bonds They form when two or more atoms share the electrons in their outer shells. 12

13 ow many bonds can form? Each atom wants their outer shell filled. ydrogen only has one electron in its shell it wants two, so it can form one bond. Carbon has four electrons in its outer shell it wants eight, so it can form four bonds. Double Bond 13

14 ow many bonds can carbon form? 1. One 2. Two 3. Three 4. Four 25% 25% 25% 25% One Two Three Four ow many bonds can hydrogen form? 1. One 2. Two 3. Three 4. Four 25% 25% 25% 25% One Two Three Four ow many bonds can helium form? 1. None 2. One 3. Two 4. Three 25% 25% 25% 25% None One Two Three 14

15 ow many bonds can nitrogen form? 1. One 2. Two 3. Three 4. Four 25% 25% 25% 25% One Two Three Four ow many bonds can oxygen form? 1. One 2. Two 3. Three 4. Four 25% 25% 25% 25% One Two Three Four Covalent Bonding When two atoms with unpaired electrons in the outermost shell come together and share electrons. Each atom has an attractive force for the other atom s unshared electrons, but not enough to take them completely away. 15

16 Covalent Bonding Covalent bonds can be polar or nonpolar. Nonpolar bonds: the atoms have the same pull on the shared electrons ( 2 ). Polar bonds: the atoms don t equally share the electrons ( 2 O). Polar Covalent Bond Figure 2.11a 16

17 Polarity Some atoms have a greater pull on shared electrons 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). Polarity Polar covalent bonding occurs with strong electrophiles (electronegative): atoms with nuclei that have a strong pull on electrons. Common examples in biological molecules include: Oxygen Nitrogen Sulfur Polarity The oxygen side of water is slightly negative and the hydrogen sides are slightly positive. 17

18 Water Alcohol O C O Ketone Aldehyde 3C 2 C C 2 O C C 3 3C 2 C C 2 O C ydrocarbons 3C 2 C C 2 2 C C 2 2 C C 2 C 3 C N S C 3 C 3 C C C C C C Polar Groups Oxygen containing: Carboxyl = -COO ydroxyl (alcohol) = -O Phosphate = -PO 4 Carbonyl: Ketone = -CO Aldehyde = -CO Nitrogen containing = amino (-N 2 ) Sulfur containing = -S 18

19 Carboxyl Alcohol C3C2C2O Ketone Aldehyde Ether C3-O-C2C3 ydrocarbons C3C2C3 Nonpolar Compounds ydrocarbons lots of carbons and hydrogens bonded together. Terminology ydrophilic (water-loving) polar molecules that are attracted to water. ydrophobic (water-fearing) nonpolar molecules that are pushed aside by water. 19

20 Chemical Formulas When we write compounds, we often write them as a formula that tells how many atoms 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. Examples ow would you draw this compound? 2 O O Examples ow would you draw this compound? C 4 10 C C C C 20

21 Examples ow would you draw this compound? C 4 8 C C C C Examples ow would you draw this compound? CO 2 O C O Examples ow would you draw this compound? C 2 4 O O C C 21

22 ydrogen Bonding Weak attraction between a hydrogen atom with a partial positive charge and another atom with a partial negative charge (an electronegative atom such as oxygen, nitrogen, or sulfur). ydrogen Bonding Individually weak, but many together can be strong. Determines shape of many biological molecules, including proteins and DNA. ydrogen Bonds Figure 2.11b 22

23 Ionic Bonds Ion = atom that has gained or lost electrons It no longer has a balance between protons and electrons. It has a positive or negative charge. Ionic bond is an association between ions of opposite charge. Ionic Bond Figure

24 Chemical Bonds Table 2.2 Water The Life Giving Molecule Why are we so interested in finding evidence of water on Mars? What would it mean if we did not find evidence of water? Or if we find evidence? Does it matter what form the water is? Life exists here because water is abundant! Water s Abundance 71% of the Earth s surface is water 97.5% of the water is salt water Freshwater only accounts for 2.5% of water Only 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 24

25 Water Water is polar and forms hydrogen bonds. Water is a great example of hydrogen bonding the hydrogen bonds give water many of its unique characteristics. O O Exists in Three Forms Water exists in three forms Solid - Ice Liquid Vapor Water Exists in Three Forms (1) Ice (Solid) As water approaches 0 C, its 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. 25

26 Ice Caps The floating property of ice allows the Artic Ocean s ice cap to exist. This is the habitat for polar bears and young seals, as well as many other species. These ice caps are melting, and as they melt the habitat for these species shrinks. Properties of Water So what does all this mean? The polarity and ability to form hydrogen bonds give water its properties. There are four properties of water 26

27 1. Water is an excellent polar solvent 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. 27

28 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. Cells are made up of mainly water: the water keeps salts in your cells, blood, and tissues in solution. 2. Water has cohesion Due to the hydrogen bonding, water has cohesion (the water molecules cling together). Cohesion is the capacity to resist breaking under tension. 28

29 2. Water has cohesion 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? The cohesion of water allows blood to move more easily through the blood vessels. Also is responsible for moving water in plants 3. Water has high heat capacity It takes a great deal of energy to raise the temperature of water. When you increase the temperature of something, the molecules in it move faster. ydrogen bonds keep the water molecules in place, so it takes lots of energy to break the bonds and heat the water. 29

30 Why is this property important? Water in our bodies keeps us at a constant temperature. 4. Water has high heat of vaporization 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? Sweat is mainly water, so when we sweat the body uses its heat to vaporize the water cooling us off. 30

31 2 is a(n) 1. Atom 2. Molecule 3. Compound molecule 33% 33% 33% Atom Molecule Compound molecule ydrophobic molecules are by water. 1. Attracted 2. Repelled 50% 50% Attracted Repelled What type of bond between water molecules creates surface tension that gives water cohesion? 1. Ionic 2. Covalent 3. ydrogen 33% 33% 33% Ionic Covalent ydrogen 31

32 Water 1. Makes ionic bonds 2. Is nonpolar 3. Is polar 33% 33% 33% Makes ionic bonds Is nonpolar Is polar Which property of water provides the cooling effect of sweating? 1. Cohesiveness 2. igh heat capacity 3. igh heat of vaporization 4. Excellent solvent 25% 25% 25% 25% Cohesiveness igh heat capacity igh heat of vaporiz... Excellent solvent Acids and Bases We are already familiar with acids and bases. Common acids: Lemon juice Sodas Vinegar Common bases: Ammonia Many household cleaners Bleach 32

33 Acids and Bases Acids substances that donates hydrogen ions when in solution: Cl + + Cl - Bases substances that accept hydrogen ions when in solution: NaO Na + + O - In solution: + + Cl - + Na + + O - 2 O + NaCl p Scale The strength of acids and bases is measured using the p scale. p = -log 10 [ + ] [ + ] = concentration in moles per liter It is an inverse relationship: igher p = lower concentration of + Logarithmic: Each point increase in p represents a ten-fold decrease in + concentration. p Scale Scale from is the most acidic 14 is the most basic 7 is neutral (pure water) 33

34 Acids and Bases Table 2.3 The higher the p a solution has, the higher the + concentration. 1. True 2. False 50% 50% True False 34

35 Is a p of 8 acidic or basic? 1. Acidic 2. Basic 50% 50% Acidic Basic Biological Fluids Blood p 7.35 Changes 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 Buffers Buffers resist p changes because they are chemicals that can take up excess + or O-. Our body wants to keep its fluids at an even p. Blood contains buffers that are weak acids that can dissociate into ions. 35

36 Buffers For example, when CO 2 enters the blood it combines with 2 O to form carbonic acid ( 2 CO 3 ). This weak acid dissociates to form + and bicarbonate ion (CO 3- ). Acids in the Environment Acid Rain The two main sources of acid rain are 2 SO 4 and NO 3. Most of 2 SO 4 pollution comes from electric power plants. Most of NO 3 pollution comes from cars, buses, etc. 36

37 Effects of Acid Rain 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. Important Concepts Reading for next lecture: Chapter 2 (pages 29 39) What are the three particles of an atom, where are they located, what are their charges, and masses? Be able to determine how many bonds each element can form. Be able to recognize if a molecule is drawn correctly. 37

38 Important Concepts 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(s). Important Concepts Be able to identify polar and nonpolar molecules. Be able to describe the types of chemical bonds. Be able to draw a water molecule and hydrogen bonding between water molecules. l Be able to describe the four properties of water and their importance in living organisms. Understand the p scale. Important Concepts What are three electronegative elements found in biological molecules? 38

39 Definitions Matter, atom, element, isotope, radioisotope, chemical bond, single bond, double bond, molecule, compound molecule, ion, ionic bond, covalent bond, nonpolar bond, polar bond, electronegativity, hydrogen bond, hydrophilic, hydrophobic, h cohesion, acid, base, buffer, logarithmic, inverse, p, solvent, solute, solution 39