Chemistry BUILDING BLOCKS OF MATTER

Chemistry BUILDING BLOCKS OF MATTER

Outline I. Why study Chemistry II. Elements Atoms Isotopes Periodic Table Electrons Bonding III. Bonds Covalent bonds Polarity Ionic bonds Hydrogen bonding IV. Water V. 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 kind of things will cross a membrane, and what are biological compounds make up cells. What is a protein?

Definitions and the Basics Matter is anything that takes up space and have mass. Atoms are units of matter that cannot be broken down into simpler substances that still retain all the properties of the substance. An element is a pure form of matter containing only one kind of atom.

Elements in nature Text page 22

Atom We used to think (hundreds of years ago) that an atom could not be divided, now we know they are composed of parts (sub atomic particles): Protons carry a positive charge Neutrons have no charge (neutral) Protons and neutrons are made of quarks Electrons carry a negative charge Electrons are massless

Table 2.1 Review of Subatomic Particles

The Atom Cont. Protons and neutrons are in the center of the atom Electrons orbit around the outer edge in orbitals In each atom the # electrons = # protons Ions have added or lost electrons Example: Cl- is a chlorine ion that has gained an electron

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 can have up to eight electrons The third, fourth shells can have up to eight electrons

Protons are found in the 1. Nucleus 2. Orbital shells

How many electrons can be in the 1 st shell? 1. One 2. Two 3. Four 4. Eight

How many electrons can be in the 2cd shell? 1. One 2. Two 3. Four 4. Eight

Periodic Table of Elements Figure 2.2

Reading the Periodic Table 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

How many electrons does Be have? 1. 4 2. 5 3. 9 4. 13

Isotopes Atoms with the same number of protons but different numbers of neutrons are called isotopes

Isotopes of Hydrogen

Radioactive Isotopes In 1896, Henri 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

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

Isotopes are atoms of the same element that differ in their number of 1. Protons 2. Electrons 3. Neutrons 4. 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

Carbon has 6 protons, 6 electrons and 6 neutrons. Its atomic weight is? 1. Six 2. Eight 3. Twelve 4. Twenty-four

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) Number of Neutrons = Mass number - # of Protons

For any element: Number of Protons = Atomic Number Number of Electrons = # Protons = Atomic Number Number of Neutrons = Mass Number - Atomic Number

For Be: Number of Protons = Atomic Number = 4 Number of Electrons = # of Protons = 4 Number of Neutrons = Mass Number - Atomic Number = 9-4 = 5

Chemical Bonds Chemical bonds are unions between electron structure from different atoms Molecules are when two or more atoms join together. They can be the same element (H 2 ) or different elements (H 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 reactive and will form chemical bonds. How many bonds it can form depends on how many empty spots in outer shell

How many neutrons does Li have? 1. 3 2. 4 3. 7 4. 10

Chemistry and Biology Figure 2.8

Chemical Bonds Covalent bonds Ionic Hydrogen

Covalent bonds Covalent bonds The strongest bonds They form when two or more atoms share the electrons in their outer shells

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

Double Bond

How many bonds can carbon form? 1. One 2. Two 3. Three 4. Four

How many bonds can hydrogen form? 1. One 2. Two 3. Three 4. Four

How many bonds can helium form? 1. None 2. One 3. Two 4. Three

How many bonds can nitrogen form? 1. One 2. Two 3. Three 4. Four

How many bonds can oxygen form? 1. One 2. Two 3. Three 4. Four

Types of Covalent Bonds Covalent bonds Polar Nonpolar

Covalent 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

Covalent Bonding Covalent bonds can be polar or nonpolar Nonpolar bonds the atoms have same pull on the shared electrons (H 2 ) Polar bonds the atoms don t equally share the electrons (H 2 O)

Polar Covalent Bond Figure 2.11a

Polarity 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)

Polarity Con t 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

Water Alcohol H H O H C O H H H Ketone Aldehyde H 3 C H 2 C C H 2 O C CH 3 H 3 C H 2 C C H 2 O C H Hydrocarbons H 3 C H 2 C C H 2 H 2 C C H 2 H 2 C C H 2 CH 3 H H C H H

H N H H S CH 3 CH 3 HC H C CH HC C H CH

Polar Groups Oxygen containing: Carboxyl = - COOH Hydroxyl (alcohol) = - OH Phosphates = -PO 4 Carbonyl Ketone = - CO Aldehyde = - CHO Nitrogen containing: Amino (-NH 2 ) Sulfur containing: -SH

Carboxyl Alcohol CH3CH2CH2OH Ketone Aldehyde Ether CH3-O-CH2CH3 Hydrocarbons CH3CH2CH3

Nonpolar compounds Hydrocarbons lots of carbons and hydrogens bonded together

Terminology Hydrophilic (water-loving) polar molecules that are attracted to water Hydrophobic (water-fearing) nonpolar molecules that are pushed aside by water

Chemical formulas 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.

Examples How would you draw this compound? H 2 O H O H

Examples How would you draw this compound? C 4 H 10 H H H H H C C C C H H H H H

Examples How would you draw this compound? C 4 H 8 H H H H C C C C H H H H

Examples How would you draw this compound? CO 2 O C O

Examples How would you draw this compound? C 2 H 4 O H O H C C H H

2. Hydrogen Bonding 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).

2. Hydrogen Bonding Individually weak, but many together can be strong. Determines shapes of many biological molecules including proteins and DNA

2. Hydrogen bonds Figure 2.11b

3. Ionic Bonds 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

3. Ionic bond Figure 2.10

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 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

Water Water is polar and forms hydrogen bonds

Hydrogen bonding H O H O H H

Exists in Three Forms Water exists in three forms Solid - Ice Liquid Vapor

Ice As water approaches 0 C, 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

Ice caps The floating property of ice allows the Artic Ocean 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 So what do all this mean? The polarity and ability to form hydrogen bond give water its properties There are four properties of water

1. Water is an excellent polar solvent 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

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

2. Water has Cohesion What allows bugs to walk on water? Hydrogen-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 move easier in 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. 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

Why is this property important? Water in our bodies keep us at a constant temp.

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). Hydrogen bonds must be broken in order to change water from liquid to vapor

Why is this property important? Sweat is mainly water, when we sweat the body uses its heat to vaporize the water cooling us off.

H 2 is a(n) 1. Atom 2. Molecule 3. Compound molecule

Hydrophobic molecules are by water 1. Attracted 2. Repelled

What type of bond between water molecules creates surface tension that gives water cohesion? 1. Ionic 2. Covalent 3. Hydrogen

Water 1. Makes ionic bonds 2. Is nonpolar 3. Is polar

Which property of water provides the cooling effect of sweating 1. Cohesiveness 2. High heat capacity 3. High heat of vaporization 4. 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

Acids and Bases Acids Substances that donates hydrogen ions when in solution HCl H + + Cl - Bases Substances that accept hydrogen ions when in solution NaOH Na + + OH - In solution: H + + Cl - + Na + + OH - H 2 O + NaCl

ph Scale The strength of acids and bases is measured using the ph scale. ph = -log 10 [H + ] [H + ] = conc in moles per liter It is inverse relationship: Higher the ph the lower the concentration of H + Logarithmic: Each point increase in ph represents a ten-fold decrease in H+ concentration.

ph Scale Scale from 0 14 0 is the most acidic 14 is the most basic 7 is neutral (pure water)

Acids and Bases Table 2.3

The higher the ph a solution has, the higher the H+ concentration 1. True 2. False

Is a ph of 8 acidic or basic? 1. Acidic 2. Basic

Biological Fluids Blood ph 7.35 Changes in ph of ± 0.1 can damage cells, ph of 7.8 can be lethal Biological fluids have buffers to keep the ph stable. Most biological fluids are between 6 8 Stomach fluid ph of under 2

Buffers Buffers resist ph changes because they are chemicals that can take up excess H+ or OH- Our body wants to keep its fluids at an even ph. Blood contains buffers that are weak acids that can dissociate into ions.

Buffers For example when CO 2 enters the blood it combines with H 2 O to form carbonic acid (H 2 CO 3 ). This weak acid dissociates to form H + and bicarbonate ion (HCO 3- )

Acids in the Environment

Acid Rain Read the section on page 25 The two main sources of acid rain are H 2 SO 4 and HNO 3 Most of H 2 SO 4 pollution comes from electric power plants Most of HNO 3 pollution comes from cars, buses etc

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 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.

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. Be able to identify polar and nonpolar molecules

Important Concepts 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 ph scale

Important Concepts 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, Chemical bonds, single bond, double bond, Molecules, Compound Molecules, Ion, Ionic bond, Covalent bond, Nonpolar bonds, Polar bonds, electronegativity, Hydrogen bond, Hydrophilic, Hydrophobic, Cohesion, acid, base, buffers, logarithmic, inverse, ph, solvent, solute, solution