I Biology I Lecture Outline Basic Chemistry Life Basic Chemistry of Life.pdfI Biology I Lecture Outline Basic Chemistry ofLife . References (Textbook - pages . 20 -36: Lab . Manual

I Biology I Lecture Outline Basic Chemistry of Life

References (Textbook - pages 20 - 36: Lab Manual - pages 8 - 11)

Matter

Elements

The Atom

Atomic Theory and Definition Atomic Symbols Anatomy of an Atom - Subatomic Particles Atomic Number and Mass Number Electrons and Energy Levels

The Periodic Table of Elements

Isotopes

Compounds and Molecules

Definitions

Ionic Bonding

Covalent Bonding

Water and Hydrogen Bonding

Acids and Bases

IBiology I Lecture Notes 3 Basic Chemistry of Life

References (Textbook - pages 20 - 36: Lab Manual- pages 8 - 11)

Organisms (living things) are made of chemicals. Organisms are made of the same chemicals as inanimate (non-living) things. In other words, many of the same chemicals that make up your body can be found in rocks, water, asphalt, steel, etc.

Everything in and around you is "chemistry". You might actually call your physical body a "bag ofchemicab'"

An understanding of the basic principles of Chemistry is necessary to understand biology. So, we will spend the next lecture or two studying afew important topics of chemistry.

Webster's Dictionary definition ofchemistry - science dealing with composition and properties ofsubstances, and with the reactions by which substances are produced or changed.

Matter

1. Matter is defined in our textbook as - anything that occupies space and possesses mass.

2. Space is defined in Webster's dictionary as - the continuous 3- dimensional expanse in whicb aU things are contained.

3. Mass is defined in Webster's dictionary as - a quantity of matter of indefinite shape and size, a lump.

4. There are 2 kinds ofmatter.

A. Living - like you and other animals and plants

B. Non-living - like rocks. aspbalt, water, steel, etc.

5. Matter exists in only 3 distinct states. One state can be converted to another by addition or subtraction of heat.

A. Solid - HOH exists as a solid (ice) below 31 degrees F

B. Liquid - HOH exists as a liquid between 31 degrees F and 111 degrees F

C. Gas - HOH exists as a gas (water vapor) above 111 degrees F

Elements

I. All matter (both living and non-living) is made up of elements.

2. Our textbook defines an element as - a substance that cannot be broken down into simpler substances with different properties by ordinary chemical means.

3. A property is this definition is a physical or chemical trait such as melJing point, solubility, density, etc).

4. Chemists have identified 92 naturally occurring elements. Some examples include hydrogen, helium, nurogen, carbon, etc.

5. Of these 92 naturally occurring elements, only 6 elements are basic to life and make up about 95% of the body weight of organisms. These six are: (CHNOPS)

A. Carbon - primary element of all organic molecules including carbohydrates, lipids, and proteins.

B. Hydrogen - a component of most organic molecules and in ionicform influences the acidity of body fluids.

C. Nitrogen - a component of proteins and nucleic acids (genetic material)

D. Oxygen - major component of both organic and inorganic molecules and as a gas is essential to the oxidation ofglucose and other food fuels during which cellular energy ATP is captured.

E. Phosphorus - present as a salt and in combination with calcium in bones and teeth. Also present in nucleic acids.

F. Sulfur - a component ofproteins, especially proteins of muscles.

The Atom

l. Atomic Theory and Definition

A. The atomic theory states that ekments consist of tiny particles called atoms.

B. The word atom comes from the Greek word "atomos" which means uncut or indivisible

c. Our textbook defines an atom as - the slIUlllest part of an element that displays the properties of the element.

D.Atoms are SIfUlU. A line of about 1 million wouldjit in the period at the end of a sentence in our textbook. 100 million arranged in a row would measure about 1 inch.

2. Atomic Symbols

A. Scientists have developed a 1 or 2 letter symbol as an abbreviation for each kind of atom.

B. These abbreviations are called the Atomic Symbol. Note that the Atomic Symbol is also used as the symbol for the co"esponding element.

C. Examples of atomic symbols include:

Hydrogen- H Radon - Ra Sodium - Na Carbon - C

3. Anatomy of an Atom - Subatomic Particles

Provide Handout or Model or Hydrogen and Helium Atoms (tbr slmplr!lt two atoms)

A.Physicist's have split atoms apart and identified over 100 kinds ofsubatomic particles. We will only study 3.

Protons Neutrons Electrons

B. Protons

1) arefound in the nucleus of the atom 2) possess a positive + charge.

C.Neutrons

1) are found in the nucleus of the atom 2) possess a neutral 0 charge.

D. Electrons

1) Are found moving around the nucleus in an area often called the electron shell.

2) Modem theory is that electrons fonn a haze or cloud about the atomic nucleus.

3) Electrons have a negative - charge.

4) Electrons travel around a positively + charged nucleus at varying distances from the nucleus at high velocities.

E. Note that atoms are mostly empty space.

F. An analogy from our textbook on page 22 says:

I) If an atom were the size of afootbaUfreld.

2) the nucleus would be the size of a gumbal/ at the 50 yard line in the center of the field,

3) electrons would be tiny specks whirling around the upper stands.

4. Atomic Number and Mass Number

A. All atoms of an element have the same number ofprotons in the nucleus.

B. The Atomic Number is the number ofprotons in the atom's nucleus. Using our handout, what is the Atomic Number for Helium? (2)

c. The Mass Number is the number ofprotons and neutrons in the atom's nucleus. Using our handout, what is the Mass Number for Helium? (4)

D. For a given atom, the Atomic Symbol, Atomic Number, and Mass Number are written as follows:

E. Why are these two values important in biology? They help predict how substances might behave in individual cells, in multi-cellular organisms, and in the environment.

5. Electrons and Energy Levels (See Handout of Bohr Models of Atoms., page ~ ofTntbook, Mader ]0lIl ed)

A. An atom is electrically neutral when the (+) positive charges ofprotons in the nucleus equals the (-) negative charges ofelectrons orbiting about the nucleus.

B. The Bohr Model uses a 2- dimensional approach to show electron positions and levels. (Note - thai tire alom ;11 nality is 3-~nsio,.lll)

c. Electrons orbit around the atom nucleus at different levels or shells. For example see chart below with electron values taken from Bohr Model Handout.

ELEMENT SheD 1 SheD 2 SheD 3 Hydrogen I electron N/A N/A

Carbon 2 electrons " electrons N/A Nitrogen 2 electrons 5 electrons N/A Oxygen 2 electrons 6 electrons N/A

Phosphorus 2 electrons 8 electrons 5 electrons Sulfur 2 electrons 8 electrons 6 electrons

D. Each shell (or level) is restricted to the number of electrons it can contain.

1) Thefirst shell surrounding the nucleus never contains more than 2 electrons. (Note - hydrogell is tire ollly alom to POSSDS ollly I electron)

2) The second shell may contain up to 8 electrons, but never more than 8. (Note ­oxygen has only 6 electroll$ ill second shd} while phosplrorus Ir(l$ 8)

3) The Octet Rule states - the outer electron shell is most stable when it has 8 electrons. (Note - thue art! SOtru! alorm thai corual" 7 dedron slrdls or ,~Is)

4) The outer shell is caned the valence shell.

• The number ofelectrons in the valence shell determines whether an atom gives up, accepts, or shares electrons to get to the needed 8 electrons to achieve stability. (ReltfDrfbu the Octet JlJJIe)

• Atoms with more than -I electrons in the outer shell have a tendency to gain or accept eLectrons.

• Atoms withfewer than -I electrons in the outer shell have a tendency to lose or give up electrons

• The bonding capacity of atoms during chemical reactions is determined by the number of electrons of its outer orbiJ - the valence orbiJ.

E. Electron Energy Levels

1) Electron shells or orbits can also be thought of as energy levels.

2) For example the sulfur atom has 3 electron shells and therefore 3 energy levels.

3) Negatively (-) charged electrons are attracted to the (+) positively charged protons in the nucleus.

4) It takes energy to push electrons away from the (+) positively charged nucleus and keep them in their own shell or orbiJ.

5) Thefarther away from the nucleus the more energy it takes to keep electrons in their own shell.

6) Therefore - the farther away from the nucleus the greater the amount of energy contained in the electron shell.

7) Question - Which orbiJ contains more energy in the sulfur atom? The innermost electron orbiJ or the outer (3rd

) orbiJ.

I

8) Electron energy levels play an important role in nature in a critical biological process called photolynthesis. (Why is pltolosymhesis ;mporttull to life on earth '/)

• During photosynthesis, energy from the sun is absorbed by certain atoms in the plant cell and electrons are boosted to a higher electron orbit. (a higltu energy IneJ) (We wiU study photosynthesis in mo,e dl!1l1illaJe, in tile semester)

• Later these electrons return to a lower electron orbit (a lower energy level) and energy is released that is used by the plant cell to complete photosynthesis and produce oxygen.

• Our textbook states on page 25 - "Our (humans) very existence is dependent on the energy ofelectrons".

The Periodic Table of Elements

(See Handout ofPeriodic Table from page 9 ofLab Manum)

1. The Periodic Table ofElements is a table that organizes all the known elements (atoms) according to certain characteristics like their atomic number, the number of electron shells, and other characteristics.

Isotopes

Textbook definition -Isotopes are atoms of the same element that differ in the "umber of neutrons. (RI!nII!mbu that aU atoms of'he same element have 'he same 1IIImber ofprotons)

2. Another definition could be - Isotopes are atoms of the same element which have the same Atomic Number, but different Mass Numbers. WHY? (Remembuthat Ihe MaY Number ofan atom ;s Ihe 1IIImber of protons plus the numbe, ofneutrons)

3. Isotopes differ physically, but behave in a similar fashion both chemically and physically.

4. Many elements found in nature have several isotopes; however, a great many isotopes have been made by man.

5. The carbon atom has three common isotopes that can be written as:

Carbon 12 - - (has 6 neurtons)

Carbon 13 - - (has 7 neutrons)

Carbon 14 - - (has 8 electrons, radioactive, and unstable)

6. There are many medical uses of radioactive isotopes.

A. To diagnose cancer and other diseases

B. To treat cancer.

C. To sterilize medical and dental products

Compounds and Molecules

1. Compounds and molecuks are the result of chemical reactions where atoms of different elements bond together.

2. Atoms do not normally exist singly or alone.

3. Atoms are most often joined to other atoms to form molecules.

4. Atoms forming molecules are held together by chemical bonds.

5. Recall these two facts we have already discussed.

A. Chemical reactions take place primarily between electrons in the outer shell or outer energy level of separate atoms.

B. The bonding capacity of atoms is determined by the number of electrons in its outer shell - the valence shell.

6. Defmitions

A. Textbook definition ofcompound - a compound exists when 2 or more elements have bonded together. (EumpiH are NaCI - "ble ,aIt. H2O- Water, CH4 - methane)

B. Textbook states - a molecule is the smaDest part of a compound that still has the properties of the particular compound.

C. A molecule is composed of 2 or more atoms.

D. A glass of water can be said to contain the compound water, including lOs of thousands of water molecules

E. In practice these two terms (compound and molecule) can be used interchangeably.

F. A chemicalformula tells the number of each kind ofatom in a molecule.

G. One molecule ofglucose can be written as

Indicating 6 atoms ofcarbon 12 atoms of hydrogen 6 atoms ofoxygen

H. The electron bonds contain energy.

I. During chemical reactions where glucose is broken down, electrons shift their energy levels and energy is released.

7. Ionic Bonding (see HaDdout of Figure 2.7, page 26 of TeItbook, Mader 10'" Ed.)

A. Textbook defines an ionic bond as - a chemical bond in which ions are attracted to one another by opposite charges.

B. Textbook definition of ion - a charged particle that carries a negative or positive charge.

C. Example of Ionic Bonding - Na (sodium) and CI (chloride)

1) Na (sodium) atom

• Has only 1 electron in its outer (3 rd) sheD and tends to be an electron

donor

• Once it gives up this electron its 2"" shell with 8 eleclrons becomes the outer shell (remember the octet rule).

2) CI (chloride) atom

• Has 7 electrons in its outer (3Td) shell and tends to be an electron acceptor

• By accepting 1 more electron it its outer shell it will have 8.

3) When a Na atom and CI atom come together - an electron is trans/erred from the Na atom to the Cl atom.

4) Now both have 8 electrons in their outer shell

5) But now they are ions. WHY???

• Before bonding each atom (Na and CI) were electrically neutral because each bad the same number ofprotons and neutrons.

• After bonding the Na atom now has 1 more proton (11) than electrons (10) and therefore has a +1 charge. It is positively charged, can be called the sodium ion and is written as Na+.

• After bonding, the CI atom now has 1 more electron (18) than protons (17) and has a -1 charge. It is a negatively charged, can be called the chloride ion and is written as CI-.

6) NaCI or table salt is an ionic compound held together by ionic bonding - the attraction between positive and negative ions.

7) Table salJ occurs in soldforln as a 3-dimensionallottice ofcrystals.

8) When mixed with water, table salt dissolves and the ions separate in the water.

8. Covalent Bonding (see Handout of Figure 2.8, plge 27 of Tutbook, Mader IO&ao E)

A. Definition - covalent bond is a chemical bond where atoms share pairs of electrons.

B. Example ofHydrogen gas - H2

J) The H atom has only J electron shell which needs 2 electrons to be complete.

2) When 2 hydrogen atoms come together they share their electrons so that each atom now has a complete outer shell (R~member tJr~ I" eJ~ctron shell is complete with only 2 electrons)

3) 1 pair of electrons is shared and this is called a single covalent bond.

C. Example of Oxygen gas - 02.

1) Oxygen atoms come together and share 2 pair (4 electrons) to achieve an outer shell of 8 electrons (called an octet) tor each oxygen atom.

2) 2 pairs ofelectrons are shared and this is called a double covalent bond.

D. Example ofMethane - CH4.

1) 4 pairs of electrons are shared between 4 atoms of hydrogen and 1 atom ofcarbon.

2) Bonds result in all 4 hydrogen atoms having a 2 electron outer shell and carbon atom having 8 electrons in its outer shell.

Water

Water is truly a remarkable molecule and compound.

It has several properties that make it essential for the survival of life on earth.

1. Hydrogen Bonding

A. The water molecule is V-shaped (DTtlW 011 blackboaTrl) and this shape results in a polarity (uneven charges) with the 2 hydrogen atoms being slightly (+) positive and the oxygen atom being slightly (-) negative.

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B. This polarity allows a water molecule to form a weak bond with other water mokcules and other atoms and molecules.

C. The slightly (+) positive hydrogen (Draw on bladboord) atom in one water molecule is attracted to the sligh,tlyj -J oxygen atom in an adjacent water molecule.

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D. Due to hydrogen bonding, water molecules cling together and give water many of its important properties. (your latbook has tJ very good discussion of5 o/Iheu properties)

E. All living things are made of 70% to 90% waleI'.

F. Recall - we said that nonnally water melJs at 32 degrees F (0 degrees C) and boils at 212 degrees F (100 degrees C). You can say that water remains a liquid in a temperature range of 180 degrees F.

G. Without hydrogen bonding - water molecules would mell at -148 degrees F (­100 degrees C) and boil at -132 degrees F (-91 degrees C). You can say that water would only remains a liquid in a much smaller temperature range of16 degrees F.

H. So - without hydrogen bonding most of the water on earth would be steam!!!

I. Note that hydrogen bonding is not unique to water - but occurs in other molecules (like DNA) that possess hydrogen atoms.

1. Textbook definition of hydrogen hond - the attraction of a slightly positive hydrogen atom to a slightly negative atom in the vicinity.

Acids and Bases

1. Chemical suhstances can be classified as being either acids or bases.

2. Acids - suhstances that dissociate in water, releasing hydrogen ions (H+).

(RtMeMI defi"ition ofion - a charged (HUtick t/tal carries Q " egative or positive charge)

3. Examples of acid solutions are lemon juice, vinegar, coffee, hydrochloric acid.

4. Acids can be either weak or strong depending on the number of (H+) ions released. Example - hydrochloric acid is a stronger acid than vinegar.

5. Bases are substances that either take up (H+) ions or release hydroxide (OH-) ions.

6. Examples of basic solutions are milk ofmagnesia and ammonia.

7. The pH scale is used to indicate the degree ofacidity or basicity of a solution.

8. The pH scale ranges from a pH of0 to a pHof14.

9. A pH of 7 indicates neutrality.

10. Solutions with a pH of below 7 are considered acidic

II. Solutions with a pH of above 7 are considered basic

12. In living organisms, the pH of body fluids is maintained at a narrow range. The pH of human blood is always around 7.4 which is slightly basic.

13. Buffers are chemicals that take up excess (H+) ions or (OH-) ions and keep the pH of body fluids within normal limits. Examples of buffers ?

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I sodium chloride (NaCO

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FIGURE 2.7 Formation of sodium chloride (table salt).

<t. During the formation of sodium chloride, an electron is transferred from the sodium atom

to the chlorine atom. At the completion of [he reaction, each atom l1las eight electrons in

the outer shell, but each also carries a charge as shown. b. In a sodium chloride Cl"ystal. ionic

bonding between Na+ and CI- causes the atoms to assume a three-dimensionallanice in

which each sodium ion is surrounded by six chloride Ions, and each chloride ion is surrounded

by six sodium ions . The res Lilt IS crystals of salt as in table salt .

Electron Model I Structural Formula

Molecular Formula

~r\ (\~ H - H H~

a. Hydrogen gas

b. Oxygen gas

H I

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C. Melhane

FIGURE 2.8 Covalently bonded molecules.

In a covalent bond, atoms share electrOnS, allowing each atom to have a com pleted Outel' shell. a. A molecule of hydrogen (H,) conoins two hydrogen atoms sharing a pair of electrons. This single covalem bond can be represented in any of the three

ways shown. b. A molecule of oxygen (01) concains two oxygen aroms sharing [Wo pairs of electrons. This results in a double covalent booet Co A molecule of methane

(CHJ concains one carbon atom bonded to four hydrogen atO<T1S­