Chapter 2

The Chemical Context of Life

Levels of OrganizationAtom

Molecule/Compound

Organelle

Cell

Tissue

Organ

System

Organism

Population

Community

Ecosystem

Biosphere

General A. Elements - cannot be broken down to other substances

1. 92 occur naturally2. 25 are essential to life

- 4 major elements (O, H, C, N) = 96% of living matter- Also; P, K, S, Ca, Na and trace elements-figure 2.1a, page 20 lists all the elements found in a human body

3. All substances consist of one or more elementsB. Compound = combination of 2 or more different elements chemically bonded in a specific ration

-Examples: NaCl, CO2, CH4 C. Elements & compounds are made of atoms

AtomsA. Structure of Atoms

1. An atom is the smallest unit of matter that retains the properties of a particular element.2. Atoms are composed of three primary subatomic

particles:a. Protons (p+) are part of the atomic nucleus and have a positive charge. b. Neutrons are also a part of the nucleus; they are neutral. c. Electrons (e–) have a negative charge. In a neutral atom their quantity is equal to that of the protons. They move around the nucleus.

3. Atomic number equals the number of protons in the nucleus (and # of e-). This determines the type of element.

4. The mass number of an atom is equal to the number of protons plus the number of neutrons.

A. The number of electrons and neutrons can differ between atoms of a certain element, but the number of protons is the same for all of the atoms in an element.B. Isotopes 1. Atoms with the same number of protons but a different number of neutrons (and therefore mass) are called isotopes.

a. all isotopes of the same elements interact with other atoms in the same way, this is because the number of neutrons does not affect atomic interactions (the number of e- does)b. remember, the atomic mass given on the periodic chart is actually the average atomic mass for all isotopic forms of that element

Radioactive Isotopes• Radioactive Isotopes:

– Nucleus decomposes spontaneously, giving off particles and/or energy • alpha particles – a helium nucleus or 2P and 2N

beta particles – high speed electronsgamma rays – high energy X-rays

• Uses:– Dating fossils– Tracers

• marking something and finding it again later• to follow the path of an atom in a series of

reactions or to diagnose disease

In Biology: think energy levels or shells – you don’t have to know all of the level, sublevel and orbital stuff like in chemistry

1. Electrons move around the nucleus in orbitals that can be thought of as occupying levels. Each level can hold a specific number of electrons.

A. The level closest to the nucleus can hold a maximum of 2 electrons.

B. The next level can hold a maximum of 8electrons.

C. The 3rd level can hold a mazimum of 18 electrons.

Valence Shells• Valence shell = outermost energy level: determines an

atom’s reactiveness• Full = nonreactive/happy !• Not full = reactive/unhappy!

– they react to become more stable– they do this by gaining, sharing or losing electrons

Chemical Bonding

• 2 types of bonding that occurs between atoms:– Covalent bonding– Ionic bonding

From Atoms to Molecules1. A chemical bond is a union between atoms formed when they give up, gain, or share electrons (this forms a compound).

A. 2 main types of bonds between atoms-ionic – give and take of electrons between a metal and a nonmetal-covalent – sharing electrons between two

nonmetals*A molecule is a compound with covalent bonds.

Covalent Bonds• atoms share valence electrons• 2 types = polar and nonpolar: depends on how the

electrons are shared– electronegativity is the attraction a specific type of

atom has for shared electrons– each element has its own electronegativity value: if

the elements involved in a covalent bond do not have close or equal electronegativity values, the atom with the largest electronegativity value will “hold” the electrons more often than the other atom(s) therefore giving it a partial negative charge and the other atom(s) a partial positive charge.

Covalent Bonding1. A covalent bond holds together two atoms that share one or more pairs of electrons.

A. if the atoms share one pair of electrons it is called a single bond –

B. if the atoms share two pairs of electrons it is called a double bond =

C. if the atoms share three pairs of electrons it is called a triple bond =

Covalent Bonding

1. In a nonpolar covalent bond, atoms have similar electronegativity values and therefor share electrons equally.

A. no partial charge2. In a polar covalent bond, atoms have very different electronegativiy values and share the electron(s) unequally, therefore there is slight difference in charge between the atoms; water is an example. A. partial charges

Hydrogen Bonding1. In a hydrogen bond, an atom or a molecule interacts weakly with a hydrogen atom already taking part in a polar covalent bond.

A. remember, polar molecules have partial charges; one polar covalently bonded atom that has a slight negative

charge is weakly attracted to the positive charge of a hydrogen atom taking part in a different polar covalent bond

B. see figure 2.11, page 27

2. These bonds impart structure to liquid water and stabilize nucleic acids and other large molecules.

Water molec

ule

Ammonia

molecule

Ion Formation and Ionic Bonding1. When an atom loses or gains one or more electrons, it no longer has the same number of protons and electrons and therefore is no longer neutral

A. the atom is now charged; we call charged atoms — ionsB. atoms that lose electrons become + and are called cationsC. atoms that gain electrons become – and are called anionsD. these oppositely charged ions are then attracted to each other and this attraction forms an ionic bondE. these are strong bonds

2. In an ionic bond, (+) and (–) ions are linked by mutual attraction of opposite charges, for example, NaCl.

A. see figure 2.9, page 26

Ionic Bonds

• Def’n: one atoms “donates” its electrons to the other – Cation = atom that donates, +– Anion = atom that receives, -

Ionic Bonding

Hydrogen Bonds• A hydrogen atom that is

covalently bonded to one electronegative atom is also attracted to another electronegative atom

• Usually between oxygen of one water molecule and hydrogen of another

• Individually weak, but strong together!

Molecular Shape & Function

• Molecules have characteristic sizes and shapes

• Molecular shape is crucial in biology because it determines how biological molecules recognize and respond to each other with specificity– Examples: ??

Applications• Morphine

– Lock and key concept– Morphine is designed to

be the same shape as endorphins

• Therefore, morphine will bind to the endorphin binding site in the brain

• Brain will be tricked!

– Heroin works in the same way

Chemical Reactions• Def’n: the making and

breaking of chemical bonds

• Reactants Products• 1st Law of

Thermodynamics:– Energy can be neither

created nor destroyed

Chpt 3

Water and Life

Properties of WaterA. Polarity of the Water Molecule

1. Because of the electron arrangements in the water molecule, a polarity results that allows water to form hydrogen bonds with one another and other polar substances.

a. see figure 2.12, page 28

b. water is a good solvent for polar substances

2. Polar substances are hydrophilic (water-loving) and are attracted to water; nonpolar ones are hydrophobic

(water-dreading) and are repelled by water.

Water's Temperature-Stabilizing Effects1. Water tends to stabilize temperature because it can absorb considerable heat before its temperature changes.

A. water has a high specific heat and a high heat of vaporizationB. this helps living things counter drastic temperature shifts in their environment

1. This is an important property in evaporative and freezing processes.

2. Water's CohesionA. Hydrogen bonding of water molecules provides cohesion (capacity to resist rupturing).B. Cohesion imparts surface tension and capillary action (which helps pull water through plants for example)

Water's Solvent Properties

1. Water is a great solvent because ions and polar molecules (solutes) dissolve in it.

2. The solvent properties of water are greatest with respect to polar molecules because “spheres of

hydration” are formed around the solute molecules.

Water expands when it freezes

1. this allows ice to be less dense than liquid water; so ice floats

Acids, Bases, and BuffersA. The pH Scale

1. pH is a measure of the H+ concentration in a solution; the greater the H+ the lower the pH scale.

a. H+ is a hydrogen ion, OH- is a hydroxide ion, H3O+ is a hydronium ion (a H+ that has combined with H2O.)

2. The scale extends from 0 (acidic) to 7 (neutral) to 14 (basic).

a. pH = -log(H3O+ concentration)b. so the higher the H+ concentration, the lower the pH

3. The interior of living cells is near pH = 7.a. therefore, high concentrations of acids or bases can disrupt the internal and external environmentsand pose a danger to life

How Do Acids Differ From Bases?1. A substance that releases hydrogen ions (proton donors) in solution is an acid; for example, HCl.

A. weak acids are reluctant proton donors and strong acids readily give up protons

B. acids react with metals, are sour (take my word for it, never taste chemicals!), and turns litmus paper red

2. Substances that release ions such as hydroxide ions (proton acceptors) that can combine with hydrogen ions are called bases.

A. bases do not react with metals, taste bitter (take my word for it, never taste chemicals!), are slippery (never touch strong bases, they are just as harmful as strong acids), turn litmus paper blue, and are also called alkaline3. both can be harmful and should be handled with care

Buffers Against Shifts in pH1. A buffer system is a partnership between a weak acid and the base that forms when the acid dissolves in water.

A. the two substances work together as a team to counter slight shifts in pH

2. Buffer molecules combine with, or release, H+ to prevent drastic changes in pH.

A. if a base enters the body fluid, the weak acid donates H+ ion to neutralize itB. if an acid enters the body fluid, the weak base can

accept its H+ ionsC. notice, the buffer system cannot make or eliminate H+ ions, it can only bind and release themD. a buffer system can only handle so much acid or base, thus once its capacity is exceeded, the system s pH

destabilized3. Carbonic acid is one of the body’s major buffers.

Carbonic Acid-Bicarbonate Buffer System

• When blood pH rises, carbonic acid

dissociates to form bicarbonate and H+

H2C03 -----> HC03- + H+

• When blood pH drops, bicarbonate binds H+

to form carbonic acid

HC03- + H+ -----> H2C03

A. Salts

1. A salt is an ionic compound formed when an acid reacts with a base; example: NaOH + HCl ——> NaCl + H2O.

2. Many salts dissolve into ions that serve key functions in cells; nerve function, for example, is dependent on ions of sodium, potassium, and calcium.

3. acids, bases, and salts (in liquid form) are electrolytes (substances that conduct electricity)

B. Neutralization reaction

1. Acid + Base Salt + Water