Essential Chemistry

Studying Life from The Chemical Level • Biology is a multidisciplinary science

• Biology includes the study of life at many levels

• Living organisms are subject to basic laws of physics and chemistry

• We will take the reductionist approach. We will start at the atomic level and work our way up to the level of cell activity

• Cells consist of enormous numbers of chemicals that give the cell the properties we recognize as life

Matter: Elements and Compounds

• Organisms are composed of matter

• Matter is anything that takes up space and has mass

• Matter is found on the Earth in three physical states

– Solid

– Liquid

– Gas

• Matter is composed of chemical elements

– Elements are substances that cannot be broken down into other substances

– There are 92 naturally occurring elements on Earth

Elements and Compounds• An atom is the smallest unit of matter that still retains the

properties of an element, it cannot be broken down to other substances by chemical reactions

• Each element consists of one kind of unique atom

• A compound is a substance consisting of two or more elements in a fixed ratio

Sodium Chlorine Sodium chloride

Essential Elements of Life

• About 25 of the 92 elements are essential to life

• Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter

• Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur

• Trace elements are those required by an organism in minute quantities

– Four of these make up about 96% of the weight of the human body

– Trace elements occur in smaller amounts

Figure 2.3

Elements Essential to Life

Essential Elements of Life

S P O N C H

Subatomic Particles• Atoms are composed of subatomic particles

• Relevant subatomic particles include:

– Neutrons (no electrical charge)

– Protons (positive charge)

– Electrons (negative charge)

• Neutrons and protons form the atomic nucleus

• Electrons form a cloud around the nucleusNucleus

Cloud of negativecharge (2 electrons)

(a)

(b)

2 Protons

2 Neutrons

2 Electrons

Atomic Number and Atomic Mass

• Atoms of the various elements differ in number of subatomic particles

• An element’s atomic number is the number of protons

• The number of protons (atomic number) determines the element’s properties

• An element’s mass number is the sum of protons plus neutrons in the nucleus

• Atomic mass, the atom’s total mass, can be approximated by the mass number

Atomic number

Element symbol

Mass number

Periodic Chart

Isotopes• Atoms of an element have the same number of protons but may differ in

number of neutrons

• Isotopes are two atoms of an element that differ in number of neutrons

• Most isotopes are stable, but some are radioactive, giving off particles and energy

• Some applications of radioactive isotopes in biological research:

– Tracing atoms through metabolic processes

– Diagnosing medical disorders

Energy Levels of Electrons• Energy is the capacity to cause change

• Potential energy is the energy that matter has because of its location or structure

• The electrons of an atom differ in their amounts of potential energy

• An electron’s state of potential energy is called its energy level, or electron shell

A ball bouncing down a flight

of stairs provides an analogy for

energy levels of electrons.

Third energy level (shell)

Second energy level (shell)

First energy level (shell)

Atomicnucleus

Energyabsorbed

Energylost

Electron Configuration and Chemical Properties

• The chemical behavior of an atom is determined by the distribution of electrons in electron shells

• The periodic table of the elements shows the electron distribution for each element

Firstshell

Hydrogen

1H

Lithium

3Li

Secondshell

Thirdshell

Sodium

11Na

Beryllium

4Be

Magnesium

12Mg

Boron

5B

Aluminum

12AlSilicon

14Si

Carbon

6CNitrogen

7N

Phosphorus

15P

Oxygen

8O

Sulfur

16SChlorine

17Cl

Fluorine

9FNeon

10Ne

Argon

18Ar

Helium

2HeAtomic number

Element symbol

Electron-shelldiagram

Atomic mass

2

He4.00

Electron Orbitals• An orbital is the three-dimensional space where an electron

is found 90% of the time

• Each electron shell consists of a specific number of orbitals

Electronorbitals

Electron-shelldiagrams

1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals

First shell(maximum2 electrons)

Second shell(maximum8 electrons)

Neon, with twofilled shells(10 electrons)

x

z

y

Electron Shell Significance• Each Orbital holds a maximum of 2 electrons each

• Several orbitals may be the same distance from the nucleus and thus contain electrons of the same energy

• Such electrons are said to occupy the same energy level or shell

• The chemical behavior of an atom is mostly determined by the valence electrons

• Valence electrons are those in the outermost shell, or valence shell

Electron

Firstelectron shell(can hold2 electrons)

Outermostelectron shell(can hold8 electrons)

Carbon (C)Atomic number = 6

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Hydrogen (H)Atomic number = 1

Valence and Chemical Reactions• Atoms with incomplete valence shells can share or

transfer valence electrons with certain other atoms

• Atoms “desire” full outer orbitals

– Give up electrons (Na)

– Take electrons (Cl)

– Share electrons (O2)

• Rule of Eights for filling each shell

• Noble gases - full outer shells (inert)

• Cells constantly rearrange molecules by breaking existing chemical bonds and forming new ones

• Such changes in the chemical composition of matter are called chemical reactions

• Chemical reactions enable atoms to give up or acquire electrons in order to complete their outer shells

– These interactions usually result in atoms staying close together

– The atoms are held together by chemical bonds

Chemical Reactions

Hydrogen gas Oxygen gas Water

Reactants Products

Chemical Reactions

• Are dependent on :

– Concentration

– Speed

– Energy (energy of activation)

– Orientation

Types of Chemical Reactions

• Synthesis reactions - atoms or molecules combine to form a product

• Decomposition reactions - molecules breakdown into smaller molecules or atoms

• Exchange reactions - molecules exchange constituent components (swap partners)

• Reversible reactions - the product of a previous reaction can revert to the original reactants.

Chemical Products• Element: a substance composed of only one type of atom

(all the atoms have the same number of protons).

• Molecule: a unit composed of two or more atoms joined together by chemical bonds

• Compound: a substance composed of 2 or more elements that have been joined by chemical bonds

• Mixture: a combination of 2 or more substances that do NOT chemically bond e.g. sugar mixed with salt

Periodic Chart

Ionic Bonds• Atoms sometimes strip electrons from their bonding partners

• An example is the transfer of an electron from sodium to chlorine

• After the transfer of an electron, both atoms have charges

• A charged atom (or molecule) is called an ion

– An anion is a negatively charged ion

– A cation is a positively charged ion

• An ionic bond is an attraction between an anion and a cation - oppositely charged ions

Ionic Compounds

• Compounds formed by ionic bonds are called ionic compounds, or salts

• Salts, such as sodium chloride (table salt), are often found in nature as crystals

Na+

Cl–

Periodic Chart

Covalent Bonds• Molecules are formed by covalent bonds

• A covalent bond is when two atoms share one or more pairs of outer-shell electrons (valence electrons)

• In a covalent bond, the shared electrons count as part of each atom’s valence shell

• Much stronger than ionic bonds – holds lots of Energy

• A single covalent bond, or single bond, is the sharing of one pair of valence electrons

• A double covalent bond, or double bond, is the sharing of two pairs of valence electrons

• Covalent bonds can form between atoms of the same element or atoms of different elements

Hydrogen atoms (2 H)

Hydrogenmolecule (H2)

Covalent Bonds

Oxygen (O2)

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

Covalent Bonds

Methane (CH4)

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

Water (H2O)

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

Covalent Bonds

Figure 2.9

• Outer orbital (valence shell) determines reactivity of atom - Electronegativity

• Electronegativity is an atom’s attraction for the electrons in a covalent bond

• The more electronegative an atom, the more strongly it pulls shared electrons toward itself

Electronegativity

H

O

H

H2O+ +

–

Polar Covalent Bond

• In a nonpolar covalent bond, the atoms share the electron equally

• In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally

The Structure of Water– Its two hydrogen atoms are joined to one oxygen atom by

single covalent bonds

– But the electrons of the covalent bonds are not shared equally between oxygen and hydrogen

– This unequal sharing makes water a polar molecule

Unnumbered Figure 2.2

() ()

() ()

Hydrogen Bonds

• A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

• In living cells, the electronegative partners are usually oxygen or nitrogen atoms (b)

()Hydrogen bond

()

()()

()

()

()()

Figure 2.11b

–

Water(H2O)

Ammonia(NH3)

Hydrogen bond

+

+

–

+

+

+

Hydrogen Bonds

Van der Waals Interactions

• Molecules or atoms that are very close together can be attracted by fleeting charge differences

• These weak attractions are called van der Waals interactions

• Collectively, such interactions can be strong

Weak Chemical Bonds

• Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules

• Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important

• Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other

Biological Importance• Acts as a powerful solvent

• Participates in chemical reactions

• Water has a high specific heat which moderates temperature - absorbs and releases heat very slowly, minimizes temperature fluctuations to within limits that permit life

– Heat is absorbed when hydrogen bonds break

– Heat is released when hydrogen bonds form

• Requires a great amount of heat to change to a gas

– Heat of vaporization - the quantity of heat a liquid must absorb for 1 gram of it to be converted from a liquid to a gas

– Evaporative cooling - Allows water to cool a surface due to water’s high heat of vaporization

• Acts as a lubricant

Polarity & Hydrogen Bonds• Cohesion - molecules attract other

water molecules

• Capillarity

– Water molecules are drawn up a narrow tube

– Helps pull water up through the microscopic vessels of plants

• Surface tension

– water molecules on the surface cling to each other – related to cohesion

– Is a measure of how hard it is to break the surface of a liquid

• Adhesion - water molecules attract other charged substances

Water as a Solvent• Water is a versatile solvent due to its polarity

• It can form aqueous solutions

• The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them

Negative oxygen regions

of polar water molecules are attracted to sodium

cations (Na+).+

+

+

+Cl –

–

–

–

–

Na+

Positive hydrogen regions

of water molecules cling to chloride anions

(Cl–).

++

+

+

–

–

–

–

–

–Na+

Cl–

Acids, Bases, and pH• Dissociation of water molecules leads to acidic and basic

conditions that affect living organisms

– Water dissociates into hydronium ions and hydroxide ions

– Changes in the concentration of these ions can have a great affect on living organisms

H

Hydroniumion (H3O+)

H

Hydroxideion (OH–)

H

H

H

H

H

H

+ –

+

Acids, Bases, and pH• Acid - A chemical compound that dissociates into

one or more hydrogen ions (H+) and one or more negative ions (anions). An acid donates H+ ions (protons) to solutions

• Base - Dissociates into one or more positive ions (cations) and one or more hydroxide ions (OH-). A base accepts H+ ions and removes them from solution, reducing the hydrogen ion concentration of a solution

• To describe the acidity of a solution, we use the pH scale

• Is a measure of the concentration of H+ ions in a solution

• Is determined by the relative concentrations of H+

– Basic = High pH = few H+, many OH-

– Acidic = Low pH = many H+, few OH-

Basicsolution

Neutralsolution

Acidicsolution

Oven cleaner

Household bleach

Household ammonia

Milk of magnesia

Seawater

Human bloodPure water

Urine

Tomato juice

Grapefruit juice

Lemon juice;gastric juice

pH scale Figure 2.17

pH

pH Scale• The pH scale is a logarithmic scale

used to express the amount of H+ ions in a solution.

• pH is defined as the negative log of the [H+] of a solution

• A change of one whole number represents a tenfold (10X) change in the number of H+ ions.

• A solution with pH 3 has ten times as many H+ ions as a solution with pH 4

Buffers• A buffer is a substance that helps minimize the change in the pH of a

solution when acids or bases are added.

• Consist of an acid-base pair that reversibly combines with hydrogen ions

• Buffers work by releasing H+ when their concentration falls, and absorbing H+ when their concentration rises.

• Buffers are important to living organisms because most cells can survive and function normally only within a relatively narrow range

-

pH

[H+]

1

14