Chapter 2

Chemical Principlespart A

LIFE in term of biology

• Life fundamental feature: – Growth - through metabolism (catabolism and anabolism) - the set of

chemical reactions that occur in living organisms in order to maintain life

– Reproduction - process by which organisms generate new individuals of the same kind - heritable genetic information (the molecular basis for genes is deoxyribonucleic acid (DNA))

• Biochemistry - biological chemistry, is the study of chemical processes within, and relating to, living organisms

• Chemistry is the study of interactions between atoms and molecules.

Chemistry

• The atom is the smallest unit of matter that enters into chemical reactions.

• Atoms interact to form molecules.

Atoms are composed of:

• Nucleus:

– Protons: • positively charged particles,

• have a mass about 1.6726×10−27  kg – Neutrons:

• no charge particles,

• have a mass slightly larger than that of a proton

• Electrons: • negatively charged particles, mass is approximately 1 / 1836 of that of the

proton

• Electrons are arranged in electron shells corresponding to different energy levels

• Number of electrons = Number of protons

The Structure of Atoms

• A chemical element is a type of atom that is distinguished by its atomic number;

• Atomic number that is the number of protons in its nucleus.

• Atomic mass - the total number of protons and neutrons (atomic weight)

• Isotopes of an element are atoms with different numbers of neutrons. Isotopes of oxygen are:

Chemical Elements

16

8O 17

8O 18

8O

• The sum of the atomic weights in a molecule is the molecular weight.

• One mole of a substance is its molecular weight in grams.

Molecular Weight and Moles

H2O

2H = 2 1 = 2

O = 16

MW = 18

1 mole weighs 18 g

Electronic Configurations

Table 2.2.1

• Protons and neutrons are in the nucleus• Electrons move around the nucleus• Electrons are organized into shells around the nucleus (regions corresponding to different energy

levels)• The number of missing or extra electrons in outermost shell is the valence.• Atoms combine to complete the shell.

• Chemical bond - the forces holding atoms in molecules ( the attraction between atoms)

• A molecule – any two or more atoms held together

O2 H2

• A compound - at least two different kinds of atoms chemically bonded.

H2O

Bond strength = Bond energy

How Atoms Form Molecules? Chemical Bonds

• 1. Covalent Bonds

• Covalent bonds form when two atoms share one or more pairs of electrons.

Types of chemical bonds

Figre 2.3a

Carbon atom

Hydrogen atomsMethane molecule

• The number of protons and electrons is equal in an atom.

• Ions are atoms that have gained or lost electrons and are charged.

• Ionic bonds are attractions between ions of opposite charge.

2. Ionic Bonds

Sodium ion(Na+)

Sodium atom(electron donor) Chlorine atom

(electron acceptor)Chloride ion

(Cl–)

Loss ofelectron

• Hydrogen bonds form when a hydrogen atom (H) that is covalently bonded to an O or N atom is attracted to another N or O atom in another molecule

• These bonds can occur between molecules (intermolecularly), or within different parts of a single molecule (intramolecularly).

• Weaker than covalent or ionic bonds

3. Hydrogen Bonds

Figure 2.4

• Chemical reactions involve the making or breaking of bonds between atoms.

• A change in chemical energy occurs during a chemical reaction.

– Endergonic reactions absorb energy.

• Synthesis reaction (making bonds)

– Exergonic reactions release energy.

• Decomposition Reactions (breaking bonds)

Chemical Reactions

• Occur when atoms, ions, or molecules combine to form new, larger molecules

• Anabolism is the synthesis of molecules in a cell – use of energy

1. Synthesis Reactions

A + B ABAtom, ion,

or molecule A

Atom, ion,

or molecule BNew molecule

AB

+ Energy

• Occur when a molecule is split into smaller molecules, ions, or atoms.

• Catabolism is the decomposition reactions in a cell – release energy.

2. Decomposition Reactions

A + BABAtom, ion,

or molecule A

Atom, ion,

or molecule BNew molecule

AB

Breaksdown into

+ Energy

• Are part synthesis and part decomposition.

3. Exchange Reactions

NaCl + H2ONaOH + HCl

• Can readily go in either direction.

• Each direction may need special conditions.

4. Reversible Reactions

A + BWater

AB

Heat

Table 2.1

Important Biological Molecules

1. Inorganic compounds typically lack carbon and Carbon-Hydrogen connected.

2. Organic compounds always contain Carbon-Hydrogen connected.

Methane CH4

(organic)

Carbonic-acid H2CO3

(inorganic)

Inorganic Compounds: Water• It can be quite correctly argued that life exists on Earth because of

the abundant liquid water 1. Polar molecule

2. Temperature buffer• Formation of a hydrogen bond between the hydrogen side of one water

molecule and the oxygen side of another water molecule

• Hydrogen bonds absorb heat

• Hydrogen bonding between water molecules makes water a

temperature buffer.

• A solvent is a liquid or gas that dissolves a solid, liquid, or gaseous solute, resulting in a solution.

• Water is a good solvent due to its polarity – Polar substances will mix well and dissolve in water (e.g. salts)

• they are known as hydrophilic ("water-loving") substances,

– Non-polar substances do not mix well with water (e.g. fats and oils),

• are known as hydrophobic ("water-fearing") substances

3. Water is Universal Solvent

Figure 2.5

Inorganic Compounds: Acids, Bases, and Salts• An acid is a substance that dissociates into one or more H+.

HCl H+ + Cl

• A base is a substance that dissociates into one or more OH.

NaOH Na+ + OH-

• A salt is a substance that dissociates into cations and anions, neither of which is H+ or OH.

NaCl Na+ + Cl

Figure 2.6a

• Dissociation

– NaOH Na+ + OH

– HCl H+ + Cl

– NaCl Na+ + Cl

• The concentration of H+ ( [H+] ) in a solution

is expressed as pH.

– Increasing [H+], increases acidity.

– Increasing [OH] increases alkalinity.

– pH = log[H+]

• Most organisms grow best between pH 6.5 and 8.5.

Acid-Base Balance

Carbon and Organic Compounds

• Carbon atom

• Carbon can make covalent bonds with another carbon atom and form long carbon chains and rings.

Organic compounds

• Organic compounds always contain carbon (C) - hydrogen (H) connected together.• Carbon has four electrons in outer shell, and can bond with up to four other atoms (usually H, O, N, or

another C).

• Since carbon can make covalent bonds with another carbon atom, carbon chains and rings that serve as the backbones of organic molecules are possible.

Organic Compounds

• The chain of carbon atoms in an organic molecule is the carbon skeleton.

H Methane

H – C – H

H

H H Ethane

H – C – C - H

H H

H H H Propane

H – C – C – C – H

H H H

Specific groups of atoms within molecules that are responsible for the chemical properties of those molecules. •The same functional group will undergo the same or similar chemical reaction(s) regardless of the size of the molecule it is a part of.

• However, its relative reactivity can be modified by nearby functional groups

Organic Compounds - Functional groups

Alcohols

Formic acidAcetic acid

Propanoic acidPropionic acid

Acids

Functional Group

R

Learning objectives

• Describe the structure of an atom and its relation to the chemical properties of elements.

• Define ionic bond, covalent bond, hydrogen bond, molecular weights, and mole.

• Diagram three basic types of chemical reactions. • List several properties of water that are important to

living systems. • Define acid, base, salt, and pH. • Distinguish between organic and inorganic compounds.• Distinguish between alcohol, carboxyl, amino, methyl,

phosphate and sulfhydryl functional groups.