How to access School Files

1) Google “ocdsb”

2) Go to the students drop down menu and select “My Docs-Active Directory”

3) Enter student number and password

4) Then choose: Data 1 on “ADLTFS1.ad.osdsb.ca”(X:)

5) Click on “Handout”

6) Scroll down and click “SBI4U”

The Chemical Basis of Life

Atoms, elements, compounds, & molecules

How molecules interact

Water is essential for life

pH and buffers

ELEMENTS, ATOMS, AND MOLECULES• Living organisms are

composed of matter

• Matter has mass and occupies space

Atom: A unit of matter, the smallest unit of an element.

Living organisms are composed of about 25 chemical elements

Trace elements

– Are essential to life, but occur in minute amounts

Element: A substance composed of atoms having an identical number of protons in each nucleus. Elements cannot be reduced to simpler substances by normal chemical means.

Carbon, hydrogen, oxygen, and nitrogen Make up the bulk of living matter

Trace elements are common additives to food and water

•Dietary deficiencies in trace elements can cause various physiological conditions

Elements can combine to form compounds• Chemical elements

– Combine in fixed ratios to form compounds

Sodium Chlorine Sodium Chloride

Subatomic Particles• An atom is made up of protons, neutrons and electrons

• The nucleus contains neutrons and protons and is surrounded by electrons

+

+

– –

+

–

2

2

2

Protons

Neutrons

Electrons

Massnumber = 4

++

2e–

Electroncloud

Nucleus

Atoms consist of protons, neutrons, and electrons

• Atom: The smallest particle of matter that still retains the properties of an element

Differences in Elements

•Atoms of each element are distinguished by a specific number of protons

+6

6

6

Protons

Neutrons

Electrons

Massnumber = 12

++

6e–

Nucleus

Electroncloud

6

Isotopes The number of neutrons in an atom may vary

• Variant forms of an element are called isotopes • Some isotopes are radioactive

Table 2.4

Radioactive isotopes are useful as tracers for monitoring the fate of atoms in living organisms

The half-life of a radioisotope is the time required for half of the atoms in a sample to decay

During beta-minus decay, a neutron in an atom's nucleus turns into a proton, an electron and an antineutrino.

Medical Diagnosis• Radioactive tracers are often used for diagnosis

- In combination with sophisticated imaging instruments

Research

• Biologists often use radioactive tracers to follow molecules as they undergo chemical changes in an organism

How brain function is studied PET, CAT, MRI, etc.

Music Appreciation

Hearing, speaking, seeing, thinking about words

PET•Positron emission tomography (PET) is a nuclear medicine imaging technique which produces a three-dimensional image or picture of functional processes in the body.

•The system detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule

PET Scan

CT•Computed tomography (CT) is a medical imaging method employing tomography created by computer processing.

•Digital geometry processing is used to generate a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation

MRI•Magnetic resonance imaging (MRI), or nuclear magnetic resonance imaging (NMRI), is primarily a noninvasive medical imaging technique used in radiology to visualize detailed internal structure and limited function of the body

•Unlike CT, MRI uses no ionizing radiation. Rather, it uses a powerful magnetic field to align the nuclear magnetization of (usually) hydrogen atoms in water in the body

MRI

Electron arrangement determines the chemical properties of an atom

•Electrons in an atom are arranged in shells, which may contain different numbers of electrons

Hydrogen (H)Atomic number = 1

Electron

Carbon (C)Atomic number = 6

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Outermost electron shell (can hold 8 electrons)

First electron shell (can hold 2 electrons)

•Atoms whose shells are not full, tend to

interact with other atoms

•Atoms gain, lose, or share

electrons

•These interactions form

chemical bonds

Electron arrangement

Chemical Bonds

Types of Bonds

1) Ionic bonds are attractions between ions of opposite charge

• When atoms gain or lose electrons

– Charged atoms called ions are created

Transfer of electron

NaSodium atom

ClChlorine atom

Na+

Sodium ion

Cl–

Chloride ion

Sodium chloride (NaCl)

Na Cl ClNa

+ ––

–

• Sodium and chloride ions

– Bond to form sodium chloride, common table salt

Na+

Cl–

• An electrical attraction between ions with opposite charges

– Results in an ionic bond

2) Covalent bonds join atoms into molecules through electron sharing

• In covalent bonds, two atoms share one or more pairs of outer shell electrons, forming molecules

Electronegativity•Electronegativity refers to the tendency of an atom to attract electrons in a covalent bond

•Oxygen (3.5) has a high electronegativity

•Hydrogen (2.1) and Carbon (2.5) have lower affinities

•A bond between carbon and hydrogen will have nearly equal sharing of electrons (non polar)

•A bond between oxygen and hydrogen will be highly polar

•If the atoms have a large difference in electronegativity (>1.8) then the electron is shared so unevenly that it produces an ionic bond.

Electronegativity

In a polar covalent bond electrons are shared unequally between atoms, creating a polar molecule

(–) (–)

(+) (+)

O

HH

3) Hydrogen Bonds

Hydrogen bonds are weak bonds important in the chemistry of life

• The charged regions on water molecules are attracted to the oppositely charged regions on nearby molecules

• This attraction forms weak bonds called hydrogen bonds

• Hydrogen bonding occurs in other biologically important compounds such as proteins and DNA.

Hydrogen

bond (+)

(+)

H

H(+)

(+)

(–)

(–)

(–)

(–)

O

Molecular Shape

Shapes of Molecules

Water is the solvent of life• Polar or charged solutes dissolve when water molecules surround them, forming aqueous solutions

+

–

–

–

–

–

–

–

–

––

++

+

++

Na+

+

Na+

Cl–

Ion insolution Salt

crystal

Cl–

WATER’S LIFE-SUPPORTING PROPERTIES

Hydrophobic and Hydrophilic molecules•Nonploar molecules do not form hydrogen bonds with water and are ‘excluded’ from associating with water

•These molecules are said to be hydrophobic

•Hydrophobic molecules such as oxygen require carrier proteins for transportation in the body

•Polar molecules can form hydrogen bonds with water and are said to be hydrophilic

Cell Membrane

WATER’S LIFE-SUPPORTING PROPERTIES

Hydrogen bonds make liquid water cohesive

• Due to hydrogen bonding

– Water molecules can move from a plant’s roots to its leaves by adhesion• Insects can walk on water due to surface

tension

• Created by cohesive water molecules

Water’s hydrogen bonds moderate temperature

• Water’s ability to store heat

– Moderates body temperature and climate

• It takes a lot of energy to disrupt hydrogen bonds

- So water is able to absorb a great deal of heat energy without a large increase in temperature

• As water cools

- A slight drop in temperature releases a large amount of heat

WATER’S LIFE-SUPPORTING PROPERTIES

Liquid waterHydrogen bonds

constantly break and re-form

IceHydrogen bonds are stable

Hydrogen bond

Figure 2.13

Ice is less dense than liquid water• Hydrogen bonds hold molecules in ice farther apart than in liquid water

• Ice is therefore less dense than liquid water which causes it to float

• Floating ice protects lakes and oceans from freezing solid

The chemistry of life is sensitive to acidic and basic conditions

A compound that releases H+ ions in solution is an acid

And one that accepts H+ ions in solution is a base• Acidity is measured on the pH scale from 0 (most

acidic) to 14 (most basic or alkaline)

The pH scale

Basic solution

Oven cleaner

Acidic solution

Neutral solution

pH scale0

1

2

3

4

5

6

7

8

9

10

11

12

Lemon juice, gastric juice

Grapefruit juice, soft drink

Tomato juice

Human urine

Pure waterHuman blood

Seawater

Milk of magnesia

Household ammonia

Household bleach

Incr

easi

ngly

AC

IDIC

(Hig

her

conc

entr

atio

n of

H+)

NEUTRAL[H+]=[OH–]

H+ H+

H+ OH– H+

H+ H+

OH– H+ H+

OH–

OH–

H+ H+OH–

OH– OH–

H+ H+H+

OH–

OH–

OH– OH–

OH–OH– H+

Incr

easi

ngly

BA

SIC

(Low

er c

once

ntra

tion

of H

+)

OH–

H+

14

13

Figure 2.15

• The pH of most cells

Is kept close to 7 (neutral) by buffers

• Buffers are substances

that resist pH change

Acid precipitation threatens the environment

• Some ecosystems are threatened by acid precipitation

• Acid precipitation is formed when air pollutants from burning fossil fuels combine with water vapor in the air to form sulfuric and nitric acids

• Can kill trees and damage buildings

Acid, Bases and Buffers

Ionization of Water

• in pure water the concentration of the hydronium ion is 1.0x10-7mol/L

• the pH is defined as the negative logarithm of the hydronium ion concentration

• In pure water the pH=-log1.0x10-7

= 7

Strong Acids and Bases• Strong acids and bases completely ionize in water

Weak Acids and Bases

•Ionize partially in water

Weak Base

•10% ionization

Buffers

• a chemical system containing a substance that can donate H+ ions when required or remove H+ when too many are in solution

•therefore resist changes in pH

Functional groups

Functional groups are reactive clusters of atoms attached to the carbon backbone of organic molecules

Bonding Capacity

Element Bonding Capacity

Examples

H 1 Water, ethane

O 2 Oxygen, methanol

S 2 Hydrogen sulphide,

N 3 Nitrogen (N2), hydrogen cyanide (HCN)

C 4 Methane, carbon dioxide

P 5 Phosphate ion

Four classes of Biological Macromolecules

Macromolecule Subunit

Complex carbohydrate (starch)

Simple sugars (glucose)

Lipid (triacylglycerol) Glycerol and fatty acids

Protein Amino acids

Nucleic acid (DNA or RNA)

nucleotides

Condensation reaction (dehydration synthesis)

•A chemical reaction that creates a covalent bond between two interacting subunits, linking them to each other

•An anabolic reaction is a reaction that produces large molecules from smaller subunits

Hydrolysis Reaction

A hydrolysis reaction is a catabolic reaction in which a water molecule is used to break a covalent bond holding subunits together