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The Chemistry of Life
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Elements: make up earth & organisms
(O, C, H, N,S, P, K, Si, Al, Fe,
Ca)cannot be broken down by a
chemical process into a simpler substance
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Molecules: a substance made up of two or more non-metal atoms that are covalently bonded together
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Compounds: substances formed by the combination of two or more elements in a fix ratio. (ex. Hemoglobin (compound) contains Fe (element)
Organic compounds: all contain carbon -ex. Carbohydrates,
lipids, proteins, nucleic acids
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Inorganic compounds: not based on carbon example: Table salt (NaCl)
Chemical Formula: C6H12O6 – 24 total atoms
6 carbon atoms12 hydrogen atoms6 oxygen atoms
SBI4U, Biology, Grade 12, University Preparation
How many atoms are in this molecule?
C55H72MgN4O5
137
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Atoms: smallest particle of an element that can exist and still have the properties of that element
SBI4U, Biology, Grade 12, University Preparation
Atomic Structure
Bohr-Rutherford Model atoms are made of a dense positively charged
central nucleus with negative particles surrounding it at specific energy levels
protons (+) neutrons (no charge) electrons (-)
protons and neutrons together make up the nucleus
electrons are used to form bonds with other elements
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Changes in the number of electrons cause atoms to become + or –
Outermost energy level (orbit) likes to be full – more stable that way
Atoms will give up, gain, or share electrons to fill the outer orbit
1st level – 2 electrons 2nd level – 8 electrons 3rd level – 8 or 18 electrons
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Sodium – 11 protons and 11 electrons 2 electrons in the 1st level 8 electrons in the 2nd
1 electron in the 3rd
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Chlorine – 17 protons, 17 electrons 2 electrons in the 1st level 8 electrons in the 2nd level 7 electrons in the 3rd level
Sodium wants to give up the last electron whereas Chlorine wants to gain an electron to fill the 3rd level with 8 electrons
Atoms bond with other atoms to become more stable
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Chemical Bond The force that holds atoms together
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Ionic bond: a bond b/w oppositely charged ions. One element loses e- & the other element gains e-. These bonds are formed between metals and nonmetals.
Covalent bond: a bond where electrons are shared (carbs, lipids, proteins & nuc. Acids); Three types: single, double, triple
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
SBI4U, Biology, Grade 12, University Preparation
IONIC BOND
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Ions - atoms that gain or lose an electron and have a
chargeCharged particle
SBI4U, Biology, Grade 12, University Preparation
IONIC BONDING
Electrons are lost by one element and gained by another
Outer energy level in both elements is full (stable)
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
SBI4U, Biology, Grade 12, University Preparation
COVALENT BONDING
Electrons shared in a chemical bond (each atom donates one electron)
Outer energy level in both elements is full (stable)
Double covalent bonds have four electrons
Triple covalent bonds have six electrons
SBI4U, Biology, Grade 12, University Preparation
COVALENT BOND
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Polar Covalent – bond w/ unequal sharing of electrons that results in slightly positive & slightly negative ends
Water – an example of a polar covalent molecule
SBI4U, Biology, Grade 12, University Preparation
POLAR COVALENT
SBI4U, Biology, Grade 12, University Preparation
NONPOLAR COVALENT
SBI4U, Biology, Grade 12, University Preparation
COVALENT VS. IONIC
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
There are three types of intermolecular bonds (collectively referred to as van der Waals forces)
London Forces – exist between all atoms, very weak, unequal distribution of electrons
Dipole-Dipole forces – hold molecules together (+-+-)
Hydrogen Bonds – H of one molecule and N, O, F of a nearby polar molecule
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Hydrogen Bonds – bonds that hold molecules together rather than atoms. These bonds are weaker than ionic or covalent bonds
* like in water – hydrogen bonds are the force that holds water molecules together
1.1 Chemical Fundamentals
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Isotopes atoms of the same element that
have a different number of neutrons
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
radioisotopes - have an unstable nucleus that breaks apart giving off energy in the form of radiation
used to tell age of fossilspreserve foodtreat cancerSBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Water is found in all living organisms Water is a polar molecule Being polar allows water to dissolve ionically
bonded compounds easily When compounds dissolve in water they form
a solution Living things are composed of 70-90% water
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
SBI4U, Biology, Grade 12, University Preparation
Properties of water
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Solutions Water is known as the universal
solventChemical properties of water are
important b/c they allow it to form solutions (aka. Uniform mixtures)
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Solute :That which is being dissolved (sugar)
Solvent: That which does the dissolving (water)
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Ionic compounds: dissolve readily in water b/c water
is polar Polar covalent compounds
dissolve in water
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Properties of water: Cohesion – “sticking together” b/c of
hydrogen bondingr Adhesion _ water molecules are
attracted to other substances
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
surface tension – water is pulled together creating the smallest surface area possible water strider walking on water
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Capillary Action
Because water has both adhesive and cohesive properties, capillary action is present.
Capillary Action = water’s adhesive property is the cause of capillary action. Water is attracted to some other material and then through cohesion, other water molecules move too as a result of the original adhesion.
Ex: Think water in a straw
Ex: Xylem in plants carry water this way
1.1 Chemical Fundamentals
Expansion – water expands when it freezes, which is opposite to most substances results in ice having a lower
density than liquid water so the ice floats
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
ponds “freeze on top” so organisms are able to
live underneathProblem for roads
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
High Heat CapacityIn order to raise the temperature of water, the average molecular speed has to increase.
It takes much more energy to raise the temperature of water compared to other solvents because hydrogen bonds hold the water molecules together!
Water has a high heat capacity.
“The specific heat is the amount of heat per unit mass required to raise the temperature by one degree Celsius.”
Properties of Water
Density
Water is less dense as a solid! This is because the hydrogen bonds are stable in ice – each molecule of water is bound to four of its neighbors.
Solid – water molecules are bonded together – space between fixed
Liquid – water molecules are constantly bonding and rebonding – space is always changing
1.1 Chemical Fundamentals
Acids, Bases & Salts Acids – release Hydrogen
ions (H+) in water (ex. HCl in stomach acid)
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Bases – Produce hydroxide (OH-) ions in solution (ex. NaOH in soap & egg whites)
Salts – yields other ions (ex. NaCl and KCl)When salt is dissolved in water; sodium & chlorine “disassociate” or temporarily separate
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
pH --“power of H+”
-pH scale measures the concentration of
Hydrogen ions
Scale 0-14
acid: 0 to < 7bases: > 7 to 14
SBI4U, Biology, Grade 12, University Preparation
1.1 Chemical Fundamentals
Blood - 7.4 (lethal if more acidic than 7 and more basic than 7.8)
Stomach acid - 2
A change in pH --in your body results in halting some enzyme functions
SBI4U, Biology, Grade 12, University Preparation
51
•Buffers resist changes to the pH of a solution when H+ or OH- is added to the solution.
•Buffers accept hydrogen ions from the solution when they are in excess and donate hydrogen ions when they have been depleted.
1.1 Chemical Fundamentals
Acid rain - contains sulfuric acid and nitric acid
Acid rain pH < 5.6 Acid rain washes away vital minerals from soil,
kills aquatic organisms & strips nutrients from plants
SBI4U, Biology, Grade 12, University Preparation
1.2The Chemicals of Life (most contain carbon)
Carbohydrates - store energy & provide shape (composed of C,H&O)
Starch - plants stored energy that is made of sugars
(monosaccharides,disaccharides &polysaccharides)
SBI4U, Biology, Grade 12, University Preparation
1.2 CARBON
Carbon is an important biological element because it can form four bonds with other elements and long chains or rings
Polymer – large molecule made up of many smaller units like starch
Monomer – unit that makes up polymer; glucose is the monomer for starch
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Glycogen - animals stored
energy made from sugars
(same saccharides)Cellulose - simple sugars that
make structural carbohydrates in plants
SBI4U, Biology, Grade 12, University Preparation
GLUCOSE
Monomer of starch, glycogen, and cellulose
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Lipids - long term energy storage; four types; not soluble in water
Fats - provide insulationWax - repel waterPhospholipids – give structure
to cell membranesSBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Steroids - cholesterol in cell membranes
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Proteins - large, complex molecules composed of many smaller molecules called amino acids (only 20 amino acids make different combinations & proteins)
SBI4U, Biology, Grade 12, University Preparation
A protein’s structural characteristics determine its function.
The genetic information in DNA codes specifically for the production of proteins and nothing else.
Proteins accomplish more tasks than any other group of biological molecules.
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Proteins - make enzymes that help control chemical reactions (ex. Speed up digestion, releasing energy during cellular respiration, building up proteins)
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
1. Defense2. Movement3. Structure
4. Regulation5. Transport6. nutrition
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Amino Acids Amino acids are held together by peptide bonds to form proteins
An amino acid is an organic molecule possessing a central atom to which are attached an amino group, a carboxyl group, a hydrogen and a variable group of atoms called a side chain (R)
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Globular Proteins Protein molecules composed of one or more
polypeptide chains that take on a rounded spherical shape
Primary Structure – the sequence of amino acids in a polypeptide strand
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Secondary Structure Coils and folds in a polypeptide caused by
hydrogen bonds between nearby amino acids Alpha helix – a type of polypeptide secondary
structure characterized by a tight coil that is stabilized by hydrogen bonds
Beta pleated sheets – polypeptide secondary structures that form between parallel stretches of polypeptides and are stabilized by hydrogen bonds
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Tertiary Structure – supercoiling of a polypeptide that is stabilized by side-chain interactions, including covalent bonds, such as disulphide bridges
Disulphide Bridges – a covalent bond between cysteine residues in a polypeptide that stabilize tertiary structure
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Quaternary Structure (QS)– two or more polypeptide subunits forming a functional protein
Examples of proteins with a QS: collagen- found in bones, skin, tendons, and
ligaments keratin – found in hair hemoglobin – found in red blood cells
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
The Denaturing of Proteins The final shape of a polypeptide (tertiary
structure) can be altered by environmental factors.
These include: Temperature changes pH Ionic concentration
A denatured protein cannot carry out its biological functions
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Chaperone proteins – special proteins that aid a growing polypeptide to fold into tertiary structure
SBI4U, Biology, Grade 12, University Preparation
1.2 The Compounds of Life
Nucleic Acids - large, complex molecules that contain hereditary or genetic info – two types
monomer – nucleotide (made up of a nitrogenous base, a phosphate group, and a five carbon sugar)
SBI4U, Biology, Grade 12, University Preparation
1.2 The Compounds of Life
DNA - carries instruction that control activities of cell (blueprint)
SBI4U, Biology, Grade 12, University Preparation
1.2 The Compounds of Life
RNA - makes the proteins (builder)Reads the information in DNA
and transports it to the protein building apparatus of the cell
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Comparing DNA and RNADNA contains the sugar
deoxyriboseRNA contains riboseThe only difference between these
two monosaccharides is the lack of an oxygen atom at carbon 2 in deoxyribose.
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
There are five types of organic bases found in nucleic acids: adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U)
DNA has nucleotides containing the bases A, G, C, and T, while RNA contains A, G, C and U.
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
DNA Helical in structure Composed of two strands There is a strict rule regarding base pairing: The two strands are held together by
hydrogen bonds between nitrogenous bases Adenine (A) will always bond to Thymine (T) with
two hydrogen bonds; Guanine (G) will always bond to Cytosine (C) with
three hydrogen bonds
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Each strand of the DNA molecule has a free phosphate group at one end and a free sugar (deoxyribose) at the other end.
Hydrogen bonds will only form if one strand is upside down compared to the other (antiparallel)
Every nucleotide pair consists of a purine (double ring) facing a pyrimidine (single ring)
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
Other nucleotides Nucleotides are not only used in the
construction of DNA and RNA They are important intermediates in a cell’s
energy transformations
SBI4U, Biology, Grade 12, University Preparation
1.2 The Chemicals of Life
ATP (adenosine triphosphate) – drives energy requiring reactions
Nucleotide derivatives such as nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD), are used in the production of ATP.
cAMP is used as a “second messenger” in various hormone interactions.
SBI4U, Biology, Grade 12, University Preparation
1.2 Chemical Reactions and Enzymes
Chemical Reaction creation of new substances by
breaking or forming chemical bonds
Carbohydrates broken for energyAll chemical reactions involve
energy (absorbed or released)
SBI4U, Biology, Grade 12, University Preparation
1.2 Chemical Reactions and Enzymes
2H2 + O2 2H2O
_C6H12O6 + __ O2 __C02 + __ H2O
SBI4U, Biology, Grade 12, University Preparation
1.2 Chemical Reactions and Enzymes
Reactions happen in living & nonliving things all the time Can be sped up by increasing temp or by involving a catalyst Catalyst - in organisms are called
enzymes (see sucrose example, fig. 2.15)
Enzymes - break bonds others help form bonds
SBI4U, Biology, Grade 12, University Preparation
1.2 Chemical Reactions and Enzymes
*Type of protein
*Act as a catalyst, speeding up chemical reactions
1. Substrate- substance being changed by enzyme
2. Active site- region on enzyme where substrate attaches (this is the enzyme substrate complex)
SBI4U, Biology, Grade 12, University Preparation
1.2 Chemical Reactions and Enzymes
3. Substrate is altered (bond weakened) so that bond is broken
4. Products released and enzyme is unchanged (only the substrate changes)
5. Enzyme is free to bond with another substrate
SBI4U, Biology, Grade 12, University Preparation
*Enzymes catalyze specific reactions- only specific substrates will fit into the active site
*Enzymes work by either breaking or forming compounds
*Enzymes work only within specific ranges of temperature and pH.
1.2 Chemical Reactions and
Enzymes
SBI4U, Biology, Grade 12, University Preparation
*Enzyme affected by high temperature
SBI4U, Biology, Grade 12, University Preparation
SBI4U, Biology, Grade 12, University Preparation
*Enzymes are also affected by the concentration of the substrate and the enzyme
Application: bee sting home remedy- meat tenderizer (enzyme) on bee
sting (protein in venom)
SBI4U, Biology, Grade 12, University Preparation