Transcript File

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 atoms
 12 hydrogen atoms
 6 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
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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
charge
 Charged 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
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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
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NONPOLAR COVALENT
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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
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
SBI4U, Biology, Grade 12, University Preparation
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 fossils
 preserve food
 treat cancer
SBI4U, 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
solvent
 Chemical properties of water are
important b/c they allow it to form
solutions (aka. Uniform mixtures)
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1.1 Chemical Fundamentals
Solute :That which is being
dissolved (sugar)
 Solvent: That which does the
dissolving (water)
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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

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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
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1.1 Chemical Fundamentals
ponds
“freeze on top” so
organisms are able to
live underneath
Problem for roads
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1.1 Chemical Fundamentals
High Heat Capacity
In 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)
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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 < 7
bases: > 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
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•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.
51
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 insulation
Wax - repel water
Phospholipids – give structure
to cell membranes
SBI4U, 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)
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 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. Defense
4. Regulation
2. Movement
5. Transport
3. Structure
6. 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
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1.2 The Chemicals of Life
 Chaperone proteins – special proteins that
aid a growing polypeptide to fold into tertiary
structure
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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 RNA
 DNA
contains the sugar
deoxyribose
 RNA contains ribose
 The 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 energy
 All chemical reactions involve
energy (absorbed or released)
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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)
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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
1.2 Chemical Reactions and
Enzymes
*Enzymes work by either breaking or forming
compounds
*Enzymes work only within specific ranges of
temperature and pH.
*Enzymes catalyze specific reactions- only specific
substrates will fit into the active site
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*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 remedymeat tenderizer (enzyme) on bee
sting (protein in venom)
SBI4U, Biology, Grade 12, University Preparation