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The Chemical Basis of Life – A Biology Prerequisite
Chapter 1, “The Molecules of Life”, is a review of chemical concepts from the grade 11
biology and chemistry courses. Coverage of material for this section will be primarily of an
independent nature, with only some topics covered by the biology teacher. The most
effective method to complete this diagnostic assessment is to complete what you know
first, and then refer to your textbook/course notes for details or understanding gaps.
1.
Distinguish between:
a) atom
b) element
c) molecule
d) compound
2.
Give five examples of elements and five examples compounds that are found in
the human body.
3.
Draw a representative (chemistry appropriate) diagram of a carbon atom
showing the placement of protons, neutrons, and electrons.
4.
Show your elemental atom in standard atomic notation. Use labels to show
what each item represents.
5.
a) Carbon-14 is considered to be an isotope of carbon. What does this mean?
Draw a Bohr diagram to represent it.
b) How is carbon-14 different than some other isotopes? What happens to it
over time?
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c) Define half-life.
d) What are three biological uses of isotopes?
6.
Distinguish between an energy level and an orbital? What is an orbital’s
maximum capacity?
7.
What are valence electrons? Why are they particularly of interest to scientists?
8.
Show a biological element with a Lewis dot diagram.
9.
a) What is meant by an atom being neutral?
b) What is an ion? Describe its electron arrangement.
c) Differentiate between a cation and anion.
d) Give 5 examples of ions found in the human body.
10.
a) What is a chemical bond?
b) Why is this an important term for biologists to understand?
11.
a) Differentiate between:
i) ionic bond
ii) pure covalent bond
iii) polar covalent bond
b) What types of atoms form these types of bonds?
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c) What does the term electronegativity refer to? What is the importance of such a
measure?
12.
Draw Lewis dot/electron dot diagrams or structural diagrams for the compounds
below. State the type of bonding that is taking place (pure covalent, polar covalent,
ionic)
a) O2
b) H2O
c) NaCl
d) CH4
13.
What happens to orbitals of different atoms during bonding? Why is this significant
with respect to the molecule?
14.
What does it mean if a molecule is polar?
15.
How can a molecule have polar covalent bonds but be classified as non-polar?
16.
Why would polarity be an important idea for biologists to understand?
17.
Differentiate between an intermolecular and intramolecular force. Give an example
of each.
18.
Give three examples of biological reactions? (See Page 32 – 35).
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19.
a) Differentiate between an acid and base.
b) What does pH mean?
c) Draw and label the pH scale demonstrating where the acids would be found, and
where the bases would be found.
d) What is the approximate pH of your stomach? blood? small intestine?
e) What is a hydronium ion? Why is it technically incorrect to call a hydronium ion a
hydrogen ion?
f) What is it called when an acid is added to a base in equal proportions? Provide a
sample equation. Identify the products.
g) What is the difference between a strong acid and a weak acid?
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Review of Atomic Structure
All elements and compounds are composed of tiny particles called _______________.
The majority of the atom is made up of empty space. At the centre, of the atom is the tiny,
dense nucleus, where the majority of the mass lies. The components of the atom are
found in the chart:
Part of the Atom Charge
Symbol
Location in
Atom
Relative Mass
(1 amu = 1.67 x 10-24 g)
PROTON
ELECTRON
NEUTRON
________________ define the identity of an element. This is represented by the atomic
number. If the number changes, so does the element. Compare carbon (6) vs nitrogen
(7).
Practice: Compare the number of protons in magnesium and phosphorous
Mg – _____ protons
P – _____ protons
________________ can vary for atoms of the __________element (called
________________). Isotopes can be recognized by their differing atomic masses.
On earth, one will find a different percentage of each isotope (this is why the atomic mass
on periodic tables are not whole numbers)
EXAMPLE: Carbon  three different isotopes, ______, _______, and _______
Carbon-12 (12C)  ____ protons and ____ neutrons
Carbon-13 (13C)  ____ protons and ____ neutrons
Carbon-14 (14C)  ____ protons and ____neutrons
 indicates radioactive form (radioisotope); this means that the nucleus is unstable and
will release radiation over time
Question: What are some applications of these radioisotopes for biologists?
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ELECTRONS
- electrons occupy specific distances away
from the nucleus corresponding to energy
levels (n = 1,2,3….. further away)
P+
N0
e
Increasing
energy
- it is impossible to know the exact position of
an electron, but there are volumes of space
where the electrons are MOST likely to be
found
- volumes of space called _________________
Orbitals can be different shapes:
Spherical shape (s)
Dumb-belled shape (p)
“Too Complex for Biology” shape (d)
- only 2 electrons can occupy an orbital (that’s why we draw electrons in pairs on Bohr
diagrams)
- there is a special stability associated with complete orbitals (that’s why we often say that
atoms are stable when they have a complete outer electron shell  noble gas
configuration)
Energy Level
1
Maximum # of e- in Orbitals
1s2
2
2s2p6
3
3s2p6d10
Max # of e- per Energy Level
- Because the d orbitals are not bonding orbitals in biological elements, we will ignore
these electrons from now on. So, effectively, aside from the first shell, the maximum
number of electrons we will talk about in an outer shell is 8 (consistent with what you’ve
learned in younger grades)
SORRY CHEMISTS!!!
For Biologists in this Class
Energy Level
1
2
3
4
Max # of e- per Energy Level
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______________ electrons  refer to those electrons in the outermost energy level (s
and p orbitals*)
- are important because these are the electrons most likely involved in chemical
reactions
- Lewis structures can be used to illustrate the valence electrons, predict the
number of bonds formed and/or to determine the ionic charge they will have:
Chlorine  2, 8, 7*
Why?
If the electron orbitals are not complete, atoms will want to react with other “willing”
elements in such a way to fill these orbitals
- when atoms lose or gain electrons to become stable, they become ____________
- when most biological elements lose or gain electrons to become stable, they will end up
with 0 or 8 e- in their outermost shell; this is called a ____________________
ION  charged atom, resulting from a loss or gain of electrons
Consider 11Na  It has an electron arrangement of ___, ___, ___; it will want to ______
electron to have a stable octet (2, 8  )
Results - one extra proton (+11) vs electrons (-10); it will be positively charged. We
write this as _______.
Consider 16S  It has an electron arrangement of ___, ___, ___; it will want to ______
electrons to have a stable octet (2, 8, 8   )
Result - two extra electrons (-18) vs protons (+16); it will be negatively charged. We
write this as ________.
You try: What is the electron arrangement of 7N? How many electrons would it lose
or gain? What is the ionic charge?
Most metallic and non-metallic elements existing in your body will be in the form of ions.
This means that they are already in stable form.
KEEP IN MIND…
When atoms lose or gain electrons, there must be a “willing” element to exchange with.
This leads us into the topic of CHEMICAL BONDING.
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Recall from yesterday:
- Elements identified by atomic # (# of protons)
- isotopes of an element have different # of neutrons
- nucleus of atom hold protons and neutrons
- electrons found in orbitals around nucleus of atom; can have different shapes:
spherical (s) , dumb-bell (p)
- valence electrons are in outermost orbital and are involved in reactions; Lewis
structures show valence electrons around the element symbol
- atoms react to create a stable octet in the valence shell (either gain or lose
electrons to become stable)
o cations are positive ions (lost electrons)
o anions are negative ions (gained electrons)
_______________________________ (En)– the measure of an atom’s ability to attract
electrons (see table pg 14);
_______________________________ - attractive forces existing between atoms that allow
molecules to form
2 Types:
1. _____________________________bond: the bonds that form
molecules or compounds
A) _______________– form between a __________and ______________.
– electrons are transferred, forming a cation and an anion; the
attraction forms the bond; ionic compounds form crystalline structures
that dissolve in water (dissociate into ions in water) ΔEn > 1.7
Example: NaCl
B) ________________– form between ____ ________________.
- electrons are _______________between atoms to achieve a stable
octet: orbitals overlap and change shape (hybridize)
i) __________covalent – ____________ sharing of electrons ΔEn = 0
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SINGLE
DOUBLE
TRIPLE
– share one pair
-share 2 pairs
– share 3 pairs
(CH4)
(O2, CO2, unsaturated fat) (N2, HCN)
ii) __________________covalent – ______________ sharing of electrons, creates a slight
charge separation due electronegativity differences: 0 < ΔEn < 1.7
- the atom with higher En will pull the shared pair closer becoming δ- (dipole) while
the other atom with the lower En becomes δ+ (dipole)
e.g. H2O
Polarity of Molecules
ICl
p. 11-12
- we often need to look at the 3-D shape to determine if a molecule is polar (it may have
polar bonds and yet still be a non-polar molecule if it has a symmetrical shape)
POLAR
NON-POLAR
H2O
CH4
NH3
CO2
- polarity of molecules allows interactions to occur between molecules; this explains
_______________________ of covalent compounds (the ability of a substance to dissolve in
a solvent)
Like dissolves like 
“Polar dissolves Polar”
“Non-polar dissolves Non-polar”
_____________ – liquids that will dissolve in each other
_________________– liquids that will form separate layers instead of dissolving when
mixed
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Hydrophilic  “water loving”
- polar molecules dissolve in water
Hydrophobic  “water fearing”
- non-polar molecules DO NOT dissolve in water
2. __________________________________ forces *weaker than ionic and covalent
– collectively called the van der Waals forces
i) _____________________________ –weakest; found between all molecules (nucleus and
electron orbitals); the only force holding nonpolar molecules to one another
ii) _________________________________________– hold polar molecules to one another;
attraction between δ- and δ+ ends of polar molecules; stronger than London forces
iii) _____________________________ – found between H of one polar
molecule and N, O, F or S of another polar molecule
 water molecules held together by H bonds
 gives it unique properties
Unique Properties of Water
1. has the ability to “_________________”; surface tension is created by:
- ___________________ (H bonding between water molecules)
- ___________________ (H-bonding with other polar molecules)
2. absorbs a lot of ___________– high specific heat capacity and specific heat of
vaporizations (H bonding cause large amounts of heat to be absorbed before
changing temp or vaporizing) allowing for temp moderation, evaporation and
cooling
3. solid water is __________ _____________ than liquid water – below 00 a crystal
lattice forms (freeze) and H bonds between molecules spread further apart, thus
reducing density
*Ionic compounds will dissociate in water; a hydration shell forms around ions (charge separation)
– see diagram in text
Homework: Text p. 17 Do #1-6, 8-9, 11-13.
Additional Questions:
1. What is the reason for water’s ability to dissolve a variety of substances?
2. Give examples of substances that dissolve easily in water.
3. Give examples of substances that do not dissolve easily in water.
4. Why do small, non-polar substances like O2 not dissolve in water?
5. How are substances like O2 transported?
6. Give an example of hydrophobic and hydrophilic substances.
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Unique Properties of Water
Water is the _____________________________. More substances dissolve in
water than in any other liquid solvent, mostly due to it’s polarity and Hbonding:
Water has the ability to “cling” due to _______________ ( H-bonding between
water molecules – creates high surface tension) and _____________________ (Hbonding with other polar molecules – allows for capillary action and solubility
of polar molecules); water molecules create a _________________; H-bonds
constantly break and reform giving water it’s fluid properties.
Solid water is __________ ____________ than liquid water – below 00, crystal
lattice forms and H-bonds between molecules spread further apart, thus
reducing density  ice floats on water.
Water is able to ___________________________________– it has a high specific
heat capacity and specific heat of vaporization  energy is used to break Hbonds, thus large amounts of heat are absorbed before changing temperature,
evaporating or cooling.
Aqueous solutions
Water molecules will readily surround polar, charged molecules and ions of
other substances, forming a _________________________________ which reduces
attraction between molecules and promotes separation.
This allows substances to form __________________________________ in which
the water is the solvent and the substance is the solute.
__________________________ – polar or charged molecules that are strongly attracted
to water (‘water-loving’)  ______________________
__________________________– non-polar molecules that are not strongly attracted to
water (‘water fearing’)  ______________________________
**Water dissolves thousands of solutes necessary for life  these solutes are able to
float around and collide, allowing chemical reactions to occur.
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Instructions: The following are scenarios that can all be explained by water’s unique
personality (eg. physical properties). Use the handout from Biology 12 to help you
complete the following table.
Scenario
A toddler takes some salt,
puts some on his tongue,
and watches in amazement
as it disappears.
Property
Polarity
That same toddler makes
some Kool-aid and watches
as the sugar he adds
disappears. Is it the same
magical trick?
Polarity
When the stems of red
carnations are placed in
black dye, the carnations
eventually turn black.
Lakes are always slower to
warm up in the spring
(versus the air) and slower
to cool down in the fall. So
why does this happen?
Oh to be a water strider! If
they see water, they walk on
it. When we see water, we
take a bridge.
Oceans and lakes don’t
freeze solid; instead the ice
floats on the water, and acts
to help preserve the aquatic
life below with an insulating
effect. So, why does solid
water float?
Explanation
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Ionization
Pure water will ______________________ into _____________________(H3O+) and
________________________(OH-) ions in equal proportions.
Other substances will alter the balance between these ions, creating acidic and basic
solutions.
ACIDS, BASES, pH, BUFFERS
When _________ is greater than _________, the solution has properties of an
____________ ______________taste, conduct electricity, turn ______ litmus ___
___________ are substances that increase [_______] in solution (donate protons).
*________________ acids tend to dissociate completely, whereas _________
acids have little dissociation.
e.g.
When __________ is greater than __________, the solution has properties of a
_____________  ______________ taste, _______________ feel, conduct
electricity, turn ____________ litmus _________
____________ are substances that increase [_______] in solution (accept protons)
*Strong bases tend to dissociate completely, whereas other bases combine
directly with H+ ions.
e.g.
pH
– “Power of Hydrogen” - a measure of the ___________________ of a
solution; describes the [H3O+]; can be calculated using the formula: pH = – log [H+]
Note: [H+] represents the concentration of H+ or H3O+
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pH scale – also see pg. 32 in text.
Note: Each whole number on the pH scale represents a 10X difference; pure water at room temp.
has a [H3O+] = 1.0 x 10-7  pH 7
Components of living cells are sensitive to pH levels - most* cellular processes
operate best within a range of pH ________ __________; very small changes in pH
can have huge impacts on biological reactions and molecule functioning.
Various factors can alter/change pH:
o cellular processes (produce acids or bases)
o foods we consume
o health; vomiting pH, diarrhea pH
When strong acid and bases dissolve, they dissociate completely;
HCl  donate all H+ to water - [_________] goes up – pH ____________
NaOH  donate all OH- to water - [_______] goes up – pH _____________
Weak acids and bases only partially ionize in water - this is a
_____________________ reaction (ions can reassociate once in solution)
In order to keep pH levels constant, living organisms have
______________________, consisting of _______________________and
_____________, that minimize changes in pH (they do this by absorbing or releasing
H+ ions)
One of the most important buffers in human
extracellular fluid and blood is ___________
____________________________________:
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When reactions increase H+ in the blood, ________ ions react with extra protons
(H+) to produce __________.
When reactions increase OH- levels in the blood, OH- ions react with ______ forming
________, then H2CO3 dissociates to replace the H+
Result: [H+/H3O+] is maintained within narrow limits, keeping the pH constant
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The Chemicals of Life
_________________ atoms make up the base of every organic compound, including
the 4 major classes of biologically important molecules:
_____________________, ____________, _____________,
____________________
Why Carbon?
 it is the ______ _____________ ___________– has _____ unpaired valence
electrons and can form 4 bonds with other atoms
 covalent bonds of carbon are _____________ and ______________
 joins with other carbons in various ways: straight chains, branched chains, rings
of various size/complexity
 form covalent bonds with Hydrogen; molecules called
_______________________:
Methane (CH4)
Propane (C3H8)
Benzene (C6H6)
*These structures are ________________________ due to symmetry, even
though individual C-H bonds are ______________.
Molecules of living organisms contain other elements in addition to C and H;
__________ ______________________ contain _________________groups of
atoms, called __________________ _________________, which give the molecule
distinct characteristics (usually ionic or strongly polar).
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Biological Functional Groups are often the site of chemical reactions between
molecules:
Try these……circle and name the functional groups:
H
H O
H–C–H O
H2N–C–C=C–C–H
O
H
H2N–C–C–OH
H–C–C–SH
H O
O
H O H
HO–P–O–C–C –C–OH
O
H
H
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Biologically Important Molecules
Macromolecules are large organic molecules composed of
____________________ simple/single molecular units
______________________– consist of many identical or similar monomers linked by
bonds; include carbohydrates, proteins, nucleic acids
__________________________________ – consist of different monomers; include
lipids
There is unity in life, as there are only ~40-50 common monomers used to construct
macromolecules.
Special reactions that require catalysts or enzymes are needed to build and break
macromolecules:
_________________________________: require energy to build macromolecules
(usually ____________________________________ reactions  water is
__________________ at the union site)
______________________________________: releases energy when bonds of
macromolecules are broken (______________________– a water molecule is
____________________ where the bond is broken)
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Carbohydrates
a) Monosaccharides
b) Disaccharides/Oligosaccharides
c) Polysaccharides
 contain ____:_____:_____in the ratio ____:_____:_____
 empirical formula (___________)
where n = # of C atoms
 the ______________ source of __________ due to the high number of C-H bonds
 also found as structural compounds and energy reserves
 almost exclusively from _________________ sources
 contain ____________________________ groups; ____________________
a. Monosaccharides
- simplest, _____________ sugars; most common with 3, 5 or 6 C
- 5 carbons  __________; 4 alcohol groups, 1 aldehyde or ketone; C5H10O5
- 6 carbons  __________; 5 alcohol groups, 1 aldehyde or ketone; C6H12O6
Examples:
Glucose, Galactose, Fructose; all have the same molecular formula
(C6H12O6),but different structural formulae  called ______________.
- in _________________, monosaccharides react intramolecularly to form
___________ (making it easier to move around):
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b. Disaccharides/Oligosaccharides
 _________________________ covalently bonded together (________________);
the covalent bond is called a _________________________________.
Disaccharide
Monomers
Sources
Dehydration Synthesis:
pg. 34 -35
+ H2O
+ H2O
c. Polysaccharides
- ________________ of glucose (100’s – 1000’s); ___________, but _____________
in water due to large size
- formed by dehydration linking C1 with C4 or C6 of another monomer
Key functions:
1. ENERGY STORAGE:
i.
*___________________  long, ______________ chain of several hundred
glucose; α-1,4 linkage
ii.
*___________________  highly ______________ (every 30th glucose has
short side chain attached to C6); α-1,4 and α-1,6 linkages
* both forms of _____________________ from ____________
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iii. ____________________  similar
structure
to amylopectin, but with ____________
branches and ___________ side
chains; storage in _______________
(liver and muscle)
2. STRUCTURAL INTEGRITY
iv.
_____________________long, ________________ chains, with
_____________________ glucose molecules – β-1,4 linkages; allow
___________________ to form between parallel chains; creates a
_________, ______________ fibre; (______________________ walls)
a. ________________  modified form of cellulose (contains ______);
abundant in nature (_____________,__________________________)
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Lipids
- ________________, _____________________,________________* in water
- Smaller than carbohydrates; have H, C and fewer O
There are 5 main categories of lipids:
Fatty acids, fats, phospholipids, steroids, waxes.
1.
Fatty Acids
 a _______________________chain with a _________________
functional group (gives it acidic properties)
 have 4 or more C in the carbon chain (most common are even
numbered chains)
 as chain length increases, solubility __________________________
 if C are all __________________ bonded and contain the max. # of
hydrogen, it is a __________________________ chain
 if there are __________________ bonds between carbons, it is an
__________________________ chain (only 1: mono-, more than 1:
poly-)
2.
Fats
 Energy __________________________(long periods of time)
 contain many more C – H bonds and fewer polar –OH
Structure:
- ______________________are a composite molecule made up of:
- __________________________
o a 3 carbon alcohol with each carbon bearing a
hydroxyl group (-OH)
- ___________________________ side chains (see
above)
*can be the same or different fatty acids
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Triglycerides are formed through ____________________________ reactions;
an _______________________ bond or linkage holds the fatty acid to the
glycerol backbone.
The properties of the fatty acid side chain determine
the type of fat:
i) _____________________ - only __________ bonds
(C-C) in the carbon chain; mainly from
_____________________ sources; ____________ at
room temperature due to close fit of the side chains
(many van der Waals forces at work)
ex: ______________,_______________
ii) _____________________(a.k.a. oils)– one or more
_________________ bonds (C=C) in the carbon chain;
mainly from ______________ sources; ___________ at
room temperature due to the bends in the chain @
double bond sites (fewer van der Waals forces)
The more double bonds the side chains contain, the
more fluid the fat. ________________________ fatty
acids contain many double bonds (C=C)
ex: ___________ oil, __________oil, _________oil
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_________________________ is the process of adding H’s to an unsaturated fat
(splitting double bonds); the fatty acids becomes more saturated, thus the fat
becomes more solid (e.g. margarine)
3. Phospholipids
 Primary component of __________________________________ 
create a phospholipid bilayer: _______________outside,
_________________ inside
 composed of a glycerol backbone attached to 2 non-polar fatty acid
chains and a highly polar phosphate
 ___________________________ molecule: the phosphate “head” is
hydrophilic and the fatty acid “tails” are hydrophobic
4. Steroids
 mostly _______________________*, very __________________
 contain 4 ____________ hydrocarbon ______________ with several
functional groups
 sterols have an –OH group (hydrophilic)
 _______________________ is an important steroid in cell membranes;
cells convert cholesterol into vitamin D and bile salts
 other steroids include ________ hormones – testosterone, estrogen,
progesterone (different side-chains)

5. Waxes
 large, contain long-chain fatty acids linked to alcohols or carbon
rings
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 extremely _____________________, _____________________,
__________ with a firm, pliable consistency
 form ____________________________ coatings on plant and animal
parts
eg. stems, leaves, fruit – (cutin); bird feathers; beeswax
Proteins
- most diverse molecules in living organisms; consist of C, H, O, _____ &
______
- proteins are _______________ ____________ polymers, folded into _______
structures
- proteins accomplish more tasks than any other group of biological
molecules:
1) ___________________ – catalyze chemical reactions in the body
2) ___________________ – hair, nails, skin, tendon
3) ___________________ – fight infection, form antibodies, form blood
clots
4) ___________________ – Hormone messenger
5) ___________________ - Transport i.e. hemoglobin (CO2/O2)
6) ___________________ /___________________ - Cell markers/protein
channels
7) ___________________ – form muscle fibres (actin/myosin)
General Structural of an Amino Acid:
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- in solution, _____________ group releases H+ and _______ accepts H+
- each amino acid has it’s own _____________ _______________ (Rgroup), which gives it unique properties; there are _______ different R
groups ( 20 different amino acids)
- side groups can be polar, non-polar, charged, acidic or basic; they may
contain __________ , _________, __________, or __________ which can
interact with other molecules both in and outside of the same protein.
- 8 amino acids are ____________________ (we cannot make them – must
come from our food)
- amino acids are linked together in _______________________ reactions
between the __________ group of one a.a. and the _________________group of
another a.a.; the link is called a ____________________________ ; thus
_______________ _____________ are formed
*Note: in cells, a.a. are added only to the carboxyl end (1 direction)
- amino acid polymers are called _______________________ (have >50 aa)
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- a protein is one or more polypepetides folded into precise 3-D shapes.
- the _____________________________ (shape) of the protein is determined by
the sequence of amino acids; 3D structure is directly related to the protein’s
function
Protein Structure and Function
Proteins have 4 levels of structure:
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a)
______________________ structure – the _________________
____________________ of amino acids that make up the polypeptide
chain (DNA codes specifically for this order)
Example:
b)
Cys – gly – ala
Gly – ala – cys
Ala – cys – gly
Each sequence is different
 each would form a different
protein
______________________ structure – the _________ or
______________ that develop in a polypeptide chain due to
_____________________ between amino and carboxyl groups of
neighbouring a.a.
There are 2 types of secondary structures:
c)
i)
________________(every 4th a.a.)
ii)
________________(side-by-side)
____________________ structure – the overall 3D shape of the
protein; depends on secondary structure
 if secondary is β-pleats, the 3D shape will be ________________, and the
protein function will be ______________________ e.g. hair, nails, silk
 if secondary is α-helices, the 3D shape will be ________________, and
the protein function will be ______________________ e.g. enzymes
* 3D shape folding occurs due to ____________________________________:
Weak
interactions;
Have a
cumulative
effect
Strong
interactions;
Increase
stability
- hydrophobic interactions  these a.a. congregate at the
core/centre of protein (away from water)
- van der Waals forces  these strengthen/reinforce
hydrophobic interactions
- H-bonding  occurs between polar side chains
- Ionic bonding – occurs between negatively and positively
charged side chains (R groups)
- Disulfid bridge (covalent) – occur when 2 cysteine amino acids
are close together
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d)
_______________________ structure – a.k.a functional protein; result
from the interaction of ____________________ polypeptide chains
(each is called a
subunit)
E.g. hemoglobin
(4 chains)
*These contain prosthetic groups (non-protein) that help the protein function
Factors that affect protein shape:
- in primary structure, altering the __________________ of a.a. will alter
the shape of the protein, since each side chain has different chemical
properties
- cell conditions: pH, temperature, [salt] can cause
____________________
-the protein loses its shape (bonding interactions disrupted); protein
can become inactive. **This is reversible or permanent depending on
nature of external stimulus.
Dangers and uses of denaturation:
- gastrin works best at pH 2, is denatured in small intestine at pH 10
- fever above 39C could denature critical brain enzymes
- curing meat with salts denatures bacterial enzymes (prevent spoil)
- heat denatures hair proteins; temporarily straighten/curl
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N
Nuucclleeiicc AAcciiddss
-
are informational polymers; serve as assembly instructions for ______________
production
-
two main types exist:
o ______________________________________ (DNA) – stores hereditary info for all
organisms (prokaryote, eukaryote, most viruses)
o ______________________________________ (RNA) – hereditary molecule of some
viruses; also involved in protein synthesis
-
the __________________________ is the monomer of nucleic acids; each nucleotide consists
of 3 subunits:
o ________________ group(s)
o a 5-C _____________ (pentose)
o a ___________________ base
-
the sugars in DNA and RNA differ:
-
There are 2 different groups of
Nitrogenous
bases:_______________________
– have a ________________ ring;
_________________ (C),
________________ (T)-DNA only,
________________ (U)-RNA only
________________
Glycosyl
bond
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– larger, have _____________ rings
(in both DNA and RNA);
___________________(A) and
__________________ (G)
-
nucleotides form a polymer or ______________________ strand through
_______________________ reactions between the phosphate group of 1
nucleotide and the –OH group on the 3-C (sugar) of another nucleotide; this is
called
a _______________________________ bond (polar covalent, hydrophilic)
*the alternating phosphates and sugars form the
___________________ of a nucleic acid chain
-
DNA coils into a ___________________________________
(twisted staircase); the 2 strands are held together by
_________________between N-bases
DNA base pairs will always match a purine with a pyrimidine
___________
____________
Note: this central region with N-bases is hydrophobic
-
to form the H-bonds properly between N-bases, the 2 strands
must run in opposite directions, called __________________
(one DNA strand is upside down compared to the other)
-
DNA strands are very long (coiled around histones to fit into a
nucleus),
are soluble in water and insoluble in alcohol
-
RNA remain single stranded as short chains that can be straight
or folded (clover or hairpin)
The nucleotides *_________* (adenosine triphosphate)
and __________ (guanosine triphosphate) are the
primary energy-transferring molecule in living
organisms which drive almost all reactions in a cell
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(they regulate and adjust cellular activity).
Enzymes
 spontaneous chemical reactions may occur very slowly; energy must be absorbed
by reactants in order to rearrange bonds, called
____________________________ ______________ - ______ (reactants must
collide with enough force and proper geometry to break bonds, reach transition
state and form products)
 heat can speed up the rate of a chemical reaction, but high temperatures can kill
cells
 enzymes are ________________ ___________________ they
______________
the rate of chemical reaction without being ______________ or
_______________ and keep ________________________ in acceptable ranges
 enzymes have specific shapes and will bind and orient reactant molecules, called
_________________________, to _________________ the activation energy and
speed up reactions
HOW?
A substrate binds to the __________________________ of an enzyme (pocket or
groove that matches the shape of the substrate). The enzyme _______________ its
shape to ____________________ the connection to the substrate, called an
___________________ _________; this alteration stresses the substrate bond,
lowering the activation energy, driving the reaction.
Enzyme-substrate specificity
- Each enzyme has a unique 3D shape, this makes it specific to the
substrate(s) it works on:
e.g. amylose + ________
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maltose + ________
Cofactors and Coenzymes
_____________________ – _______________________ group that binds to an
enzyme and is essential for catalytic activity; often _________________ (e.g. ____,
______, ______, ______)
_____________________ – ________________ molecules that act as cofactors;
many
derived from ___________________; many will ____________________ molecules
from one enzyme to another e.g. NAD+ from Vit.B3 (niacin)  electron carrier in
c.r.
Conditions and Factors Affecting Enzyme Activity
1.
Concentration of Enzyme and/or Substrate
_________________________: Excess substrate is proportional to enzyme
concentration: if [enzyme] is _________________, then more substrate =
________________________________ up to the saturation level
______________________: There are a ________________ number of enzyme
molecules in a cell at one time; each reaction takes time to complete; when all
enzymes are ____________________ working, the rate of reaction is much
faster; the more enzymes present/working, the
__________________ the reaction
2.
_______________________
Reactions increase in _______________ as temperature
______________________ BUT beyond a ___________
temperature (for most enzymes <55C), an enzyme will
__________________________ first, slowing enzyme
activity then stopping it completely
3.
_________
Each enzyme works at an optimal pH (depends on properties
of the enzyme); altering the pH can cause
_________________________ changes and ____________
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the enzyme’s ability to catalyze a reaction
(e.g. pepsin – pH ______, trypsin – pH ______)
4. _______________________________
Chemicals bind to an enzyme, decreasing its activity (lower
rate of reaction).
a) _____________________ inhibition – a
___________________ molecule that
resembles the normal substrate binds to the
________________ site, blocking the
substrate and ________________ the
reaction.
b) _______________________ inhibition
– molecules that bind to the enzyme at _________
locations (NOT the active site) causing a change
in ______________; the active site is not longer
____________________ (substrate cannot bind)
Weak inhibitors can be _______________________; Strong inhibitors are not
released  _______________________ (e.g. Toxins  cyanide, antibiotics). The cell
must produce more enzyme to overcome irreversible inhibition.
c) _______________________________________(reversible non-competitive)
________________________ molecules bind to an enzyme on its
______________ site, causing a ___________________________ to the active
site. This can either ____________________ or ___________________ enzyme
activity, referred to as allosteric ____________________and allosteric
__________________ respectively.
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Feedback inhibition
A method used to control or regulate ________________________ pathways
 one of the __________________ of this pathway acts as an
_________________ to earlier enzymes, thus ________________ or
_________________ the process. If the [inhibitor] is __________ , it will
___________________ from the enzyme, allowing it to function, thus turning
______ the pathway.
**See handout
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Cells: The Basic Units of Life: PowerPoint Notes
Types of Cells
Prokaryotic Cells
 Earliest Cells
 Do not have a nucleus
 Have very few organelles
 Examples: bacteria and archaea
Eukaryotic Cells
 Evolved from prokaryotic cells
 Do have a nucleus
 Have many organelles
 Examples: plants, animals, fungi and protists
Organelles*(Eukaryotes)
 An organelle is a small structure inside the cell that is specialized to perform a particular job.
 Animal cells and plant cells have many organelles in common, but also have some
differences.
 The following are important organelles:
Cell or Plasma Membrane
 All cells have a cell or plasma membrane; it is the outer most portion of a cell, or it lies just
inside the cell wall (plant, fungi, bacteria).
 It forms a dynamic barrier around the cytosol to maintain the internal environment of the
cell.
 It is semi-permeable, and controls the movement of material in and out of the cell
**more on this later**
Cytosol
 The jelly-like fluid inside the cell; suspends the organelles.
 **Cytoplasm is a term that refers to all of the internal components of the cell, excluding the
nucleus
Nucleus
 The control center of the cell.
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 It is keep separate from the rest of the cell by the nuclear membrane (double membrane;
outer part of E.R.).
 The nuclear membrane has holes in it called nuclear pores which allow items in and out.
 Inside the nucleus there is DNA and usually a nucleolus.
 DNA when uncoiled is called chromatin.
Nucleolus
 Dense, irregular shape
 It makes the subunits of ribosomes out of proteins and RNA
Ribosomes
 Can be free-floating or attached to an endoplasmic reticulum.
 The site of protein synthesis.
**more on structure and function in Molecular Genetics unit**
Endoplasmic Reticulum (ER)
 A series of canals that connect the nucleus to the cell membrane; flattened & folded tubes.
 It is like a subway system in which molecules made by the cell can travel all over.
 Rough ER have ribosomes on them; make proteins.
 Smooth ER do not have ribosomes ; make lipids and break down carbs, fatty acids, drugs
and poisons.
 Molecules made in the ER are packaged into vesicles.
Vesicles
 Membrane bound, saclike organelles
 Transports, stores or digests substances within a cell
 Several types include: peroxiosomes, vacuoles and lysosomes.
Peroxisomes
 Mainly found in liver and kidney cells.
 Contain enzymes; they are used to break down toxins like hydrogen peroxide, alcohol and
heavy metals.
 Similar in appearance to lysosomes.
Vacuoles
 Large, fluid-filled, storage organelles that isolates water, metabolic wastes, and can store
nutrients.
 Usually very large in plant cells – its fluid pressure keeps the plant cell firm (turgid).
Lysosomes
 Small, membrane-bound sacs that contain digestive enzymes.
 They fuse with vacuoles and the enzymes breakdown broken cell parts or are used to digest
nutrients.
 Found in animal cells.
Golgi Bodies
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 Stacked, folded membranes
 It processes the lipids and proteins made in the ER and then ships them to the cell membrane
or to lysosomes.
 Vesicles are the bubbles of protein/lipid that it receives from the ER and ships out towards
the cell membrane.
Mitochondria (pl.)
 Cellular respiration occurs in the mitochondrion, making energy (ATP)for the cell. (# vary
depending on cell type)
 It has two membranes: an outer membrane and the inner called the cristae; the space
between the membranes is the intermembrane space (IMS); the mitochondrial matrix lies
inside the cristae.
Plastids
 Found only in plants and algae.
 Used for photosynthesis or storage.
Chromoplasts – make and store pigments other than chlorophyll
Amyloplasts – store starch
Chloroplasts
 Site of photosynthesis (make sugars); green due to chlorophyll pigment (reflects green
light).
 Oval or disc shape with two outer membranes.
 Has an inner membrane that surrounds a compartment called a thylakoid.
 The thylakoids stack up on one another to make grana.
 The fluid inside the chloroplast is the stroma.
Cytoskeleton
 Made up of microfilaments (with actin protein) and microtubules ( hollow tubes) which
strengthen the cell, help maintain the shape, and move organelles and other structures
through the cytoplasm.
Centrosome
 Located near the nucleus, this organelle organizes the cytoskeleton and contains centrioles
which help separate chromosomes during mitosis.
Flagella (sing. Flagellum)
 Whip-like tails found in some animal cells, bacteria and protists.
 Usually quite long compared to the cell.
 Used for propulsion
Cilia
 Tiny hair like projections found in some animal and protist cells.
 Move water and mucus in eukaryotes; used for movement/propulsion of prokaryotes
Pseudopods
 Extensions (lobes) that stretch out from the cell to engulf a target, or to move the cell
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Cell Wall
 The outer most portion of a plant, fungal or protist cell.
 It protects, supports and keeps the cell’s shape.
 It is not as selective as the cell membrane; porous.
 Plant cell walls are made of cellulose, a sugar filled with lots of energy, however humans
cannot digest it.
*Primary wall – cellulose
*Secondary wall – thicker coating;
internal
Extra-cellular matrix
 Found in multi-cellular organisms; non-living mixture of proteins and polysaccharides
secreted by cells; varies depending on cell type.
 Functions: support and anchors cells, separates tissues, function in cell signaling
 Examples: Plant cell wall (cellulose), Fungi cell wall (chitin), animals bone, insect
exoskeleton, shells.
 Cell junctions are structures that allow cells to interact with each other and the surrounding
environment
The Structure of the Cell Membrane: PowerPoint Notes
 Cell membranes are very intricate. They are made up of fat molecules called phospholipids,
cholesterol and some proteins and carbohydrates.
 All of these make sure the membrane stays fluid so it can do its job.
 The plasma membrane is a thin outer layer that surrounds all cells. This membrane has four
main functions:
1. allow the transport of raw materials into the cell
2. allow the transport of manufactured products and wastes out of the cell
3. prevent the entry of unwanted material into the cell
4. prevent the leakage of essential matter out of the cell
Cellular functions depend on a watery environment like the one that is found on the inside of the
cell.
In order to maintain their integrity, cells need to be surrounded by an environment through which
water cannot flow. A membrane composed of fatty molecules serves this purpose.
History of the Cell Membrane
In 1924, using an electron microscope, two Dutch physicians, E. Gorter and F. Grendel found that
the cell membrane was composed primarily of phospholipids (shown on the right).
 Phospholipids are made up of a glycerol backbone with a hydrophilic head region containing
a phosphate group and a hydrophobic tail region containing a saturated fatty acid and an
unsaturated fatty acid.
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 The fact that it has both types of fatty acids ensures the cell membrane is fluid.
 They deduced, based on the properties of phospholipids, that the cell membrane was in fact
a bilayer.
 By the 1930s experimental evidence showed that proteins were also part of the cell
membrane.
 In 1935, James Danielli and Hugh Davson proposed the sandwich model: a phospholipid
bilayer between two layers of protein with pores for molecules to travel through.
Stronger electron microscopes would show that the cell membrane was not covered in protein, but
rather had protein embedded in it.
In 1972, S. J. Singer and Garth Nicholson presented the fluid mosaic model of the cell membrane,
which displayed the cell membrane as an integration of proteins and other molecules into the
phospholipid bilayer.
Structures in the Fluid Mosaic Model of the Cell Membrane
Cholesterol is interspersed throughout the cell membrane to add rigidity to it. It also allows the cell
membrane to stay fluid over a wider range of temperatures. Various proteins are associated with the
cell membrane with 4 main functions: transport, enzymatic activity, triggering signals, and
attachment/recognition.
Integral Proteins (a.k.a. trans-membrane proteins) span the width of the cell membrane: these
create channels through which charged molecules or large molecules can pass through
Peripheral Proteins are found on the surface of the cell membrane and are primarily used in cell to
cell signaling with surface carbohydrate chains or linking with the cytoskeleton for support.
The cytoskeleton is attached to the cell membrane for added stability, since membrane proteins and
phospholipids can shift places in the membrane.