Unit 1: Metabolic Processes
Are You Ready?
SBI4U1
DAY 1
1.1 Chemical
Fundamentals
Scanning
electron
micrograph
Animation
http://micro.magnet.fsu.ed
u/primer/java/electronmicr
oscopy/magnify1/index.ht
ml
Atoms of the same element with the same number of protons,
but a different number of neutrons
Uses of Isotopes
• Radioisotopes can be used to help
understand chemical and biological
processes in organisms.
• They can also be used in radiometric dating
which is useful in determining the age of
fossils
• They also have numerous medical
applications
• Example:
A solution of phosphate,
containing radioactive
phosphorus-32, is injected
into the root system of a plant.
• Since phosphorus-32 behaves
identically to that of
phosphorus-31, the more
common form of the element,
it is used by the plant in the
same way.
• A Geiger counter is used to
detect the movement of the
radioactive phosphorus-32
throughout the plant.
• This information helps
scientists understand the
detailed mechanism of how
plants utilized phosphorus to
grow and reproduce.
• Brachytherapy is a form of
radiation therapy where
radioactive isotopes in the
form of small pellets (called
seeds) are inserted into
cancerous tumours to destroy
cancer cells while reducing
the exposure of healthy tissue
to radiation.
• It is currently approved for
treatment of prostate cancer
and cancers of the head and
neck. There are also studies
underway to see whether it
can be used in the treatment of
lung cancer.
• In radioimmunotherapy,
doctors inject antibodies
that have isotopes attached.
• The antibodies flow through
the bloodstream and deliver
the radioactivity by seeking
out and latching onto
proteins on the cancerous
cells.
• RIT is used the treatment of
blood cell cancers, such as
leukemia and lymphoma. It
is also being looked at for
treatment of prostate,
colorectal and pancreatic
cancers.
Valence electrons are those electrons that are available for
bonding.
The electrons in the outermost s and p orbitals
Orbitals: volumes of space around the nucleus where
electrons are most likely found
Ionic and Molecular Compounds
• Formation of sodium chloride:

 Na+ [ Cl

]


Cl

Na  +



• Formation of hydrogen chloride:


H Cl



Cl

H +



A metal and a nonmetal transfer electrons to
form an ionic compound. Two nonmetals
share electrons to form a molecular compound.
Ionic Compounds
Ionic compounds consist of a lattice of
positive and negative ions.
NaCl:
Covalent Bond
How many electrons are involved in each covalent bond?
Double and Triple Bonds
• Atoms can share four electrons to form a double
bond or six electrons to form a triple bond.


N2 :
N N

O
=O



O 2:
• The number of electron pairs is the
bond order.
Electronegativity is a
measure of an atom's ability
to attract a shared electron
pair when it is participating
in a covalent bond with
another atom
By calculating the net
Electronegativity of the
atoms, we can determine the
distribution of electrons and
the nature of the molecule
The Pauling scale of
electronegativity
Electronegativity
• nonpolar bond: electrons are shared equally
H 2,
Cl2:
• polar bond: electrons are shared unequally
because of the difference in electronegativity.
HCl:
Electronegativity
• Number assigned to each element (En)
• Difference in En helps determine the nature of
the bond: ionic or covalent
• Covalent bonds can be either nonpolar
covalent or polar covalent –
• This difference has Biological Consequences
Bond Polarity
A polar bond can be pictured using partial
charges:
+

H
Cl
2.1
 = 0.9
3.0
Electronegativity
Difference
Bond Type
0 - 0.5
Nonpolar
0.5 -1.7
Polar
1.7
Ionic
MOLECULAR SHAPE
• When atoms form a covalent bond, the valence
electron pairs arrange themselves to be as far
away from each other as possible.
• This change to the orientation of the valence
electrons is Hybridization.
• Symmetry of shape will also determine
polarity of molecule or functional group.
•Methane: CH4 – tetrahedral shape – equal 109.5 angle
between valence electrons; symmetrical; nonpolar
Ammonia: NH3 – pyramidal shape – equal 107 angle
between valence electrons; asymetrical shape –
polar molecule
To determine if a molecule is polar
or nonpolar, must consider both
electronegativity and shape
Which of the following is the essential
characteristic of a polar molecule?
a.Contains double or triple bonds
b.is formed at extremely low temperatures
c.contains ions as part of the structure
d.has an asymmetrical distribution of electrical
charge
e.contains the element oxygen
Van der Waals forces:
•intermolecular forces of attraction
Examples: London forces, dipole-dipole forces, hydrogen
bonds
London forces
- weak/temporary/
random charges
-gases at room
temperature
- volatile e.g.; octane
Dipole-dipole
-between polar
molecules
-stronger
- e.g.; HCl
• London forces are weak because (1.) partial charges are involved and
(2.) because they are temporary. They arise from the random
movement of electrons in atoms and molecules.
a) small collection of nonpolar molecules
b) a nonpolar molecule may temporarily have a slight excess of electrons
in one portion of the molecule
c) During the brief interval that these temporarily polar molecules exist,
they are attracted to each other
•Hydrogen bonds: strongest intermolecular bonds
Properties of water are due to hydrogen
bonds
I. They are responsible for the surface tension
properties of water.
II. They are responsible for the relatively high boiling
point of water.
III. They are responsible for adhesion- cohesion
IV. The make water a good heat sink.
V. The maximum density of water occurs at 4°C
Solubility
• The solubility of many molecules is determined by
their electronegativity and molecular structure.
• Sugars, such as glucose, have many hydroxyl
(OH) groups, which tend to increase the solubility
of the molecule.
• Molecules that lack polar covalent bonds, such as
lipids, clump together in water because they are
excluded from interacting with the polar groups.
Hydrophobic
http://programs.northl
andcollege.edu/biolog
y/Biology1111/animat
ions/hydrogenbonds.h
tml
…and hydrophilic
-“like dissolves like”;
--polar nature; excellent
solvent
-http://programs.northlan
dcollege.edu/biology/Biol
ogy1111/animations/disso
lve.html
Functional Groups
• Functional groups are clusters of atoms with
characteristic structure and functions.
• Generally, they are polar covalent groups
• They increase the solubility of a substance
in water.
• The hydroxyl (OH) groups in glucose are
what make this sugar soluble
Acids and Bases
• pH scale is used
to measure
• Is an inverse
logarithmic scale
• pH=7 is neutral
• pH  7 means
high H+
• pH > 7 means
high OH-
Conjugate Acids and Bases
• Weak/reversible
• Act to “absorb” protons or release proton to maintain
constant pH
If an acid has the formula CH3COOH, then the
conjugate base would be
CH3COO-.
Buffers are compounds that tend to neutralize the pH of
a solution by combining with either H+ ions or OH- ions to
keep the solution neutral. Buffers play a very important role
in most organisms, as many organisms cannot live at pHs
that are too acidic or too basic.
CH3COOH
< -------- >
CH3COO-
+ H+
The acetic acid molecule (CH3COOH) acts as a store of base
and acid ions.
The acetate ion (CH3COO-) acts like a base which accepts H+
and neutralizes them.
The hydrogen ion (H+) acts like an acid which accepts OH- and
neutralizes them.
In living organisms, buffers maintain pH in the cells
within a narrow range, allowing enzymes to function
Buffer Animation!
http://www.mhhe.com/physsci/chemistry/essentialchemistry/flash/buffer
12.swf
Review 1.1 ‘Chemical
Fundamentals’
Answer p.23 #4,6,7,8,10,12,14,15
• What type of intermolecular forces of attraction must be
overcome to melt each of the following solids?
A) ice, H2O (s)
B) iodine, I2 (s)
4 a) Hydrogen bonds must be broken to melt ice, H2O (s) , into water
H2O (l) .
b) London forces must be broken to melt I 2 (s) into I 2 (l) .
- the only intermolecular forces that hold nonpolar molecules
to one another
Is carbon tetrachloride, CCl 4 , and ammonia, NH 3 , polar or
nonpolar?
6. Based on VSEPR theory and electronegativity values,
carbon tetrachloride, CCl 4 , is nonpolar due to the
symmetrical arrangement of its polar C – Cl bonds and
ammonia, NH 3 , is polar due to the nonsymmetrical
arrangement of its polar N-H bonds.
Why is table salt, NaCl (s), soluble in ethanol, CH 3 OH (l), but
not soluble in gasoline, C 8 H 18 (l) ?
7. Table salt, NaCl (s), is soluble in ethanol, CH 3 OH (l) ,
because Na + and Cl – ions are attracted to polar ethanol
molecules.
Na + and Cl – ions are not attracted to nonpolar gasoline
molecules (C 8 H 18 (l) ).
What is the difference between a weak acid and a dilute
solution of a strong acid?
• 8. A weak acid only partially dissociates to release
H+ ions, while a strong acid completely dissociates.
Describe the components of a buffer and the role each plays in
helping maintain a constant pH.
10. A buffer is formed from a weak acid and a weak
base in approximately equal concentrations. The
weak acid will donate a hydrogen ion to a base,
neutralizing it, and its conjugate base will accept a
hydrogen ion form an acid, neutralizing it.
What is the difference between ionic and polar covalent
bonds?
12. Ionic bonds are formed because of a complete transfer of
electrons from one element to another element.
Polar covalent bonds result from the unequal sharing of
electrons between two different elements.
1. Hydrophobic: the tendency of nonpolar molecules to
exclude water.
Hydrophilic: the tendency of polar and ionic substances
to dissolve in water.
a) C6H 6 (l) is …
hydrophobic
b) C2H5OH (l) is …
hydrophilic.
c) CCl 4 (l) is …
hydrophobic
15. What property of water accounts for each of the
following observations?
a) A steel sewing needle floats on water but a large steel nail
sinks.
A steel sewing needle floats on water because the
surface tension of the water holds it there, while a
large steel nail sinks because the force of gravity on
the nail is greater than the surface tension of the water.
b) Dogs pant on a hot summer day.
Dogs pant to cool their bodies. The evaporation of water requires
heat, due to its high latent heat of evaporation, which it gets from
the dog’s tongue.
c) Water creeps up the wall in a flooded room.
Water creeps up the walls of a flooded room due to the cohesion of water
molecules to molecules in the wall because of hydrogen bonding.
d) Hands are usually washed in water.
Hands are usually washed in water because water is considered the
universal solvent and most substances will be dissolved and washed
away.
DAY 3 - Carbohydrates. Structure/function. Biological
importance. Model kits: build glucose, maltose, amylase,
glycogen and cellulose. Relate structure to properties to
function
1.2 The Chemicals of Life
The following structural formula is
representative of which functional group?
a.sulfhydryl
b.carboxyl
c.hydroxyl
d. amino
e.carbonyl
carboxyl
The following structural formula is
representative of which functional
group?
a.sulfhydryl
b.carbonyl
d.hydroxyl
d.amino
e.carboxyl
AMINO
The following structural formula is
representative of which functional group?
a.sulfhydryl
b.carbonyl
c.hydroxyl
d.amino
e.carboxyl
CARBONYL
Biological macromolecules
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids
Anabolic reactions
•Require energy “endothermic reaction”
•Produce big molecules
•By removing water and forming new covalent bonds
(dehydration synthesis)
•Require enzymes
Catabolic reactions
• Produce energy: exothermic
• Break big molecules into smaller
• Adding water to break covalent bonds (hydrolysis
reactions)
• Require enzymes
CARBOHYDRATES
[CH2O ]n
•
•
•
•
Monosaccharides: 1
Disaccharides: 2
Oligosaccharides: 3 – 10
Polysaccharides: greater than 10
Function
1. Energy ~ glucose
2. Longer term energy needs/storage ~
glycogen (animals) and starch (plants)
3. Structural ~ cell wall of plants (cellulose)
4. Recognition & communication (cell surface
markers & identification of self vs non-self~
glycoproteins)
carbohydrates…
• Classified based on
– Size of base carbon chain
– Number of sugar units
– Location of C=O
– stereochemistry
Monosaccharides
(various isomers – same chemical formula;
different chemical and physical properties)
Some important monosaccharides
• D-glyceraldehyde: simplest sugar
• D-glucose: Most important in diet; common
names include dextrose, grape sugar, blood sugar
• D-fructose: sweetest of all sugars
• D-galactose: Part of milk sugar
• D-ribose: used in RNA
Glycosidic linkages (ether): covalent bonds
holding monosaccharides to one another
Dehydration synthesis (mostly 1-4 linkage)
- starch
-glycogen
-cellulose
Several simple sugars attached to one another
In humans the function of glycogen is to keep glucose
available.
Glucose in Water Animation
• http://www.stolaf.edu/people/giannini/flasha
nimat/carbohydrates/glucose.swf
Based on location of C=O
• Aldose
– Aldehyde C=O
• Ketose
– Ketone C=O
Steochemistry: study of the spatial
arrangement of molecules
• Stereoisomers have
– The same order and type of bonds
– Different spatial arrangements
– Different properties
– Many biologically important chemicals, like
sugars, exist in stereoisomers.
Enantiomers molecules that have opposite spatial
configuration and are optically active.
Day 4: Lipids
• Lipids. Structure/model of fatty acid, glycerol,
triglyceride. Saturated, unsaturated, cis/trans:
properties and function. Steroids, waxes and
phospholipids.
Homework
• Read and summarize proteins for next class.
• http://www.tvdsb.on.ca/westmin/science/sbioac/bioc
hem/triglyc.htm
• Lipids Animations!
• http://www2.nl.edu/jste/lipids.htm
Lipids: Also called Fats and Oils
Lipid Facts
• Fat: Solid at room temperature
• Oil: Liquid at room temperature
• Contribute 30-50% of calories for Americans
• Soluble in organic solvents, i.e., not soluble in
water (They are all hydrophobic)
• Lipids are primarily consumed for energy
• Diverse groups: no basic sub-unit
Function
1. Energy storage [fats] long-term (2x energy of CHO’s)
2. Cushions/protects organs e.g.; kidney, reproductive organs,
etc.
3. Insulation: helps maintain constant internal temperature
4. Structural: cell membrane
-phospholipid
- cholesterol (fluidity to memb)
5. Vitamins and Hormones (regulation of biological processes)
-steroids
-testosterone, estrogen, progesterone
-vit. D (co-enzyme)
6. Waxes: waterproof/protective coating
When a molecule of glycerol reacts with one or
more fatty acids an ester linkage results. The
formation of this linkage is a result of a reaction
between an alcohol and a carboxylic acid
Formation of a triglyceride
Fatty Acid Nomenclature
Based on:
• Number of carbons
• Number of double bonds
Oleic Acid
Saturated
• No double bonds
• Solid at room temperature
• Implicated in coronary heart disease (CHD)
• Meats, dairy
Unsaturated
• Has double bonds
• Fluid at room temperature
• Less stable to off flavor development
• Vegetables, legumes, fish
LIPIDS
Saturated: only single
bonds
Unsaturated: double
bonds between 1 or
more carbons
• Polyunsaturated: 2-5 double bonds
• Highly Unsaturated: >5 double bonds
• Omega 3 Fatty Acids
– Good for reducing CHD
– High in fish
Linolenic Acid, an Omega 3 Fatty Acid
Micelle
- fatty acids are the main
component of soaps, where
their tails are soluble in oily
dirt and their heads are
soluble in water to emulsify
and wash away the oily dirt
(However, when the head
end is attached to glycerol to
form a fat, that whole
molecule is hydrophobic)
Phospholipids
• Modified fatty acid
• Two fatty acids tails and a cholinephosphate head
• Tails are hydrophobic
• Head is hydrophilic
• Cell membrane
(4 ring compounds)
Cholesterol
Why is cholesterol important in the
body?
• Hormone production
• Membranes
• Vitamin D
• Absorption of fats
Foods high in cholesterol
• Organ meats
• Eggs
• Shellfish
Waxes
• Extremely hydrophobic
• Cutin: cuticle of leaf
When one fat molecule is broken down to glycerol and fatty
acids, the number of hydroxyl ions consumed in order to
neutralize the fatty acids would be
a.0,
b.3,
c.1,
d.4,
e.2
Fat uses in Foods
Flavor
• Fried Foods
• Popcorn
Texture
• Shortening (Flakiness)
• Moistness
Stabilizers (emulfsifiers)
• Lecithin
• Mono and diglycerides
Relationship of Fat and
Cholesterol on CHD
• CHD is No. 1 killer of
Americans
• Approximately1 million
deaths/year
General Agreement
• Cholesterol and tryglycerides
build up in arteries and
reduce blood flow to heart.
Hypothesis
• Reduce cholesterol and fat in
diet and reduce CHD
Issues w/ Fat and CHD
Cholesterol not only Factor in CHD
• Heredity
• Stress
• Smoking
Response from Industry
Theory: Produce fat-like
substance that has reduced
metabolism
Examples
– Olestra - sucrose polymer
• Expected for use in all types
of foods
• Issues: Anal leakage and
vitamin loss
EXPERTS SAY...
• Lower fat intake to 30% of daily calories
• Consume “proper amount” of fatty acids in diet
• Have approximately 1:1.5:1 ratio of saturated,
monounsaturated and polyunsaturated fats
• Dietary fiber may be of some benefit
• Some suggest increase intake of Omega 3 Fatty
Acids
– May reduce blood cholesterol
Day 5: Proteins
• Functions. Amino acid structure and properties of R groups.
Primary, secondary, tertiary and quaternary structure and
bonds.
Homework:
• Read and summarize nucleic acids
• http://www.tvdsb.on.ca/westmin/science/sbioac/biochem/am
ino.htm
Proteins
Next to water, protein is the major component of
living cells!
The 20
amino acids
– see pg. 42
Polypeptide structure - Animation
http://science.nhmccd.edu/biol/dehydrat/dehydrat.html
Essential Amino Acids
• Humans can not synthesize them; they are
dietary requirements (there are 8)
Protein structures Animation
http://www.stolaf.edu/people/giannini/flashanimat/proteins/protein%20structure.swf
Primary
Structure
"The sequence
of amino acids in
the polypeptide
chain."
Secondary
structure
The Helix
nature of wool is
what makes it
shrink.
The pleated sheet structure is often found in many structural
proteins, such as "Fibroin", the protein in spider webs.
Tertiary
structure
Globular proteins
-spherical in nature
-Common globular proteins include egg albumin, hemoglobin, insulin,
and many enzymes.
Quaternary Structure
Proteins when heated can unfold or "Denature". This loss of three
dimensional shape will usually be accompanied by a loss of the
proteins function. If the denatured protein is allowed to cool it will
usually refold back into it’s original conformation.
Dipeptide hydrolysis
Day 6
Nucleic acids: DNA and RNA: structure and differences. Bonds in
DNA. Nucleoside, nucleotide, purine pyrimidine. Other nucleic acids:
ATP, NAD, NADP, FAD
p.56 #1,3,4,5 ,6,9,10, 11,13,14, 16 ,17,18,19
Base
pairing
in DNA
anitiparallel
Nucleotides (Both Sides of Double Helix)
Adenosine triphosphate (ATP):
major energy carrier
Coenzyme A
(CoA)
Flavin
Adenine
Dinucleotide
(FAD)
Nicotinamide
Adenine
Dinucleotide
(NAD+)
Nicotinamide
Adenine
Dinucleotide
Phosphate
(NADP+)
PRACTICE QUESTIONS
A) Structurally, a sulfhydryl group is most similar to
which of the following?
a.carbonyl,
b.hydroxyl,
c.carboxyl,
d.amino,
e.acetyl
B) A nitrogen atom would be found bonded to a
hydrogen atom in which of the following functional
groups?
a.sulfhydryl, b.carbonyl,
c.hydroxyl,
d.amino,
e.carboxyl
C) In terms of maintaining the shape of an enzyme, the
strongest bonds involved are
a. covalent (disulfide) bonds,
c.dipole-dipole interactions,
e.ionic interactions
b.hydrogen bonds,
d.hydrophobic bonds,
D) Which
of the following functional groups would be
found in a monosaccharide?
a. carbonyl and hydroxyl,
c.glycosidic and hydroxyl,
e.carboxyl an amino
b.carboxyl and carbonyl,
d.hydroxyl and sulfhydryl,
E) Of the following, which is not considered to by a
polymer?
a. cellulose,
b.protein,
c.RNA,
d.fat,
e.starch
Name Of Reaction
Summary Of Changes
dehydration
synthesis
(condensation)
two molecules joined; water
removed from the point
where the molecule join
synthesis of
macromolecules for
storage of energy or
information
hydrolysis
large molecule split into two
smaller ones; water added at
the point where the
molecules split
digestion: breakdown to
smaller molecules of
fewer kinds for active
transport
redox
hydrogen atoms or electrons
transferred between
reactants
energy storage and
transfer in cells
acid + base – > water and
salt
stomach acid neutralized
by bile and sodium
bicarbonate in pancreatic
juice in the duodenum
neutralization
Example
TEXT ANSWERS p.56
1. Why are hydrocarbons all nonpolar molecules?
Hydrocarbons are all nonpolar molecules because
of the symmetrical arrangement of their C-C and CH bonds.
2. List the elements found in all carbohydrates,
indicating the atomic ratio in which they are found.
carbon, hydrogen, and oxygen in the ratio 1:2:1
3. A) Define functional group.
b) What advantage is conferred to biological
molecules by having functional groups?
A) In organic chemistry, a functional group is a
reactive cluster of atoms attached to the carbon
backbone of organic molecules.
B) Biological molecules with functional groups are
more reactive than molecules without functional
groups.
4. Why are monosaccharides more soluble in water
than are triacylglycerols?
Monosaccharides are more soluble in water than
triacylglycerols because of the large number of
asymmetrical polar bonds.
Carbohydrate (or
derivative)
Main function
Glucose
Primary source of energy in
most living organisms
Starch (amylose)
Energy storage in plant cells
Chitin
Structural carbohydrate in
insects, crustaceans, and
mushrooms
Cellulose
Plant cell wall component
glycogen
Energy storage in animal cells
6. Describe the difference between a condensation
reaction and a hydrolysis reaction.
A condensation (dehydration synthesis) reaction
releases a water molecule in an anabolic reaction,
while a hydrolysis reaction adds a water molecule
across a chemical bond in a catabolic reaction.
9. Why are glucose and galactose monomers?
Glucose and galactose are isomers because they have
the same chemical formula (C 6 H 12 O 6 ) but different
arrangements of atoms.
10. Why do animals use lipids instead of carbohydrates as
energy-storing molecules?
First, lipids contain more energy per gram than
carbohydrates.
Secondly, lipids offer greater thermal insulation than
carbohydrates and allow animals to survive in frigid
environments.
11. A) How many fatty acids are attached to a glycerol
molecule in a triacylglycerol? In a phospholipid?
b) What two functional groups react when a fatty acied bonds
to a glycerol molecule?
A) Three fatty acids are attached to a glycerol
molecule in a triacylglycerol and two fatty acids are
attached to a glycerol in a phospholipid.
B) Hydroxyl and carboxyl groups react when a fatty
acid molecule bonds to a glycerol molecule.
13. Distinguish between a polypeptide and a protein.
A polypeptide refers to a single chain of amino acids
with primary, secondary, or tertiary structures,
while a protein consists of one or more polypeptide
chains twisted and folded together into a specific
shape.
The amino acid sequence of a polypeptide chain
determines the three-dimensional shape of the protein.
14. B) The functional group found on the R-group side
chain is a carboxyl group.
C) This amino acid is acidic because of its acidic
functional group.
16. State two similarities and two differences between an
alpha helix and a beta-pleated sheet.
Similarities between alpha-helix and beta-pleated
- they determine the secondary structure
- they occur because of hydrogen bonding
Differences
- the type of structure formed (spiral helix vs. flat sheets)
- alpha helix is formed by hydrogen bonding between successive amino
acids along a polypeptide chain, while a beta-pleated sheet is formed
from hydrogen bonds between two parallel polypeptide chains.
17. A) List the four types of bonds that stabilize a protein’s
tertiary structure.
b) Which of these bonds is the strongest?
A) The four types of bonds that stabilize tertiary
structure are:
- hydrogen bonds (a type of van der Waals force),
- disulfide bridges (covalent bonds),
- ionic bonds, and
-hydrophobic interactions ( a type of van der Waals
force).
B) The strongest of the above are the disulfide bridges
because they are the only covalent bond.
18. Describe two differences between RNA and DNA
nucleotides.
Two differences between RNA and DNA are the
sugar found in the nucleotide, RNA has ribose and
DNA has deoxyribose, and that RNA is single
stranded while DNA is double.
Also DNA contains the nitrogenous base thymine,
(T) while RNA contains uracil (U) instead.
19. State the rule for base pairing in DNA, indicating the
number of hydrogen bonds that forms in each case.
The rule for DNA base pairing is adenine with
thymine, forming two hydrogen bonds, and cytosine
with guanine, forming three hydrogen bonds.
DAY 7: SEE HANDOUT
1.3 An Introduction to Metabolism (DAY 8)
Read section 1.3 p.58-68 Answer #2,3,6,7,8
Thermodynamics: the
science of energy
transformations (flow of
energy through living and nonliving systems)
All living things require ENERGY –
which is the capacity for doing work
Forms of energy:
•thermal
•light
•chemical
•electrical
KINETIC ENERGY
• Energy of motion:
–Falling water
–Pistons in a car engine
–Skier going down a hill
– examples on a molecular
scale include the energy of
vibrations, random
diffusion, and heat.
POTENTIAL ENERGY
• stored energy
• Example:
Molecules of
glucose have
potential energy,
stored in bonds
FIRST LAW OF THERMODYNAMICS
• Energy can neither be created nor destroyed,
but can be transformed from one form to another.
• E.g.; during photosynthesis, light energy from the
Sun is transformed into chemical energy stored in
the bonds of glucose
• During cellular respiration, the energy in
the bonds of glucose is released and is
transformed into new molecules, motion,
and heat energy.
The Second LAW OF THERMODYNAMICS:
Every energy transformation increases the
entropy of the universe.
• There is ALWAYS
some loss of useful
energy.
The second law of thermodynamics
In all processes or reactions, some of the energy
involved irreversibly loses its ability to do work.
or
In any reaction the amount of molecular
disorder always increases
Entropy is a measure of the randomness
or disorder in a collection of objects
Entropy increases…
• when solids become liquids or gases
• Complex molecules react to form simpler molecules
(catabolic reactions)
• During diffusion
Living systems seem to break the
second Law of Thermodynamics
• Anabolic processes
in cells build
highly ordered
structures (e.g.;
proteins and
DNA) from a
random assortment
of molecules
(amino acids and
nucleotides) in the
cell fluids.
• On a large scale, living organisms build and
maintain highly ordered structures such as cells,
tissues, organs and systems, as well as nests, webs
and homes.
• All of these changes cause the universe to become a
little more ordered.
But these anabolic processes are coupled to catabolic
processes
• Which release free energy
and thermal energy and
increase the entropy of the
universe.
• Living organisms create
order in a local part of the
universe at the expense of
greater a greater amount of
disorder in the universe as
a whole.
Free energy
It is clear that
we should be
concerned only with
energy available to do
useful work, so-called
free energy or Gibbs
energy.
Josiah Willard
Gibbs
(1839 - 1903)
The relationship between energy
change, entropy change, and the
temperature of a reaction is best
described in terms of free energy
A)Exothermic Reactions
• Produce energy (exergonic reactions)
• Tend to increase entropy (therefore,
spontaneous)
–
- delta G value
• E.g.; cellular respiration
Exothermic Reaction
During this part of the reaction the molecules are said to be in a
transition state.
Activation Energy :amount of energy needed to strain
and break the reactants' bonds in a biochemical
reaction
B) Endothermic Reactions
•Require energy (endergonic reactions)
•Tend to decrease entropy (because they create
big/organized molecules)
•Are not spontaneous
–+ delta G values
•E.g.; photosynthesis
REDOX REACTIONS
• Biochemical reactions are essentially energy
transfers.
• Often they occur together, "linked" in
oxidation/reduction reactions.
• Reduction is the gain of an electron. Sometimes
we also have H ions along for the ride, so
reduction also becomes the gain of H.
• Oxidation is the loss of an electron (or hydrogen).
• In oxidation/reduction reactions, one chemical is
oxidized, and its electrons are passed (like a hot
potato) to another chemical.
• OIL RIG (oxidation is loss, reduction is
gain)
• Many metabolic processes (glycolysis,
Kreb's Cycle, and Electron Transport
Phosphorylation) involve the transfer of
electrons by redox reactions.
a.the synthesis of glucose in a plant
All but one of the following are examples of oxidizing reactions.
Which one is not an oxidizing reaction?
a.the synthesis of glucose in a plant
b.a log burning in a fireplace
c.the breakdown of glucose in a cell
d.a newspaper turning yellow as it ages
e.the rusting of a nail
In the following chemical reaction, a oxidation/reduction
reaction is occurring.
C6H12O6 + 6 H2O + 6 O2  12 H2O + 6 CO2
because electrons are transferred from
one substance to another
Chemical intermediates - Nucleotides
Some compounds contain high-energy bonds, e.g. the bond
between phosphate groups of tri- and diphosphate
nucleotides
Physical energy intermediates
An equally common way of storing energy is in the form of
potential energy, as an electrical gradient (potential),
concentration gradient, or pH gradient.
Some proteins (e.g. cotransporters) are able to utilize the flow
of ions directly to power their endergonic reactions.
ANSWERS - p.58-68
1.3 An Introduction to Metabolism
2. Identify each of the following activities as either anabolic or
catabolic.
A) protein synthesis is anabolic
b) Digestion is catabolic
c) DNA synthesis is anabolic
d) Photosynthesis is anabolic
e) Cellular respiration is catabolic.
3. Metabolism represents the sum of all anabolic and
catabolic reactions in a cell or organism.
6. A) an arm raised: a decrease in entropy because
potential energy is increased.
b) Protein is digested into amino acids in the
duodenum: an increase in entropy, because a large
number of amino acids ae more randomly arranged
than in a protein molecules in which the amino acids
are attached to one another in a particular sequence.
c) Chromosomes move along spindle fibres: the cells
free energy is used to move chromosomes into a
more ordered arrangement; entropy decreases as
organization increases.
6. D) oxygen diffuses into alveoli in the lungs: an
increase in entropy as oxygen molecules trapped in
alveoli diffuse into capillaries and move randomly
through the circulatory system.
e) A cell divides: an increase in entropy as the system
is becoming more random, and much of the cell’s
free energy is used in cell division; two cells
represent a more random arrangement of objects
than a single cell
7. Gibbs free energy represents energy that can do
useful work.
8. A) Heat death of the universe refers to the state
where all the particles and energy of the universe
will move randomly, unable to do useful work. All
energy will still be present, but it will be uniformly
distributed and unable to apply a push or pull to
anything.
b) Heat death of the universe is related to the death of
an organism because a dead organism is unable to
do work. Energy is still present, but it cannot
perform the work that is necessary to keep the
organism alive.
1.4 ENZYMES
An enzyme is a
biological
protein-based
catalyst
Enzyme nomenclature
Enzymes are divided into 6 groups based on the
chemical reactions they catalyze.
1.
2.
3.
4.
5.
6.
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases (synthetases)
Enzymes online tutorial
• Excellent animations:
• http://www.lewport.wnyric.org/jwanamaker/animati
ons.htm
• http://www.northland.cc.mn.us/biology/Biology1111
/animations/enzyme.html
• http://highered.mcgrawhill.com/sites/0072437316/student_view0/chapter8/a
nimations.html#
Substrate: the
reactant that an
enzyme acts on
when it
catalyzes a
chemical
reaction
The Induced-fit model of enzyme-substrate
interaction describes a protein as a dynamic molecule that
changes its shape to better accommodate the substrate
Factors Affecting Enzyme Activity
1.Temperature
2. pH
3. Substrate Concentration
37C
is the optimum
temperature in
most living
systems
(at high/temperatures
enzyme function is
altered ~denatured
enzyme)
- most enzymes work best at pH ~7 (narrow range)
- however, some such as “pepsin” have a pH of ~3
- changing the pH will alter the enzymes 3D shape
pH
Substrate Concentration
• As concentration increases, the rate of
reaction increases
• Maximum occurs when all the enzymes are
working
cofactors
•Inorganic atoms
(Zn, Ca, Fe,…)
which bind
temporarily to
enzyme
coenzyme
•Organic molecules
•E.g.; vitamins
•Necessary to activate enzyme and allow
it to bind to substrate
•Also can help weaken bonds in
substrates
Controlling Enzyme Activity
•
1. Regulating transcription/translation .
–
By regulating transcription/translation,
production of enzymes can be turned
off/on.
– Some end products can act as transcription
factors and inhibit the
transcription/translation of enzymes
• 2. Competitive Inhibition : A substrate mimic
(molecule that has the same configuration as the
substrate) can enter into ACTIVE SITE and block
enzyme action.
• Some antibiotics are competitive inhibitors
– E.g.; HIV (protease inhibitors)
– Penecillin (inhibits a bacteria transpepsidase: cell wall is
not built properly)
• When bind permanently (poisons or toxins)
• When bind temporarily (can be “disloged” by
increasing concentration of substrate)
Inhibitors
• 3. Allosteric Inhibition (Feedback
inhibition). Allows an enzyme to be
temporarily inactivated.
• Binding of an allosteric inhibitor changes
the shape of the enzyme, inactivating it
while the inhibitor is still bound.
• This mechanism is commonly employed in
feedback inhibition. Often one of the
products of a series of reactions act as an
allosteric inhibitor and blocks the pathway.
• AKA non-competitive inhibition
3.
Regulation of Enzyme Action
4. Allosteric Activators
• Substances bind to an allosteric site on
enzyme and increase efficiency
a) Substrate and
enzyme
b) Competitive
Inhibitor
c) Non competitive
inhibitor
Applications of enzymes for
commercial or industrial use!
a. starch hydrolysis for the food industry
b. proteases to coagulate milk for the manufacture of
cheese
c. removal of lactose from dairy products for lactose
intolerant people
d. proteases added to detergents to remove proteinbased stains
Enzymes are _________________________ catalysts, and as
such they _________________________ a chemical reaction
without being _________________________ in the process.
Enzymes work by reducing the
_________________________. The
_________________________ is the reactant that an enzyme
act on. This reactant binds to a particular spot on the enzyme
known as the _________________________. Enzymes are
very _________________________ for the reactant to which
they bind. The names of enzymes usually end in
_________________________.
ANS: protein, speed up, consumed, activation energy,
substrate, active site, specific, ase
Temperature and pH affect enzyme activity. As with all other reactions, enzymecatalyzed reactions _________________________ in speed with an increase in
temperature. However, as the temperature increases beyond a critical point, the protein
structure begins to get disrupted , resulting in _________________________ and loss
of enzyme function. Every enzyme has a(n) _________________________ temperature
at which it works best and activity tends to decrease on either side of this temperature.
Most human enzymes work best at around _________________________. Some
enzymes require nonprotein _________________________, such as zinc and
manganese ions. Other enzymes may require organic _________________________
such as NAD+ and NADP+. A variety of substances inhibit enzyme activity.
___________________________________ are so similar to the enzyme's substrate that
they are able to enter he enzyme's active site and block the normal substrate from
binding. This process is reversible and can be overcome be increasing the concentration
of the enzyme's substrate. Another class of inhibitors does not affect an enzyme at its'
active site, they are called ___________________________________ and their effect
cannot be overcome by adding more substrate.
ANS:
increase, denaturation, optimal, 37C, cofactors, coenzymes, Competitive inhibitors, noncompetitive inhibitors
Practice!
1. Define catalyst
• A chemical that speeds up the rate of
reaction without being consumed in the
reaction.
2. Draw a labeled free-energy diagram to illustrate the effect of an
enzyme on the activation energy of a hypothetical reaction. (Assume
it is an exergonic reaction.)
3. What is meant by the statement, “an enzyme cannot affect the freeenergy change of a reaction”?
• 5. How does an enzyme lower the activation energy
of a biochemical reaction?
The enzymes do this by bringing the substrates into the correct
geometry and by putting stress on the necessary chemical
bonds.
6. How do competitive enzyme inhibition and
noncompetitive enzyme inhibition differ?
A competitive inhibitor binds to the active site of an enzyme,
preventing the substrate(s) from binding. In this case, the
inhibitor competes with the substrate for the active site. A
noncompetitive inhibitor attaches to an enzyme at a binding
site other than the active site. This causes a conformational
change in the enzyme’s protein structure that causes a loss of
affinity of the active site for its substrate.
8. What happens to an enzyme after it has catalyzed a
reaction?
After an enzyme catalyzes a reaction, it will catalyze the same
reaction again.
For an exothermic reaction, H is negative.
For an endothermic reaction, H is positive.