Biology Journal 9/25/2014
Describe this chemical reaction in as much
detail as you can!
• Synthesis of two amino acids (aka monopeptides)
into a dipeptide.
• Condensation (because it makes H2O out of the H
and OH of the amino and carboxyl groups)
• Anabolism (because it is building a larger molecule
• It’s making a peptide bond (the bond holding amino
acids to each other in proteins, aka polypeptides)
Schedule
Thursday: review for 2.4 and 2.5
Quiz
Friday: 2.4 and 2.5 Quiz
Tuesday: 2.6 homework due
Wednesday: Notebooks
collected, for practice and
evidence!
Topic 2: Molecular biology (21 hours)
2.4 Proteins: Proteins have a very wide range of functions in living organisms.
Nature of science: Looking for patterns, trends and discrepancies—most but not all organisms assemble
proteins from the same amino acids.
Understandings:
• Amino acids are linked together by condensation to form
polypeptides.
• There are 20 different amino acids in polypeptides synthesized on
ribosomes.
• Amino acids can be linked together in any sequence giving a huge
range of possible polypeptides. Most organisms use the same 20
amino acids in the same genetic code although there are some
exceptions. Specific examples could be used for illustration.
• The amino acid sequence of polypeptides is coded for by genes.
• A protein may consist of a single polypeptide or more than one
polypeptide linked.
• The amino acid sequence determines the 3-D conformation of a
protein.
• Living organisms synthesize many different proteins with a wide
range of functions.
• Every individual has a unique proteome.
Applications and skills:
Application: Rubisco, insulin,
immunoglobulins, rhodopsin, collagen
and spider silk as examples of the range
of protein functions.
Application: Denaturation of proteins
by heat or by deviation of pH from the
optimum. Egg white or albumin
solutions can be used in denaturation
experiments.
Application: Proteomics and the
production of proteins by cells cultured
in fermenters offer many opportunities
for the food, pharmaceutical and other
industries.
Skill: Drawing molecular diagrams to
show the formation of a peptide bond.
Aims: Obtaining samples of human blood for immunological, pharmaceutical and anthropological studies is an
international endeavour with many ethical issues.
Topic 2: Molecular biology (21 hours)
2.5 Enzymes: Enzymes control the metabolism of the cell.
Nature of science: Experimental design—accurate, quantitative measurements in enzyme experiments
require replicates to ensure reliability.
Understandings:
• Enzymes have an active site
to which specific substrates
bind.
• Enzyme catalysis involves
molecular motion and the
collision of substrates with
the active site.
• Temperature, pH and
substrate concentration
affect the rate of activity of
enzymes.
• Enzymes can be denatured.
Applications and skills:
 Application: Methods of production of lactose-free milk and its
advantages. Lactase can be immobilized in alginate beads and
experiments can then be carried out in which the lactose in milk is
hydrolysed.
PRACTICAL
Design of experiments to test the effect of temperature, pH and
substrate concentration on the activity of enzymes. Students should be
able to sketch graphs to show the expected effects of temperature, pH
and substrate concentration on the activity of enzymes. They should be
able to explain the patterns or trends apparent in these graphs.
Theory of knowledge: Development of some techniques benefits particular human populations more
than others. For example, the development of lactose-free milk available in Europe and North America
would have greater benefit in Africa/Asia where lactose intolerance is more prevalent. The development
of techniques requires financial investment. Should knowledge be shared when techniques developed in
one part of the world are more applicable in another?
Enzymes (almost) always end in what 3 letters?
Identify the parts for each of the letters.
State what kind of reaction is occurring in as
much detail as you can.
A = Substrate
B = Enzyme
C = Active site
D = Enzyme-substrate complex
E = Products
This is the enzyme-catalyzed catabolic reaction of A
into E’s. We can’t say if it’s hydrolysis (but, it might
be)
What determines what the 3D
shape of a protein will be?
The sequence of amino acids!
These interact and fold up into the
final enzyme shape.
Make a drawing of a generalized
amino acid.
R group
(could be 20 different
things in human proteins)
Amine
(NH2)
Carboxyl
(COOH)
Alpha carbon
(the middle C where the R group is attached)
What is a proteome?
Just like a genome is all of the
genes an organism has
(ATCG’s), a proteome is all of
the proteins (sequence of
amino acids) that an organism
makes.
What is activation energy?
The energy required to start a
chemical reaction. The activation
energy converts the reactants
into a transition state, which then
progress to the products.
Activation energy is the energy which
must be put into reactants to break some
bonds to get a reaction started
Enzymes lower activation energy,
making reactions happen faster.
An Explosive Example…
These reactants (TNT) really
want to be the products (a
bunch of gasses). It just needs
the activation energy to do the
reaction….
Where does the activation
energy come from?
What does
the protein
insulin do?
Insulin is made by the pancreas. When
blood-sugar is high, it is released and
decreases the amount of glycogen
(blood sugar) in the blood and stores it
in the liver, or as fat.
Define what it means for a protein to denature.
When a protein loses its shape it is called denaturing. It is
irreversible. It can happen when the protein is exposed to:
Different
Different
Energy in Reactants/Products
What do enzymes have to do with activation
energy?
Intermediaries
Start
(reactants)
Activation Energy
Reaction Complete
(products)
TIME
Without
enzyme
With
enzyme
This graph shows the enzyme activity (rate of
reaction) for salivary amylase, which digests
starches in the mouth.
1. Why is the highest rate at 38°C?
2. Why does enzyme activity decrease rapidly
at temperatures higher than 38°C?
Optimum Temperature
Reaction rate
increases with
increase in
temperature, as
molecules move
faster
Amylase
denatures, and
quickly stops
facilitating
chemical
reaction
1. 38°C is the highest rate because the enzyme is optimized to
operate fastest at normal human body temperature.
2. At temperatures higher than 38°C, the enzyme denatures.
What does the
protein
RuBisCO do?
RuBisCO (Ribulose-1,5-bisphosphate
carboxylase/oxygenase) is a protein used in
carbon-fixation (taking carbon from the
atmosphere and making carbohydrates out of
it). It is found in most plants, and autotrophic
single-celled organisms. It’s probably the
most abundant protein on Earth!
State the effect of pH on enzyme
rate.
All enzymes have an optimal pH.
Deviation from this results in the
denaturaziation of enzymes, and
thus a reduction in reaction rate.
How is lactose-free milk made?
1. Adding lactase to
milk.
2. Running milk
through an apparatus
with immobilized
lactase.
Note: This can be done
to any substance to
treat it with an
enzyme!
Describe the lock and key model of enzyme
function.
Enzymes are specific to one (although sometimes multiple)
substrate. How?
1. Structurally: the 3D shape of the active site matches the
substrate
2. Chemically: the polar / nonpolar parts of the active match
the substrate
a.
b.
c.
d.
What kind of reaction is this?
Write out the reaction as words
Which are the reactants?
Which are the products?
+
→
+
H2O
a. What kind of reaction? Anabolic Condensation
b. Write out the reaction as words: below
c. Which are the reactants? fructose, glucose
d. Which are the products? sucrose, water
→
+
fructose
+
glucose
→
+
sucrose
+
H2O
water