Topic 2: Molecular biology (21 hours)

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Topic 2 Molecular biology (21 hours)
2.5 Enzymes Enzymes control the metabolism of the cell. 2.5 Enzymes Enzymes control the metabolism of the cell.
Nature of science Experimental designaccurate, quantitative measurements in enzyme experiments require replicates to ensure reliability. Nature of science Experimental designaccurate, 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.
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. 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? 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?
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Biology Journal 9/19/2014

• What is a rate? What is the rate we are
  measuring in this lab?

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Biology Journal 9/18/2014

1. What does a broken toothpick represent?
2. What represents the enzyme?
3. You need 3 to 5 people in your group. What does
   each one do?

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Biology Journal 9/22/2014
Describe the lock and key model of enzyme
function.

• Enzymes are specific to one (although sometimes
  multiple) substrate. How?
• Structurally the 3D shape of the active site
  matches the substrate
• Chemically the polar / nonpolar parts of the
  active match the substrate

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Some Jobs for this Experiment

1. Enzyme person who breaks the toothpicks
2. Organizer person who sets up the trial
3. Cleaner makes sure all materials are returned /
   disposed of after each trial
4. Timer keeps track of and announces time
5. Counter keeps track of number of broken
   toothpicks during trial
6. Recorder writes down data

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There are 3 Trials in this Experiment

• Rate and time
• Start with 100 toothpicks
• Lasts 180 seconds (3 minutes)
• Count number of toothpicks broken at 10, 20, 30,
  60, 120, 180 seconds
• Rate and concentration
• Start with different numbers of toothpicks (10,
  20, 30, 40, 50, 60, 70, 80, 90, 100) and 100
  paperclips.
• Lasts 20 seconds only
• Count number of toothpicks broken at end
• Rate and temperature
• Start with 10 toothpicks
• Time is now dependent variable (you measure how
  long it takes the enzyme to break all 10
  toothpicks)

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Biology Journal 9/17/2014

• What kind of reaction is shown?
• Write out the reaction as words
• fructose _______ ? ________ _______
• c. Which are the reactants?
• d. Which are the products?

?


H2O
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Biology Journal 9/5/2013

• 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

?


H2O
fructose glucose ?
sucrose water
Today we will learn how enzymes make this happen!
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Biology Journal 9/17/2014
What is a genome? What is a proteome? Do you
think all humans have mostly the same genome, or
naw? Do you think all humans have mostly the
same proteome, or naw?
Where could be some places that our biological
differences come from?
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Humans share over 99 the same DNA. DNA codes
for proteins, so our proteins are over 99
identical as well.
Our differences come from 2 things mutations,
and the recombination of genes during every
sexual reproduction!
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Review!
What is a catalyst?
Catalysts speed up chemical reactions (and
theyre not used up by the reaction)
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2.5 Enzymes
Hair is a protein called Keratin
Enzymes speed things up.
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Enzymes Specially shaped proteins that are
catalysts. Enzymes are specific, like a lock and
key.
Enzymes make reactions fast! (but they usually
dont blow up thatd be bad for a living thing)
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Energy-Time Graph for a Chemical Reaction
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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?
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Substrate the reactant that goes into the
enzyme Active site where the substrate bonds on
the enzyme Products what the substrate turns into
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Enzymes do not run out. They keep making the
product over and over.
How is this chemical reaction different from the
previous one?
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Enzymes are specific

• Each enzyme catalyses very few reactions

• Each enzyme acts on only one (or a limited
  number) of substrates

• Each enzyme will only act on substrates that
  will fit into its active site

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Like any protein, an enzyme can denature (lose
its shape and thus stop working).
Active site fits around substrate
Active site no longer fits round substrate
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Enzymes end in -ase (almost always)
What do you think these enzymes
do? Protease Lactase Lipase Cellulose
synthase Glucose phosphotransferase
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Sketch this picture into your journal and label
the parts. Describe what kind of reaction is
occurring in as much detail as you can.
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A Substrate B Enzyme C Active site D
Enzyme-substrate complex E Products This is
the enzyme-catalyzed decomposition of A into Es.
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Your Assignment

• Read the entire toothpickase lab. Re-read until
  you understand the directions completely!
• Do all of the parts of the lab in your graph
  notebook through Data lab group data.
  Specifically
• Write the title
• Do the pre-lab questions
• Write the first heading
• Write the Procedure for this part
• Write Data class data and prepare a data table
  that you will have ready to fill in tomorrow!

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Enzymes are an example of a kind of molecule
called a protein. Tissues like hair, muscle, and
skin are also made out of this polymer the
polymer is composed of monomers called amino
acids.
Enzymes are an example of a kind of molecule
called a ______. Tissues like hair, muscle, and
skin are also made out of this polymer the
polymer is composed of monomers called
___________.
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Enzymes (almost) always end in what 3 letters?
ASE
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Do all enzymes catalyze (speed up) decomposition
reactions?
No! What kind of reaction is this?
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Are enzymes consumed in a chemical reaction?
What happens to the enzyme in this picture? What
happens to the product?
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Describe the lock and key model of enzyme
function.

• Enzymes are specific to one (although sometimes
  multiple) substrate. How?
• Structurally the 3D shape of the active site
  matches the substrate
• Chemically the polar / nonpolar parts of the
  active match the substrate

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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 temperatures
• Different pHs

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All enzymes have an optimal temperature and pH.
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What is activation energy? How does an enzyme
catalyse a reaction?
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What is lactose intolerance?
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A person with lactose intolerance is not
producing the enzyme lactase.
Lactase is the enzyme that catalyzes the
catabolic hydrolysis of lactose into galactose
and glucose.
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Percentage of Population with Lactose Intolerance
Where are you from? The chances of having
lactose intolerance are genetically tied to
cultural and historical uses of animal milk as a
food source. For example, in Northern European
culture cow milk was used as a food source for
many centuries in South America, it was not.
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• To cope with lactose intolerance
• Take a lactase supplement, made by a genetically
  engineered fungus.
• Drink lactose-free milk.

Aspergillus niger is also known as black mold.
Youve most likely seen it before.
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• Lactose-free milk can be made by
• Adding lactase to milk.
• Running milk through an apparatus with
  immobilized lactase.

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Scientific Method
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What is the dependent and independent variables
in this experiment? What could be controls?
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• Independent Variable The cause that is more
  directly controlled or measured. Graphed on x
  axis.
• Dependent Variable The effect you measure.
  Graphed on y axis.
• Independent causes Dependent
• The dependent variable depends on the
  independent variable
• Controls Anything that could effect the outcome
  of the dependent variable.
• Some controls can be controlled (purposely kept
  constant), but some can only be acknowledged as
  variables impacting the data.

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Independent Variable