Download Class4 1-6 Win16 Enzymes and Nucleic Acids Notes

Exam format for Bio200
•  Step 1: The ‘Public Version’
–  60% or more of test released one week prior to exam-time
–  This is the basis for an extra RQ question (due Monday)
•  Step 2: Understand & Edit
–  Help to produce a readable and correct final version
–  Public Version with Edits will be released on the pre-exam Tuesday
•  Step 3: Study
–  A lot.
–  In ways that maximize your time.
•  Step 4: Perform
–  Friday exam
–  Overcome the stress and do the best you can.
•  Step 5: Grade
–  And re-grade
–  Points: 5 pts for submitting a regrade (or a null) on one of the first four exams
•  Step 6: Understand your performance and adjust for success
REACTION MECHANISM
1.
2.
3.
6.
5.
4.
Respond at PollEv.com/biology200
(or text BIOLOGY200 to 22333 once to join)
Clicker Question #1
The His119 side chain:
1. 
2. 
3. 
4. 
5. 
6. 
Is part of a single amino acid
Can lose a proton
Can perform a condensation reaction
Is part of a tertiary structure
Cannot gain a proton
Has a completely useless C=N portion
Clicker Question #2
The water molecule shown in Panel 5:
1. 
2. 
3. 
4. 
5. 
6. 
Is necessary to regenerate the enzyme
Is the most important substrate
Is rarely found near the enzyme
Slows the reaction rate
Is more polar than a normal water molecule
Is in the active site of the enzyme
Clicker Question #3
How many times can an enzyme catalyze a
particular reaction?
You can assume there are infinite substrate
molecules present. Choose the best answer.
1.  1
2.  3-5
3.  An infinite number of reactions
4.  Many, but not infinite
5.  It depends on the enzyme
6.  Only 1 per type of substrate, but it can
catalyze many different kinds of chemical reactions
Peer Instruction
Why is this enzyme sensitive to changes in pH?
Why might this enzyme be sensitive to change in
temperature?
If you could change the amino-acids in this
enzyme, how would you change them to make
the enzyme functional at higher temperatures?
You will be analyzing β-galactosidase activity in
lab next week.
β-galactosidase is an enzyme
that can break down lactose.
Why would enzyme supplements be
more useful for lactose-intolerant
individuals than glucose supplements?
7
Peer Instruction
Competitive inhibition directly blocks the active site.
Competitive
inhibitor
Substrate
Enzyme
When a regulatory molecule binds the active site, the substrate cannot bind.
When the concentration of competitive inhibitors goes up,
the reaction rate tends to go (up?/down?).
Increasing the binding strength of the substrate for the enzyme
would (increase?/decrease?) the competitive inhibition.
Peer Instruction
Allosteric regulation occurs when a regulatory molecule
binds somewhere other than the active site.
Substrate
Enzyme
or
Regulatory
molecule
1) When the regulatory molecule binds to a different site on the enzyme,
it induces a shape change that makes the active site either:
Left) more available to substrate, or Right) less available to substrate
Which allosteric regulator (right or left) increases the reaction rate?
Clicker Question #4
Can a single protein have more than one allosteric site?
Why or why not?
1. 
2. 
3. 
4. 
No, more than one would be too complicated.
No, multiple sites would interfere with each other.
Yes, every amino acid is always an allosteric site.
Yes, any region that could bind another molecule
is a potential allosteric site.
Friday, January 6th, 2017
Class 4 Learning Goals
Nucleic Acids
•  After this class, you should be able to:
–  Identify the structural features of nucleic acid monomers that:
–  Form the bonds in polymers
–  Form the bonds in base pairs
–  Contain charge distribution energy
–  Give the monomer a specific identity (A, G, U, etc)
–  Give the nickname for a nucleic acid from a simplified structure
–  Analyze the mechanism through which ATP provides energy to
biochemical reactions
–  Describe the double-helix structure of DNA and RNA in terms of
phosphodiester bonds, base pair bonds and polarity
–  Predict nucleotide abundances of A, T, G and C given the
abundance of any one of them.
Peer Instruction
Identify the:
phosphate group
sugar
nitrogenous base
Is this from a ribonucleotide or a deoxyribonucleotide?
How do you know?
In life on Earth, nucleic acid monomers are
named A, T, G, C and U. Which bonds with which?
The Nucleotide: Energy Storage Molecule
ATP
The addition of phosphate
groups raises the potential
energy of the monomer
Naming:
__P= tri-phosphate (could be
mono- or di-phosphate A=adenosine base
N=____ base
______=any triphosphate
deoxynucleotide base
Why ATP is Useful
The problem with endothermic biological reactions
+
Free
Energy
Reaction Progress
Why ATP is Useful
Phosphate hydrolysis is massively exothermic
+
Free
Energy
Reaction Progress
Why ATP is Useful:
Enzymes combine reactions to become exothermic (aka exergonic)
+
+
+
+
Free
Energy
Reaction Progress
Building DNA: The Double Helix
Cartoon of base pairing
Cartoon of double helix
Double-stranded DNA: Base Pair Bonding
Only purine-pyrimidine pairs fit inside the double helix.
Hydrogen bonds form:
between G-C pairs and A-T pairs.
Purine-pyrimidine pair
JUST RIGHT
Purine-purine pair
NOT ENOUGH SPACE
Pyrimidine-pyrimidine pair
TOO MUCH SPACE
Space inside sugarphosphate backbones
Sugar-phosphate backbone
5ʹ
3ʹ
Guanine
Cytosine
Adenine
Thymine
3ʹ
5ʹ
DNA contains thymine,
whereas RNA contains uracil
Note: Base pairs form with antiparallel backbone structure
Building a Nucleic Acid: The Phosphodiester Backbone
Electrons attack the
phosphate core at
the ___ carbon
This creates a
phosphodiester
linkage
__________
Reaction
Building a nucleic acid: Double Helix Measurements
Distance between
bases: 0.34 nm
Length of one complete
turn of helix: 3.4 nm
(__ rungs per turn)
Width of the helix: 2.0 nm
Clicker Question #3
Chargaff’s Rule:
We know that in DNA there are A-T and G-C base-pairs.
If I tell you that a DNA molecule is 30% guanine, what is the % of
thymine in that molecule?
1. 
2. 
3. 
4. 
5. 
6. 
0%
10%
20%
30%
40%
50%
Peer Instruction
RNA: Structure and Function
The primary structure of
RNA
differs from DNA
in two ways:
-
-
Loop
Stem
Single
stranded
Double
stranded
The presence of the 2’–OH
group on ribose makes RNA
much (more/less) reactive and
(more/less) stable than DNA.
Building DNA: Making a Copy
“It has not escaped our attention that the specific pairing we have postulated
immediately suggests a possible copying mechanism for the genetic material.” -Watson and Crick, 1953
Concept Questions
•  Find the structure of a nucleotide, and point out the nitrogenous base,
the phosphate group(s), the ribose ring, whether it is DNA or RNA,
what base it is, and whether this is a relatively high-energy or lowenergy molecule compared to other nucleotides.
•  What is the nickname for this nucleotide? (for example: ‘dGMP’)
•  Explain, without skipping over any parts, why adding ATP hydrolysis to
a reaction can allow an organism to drive an otherwise impossible
reaction.
•  Imagine that the genome of a new bacteria found on Mars is 35%
Guanine. What percentage of the new genome is likely to be Cytosine?
What assumptions are you making in your calculation?
•  Why is RNA more like protein than DNA?
•  Why is it more like DNA than protein?
•  What extra work must you do to complete a Bio200 exam?
•  Is this a good or bad exam system? Why?