Download 1.4+ billion cows X 200 liters of methane per day = > 7 million tons of

Cellulose, methane, and climate change
+
Stomach bacteria
=
Meat (good) and methane (greenhouse gas)
1.4+ billion cows X 200 liters of methane per day =
> 7 million tons of methane annually
What does this big number mean?
Cellulose, methane, and climate change
+
Stomach bacteria
=
Meat (good) and methane (greenhouse gas)
1.4+ billion cows X 200 liters of methane per day =
> 7 million tons of methane annually
Methane production of the oil & gas industry =
> 13 million tons of methane annually
Thursday January 5th, 2017
Class 3 Learning Goals
Proteins, especially Enzymes
•  After this class, you should be able to:
–  Relate the diversity of protein function in cells to the special
flexibility of polymers of amino acids.
–  Compare and contrast amino acids by R-group components
–  Classify changes into categories by differences in level of
structure (primary, secondary, tertiary, quarternary)
–  Predict reaction consequences of structural changes in enzymes
–  Rationalize the special value of molecular catalysts for living cells
Big list:
What do organisms need to do?
Peer Instruction
Peer Instruction
Explain which parts of the amino acid are the:
•  Tetrahedral Carbon
R
H
O
•  Carboxyl Group
•  Amino Group
N
C
C
•  Singular Hydrogen
H
H
O
•  Side-Chain
H
Because life on Earth is primarily found in water, proteins
typically reside in a different form. What is the difference?
H
H
H
+
N
R
C
H
O
C
O
This is called the ‘zwitterion’ form
Peer Instruction
When amino acids are polymerized:
1) What are the reactive parts?
2) What are the by-products?
3) Is entropy of the amino acids increasing or decreasing?
4) Describe the ‘peptide bond’.
H
H
+
N
H
H
O
C
C
H
R1
+
H N
H
R2
R1
O
+
H
H
+
N
H
-
O
O
C
H
H
C
O
-
R2
O
+
C
C
N
C
H
H
C
-
+
O
This new bond is a special covalent bond known as the ‘peptide bond’
H
O
H
Respond at PollEv.com/biology200
(or text BIOLOGY200 to 22333 once to join)
1
H
H
O
2
+
N
H
O
+
C
C
Clicker Question #1
N
H
C
H
C -
=
O
There are three amino-acid polymers shown. One is very rigid and
stable. Another is very flexible and does not hold a defined shape.
Which polymer is semi-stable but still has some flexibility?
1)
2)
3)
Nonpolar
side chains
Polar
side chains
Glycine (G)
Gly
Alanine (A)
Ala
Methionine
(M)
Met
Serine (S)
Ser
Valine (V)
Val
Phenylalanine
(F)
Phe
Threonine
(T)
Thr
Cysteine (C)
Cys
Leucine (L)
Leu
Tryptophan (W)
Trp
Tyrosine (Y)
Tyr
Acidic
Asparagine
(N) Asn
Isoleucine
(I) Ile
Proline (P)
Pro
Glutamine (Q)
Gln
Basic
Electrically
charged
side chains
Aspartate
(D)
Asp
Glutamate
(E)
Glu
Lysine (K)
Lys
Arginine (R)
Arg
Histidine (H)
His
Clicker Question #2
A particular part of a structural protein needs to
interact tightly with a negatively charged ion.
Which of these amino acids is most likely to be found
in this part of the protein?
3) Alanine
1)
4) Lysine
2)
<proteins>
Structure levels in proteins
The grey molecule is a protein. It is shown here
interacting with a red/blue DNA molecule.
What is the:
•  Primary structure:
•  Secondary structure:
•  Tertiary structure:
14
Peer Instruction
1) Describe the differences and
similarities between alpha-helix
and beta-sheet configurations.
α-helix
2) Find a region in this protein of:
Alpha-helix
Beta-Sheet
Unstructured ‘loop’
β-pleated
sheet
α-helix
Protein Tertiary Structure
Peer Instruction
Label the 4-5 intramolecular bonds shown here.
Why are these bonds important?
Protein Structure: Quaternary Structure
Cro protein, a dimer
Hemoglobin, a tetramer
Stretch break
Get one worksheet for each person.
You will turn this in at the end of Friday’s class.
Peer Instruction
Enzymes: A Three-Step Model
Substrates
Transition state
Enzyme
Shape changes
1. Initiation: What
rolesite
ofinthe
Reactants
bindis
to the
the active
a specific orientation, forming an
enzyme-substrate complex.
Products
enzyme?
Could the reaction occur without the enzyme?
Does the
2. Transition state facilitation: Interactions between enzyme and substrate
enzyme
contribute
lower the activation
energyenergy?
required.
3. Termination: Products have lower affinity for active
site and are released. Enzyme is
unchanged after the reaction.
Enzymes: Catalysis of Biological Chemistry
Peer Instruction
Task: Define all terms shown.
Transition state
Reactants
Activation Energy
Products
Clicker Question #3
The amino-acid side chains:
1.  Help to create an open space that is a good
fit for the substrate molecule.
2.  Interact chemically with parts of the
substrate molecule.
3.  Interact with other amino-acid side chains to
stabilize the structure of the enzyme.
4.  <More than one of these options is true.>
5.  <None of these options is true.>
Respond at PollEv.com/biology200
(or text BIOLOGY200 to 22333 once to join)
Concept Questions
• 
• 
Why are proteins not completely flexible?
Why are proteins not completely stiff?
• 
Discuss the properties of a protein that was a simple chain of
threonines.
• 
Define the protein structure level of change for:
–  A lost hydrogen bond
–  An extra disulfide interaction
–  Three reordered peptide bonds
• 
Predict two consequences for an enzyme that loses four important
hydrophobic side chains.
• 
Most living organisms make their own molecular catalysts. These
sometimes-huge molecules can be very expensive in terms of
molecular energy to build. Why is this worthwhile for the organism?
Clicker Question #2.5
All but one of these are 100%OK. For which will you
lose all clicker points for the day without warning?
1. 
2. 
3. 
4. 
Watching basketball on ESPN while sitting in the last row
of the classroom.
Using any device for any class-related task in any seat.
Using a device to access the UW registration page or
Facebook in the 3rd row.
Using a cell phone to do an Google search about a
Bio200-related science topic during class in the 6th row.
Research shows that device use distracts nearby students and disrupts their learning.
We’ve had several complaints already in this Winter Bio200 class.
Our system isn’t perfect, but it is the best we have.