Transcript O > N > C ≅ H

Tuesday January 3rd,
2017
Class 1 Learning Goals
Biochemistry: Elements in water
• After this class, you should be able to:
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–
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Decide if a molecule is primarily polar or primarily non-polar
Determine if a molecule is likely to dissolve in water
Predict likely hydrogen bonds
Explain Bio200 course logistics to a classmate
Assess life as mixture primarily of a few elements and judge
any particular element as a potential primary building block
for life
Chemical compositions:
The planet:
The crust:
The atmosphere:
The ocean:
A bacteria:
A squid:
You:
Fe
O
other elements…
O
N
O
O
O
O
other elements…
O
other elements…
other elements…
C
H
N
other elements…
C
H
N
other elements…
C
H
N
other elements…
H
Peer Instruction
Elemental biology
C N O
1) Does life on
Earth have very
large elements?
Why or why not?
2) What can C, N, and O do that He and Rb can’t?
O > N > C ≅ H
‘Pauling Scale’
of electronegativity: 3.44
3.04
2.55
2.20
(reference)
3) What is electronegativity?
4) What does this mean for bonds in living creatures?
Peer Instruction
Is this molecule hydrophobic or hydrophilic?
In aqueous solution, which scenario is more likely? Why?
Scenario #1
Scenario #2
4 common ways to organize H, C, N and O:
Carbohydrates
(CH2O)n
Proteins
(C2H4O2N+[X])n
Nucleic Acids
~(C5H5N2O2)n
Lipids
~C44H72O8NP
Concept Questions
•
The element Argon does not make up a large portion of living organisms. Is this
something that you would expect? Why or why not?
•
•
•
Can benzene hydrogen bond with water?
Can formaldehyde hydrogen bond with water?
Can formaldehyde hydrogen bond with benzene?
•
Imagine two massive proteins composed of 10,000 atoms. At the end of one protein
is a hydroxyl group, while the other protein has a phosphate group in the same
place. How are these massive molecules similar or different? Does it matter?
•
•
•
How well do you expect octane to dissolve in a pure solution of liquid ethanol?
How well do you expect nitrate to dissolve in a pure solution of liquid methane?
Butane does not dissolve well in water. Why? Explain your answer in terms of water
molecules and their weak binding to each other.
•
What Bio200 assignments should you complete each week?
You:
O
C
H
N
other elements…
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Logistics
Course Coordinators: Liz Warfield and Christine Savolainen
Your TAs (who you’ll meet in lab)
Getting a spot in the lab
– You MUST show up to your first lab (or you may be dropped from the entire course)
– Looking for a spot? Communicate with Course Coordinator Liz Warfield
Class discussion board: Engagement and proper academic conduct is expected (10 points)
Points breakdown
– 5 exams (The first four are worth 80, and the final is worth 120)
– Clickers (80 points)
– Daily Reading Quizzes (2 pts per day, lowest 3 quizzes dropped)
– 9 Labs (Each worth 10 points, including the 2 point online pre-lab)
– Seminar (30 points)
Polling points
– Using PollEverywhere, so get registered as per the website
– A variety of grading schemes depending on question
Reading Quizzes
– Why we use them
– How best to read for this class
Homework this week:
– Chemistry skills quiz (as many chances as you’d like for a high score
– Pre-Lab #1
– 3 more Reading Quizzes
Seminar: finding more later this week.
Exams: finding out more later this week
Most importantly, you.
Wednesday January 4th,
2017
Class 2 Learning Goals
Entropy and Carbohydrates
• After this class, you should be able to:
–Determine if entropy is increasing or decreasing for a given scenario
–Use entropy to determine if a system is becoming more stable
(lower energy) or less stable (higher energy)
–Identify a carbohydrate molecule by name, composition or structure
–Describe multiple carbohydrate compounds comprised of the same
elemental components
–Predict biological roles (structural, energy storage, identification) for
carbohydrate polymers based on structural characteristics
Entropy: Energy spreading out
Peer Instruction
1) In which situation is energy more spread out?
Situation 1
Situation 2
2) Do these situations give you any information about bond enthalpy?
For #3, assume total bond enthalpy is the same in both situations.
3) In which situation is the overall energy higher?
Overall entropy in the universe is increasing.
4) What does the universe look like in the far distant future?
5) Is this reaction possible? If so, how?
+
+

Creating polymers: A general process
• Many biological macromolecules are made by:
– linking individual molecular units
• (___________, like a monosaccharide or a nucleotide)
– into a chain-form macromolecules
• (a _________, like a polysaccharide or DNA)
• The two reaction directions have special names:
– Condensation reactions (adding monomers together)
– Hydrolysis reactions (taking polymers apart)
Peer Instruction
Is this a carbohydrate?
(CH2O)3
Glucose
Are these two
molecules the same?
Galactose
(CH2O)_
Are glucose and galactose
different molecules?
Notice the suffix:
Peer Instruction
Carbohydrates: Ring configurations
Linear form of glucose
Ring forms of glucose
-Glucose
-Glucose
Do alpha-glucose and beta-glucose differ:
In molecular formula?
In general shape?
In # of carbons?
In precise shapes and charges?
C-H and C-C bonds
can be harvested for redox energy to
be used in other chemical reactions
C-H and C-C can be harvested for energy. Memorize this.
Why these bonds? It’s complicated.
How it this energy harvested? Week 6!
What Do Carbohydrates Polymers Do?
• Carbohydrates are important building
blocks in the synthesis of other molecules.
• Carbohydrates can:
– Store chemical energy.
– Provide cells with fibrous structural materials.
– Help create cell identity.
Peer Instruction
Carbohydrates: Energy Storage
What is the monomer in the polymers shown?
What is similar/different about the polymers shown?
Carbohydrates: Protective Barriers
Which polymer forms a tougher layer?
Which polymer is more expensive to build?
Peer Instruction
Peer Instruction
How can carbohydrates help cells tell each other apart?
Outside of cell
Inside of cell
Concept Questions
• Is entropy increasing or decreasing as a game of chess is played?
– What about while wood is burned to give CO2 and water?
– What about during a hydrolysis reaction for a carbohydrate polymer?
• Is acetic acid a carbohydrate? How do you know?
–
•
A harder one: Is chitin a carbohydrate? Why or why not?
Find a molecular formula of the form (CH2O)N from which you can make three
different molecular structures.
•
Find a structure for the carbohydrate polymer inulin. Predict whether or not this
polymer:
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–
–
–
Can pack tightly for storage of lots energy? Where in the molecule is most of the energy stored?
Can allow rapid energy usage?
What glucose polymer is most similar to inulin?
Would inulin be a useful molecule for cellular identification? Why or why not?
Bio200 has 14+ office hours per
week.
In Hck 302 (unless otherwise noted):
• Mondays: 9:20am
• Tuesdays: 9:30am, 1:30pm, 2:30pm
• Wednesdays: 9:20am, 12:40pm, 1:30pm, 3:30pm,
• Thursdays: 12:40pm, 1:30pm, 3:30pm, 4:30pm
• Fridays: 10:30-12:30 (in Kane 120 on non-exam weeks)
• Also:
– By appointment with Liz Warfield or Ben Wiggins
– Help on Piazza from students and staff
– During labs or immediately after if the TA has time
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
Peer Instruction
Big list:
What do organisms need to do?
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
R
+
N
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
H
H
O
C
C
H
R1
+
N
R2
R1
O
H
+
-
H
+
N
H
O
O
C
H
H
C
O
-
R2
O
+
C
C
N
C
H
H
C
-
H
+
O
This new bond is a special covalent bond known as the ‘peptide bond’
O
H
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
Structure levels in proteins
The grey molecule is a protein. It is shown here
interacting with a red/blue DNA molecule.
What is:
Primary structure:
Secondary structure:
Tertiary structure:
25
Peer Instruction
1) Describe the differences and
similarities between alpha-helix
and beta-sheet configurations.
-helix
2) Find a region in this protein of:
Alpha-helix
Beta-Sheet
Unstructured ‘loop’
-pleated
sheet
-helix
Protein Tertiary Structure
Peer Instruction
Label the 4-5 intramolecular bonds shown here.
Why are these bonds important?
Peer Instruction
Enzymes: A Three-Step Model
Substrates
Transition state
Enzyme
Shape changes
1. Initiation:
What
role site
of in
the
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
energy?
lower the activation
energy
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
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?
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
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?
32
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?
33
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?
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
5
3
Guanine
Cytosine
Adenine
Thymine
3
5
DNA contains thymine,
whereas RNA contains uracil
Note: Base pairs form with antiparallel backbone
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
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?