Download The Basics: A general review of molecular biology: DNA

The Basics: A general review of
molecular biology:
DNA
Transcription
RNA
Translation
Proteins
DNA (deoxy-ribonucleic acid) is the genetic material
It is an informational super polymer
-think of it as the blueprint
DNA structure-- a polymer of nucleotides
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Central dogma
Protein synthesis: translation (mRNA to protein)
Proteins have catalytic and structural functions
Proteins with catalytic functions are enzymes
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Proteins fold in an aqueous environment
Life happens in water
70% of the cell is water
Water is polar
Water plays an important part in
determining the final shape of proteins
Water
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How does it interact with other substances?
Does it interact with other water molecules?
If so, which atoms?
Does it interact with Na+ (Blue)
If so, which atoms?
Does it interact with Cl- (Green)
If so, which atoms?
Does it interact with ethane
If so, which atoms?
Does it interact with ethanol?
If so, which atoms?
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http://www.3dchem.com/molecules.asp?ID=234
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Amino acids are the building blocks of proteins:
Common to all:
Hydrogen atom
Amino group
Carboxyl group
Distinguishing feature: R group; side chain
conveys specific chemical properties
Each table should construct two amino acids
Short white bonds - hydrogens
Thick gray bond - covalent bonds
Long gray bond - covalent double bonds
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Use MolyMod to have the students investigate the structure of
the amino acid backbone and formation of a dipeptide
1.
Examine the structure of 2 preassemble aa (side chains are green spheres)
2.
Take aa apart and put them back together.
3.
Join 2 aa to make a dipeptide, releasing water.
4.
Join several dipeptides to make a longer peptide.
5.
Examine structural constraints on the peptide chain -rotation of the phi (N-C)
bond and psi (C-C) angles.
Your structure should look like this
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Protein synthesis--chain elongation mechanism
Each table should make a dipeptide
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Proteins also have a polarity to them-distinct beginning and end
Free amino group
At the first residue
Free carboxy group
at the last residue
OH
Fig 1-15
Different amino acids have different side chains
file:///Volumes/AASK%2010-2006/Jmols/amino.html
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Different amino acid chains have different chemical properties
Activities for Amino Acid Side Chains and Properties
1. WSSP Amino Acid game:
http://avery.rutgers.edu/WSSP/WSSPSummer06/WSSPSummer/AAGame/AAQuizPlusPenalty.php
2. Amino Acid matching game http://www.studystack.com/matching-23027
3. Amino Acid Quiz http://www.funtrivia.com/playquiz/quiz2422051bbb2a0.html
4. Asteroids AA game
http://www.wiley.com/legacy/college/boyer/0470003790/animations/acideroids/acideroids.htm
5. Amino Acid Starter Kit (toobers with side chains)
Helps sort the aa into different groups
Using the chart, students mark the atoms in the side
chains with stickers and sort the side chains.
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Amino acid starter kit
Use the key chart to arrange the amino acids on the circle
Turn the circle around to look at the atoms of each side
chain
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Amino Acid Starter Kit (continued)
Principals of protein folding
1. Have students choose 6 hydrophobic, 2 acidic, 2
basic, 2 cysteine, 1 methione and 2 poly side chains.
2. Mix and place aa along the toober. The aa order is
the primary structure of the protein (Note: No two
groups will get the same order).
3. Have the students fold the toobers using the
following principals (not laws):
1. Hydrophobic aa should be hidden from polar water
2. Charged aa should be on the surface.
3. Positive and negative aa can be paired within one
inch to neutralize the side chains
4. Polar side chains should be on the surface
5. Pair the cysteines to form a disulfide bond.
Amino Acid Starter Kit (continued) Questions
1.
Why should the Met be next to the blue cap? Proteins start with
Met
2. As you added each new property what happened to the fold of the
protein? The protein became more compact and complicated
3. Were you able to satisfy all the chemical properties?
4. Does your protein look like other students proteins? No, because
they each have different aa sequences.
5. Given unlimited aa how many protein are there of 15 aa long? 2015
6. The average protein is 300 aa long. How many different proteins
are possible? 20300 = 2 X 10390
7. How many proteins (genes) are in the human body? 50,000 (5 X
104)
8. What fraction of the total possible protein sequences are present in
the human body? 2 X 10-386
9. Why are there so few? Relatively few sequences can satisfy all
the chemical principals to form a stable shape.
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Amino Acid Start Kit Variations:
1. Reversible Denaturation:
a)
b)
c)
Fold the protein and take a picture
Unfold the protein then try to refold it.
How does it compare to the original?
2. Reverse Engineering: Sometimes the protein sequence
can not satisfy all the chemical principals. Try it in
reverse
a)
b)
c)
d)
Fold the toober into a compact shape without side chains
Add the side chains so that they obey the chemical properties
Unfold the toober and document the aa sequence. Are they similar to
other groups?
Unfold the protein
3. Effect of Mutations: Make changes in one of the
hydrophobic side chains to a positive side chain
What would happen to the protein fold?
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Secondary Structure
α-helices - right handed helix, 3.6 aa/turn,
aa point outward
stabilized by H-bonds between NH of aa X and CO of
aa X+4
β-sheet - extended zig-zag structure
parallel or antiparallel chains to form flat sheets
aa side chains are above or below the sheets
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a-helix and b-sheet construction kit
1. Assemble α-helix and β-sheet with components from
the kit
2. What are the similarities and differences of the
backbone aa?
3. Build an α-helix (10 aa) and 2 β-strands (5 each)
a) How are these secondary structures the same or
different?
b) What does the effect of adding the H-bonds do to
the structure?
4. Which atoms share these H-bonds?
5. Are these backbone or side chain atoms?
6. Measure the length of each structure
Which is longer? Why?
What implications does this have on protein folding?
α-helix and β-sheet construction kit (cont.)
5. Organize the aa into groups and justify your groupings
Nonpolar - Ala, Val, Leu, Ile, Phe,
Polar -Gly, Ser, Thr, Asn, Gln, Trp, Tyr
Postively charged - Arg, Lys, His
Negatively charged - Asp, Glu
Sulfur - Cys, Met
6. Why is there no Proline in the kit?
7. Assemble the side chains on the α-helix and β-strands
How does the addition of these side chains affect
its possible structure and interactions with water?
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Use your assembled α-helix and add the amino acids side
chains in the following order:
N+- Glu-Glu-Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp-Gly-CWhat effect to you think water has on folding this peptide?
Sickle Cell Anemia is caused by a mutation in the β-globin
gene of a Glutamate residue to Valine.
N+- Glu-Glu-Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp-Gly-CVal
The mutation leads to deformed red blood cells resulting in
anemia. What effect to you think this mutation has on
folding this peptide?
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Use your assembled β-strands and add the amino acids side
chains in the following order:
Strand#1 N+- Ile-Leu-Val-Glu-Leu -CStrand#2 C-- Ser-Val-Ser-Gly-Glu -N+
What differences do you see on one side of the sheet than
the other?
Examine secondary structure models with and without
side chains
What sides of these structures are likely to be in the
interior of the protein?
What sides of these structures are likely to be in the
exterior of the protein?
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Examine tertiary structure models of GFP and β-Globin
Define the function of the proteins
Identify and count the secondary structures
Follow the chains through the entire protein. Are regions
of the protein that are near each other on the primary
sequence near each other in the tertiary structure?
Zinc Finger Kit: Use toobers to form secondary structures
and fold a protein
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Form the β-strands
Form the α-helix
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Fold the secondary structures into the tertiary structure
Zn Finger Kit Folding Questions
1.
Describe the secondary structure elements that
make up a Zn finger
2. How does the Zn atom stabilize the Zn finger motif?
3. Zn Finger proteins bind DNA. How might the arginine
side chain in the model be involved in DNA binding?
4. How close is your model of the Zn finger to the model
provided?
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