dancing spiders. dna instructions for the parts of living things why the instructions for you
TRANSCRIPT
DNA
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Instructions for the parts of living things
Why the instructions for you are stored as hydrogen interactions between ringy things
DNA
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• It’s in all living things
• Interface between chemistry and ‘life’
• Easily understood molecule
• doesn’t ‘do’ anything
• Structure is based on H-bonding
• Structure IS function
DNA
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• So what does it mean to be “living”
•Give me adjectives!
Things to do today:• Make leap from Chemistry to Biology: how can you get ‘you’ from C, H, O, N and P (finish next week)
• Describe HOW/WHY A goes with T and G with C (and ‘not’ G with T)
• Discuss what took ‘them’ so long
• Mutations happen ALL THE TIME!
• Begin investigation into genetic diseases
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General & SpecificShake hands with everybody on the side of the bench facing yours
How many of these interactions failed?
Pair up. Design a handshake where A can shake with B, but not A:A nor B:B
How can we achieve this with C, H, N, O?
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Four ‘bonds’
• Covalent: like a dowel. Arises from?• Ionic: like a rare earth magnet. Arises from?• Hydrogen: like a wimpy old fridge magnet.
Arises from?• Hydrophobic: like nothing else. Arises from?
Some things…
• Polarity describes a covalent bond. If something is polar what does that mean? What about nonpolar?
• Ions arise from what type of bond? Is there a charge? If so, what type of charge?
• Electronegativity describes atoms NOT molecules. – Water is not electronegative! The atoms that make
up water are, which creates an uneven distribution of electrons.
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DNA
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• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
DNA
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• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
•Based on electronegativity
DNA
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• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
•Based on electronegativity
• Why not Carbon-Hydrogen?
DNA
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• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
• H-Bond Donors
DNA
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• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
• H-Bond Donors
• Positive charge (Hydrogen)
DNA
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• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
• H-Bond Donors
• Positive charge (Hydrogen)
• H-Bond Acceptors
DNA
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• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
• H-Bond Donors
• Positive charge (Hydrogen)
• H-Bond Acceptors
• Negative charge (O, N)
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• Adenine: from the Greek word for gland
• Thymine: first isolated from the thymus
• Cytosine isolated from ‘cells’ (think cytoplasm)
• Guanine: Yep--first isolated from bird guano
Why do we call them that?
• Party hats on- • Starting point:
– BLUE hats – 0 - +– GREEN hats – + + -– YELLOW hats – - + -– RED hats – + - -
• START with a strand of GGTT ,‘right hand’ on neighbor’s shoulder
• Make a matching strand (dbl-stranded DNA)• Why do bases go together?
• Each strand ‘count off’ from their L to R, how do the two directions compare?
Gua = GreenCyt = RedAde = BlueThy = Yellow
• Separate strands; who partners with whom? What external info do we need to re-create the missing strand?
• Restart; RED hat changes to - + - (put on purple hat)
• it’s undergone chemical change… replicate &…?
Gua = GreenCyt = RedAde = BlueThy = Yellow
GGGTT
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Things you already ‘know’
• Pyrimidine (single ring), Purine (double)
– PUR As Gold
– Cut The PY
– Big base = little name
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Take a look at the models
• Each group gets GC or AT pair. Investigate.
• Superimposability of GC, CG, AT, TA pairs
• High crimes and misdemeanors
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Anatomy of a basepairOrnaments
-NH2
=O
-H
-OH
=NH
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Make your own GC or ATHydrogen bonds form between G-C pairs and A-T pairs.
Guanine Cytosine
ThymineAdenine
Su
ga
r-p
ho
sp
ha
te b
ac
kb
on
e
Hydrogen bonds
DNA contains thymine,whereas RNA contains uracil
5′
5′3′
3′
Freeman, Biological Science, 4.6b
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Rubric is available via web page
BasePairer
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• Go to the ‘Lab03_DNA’ folder
• Launch ‘BasePairer’
• DON’T log in, that’s for homework
• Work through the activity guide for homework
• HOMEWORK answers in Dropbox on D2L page
• Can work in pairs (contract)
Basepairer
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Bad things happen to good bases
• Chart
• tautomers
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Bad things happen to good bases
• What happens when cytosine gets deaminated?
• What would the consequences be?
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Deamination
Cytosine
just add water…and heat
H2ONH3
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Deamination
Cytosine
Hmmm, this is IDENTICAL to THIS
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Deamination
Cytosine
We started with Cytosine
Deaminated it to
URACIL
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What’s up with U?• Just a T without the -CH3• In terms of basepairing, identical in
the partnering with A• Historically, U came first (as RNA
preceded DNA); FYI, the ‘marking’ of T allows better maintenance/repair of DNA than is available in RNA
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Nitrogen-containing bases
Cytosine (C) Uracil (U)
Pyrimidines
Thymine (T)
Guanine (G) Adenine (A)
Purines
Freeman, Biological Science, 4.1
Bad things happen to Good BasesChargaff’s Rules didn’t lead to structure
WHY?
%A%A %T%T %G%G %C%C
MycobacteriumMycobacterium 15.1 14.6 34.9 35.4
YeastYeast 31.3 32.9 18.7 17.1
WheatWheat 27.3 27.1 22.7 22.8
Sea UrchinSea Urchin 32.8 32.1 17.7 17.3
Marine CrabMarine Crab 47.3 47.3 2.7 2.7
TurtleTurtle 29.7 27.9 22 21.3
RatRat 28.6 28.4 21.4 21.5
HumanHuman 30.9 29.4 19.9 19.8
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Genetic Disease
• Spans the next month– SYMPTOMS AND DISTRIBUTION
– DNA mutation, amino acid change
– Probable influence on protein structure
– Then you’ll share your findings with the class
• Lets you apply your learning and thinking to an actual disease
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Genetic Disease• Write your names on the paper I hand
out; return it at end of class or zero credit
• Make note or your group name and disease in your lab notebook
• What is most important is that you think well and integrate what you are learning; being ‘right’ is secondary
* Letters and underlines only. CAN BE SEEN BY ME!
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Genetic Diseases
Due Today!!!Part 1 of assignment
Page I-1 of your lab manual
Turned in to me with all group members’ names on it.
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Genetic Diseases
Due Today!!!Part 1 of assignment
Turned in to me with all group members’ names on it.
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Genetic Diseases
• An example: hemoglobin/sickle cell anemia
– Sufferers: one in 12 African Americans has the TRAIT; overall, 1/5000 Americans suffer
– Common in areas with malaria– symptoms: shortened lifespan (48-52),
see next slide
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A few thoughts
• “Google” is a great search engine– Use quotes if needed– Advanced search– ‘scholar’
• Wikipedia– User contributions
• Anybody can have a web page
Homework• Examining DNA/Intro Translation Assessor
• Solving the Structure Assessor
• Transcribe & Translate (Vocab)
• READ next weeks lab and ‘Dicty”
insert
•Quiz next week next week’s lab AND previous labs
Your genome1. Get a cup of saltwater solution; swish vigorously in mouth for
30 seconds. {other protocols suggest gently chewing your cheeks as well}. This will remove dead cells lining the mouth and provide students with a source of their own DNA.
2. Spit back into cup; then pour it into a large test tube containing 5ml of detergent solution.
3. Cap the test tube {let's try with parafilm; it MAY dissolve in detergent} and gently rock it on its side for 2-3 minutes.
4. Uncap the tube and then slightly tilt it and carefully pour 5ml chilled ethanol down the inside of the tube so that it forms a layer on the top.
5. Allow the tube to stand for one minute. Use a thin wood or glass rod to slowly move some of the ethanol into the soap layer. Spool the DNA strands around it. If too much shearing has occurred, the DNA fragments may be too short to wind up, and they may form clumps instead.