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1Four ‘bonds’(review)
• Covalent: like a dowel. Arises from?
• Ionic: like a rare earth magnet. Arises from?
• Hydrogen: like a wimpy old fridge magnet. Arises from? (we will talk about this again today extensively)
• Hydrophobic: like nothing else. Arises from?
2Why is one of these the genetic code?
DNA
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Instructions for the parts of living things
Why the instructions for you are stored as hydrogen
interactions between ringy things
DNA
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Why care about DNA?
55
Spider dance!Spider dance!Now that’s ‘information’!Now that’s ‘information’!
6Who cares about DNA?• It’s what’s in you (and every other living thing)
• It’s (part of) the magical interface between chemistry and life
• It is perhaps the single most easily understood biomolecule you’ll ever meet
• doesn’t ‘do’ anything
• key is in H-bonding donor/acceptor pairing
• its structure IS its function
77
DNA: instructions for the
parts of living things
DNA: instructions for the
parts of living things
Why the instructions for you are stored as hydrogen interactions between
ringy things
Why the instructions for you are stored as hydrogen interactions between
ringy things
How? Why?
88
Primary goals for today
Primary goals for 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
9Is today ‘science’?Are these
‘investigations’?• The goal of science is to create simplifying worldview that is predictive and explanatory.
• You’ll never feel the pull of electronegativity, the ‘pH-ey’ presence of a proton. But thinking in this way helps you explain, predict?
• That’s what we’re going for today in this way of looking at the bases
• We are working with MODELS today
10Life: gimme adjectives
What’s the difference between you, the bench top, a rock, a candle flame?
11
Use: GGGTT Green = GuanineRed = Cytosine
Blue = AdenineYellow = Thymine
• Party hats on-
• Starting point:
• BLUE hats – L hand out, palm down
• GREEN hats – L hand out, palm out (shake)
• YELLOW hats – L hand out, palm up
• RED hats – L hand out, palm out (shake)
• 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 = Green
Cyt = RedAde = Blue
Thy = Yellow
• Separate strands; who partners with whom? What external info do we need to re-create the missing strand?
• Restart; RED hat turns hand palm up (put on purple hat)
• it’s undergone chemical change… replicate &…?
Gua = Green
Cyt = RedAde = Blue
Thy = YellowGGGTT
DNA• Why do atoms make bonds?
DNA• Why do atoms make bonds?
• What types of ‘bonds’ are there?
DNA• Why do atoms make bonds?
• What types of ‘bonds’ are there?
• Not all atoms play fair
DNA• Hydrogen bond/interaction
DNA• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
DNA• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
•Based on electronegativity
DNA• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
•Based on electronegativity
• Why not Carbon-Hydrogen?
DNA• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
• H-Bond Donors
DNA• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
• H-Bond Donors
• Positive charge (Hydrogen)
DNA• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
• H-Bond Donors
• Positive charge (Hydrogen)
• H-Bond Acceptors
DNA• Hydrogen bond/interaction
• When H bonds with ‘O’ or ‘N’
• H-Bond Donors
• Positive charge (Hydrogen)
• H-Bond Acceptors
• Negative charge (O, N)
Basil
Oregano
Salt
Garlic
Basil
Oregano
Salt
Garlic
Basil
Oregano
Salt
Garlic
Adenine
Guanine
Cytosine
Thymine
3131
First lookFirst lookTouching, feeling basesTouching, feeling bases
32Blinding you with science (jargon)
• Pyrimidine (single ring), Purine (double)
• PUR As Gold
• Big base gets the little name
• Hydrogen interaction, H-bond: O-H :N-
• Donor: the group possessing the H, sharing it
• Acceptor: the partial (-) atom partaking of the H
33
Fantastic plastic• Each group gets GC or AT pair. Investigate.
• Superimposability of GC, CG, AT, TA pairs
• High crimes & misdemeanors
34Anatomy of a basepair
H
Ornaments: -NH2=O-H-OH=NH
----- Dashed lines indicate double bonds present in some purines or pyrimidines
35
Hydrogen 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
Text
Grow your own--make GC or AT
36Building block
3737
Closer look:Pairing BasesCloser look:
Pairing Basesthe Truth about the Codethe Truth about the Code
38Rubrics
• Homepage = > my instructor link => this week => BasePairer rubric
• http://blc.arizona.edu/courses/181Lab/Rubrics/BasePairer_rubricF12.pdf
39
Basepairer• Launch ‘BasePairer’
• Homepage = > my instructor link => this week => Activity guide
• Don’t log in; that’s for homework
• Write your names on the paper I hand out; return it at end of class or zero credit
• make a note of your tautomer in your lab notebook
Base Pairer Rubric 40
41Chemistry Happens II• Dr. Base & Mr. Tautomer
• Why Chargaff’s rules didn’t => the structure
%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
42
http://www.nature.com/scitable/nated/content/ne0000/ne0000/ne0000/ne0000/97271/pierce_17_11_FULL.jpg
Stuff happens (baaaad stuff)
What to do with your piece of
paper• Look at the paper I handed out again
• Explore the tautomer that is on your paper now that we have talked about what a tautomer is
• Write down the tautomer on your piece of paper in your lab notebook because that is the one you will need to use for your homework
43
44Precision & Pickiness
• H-bonds: because weak, picky
• Combined with stiff bases: it’s all right or it it’s wrong
• Geometry of an H-bond
45
“Rather than believe that Watson and Crick made the DNA structure, I would rather stress that the structure made Watson and Crick.... what I think is overlooked in such arguments is the intrinsic beauty of the DNA double helix. It is the molecule which has style, quite as much as the scientists.”
—F. H. C. Crick
4646
Genetic DiseasesGenetic DiseasesWhy mutations matter
What loss of genetic information looks likeWhy mutations matter
What loss of genetic information looks like
Back to the little sheet of paper
again
Back to the little sheet of paper
again- make a note of your group name & genetic
disease in your lab notebook
- Make sure all of your names are on the back of that sheet of paper and that you TURN IT IN TODAY or no credit
- make a note of your group name & genetic disease in your lab notebook
- Make sure all of your names are on the back of that sheet of paper and that you TURN IT IN TODAY or no credit
4747
48
This exercise...• Spans the next month
• Lets you apply your learning and thinking to an actual disease
• What is most important is that you think well and integrate what you are learning; being ‘right’ is secondary
49Google & WikipediaGoogle & Wikipedia
• GOOGLE.com (or Blackle.com)
• search several terms
• “phrases in quotes”
• google.com/advanced_search
If you want to Bing, I’m not stopping you
Caveat emptor! The web is a wonderful, rich source of information. ***But anybody can have a webpage***
• Wikipedia.org
• User contributed
• User policed
• But pretty good!
50The task
• Over the coming weeks, you’ll characterize a genetic disease
• Symptoms and distribution
• DNA mutation, amino acid change
• Your ideas about influence on protein structure
• Then you’ll share your findings with the class
51Due today!• Genetic disease part 1, from today on calendar
• Handed in to the d2l drop box with all group member names on it
• FILE NAME: Name of genetic_net id_net id_net id_net id
• 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
52
53My sources
• Wikipedia: I generally trust it based on personal experience and b/c it is community edited and putting up lies about science just isn’t that interesting
• NIH: Federally funded science & health professionals, I judge it generally very trustworthy
• Campbell textbook: textbook authors are not experts in every area of content, they consult with experts and their work is critically read by thousands, so I trust it
5454HomeworkHomework
Next week’s quiz emphasizesQuestions from the manual reading
HALF of your quiz for next week will be questions based on the lab manual reading for lab 4. Make sure you have some idea of what transcription/translation is!!!!