four ‘ bonds ’ (review)

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?

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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

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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?

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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?

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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

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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

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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

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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

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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

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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

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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

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“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

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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

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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!!!!