11

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?

2Why is one of these the genetic code?

33

Spider dance!Spider dance!Now that’s ‘information’!Now that’s ‘information’!

4Who 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

Who cares?

•A goes with T •G goes with C

5

66

Primary goalsPrimary goalsConsider the necessary properties of a

chemical that ‘is’ information

Understand HOW the bases go together

See how pairing is replication

See how mutations arise

and why they cannot be prevented

Genes in (in)action: genetic diseases

Consider the necessary properties of a chemical that ‘is’ information

Understand HOW the bases go together

See how pairing is replication

See how mutations arise

and why they cannot be prevented

Genes in (in)action: genetic diseases

7

Life: gimme adjectives

What’s the difference between you, the bench top, a rock, a candle flame?

8

Use: GGGTT Green = GuanineRed = Cytosine

Blue = AdenineYellow = Thymine

9Pas de deux*

• Party hats on--we’re going to do some line dancing!

• Starting point: a double strand of DNA, each base facing partner with their ‘right hand’ on neighbor’s shoulder

• Each strand ‘count off’ from their L to R, how do the two directions compare?

• Separate strands; who partners with whom? What external info do we need to re-create the missing strand?

• Restart; ‘Mask’ one with a purple hat; it’s undergone chemical change

• replicate &…?

*Dictionary.com: a dance by two persons

Gua = GreenCyt = RedAde = BlueThy = Yellow

GGGTT

Movie

• http://www.youtube.com/watch?v=zdDkiRw1PdU

10

11

“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

12

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?

Would a loose flexible handshake be a good one for DNA base pair interaction?

1313

ModelingModelingWhy we do it

How to tell if we’re doing it right

Why we do itHow to tell if we’re doing it

right

14Is 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 – all about feel

1515

Review: bondsReview: bondsA few more pieces of reviewA few more pieces of review

16Four ‘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?

1717

First lookFirst lookTouching, feeling basesTouching, feeling bases

18Blinding 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

19Fantastic plastic

• Each group gets GC or AT pair. Investigate.

• Superimposability of GC, CG, AT, TA pairs

• High crimes & misdemeanors

20Anatomy of a basepair

H

Ornaments: -NH2=O-H-OH=NH

----- Dashed lines indicate double bonds present in some purines or pyrimidines

21

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

22Building block

2323

Closer look:Pairing BasesCloser look:Pairing Bases

the Truth about the Codethe Truth about the Code

24Rubrics

• Homepage = > my instructor link => this week => BasePairer rubric

25

Basepairer• Launch ‘BasePairer’

• 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 group name & genetic disease in your lab notebook

26Chemistry 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

27

http://www.nature.com/scitable/nated/content/ne0000/ne0000/ne0000/ne0000/97271/pierce_17_11_FULL.jpg

Stuff happens (baaaad stuff)

28Precision & Pickiness

• H-bonds: because weak, picky

• Combined with stiff bases: it’s all right or it it’s wrong

2929

Genetic DiseasesGenetic Diseases

Why mutations matterWhat loss of genetic information

looks like

Why mutations matterWhat loss of genetic information

looks like

30This 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

Things to think about:

• Genetic diseases are caused by mutation, failure to make protein at the right time or in the right quantity or in the right way

• Why does this prevent that protein from being a good protein?

31Google & WikipediaGoogle & Wikipedia• GOOGLE.com (or Blackle.com)

• search several terms

• “phrases in quotes”

• google.com/advanced_search

• Wikipedia.org

• User contributed, User policed

Caveat emptor! The web is a wonderful, rich source of information. ***But anybody can have

a webpage***

32The task

• Over the coming weeks, you’ll characterize a genetic disease

• Symptoms and distribution (part 1)

• DNA mutation, amino acid change (part 2)

• Your ideas about influence on protein structure (part 3)

• Then you’ll share your findings with the class (part 4)

33Due today!• Genetic disease part 1, rubric on calendar for

today

• Handed in to me with all group member names on it

• 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

34My 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

3535HomeworkHomeworkVocab: Transcription & Translation words

Assessor: Examining DNA/Introducing translation

Basepairer as individual or pair

Vocab: Transcription & Translation wordsAssessor: Examining DNA/Introducing

translationBasepairer as individual or pair

Next week’s quiz emphasizesQuestions from the manual reading