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Wed @ 11 meeting:Andrea- Sara-RyanLynn - Bob SteveKatie- Heidi LeslieAleksi- DeborahEmily- Sarah JingTyler- Candice Jessica

Pics: homepage => Instructors

GradingMovie: BruceStuff => Tutorial Movies => ‘Grading Tao”

taProg: BruceStuff => TA Software

Must have VPN client running (available same page)

They (and you!) can see their grades from the homepage grade link

Master_of_Patterns; DNA walk-throughs posted

Emily will contact you about PMaster write-up conferences (guidance in rubric interpretation)

Expectations

Surface tension is a word.

“Billions of interlinings creating a tight mesh that doesn’t readily separate” is an explanation

It truly is exactly like popping the water balloon

stuff pulls back from the introduced point of weakness

See ‘TA_Guide’ for this type of walk through

Answers should be mechanistic, cause-effect!

Building Quizzes

See the QuizBank; it has examples and point distros

New as a 181L instructor? Please send your quiz draft to me 24-48 hours before you intend to distro

New

Party hats & replication, mutation demo

Desk drawing bases, charges

Paired homework

Nucleobases argument map (ID the claims & their support)

What is teaching?

How is it different from teaching a parrot to say words?

All the news that’s fit to print

A goes with TG goes with C

88

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

99

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?

10Who 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, its more or less inert

• key is in Hydrogen interaction pairing

• its structure IS its function

11

Use: GGGTT Green = GuanineRed = Cytosine

Blue = AdenineYellow = Thymine

1212

Primary goalsPrimary goalsConsider the necessary properties of a

chemical (DNA) that ‘is’ information

Understand HOW the bases go together

See how base pairing is replication

See how mutations arise

and why they cannot (always) be prevented

Genes in (in)action: genetic diseases

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

Understand HOW the bases go together

See how base pairing is replication

See how mutations arise

and why they cannot (always) be prevented

Genes in (in)action: genetic diseases

13Is today ‘science’?Are these

‘investigations’?• The goal of science is to create simplifying worldview

that is predictive and explanatory.

• We’re working with computers today: 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

14

Life: gimme adjectives

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

1515

Review: bonds and

“interactions”

Review: bonds and

“interactions”A few more pieces of reviewA few more pieces of review

16Four ‘bonds’/’interactions’

• Covalent: like a dowel. Arises from?

• Hydrogen interactions: like a wimpy old fridge magnet. Arises from?

• Hydrophobic interaction/exclusion: like nothing else. Arises from?

• Ionic: like a rare earth magnet. Arises from?

H-bond donors and acceptors

• Hydrogen interaction, H-bond: R-O-H - - - :N-R

• Donor (+): the group possessing the H, sharing it

• Acceptor (-): the partial (-) atom partaking of the H

17

19Which one of these is a part of the genetic code? Why

20Which one of these is a part of the genetic code? Why

Monomers Polymers Nucleotide Nucleic acid

Amino Acid Protein

21Building block

http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

Basil

Oregano

Salt

Garlic

http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

Adenine

Guanine

Cytosine

Thymine

24Blinding you with science (jargon)

• Pyrimidine (single ring), Purine (double)

• PUR As Gold

• Big base gets the little name

25

Use: GGGTT Green = GuanineRed = Cytosine

Blue = AdenineYellow = Thymine

26Pas 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

27

Fantastic plastic• Each group gets GC or AT pair. Investigate.

• Superimposability of GC, CG, AT, TA pairs

• High crimes & misdemeanors

28Anatomy of a basepair

H

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

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

29

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

3030

Closer look:Pairing BasesCloser look:

Pairing Basesthe Truth about the Codethe Truth about the Code

31BasePairer

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

• ‘Activity Guide’ is also on the web page

32

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

DNA

• What properties of DNA…

• Make it a good molecule to store info?

• Make it easy to copy?

33

34Precision & Pickiness

• H-bonds: because weak, picky

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

35Chemistry 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

36

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

Stuff happens (baaaad stuff)

Bad things happen to good bases

http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

Deamination

Cytosine

http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

DeAMINation

Cytosine

http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

Deamination

Cytosine

just add water…and heat

H2

O

NH3

http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

Deamination

Cytosine

http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

Deamination

Cytosine

Hmmm, this is IDENTICAL to THIS

http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

Deamination

Cytosine

We started with Cytosine

Deaminated it to

URACIL

http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

Deamination

CytosineUracil

Thymine

4545

Genetic DiseasesGenetic DiseasesWhy mutations matter

What loss of genetic information looks likeWhy mutations matter

What loss of genetic information looks like

46

This exercise...• Spans the next month – same groups all 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

47The task

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

• Symptoms and distribution (DUE AT END OF THIS LAB!)

• DNA mutation, amino acid change

• Your ideas about influence on protein structure

• Then you’ll share your findings with the class

48Google & WikipediaGoogle & Wikipedia

• GOOGLE.com (or Blackle.com)

• search several terms

• “phrases in quotes”

• google.com/advanced_search

• Wikipedia.org

• User contributed

• User policed

• But pretty good! 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***

49My 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

50Due today!• Genetic disease part 1, from today on calendar

• 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”

Homework 51

5252HomeworkHomeworkVocab: Transcription & Translation words

Assessor: Examining DNA/Introducing translationAssessor: Solving the Structure (remember your

tautomer)Basepairer as individual or pair

READ LAB 4!!!*

Turn in your Mix and Match Liquids lab in my TA dropbox Bio Sci East rm. 109

Vocab: Transcription & Translation wordsAssessor: Examining DNA/Introducing translationAssessor: Solving the Structure (remember your

tautomer)Basepairer as individual or pair

READ LAB 4!!!*

Turn in your Mix and Match Liquids lab in my TA dropbox Bio Sci East rm. 109

*Next week’s quiz emphasizesQuestions from the manual reading

Grading BasePairer

How the grading software works: UberPlayer

Movie: ‘Grading BasePairer

Entering grades: taProg

5454

HonorsHonorsDeaminationDeamination

55Things left out in water

and oxygen)

http://simple.wikipedia.org/wiki/File:Rust.rost.JPG

http://upload.wikimedia.org/wikipedia/commons/6/6e/Statue_of_Liberty_frontal_2.jpg

5656

Old walk-thruOld walk-thru

TA note

Following slides are old version to help you stay organized

They exactly parallel the instructions now linked from assignment & software calendars

Alert! Added ability to store A:C pair after manual printing, so it’s in instructions, but not in the manual version of the rubric

58BasePairer

Choose Guanine. Leave it be.

Describe it’s ‘pairing positions’

Deduce the face of its partner

On the right, select Cytosine

Analyze

Execute! (keep track of movements [watch the big letter ‘C ’)

Record

Turn on ‘show backbone’

59

Repeat with AT

60

Crosswise pairing

What can you do with G-T, A-C (antiparallel, 3-aligned)

Record it when you get it

Consider codes. How does it work with ‘pick your partner?

STOP!

Whatever you are doing, ask

What challenges might students be encountering with the software here?

...with the concepts?

How will you answer questions they ask you?

62Uh-oh

Click ‘Just look’ checkbox so it is on/checked

Pull up Adenine on the left; Hypoxanthine right

What’s the difference?

Consequences: go back to ‘Examine pairs’

Now look at Hypoxanthine:Cytosine

Record it

6363

Old: The wetstuffOld: The wetstuffDNA: Is it in you?DNA: Is it in you?

6464

Old/unusedOld/unused

65Sense-making

http://dd.dynamicdiagrams.com/wp-content/uploads/2011/01/orrery_2006.swf

created by Piotr Kaczmarek

66

“Nowhere is there anything resembling a blueprint of the body. At most, the genome is a set of instructions for making a body: it is not a description of a body.”

The Major Transitions in Evolution, J. M. Smith & E. Szathmary p. 257

6767

Implications & Uses

Implications & Uses

68Copying: easy as falling down

• Note that A & T; G & C ‘know’ each other by touch

• No machine needs (or uses) a ‘dictionary’ to pair them; only needs to know when a partner has been found for whatever is already there

• DNA Polymerase (the copy-maker!) indeed has no great attachment to A, T, G, C; can work with others if they H-bond*

The Examining DNA assessment will display some basepairs NOT found in our genetic code that can nonetheless be copied with good fidelity by some DNA polymerases--it’s the match, not the participants

69Ending notes

• Polymerase Chain Reaction

• Picky Pairing of short DNA strands

• the Rest is Replication

• Sensitivity: who smoked that cigarette?

• The PCR song (Bio-Rad)

70

How is RNA different from DNA?

Two, maybe 3 reasons

7171

DNA toysDNA toys

72Fun with basepairing

73

How does this work?http://www.sciencedaily.com/releases/2009/04/090402143507.htm

Movie in TA desktop folder

7474

Rube Goldberg in your genome

Rube Goldberg in your genome

The twisted tail of the ‘innovation’ of thymine from the ground state of uracil

The twisted tail of the ‘innovation’ of thymine from the ground state of uracil

75What’s the big deal?

76

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

7777

My older, more extensive code

stuff

My older, more extensive code

stuff

78Information and Copying

• Morse code: .... . ._.. ._.. _ _ _

• English: Hello

• French: Bonjour

• Chinese

• Arabic

http://www.chinese-symbols.com/h-chinese-symbol-for-hello

http://members.virtualtourist.com/m/9cfaf/1c5710/a/

Chinese, Arabic contr. by Libby Landeen

79

Making copiesImagine a two-part machine--one part sees/feels the old, one generates the new. Verbalize the minimum instruction set (terms) needed to transcribe*...

Morse?

English?

Chinese?

Example: English

E: make vertical line. Make half-length horizontal lines from top, middle and bottom of vertical line, with one endpoint on the vertical line and extending to the right

Q: ???

*A term we’ll see again; lit. “write across”

80Nitrogen-containing bases

Cytosine (C) Uracil (U)

Pyrimidines

Thymine (T)

Guanine (G) Adenine (A)

Purines

Freeman, Biological Science, 4.1

81Hydrogen bonds form between G-C pairs and A-T pairs.

Guanine Cytosine

ThymineAdenineS

ug

ar-

ph

os

ph

ate

ba

ck

bo

ne

Hydrogen bonds

DNA contains thymine,whereas RNA contains uracil

5′

5′3′

3′

Freeman, Biological Science, 4.6b

82

Printing pressesImagine you had a 3D (think braille) representation of a message

If you pressed clay over it, what kind of ‘copy’ would you get?

What process would you need to make a duplicate of the original?

83

ExamplesHow many ‘binary copy systems’* can you think of in the macro world?

snaps on jeans

*If you could only do things by feel, you could take an existing string and partner each element with another element that somehow ‘matched’ it

84

• 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?