Lab 3: Codes, Meaning, Copying. DNA Instructions for the parts of living things Why the instructions.

Lab 3: Codes, Meaning, Copying

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


Why care about DNA?

DNA


• 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


• So what does it mean to be “living”

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

DNA


Why Does A “go with” T?

• 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 GGGTT ,‘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 turns hand palm up (put on purple hat)

• it’s undergone chemical change… replicate &…?

Gua = GreenCyt = RedAde = BlueThy = YellowGGGTT

DNA


• Why do atoms make bonds?

DNA



• What types of ‘bonds’ are there?

DNA



• What types of ‘bonds’ are there?

• Not all atoms play fair

DNA


• Hydrogen bond/interaction

DNA



• When H bonds with ‘O’ or ‘N’

DNA




•Based on electronegativity

DNA




•Based on electronegativity

• Why not Carbon-Hydrogen?

DNA




• H-Bond Donors

DNA




• H-Bond Donors

• Positive charge (Hydrogen)

DNA




• H-Bond Donors


• H-Bond Acceptors

DNA




• H-Bond Donors


• H-Bond Acceptors

• Negative charge (O, N)


Basil

Oregano

Salt

Garlic


Adenine

Guanine

Cytosine

Thymine


Things you already ‘know’

• Pyrimidine (single ring), Purine (double)

– PUR As Gold

– Big base = little name


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


Anatomy of a basepairOrnaments

-NH2

=O

-H

-OH

=NH


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


Rubric is available via web page

BasePairer


• Go to the ‘Lab03_DNA’ folder

• 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

• Basepairer group = genetic disease group

• make a note of your group name & genetic disease in your lab notebook

Basepairer


Bad things happen to good bases

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

Tautomers

Bad things happen to Good Bases

Tautomers

Bad things happen to Good Bases


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


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!


Genetic Diseases

Due Today!!!Part 1 of assignment

Turned in to me with all group members’ names on it.


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


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

• Transcribe & Translate (Vocab)

•Basepairer –Group assignment (1/group)

–Written portion to Dropbox

•Quiz next week –Emphasizes next week’s lab

–Study today’s material, too

Lab 3: Codes, Meaning, Copying. DNA Instructions for the parts of living things Why the instructions.

Documents