dancing spiders. dna instructions for the parts of living things why the instructions for you

Dancing Spiders

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”

•Give me adjectives!

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?

8

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?

9

Four ‘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?

Some things…

• Polarity describes a covalent bond. If something is polar what does that mean? What about nonpolar?

• Ions arise from what type of bond? Is there a charge? If so, what type of charge?

• Electronegativity describes atoms NOT molecules. – Water is not electronegative! The atoms that make

up water are, which creates an uneven distribution of electrons.

10

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)

Charges… Again


Basil

Oregano

Salt

Garlic


Adenine

Guanine

Cytosine

Thymine

25

• 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?

Party time!

26

• Party hats on- • Starting point:

– BLUE hats – 0 - +– GREEN hats – + + -– YELLOW hats – - + -– RED hats – + - -

• 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 = 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 changes to - + - (put on purple hat)

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

Gua = GreenCyt = RedAde = BlueThy = Yellow

GGGTT


Things you already ‘know’

• Pyrimidine (single ring), Purine (double)

– PUR As Gold

– Cut The PY

– 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

• Work through the activity guide for homework

• HOMEWORK answers in Dropbox on D2L page

• Can work in pairs (contract)

Basepairer

DNA

• What properties of DNA…– Make it a good molecule to store info– Make it ‘easy’ to copy

http://www.flickr.com/photos/66831827@N00/5318810/in/photostream



Bad things happen to good bases

• Chart

• tautomers



• What happens when cytosine gets deaminated?

• What would the consequences be?


• Take a look at your tautomers -- basepairer


Deamination

Cytosine


DeAMINation

Cytosine


Deamination

Cytosine

just add water…and heat

H2ONH3


Deamination

Cytosine


Deamination

Cytosine

Hmmm, this is IDENTICAL to THIS


Deamination

Cytosine

We started with Cytosine

Deaminated it to

URACIL


Deamination

CytosineUracil

Thymine

48

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

49

Nitrogen-containing bases

Cytosine (C) Uracil (U)

Pyrimidines

Thymine (T)

Guanine (G) Adenine (A)

Purines

Freeman, Biological Science, 4.1

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


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

Page I-1 of your lab manual

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


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


Genetic Diseases


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

• Solving the Structure Assessor

• Transcribe & Translate (Vocab)

• READ next weeks lab and ‘Dicty”

insert

•Quiz next week next week’s lab AND previous labs

Your genome1. Get a cup of saltwater solution; swish vigorously in mouth for

30 seconds. {other protocols suggest gently chewing your cheeks as well}. This will remove dead cells lining the mouth and provide students with a source of their own DNA.

2. Spit back into cup; then pour it into a large test tube containing 5ml of detergent solution.

3. Cap the test tube {let's try with parafilm; it MAY dissolve in detergent} and gently rock it on its side for 2-3 minutes.

4. Uncap the tube and then slightly tilt it and carefully pour 5ml chilled ethanol down the inside of the tube so that it forms a layer on the top.

5. Allow the tube to stand for one minute. Use a thin wood or glass rod to slowly move some of the ethanol into the soap layer. Spool the DNA strands around it. If too much shearing has occurred, the DNA fragments may be too short to wind up, and they may form clumps instead.

dancing spiders. dna instructions for the parts of living things why the instructions for you

Documents

h bonds

n hbond donorsdnahttp

hydrogen interactions

hbonding structure

type of bond

covalent bond

type of charge

living things interface