Dancing Spiders

DNA 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 & Specific Shake 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 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)

Charges… Again

Basil Oregano Salt Garlic

Basil Oregano Salt Garlic

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 – –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 = Green Cyt = Red Ade = Blue Thy = 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 = Green Cyt = Red Ade = Blue Thy = Yellow GGGTT

Things you already ‘know’ Pyrimidine (single ring), Purine (double) –PUR A s G old –C ut T he 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 basepair Ornaments -NH2 =O -H -OH =NH

Make your own GC or AT Hydrogen bonds form between G-C pairs and A-T pairs. GuanineCytosine ThymineAdenine Sugar-phosphate backbone Hydrogen bonds DNA contains thymine, whereas RNA contains uracil 55 55 33 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

Bad things happen to good bases Chart tautomers

Bad things happen to good bases What happens when cytosine gets deaminated? What would the consequences be?

Bad things happen to good bases Take a look at your tautomers -- basepairer

Deamination Cytosine

DeAMINation Cytosine

Deamination Cytosine just add water… and heat H2OH2O NH3

Deamination Cytosine

Deamination Cytosine Hmmm, this is IDENTICAL to THIS

Deamination Cytosine We started with Cytosine Deaminated it to URACIL

Deamination Cytosine Uracil 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 Bases Chargaff’s Rules didn’t lead to structure WHY? %A%T%G%C Mycobacterium Yeast Wheat Sea Urchin Marine Crab Turtle Rat Human

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 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 genome 1.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.