Lab 3: Codes, Meaning, Copying

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”

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 = 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 turns hand palm up (put on purple hat) it’s undergone chemical change… replicate &…? Gua = Green Cyt = Red Ade = Blue Thy = Yellow GGGTT

DNA Why do atoms make bonds?

DNA Why do atoms make bonds? What types of ‘bonds’ are there?

DNA Why do atoms make bonds? What types of ‘bonds’ are there? Not all atoms play fair

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)

Basil Oregano Salt Garlic

Adenine Guanine Cytosine Thymine

Things you already ‘know’ Pyrimidine (single ring), Purine (double) –PUR A s G old –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 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 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 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