Transcript basepairing - Biology Learning Center

Pics: homepage => Instructors
Wed @ 11 meeting:
Andrea- Sara-Ryan
Lynn - Bob Steve
Katie- Heidi Leslie
Aleksi- Deborah
Emily- Sarah Jing
Tyler- Candice Jessica
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Grading
Movie: 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 T
G goes with C
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Spider dance!
Now that’s ‘information’!
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How?
Why?
DNA:
instructions for the parts of
living things
Why the instructions for you are stored as
hydrogen interactions between ringy things
Who cares about DNA?
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•
It’s what’s in you (and every other living thing)
•
It’s (part of) the magical interface between chemistry and life
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It is perhaps the single most easily understood biomolecule you’ll
ever meet
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doesn’t ‘do’ anything, its more or less inert
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key is in Hydrogen interaction pairing
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its structure IS its function
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Use: GGGTT
Green = Guanine
Red = Cytosine
Blue = Adenine
Yellow = Thymine
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Primary goals
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
Is today ‘science’?
Are these ‘investigations’?
13
•
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
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Life: gimme adjectives
What’s the difference between you, the bench
top, a rock, a candle flame?
15
Review: bonds and
“interactions”
A few more pieces of review
Four ‘bonds’/’interactions’
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Covalent: like a dowel. Arises from?
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Hydrogen interactions: like a wimpy old fridge magnet.
Arises from?
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Hydrophobic interaction/exclusion: like nothing else.
Arises from?
•
Ionic: like a rare earth magnet. Arises from?
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H-bond donors and
acceptors
•
Hydrogen interaction, H-bond: R-O-H -
- - :N-R
•
Donor (+): the group possessing the H, sharing it
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Acceptor (-): the partial (-) atom partaking of the H
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Which one of these is a part of the genetic19
code? Why
Which one of these is a part of the genetic20
code? Why
Monomers
Polymers
Nucleotide
Nucleic acid
Amino Acid Protein
Building block
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Oregano
Salt
Garlic
Basil
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Guanine
Cytosine
Thymine
Adenine
http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Blinding you with science
(jargon)
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Pyrimidine (single ring), Purine (double)
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PUR As Gold
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Big base gets the little name
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Use: GGGTT
Green = Guanine
Red = Cytosine
Blue = Adenine
Yellow = Thymine
GGGTT
Pas de deux*
Gua = Green 26
Cyt = Red
Ade = Blue
Thy = Yellow
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Party hats on--we’re going to do some line dancing!
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Starting point: a double strand of DNA, each base facing partner
with their ‘right hand’ on neighbor’s shoulder
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Each strand ‘count off’ from their L to R, how do the two
directions compare?
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Separate strands; who partners with whom? What external info
do we need to re-create the missing strand?
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Restart; ‘Mask’ one with a purple hat; it’s undergone chemical
change
•
replicate &…?
*Dictionary.com: a dance by two persons
Fantastic plastic
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Each group gets GC or AT pair. Investigate.
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Superimposability of GC, CG, AT, TA pairs
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High crimes & misdemeanors
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Anatomy of a basepair
Ornaments:
-NH2
=O
-H
-OH
=NH
H
----- Dashed lines indicate
double bonds present in
some purines or
pyrimidines
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Grow your own--make GC or AT
Hydrogen bonds form between G-C pairs and A-T pairs.
Hydrogen bonds
Sugar-phosphate backbone
5
Guanine
Adenine
3
Cytosine
Text
3
Thymine
DNA contains thymine,
whereas RNA contains uracil
Freeman, Biological Science, 4.6b
5
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Closer look:
Pairing Bases
the Truth about the Code
BasePairer
•
Homepage = > my instructor link => this week => BasePairer
rubric
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‘Activity Guide’ is also on the web page
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Basepairer
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Launch ‘BasePairer’
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Don’t log in; that’s for homework
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Write your names on the paper I hand out; return it at end
of class or zero credit
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make a note of your group name & genetic disease in
your lab notebook
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DNA
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What properties of DNA…
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Make it a good molecule to store info?
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Make it easy to copy?
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Precision & Pickiness
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H-bonds: because weak, picky
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Combined with stiff bases: it’s all right or it it’s wrong
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Chemistry Happens II
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Dr. Base & Mr. Tautomer
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Why Chargaff’s rules didn’t => the structure
%A
%T
%G
%C
Mycobacterium
15.1
14.6
34.9
35.4
Yeast
31.3
32.9
18.7
17.1
Wheat
27.3
27.1
22.7
22.8
Sea Urchin
32.8
32.1
17.7
17.3
Marine Crab
47.3
47.3
2.7
2.7
Turtle
29.7
27.9
22
21.3
Rat
28.6
28.4
21.4
21.5
Human
30.9
29.4
19.9
19.8
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Stuff happens (baaaad stuff)
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http://www.nature.com/scitable/nated/content/ne0000/ne0000/ne0000/ne0000/97271/pierce_17_11_FULL.jpg
Bad things happen
to good bases
Deamination
Cytosine
//jennifersaylor.files.wordpress.com/2006/08/dna.jpg
DeAMINation
Cytosine
//jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Deamination
NH3
H2
O
just add water…
and heat
Cytosine
//jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Deamination
Cytosine
//jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Deamination
Hmmm, this is IDENTICAL to
THIS
Cytosine
//jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Deamination
We started with Cytosine
Deaminated it to
URACIL
Cytosine
//jennifersaylor.files.wordpress.com/2006/08/dna.jpg
Deamination
Thymine
Uracil
Cytosine
//jennifersaylor.files.wordpress.com/2006/08/dna.jpg
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Genetic Diseases
Why mutations matter
What loss of genetic information looks like
This exercise...
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Spans the next month – same groups all month!
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Lets you apply your learning and thinking to an actual
disease
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What is most important is that you think well and
integrate what you are learning; being ‘right’ is
secondary
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The task
•
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Over the coming weeks, you’ll characterize a genetic disease
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Symptoms and distribution (DUE AT END OF THIS
LAB!)
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DNA mutation, amino acid change
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Your ideas about influence on protein structure
Then you’ll share your findings with the class
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Google & Wikipedia
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GOOGLE.com (or Blackle.com)
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search several terms
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“phrases in quotes”
•
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Caveat emptor! The web is a
wonderful, rich source of
google.com/advanced_search information. ***But anybody can
have a webpage***
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Wikipedia.org
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User contributed
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User policed
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But pretty good!
If you want to Bing, I’m not stopping you
My sources
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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
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NIH: Federally funded science & health professionals, I judge it
generally very trustworthy
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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
Due today!
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Genetic disease part 1, from today on calendar
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Handed in to me with all group member names on it
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An example:
hemoglobin/sickle cell anemia
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Sufferers: one in 12 African Americans has the TRAIT;
overall, 1/5000 Americans suffer
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Common in areas with malaria
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symptoms: shortened lifespan (48-52), see next slide”
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Homework
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Homework
Vocab: Transcription & Translation words
Assessor: Examining DNA/Introducing translation
Assessor: 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 emphasizes
Questions from the manual reading
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Grading BasePairer
How the grading software works: UberPlayer
Movie: ‘Grading BasePairer
Entering grades: taProg
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Honors
Deamination
Things left out in water
and oxygen)
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http://simple.wikipedia.org/wiki/File:Rust.rost.JPG
http://upload.wikimedia.org/wikipedia/commons/6/6e/Statue_of_Liberty_frontal_2.jpg
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Old 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
BasePairer
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’
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Repeat with AT
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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?
Uh-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
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Old: The wetstuff
DNA: Is it in you?
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Old/unused
Sense-making
created by Piotr Kaczmarek
http://dd.dynamicdiagrams.com/wp-content/uploads/2011/01/orrery_2006.swf
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“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
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Implications & Uses
Copying: easy as falling
down
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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
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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
Ending notes
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Polymerase Chain Reaction
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Picky Pairing of short DNA strands
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the Rest is Replication
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Sensitivity: who smoked that cigarette?
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The PCR song (Bio-Rad)
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How is RNA different
from DNA?
Two, maybe 3 reasons
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DNA toys
Fun with
basepairing
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How does this work?
http://www.sciencedaily.com/releases/2009/04/09040
2143507.htm
Movie in TA desktop folder
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Rube Goldberg in
your genome
The twisted tail of the ‘innovation’ of thymine
from the ground state of uracil
What’s the big deal?
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What’s up with U?
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Just a T without the -CH3
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In terms of basepairing, identical in the partnering
with A
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Historically, U came first (as RNA preceded DNA);
FYI, the ‘marking’ of T allows better
maintenance/repair of DNA than is available in RNA
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My older, more
extensive code stuff
Information and Copying
.... . ._.. ._.. _ _ _
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Morse code:
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English: Hello
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French: Bonjour
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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
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Making copies
Imagine a two-part machine--one part sees/feels the old, one generates the
new. Verbalize the minimum instruction set (terms) needed to transcribe*...
*A term we’ll see again; lit. “write across”
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: ???
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Nitrogen-containing bases
Cytosine (C)
Uracil (U)
Pyrimidines
Thymine (T)
Adenine (A)
Guanine (G)
Purines
Freeman, Biological Science, 4.1
Hydrogen bonds form between G-C pairs and A-T pairs.
Hydrogen bonds
Sugar-phosphate backbone
5
3
Guanine
Cytosine
Adenine
Thymine
DNA contains thymine,
whereas RNA contains uracil
Freeman, Biological Science, 4.6b
3
5
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Printing presses
Imagine 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?
Examples
How 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
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Why do we call them that?
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Adenine: from the Greek word for gland
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Thymine: first isolated from the thymus
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Cytosine isolated from ‘cells’ (think cytoplasm)
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Guanine: Yep--first isolated from bird guano
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