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Why. How?. Lab 4: DNA – the instructions for life. First things first:. Why do we teach the way that we teach?. Modeling. Why we do it How to tell if we ’ re doing it right. What ’ s the difference. Between assertion and evidence ?

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first things first
First things first:
  • Why do we teach the way that we teach?
modeling
Modeling
  • Why we do it
  • How to tell if we’re doing it right
what s the difference
What’s the difference...
  • Between assertion and evidence?
  • What constitutes a valid, coherent scientific argument that X is true?
  • Is the earth the center of the solar system? Justify!
sense making
Sense-making

created by Piotr Kaczmarek

http://dd.dynamicdiagrams.com/wp-content/uploads/2011/01/orrery_2006.swf

is today science are these investigations
Is today ‘science’?Are these ‘investigations’?
  • The goal of science is to create simplifying worldview that is predictive and explanatory.
  • 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
why use analogies 181 only
Why use analogies? (181 only)
  • http://www.technologystudent.com/struct1/arch1.htm
where we ve been
Where we’ve been
  • Proteins and how they get their shape
  • Hemoglobin – explored one awesome protein in detail
where we re going
Where we’re going
  • HOW does the cell know how to make Hemoglobin (and every other protein)?
  • Where are the instructions?
  • How are these instructions ‘read’?
  • Who does the building?
  • How can it be that none of the builders can ‘think’, ‘read’ or ‘understand’?
slide10
DNA!
  • Is the instruction molecule of the cell
  • Proteins are the action molecules of the cell
  • DNA contains the instructions for building proteins
atoms they re how life works
Atoms: They’re how life works
  • DNA, RNA: C, H, N, O, P, [Mg++]
  • Carbs: C, H, O
  • Protein: C, H, N, O, (S), (P)

How can this small assortment of atoms be used to both build the machines of the cell (proteins) AND store the instructions for the machines (DNA)?

primary goals
Primary goals
  • Consider the necessary properties of a chemical that ‘is’ instructions
  • Understand DNA stores and relays the instructions
  • Understand HOW the bases go together
  • See that pairing is replication (storing) and transcription (relaying)
how to make sense of dna
How to make sense of DNA?
  • Recipe book analogy
now it s your turn
Now it’s your turn!
  • Have students do the Info-flow exercise
once you have finished information flow come up and get a worksheet
Once you have finished Information Flow, come up and get a worksheet.
  • The worksheet is a series of questions concerning how the analogy relates to the processes of replication and transcription/translation, so it will be beneficial to pay attention to what is written in the exercise as you do it
  • It will be worth points on your quiz next week
how does the recipe analogy make us smarter1
How does the recipe analogy make us smarter?
  • The whole recipe book = ?
  • all the DNA in a cell (the whole genome)
how does the recipe analogy make us smarter2
How does the recipe analogy make us smarter?
  • The whole recipe book = ?
  • all the DNA in a cell (the whole genome)
    • What does a recipe represent?
how does the recipe analogy make us smarter3
How does the recipe analogy make us smarter?
  • The whole recipe book = ?
  • all the DNA in a cell (the whole genome)
    • What does a recipe represent?
    • Gene = section of DNA = instructions for making a protein
how does the recipe analogy make us smarter4
How does the recipe analogy make us smarter?
  • The whole recipe book = ?
  • all the DNA in a cell (the whole genome)
    • What does a recipe represent?
    • Gene = section of DNA = instructions for making a protein
    • The recipes for how many different dishes are in the book?
how does the recipe analogy make us smarter5
How does the recipe analogy make us smarter?
  • The whole recipe book = ?
  • all the DNA in a cell (the whole genome)
    • What does a recipe represent?
    • Gene = section of DNA = instructions for making a protein
    • The recipes for how many different dishes are in the book?
    • How many different types of genes are in the genome (all the DNA in a cell)?
how does the recipe analogy make us smarter6
How does the recipe analogy make us smarter?
  • The process of making a copy of the whole recipe book = ?
how does the recipe analogy make us smarter7
How does the recipe analogy make us smarter?
  • The process of making a copy of the whole recipe book = ?
  • The process of REPLICATION
how does the recipe analogy make us smarter8
How does the recipe analogy make us smarter?
  • The process of making a copy of the whole recipe book = ?
  • The process of REPLICATION
    • How much of the book would you want a copy of?
how does the recipe analogy make us smarter9
How does the recipe analogy make us smarter?
  • The process of making a copy of the whole recipe book = ?
  • The process of REPLICATION
    • How much of the book would you want a copy of?
    • How much of the DNA would a new cell want a copy of?
how does the recipe analogy make us smarter10
How does the recipe analogy make us smarter?
  • The copy of the recipe book that was given to you = ?
how does the recipe analogy make us smarter11
How does the recipe analogy make us smarter?
  • The copy of the recipe book that was given to you = ?
  • the copy of all the DNA that a new cell gets when it is made
how does the recipe analogy make us smarter12
How does the recipe analogy make us smarter?
  • The copy of the recipe book that was given to you = ?
  • the copy of all the DNA that a new cell gets when it is made
  • Things to think about:
    • If you had just been given the recipe book, would you make EVERY recipe in the book?
how does the recipe analogy make us smarter13
How does the recipe analogy make us smarter?
  • The copy of the recipe book that was given to you = ?
  • the copy of all the DNA that a new cell gets when it is made
  • Things to think about:
    • If you had just been given the recipe book, would you make EVERY recipe in the book?
    • Does a cell make all of the proteins that it has the instructions for?
how does the recipe analogy make us smarter14
How does the recipe analogy make us smarter?
  • The copy of the recipe book that was given to you = ?
  • the copy of all the DNA that a new cell gets when it is made
  • Things to think about:
    • If you had just been given the recipe book, would you make EVERY recipe in the book?
    • Does a cell make all of the proteins that it has the instructions for?
    • Put another way – does a ‘liver cell’ make all the proteins the DNA it contains has the instructions for?
how does the recipe analogy make us smarter15
How does the recipe analogy make us smarter?
  • Clarifications:
    • REPLICATION is just the very first part of the analogy (making a copy of the recipe book).
    • It is a separate process from everything else that follows
how does the recipe analogy make us smarter16
How does the recipe analogy make us smarter?
  • Process of making a photo copy of the recipe =
  • the processes of TRANSCRIPTION (making a copy of RNA from DNA)
  • Photo copy of the recipe =?
  • Strand of mRNA
    • How much of the recipe book should be taken to a picnic to make just one recipe?
    • How much of the DNA would need to be copied to make just one protein?
    • How permanent does the recipe copy need to be?
    • How permanent does the copy of the DNA (copy = mRNA) need to be?
how does the recipe analogy make us smarter17
How does the recipe analogy make us smarter?
  • Process of making a photo copy of the recipe =
how does the recipe analogy make us smarter18
How does the recipe analogy make us smarter?
  • Process of making a photo copy of the recipe =
  • the processes of TRANSCRIPTION (making a copy of RNA from DNA)
how does the recipe analogy make us smarter19
How does the recipe analogy make us smarter?
  • Process of making a photo copy of the recipe =
  • the processes of TRANSCRIPTION (making a copy of RNA from DNA)
  • Photo copy of the recipe =?
how does the recipe analogy make us smarter20
How does the recipe analogy make us smarter?
  • Process of making a photo copy of the recipe =
  • the processes of TRANSCRIPTION (making a copy of RNA from DNA)
  • Photo copy of the recipe =?
  • Strand of mRNA
how does the recipe analogy make us smarter21
How does the recipe analogy make us smarter?
  • Process of making a photo copy of the recipe =
  • the processes of TRANSCRIPTION (making a copy of RNA from DNA)
  • Photo copy of the recipe =?
  • Strand of mRNA
    • How much of the recipe book should be taken to a picnic to make just one recipe?
how does the recipe analogy make us smarter22
How does the recipe analogy make us smarter?
  • Process of making a photo copy of the recipe =
  • the processes of TRANSCRIPTION (making a copy of RNA from DNA)
  • Photo copy of the recipe =?
  • Strand of mRNA
    • How much of the recipe book should be taken to a picnic to make just one recipe?
    • How much of the DNA would need to be copied to make just one protein?
how does the recipe analogy make us smarter23
How does the recipe analogy make us smarter?
  • Process of making a photo copy of the recipe =
  • the processes of TRANSCRIPTION (making a copy of RNA from DNA)
  • Photo copy of the recipe =?
  • Strand of mRNA
    • How much of the recipe book should be taken to a picnic to make just one recipe?
    • How much of the DNA would need to be copied to make just one protein?
    • How permanent does the recipe copy need to be?
how does the recipe analogy make us smarter24
How does the recipe analogy make us smarter?
  • Process of making a photo copy of the recipe =
  • the processes of TRANSCRIPTION (making a copy of RNA from DNA)
  • Photo copy of the recipe =?
  • Strand of mRNA
    • How much of the recipe book should be taken to a picnic to make just one recipe?
    • How much of the DNA would need to be copied to make just one protein?
    • How permanent does the recipe copy need to be?
    • How permanent does the copy of the DNA (copy = mRNA) need to be?
how does the recipe analogy make us smarter25
How does the recipe analogy make us smarter?
  • Following the instructions on the copy of the recipe =
how does the recipe analogy make us smarter26
How does the recipe analogy make us smarter?
  • Following the instructions on the copy of the recipe =
  • Translation
how does the recipe analogy make us smarter27
How does the recipe analogy make us smarter?
  • Following the instructions on the copy of the recipe =
  • Translation
    • How many sandwiches could be made from the photo copy of the recipe at the picnic?
how does the recipe analogy make us smarter28
How does the recipe analogy make us smarter?
  • Following the instructions on the copy of the recipe =
  • Translation
    • How many sandwiches could be made from the photo copy of the recipe at the picnic?
    • How many proteins can be made from the mRNA?
how does the recipe analogy make us smarter30
How does the recipe analogy make us smarter?
  • Turkey club sandwich =
  • a specific protein
how does the recipe analogy make us smarter31
How does the recipe analogy make us smarter?
  • Turkey club sandwich =
  • a specific protein
  • Every different dish in the recipe book =?
how does the recipe analogy make us smarter32
How does the recipe analogy make us smarter?
  • Turkey club sandwich =
  • a specific protein
  • Every different dish in the recipe book =?
  • all the different types of proteins
how does the recipe analogy make us smarter33
How does the recipe analogy make us smarter?
  • Turkey club sandwich =
  • a specific protein
  • Every different dish in the recipe book =?
  • all the different types of proteins
  • **Remember: A genome (all the DNA in a cell) stores the information needed to make every different protein
  • **However, only a small subset of proteins is ever made by a specific type of cell
important point to remember
Important point to remember:
  • REPLICATION is a completely separate process from TRANSCRIPTION/TRANSLATION
    • Transcription DOES not directly follow Replication
  • REPLICATION is the copying of the entire genome (ALL the DNA) in order to provide a new cell with a copy
  • TRANSCRIPTION is the copying of a section of DNA (gene) to make mRNA (a temporary messenger molecule)
  • TRANSLATION is the ‘reading’ of the mRNA in order to build a protein
getting down to the nitty gritty
Getting down to the nitty gritty
  • HOW does DNA store and transmit instructions?
  • What is happening at the molecular level?
review bonds
Review: bonds
  • A few more pieces of review
  • For sure we need to review hydrogen bonds in this lab
four bonds
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?
let s investigate
Let’s investigate
  • What fits? How does it fit?
blinding you with science jargon
Blinding you with science (jargon)
  • Pyrimidine (single ring), Purine (double)
    • PURAs Gold
    • Big base gets the little name
  • Hydrogen interaction, H-bond: O-H :N-
    • Donor: the group possessing the H, sharing it
    • Acceptor: the partial (-) atom partaking of the H
slide58

Guanine

Adenine

Thymine

Cytosine

Where can hydrogen bonds form?

slide59

Hydrogen bonds form between G-C pairs and A-T pairs.

Hydrogen bonds

5′

3′

Guanine

Cytosine

Sugar-phosphate backbone

Adenine

Thymine

DNA contains thymine,whereas RNA contains uracil

5′

3′

Freeman, Biological Science, 4.6b

Grow a basepair

closer look pairing bases
Closer look:Pairing Bases
  • the Truth about the Code
rubrics
Rubrics
  • ContCent week4 => Calendar => BasePairer
  • Click on How To for instructions on how to do the assignment
  • Go to not-for-credit in order to access BasePairer to work with now in class (is this the best way for them to access it?)
  • The Rubric will explain how you will be scored on what you turn in for the BasePairer homework
basepairer
Basepairer
  • Launch ‘BasePairer’
  • Don’t log in; that’s for homework
  • Write down the name of the person you are working with for this assignment
more detailed view
More detailed view

http://www2.estrellamountain.edu/faculty/farabee/biobk/biobookdnamolgen.html

slide67

Hydrogen bonds form between G-C pairs and A-T pairs.

Hydrogen bonds

5′

3′

Guanine

Cytosine

Sugar-phosphate backbone

Adenine

Thymine

DNA contains thymine,whereas RNA contains uracil

5′

3′

Freeman, Biological Science, 4.6b

dna replication
DNA Replication

ALL the DNA is replicated – the whole genome

DNA replication = making copy of entire recipe book

dna transcription
DNA Transcription

Only part of the DNA is transcribed – the gene that is the instructions for making the protein

DNA transcription = making photo copy of one recipe

http://biochem.co/wp-content/uploads/2008/08/trascription-dna-to-rna.png

homework see control center
Homework- See Control Center

Next week’s quiz emphasizes

Questions from the manual reading

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