Lab 4 dna the instructions for life
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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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Lab 4: DNA – the instructions for life

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Lab 4 dna the instructions for life

Why

How?

Lab 4: DNA – the instructions for life


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’?


Lab 4 dna the instructions for life

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 smarter

How does the recipe analogy make us smarter?

  • The whole recipe book = ?


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 smarter29

How does the recipe analogy make us smarter?

  • Turkey club sandwich =


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


Why does a g go with a c and an a go with a t

WHY does a G go with a C and an A go with a T???


Lab 4 dna the instructions for life

Where can hydrogen bonds form?


Lab 4 dna the instructions for life

Guanine

Adenine

Thymine

Cytosine

Where can hydrogen bonds form?


Lab 4 dna the instructions for life

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


Building block

Building block


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


Flip and rotate cytosine

Flip and Rotate Cytosine


Why did cytosine need to be flipped and rotated

Why did Cytosine need to be ‘flipped’ and ‘rotated’?


More detailed view

More detailed view

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


Lab 4 dna the instructions for life

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


What do you notice here

What do you notice here?


Summary

Summary


Base pairing is replication

Base pairing is REPLICATION


Dna replication

DNA Replication

ALL the DNA is replicated – the whole genome

DNA replication = making copy of entire recipe book


Re set

Re-set


Base pairing is transcription

Base Pairing is Transcription


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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