Translation & ProteinsTranslation & Proteins

Lab manual objectivesLab manual objectives

• Witness once again how molecular Witness once again how molecular rules influence higher order structure! rules influence higher order structure!

• Explore how monomers function to Explore how monomers function to make molecules.make molecules.

• Why does A go with T and C with G Why does A go with T and C with G again?again?

• Consider how DNA is dislike/like any Consider how DNA is dislike/like any other protein.other protein.

• Think about how these molecules Think about how these molecules function in our bodies!function in our bodies!

Biochemical Properties of Biochemical Properties of MacromoleculesMacromolecules

In lab today we will:In lab today we will: Look at physical models of these Look at physical models of these

molecules.molecules. Use computer software to Use computer software to

understand the understand the feelfeel of these of these molecules and how their surfaces molecules and how their surfaces interact with the worldinteract with the world

Big Rigs – from DNA to Big Rigs – from DNA to proteinprotein

We have a busy day!!! Let’s try to work We have a busy day!!! Let’s try to work together to make it go faster!together to make it go faster!

We have a “play” (not my idea… ahem)We have a “play” (not my idea… ahem) A oil/water and carbon exercise, a A oil/water and carbon exercise, a

“identify” amino acids exercise (this will “identify” amino acids exercise (this will be quick).be quick).

And an in-class Assessor exercise.And an in-class Assessor exercise. If anyone has ideas on how to bang this If anyone has ideas on how to bang this

out faster… speak up! We can do the out faster… speak up! We can do the hemoglobin work first, ditch the hemoglobin work first, ditch the powerpoint until later - etc… this is powerpoint until later - etc… this is YOUR class, so let me know! YOUR class, so let me know!

Revisiting AA - So lets begin Revisiting AA - So lets begin with 20 toys… pass ‘em outwith 20 toys… pass ‘em outEVERY one has a blue part. Chem EVERY one has a blue part. Chem

name?name?

EVERY one has a red part. Chem EVERY one has a red part. Chem name?name?

Thus these are all...?Thus these are all...?

How many are there? Uhhhh….How many are there? Uhhhh….

: matcmadison.edu/.../labManual/chapter_2.htm

Amino acid powerAmino acid power Like this, the right handed side of the Like this, the right handed side of the

picture is called the native state, the right is picture is called the native state, the right is the result of the process of largely hydrogen the result of the process of largely hydrogen bonding, bonding, resulting in a three-resulting in a three-dimensional structure determined by a dimensional structure determined by a sequence of amino acids.sequence of amino acids.

Different tools; different Different tools; different jobsjobs

Your group has an amino acid; which is it?Your group has an amino acid; which is it? In what ways are all bases identical? In what ways are all bases identical?

Different?Different? In what ways are all amino acids In what ways are all amino acids

identical? Different?identical? Different? Which group is more diverse in terms of Which group is more diverse in terms of

‘feel’?‘feel’? Which is more diverse in terms of shape?Which is more diverse in terms of shape? Which would allow you to build more Which would allow you to build more

diverse shapes & surfaces?diverse shapes & surfaces? How many?How many?

Tah Dah! But of course! There have to be 20, not including start and stop codons.

And these amino acids lead the way to all kinds of protein fun and folding.

While I talk….While I talk….

• Lets make things go quicker today..Lets make things go quicker today..

• I talk, listen – but while doing so, take I talk, listen – but while doing so, take a pencil and follow the instructions on a pencil and follow the instructions on the next slide.the next slide.

• What’s in a pencil?What’s in a pencil?

• Graphite! Graphite!

• What’s graphite? – all What’s graphite? – all allotropes of carbonallotropes of carbon

Get the oil and water…Get the oil and water…

• Use the pencils (sideways) to make Use the pencils (sideways) to make an area on the cards where you can an area on the cards where you can punch out about 6 or so little circles.punch out about 6 or so little circles.

• Make sure the penciled region is Make sure the penciled region is thick enough and then drop those thick enough and then drop those little suckers into the oil/water little suckers into the oil/water mixture, mix ‘em up.mixture, mix ‘em up.

• Do this while I jabber away – I’m not Do this while I jabber away – I’m not offended!offended!

So…So…• ‘‘hiding greasy spots’ is the primary hiding greasy spots’ is the primary

driver in protein foldingdriver in protein folding

• maximizing the number of charge-maximizing the number of charge-charge and H-bonding interactions charge and H-bonding interactions mattersmatters

• Tell me about your results and Tell me about your results and carbons role !carbons role !

So now, why should I bother So now, why should I bother with this?with this?• TherapyTherapy

• Drug designDrug design

• Natural products & chemistryNatural products & chemistry

• Like - green fluorescent protein (GFP) Like - green fluorescent protein (GFP)

Comes from a fluorescent Comes from a fluorescent jellyfish!jellyfish!• This protein has become one of the This protein has become one of the

most important tools in most important tools in contemporary bioscience. Using GFP, contemporary bioscience. Using GFP, researchers have developed ways to researchers have developed ways to watch processes that were previously watch processes that were previously invisible, like the development of invisible, like the development of nerve cells or how cancer cells nerve cells or how cancer cells spread! spread!

• These guys won a Nobel Prize for this These guys won a Nobel Prize for this discovery! discovery!

So how do we get here from So how do we get here from there? Or anywhere…there? Or anywhere…

• These are a lot of new terms. This These are a lot of new terms. This language can be bizarre. These concepts language can be bizarre. These concepts could even be a little overwhelming at could even be a little overwhelming at first.first.

• In a slide or two we will remind you that In a slide or two we will remind you that this can all really be as simple as a this can all really be as simple as a process the cells in your body undergo process the cells in your body undergo every day. Now. And now. And again.every day. Now. And now. And again.

• Lets review the “Central Dogma” one Lets review the “Central Dogma” one more time. more time.

Blinding you with Blinding you with ScienceScience

mRNA: mRNA: messengermessenger RNA; the RNA string copied RNA; the RNA string copied (‘transcribed’) from DNA(‘transcribed’) from DNA

tRNA: tRNA: transfertransfer RNA; one of many RNA molecules RNA; one of many RNA molecules that carry specific amino acidsthat carry specific amino acids

ribosome: giant machine (>200 proteins, 4 RNAs ribosome: giant machine (>200 proteins, 4 RNAs (2 > 1000 nucleotides) that oversees the reading (2 > 1000 nucleotides) that oversees the reading of the mRNA and the creation of polypeptideof the mRNA and the creation of polypeptide

aminoacyl tRNA synthetase: a protein machine aminoacyl tRNA synthetase: a protein machine that adds a specific amino acid to tRNAs it that adds a specific amino acid to tRNAs it recognizesrecognizes

Termination factor: ‘reads’ UAA et al., causes Termination factor: ‘reads’ UAA et al., causes ribosome to cut loose the peptide and fall apartribosome to cut loose the peptide and fall apart

Dogma, Dogma…Dogma, Dogma…

www.answers.com

www.cbs.dtu.dk/.../roanoke/central_dogma.gif

So the amino acids do So the amino acids do what?what?

serc.carleton.edu/.../research_methods/genomics

Transcription & Translation have many players.

Now lets tackle the nomenclature, so we all know the right words.

Then, I think this process/concept becomes more manageable.

More “central dogma”More “central dogma”

And then the proteins And then the proteins are made…are made…

So it all boils down to this…So it all boils down to this…

But we have to start But we have to start somewhere…somewhere…

• And then we can understand…

The importance of mutation: easy to understand (and foundational to today & to general understanding of disease, evolution...)

Mutations on a larger scale Mutations on a larger scale - DNA- DNA

Livable mutations too!Livable mutations too!

Smaller scale – proteins like Smaller scale – proteins like hemoglobinhemoglobin

Then it all fell apart...Then it all fell apart...

*Moby, “Extreme ways” (theme from Bourne II & III)

Hartl & Jones, Genetics: Analysis of Genes and Genomes, Figure 7-35

We will be looking at this in We will be looking at this in depth pretty darn soon…depth pretty darn soon…

But a little more on protein folding But a little more on protein folding and the like first.and the like first.acid + milk, boiling eggs, making acid + milk, boiling eggs, making cheese all good examples of cheese all good examples of charge/phobicity => folding & charge/phobicity => folding & structurestructure

but most have seen these, and but most have seen these, and other than gee-whiz, is there a way other than gee-whiz, is there a way to tie to this week’s concepts?to tie to this week’s concepts?

But to talk about these we But to talk about these we gotta go way back to where gotta go way back to where

we began, much like my we began, much like my little friend here…little friend here…

And that And that “somewhere” “somewhere”

was here!was here!This amino acid chain being “built”

ultimately participates in the shaping and folding of proteins in water (which

we are mostly made up of!)

Proteins are about 50% of the dry weight of most cells, and are the most structurally complex macromolecules known. Each type of protein has its own unique structure and function.Polymers are any kind of large molecules made of repeating identical or similar subunits called monomers. The starch we previously saw in action are polymers of glucose, which in that case, is the monomer. Proteins are polymers of about 20 amino acids (the monomer).

tRNA hangs on to the AA chain

Two important things happen here re: joining

up