Translation & Proteins

Lab manual objectives Witness once again how molecular rules influence higher order structure! Witness once again how molecular rules influence higher order structure! Explore how monomers function to make molecules. Explore how monomers function to make molecules. Why does A go with T and C with G again? Why does A go with T and C with G again? Consider how DNA is dislike/like any other protein. Consider how DNA is dislike/like any other protein. Think about how these molecules function in our bodies! Think about how these molecules function in our bodies!

Biochemical Properties of Macromolecules In lab today we will: In lab today we will: Look at physical models of these molecules. Look at physical models of these molecules. Use computer software to understand the feel of these molecules and how their surfaces interact with the world Use computer software to understand the feel of these molecules and how their surfaces interact with the world

Big Rigs – from DNA to protein We have a busy day!!! Let’s try to work together to make it go faster! We have a busy day!!! Let’s try to work 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 “identify” amino acids exercise (this will be quick). A oil/water and carbon exercise, a “identify” amino acids exercise (this will be quick). And an in-class Assessor exercise. And an in-class Assessor exercise. If anyone has ideas on how to bang this out faster… speak up! We can do the hemoglobin work first, ditch the powerpoint until later - etc… this is YOUR class, so let me know! If anyone has ideas on how to bang this out faster… speak up! We can do the hemoglobin work first, ditch the powerpoint until later - etc… this is YOUR class, so let me know!

Revisiting AA - So lets begin with 20 toys… pass ‘em out EVERY one has a blue part. Chem name? EVERY one has a blue part. Chem name? EVERY one has a red part. Chem name? EVERY one has a red part. Chem 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 power Like this, the right handed side of the picture is called the native state, the right is the result of the process of largely hydrogen bonding, resulting in a three-dimensional structure determined by a sequence of amino acids. Like this, the right handed side of the picture is called the native state, the right is the result of the process of largely hydrogen bonding, resulting in a three-dimensional structure determined by a sequence of amino acids.

Different tools; different jobs 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? Different? In what ways are all bases identical? Different? In what ways are all amino acids identical? Different? In what ways are all amino acids identical? Different? Which group is more diverse in terms of ‘feel’? Which group is more diverse in terms of ‘feel’? Which is more diverse in terms of shape? Which is more diverse in terms of shape? Which would allow you to build more diverse shapes & surfaces? Which would allow you to build more 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…. Lets make things go quicker today.. Lets make things go quicker today.. I talk, listen – but while doing so, take a pencil and follow the instructions on the next slide. I talk, listen – but while doing so, take a pencil and follow the instructions on the next slide. What’s in a pencil? What’s in a pencil? Graphite! Graphite! What’s graphite? – all allotropes of carbon What’s graphite? – all allotropes of carbonallotropes of carbonallotropes of carbon

Get the oil and water… Use the pencils (sideways) to make an area on the cards where you can punch out about 6 or so little circles. Use the pencils (sideways) to make an area on the cards where you can punch out about 6 or so little circles. Make sure the penciled region is thick enough and then drop those little suckers into the oil/water mixture, mix ‘em up. Make sure the penciled region is thick enough and then drop those little suckers into the oil/water mixture, mix ‘em up. Do this while I jabber away – I’m not offended! Do this while I jabber away – I’m not offended!

So… ‘hiding greasy spots’ is the primary driver in protein folding ‘hiding greasy spots’ is the primary driver in protein folding maximizing the number of charge- charge and H-bonding interactions matters maximizing the number of charge- charge and H-bonding interactions matters Tell me about your results and carbons role ! Tell me about your results and carbons role !

So now, why should I bother with this? Therapy Therapy Drug design Drug design Natural products & chemistry Natural products & chemistry Like - green fluorescent protein (GFP) Like - green fluorescent protein (GFP)

Comes from a fluorescent jellyfish! This protein has become one of the most important tools in contemporary bioscience. Using GFP, researchers have developed ways to watch processes that were previously invisible, like the development of nerve cells or how cancer cells spread! This protein has become one of the most important tools in contemporary bioscience. Using GFP, researchers have developed ways to watch processes that were previously invisible, like the development of nerve cells or how cancer cells spread! These guys won a Nobel Prize for this discovery! These guys won a Nobel Prize for this discovery!

So how do we get here from there? Or anywhere… These are a lot of new terms. This language can be bizarre. These concepts could even be a little overwhelming at first. These are a lot of new terms. This language can be bizarre. These concepts could even be a little overwhelming at first. In a slide or two we will remind you that this can all really be as simple as a process the cells in your body undergo every day. Now. And now. And again. In a slide or two we will remind you that this can all really be as simple as a process the cells in your body undergo every day. Now. And now. And again. Lets review the “Central Dogma” one more time. Lets review the “Central Dogma” one more time.

Blinding you with Science mRNA: messenger RNA; the RNA string copied (‘transcribed’) from DNA mRNA: messenger RNA; the RNA string copied (‘transcribed’) from DNA tRNA: transfer RNA; one of many RNA molecules that carry specific amino acids tRNA: transfer RNA; one of many RNA molecules that carry specific amino acids ribosome: giant machine (>200 proteins, 4 RNAs (2 > 1000 nucleotides) that oversees the reading of the mRNA and the creation of polypeptide ribosome: giant machine (>200 proteins, 4 RNAs (2 > 1000 nucleotides) that oversees the reading of the mRNA and the creation of polypeptide aminoacyl tRNA synthetase: a protein machine that adds a specific amino acid to tRNAs it recognizes aminoacyl tRNA synthetase: a protein machine that adds a specific amino acid to tRNAs it recognizes Termination factor: ‘reads’ UAA et al., causes ribosome to cut loose the peptide and fall apart Termination factor: ‘reads’ UAA et al., causes ribosome to cut loose the peptide and fall apart

Dogma, Dogma…

So the amino acids do 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”

And then the proteins are made… So it all boils down to this… So it all boils down to this…

But we have to start 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 - DNA

Livable mutations too!

Smaller scale – proteins like hemoglobin

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 depth pretty darn soon… But a little more on protein folding and the like first. But a little more on protein folding and the like first. acid + milk, boiling eggs, making cheese all good examples of charge/phobicity => folding & structure but most have seen these, and other than gee- whiz, is there a way to tie to this week’s concepts?

But to talk about these we gotta go way back to where we began, much like my little friend here…

And that “somewhere” 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!) ProteinsProteins 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.macromolecules PolymersPolymers 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).monomers tRNA hangs on to the AA chain Two important things happen here re: joining up