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Do you remember that we decided that DNA and RNA are two separate languages? Transcription factors read “TATAAA” as “park here.” There are hundreds of other examples of how enzymes recognize only certain sequences, but we’re gonna keep it simple for now.

Well during translation, Dr. Ribosome and his tRNA graduate students “translate” the mRNA into yet ANOTHER language: polypeptide. Ok, after some thought, that’s too cheesy even for me. But since it gets the point across, I’ll leave it at that.

Once the mRNA strand has left the nucleus and entered the cytoplasm (or “cytosol” to some people), it is fair game for ribosome binding. That 5′ cap is EXTREMELY important here because it marks the location for the ribosome to bind.

WAIT! I want to add a little sidenote here that would have REALLY aided me in getting the concept of why all the little proteins are necessary. Remember how we needed transcription factors to start transcription? We’re gonna need translation initiation factors in order to start translation as well. But what’s really the point? You’ll have to read that article to find out, but for now, read on.

SO, the ribosome uses initiation factors to bind on the RNA, more factors find the AUG start codon, then the ribosome uses factors to bring the tRNA molecule with Methionine to the AUG Start codon… WHEN DOES THE RIBOSOME ACTUALLY DO SOME WORK BY ITSELF!?!?

Ummmmmmm, pretty much after that first methionine. You see, once everything is set up, the rest is automatic. If you look at the picture above, you’ll see that there is an “A Site,” a “P Site,” and a tRNA molecule floating away. The “A Site” is short of aminoacyl site, or “amino ACID” site. This is where tRNA molecules land if their anticodon matches the codon that is showing.The “P Site” is short for the peptidyl, or “PEPTIDEyl” site. This is where the amino acids bound to the tRNA molecules are added to the growing protein using a peptide bond. Finally, there is the exit site, where the empty tRNA molecule is allowed to float off and become recharged with another amino acid (of the same type).

In the case of the methionine start codon, the ribosome was moved so that the AUG codon was the only one that was showing in the Aminoacyl site. Once the methionine tRNA was bound, the RIBOSOME MOVED (not the tRNA molecule) and this pushed the tRNA molecule over to the Peptidyl site. This left an empty A-Site for another tRNA to enter and bind, causing the ribosome to move again. This time, the methionine tRNA is pushed into the exit site and ejected from the ribosome.

This move-eject-bind procedure will go on until the ribosome encounters a stop codon. If you look at the chart above, you’ll see three different combinations that will result in a stop. This happens because there’s a special molecule that possess and anticodon but NOT an amino acid. When this molecule moves into the P site, the ribosome will attempt to move the growing amino acid chain to bind with the new amino acid. The only problem is that with this special molecule, there is no amino acid. So the protein just floats off, and the ribosome falls apart, thereby ending translation.

Short Version

1. Factors bind ribosome to mRNA
2. Methionine tRNA initiates reading
3. Move – peptide bond/eject – Move – peptide bond/eject
4. Stop codon ends it all

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Best of Luck,

Grey

To do well with organic molecules, all you need to know is a few facts and to recognize some specific structures. That’s it. I rewrote this article three times, and every time was more detailed than the last. It eventually became ridiculous. I started by comparing a cell to a city, then to a house, then just explaining it in terms of how it relates to the body – UNNECESSARY. So, enjoy this; it’s short, sweet, and to the point.

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CARBOHYDRATES (sugars)

Ribose Monomer (5-Carbon Sugar)

Dimer of Glucose and Fructose

Cellulose (Glocose Polymer)

• Carbon, Hydrogen, and Oxygen. All sugars that you will deal with for a long time will be made up of a combination of these three elements. Many of them will be in a ring, like those pictured above.

D-Fructose

• Look for those elements in order to identify sugars. You can also look for a carbon backbone. Because carbon has 4 bonds, it can bond to another carbon on each side and still have room for binding to hydrogen or oxygen. Sometimes, the shape can give it away too, like glucose has six sides and ribose has five. But as you can see above, it isn’t necessary for sugars to be in a ring.

POLYPEPTIDES (proteins)

• ALL polypeptides are composed of amino acids, and ALL amino acids will have the following structure.

Amino Acid Structure by Tyagi Anuj

• There will be a Carboxyl Group, an Amino Group, a Hydrogen, and the dreaded “R-Group,” all bound to a central Carbon.

• Amino acids are the building blocks of proteins, in case you forgot. The “R-Group” is what makes one amino acid different from another; other than the R-Group, all amino acids are exactly the same.

• In order to identify a protein, look for a carbon bound to another carbon bound to a nitrogen, like in the schematic below. Although there are Hydrogens, Oxygens, and R-Groups bound to the middle ( you can ignore the arrows and dotted lines), you can see that there is a clear pattern of N-C-C-N-C-C-N-C-C-N… along the backbone of the protein.

Polypeptide Schematic by Dagmar and Ringe

• Your teacher may also hit you with a larger representation of a protein. Ribbons or blobs, like these pictured below, are usually proteins.

Src Protein

G Protein

LIPIDS

• Lipids have ONLY Hydrocarbons. Can you guess the elements that make those up? Carbon and Hydrogen? YES!

Octane

• That’s all you really need to know in order to recognize them. They are the only organic molecules that are made of just hydrocarbons.

Triglyceride

• You may need to know that squiggly lines like the ones pictured above are a shorthand way of writing carbon-carbon bonds. If you don’t see anything else written in on the squiggly line, you can assume that it’s just carbon and hydrogen.

NUCLEIC ACIDS

DNA Structure by Dr. Frank Boumfrey

• Three parts: Pentose (5-carbon sugar) + Nitrogenous Base (A,T,G,C) + Phosphate Group. These have a very distinctive shape, and you shouldn’t have any trouble recognizing them because they HAVE TO bond this way to be recognized as a nucleic acid. As you can see above, it’s got a structure that should be fairly easy to recognize.

• And don’t worry about the differences between different kinds of nucleic acids, the difference comes in the TYPE of nitrogenous base that is used. The overall structure of DNA, tRNA, mRNA, and whatever other -NA that you come across will all have the same basic structure… else they wouldn’t be a nucleic acid.

So Remember:

1. Protein: carbon bonded to nitrogen bonded to oxygen. and R group.
2. Sugar: carbon, hydrogen, oxygen
3. Lipids: carbon and hydrogen ONLY
4. Nucleic Acids: sugar, phosphate, nitrogenous base.

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Best of Luck,
Grey

EACH “LEVEL” OF PROTEIN STRUCTURE DESCRIBES SOME PART OF THE PROTEIN… and “PROTEIN”=”POLYPEPTIDE”… remember that. Keep them in your mind as you read the rest of the article.

A.) There are four levels of protein structure: Primary (first), Secondary (second), Tertiary (third), and Quaternary (fourth). Think about this like a stack of books: you can’t get to the third book without there being two books underneath, but you can have a stack of only two books without the need of a third or fourth.

Likewise, you can have primary structure without having secondary, or you can have tertiary structure without quaternary. If, at this point, you’re still unsure about exactly WHAT each of those are, it’s ok. Just make sure that you know that you must start at the bottom and work your way up and that every protein won’t have all four.

B.) The first level of protein structure DESCRIBES the order of amino acids in the protein. It has NOTHING to do with shape at this point. Eventually, these amino acids will effect the shape of the protein, but for now don’t worry about that.

When you think of Primary Structure, think back to kindergarten, when you were forced to stand in line between the same two people everywhere your class went. The primary structure of a protein is similar to the kindergarten line in that it focuses on the ORDER of the CERTAIN amino acids that make up that polypeptide. These lines of amino acids, bound to one another by peptide bonds, are the building blocks of the next level of structure…

C.) The second level of protein structure DESCRIBES the ways that the primary structure of the protein interacts with itself. This is the first instance of 3D shape that you see in polypeptides.

There are two major configurations that you need to know at this point, Aplha Helix and Beta Pleated Sheet. Actually, just to make things simpler, we’ll just call them helix and pleated sheet. The “alpha” and “beta” are just “the man” trying to keep you down. A helix is shaped like a tube and a pleated sheet is has ridges like a “Ruffle’s” potato chip.

In schematic representations of proteins, like these pictured here, flat ribbons are the accepted representation of beta sheets. Although they look flat, you’re just supposed to know that they are actually ridged.

fhuA transport protein

Bacterial Potassium Channel

In the examples given, the red alpha helices are shown in a bacterial potassium pump that is composed of only alpha helices, and the bets sheets are shown in the fhuA transport protein that is composed of only beta sheets. I’ll show in another post why these structures make them the best for their function.

Some amino acids will interact with each other to form shapes (helices or sheets). Remember concept A? It applies here. THERE IS NOTHING THAT SAYS THAT ALL AMINO ACIDS IN A PROTEIN HAVE TO FORM INTO HELICES OR SHEETS. Some just remain as strings of amino acids.

C.)  Tertiary structure is one of the easiest ones to remember. It DESCRIBES the way that the secondary structures interact… (there goes that “building blocks” thing again).

Blob. There you go. That’s tertiary structure. If you take your polypeptide “string” (primary), with all of its helix and pleated sheet “beads” (secondary), and you drop it on the floor, you’ll likely find that it falls into a bunch. Or maybe if you put the whole thing in your hand so that none of the strings hang off your palm, you’ll notice that you have to ball it up in order to get it all into your palm.

Tertiary structure is the EXACT SAME THING… kinda. it describes the way that the secondary structures interact with each other. Blob. Simple, huh? Theoretically, yes, but it’s at this point that proteins really begin to take on the shapes that they need to carry out functions in the cell.

Remember proteins are tools that the cell uses to do jobs. They aren’t the only tools, but they make up a whopping majority. The jobs that proteins can do depend COMPLETELY on their shape. You cant screw a screw with a hammer because it doesn’t have the correct shape.

D.) Finally… lets speed this up a little… Make four of those blobs from concept C and glue them together somehow. That’s quaternary structure. It describes the way that those tertiary structure blobs interact to form new and novel proteins that can do NEW JOBS. If you glue a hammer to a screwdriver… well, there’s probably not a lot that you can do with that, BUT THEORETICALLY, the possibilities are endless!

So, that’s it. Protein structure really gets more hype than it  deserves. But for your memory, here’s the condensed version:

• Primary – Kindergarten Line – certain arrangement of amino acids
• Secondary – Pringle’s tubes and Ruffle’s chips – alpha helices and beta pleated sheets
• Tertiary – Blob – interactions between primary and secondary structures
• Quaternary – BIG Blob – interactions between different polypeptide chains to form new shapes.

Here are some more links that may come in handy:

http://webhost.bridgew.edu/fgorga/proteins/proteins.htm#Primary

http://themedicalbiochemistrypage.org/protein-structure.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/DenaturingProtein.html

http://wiz2.pharm.wayne.edu/biochem/prot.html

Images courtesy of

Best of Luck,
Grey