PROTEIN STRUCTURE AND FOLDINGCover work and Web Quest

AS Biology17th September

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PROTEINS - THE BASICSsubunits and how they bond

Why study proteins?As far as you’re concerned - because they will definitely be on the exam. As far as scientific study in general is concerned - because they are both vital and fascinating. Protein is not just a food group you have to make sure you consume - protein is a small building block that is vital to a functioning life. Proteins are in all of your cells, providing structure, giving support and speeding up reactions. Without them, you’d be no more than a pile of goo and completely un-able to do this cover work....

images #om flickr - a% under creative commons

The amino acidThe basic subunit of a protein is an amino acid. It is made of three main groups. The carboxyl group (COOH) the amino group (NH2) and the R group or side chain.

Copy this image and label each of the groups mentioned above.

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The side chain - R (or residual group varies from amino acid to amino acid. The simplest is glycine that has a single hydrogen as its side chain

Some side chains are more complicated than this.

Find and draw the following amino acids:

Arginine

Cysteine

Valine

Glutamine

Primary Structure of a ProteinThe primary structure of a protein is a polypeptide chain. Whenever you see the prefix poly- in a biological context you can assume it means many. But what does peptide refer to?

This bond is a peptide bond and it forms between two amino acids. What must be lost from the two amino acids in order for this bond to form? If you ask them nicely a technician may allow you to use the molymod kits to make two 3D amino acids and join them together.

The primary structure of amino acids is a polymer or polypeptide made up of a long chain of amino acids.

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Secondary Structure of a ProteinThe chain of amino acids will twist to make one of two different shapes or motifs. The way that this twisting and folding takes place is entirely dependent on the R chains present in the polypeptide.

Sometimes Hydrogen bonds form between the C=O of the carboxylic acid and the -NH of the amine group stabilising a structure called an alpha helix. Do you know the greek symbol for alpha?

Sometimes the bonding may stabi-lise the structure into a motif called a beta sheet. This appears as a pleated sheet. Within any single protein there may be many regions of alpha helices and beta sheets. If you look at this image, the arrows are represented by sheets and the helices by helices. Copy the image into paint and label it with alpha helix or beta sheet whenever they occur.

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Tertiary and Quaternary Structure of a ProteinThis is when the polypeptide chain begins to become three dimensional.

If you had an amino acid with a positive side chain in the polypeptide chain; as well as an amino acid with a negative side chain - how would they behave towards each other?

How about if they were both positive? Would they behave the same way?

If you had a hydrophobic water-hating side chain, would it want to point towards the dry in-side of the protein or the wet outside?

What about if it was hydrophillic water-loving?

In the tertiary structure the protein folds to become more 3 dimensional. The folding is de-pendent on exact type and sequence of side chains. We will model this in class next time I see you so don’t worry too much if it seems confusing now.

The quaternary structure is when one tertiary polyptide chain joins up with others to make a larger molecule - like haemoglobin for example.

The importance of the amino acid sequence can be seen very clearly with the disorder Sickle Cell Anaemia. One single amino acid in a massive polypeptide chain is swapped for another, and this causes all of the problems exhibited in Sickle Cell.

What I’d like you to do...Go to www.slideshare.net and set up an account. I think you *should* have already done this.

Create a powerpoint presentation about at least the primary and secondary structure of amino acids. Your slides must have pictures (flickr is usually a good source) and no slide may have more than 15 words on it. I’ll be very strict about this one. I hate wordy powerpoints with a passion. Upload your presentation to slideshare and email me the link.

If you whizz through this in no time and think you’d like to - have a crack at tertiary and qua-ternary. Maybe having a specific look at haemoglobin and sickle cell anaemia.

Make sure you answer all of the questions in this document before you do this though. I’ll be happy with emailed answers, or answers scribbled down on bits of paper.

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