Monday, 7 December 2009

Biochemistry Exams - 2008/2009 3rd year Undenominated Science Semester I - Question 4


It is time for Question 4.

We are refering to paper that can be found here: 2008/2009 3rd year Undenominated Science Exam Paper Semester I

Question 4 EITHER complete both parts A and B below (each part is worth equal marks)
A. Name two different types of post-translational modifications, specify the
amino acids involved and the chemical effect of the modification. Describe
how each modification enables biochemical function using examples.
B. Explain how the repeating chemical structure of the polypeptide
backbone gives rise to protein secondary structure.
Write an essay on the processing and targeting of newly synthesized
proteins in eukaryotic cells.

This one is a little bit longer but still very easy:)

Let's taka care of the Part A first with a short background:
As you know proteins can be post-translationaly modified. Those modifications affect protein function, stability, activity, binding affinity etc.
List of protein modifications is still growing:
- phosphorylation (phosphate group attachment),
- methylation (methyl group attachment),
- acetylation (acetyl group attachment),
- ubiquitination (attachment of ubiquitin peptide),
- sumoylation (attachment of SUMO peptide),
- argininylation (attachment of arginine),
- ADP-rybosylation (attachment of ADP-ribose),
- citrulination (deamination of arginine),
- myristoylation (atachment of myristic acid group),
- hydroxylation (attachment of hydroxyl group),
- prenylation (attachment of prenyl groups),
- palmitoylation (attachment of palmitic acid group),
- glycosylation (attachment of sugar residues),
- and others.
Remember that also:
- proteolytic protein cleveage is a post-translational modification.

To answer the Part A we need to discuss only two modifications. In my opinion the easiest two to describe would be protein phosphorylation and protein modification by proteolytic cleveage. So:
Protein phosphorylation - is a protein modification where phosphate group is attached to a serine or threonine residues (rarely to tyrosine residue) by a protein kinases (removal of the phosphate groups is mediated by phosphatases). See figure below:

Very important to remember is that phosphate group bears negative charge. Modification of protein by phosphorylation cause conformational change in the target protein (negative charge on the phosphate group will attract positively and repell negatively charged parts of the protein). Conformational change of the protein can affect its activity, stability, binding affinity and others. Imagine that enzyme active site of protein X is not accesible (let say it is hindered by a part of the protein) but upon the phosphorylation its conformation changes, active site becomes opened and substrate can bind. See figure below.

ATM protein is a good example of activation by phosphrylation. ATM protein is a kinase which in unperturbet cell cycle is present as a dimer and stays inactive. ATM is activated by ionizing radiation (IR) which cause DNA strand brakes. As a part of the DNA damage response each ATM protein phosphorylates its partner within the dimer (autophosphorylation). Upon phosphorylation ATM protein is released from the dimer and kinase is able to modifiy other protiens through phosphorylation.

Protein Cleaveage is easy to explain as well. There is a lot of proteins that are cleaved by proteases in order to became active. You know that most of the proteolytic enzymes like trypsin or chymotrypsin are produced as zymogens (not-active enzymes). After zymogen secretion, they are cleaved and became active.
Remember that in general most of the protein modifications work in a simillar way. They change protein conformation (you can easily imagine that if you chop out a piece of the protein that it will change its structure) what leads to change in protein activity, stability etc etc.

In Part B we need to explain how protein aminoacid backbone affects protein secondary structure. As you know there is only two major types of protein secondary structure:
- alfa-helis,
- beta-strand.
See fiigure:

 Picture taken from

Both alpha-helix and beta-strands are stabilized by hydrogen bonds formed between hydrogen of the backbone alpha-amino group and oxygen from the backbone carboxyl group. Depending on the aminoacid sequence protein can either accomodate beta-strand or alpha-helix conformation. Remember that alph-helices and beta-strands can occure simultaneously in the same protein (one part of the protein folds this way the other one folds differently).

This is it:)

In this question you either answet part A and B or you have to write a short assay about: processing and targeting of newly synthesized proteins in eukaryotic cells.
Of course I am not goind to write an assay here beacuse that does not make any sense but I will put an essential information that you should include in your assay (write about). This part of the question is actually very similar to Part A because protein processing and targeting is achieved by protein modification.

Ok so let's start. You have to remember that after synthesis protein has to be: 
- folded. In this process proteins called cheparones play a crucial role. Proteins in the presence of cheparones fold properly and efficiently (Have a look at this animation - Willey Interactive - Protein Folding). Unfolded protein is useless for the cell and therefore it is degraded.

- targeted.  Proteins contain a signal sequence which is specific for each cell compartment. They are often called sorting signals and these signals interact with specific receptors, either on the target organelle or a carrier protein. For example there is a nuclear location sequence as well as a membrane location sequence etc.
Remember that proteins can be targeted to the different locations by a post-translational modifications as well (to see what I mean see the top of that post:). Good example of such is a SUMOylation process. Protein which was modified by attachment of SUMO peptide is usually targeted to the nucleus.
Different examples are myristoylation and prenylation modifications which target proteins to membranes (it makes sense as myristic acid and prenyl group are hydrophobic molecules).
Notice also that proteins which suppose to be targeted to the cytoplasm usually do not bear any location signal (those are proteins like enzymes, structural proteins, translational machinery protiens).

To sum up please see this animation Protein Targeting.

- processed. Some proteins have to be modified before they became active or fulfill their function (see the Part A of that question as well). For example proteolytic enzymes have to be cleaved at specific sites to became catalytically active (like trypsin). Other proteins have to bele phosphorylated, methylated or glycosylated to perform their function.
You can imagine protein processing as a set of essential protein modifications/alterations processes which lead to protein activation, localization etc.

Essential animations that will help you to see what is going on:)

Protein Modification
Protein Trafficking

Ufff that was a loooooong one:)

CyA, next time question 5.


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