number Done by Corrected by Doctor Dr. Diala

Transcription

1 number 30 Done by Dergam Al-Tarawneh Corrected by Zaid Emad Doctor Dr. Diala 1

2 After we ve finished talking about lipids metabolism pathways, today we will start talking about another pathway that takes in concern the metabolism of proteins and Amino Acids. DrDiala didn t go over everything in her slides so I ll try my best to include everything that she said in this sheet. Let s begin After what we ve taken before, we have almost talked about all molecules such as carbohydrates and lipids and we ve known their different pathways in the body and the ways they are synthesized,degraded and how the body get them out of our system or get rid of them. Now we will start talking about another or a new type of pathway that is the pathway of protein metabolism or to be more specific the pathway of Amino Acids metabolism. The Amino Acids metabolism pathway is a more complicated pathway from what we ve taken earlier but even though we won t be taking each and every amino acid in a specific manner, rather we will be talking about similarities that link some different Amino Acids. Before we start the real stuff we should know some info about Amino acids and how our bodies deal with them. There are some differences between Amino acids and other compounds and molecules that our bodies deal with, for example upon glucose uptake our body initiates the process of glycogen synthesis and store the excess glucose in the form of glycogen in the liver and other places.however, the Amino Acids, which are the source of nitrogen for the body (having the N-terminus in their structures ), are actually not stored in the body, even the people with high protein intake rate ( having a protein based diets ) such as body builders the amino acids aren t stored in the body in any manner. Amino Acids are mainly used in our bodies in two ways: 1 st they are used in the synthesis of new proteins. 2 nd they are degraded into basic row material that can be utilized in the production of other compounds such as glucose by gluconeogenesis and other essential compounds. And if we don t use Amino Acids then we get rid of them that s the RULE we should remember. But since we ve given the issue of Amino Acids storage a big spotlight, why don t we store Amino Acids as we store other compounds in the body?! 2

3 The answer is toxicity related to the nitrogen atom within the Amino Acids. Individuals with a relatively high protein intake will develop a situation of Ammonia toxicity which is a very dangerous situation, and as we know ammonia in our bodies is rapidly converted into urea which is excreted in urine, but when we have a high protein and amino acids intake then we will have a large amount of nitrogen and thus a large amount of ammonia that our bodies can t deal with, so we will develop toxicity from ammonia and that s why we don t store Amino Acids in our bodies like other harmless compounds. NOTE : The usage of Amino Acids is not mainly for the production of energy containing compounds, they are used in the first place to produce signaling compounds, hormones and regulatory compounds, then we use the EXCESS Amino Acids left to produce those energy containing compounds. Now we get to the point of asking ourselves, from where can we get those Amino Acids or what are the sources of Amino Acids that can supply us with a sufficient amount of them? 1. The firstsource is from our DIETthatcontain proteins and by digesting them we get a relatively high amount of Amino Acids. 2. The second source is by the process of ENDOGENOUS SYNTHESIS but we can only synthesize specific Amino Acids and not every type our bodies need. 3. The third and most important source is by DEGRADING PROTEINS in our bodies to free Amino Acids so the body can utilize them according to its needs, ( for example if a body builder with a high protein amount diet stops working out a noticeable loss of muscle mass will be seen and this loss is due to degradation of muscle proteins for body usage, another example is that as our bodies age, a loss of muscle mass will also be seen as the rate of protein degradation is higher than synthesis ). So as we saw there are some different sources and ways that we can get Amino Acids from and all of these sources contribute to what we call Amino Acids pool. 3

4 And when we say pool we mean an INPUT and an OUTPUT of Amino Acids, the input process is done by the sources we mentioned earlier and the output is done by the exact opposite of the input which include the synthesis of proteins instead of degrading them and the production of other different compounds in the body ( output means how can we consume Amino Acids ). But an important thing to consider is that we have a balance in this pool which means a balance between the sources of Amino Acids and the fate of Amino Acids. As we ve seen earlier there is an exact opposite pathways in the pool which are protein degradation and synthesis and since we re producing and breaking proteins we contribute to a process of PROTEIN TURNOVER. when we say turnover we say that the proteins are converted from one form to another and this method is used to recycle or replenish proteins in our bodies to compensate for the degraded ones, but here also we require a balance and this balance is to maintain a steady mass for the body so we do not increase it nor decrease it rather keeping it constant, not taking the state of a bodybuilder nor an aging individual in consideration because we are talking about normal healthy individuals here. So another rule to be known : We should always maintain a constant protein turnover rate. Now i suppose that we re all familiar with the concept of half life and what does it represent,proteins half life is an important determinant of the protein turnover rate as some proteins exhibit short half-lives for some seconds and others may have a years long half lives,other factors that affect the turnover rate are the type and function of proteins. Some proteins have very long half-lives such as structural proteins since they are usually in balance and they don t change upon time to induce functions, other proteins with short half lives include proteins that we need to rapidly activate and then deactivate them such as regulatory proteins, hormones and enzymes so those proteins are rapidly synthesized and degraded according to the cellular demand of their presence. Another conclusion is that proteins turnover can be manifested in the regulatory processes of the cell by controlling the production and elimination of the activators or inhibitors of some cellular machineries. 4

5 Another way to regulate proteins in the cells is the MODE OF EXPRESSION method in which we synthesize proteins that we are always in need of their presence in a constant matter in a Constitutive expression mode, on the other hand we produce proteins that we need to keep turning on and off in an INDUCABLE EXPRESSION mode that produces them upon need. Now let s assume that we have a certain kinase that I need to degrade, how can I make the degradation machineries distinguish this kinase upon all present kinases in the cell? A simple answer is that we mark it or tag it, so the cell degrades it without missing it with the other kinases which I need. We call this process PROTEIN TAGGING in which a certain compound is added to the intended protein we want to degrade producing a chemical signal for cellular degradation machineries to degrade the tagged protein. An example of molecules which we use for tagging, is a small protein called UBIQUITIN. Another way of tagging is to produce a chemical change of the molecule I want to degrade to make it visible for the degradation machineries, one of these changes is getting the protein undergo an OXIDATION to signal the need for its degradation. And now since we have been repeating the term Degradation a lot,lets talk about it for a little bit There are mainly TWO machineries that the cell uses for protein degradation which are : 1- Ubiquitin-mediated proteasomal system. 2- The Lysosomal Enzymes system. Why would we have two degradation methods?why don t we use just one of them?! That s because not all proteins go to the first machinery and it is the same with the second one. 5

6 The Lysosomal Enzymes system. The proteins that undergo degradation by this system are mainly Membrane proteins such as membrane receptors which we don t need them functioning all the time to produce a cellular effect so we need to put them to rest sometimes (eg ; oxytocin receptors in pregnant female ) Other than membrane proteins we also degrade Extracellular proteins that exist in the extracellular matrix by the same pathway, and they are mainly structural proteins. The process of lysosomal degradation of those proteins require the mechanism of ENDOCYTOSIS( receptor-mediated endocytosis )so I can engulf those proteins forming a vesicle and fuse them with the lysosome where they are denatured first by the high acidity then they get degraded by the lysosomal enzymes which are acid stable. NOTE : Endocytosis is an ATP independent process that does not require energy to proceed. Ubiquitin-mediated proteasomal system The other machinery which is an ATP DEPENDENT machinery is the Ubiquitinmediated proteasomal system, and it is different from the lysosomal system by the fact that it s not an organelle rather it is a machinery which takes place inside the proteasome. 6

7 It is present in the proteasome( a barrel shaped complex with a hollow center that is composed of large number of protein subunits that contribute in the process of degradation and hydrolysis of proteins ), so here the protein enters as an intact protein from one side and exits as small peptide fragments from the other side, then they can be degraded completely by the action of proteases outside the proteasometo yield Amino Acids. Here in this system the process of degradation takes place right after the Ubiquitin tagging process,we use ubiquitin ( a small globular or rounded protein ) to tag the protein we want to degrade, and it is always preferred to tag the protein with more than one ubiquitin molecule in a process of Polyubiquitination. Here is a picture that gives a general concept of this system: But we should know that ubiquitin here is only used for tagging and it does not contribute to the process of degradation and hydrolysis of proteins, it only gives the signal that the machinery needs to detect the molecule and degrade it, and we also should know that both processes of tagging and degradation here need ATP independently. After all this talking about ubiquitin-mediated proteasomal system and tagging, let s talk about some applications on this system. HPV ( HumanPapilloma Virus ) As we know from virology it is a DNA virus, this virus is distinguished among others by having the capability to develop cancer in females on long term 7

8 bases ( up to years ), it only produces cancer in females while it can be found in males but without causing cancer, and it is transferred by the sexual intercourses. This virus does so by having the ability to produce the E3 enzyme, which is the last enzyme in the process of ubiquitination in tagging, and it comes after the enzymes E1 & E2 and it is the most important one, this E3 enzyme tags the P53 protein ( a cellular division suppressor and a tumor suppressing protein protecting from cancer development by abnormal divisions ) with ubiquitin resulting in its degradation, producing abnormal divisions of cells resulting in CERVICAL CANCER in females. Now since we ve acquired the info about the ways of protein degradation we can talkabout metabolism but before that lets talk a little about the process of DIGESTION. Digestion As we mentioned before one of the main sources of Amino Acids is the diet, and we know that proteins acquired from diet are complex structures that cannot be digested in the oral cavity so the digestion process starts in the stomach and here we go back to the idea of lysosomal degradation and the utilization of acidity to do so, in the stomach it is the same idea, the acidity and the enzymes of the stomach helps denaturing and making the protein more accessible to further digestion. In the stomach we have the enzyme PEPSIN and it is a zymogen (found in the inactive form ), it is found as pepsinogen that is activated by the acidity provided by the hydrochloric acid HCL found in the stomach. Pepsin is a non-specific enzyme that hydrolyses and cleaves peptide bonds randomly without taking in consideration the type of the peptide bonds, and as we know peptide bonds are bonds between the backbone components of the proteins and they differ among different proteins due to the presence of the R-Groups in the proteins in different positions and orientations, so a peptide bond between Arg and Lys is different from a one between Glu and Ser and that s because of different R-Groups around those molecules. 8

9 And now before moving to our next station for further digestion we should mention the role of HCL in the stomach, which plays some roles such as : 1- Denaturing proteins by providing the acidity 2- Activating enzymes such as pepsin 3- Killing and cleaning bacterial content and microbes that we are introduced to from the dietary products we ingest. Now lets get back to the partially digested proteins, HCL and Pepsin mixture which we give the name Chyme that will move to the duodenum in the small intestines as its next station of digestion. Now we have a new environment which exhibits a new ph and a new Enzymatic content ( we know that different enzymes have different activities in different ph values, and they also have different specificities ), we said earlier that pepsin is a non-specific enzyme but here the enzymes have some specificity as they will cleave certain peptide bonds only. The process of digestion continues by the secretion of Pancreatic Enzymes over the mass of chime that came from the stomach with an acidic state ( low ph ) and an active form of pepsin, but since here the situation is different in the means of ph value ( nearly 6 ) the pepsin will be inactivated and there will be an activation of the pancreatic enzymes. We have two types of pancreatic enzymes with different positions of peptide bond cleavage and hydrolysis and they are : ENDOPEPTIDASES : cleaving the peptide bonds in the MIDDLLE. EXOPEPTIDASES : cleaving bonds on the EDGES mainly working on the C- TERMIUS. All of these enzymes are Zymogens produced in an inactive form in the pancreas and activated in the duodenum, WHY?! We don t want them to digest the pancreatic proteins and proteins in the ducts they will travel through. 9

10 The Dr. mentioned the sequence in which every enzyme work after but we don t need to memorize them we just need to distinguish if the enzyme is and ENDO or EXO Now after we ve almost covered all of the protein parts with the enzymes that act on them we still have the N-Terminus which is acted upon by the enzyme AMINOPEPTIDASE which is an exopeptidase that protrudes from the intestinal cells membrane( it s a membrane bound enzyme ) and it is not a pancreatic enzyme. Now we will be in the state where we have free Amino Acids and some Di & TRI peptides that should now go to the stage of absorption that we will talk about in the next lecture. Hope all of you all the best And sorry for any mistakes Thank you 10