Month: August 2013

Financial Cost

Consider a situation where you are studying lab rats and hypothesize that Peptide A causes a particular rodent to get sick when eating a specific kind of cheese. Once you isolate this particular peptide from the rodent, you will need to be able to follow the scientific method in order to prove your hypothesis.

This will include running a number of tests to prove that Peptide A is the cause of the rodent’s problem instead of some other factor. If you have to purchase and care for other rodents, plus keep trying to isolate Peptide A from all of them, it will cost a fortune. At the very least, if you create a synthetic version of Peptide A, you can study it in less expensive settings during the earlier stages.

Sample Purity and Research Development

Within the cellular environment, a single molecule can create an endless number of changes. Therefore, when it comes to trying to study peptides, you may have a difficult time isolating them from cells in sufficient quantity.

In addition, no matter how careful you are during the isolation process, you may wind up making mistakes that cause impurities in the peptide stock solution. Needless to say, this can easily cause you to get all the wrong results later on in your research efforts.

By contrast, when you create synthetic peptides, the process involved will yield only that particular peptide. As an added bonus, if you want to try changing a few amino acids, or even their position within the peptide, you can do so with ease. You may even find that using variations will help you predict what would happen in a natural cell, or in a complex organism at a later time.

Ethical Issues

Have you ever been mildly offended to hear a doctor say that animal studies imply nothing about what will happen to a human being taking any given medication? Did you feel even more upset when news was released indicating that your concerns were valid? While modern science has come a long way, it is sad to say that animal studies are performed over and over again, only to have the information ignored.

Even though you may not realize it, the vast majority of lab animals are killed at the end of any given experiment. In many cases, these animals suffer in excruciating pain, are denied proper food and hydration, or are forced to remain tied up so that various processes can be “studied”. To add insult to injury, many lab animals are killed in inhumane ways in order to prevent other chemicals from interfering with the gathering of tissue samples. Regardless of whether a frog or fish is pithed or a dog heart stuck, the vast majority of people would choose some other way to gather information, or simply not have it at all.

When it comes to studying peptides, synthetic ones can easily be studied in cellular environments or even in lab grown tissue samples. As computer models and other simulated models become more accurate, it becomes easier to end reliance on lab animals. Using synthetic peptides can speed up this process as well as reduce the number of animals that suffer because of research methods based largely upon human ignorance.

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How are They Created by Nature

In order to be organized into peptides and proteins, cells must arrange amino acids based on a template. Once the amino acids are organized into an appropriate structure, they are released from the template and moved to other locations within or outside the cell.

Needless to say, the process that converts amino acids into functional peptides is as fascinating as it is complicated. If you keep a few basic steps in mind, it will be much easier to remember and understand how they fit into the overall structure of cell function and the capacity to carry out basic life needs.

Cellular Machinery

There are two basic organelles required to make peptides. First, the endoplasmic reticulum (ER) is a ribbon like organelle that runs throughout the cell. It acts as an anchor point as well as transmission channel for completed proteins and peptides. Depending on the phase any given cell is in, the ER may be involved in producing proteins and peptides or some other molecule.

Ribosomes (small granular organelles) attach to the endoplasmic reticulum and assemble peptides based on a template that feed through them. At this stage, the ER is often referred to as “rough” since ribosomes can be seen attached to it under a microscope. Typically, ribosomes will not bond to the ER unless the ribosomes are already bound to a template. Interestingly enough, the start and stop sequences on any given template are composed of peptides that facilitate bonding or breaking away from the ER.

The Template

If you have done any research on protein, genetic material, and peptide synthesis, then you may already realize that a special set of nucleic acids are used to form templates. For example, if the origin template utilizes RNA, the four nucleic acids involved are adenine, cytosine, guanine, and uracil. If the cell uses DNA for its genetic material, uracil is exchanged for thymine.

No matter whether the cell makes use of RNA or DNA, ribosomes cannot simply attach to the chromosome and begin transcribing proteins. Instead, special peptides and other molecules attach to the genetic material and create copies, or transcriptions of the required template pieces. Typically, this process will start at a specific code within the nucleic acid, and then end at a different point. Even though messenger RNA and transfer RNA are still formed from nucleic acids, they are able to bond with, and act as the template for arranging amino acids within ribosomes.

Why Manufacture Synthetic Peptides

There is no question that there are billions of molecules of peptides available in nature. On the other hand, gaining access to pure quantities of them can be very difficult. This is just one of many reasons why researchers are increasingly relying on ways to manufacture synthetic peptides. While discovering brand new ones still requires the usage of organic, living cells, producing them in useful quantities tends to make it easier to go past that point.

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A Guide to Amino Acids

It can be said that amino acids are a special group of molecules that have a basic form. No matter whether the amino acid is found in the cell of a bacteria, human being, or a plant, it will have the same structure and may even carry out the same functions within the cell. Even though there are well over 500 amino acids, most organisms make use of 22 standard amino acids, and a handful of others that may be useful based on certain conditions.

For example, specialized amino acids may be produced to function based on PH levels within a cell, variable temperatures, or the presence of oxygen. Unfortunately, more research needs to be done in order to determine how many non-standard amino acids are used, as well as their role in any given organism under any given environmental condition.

Standard Amino Acid Shape

Amino acids are usually composed of a handful of atoms, (Carbon, Hydrogen, Nitrogen, and Oxygen) that are arranged into specific structures. This includes a side chain, a COOH (carboxylic acid) unit, and an NH2 (amine) unit. Visually, it is easiest to imagine the COOH unit at one end of the amino acid, a chain or ring of carbons down the center, and NH2 at the other end.

The side chain is usually attached to the backbone. Depending on the amino acid in question, this side chain may form a chain of atoms, or form a carbon ring with other atoms attached to it.

Basic Ways Organisms Use Peptides

Regardless of whether you are studying a cell with a single strand of RNA for its genetic material or hundreds of strands of DNA, you can rest assured that coding information exists for hundreds, if not millions of peptides. Therefore, it should come as no surprise that peptides represent some of the most important molecules found within any given cell.

In single cell organisms they can be used to signal the start and stop of cellular division, open RNA or DNA for replication or transcription, and determine which molecules are made at any given moment. Peptides may also be used to facilitate the conversion of glucose and other forms of fuel into energy.

When it comes to multi-cellular organisms, peptides become even more important. For example, the vast majority of plants and animals would not be able to survive without insulin. This particular peptide bonds to glucose in the blood or sap of an animal or plant, and then encourages transport across cellular membranes.

Without this particular peptide, it would be impossible for cells to take in glucose. In a similar way, peptides can act as hormones, neurotransmitters, and signaling molecules. You may even find that peptides play roles in immune responses, and just about any other process that requires a signaling cascade within cells or specific tissues.

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