HIV cure has not been found yet

A HIV cure is difficult. Recently, I noticed that there has been many websites pointing out that a HIV cure has been found. Unfortunately, this is not the case. HIV has only really been cured in rare cases, most of which are currently being studies. Examples of these rare cases are the two American men that have received bone marrow stem cell transplants and the baby that received high doses of antiviral therapy within 30 hours of birth.

The point of this post was to dispel the rumours of Indian herbal remedies and other treatment methods could cure HIV/AIDS. If you believe one exists, post a comment below and I will check it up and amend my post if necessary. However, the most current literature I have read suggest otherwise.

Biology basics: Protein folding

Protein folding is a fascinating area of science for several reasons. Understanding protein folding may well open up the path to find cure to the diseases that arise from incorrect folding. Also, programming and algorithms have not been all that successful in predicting how a protein will form.

Biology basics: Proteins

Proteins are present in biology everywhere. Without we wouldn't exist. Nor would bacteria, fungi, viruses, pet dogs and our gold fishes..... Proteins are essential to all forms of life and this is why it is important to understand them.

What is a protein?

Proteins are long molecules that consist of reoccurring subunits called amino acids. Proteins are needed for our bodies and the cells in our bodies to function properly. Our body structures: cells, tissues and organs cannot exist without proteins.

Enzymes, many hormones and antibodies that we hear about are proteins. Hemoglobin which carries oxygen in the blood are also proteins. Many neurotrasmitters, involved in the transmission of messages between nerve cells, are also proteins.

Almost every biological process involves, in one way or another, proteins. Examples of the functions of proteins in the human body are:

• Enzymes which makes biochemical reactions occur faster
• As antibodies for our immune system
• As hormones, which help cells signal between each other and coordinate events in the body (such as menstruation in females.
• The hemoglobin protein transports oxygen through the blood.
• The rhodopsin is a protein in the eye is vital for vision
• Muscle contractions involves two types of proteins (actin and myosin) are involved in muscle contraction and movement.

What are amino acids?

These 20 amino acids are make up proteins can be arranged in many different ways to create millions of different proteins, each one with a specific shape and specialised function in the body. Anfinsen showed that the sequence of amino acids (primary structure) was what determined the final shape of the protein. The twenty amino acids are:

• Alanine
• Arginine
• Asparagine
• Aspartate
• Cysteine
• Glutamate
• Glutamine
• Glycine
• Histidine
• Isoleucine
• Leucine
• Lysine
• Methionine
• Phenylalanine
• Proline
• Serine
• Threonine
• Tryptophan
• Tyrosine
• Valine

How proteins fold?

Proteins need to fold into specific three-dimensional shapes to work properly. Anfinsen's experiment showed that many proteins can fold without help. Some proteins can still need a bit of help from special proteins called chaperones. These protein separate the folding protein from other cellular components so the protein can fold in peace, without being disrupted by multitude of other things present in the cell. To get a feel of how proteins fold, have a look at the video below that shows a protein folding.

This simulation requires lots and lots of computational power. The simulation was made possible with folding@home, where more than 280,000 people all around the world donated unused computer power (when their computer was idling). Protein folding is very sophisticated and often does require the combined power of 280,000 to model.

Advertisement for Folding@Home
From their website:

We are scientists. Citizens. Gamers. Thinkers. Parents. Friends. Family. We've joined forces to donate our unused computer power to help uncover the mysteries of protein folding and fight diseases. We are Folders, and this is our home.
Get support, join a team, and learn how your computer and (as of today) 281,427 others contribute to finding cures for some of life’s most threatening illnesses.

Visit their site at http://folding.stanford.edu/. I think it's a lovely movement. Hundreds of thousands of people uniting to fight disease. Sounds incredible, doesn't it?

Determination of structures of small molecules: NMR spectroscopy

The third and final segment of small molecular structure determination is nuclear magnetic resonance (NMR) spectroscopy, as is one of the strongest tools that chemists have in their arsenal. Like infrared (IR) spectroscopy, it involves illuminating molecules with light of the radiofrequency.

Nuclear magnetic resonance spectroscopy is based on the same technology as MRI, magnetic resonance imaging, that is used for medical and research. MRI will be the focus of another article.

What is spectroscopy?
Molecules can absorb or emit light. How they absorb and emit light can tell us about the molecule itself. The science that involves shining light onto a molecule is called spectroscopy. Studying how molecules emit light is also called spectroscopy.

What is NMR spectroscopy?
Nuclei have their own magnetic field, so when they are placed in an external magnetic field (inside an electromagnet), they will line up with and against the field.

Shining electromagnetic radiation (radiofrequency) onto the molecules can change the numbers aligned with and against the external magnetic field.

What does NMR spectroscopy tell us?
The types and amount of radiofrequency radiation absorbed can tell us several things.

• What atoms are present- carbon, hydrogen, titanium and many others
• How many of each atom is present
• Whether the molecule is symmetric (for example: aniline is symmetric)

• Which atoms are connected to with atoms. Chemists have advanced NMR techniques such as COSY (pronounced like nice and cosy), TOCSY (pronounced toxy) and ROESY (pronounced rosy).
• Which atoms are close in space to other atoms. Chemists have special NMR techniques such as NOESY (pronounced nosy) 

This concludes these series of articles on small molecule structure determination. Hopefully, it was entertaining and gives a glimpse of the world of chemistry. 

I would like to apologize for giving a very abridged stories of mass spectroscopy, NMR spectroscopy and IR spectroscopy. I intentionally wrote this for people with very little chemistry knowledge.

Determination of structures of small molecules: IR spectroscopy

The second segment of small molecular structure determination is IR spectroscopy. IR spectroscopy stands for infrared spectroscopy. IR spectroscopy tells us specific characteristics that the molecule has, which helps to narrow down possibilities.

It's like CSI and other detective dramas. Consider a group of people, one of which is the culprit. If I know that the culprit has black hair, I can narrow down the potential suspects. 

What is spectroscopy?
Molecules can absorb or emit light. How they absorb and emit light can tell us about the molecule itself. The science that involves shining light onto a molecule is called spectroscopy. Studying how molecules emit light is also called spectroscopy.

What is IR spectroscopy?
Infrared spectroscopy is where infrared light is shone onto a molecule and seeing what it absorbs. Consider aniline, which was introduced in mass spectrometry.

Aniline has a nitrogen connected to a hydrogen (an N attached to a H).

This causes the molecule to absorb specific types (wavelengths) of IR light. This shows up in the IR spectrum of aniline is shown below and the N-H dip is seen, where IR light is absorbed by aniline.

So if a scientist finds a molecule that he thinks is aniline. It has a mass of 93 Daltons, which is shown by mass spectrometry. It also has N-H which is shown by IR spectroscopy. This helps confirm to the scientist that they are correct.

If infrared spectroscopy is still not enough to work out what molecule the molecule is, we can the ultimate weapon: NMR spectroscopy.