Nanotechnology – a very old story

What genes are series – part 4

Nanotechnology became a real buzz word in the last two decades and it seems like a new revolutionary idea, that physicists and chemists are looking for in their fields.
The concept of nanotechnology is to build nano-scale (billionth of a meter) machines that will be able to do amazing things by manipulating atoms and molecules in a very precise way. But this technology was invented billions of years ago, and it is called – biology...

Genes are the manuscript of nanotechnology
As we already talked about how genes are written and read, I mentioned that large part of the genome is being translated to long chains, composed of 20 small building blocks called “amino acids”. Each of these blocks has unique chemical properties. The large chains of amino acids are then “folded” to three-dimensional structure, we call “protein”.

There are many proteins, with many functions and structures. Proteins are the machinery and the building blocks of life. So in general, when speaking about genetics, we usually refer to the genes that translated to proteins as the most important genes for biotechnology.


Proteins general functions
So what do these proteins do? Well, there are 3 main functions that proteins play in life:



1. Enzymes



Most of the proteins are enzymes. Enzymes are the essence of nanotechnology. They are small machines, which work alone or with others to accelerate and mediate chemical reactions. The power of enzymes is unimaginable. Enzymes can speed up reactions up to billion billions times faster then they would have been accrued naturally. This power allows life to break and build molecules, store energy, build complex structure, and maintain the DNA code, in quick way, and in moderate temperature. Virtually no man-made machine can even get closer to the efficiency, accuracy and power of enzymes. To achieve a fraction of the energy production and chemical synthesis of enzymes, we need to use high heat and strong pressure, or employ very reactive chemicals.
The way proteins do that is by using their special fold with many functional groups (the amino acids), to break molecules, bind to them, or move them closer together. They function as little robots that physically manipulate atoms and molecules, like the nanotech guys can only dream-of.


2. Structural proteins
Some of the proteins are not used as little machines, but as sophisticated building blocks. Proteins are used to build strong materials, like spider silk or nails. Proteins construct the basic scaffolds of organs, and they used in biological motors to create energy.
Structural proteins are everywhere, and they are involved in every aspect of life.

3. Recognition
The third specialty of proteins is the ability to use their highly complex structure as a tool to recognize other molecules. Many proteins are receptors – they can receive signals from outside the cell and respond to it. Information in biology does not stop at genes. There is a continue communication between cells and between parts in the cells, and all of this communication is carried out by proteins.
In some cases proteins can be gently modified to be able to recognize small molecules in a very specific manner, this is the case of antibodies. Antibodies are proteins that can recognize and react to very specific molecules that are foreign to the body.

Can we use it?
We already do. from fermenting of wine to manufacturing drags, we use proteins everywhere – in the chemical industry, in textiles, in medicine and more. The real bio-tech is in using proteins to our advantages. Nano-technology is already in our hands.

Information and us

What genes are? – Part 3

After discussing about the place where the data of life is stored (nucleic acids), and the way this data is read (The assembly lines of bio-tech), and before we will talk about what makes life so wonderful, I’ll explain why I think that living is all about information.

Information is the core of biology.
One of the things that biological systems master is information saving and manipulating. As already said, many of the cell resources are dedicated to protecting, maintaining, and reading this data. The way biology invent new designs and functions, is by slowly moderating this data, in a way called evolution. I am not going to enter into it right now, but this it is a very important notion.

The living world invented an amazing set of innovations, which are much more advanced than humans have ever invented. The animal and plant world is still ahead of us in energy harvesting and manipulation, in building complex structures and materials and many other functions.

The meaning of this data.
All of this data is stored in tiny nucleus, and is transferred from generation to generation for billions of years. Anything else is extremely temporary, the materials that make life are degraded and gone very fast, but the data remains. This is the secret of life.
When we consider the chemical differences between organisms, we will found out that basically all the living world is build from virtually the same building blocks. Much of our membranes, proteins and other small materials is the same. The only thing that really differ one species from another is the information that lineate the manuscript of life.
Consequently, the key to understand and utilize the power of life to our advantage is to understand the information. Once we will understand the “genome” and how the information is stored and used; we will be the kings of all life. But this is not so easy...

Biological information is complex.
When scientists understood the importance of data processing in biology, a new field of research was born – bioinformatics. This is the science of understanding the data behind the chemistry of life. Now we collected a huge amount of data, and we have strong computers that allow us to dive into the enormous information of life, and the vision is mesmerizing. It quickly became clear that reading and understanding, even the simplest genome is very hard. The information is more than just words of DNA that translated to proteins. The biological data is encrypted in each aspect of life, starting with the way data is altered in the DNA itself, by chemically modifying the code of life, and ending in the way the proteins themselves are edited and changed after their were already translated.

How to read the data?
Although we are still very far away from reading the whole picture, we can already manipulate some of the genetic data to our advantages. We learn how to read the data stored in the DNA by a method called sequencing. We also learned how to control the expression of genes, and we can sometimes alter the amount of their expression. These tools are constantly increasing our knowledge of what genes are and how they work.
As genes are not working as single units but as a network of genes, small machines that work together, a new kind of science was invented called system biology. This research field is trying to understand the system as a whole, and already gave new insight of how the bigger picture of life information looks.




How can we use this data?
Well, as we understanding the information and the biological system more and more, we can use out knowledge to understand how living creatures use this knowledge to alter themselves and the environment, and then use this data to invent new technologies.
This understanding opened new grounds to medical, industrial and agricultural technologies already, and it is developing rapidly.

So if you want to deeply understand biotechnology, you must recognize the importance of the biological data, and how it is work, before trying to understand how to use it as a technology.

The assembly lines of bio-tech

What genes are? – part 2

After introducing the molecules that store the information of how to create life - the nucleic acids, I will now shortly introduce the way these long chains of information is translated into the small machines that creates life.
In biotechnology we use this machinery to our advantages, to control the way this precious biological data is used.

As you already know, the huge data-base of life is stored in a highly packed ans stable DNA molecules, which can be billions of letter long. These molecules are highly preserved and maintained, and cannot "make life" by themselves. Something have to read the data and use it. The way it is done, is by using a nano scale assembly line, that can read the manuscripts written in the genes and translate it to small machines. Most of the small machinery of life are called proteins, and we will discuss it later.

A large part of the genome contain the information of the machines that use to translate the information in the genome itself. Many small machines are called "transcription factors". These factors control the timing and amount of reading the genome, by binding and modifying, specific locations on the long DNA molecules. The main purpose of these factors is to control the binding of large assembly line, build from several proteins (we call it "complex"), that are used to translate the 4 letters code of the DNA to the 4 letter code of a smaller RNA molecule. This process is called "transcription" since you create the RNA transcript which represent small parts of the DNA code that bear specific functions.




After the RNA is created, it is used as the key to create the functionality of the living cell. RNA have many purposes. First some of the RNA are actually nano-machine by themselves. RNA unlike DNA is not very stable, and its long chines is not packed is a stable helix. The RNA chain can twist and fold, and create a specific form that may have special chemical properties. The folded RNA can be use as a small catalyst to some reactions, like cleaving other RNA. It is also used as part of the transcription complex, and small RNA can be used to cleave other RNA as well, and be part of the transcription control. Finally, most of the RNA are used as a message to further build much more complex machines called proteins. Proteins are the real secret of life, and I will dedicate a different article for them later.

Before being translated into proteins, this messenger RNA is sometimes being modified and changed, parts of it may b cleaved out, and some of its letters are edited. I have to mention it, since you must understand, that not everything that is written in the DNA is translated as is to the RNA message. This message RNA is transferred to a very large protein and RNA complex, a nano-factory called ribosome. This ribosome reads the RNA and translate each 3 letters to one amino-acid. There are 20 amino-acids that the ribosome knows how to connect, and the long RNA message is translated to a long chains of amino acids. Each amino acids have different chemical properties - some are acidic and some are more basic, some can break chemical bonds, and some can assist in creating one, some can bind metals, and so on. Creating this long chains of amino acids with different qualities, is the secret of creating new molecules that can have very different chemical and physical properties, these are called proteins.



In ancient, simple creatures like bacteria, all of these processes are taking place in one large space, inside the cell, which is covered by oily membrane. In more advanced organisms, there are many internal membranes that divide and compartmentalize the cell, so every part of this assembly line is being placed is a dedicated area. the DNA is stored in the nucleus, which protect and maintain the genetic material. In the nucleus the DNA is being transcribed to RNA, and the RNA message is transferred outside of the nucleus, and being translated to proteins on a ribosomes outside of the nucleus.

That's all for now.
lets summarized:
1. The genetic material is being controlled and read by proteins called transcription factors.
2. then a transcription complex assembly line read the DNA is specific locations and create a complementary RNA molecules.
3. RNA can be used as machines by themselves, and help in the processes of controlling the transcription and translation process.
4. The RNA message can go to the ribosome, in which it is being translated to long chain of amino acids, called protein.

Before I'll go into the functions of proteins, I will discuss the way information of the basis to lifr on earth.

The acids in the nucleus.

What genes are? – part 1

During the 20th century, biologists started to understand the concept of genes, and the way basic chemicals can produce the diversity and phenomena of life. The big explosion of this knowledge was, when scientists proved that the material that is accountable to store and transfer the hidden data of how to create and maintain a living creatures, is coded in a complex, acidic molecules inside our cells nuclei.

These molecules are long chains of simple sugar molecule called ribose, in which each unit in the chain have a slightly different chemical structure. The ribose chains that were found in the nucleus were called Ribo – Nucleic – Acids (RNA) and Deoxy-ribo Nucleic Acids (DNA).
It the 1950’s, scientists understood the structure of these molecules, and from then to now, we gradually figuring out, how these molecules, store and use biological information.

So what is a gene?
A gene is a very old concept in modern biology that is a virtual unit of information that can be passed on to next generations. Today, we usually call to a unit of information written in the DNA language, which can be translated to one protein – a gene. I will explain that sentence later.

The language of life
It is funny to call to the basic molecules of life “nucleic acids”, since they do not have to be in the nucleus. Any creature on earth have DNA and RNA, from the simplest bacteria (which have no nucleus), to mammals and plants. And although the letters of the language are the same, there is huge different in the way different creatures use the universal language of DNA and RNA to store and retrieve information. In its basics, the DNA has 4 “letters” – four different ribose base molecules that can be combined to produce “words”. Part of the huge DNA molecules contains chains of three letter words that can be copied from the DNA to a RNA molecule and then each 3 letter word is translated with sophisticated machinery to long chains of different of amio-acids that build the small machinery of life. More about that later.

Storing the data
The information of how to build the small chemical machines of life is stored in the DNA, a very stable molecule. The DNA has two parallel chains, and each piece of information is actually backed up by the complementary chain. Advanced organisms usually store a backup of the entire gene repertoire in two different molecules. The information is carefully taking care of, by a big inventory of preserving and repairing machines. The DNA is held in every single cell. The information is passed on from generation to generation by duplicating the entire genetic material and passing half of it to the sibling.
We have to understand that most of the data stored in the DNA is not genes themselves, but a huge information on how to read them and when.

Reading the data
Like mentioned before, the data is read by a dedicated machines that knows how and when to translate the information to small molecular machines. Most of the genome contains information on where genes begin and end, when to read them, and in which organ. A lot of nano-machines (that the information to build them is also stored in genes), are used to read, and translate the data to the life processes.

The code of life
When we look on different organisms we can say that most of the gene repertoire was not dramatically changed from the ancient uni-cellular organisms to big animals. Many of life processes are the same. The change in many cases is in the code surrounded the genes, that dictate how and when to read these genes. For example, the hidden different between us and chimps, is probably not in the pool of genes, which is virtually identical, but in the control of how and when to use them.

Complicating things.
When we first solved the way genes are translated to the machinery of life (that will be explained in later articles), we thought that we can easily control the way genes are used, and if we will understand the genome, we will control the processes of life.
That was the beginning of “genetic engineering”. but soon we found out that things are much more complicated.
First, it turn out that most of the genome is not coding to “real genes”. Later we found that a lot of information is not stored in the DNA code, but in other form of data, like RNA, small molecules, and modification of the DNA. We found that genes can be edited after they were transcribed from the genome.
So today we stand with basic understanding of the information of life, but with many questions that have to be solved before we can really “genetically engineer” life.

So what biotechnology and genetic engineering really is?
Well, we do understand some of the way genes work, and we can use the information to manipulate living creatures to do what we want. How do we do so? – on this in later posts...

Let’s summarized:
1. Life’s data is stored in long molecular chains called DNA.
2. DNA is highly maintained and is the genetic material that passed between generations.
3. Part of the DNA contains the information on how to build the life machinery, and some contain the instructions of how to use this data.
4. The way the data is stored and read is very complex and we do not understand the whole picture yet.

Where to begin? - What genes are series

Where to begin?
When you start to think about scientific topic, it is very hard to know where to begin.
Bio-technology is a very broad subject, and if we where at school, we would start by learning basic biology and chemistry. However, this is not the purpose of this website.
So I think that we will skip the basics in biochemistry, and jump right to the most amazing discovery in the history of science - Our genes.

Biology as information science.
Instead of trying to define what life is and what genes are, and how we can make technology out of it, I'll jump right into the water and write a series, trying to explain why life is all about information, what genes are and how they work. I m sure that all of you already heard that we are build of cells, that we have genes that can be inherited, you might even heard something about DNA, RNA and other strange words like that.

The series will include the following:

1. The acids in the nucleus.
This part will discuss the basic (very basic, I promise) chemistry of data storage in our cells.

2. The assembly lines of biotech
We will see how nature invented the assembly lines and how it is use to make the coded information in our genes, becoming alive.

3. Information and us
We will talk about living creatures as information and how information can do all these staff.

4. Nanotechnology – a very old story
Here we will talk about the only real nanotechnology known today, the way it works, and what the connection to life.

What is biotech any way?

Maybe this question sounds strange to you, but before we can dive into the biotech science and practice, you have to understand what do I mean when I say "biotech".
Bio-technology, is a general term, referring to any kind of technology that uses living organisms or materials from living organisms.

The Wiktionary define biotechnology as:

"1. the use of living organisms (especially microorganisms) in industrial, agricultural, medical and other technological applications 2. the application of the principles and practices of engineering and technology to the life science"

I disagree with that. This definition is not enough. A huge amount of technologies uses bio materials, but does not considered as biotech - for example - riding on horses uses living organisms (horses), but is not considered biotech, so does egg produced by chickens.

So in order to call some technology "biotech" it must hold another quality. For my opinion this quality is science.
What distinguish regular technology that exploit biological processes, and biotechnology? - the understanding. In biotech, we use our advanced understanding of biology to create the technology. Usually this mean understanding the chemical processes behind the biological world.

In more details, bio-tech is usually referring to the following technologies:

1. Medical technology - when we use biological understanding to invent new medical procedures, drags, treatments or devices, it might be called "biotechnology".
2. Agricultural technology - Using our knowledge of plants and animals biology to create more advanced crops , live stocks and agricultural techniques.
3. Research techniques - some times we use bio-technology to invent new kind of research methods that creates new scientific data.
4. Chemical industry - Many useful materials can be produced by using biological principles and reactions. When using advanced biological methods to produce new materials, it is also bio-tech.
5. Food industry - Since all of our foods are essentially biological, a lot of modern food production practices uses bio-tech.
6. Energy industry - In recent years, a lot of efforts are invested in the research of renewable energy resources, and one of the important ways to achieve that is bio-tech.

What is the basic knowledge required for understanding bio-tech?
Biotechnology is eventually about understanding how biological processes work from two main angles: One is the chemical side of the process and the other is the way information is used to shape the machinery of life. Biology is about super advanced information processing and super efficient chemical reactions.
So, in order to understand bio-tech we will talk about these two aspects of biology and how understanding them, can help us engineer new technologies.
This site does not assume any previous knowledge of these subject, and it will explain any piece if science when it will be needed.

To conclude, it is quite hard to define what bio-tech is. but I think I passed on the main idea. hopefully, you'll keep reading the material on this site, and will get to know the subject and it aspects deeply.

D.H.

About this site

"Biotech for smart dummies", is a blog, writing about advanced biotechnology ideas, techniques and news, targeted to people that are not professional scientists, but smart enough to understand the importance of learning bio-tech in our developing world.
This site is not intended to replace textbooks or scientific literature, but to provide my insights about biology and biotechnology.

During the posts, I'll try to pass my knowledge of biology and new technological methods in simple, fun way. The idea is to bring the joy and mystery of science to anyone who is interested in the field, from any reason it might be.

Another goal of the material I will be discussing here is to make some order in the blowing news of the biotech industry we see every day. That industry gives a great deal of promises, raising a monstrous amount of money, from people who usually have no idea what the technology is all about. So here is the place for catching up.

I hope to wake some discussions about scientific ideas from different perspectives, so your comments are most welcome.

D. Hilman