Biology - The Study of Life

What is biology? Simply put, it is the study of life -- life in all of its grandeur. From the very small algae to the very large elephant, life has a certain wonder about it. With that in mind, how do we know if something is living? Is a virus alive or dead? What are the characteristics of life? These are all very important questions with equally important answers.


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Characteristics of Life

Living things include both the visible world of animals and plants, as well as the invisible world of bacteria. On a basic level, we can say that life is ordered. Organisms have an enormously complex organization. We're all familiar with the intricate systems of the basic unit of life, the cell.

Life can also "work." No, not the daily employment variety, but living creatures can take in energy from the environment. This energy, in the form of food, is transformed to maintain metabolic processes and for survival.

Life grows and develops. This means more than just getting larger in size. Living organisms also have the ability to rebuild and repair themselves when injured.

Life can reproduce. Have you ever seen dirt reproduce? I don't think so. Life can only come from other living creatures.

Life can respond. Think about the last time you accidentally stubbed your toe. Almost instantly, you flinched back in pain. Life is characterized by this response to stimuli.

Finally, life can adapt and respond to the demands placed on it by the environment. There are three basic types of adaptations that can occur in higher organisms.

• Reversible changes occur as a response to changes in the environment. Let's say you live near sea level and you travel to a mountainous area. You may begin to experience difficulty breathing and an increase in heart rate as a result of the change in altitude. These symptoms go away when you go back down to sea level.


• Somatic changes occur as a result of prolonged changes in the environment. Using the previous example, if you were to stay in the mountainous area for a long time, you would notice that your heart rate would begin to slow down and you would begin to breath normally. Somatic changes are also reversible.


• The final type of adaptation is called genotypic (caused by mutation). These changes take place within the genetic makeup of the organism and are not reversible. An example would be the development of resistance to pesticides by insects and spiders.

In summary, life is organized, "works," grows, reproduces, responds to stimuli and adapts. These characteristics form the basis of the study of biology.

Basic Principles of Biology

The foundation of biology as it exists today is based on five basic principles. They are the cell theory, gene theory, evolution, homeostasis, and laws of thermodynamics.

• Cell Theory: all living organisms are composed of cells. The cell is the basic unit of life.
  
  
• Gene Theory: traits are inherited through gene transmission. Genes are located on chromosomes and consist of DNA.
  
  
• Evolution: any genetic change in a population that is inherited over several generations. These changes may be small or large, noticeable or not so noticeable.
  
  
• Homeostasis: ability to maintain a constant internal environment in response to environmental changes.
  
  
• Thermodynamics: energy is constant and energy transformation is not completely efficient.

Subdiciplines of Biology

The field of biology is very broad in scope and can be divided into several disciplines. In the most general sense, these disciplines are categorized based on the type of organism studied. For example, zoology deals with animal studies, botany deals with plant studies, and microbiology is the study of microorganisms. These fields of study can be broken down further into several specialized sub-disciplines. Some of which include anatomy, cell biology, genetics, and physiology.

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How Proteins Find The Right DNA Sequences

Illustration of how proteins find the right DNA sequences. (Credit: Image courtesy of Uppsala University)

Researchers at Uppsala University and Harvard University have collaboratively developed a new theoretical model to explain how proteins can rapidly find specific DNA sequences, even though there are many obstacles in the way on the chromosomes.





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In living cells, DNA-binding proteins regulate the activity of various genes so that different cells carry out the right tasks at the right time. For this to work, the DNA-binding proteins need to find the right DNA site sufficiently quickly. The research team behind the new study has previously succeeded in determining that it takes only a few minutes for an individual protein molecule to look through the millions of nearly identical binding alternatives and find the right place to bind. This is nevertheless slower than what is predicted by the established theoretical model for how DNA-binding proteins find their way to the proper place by alternating between diffusing in the cell cytoplasm and along DNA strands.
"By also taking into consideration the fact that there are many obstacles in the way when proteins are to diffuse along DNA strands, we can now calculate more exactly how long it takes them to find their way," says Johan Elf, associate professor of molecular biotechnology at the Center for Bioinformatics.
Besides offering a more precise prediction regarding the time needed to find the right site on DNA, the new theoretical model explains why there is an optimal total concentration of DNA-binding proteins. If there were more, it would simply be impossible for them to find a binding place in a reasonable time, since the proteins would be in each other's way. If there were fewer it would go slower as well, since not enough proteins would be searching. Finally, the new model provides an explanation why so many DNA-binding proteins also bind auxiliary binding sites close to the regulatory site, thus forming DNA loops. It turns out that this can shorten the time to find the right sites.
"This more detailed understanding of gene regulation is important, since it can ultimately provide a better understanding of diseases that occur as a result of problems in the control functions of cells, such as in cancer" says Johan Elf.
The researchers behind the study are Gene-Wei Li, Otto G. Berg, and Johan Elf. The findings are being published March 16 in the scientific journal Nature Physics.
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New Antibiotics Could Come From A DNA Binding Compound That Kills Bacteria In 2 Minutes

A synthetic DNA binding compound has proved surprisingly effective at binding to the DNA of bacteria and killing all the bacteria it touched within two minutes. The DNA binding properties of the compound were first discovered in the Department of Chemistry at the University of Warwick by Professor Mike Hannon and Professor Alison Rodger (Professor Mike Hannon is now at the University of Birmingham). However the strength of its antibiotic powers have now made it a compound of high interest for University of Warwick researchers working on the development of novel antibiotics.

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Dr Adair Richards from the University of Warwick said: "This research will assist the design of new compounds that can attack bacteria in a highly effective way which gets around the methods bacteria have developed to resist our current antibacterial drugs. As this antibiotic compound operates by targeting DNA, it should avoid all current resistance mechanisms of multi-resistant bacteria such as MRSA."
The compound [Fe2L3]4+ is an iron triple helicate with three organic strands wrapped around two iron centres to give a helix which looks cylindrical in shape and neatly fits within the major groove of a DNA helix. It is about the same size as the parts of a protein that recognise and bind with particular sequences of DNA. The high positive charge of the compound enhances its ability to bind to DNA which is negatively charged.
When the iron-helicate binds to the major groove of DNA it coils the DNA so that it is no longer available to bind to anything else and is not able to drive biological or chemical processes. Initially the researchers focused on the application of this useful property for targeting the DNA of cancer cells as it could bind to, coil up and shut down the cancer cell's DNA either killing the cell or stopping it replicate. However the team quickly realised that it might also be a very clever way of targeting drug-resistant bacteria.
New research at the University of Warwick, led by Dr Adair Richards and Dr Albert Bolhuis, has now found that the [Fe2L3]4+ does indeed have a powerful effect on bacteria. When introduced to two test bacteria Bacillus subtilis and E. coli they found that it quickly bound to the bacteria's DNA and killed virtually every cell within two minutes of being introduced - though the concentration required for this is high.
Professor Alison Rodger, Professor of Biophysical Chemistry at the University of Warwick, said: "We were surprised at how quickly this compound killed bacteria and these results make this compound a key lead compound for researchers working on the development of novel antibiotics to target drug resistant bacteria."
The researchers will next try and understand how and why the compound can cross the bacteria cell wall and membranes. They plan to test a wide range of compounds to look for relatives of the iron helicate that have the same mechanism for action in collaboration with researchers around the world.


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Glutamate Receptor Believed Dead Comes To Life

Schematic presentation of the exchange of the delta2 receptor's intrinsic ligand recognition site (red). The recognition site from another glutamate receptor (blue) enables conversion of chemical into electrical signals: the reputedly dead ion channel springs to life. (Credit: Image courtesy of Ruhr-Universitaet-Bochum)

To all intents and purposes, the delta2 receptor is an unequivocal member of the family of glutamate receptors, the most important receptors for excitatory neurotransmitters in our brain. To date, however, this receptor has been considered the “black sheep” of the family because it does not react to glutamate, which, by definition, a glutamate receptor ought to do.


This riddle fascinated the neuroscientists working with Prof. Michael Hollmann (Chair of Biochemistry I – Receptor Biochemistry) at the Ruhr University.
To unlock the secret of this receptor, they “crossed” it with another glutamate receptor that functions normally. The resulting chimera is functional and opens an ion channel. The task now at hand is to identify a transmitter that triggers this mechanism in an unchanged, physiological delta2 receptor. The scientists have published their observations in the current edition of the Proceedings of the National Academy of Sciences, USA (PNAS).


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Lively communication between brain cells



Our brain consists of a gigantic network of about 100 billion neurons. Every one of them is linked to other neurons by more than ten thousand contact sites. The universal language within this network consist of electrical impulses, the sum of which lead to the development of our world of thought in a hitherto completely unknown manner. The majority of contacts between neurons are not direct, as a few millionth of a cm separate the cells from one another. This distance must be overcome if a signal from a transmitting cell is to reach a receptor cell.
This occurs at special contact sites, so-called synapses, which conduct incoming signals with the assistance of a chemical messenger, a so-called neurotransmitter. The activated transmitting cell discharges the messenger, which then crosses the synaptic cleft and is recognized by the receiving cell. This is where the glutamate receptors come into play. Protruding from the plasma membrane into the synaptic cleft they are specialized in registering the messenger most frequently found in the brain, namely glutamate – the well-known flavor enhancer in Chinese dishes, and subsequently convert the chemical signal into an electrical signal.



Conversion of chemical into electrical signals



Key to the secret of conversion of chemical into electrical signals is the structure of the receptors. They consist of three important parts: a glutamate recognition site, a joint, and a channel. The extracellular, bipartite recognition site protruding from the plasma membrane recognizes glutamate, binds it and then snaps shut like a mouse trap. Via a sophisticated joint mechanism, this closing movement is transmitted to the channel that traverses the cell membrane and causes the channel to open. Positive ions that have accumulated outside the cell can now flow into it and thereby generate an electrical signal.



Important but mysterious role



The delta2 receptor also has the three elements discussed above. Why then is it not activated by glutamate? Prof. Hollmann summarizes the problem by stating: "We know that the delta2 receptor is located at specific sites within the cerebellum, that it plays an extremely important role for the fine coordination of motor behaviour, and that it evidently contributes to the correct circuitry of the neurons during development of the cerebellum. What we don't know is just how the receptor fulfils these functions". The scientists thus decided to pursue the principal question whether the delta2 receptor is at all capable of functioning in a manner similar to that of the other glutamate receptors, namely as a neurotransmitter-activated ion channel.



Greek mythology helps



To answer this question the scientists recalled a very old idea: they produced a chimerical receptor. In Greek mythology, the chimera is a monstrous figure with a lion’s head, the body of a goat, and a snake's tail. Within the framework of her dissertation at the IGSN (International Graduate School of Neuroscience), Sabine Schmid created a chimeric delta2 receptor with the joint and channel of the delta2 receptor, but the ligand recognition site transplanted from a normally functioning relative.
This chimeric receptor did indeed react to glutamate and opened its ion channel, which had previously been belived to be dead. Prof. Hollmann comments: "We thus have developed a tool that, for the first time, enables us to investigate of the unique properties of the joint and the ion channel of the delta2 receptor. Moreover, our results suggest that the secret of the delta2 receptor is to be found in the difference in its recognition site for neurotransmitters". To a certain degree, the scientists have thus managed to unveil the function of the “black sheep.” The next step is to determine to which signal the actual recognition site of the delta2 receptor reacts and which role this plays for its essential function in the cerebellum.

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Circadian Rhythm: How Cells Tell Time

The fuzzy pale mold that lines the glass tubes in Dr. Yi Liu’s lab doesn’t look much like a clock.
But this fungus has an internal, cell-based timekeeper nearly as sophisticated as a human’s, allowing UT Southwestern Medical Center physiologists to study easily the biochemistry and genetics of body clocks, or circadian rhythms.
In a new study appearing online this week in the Proceedings of the National Academy of Sciences, Dr. Liu and his co-workers have found that this mold, which uses a protein called FRQ as the main gear of its clock, marks time by a sequence of changes in the protein’s chemical structure.
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Dr. Liu said the new finding might someday help researchers develop treatments for human sleep disorders and other problems associated with a faulty biological clock.
“This timekeeping protein is really the core component of the circadian clock,” said Dr. Liu, professor of physiology at UT Southwestern and senior author of the study.
Despite the evolutionary distance from mold to man, mechanisms controlling their circadian clocks are very similar. In both, circadian rhythms control many biological processes, including cell division, hormonal release, sleep/wake cycles, body temperature and brain activity.
The researchers employed a fungus called Neurospora, an organism frequently used in studies on genetics and cell processes, especially circadian rhythms. It reproduces in the dark and rests in the light.
A decade ago, Dr. Liu discovered that FRQ controlled the cellular clock in Neurospora by chemical changes of its protein structure. As the day goes on, the cell adds chemical bits called phosphates to the protein. Each new phosphate acts like a clock’s ticking, letting the cell know that more time has passed.
When the number of phosphates added to FRQ reaches a certain threshold, the cell breaks it down, ready to start the cycle again.
The researchers, however, did not know where the phosphates attached to FRQ, how many got added throughout a day, or how they affected the protein’s ability to “tell” time.
In the current study, the researchers used purified FRQ to analyze the specific sites where phosphate groups attach. In all, the researchers found 76 phosphate docking sites.
“This is an extremely high number,” Dr. Liu said. “Most proteins are controlled by only a handful of phosphate sites.”
They also studied how these phosphates are added to FRQ daily and found that two enzymes are responsible for adding most of the phosphate groups in Neurospora. They also found that the total number of phosphates oscillates robustly day by day.
In addition, the researchers created a series of mutations in many of the phosphate docking sites, creating strains of mold that had abnormally short or long daily clocks.
In upcoming studies, the researchers plan to identify which enzymes add phosphates to specific sites and exactly how changes in a particular site affect a cell’s clock.
Other UT Southwestern physiology researchers contributing to the work were co-lead authors Dr. Chi-Tai Tang, postdoctoral researcher, and Dr. Shaojie Li, former postdoctoral researcher; Dr. Joonseok Cha, postdoctoral fellow; Dr. Guocun Huang, assistant instructor; and Dr. Lily Li, former postdoctoral researcher. Researchers from the National Institute of Biological Sciences in China and the Chinese Academy of Sciences also participated.
The study was supported by the National Institutes of Health and the Welch Foundation.


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