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Biomolecular Adaptations to Extreme Environments
   Chris Bennett, David Harrington, & Mark Pitts
Based on the presentation at the Astronomy 734 Astrobiology Seminar by Andrew Boal,Fall 2004


1. Biomolecular Structures

1.1 Introduction
When we talk about biomolecules, we are referring to the molecules found within an organism that have some kind of biological function necessary to keep the organism alive. In recent years, scientists have discovered forms of life on Earth that possess biomolecules very similar to those that make up our own cells, yet live in conditions that we once thought would be lethal to living organisms (such as intense heat, pressure, or acidity). To survive in these extreme environments, it is necessary for the organisms to make structural alterations to many of their biomolecules so that they can still carry out their desired function. The study of these altered structures could be of great importance when searching for signs of life elsewhere in the Universe, where extreme conditions might be common. To understand the adaptive changes in these biomolecules, it is necessary to have an understanding of some of the basic biomolecules that make up a cell. We then proceed to list some examples of how these structures have changed to better suit their environment. Finally, we describe several terrestrial locations where these exotic organisms are found, and possible off-world analogs to their extreme environments.

1.2 Polarity: Are they scared of the water?
One of the most important concepts to bear in mind when discussing biomolecules is that of polarity. When a covalent bond is formed between two different atoms (for example, in water, a hydrogen atom, H, and an oxygen atom, O), the shared electrons between the atoms will feel a slightly larger attraction toward the atom with a larger electronegativity. The electron will dwell near that atom more often, giving it a slight negative charge and the companion atom a slight positive charge. This asymmetrical electron distribution between the bonding atoms is described as polarity. Considering the most common elements found in biomolecules, we find that the bond between O and H is very polar, the bond between nitrogen, N, and H is slightly polar, and the bond of carbon, C, with H is essentially nonpolar. Thus, water (H2O) is a very polar molecule. Oils, on the other hand, are made up of hydrocarbons that have only C-H and C-C bonds present, and are described as being nonpolar. When oil and water are mixed, we discover that two separate layers form (Figure 1, Oil and water form two separate layers when mixed. (Ref. 9)). The reason for this is that polar molecules such as water are attracted to other polar molecules. Likewise, nonpolar molecules prefer to be surrounded by other nonpolar molecules. Another way of putting this is to say that nonpolar compounds are hydrophobic (water fearing), whereas polar molecules are said to be hydrophilic (water loving).

The concept of hydrogen bonding (Figure 2) can be described in a similar way. When an electronegative atom (such as N or O) is attached to a hydrogen atom, the slightly positive hydrogen atom can form a weak bond to another electronegative atom known as a hydrogen bond. Although an individual hydrogen bond is far weaker than a covalent bond, large numbers of hydrogen bonds are incredibly strong. Hydrogen bonds are responsible for some of water's unique properties, such as its high melting point, which have been vital to the creation and sustaining of life on Earth.

1.3 Lipids: A matter of heads or tails
Lipids, also known as fatty acids, are the biomolecules responsible for forming cell membranes, which are boundaries between the interior of a living cell and the rest of the environment (Figure 3, An illustration of the cell-membrane forming the outer layer of the cell. (Ref. 4)). These lipid membranes are formed by an application of polarity (discussed above). Lipids have a polar, hydrophilic "head" and a nonpolar, hydrophobic "tail." As they are introduced to water, what results is the self-assembly of a lipid bilayer, where all of the hydrophobic tails have been pushed together, and only the polar heads are in contact with the water surrounding the membrane on both sides (Figure 4, An example of the formation of a lipid bilayer. Note the hydrophobic tails come together on the inside, and the hydrophilic heads are on the outside. (Ref. 4)).

A closer look at an individual lipid is shown in Figure 5. The polar head is shown in blue and the nonpolar chain is shown in red (note how the nonpolar hydrocarbon chain contains only C-H bonds). The right part of the figure demonstrates how chemists draw lines to represent chains of hydrocarbons. Each "kink" represents a carbon atom, and unless something else is bonded to it, we assume there are two bonded hydrogen atoms present.

1.4 Nucleic Acids: Everyone pair up!
1.4.1 Primary structure:
DNA (Deoxyribonucleic acid) and RNA (ribonucleic acid) are the blueprints and messengers of the cell, respectively. DNA stores all of the instructions for a cell's function, and the RNA helps to transport and translate these instructions to the other parts of the cell. Both DNA and RNA are composed of long chains of shorter subunits called nucleotides. Each nucleotide is made up of three parts:
  • Nucleobase: These are the molecules within DNA that actually carry the genetic code, the blueprint for all of the biomolecules required for that organism to develop and function. There are four different bases that can be used in any order; adenine and guanine have a purine (two-membered ring) structure, whereas thymine (in DNA only), uracil (in RNA only), and cytosine are based on pyrimidine (single-ring structure) (Figure 6).
  • Sugar: Figure 7 shows the five-carbon sugars used as part of the structural backbone of DNA and RNA. The ribose used in RNA has a hydroxyl group (-OH) attached to one of the carbons not present in the deoxyribose equivalent in DNA, which leads to a decrease in RNA's stability. We therefore can expect RNA molecules to degrade faster than DNA molecules (i.e., they are only temporary carriers of information). Sugars like ribose are composed of C, H, and O, are plentiful in the cells of organisms, and provide a variety of different functions (for example, cellulose as a structural component in plants).
  • Phosphate: The phosphates are usually bridge two sugars together and make up the second part of the structural backbone (Figure 8). They can be found as mono-, di-, and triphosphates (the monophosphate is shown here. All of these have negative charges that make them hydrophilic. As a result, this side of the nucleotide is the one in contact with the water medium within the cell.

1.4.2 Secondary structure:
The primary structure of DNA refers to the order of the nucleotides within the nucleic acid chain, whereas the secondary structure refers to the shape that the chain folds up into. Normally, DNA forms a double-helix structure. This is the most famous representation of DNA. It looks like a twisted ladder, which completes a complete circle every 10 base pairs, stabilized by hydrogen bonding. In this double helical structure; there are actually two separate strands of DNA, which are complementary. What this means is that each nucleotide has a specific partner that it must bond to. Within the space of the double-helical structure, a purine must bond with a pyrimidine, thymine (or uracil in RNA) is complementary to Adenine (T:A, or U:A), and guanine is complementary to cytosine (G:C). The double helix structure, although the most common, is not the only secondary structure that DNA have. Figure 9 shows a few of the other possible structures.

1.5 Proteins: The chemical machines of the biological world
Similar to the way nucleic acids are built from smaller subunits, proteins are made from smaller molecules known as amino acids that form chains of peptides. The functional groups of an amino acid are shown in Figure 10, the R-group can be varied to give the amino acid different chemical functionality. For example, it can be a side group that is hydrophobic or hydrophilic. This will determine which amino acids will be on the outside of the protein (hydrophilic groups), and which are more likely to be pushed into the inside (hydrophobic groups) when the peptide chain begins to fold. Polarity is not the only chemical functionality that can be altered by the side group. In fact, each protein has a specific architecture determined by the location of amino acids (and often also a transition metal) that is known as its active site, which has been perfected to carry out a specific biological function. Some examples of different amino acids are shown in Figure 11.

The basic outline of how we get from the genetic code for creating a protein stored in DNA to the peptide chain that folds into the functional protein is outlined in Figure 12. The appropriate section is copied from a gene in DNA to mRNA (messenger RNA), which is complementary to the original DNA strand, in a process called transcription (i.e., copying a section of the genetic code). The process for converting the actual genetic code into a sequence of amino acids is called translation, and requires knowledge of the universal genetic code (Figure 13). Here, we can see that the genetic code is made up of codons (3 nucleobases long), each of which codes for a specific amino acid, for example, UAG = Trp (tryptophan). A large biomolecule called ribosome RNA moves along the mRNA strand codon by codon eventually creating a long peptide chain. A transfer RNA (tRNA) molecule is responsible for recognizing a codon, and has the appropriate amino acid attached to it, which is incorporated into the growing peptide chain by the ribosome RNA, with each amino acid linked by a peptide bond that is formed between the carboxylic acid (COOH) and amino (NH2) groups of neighboring amino acids coupled with the loss of water (H2O) (Figure 14, The formation of a peptide bond between two amino acids. (Ref. 7)). The order of amino acids in a peptide chain is referred to as the primary structure of the protein (Figure 15).

The secondary structure of a protein refers to the way certain parts of the peptide chain can fold locally to give rise to α-helix coils (Figure 16) and β-sheets (Figure 17) that are held together again by hydrogen bonding. Note that the arrows indicate the direction of the folding sheets. They can be arranged either parallel or antiparallel. Tertiary structure refers to the overall shape of a folded protein (Figure 18, The tertiary structure of a protein refers to its overall shape once folded. Note that the structure is not rigid and maintains a certain amount of flexibility required to carry out its function. (Ref. 8)) and quaternary structure refers to the process whereby single protein subunits combine to form a larger functional structure (Figure 19, The quaternary structure is the overall structure of a biomolecule that consists of more than one separate protein. This diagram demonstrates how they combine together to provide functionality. (Ref. 8)).

2. Biomolecular Stability

With a basic understanding of the major biochemical structures (e.g., lipids, nucleic acids, and proteins), we can now explore the resilience of these structures under extreme environmental conditions. We will find that increased stability comes as a direct result of subtle chemical changes in the structures that allow them to maintain their shape and functionality. Such changes might be vital not only for terrestrial life in extreme conditions, but could also be important for forms of life elsewhere in the Universe where such conditions are frequent.

2.1 Are they loving or just tolerant?
In discussing life-forms dwelling within extreme environments, three groups characterize life in the broadest sense: mesophilic life, extremeotolerant life, and extremeophilic life. Mesophilic life are living things that survive and flourish at typical conditions on Earth's surface and shallow ocean depths. (Humans are an example of mesophilic life.) Extremeotolerant organisms can survive under certain extreme conditions, but they often do not flourish. Extremeophilic organisms not only survive in extreme environments, but actually require such an environment to grow and thrive. Extremeophiles are further grouped into various subcategories based on what extreme conditions they prefer. A brief list of some of these subcategories is given in Figure 20.

2.2 Rescuing their fat from the fire
As discussed above, lipids are vital to living cells, because they provide the barriers that give cells their definition and support. Without a functioning lipid bilayer, a cell cannot regulate the transfer of materials in and out of the cell, nor can it protect itself from the extreme conditions that lie outside the cell. Fortunately, as scientists have discovered, the lipids of extremeophiles have distinct chemical differences from those of other life-forms that increase their structural stability.

In the specific case of thermophiles, the lipids must withstand a liquid water environment many times hotter than room temperature (i.e., from 45° C to more than 100° C). In such an environment, water molecules have greater kinetic energy, and can more easily cause biochemical structures to warp and break apart under the increased bombardment. For these high-temperature life-forms, three major changes have served to strengthen the lipid layer and maintain the cell's structure. First is an increase in the number of hydrogen-carbon single bonds in the lipid tails. This increases the strength of the lipid bilayer because there is a greater surface area for attraction between the nonpolar tails. Secondly, double-bonded oxygen is removed from the hydrophilic heads, which increases their structural stability. In very high temperature environments, a third alteration joins the lipid tails together, turning the bilayer into a stronger, single layer. The self-assembly of these bilipid layers requires less individual molecules and is therefore more likely to occur. Also, the destruction of the lipid will become more difficult. These three chemical changes are illustrated in Figure 21.

2.3 Three are better than two
Just as important as the lipids that make up cell boundaries is the DNA that encodes the cell's instructions. While DNA usually exists in a double-helix structure, scientists have found that the structure can "unzip" and warp at a sufficiently high temperature. This process, known as DNA melting, is characterized by a specific temperature (Figure 22). In examining the hydrogen bonding between base pairs that hold the DNA together, two hydrogen bonds join the A:T pair, while three such bonds connect the G:C pair. As one might expect, three bonds prove to be stronger than just two, and data suggest that the higher percentage of G:C pairs in a DNA strand, the higher the temperature it can survive without melting (Figure 23).

2.4 Things are unraveling fast
Like DNA, the RNA and proteins within a cell will loose their structure as the temperature increases. In addition to simply observing at what temperature the RNA or proteins disintegrate, we can calculate the free energy of complex formation (ΔGf) to better quantify a structure's stability at high temperatures. This ΔGf value can be derived directly from which amino acids and secondary structures are present. The lower the ΔGf value, the more stable the structure and the more resistant it is to melting. The study of thermophiles has demonstrated that these organisms do indeed possess proteins with a lower ΔGf value than other organisms (Figure 24).

One might ask the question, if these thermophile structures are so stable, why don't all organisms have them? The answer is that stability and flexibility are both needed for biomolecules to be functional. The biological world is a dynamic place, and all biochemical structures must retain an amount of flexibility if they are to adequately serve their purpose. Some thermophilic biomolecules are so stable that, at the lower temperatures of mesophiles, the structures would be too rigid to be useful. Likewise, mesophilic biomolecules, while very flexible at higher temperatures, would fall apart due to their decreased stability. An example of this concept is the RecA protein. RecA is involved is such processes as DNA repair and cell division, fundamental operations that every organism on the Earth must accomplish. The 3D structure of RecA is shown in Figure 25. (Three-dimensional structure of the RecA protein. (Ref. 8)) Across multiple organisms, from the E. coli that live in the human digestive system to thermophiles that thrive at ~80° C, the RecA protein was found to have the same ΔGf value at its optimal working temperature. This demonstrates that the protein requires a proper balance of flexibility and stability to be useful to the cell.

3. Biomolecular Structural Endemism

An endemic species is a species found only in specific areas or environments. For instance, many birds are endemic to Hawaii because of the extreme isolation and unique environment without major predators. This lack of competition allowed them to develop unique colors, sizes, and life habits. Likewise, an endemic structure is a structure found only in a specific area. A type of endemic structure might be the marsupial pouch of Australia, since the pouch is unique to the marsupials and is only found in Australia. Biomolecular structural endemism then refers to biomolecules that have specific structures found in a unique environment.

3.1 Unique molecules
The first step in finding unique and endemic biomolecules is identifying environment-specific biomolecules. Extreme environments like the high temperature hydrothermal vents or salty lakes such as the Dead Sea or Utah's Great Salt Lake are of particular interest because of their similarity to possible environments on other planets as well as their widely different chemistry. A list of known molecular structures, such as proteins and RNA sequences, will be compiled from public databases. This list will then be searched for such specific environmental parameters as their response to high pressure, extreme temperature, or acidic conditions. Finding and returning samples from these kinds of environments will also help identify the molecular structures and find their particular characteristics.

3.2 Finding unique structures
The first step in the actual field work is to examine the biogeography of a few specific environments. The first environments to be tested will be several lakes in the Hawaiian islands: Kauhako on Molokai, Waieleele on Maui, and Green Lake and Waiau on Hawaii. These will provide easily accessible environment to develop methods of sampling and analysis as well as providing initial results for comparison with others. Once this work in Hawaii is completed, we will examine South American lakes. These lakes have not been well studied and are geographically isolated from similar environments so that any new endemic biomolecules will have had time to develop, creating greater geographic diversity. Cataloging this diversity and any structures that are specific to the environment will shed light on which types of chemistries are likely to develop under different circumstances. This understanding can then be generalized to different environments on other planets and help give clues to the key molecules that might be found there.

3.3 What structures have we found already?
One specific type of protein that can be examined is called an adaptive protein. These molecules have a specific function that allows a cell to adapt to its surrounding environment. For instance, one type of protein acts as antifreeze by inhibiting ice crystal formation (Figure 26, An "antifreeze" protein that hinders the formation of ice. (Ref. 8)).Others respond to pressure and help keep cell structures intact at high pressure by expanding and contracting with pressure (Figure 27, A protein structure used to regulate cell pressure. (Ref. 8)).These types of adaptations can be characterized and traced in the same way a biologist would characterize fins on different fish, to learn how they work and what environments they are found in.

Another specific type of protein is called a conserved protein. These proteins are expected to have similar functions in all environments. One example is the protein rhodopsin (Figure 28, A light-sensitive protein. (Ref. 8)). This protein aids in sensing light and should perform the same function in all environments where it is found. Another example would be adenosine triphosphate (ATP) proteins, which help synthesize cell energy, a basic need for all living cells regardless of the environmental conditions (Figure 29, ATP protein involved in the vital task of energy production for the cell. (Ref. 8)).

3.4 Diversity abroad (and off world)
With the samples collected in Hawaii and South America, we can study DNA in a wide variety of environments to gain clues about what biomolecules are present under what conditions. By knowing the temperature, salinity, nutrients, pressure, and other physical factors of the environments, we will be able to establish the correlation between the DNA, the molecular sequences, and the type of environment. Knowing this correlation helps to determine the types of molecules we would expect in any new environment with known traits. This applies directly to the search for life on other planets because environments outside Earth are drastically different, and knowing how to find life there is greatly helped by knowing what life does here. If all hot springs studied have organisms with similar heat-shielding structures, then those structures are likely to be found in all hot springs. Hot springs on Europa may have organisms with similar adaptations. Knowing what to look for will greatly aid the search for extraterrestrial life.

3.5 A public toolbox
Another useful tool for researchers is a database of molecules and molecular sequences for quick and easy comparison. This database will have many sequences and structures in it to compare with molecules found in the samples taken in different environments. This database will help establish specific environmental targets and help guide searches in new, unstudied environments. This database can also be expanded by adding any new information found in the biogeographical studies. Databases like this are a new tool for researchers to use when comparing different environments, and as with any public database, should be kept up to date and contain as much new information as possible.

3.6 How does a molecule help an organism?
All these results will then be put together to understand the relationships between the specific traits of the environment, the molecules that are found in these environments, and the diversity of these molecules across the globe. Such experiments can be summarized by saying that the similarity of structures will show how important the specific structures are. If a specific environment, for instance high temperature, contains only one specific type of structure for letting a cell respond to pressure on the cell wall, then we would have learned that the specific structure is very important and very specifically adapted to high temperature environments (Figure 30). The reverse situation could also happen. If structures allowing a cell to respond to pressure on the cell wall had almost no similarity even in a single location, then we would know that the structures can vary widely and that the cells are very stable in a number of different configurations

This type of stability and structural analysis can be done for each environment to characterize the molecules found there. A small range of stable molecules would indicate that the environment is very selective of which molecules can exist there. A small number of different structures would indicate that all life that survives there must have very specific adaptations. If both the number of molecules and the variety of molecular structures are small, that would suggest that these molecules evolved to meet the demands of that specific environment and the window for variance is small.

3.7 Extraterrestrial implications?
The information gained by studying what kinds of structures organisms use in different environments will tell us how life can work in different places. Many places in the solar system have some of the conditions for life as we know it, but are extreme in many ways. Mars has an atmosphere of mostly carbon dioxide, very cold temperatures, and low surface pressure. Europa may have oceans under a surface of ice at very cold temperatures and unknown mineral content. Other places may have other possibilities. Since we hardly understand how organisms can survive in the more exotic environments on Earth, the clues these environments may offer will make a search for life beyond our little blue planet more successful and thorough.

References

1. Berg, S. Free Illustrations (Hydrogen Bonding), http://bio.winona.edu/berg/ILLUST/H-bond.gif

2. Boal, A. 2004, Astrobiology Seminar Presentation: “Biomolecular Adaptations to Extreme Environments” (and references therein)

3. Drukker, K., & Schatz, G. C. 2000. A Model for Simulating Dynamics of DNA Denaturation. Journal of Physical Chemistry B, 04, 6108-6111

4. Johnson, J. G. Structure of the Lipid Bilayer, http://www.sirinet.net/~jgjohnso/bilayer.html

5. National Park Service. www.nps.gov

6.Owczarzy, R., You, Y., Moreira, B. G., Manthey, J. A., Huang, L., Behlke, M. A., & Walder, J. A. 2004. Effects of Sodium Ions on DNA Duplex Oligomers: Improved Predictions of Melting Temperatures. Biochemistry, 43, 3537-3554

7. Peptide Bond Formation, Stanford University School of Medicine, Biochemistry 201 Slides. http://cmgm.stanford.edu/biochem201/Slides/Protein%20Structure/Peptide%20Bond%20Formation.jpg

8. Protein Data Bank. www.rcsb.org/pdb/education.html

9. SimScience. Membranes. http://simscience.org/membranes/intermediate/page3.html

10. University of Cambridge, Cambridge Institute for Medical Research, The Genetic Code: Codons. http://www.cimr.cam.ac.uk/links/codon.htm

Glossary

Active site: The portion of a protein where an incoming molecule binds and reacts.

Adaptive protein: A protein that allows a cell containing the protein to adapt to its environment.

Amino acid: The basic chain unit of proteins and polypeptides. There are 20 amino acids found within life forms on Earth, all of which are chiral (except glycine). They have four different functional groups attached to a central carbon; a carboxylic acid (-COOH), an amino group (-NH 2), a hydrogen (-H), and a R-group (-R) which differs from amino acid to amino acid.

ATP: Adenosine triphosphate. This is a universal energy storage molecule. It is made up of an adenosine molecule and three phosphate group molecules. When ATP breaks down, one of the phosphate group molecules is released and that creates energy.

Biogeography: The study of how different living things are distributed in the world.

Biomolecules: Molecules created by an organism that have some biological function.

Cell membranes: A sheet, usually composed of a mixture of lipids and proteins, that encloses a cell, or part of an organelle (specialized part) within a cell.

chiral: Referring to a molecule that is nonsuperimposable on its mirror image.

Codon: A triplet of consecutive bases in DNA, RNA, or mRNA that is specific for a particular amino acid.

Complementary DNA: Base pairing rules between strands of DNA and RNA are said to be complementary as they must bind C:G and A:T (or A:U in RNA), i.e., ATCG is complementary to TAGC.

Conserved protein: a protein that has the same function in all cells.

Covalent bond: A chemical bond in which two or more atoms are held together by the interaction of their outer electron clouds.

DNA: Deoxyribonucleic acid. These molecules hold the genetic information of most living cells. It is made up of linked nucleotides, often found in a double helical structure composed of two complementary DNA strands.

DNA melting: The warping and disintegration of biochemical structures as a result of increasing temperature.

Electronegativity: The relative ability of an atom to retain or gain electrons. The commonly used scale is the Pauling scale where elements are given values ranging from 1 (alkali metals) to 4 (fluorine).

Endemic: Limited to a certain area, or native to a certain region.

Extreme environments: An environment which has some undesirable characteristic such as pH, temperature, salt content, lack of water, high radiation, etc., in which mesophilic life could not survive.

Extremeophilic: The condition of an organism needing an extreme environment to thrive.

Extremeotolerant: The ability of an organism to survive in extreme conditions that are not ideal for its growth and development

Free energy of complex formation (ΔGf): A measurement of how favorable the formation of a biochemical structure is. A lower free energy value indicates a more stable structure.

Hydrogen bond: A weak inter- or intramolecular force resulting from the interaction of a slightly positive hydrogen atom attached to an electronegative atom and a second electronegative atom, often with a free lone-pair of electrons such as oxygen, or nitrogen.

Hydrophilic: "Water loving," often polar molecules.

Hydrophobic: "Water fearing," often nonpolar molecules.

Lipids: Generic term for oils, fats, waxes, and related products found in living cells.

Lipid bilayer: When lipids are introduced into water, they form two layers of lipids where the hydrophobic tails are in contact with each other and not in contact with the water. The hydrophilic heads face outward on either side and are in contact with the water medium.

Mesophilic: Organisms which thrive under gentle or "ordinary" environmental conditions.

mRNA: Messenger RNA is a short-lived molecule that carries the information for a protein from DNA, and is translated into a protein by ribosome RNA.

Nucleobase: The molecules within DNA that actually carry the genetic code.

Nucleotide: The subunit of nucleic acids, composed of a nucleobase (either a purine or pyrimidine), a sugar (either ribose or deoxyribose), and a phosphate group.

Peptide: A sequence of amino acids held together by peptide bonds.

Peptide bond: The bond formed by the condensation of the amino group (NH 2) and carboxylic group (COOH) of a pair of amino acids.

Phosphate: One of the molecular components of a nucleotide; a small molecule made up of phosphorus and oxygen.

Polarity: A permanent property of a molecule that has an unsymmetrical electron distribution.

Protein: A biomolecule that plays a central role in the structure and functioning of all living cells (all enzymes for example, are proteins). Proteins are macromolecules composed from 20 different amino acids linked by peptide bonds to form peptide chains. The completed chain structure adopts a specific three-dimensional structure that gives it its unique properties.

Purine: A group of cyclic diureides, including adenine, guanine (present in DNA and RNA). Caffeine is also an example of a purine molecule.

Pyrimidine: A six-membered heterocyclic compound containing two nitrogen atoms. Cytosine, uracil, and thymine are important examples found in DNA and RNA.

R-Group: The R-group is an interchangeable part of the molecule (e.g., it can be -CH 3, -CH 2OH, etc.). In the case of amino acids, this group can give the amino acid a distinct property such as whether or not the amino acid is hydrophobic or hydrophilic.

Rhodopsin: A light-sensitive protein commonly found in the retina of "higher" organisms like mammals. Formed when a protein called opsin develops a chemical bond with a special type of vitamin A molecule, it is found mostly in the outer parts of the rod cells and can be formed only in the dark. When light strikes the rhodopsin molecule, it changes its shape, causing the bond between the opsin and vitamin A to break. This signals the detection of light in a cell in your eye.

Ribosome RNA: A large biomolecule composed of RNA and protein. It is an example of a ribozyme (RNA with catalytic activity), which binds to mRNA and is the site of synthesis for polypeptides encoded by the mRNA.

RNA: Ribonucleic acid. RNA is a nucleic acid (often single stranded) made up of bound nucleotides. It is can be found in different forms, for example, as messenger RNA, transfer RNA, and as ribozymes, which show catalytic activity. Both mRNA and tRNA are involved in the creation of proteins inside cells.

Thermophile: An organism that requires a high-temperature environment, e.g., hydrothermal vents or hot springs, to flourish .

Transfer RNA (tRNA) - An RNA molecule roughly 80 nucleotides long, with complementary sequences that result in several hairpinlike secondary structures. The loop on one end carries an anticodon triplet that binds to mRNA, while the corresponding amino acid is bound to the other end.

Transcription: The process by which a complementary RNA strand is produced from a DNA template by a molecule called RNA polymerase.

Translation: The process by which ribosome RNA, with help of tRNA, deciphers the universal genetic code in mRNA to synthesize a polypeptide.

Universal genetic code: The rules that relate the four bases found in nucleic acids, adenine, cytosine, guanine, and thymine (or uracil in RNA) with the 20 naturally occurring amino acids found in proteins. There are 64 possible combinations of different three-base sequences known as codons, each of which potentially could uniquely specify one amino acid; however, there is degeneracy within the genetic code, and there are also start and stop codons that determine where the beginning and end of a particular peptide sequence is located.