DNA, RNA and proteins: The three essential macromolecules of life

 

From Wikipedia, the free encyclopedia

All living organisms are dependent on three types of very large molecules for essentially all of their biological functions. These molecules are DNA, RNA and proteins, and are classified as biological macromolecules.^[1] Without DNA, RNA and proteins, no known forms of life could exist. This is because each molecule plays an indispensable role in biology.^[2] The simple summary is that DNA makes RNA, and then RNA makes proteins.

DNA is an informational macromolecule that encodes the complete set of instructions (the genome) that are required to assemble, maintain, and reproduce every living organism.^[3]

Proteins are responsible for catalyzing the myriad biochemical reactions that are required to provide food and energy for every organism, and for all forms of movement. In addition proteins carry out all of the other functions of any given organism, for example photosynthesis, or, for example in animals, neural function, vision, and structure (skin, tendons, exoskeleton, etc.).^[4]

RNA is multifunctional, its primary responsibility is to make proteins, according to the instructions encoded within a cell’s DNA. They control and regulate many aspects of protein synthesis in eukaryotes.

 

Contents

• 1 Comparison of DNA, RNA and proteins
• 2 Common structural features of DNA, RNA and proteins
• 3 Divergent structural features
• 4 Why DNA is best for encoding genetic information
• 5 Why proteins are best for catalyzing biological reactions
• 6 Why RNA is multifunctional
• 7 DNA, RNA and proteins in molecular evolution
• 8 See also
• 9 References

Comparison of DNA, RNA and proteins

Common structural features of DNA, RNA and proteins

While many typical cellular molecules (for example sugars and fats) contain tens, or rarely hundreds, DNA, RNA and proteins are typically composed of thousands of atoms (millions for most DNA molecules).

DNA, RNA and proteins are all polymers, long molecules that consist of a repeating structure of related building blocks (also termed monomers; nucleotides in the case of DNA and RNA, amino acids in the case of proteins). In general, DNA, RNA and proteins are all unbranched polymers, and so can be represented in the form of a string. Indeed, they can be viewed as a string of beads, with each bead representing a single nucleotide or amino acid monomer linked together through covalent chemical bonds into a very long chain.

In most cases, the monomers within the chain have a strong propensity to interact with other amino acids or nucleotides. In DNA and RNA, this can take the form of Watson-Crick base pairs (G-C and A-T or A-U), although many more complicated interactions can and do occur.

Divergent structural features

Because of the double-stranded nature of DNA, essentially all of the nucleotides take the form of Watson-Crick pairs between nucleotides on the two complementary strands of the double helix.

In contrast, both RNA and proteins are normally single-stranded. Therefore, they are not constrained by the regular geometry of the DNA double helix, and can and do fold into a vast number of complex three-dimensional shapes. These different shapes are responsible for many of the common properties of RNA and proteins, including the formation of specific binding pockets, and the ability to catalyze biochemical reactions.

 

Why DNA is best for encoding genetic information

DNA and RNA are both capable of encoding genetic information, because there are biochemical mechanisms which read the information coded within a DNA or RNA sequence and use it to generate a specified protein. On the other hand, the sequence information of a protein molecule is not used by cells to functionally encode genetic information.

DNA has three primary attributes that allow it to be far better than RNA at encoding genetic information. First, it is normally double-stranded, so that there are a minimum of two copies of the information encoding each gene in every cell. Second, DNA has a much greater stability against breakdown than does RNA, an attribute primarily associated with the absence of the 2'-hydroxyl group within every nucleotide of DNA. Third, highly sophisticated DNA surveillance and repair systems are present which monitor damage to the DNA and repair the sequence when necessary. Analogous systems have not evolved for repairing damaged RNA molecules.

 

Why proteins are best for catalyzing biological reactions

The single-stranded nature of protein molecules, together with their composition of 20 or more different amino acid building blocks, allows them to fold in to a vast number of different three-dimensional shapes, while providing binding pockets through which they can specifically interact with all manner of molecules. In addition, the chemical diversity of the different amino acids, together with different chemical environments afforded by local 3D structure, enables many proteins to act as enzymes, catalyzing a wide range of specific biochemical transformations within cells. In addition, proteins have evolved the ability to bind a wide range of cofactors and coenzymes, smaller molecules that can endow the protein with specific activities beyond those associated with the polypeptide chain alone.

 

Why RNA is multifunctional

RNA encodes genetic information that can be translated into the amino acid sequence of proteins, as evidenced by the messenger RNA molecules present within every cell, and the RNA genomes of a large number of viruses. The single-stranded nature of RNA, together with tendency for rapid breakdown and a lack of repair systems means that RNA is not so well suited for the long-term storage of genetic information as is DNA.

In addition, RNA is a single-stranded polymer that can, like proteins, fold into a very large number of three-dimensional structures. Some of these structures provide binding sites for other molecules and chemically-active centers that can catalyze specific chemical reactions on those bound molecules. The limited number of different building blocks of RNA (4 nucleotides vs >20 amino acids in proteins), together with their lack of chemical diversity, results in catalytic RNA (ribozymes) being generally less-effective catalysts than proteins for most biological reactions.

 

References

Berg, Jeremy Mark; Tymoczko, John L.; Stryer, Lubert (2010). Biochemistry, 7th ed. (Biochemistry (Berg)). W.H. Freeman & Company. ISBN 1-4292-2936-5. Fifth edition available online through the NCBI Bookshelf: link

Walter, Peter; Alberts, Bruce; Johnson, Alexander S.; Lewis, Julian; Raff, Martin C.; Roberts, Keith (2008). Molecular Biology of the Cell (5th edition, Extended version). New York: Garland Science. ISBN 0-8153-4111-3.. Fourth edition is available online through the NCBI Bookshelf: link

Golnick, Larry; Wheelis, Mark. The Cartoon Guide to Genetics. Collins Reference. ISBN 978-0-06-273099-2.

Takemura, Masaharu (2009). The Manga Guide to Molecular Biology. No Starch Press. ISBN 978-1-59327-202-9.

http://en.wikipedia.org/wiki/DNA,_RNA_and_proteins:_The_three_essential_macromolecules_of_life

Why thymine instead of uracil?

 

by Piter Kehoma Boll | September 29, 2012 · 12:05 pm

About a year ago, while I was in my class of Techniques of Molecular Diagnosis, an interesting doubt sprouted: why does DNA use thymine instead of uracil as RNA does?

I hope everybody reading this knows about nucleic acids and the difference between DNA and RNA. As a very quick review:

RNA (ribonucleic acid) is a polymer made of ribonucleotides, compound molecules made of three parts, or smaller molecules: a nitrogenous base (adenine, uracil, cytosine or guanine), a ribose sugar and a phosphate group.

DNA (deoxyribonucleic acid) is similar, but instead of uracil it has thymine, and instead of a ribose sugar is has a deoxyribose, so that it is made of deoxyribonucleotides. Another difference is that DNA is a double chain twisted helicoidally, where two nitrogenous bases (each from one of the chains) are connected. Adenine is always connected to thymine and cytosine always to guanine, so that one chain is always dependent on the other.

Currently it’s highly accepted that RNA was the first nucleic acid to exist and that DNA evolved from it, so the changes in the sugar and one of the nitrogenous bases must have some advantage.

To understand that, let’s take a look at the structure of the uracil:

Uracil

The only difference between it and thymine is the presence of a methyl group at the last one:

Thymine

In fact, thymine is also called 5-methyluracil. But let’s go to the explanation:

While nucleotides are synthesized, the nucleotide-monophosphates (NMPs), i.e., the set nitrogenous base + sugar + phosphate is dehydroxylated, creating 2’-deoxy-nucleotide-monophosphate (dNMPs), i.e., GMP, AMP, CMP and UMP (for guanine, adenine, cytosine and uracil) are changed to dGMP, dAMP, dCMP and dUMP.

This modification by dehydroxylation has been shown to make the phosphodiester bonds (the bonds of phosphates on the sugar) less susceptible to hydrolysis and damage by UV radiation. It assures that a DNA molecule will not be as easy to be broken as an RNA molecule, which is very useful since DNA carries all the information to build up the organism.

After the dehydroxilation of the nucleotide-monophosphates, the next step, catalyzed by folic acid, add a methyl group to the uracil to form a thymine, so turning dUMP into dTMP.

There are many explanations for that:

1. Despite uracil’s tendency to pair with adenine, it can also pair with any other base, including itself. By adding a methyl group (which is hydrophobic) and turning it into thymine, its position is reorganized in the double-helix, not allowing those wrong pairings to happen.

2. Cytosine can deaminate to produce uracil. You can see in the picture below that the only difference between them is the change from an O in uracil to an NH2 in cytosine. The problem is that, if uracil were a component of DNA, the repair systems would not be able to distinguish original uracil from uracil originated by deamination of cytosine. So using thymine instead makes it way easier and more stable, as any uracil inside DNA must come from a cytosine and so it can be replaced by a new cytosine.

Cytosine

This didn’t evolve for that purpose, of course. Evolution cannot predict what happens. Probably during the earliest times of life, eventually an error changed uracil for thymine and it was found to be more stable to carry information, since such a molecule wouldn’t be destroyed so easily and thus would succeed in passing its “layout” to the next generation.

It makes me wonder… Could some alien life form have found an alternative way to deal with RNA’s (or something equivalent) instability?

– – –

Main Reference:

Jonsson, J. (1996). The Evolutionary Transition from Uracil to Thymine Balances the Genetic Code Journal of Chemometrics, 10, 163-170 DOI: 10.1002/(SICI)1099-128X(199603)10:2

https://earthlingnature.wordpress.com/2012/09/29/why-thymine-instead-of-uracil/

DNA, genes and chromosomes

 

Your genes are part of what makes you the person you are. You are different from everyone alive now and everyone who has ever lived.

 

DNA

But your genes also mean that you probably look a bit like other members of your family. For example, have you been told that you have 'your mother's eyes' or 'your grandmother's nose'?

Genes influence what we look like on the outside and how we work on the inside. They contain the information our bodies need to make chemicals called proteins. Proteins form the structure of our bodies, as well playing an important role in the processes that keep us alive.

Genes are made of a chemical called DNA, which is short for 'deoxyribonucleic acid'. The DNA molecule is a double helix: that is, two long, thin strands twisted around each other like a spiral staircase.

The DNA double helix showing base pairs

The sides are sugar and phosphate molecules. The rungs are pairs of chemicals called 'nitrogenous bases', or 'bases' for short.

There are four types of base: adenine (A), thymine (T), guanine (G) and cytosine (C). These bases link in a very specific way: A always pairs with T, and C always pairs with G.
The DNA molecule has two important properties.

• It can make copies of itself. If you pull the two strands apart, each can be used to make the other one (and a new DNA molecule).
• It can carry information. The order of the bases along a strand is a code - a code for making proteins.

Genes

A gene is a length of DNA that codes for a specific protein. So, for example, one gene will code for the protein insulin, which is important role in helping your body to control the amount of sugar in your blood.

Genes are the basic unit of genetics. Human beings have 20,000 to 25,000 genes. These genes account for only about 3 per cent of our DNA. The function of the remaining 97 per cent is still not clear, although scientists think it may have something to do with controlling the genes.

Chromosomes

If you took the DNA from all the cells in your body and lined it up, end to end, it would form a strand 6000 million miles long (but very, very thin)! To store this important material, DNA molecules are tightly packed around proteins called histones to make structures called chromosomes.

The packaging of DNA into chromosomes

Human beings have 23 pairs of chromosomes in every cell, which makes 46 chromosomes in total. A photograph of a person's chromosomes, arranged according to size, is called a karyotype.

The sex chromosomes determine whether you are a boy (XY) or a girl (XX). The other chromosomes are called autosomes.

The karyotype of a male human being

The largest chromosome, chromosome 1, contains about 8000 genes. The smallest chromosome, chromosome 21, contains about 300 genes. (Chromosome 22 should be the smallest, but the scientists made a mistake when they first numbered them!).

The DNA that contains your genes is stored in your cells in a structure called the nucleus.

A diagram of animal cell showing the nucleus

Back to top

This work is licensed under a Creative Commons Licence.

http://www2.le.ac.uk/departments/genetics/vgec/highereducation/topics/dnageneschromosomes

NASA Rebuilds 3 Building Blocks of Life, What Next?

Left to right: Ames scientists Michel Nuevo, Christopher Materese and Scott Sandford reproduce uracil, cytosine, and thymine, three key components of our hereditary material, in the laboratory. Image Credit: NASA/ Dominic Hart

 

in SCIENCE March 4, 2015

Now that NASA scientists have reproduced uracil, cytosine, and thymine, three key components of our hereditary material, in the laboratory, the question is how would it help the mankind or replicate the mankind in outer space.

NASA said its scientists discovered that an ice sample containing pyrimidine exposed to ultraviolet radiation under space-like conditions was able to produce the three essential ingredients of life.

Pyrimidine is a ring-shaped molecule made up of carbon and nitrogen and is the central structure for uracil, cytosine, and thymine, which are found in RNA and DNA. Image Credit: NASA

The ring-shaped molecule pyrimidine is found in cytosine and thymine. Image Credit: NASA

Pyrimidine molecule is made up of carbon and nitrogen and is the central structure for uracil, cytosine, and thymine, which together form the genetic code found in ribonucleic (RNA) and deoxyribonucleic acids (DNA). RNA and DNA are key to protein synthesis, besides other uses.

“We have demonstrated for the first time that we can make uracil, cytosine, and thymine, all three components of RNA and DNA, non-biologically in a laboratory under conditions found in space,” said Michel Nuevo of NASA’s Ames Research Center in California.

“We are showing that these laboratory processes, which simulate conditions in outer space, can make several fundamental building blocks used by living organisms on Earth,” said Dr. Nuevo.

Nobody really understands how life began on Earth but now these scientists say their experiments suggest that once the Earth formed, many of the building blocks of life were likely present from the beginning. “Since we are simulating universal astrophysical conditions, the same is likely wherever planets are formed,” says Scott Sandford, a space scientist at Ames, which means replication of life in outer space is the next step that NASA may undertake.

The research was funded by the NASA Astrobiology Institute (NAI) and the NASA Origins of Solar Systems Program.

http://www.microfinancemonitor.com/2015/03/04/nasa-rebuilds-3-building-blocks-of-life-what-next/

NASA to send submarine to Saturn’s moon Titan

 

By: PTI | Washington | February 17, 2015 7:08 pm

US Space agency NASA's single-tonne concept robot submarine is equipped with a seafloor camera and sampling system. (Reuters)

 

NASA is planning to send a nuclear-powered submarine to explore one of the methane seas located on Saturn’s moon Titan.

The single-tonne concept robot submarine is equipped with a seafloor camera and sampling system.

The submarine could fit into a space plane such as Boeing’s X-37, which was recently used for a classified Air Force mission.

The plane could land on Kraken Mare, the largest known body of liquid on Titan that consists mostly of liquid methane, or possibly drop the submarine using a parachute, ‘ibtimes.com’ reported.

“The vehicle would use conventional propulsors to yaw around, using a sun sensor to determine the initial azimuth to Earth and begin communication using a terrestrial radio as a more precise reference,” NASA said.

NASA hopes to use the submarine to explore the chemistry of Titan’s seafloor and sea composition, as well as study its tides, weather, shoreline, islands and search for any type of life.

The submarine concept was showcased by NASA Glenn’s COMPASS Team and researchers from Applied Research Lab at the NASA Innovative Advanced Concepts (NIAC) Symposium in Florida.

The concept of the submarine is still in its very early stages, but the team expects that it may be up and running by 2047.

“Measurement of the trace organic components of the sea, which perhaps may exhibit prebiotic chemical evolution, will be an important objective, and a benthic sampler (a robotic grabber to sample sediment) would acquire and analyse sediment from the seabed,” the US space agency explained.

These measurements, and seafloor morphology via sidescan sonar, may shed light on the historical cycles of filling and drying of Titan’s seas.

Models suggest Titan’s active hydrological cycle may cause the north part of Kraken to be ‘fresher’ (more methane-rich) than the south, and the submarine’s long traverse will explore these composition variations.

http://www.financialexpress.com/article/lifestyle/science/nasa-to-send-submarine-to-saturns-moon-titan/44138/

Mysterious giant clouds spotted on Mars

 

Feb 17, 2015, 04.59 PM IST

On two separate occasions in March and April 2012, amateur astronomers reported definite plume-like features developing on the planet.

LONDON: Mysterious cloud-like plumes seen reaching high above the surface of Mars have puzzled scientists studying the atmosphere of the Red Planet.

On two separate occasions in March and April 2012, amateur astronomers reported definite plume-like features developing on the planet.

The plumes were seen rising to altitudes of over 250km above the same region of Mars on both occasions. By comparison, similar features seen in the past have not exceeded 100km.

"At about 250km, the division between the atmosphere and outer space is very thin, so the reported plumes are extremely unexpected," said Agustin Sanchez-Lavega of the Universidad del Pais Vasco in Spain, lead author of the paper published in the journal Nature.

The features developed in less than 10 hours, covering an area of up to 1000 x 500 km, and remained visible for around 10 days, changing their structure from day to day.
None of the spacecraft orbiting Mars saw the features because of their viewing geometries and illumination conditions at the time, researchers said.

However, checking archived Hubble Space Telescope images taken between 1995 and 1999 and of databases of amateur images spanning 2001 to 2014 revealed occasional clouds at the limb of Mars, albeit usually only up to 100km in altitude.

But one set of Hubble images from May 17, 1997 revealed an abnormally high plume, similar to that spotted by the amateur astronomers in 2012.

Scientists are now working on determining the nature and cause of the plumes by using the Hubble data in combination with the images taken by amateurs.

"One idea we've discussed is that the features are caused by a reflective cloud of water-ice, carbon dioxide-ice or dust particles, but this would require exceptional deviations from standard atmospheric circulation models to explain cloud formations at such high altitudes," said Agustin.

"Another idea is that they are related to an auroral emission, and indeed auroras have been previously observed at these locations, linked to a known region on the surface where there is a large anomaly in the crustal magnetic field," added Antonio Garcia Munoz, a research fellow at ESA's ESTEC and co-author of the study.

RELATED

• UK students aim to grow lettuce on Mars by 2018
• On New Year, MOM celebrates 100 days in Mars skies
• Out of 43 attempts, only 20 Mars mission have been successful
• Curiosity rover finds evidence of large lakes on Mars
• Ancient rock shows signs of water on Mars

READ ALSO: Kerala girl a step away from ticket to Mars
3 Indians in 100 shortlisted for one way trip to Mars

http://timesofindia.indiatimes.com/Home/Science/Mysterious-giant-clouds-spotted-on-Mars/articleshow/46274950.cms

Life on Earth May Have Begun 1 Billion Years Earlier Than Thought, Scientists Say

 

Feb 17, 2015, 10:02 AM ET

By ALYSSA NEWCOMB

The earliest life forms may have blossomed on Earth 1 billion years earlier than previously thought.

Working together, scientists at the University of Washington and the University of Johannesburg in South Africa found evidence that life may have thrived on Earth 3.2 billion years ago, upending the belief that Earth's atmosphere at the time was uninhabitable.

The study is based on an analysis of 52 rock samples collected in South Africa and northwestern Australia and range in age from 2.75 to 3.2 billion years old.

Roger Buick, a University of Washington professor and co-author of the article that was published Monday in the journal Nature, said the rock samples his team analyzed showed that there was plentiful nitrogen 3.2 billion years ago to sustain the most basic life forms, including bacteria, viruses and other organisms.

While life can exist without oxygen, nitrogen is an essential building block for genes.

"People always had the idea that the really ancient biosphere was just tenuously clinging on to this inhospitable planet, and it wasn't until the emergence of nitrogen fixation that suddenly the biosphere become large and robust and diverse," Buick told UW Today.

Rosetta Space Probe Takes Sharp, Close-up Images of Comet

Titan: How NASA Got the Clearest Photo Ever of Saturn's Moon

Astronomers Discover Ancient Solar System With 5 Earth-Like Planets

 

http://abcnews.go.com/Technology/life-earth-begun-billion-years-earlier-thought-scientists/story?id=29017106

Einstein's Theory of General Relativity

by Nola Taylor Redd, SPACE.com Contributor   |   September 18, 2012 06:52pm ET

Einstein's theory of general relativity predicted that the space-time around Earth would be not only warped but also twisted by the planet's rotation. Gravity Probe B showed this to be correct.

In 1905, Albert Einstein determined that the laws of physics are the same for all non-accelerating observers, and that the speed of light in a vacuum was independent of the motion of all observers. This was the theory of special relativity. It introduced a new framework for all of physics and proposed new concepts of space and time.

Einstein then spent ten years trying to include acceleration in the theory and published his theory of general relativity in 1915. In it, he determined that massive objects cause a distortion in space-time, which is felt as gravity.

The tug of gravity

Two objects exert a force of attraction on one another known as "gravity." Even as the center of the Earth is pulling you toward it (keeping you firmly lodged on the ground), your center of mass is pulling back at the Earth, albeit with much less force. Sir Isaac Newton quantified the gravity between two objects when he formulated his three laws of motion. Yet Newton's laws assume that gravity is an innate force of an object that can act over a distance.

Albert Einstein, in his theory of special relativity, determined that the laws of physics are the same for all non-accelerating observers, and he showed that the speed of light within a vacuum is the same no matter the speed at which an observer travels. As a result, he found that space and time were interwoven into a single continuum known as space-time. Events that occur at the same time for one observer could occur at different times for another.

As he worked out the equations for his general theory of relativity, Einstein realized that massive objects caused a distortion in space-time. Imagine setting a large body in the center of a trampoline. The body would press down into the fabric, causing it to dimple. A marble rolled around the edge would spiral inward toward the body, pulled in much the same way that the gravity of a planet pulls at rocks in space.

Experimental evidence

Although instruments can neither see nor measure space-time, several of the phenomena predicted by its warping have been confirmed.

 Einstein's Cross is an example of gravitational lensing.
Credit: NASA and European Space Agency (ESA)

Gravitational lensing: Light around a massive object, such as a black hole, is bent, causing it to act as a lens for the things that lay behind it. Astronomers routinely use this method to study stars and galaxies behind massive objects.

Einstein's Cross, a quasar in the Pegasus constellation, is an excellent example of gravitational lensing. The quasar is about 8 billion light-years from Earth, and sits behind a galaxy that is 400 million light-years away. Four images of the quasar appear around the galaxy because the intense gravity of the galaxy bends the light coming from the quasar.

Changes in the orbit of Mercury: The orbit of Mercury is shifting very gradually over time, due to the curvature of space-time around the massive sun. In a few billion years, it could even collide with the Earth.

Frame-dragging of space-time around rotating bodies: The spin of a heavy object, such as Earth, should twist and distort the space-time around it. In 2004, NASA launched the Gravity Probe B. The precisely calibrated satellite caused the axes of gyroscopes inside to drift very slightly over time, a result that coincided with Einstein's theory.

Gravitational redshift: The electromagnetic radiation of an object is stretched out slightly inside a gravitational field. Think of the sound waves that emanate from a siren on an emergency vehicle; as the vehicle moves toward an observer, sound waves are compressed, but as it moves away, they are stretched out, or redshifted. Known as the Doppler Effect, the same phenomena occurs with waves of light at all frequencies. In 1959, two physicists, Robert Pound and Glen Rebka, shot gamma rays of radioactive iron up the side of a tower at Harvard University and found them to be minutely less than their natural frequency due to distortions caused by gravity.

Gravitational waves: Violent events, such as the collision of two black holes, are thought to be able to create ripples in space-time known as gravitational waves. The Laser Interferometer Gravitational Wave Observatory is presently searching for the first signs of these tell-tale indicators.

— Nola Taylor Redd, SPACE.com Contributor

Related:

• Video: Flying Space-time's Warps and Twists
• Top 10 Strangest Things in Space
• Twisted Physics: 7 Mind-Blowing Findings

http://www.space.com/17661-theory-general-relativity.html?cmpid=514630_20150207_40021356&adbid=10152625773696466&adbpl=fb&adbpr=17610706465