What is the Nucleic Acid?

What is the Nucleic Acid?

By: Gabe Buckley

Definition

A nucleic acid is a chain of nucleotides that stores genetic information in biological systems. It creates DNA and RNA, which store the information needed by cells to create proteins. This information is stored in multiple sets of 3 nucleotides, known as codons.

How Nucleic Acids Work

The name comes from the fact that these molecules are acids – that is, they are good at donating protons and accepting electron pairs in chemical reactions – and the fact that they were first discovered in the nuclei of our cells. Typically, a nucleic acid is a large molecule made up of a string, or “polymer,” of units called “nucleotides.” All life on Earth uses nucleic acids as their medium for recording hereditary information – that is nucleic acids are the hard drives containing the essential blueprint or “source code” for making cells. For many years, scientists wondered how living things “knew” how to produce all the complex materials they need to grow and survive, and how they passed their traits down to their offspring. Scientists eventually found the answer in the form of DNA – deoxyribonucleic acid – a molecule located in the nucleus of cells, which was passed down from parent cells to “daughter” cells. When the DNA was damaged or passed on incorrectly, the scientists found that cells didn’t work properly. Damage to DNA would cause cells and organisms to develop incorrectly, or be so badly damaged that they simply died. Later experiments revealed that another type of nucleic acid – RNA, or ribonucleic acid – acted as a “messenger” that could carry copies of the instructions found in DNA. Ribonucleic acid was also used to pass down instructions from generation to generation by some viruses.

Multiple Choice

Identify the purine base of nucleic acids in the following

• Cytosine

• Thymine

• Uracil

• Adenine

Functions of Nucleic Acids

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Nucleic Acids Store Information Like Computer Code

By far the most important function of nucleic acids for living things is their role as carriers of information. Because nucleic acids can be created with four “bases,” and because “base-pairing rules” allow information to be “copied” by using one strand of nucleic acids as a template to create another, these molecules can both contain and copy information. To understand this process, it may be useful to compare the DNA code to the binary code used by computers. The two codes are very different in their specifics, but the principle is the same. Just as your computer can create entire virtual realities simply by reading strings of 1s and 0s, cells can create entire living organisms by reading strings of the four DNA base pairs. As you might imagine, without binary code, you’d have no computer and no computer programs. In just the same way, living organisms need intact copies of their DNA “source code” to function. The parallels between the genetic code and binary code have even led some scientists to propose the creation of “genetic computers,” which might be able to store information much more efficiently than silicon-based hard drives. However as our ability to record information on silicon has advanced, little attention has been given to research into “genetic computers.”

Protecting the Information

Because the DNA source code is just as vital to a cell as your operating system is to your computer, DNA must be protected from potential damage. To transport DNA’s instructions to other parts of the cell, copies of its information are made using another type of nucleic acid – RNA. It’s these RNA copies of genetic information which are sent out of the nucleus and around the cell to be used as instructions by cellular machinery. Cells also use nucleic acids for other purposes. Ribosomes – the cellular machines that make protein – and some enzymes are made out of RNA. DNA uses RNA as a sort of protective mechanism, separating the DNA from the chaotic environment of the cytoplasm. Within the nucleus, the DNA is protected. Outside of the nucleus, movements of organelles, vesicles, and other cellular components could easily damage the long, complex DNA strands. The fact that RNA can act both as hereditary material and an enzyme strengthens the case for the idea that the very first life might have been a self-replicating, self-catalyzing RNA molecule.

Examples of Nucleic Acids

The most common nucleic acids in nature are DNA and RNA. These molecules form the foundation for the majority of life on Earth, and they store the information necessary to create proteins which in turn complete the functions necessary for cells to survive and reproduce. However, DNA and RNA are not the only nucleic acids. However, artificial nucleic acids have also been created. These molecules function in the same way as natural nucleic acids, but they can serve a similar function. Scientists are using these molecules to build the basis of an “artificial life form”, which could maintain the artificial nucleic acid and extract information from it to build new proteins and survive. Generally speaking, nucleic acids themselves differ in every organism based on the sequence of nucleotides within the nucleic acid. This sequence is “read” by cellular machinery to connect amino acids in the correct sequence, building complex protein molecules with specific functions.

Multiple Choice

Which of the following statements is true?

• Sugar component of a nucleotide is ribose

• Sugar component of a nucleotide is deoxyribose

• The bases in nucleotides are attached to a pentose sugar moiety by a glycosidic linkage

• The sugar molecule of the nucleotide is in L-configuration

Nucleic Acids and Genetics

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The Genetic Code

Scientists know that the source code for cells is quite literally written in nucleic acids. Genetic engineering changes organisms’ traits by adding, removing, or rewriting parts of their DNA – and subsequently changing what “parts” the cells produce. A sufficiently skilled genetic “programmer” can create the instructions for a living cell from scratch using the nucleic acid code. Scientists did exactly that in 2010, using an artificial DNA synthesizer to “write” a genome from scratch using bits of source code taken from other cells. All living cells on Earth “read” and “write” their source codes in almost the same “language” using nucleic acids. Sets of three nucleotides, called codons, can code for any given amino acid, or the stop or start of protein production. Other properties of nucleic acids may influence DNA expression in more subtle ways, such as by sticking together and making it harder for transcription enzymes to access the code they store. The fact that all living cells on Earth “speak” almost the same genetic “language” supports the idea of a universal common ancestor – that is, the idea that all life on Earth today started with a single primordial cell whose descendants evolved to give rise to all modern living species. From a chemical perspective, the nucleotides that are strung together to create nucleic acids consist of a five-carbon sugar, a phosphate group, and a nitrogen-containing base. The image below shows structural drawings of the four DNA and the four RNA nitrogenous bases used by living things on Earth in their nucleic acids. It also shows how the sugar-phosphate “backbones” bond at an angle that creates a helix – or a double helix in the case of DNA – when multiple nucleic acids are strung together into a single molecule.

Difference between DNA and RNA

Nucleic Acids are Polymers of Nucleotides

DNA and RNA are both polymers made of individual nucleotides. The term “polymer” comes from “poly” for “many” and “mer” for parts, referring to the fact that each nucleic acid is made of many nucleotides. Because nucleic acids can be made naturally by reacting inorganic ingredients together, and because they are arguably the most essential ingredient for life on Earth, some scientists believe that the very first “life” on Earth may have been a self-replicating sequence of amino acids that was created by natural chemical reactions. Nucleic acids have been found in meteorites from space, proving that these complex molecules can be formed by natural causes even in environments where there is no life. Some scientists have even suggested that such meteorites may have helped create the first self-replicating nucleic acid “life” on Earth. This seems possible, but there is no firm evidence to say whether it is true.

Nucleic Acid Structure

Because nucleic acids can form huge polymers which can take on many shapes, there are several ways to discuss the “structure of nucleic acid”. It can mean something as simple as the sequence of nucleotides in a piece of DNA, or something as complex as the way that DNA molecule folds and how it interacts with other molecules. Nucleic acids are formed mainly with the elements carbon, oxygen, hydrogen, nitrogen, and phosphorus.

The monomer of Nucleic Acids

Nucleotides are the individual monomers of a nucleic acid. These molecules are fairly complex, consisting of a nitrogenous base plus a sugar-phosphate “backbone.” There are four basic types of nucleotide, adenine (A), guanine (G), cytosine (C), and thymine (T). When our cells join nucleotides together to form the polymers called nucleic acids, it bonds them by replacing the oxygen molecule of the 3′ sugar of one nucleotide’s backbone with the oxygen molecule of another nucleotide’s 5′ sugar. This is possible because the chemical properties of nucleotides allow 5′ carbons to bond to multiple phosphates. These phosphates are attractive binding partners for the 3′ oxygen molecule of the other nucleotide’s 3′ oxygen, so that oxygen molecule pops right off to bond with the phosphates, and is replaced by the oxygen of the 5′ sugar. The two nucleotide monomers are then fully linked with a covalent bond through that oxygen molecule, turning them into a single molecule. Nucleotides are the monomers of nucleic acids, but just as nucleic acids can serve purposes other than carrying information, nucleotides can too. The vital energy-carrying molecules ATP and GTP are both made from nucleotides – the nucleotides “A” and “G,” as you might have guessed. In addition to carrying energy, GTP also plays a vital role in G-protein cell signaling pathways. The term “G-protein” actually comes from the “G” in “GTP” – the same G that’s found in the genetic code. G-proteins are a special type of protein that can cause signaling cascades with important and complex consequences within a cell. When GTP is phosphorylated, these G-proteins can be turned on or off.

Multiple Choice

What is the composition of nucleoside?

• a sugar + a phosphate

• a base + a sugar

• a base + a phosphate

• a base + a sugar + phosphate

Nucleic Acid Types and Structure

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Nucleic Acid Types

There are 2 types of nucleic acid: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Both play a central role in every function of every living organism. Nucleic acids have similar basic structures with important differences. They are composed of monomer nucleotides connected like links in a chain to form nucleic acid polymers. Nucleotides consist of a nucleoside (the combination of a pentose monosaccharide molecule and a nitrogenous base) and a phosphate group. The difference between RNA and DNA lies in a single nitrogenous base and a single atom of oxygen within a sugar molecule.

DNA

DNA is the genetic blueprint of a living organism in which all information is stored and from which all information can be passed on. It has a distinctive double-helix form – two single strands which entwine around each other. A strand of DNA is much longer than that of a singular strand of RNA. This is because every strand of DNA in every cell contains the blueprint for the entire organism. Deoxyribonucleic acid is found primarily in the nucleus. However, DNA in a much shorter version can also found in the mitochondria (mtDNA) where it supplies the genes necessary for adenosine triphosphate production, the most important source of cellular energy. Any cell which has a nucleus contains nucleic acid in the form of DNA. There are various exceptions to the rule. Some cells lose their nucleus and DNA during the aging process, such as mature red blood cells, corneocytes, and keratinocytes. Blood platelets are sometimes mentioned as containing neither nucleus nor DNA; however, platelets are fragments of megakaryocytes and not considered to be actual cells. Single-cell organisms (prokaryotes) such as bacteria have no nucleus but contain loose strands of DNA in the cytoplasm, as shown on the next slide.

Nucleic Acid Structure of DNA

The structure of DNA, a globally recognized double-helix, is based upon the two strands of a sugar-phosphate backbone held together by nitrogenous base spindles. DNA contains four nitrogenous bases, or nucleobases: adenine, thymine, cytosine, and guanine. These are naturally occurring compounds that give each nucleotide its name, and are divided into two groups – pyrimidines and purines. While the pyrimidines cytosine, thymine, and uracil (see RNA) are small, single-ringed constructions, adenine, and guanine are larger and double-ringed. This difference in shape and size and a subsequent difference in electrical charge is important, as it allows only specific complementary pairings between different group types; in DNA, adenine will only bond with thymine and cytosine will only bond with guanine. This creates nitrogenous base spindles of the same length and a mirror image on the opposite strand. The double-helix form of DNA is caused by the shape of the monomer nucleotides. When asymmetrical molecules are stacked one on top of the other, a helix is often the result. In DNA, each strand runs antiparallel from the other, or in opposite directions. The nucleotide monomer that makes up a single link of the DNA polymer chain is formed from a nucleobase, a phosphate group, and a five-carbon (pentose) sugar called 2-deoxyribose. ‘Deoxy’ refers to the loss of an oxygen atom about another form of pentose sugar known as ribose (see RNA). This lack of an oxygen atom also plays a role in the helical structure of DNA. The following image shows the difference in the chemical structure of these two pentose sugars. Note the absence of the red oxygen molecule on the second carbon of deoxyribose on the left.

Deoxyribose bonds covalently with a phosphate group. This produces a chain known as the sugar-phosphate backbone. This structure leaves each nucleotide base open and free to bond with the correct nucleotide base on the opposite strand.

Fill in the Blank

The sugar molecule in a nucleotide is

RNA

RNA is found in every type of cell. It is essential for the production of proteins via the replication of genetic information. Using the DNA blueprint, RNA in various forms copies and transfers encoded genetic data to cellular ribosomes. In turn, the ribosomes translate this data into the form of proteins. RNA is not associated with the double-helix structure of DNA. However, it can form this structure for a temporary period and exists in single strands of varying lengths. Even in denucleated red blood cells, RNA continues to carry out the process of transcription. This is because protein biosynthesis is necessary for every reaction within a living organism.

RNA Types

RNA has 4 main forms named according to its specific role. These are known as messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and non-coding RNA (ncRNA). Three of these – mRNA, tRNA, and rRNA – are responsible for the production of proteins from single amino acids according to the DNA blueprint. Non-coding RNA is a broad group of ribonucleic acids which do not produce proteins through DNA codes. Research into this group is still in its infancy, and many types are relegated to a category known as ‘junk’ RNA. However, large quantities of certain RNA types may indicate functions in areas such as chromosome structure, homeostasis, and cell physiology.

Nucleic Acid Structure of RNA

About structure, RNA is very similar to DNA. The main differences are the absence of a double-helix structure, ribose instead of deoxyribose, and uracil instead of thymine. RNA is primarily found in single strands of folded forms. It tends to form a double-helix only temporarily. The pentose sugar in the form of ribose that forms part of the sugar-phosphate backbone of RNA has an additional oxygen atom on the second carbon atom which forms a hydroxyl group. The nucleobase uracil – specific to RNA – replaces the thymine found in DNA. The image below clearly shows these structural and elemental differences.

Multiple Choice

Arrangement of nucleotides in DNA can be seen by

• Ultracentrifuge

• X-Ray crystallography

• Light microscope

• Electron microscope

Nucleic Acid Structure

Nucleic acids can form huge polymers which can take on many shapes. As such, there are several ways to discuss nucleic acid structure. “Nucleic acid structure” can mean something as simple as the sequence of nucleotides in a piece of DNA. Or, it could mean something as complex as the way that DNA molecule folds and how it interacts with other molecules. Here’s a little about each level of nucleic acid structure.

Primary Structure

Nucleotides – the building blocks of nucleic acids, and the “letters” of the genetic “code” – are made of two components:

• A nitrogenous base such as adenine, cytosine, guanine, and thymine or uracil. DNA and RNA each have four possible nitrogenous bases; where DNA uses thymine, or “T,” RNA uses uracil, or “U” instead of thymine. Each of these four bases has different bonding properties, ensuring that the cell doesn’t “mix up” one letter with the other. Thymine and uracil have almost identical structures and properties, allowing them to fulfill similar roles in the two different types of nucleic acids.

• A sugar-phosphate backbone, which allows the nitrogenous bases to be strung together. Each nucleotide’s sugar can link to another nucleotide’s phosphate to become a single molecule.  When many nucleotides are strung together, the angle of this phosphate-sugar bond most often makes the string into a helix. This is why DNA, which is 2-stranded, naturally takes on the shape of a double helix. The primary structure of nucleic acid refers to the sequence of its nucleotide bases, and the way these are covalently bonded to each other. The sequence of “letters” in a strand of DNA or RNA, then, is part of its primary structure, as is the helical or double-helical shape.

Secondary Structure

Secondary structure refers to how nucleotide bases hydrogen bond with each other, and what shape this creates out of their 2 strands. The hydrogen bonds that form between complementary bases of two nucleic acid strands are quite different from the covalent bond that forms between sister monomers in a nucleic acid strand. The bonds between bases in a single strand of nucleic acid are covalent – they fully share their electrons, and are bonded in a way that’s very difficult to break. Atoms linked by covalent bonds are all part of the same molecule. Hydrogen bonds, on the other hand, are weak bonds that come from weak, temporary attractions between positively charged hydrogen nuclei and the electrons of other atoms. The molecules don’t actually share electrons, so they can be separated fairly easily. Changes to environmental factors like acidity can also disrupt hydrogen bonds. The most common secondary structure we’re familiar with is the double helix that forms when two complementary strands of DNA hydrogen bond with each other. Other structures are also possible, such as a “stem-loop” – which occurs when a single RNA molecule folds back and hydrogen bonds with itself – or a four-armed structure that can occur when four different strands of nucleic acid hydrogen bond with different parts of each other. It is thought that some of these secondary structure possibilities are used to help control gene expression and perform other biological functions. In general, transcription enzymes will only express genes they can access. If a gene or RNA snippet is “tied up” in a tangle of nucleic acids, the enzymes may be less likely to reach it. Genes in more open, simple secondary structures, on the other hand, maybe more likely to be expressed.

Fill in the Blank

One of the following nucleic acids has a left-handed helix

Tertiary Structure

Tertiary structure refers to the position of the atoms of a nucleic acid in space. Several common measurements are discussed when talking about the tertiary structure of a nucleic acid, including:

1. “Handedness”

Asymmetrical molecules are very much like our hands. Each of our hands has the same shape, for example – the same components linked together in the same way. But our hands are not interchangeable. That’s because one of our hands has the thumb on the right side, while the other has the thumb on the left. Rather than being identical, interchangeable structures, our hands are mirror images of each other. In just the same way, asymmetrical molecules with the same parts and connectivity can be identical, or they can be mirror images of each other. Some molecules are “right-handed” while others are “left-handed” mirror images of these. When it comes to biological molecules, “handedness” can be crucial to determining the effect that a chemical has on an organism. For some medicines and poisons, only one stereoisomer interacts with our body’s enzymes. One molecule may not affect us, while its mirror image may be beneficial or deadly.

2. Length of helix turn.

While any asymmetrical molecule can have a stereoisomer, as you might guess, the “length of helix turn” is fairly unique to nucleic acids. The angle of bonds between nucleotides causes most nucleic acids to form a helix shape. But small differences in the shape of the helix can cause differences in how the helix interacts with our enzymes and other molecules. So the details of this helix shape can be important!

3. The number of base pairs per turn.

This is another measure of the exact shape and properties of a nucleic acid helix. This can be chemically and biologically important, as it determines which enzymes and molecules can affect the DNA or RNA.

4. The difference in size between major and minor grooves.

In a nucleic acid double helix, the “major groove” is the wider path that opens between two 2 nucleic acid strands. The “minor groove” is the narrower one. In some cases, these grooves may serve as binding sites for other molecules. The size of the major and minor grooves can vary depending on several factors, including the chemical environment of the double helix. Anything that affects the strength of hydrogen bonds can affect the size of the major and minor grooves.

Multiple Choice

Which of the following is true about the Z-DNA helix?

• It has alternating GC sequences

• It is a permanent conformation of DNA

• It tends to be found at the 3’ end of the genes

• It has fewer base pairs per turn than B-DNA

Quaternary Structure

Quaternary structure refers to the large shapes and structures that can be made by nucleic acids. Much like amino acids and proteins, nucleic acids can form large structures. The shape of these structures can be important to their functions. Examples of nucleic acid quaternary structures include chromatids – huge molecules of DNA that are packed tightly for storage and transportation during cell division – and ribosomes, which are organelles made partially of RNA. Some ribozymes also accomplish their jobs partially through the use of quaternary structure. This allows them to interact with their substrates. Just like enzymes made of protein, ribozymes must precisely fit their substrate to catalyze their chemical reactions.

Multiple Choice

Which of the following is NOT a reason why some scientists think the first life might have been made of RNA?

• A. Natural processes can create RNA

• B. RNA can carry hereditary information, just like DNA

• C. RNA can form enzymes that can catalyze chemical reactions, just like proteins

• D. None of the Above

Explanation

All of the above are reasons why some scientists think RNA may have been the first life form!

Multiple Choice

If there are only four base pairs of RNA and DNA, then why do we list 5? (A, G, C, T, and U?)

• A. Uracil isn't a true nucleotide.

• B. Uracil is the RNA equivalent of Thymine.

• C. Uracil and Thymine are interchangeable.

• D. None of the above.

Explanation

Uracil is the RNA equivalent of Thymine. Although there are tiny chemical differences between the 2, U and T can play the same role in base-pair hydrogen bonding. The four DNA base pairs are A, T, C, and G, while the four RNA base pairs are A, U, C, and G.

Multiple Choice

Why might the “handedness” of our nucleic acids be important?

• A. Left-handed nucleic acids might take up more room in our cells than right-handed ones.

• B. If you are right-handed, you have right-handed nucleic acids.

• C. Some enzymes can only interact with molecules that have the correct “handedness” for their active sites.

• D. None of the above.

Explanation

While “handedness” in molecules has nothing to do with whether your right or left hand is dominant, it can determine whether your enzymes can interact with the molecule. Enzymes might interact very differently with the right-handed vs. left-handed version of a molecule.

Multiple Choice

What is the difference between deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)?

• A. There is no difference

• B. The difference is in the structure of the nucleic acids, and how they bind together

• C. Only strange organisms like viruses use RNA

Explanation

The only difference between DNA and RNA is the sugar molecule that forms the base of each monomer. With DNA, the monomer lacks an oxygen atom. This affects how the monomers bind together and interact, causing RNA to be single-stranded and DNA to exists as a double-strand.

Multiple Choice

Which of the following is NOT a function of a nucleic acid?

• A. Aiding in the transfer of cellular signals

• B. Building and maintaining the genetic information

• C. Creating new proteins

• D. None of the above

• E. All of the above

Explanation

All of these are functions of nucleic acids, as they are used in many different ways in each cell.

Multiple Choice

A new virus, virus X, is isolated and studied. Which molecule is most likely to be the genetic material of virus X?

• a linear DNA molecule containing 10,000 base-pairs

• a linear RNA molecule containing plasmids

• a circular DNA molecule containing nucleosomes

• a circular RNA molecule with a molecular weight of 10 billion