Biochemistry_Medical_School_Crash_Course_Unabridged_008_A_T_F

DNA, RNA, and nucleotides are important molecules in biochemistry and life. Nucleotides are the building blocks of RNA and DNA, which make up the genetic code. Nucleotides consist of a 5-carbon sugar, a nitrogenous base, and a phosphate group. Nucleotides play a fundamental role in cell metabolism and provide energy for various processes. They can form pairs and create long strands in DNA or RNA. Nucleotides can be synthesized through different pathways. DNA is a macromolecule located in the nucleus and carries the genetic code. It consists of two strands of nucleotides that form a double helix. DNA's main function is to store information and transcribe itself into messenger RNA to make proteins. Humans have 23 pairs of chromosomes, and DNA is also found in mitochondria. Histones help organize and compact DNA. Chapter 5. DNA, RNA, and Nucleotides. Another important molecular type in biochemistry and in life is the nucleotide molecule, which is the building block molecule for both RNA and DNA, which make up the genetic code and the mechanism by which the genetic code gets translated from messenger RNA to the proteins of the cell. This chapter will discuss nucleotides, DNA, and RNA, their structure and function within the cell. Nucleotides. Nucleic acids are biopolymers or large biomolecules that are necessary to create all forms of life. They are made from monomers, which are nucleotides, that are themselves made in several different and unique forms. A nucleotide is basically made from a 5-carbon sugar, a nitrogenous base, and a phosphate group. Nucleotides are organic molecules that are the basic monomer unit for nucleic acids, DNA or deoxyribonucleic acid, and RNA or ribonucleic acid. The 5-carbon sugar is different if the molecule is to be DNA or RNA in the end. It is ribonucleic acid in RNA and deoxyribonucleic acid in DNA. Nucleic acids are found in all life forms. These are also known as phosphate nucleotides. A nucleoside is just the nitrogenous base and the 5-carbon sugar without the phosphate group. Nucleotides play a fundamental role in life-form metabolism. They carry packets of chemical energy in the form of nucleoside triphosphates, ATP, GTP, CTP, and UTP. They provide the energy to do almost all energetic processes required by the cell, including amino acid synthesis, protein synthesis, and cell membrane synthesis. They take part in cell division, cell signaling, and the incorporation of important cofactors in enzymatic reactions. Nucleotide structure. Nucleotides like to form pairs. For example, thiamine and adenine are connected by double hydrogen bonding, while guanine and cytosine are connected by triple hydrogen bonds. Each nucleotide monomer is chain joined at their sugar and phosphate components, forming the backbone of the double helix molecule in DNA. As mentioned, the nucleotide has three components, a 5- carbon sugar molecule, a nitrogenous base that together makes a nucleoside, and a phosphate group. These together form the nucleotide or the nucleoside monophosphate. Technically, a nucleotide has only one phosphate group, but some textbooks call a molecule a nucleotide if it has two or three phosphate groups termed nucleoside diphosphates or nucleoside triphosphates. The nitrogenous base molecule or nucleobase is a purine or a pyrimidine. The sugar is a ribose sugar when it makes RNA, while the sugar is a deoxyribose when it makes DNA. Deoxyribonucleotides make DNA and ribonucleotides make RNA. Individual phosphate groups connect the sugar ring molecules, connecting them together to create a backbone that is either double-stranded in DNA or single- stranded in RNA. They ultimately create a very long strand. The strands run from the 5 end to the 3 end. In a double strand, the strands are connected in an opposite way, with one strand going from 5 to 3 and another strand going from 3 to 5. Singular cyclic nucleotides are made when the phosphate group is bound twice to the same sugar molecule at the corners of the hydroxyl groups on the sugar. These don't make nucleic acids, but are important in cellular metabolism. Nucleic acids are basically nothing more than polymers or macromolecules made from strands of nucleotides. The purines are adenine and quinine, while the pyrimidines are cytosine, thymine, and uracil. Thymine is only found in DNA and uracil is only found in RNA. The hydrogen bonding occurs between adenine and thiamine, adenine and uracil, and guanine and cytosine. Nucleotide synthesis. Nucleotides can be synthesized by several different means. There are de novo ways of making nucleotides and ways of recycling molecules to make nucleotides through salvage pathways. The basic precursors to the making of nucleotides are both carbohydrates and nucleic acids, and even more basically from ammonia and carbon dioxide. The liver is where the de novo synthesis of nucleotides happens. However, the de novo synthesis of the purines and pyrimidines are different. The nucleotides aren't made in an organelle, but are instead made by the cytoplasm of the cell. The main pyrimidines, CTP and UTP, are made in the cytoplasm of the cell and their synthesis begins with the formation of carbamoyl phosphate from carbon dioxide and glutamine. Then aspartate carbamoyl transferase catalyzes a condensation reaction between aspartate and carbamoyl phosphate to make carbamoyl aspartate acid, which gets cyclized into 4.5 dihydroerotic acid by dihydroorotase. The dihydroorotase is converted into orotate by dihydroorotate oxidase in a reaction that looks like this. S-dihydroorotate plus O2 yields orotate plus H2O2. After this, the orotate is covalently bonded to a phosphorylated ribosyl molecule at the point on the ribose molecule, which contains a pyrophosphate and N atom of the pyrimidine ring. The enzyme orotate phosphoribosyltransferase, PRPP transferase, catalyzes the next reaction, which gives rise to orotidine 5' phosphate and pyrophosphate. The orotidine 5' monophosphate is then decarboxylated by the orotidine 5' phosphate decarboxylase to make uridine monophosphate, UMP. The PRPP transferase enzyme catalyzes both the ribosylation process and the decarboxylation process, making UMP from a molecule of erotic acid. All pyrimidine nucleotides are made from this. UMP becomes phosphorylated by two kinase enzymes to make UTP by two different reactions that need ATP in order to happen. First UMP goes to UDP and then UDP goes to UTP with the use of one ATP molecule per reaction. CTP is made by emanating UTP by the catalytic activity of CTP synthetase. The donor molecule that gives the NH3 is glutamine, which is a reaction that also requires ATP and gives off ADP and phosphate. CMP is made by the loss of two phosphates from CTP. Purine synthesis happens slightly differently. The intermediate molecule that makes all of these purines is called IMP. There are several amino acids that give carbon and nitrogen atoms to make the purine molecule, include aspartate, glycine, and glutamine, with molecules also donated from bicarbonate and formate. This is a 10-step process that starts with the basic precursor molecules and turns them into IMP, which is the nucleotide base of hypoxanthin. Both AMP and GMP are synthesized by this molecule by two different pathways. Purines then are first made from ribonucleotides rather than from free bases. There are six different enzymes that take part in the 10-part process that makes IMP. Three of the enzymes are multifunctional and do more than one step. Phosphoryl ribosyl glycinamide transferase does reactions 2, 3, and 5. Phosphoryl ribosyl aminoimidazole carboxylase does reactions 6 and 7, and inosine monophosphate synthase does reactions 9 and 10. IMP or inosine monophosphate is the intermediate that gets converted to GMP by the oxidation of IMP to make xantholate, which then gets an amino group, giving up an electron to NAD positives, making an amide group come also from glutamine with the energy input of ATP. In degradation, the C, T, and U pyrimidine rings get completely degraded into CO2 and NH3. The purine rings G and A cannot do this but are instead degraded to uric acid, which is excreted by the kidney. The last reaction to uric acid is irreversible. Uric acid can also be made when AMP gets deaminated into IMP and the ribose unit is removed to make hypoxanthine. This gets oxidized to xanthine and finally becomes uric acid. Both guanine and IMP can be recycled to make new nucleotides. Deoxyribonucleic acid or DNA. DNA is a large macromolecule located mainly in the nucleus of the cell and that carries the genetic code for the organism and cell, functioning in both cell division and cellular reproduction. They represent one of the four main types of macromolecules, nucleic acids, proteins, lipids, and carbohydrates. DNA consists of two polymer strands of nucleotides that are bonded loosely together to form a double helix. The two DNA strands are called polynucleotides as they are made from nucleotide bases. The four nucleotide bases found in DNA are adenine, guanine, cytosine, and thymine. Each of these are a five carbon sugar, a nitrogen base, and a phosphate group. The sugar of one nucleotide attaches to the phosphate group of the next nucleotide, making an alternating phosphate sugar backbone. A always binds with T and G always binds with C. There are about five times ten to the 37th base pairs on earth or about 50 billion tons of DNA. This compares to a total carbon mass in the biosphere of about 4 trillion tons. The main function of DNA is to store information and both strands of DNA carry the same piece of information in reverse order of each other. Interestingly, more than 98% of DNA is not coded at all and don't match to any known proteins. The basic thing that DNA does is transcribe itself into messenger RNA fragments that then undergo further processes to become mature messenger RNA that goes to the ribosomes and makes a given protein. In order for transcription to happen, the DNA fragment must separate for a period of time so that a matching RNA strand can be made from a parted double strand of DNA. Each set of three nucleotides on a DNA fragment is called a codon and each codon eventually stands for a specific protein with some redundancy as there are more codons than there are available proteins. DNA in humans and eukaryotes is coiled into pairs of chromosomes. The human has 23 pairs of chromosomes with 22 pairs being basically the same and one pair being the same in females and different in males. The DNA is located in the nucleus primarily but in small amounts it exists in the mitochondria of the cell. Histones are the proteins that cause the compaction and organization of DNA. They help control which parts of the DNA are separated in order to be transcribed onto the RNA molecule. DNA chemical properties. As mentioned, DNA is a very long polymer made from nucleotides. It has the capacity to exist in a straight line but is usually coiled and looped preventing transcription. In all organisms, it is a double helix consisting of two identical helical strands that are bound together by hydrogen bonds. Both strands are coiled around the same axis and are of the same length. Each strand can contain millions to hundreds of millions of nucleotides with the largest chromosome, chromosome one, being 220 million nucleotides long. Each DNA strand is paired with another and is tightly held to it. DNA is referred to as a polynucleotide because it has a nucleobase molecule linked to a sugar which is called a nucleoside that is itself connected to a phosphate group making it a nucleotide. A sugar is attached to the phosphate group on the adjacent nucleotide making a backbone of sugars alternating with phosphate groups. The sugar in DNA is called a 2-deoxyribose sugar which is a 5-carbon pentose sugar. Each strand of DNA has a 5 prime end and a 3 prime end. The strands are located anti-parallel to each other so that the 5 prime end of one DNA strand is associated with the 3 prime end of the other DNA strand. The 5 prime end is a phosphate group while the 3 prime end is a hydroxyl group. The only real differences between RNA strands and DNA strands is that DNA strands have deoxyribose sugars on them while the RNA strands have ribose sugars on them. The two main structural forces that keep the DNA molecule stable include the hydrogen bond between the nucleosides and the base stacking interactions between the aromatic nucleobases. The nucleobases line up in a perpendicular fashion when compared to the DNA axis maximizing their interaction with the solvation shell. As mentioned, the base pairs are very specific with A always attaching to T and G always attaching to C. These are hydrogen bonds meaning that they are not covalent and can easily be unzippered in the transcription process. The fact that each strand is identical is crucial to the mitotic process so that when DNA gets duplicated the strands made are identical. Strands that have more GC pairs are more stable than strands with AT pairs because there are three hydrogen bonds between the GC pairs and only two hydrogen bonds between the TA pairs. A sequence of DNA is called a sense sequence if its sequence is identical to that of the mRNA copy that gets transcribed from it. The opposite strand contains the anti-sense sequence and does not get transcribed in most situations. The exact purpose of anti-sense transcription is unknown but it may have something to do with the regulation of gene expression. Strands of DNA can be relaxed or supercoiled. A relaxed strand of DNA circles the double helix axis every 10.4 base pairs. Supercoiled DNA is more tightly bound with the base pairs held more tightly together. Most DNA is very relaxed in nature allowing for it to be acted upon by topoisomerases that relieve the twisting stresses that can happen to DNA during DNA replication or DNA transcription. At the ends of each chromosome are a series of base pairs called telomeres. They allow the cell to replicate the entire genome using the enzyme telomerase to replicate the far three prime ends of the chromosomes effectively allowing for a capping of the end of the chromosome. They protect the ends of the DNA and get shortened somewhat during the replication phase. Telomeres in humans are thousands of repeating sequences involving TTAGGG. Telomeres form large telomere loops at the end of the DNA segment that is stabilized by DNA binding proteins. It forms a triple stranded structure called the displacement loop or D loop. Base pairs can undergo modification but this usually happens in the part of the DNA that isn't encoding for any protein. Some of these areas have high amounts of methylated cytosine bases associated with them that influences the packaging of DNA. There is crosstalk between the histone protein core and the DNA methylation process that helps coordinate the expression of the different genes. Interestingly, methylated cytosine or 5-methylcytosine is more prone to mutations because it can deaminate into thymine so those DNA segments with a lot of this molecule on them are more highly prone to genetic mutations. DNA can be damaged in several ways. Mutagens can damage the DNA sequence and can consist of oxidizing agents, electromagnetic radiation, X-rays, UV light, and alkylating agents. UV light can damage DNA by making thymine dimers which cross-link to pyrimidine bases. Oxidants, free radicals or hydrogen peroxide, can modify bases, particularly guanosine. The most dangerous DNA damage involves breakage of the DNA segment because these are hard to repair and can result in many types of mutations or chromosomal translocations to occur. DNA mutations can result in cancerous cells. Some mutagens work by inserting themselves between base pairs. These mutations can cause what is known as intercalation. These are usually aromatic molecules that have been turned into effective chemotherapy agents as they damage DNA particles. Intercalators cause problems by inhibiting both replication and transcription of the DNA resulting in mutations and toxicity to the DNA molecule. DNA intercalators may be carcinogens or teratogens. One intercalator that was known to be a teratogen was thalidomide. Others like aflatoxins and benzopyrene epoxide cause replication errors. Doxorubicin is an intercalator used as a chemotherapy agent. Function of DNA. DNA occurs as linear chromosomes in the nucleus of the cell and in circular chromosomes in prokaryotes. Each set of chromosomes makes up the cell's genome. There are three million base pairs in the human genome, packed into 46 chromosomes. The chromosomes have genes on them that code for different proteins. The transmission of genetic information happens when a cell transcribes the information on the DNA molecule into RNA which translates it into a protein in the ribosomes of the cells. DNA can be passed from one cell to another through the replication process in mitosis. Genomic DNA is tightly and orderly packed in a condensation process in order to fit a lot of DNA into a very small amount of space. The complete package of genes and what is on them is called the genotype. The gene is a single unit of heredity and is the part of the genome that influences the characteristics of the organism. Genes each contain a reading frame that is transcribed as well as regulatory sequences such as promoters and enhancers that don't get transcribed. Telomeres don't get transcribed either. Less than 2% of the human genome actually gets transcribed with over half of the DNA consisting of repetitive non-coded sequences. No one knows the exact purpose of these non-coded DNA sequences. Transcription takes place by means of unwrapping of the helix in small fragments and undoing the hydrogen bond between the base pairs. RNA polymerase is the enzyme that copies the piece of DNA to make a matching copy of messenger RNA from it. The genetic code consists of triplets of bases that each stand for a specific coded protein. The messenger RNA must rely on the transfer RNA to take the message and make it into an actual protein. The transfer RNA carries the amino acids that get combined again to make the ribosomal protein. There are 64 possible codons which means that some codons are either nonsensical, stop codons, and codons that code for the same protein. TAA, TGA, and TAG are all stop codons. In the replication process, DNA polymerase is the main enzyme responsible. It helps take apart the strands of DNA and can make a complementary strand by finding the correct base on the strand and matching it with its corresponding base pair so there will be two identical DNA helices, one for each cell that is to be made or divided up into. DNA polymerases can only work from the 5' end to the 3' end so that other mechanisms are necessary to copy the anti-parallel strands of DNA. Proteins associated with DNA. Specific proteins are available that bind to DNA and perform different functions. These proteins help compact the DNA so that it can fit into its tight chromatin pattern. In humans, these proteins are called histone proteins. They form a disc-shaped complex called a nucleosome that wraps two turns of DNA around its surface, making ionic bonds with the acidic sugar phosphate band on the DNA so it is independent of the actual base sequence. Another important protein that interacts with DNA is called replication protein A. It helps separate the DNA bonds on the helix so that it can be replicated, recombined, and repaired during the process of DNA replication and cell division. These binding proteins help stabilize the single strand of DNA so that it is protected by being degraded by nucleases or so that it doesn't form stem loops. Other proteins have evolved that bind to specific DNA sequences. Those that have been studied the most include transcription factors that are proteins which bind to DNA to regulate the transcription process. Some activate a gene while others suppress a gene. They can bind to RNA polymerase in order to promote transcription either directly or indirectly. They can help the RNA polymerase find the promoter chain so it can begin transcription. They can bind to other transcription factors that help modify the histones at the promoter region. This changes the ability of DNA to be accessible to the polymerase. Nucleases are enzymes that degrade DNA by cutting DNA strands or by catalyzing the hydrolysis of the phosphodiester bond. There are exonucleases that DNA strands outside of the strands and endonucleases that cut DNA within the strands. Restriction endonucleases are the most popular enzyme of this type. They cut the DNA strands at specific places. Enzymes called DNA ligases can rejoin areas of cut or broken DNA strands. They are used in DNA repair and in the genetic recombination process. Topoisomerases are enzymes that have both nuclease and ligase activity. They change the amount of supercoiling that happens in DNA and work by cutting the DNA helix allowing one section to rotate and decrease its degree of supercoiling. It then seals the break in the DNA strand. These enzymes are important in DNS transcription and DNA replication. Helicases are proteins that act as a motor protein with regard to DNA. They use chemical energy in nucleoside triphosphates like ATP in order to break hydrogen bonds between the bases so that DNA can unwind to form a single strand so that enzymes can gain access to the DNA bases. Polymerases are enzymes that synthesize polynucleotide chains from nucleotide triphosphates. They work by adding a nucleotide to the three prime hydroxyl group on the existing chain, one nucleotide at a time. They all work by adding from the five prime end to the three prime end allowing the synthesis of a complementary strand to a DNA template. There are many polymerases that allow for proofreading activity that will catch mistakes in the synthesis reaction so that mistakes are not made. The incorrect base is removed and the correct base is reinserted. All of this happens inside a replisome that has several enzymes operating at once. RNA-dependent DNA polymerases are a type of polymerases that copy the sequence of an RNA strand into DNA. These include reverse transcriptase which comes from a virus and allows virus RNA to be placed into the host's DNA molecule. Retroviruses will do this. Telomerase is another example that works only on the telomere of the DNA molecule and adds telomere subunits on a DNA molecule. Transcription happens by means of RNA polymerase which makes an RNA copy based on a gene sequence on a DNA molecule. The RNA polymerase first binds to a promoter region and then binds to the DNA sequence copying RNA based on the base pairs present on the DNA molecule. There are then terminator or stop regions that tell the RNA to stop coding a particular gene. Then it detaches from the DNA molecule exiting the nucleus to make a protein. As a helix, DNA doesn't significantly interact with other helices of DNA and in humans each chromosome exists in its own territory so that the only time they interact with one another is during DNA crossover in sexual reproduction when a greater degree of genetic recombination occurs. When this happens the helix unwinds chromosomes swap segments which either increases or decreases the efficiency of natural selection of the cells made when they divide. Those cells that are genetically favorable survive while others do not survive very well. The most common type of recombination is called homologous recombination in which the same segments on a chromosome will swap during the replication process. Recombinases such as RAD51 take part in this recombination process starting with the breakage of a DNA fragment. An endonuclease or damage to the DNA can cause this breakage to occur. Then a recombination occurs and separate helices take on large segments of DNA from another DNA helix at a holiday junction. Only strands of similar polarity will exchange segments. This aids in genetic diversity. Ribonucleic acid or RNA. RNA or ribonucleic acid is a polymer consisting of ribonucleotides that combine to share genetic information as part of the protein making process. They are part of the four main macromolecules found in nature and are clustered with DNA as being similar molecules. The main difference between RNA and DNA is that RNA is single-stranded while DNA is double-stranded. It uses G, A, U, and C in order to make its strands and folds onto itself rather than having a double strand. Many viruses are made exclusively from RNA fragments and don't have DNA fragments. The three main differences between RNA and DNA are that RNA is single-stranded and usually of a shorter chain length than DNA. It also consists of ribose sugars instead of deoxyribose sugars as there is no hydroxyl group at position 2' of the sugar. This makes the RNA molecule less stable than DNA, more prone to breakdown through the hydrolytic process. It has uracil instead of thymine which is actually an unmethylated type of thymine. There are several types of RNA including mRNA, rRNA, tRNA, and snRNA along with other non-coding RNAs. Only mRNA is actually a coding type of RNA that interacts directly with DNA. These are all highly structured molecules that consist of short single-stranded helices that are packed into structures that aren't unlike protein structures. This means that RNAs can achieve chemical catalysis and can catalyze chemical reactions. Structure of RNA. Each nucleotide in RNA consists of a ribose sugar with five carbon atoms, each numbered 1' through 5'. A base is attached to the 1' position being adenine, cytosine, guanine, or uracil. Adenine and guanine are purine bases while cytosine and uracil are pyrimidines. Thymine in DNA is a pyrimidine as well. A phosphate group is attached to the 3' carbon atom on the ribose molecule and on the 5' carbon atom on the next molecule. The phosphate groups are negatively charged making RNA a polyanion that is negatively charged. The bases form hydrogen bonds between the cytosine and guanine, between the adenine and uracil, and between the guanine and uracil bases. Adenine bases can also bind to each other with hydrogen bonds forming large clumps of adenine bases. There is also what is known as a gRNA tetraloop that is made by a binding of guanine to adenine. An important structural feature that makes RNA different from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar. This causes the helix to form an A-form geometry although it can form a B-form geometry similar to DNA. The A-form geometry results in the presence of a deep narrow major groove and a shallow wide minor groove. Because of its 2' hydroxyl group, it can also chemically cleave the adjacent phosphodiester bond causing cleavage of the backbone. While the transcription of RNA involves guanine, cytosine, adenine, and uracil, these bases can be modified in many ways to make the mature RNA molecule. A molecule called pseudouridine can be made which involves a linkage between uracil and ribose that changes a carbon-nitrogen bond to a carbon-carbon bond. Another molecule, ribosimidine, can be made as well as hypoxanthine which is a deaminated adenine base with a nucleoside that is called inosine, I. Inosine is important in the wobble hypothesis of the genetic code. There are more than a hundred naturally occurring nucleosides in RNA with the greatest structural changes happening in tRNA with pseudouridine and nucleosides with a 2'-O-methylribose being the most common. These chemical changes are important to the function of the tRNA molecule and occur in the most active parts of the molecule. There is a specific tertiary structure associated with RNA because they are single-stranded. The tertiary structure is formed by hydrogen bonds between bases in the structure. This leads to several distinctive shapes associated with RNA such as hairpin loops, bulges of RNA, and internal loops. As RNA is a charged molecule, it needs positively charged ions like magnesium to stabilize its secondary and tertiary structures. The naturally occurring enantiomer of RNA is dRNA, meaning that it consists of mostly d-ribonucleotides. LRNA can only be artificially synthesized where it is much more stable and can't be easily degraded by RNase, while the dRNA is easily degraded by RNase. As mentioned, while RNA is a linear molecule, it is not a straight structure in nature and is folded in specific ways. Synthesis of RNA. RNA is made by RNA polymerase with DNA as the major template that determines the base configuration of the RNA molecule. The synthesis of RNA is known as transcription. The enzyme binds to the promoter region of the DNA molecule, which is upstream of the actual gene. The DNA is unwound by the enzyme called helicase, with transcription occurring along a part of the DNA molecule that is unwound and separated into a single strand. The sequence of DNA has a stop codon that tells the RNA polymerase molecule when to stop making an RNA strand. After transcription, there is a lot of modification that must happen in order to make a mature mRNA molecule. A poly-A tail and a 5' cap are added to the pre-mRNA and introns are removed by the spliceosome. New strands of RNA are made by other types of RNA-dependent RNA polymerases that use RNA as the template for the making of new types of RNA strands. This is used by viruses and other microorganisms to replicate their RNA molecules. Types of RNA molecules. There are several types of RNA. The initial type is mRNA that is directly transcribed from the DNA molecule and that goes to the ribosome, where translation takes place. The coding sequence of the mature mRNA molecule determines the protein amino acid sequence. Interestingly, most RNA is non-coding RNA. Only about 3% of the transcribed RNA is actually coded for a protein. Non-coding RNA, or ncRNA, can be encoded by their own genes on the DNA molecule or can be made by introns spliced out of pre-mRNA. The most common non-coding RNA molecules are transfer RNA, or tRNA, and ribosomal RNA, or rRNA, both of which are necessary for the translation process. There is also non-coding RNA molecules that are not involved in translation but are involved in gene regulation, the processing of RNA, and other specific roles in the cell. Some RNAs have catalytic properties that mean they can splice other RNA molecules. RNA can be defined according to its length. RNA can be small RNA, medium RNA, or long RNA. Long RNA molecules are usually long non-coding RNA, lncRNA, and mRNA. Small RNAs include certain ribosomal RNA molecules, transfer RNA, micro RNA, small interfering RNA, small nucleolar RNA, Peewee interacting RNA, small rDNA derived RNA, and tRNA derived small RNA molecules. Messenger RNA, or mRNA, is the only RNA that encodes from DNA and that carries the protein sequence to the ribosomes. The other types of RNA have other functions in the cell, mostly involved in translation. It is actually pre-mRNA that gets transcribed with mRNA being extremely modified before actually being turned into a translating molecule. It takes tRNA to actually code for a protein as this is necessary for bringing the amino acids into the ribosome for translation. Introns must be removed from pre-mRNA in order to make mature mRNA. Ribonucleases eventually degrade the mRNA if it isn't used and after it is translated into many copies of the protein. Transfer RNA is extremely small, only about 80 nucleotides long. Its purpose is to transfer specific amino acids to the polypeptide in order to make the protein in the ribosome. It has sites for amino acid attachments and an anticodon that matches to a specific codon on the mRNA molecule, linking to it through a hydrogen bond. Ribosomal RNA, or rRNA, is a catalyst for the translation of mRNA into protein. There are differently sized rRNA molecules, some of which are made in the nucleolus, and one that is made elsewhere in the cell. Ribosomal RNA and protein combine together to form a ribosome that binds mRNA and helps carry out protein synthesis. Several ribosomes can attach to the same piece of mRNA at any given time. The vast majority of RNA in the cells is ribosomal RNA. Transfer messenger RNA, or tmRNA, is found mainly in bacterial organisms and plastids. It is involved in the tagging of proteins encoded by messenger RNA that don't have stop codons. It prevents the stalling of the ribosome in the translational process. There are a number of regulatory RNA molecules that can upregulate or downregulate the expression of genes. For example, microRNA, or miRNA, are found in eukaryotic cells and act through RNA interference, where an effector complex of miRNA and enzymes are able to cleave mRNA, blocking it from being translated or accelerating its degradation. Small interfering RNA, or siRNA, comes from the breakdown of viral RNA. There are also endogenous sources of siRNA that interfere with messenger RNA in a way that is similar to microRNA. They can methylate their target so that the transcription of the genes is upregulated or downregulated. Animals also have PIWI-interacting RNA, or piRNA, which is only found to be active in germline cells and is believed to be a defense against transpathons. They may also play a role in the making of gametes. Many of the non-coding RNAs are involved in modifying other RNAs. Introns need spliceosomes made from small nuclear RNAs to be taken out of messenger RNA. Introns themselves can become part of ribosomes that are intact or spliced themselves. RNA can be changed by having its nucleotides modified into non-ordinary nucleotides. In eukaryotes, modifications of RNA nucleotides are directed or regulated by small nucleolar RNAs, SnO RNAs, found in the nucleolus and in calel bodies. They can be associated with enzymes that guide them to be base paired to the RNA needing modifying. Ribosomal RNA and transfer RNA are both extensively modified before being utilized by the cell. Any type of RNA can be methylated. Key takeaways. Nucleic acids are made from monomers that are called nucleotides. Nucleotides are partly sugar and partly side chains that help the monomers attach to one another. The major nucleotides are adenine, guanosine, thymine, and cytosine in DNA. The major nucleotides are adenine, guanosine, cytosine, and uracil in RNA. There are multiple types of RNA that perform different functions in the making of proteins. Quiz. Number one. A nucleotide is made from three components. What chemical component is not part of a nucleotide? A. Five-carbon sugar. B. Carboxyl group. C. Nitrogenous base. D. Phosphate group. Answer. B. Nucleotides have all of these components but do not have a carboxyl group as part of their chemical makeup. Number two. What type of bonding takes place between the base pairs between each strand of DNA? A. Covalent bonding. B. Ionic bonding. C. Hydrogen bonding. D. Van der Waals forces. Answer. C. It is hydrogen bonding that connects the different base pairs each strand of DNA. Number three. Which nucleotide is only found in RNA and isn't found in DNA? A. Adenine. B. Cytosine. C. Guanine. D. Uracil. Answer. D. Uracil is a nucleotide base found only in RNA while in its place thymine is used in DNA. Number four. The base pairing of nucleotides in DNA is very specific. What nucleotide does thymine always bind to in the making of the DNA helix? A. Thymine. B. Adenine. C. Guanine. D. Uracil. Answer. B. Thymine always binds to an adenine molecule as a base pair in the DNA helix of the DNA molecule. Number five. In humans not all of the DNA in the cell is coded for. About what percentage of DNA in the human cell is actually encoded into proteins? A. 2%. B. 8%. C. 12%. D. 20%. Answer. A. Less than 2% of the available DNA on a cell is actually coded into a protein. Number six. What molecule controls the organization, coiling, and uncoiling of the DNA strands? A. Centromere. B. Histone. C. RNA transcriptase. D. DNA carboxylase. Answer. B. It is histone proteins that coil the DNA, organize it, and decide which parts get separated as part of the transcription process. Number seven. DNA molecules all have telomeres. In a basic sense, what is a telomere? A. A non-coding segment of DNA. B. The replicated cap on the 5 prime end of the DNA strand. C. The replicated cap on the 3 prime end of the DNA strand. D. The part of the DNA where the RNA first attaches to. Answer. C. The telomere is the replicated cap on the 3 prime end of the DNA strand that protects it from being incompletely replicated during the mitotic process. Number eight. What is the main problem with having a lot of 5 methylcytosine on a DNA fragment? A. It has a higher mutation rate because 5 methylcytosine mutates more easily. B. It gets transcribed more often than the segments with less 5 methylcytosine. C. The double helix is less stable whenever there is a lot of 5 methylcytosine. D. 5 methylcytosine doesn't form a hydrogen bond with guanine. Answer. A. The biggest problem is that 5 methylcytosine has a higher mutation rate so segments with a lot of this molecule can mutate more easily. Number nine. What is considered the most dangerous type of DNA damage that can occur? A. Methylation of a cytosine base. B. Breakage of the DNA chain. C. Point mutation of a single base pair. D. A base pair deletion. Answer. B. The most dangerous type of DNA damage is the breakage of the DNA chain because it can cause a great deal of chromosomal translocation errors and is very difficult to fix. Number ten. Which kind of RNA is considered the most common RNA made by the eukaryotic cell? A. mRNA. B. tRNA. C. tmRNA. D. rRNA. Answer. D. The most common type of RNA is ribosomal RNA or rRNA which when combined with certain proteins makes ribosomes which are very common in a eukaryotic cell.