Information

How are lesions in the RNA corrected?


I quite understand why thymine is present in DNA. So we can mark it out where cytosine undergoes a reaction and is converted to uracil. Then we can repair the DNA.

But how can we make that out in RNA ??


RNA is shortlived and need not undergo repair. A "mutated" RNA will degrade and will be replaced by the correct RNA.

Even though RNAs are shortlived compared to DNA (which does not really undergo turnover), some RNAs are stable and have low turnover. Nonetheless RNA would be present in multiple copies it is improbable that all of them would have undergone mutation.

Moreover RNA with certain mutated codons e.g. non-sense mutations are cleared off by the exosome.

Thanks to har-wradim for pointing out about RNA repair mechanisms. There are few reports that say that methylations in the RNA can be corrected by the enzymes AlkB (in E.coli) and its eukaryotic homologue hABH3. These enzymes were known to repair methyl lesions in the DNA (1-methyladenine and 3-methylcytosine), but it was subsequently shown that they can act on RNA as well [1,2].

However there seems to be no mechanism for repairing deamination damage; this study has demonstrated an artificially designed system which is capable of targeted RNA deamination (but there is no system yet that can fix a deaminated base in RNA).

This article comments that AlkB is tightly regulated because if uncontrolled it can demethylate functional methylations too. Overexpression of AlkB is actually toxic to the cells unless they are under alkylation stress by agents such as EMS/MMS (Ethyl/Methyl MethaneSulphonate).

But IMO RNA repair is not as essential as DNA repair because of aforementioned reasons.


7.5: DNA Lesions

  • Contributed by E. V. Wong
  • Axolotl Academica Publishing (Biology) at Axolotl Academica Publishing

The robust nature of DNA due to its complementary double strands has been noted several times already. We now consider in more detail the repair processes that rescue damaged DNA. DNA is not nearly as robust as popular media makes it out to be. In fact, to take the blockbuster book and film, Jurassic Park, as an example, Although there is unquestionably some DNA to be found either embedded in amber-bound parasites, or perhaps in preserved soft tissue (found deep in a fossilized femur, Schweitzer et al, 2007). It is likely to be heavily degraded, and accurate reproduction is impossible without many samples to work from.

The most common insult to the DNA of living organisms is depurination, in which the &beta-N-glycosidic bond between an adenine or guanine and the deoxyribose is hydrolyzed. In mammalian cells, it is estimated at nearly 10000 purines per cell generation, and generally, the average rate of loss at physiological pH and ionic strength, and at 37°C, is approximately 3 x 10 -11 /sec. Depyrimidination of cytosine and thymine residues can also occur, but do so at a much slower rate than depurination. Despite the high rate of loss of these bases, they are generally remediated easily by base excision repair (BER), which is discussed later in this section. Therefore it is rare for depurination or depyrimidination to lead to mutation.

Figure (PageIndex<15>). Depurination of guanines (or adenines) is a common DNA lesion.

Three of the four DNA bases, adenine, guanine, and cytosine, contain amine groups that can be lost in a variety of pH and temperature-dependent reactions that convert the bases to hypoxanthine, xanthine, and uracil, respectively. This can sometimes lead to permanent mutations since during replication, they serve as a template for the synthesis of a complementary strand, and where a guanine should go, for example (complementary to cytosine), an adenine may be inserted (because it complements uracil, the deamination product of cytosine).

Figure (PageIndex<16>)A. Deamination of adenine and guanine can lead to mutations upon replication if unrepaired.

Another deamination, of the modified base methylcytosine, can also lead to a mutation upon replication. Some cytosines may be methylated as part of a regulatory process to inactivate certain genes in eukaryotes, or in prokaryotes as protection against restriction endonucleases. When the methylated cytosine is deaminated, it produces a thymine, which changes the complementary nucleotide (upon replication) from a guanine to an adenine. Deamination of cytosines occurs at nearly the same rate as depurination, but deamination of other bases are not as pervasive: deamination of adenines, for example, is 50 times less likely than deamination of cytosine.

Figure (PageIndex<16>)B. Deamination of cytosine, and methylcytosine can lead to mutations upon replication if unrepaired.

Thymine good, Uracil bad. Why is thymine found in DNA rather than uracil? It turns out that the frequency of cytosine deamination may yield a clue as to why cells have gone the extra step (literally, since uracil is a precursor in thymine biosynthesis) to make a new &ldquostandard&rdquo nucleotide for DNA when uracil worked just fine for RNA, presumably the older genetic molecule. Consider this: if uracil was standard for DNA, then the very frequent deamination conversions of C to U would not be caught by error-checking for non-DNA bases, and the mutation rate would skyrocket. Fortunately, since T has evolved to be the standard base-pairing partner of adenine in DNA, uracil is quickly recognized and removed by multiple uracil DNA glycosylases (more on that later in this chapter), and the integrity of our DNA sequences is much safer.

All DNA bases can spontaneously shift to a tautomeric isomer (amino to imino, keto to enol, etc), although equilibrium leans heavily toward one than the other. When a rare tautomer occurs, it base-pairs differently than its more common structural form: guanines with thymines and adenines with cytosines. Here again, a mutation can be propagated during replication of the DNA.

DNA inside a cell must also contend with reactive oxidative species (ROS) generated by the cell&rsquos metabolic processes. These include singlet oxygen, peroxide and peroxide radicals, as well as hydroxyl radicals. although it is thought that the hydrogen peroxide and peroxide radicals do not directly attack the DNA but rather generate hydroxyl radicals that do. Most of these ROS are generated in the mitochondria during oxidative phosphorylation and leak out, although some may be generated in peroxisomes, or in some cytosolic reactions. Depending on what part of the DNA is targeted, ROS can cause a range of lesions including strand breaks and removal of bases.

Ionizing radiation (e.g. X-rays) and ultraviolet radiation can each cause DNA lesions. Ionizing radiation is often a cause for double-stranded breaks of the DNA. As described later in the chapter, the repair process for double-stranded breaks necessarily leads to some loss of information, and could potentially knock out a gene. Ultraviolet radiation that hits adjacent thymines can cause them to react and form a cyclobutyl (four carbons bonded in closed loop) thymine dimer. The dimer pulls each thymine towards the other, out of the normal alignment. Depending on the structural form of the dimer, this is sufficient to stymie the replication machine and halt replication. However, some data suggests that normal base-pairing to adenine may be possible under some conditions, although, it is likely only one base-pair would result, and the missing base could lead to either random substitution or a deletion in the newly synthesized strand.

Figure (PageIndex<17>). Ultraviolet radiation can be absorbed by some DNA and commonly causes pyrimidine cyclobutyl dimers connecting adjacent nucleotide bases.

Finally, we consider the formation of chemical adducts (covalently attached groups) on DNA. They may come from a variety of sources, including lipid oxidation, cigarette smoke, and fungal toxins. These adducts attach to the DNA in different ways, so there are a variety of different effects from the adducts as well. Some may be very small adducts - many environmental carcinogens are alkylating agents, transferring methyl groups or other small alkyl groups to the DNA. Other adducts are larger, but also attach covalently to a nitrogenous base of DNA. Common examples are benzo(a)pyrene, a major mutagenic component of cigarette smoke, and aflatoxin B1, produced by a variety of Aspergillus-family fungi. Benzo(a)pyrene is converted to benzo(a)pyrene diol epoxide, which can then attack the DNA. When this happens, the at pyrene ring intercalates between bases, causing steric changes that lead to local deformation of the DNA and disruption of normal DNA replication.

Figure (PageIndex<18>). Benzo(a)pyrene is converted to an epoxide form by the cell. The epoxide can form an adduct on DNA.

Aflatoxin B1 is the primary aflatoxin produced by some species (esp. flavus, parasiticus) of Aspergillus, a very common mold that grows on stored grain (as well as detritus and other dead or dying plant matter). In addition to infecting grain, it is a common problem with stored peanuts. At high levels, aflatoxin is acutely toxic, but at lower levels, it has the insidious property of being unnoticeably toxic but mutagenic. Like benzo(a) pyrene, it is metabolized into an epoxide and will then react with DNA to form an adduct that can disrupt replication.

Figure (PageIndex<19>). The epoxide form of aflatoxin also forms adducts on DNA.

Some alkylating agents, particularly N-nitroso compounds, are formed in the acidic conditions of the stomach from nitrosation of naturally occurring nitrites produced from food (reduction of nitrates), or environmental nitrites in drinking water. Ironically, while some alkylating agents can cause cancers, others are used therapeutically as anticancer treatments, e.g. mitomycin, melphalan. The idea, as with many cancer treatments, is that although such drugs cause DNA damage to non-cancerous cells as well as cancer cells, the high rate of cancer cell proliferation gives them fewer chances for repair of damaged DNA, and thus greater likelihood that the damage might halt replication and lead to cell death.

In a similar vein, crosslinking chemotherapeutic agents such as cisplatin (a platinum atom bonded to two chloride groups and two amino groups) also bind to DNA. The chloride groups are displaced first by water and then by other groups including sites on DNA. Although sometimes classified as an alkylating agent, it obviously is not, but it acts similarly. Cisplatin goes a step further than a simple alkylating agent though, because it has another reactive site and can thus crosslink (covalently bond) another nucleotide, possibly on another strand of DNA, making a strong obstruction to DNA replication. Cisplatin can also crosslink proteins to DNA.

Benzo(a)pyrene and aflatoxin B1 are not themselves mutagens. Once they are in the cell, the normal metabolism of these compounds leads to diol epoxide formation, which can then attack the DNA. Although the 7-nitrogen (N7) of guanine is more nucleophilic, and is a target for aflatoxin, most benzo(a)pyrene diol epoxide adducts attach to the 2-nitrogen of guanine residues.

There are federal standards (20-300 parts per billion depending on usage) for aflatoxin in various forms of grain-based animal feed, especially corn-based feeds, because the toxin can pass through the animal into milk, as well as linger in the meat. In addition to feed, there are federal maximums for peanuts and peanut products, brazil nuts, pistachios, and other foodstuffs (actionable at 20 ppb).

Well then, what&rsquos a poor cell to do when its DNA is being constantly ravaged? As it turns out, there are some very good repair processes that are constantly at work on the DNA, scanning it for defects, and where possible, making repairs. Often the repairs are perfect, if the complementary strand is intact, sometimes mutations must be introduced, and finally there are occasions when repair is impossible, and apoptosis is triggered to kill the cell and prevent propagation of damaged DNA.


How are lesions in the RNA corrected? - Biology

Most mistakes during replication are corrected by DNA polymerase during replication or by post-replication repair mechanisms.

Learning Objectives

Explain how errors during replication are repaired

Key Takeaways

Key Points

  • Mismatch repair enzymes recognize mis-incorporated bases, remove them from DNA, and replace them with the correct bases.
  • In nucleotide excision repair, enzymes remove incorrect bases with a few surrounding bases, which are replaced with the correct bases with the help of a DNA polymerase and the template DNA.
  • When replication mistakes are not corrected, they may result in mutations, which sometimes can have serious consequences.
  • Point mutations, one base substituted for another, can be silent (no effect) or may have effects ranging from mild to severe.
  • Mutations may also involve insertions (addition of a base), deletion (loss of a base), or translocation (movement of a DNA section to a new location on the same or another chromosome ).

Key Terms

  • mismatch repair: a system for recognizing and repairing some forms of DNA damage and erroneous insertion, deletion, or mis-incorporation of bases that can arise during DNA replication and recombination
  • nucleotide excision repair: a DNA repair mechanism that corrects damage done by UV radiation, including thymine dimers and 6,4 photoproducts that cause bulky distortions in the DNA

Errors during Replication

DNA replication is a highly accurate process, but mistakes can occasionally occur as when a DNA polymerase inserts a wrong base. Uncorrected mistakes may sometimes lead to serious consequences, such as cancer. Repair mechanisms can correct the mistakes, but in rare cases mistakes are not corrected, leading to mutations in other cases, repair enzymes are themselves mutated or defective.

Mutations: In this interactive, you can “edit” a DNA strand and cause a mutation. Take a look at the effects!

Most of the mistakes during DNA replication are promptly corrected by DNA polymerase which proofreads the base that has just been added. In proofreading, the DNA pol reads the newly-added base before adding the next one so a correction can be made. The polymerase checks whether the newly-added base has paired correctly with the base in the template strand. If it is the correct base, the next nucleotide is added. If an incorrect base has been added, the enzyme makes a cut at the phosphodiester bond and releases the incorrect nucleotide. This is performed by the exonuclease action of DNA pol III. Once the incorrect nucleotide has been removed, a new one will be added again.

DNA polymerase proofreading: Proofreading by DNA polymerase corrects errors during replication.

Some errors are not corrected during replication, but are instead corrected after replication is completed this type of repair is known as mismatch repair. The enzymes recognize the incorrectly-added nucleotide and excise it this is then replaced by the correct base. If this remains uncorrected, it may lead to more permanent damage. How do mismatch repair enzymes recognize which of the two bases is the incorrect one? In E. coli, after replication, the nitrogenous base adenine acquires a methyl group the parental DNA strand will have methyl groups, whereas the newly-synthesized strand lacks them. Thus, DNA polymerase is able to remove the incorrectly-incorporated bases from the newly-synthesized, non-methylated strand. In eukaryotes, the mechanism is not very well understood, but it is believed to involve recognition of unsealed nicks in the new strand, as well as a short-term continuing association of some of the replication proteins with the new daughter strand after replication has been completed.

Mismatch Repair: In mismatch repair, the incorrectly-added base is detected after replication. The mismatch-repair proteins detect this base and remove it from the newly-synthesized strand by nuclease action. The gap is now filled with the correctly-paired base.

In another type of repair mechanism, nucleotide excision repair, enzymes replace incorrect bases by making a cut on both the 3′ and 5′ ends of the incorrect base. The segment of DNA is removed and replaced with the correctly-paired nucleotides by the action of DNA pol. Once the bases are filled in, the remaining gap is sealed with a phosphodiester linkage catalyzed by DNA ligase. This repair mechanism is often employed when UV exposure causes the formation of pyrimidine dimers.

DNA Ligase I Repairing Chromosomal Damage: DNA damage, due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day. A special enzyme, DNA ligase (shown here in color), encircles the double helix to repair a broken strand of DNA. DNA ligase is responsible for repairing the millions of DNA breaks generated during the normal course of a cell’s life. Without molecules that can mend such breaks, cells can malfunction, die, or become cancerous. DNA ligases catalyse the crucial step of joining breaks in duplex DNA during DNA repair, replication and recombination, and require either Adenosine triphosphate (ATP) or Nicotinamide adenine dinucleotide (NAD+) as a cofactor.

Nucleotide Excision Repairs: Nucleotide excision repairs thymine dimers. When exposed to UV, thymines lying adjacent to each other can form thymine dimers. In normal cells, they are excised and replaced.

DNA Damage and Mutations

Errors during DNA replication are not the only reason why mutations arise in DNA. Mutations, variations in the nucleotide sequence of a genome, can also occur because of damage to DNA. Such mutations may be of two types: induced or spontaneous. Induced mutations are those that result from an exposure to chemicals, UV rays, X-rays, or some other environmental agent. Spontaneous mutations occur without any exposure to any environmental agent they are a result of natural reactions taking place within the body.

Mutations may have a wide range of effects. Some mutations are not expressed these are known as silent mutations. Point mutations are those mutations that affect a single base pair. The most common nucleotide mutations are substitutions, in which one base is replaced by another. These can be of two types: transitions or transversions. Transition substitution refers to a purine or pyrimidine being replaced by a base of the same kind for example, a purine such as adenine may be replaced by the purine guanine. Transversion substitution refers to a purine being replaced by a pyrimidine or vice versa for example, cytosine, a pyrimidine, is replaced by adenine, a purine. Mutations can also be the result of the addition of a base, known as an insertion, or the removal of a base, known as a deletion. Sometimes a piece of DNA from one chromosome may get translocated to another chromosome or to another region of the same chromosome.


RNA ties itself in knots, then unties itself in mesmerizing video

Striking new videos show how RNA — the genetic molecule that tells cells how to build proteins — tangles up in insane knots as it forms, only to disentangle itself at the last second, and in a way that took scientists by surprise.

The high-resolution videos depict a bouncing conga line of nucleotides, the building blocks of RNA as the single strand of RNA grows longer, these nucleotides dance and twist into different three-dimensional shapes, wiggling first into one conformation and then another. Once fully assembled, the RNA assumes its final shape, which dictates how it can interact with other molecules and proteins in the cell.

But on the way, the RNA can get trapped in "knots" that must be undone for this final shape to emerge.

"So the RNA has to get out of it," said study author Julius Lucks, an associate professor of chemical and biological engineering and a member of the Center for Synthetic Biology at Northwestern University. The RNA won't function correctly if it remains trapped in the wrong knot, meaning a knot that gets in the way of its final shape, he said. "What was surprising is how it got out of that trap. … This was only discovered when we had the high-resolution videos."

In the new study, published Jan. 15 in the journal Molecular Cell, Lucks and his colleagues generated their videos of RNA using experimental data and a computer algorithm. The goal was to zoom in on how RNA forms, both to better understand basic cell biology and to pave the way to better treatments for RNA-related diseases.

In the experiments, the team used a specific kind of RNA called signal recognition particle (SNP) RNA, an evolutionarily ancient molecule found across all kingdoms of life. They used this RNA as a model since it serves a fundamental function in many kinds of cells.

To zoom in on how cells build this RNA, the team used chemicals to pause the construction process. So as new nucleotides got added to the RNA, the researchers hit pause and then recorded how those nucleotides interacted with others already in the lineup, and what shapes they all formed together. By capturing the data from many individual RNA molecules, the team developed snapshots of how RNA generally builds itself through time.

These snapshots served as individual frames in what would become their final videos of RNA formation. That's where the computer model came in. The algorithm essentially strung together the individual frames into mini-movies and filled in the gaps between frames with the most likely nucleotide interactions. In these videos, the team noticed how the RNA got tangled into complex knots that, if left tied, would render the whole molecule useless.

"It folds into this trap state, and it kind of stays there," Lucks said. SNP RNA is meant to form in a signature "hairpin-like" shape, and these traps seem to get in the way. But as more nucleotides get added to the sequence, the new nucleotides swoop in to unravel the knot by displacing the nucleotides tangled up inside.

"That last little nucleotide is like a trigger" that allows the whole RNA to pop into the correct conformation, Lucks said. Think of the last fold in an origami project, which suddenly transforms a crinkly piece of paper into a lovely butterfly. In the videos, the nucleotides highlighted in dark purple knot themselves up, and the dark pink nucleotides help free them, Lucks noted.

Learning how RNA tangles and untangles is key to understanding how cells function and how proteins form the research can also help address diseases where RNA doesn't function properly or a specific protein can't form, such as spinal muscular atrophy, and infectious diseases such as COVID-19 that are caused by RNA viruses, according to a statement.

A big question is whether RNA can mostly untangle itself from these knots, or whether it sometimes needs helper proteins to ease the process. It's possible that some proteins act as so-called "RNA chaperones" and help sculpt the molecule into its final form, Lucks said. He added that it may be a combination of both, although at this point, that's speculative.


What are the differences between DNA nucleotides and RNA nucleotides?

How is the information stored within the base sequence of DNA used to determine a cell&rsquos properties?

How do complementary base pairs contribute to intramolecular base pairing within an RNA molecule?

If an antisense RNA has the sequence 5ʹAUUCGAAUGC3ʹ, what is the sequence of the mRNA to which it will bind? Be sure to label the 5ʹ and 3ʹ ends of the molecule you draw.

Why does double-stranded RNA (dsRNA) stimulate RNA interference?


Symptoms and Causes

What causes brain lesions to develop?

Brain lesions can be caused by many different triggers. The following factors put a person at greater risk to get brain lesions:

  • Aging
  • Family history of brain lesions. The risk increases if someone else in the family has had the condition.
  • Vascular conditions, such as stroke, high blood pressure, and cerebral artery aneurysms
  • Trauma to the brain, which can cause internal bleeding. If not remedied, it could lead to death.
  • Infections, harmful germs or bacteria in the brain. These can cause diseases like meningitis and encephalitis (both types of swelling (inflammation) of the brain).
  • Tumors that either start in the brain (primary tumors) or travel there (metastatic) via blood or lymphatic vessels
  • Autoimmune diseases, such as lupus and multiple sclerosis. These result when the body’s antibodies start to attack the body’s own tissues, such as those tissues in the brain.
  • Plaques, or excess build-up of abnormal protein in the brain tissues or in the blood vessels, slowing down the supply of blood to the brain, as seen in clogged arteries. Alzheimer’s disease, a condition that affects a person’s memory, thinking and behavior, develops because of plaques in brain tissues. Multiple sclerosis can also cause plaques in the brain secondary to damaged tissue.
  • Exposure to radiation or certain chemicals that increase the chance of tumors and lesions in the brain
  • Toxins, such as excessive amounts of alcohol or cigarette smoke, in the body. Other toxic substances are elevated levels of ammonia and urea in the body due to kidney issues (can affect brain function but may not show discrete brain lesions).
  • Poor diet, especially eating foods with excess fats and cholesterol

What diseases cause brain lesions?

    , vascular injury, or impaired supply of blood to the brain is perhaps the leading cause of lesions on the brain. , is a disease where brain lesions are located in multiple sites of the brain. Those suffering from MS have significant problems with motor and sensory functions. , an autoimmune disease, affects almost all systems of the body ranging from skin to heart, liver, muscles and brain. Brain lesions are typically a symptom of this disease.
  • Tumors are also a cause of brain lesions and abnormal growth of brain cells.

What are the symptoms of brain lesions?

Symptoms of brain lesions vary depending on the type of lesion, its extent, and where it is found. Everyone is different and symptoms will vary in individual cases. Many lesions, however, may be in areas of the brain that don’t produce symptoms.

Typical symptoms may include:

  • Headaches are usually the first symptom to appear with brain lesions. The pain appears suddenly and worsens as time passes. Over-the-counter medicine usually offers no relief for the pain. and possible vomiting
  • Impaired movement, if the lesion affects the part of the brain responsible for motor skills
  • Lack of concentration, the inability to make quick decisions, and agitation
  • Delayed speech, blurred vision, and impaired hearing
  • Involuntary movements of body parts, which may progress to convulsions in severe cases

The following symptoms are specific to lesions of the frontal lobe:

  • Absence of sense of smell, usually limited to one nostril
  • Speech impairment
  • Loss of motor activity on one or both sides of the body
  • Behavioral changes

The following symptoms are specific to lesions of the temporal lobe:

  • A change in behavior and emotions
  • Disruption in the sense of smell, taste, and hearing
  • Language and speech disorders
  • Problems with field of vision
  • Forgetfulness and the inability to focus

The following symptoms are specific to lesions of the parietal lobe:

  • Loss of sensations like touch
  • Astereognosis, or the inability to identity things placed in the hand
  • Weakening of language development

The following symptoms are specific to lesions of the occipital lobe:


15.4 RNA Processing in Eukaryotes

In this section, you will explore the following questions:

  • What are the steps in eukaryotic transcription?
  • What are the structural and functional similarities and differences among the three RNA polymerases?

Connection for AP ® Courses

Scientists discovered a strand of mRNA translated into a sequence of amino acids (polypeptide) shorter than the mRNA molecule transcribed from DNA. Before the information in eukaryotic mRNA is translated into protein, it is modified or edited in several ways. A 5′ methylguanosine (or GTP) cap and a 3′ poly-A tail are added to protect mature mRNA from degradation and allow its export from the nucleus. Pre-mRNAs also undergo splicing, in which introns are removed and exons are reconnected. Exons can be reconnected in different sequences, a phenomenon referred to as alternative gene splicing, which allows a single eukaryotic gene to code for different proteins. (We will explore the significance of alternative gene splicing in more detail in other chapters.)

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP ® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices.

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes.
Enduring Understanding 3.A Heritable information provides for continuity of life.
Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information.
Science Practice 6.5 The student can evaluate alternative scientific explanations.
Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information.

Teacher Support

Have students work in groups of 4–5 and ask them to prepare models of RNA molecules undergoing processing. Supply scissors, glue, large sheets of white paper, and colored construction paper to differentiate the components of RNA molecules, exons and introns, and the other molecules such as transcription factors and enzymes associated with the process. Emphasize the importance of the order of the steps. Ask students to specify whether these steps happen in the nucleus or in the cytoplasm.

Ask students which mRNAs would they expect to be stable and which mRNAs should have short half-lives. Proteins that control growth and cell cycles are associated with short-lived RNAs. The globin mRNAs which encode the protein parts of hemoglobin are unusually stable. Synthesis of globin continues in red blood cells without the nucleus being present.

Explain that introns and exons vary in number and length. Mention that not all exons will be included in the final polypeptide and that there is alternative splicing which allows cells to produce different proteins using the same gene.

After transcription, eukaryotic pre-mRNAs must undergo several processing steps before they can be translated. Eukaryotic (and prokaryotic) tRNAs and rRNAs also undergo processing before they can function as components in the protein synthesis machinery.

MRNA Processing

The eukaryotic pre-mRNA undergoes extensive processing before it is ready to be translated. The additional steps involved in eukaryotic mRNA maturation create a molecule with a much longer half-life than a prokaryotic mRNA. Eukaryotic mRNAs last for several hours, whereas the typical E. coli mRNA lasts no more than five seconds.

Pre-mRNAs are first coated in RNA-stabilizing proteins these protect the pre-mRNA from degradation while it is processed and exported out of the nucleus. The three most important steps of pre-mRNA processing are the addition of stabilizing and signaling factors at the 5' and 3' ends of the molecule, and the removal of intervening sequences that do not specify the appropriate amino acids. In rare cases, the mRNA transcript can be “edited” after it is transcribed.

Evolution Connection

RNA Editing in Trypanosomes

The trypanosomes are a group of protozoa that include the pathogen Trypanosoma brucei, which causes sleeping sickness in humans (Figure 15.13). Trypanosomes, and virtually all other eukaryotes, have organelles called mitochondria that supply the cell with chemical energy. Mitochondria are organelles that express their own DNA and are believed to be the remnants of a symbiotic relationship between a eukaryote and an engulfed prokaryote. The mitochondrial DNA of trypanosomes exhibit an interesting exception to The Central Dogma: their pre-mRNAs do not have the correct information to specify a functional protein. Usually, this is because the mRNA is missing several U nucleotides. The cell performs an additional RNA processing step called RNA editing to remedy this.

Other genes in the mitochondrial genome encode 40- to 80-nucleotide guide RNAs. One or more of these molecules interacts by complementary base pairing with some of the nucleotides in the pre-mRNA transcript. However, the guide RNA has more A nucleotides than the pre-mRNA has U nucleotides to bind with. In these regions, the guide RNA loops out. The 3' ends of guide RNAs have a long poly-U tail, and these U bases are inserted in regions of the pre-mRNA transcript at which the guide RNAs are looped. This process is entirely mediated by RNA molecules. That is, guide RNAs—rather than proteins—serve as the catalysts in RNA editing.

RNA editing is not just a phenomenon of trypanosomes. In the mitochondria of some plants, almost all pre-mRNAs are edited. RNA editing has also been identified in mammals such as rats, rabbits, and even humans. What could be the evolutionary reason for this additional step in pre-mRNA processing? One possibility is that the mitochondria, being remnants of ancient prokaryotes, have an equally ancient RNA-based method for regulating gene expression. In support of this hypothesis, edits made to pre-mRNAs differ depending on cellular conditions. Although speculative, the process of RNA editing may be a holdover from a primordial time when RNA molecules, instead of proteins, were responsible for catalyzing reactions.

  1. mRNA editing changes the coding sequence of the mRNA, but mRNA processing does not.
  2. mRNA editing splices out noncoding RNA, but mRNA processing does not.
  3. mRNA editing adds a cap of 5’-methylguanosine to the mRNA, but mRNA processing does not.
  4. mRNA editing adds a 3’ poly-A tail, but mRNA processing does not.

5' Capping

While the pre-mRNA is still being synthesized, a 7-methylguanosine cap is added to the 5' end of the growing transcript by a phosphate linkage. This moiety (functional group) protects the nascent mRNA from degradation. In addition, factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes.

3' Poly-A Tail

Once elongation is complete, the pre-mRNA is cleaved by an endonuclease between an AAUAAA consensus sequence and a GU-rich sequence, leaving the AAUAAA sequence on the pre-mRNA. An enzyme called poly-A polymerase then adds a string of approximately 200 A residues, called the poly-A tail . This modification further protects the pre-mRNA from degradation and signals the export of the cellular factors that the transcript needs to the cytoplasm.

Pre-mRNA Splicing

Eukaryotic genes are composed of exons , which correspond to protein-coding sequences (ex-on signifies that they are expressed), and intervening sequences called introns (int-ron denotes their intervening role), which may be involved in gene regulation but are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins.

The discovery of introns came as a surprise to researchers in the 1970s who expected that pre-mRNAs would specify protein sequences without further processing, as they had observed in prokaryotes. The genes of higher eukaryotes very often contain one or more introns. These regions may correspond to regulatory sequences however, the biological significance of having many introns or having very long introns in a gene is unclear. It is possible that introns slow down gene expression because it takes longer to transcribe pre-mRNAs with lots of introns. Alternatively, introns may be nonfunctional sequence remnants left over from the fusion of ancient genes throughout evolution. This is supported by the fact that separate exons often encode separate protein subunits or domains. For the most part, the sequences of introns can be mutated without ultimately affecting the protein product.

All of a pre-mRNA’s introns must be completely and precisely removed before protein synthesis. If the process errs by even a single nucleotide, the reading frame of the rejoined exons would shift, and the resulting protein would be dysfunctional. The process of removing introns and reconnecting exons is called splicing (Figure 15.14). Introns are removed and degraded while the pre-mRNA is still in the nucleus. Splicing occurs by a sequence-specific mechanism that ensures introns will be removed and exons rejoined with the accuracy and precision of a single nucleotide. The splicing of pre-mRNAs is conducted by complexes of proteins and RNA molecules called spliceosomes.

Visual Connection

  1. Mutations in the spliceosome recognition sequence at each end of an intron, or in the proteins and RNAs that make up the spliceosome, may occur. Mutations may also add new spliceosome recognition sites.
  2. Mutations in the spliceosome recognition sequence at each end of an exon, or in the proteins and RNAs that make up the spliceosome, may occur. Mutations may also add new spliceosome recognition sites.
  3. Mutations in the spliceosome recognition sequence at each end of an intron, or in the proteins and RNAs that make up the spliceosome, may occur. Mutations may also delete existing spliceosome recognition sites.
  4. Mutations at the each end of intron and exon, or in the proteins and RNAs that make up the spliceosome, may occur. Mutations may also add new spliceosome recognition sites and delete existing sites.

Note that more than 70 individual introns can be present, and each has to undergo the process of splicing—in addition to 5' capping and the addition of a poly-A tail—just to generate a single, translatable mRNA molecule.

Link to Learning

See how introns are removed during RNA splicing at this website.

  1. Helper proteins attach themselves to the ends of introns so that they can be spliced out during RNA splicing and coded areas are spliced together to form mRNA which then codes for the final protein.
  2. Helper proteins attach themselves to the ends of exons so that they can be spliced out during RNA splicing and coded areas are spliced together to form mRNA which encodes the final protein.
  3. Helper proteins attach themselves to mRNA in order to remove the non-coded areas and thus form the pre-mRNA which codes for the final protein.
  4. Helper proteins help the pre-mRNA to recruit various other components which splice out the non-coded regions and form mRNA which codes for the final protein.

Processing of tRNAs and rRNAs

The tRNAs and rRNAs are structural molecules that have roles in protein synthesis however, these RNAs are not themselves translated. Pre-rRNAs are transcribed, processed, and assembled into ribosomes in the nucleolus. Pre-tRNAs are transcribed and processed in the nucleus and then released into the cytoplasm where they are linked to free amino acids for protein synthesis.

Most of the tRNAs and rRNAs in eukaryotes and prokaryotes are first transcribed as a long precursor molecule that spans multiple rRNAs or tRNAs. Enzymes then cleave the precursors into subunits corresponding to each structural RNA. Some of the bases of pre-rRNAs are methylated that is, a –CH3 moiety (methyl functional group) is added for stability. Pre-tRNA molecules also undergo methylation. As with pre-mRNAs, subunit excision occurs in eukaryotic pre-RNAs destined to become tRNAs or rRNAs.

Mature rRNAs make up approximately 50 percent of each ribosome. Some of a ribosome’s RNA molecules are purely structural, whereas others have catalytic or binding activities. Mature tRNAs take on a three-dimensional structure through intramolecular hydrogen bonding to position the amino acid binding site at one end and the anticodon at the other end (Figure 15.15). The anticodon is a three-nucleotide sequence in a tRNA that interacts with an mRNA codon through complementary base pairing.

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    RNA Processing and the Human Genome

    The fact that most human genes are composed of many exons has some important consequences for the expression of genetic information. First, we now know that many genes are spliced in more than one way, a phenomenon known as alternative splicing. For example, some types of cells might leave out an exon from the final mRNA that is left in by other types of cells, giving it a slightly different function. This means that a single gene can code for more than one protein. Some complicated genes appear to be spliced to give hundreds of alternative forms. Alternative splicing, therefore, can increase the coding capacity of the genome without increasing the number of genes.

    A second consequence of the exon/intron gene structure is that many human gene mutations affect the splicing pattern of that gene. For example, a mutation in the sequence at an intron/exon junction that is recognized by the spliceosome can cause the junction to be ignored. This causes splicing to occur to the next exon in line, leaving out the exon next to the mutation. This is called exon skipping and it usually results in an mRNA that codes for a nonfunctional protein. Exon skipping and other errors in splicing are seen in many human genetic diseases.

    see also Alternative Splicing Nucleotide Nucleus Ribosome RNA RNA Polymerases.

    Richard A. Padgett

    Bibliography

    Lewin, Benjamin. Genes VII. Oxford, U.K.: Oxford University Press, 2000.

    Lodish, Harvey, et al. Molecular Cell Biology, 4th ed. New York: W. H. Freeman, 2000.


    Nucleic acid structure

    Nucleic acids are long chains (polymers) created by the joining of monomers, which are the nucleotides. Nucleotides are therefore the building blocks of a nucleic acid. They are small molecules composed of 3 subunits: a nitrogenous base, a five carbon sugar and a phosphate group.

    The nitrogenous base is the part of the nucleotide that dictates the specificity of the sequence. The sugar in DNA is called deoxyribose (the clue is in the name, deoxyribonucleic acid). The sugar of RNA is called ribose (hence ribonucleic acid), an unmodified version of this sugar. The sugar occupies a central position, with the nitrogenous base attached to its first carbon (1′) and the phosphate group attached to its fifth carbon (5′)


    Short Notes on Aminoacylation of tRNA | Cell Biology

    Transfer RNA molecules play a key role in the process by deli­vering amino acids to the ribosome in an order specified by the mRNA sequence this ensures that the amino acids are joined together in the correct order. Cells usually contain many species of tRNA, each of which binds specifically to one of the 20 amino acids.

    Consequently, there may be more than one tRNA for each amino acid. Transfer RNAs that bind the same amino acid are called iso-acceptors.

    Before translation begins, amino acids become covalently linked to their tRNAs which then recognize codons in the mRNA specifying that amino acid. The attach­ment of an amino acid to its tRNA is called amino acylation or charging. The amino acid is covalently attached to the end of the acceptor arm of the tRNA which always ends with the base sequence 5′ CCA 3′.

    A bond forms between the carboxyl group of the amino acid and the 3′-hydroxyl of the terminal adenine of the accep­tor arm. Charging is catalyzed by enzymes called aminoacyi tRNA synthetizes in a reaction requir­ing the hydrolysis of ATP. A separate enzyme exists for each amino acid and each enzyme can charge all the iso-acceptors tRNAs for that amino acid.

    The aminoacyi tRNA synthetase recognizes both the appropriate amino acid and the corre­sponding tRNA.

    When the correct amino acid has been attached to the tRNA, it recognizes the codon for that amino acid in the mRNA allowing it to place the amino acid in the correct position, as speci­fied by the sequence of the mRNA. This ensures that the amino acid sequence encoded by the mRNA is translated faithfully.

    Codon recognition takes place via the anticodon loop of the tRNA and specifically by three nucleotides in the loop known as the anticodon which binds to the codon by complementary base-paring.

    The entire codon – anticodon fitting is comparable to recognition of a 3-pin plug with the socketed base. Both the pin and the socket are highly spe­cific. The four bases present in DNA can com­bine as 64 codons. Three codons act as signals for translation to stop and the remaining 61 encode the 20 amino acids present in proteins. Consequently, most amino acids are represented by more than one codon.

    Activation of Amino Acid and Attachment with tRNA:

    Amino acid in cytoplasm occurs in inactive state. They are activated by gaining energy which comes from ATP. The reaction is brought about by the binding of amino acid with ATR. The step is mediated by specific activating enzyme known as aminoacyi RNA synthetase.

    A high energy acyl bond is formed between the a-phosphate of ATP and the carboxyl group of amino acid with the formation of aminoacyi adenylate. The β and γ phosphates of ATP break away as inorganic pyrophosphate.

    The activated amino acid is transferred to its specific t-RNA. A high energy ester bond is formed between the carboxyl group of the amino acid and the 3′-hydroxyl group of the terminal adenosine of tRNA. The aminoacyi AMP-enzyme complex reacts with the specific tRNA to form an aminoacyl-tRNA complex.


    Watch the video: Virology Lectures 2020 #6: RNA directed RNA synthesis (December 2021).