Types and Function of RNA

DNA of the nucleus. This DNA is circular, which is what is seen in bacteria as well. There are also no introns in this DNA. The DNA in mitochondria is transcribed and code for proteins that are involved in electron transport within the mitochondrion.

The DNA double helix can unwind under certain circumstances. Heat, extremes of pH, and certain chemicals will cause denaturation of the DNA molecule. Low salt concentrations, dimethyl sulfoxide, and formamide will all help to denature DNA. DNA can be denatured and will reanneal or come together, coming together to bind in the same way that existed before the molecules became denatured.

TYPES AND FUNCTION OF RNA

RNA or ribonucleic acid is extremely similar to DNA. Two major differences are that RNA strands are shorter and are typically single-stranded molecules. RNA is mainly involved in the synthesis of proteins and in the regulation of the translation process. RNA is made from ribonucleotides linked together through many phosphodiester bonds, which is similar to DNA. The four bases are adenine, guanine, cytosine, and uracil. These different aspects of RNA make it less stable than DNA. Even though RNA is single-stranded, it can fold on itself and make bonds with itself; this tends to stabilize the molecule.

There are three main types of RNA—each of which has different structures and functions. All of them participate in the translation process. The three main types are messenger RNA or mRNA, ribosomal RNA or rRNA, and transfer RNA or tRNA.

Messenger RNA is what gets transcribed as the chemical messenger between DNA and protein synthesis. DNA is quite large and cannot leave the nucleus. For this reason, messenger RNA is made by “reading” genes on the DNA molecule, making an exactly opposite match to the gene, only the structure made is messenger RNA instead of another DNA strand. The entirety of the transcription process happens through the activity of RNA polymerase, which takes the DNA strand and turns it into a complementary strand of RNA. The strand is read from the five-prime end to the threeprime end.

There are three stages of transcription: initiation, elongation, and termination. In prokaryotes, the process is relatively simple. RNA binds to the promotor region near the gene’s beginning. Each gene has its own promotor sequence. At this level, the RNA polymerase separates the DNA strands so that there is a strand to read in the transcription process.

Next comes elongation. There is a template strand on the DNA molecule that is read by RNA polymerase one base at a time. The process ends up building a messenger RNA molecule out of nucleotides that are complementary to the DNA strand. The RNA strand starts at the five-prime end and adds on at the three-prime end. The messenger RNA strand is the same as the noncoding DNA strand with the exception that it has uracil instead of thymine. The RNA strand only hangs onto the DNA it is reading for a short period of time. Most of it dangles freely so that the DNA molecule gets reconnected almost as soon as it is read.

There are also sequences on the DNA molecule called terminators. These sequences signal that the transcription process is finally completed. The reading of this sequence means that the transcripted messenger RNA will be released from the RNA polymerase molecule. The terminator sequence encodes for a portion of the RNA molecule that forms a hairpin, which is when RNA folds back upon itself to make a hairpin structure. This is followed by a number of U-nucleotides that cause stalling of the RNA polymerase molecule. The uracil nucleotides cause the transcript to separate from the template DNA molecule.

In eukaryotes, the initially coded messenger RNA is called pre-mRNA because it is not completely ready to be translated. As mentioned previously, there are introns and exons that need to be separated to make the whole mRNA molecule. There is also the addition of a five-prime cap and a three-prime poly-A tail. Remember, it is the introns that are chopped out and the exons remain in. Figure 38 shows the splicing and addition of the cap and tail:

Figure 38.

These end modifications serve to increase the stability of the messenger RNA molecule, while the splicing out of introns will give the RNA the proper sequence. The mRNA molecule will not read properly if the introns remain in the sequence.

Not all genes are transcribed at the same time. Each gene is opened up for transcription individually when needed so that only necessary genes are transcribed at any given

period of time. In some cases, many RNA transcripts are made over a short period of time, while others are not made at all.

In the process of transcription, the histone proteins unwind and DNA polymerase opens up a transcription bubble, in which the strands separate so that the template strand can be transcribed. The coding strand is the strand of RNA that is made from the template strand. It is the mRNA transcript that gets made into the protein molecule. The coding strand is also referred to as the non-template strand.

In eukaryotes like humans, there are general transcription factors that help RNA polymerase to bind to the DNA molecule. There is a promotor sequence known as the TATA box. It is recognized by the transcription factors, allowing RNA polymerase to bind to the molecule. This TATA sequence allows the DNA strand to pull apart more easily.

The DNA template always gets read from the three-prime end to the five-prime end. The RNA nucleotides get added at the three-prime end, one nucleotide at a time with the tail hanging off the DNA template as the nucleotides are added. There are three phosphates on each RNA nucleotide, with two phosphates dropping off to provide the energy to make the phosphodiester linkage between the bases.

Termination happens differently in bacteria compared to eukaryotes. In bacteria, termination can be Rho-dependent or Rho-independent. There is a Rho-factor binding site in rho-dependent termination. The Rho-factor attaches to the RNA transcript and gradually works its way toward the transcription bubble. When it reaches the transcription bubble, the RNA transcript falls off the DNA template strand.

In Rho-independent termination, there are specific sequences of the DNA template strand that have a great deal of cytosine and guanine nucleotides. The RNA transcribed from this region will fold back on itself, making a hairpin that is stable enough to fall off. The hairpin also has a long stretch of Uracil nucleotides that have a weak connection to the template. This also encourages the falling off of the transcript.

In bacteria, the messenger RNA doesn’t need to be spliced. Instead, translation happens at the same time as translation. Transcription also happens at the same time throughout the DNA molecule. This means that DNA transcription and translation

happen all throughout, leading to polyribosomes that look like beads on a string connected to the mRNA transcript, which are themselves connected to a long stretch of DNA. There are no organelles to separate these processes. This isn’t the case with eukaryotes, where there is splicing as well as separation of the translation process from the transcription process.

The five-prime cap and poly-A tail (which stands for poly-adenosine) are used to protect the messenger RNA from becoming damaged. These will protect the messenger RNA so that it can get exported from the nucleus. The five-prime cap gets added during the transcription process. It is a modified guanine molecule that prevents breakdown of the transcript and helps in the translation process. There is another enzyme that adds the poly-A tail, which is also to add stability to the molecule.

There is a process known as alternative splicing, in which different introns get spliced out, depending on the circumstances. When some introns get spliced out, certain proteins are made; when other introns get spliced out, other proteins are made. It is a way to make two different proteins from the same piece of DNA.

Transfer RNA or tRNA and ribosomal RNA or rRNA are more stable. Transfer RNA transfers the amino acid to the growing polypeptide chain. Ribosomal RNA is seen in eukaryotes. It goes into the making of ribosomes as part of the translation process. Ribosomal RNA gets made and assembled in the nucleolus of the cell. These do not carry a DNA message but are important in the translation process.

Ribosomal RNA has enzymatic properties. It ensures the adequate alignment of the messenger RNA and transfer RNA in order to facilitate the process of translation. This part of ribosomal RNA is called peptidyl transferase.

Transfer RNA is very small. It is only about 80 nucleotides long. There is different transfer RNA for each of the amino acids that get connected to the growing polypeptide chain. The transfer RNA is a hairpin molecule that has an amino acid attached to the three-prime end. There are multiple hairpins in the transfer RNA molecule so that it has a three-dimensional shape.