RNA - Biology

The first stage of transcription is initiation, in which RNA polymerase II (PolII) engages the promoter and recruits the general transcription machinery. Following initiation, PolII travels down the length of the gene, producing a transcript (elongation). Finally, transcription is terminated, and PolII is removed from the gene. Following transcription, immature heterogeneous RNA (htRNA) can be processed during splicing to become mature messenger RNA (mRNA).

Summary of steps:

Initiation, elongation, termination, splicing

When transcribing from a template strand, the new strand is synthesized in the opposite direction, much like in DNA replication. This will result in antiparallel strands. Also, we need to replace thymine with uracil, because RNA uses uracil in place of thymine.

Template: 5'-CGAATGGCAT-3'

Answer: 5'-AUGCCAUUCG-3'

To see these pairs match up, the 3' end of the answer must align with the 5' end of the template.

Template: 5'-CGAATGGCAT-3'

Answer (3'-5'): 3'-GCUUACCGUA-5'

There are several types of RNA, but four main types: messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and heteronuclear RNA (htRNA).

Heteronuclear RNA is the direct product of transcription, prior to post-transcriptional modification. htRNA is unable to exit the nucleus until it has undergone RNA splicing to remove introns, addition of the poly-A tail, and addition of the 5' cap. At this point, the htRNA has matured to become functional mRNA.

Messenger RNA is the final transcription product from DNA and used as the template for protein translation. It carries genetic information in the form of codons from the nucleus to the cytosol to create protein chains.

Transfer RNA binds to specific amino acids and helps add them to protein chains during translation. tRNA molecules enter active sites in the ribosome and match an anticodon region to the mRNA template codon before transferring their amino acid cargo to the polypeptide chain.

Ribosomal RNA associates with proteins and is used to form the structure of the ribosomes.

The process of forming messenger RNA from a strand of DNA is called transcription. Replication is the creation of new DNA from the original DNA strands. Translation is the creation of a protein chain from the messenger RNA strand using transfer RNA.

RNA polymerase II is the primary protein responsible for generating mRNA.

RNA polymerases I and III transcribe other RNAs (such as tRNA and rRNA). DNA polymerase is responsible for DNA replication during the S phase of the cell cycle.

During transcription, transcription factors will bind to promoter sites on the 5' side of the gene to be transcribed. Although the answer "a gene" is technically correct, the more accurate answer is promoter site—the region of DNA that initiates transcription.

A peptide strand is the product of translation, and does not bind transcription factors.

Ribosomes help read the RNA that is eventually transcribed from the DNA, but transcription factors do not interact directly with the ribosomes.

Plant cells are eukaryotic, thus they have nuclei. The process of mRNA synthesis is called transcription. Transcription occurs in the nucleus in eukaryotes. In prokaryotes, it occurs in the cytoplasm. Note that rRNA synthesis and ribosome assembly takes place in the nucleolus.

The genetic code is read in triplets. The addition of a single nucleotide would shift the triplets such that they are no longer read in the correct frame. This is called a frameshift mutation. A truncated protein could be a result of an insertion, but this is not the most likely result. Early transcriptional termination would not be a likely result of an insertion, since this is mediated by long GC repeats or a protein called rho in prokaryotes. Eukaryotic transcriptional termination is not well-understood.

Prokaryotes do not have nuclei. It is translation, not transcription, that occurs on ribosomes. tRNA is the type of RNA that brings amino acids to the ribosome; again, translation is the process of protein synthesis from amino acids. There are many differences between eukaryotic and prokaryotic transcription! These differences are monumental in differentiating between eukaryotes and prokaryoes. For example, in eukaryotes, transcription occurs in the nucleus and involves mRNA processing—adding a 5' cap, adding a 3' poly-A tail, and splicing out introns; none of these things are true for prokaryotes.

The genetic code is based on codons, which are sets of three nucleotides. mRNA is read in the triplet code; each codon specifies for an amino acid. The genetic code is redundant (one amino acid may be coded for by multiple codons), but each codon only codes for one amino acid, or the stop codon.

It is important to remember the base-pairing rules when discussing both DNA and RNA because they are the rules by which all of transcription and translation occur. In RNA, uracil takes the place of thymine, creating an A-D pair instead of an A-T pair. The structure of RNA is a single strand of alternating ribose and phosphate groups with nitrogenous bases attached to the ribose. One way that DNA and RNA differ is that DNA contains deoxyribose sugar while RNA contains the ribose sugar.

Transcription must occur first because it is the process that copies the genetic code from the DNA, and it must occur in the nucleus because DNA is too large a molecule to leave the nucleus. Next comes translation, which is the reading of the "photocopied" code (mRNA) after it leaves the nucleus and connects with a ribosome. After this, the mRNA binds with ribosomes and is translated to create proteins.

RNA is the key molecule involved in protein synthesis. During translation, the mRNA binds to a ribosome carrying a sequence of codons. The tRNA then binds to the ribosome/mRNA complex with the matching anticodon. The anticodon contains the three complimentary nucleotides to the codon.

Each type of RNA is designed to complete a different function in the cell. Messenger RNA (mRNA) has a linear structure and provides the codon template for translation. Transfer RNA (tRNA) has a hairpin loop structure and carries amino acid residues to ribosomes for elongation of the polypeptide created from translation. Ribosomal RNA (rRNA) has a globular structure and forms an integral component of the ribosome subunits.

Despite their differences, all RNA molecules have the same backbone structure, which contains ribose sugars and phosphate groups, and the same nitrogenous bases: adenine, cytosine, guanine, and uracil.

Ubuiqitin is a protein synthesized to tag worn out or defective proteins for recycling. Since this would only eliminate proteins that have already been synthesized, it would be more of a translational regulation process.

The other choices are common transcription regulators. Chromatin remodeling complexes are proteins that interact with the histones in chromatin. They are able to expand or condense the amount of coiling around histones and therefore allow greater or lesser access by transcription machinery to the DNA; thus, when the DNA is more tightly bound, it is less accessible and transcription is regulated. Our genes are broken into coding and non-coding sequences called exons and introns respectively. Alternative splicing is a process that alters the mRNA transcription product by selecting different combinations of exons to be joined together. This is an important process and allows the body to produce many more proteins than it normally would from the same quantity of genes. DNA binding motifs and their associated proteins are called transcription factors when interacting and they regulate transcription. They regulate by blocking a genes' promoter region (reduces the expression of that sequence) or they bond to the promoter to help the transcription machinery recognize that sequence and assemble itself (increases expression). Last, repressor proteins bond to promoter regions of genes they regulate. Often times the product of that gene is responsible for activating and inactivating that repressor. For example, a large quantity of a gene product can make it more likely for the repressor and that gene product (protein) to meet and join. This activity generally turns repressors on and transcription of that gene is reduced or stopped.

rRNA forms ribosomes.

tRNA is transport RNA, it joins amino acids to ribosomes to assemble a protein molecule

SnRNA is small nuclear RNA, it splices pre-mRNA to form mRNA

miRNA is microRNA, which regulates gene transcription and translation

mRNA is messenger RNA, carries the genetic code for controlling the protein formed.

Although RNA and DNA have some key differences that result in different functions, they also have some key similarities. Both are composed of nucleotide monomers linked together by phosphodiester bonds. They are also both read in the 5'-3' direction. It is important to know that the backbone of both DNA and RNA is made by phosphodiester bonds, but it is hydrogen bonds that bind two strands to DNA together to form the double-helix.

DNA and RNA both use adenine, cytosine, and guanine, but only DNA uses thymine and only RNA uses uracil. Only DNA is double-stranded; RNA is single-stranded. Deoxyribose, in DNA, is deoxygenated at the 2' carbon, but ribose in RNA is oxygenated.

DNA uses four nitrogenous bases: adenine, thymine, cytosine, and guanine. Adenine residues bond to thymine residues, and cytosine binds to guanine.

During transcription, DNA is used as a template to generate mRNA. During this process, bases are matched to the DNA template and used to build a single strand of RNA. In RNA, there are also four nitrogenous bases: adenine, cytosine, guanine, and uracil. Thymine is not found in RNA.

DNA sequences contain the following nucleotides: adenine (A), thymine (T), cytosine (C), and guanine (G). Guanine and cytosine bases pair together, while adenine and thymine bases pair together. In RNA, thymine is replaced by uracil (U).