RIBONUCLEIC ACID (RNA)

-------------------------------------------------------------------Objectives: 1. To understand the cell in eukaryotes and prokaryotes 2. To understand structure of RNA 3. To understand the types of RNA SECTION A: THE CELL Prokaryotes and Eukaryotes Basic structure of Eukaryotic cell The basic eukaryotic cell contains the following: 1. 2. 3. 4. plasma membrane glycocalyx (components external to the plasma membrane) cytoplasm (semifluid) cytoskeleton - microfilaments and microtubules that suspend organelles, give shape, and allow motion presence of characteristic membrane enclosed subcellular organelles.

Characteristic biomembranes and organelles Plasma Membrane A lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems.

Nucleus Double membrane surrounding the chromosomes and the nucleolus. Pores allow specific communication with the cytoplasm. The nucleolus is a site for synthesis of RNA making up the ribosome.

Mitochondria Surrounded by a double membrane with a series of folds called cristae. Functions in energy production through metabolism.

Chloroplasts (plastids) Surrounded by a double membrane. Responsible for photosynthesis, the trapping of light energy for the synthesis of sugars. Contains DNA.

Rough endoplasmic reticulum (RER) A network of interconnected membranes forming channels within the cell. Covered with ribosomes (causing the "rough" appearance) which are in the process of synthesizing proteins for secretion or localization in membranes. Ribosomes Protein and RNA complex responsible for protein synthesis. Smooth endoplasmic reticulum (SER) A network of interconnected membranes forming channels within the cell. A site for synthesis and metabolism of lipids.

Golgi apparatus A series of stacked membranes. Vesicles (small membrane surrounded bags) carry materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are "processed" to a mature form. Vesicles then carry newly formed membrane and secreted proteins to their final destinations including secretion or membrane localization. Lysosymes A membrane bound organelle that is responsible for degrading proteins and membranes in the cell, and also helps degrade materials ingested by the cell.

Vacuoles Membrane surrounded "bags" that contain water and storage materials in plants.

Peroxisomes or Microbodies Produce and degrade hydrogen peroxide, a toxic compound that can be produced during metabolism.

Cell wall Plants have a rigid cell wall in addition to their cell membranes. Prokaryotic Cells Cells that lack a membrane-bound nucleus are called prokaryotes (from the Greek meaning before nuclei). These cells have few internal structures that are distinguishable under a microscope. Cells in the monera kingdom such as bacteria and cyanobacteria (also known as blue-green algae) are prokaryotes. Prokaryotic cells differ significantly from eukaryotic cells. They don't have a membranebound nucleus and instead of having chromosomal DNA, their genetic information is in a circular loop called a plasmid. Prokaryotic cells feature three major shapes: rod shaped, spherical, and spiral.

Diagram of a prokaryotic cell SECTION B: WHAT IS RNA? Ribonucleic acid, or RNA, is a nucleic acid polymer consisting of nucleotide monomers, which plays several important roles in the processes of translating genetic information from deoxyribonucleic acid (DNA) into proteins. RNA is a nucleic acid made from a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA acts as a messenger between DNA and the protein synthesis complexes known as ribosomes, forms vital portions of ribosomes, and serves as an essential carrier molecule for amino acids to be used in protein synthesis. RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. Some of these RNA-processing enzymes contain RNA as part of their structures. RNA is also central to the translation of some RNAs into proteins. It has also been known since the 1990s that several types of RNA regulate which genes are active.

I.

Structure of RNA

(A)

(B)

(A) A hairpin loop from a pre-mRNA. Notice its nitrogen-rich (blue) bases and oxygenrich (red) backbone. (B) Watson-Crick base pairs in a siRNA (hydrogen atoms are not shown) Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, generally adenine (A), cytosine (C), guanine (G) or uracil (U). Adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule (polyanion). The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.[1] However other interactions are possible, such as a group of adenine bases binding to each other in a bulge.

Chemical structure of RNA RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil), but there are numerous modified bases and sugars in mature RNAs. Classes of RNA molecules (1) Messenger RNA (mRNA) is the RNA that carries information from DNA to the ribosome, the sites of protein synthesis (translation) in the cell. The coding sequence of the mRNA determines the amino acid sequence in the protein that is produced. mRNA is transcribed by RNA polymerase II in eukaryotes. (mRNA) carries information about a protein sequence to the ribosomes. It is coded so that every three nucleotides form a codon which corresponds to one amino acid. In eukaryotic cells, once precursor mRNA (pre-mRNA) has been transcribed from DNA, it is processed to mature mRNA. This removes its intronsnon-coding sections of the premRNA. The mRNA is then exported from the nucleus to the cytoplasm, where it is bound to ribosomes and translated into its corresponding protein form with the help of tRNA. In prokaryotic cells, which do not have nucleus and cytoplasm compartments, mRNA can bind to ribosomes while it is being transcribed from DNA. After a certain amount of time the message degrades into its component nucleotides with the assistance of ribonucleases. (2) Non-coding RNAs: many RNAs do not code for protein. These non-coding RNAs can be encoded by their own genes (RNA genes), but can also derive from mRNA introns. Examples: (i) the most prominent examples of non-coding RNAs are transfer RNA (tRNA). Transfer RNA (tRNA) is a small RNA chain of about 80 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino acid attachment and an anticodon region for codon recognition that binds to a specific sequence on the messenger RNA chain through hydrogen bonding. It is transcribed by RNA polymerase III in eukaryotes.

(ii) ribosomal RNA (rRNA), both of which are involved in the process of translation. Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. rRNAs are transcribed by RNA polymerase I in eukaryotes. (iii) Ribozymes: there are also non-coding RNAs involved in gene regulation, RNA processing and other roles. Certain RNAs are able to catalyse chemical reactions such as cutting and ligating other RNA molecules, and the catalysis of peptide bond formation in the ribosome; these are known as ribozymes. Transfer-messenger RNA (tmRNA) is found in many bacteria and plastids. It tags proteins encoded by mRNAs that lack stop codons for degradation and prevents the ribosome from stalling.