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RIBONUCLEIC ACID (RNA)--------------------------------------------------------------------

Objectives:

1. To understand the cell in eukaryotes and prokaryotes2. 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. plasma membrane2. glycocalyx (components external to the plasma membrane)

3. cytoplasm (semifluid)

4. cytoskeleton - microfilaments and microtubules that suspend organelles, giveshape, and allow motion presence of characteristic membrane enclosed

subcellular organelles.

Characteristic biomembranes and organelles

Plasma MembraneA 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 thecytoplasm. The nucleolus is a site for synthesis of RNA

making up the ribosome.

MitochondriaSurrounded by a double membrane with a series of folds

called cristae. Functions in energy production through

metabolism.

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Chloroplasts (plastids)

Surrounded by a double membrane. Responsible for

photosynthesis, the trapping of light energy for the synthesisof 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 channelswithin 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 Golgiapparatus. 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 helpsdegrade materials ingested by the cell.

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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 membrane-

bound nucleus and instead of having chromosomal DNA, their genetic information is in acircular loop called a plasmid.

Prokaryotic cells feature three major shapes: rod shaped, spherical, and spiral.

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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 along chain ofnucleotide units. Each nucleotide consists of a nitrogenous base, a ribose

sugar, and aphosphate.

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 moleculefor 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 intoproteins. It has also been knownsince the 1990s that several types of RNA regulate which genes are active.

http://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Nucleotidehttp://en.wikipedia.org/wiki/Nucleobasehttp://en.wikipedia.org/wiki/Ribosehttp://en.wikipedia.org/wiki/Phosphatehttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Enzymeshttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Gene_regulationhttp://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Nucleotidehttp://en.wikipedia.org/wiki/Nucleobasehttp://en.wikipedia.org/wiki/Ribosehttp://en.wikipedia.org/wiki/Phosphatehttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Enzymeshttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Gene_regulation

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I. Structure of RNA

(A) (B)

(A) A hairpin loop from a pre-mRNA. Notice its nitrogen-rich (blue) bases and oxygen-rich (red) backbone.

(B) Watson-Crick base pairs in asiRNA (hydrogen atoms are not shown)

Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. Abase 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] Howeverother interactions are possible, such as a group of adenine bases binding to each other in a

bulge.

http://en.wikipedia.org/wiki/SiRNAhttp://en.wikipedia.org/wiki/SiRNAhttp://en.wikipedia.org/wiki/Adeninehttp://en.wikipedia.org/wiki/Cytosinehttp://en.wikipedia.org/wiki/Guaninehttp://en.wikipedia.org/wiki/Uracilhttp://en.wikipedia.org/wiki/Purinehttp://en.wikipedia.org/wiki/Pyrimidinehttp://en.wikipedia.org/wiki/Phosphatehttp://en.wikipedia.org/wiki/Hydrogen_bondhttp://en.wikipedia.org/wiki/RNA#cite_note-pmid15561141-0%23cite_note-pmid15561141-0http://en.wikipedia.org/wiki/Image:Piwi-siRNA-basepairing.pnghttp://en.wikipedia.org/wiki/Image:Pre-mRNA-1ysv.pnghttp://en.wikipedia.org/wiki/SiRNAhttp://en.wikipedia.org/wiki/Adeninehttp://en.wikipedia.org/wiki/Cytosinehttp://en.wikipedia.org/wiki/Guaninehttp://en.wikipedia.org/wiki/Uracilhttp://en.wikipedia.org/wiki/Purinehttp://en.wikipedia.org/wiki/Pyrimidinehttp://en.wikipedia.org/wiki/Phosphatehttp://en.wikipedia.org/wiki/Hydrogen_bondhttp://en.wikipedia.org/wiki/RNA#cite_note-pmid15561141-0%23cite_note-pmid15561141-0

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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 theribosome, 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. Ineukaryotic 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 pre-

mRNA. 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 oftRNA. Inprokaryotic 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 ofribonucleases.

(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 anticodonregion 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.

http://en.wikipedia.org/wiki/Image:RNA_chemical_structure.GIFhttp://en.wikipedia.org/wiki/Ribosomehttp://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/Amino_acidhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Ribosomehttp://en.wikipedia.org/wiki/Genetic_codehttp://en.wikipedia.org/wiki/Eukaryotichttp://en.wikipedia.org/wiki/Intronhttp://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/TRNAhttp://en.wikipedia.org/wiki/Ribonucleasehttp://en.wikipedia.org/wiki/Non-coding_RNAhttp://en.wikipedia.org/wiki/Intronhttp://en.wikipedia.org/wiki/Transfer_RNAhttp://en.wikipedia.org/wiki/Transfer_RNAhttp://en.wikipedia.org/wiki/Nucleotidehttp://en.wikipedia.org/wiki/Polypeptidehttp://en.wikipedia.org/wiki/Anticodonhttp://en.wikipedia.org/wiki/Codonhttp://en.wikipedia.org/wiki/Image:RNA_chemical_structure.GIFhttp://en.wikipedia.org/wiki/Image:RNA_chemical_structure.GIFhttp://en.wikipedia.org/wiki/Ribosomehttp://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/Amino_acidhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Ribosomehttp://en.wikipedia.org/wiki/Genetic_codehttp://en.wikipedia.org/wiki/Eukaryotichttp://en.wikipedia.org/wiki/Intronhttp://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/TRNAhttp://en.wikipedia.org/wiki/Ribonucleasehttp://en.wikipedia.org/wiki/Non-coding_RNAhttp://en.wikipedia.org/wiki/Intronhttp://en.wikipedia.org/wiki/Transfer_RNAhttp://en.wikipedia.org/wiki/Transfer_RNAhttp://en.wikipedia.org/wiki/Nucleotidehttp://en.wikipedia.org/wiki/Polypeptidehttp://en.wikipedia.org/wiki/Anticodonhttp://en.wikipedia.org/wiki/Codon

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(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 ascutting and ligating other RNA molecules, and the catalysis ofpeptide 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.

http://en.wikipedia.org/wiki/Ribosomal_RNAhttp://en.wikipedia.org/wiki/Ribosomal_RNAhttp://en.wikipedia.org/wiki/RNA_processinghttp://en.wikipedia.org/wiki/RNA_processinghttp://en.wikipedia.org/wiki/Catalysishttp://en.wikipedia.org/wiki/Ligasehttp://en.wikipedia.org/wiki/Peptide_bondhttp://en.wikipedia.org/wiki/Ribosomehttp://en.wikipedia.org/wiki/Ribozymehttp://en.wikipedia.org/wiki/TmRNAhttp://en.wikipedia.org/wiki/Bacteriahttp://en.wikipedia.org/wiki/Plastidhttp://en.wikipedia.org/wiki/Ribosomal_RNAhttp://en.wikipedia.org/wiki/Ribosomal_RNAhttp://en.wikipedia.org/wiki/RNA_processinghttp://en.wikipedia.org/wiki/RNA_processinghttp://en.wikipedia.org/wiki/Catalysishttp://en.wikipedia.org/wiki/Ligasehttp://en.wikipedia.org/wiki/Peptide_bondhttp://en.wikipedia.org/wiki/Ribosomehttp://en.wikipedia.org/wiki/Ribozymehttp://en.wikipedia.org/wiki/TmRNAhttp://en.wikipedia.org/wiki/Bacteriahttp://en.wikipedia.org/wiki/Plastid