what is the protein sythesis in eukaryotic cells?

Question

1.giving account to transcription and translation
2.step by step process of dna transcription which takes place in nucleus
3.dna translation into amino acids sequence in the cytoplasma of the cells

Answer 1

1. The gene is the part of the DNA with the instructions for making the particular protein. Enzymes unzip the DNA in the area of the gene.
2. More enzymes bring RNA nucleotides to match the unpaired nitrogen bases of the gene. A molecule of mRNA is made in this way, and the process of copying the DNA's instructions into a molecule of mRNA is called transcription.
3. The mRNA separates from the gene and goes out of the nucleus through a pore in the nuclear envelope. The DNA closes back up the way it was.
4. A ribosome attaches to the mRNA and translation can begin.
5. The mRNA is "read" one codon at a time. A codon is a series of 3 bases that call for a particular amino acid to be brought to the protein assembly site.
6. tRNA molecules deliver the amino acids to be added to the growing polypeptide chain. tRNA molecules have a series of three bases called an anticodon which much match up with mRNA's codon. Whichever tRNA can match the codon gets to add its amino acid to the chain next.
7. This process continues until the ribosome reaches a stop codon on the mRNA. The polypeptide chain breaks off, folds into its characteristic shape, and a protein is complete.

Answer 2

Transcription is the process in which genetic information stored in a strand of DNA is copied into a strand of RNA. The sequence of the four bases in DNA, which are adenine (A), cytosine (C), guanine (G), and thymine (T), is preserved in the sequence of the four bases in RNA, which are A, C, G, and uracil (U).

Functions of Rna Transcripts

RNA molecules have various functions in the cell. Many of the functions are associated with translation, in which the genetic code of messenger RNA molecules is used to help the ribosomes synthesize a specific protein. In addition, ribosomal RNA is the main component of the ribosome, and transfer RNA does the actual translating from nucleotide sequence into amino acid sequence.

RNA molecules may also function as enzymes. They do so either alone or in association with proteins. RNA molecules associate with proteins, for example, when they serve as components of machinery that helps make other, newly formed RNA molecules functional.

RNA is chemically better suited to carry out certain tasks than is DNA. There are also other reasons RNA, not DNA, is used for these tasks. First, it is desirable to keep DNA available for replication and not tied up with other functions. Second, the small number of DNA molecules in the cell is often insufficient. Creating many identical RNA molecules that are copies of a single segment of DNA provides the necessary numbers. Third, RNA can be differentially degraded when it is no longer needed, providing an important regulatory mechanism that would be unavailable if there were only one type of nucleic acid.

Promoters

Transcription is initiated at regions of DNA called promoters, which are typically 20 to 150 base pairs long, depending on the organism. The sequence of bases at a promoter is recognized by RNA polymerase, the enzyme that synthesizes RNA.

The RNA polymerases in bacteria, as well as in viruses in bacteria, are able to recognize particular promoter sequences without the help of any other cellular proteins. However, in eukaryotes and Archaea, other proteins, called initiation factors, recognize the promoter sequence, "recruit" RNA polymerase and other proteins, help the RNA polymerase bind to the DNA, and regulate the enzyme's activity.

RNA polymerase is assembled on promoters in a particular orientation (Figure 1A). This allows RNA synthesis to start at a precise location and proceed in only one direction, "downstream" toward the gene (Figure 1B).

Rna Synthesis

RNA, like DNA, is a polymer of nucleotides. Each nucleotide consists of a sugar that is attached to a phosphate group and any one of four bases. The RNA polymerase, as it builds the chain of nucleotides, processes only one of the two complementary strands of DNA. This DNA strand is referred to as the template strand. The least confusing name for the other DNA strand is "the nontemplate strand."

The bases in the newly synthesized RNA are complementary to the bases in the template DNA strand and, therefore, identical in sequence to the bases in the nontemplate strand, except that the RNA contains U where the nontemplate strand of DNA contains T.

Before the nucleotides are linked together, they exist separately as ribonucleoside triphosphates (NTPs). As shown below, the NTPs contain one of the four common RNA bases, A, C, G, and U, linked to a five-carbon ribose sugar, linked, in turn, to a chain of three phosphate groups. During RNA synthesis, a covalent, "phosphodiester" bond is formed between one of the three phosphate groups on one NTP and a hydroxyl group on another. The two other phosphate groups that were part of the original NTP are released.

RNA synthesis is said to proceed in the 5′ to 3′ direction, reflecting the fact that the attachment of new nucleotides always occurs at the 3′ hydroxyl group of the growing RNA chain. RNA synthesis goes through phases that are typical of polymerization processes: initiation, elongation, and termination, yielding an RNA product of defined size and sequence.

Initiation

The first phase of RNA synthesis is initiation (Figure 1B). Initiation starts when the first phosphodiester bond is formed. At precise locations, determined by the promotor DNA sequence, the first and second RNA bases bind to the complex, and RNA polymerase catalyzes the formation of a covalent bond between them.

When the growing RNA chain reaches a length of about ten nucleotides, the complex loses contact with the promoter and starts moving along the DNA. This is referred to as promoter "clearance" or "escape."

Only a fraction of initiation events lead to promoter clearance. In many instances, an "abortive" RNA molecule, shorter than ten nucleotides, is released from the RNA polymerase, and RNA synthesis begins all over again. Such an abortive molecule is shown in the figure as a thick line.

Once the growing RNA chain has reached the critical length of about ten nucleotides, the initiation stage is considered to have ended, and elongation begins. In eukaryotes, the transition from initiation to elongation can be triggered by enzymes called kinases, which attach phosphate groups to RNA polymerase, facilitating promoter clearance.

Elongation

Genes range in length from about 80 base pairs of DNA, as is the case for those transcribed into transfer RNA, to more than 1 million base pairs, as is the case for those encoding very long proteins. An RNA polymerase molecule that has disengaged from DNA during elongation would be unable to finish synthesizing the RNA molecule. Thus the enzyme has to traverse even the longest genes (Figure 1C), without falling off.

Along the way, there are DNA sequences that the RNA polymerase traverses considerably more slowly than at its usual rate of about 50 nucleotides per second. At regions called pause sites, it may take longer than 1 second for a single nucleotide to be added to the growing polymer.

In eukaryotes, many genes contain blocks of DNA called introns, which disrupt the coding information of the gene. Introns are removed from the newly made RNA by a process called splicing. It is thought that the proteins which carry out the splicing are carried by the RNA polymerase as it is transcribing the gene, allowing the processing of the RNA to occur at the same time as the RNA molecule is synthesized.

Termination

When the RNA polymerase reaches a specific DNA sequence known as a terminator, it slows down and the transcription complex dissociates from the DNA, as shown in Figure 1D. The released RNA polymerase is then free to participate in a new initiation event.

At some terminators, primarily in bacteria, the RNA polymerase is able to respond to the release signal without being helped by any other proteins. Such sites are called intrinsic terminators. At other sites, termination is accomplished only with the aid of additional proteins. These proteins, called termination factors, are also instrumental in causing RNA to be released from the transcribing complex.

"Factor-dependent" terminators have been found in organisms from each of the three domains of life, the eukaryotes, bacteria, and Archaea. In eukaryotes, but usually not in bacteria, transcription of most genes proceeds past the end of the gene, as shown in Figure 1D.

The initial RNA molecules are often referred to as "primary" transcripts. In many instances, the primary transcripts must be processed to yield functional, or "mature," RNA. The processing can involve shortening them by removing their terminal or internal regions, or modifying specific nucleotides in other ways.

Regulation of Transcription

Only a few of an organism's genes are active or "expressed" at any particular time. Which genes are expressed in a particular cell depends on such factors as the nutrients available, the cell's state of differentiation, and the cell's age. There are intricate mechanisms that let the cell regulate the expression of many of its genes. Transcription, the first step in the expression of the genetic information, is an important point at which gene expression can be regulated.

There are two types of regulation: positive control, in which transcription is enhanced in response to a certain set of conditions; and negative control, in which transcription is repressed. Usually, positive control is used at promoters that are otherwise engaged in the initiation of few RNA molecules. Negative control is used at promoters where many molecules of RNA are initiated.

Activator proteins enable positive control by binding to the promoter to recruit RNA polymerase or other required initiation proteins. Such activator proteins usually bind upstream of the promoter (Figure 1). Increased recruitment then leads to an increased rate of synthesis of RNA for a particular gene. The more regulatory sites that are bound, the greater the increase in the rate of RNA synthesis. Repressor proteins can inhibit initiation of transcription by binding to the promoter and preventing RNA polymerase or a required initiation protein from binding.

In eukaryotes, DNA is "packaged" into nucleosomes by being wrapped around histone proteins. This can dramatically reduce the ability of genes to be transcribed, because the packaging may hide promoter sequences that are recognized by initiation factors.

Two mechanisms are used to alter the DNA packaging, to regulate transcription. First, enzymes called chromatin remodeling factors can move his-tone proteins around on the DNA, so that promoter sequences are more accessible or less accessible to the transcription initiation machinery. Second, enzymes can attach small chemical groups, including acetyl, phosphate, methyl or other groups, to the histone proteins. This modification of his-tone proteins may alter the interaction between the DNA and the histones, or between histones and other proteins, either facilitating or blocking the ability of initiation factors to bind DNA.

Transcription also is regulated by proteins that influence how quickly RNA polymerase moves along the DNA. These proteins, called regulatory elongation factors, may help the polymerase traverse pause sites, and they may facilitate elongation through packaged DNA. On the other hand, they may also facilitate the termination of transcription at specific sites.

Translation is the cellular process in which the genetic information carried by the DNA is decoded, using an RNA intermediate, into proteins. This process is also known as protein synthesis.

Deciphering the Genetic Code

There are two steps in the path from genes to proteins. In the first step, called transcription, the region of the double-stranded DNA corresponding to a specific gene is copied into an RNA molecule, called messenger RNA (mRNA), by an enzyme called RNA polymerase. In the second step, called translation, the mRNA directs the assembly of amino acids in a specific sequence to form a chain of amino acids called a polypeptide. This process is accomplished by ribosomes, special amino acid-bearing RNA molecules called transfer RNAs (tRNAs), and other translation factors. The newly synthesized polypeptides form proteins, which have functional and structural roles in cells. All proteins are synthesized by this process.

The precise order of amino acids assembled during translation is determined by the order of nucleotides in the mRNA. These nucleotides are a direct copy of the linear sequence of the nucleotides in one of the two complementary DNA strands, which have been transcribed using a code in which every three bases of the RNA specify an amino acid. DNA and RNA molecules both have directionality, which is indicated by reference to either the 5′ ("five prime") end or the 3′ ("three prime") end.

The code is always read in the 5′ to 3′ direction, using adjacent, non-overlapping three-base units called codons. Since there are four different nucleotides (also called bases) in RNA (abbreviated A, C, G, and U), there are sixty-four (43) different codons, and each codon specifies a particular amino acid. There are only twenty different amino acids, however, so many of the amino acids can be specified by more than one codon, a circumstance that is known as degeneracy. The list of mRNA codons specific for a given amino acid is called the genetic code. The start signal, or initiation codon, for translating the mRNA is usually specified by an AUG, which codes for the amino acid methionine. Three codons (UAA, UGA, and UAG) do not specify an amino acid. Instead, these codons serve as stop signals to indicate that the end of the gene has been reached. During the translation process, they signal that no further amino acids are to be assembled.

The process of translation is carried out by ribosomes, which bind the mRNA and conduct a catalytic activity, called peptide bond formation, for joining the amino acids. The amino acids are carried to the ribosome by the tRNAs. Each tRNA has a specific amino acid attached to it and contains a nucleotide triplet called an anticodon. The anticodon recognizes a specific codon on the mRNA by pairing with it, using base-pairing rules like those used by DNA: A pairs with U and G pairs with C. For example, a tRNA with a UUU anticodon recognizes the AAA codon. The amino acid lysine is attached to this tRNA, so every time the ribosome "reads" an AAA codon, the lysine-bearing tRNA is brought in, base pairs via its anticodon to the codon, and delivers a lysine to the growing protein chain.

Mutations arise when one or more bases in the DNA is changed. When the mutated DNA is transcribed, the resulting mRNA will carry the same mutation. Then, when the mRNA is translated, the amino acid sequence of the resulting protein will be different from the original, or wild-type, sequence because the codons affected by the mutation will recruit the wrong amino acids. The resulting mutant protein may have neutral, harmful, or even beneficial effects on the individual. These changes are the basis for evolution.

Stages of Translation

The process of translation can be broken down into three stages. The first stage is initiation. In this step, a special "initiator" tRNA carrying the amino acid methionine binds to a special site on the small subunit of the ribosome (the ribosome is composed of two subunits, the small subunit and the large subunit). The mRNA is also loaded on, and positioned so that the initiation codon (usually AUG) is base paired with the anticodon of the initiator tRNA. The large subunit then binds to the small subunit. The resulting complex of ribosome, mRNA, and methionine-bearing initiator tRNA is called an initiation complex. Formation of this complex also requires a number of helper proteins called initiation factors.

The second stage is called chain elongation. During this stage, additional amino acids are progressively added. The methionine-bearing initiator tRNA sits on a site of the ribosome called the P (peptidyl) site. A new tRNA, bearing the next amino acid is base paired via its anticodon to the next codon of the mRNA, using a site called the A (acceptor) site. This new amino acid is then attached to the amino acid carried by the P site tRNA, forming a peptide bond. This enzymatic step is carried out by the ribosome, at a site called the peptidyl-transferase center.

The tRNA that has so far been attached to the amino acid in the P site is then released through the E (exit) site, and the new tRNA, now carrying both its own amino acid and the methionine moves into the P site. The mRNA also slides three bases to bring the next codon into position at the A site. A third tRNA, again carrying a specific amino acid and recognizing the third codon of the mRNA, moves into the A site, and the cycle is repeated. As these steps are continued, the mRNA slides along the ribosome, three bases at a time, and the peptide (amino acid) chain continues to grow. As with initiation, elongation requires helper proteins, called elongation factors. Energy is also required for peptide bond formation.

The final stage of translation is termination. The signal to stop adding amino acids to the polypeptide is a stop codon (UAA, UAG, or UGA), for which there is no partner tRNA. Rather, special proteins called release factors bind to the A site of the ribosome and trigger an enzymatic reaction by the ribosome. This reaction causes the ribosome to release the polypeptide and mRNA, ending the elongation process.

At a given time, more than one ribosome may be translating a single mRNA molecule. The resulting clusters of ribosomes, which resemble beads on a string, are called polysomes.

Recognition of Initiation Codons

Not all AUG codons serve as the site of initiation. Most AUGs are intended to code for methionines within the polypeptide chain. Therefore, in addition to the methionine-bearing initiator tRNA, another set of methionine-specific tRNAs are used for these internal AUG codons. The ribosome must be able to distinguish between these two kinds of AUG codons. In bacteria, additional information contained within the mRNA sequence immediately before the intended initiating AUG, called a Shine-Dalgarno sequence, helps the ribosome to recognize where it should start translating. Any AUG sequences on the 5′ side of the initiation codon are ignored. In eukaryotic cells, a different strategy is used to recognize the initiating AUG codon. The mRNA contains a special structure at its 5′ end, which helps the ribosome to attach and then to scan down the RNA molecule until it reaches the first AUG triplet. In bacteria and eukaryotes, AUG codons encountered during translation after initiation are recognized by a non-initiator methionine-bearing tRNA.