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Terms in this set (86)

- In a eukaryotic cell, the nuclear envelope separates transcription from translation in space and time
- Transcription occurs in the nucleus, and mRNA is then transported to the cytoplasm, where translation occurs
- Before eukaryotic RNA transcripts from protein-coding genes can leave the nucleus, RNA transcripts (pre-mRNA) must be modified in various ways to produce functional mRNA
- Transcription progresses at a rate of about 40 nucleotides per second in eukaryotes
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- Triplets of nucleotide bases are the smallest units of uniform length that can code for all the amino acids
- If each arrangement of three consecutive nucleotide bases specifies an amino acid, there can be 64 possible code words (which is more than enough to specify all the amino acids)
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- The triplet code: The genetic instructions for a polypeptide chain are written in the DNA as a series of nonoverlapping, three-nucleotide words
- The series of words in a gene are transcribed into a complementary series of non-overlapping, three-nucleotide words in mRNA, which is then translated into a chain of amino acids during translation
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- 61 of the 64 triplets code for amino acids; the three codons that do not designate amino acids are "stop" signals or termination codons, which mark the end of translation
- Note that the mRNA codon AUG has a dual function: It codes for the amino acid, methionine, and also functions as a "start" signal or initiation codon
- Genetic messages usually begin with AUG, which signals the protein-synthesizing machinery to being translating the mRNA at that location
- Note that AUG also stands for methionine, thus most polypeptide chains begin with methionine when they are synthesized--however, an enzyme may subsequently remove methionine from the polypeptide chain
- There is redundancy in the genetic code, but no ambiguity (Example: GAA and GAG both specify glutamic acid, but neither of them ever specifies any other amino acid so there is no ambiguity)
- In many cases, codons that are synonyms for a particular amino acid differ only in the third nucleotide base of the triplet
- The ability to extract the intended message from a written language depends on reading the symbols in the the correct reading frame--a short stretch of polypeptide will be made correctly only if the mRNA nucleotides are read from left to right (5' --> 3') and if the message is read as series of non-overlapping three-letter words
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- Initiation
- Elongation
- Termination
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- As RNA polymerase moves along the DNA, it continues to untwist the double helix, exposing about 10-20 DNA nucleotides at a time for pairing with RNA nucleotides
- RNA polymerase adds nucleotides to the 3' end of the growing RNA molecule as it continues along the double helix
- Behind the RNA polymerase, the new RNA peels away from the template strand, which re-forms a double helix with the non-template strand
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- A single gene can be transcribed simultaneously by several molecules of RNA polymerase following each other
- A growing strand of RNA trails off from each polymerase, with the length of each new strand reflecting how far along the template the enzyme has traveled from the start point
- The congregation of many RNA polyermase molecules simultaneously transcribing a single gene increases the amount of mRNA transcribed, which helps the cell make the encoded protein in large amounts
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- Enzymes in the eukaryotic nucleus modify pre-mRNA in specific ways before the genetic messages are dispatched to the cytoplasm
- During this RNA processing, both ends of the primary transcript are altered (and in most cases, certain interior sections of the RNA molecule are cut out and the remaining parts are spliced together)
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- RNA splicing is a stage of RNA processing in the eukaryotic nucleus that involves the removal of large portions from a RNA molecule that is initially synthesized
- In humans, it takes only 1,200 nucleotides in RNA to code for the average-sized protein (400 amino acids)
- Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides (most of these noncoding sequences are interspersed between coding segments of the gene and thus between coding segments of the pre-mRNA)
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1) snRNPs and other proteins form a spliceosome on a pre-mRNA molecule containing exons and introns
2) Within the spliceosome, snRNA base-pairs with nucleotides at specific sites along the intron
3) The spliceosome cuts the pre-mRNA, releasing the intron for rapid degradation, and at the same time splice the exons together, the spliceosome then comes apart, releasing mRNA, which now contains only exons
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- Translation is the synthesis of a polypeptide using the information in the mRNA
- The cell must translate the nucleotide sequence of an mRNA molecule into the amino acid sequence of a polypeptide
- The sites of translation are ribosomes
- During translation, the sequence of codons along an mRNA molecule is decoded, or translated, into a sequence of amino acids making up a polypeptide chain, the codons are read by the translation machinery in the 5' --> 3" direction along the mRNA
- Each codon specifies which one of the 20 amino acids will be incorporated at the corresponding position along a polypeptide
- Because codons are nucleotide triplets, the number of nucleotides making up a genetic message must be three times the number of amino acids in the protein product
- As a molecule of mRNA is moved through a ribosome, condons are translated into amino acids, one by one
- The interpreters are tRNA molecules, each type with a specific anticodon at one end and a corresponding amino acid at the other end
- A tRNA adds its amino acid cargo to a growing polypeptide chain when the anticodon hydrogen-bonds to a complementary codon on the mRNA
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- Like mRNA and other types of cellular RNA, tRNA molecules are transcribed from DNA templates
- In a eukaryotic cell, tRNA, like mRNA, is made in the nucleus and then travels from the nucleus to the cytoplasm, where translation occurs
- A tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long (compared to hundreds of nucleotides for most mRNA molecules)
- Because of the presence of complementary stretches of nucleotide bases that can hydrogen bond to each other, this single strand can fold back upon itself and from a molecule with a three-dimensional structure
- Flattened into on plane, a tRNA molecule looks like a cloverleaf
- The tRNA actually twists and folds into a compact three-dimensional structure that is roughly L shaped
- The loop extending from one end of the L includes the anticodon
- From the other end of the L-shaped tRNA molecule protrudes its 3' end, which is the attachment site for an amino acid
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- The correct matching up of tRNA and amino acid is carried out by a family of related enzymes called aminoacyl-tRNA synthetases
- The active site of each type of aminoacyl-tRNA synthetase fits only a specific combination of amino acid and tRNA
There are 20 different synthetases, one for each amino acid; each synthetase is able to bind all the different tRNAs that code for its particular amino acid
- The synthetase catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the hydrolysis of ATP
- The resulting aminoacyl tRNA, also called a charged tRNA, is released from the enzyme and is then available to deliver its amino acid to a growing polypeptide chain on a ribosome

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- A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more ribosomal RNAs (in eukaryotes, the subunits are made in the nucleolus)
- About 1/3 of the mass of a ribosome is made up of proteins; the rest consists of rRNAs (either three molecules in Bacteria and four in eukaryotes)
- Ribosomal RNA genes are transcribed, and the RNA is processed and assembled with proteins imported from the cytoplasm and the resulting ribosomal subunits are then exported via nuclear pores to the cytoplasm
- In both bacteria and eukaryotes, large and small subunits join to form a functional ribosome only when they attach to an mRNA molecule
- About 1/3 of the mass of a ribosome is made up of proteins; the rest consists of rRNAs (either three molecules in Bacteria and four in eukaryotes)
- Eukaryotic ribosomes are slightly larger and differ somewhat from bacterial ribosomes in their molecular composition
- Evidence strongly supports the hypothesis that rRNA, not protein, is primarily responsible for the both the structure and the function of the ribosome because the proteins are largely on the exterior, support the shape changes of the rRNA molecules as they carry out catalysis during translation
- rRNA is the main constituent of the interface between the two subunits and of the A and P sites, and it is the catalyst of peptide bond formation
- A ribosome can be regarded as one colossal ribozyme
- In addition to a mRNA binding site, each ribosome has three binding sites for tRNA:
1) P site (peptidyl-tRNA) holds the tRNA carrying the growing polypeptide chain
2) A site (aminoacyl-tRNA) holds the tRNA carrying the next amino acid to be added to the chain
3) E site (exit) is where discharged tRNAs leave the ribosome
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- The ribosome adds amino acid brought to it by tRNA to the growing end of a polypeptide chain
- Ribosomes facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis
- The ribosome holds the tRNA and mRNA in close proximity and positions the new amino acid for addition to the carboxyl end of the growing polypeptide
- It then catalyzes the formation of the peptide bond
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- Once a ribosome is far enough past the start codon, a second ribosome can attach to the mRNA, ecentually resulting in a number of ribosomes trailing along the mRNA
- Strings of ribosomes
- Found in both bacterial and eukaryotic cells
- Enable a cell to make many copies of a polypeptide very quickly
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- Brings together mRNA, a tRNA bearing the first amino acid of the polypeptide, and the two subunits of a ribosome
- First, a small ribosomal subunit binds to both mRNA, and a specific initiator tRNA, which carries the amino acid methionine
- In bacteria, the small subunit can behind these two in either order; it binds the mRNA at a specific RNA sequence, just upstream of the star codon, AUG
- In eukaryotes, the small subunit, with the initiator tRNA already bound, binds to the 5'cap of the mRNA and then moves, or scans, downstream along the mRNA until it reaches the start codon; the initiator tRNA then hydrogen bonds to the AUG start codon
- The union of mRNA, initiator tRNA, and a small ribosomal subunit is followed by the attachment of a large ribosomal subunit, completing the translation initiation complex
- Proteins called initiation factors are required to bring these components together
- The cell also expends energy obtained by hydrolysis of a GTP molecule to form the initiation complex
- At the completion of the initiation process, the initiator tRNA sits in the P site of the ribosome, and the vacant A site is ready for the next aminoacyl-tRNA
- Note that a polypeptide is always synthesized in one direction, from the initial methionine at the amino end, also called the N-terminus, toward the final amino acid at the carboxyl end, also called the C-terminus
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- In the elongation stage of translation, amino acids are added one by one to the previous amino acid at the C-terminus of the growing chain
- Each addition involves the participation of several proteins called elongation factors and occurs in a three-step cycle
- Energy expenditure occurs in the first and third steps
- Codon recognition requires hydrolysis of one molecule of GTP which increases the accuracy and efficiency of this step
- One more GTP is hydrolyzed to provide energy for the translocation step (third step)
- The mRNA is moved through the ribosome in one direction only, 5' end first; this is equivalent to the ribosome moving 5' --> 3' on the mRNA
- The elongation cycle takes less than a tenth of a second in bacteria and is repeated as each amino acid is added to the chain until the polypetide is completed
- Elongation continues until a stop codon in the mRNA reaches the A site of the ribosome
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- The nucleotide base triplets UAG, UAA, UGA do not code for amino acids but instead act as signals to stop translation
- A release factor (a protein shaped like an aminoacyl tRNA) binds directly to the stop codon in the A site which causes the addition of a water molecule instead of an amino acid to the polypeptide chain
- The bond between the completed polypeptide and the tRNA in the P site is hydrolyzed, releasing the polypeptide through the exit tunnel of the ribosome's large subunit
- Breakdown of the translation assembly requires the hydrolysis of two more GTP molecules
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1) Polypeptide synthesis begins on a free ribosome in the cytosol
2) An SRP binds to the signal peptide, halting synthesis momentarily
3) The SRP binds to a receptor protein in the ER membrane. This receptor is part of a protein complex (a translocation complex) that has a membrane pore and signal-cleaving enzyme
4) The SRP leaves, and polypeptide synthesis resumes, with simultaneous translocation across the membrane (the signal peptide stays attached to the translocation complex)
5) The signal cleaving enzyme cuts off the signal peptide
6) The rest of the completed polypeptide leaves the ribosome and folds into its final conformation
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- Sickle-cell disease
- Familial cardiomyopathy
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- Substitutions that change one amino acid to another one are called missense mutations
- Such a mutation may have little effect on the protein (the new amino acid may have properties similar to those of the amino acid it replaces, or it may be in a region of the protein where the exact sequence of amino acids is not essential to the protein's function
- Substitution mutations are usually missense mutations; that is, the altered codon still codes for an amino acid and thus makes sense, although not necessarily the right sense
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- A point mutation can also change a codon for an amino acid into a stop codon
- A nonsense mutation causes translation to be terminated prematurely; the resulting polypeptide will be shorter than the polypeptide encoded by the normal gene
- Nearly all nonsense mutations lead to nonfunctional proteins
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- A frameshift mutation, will occur whenever the number of nucleotides inserted or deleted is not a multiple of three
- All the nucleotides that are downstreeam of the deletion or insertion will be improperly grouped into codos, and the result will be extensive missense, usually ending sooner or late in nonsense and premature termination
- Unless the frameshift is very near the end of the gene, the protein is almost certain to be nonfunctional
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