translation Flashcards
How is the information in a linear sequence of nucleotides in an RNA molecule translated into the linear sequence of a chemically quite different set of subunits—the amino acids in a protein?
The set of rules by which the nucleotide sequence of a gene, through an intermediary mRNA molecule, is translated into the amino acid sequence of a protein is known as the genetic code.
The sequence of nucleotides in an mRNA molecule is read consecutively in groups of three. And because RNA is made of 4 different nucleotides, there are 4 × 4 × 4 = 64 possible combinations of three nucleotides: AAA, AUA, AUG, and so on. However, only
20 different amino acids are commonly found in proteins. Either some nucleotide triplets are never used, or the code is redundant, with some amino acids being specified by more than one triplet. Each group of three consecutive nucleotides in RNA is called a codon, and each codon specifies one amino acid.
Mitochondria have their own DNA replication, transcription, and protein-synthesis
machinery, which operates independently of the corresponding machinery
in the rest of the cell, and they have been
able to accommodate minor changes to the otherwise universal genetic
code. Only one of the three possible reading frames in an mRNA specifies the correct protein.
Explain how tRNA molecules match amino acids to codons in mRNA
the translation of mRNA into protein depends on adaptor molecules that bind to a codon with one part of the adaptor and to an amino acid with another. Adaptors consist of a set of small RNA molecules known as transfer RNAs (tRNAs), each about 80 nucleotides in length. The base-paired regions are sufficiently extensive, they will fold back on themselves to form a double-helical structure, like that of double-stranded DNA. Such is the case for the tRNA molecule. Four short segments of the folded tRNA are double-helical, producing a distinctive structure that looks like a cloverleaf when drawn schematically. The anticodon, a set of three consecutive nucleotides that bind, through base-pairing, to the complementary codon
in an mRNA molecule.
We saw in the previous section that the genetic code is redundant; that is, several different codons can specify a single amino acid. This redundancy implies either that there is more than one tRNA for many of the amino acids or that some tRNA molecules can base-pair with more than one codon. In fact, both situations occur. Some amino
acids have more than one tRNA, and some tRNAs require accurate basepairing
only at the first two positions of the codon and can tolerate a mismatch (or wobble) at the third position. This wobble base-pairing explains why so many of the alternative codons for an amino acid differ only in their third nucleotide. Wobble base-pairings make it possible to fit the 20 amino acids to their 61 codons with as few
as 31 kinds of tRNA molecules. The exact number of different kinds of tRNAs, however, differs from one species to the next. For example, humans have approximately 500 different tRNA genes, but this collection includes only 48 different anticodons.
Explain why life requires Autocatalysis
The origin of life requires molecules that posses, if only to a small extent, one crucial property: the ability to catalyze reactions that lead - directly or indirectly - to the production of more molecules like themselves.
Make a timeline over the RNA world
Explain why RNA can store information and catalyze chemical reactions
Complementary base-pairing enables one nucleic acid to act as a template for the formation of another. A single stand of RNA or DNA contains the information needed to specify the sequence of a complementary polynucleotide, which can specify the sequence of the original molecule, allowing the original nuceleic acid to be replicated.
Synthesis of polynucleotides by complementary templating mechanisms require catalysts to promote polymerization reaction: without catalysts, polymer formation is slow. Nucleotide polymerization is catalyzed by protein enzymes - such as DNA and RNA polymerases.
RNA molecules can themselves act as catalysts. RNA is synthesized as a single-stranded molecule, and complementary base-pairing can occur between nucleotides in the same chain. This base-pairing, along with nonconventional hydrogen bonds, can cause each RNA molecule to fold up in a unique way that is determined by its nucleotide sequence. Such associtations produce complex three-dimensional shapes.
Protein enzymes are able to catalyze biochemical reactions because they have surfaces with unique contours and chemical properties. In the same way, RNA molecules, with their unique folded shapes, can serve as catalysts. Catalytic RNAs do not have the same structural and functional diversity as protein enzymes do (RNA are only built of four different subunits). Nonetheless, ribozymes can catalyze many types of chemical reactions. Although relatively few catalytic RNAs operate in present-day cells, they play major roles in some of the most fundamental steps where RNA molecules themselves are spliced or translated into protein.
RNA has all the properties required of an information-containing molecule that could also catalyze its own synthesis.
Show how an RNA molecule can in principle guide the formation of an exact copy of itself
Table over biochemical reactions that can be catalyzed by ribozymes
Show how A ribozyme is an RNA molecule that possesses catalytic activity.
Could an RNA molecule catalyze its own synthesis?
Explain how RNA is thought to predate DNA in evolution
Ribose, like glucose and other simple carbohydrates, is readily formed from formldehyde (HCHO). The sugar deoxyribose is harder to make, and in present-day clls it is produced from ribose in a reaction catalyzed y a protein enzyme, suggesting that ribose predates deoxyribose in cells. the deoxyribose in its sugar-phosphate backbone makes chains of DNA chemically much more stable than chains of RNA, so that DNA can grow to greater lengths without breakage.
The other differences between RNA and DNA - the double-helical structure of DNA and the use of thymine rather than uracil - further enhance DNA stability by making the molcule easier to repair. A damaged nucleotide on one strand of the double helix can be repaired by using the other strand as a template.
Deamination in polynucleotides, is easier to detect and repair in DNA than in RNA. This is because the product of the deamination of cytosine is, by chance, uracil, which already exists in RNA, so that such damage would be impossible for repair enzyes to detect in an RNA molecule.
Show how A single prokaryotic mRNA molecule can encode several different proteins.
Show how Antibiotics that inhibit bacterial protein or RNA synthesis
Show how Producing mRNA molecules is more complex in eukaryotes than it is in prokaryotes.
(A) In eukaryotic cells,
the pre-mRNA molecule produced by
transcription contains both intron and
exon sequences. Its two ends are modified
by capping and polyadenylation, and the
introns are removed by RNA splicing. The
completed mRNA is then transported
from the nucleus to the cytosol, where
it is translated into protein. Although
these steps are depicted as occurring
one after the other, in reality they occur
simultaneously. For example, the RNA cap
is usually added and splicing usually begins
before transcription has been completed.
Because of this overlap, transcripts of
the entire gene (including all introns
and exons) do not typically exist in the
cell. Ultimately, mRNAs are degraded by
RNAses in the cytosol and their nucleotide
building blocks are reused for transcription.
(B) In prokaryotes, the production of
mRNA molecules is simpler. The 5ʹ end
of an mRNA molecule is produced by
the initiation of transcription by RNA
polymerase, and the 3ʹ end is produced
by the termination of transcription.
Because prokaryotic cells lack a nucleus,
transcription and translation—as well as
degradation—take place in a common
compartment. Translation of a prokaryotic
mRNA can therefore begin before its
synthesis has been completed. In both
eukaryotes and prokaryotes, the amount of
a protein in a cell depends on the rates of
each of these steps, as well as on the rates
of degradation of the mRNA and protein
molecules.
Show how Each ribosome has a binding site for an mRNA molecule and three binding sites for tRNAs
Show how In principle, an mRNA molecule can be translated in three possible reading frames
Show how Initiation of protein synthesis in eukaryotes requires translation initiation factors and a sepcial initiator tRNA
Show how Many proteins require posttranslational modifications to become fully functiona
Show how Produing mRNA molecules is more complex in eukaryotes than it is in prokaryotes
Show how Protein production in a eukaryotic cell requires many steps
Show how Proteins are degraded by the proteasome
Show how Proteins are synthesized on polyribosomes
Show how Proteins marked by a polyubiquitin chain are degraded by the proteasome
Show how the eukaryotic ribosome is a large complex of four rRNAs and more than 80 small proteins
Show how The genetic code is translated by aminoacyl-tRNA synthetases and tRNAs
show how the nucleotide of an mRNA is translated into the amino acid sequence of a protein via the genetic code
Show how Translation halts at a stop codon
Show how Translation takes place in a four-step cycle, which is repeated over and over during the synthesis of a protein
Show how tRNA molecules are molecular adaptors, linking amino acids to codons
