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Gene expression (central dogma) DNA is the genetic material of all organisms on Earth. When DNA is transmitted from parents to children, it can determine some of the children's characteristics (such as their eye colour or hair colour). But how does the sequence of a DNA molecule actually affect a human or other organism's features? For example, how did the sequence of nucleotides (As, Ts, Cs, and Gs) in the DNA determine the human features? Genes specify functional products (such as proteins) A DNA molecule consists of functional units called genes. Each gene provides instructions for a functional product (a molecule needed to perform a job in the cell). In many cases, the functional product of a gene is a protein. The functional products of most known genes are proteins, or, more accurately, polypeptides. Polypeptide: is just another word for a chain of amino acids. Although many proteins consist of a single polypeptide, some are made up of multiple polypeptides. Genes that specify polypeptides are called protein-coding genes. Not all genes specify polypeptides. Instead, some provide instructions to build functional RNA molecules, such as the transfer RNAs and ribosomal RNAs that play roles in translation. How does the DNA sequence of a gene specify a particular protein? Many genes provide instructions for building polypeptides. How, exactly, does DNA direct the construction of a polypeptide? This process involves two major steps: transcription and translation. In transcription: the DNA sequence of a gene is copied to make an RNA molecule. This step is called transcription because it involves rewriting, or transcribing, the DNA sequence in a similar RNA "alphabet." In eukaryotes, the RNA molecule must undergo processing to become a mature messenger RNA (mRNA). In translation: the sequence of the mRNA is decoded to specify the amino acid sequence of a polypeptide. The name translation reflects that the nucleotide sequence of the mRNA sequence must be translated into the completely different "language" of amino acids. Thus, during expression of a protein-coding gene, information flows from DNA→RNA →protein. This directional flow of information is known as the central dogma of molecular biology. Non-protein-coding genes (genes that specify functional RNAs) are still transcribed to produce an RNA, but this RNA is not translated into a polypeptide. For either type of gene, the process of going from DNA to a functional product is known as gene expression. Transcription In transcription, one strand of the DNA that makes up a gene, called the non-coding strand, acts as a template for the synthesis of a matching (complementary) RNA strand by an enzyme called RNA polymerase. This RNA strand is the primary transcript. The primary transcript carries the same sequence information as the non-transcribed strand of DNA, sometimes called the coding strand. However, the primary transcript and the coding strand of DNA are not identical, due to biochemical differences between DNA and RNA. One important difference is that RNA molecules do not include the base thymine (T). Instead, they have the similar base uracil (U). Like thymine, uracil pairs with adenine. Transcription and RNA processing: Eukaryotes vs. bacteria: In bacteria, the primary RNA transcript can directly serve as a messenger RNA, or mRNA. Messenger RNAs get their name because they act as messengers between DNA and ribosomes. Ribosomes are RNA-and-protein structures in the cytosol where proteins are actually made. In eukaryotes (such as humans), a primary transcript has to go through some extra processing steps in order to become a mature mRNA. During processing, caps are added to the ends of the RNA, and some pieces of it may be carefully removed in a process called splicing. These steps do not happen in bacteria. The location of transcription is also different between prokaryotes and eukaryotes. Eukaryotic transcription takes place in the nucleus, where the DNA is stored, while protein synthesis takes place in the cytosol. Because of this, a eukaryotic mRNA must be exported from the nucleus before it can be translated into a polypeptide. Prokaryotic cells, on the other hand, don't have a nucleus, so they carry out both transcription and translation in the cytosol. Translation: After transcription (and, in eukaryotes, after processing), an mRNA molecule is ready to direct protein synthesis. The process of using information in an mRNA to build a polypeptide is called translation. The genetic code: During translation, the nucleotide sequence of an mRNA is translated into the amino acid sequence of a polypeptide. Specifically, the nucleotides of the mRNA are read in triplets (groups of three) called codons. There are 616161codons that specify amino acids. One codon is a "start" codon that indicates where to start translation. The start codon specifies the amino acid methionine, so most polypeptides begin with this amino acid. Three other “stop” codons signal the end of a polypeptide. These relationships between codons and amino acids are called the genetic code. Steps of translation: Translation takes place inside of structures known as ribosomes. Ribosomes are molecular machines whose job is to build polypeptides. Once a ribosome latches on to an mRNA and finds the "start" codon (AUG), it will travel rapidly down the mRNA, one codon at a time. As it goes, it will gradually build a chain of amino acids that exactly mirrors the sequence of codons in the mRNA. How does the ribosome "know" which amino acid to add for each codon? As it turns out, this matching is not done by the ribosome itself. Instead, it depends on a group of specialized RNA molecules called transfer RNAS (tRNAs). Each tRNA has a three nucleotides sticking out at one end, which can recognize (base-pair with) just one or a few particular codons. At the other end, the tRNA carries an amino acid – specifically, the amino acid that matches those codons. There are many tRNAs floating around in a cell, but only a tRNA that matches (base-pairs with) the codon that's currently being read can bind and deliver its amino acid cargo. Once a tRNA is snugly bound to its matching codon in the ribosome, its amino acid will be added the end of the polypeptide chain. This process repeats many times, with the ribosome moving down the mRNA one codon at a time. A chain of amino acids is built up one by one, with an amino acid sequence that matches the sequence of codons found in the mRNA. Translation ends when the ribosome reaches a stop codon and releases the polypeptide. Once the polypeptide is finished, it may be processed or modified, combine with other polypeptides, or be shipped to a specific destination inside or outside the cell. Ultimately, it will perform a specific job needed by the cell or organism – perhaps as a signalling molecule, structural element, or enzyme. Codons: Cells decode mRNAs by reading their nucleotides in groups of three, called codons. Here are some features of codons: Most codons specify an amino acid Three "stop" codons mark the end of a protein One "start" codon, AUG, marks the beginning of a protein and also encodes the amino acid methionine Codons in an mRNA are read during translation, beginning with a start codon and continuing until a stop codon is reached. mRNA codons are read from 5' to 3' , and they specify the order of amino acids in a protein from N-terminus (methionine) to C-terminus. The genetic code table: The full set of relationships between codons and amino acids (or stop signals) is called the genetic code. The genetic code is often summarized in a table. Notice that many amino acids are represented in the table by more than one codon. For instance, there are six different ways to "write" leucine in the language of mRNA (see if you can find all six). An important point about the genetic code is that it's universal. That is, with minor exceptions, virtually all species (from bacteria to you!) use the genetic code shown above for protein synthesis. Reading frame: To reliably get from an mRNA to a protein, we need one more concept: that of reading frame. Reading frame determines how the mRNA sequence is divided up into codons during translation. That's a pretty abstract concept, so let's look at an example to understand it better. The mRNA below can encode three totally different proteins, depending on the frame in which it's read: So, how does a cell know which of these protein to make? The start codon is the key signal. Because translation begins at the start codon and continues in successive groups of three, the position of the start codon ensures that the mRNA is read in the correct frame (in the example above, in Frame 3). Mutations (changes in DNA) that insert or delete one or two nucleotides can change the reading frame, causing an incorrect protein to be produced "downstream" of the mutation site: Summary: DNA is divided up into functional units called genes, which may specify polypeptides (proteins and protein subunits) or functional RNAs (such as tRNAs and rRNAs). Information from a gene is used to build a functional product in a process called gene expression. A gene that encodes a polypeptide is expressed in two steps. In this process, information flows from DNA→RNA→ protein, a directional relationship known as the central dogma of molecular biology. Transcription: One strand of the gene's DNA is copied into RNA. In eukaryotes, the RNA transcript must undergo additional processing steps in order to become a mature messenger RNA (mRNA). Translation: The nucleotide sequence of the mRNA is decoded to specify the amino acid sequence of a polypeptide. This process occurs inside a ribosome and requires adapter molecules called tRNAs. During translation, the nucleotides of the mRNA are read in groups of three called codons. Each codon specifies a particular amino acid or a stop signal. This set of relationships is known as the genetic code.