Protein Synthesis PDF

READ & STUDY – S7 7.1.2. – Protein Synthesis Transcription Transcription involves making an RNA copy of a bit of DNA code. The initial steps in transcription are similar to the initial steps in DNA replication. The obvious difference is that, whereas in replication we end up with a complete copy of...

READ & STUDY – S7 7.1.2. – Protein Synthesis Transcription Transcription involves making an RNA copy of a bit of DNA code. The initial steps in transcription are similar to the initial steps in DNA replication. The obvious difference is that, whereas in replication we end up with a complete copy of the cell’s DNA, in transcription we end up with only a tiny specific section copied into an mRNA. This is because only the bit of DNA that needs to be expressed will be transcribed. If you wanted to make a cake, but your cookbook couldn’t leave your vault (a.k.a. the nucleus), you wouldn’t copy the entire cookbook! You would copy only the recipe for the cake. Since each recipe is a gene, transcription occurs as-needed on a gene-by-gene basis. The exception to this is prokaryotes because they will transcribe a recipe that can be used to make several proteins. This is called a polycistronic transcript. Eukaryotes tend to have one gene that gets transcribed to one mRNA and translated into one protein. Our transcripts are monocistronic. Transcription involves three phases: initiation, elongation, and termination. As in DNA replication, the first initiation step in transcription is to unwind and unzip the DNA strands using helicase. Transcription begins at special sequences of the DNA strand called promoters. You can think of a promoter as a docking site or a runway. We will talk about how promoters are involved in regulating transcription later in the chapter. Because RNA is single-stranded, we have to copy only one of the two DNA strands. The strand that serves as the template is known as the antisense strand, the non-coding strand, transcribed-strand, or the template strand. The other strand that lies dormant is the sense strand, or the coding strand. Just as DNA polymerase builds DNA, RNA polymerase builds RNA, and just like DNA polymerase, RNA polymerase adds nucleotides only to the 3’ side, therefore building a new molecule from 5’ to 3’. This means that RNA polymerase must bind to the 3’ end of the template strand first (which would be the 5’ end of future mRNA). RNA polymerase doesn’t need a primer, so it can just start transcribing the DNA right off the bat. The promoter region is considered to be “upstream” of the actual coding part of the gene. This way the polymerase can get set up before the bases it needs to transcribe, like a staging area before an official parade starting point. The official starting point is called the start site. When transcription begins, RNA polymerase travels along and builds an RNA that is complementary to the template strand of DNA. It is just like DNA replication except when DNA has an adenine, the RNA can’t add a thymine since RNA doesn’t have thymine. Instead, the enzyme adds a uracil. Once RNA polymerase finishes adding on nucleotides and reaches the termination sequence, it separates from the DNA template, completing the process of transcription. The new RNA is now a transcript or a copy of the sequence of nucleotides based on the DNA strand. Note that the freshly synthesized RNA is complementary to the template strand, but it is identical to the coding strand (with the substitution of uracil for thymine). RNA Processing In prokaryotes, the mRNA is now complete, but in eukaryotes the RNA must be processed before it can leave the nucleus. In eukaryotes, the freshly transcribed RNA is called a pre-mRNA or RNA transcript, and it contains both coding regions and noncoding regions. The regions that express the code that will be turned into protein are exons. The noncoding regions in the mRNA are introns. The introns—the intervening sequences—must be removed before the mRNA leaves the nucleus. This process, called splicing, is accomplished by an RNA-protein complex called a spliceosome. This process produces a final mRNA that is shorter than the transcribed RNA. The way that a transcript is spliced can vary, and alternative splicing variants will result with different exons included. In addition to splicing, a poly(A) tail is added to the 3’ end and a 5’ GTP cap is added to the 5’ end. Translation Translation is the process of turning an mRNA into a protein. Remember, each protein is made of amino acids. The order of the mRNA nucleotides will be read in the ribosome in groups of three. Three nucleotides is called a codon. Each codon corresponds to a particular amino acid. The genetic code is redundant, meaning that certain amino acids are specified by more than one codon. The mRNA attaches to the ribosome to initiate translation and “waits” for the appropriate amino acids to come to the ribosome. That’s where tRNA comes in. A tRNA molecule has a unique three- dimensional structure that resembles a four-leaf clover: One end of the tRNA carries an amino acid. The other end, called an anticodon, has three nitrogenous bases that can complementarily base pair with the codon in the mRNA. Usually, the normal rules of base pairing are set in stone, but tRNA anticodons can be a bit flexible when they bind with a codon on an mRNA, especially the third nucleotide in an anticodon. The third position is said to experience wobble pairing. Things that don’t normally bind will pair up, like guanine and uracil. Transfer RNAs are the “go-betweens” in protein synthesis. Each tRNA becomes charged and enzymatically attaches to an amino acid in the cell’s cytoplasm and “shuttles” it to the ribosome. The charging enzymes involved in forming the bond between each amino acid and tRNA require ATP. Translation also involves three phases: initiation, elongation, and termination. Initiation begins when a ribosome attaches to the mRNA. What does the ribosome do? It helps the process along by holding everything in place while the tRNAs assist in assembling polypeptides. Initiation Ribosomes contain three binding sites: an A site, a P site, and an E site. The mRNA will shuffle through from A to P to E. As the mRNA codons are read, the polypeptide will be built. In all organisms, the start codon for the initiation of protein synthesis is A–U–G, which codes for the amino acid methionine. Proteins can have AUGs in the rest of the protein that code for methionine as well, but the special first AUG of an mRNA is the one that will kick off translation. The tRNA with the complementary anticodon, U–A–C, is methionine’s personal shuttle; when the AUG is read on the mRNA, methionine is delivered to the ribosome. Elongation Addition of amino acids is called elongation. Remember that the mRNA contains many codons, or “triplets,” of nucleotide bases. As each amino acid is brought to the mRNA, it is linked to its neighboring amino acid by a peptide bond. When many amino acids link up, a polypeptide is formed. Termination How does this process know when to stop? The synthesis of a polypeptide is ended by stop codons. A codon doesn’t always code for an amino acid; there are three that serve as a stop codon. Termination occurs when the ribosome runs into one of these three stop codons. How about a little review? In transcription, mRNA is created from a particular gene segment of DNA. In eukaryotes, the mRNA is “processed” by having its introns, or noncoding sequences, removed. A 5’ cap and a 3’ tail are also added. Now, ready to be translated, mRNA proceeds to the ribosome. Free-floating amino acids are picked up by tRNA and shuttled over to the ribosome, where mRNA awaits. In translation, the anticodon of a tRNA molecule carrying the appropriate amino acid base pairs with the codon on the mRNA. As new tRNA molecules match up to new codons, the ribosome holds them in place, allowing peptide bonds to form between the amino acids. The newly formed polypeptide grows until a stop codon is reached. The polypeptide or protein folds up and is released into the cell. At the Same Time! In prokaryotes, transcription and translation can be occurring at the same time. This is because prokaryotes lack a nucleus and their transcription and translation are both occurring in the same place, the cytoplasm.