Proteins are Polymers of Amino Acids - Lecture notes

PROTEIN SYNTHESIS Proteins are polymers of amino acids. Proteins are made through two stages, which are translation and transcription. Protein synthesis takes place within the nucleus and ribosomes of a cell and is regulated by DNA and RNA. Protein synthesis steps are twofold. Firstly, the code for a protein (a chain of amino acids in a specific order) must be copied from the genetic information contained within a cell’s DNA. This initial protein synthesis step is known as transcription. Transcription produces an exact copy of a section of DNA. This copy is known as messenger RNA (mRNA) which must then be transported outside of the cell nucleus before the next step of protein synthesis can begin. The second protein synthesis step is translation. Translation occurs within a cell organelle called a ribosome. Messenger RNA makes its way to and connects with the ribosome under the influence of ribosomal RNA and enzymes. Transfer RNA (tRNA) is a molecule that carries a single amino acid and a coded sequence that acts like a key. This key fits into a specific sequence of three codes on the mRNA, bringing the correct amino acid into place. Each set of three mRNA nitrogenous bases is called a codon. Understanding protein synthesis is easy when we imagine our DNA as a recipe book. This book lists the instructions that show a cell how to make every tiny part of every system, organ, and tissue within our bodies. All of these individual parts are polypeptides. From the keratin in your hair and fingernails to the hormones that run through your bloodstream, polypeptides and proteins are the foundation stones of every structure. Our DNA does not code for lipids or carbohydrates – it only codes for polypeptides. The enzyme RNA polymerase opens the DNA recipe book that sits inside the cell nucleus. It uses certain pieces of code as bookmarks to find the right page. This recipe book is written in a foreign language – mRNA copies what is written without understanding it. The recipes are translated into a language that other molecules can decipher at a later stage. The TRANSLATORS are ribosomes and tRNA They read the recipe and can collect the right ingredients and, in the correct order, make the finished polypeptide product. DNA Sequences In the nucleus, two strands of DNA are held together by nitrogenous bases (also called nucleobases or bases). Four bases – cytosine, guanine, adenine, and thymine – form the letters of the words in the DNA recipe book. One strand of DNA holds the original code. If the instructions of this code are carefully followed, a specific correct polypeptide can be assembled outside the nucleus. The second DNA strand – the template strand – is a mirror image of the original strand. It must be a mirror image as nucleobases can only attach to complementary partners. For example, cytosine only ever pairs with guanine and thymine only pairs with adenine. You will probably have seen codes such as CTA, ATA, TAA, and CCC in various biology textbooks. If these are the codons (sets of three bases) of the original strand of DNA, the template strand will attach to these using their partners. So, using the given examples, template DNA will attach to the original DNA strand using GAT, TAT, ATT, and GGG. Messenger RNA then copies the template strand. This means it ends up creating an exact copy of the original strand. The only difference is that mRNA replaces thymine with a base called uracil. The mRNA copy of the template strand using the given examples would read CUA, AUA, UAA, and CCC. These codes can be read by transfer RNA outside the nucleus; the recipe can be understood by a molecule that does not fully understand the language used in the original (it does not understand thymine, only uracil). Transfer RNA helps to bring the right parts to the assembly line of the ribosome. There, a protein chain is constructed that matches the instructions in the original DNA strand. Protein Synthesis Contributors To make the copied stretch of code (transcription) we need enzymes called RNA polymerases. These enzymes gather free-floating messenger RNA (mRNA) molecules inside the nucleus and assemble them to form the letters of the code. Each letter of DNA code has its own key and each new letter formed by mRNA carries a lock that suits this key, a little like tRNA. Notice that we are talking about letters. This is important. Inside the nucleus, the DNA code is not understood, simply copied down – transcribed. Understanding the code by spelling out the words formed by these letters – translating – happens at a later stage. RNA polymerase must find and bring over the appropriate mRNA molecule for each nitrogenous base on the template strand. Selected mRNA molecules link together to form a chain of letters. Eventually, these letters will spell out the equivalent of a phrase. Each phrase represents a specific (polypeptide) product. If the recipe is not exactly followed, the final product might be completely different or not work as well as it should. Messenger RNA has now become the code. It travels to the next group of important contributors that work as manufacturing plants. Ribosomes are found outside the cell nucleus, either in the cell cytoplasm or attached to the rough endoplasmic reticulum; it is ribosomes that make the endoplasmic reticulum ‘rough’. A ribosome is split into two parts and the strand of mRNA runs through it like ribbon through an old-fashioned typewriter. The ribosome recognizes and connects to a special code at the start of the translated phrase – the start codon (AUG). Transfer RNA molecules enter the ribosome, bringing with them individual ingredients. As with all of these processes, enzymes are required to make the connections. If each mRNA codon has a lock, tRNA possesses the keys. The tRNA key for an mRNA codon is called an anticodon. When a tRNA molecule holds the key that matches a three-nucleobase code it can open the door, drop off its load (an amino acid), and leave the ribosome factory to collect another amino acid load. This will always be the same type of amino acid as the anticodon. Messenger RNA shifts along the ribosome as if on a conveyor belt. At the next codon another tRNA molecule (with the right key) brings the next amino acid. This amino acid bonds to the previous one. A chain of bonded amino acids begins to form– a polypeptide chain. When completed, this polypeptide chain is an accurate final product manufactured according to the instructions in the DNA recipe book. Not a pie or a cake but a polypeptide chain. The end of the mRNA code translation process is signalled by a stop codon. Start and stop codons do not code for amino acids but tell the tRNA and ribosome where a polypeptide chain should begin and end. The finished product – the newly synthesized polypeptide – is released into the cytoplasm. From there it can travel to wherever it is needed. Site of Protein Synthesis The site of protein synthesis is twofold. Transcription (copying the code) occurs within the cell nucleus where DNA is located. Once the mRNA copy of a small section of DNA has been made it travels through the nuclear pores and into the cell cytoplasm. In the cytoplasm, the strand of mRNA will move towards a free ribosome or one attached to the rough endoplasmic reticulum. Then the next step of protein synthesis – translation – can begin.