Central dogma and production of proteins

Introduction:

The  topic is central dogma. So what we're gonna do here is take all the information we have from topic be anything from chemical reactions from bonding into building with macromolecules including things like dehydration synthesis and hydrolysis to build our final macromolecule DNA and RNA and protein to produce life. Reminding everybody that protein since this is what we start our macromolecules that are built from monomers the polymers using dehydration synthesis and that each individual protein has an individual function or multiple functions that they're all based specifically on their three-dimensional structure. No structure means no function. But this particular topic is going to deal with how we produce them, what are the instructions to make them ,how are they made and what exactly is more than in detail of their composition based on three concepts or three components DNA, RNA and protein. And the three processes involved in this which are going to be

1. Replication
2. Transcription and
3. Translation

 In the idea that this all revolves around a cycle in which DNA acts like the blueprint or the carrier of genetic information which then needs to be decoded by a process called transcription into RNA which is the decoded message that can be understood by ribosomes to produce protein. So that idea puts together the entire concept of central dogma. As the source and order of all genetic information turning it into something functional here. In this  page we will understand what that central dogma is, starting with DNA which is usually found in a eukaryotic cell inside the nucleus versus at prokaryotic cell in the nuclear region and DNA undergoes the first process called replication to make more of itself and more cells and then it needs to be decoded by a process called transcription into RNA that is the version that most living things can use to understand and produce protein and then that further is decoded by process called translation into the functional units of life called protein. Reminding everybody that this is a cycle because it is those proteins to perform all those processes mentioned. Repliclication is performed by protein called RNApolymerase. Transcription by RNApolymerase and translation itself is performed by a combination of protein and RNA called ribosomes.

How proteins are made?

Central dogma and production of proteins

 In this first section we're going to look at how protein is made in detail. Obviously there's plenty of examples of proteins what do they do most of us have heard variations behind them. The idea however is they said you have specific shapes and depending on what the shape is they perform different functions. In this topic we learn how proteins are built from monomers to the polymers utilizing amino acids both having a carboxylic acid on one side and amino terminus on the other side. And usually having this R group or variable group that made twenty available amino acids slightly different from one another. So we know that based on the R group or variable group there's xx naturally occurring amino acids and several more synthetic ones. And out of those xx there are about nine that are so called essential,simply because we cannot produce them that means we usually have to obtain them from an additional source usually by consuming them. Amongst those variations that we can divide the amino acids into groups based on their properties so that means some of them can be acidic or basic some of them can be neutral or electrically charged and depending on those R groups they will interact with each other within the protein to produce different shapes. As they start interacting we get a series of levels or structures that indicate how complex the protein gets when an amino acid undergoes dehydration synthesis and combines with a second amino acid and so on and so forth what we call a primary sequence. This means literally the order in which each aminoacid is being linked to one another.

 So just as much as we can talk about several letters in an alphabet and talking about an ABC and D in that particular order a primary sequence literally means that it is a specific order of the amino acids. In that chain two fold with one another because of those groups they start achieving a three-dimensional structure. Typically the hydrogen bonds present between the amino and the carboxylic acid group produce two typical shapes, the first one is called an alpha helix and other beta pleated sheet. Both of these kind of side by side get unique looks or three-dimensional shapes and as they start combining with one another there's something called a tertiary structure in which part of their groups or the variable groups additional hydrogen bonds and other chemical interactions like ionic bonds and disulfide bridges all start building what we call a tertiary structure. This is more or less the overall three-dimensional shape of the proteins.

Structure of proteins

So it now takes a full-blown shape from it however this is not necessarily only shape it can take. Sometimes they can continue to interact with additional proteins into what we call a quaternary structure. Meaning multiple proteins interaction with one another probably a typical example that most people are familiar with is haemoglobin. In the blood that is composed out of four separate proteins assemble into a much larger structure so in the lower right-hand side we see kind of the step-by-step assembly into these larger structures going from the first sequence or the primary structure which is literally just the order into the secondary structure into alpha helixes and beta sheets which are in this case the interactions of hydrogen bonds between those same amino acids and then ultimately those secondary structures are similar to these final tertiary structures or three-dimensional shapes. Nonetheless those two-dimensional shapes can interact with additional three-dimensional shapes to form into what we call a coronary structure so if we just keep on trying to define proteins and their shapes or how we determine function as we start giving them shapes we categorize them into two typical shapes.

 Our structure is referred to as the globular ones which looks very cool or more fibrous ones which are usually thin. Now depending on which type of these did they fall into. Most of them the globular ones end up having some sort of activity that they can perform or the fibrous ones end up a more structural to build things or hold things together. However based again on their three-dimensional shape it's important to maintain it because any disruption of that coronary structure or these ones below tertiary and secondary can completely destroy their ability to function. What we learned as the initiation in the past and this can be performed by various different methods. Easiest one to use this temperature or heat or the association with certain organic solvents which easily destroy hydrogen bonds also acids and bases based on their electricity can disrupt the protein shape and similarly heavy metal ions, so in this case things like iron and copper can all disrupt these proteins simply because of their large charges. And then similar to heat, the process of agitation by moving things constantly and high velocities increases heat which in turn also the nature’s things this is nothing that is outside the ordinary performance. Initiation occurs on daily life all the time by destroying proteins that are performing a function simply by adding either heat or an acid by pretty much everyday activities.

Central Dogma:

1.Replication

Dna replication

 For the process of DNA replication to begin it is important for the two strands of the DNA to open up. This job is done by the enzyme helicase which is also known as the unzipping enzyme. The enzyme helicase performs this function by acting on the hydrogen bonds which are present between the base pairs of the opposite DNA strands. The helicase breaks these hydrogen bonds due to which the double helix opens up leading to the creation of the structure known as the replication fork. This exposes a sequence of DNA base pairs upon which many enzymes will subsequently act. Now the process of unzipping of DNA involves action of multiple helices enzymes on different segments of DNA. These segments of DNA where the enzyme helicase acts are also known as the sites of origin. Now since the helices acts on the DNA at multiple sites, multiple replication forks are created upon which the process of DNA replication will proceed. Now to prevent the two separated strands of DNA from joining together a special type of protein known as the single stranded binding protein holds the two strands of the DNA apart.

 According to the concept of directionality, let's suppose from the above picture,one is the 3 prime end of the upper strand and the other is the 5 prime end of the upper strand. And similarly we have the 3 prime end of the lower strand in the opposite direction and 5prime end in the other direction. Now the main enzyme the DNA polymerase which has the job of formation of new strands of DNA can only form a strand from the 5 prime to 3 prime direction. Now since the upper daughter strand of this DNA is running from three prime to five prime direction theDNA polymerase can easily form the replicated opposite strand from the five prime to three prime direction. And since the helices is also unzipping the DNA in the same direction, the DNA polymerase can form the new strand continuously. But when we look at the opposite strand ofDNA which is running in the opposite direction, things are very different.

 Since the DNA polymerase has to act  it has to form the new strand in the direction which is in the 5 prime to 3prime direction but since the helicases opening the DNA helix  are in the opposite direction the DNA polymerase cannot synthesize the new strand continuously. Well this problem is solved by formation of the new strand of DNA in short segments known as the Okazaki fragments. These fragments are littering by a different enzyme to produce one continuous strand. Due to this reason the opposite strand is known as the lagging strand and the replication on the lagging strand is discontinuous replication as compared to the continuous replication on the leading strand. Now we will take the leading and the lagging strand separately and understand the process of DNA replication.

Formation of RNA primer

 Further so after the formation of the replication fork, the next important step is the process of formation of RNA primer. Now what happens is that the DNA polymerase enzyme can only add new nucleotides to the three prime end of the existing nucleotide strand. Which basically means that the DNA polymerase cannot start synthesizing new DNA out of nowhere and basically requires a short segment of nucleotides. So that it can add new nucleotides as a three prime end of this sequence to form the new DNA. This problem is solved by the enzyme RNA primase the primase makes an RNA primer which is a short stretch of nucleic acids complementary to the template that provides the 3 prime end for the DNA polymerase to work on. So now we have a leading strand of DNA which is running from the 3 prime to the 5 prime direction and we already have the short primer synthesized by the enzyme primase. Now it is a turn of the enzyme DNA polymerase to do its job and a few important points that you should know about DNA polymerase are that it always requires a primer to work with, which is a short sequence of nucleotides and it cannot start synthesizing the new DNA from scratch. The DNA polymerase can only add new nucleotides at the three prime end of the DNA and can only synthesize a new DNA in one direction. And also the DNA polymerase requires energy for polymerization reactions that it gets from the nucleotides itself. Now once the primer is synthesized the DNA polymerase can perform the vital function of elongation of DNA strand by addition of new nucleotides through the three prime end of the growing chain. The DNA polymerase uses the deoxyribonucleotides which contain either of the four bases the adenine, cytosine, guanine or thymine. The DNA polymerase adds these nucleotides to one by one to the three prime end of the new DNA strand. Now since the enzyme helicase is opening the DNA helix in the same direction the DNA polymerase can synthesize a long chain of new DNA before separating and this is known as the continuous synthesis on the leading strand. The DNA polymerase also requires energy for this polymerization reaction which it basically gets from breaking the phosphate bonds present between the triphosphates of deoxyribonucleotides. These phosphate bonds are high energy bonds which when broken provide the energy for this polymerizatioreactition.

 Now we will take a look at a lagging strand which runs from the 5 prime to the 3 prime direction we can see that the main problem on this strand is that the DNA helix is being opened up in the opposite direction of the direction in which the DNA polymerase synthesizes the new DNA which is from the 5 prime to 3 prime direction. But this problem is solved by formation of new DNA in short segments known as the Okazaki fragments. What happens is that on the lagging strand the primary synthesizes a short piece of primer and then the DNA polymerase synthesizes a short segment of DNA and then separates from the growing end. After this the enzyme helicase would have opened up more of the DNA helix in this direction then again the enzyme primase synthesizes a new primer further up on the DNA which is followed by formation of another short segment ofDNA. This process is repeated multiple times thus known as the discontinuous DNA synthesis. Now after the DNA polymerase has done its job, the newly DNA looks something like it has short segments of DNA with interrupting segments consisting of RNA primer. After this another enzyme known as the Exonuclease comes into play which removes these short segments of primers which are then replaced by short new segments of DNA by another type of DNA polymerase. After this the enzyme DNA ligase seals or joins the DNA fragments to produce a continuous DNA strand even on the lagging strand.

Proofreading mechanism

 Lastly it is also important to check for errors in the newly synthesized DNA and this is done by another type of DNA polymerase which proofreads the newly synthesized DNA for any wrong bases that may have been inserted. And if it finds a wrong base or sequence, it removes the base and then replaces it with a correct one. After the process of DNA replication is completed, the two newly synthesized DNA molecules coil up again into the DNA helix model.

 2.Transcription

 Why do our cells want to go through the process of transcription?
 It is all about making a protein. Our DNA contains units called genes and these genes have in their sequences of nucleotides. The instructions for building a protein there are two major steps. For being able to use this information in the DNA to build a protein. You must first make a copy of the protein building information stored in the gene. The first step of the production of a copy of the gene is called transcription.

The copy of the DNA instructions this temporary copy of theDNA sequence is in the form of RNA (ribonucleic acid). RNA is like DNA in that it is made up of nucleotides but unlike DNA RNA is single-stranded and contains the nucleotide base uracil instead of thymine. There are many types of RNA found in cells. The specific type of RNA that is built in transcription is called messenger RNA or mRNA because it is carrying the message from the DNA to the protein building machinery in the cell. To build this mRNA transcript of a gene we need to use a few types of proteins. RNA polymerase is the enzyme responsible for unwinding the DNA and building the mRNA. And proteins called transcription factors are responsible for promoting transcription of a gene by recruiting the RNA polymerase to that gene.

Process of sequencing RNA

First we have a promoter region which is where transcription factors and RNA polymerase bind to the DNA to prepare for transcription. Then we have the transcription unit which contains the actual nucleotide sequence that codes for the protein. Finally we have a termination sequence which bind to the DNA. Once the transcription factors have bound to the Tata box, they will recruit RNA polymerase to the  promoter of the gene preparing that gene for transcription. One more thing to note about the gene is that it contains two strands of DNA running anti parallel. One strand holds the nucleotide sequence that acts as the instructions to buildnthe protein this is called the coding strand.  The other strand is called the template strand. To make a strand of mRNA that is a copy of the coding strand of the DNA, the mRNA will be built complementary to the template strand. This way the sequence of the mRNA is exactly the same sequence of the coding strand except that mRNA will have a uracil where the DNA will have a thymine. Once the RNA polymerase has bound to the promoter region of the gene, transcription can start the RNApolymerase will unwind. The DNA creating a transcription bubble the RNApolymerase will use RNA nucleotides to build a strand of mRNA complementary to the template strand. The transcription bubble notice that when DNA contains adenine the complementary RNA nucleotide is uracil and when DNA contains thymine the complementary RNA nucleotide is adenine. As the RNA polymerase moves along the gene the transcription bubble will remain the same size. Meaning that theDNA that has already been built on -will need to wind back together. For this to happen the newly built mRNA will begin to detach from the DNA toward the back of the transcription bubble as the RNA polymerase moves down the gene. An mRNA tail will start to trail the bubble getting longer and longer. As transcription continues when the RNApolymerase reaches the end of the transcription unit it will run into the terminator sequence of the gene. This sequence of DNA causes the RNApolymerase and the mRNA to detach from the DNA and the remaining transcription bubble winds back together. Notice that the original DNA strand is left completely unaltered from its original state. At this point the RNApolymerase has created an mRNA version of the coding strand of the gene and this mRNA can now leave the nucleus and enter the cytoplasm of the cell where it will go through the process of translation to build a protein.

3.Translation

The process of translation is the final step in gene expression. Gene expression is the process by which information stored in your DNA in the form of genes is used in the synthesis of functional gene products. These gene products are mainly proteins which have numerous functions in our cells like repair and maintenance of cell's energy synthesis and enzymatic actions on biochemical reactions. Gene expression essentially occurs in two steps. 

It begins in the nucleus with the process of transcription in which the information on the DNA is copied into a RNA. This RNA is known as the messenger RNA or the mRNA. Since the main job of this RNA is to carry this information or message outside the nucleus and use it to perform the second step of gene expression known as translation. In translation the message stored on the mRNA is decoded in a ribosome to produce specific amino acid chain or polypeptide.

 Let's first have a brief look onto what are the structures in the cell that make the process of translation possible. Besides the messenger RNA translation also requires another type of RNA known as the transfer RNA or the tRNA. Ribosomes are dedicated cellular machineries that make this whole process possible. The ribosomes that read the message on the mRNA and the tRNA transfers individual amino acids to the ribosome. According to the sequence of base pairs on the mRNA these amino acids are then joined together by bonds to form a protein. So the process of translation occurs in three basic steps. 

3.1 Initiation

First step is known as initiation, in which the ribosome assembles around the target mRNA. In the second step known as elongation the tRNA transfers amino acids to the ribosome which are joined together to form a polypeptide chain. In the last step known as termination the ribosomes release the polypeptide when it reads a stop signal on the mRNA. The cell it's slightly different for eukaryotes and prokaryotes. In prokaryotes the translation takes place in the cytoplasm. In eukaryotes the translation occurs in the cytoplasm or across the membrane of the endoplasmic reticulum. What happens is that when the ribosomes bind to the mRNA this whole complex then attaches to the endoplasmic reticulum the new protein is synthesized and released into the endoplasmic reticulum this protein can be stored inside the endoplasmic reticulum or released in the future or it can also be secreted immediately.

Function of ribosomes

Before going into the details of process of translation it's important to learn about a few concepts, the main machine which plays a central role in translation is ribosome. Ribosomes are complex molecular structures found inside all living cells and they act as a site for protein synthesis. The ribosomes essentially consists of two major components, a small subunit and a large subunit. The unit of measurement used to describe the ribosomal subunits is the Svedberg unit which is a measure of the rate of sedimentation in centrifugation rather than size. In eukaryotic ribosomes the smaller subunit is 40 s and the larger subunit 60 s. When they join they are denoted as ATS. These subunits lies separately in the cytoplasm until they need to come together for translation. These subunits have different jobs as well. The small subunit reads the mRNA whereas the large subunit joins the minor acids to form a polypeptide chain. Now assuming you know about structure of nucleic acids and DNA you know that the information of the genetic code is stored in the form of base pairs with four main bases adenine, guanine, cytosine and thymine. In RNA we have uracil in place of thymine.

 Now the cornerstone to understand the process of translation is to understand what is a codon. A codon is basically a sequence of three DNA or RNA bases. When a mRNA goes inside a ribosome the ribosome does not read individual bases but rather these sequences of three bases which are known as triplet codons. Each of these sequences of three base pairs corresponds to a specific amino acid. For example if three uracil bases are in sequence which means the code will be UUU. The ribosome will read this code and amino acid that is used will be phenylalanine. Similarly if the core is UCC the amino acid that will be used is serene. And so on the codon AUG codes for the methionine and is also the start codon which signals the ribosome to start synthesizing the protein. Similarly we have three special codons which signal the ribosome to stop synthesizing the protein. These are  UAG, UAA and UGA. These are known as stop codons and when the ribosome read these, they know that the protein is now complete and their job is done. 

3.2 Elongation

Now let's get into the details of translation. So the first step in translation is known as initiation. There is a transfer RNA or tRNA which has an amino acid methionine bound to it. This tRNA attaches to the smaller subunit of ribosome and when it encounters a mRNA it starts reading the code on the mRNA from its 5 prime end. As soon as a tRNA ribosome finds the start signal, the AUG codon it immediately binds to the larger subunit to form the complete ribosome and the protein synthesis is initiated. The next step in the process is elongation. Elongation is when the polypeptide chain gets longer in the larger subunit of ribosome. We have three slots or sites which are named as E, P and A. I told you the first tRNA to attach to this mRNA complex is a tRNA with amino acid methionine. This tRNA occupies the P side. (P stands for peptidyl side). Now on each side of the P side we have two more sites the E and the A side. And here the mRNA in the smaller subunit now what happens is the A site receives the next tRNA which matches the codon next in the sequence. Now if the next codon is UAU the trna attached to the A site will have amino acid tyrosine. So this tRNA is now occupying the A site. Now we know the main job of translation is to form a protein whichis essentially a chain of a minor sets. So what we need next is to form a bond between the amino acid on the tRNA in the p-site and the amino acid on the tRNA in the A side. After this the tRNA in the P-site loses its amino acid and becomes empty. Out of which the ribosome moves and now the tRNA in the p-site moves to the other side which is the exit site, and the tRNA in the A site moves into the P-site. The A site thus becomes empty and ready to receive the next tRNA. So the P site always holds the growing polypeptide chain. This process is repeated again  repeating the whole process until we get a polypeptide chain of desired length. 

3.3 Termination

Termination or the cutting down of fragments

The next step in the process is known as the termination the ribosomes must have a way to know where to stop so that we get a final protein of desired number of amino acids. This is possible because the mRNA actually contains stop signals which is known as the stop codon.  When the ribosome reads any of the three codons the  UAG ,UAA or the UGA it stops the process of translation and the polypeptide chain is released from the translatiocomplplex. So after the ribosome finishes the protein synthesises the protein complete not really after that the protein is formed it goes through some additional processing likesome amino acids may be deleted and some proteins also undergo folding to form a more stable structure.