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DNA: It is formed by two different strands bonded together.

It's called the doble helix structure.

The strands are formed by nucleotides, the nucleotides are made of 3 parts essentially, the phosphate group(acid), the deoxyribose and the nucleobase by which they join.

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1. DNA contains deoxyribose, while RNA contains ribose. When it is deoxyribose, carbon 2' has only two hydrogens and not an OH group and a separate hydrogen.

2. DNA is a double-strand molecule, while RNA is formed by just one strand as it only needs the information on the coding strand.

3. One of DNA's four nucleobases is thymine, while RNA replaces thymine for uracil.

4. DNA is stable, while RNA is very reactive and disintegrates with time.

5. DNA CANNOT leave the nucleus of the cell because it is too important, but RNA does leave the nucleus to perform different functions.

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The strands are formed by nucleotides, the nucleotides are made of 3 parts essentially, the phosphate group(acid), the deoxyribose and the nucleobase by which they join.

Deoxyribose: The deoxyribose is formed by 5 carbons, and one oxygen, completed with hidrogens and oxigens.

Difference between oxygenated and deoxygenated: The difference between a ribose and a deoxyribose is that the riboses carbons all have an OH and an H, so when it is deoxiribosed one carbon, the bottom right (2nd) C has only two H, and not OH and H.We number carbons in clockwise order to localize them in the nucleotyde.

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*in the image of a line with letter, the line represents the ribose and phosphates of thestrand, and the letters the proteins of the nucleobase.

The nucleotides are all mostly the same, except for the nucleobase's proteins.

An example to compare it to is a language, the language is form by a number of digits(letters) when combined they can create sentences. Dna is the same with the nucleobase's proteins, that would be the equivalent to letters and the strand of dna a sentence.

Nucleobase: The nucleobase can have four possibilities for its proteins:

Adenine: Only goes with Thymine

Thymine: Only goes with Adenine

Citosine: Only goes with Guanine

Guanine: Only goes with Citosine

A-T C-G

*CHANGE IN RNA

The rna is almost the same as dna, but the most significant difference appart from them being different things(rna is a messenger of only a part of the genes), The rna s¡doesn't have Thymine, instead it uses Uracil to complete the Adenine

|Adenine goes with Uracil|

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Enzyme: Protein with an soecific function

Topoisomerase: Enzyme that un-twists the doble helix

Helicase: Enzyme that separates the tw strands.

Single Strand bindind Proteins (SSBP): They stalbilize the replication complex, both strands to stay separate and in place.

Primase: Enzyme that adds primer, which adds a short sequence of the first nucleotides when filling up the strand.

Primer: Short sequence of nucleotides. It's an RNA

DNA Polymerase III: Enzyme that synthetizes the new DNA strand. (It can't start adding nucleotides to the strand from the beginning, so it waits for the primer to put the first 3, and then the DNA Polymerase III finish filling up the strand with the correct nucleotides)

DNA Polymerase II: Cheks for any mutation in the cell, and if there is tries to solve it, if its not possible the process continues.

DNA Polymerase I: Changes primer form RNA to DNA. It takes out the RNA that was there and changes it for a DNA

Ligase: Closes gaps in lagging strand

RNA Polymerase : It attaches to the promoter and completes the strand with its complementary nucelotides. It moves from 5' to 3'.

Codon: Sequence of three nucleotides in a geneitc strand

AUG: Starting codon that codifies for metionine(Met), meaingin that metionine is the starting process of everything.

Mutation: gene which produces or facilitates a mutation to occur.

RNA messenger: Copy created during transcription that is used as a template to produce the protein that codifies for that sequence

Exons: these are the sections of the molecule that contain useful information for whatever that specific RNA molecule is aiming to do.

Introns: these are the sections that contain useless information for the function taking place.

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In order to create an exact same copy of the doble helix structure for no confusions to be made and provoke a genetic disease, the two strands need to me separated vertically, through the hydrogen bond.

1. Separate strands

2. Complete the proteins from both strands with the adecuate one.

3. The two strands are now exactly the same

Central dogma of molecular biology:

DNA- Transcription - RNA - Translation - Protein

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Replication

1. Replication: Replication in DNA is the process by which a cell copies its DNA to ensure that each daughter cell receives an identical set of genetic instructions during cell division.

2. Transcription: Human have a instruction book for 26 thousand, which is DNA. So when a protein must be created, as the DNA cannot exit the nuecleus, a RNA messenger is created to transport it. Creating an RNA messenger of the gene that is needed to be translated.

3. Translation: the rna messenger is codified into proteins

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In order to create the copy first the topoisomerase (a ring-shaped enzyme) helps untwist the DNA molecule,for it to work it needs the help of the the helicase (another enzyme) in order to separate the two strands (as if opening a zipper).

In each strand, there are proteins attached called SSBP, which help stabilize the molecule after this process, to avoid the molecule from twisting back to the initial position. THen the primase situates itself in the strands and starts completing it.

Limitations:

1. It cannot put the first nucleotide of the new strand. (It cannot start from 0) That's why the primase is needed

2. Can only build in the direction of 5'-->3'

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1- Untwist the two strands with the topoisomerease: This enzyme surrounds the dna molecule and un-twistes it making it two parallel strands of dna together.

2- Separate the strands from each other: the Helicase is an enzyme that goes through the middle of the two strands and brakes the hydrogen bonds between both strands

3- Stabilize the strands: SSBP is another enzyme that acts as a clip for the two strands to not get tangled and stay in place.

4- Primer placing: The primase arrives, places the primer and leaves, this primer has new nucleotides that attach to the separated strand's nucleotides, the primer places the first 3 nucleotides to give then the strand to the polymerase III in order to complete it and create the copy.

Whenever the topoisomerase and helicase untwist one, the polymerase moves as well placing new nucelotides.

5- There are two strands, the leading strand and lagging strand.

Leading: The strand that moves easily and is first completed without gaps, moves from 3' to 5'

Lagging: the lagging strand has to move the other way around, from right to left, form 5' to 3' which is much more complex than advancing with the helicase and topoisomerase in the leading strand. In the lagging strand, the primase will stablish itself just at the almost end of the strand and completes that little piece. Then another primer is places a little bit further the last one and complete its piece, and that occurs over and over again until the whole strand is completed

6- RNA transformation: The polymerase I transforms the rna from the primer into dna, but in the lagging strand there are still gaps in between the strand so the Ligase is in charge of filling up those gaps.

7- The complementing of the lagging strand with its complementary strand is also done in fragments.

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1- Initiation: Initiation starts in the transcription site, which is a section of the DNA that contains the information for the creation of the protein needed. In front of this transcription site is the promoter, which is a signal in order to now that the instructions needed are there. At the end of the transcription site there is a termination signal which acts the same way as the promoter, but for when the information needed finishes. The RNA polymerase situates itself at the promoter

2- Elongation: Elongation comes after initiation when the RNA polymarase II starts moving and creating the RNA, which would only need one strand. The polymerase puts nucleotides of RNA in one of the strands with the complementary nucleotide of the ones in the strands. The RNA polymarase works from 5' to 3' as well as the DNA polymerase III.

The top strand that is not being replicated with the rna polymarase, is called Coding strand, and the other one is template strand. The template is called this way because is the one used to complete the rest of the strand as a template.

3- Termination: Once the polymerase gets to the termination signal, the process stops, polymerase detaches from the DNA strand and the copy is finished, with the polymerase ready to be used again. This copy is know called rna messenger

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After termination ends, the RNA messenger is still not capable of translating the information.

In an RNA molecule, we find two types of sections.

Exons: these are the sections of the molecule that contain useful information for whatever that specific RNA molecule is aiming to do.

Introns: these are the sections that contain useless information for the function taking place.

In order to get rid of the useless information, the RNA molecule goes through splicing. This process consists of cutting through the covalent bonds that separate each exon from an intron. After having extracted every intron, the resulting exons bond together to form a completely useful nucleotide sequence.

It is important to note that, depending on the way the exons are removed and put back together, the RNA can have different instructions. If they are put back together in the same order they initially were, it is simply called splicing, but if they appear in a different order, we call that alternative splicing.

After splicing, the RNA seems ready to take action. However, as RNA is highly reactive and it disintegrates starting from its ends as time passes, the ends get protected by a 5' cap and a 3' poly A tail, as depicted in the drawing.

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Initiation: This process starts with the mRNA outside the nucleus. The RNA will travel into a ribosome.

Ribosome: It has 2 subunits, one bigger than the other that can move independently, inside the big one there are three parts called A, P, E.

The small sub unit of the ribosome arrives first, separately, and positions itself under the starting codon (AUG).

Each codon will have its transfer RNA that will have the anti-codon complementary to the codon, with a amino acid stuck to it. This amino acid, will be only the one that the original codon codifies for.

Once this anti-codon is placed in the rna strand, the Big sub unit of the ribosome arrives to stick over it and complete it. This will always start on the starting codon.

The A part of the bigger sub unit will attach to the next codon, and another anti codon complementary for that sepcific combination, ataches to it. Site P and site A amino acids will bond by a peptide bond. After it, site P detaches from the RNA strand.

With the first nucleotide, the E site will stay the same as it is empty, regards in the next parts it will repeat again.

Elongation: In the repetition the ribosome moves as a monster eating the rna strand with its anticodons. On site A that now is empty a transfer can attach to that part of the strand. Now the transfer that was placed in E detaches and will go to pick up another aminoacid and do the same. At the same time the amino acid that was transported, is bonded to the ribosome. This way what we have is a ribosome that contains the aminoacids we want, the transfers go to its original place and, the ribosome continues advancing through the rna strand. The process starts again over and over again, so the bonding between each rna creates a strand of amino acids, that can now be called a protein.

Termination: to end the process, a stop codon will end the process. THere are several codons that are specifically for stoping the process, so when the ribosme gets to this stoping codon, there is no aminoacid so when the last aminoacid tries to atach to the next one, it is empty. As there is no other aminoacid that ataches, the aminoacid continues to detach from the transfer being free. The strand goes through the next sites until the last transfer is detached from the strand.

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The table helps to interpret what the genitc code is hiding. To do it we divide it in sections of 3 nucleotides called codon. For example:

AUG UUA CGC CAA UCG

= = = = =

Met Leu Arg Gln Ser

The starting codon is always going to be AUG which codifies for metionine, regards the ending codons are called the stop codon.

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A mutation is defined as any change that occurs either on dna or rna, there are pretty common and depending on the importante of that mistake different consequences can occur:

· For example if the polymerase 3 puts the incorrect protein, that would be callecd a mutation ·

THis mutations can occur in replication or transcription as in translation there is no dna changed

In case a mutation occurs, the first thing the cell will do is try to fix it. If it is not possible to solve the mutation the cell goes through apoptosis which is the cell's auto-death. In case that doesn't work the body will try to kill it.

The probability of getting any mutation increases with mutagens. This mutagens create a higher probability of not being able to kill a mutant cell and to produce more mutant cells.

Types of mutagens:

Physical mutations: Radiation (X-rays or UV light)

Chemical mutagens: Pollutants, tobacco, alcohol...

Biological mutagens: Viruses (VIH)

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Base substitution: one of the bases of a strand is changed for another one

Missense mutation: The change of a base that causes the change of the amino-acid created by that codon.

Non-sense mutation: The change of that base changes into a stop codon, instead of producing a amino-acid.

Silent mutation: the change in the base does not have any repercussion in the creation of the amino-acid as it belongs to the same box as before.

Insertion mutation: Is when a nucleobase that wasn't supposed to be there is inserted in the dna or rna strand. This causes a decolocation of the codons as they must be in groups of 3. Now all the codons left are changed.

Deletion mutations: is when one of the nuelobase is deleted from the strand. This provokes a movement in the order of codons.

*This last two, both produce a frameshift mutations which is when the mutation changes the rest of codons

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Genetic engeneering is basically modifiing the genetic material of an organism in order to change some aspect or characteristic of it.

PCR - Polimerase Chain Reaction: in order to make a pcr you'll need a sambple, nucleotides, polymerases and primers that codify specifically for the illness that is being analyzed. If the genetic material of the virus is not present the primers will not attach at all to the chain, which would make no difference. If that genetic material is present, the primers will attach to it and duplicate. This is used to amplify specific genetic material, as when it is duplicated several times, the virus is more present.

+

Electrophoresis: The electrophoresis is a huge block of gelly where the samples are placed, then it is connected to electricity. When this happens, the smallest strands of DNA will go faster and consequently will place themselves at the lowest part of the jelly block. This is compared to a marker that states what length of strand belongs to what is being analyzed.

* The pcr is useless if is not followed by electrophoresis, and an electrophoresis can be only done after the pcr *

DNa sequency: its a process by which you can identify all the dna sequence of a organism.

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Plasmid's manipulation: a plasmid is a part of DNA in a circular shape. This plasmids can be extracted from the bacteria and modified. We can change some of the genetic material of this plasmid and return it to the bacteria. For example, if the genetic code of a bacteria is changed to produce human insulin, the bacteria will not differ from his own and the one inserted, so this bacteria will be able to produce insulin, and as it doesn't need it, it will expel it and can be used as normal insulin for a human being. When inserting a gene a marker gene must be added too, this way, we will be able to identify the bacterias genetically modifeied form the general ones.

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Biological: Use a virus modified to not be pathological, meaning it is no longer dangerous. The gene desired is put in the non-dangerous virus. Once that is done, the cell is infected with the modified virus and therefore adopts the gene.

Chemical: it is the same as biological, but the molecules are created in a lab rather than making use of a virus.

Electroporactor: this machine uses electricity to make cells permeable to genetic material (meaning the genetic material can easily pass through the cell membrane)

Microinjection: to inject the gene with a needle inside a cell. This can only be done with big cells, like an ovum. For example, in vitro fertilization, where a sperm cell is injected inside an ovum.

Gene gun: a gene gun uses gold particles coated in genetic material containing the gene desired and shoots them at other cells to modify them. This process uses gold because very few people in the world are allergic to this element.

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The organisms genetically modified are GMOs (genetically modified organisms).

GMO's are usually patented, as those organisms can reproduce by themselves.

Genetic modification in viruses:

Modifying viruses can be used in several ambits, they are commonly used for vaccines, proteins production, and genetic modification of other living organisms. We can do this because the virus is first treated to not be dangerous and to do only the task they are assigned to and not infect the individual. This "disinfected" viruses are called Viral Vectors, and there are several types:

Adenovirus

Lentivirus

Adeno-associated virus

Plant viruses (for plants)

Deciding what virus to use will depend on the magnitude of the gene, the target of the virus and the duration.

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Modification in plants can be done by several methods, changing their plasmids. They are usually done to prove resistance in pesticides, or to produce vitamins or other molecules.

The process involves the use of a bacteria to which the gene desired is inserted to, then the chromosomes of a plant cell that has been infected with this bacteria is introduced on a plant cell in order to produce that gene in the plants that would grow from it.

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Genetic modificated animals are called transgenic animals, which are species that are born with the modification desired. Modificated animals are usually used for testing drugs or food. There are two different processes by which an animal can be genetically modified.

Microinjection of DNA: The process is produced during the first stage of reproduction, inserting the gene on the egg before it is even fertilized. this egg is then introduced i the surrogated mother that will carry the baby until it is born.This way the result comes up as a genetically modified animal. It works the same way for humans.

Embryotic stem cells: The process comes through changing embryotic stem cells. Embryotic stem cells can develop into any kind of cell inside the body. This allows the scientist to specificlly instert the mutation wherever it is desired and choose the embryoes that will carry the mutation. This embryoe is then inserted in the surrogated mother and the resulting offsprings will have this mutation.