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Deoxyribonucleic Acid(DNA):

It is made up of a lots of nucleotides joined together. One molecule of DNA consist of 2 strands of repeating units called nucleotides, which are twisted into double helix structure.

The parts of the nucleotide:

1. Phosphate group: attach to the 5' carbon and 3' carbon of the next deoxiribose sugar.

2. Deoxiribose sugar(DNA: hasn't hydroxyl group (-OH) at the 2' carbon position ) or Ribose sugar(RNA: has a hydroxyl group (-OH) at the 2' carbon position)

3. Nitrogenous base: adenine, thymine, cytosine, or guanine

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Covalent bonds

The bond that join together the phosphate of one nucleotide with the 3' hydroxyl of the deoxyribose sugar of the next nucleotide are covalent, which are really strong. Therefore, it is really difficult to separate or break that part(bonds between the sugar and phosphate groups).

Hydrogen bonds

But it is easy to break between the nitrogenous bases (A-T and C-G) in the middle of the DNA double helix. As they are hydrogen bonds, not covalent bonds. However, collectively can be strong also.

A polynucleotide

1. The sugar and phosphate units make up the “backbone” of the nucleic acid.

2. A base is attached to each sugar molecule.

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There are 4 different types of bases in DNA and they pair in a specific, complementary way:

1. Guanine(Purine bases)-Cytosine(Pyrimidine bases)

2. Adenine(Purine bases)-Thymine(Pyrimidine bases)

There is not other way of joining two bases, as the hydrogen bond wouldn't appear if any base joined with another base, which is not his complementary base pair.

During DNA replication, the two strands of the double helix will reparate to allow the original strand matche or create its complementary base.

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Is a theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein.

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Information:

1. From notes taken in class and the information given by the teacher in his PPT.

2. Transcription: Professor Dave Explains. (2016, September 9). Transcription and Translation: From DNA to protein [Video]. YouTube. https://www.youtube.com/watch?v=bKIpDtJdK8Q

Photos:

1. The Editors of Encyclopaedia Britannica. (2025b, January 14). DNA | Definition, Discovery, Function, Bases, Facts, & Structure. Encyclopedia Britannica. https://www.britannica.com/science/DNA

2. Project, H. O. (2019, June 19). DNA structure & function: A simple guide. https://humanoriginproject.com/dna-structure-function/

3. DNA as a molecule. (n.d.). https://www.labxchange.org/library/items/lb:LabXchange:c1171748:lx_image:1

4. Nitrogenous bases | BioNinja. (n.d.). https://old-ib.bioninja.com.au/standard-level/topic-2-molecular-biology/26-structure-of-dna-and-rna/nitrogenous-bases.html

5. Wikipedia contributors. (2024, January 1). Replisome. Wikipedia. https://en.wikipedia.org/wiki/Replisome

6. Baniya, S., & Baniya, S. (2023, December 30). DNA transcription: steps and mechanism. Microbe Online. https://microbeonline.com/dna-transcription/

7. Translation | BioNinja. (n.d.). https://old-ib.bioninja.com.au/standard-level/topic-2-molecular-biology/27-dna-replication-transcri/translation.html

8. Hickman, R. J., MD. (2024, May 3). Genetic mutation. Health. https://www.health.com/genetic-mutation-8619244

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RNA(characteristics):

1. Ribo nucleic acid

2. Structurally different in 3 ways from DNA:

a. DNA: Deoxiribose RNA: Ribose

b. DNA: 2 strands RNA: 1 strand

c. DNA: Thymine RNA: Uracil

3. Functionally different in 2 ways from DNA:

a. DNA: can't leave from nucleus RNA: can leave from nucleus

b. DNA: is stable(stays the same in log period of time, as if it changes, there would be troubles. That's why the RNA exist, to prevent changes from DNA)

RNA: is reactive(short time, it only need to be taken outside the nucleus)

Transcription:

1. Transcription is the name of the process in which a copy of DNA is made.

2. The copy is known as messenger RNA.

3. This process occurs in the nucleus of the cell

Transcription of a gene takes place in three stages: initiation, elongation, and termination.

1. Initiation: During the initiation, RNA polymerase binds to the promoter region(a short sequence of DNA and in eukaryotic DNA it's TATA box, which is located 25 nucleotides upstream of the site where transcription begins) of DNA. Each gene (or group of cotranscribed genes, in bacteria) has its own promoter. Once bound, RNA polymerase separates the DNA strands, providing the single-stranded template needed for transcription.

2. Elongation: During the elongation, one of the strand will be the template strand(it will be used to generate the mRNA) and the other strand will be the nontemplate strand or coding strand, which has the same sequence as the mRNA (except that thymine is replaced with uracil in RNA).

RNA polymerase doesn't need a primer, it initiates mRNA synthesis at the promoter and moves downstream along the gene, reading the template strand from 3' to 5' and generating the mRNA from the 5' end, attaching RNA nucleotides to the 3' end. The RNA transcript carries the same information as the nontemplate strand of DNA, but it contains the base uracil, instead of thymine, as it is RNA and not DNA.

3. Termination: Once RNA polymerase reaches the end of the gene, the termination occurs, the enzyme detaches from the gene and the DNA returned to its original state. We will have the mRNA produced, which carries the code in the gene, ready for the next step.

Post transcription modifications(only in Eukaryotes):

Eukaryotic pre-mRNAs must have their ends modified, by addition of a 5' cap (at the beginning) and 3' poly-A tail (at the end).

1. Splicing: Many EUKARYOTIC pre-mRNAs undergo splicing, where the introns(non-coding regions) are removed and exons(coding regions) are joined together.

2. Alternative splicing: a type of splicing, where the cell randomly removes or joines different exons to create or make multiple mRNA versions from the same gene(making different proteins).

Why splicing is that important?(explained by professor Rafa)

1. Efficiency and saves genetic space

2. This process explain us why proteins are that big.

3. Increases protein diversity

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Each codon(a sequence of 3 nucleotides) codes for a specific animo acids, which also can be called: aa, carried by a transfer RNA.

There are four bases, and each codon has three bases, which give us 64 differen/possible combination, encoding 20 different amino acids.

Humans are able to produce 11 out of the 20 amino acids. The ones that humans can't produce can be obtained by eating foods that contain those 9 amino acids. If these are not consumed efficiently, it could lead to serious health issues or death.

Each codon correspond to a specific amino acid.

The most important(for us, as it going to be a question in the exam) codon are:

1. Start codon(initiates translation): AUG(Methionine)

2. Stop codons(end the translation): UAA UAG UGA

Translation occurs inside a ribosome, which has two parts:

Large subunit: It is composed of three main sites:

1. P site (Peptidyl site): Where peptide bonds are formed between amino acids.

2. A site (Aminoacyl site): Where a new tRNA carrying a complementary anticodon and amino acid arrives.

3. E site (Exit site): Where the tRNA leaves after reaching a stop codon.

Small subunit: in charge of reading the mRNA and colocate the tRNAs correctly.

The tRna that corresponds to the codon after the start codon will enter the A site of the ribosome. This tRNA will carry with it an amino acid, which will be connected to the previous amino acid, forming a bond called peptide bond.

Then, the start tRNA/codon will detach from the mRNA, as the mRNA moves to the left, where the start codon will occupy the E site(a place or process, where the tRNA detaches the mRNA). As the mRNA moves, the 2nd tRNA also will move, occupying the P site, where the start tRNA was.

Then, a new tRNA that correspond to the next codon will connect it. The amino acid that it carries will also form a peptide bond with the last amino acid.

This process repeats until a stop codon arrive. As the stop codon doesn't correspond to any tRNA.

As a result, there will be a sequence of amino acid formed, known as the protein or polypeptide chain.

Valine: if the last letters of these codons: GUA GUC GUU GUG, change, it wouldn't change or affect anything, as the first two bases are the most important(explained by the professor Rafa).

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What is mutation?

A mutation is a change of genetic material(more specifically: a change within a nucleic acid).

Anything with RNA or DNA can have a mutation, which means that any living thing can have a mutation, including the animals, plants, fungi, bacteria, etc.

Mutations are random, we can't will ourself to get a certain mutation. However, there are some factors that can make mutations more likely to occur: Mutagens.

Types of mutagens:

Physical mutagen: radiation(X-rays or UV)

Chemical mutagens: some subtances can cause changes in genes. For instance: pollutants, alcohol, substance in tabacco, etc. Risk of mutations increase with the increased exposure.

Biological mutagens: some viruses can increase the frequency of genetic mutation

Mutation in DNA and RNA:

If the mutation occurs in the DNA, the RNA of that DNA will also have the same mutation. As the RNA is a copy of the DNA. However, if the mutation only occurs in the RNA, it wouldn't affect the DNA.

Gene mutations

DNA makes up genes, which can code for proteins that influence different traits. Therefore, when a mutation in DNA happens, which means that a change in one or more DNA bases, different proteins can be produced, that can affect an organism's traits.

There's many types of gene mutations:

1. Base substitution: a wrong base is matched

1. Missense mutation: the change of the base causes a change in amino acid inserted in the protein.

2. Nonsense mutation: the change of the base(stop codon) causes the protein to be shorter than it need to be or it was supose to be.

3. Silent mutation: the change of the base doesn't cause anything. As the base that was change correspond to the same type of codon.

2. Insertion mutation: when an extra nucleotide is added to the DNA during the process of replication. This happens when the replicating trand slips or wrinkles, which allows the extra nucleotide to be added. Strand slippage can also lead to deletion mutations.

3. Deletion mutation: when a wrinkle forms on the DNA template strand and subsequently causes a nucleotide to be omitted from the replicated strand.

Frameshift mutations: when nucleotides are inserted or deleted from a DNA, which cause that there will be one more or less base than usual. As three bases form one codon, there will be one more or less bases to form another codon, which will obviously affect the proteins function.

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What is Gentetic Engineering?

A process of changing an organism's genotype using biotechnology tools or techniques.

Why is it important?

It is a really significant advancement in technologies. It helps to improve human lifes: it helps to create vaccines, to improve yields(enhance food and agricultural production), to create insulins, etc.

PCR(Polymerase Chain Reaction)

PCR (Polymerase Chain Reaction) is a technique used to amplify small amounts of DNA, which is especially useful for generating many copies of a specific DNA fragment, such as a gene. It is also used in forensic science to amplify tiny DNA samples found at crime scenes, helping to identify suspects or victims.

Moreover, PCR is also used for detecting COVID-19. In a COVID-19 test, it uses a reverse transcription PCR because the virus contains RNA, not DNA. The process consist of turning RNA into DNA and then amplifying it.

If the primers bind to the target viral genetic material and amplification occurs, the person would have COVID-19. If there is no amplification, the person wouldn't have COVID-19.

Detecting COVID-19 with PCR will be more fiable, as it can detect it without having symptoms of it. However, with those test of only 10mins, it can only detect it if the person already have symptoms of COVID-19.

If we only use PCR, it is not enough. It must be PCR + Electrophoresis or with other, but never alone, to analyze the amplified DNA properly.

Electrophoresis(the key of sequences)

Electrophoresis is a laboratory technique used to separate DNA, RNA, or proteins based on their size and electrical charge. It applies electricity to move the molecules through a gel matrix (such as agarose or polyacrylamide).The bigger they are, the slower they are going to pass through the pores. It moves towards the + pole, repelled by a – charge.

To identify a person (in forensic investigations), we compare the banding patterns/samples of DNA fragments. If two samples show the same band pattern, it means that they are the same person or are related.

DNA profiling and sequencing

DNA profiling is a technique to identify a person based on his/her DNA pattern.

DNA sequencing is the process of find out the order of the nucleobases in DNA.

Any biological sample can be used: blood, hair, etc.

How does it works:

1. PCR with fluorescent, chain-terminating ddNTPs: ddNTPs coppy and modify the DNA.

2. Size separation by capillary gel electrophoresis: Fragments are classify by size as they move through a gel(Big- slow, Small-fast)

3. Laser excitation and detection by sequencing machine: The laser will read different fragments based on the ddNTPs to form the sequence.

Every time the PCR inserts a ddNTP at random, the reaction stops, generating a fragment that ends in a specific nitrogen base. The electrophoresis will order them by size and the laser will read the ddNTPs.

Plasmids and their manipulation

Plasmid is a genetic material found in bacteria that is used for trick cells into producing a desired protein through its gene.

Structure of plasmid:

1. Promoters: a part of the DNA sequence that initiate the transcription of a mRNA.

2. Restriction site: specific sequences where restriction enzymes cut the plasmid to insert the gene.

3. Selectable marker: an antibiotic resistance gene, that allows scientist to see or identify the bacteria that have take up plasmids

4. Gene of interest: the gene that was introduced to the plasmid.

Restriction enzymes are the most important thing for plasmid engineering. Scientifics use restriction enzymes to cut the plasmid and the target gene at specific sites, creating sticky ends. Then, they use DNA ligase to seal the inserted gene into the plasmid. After the modification, the transformation process follows where the plasmid is introduced into bacterial cells. Bacteria that could not make it will be marked with selectable markers.

Viruses: Allies or enemies?

Most of the times, viruses are enemies as they produce diseases, however, they can also help in genetic engineering.

Scientifics turned viruses into a way or object that could help the medicine: Viral Vector, which is a virus that had been genetically modified. It was inserted a desired gene into the cells. This causes that viruses could produce good things like proteins for medical treatments.

There is many types of Viral Vectors:

1. Adnovirus: It can carry a lot of genes and infect many cells, but it does not resist for a long time.

2. Lentivirus: a research tool used to introduce a gene product into in vitro systems or animal models

3. Adeno-associated: a non-enveloped virus that can be engineered to deliver DNA to target cells.

4. Plant viruses: viruses that affect plants.

They can be determined by size of the gene and the permanence and place in the organism for the future.

Other methods of gene delivery

1. Electroporator: uses an electrical field to create poles in the cell membrane(short time), in which the genes or DNA enters from there.

2. Microinjection: It basically consists of the injecting DNA into cells by using fine needles.

3. Chemical(Polymer and Liposome): it is just insert gene into a small molecule(made in laboratory) and wait until it infects.

-Polymer: Synthetic molecules that help transport genetic material into cells.

-Liposomes: A very tiny, fat-like particle that is made in the laboratory that encapsulate DNA and merge with cell membranes, allowing gene transfer.

4. Gene Gun: It uses microscopic particles, which usually is gold, with DNA(high speed, shot by a "gun") to enter the cell by just pass through the membrane and leave the genetic materials.

CRISPR/Cas9

This is a gene-editing technology causing a major upheaval in biomedical research, first discovered in bacteria, that can target specific sequences and modify them.

It has multiple uses such as gene modification by using a synthetic “guide” DNA (gDNA) to target and modify what the patient needs.

Gene modification

Single-celled organisms can be genetically modified to produce proteins like insulin by inserting specific genes. This process takes place/ happens in large culture vats, where the organisms grow and produce the desired protein, which is then extracted and purified.

In bacteria

Microbial genetic engineering uses cutting, splicing, and integrating target genes into bacterial cells, allowing them to produce useful compounds.

In plants

Scientists insert a desired gene into a bacterium, which then transfers the gene into the plant’s genome, which causes the genetic modification.

In animals

DNA is inserted by the scientist using microinjection (directly into the nucleus) or viral vectors to integrate the new genetic material.

In humans

Gene modification in humans= editing, deleting, or adding DNA sequences:

Somatic Cells: Only the targeted cells are changed, and the edits won't be passed to offspring.

Gametes (Reproductive Cells): Changes affect all cells and can be passed to future generations.

GMO(genetically modified organism)

As it says in its name. It consists of any organism(plants, animals or microbes) whose genetic material has been altered or modified using genetic engineering techniques. This process includes inserting, deleting, or modifying one or more genes in the organism's DNA to achieve desired traits

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When does a DNA molecule need to replicate?

Before a cell divides, DNA replication occurs during interphase in both mitosis and meiosis. This ensures that when the cell divides, each of the two daughter cells receives the correct amount of genetic material.

DNA polymerase

The enzyme DNA polymerase is one of the key molecules in DNA replication. They are responsible for synthesizing DNA. They add nucleotides one by one to the growing DNA chain(only adding those that are complementary to the template).

Key features of DNA polymerase:

1. They always need a template.

2. They can only add nucleotides to the 3'(end of a DNA strand). So they can only synthetise in

5´->3´ direction.

3. They can't start making a DNA chain from scratch, but require a pre-existing chain or short stretch of nucleotides, primer.

Glosary and the steps of DNA replication:

1. Helicase(the unzipping enzyme) breaks through the hydrogen bonds that hold the DNA bases together.

2. To prevent the strands that the helicase separated come back together, SSB proteins(single stranded binding proteins) bind to the DNA strands to keep them together.

3. Topoisomerase works at the region ahead of the replication fork to prevent supercoiling.

4. Primase(the initializer)synthesizes RNA primers so that DNA polymerase can figure out where to go to start to work. The primers are made of RNA.

5. DNA polymerase III builds the new strand in the 5' to 3' direction. This means that it moves along the old, template strand in the 3' to 5' direction. Led by this primers have to keep being placed in order for DNA polymerase to build in the lagging strand. These fragments are known as Okazaki(name of a couple that discovered this) fragments(which is a problem).

6. RNA primers are removed and replaced with DNA by DNA polymerase I.

7. DNA ligase(the gluer) helps to glue DNA fragments together, also, it has to take care of the gaps between the Okazaki fragments, sealing them together.

They all function or work at the same time. There is no one before the other, as there is no thing that organise or orquestrate this.

When DNA is replicated, the two DNA strands will up and form identical chromatids, joined by a centromere. The amount of genetic material will double, but the chromosome number will be the same as before. In this form, chromosomes would be ready for cell division.