Central Dogma of Molecular Biology by Daniel Hu

Structure of DNA

danielhu437 — 2024-04-10 11:27:16 UTC

DNA is formed by a double helix structure that is formed by two strands that are antiparalell. The structure of a DNA consists of three fundamental parts that together form a Nucleotide, which are: Phosphate group (acid), Deoxyribose (sugar) and the Nucleobase.

Nucleobase

danielhu437 — 2024-04-10 11:27:37 UTC

Molecules that form the building blocks of DNA and RNA. These nucleobases pair up in specific combinations (A with T or U, and C with G) to form the rungs of the DNA double helix or to compose the sequence of RNA molecules.

Processes of the Central Dogma of Molecular Biology

muellerregleroalejandro — 2024-04-15 11:01:38 UTC

Phosphate group

muellerregleroalejandro — 2024-04-15 11:04:30 UTC

A chemical compound containing phosphorus, often in the form of a polyatomic ion.

Deoxyribose

muellerregleroalejandro — 2024-04-15 11:05:37 UTC

Is a type sugar molecule with five carbon atoms. It lacks one oxygen atom compared to ribose at the 2' position of the sugar pentagon.

Differences DNA & RNA

muellerregleroalejandro — 2024-04-15 11:15:11 UTC

Difference N.1

muellerregleroalejandro — 2024-04-15 11:16:26 UTC

The first difference is found on the Deoxyribose / Ribose. In DNA, Carbon two prime has two hydrogens attached to it. On the other hand, in RNA, Carbon 2 prime has one hydrogen molecule and one OH molecule

Replication (Phase 1)

danielhu437 — 2024-04-15 11:18:49 UTC

Process by which a double-stranded DNA molecule is copied to produce two identical DNA molecules. This process occurs during the cell cycle, specifically during the S phase (synthesis phase) of interphase, before cell division (mitosis or meiosis).

muellerregleroalejandro — 2024-04-15 11:28:11 UTC

Replication includes a lot of enzymes to fullfill the process. These are:

Helicase: Separate both strands

SSB: Stabilises the strands so they cant join back together

Primase: Adds primers

Topoisomerase: Untwists the DNA molecule

DNA Polimerase III (the blue ball): Adds nucleotides 5' - 3'

DNA Polimerase I: Changes primers for DNA

DNA Ligase: Bonds gaps

Difference nº2

danielhu437 — 2024-04-15 11:30:17 UTC

The second difference is that while DNA is typically double-stranded, forming the famous double helix structure. RNA is usually single-stranded, although it can fold back upon itself to form various shapes.

Difference nº3

danielhu437 — 2024-04-19 10:24:40 UTC

While DNA contains the bases adenine (A), thymine (T), cytosine (C), and guanine (G). RNA contains adenine (A), uracil (U) instead of thymine, cytosine (C), and guanine (G). Basically in RNA we have uracil instead of thymine.

Transcription (Phase 2)

danielhu437 — 2024-04-19 21:23:54 UTC

Process of copying genetic information from DNA to RNA, specifically messenger RNA (mRNA). It occurs in the nucleus of eukaryotic cells or in the cytoplasm of prokaryotic cells and involves initiation, elongation, and termination stages. Transcription is crucial for gene expression, serving as a blueprint for protein synthesis and is tightly regulated in various biological processes.

Initiation - Stage nº1

danielhu437 — 2024-04-19 21:26:02 UTC

In this stage, transcription factors and RNA polymerase bind to a specific region of DNA called the promoter.
The transcription factors help the RNA polymerase recognize the promoter region and initiate the process.
Once the RNA polymerase is bound to the promoter, it unwinds the DNA double helix to expose the template strand.

Elongation - Stage nº2

danielhu437 — 2024-04-19 21:27:59 UTC

During elongation, the RNA polymerase moves along the template strand of DNA, synthesizing an RNA molecule that is complementary to the template strand.
As the RNA polymerase moves along the DNA, it continues to unwind the double helix ahead and rewind it behind, allowing for the formation of RNA.
Nucleotides are added to the growing RNA chain in a complementary manner, following the base-pairing rules (A pairs with U in RNA, and G pairs with C).

Termination - Stage nº3

danielhu437 — 2024-04-19 21:28:36 UTC

Termination marks the end of transcription.
In prokaryotes, termination occurs when the RNA polymerase encounters a termination signal in the DNA sequence. This signal may cause the RNA polymerase to stop transcription and release the newly synthesized RNA molecule.
In eukaryotes, termination is more complex and involves the recognition of specific sequences and the action of termination factors to release the RNA polymerase from the DNA template.

Post Transcription Modifications

danielhu437 — 2024-04-19 21:31:33 UTC

Splicing is the removal of non-coding regions (introns) from pre-mRNA to create mature mRNA.

Alternative splicing selectively includes or excludes exons, generating multiple mRNA isoforms from one gene, increasing proteome diversity.

Lagging vs Leading Strands

danielhu437 — 2024-04-24 11:07:52 UTC

Leading Strand: This is the DNA strand that is synthesized continuously in the 5' to 3' direction during DNA replication. The DNA polymerase enzyme can move along this strand in the same direction that the replication fork is moving.
Lagging Strand: The lagging strand is synthesized in the opposite direction, from 3' to 5', because DNA polymerase can only add nucleotides in the 5' to 3' direction. Therefore, the lagging strand is synthesized discontinuously in short fragments.

Translation (Phase 3)

danielhu437 — 2024-04-24 11:10:17 UTC

During translation, the genetic information stored in messenger RNA (mRNA) molecules is decoded to produce specific proteins. This process involves the interaction between mRNA, transfer RNA (tRNA), and ribosomes.

KEY TERMS

danielhu437 — 2024-04-26 20:33:02 UTC

mRNA: messenger RNA: Product of transcription, contains instructions to "build" a protein.

tRNA: transfer RNA: Carries 1 aminoacid (aa)

Aminoacid (aa): Monomere of a protein. A chain of aa is a protein.

Ribosome: Where proteins synthesis takes place. Organelle with 2 subunits

Codon: Group of 3 nucleotides. Codifies for 1 aa.

Initiation - Stage nº1

danielhu437 — 2024-04-26 20:33:55 UTC

The small subunit of the ribosome binds to the mRNA molecule at a specific sequence called the start codon (usually AUG).

Elongation - Stage nº2

danielhu437 — 2024-04-26 20:38:00 UTC

The ribosome moves along the mRNA molecule in a 5' to 3' direction, and tRNA molecules bring amino acids to the ribosome according to the sequence of codons on the mRNA. Each tRNA molecule carries an amino acid specified by the codon it recognizes. The ribosome catalyzes the formation of peptide bonds between adjacent amino acids.

Termination - Stage nº3

danielhu437 — 2024-04-26 20:38:46 UTC

When the ribosome encounters a stop codon (UAA, UAG, or UGA) on the mRNA, translation terminates. Release factors bind to the ribosome, causing the completed polypeptide chain to detach from the ribosome. The ribosome then dissociates into its subunits, and the mRNA molecule is released.

Mutations

muellerregleroalejandro — 2024-05-03 13:49:32 UTC

These are the agents which produce or facilitate a mutation to occur. The Physical mutagen is primarily radiation (X-rays and UV light). The chemical mutagens are substances that cause a change in the gene. An example of this mutagen is Tobacco. The last mutagen is the Biological mutagen. These mutagens are usually viruses that attack the body

Gene mutations

muellerregleroalejandro — 2024-05-03 13:55:52 UTC

Missense mutation: The base changes and this causes a different amino acid

Nonesense mutation: This type of mutation in the base causes the protein to be terminated

Silent mutation: This is a change in the base that does not make any difference, meaning that it does not change the amino acid

Insertion mutation: an extra nucleotide is added to the DNA strand

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

Genetic Engineering

muellerregleroalejandro — 2024-05-12 10:51:23 UTC

Genetic engineering is the modification of an organism, usually a cell, that receives an ability that it was not able to do before

PCR

muellerregleroalejandro — 2024-05-12 10:58:30 UTC

A method called PCR is usually used to quickly multiply the number of identical copies of a DNA sequence. To amplify and selectively bind to particular sequences in the DNA template, customized primers are used.

Electrophoresis

muellerregleroalejandro — 2024-05-12 11:07:00 UTC

Electrophoresis is used in genetic engineering. It divides the DNA in sizes. When the DNA fragments are bigger, they move slower and they arrive to the first layers of the pores. This is usually used to identify family members, crimes amongst other things, since every person has a different combination.

Plasmids and their manipulations

muellerregleroalejandro — 2024-05-12 11:44:21 UTC

Plasmids are a DNA molecules that are used to produce proteins with a gene.

Promoters: they activate transcription of DNA

Restriction site: Here, the enzymes select this part to insert the gene

Selectable marker and Antibiotic Resistance Gene: they look for the cells that express the plasmids

Restriction enzymes are essential for plasmid engineering.
After cutting both DNAs, they will create compatible ends, or sticky ends, which ligase will subsequently link together.

This is extremely useful to create new gene combinations

Sequencing

danielhu437 — 2024-05-12 19:49:53 UTC

PCR Amplification with Fluorescently Labeled ddNTPs: The target DNA fragment is amplified via PCR, and the ddNTPs are fluorescently labeled with fluorophores, which are then incorporated into the DNA polymerase.
Capillary Gel Electrophoresis: Capillary gel electrophoresis is a technique used to separate DNA fragments based on their size, using an electric field to move them through a tube.
Laser Excitation and Detection: Fragments of fluorescently labeled DNA are emitted by a laser beam, exciting fluorophores. The emitted light is detected by a fluorescence detector, allowing the sequence of DNA fragments to be determined.
Data Analysis: The sequencing machine detects fluorescence signals, which are processed and analyzed using software to create a sequencing chromatogram, which represents fluorescence intensity along the DNA fragment.

Gene delievery

danielhu437 — 2024-05-12 19:57:43 UTC

Gene delivery methods are techniques used to introduce foreign genetic material, such as DNA or RNA, into target cells for various purposes, including gene therapy, genetic engineering, and research

Gene Modifications

danielhu437 — 2024-05-12 20:02:14 UTC

Gene modifications refer to alterations made to the DNA sequence of an organism's genome. These modifications can occur naturally through genetic mutations or can be intentionally induced through genetic engineering techniques.

Somatic gene editing: Somatic cells, non-reproductive organs of organisms, are modified individually and not passed on to offspring, often used for therapeutic purposes.purposes, such as treating genetic diseases or cancer.

Germline gene editing: Germline cells produce gametes and contribute to the organism's germ line, passing genetic material to offspring. Heritable genetic modifications affect future generations, potentially for disease prevention or trait enhancement.

Gene Modification (golden rice)

danielhu437 — 2024-05-12 20:05:57 UTC

Golden rice is a genetically modified rice variety developed to combat vitamin A deficiency by producing beta-carotene, a precursor of vitamin A, in the rice grains. Hoped to be grown in poor parts of Asia where vitamin A deficiency is a problem.

Gene Modification (AquaAdvantage salmon)

danielhu437 — 2024-05-12 20:10:41 UTC

AquAdvantage salmon is a genetically modified Atlantic salmon variety engineered to grow faster and more efficiently than conventional salmon. It contains genes from Chinook salmon and ocean pout, enabling year-round production of growth hormone. Despite controversy over safety and environmental impact, it has received regulatory approval for commercial production and consumption in certain countries.