What we are: A beginners course on biochemistry 🩸 and DNA Translation 🧬

Biochemistry is the science of life. All our life processes — walking, talking, moving, feeding — are essentially chemical reactions. So biochemistry is actually the chemistry of life, and it’s supremely interesting.

— Aaron Ciechanover

I think most people struggle with the fact that there are too many terms. In biochemistry, everything has its own fancy term, such as anabolism- ‘the process in which molecules are built’, or catabolism- ‘the process which molecules are being destroyed.’ All compounds are divided into monomers and polymers. A polymer is a ‘large molecule which is being built from many repeated identical monomers’. For example, a DNA strand is made of many repeated monomers called nucleotides.

One of the greatest discoveries in biochemistry was the central role of ATP in ‘energy transfer’. The cell is essentially an energy converting device! ATP is the main product and energy transferring molecule of the citric acid cycle and the electron transport chain. ATP synthesis takes place via the process of photosynthesis, cellular respiration, and glycolysis. The ATP is utilized to drive other biological processes, including protein and DNA synthesis. The cell is basically driven by ATP and controlled by ATP 🔥

A monomer is an example of ‘a smaller molecules’ within the chemistry of life. Monomers can be categorized into four different groups: carbohydrates, proteins, fatty acids (lipids), and nucleic acids.

The most common example of a monomer is the glucose molecule which is made of carbon, hydrogen, and oxygen (C₆H₁₂O₆).

You can make longer polymers from combinations of these monomers and connect them together by covalent bonds. These macromolecules ‘are the building blocks of cells and of life!’

• Covalent bonds are the basis for all chemistry and biochemistry in nature as far as we know it today!

The “invisible” particle- ⚛ Atoms:

Everything in nature is made up of atoms, the smallest unit of matter with a specific mass. All atoms are made from neutrons, protons, and electrons.

An model of the atom illustrated by letstalkscience.ca

In all fields of science be it biology or biochemistry, two or more atoms are linked in compounds by chemical bonds. Every bond has its unique name and properties, there are various types of bonds but there are two main types of bonds in biology- ionic and covalent bonds! The covalent bonds are the type of bond between atoms who are sharing electrons and are held to each other due to electromagnetic forces between the atoms.

The proton has a + charge, while electron has the — (minus) charge, and the neutron has no charge. The atom is held together by electromagnetic forces. When an atom gains an electron or looses an electron, we say that the atom is being oxidized and reduced respectively. This is basically what we call chemical thermodynamics. The change of oxidation means ‘we gain or loose energy’ and the change of reduction is also called as energy transfer.

The + and — charges of protons and electrons mean that they have the ‘desire to attract each other’, which is why we usually see them as a pair.

For biochemistry, the importance of having + and — charges, is because they are the driver of chemical reactions, all chemical reactions in biology require a source of energy (electrical/chemical energy). The energy transfer happens due to the flow of + and — charges between atoms, and the energy that flows when the atom gains the missing charge, which is oxidation and it drives various biological processes in organisms.

Here is a brief summary:

1. Biochemistry 💫 — The Study of Chemical Reactions in living organisms.
2. Life is driven by ATP 🎇- ATP is the energy transferring molecule, it stores the energy needed for biological processes. It is made and used in photosynthesis and cellular respiration.
3. Life is made from organic molecules 🎏- Macromolecules are polymers (large molecules) which are made from many repeated identical monomers, while monomers are small molecules which have different combinations of carbon, hydrogen, oxygen, nitrogen, and sometimes phosphorus.
4. The atom is held together by electromagnetic bonds 🔌- All chemistry and biochemistry takes place within the atom. The atom is basically a miniature working machine which acts as the fundamental unit of matter.
5. The atom consists of three types of particles 🥎:

• Protons: + charge
• Neutrons: neutral charge
• Electrons (orbiting the atom): — Charge

Check out In Pursuit of Matter: An Introduction to Chemistry 📚 if you want to learn about things like the periodic-table and how to start balancing equations!

The Elements, a brief view:

The elements which are most abundant in living organisms are carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus and the alkali metals.

What you need to know for now:

• Carbon is the basis of organic chemistry. It forms the backbone of all the complex molecules of life.
• Hydrogen and oxygen are present in water, the solvent in which life is based. They are present in most of the molecules of life.
• Nitrogen is the most abundant element in the atmosphere and in the earth’s surface. It is found in proteins and nucleic acids.
• Sulfur is a key component of the amino acids cysteine and methionine and is essential to the tertiary structure of proteins.
• Phosphorus is essential to all living organisms. It is found in the backbone of the nucleic acids, the sugar-phosphate backbone of the nucleic acids and in the high-energy compounds such as ATP and NADH.
• The alkali metals, sodium, potassium, rubidium, cesium and lithium, are found in the environment and in the body fluids of all living organisms.

The Periodic table and it’s function- a brief view:

The Periodic Table has several uses for a Biochemist, such as allowing the organization of elements by atomic number, mass, and atomic properties. It shows the reactivity of the elements and shows the properties of the compounds they form. In addition, they can use it to predict chemical composition of unknown chemicals in solution. The Table also shows how elements form bonds and the types of bonds the form.

Check out In Pursuit of Matter: An Introduction to Chemistry 📚 if you want to know the ‘how’ to concretely utilize the periodic table and balancing it’s equations!

Water 💧- the molecule of life:

Water, scientifically known as dihydrogen monoxide or DHMO, is a common inorganic compound with the formula H2O. It is an aqueous solution that plays a key role in the Earth’s water cycle and is naturally available as a liquid at standard air temperature and pressure. It is also the most widely used industrial chemical due to being the primary raw material for many processes and products.

If you were to drink too much water in a short amount of time, it could result in a condition called water intoxication or water poisoning. You get water poisoning when the concentration of water in your body is higher than the concentration of electrolytes. This condition can be fatal and cause serious health problems.

Water has strong intermolecular forces that keep the individual water molecules tightly associated with one another. This results in a variety of interesting properties. One such property is hydrogen bonding, the interaction of the lone pair on the oxygen of one water molecule with the hydrogen of another, which forms two bonds simultaneously! This strong intermolecular force is the reason for some of water’s unusual characteristics. It results in its high boiling and melting points as well as high density.

Hydrolysis is an important reaction in the human body. It is ‘the reaction between an acid and water.’ This reaction is exothermic because the energy level of one bond is broken and two bonds are formed between the acid and water molecule. Hydrolysis is essential for the digestion of proteins, for example. Digestion of proteins, known as proteolysis, is ‘the breakdown of proteins into their constituent amino acids through hydrolysis.’ This process begins with proteases, ‘an enzyme responsible for digesting the food’ to be absorbed by the body. It then continues with other hydrolytic enzymes! So, hydrolysis is something we should care about because it can tell us what is happening in the human body during a process like digestion. The reactions of hydrolysis cause many different molecules to be produced such as acids, bases and salts 🧂

Hydrolosis is the mechanism behind many chemical reactions in biochemistry. For example, enzymes (protein that promotes and facilitates chemical reactions in the body) are needed to initiate the process of protein folding. During the reaction, enzymes will react with the protein as it folds. Other reactions, such as the synthesis (chemical production) of ATP, also occur due to hydrolysis. Hydrolysis also plays a vital role in the replication of DNA!

Simple illustration of DNA and a microscope.

Water pressure and substance transportation by water:

A key factor for our being and most beings we know of are that water is required for the transport of substances in and out of the cell, for the maintenance of cell turgor, and for the generation of osmotic pressure.

• Cell turgor and osmotic pressure are both terms used to describe the pressure that water puts on a cell. For example, a plant cell has a cell wall which has an outer surface that prevents water molecules from getting through. Since the water outside the cell membrane is more than inside, the water molecules exert pressure on the cell membrane and this pressure is called turgor pressure. Osmotic pressure is the pressure exerted on the cell membrane by the water inside a cell.

One of the most important aspects of cell turgor and osmotic pressure is that they both involve the concentration of water in a solution. The amount of water a solution contains is known as its osmotic potential. This potential can be calculated using a formula called the osmolarity formula. Check out THIS paper 📜 if you want to get more specific!

Water (H20) is essential for life, as we hopefully understand. Fun fact is that the body of a human adult contains about 40 liters of water. This is about 60 percent of the body weight! That’s an incredible amount, right?!

“Without water, life would just be rock.”

― Anthony T. Hincks

Introduction to cells and more water 🚿:

Water is present in the cytoplasm of cells, in the cell membranes, in the nucleus of cells, and in the organelles of cells.

Cytoplasm ‘is the clear liquid inside of cells’. It contains all of the important organelles, ‘which are different structures within cells’ that carry out different functions. It is also known as the cytosol. Cell membrane is ‘the boundary between the outside and inside of cells.’ It surrounds cells and helps to keep out unwanted substances! Nucleus is ‘the central organelle of cells’. It contains the DNA (genetic information).

An illustration of the cell as we know it for now: Check out Micro.Magnet.fsu.du for more information.

Mitochondria play a key role in cell metabolism. They produce ATP, which is the main source of energy for most cells. Mitochodria are surrounded by two membranes: an inner and an outer membrane. Between these two membranes, there is a space called the intermembrane space where proteins that move ions across the inner membrane are found.

• Ions are atoms ‘that have an electrical charge.’ The positive charge is known as a cation and the negative charge is called an anion. Ions have different properties than atoms, mainly how they react with other things. For example, ions are able to react with one another to form salts 🧂🧂🧂

Eukaryotic cells are the most common type of cell. They contain one or more cell nuclei. Their internal membrane-bound organelles are held in place by microfilaments and act as little “factories” that keep the cell alive. They’re also the basis of tissue and organs within an organism.

• A cell nucleus is the main structure of a cell. It contains DNA which ‘tells the cell what to do and where to put things’. Around the nucleus is the nucleoplasm, which is a space of water that helps to keep the nucleus in place. Inside of the nucleus, there are chromosomes that the DNA is wrapped around. These chromosomes keep the DNA organized.

Chromosomes are tiny thread-like structures made from DNA and proteins. They are ❗❗extremely ❗❗ important because they carry the genetic information that determines how organisms develop and grow. If there is something wrong with them, it can cause lots of different problems. For example, chromosome abnormality can cause birth defects or cancer!

DNA and the biochemical building blocks of life!

tRNA (or transfer RNA) is a molecule that helps to translate genetic information from DNA to proteins. It has a three-dimensional structure and is composed of a molecule called a nucleotide. The nucleotides of tRNA bind to specific amino acids (the building blocks of proteins) and bring them to ribosomes. Ribosomes ‘are specialized organelles found in eukaryotic cells.’ They are responsible for protein synthesis.

Amino Acids- a brief course ♦:

It now seems certain that the amino acid sequence of any protein is determined by the sequence of bases in some region of a particular nucleic acid molecule.

— Francis Crick

Amino acids are the building blocks of proteins, they are the essential component for life, and therefore of all life on earth! They are organic compounds with a single amine group (NH2) and a carboxylic Acid group (COOH), and a side chain (R). The R group is a variable carbon chain which gives each amino acid a unique identity. There are 20 known amino acids in nature which are encoded by the universal genetic code.

• Proteins are one of the most abundant biological molecules on earth. Proteins perform a vast array of functions within organisms, including catalyzing metabolic reactions, acting as hormones, and responding to stimuli. The ability of proteins to perform such a variety of functions is largely dependent on the 3-dimensional shape of the protein.

What are the 20 amino acids?

1. Alanine (Ala)
2. Arginine (Arg)
3. Asparagine (Asn)
4. Aspartic Acid (Asp)
5. Cysteine (Cys)
6. Glutamic Acid (Glu)
7. Glutamine (Gln)
8. Glycine (Gly)
9. Histidine (His)
10. Isoleucine (Ile)
11. Leucine (Leu)
12. Lysine (Lys)
13. Methionine (Met)
14. Phenylalanine (Phe)
15. Proline (Pro)
16. Serine (Ser)
17. Threonine (Thr)
18. Tryptophan (Trp)
19. Tyrosine (Tyr)
20. Valine (Val)

The synthesis of amino acids occurs through a process called carbon fixation, which is the addition of carbon dioxide (CO2) to a molecule. Amino acids are broken down through the process of proteolysis, in which a peptide bond is cleaved by hydrolysis!

How are they classified?!

The Amino acids can be classified in several different ways. Firstly, they can be classified by the chemical characteristics of their R group. There are three major groups: nonpolar, polar, and charged.

1)- Nonpolar — This group is made up of amino acids which contain nonpolar R groups. These amino acids are hydrophobic and do not interact well with water. An example of a non polar amino acid is proline (Pro), in proline (Pro), the side chain is highly non polar due to the 5 member ring in proline’s (Pro) side chain. Non polar amino acids do not interact with water well and so are often found buried within protein molecules rather than exposed to water.

Proline in the form of organic chemistry from worldofmolecules.com

2)- Polar — This group is made up of amino acids which contain polar R groups. These amino acids can interact with water and are hydrophilic. An example of a polar amino acid is aspartic acid (ASP), there are two types of aspartic acid (ASP): The first is acidic and the other one is basic. Aspartic acid is a polar amino acid. Its side chain contains two oxygen atoms which form the negative end of its dipole (check the link if you want to read some before I get into it further down). The oxygen atoms are highly reactive and are able to form intermolecular hydrogen bonds with water due to their polarity.

L-Aspartic Acid (ASP) in the form of organic chemistry from wikipedia. The l- stands for levo which is a chemistry term. It is a prefix from the Latin word ‘laevum’ for ‘left’. We use these prefixes to show what direction the molecule rotates plane-polarized light.

3)- Charged — This group is made up of amino acids which contain charged R groups. These amino acids can interact with water and are hydrophilic. Lysine (Lys): C6H14N2O2, a proteinogenic amino acid, lysine (Lys) is positively charged at physiological pH. It has a role in cell signaling and has been shown to have antiviral and antimicrobial activities. Let me explain it further- a proteinogenic amino acid is basically an amino acid that is used to ‘create proteins.’ PH in chemistry is a ‘way to measure the concentration of H+ and OH- ions in a given solution’, lysine (Lys) has a role to play in cell signaling because of its positively charge and therefore it can bind to certain cells to influence them.

A pH scale for blood content found on freepik.com.

Another way to classify amino acids is by their chemical characteristics. There are four different groups:

1. Acidic — This group is made up of amino acids which contain a carboxylic acid functional group. These amino acids can accept protons and are negatively charged.
2. Basic — This group is made up of amino acids which contain an amino functional group. These amino acids can donate protons and are positively charged.
3. Neutral — This group is made up of amino acids which do not contain a carboxylic acid or amino functional group. These amino acids are not charged and are electrically neutral.
4. Sulfur-Containing — This group is made up of amino acids which contain a sulfur atom.

PH: How we measure acids and bases 🏰:

Let me start by explaining the acidic and basic ones, in chemistry, there are a lot of acids (like muriatic acid, sulfuric acid, etc) , when we mix an acid such as sulfuric acid with a base, say sodium hydroxide, it will neutralize the acid and give water. An amino acid that is acidic means that it still contains a hydrogen atom that it can give away. An amino acid that is basic means it has a hydrogen atom that can accept from another acid to neutralize the acid by combining with the free electron (or proton) present in other organic molecules.

• Lets take lysine (Lys) as an example. Lysine (Lys) is a positively charged proteinogenic amino acid. When it is dissolved in water, its side chain releases hydrogen ions (H+), thereby turning the water more acidic. This shows that lysine (Lys) can influence cell signaling by binding to cells that have a pH dependent receptor.

PH basically refers to the concentration of H+ (hydrogen ions) present in a water solution. This number is an integer and can be anywhere between 0 and 14. The lower this number is, the higher the concentration of H+, so the more acidic the water solution is.

Illustrated Ph-scale with associate elements from sciencenotes.org.

Dipoles and Lysine:

A dipole is a molecule that consists of polar bonds, and one end of the bonds is positive, and the other end is negative. Water and other Polar molecules form dipoles when dissolved in water. This allows e.g. lysine’s (Lys) polar side chain to interact with cell membrane receptors and thus influence the cell signaling pathway. The whole basis of dipoles is that each individual molecule has electric charge. That electric charge can be positive or negative. In the case of lysine’s (Lys) charged R group, it is positive, this is due to the hydrogen atoms that are covalently bonded to the rest of the lysine (Lys) molecule. These hydrogen atoms are very easily attracted to water molecules because the oxygen in water is very electronegative. When in water therefore, these highly reactive hydrogen atoms give up their single electron to the oxygen, thereby transferring their positive charge.

Proteins:

Amino acids make up the building blocks of proteins. Since the amino acids have specific properties, such as being polar or non polar, this allows the protein molecules to interact with each other in a particular manner, for example a polar amino acids can interact with another polar amino acid and make the protein more stable! The way specific protein are made up and the way the individual protein molecules interact depends on the amino acids that are present within a protein. Since every protein is made up of a unique and different set of amino acid, every protein is different!

Proteins are what we call polymers of amino acids. They have molecular weights in the range of 10,000 to 100,000,000 daltons. They have a wide range of biological functions. They are the catalysts of biochemical reactions, they are the structural elements of cells and tissues, they are the transport proteins, and they are the receptors for hormones.

• The dalton or atomic mass unit is the unit of mass used within chemistry. 1 dalton is equal to 1/12th of the average mass of the carbon atoms atom. So for example, if an element (such as Hydrogen) has a atomic mass of 1 dalton, this means that on average, the atomic weight of Hydrogen is 12% of the atomic weight of carbon. However, this may vary due to isotopes. Check out the Dalton to learn more.

All twenty different amino acids can be found in various proteins, and all of them have the same basic structure. They all have a central carbon atom, known as the carbon atom, to which is attached a hydrogen atom, an amino group, a carboxyl group, and a side chain.

The amino acids are classified into two groups. The essential amino acids are ‘those that cannot be synthesized by the body’ and therefore must be obtained from the diet. The non-essential amino acids are those that ‘can be synthesized by the body and therefore do not need to be obtained from the diet.’

The amino acids are joined together by a peptide bond. The peptide bond is formed by the reaction of the carboxyl group of one amino acid with the amino group of another. The result is the elimination of a molecule of water and the formation of a peptide bond between the two amino acids.

The peptide bond is very stable. It cannot be broken without the use of an enzyme. Let’s take insulin as an example, that’s an peptide, and the enzyme for insulin is called Recombinant Proinsulin Autocatalytic Peptidase. It breaks the peptide in protium so its ready to get into the bloodstream, it then joins it to two other amino acids to create insulin. Insulin is a (pancreatic) hormone- its main function is primarily to regulate blood sugar levels (glucose). Check this article out if you want to learn more 📄!

There are two types of protein structures. Globular proteins have a compact, well-defined structure. Membrane proteins are much less compact. They are attached to membranes.

The proteins of living organisms have been classified into families. This is based on similarities in amino acid sequence and in three-dimensional structure.

‘Amino Acid Chart’ by biologydictionary.not.

The Double Twist 🧬:

Nucleic Acids are polynucleotides, which are composed of numerous monomers known as nucleotides. They are made up of four bases, which are adenine (which pairs with Thymine), guanine (pairs with Cytosine), or Uracil. Each base also comes with a sugar and a phosphate group. The two DNA strands are held together by hydrogen bonds. Simply said: The DNA molecule is made up of two chains wound around one another to form a double helix (the structure first proposed by Watson & Crick).

There are two types of nucleic acids, deoxyribonucleic acid, DNA, and ribonucleic acid, RNA (both mentioned above). DNA is the essential biological genetic material of all organisms except for the viruses. RNA is the genetic material of the viruses. It (DNA) is a molecule that encode genetic information which is then expressed on an RNA molecule (which humans also have).

The nucleotides of DNA and RNA have the same basic structure. They all have a central nitrogenous base to which is attached a sugar, a phosphate group and a deoxyribose in the case of DNA or a ribose in the case of RNA.

The nucleotides are joined together by a phosphodiester bond. The phosphodiester bond is formed by the reaction of the 3’ hydroxyl group of one sugar with the 5’ phosphate group of another. The result is the elimination of a molecule of water and the formation of a phosphodiester bond between the two nucleotides. This might not the best metaphor, but the process of forming phosphodiester bonds in DNA is like stitching two pieces of cloth together. With cloth, you combine two pieces of material and stitch them together so that there is no chance that the two will separate. Now, imagine the phosphates on each nucleotide as the needle used to puncture the fabric to form the stitches.

Super Quick Organic Chemistry to clarify the sugar group:

Of course, a sugar group consists of three carbon atoms, with each of those atoms bonded to one oxygen and hydrogen atom. The 5' and 3' labels (To clairify) refer to how the groups are written down and oriented. The 5' refers to the fact that the phosphate group is connected to the 5th carbon atom in the sugar group, and the 3' means the 3rd carbon atom in the sugar group.

• The counting starts from the oxygen atom. When you have a ring structure in a molecule, the carbon atoms are numbered by the number of double bonds. For instance, in the above comment, I mentioned that the “sugar group” consists of three carbons. These three carbons all have a double bond with either a carbon or an oxygen atom. Hope that helps!

An illustration of the sugar group, you can find an answer on quora by Mr. Goddam that refered to this more in depth here. Also, check out this paper if you are interested in Fischer Projections and the sugars.

The phosphodiester bond is very stable. It cannot be broken without the use of an enzyme. Kinda like the Insulin we mentioned eariler in this article!

DNA and RNA are capable of forming duplexes with complementary sequences. A duplex is formed when two complementary strands of DNA or RNA interact with each other via hydrogen bonding. The structure of a DNA or RNA duplex is shown in the figure bellow:

The structure of a DNA and RNA duplexes from Biophysical Journal at ScienceDirect.

DNA and RNA duplexes have a right-handed helical structure. In the most common helical structure of DNA and RNA, the duplex is called A-form DNA or A-form RNA. While there are seven different right-handed helical structures, A-form is by far the most common for both DNA and RNA. When you see a molecule of DNA or RNA, it looks like a twisted ladder. The rungs are the backbones, which make up the ladder’s structure. The horizontal lines are the bases. These horizontal lines stack upon one another and allow for hydrogen bonding to occur, which help maintain the correct, right-handed helical structure.

• The backbone consists of a sugar group attached to a phosphate as you now know. The phosphodiester bond connects both of the parts, allowing the DNA to be more stable and not break. The backbone consists of repeating phosphate and sugar groups. In other words, they are “repeated”, or “rungs”.

B-forms have a left-handed helical structure similar to A-forms. However, the sugar groups are rotated 180 degrees, resulting in a different hydrogen bonding pattern. There is also less curvature in B-Forms as compared to A-Forms, as well as a smaller major groove.

To explain furthere we need to look back at the hydrogen:

There are two different types of hydrogen bonds: H-bonding between a base with the phosphodiester bond and a H-bond between two bases. As the major groove is smaller in B-form DNA/RNA, less H-bonding occurs in that area. In A-form DNA/RNA, the larger major groove causes more H-bonding. This results in B-form DNA/RNA being able to hybridize (form double stranded DNA/RNA) more favorably than A-form DNA/RNA, allowing for B-form to be the preferred form in living cells.

Imagine you are looking at a DNA/RNA molecule! In A-form DNA/RNA, the bases on two of the strands can stack upon one another because they are facing each other like mirrors. This leads to a ton of hydrogen bonds being made, which in turn ‘makes DNA very stable.’

In B-form DNA/RNA, the bases are not like mirrors. They are twisted to the opposite direction, meaning that the bases cannot bond efficiently. However, the DNA/RNA molecule itself is more prone to flexibility and deformation.

If A-form DNA/RNA is like steel. Hard, sturdy and inflexible.

B-form DNA/RNA is like cotton candy. Soft, light, and very flexible!

So, why do we even have B-form?!

B-form exists for two reasons:

1. While B-form is flexible, it is also very strong despite not having hydrogen bonds. It is very resistant to stretching and can help to keep cell components together.
2. B-form allows for more efficient packing of DNA in chromosomes. With double-stranded B-DNA, you can fit more DNA strands into a small area. It is also better to work with than A-form due to that.

In summary, B-form helps to stabilize the chromosome and keep DNA condensed. Its flexible nature allows it to pack onto chromosomes better.

However, when in B-Form on chromosomes, it is hard to stretch and break. There is a very specific arrangement of B-Form DNA molecules called “Z-DNA”. Z-DNA has a zigzag pattern with both strands running in the same direction. Z-DNA is very rigid and is able to resist heat.

Z-DNA: Not the zombies 🧠🦟:

Z-DNA is found typically after heat shock in bacteria or after cellular stress. It can also form under strong positive supercoiling! Z-DNA is usually stabilized through a specific protein called the DNA-binding protein called HU. It forms a complex with the DNA that stabilizes it and prevents it from forming a double-stranded helical structure like A-Form and B-Form.

An illustration of B-DNA, Z-DNA/Z-RNA and Za domain (alpha) from mdpi.com. Check it out if you want to learn more of Z-DNA!

A little bit on E. coli, the Za domain and the HU protein:

In E. coli, the Za domain is part of the HU protein. The HU protein binds to the base pairs of Z-DNA to stabilize it. The Za domain binds to the Z-DNA to stabilize it through hydrophobic interactions. This makes it even more stable and resistant to disruption.

The E. coli has a DNA repair system. When the E. coli has Z-DNA, it will activate its DNA repair system. This DNA repair system repairs the Z-DNA, converting it back to B-DNA.

The Za domain is a highly conserved domain in many HU proteins across species. It is able to sense Z-DNA through the use of its amino acids. It is responsible for stabilizing and protecting Z-DNA through hydrophobic interactions.

Through the knowledge of Z-DNA, we can find applications that are extremely useful. One application is in the treatment of cancer. The formation of Z-DNA stabilizes the chromosomes in cancer cells and prevents replication. This could allow for the targeting of cancer cells without harming the host body (Check out this 📑 if you are more interested)! Truely a groundbreaking potential 🎁

Another important application is the storage of genetic information. This is done via the stabilization of Z-DNA through the use of specific proteins and molecules! Not exciting, huh? Z-DNA can be used to store large amounts of genetic information with very high density. Since Z-DNA is stabilized, it is very stable and has long shelf life. This means that it can theoretically be used as a method of storing data digitally. In fact, Z-DNA can carry up to 6 bit data, making it one of the best methods in the biological world! If we were to put all the information stored on the internet onto Z-DNA, we would only need a few thousand grams to store it all. This means we can store multiple years worth of data in just a few kilograms! Take that into perspective! Check out this study if you are more interested researchGate.

Correspondance of Genetic Code 📕📗📘📙:

Genes are like the story, and DNA is the language that the story is written in.

— Sam Kean.

The central dogma of molecular biology describes the process by which information flows from DNA to mRNA to protein. The first step of protein synthesis is transcription. Transcription is the process of copying the information encoded in DNA into RNA. This process requires the enzyme RNA polymerase. RNA polymerase will bind to an open region of DNA (known as a promoter), which allows it to get to work. RNA polymerase converts a section of a DNA strand into a complementary RNA strand using a template strand. In order to save alot of explination, check out this animated video that explains this process in 2-ish minutes:

From DNA to protein, a visual animation by ‘yourgenome.’ It might be a little outdated, but it helps with the visualization of the process itself 👍

A template strand is a complementary RNA sequence to a given DNA strand. DNA transcription is a process in which RNA is synthesized from a DNA template using RNA polymerase. RNA Polymerase reads across the DNA strand in a 5’ to 3’ direction and forms a complementary RNA strand in a 3’ to 5’ direction. This step is called RNA processing. This process involves more technically said the removal of introns from the pre-mRNA and the addition of a 5' cap and 3' poly(A) tail to the mRNA.

• Intron: Introns are non-coding regions of DNA within a gene that are removed from a primary RNA transcript (precursor RNA). They are not translated into protein.
• Poly(A) Tail: This is a short stretch of nucleotides at the 3' end of an mRNA strand. They are believed to be important for gene expression and translation.

The final step of protein synthesis is translation. This process involves the ribosome and many other factors. The ribosome is a complex molecule composed of two subunits, a large subunit and a small subunit. These subunits come together during the process of translation. The small subunit binds to the mRNA and scans it for the start codon AUG. The start codon marks the beginning of a coding region of mRNA. The large subunit of the ribosome binds to a tRNA. Each tRNA is specific for an amino acid and brings that amino acid to the ribosome. The ribosome links amino acids together in the order specified by the codons in the mRNA.

Key points about the ribosome:

1. A ribosome is a large complex composed of proteins and a few types of RNA.
2. They are responsible for reading and decoding the RNA to synthesize proteins.
3. They also contain a specific binding site for transfer RNA (tRNA).

All three phases of translation: initiation, elongation, and termination. Greatly illustrated by lumenlearning!

There are three phases of translation: initiation, elongation, and termination. The process of translation begins with initiation. During the initiation, the mRNA is found to have a short sequence of nucleotides that are recognized by the ribosomes. This short sequence is called the Shine-Dalgarno sequence. The ribosomes also scan for a special code, known as an ATG start code, which tells the ribosomes to start protein synthesis.. The Shine-Dalgarno sequence is a sequence upstream of the start codon AUG. The small subunit scans the mRNA until it reaches the start codon AUG. There are many proteins known as Initiation Factors, such as eIF2 and eIF3. They are involved in a very fast process that we call scanning (which is referred in ‘scan’). In scanning, the small 60S subunit (of the ribosome) moves with the aid of the initiation factors along the mRNA strand until it finds the AUG start code. The ribosome is essentially a microscopic super robot that copies messages! When the ribosome receives the corresponding mRNA and the appropriate Amino Acids, it will start the translation process. The large subunit of the ribosome then binds to the small subunit! This is the start of the elongation phase of translation.

The elongation phase begins once the ribosome successfully binds to it’s respective mRNA. A tRNA carrying an Amino Acid will bind to the ribosome’s 3' end, and transfer the Amino Acid over to the mRNA. This tRNA recognizes the start codon AUG. Then ribosome links the amino acid to the growing polypeptide chain and moves along the mRNA, one codon at a time. The next tRNA in line recognizes the next codon on the mRNA. The ribosome links this amino acid to the growing polypeptide chain and moves along the mRNA. This process continues until the ribosome reaches a stop codon. This is the termination phase of translation. When the ribosome reaches a stop codon, a release factor binds to the ribosome. The release factor have the following characteristics:

1. A release factor is a protein that stops the translation of the polypeptide chain once it encounters a Stop Codon.
2. To repeat: the Stop Codons act as signals to let the ribosome know when the translation process should be over and the protein should be released.
3. Once the release factor encounters its respective Stop Codon, it stops the translation process and causes the ribosome to release the new protein.

“Wanna know the truth about yourself and this universe?
Just learn to understand your DNA code then you’ll see.”
― Toba Beta, My Ancestor Was an Ancient Astronaut

Super Simplifed Protein Folding:

Once a protein is fully synthesized, it will undergo a process known as folding. The folding process helps to allow the protein to reach its optimal shape. It’s important for proteins to have the correct shape since they cannot function properly if they are not folding properly. The formation of secondary and tertiary structures is crucial for protein folding, and there are many factors that influence this important event.

When a protein is first formed, it will be unorganized and “floppy” in regards to its shape. It is imperative that the proteins have an ideal shape in order for them to interact properly with other proteins and create the protein complex, which is essentially “just” a group of proteins that work together. In order for proteins to properly fold over themselves, they need to be within a very specific temperature, pH, and presence of molecules. It’s an extremely delicate process and it is very difficult for us to replicate this process in a lab (for now).

If we cracked the code of protein folding, we’ll be able to create designer proteins! Designer proteins are modified versions of existing proteins that are tailor-made for specific functions. A glorious example on a protein (peptide hormone) we have cracked is insulin! We’re able to artificially manufacture insulin since we know how it should properly fold, thanks to Frederick Banting and Charles Best since the year 1921. Before their revolutionary discovery, insulin was extracted from the pancreases of cattle and such animals. This is why Banting’s work was revolutionary. Artificial insulin became accessible to everyone in need! Definitely! Designer proteins can be used to treat countless diseases by making your body create the desired protein that is needed.

Another example I find (which seems very promising) is with the designer protein called M83. This designer protein was created by Professor Paul Gardner and his team at the University of Wisconsin-Madison’s Medical School. The protein is a derivative of vitamin D and, when given to mice, was found to slow down the development of tumours. Imagine if this is replicated in humans! We could possibly slow down cancer! I recommend to check out these articles bellow if you are more interested:

Alpha-synuclein spreading in M83 mice brain revealed by detection of pathological α-synuclein by…

Experimental Preemptive Immunotherapy of Murine Cytomegalovirus Disease with CD8 T-Cell Lines…

Ask yourself to subscribe to the newsletter if you haven’t 📰, become a follower of knowledge, and let’s travel this journey together 🎈 Thanks for reading and listening, have a wonderful weekend!

— Lucid Owl 🦉, out.