info.txt

Cell
Cell Membrane 
Short Description
The cell membrane is composed primarily of a phospholipid bilayer, with other molecules such as proteins and cholesterol embedded. Phospholipids have 2 unsaturated fatty acid tails and one head. The phospholipid head is hydrophilic (it's attracted to water) and the 2 unsaturated fatty acid tails are hydrophobic (they repel water). The phospholipid bilayer has many kinks and bends in it. This allows the inside of the membrane to be fluid, meaning it can get more or less solid depending on outside conditions, such as temperature. This characteristic is mainly due to the cholesterol embedded. The many proteins in the membrane have a vast array of uses, some including being used for transport, attachment, and signaling.",


Long Description 
1. **Whole Bilayer**: Expanding on (3), this is the entire cell membrane as a phospholipid bilayer. As mentioned in (3), “like dissolves like”. In other words, the phosphate group (polar) likes to face the watery cytosol and ECM (polar), but the fatty acid tails (nonpolar) hide in the middle amongst themselves, away from the watery polar regions. Between the phospholipids, many channel proteins aid the facilitated diffusion of large polar molecules through the membrane, as they cannot pass through the nonpolar region of the fatty acid tails in the phospholipid bilayer. Small nonpolar molecules may pass through without such aid as they can fit through the gaps between the polar heads and are able to comfortably pass by nonpolar regions due to the “like dissolves like” property. Proteins that require ATP called carrier proteins that move a molecule against its concentration gradient (low to high) are performing active transport, as opposed to passive transport, which can occur either naturally or with the help of facilitated diffusion, and it goes down the concentration gradient (high to low). Furthermore, cholesterol molecules are added/removed in between the membrane to increase/decrease membrane fluidity, respectively, because it either decreases/increases the compactness of the phospholipids (respectively). Additionally, there are glycoproteins and glycolipids, which are proteins or lipids attached to a sugar that serve as “ID tags'' on the cell membrane to aid in cell-to-cell recognition and the creation of tissue.

2. **Single phospholipid**: A single phospholipid consists of a phosphate group as the head and two fatty acid tails, that are held together with a glycerol backbone. The phosphate group is negatively charged, making it polar, thus making it hydrophilic and able to form bonds with other large, polar molecules. The fatty acid tails are simply two hydrocarbon chains, thus nonpolar and hydrophobic. The bend in one of the fatty acid tails is due to a double bond between two carbon atoms. The bend creates more gaps and space between adjacent phospholipids, causing some of the fluidity of the membrane.

3. **2 phospholipids across from each other**: Building off of the information from (2), these two phospholipids are oriented facing away because, as a piece of the cell membrane, it is the border between the polar cytosol and the polar extracellular matrix (ECM). Thus, the polar heads face the polar regions, while the fatty acid tails “hide” away (hence ‘hydrophobic’) from the watery polar regions.


Open Channel and Gated Channel

Gated Transmembrane Ion Channel:
A gated transmembrane ion channel is a specialized protein embedded in the cell membrane that facilitates the regulated passage of ions (charged particles) across the membrane. These channels possess a gating mechanism, which can be controlled by various cellular signals like voltage changes (voltage-gated channels), chemical messengers (ligand-gated channels), or physical deformation (mechanosensitive channels). The gating process modulates the flow of ions, crucial for electrical signaling and cellular communication.

Open Transmembrane Ion Channel:
An open transmembrane ion channel is a specific state of a transmembrane protein channel where it allows the continuous and unrestricted movement of ions across the cell membrane. This state occurs when the channel is not obstructed or closed by any regulatory mechanisms. Open channels play a vital role in maintaining ion gradients, electrical potentials, and cellular homeostasis by permitting the unimpeded flux of ions through the cell membrane.

Bacterial Cell Walls 
Most of the prokaryotes and bacterias found in your body are surrounded by a cell wall that provides them with structure and rigidity. It assists the cells in attaching with other cells, as well as protects them against osmotic forces and harmful chemicals. Scientists have distinguished bacterial cell walls into two basic types: Gram-positive cell wall, and Gram-positive cell wall. Some gram-negative and gram-positive bacterias are found in our digestive tracts and are part of our normal microbiota found in and on our body, while others are agents of infections and diseases. 
Microbiota refers to the community of microorganisms that reside in a specific environment.
Structure of the cell wall
The bacterial cell wall is composed of a mesh-like structure of polysaccharides called peptidoglycan. 
Peptidoglycan is composed mainly of two alternating sugar molecules known as N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). These two sugar molecules are covalently bonded to one another in an alternating chain. And these NAG and NAM chains are in terms attached to other NAG and NAM chains through short connecting chains of amino acids. 
Gram-positive cell walls
Gram-positive cell walls have a really thick layer of peptidoglycan facing the outer surface. This layer of peptidoglycan also contains a special chemical known as teichoic acids. Some teichoic acids are covalently linked to lipids, forming lipoteichoic acids that help anchor the peptidoglycan to the cellular membrane of the cell. Gram-positive cell walls help protect the bacteria from osmotic lysis by providing structural support. Additionally, with the teichoic acids embedded in its peptidoglycan layer, there is an overall negative charge on the surface of the bacteria as well as a potential passage of ions through the cell wall. 
Gram-negative cell walls
Gram-negative cell wall consists of a thin layer of peptidoglycan sandwiched between the cytoplasmic cellular membrane and the outer cellular membrane. 
The cytoplasmic cellular membrane is your average phospholipid bilayer composed of two leaflets that are both made up of phospholipids. The outer cellular membrane, on the other hand, is a lipid bilayer that is composed of two different leaflets. The inner leaflet consists of phospholipids, while the outer leaflet consists of lipopolysaccharides (LPS). 
LPS (lipopolysaccharide) is essentially an union of lipid and sugar. The lipid portion of the LPS is widely known as lipid A. Lipid A is harmful when it is released into the surrounding by dead gram-negative cells, and it may cause fever, inflammation, as well as blood clotting in humans. Because of the harms posed by lipid A, killing large numbers of gram-negative pathogens with antimicrobial drugs releases large amounts of lipid A that can pose a greater threat to the patient than the pathogens themselves. 

Like the cytoplasmic cellular membrane, there are proteins embedded in the outer membrane of the gram-negative cell, including channel proteins that allow movement of molecules through the membrane.

The space between the cytoplasmic membrane and the outer membrane is called the periplasmic space, which contains the peptidoglycan and the periplasm. 
Periplasm is the gel found in the periplasmic space, and it houses water, nutrients, and a variety of substances secreted by the cell.


Golgi
Short Description
The Golgi apparatus, aka the Golgi body, is an organelle composed of a series of small, flat sacs stacked in the cell's cytoplasm. The function of the Golgi apparatus is to sort out and package protein and lipid molecules synthesized by the ER or free-floating ribosomes for intercellular use or transport out of the cell. Additionally, the Golgi can add "tags" to molecules, making them more structurally stable. It can sometimes also locate where the tagged structure goes. 

Pool Maturation and Vesicle Trafficking Models
The pool maturation model and the vesicle trafficking model are two opposing theories explaining how the Golgi apparatus works in the processing and sorting of proteins and lipids. These models provide different perspectives on how the Golgi cisterns change over time and how molecules move through the Golgi. Here is an overview of the two models:

1. Tank maturity model:

In pool maturation models, Golgi cisterns are considered to be relatively stable structures that change over time as they mature. How the model works:

A. Stacking of cisterns: The Golgi apparatus consists of a series of stacked cisterns, with the cis surface (entry surface) closest to the endoplasmic reticulum (ER) and the trans surface (exit surface) furthest from the ER.

B. One-way flow: proteins and lipids enter the Golgi apparatus through vesicles fused to the cis surface. These molecules then move through the stacked pools, a process called "pool maturation." The tank itself changes over time. As the pool matures, it migrates from the cis to the trans side of the Golgi stack.

C. Advancement of enzymes: Each pool contains a specific set of enzymes responsible for modifying molecules. As the tank matures and moves through the stack, it acquires the appropriate enzymes needed for further processing. This allows for sequential modification of the molecule as it passes through the Golgi apparatus.

D. Vesicle formation: When molecules undergo the necessary modifications, they are packaged into vesicles through the transverse surface of the Golgi apparatus. These vesicles then transport the molecule to its final destination, such as transport to other cellular compartments or secretion from the cell.

Advantages: The cistern maturation model provides a more dynamic view of the Golgi apparatus and is consistent with experimental observations of cistern changes over time. It is also responsible for the sorting and processing of molecules within the Golgi stack.

2. Vesicle transport model:

On the other hand, models of vesicle trafficking suggest that Golgi cisterns are stable and do not change significantly over time. Instead, it has been proposed that molecules are sorted and processed by the Golgi apparatus via vesicles that shuttle between different compartments. How the model works:

A. Solid pool: In this model, each pool within the Golgi stack is viewed as a distinct compartment with a distinct set of enzymes. These tanks remain relatively stable and do not mature or change position.

B. Vesicle-mediated transport: Molecules entering the Golgi apparatus from the ER are sorted into transport vesicles, which emerge from the pool and fuse with the next compartment in the Golgi stack. These vesicles carry the molecules and enzymes needed for further processing.

C. Enzyme Localization: In contrast to the pool maturation model, where the enzyme moves with the pool, the vesicle trafficking model assumes that the enzyme is localized within a specific pool. Therefore, each tank has its own set of enzymes for grooming.

D. Sorting and packaging: Molecules are sorted into different vesicles according to their final destination. After processing, they are packaged into vesicles, which transport them to their intended destinations, such as lysosomes, the plasma membrane, or for secretion.

Advantages: The vesicle trafficking model simplifies the organization of the Golgi apparatus by considering the pool as a stable compartment. It also provides a clear mechanism for sorting and transporting molecules.

3. 


Mitochondria
Short Description
The mitochondria, aka the "powerhouse of the cell", is a very important organelle that primarily functions in generating energy in the form of ATP for cellular processes through cellular respiration. The anatomy of a mitochondrion is designed to maximize energy production. The inner and outer membranes increase surface area and provide a place for energy production to happen.

Long Description (Anatomy) 
The mitochondria, aka the "powerhouse of the cell", is a very important organelle that primarily functions in generating energy in the form of ATP for cellular processes through cellular respiration. Cellular respiration is a process where mitochondria  (singular: mitochondrion), takes in glucose and oxygen and releases ATP (adenosine triphosphate, which contains energy), carbon dioxide, and water.

The anatomy of a mitochondrion is designed to maximize energy production. There are two membranes, an inner and outer one, with spaces in between. The inner membrane has many folds called cristae, which provide more surface area for cellular respiration to happen. The space between the inner and outer membrane, called the intermembrane space, is where an H+ gradient is built up for ATP Synthase to use. The inner space that the inner membrane encloses is called the matrix, and that's where the electron transport chain (ETC) used during respiration is located.

One interesting thing about mitochondria is that they are thought to have originally been autonomous alpha-proteobacteria (a type of prokaryote) that merged with a larger cell, and over the eons they developed a mutualistic relationship. This is referred to as the endosymbiotic theory. There's a lot of evidence to support this:
> Mitochondria have their own DNA, separate from the cell
> They have a double membrane of their own
> They replicate independently of their cell

Mitochondria also play roles in apoptosis and calcium signaling.

Long Description (Cellular Respiration) 
Cellular respiration is a process that happens in the cytoplasm and the mitochondria and generates energy in the form of ATP (adenosine triphosphate). The equation for respiration is: C6H12O6+ 6O2 → 6CO2 + 6H2O (glucose + oxygen -> carbon dioxide + water). The process of cellular respiration can be divided into three main stages: glycolysis, the citric acid cycle (also known as the Krebs cycle), and the electron transport chain (ETC), coupled with oxidative phosphorylation.

Glycolysis: This is the first step of respiration, and happens in the cytoplasm. One molecule of glucose is broken down, or oxidized, into 2 pyruvate molecules. The cell uses 2 ATP (think of this as an energy investment), and once broken down, the reaction yields 4 ATP and 2 NADH, which are electron carriers that are transported to the mitochondria for use in the electron transport chain. The net yield of glycolysis are 2 NADH molecules and 2 ATP molecules, and 2 molecules of pyruvate which move into the mitochondria for the next stage of respiration, the Krebs Cycle.
The Krebs Cycle: This is the second step of respiration, and takes place in the mitochondrial matrix. The two pyruvate molecules produced in glycolysis are slightly structurally altered to form a compound called acetyl coenzyme A (acetyl-CoA). This is often known as the intermediate step between glycolysis and the Krebs Cycle. Next, the acetyl-CoA is turned into citric acid, which is where the name ‘citric acid cycle’ is derived. Next, the citric acid undergoes a series of chemical oxidation reactions where carbons are removed from the acid, and electron carriers NADH and FADH2  are generated. In addition, molecules of carbon dioxide are made, which are discarded as waste, and  One helpful analogy to remember the Krebs Cycle may be to remember a boxer punching a bag; each time the acetyl-CoA is “punched”, it is oxidized a bit further, releasing electrons that are transferred to carriers and carbon atoms that form CO2. For each molecule of acetyl-CoA(remember that one glucose molecule = two pyruvate molecules), 1 ATP, 3 NADH, 1  FADH2 , 2CO2
The Electron Transport Chain and Oxidative Phosphorylation: This final step of respiration takes place in the inner mitochondrial membrane and the intermembrane space. Here, the electron carriers generated in the Krebs Cycle and Glycolysis feed their electrons to the ETC (electron transport chain), which uses the energy to make ATP. NADH and FADH2 transfer their electrons to a series of proteins embedded in the inner mitochondrial membrane. The electrons then move from complex to complex, and as they move, they drop to a lower energy level, which releases energy. This released energy is used to pump H+ ions up their concentration gradient, into the intermembrane space from the matrix. This creates a proton gradient, which is electrochemically charged and stores potential energy. Any molecule tends to move down its concentration gradient, from an area of high to low concentration, and the only way the stored H+ ions can do that is through a protein called ATP Synthase, which is embedded in the inner membrane. As the ions flow through, ATP Synthase phosphorylates an ATP from ADP and P (hence the name oxidative phosphorylation), and the final electron acceptor oxygen combines with the H+ ions and electrons to form water. The overall result from this step (for one molecule of glucose) is 30-32 ATP, NAD+, FAD, and water. The NAD+ and FAD are recycled, and the cell uses the ATP for various cellular processes.

Nucleus
The nucleus serves as the control center of the cell, and is where genetic information is stored. The DNA is enclosed in a protective structure called the nuclear envelope. This is a double membrane made up of a phospholipid bilayer, much like that of the cell membrane. Holes in the envelope, called nuclear pores, regulate what goes in and out of the nucleus. The interior of the nucleus, also called the nucleoplasm, contains the genetic material of the cell. In humans, there are 23 pairs of chromosomes, and the nucleus is where processes such as DNA replication and transcription happen. The nucleolus is a condensed region inside the nucleus, and it is the location of assembly of ribosomes (rRNA), which exit the nucleus for use in protein synthesis. 


Rough ER
Short Description
The endoplasmic reticulum (ER) is a vast network of membranes, constituting over half of the total membrane in many eukaryotic cells. It consists of membranous tubules and sacs called cisternae, separating the ER lumen from the cytosol and connecting with the nuclear envelope. The ER has two interconnected regions: smooth ER, lacking ribosomes, is involved in lipid synthesis, carbohydrate metabolism, drug detoxification, and calcium ion storage. On the other hand, 

Rough ER, studded with ribosomes, plays a role in synthesizing and secreting proteins. It also acts as a membrane factory, growing by incorporating proteins and phospholipids and transporting them via vesicles to other parts of the cell.
Long Description
The endoplasmic reticulum (ER) is a prominent membrane network in eukaryotic cells, constituting over 50% of the cell's total membrane. It comprises tubules and sacs called cisternae, separating the ER lumen from the cytosol and connecting with the nuclear envelope. The ER consists of two interconnected regions: smooth ER, devoid of ribosomes, performs various metabolic functions, including lipid synthesis, carbohydrate metabolism, drug detoxification, and calcium ion storage. It is vital for producing lipids like oils, phospholipids, and steroids (e.g., sex hormones and adrenal gland steroids). The smooth ER's enzymes detoxify drugs and poisons, particularly in liver cells, by adding hydroxyl groups to increase solubility. In muscle cells, it acts as a calcium ion reservoir, regulating muscle contractions by releasing calcium ions upon stimulation. Conversely, rough ER, studded with ribosomes, primarily synthesizes and secretes proteins. For instance, pancreatic cells produce insulin in the ER, releasing it into the bloodstream. Secretory proteins are often glycoproteins with covalently attached carbohydrates. Moreover, rough ER serves as a membrane factory, growing in place by incorporating membrane proteins and phospholipids, and exchanging membrane portions with other components of the endomembrane system via transport vesicles.


Rough ER Protein Modifications
As described above, the Rough ER is composed of a network of membrane sacs studded with ribosomes. Its membranes are composed of proteins and phospholipid bilayers.

Protein Synthesis
Protein synthesis happens in the cell’s cytoplasm. Ribosomes are responsible for protein synthesis, and they read the genetic instructions from messenger RNA (mRNA) and link the amino acids together to form a polypeptide chain. Many of these polypeptides would later become membrane proteins, secreted proteins, or proteins utilized by other organelles within the cell. 

Translocation
Proteins that would later enter the rough ER contain signal peptides. Signal peptides are located at the N-terminus and they guide the ribosomes and its polypeptide chain to the rough ER. The signal peptides are recognized by the signal recognition particle (SRP), which would temporarily stop translation by binding to the ribosome upon detecting the signal sequence. The SRP would then bind to the SRP receptor in the ER membrane, which helps the ribosome-mRNA complex to attach with the translocon, a protein channel found in the membrane of the ER. The signal peptide of the polypeptide chain is then directly inserted into the translocon’s pore. Finally, the SRP receptor releases the SRP, and the ribosome continues its protein translation. 

Vocabs (the bolded words; make them additional links in the above paragraph):
N-terminus = N-terminus the end of the polypeptide chain where the first amino acid is found
Signal Recognition Particle (SRP) = SRP is a complex of RNA and protein that recognizes signal peptides of the newly synthesized protein and temporarily halts translation by binding to the ribosome. It then guides the ribosome-polypeptide complex to the ER.
Signal Recognition Particle Receptor (SRP Receptor) = The SRP receptor is a protein receptor found on the ER membrane. It interacts with the SRP to direct the ribosome-polypeptide complex to the ER for translocation. 
Translocon = Translocon is a protein channel found in the membrane of the ER. It is composed of several subunits, including the Sec61 complex, which forms the core channel.

Cotranslational Translocation
As the ribosomes continue to synthesize the polypeptide chain, it threads the growing chain directly through the translocon and in the lumen of the ER. The growing polypeptide chain passes through the Sec61 channel of the translocon, which opens to facilitate the chain’s passage. As the polypeptides enter the lumen, it would encounters the ER chaperons, which 

Vocabs (the bolded words; make them additional links within the paragraph in the sim):
Sec61 = Sec61 is a component of the core of the protein-conducting translocon. 

Protein Modifications
As the polypeptides chain is being inserted, or translocated, into the ER lumen, it encounters a specialized environment encompassing ER chaperones, which assists with protein folding to help the polypeptides chain attain its correct three-dimensional structure. 

Post-Translational Modifications
The protein undergoes various post-translational modifications, and these modifications include, proteolytic cleavage, glycosylation, and disulfide bond formation. 

Proteolytic Cleavage
When the protein is in the ER lumen, it can undergo cleavage where specific peptide segments are removed to turn itself into an active protein. For example, signal peptides could be cleaved off at a very specific site by an enzyme known as the signal peptidase such that the remaining mature protein remains in the lumen. 

N-linked Glycosylation
As the protein chain enters the Er lumen, it can undergo N-linked glycosylation. This occurs when enzymes in the ER add a carbohydrate chain to specific asparagine residues of the protein to create a glycoprotein. This sort of modification helps with protein folding, stability, and recognition. 
Vocabs (the bolded words; make them additional links within the paragraph in the sim):
Asparagine residue in this case refers to the amino acid asparagine that is part of the protein sequence. During N-linked glycosylation, the carbohydrate chain is attached to the side chain of the asparagine through an amide bond. 

Disulfide Bond Formations
As the protein undergoes folding, disulfide bonds can form between the sulfur atoms in cysteine residues within the protein to promote a protein’s structural stability. There are specific enzymes in the ER that help with forming covalent bonds between these cysteine residues. 
Vocabs (the bolded words; make them additional links within the paragraph in the sim):
Cysteine residue in this case refers to the amino acid cysteine that is part of the protein sequence. Cysteine contains sulfur atoms, which is what allows two cysteine to form a disulfide bond in disulfide bond formations.  

Quality Control
The protein folding process is monitored and carried out by chaperones and other folding enzymes. Just like it is in a factory, if a protein is not being folded, or manufactured, correctly, it would be degraded through a process called the ER-associated degradation (ERAD). 

Transport
Proteins that are folded correctly and past the quality control test in our ER factory can be assembled into more complex structures, such as protein complexes. The final protein product would then be packaged into vesicles and transported into their final cellular locations, including cellular organelles, the cellular membrane, or for secretion. 

Lysosome
Short Description
Lysosomes are membranous sacs containing hydrolytic enzymes used by animal cells to digest macromolecules. These enzymes function optimally in the acidic environment within lysosomes. When lysosomes rupture, their contents can provide nutrients for the cell. Some human cells, like macrophages, participate in phagocytosis to defend the body against invaders. Lysosomes also engage in autophagy, where damaged organelles or cytosol are encased in a double membrane and broken down by lysosomal enzymes, releasing small organic compounds for reuse. Lysosomal storage diseases result from the absence or malfunction of hydrolytic enzymes in lysosomes, causing a buildup of indigestible material that disrupts cellular activities, though these conditions are rare in the general population.

Long Description
Lysosomes in animal cells are membranous sacs filled with hydrolytic enzymes used for digesting macromolecules in an acidic environment. When lysosomes rupture, their contents mix with cytosol and provide nutrients for the cell. Some human cells, like macrophages, carry out phagocytosis, which involves engulfing and destroying invaders. Lysosomes also participate in autophagy, where damaged organelles or cytosol are enclosed by a double membrane, and lysosomes fuse with the vehicle's outer membrane to dismantle the material, releasing small organic compounds back to the cytosol for reuse. This process helps cells renew themselves, with a human liver cell recycling half of its macromolecules weekly.

Lysosomes play a vital role in maintaining cellular health and functionality. These membranous sacs filled with hydrolytic enzymes serve to digest macromolecules within the acidic environment of animal cells. Additionally, lysosomes facilitate autophagy, a process through which damaged organelles or small amounts of cytosol are broken down and their organic components are released back into the cytosol for reuse. This recycling process helps cells continually renew themselves, contributing to overall cellular homeostasis. The ability of lysosomes to break down and recycle cellular materials is essential for proper cell function and survival. Ongoing research in this area expands our knowledge of cellular biology, offering potential applications in fields like regenerative medicine and biotechnology.

People with inherited lysosomal storage diseases lack functional hydrolytic enzymes in their lysosomes, leading to an accumulation of indigestible material that hinders cellular activities. An example is Tay-Sachs disease, where a missing or inactive lipid-digesting enzyme impairs the brain due to lipid buildup. Thankfully, lysosomal storage diseases are rare in the general population.

Vacuole
Vacuoles are derived from the endoplasmic reticulum and Golgi apparatus, being an integral part of a cell's endomembrane system. They have selective membrane transport, resulting in a different composition from the cytosol. These vesicles serve various functions in different cell types, including food vacuoles formed through phagocytosis, contractile vacuoles in freshwater protists, and enzymatic hydrolysis in plants and fungi. Additionally, vacuoles in plants store organic compounds, protect against herbivores, and contain pigments to attract pollinating insects. The central vacuole, found in mature plant cells, holds cell sap with inorganic ions, aiding in cell growth as it absorbs water.

Peroxisome

The peroxisome is a specialized metabolic compartment enclosed by a single membrane. Inside, enzymes facilitate the removal of hydrogen atoms from specific molecules and transfer them to oxygen, generating hydrogen peroxide. These reactions serve various purposes, including detoxifying alcohol and harmful substances in the liver by transferring hydrogen to oxygen. Despite the toxicity of H2O2, the peroxisome houses an enzyme that converts it into water. This illustrates the vital role of the cell's compartmental structure, as it segregates the enzymes producing H2O2 from other cellular components that could be harmed. While peroxisomes grow larger by assimilating proteins and lipids from the cytosol, ER, and within the peroxisome itself, their origins and multiplication in evolution remain unresolved.

Ribosome
Ribosomes, complexes made of ribosomal RNA (rRNA) and protein, carry out protein synthesis in cells. They are made up of a larger top subunit and a smaller bottom subunit. These both interact with mRNA and tRNA molecules to perform translation. High rates of protein synthesis are associated with an abundance of ribosomes. Ribosomes function in two cytoplasmic locations: free ribosomes in the cytosol and bound ribosomes attached to the rough endoplasmic reticulum or nuclear envelope. Both bound and free ribosomes are structurally identical and can switch roles. Free ribosomes produce proteins for the cytosol, such as enzymes catalyzing sugar breakdown, while bound ribosomes create proteins for membrane insertion, packaging within organelles, or cell export, common in cells specialized in protein secretion, like the pancreas cells that secrete digestive enzymes.

Flagella
Flagella is a whiplike extension that extends from the surface of certain types of cells. Its primary function is enabling cellular organisms to move and locomote across mediums. Although its function is virtually the same across different types of organisms, its structure is different in prokaryotes and eukaryotes. 

Functions
The flagella facilitates the movements of cells through their surrounding medium. In some cases, flagella can also serve as a sensory organelle that helps certain bacteria and eukaryotic cells to respond to changes in the environment. Flagella also helps with capturing prey in some organisms by creating currents that bring food particles and prey closer. 

Prokaryotic Flagella
In prokaryotes, the flagella enables the bacterial cells to flee from harmful environments as well as move towards favorable environments where nutrients and lights are abundant. The prokaryotic flagella is composed of three parts: filament, hook, and basal body. And it’s important to note that unlike the eukaryotic flagella, the prokaryotic flagella is not covered by the cell membrane. 

Filament 
Filament is a long, helical, shaft that extends from the cell surface. It is made up of many globular molecules of proteins called flagellin. The flagella lengthens as the cell secretes molecules of flagellin through the hollow core to be deposited in a clockwise-helix manner at the tip of the filament. Contrary to the popular notion, the filament does not move in a whip-like motion, rather, it rotates like a propeller to drive the movement of the cell. 

Hook 
The hook is a curved and flexible structure that serves as a joint connecting the basal body and the filament together. It is composed of a different type of protein, and like the filament, it extends out of the cell. 

Basal Body
The basal body is a complex structure embedded in the cell envelope. It is composed of many different proteins that usually spans the cell wall and the cell membrane. It anchors the hook and the filament through a rod and a series of protein rings, including the L ring (lipopolysaccharide layer), P ring (peptidoglycan layer), MS ring (membrane-spanning), and the C ring (cytoplasmic). The basal body also drives the rotation of the flagella through the flow of ions across the cell membrane and through its own structure. 

Arrangement
Flagellums are arranged in many different ways in bacteria. 
Peritrichous flagella covers the entire surface of the bacteria. 
Single polar flagella is found at the end of the bacteria. Tuft polar flagella are a series of polar flagellums found at the end of the bacteria. 
Endoflagella is a type of flagella that wraps tightly around the spiral-shaped bacteria, spirochetes, between its cytoplasmic membrane and outer membrane rather than protruding out into the medium like the other types of flagella. Its rotation causes the spirochetes to corkscrew through its environment. 

Function
The exact mechanism behind the movement of prokaryotic flagella is still being researched. However, we do know that the prokaryotic flagella rotates like a propeller rather than whipping from side to side. Bacteria moves with a series of “runs” and “tumbles”. As the flagella rotates counterclockwise, it propels the bacteria to move in a single direction for some time. And if multiple flagella are present, the flagellum aligns and rotates as a bundle. However, runs are interrupted by tumbles when the flagella rotates clockwise, or in the case of a bundle, when they each rotate independently.
There are receptors for light and chemicals on the surface of the cell that signal the movement of the flagella and change its speed and direction. When a bacteria is approaching a favorable medium, the attractants in that medium would stimulate the bacteria to move towards it. Similarly, when a bacteria is approaching a harmful environment, the repellant would stimulate the bacteria to move in any direction away from it. 

Eukaryotic Flagella
Eukaryotic flagella enables the movement, locomotions, as well as other special properties in eukaryotes. It is also more structurally complex compared to prokaryotic flagella. In addition, it moves in a whip-like manner and is completely covered by the cell membrane, unlike those of prokaryotic flagella. 

Microtubule shaft
The shaft of the eukaryotic flagella is composed of a bundle of microtubules, which are tubular chains made up of protein subunits called tubulin. We often refer to the way in which the microtubules are organized in the eukaryotic flagella shaft as the “9+2” arrangement of PAIRS. This essentially means that nine PAIRs (so two) of microtubules surround a central PAIR. The “9+2” arrangement allows for a sturdier structure and the ability for the flagellum to bend. 

Kinetosome
Kinetosome is basically the fancy term for the basal body of the eukaryotic flagella. It anchors the flagellum and serves as a microtubule-organizing center. Unlike the microtubule shaft, the microtubules of the kinetosome are organized in a “9+0” arrangement of TRIPLETS (note the difference, triplets, not pairs). This means 9 TRIPLETS (so three) of microtubules with 0 microtubules in the center. 

Dynein Arms
Dynein arms are composed of the motor protein dynein. Dynein arms extend from one of the microtubules to the adjacent pair, and they utilize the energy from ATP hydrolysis to cause the flagella to bend and move in a whip-like motion. 



Nervous System
https://sketchfab.com/3d-models/neuron-d40557a1e4154267b78117433bc51296 (neuron)

Brain
The brain is the central organ of the nervous system. It is a highly complex organ that is responsible for controlling and regulating all vital body functions, as well as intelligence, consciousness, processing information, memories, thoughts, and much more. The brain is made up of billions of neurons, and billions of other supporting cells like glial cells. It is subdivided into many parts, each specialized to control specific tasks. For example, the brainstem controls vital functions, the hippocampus functions in long term memory, and the amygdala is a major center for processing emotions.
Brain parts

The forebrain, the largest and most complex part of the brain, is responsible for a wide variety of higher functions essential to human cognition and behavior It includes major structures such as the cerebral cortex, thalamus, and hypothalamus. It plays an important role in advanced cognitive processes such as thinking, thinking, speaking, problem solving and also in sensory perceptions such as touch, sight, hearing, taste and smell. The thalamus acts as a relay station, receiving sensory information from different parts of the body and directing it to the appropriate areas of the brain for other associated functions. Overall, the forebrain is the command center of the brain, organizing complex mental processes, regulating vital bodily functions, and organizing our behaviors and experiences 

The hindbrain, positioned at the back of the brainstem, controls vital, involuntary body functions  such as breathing, heartbeat, stability, and coordination. It consists of structures like the medulla oblongata, pons, and cerebellum, acting as a manipulate center for the body and facilitating powerful verbal exchange among the mind and the autonomic (involuntary) nervous system. Additionally, it regulates the sleep cycle, oxygen-carbon dioxide levels inside the bloodstream, and integrates sensory facts for maintaining stability and coordination in numerous activities. Overall, the hindbrain plays a crucial function in crucial bodily features and our involuntary nervous system. 

The midbrain is located between the hindbrain and forebrain. It serves as a relay station for sensory and motor signals, facilitating verbal exchange among regions of the brain. The midbrain includes systems such as the tectum, tegmentum, and substantia nigra. The tectum is responsible for processing visual and auditory information, assisting us in orienting our attention and responding to applicable stimuli in our surroundings. The tegmentum performs functions in controlling motion. and coordinating actions initiated through the motor cortex. Additionally, the substantia nigra is concerned with the production of dopamine, a neurotransmitter critical for motor manipulation and the "reward system". Furthermore, the midbrain is connected to the hindbrain and forebrain, taking into consideration the mixing of sensory inputs and coordination of complex behaviors. In summary, the midbrain plays a large role in sensory processing, motor control, and the law of important neurotransmitters, contributing to our notion, motion, and overall cognitive functioning. 

The frontal lobe, located at the front of the cerebral cortex, plays a critical role in various higher-level cognitive functions and personality traits. It is responsible for  functions such as decision-making, problem-solving, and planning. The frontal lobe also houses the primary motor cortex, which controls voluntary movements throughout the body. In addition, it is involved in regulating emotions, social behavior, and aspects of personality, including shaping our ability to interact with others and exhibit self-control. The frontal lobe's intricate neural networks and connectivity enable us to engage in complex cognitive processes, exercise self-awareness, and make conscious choices.


Frontal lobe: The frontal lobe, situated at the front of the brain's cerebral cortex, is a vital region with diverse functions. Found beneath the frontal skull bones, this lobe exists in all mammals but varies in size and complexity. It cooperates with other brain regions, contributing to memory formation and overall brain function. While the brain's complexity prevents attributing one role to a single region, the frontal lobe plays a crucial role in planning, decision-making, speech, motor skills, object comparison, memory formation, empathy, personality development, and attention management. Damage to the frontal lobe, exemplified by Phineas Gage's case, can result from factors like dementia, trauma, stroke, multiple sclerosis, or brain tumors, leading to personality changes, impaired decision-making, and disrupted emotional regulation. The brain's ability to rewire itself allows for compensation in the face of injury, highlighting its remarkable adaptability.

Parietal lobe: The parietal lobe constitutes approximately 19% of the total neocortical volume, slightly larger than the occipital lobe. Its spatial expanse extends from the central sulcus anteriorly, demarcating it from the frontal lobe, to the parieto-occipital fissure posteriorly, segregating it from the occipital lobe. Its inferolateral boundary coincides with the lateral sulcus, separating it from the temporal lobe. Medially, its confines are defined by the medial longitudinal fissure that splits both cerebral hemispheres. Primarily responsible for sensory perception and integration, the parietal lobe plays a pivotal role in processing taste, hearing, sight, touch, and smell. Within its realm lies the brain's primary somatosensory cortex, a critical area for interpreting input from various body regions. Remarkably, research underscores a direct relationship between sensory input and parietal lobe surface area, with more prominent sensory regions of the body, such as the fingers and hands, corresponding to larger dedicated sections of the parietal lobe. Yet, despite the progress in understanding, the parietal lobe remains enigmatic, with ongoing studies continually unveiling new insights into its functions, emphasizing the likelihood that its complete range of roles is yet to be fully uncovered.

Occipital lobe: The occipital lobe is a part of the brain responsible for processing visual information. On its outer surface, there are raised areas called gyri and grooves called sulci. The sides of the occipital lobe have three specific sulci that help define its shape. Inside, on the middle surface, there's a distinct calcarine sulcus, which divides it into the cuneus and lingual regions. The upper and lower parts of the calcarine sulcus contain the primary visual cortex, which is where we process what we see. This cortex gets information from our eyes and helps us understand things like shapes, colors, and distances. The occipital lobe's main job is to help us understand and recognize what we see. There are different areas in this lobe, like the primary visual cortex, which receives information directly from our eyes, and secondary visual cortex areas that work with this information to help us recognize objects and understand where they are. The occipital lobe also sends information to other parts of the brain through two pathways: the dorsal stream for recognizing where objects are and the ventral stream for recognizing what objects are.

Temporal lobe: The temporal lobes, found on both sides of the brain, have distinct functions and differences. The left temporal lobe is crucial for understanding language, memory, and verbal skills. On the other hand, the right temporal lobe is involved in processing non-verbal information, recognizing faces and expressions, and understanding drawings and music. These lobes depend on input from various brain areas and sensory information, and they can even convert sounds into mental images. For instance, without the temporal lobes, comprehending speech would be difficult. In these lobes, there's a region called Wernicke's area, vital for language comprehension and speech meaning. The auditory cortex, within the temporal lobe, processes auditory information by filtering out irrelevant details and sending meaningful information to be understood. This cortex is essential for hearing and language processing, and it's a part of the limbic system, which handles emotions, memories, and motivation. The hippocampus in the temporal lobe forms new memories, while the amygdala, also in the limbic system, processes emotions, fear, and reward, influencing memory strength based on emotional significance.

Amygdala: The amygdala, an almond-shaped structure within the brain's temporal lobe, is vital for survival. It serves as the brain's early warning system, detecting threats and inducing fear responses. Beyond fear, it influences aggression, reward-based learning, unconscious memory, social understanding, parenting emotions, memory-emotion connections, and addiction behaviors. Positioned bilaterally in the temporal lobes near sensory processing areas, it's level with the eyes vertically. Named for its almond-like shape and slightly darker hue compared to other brain tissue, it's composed of neurons and glial cells and contains 13 nuclei on average. Despite its small size, the amygdala profoundly impacts emotions, behavior, and survival instincts.

Hippocampus: The hippocampus, part of the brain's limbic system, is vital for memory, learning, and emotions. Resembling a seahorse, it's named after the Greek word for "seahorse." Each person has two hippocampi, one on each brain side, studied extensively for its role in neurological conditions. It stores short-term memories and facilitates their conversion into long-term memory, contributing to emotional processing and anxiety. Although once linked to smell, it primarily handles memory and connects with various brain regions. Key functions include storing declarative facts, transferring short-term to long-term memory (assisted by sleep), and aiding spatial navigation and mental mapping. Located about 1.5 inches deep within each temporal lobe above the ears, it comprises three main parts: the hippocampus proper (Cornu Ammonis, seahorse-shaped), the dentate gyrus (interlocking ring), and the subiculum (linking them). Unlike many body parts, the hippocampus can grow and change over time (neurogenesis). In summary, the hippocampus is a vital brain structure for memory processing, emotions, and spatial navigation.

Hypothalamus: The hypothalamus, deep within the brain, links the endocrine and nervous systems to maintain body stability (homeostasis). It interprets chemical signals from the brain and peripheral nerves, regulating vital functions like temperature, blood pressure, hunger, thirst, and mood. It also influences sex drive and sleep, controlling these processes through the autonomic nervous system and hormone regulation. Hormones serve as messengers, and the hypothalamus generates some, storing them in the posterior pituitary or sending releasing hormones to the anterior pituitary. This prompts the release of hormones that impact target organs or stimulate other glands. Notably, the posterior pituitary stores oxytocin, affecting childbirth, lactation, bonding, and vasopressin, regulating water balance and blood pressure. Additionally, the hypothalamus produces dopamine (linked to pleasure and motivation) and somatostatin (inhibiting hormone secretion). It corrects body temperature, stress, and daily rhythm imbalances. Anatomically, the hypothalamus, roughly almond-sized, is located below the thalamus, above the pituitary gland, at the base of the brain above the brainstem.



Neuron anatomy
https://sketchfab.com/3d-models/neuron-d40557a1e4154267b78117433bc51296 (based off of this 3D Model)
Neurons are the building blocks of the nervous system. They are responsible for receiving, processing, and transmitting electrochemical signals, enabling communication and functioning of our nervous system. Like all the other cells in our body, neurons are composed of several different parts, each with a specialized function. In this section of our simulation, we will explore these specialized components in detail.

1. Soma: The soma is essentially the cell body of the neuron. It houses the nucleus and various organelles that are crucial for the normal functioning of the neuron. Signals received by the dendrites are directed to the soma where they are processed and then sent further down to the axon. 

3. Dendrite: Dendrites are the branch-like structures that extend from the soma (cell body). Their primary function is to receive signals in the form of neurotransmitters from the axons of neighboring neurons. These signals are then transmitted electrically across the soma, where they are processed, and then further down into the axon.

2. Axon: The axon is a projection that extends from the cell body (soma), and electrical signals called action potentials travel down it. Once action potentials reach the end of the axon, to a place called the axon terminal, neurotransmitters (chemical messengers) are released into the synapse. The neurotransmitters released by the axon are received by dendrites of adjacent neurons, and the action potential cycle continues again. signals to adjacent neurons. 

6 & 8. Axon Terminal: Towards their ends, axons branch out into several smaller branches known as axon terminals. Each axon terminal contains small structures called synaptic vesicles. These vesicles are like tiny pods that store and release neurotransmitters, which are chemical messengers that transmit signals between neurons when stimulated by action potentials traveling down the axon.

Neurotransmitters (Follows 6 & 8; Additional): Neurotransmitters are chemical messengers that carry signals to neurons within our nervous system. They exist in various types and forms, with each type carrying a distinct signal. 

Synapse (Follows 6 & 8; Additional): The synapse is the small junction between the axon terminal of one neuron and the dendrites of another neuron. It is a crucial site where communication between neurons takes place. The communication occurs when an action potential reaches the axon terminal of one neuron, triggering the release of neurotransmitters from the synaptic vesicles into the synapse. The neurotransmitters would then travel across the synapse and bind to the specific receptors on the receiving neuron, allowing the transmission of the signal from one neuron to the next.

4. Myelin Sheath: The axons of neurons are covered by a protective layer called the myelin sheath, which consists of a thick coating of fatty substance called myelin. This myelin sheath acts as an insulator, which enhances the speed at which signals travel along the axon.

5. Nodes of Ranvier: The myelin sheath does not cover the entire length of the axon. Instead, it has periodic gaps along the myelinated axon where the myelin is absent, and these gaps are called Nodes of Ranvier. These nodes are important for the transmission of action potentials. They serve as points along the axon where the electrical signals are regenerated, which in terms allows for more efficient conduction of nerve impulses.

7. Axon hillock: The axon hillock is the part of a neuron that connects the soma to the axon. The impulses from all the dentries are integrated at the axon hillock to determine whether an action potential will occur.


Action Potential

**na k pumps**: 
Sodium-potassium pumps, also known as Na+/k+ pumps, are integral proteins that are embedded in the membranes of cells. It regulates cell volume and concentration of ions across the membrane in all cells, but in neurons it plays another essential function: causing and restoring action potentials via controlled movement of ions across the membrane. Na/K pumps do this by hydrolyzing a molecule of ATP. This gives it the energy to transport sodium ions out of the cell and potassium ions in. This happens hundreds of thousands of times per second in neurons, which disrupts the electrochemical gradient, allowing for action potentials to occur.
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**simple description**: A neuron fires by changing the electrochemical gradient across its membrane. This change in charge stimulates a signal to go down the cell, a signal which activates the subsequent neuron and causes the process to happen again. The first thing that is needed is a stimulus, which is usually a signal from the previous neuron. Once a stimulus is received, the neuron opens its Na/K pumps, which cause ions to flow into and out of the cell. This is known as **depolarization**, which is when the established resting charge of the neuron is disrupted. Once a certain voltage is reached, something called the action potential is reached, where the neuron sends a signal down the axon, which acts as a stimulus for the adjacent neuron. Once the action potential is fired off, **repolarization** occurs, where the neuron lets neurons flow back to its resting state, restoring resting potential and awaiting the next stimulus.

**all or nothing**: All or nothing refers to the message that a neuron sends. There will either be one, strong message, or no message. Neurons never emit a weak message.



Muscular System
Gluteus maximus - The largest muscle in the buttocks, responsible for hip extension and external rotation.

Quadriceps - A group of four muscles in the front of the thigh that extend the knee joint.

Hamstrings - A group of three muscles at the back of the thigh that flex the knee joint and extend the hip joint.

Gastrocnemius - The calf muscle, responsible for plantar flexion of the foot.

Biceps brachii - Located in the upper arm, this muscle is involved in elbow flexion and forearm supination.

Triceps brachii - Found on the back of the upper arm, it extends the elbow joint.

Rectus abdominis - Also known as the "abs," it flexes the spine and helps stabilize the core.

Obliques - The external and internal obliques assist in rotation and lateral flexion of the spine.

Pectoralis major - The chest muscle, responsible for shoulder flexion, adduction, and internal rotation.

Latissimus dorsi - Located in the back, it performs shoulder extension, adduction, and medial rotation.

Deltoids - The shoulder muscles responsible for arm abduction, flexion, and extension.

Trapezius - The large muscle in the upper back and neck, responsible for shoulder movement and neck extension.

Soleus - Located beneath the gastrocnemius, it assists in plantar flexion of the foot.

Tibialis anterior - Found in the front of the lower leg, it dorsiflexes the foot.

Rectus femoris - Part of the quadriceps group, it flexes the hip and extends the knee.

Adductor muscles - Located on the inside of the thigh, these muscles bring the legs together.

Supraspinatus - One of the rotator cuff muscles, it assists in shoulder abduction.

Infraspinatus - Another rotator cuff muscle, it aids in shoulder external rotation.

Teres major - Found on the back, it assists in shoulder adduction and internal rotation.

Transverse abdominis - The deepest abdominal muscle, providing core stability and compressing the abdominal contents.


Skeletal System

Skull (Cranium): Protects the brain and houses sensory organs like the eyes and ears.
Spine (Vertebral Column): Provides support and protection for the spinal cord and allows for movement.
Femur: The thigh bone, which is the longest and strongest bone in the body, supporting body weight and facilitating walking and running.
Pelvis (Pelvic Girdle): Forms the base of the spine and supports the body's weight; also protects internal reproductive organs.
Ribs: Protect the vital organs in the chest, such as the heart and lungs.
Humerus: The upper arm bone that connects the shoulder to the elbow and allows for arm movement.
Tibia and Fibula: The two bones in the lower leg, with the tibia bearing most of the body's weight and the fibula providing stability.
Radius and Ulna: The bones of the forearm that allow for forearm rotation and wrist movement.
Sternum (Breastbone): Protects the heart and lungs and anchors the ribcage.
Scapula (Shoulder Blade): Provides attachment for muscles that control shoulder and arm movement.
Phalanges: Phalanges are the smaller bones that make up the fingers and toes, with each digit typically consisting of three phalanges (proximal, middle, and distal).

Circulatory System
The heart is the central organ of the circulatory, or cardiovascular, system. Its main function is to pump blood to deliver oxygen and nutrients to all the cells and tissues in the body. The heart maintains homeostasis and plays a critical role in oxygenating blood. In addition, it regulates blood pressure and supports the entire circulatory system. The heart is divided into four chambers: two atria and two ventricles, with one atrium and one ventricle on the left side and one atrium and one ventricle on the right side. The right atrium receives deoxygenated blood from the body and pumps it into the right ventricle, which then sends the blood to the lungs through the pulmonary artery for oxygenation. The left atrium receives freshly oxygenated blood from the lungs and pushes it into the left ventricle, which pumps the oxygen-rich blood out to the rest of the body. To ensure a one-way circulation of blood, valves are located between the atria and ventricles, preventing backflow.

Right Atrium
The right atrium is responsible for receiving oxygen-poor blood from the body through the superior and inferior vena cava. It serves as a holding chamber that allows blood to accumulate before it is transferred to the right ventricle for further circulation.
Right Ventricle
The right ventricle pumps oxygen-poor blood to the lungs via the pulmonary artery, where it undergoes oxygenation. The wall of the right ventricle is relatively thinner compared to the left ventricle, as it only needs to pump blood a short distance to the lungs.
Left Atrium
The left atrium receives oxygen-rich blood from the lungs through the pulmonary veins. This chamber acts as a conduit, passing the oxygenated blood into the left ventricle, which will then pump it to the rest of the body.
Left Ventricle
The left ventricle is responsible for pumping oxygen-rich blood to the entire body through the aorta. It has the thickest wall among the heart chambers, as it needs to generate substantial force to push blood through the extensive systemic circulation.
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Digestive System
The stomach, a key part of the gastrointestinal (GI) tract, is a muscular organ that digests food using acids and enzymes. It's located in the upper left abdomen and has five sections: cardia, fundus, body, antrum, and pylorus. These sections work together to contract, mix, and process food before passing it to the small intestine.

Liver: The liver carries out numerous essential functions, such as detoxifying harmful substances from the blood, disposing of old red blood cells, producing bile to aid in digestion, metabolizing proteins, carbohydrates, and fats for energy, facilitating blood clotting, regulating blood volume, and storing glycogen and vitamins for later use. This organ is divided into two main parts: the larger right lobe and the smaller left lobe, both containing intricate networks of blood vessels and lobules. 
Urinary System
Bladder: The bladder’s key function is to store urine before the body releases the waste through the urethra.

The kidneys, each about the size of a human fist, are bean-shaped organs located on either side of the spine in the lower back. They filter waste and excess substances from the blood, playing a pivotal role in regulating electrolyte balance, blood pressure, and producing urine for waste elimination.

Respiratory System 
The lungs, crucial for breathing, sit symmetrically in the chest. The right lung has three lobes, while the left has two. Their main job is gas exchange, taking in oxygen and releasing carbon dioxide. Air enters through the nose/mouth, travels down the airway, and reaches tiny sacs called alveoli. Here, oxygen enters the blood, and carbon dioxide is removed. Protective features like nasal hairs and mucus ensure smooth airflow. Lungs are buoyant, and one can function with just one. Regular exercise boosts lung capacity, and adults have millions of alveoli. In essence, lungs play a vital role in maintaining our health and sustaining life through efficient gas exchange.

Trachea

Diaphragm 

The diaphragm is a muscular dome that separates the abdominal and thoracic (chest) chambers. Its ability to contract and relax to aid in breathing is essential to respiration. The diaphragm flattens and contracts during inhalation, expanding the thoracic cavity's volume and producing a vacuum that pulls air into the lungs. It relaxes and takes on the shape of a dome during exhalation, reducing the volume of the thoracic cavity and releasing air from the lungs. In addition to offering structural support, the diaphragm divides the heart and lungs from the abdominal organs. By raising stomach pressure, it also helps with other body processes like sneezing, coughing etc. The diaphragm is coordinated with other breathing muscles by means of the phrenic nerves that regulate its movements.