Hydrochloric acid does not break peptide bonds. Instead, it is responsible for breaking down the quaternary and tertiary structure of the protein, leaving the peptide bonds more accessible for pepsin to break. Pepsin is responsible for breaking the bonds between the amino acids, which is known as proteolysis. Lastly, the acidic environment of the stomach kills many microbes, preventing infection.

The portal vein carries blood from the small intestine to the liver. It has an extremely high nutrient content because it is fed with blood by the superior and inferior mesenteric veins along the small intestine. The small intestine absorbs most of the nutrients from the food that has been ingested into these vessels that take the blood directly to the liver to remove toxins prior to being distributed to the rest of the body. Essentially all nutrients that enter the body must first pass through the portal vein and liver before being distributed to other tissues.

The liver has a variety of functions including carbohydrate metabolism and storage, as well as blood detoxification. Most hepatocytes have a developed smooth endoplasmic reticulum to facilitate detoxification or wastes absorbed from the blood. Glucose is also taken from the blood and dimerized to create glycogen. Digested proteins are also carried to the protein for metabolism. Once fully dissociated, the amino acids of digested proteins can be used to build new molecules.

Although the liver produces bile, it does not store it. Bile storage is the function of the gall bladder.

The liver is capable of storing glucose from carbohydrates when blood sugar levels are normal or elevated. This is accomplished by the process of converting glucose to glycogen in the liver, or glycogenesis. Once the blood sugars are low, the liver will convert glycogen back to glucose in a process called glycogenolysis. Gluconeogenesis is the synthesis of glucose from non-carbohydrate molecules, such as amino acids and triglycerides. Deglutition is simply the technical term for swallowing, and is not involved in glucose metabolism.

As chyme enters the small intestine, the pancreas will release bicarbonate ions. This not only helps lower the acidity of the chyme that has just left the stomach, but also allows enzymes in the small intestine to be at their ideal pH when functioning.

Proteases, such as chymotrypsin, break down proteins and hydrochloric acid from parietal cells in the stomach contributes to the acidity of the stomach contents.

In the pancreas, islets of Langerhans are collections of alpha, beta, and gamma endocrine cells (these are most numerous in the tail of the pancreas). Beta cells are more centrally located and are responsible for insulin secretion. Alpha cells are peripherally located and release glucagon, while delta cells are interspersed and release somatostatin. Chromaffin cells are located in the adrenal medulla and produce catecholamines.

The liver detoxifies everything we consume and thus must have the ability to regenerate the damage from such intense metabolism. The liver converts fat soluble toxins to water soluble ones so that they can be secreted in urine. It also manages by products of regular digestion such as converting the ammonia formed from protein digestion into urea.

This patient most likely has vitamin B12 deficiency. B12 is found in meats and thus a vegan individual would be deficiency in this vitamin. It takes several years to develop B12 deficiency because the liver can store B12 for a few years before signs and symptoms present of the deficiency. B12 deficiency is associated with neurological symptoms (peripheral neuropath) and macrocytic/megaloblastic anemia. B9 also presents with megaloblastic/macrocytic anemia but it does not have neurological signs or symptoms. Additionally, B9 is found in green vegetables and there is nothing in the patient's history to suggest B9 deficiency. B6 presents as sideroblastic anemia. 

Pancreatic function is crucial for the absorption of fat-soluble vitamins (ADEK). Toxins, such as alcohol, have the potential to harm the pancreas, leaving it non-functional. Best treatment in this person would be to stop alcohol consumption, and to administer the deficient vitamins and pancreatic enzymes to replace those that are not working. 

As macromolecules are absorbed in the small intestine, polar molecules are able to float freely into the bloodstream due to their hydrophilic nature. Nonpolar molecules, such as fats and lipids, require a carrier protein in order to move throughout the body. Fats are carried through the lymphatic system by chylomicrons and are then dumped into the bloodstream through the thoracic duct.

Proteins, nucleic acids, and carbohydrates all contain polar regions that allow them to travel easily within aqueous environments.