Digestion

context: In the human digestive system, food enters the mouth and mechanical digestion of the food starts by the action of mastication (chewing), a form of mechanical digestion, and the wetting contact of saliva. Saliva, a liquid secreted by the salivary glands, contains salivary amylase, an enzyme which starts the digestion of starch in the food; the saliva also contains mucus, which lubricates the food, and hydrogen carbonate, which provides the ideal conditions of pH (alkaline) for amylase to work. After undergoing mastication and starch digestion, the food will be in the form of a small, round slurry mass called a bolus. It will then travel down the esophagus and into the stomach by the action of peristalsis. Gastric juice in the stomach starts protein digestion. Gastric juice mainly contains hydrochloric acid and pepsin. As these two chemicals may damage the stomach wall, mucus is secreted by the stomach, providing a slimy layer that acts as a shield against the damaging effects of the chemicals. At the same time protein digestion is occurring, mechanical mixing occurs by peristalsis, which is waves of muscular contractions that move along the stomach wall. This allows the mass of food to further mix with the digestive enzymes.
qas: answers: the action of mastication (chewing)
question: What is the first step in the human digestive system?

answers: a liquid secreted by the salivary glands
question: What is saliva?

answers: salivary amylase
question: What is in saliva that starts to digest the starches?

answers: a small, round slurry mass
question: What is the definition of bolus?

answers: peristalsis
question: What is the action of the food morving down the esophagus into the stomach called?

context: Other animals, such as rabbits and rodents, practise coprophagia behaviours - eating specialised faeces in order to re-digest food, especially in the case of roughage. Capybara, rabbits, hamsters and other related species do not have a complex digestive system as do, for example, ruminants. Instead they extract more nutrition from grass by giving their food a second pass through the gut. Soft faecal pellets of partially digested food are excreted and generally consumed immediately. They also produce normal droppings, which are not eaten.
qas: answers: eating specialised faeces in order to re-digest food
question: What is the practive of coprophagia behaviours?

answers: extract more nutrition
question: Why do some animals pass food through their gut twice?

answers: excreted and generally consumed immediately
question: What happens with these soft feacal pellets?

answers: not eaten
question: Are normal droppings also eaten? 

context: Digestive systems take many forms. There is a fundamental distinction between internal and external digestion. External digestion developed earlier in evolutionary history, and most fungi still rely on it. In this process, enzymes are secreted into the environment surrounding the organism, where they break down an organic material, and some of the products diffuse back to the organism. Animals have a tube (gastrointestinal tract) in which internal digestion occurs, which is more efficient because more of the broken down products can be captured, and the internal chemical environment can be more efficiently controlled.
qas: answers: internal and external digestion
question: What are the two types of digestion?

answers: earlier in evolutionary history
question: When did external digestion develop?

answers: most fungi
question: What still uses the external digestion system?

answers: gastrointestinal tract
question: What is the name of the tube that helps add in animal digestion?

answers: more of the broken down products can be captured, and the internal chemical environment can be more efficiently controlled
question: Why is internal digection better than external?

context: The nitrogen fixing Rhizobia are an interesting case, wherein conjugative elements naturally engage in inter-kingdom conjugation. Such elements as the Agrobacterium Ti or Ri plasmids contain elements that can transfer to plant cells. Transferred genes enter the plant cell nucleus and effectively transform the plant cells into factories for the production of opines, which the bacteria use as carbon and energy sources. Infected plant cells form crown gall or root tumors. The Ti and Ri plasmids are thus endosymbionts of the bacteria, which are in turn endosymbionts (or parasites) of the infected plant.
qas: answers: Agrobacterium Ti or Ri plasmids
question: What elements can transfer to plant cells?

answers: the plant cell nucleus
question: Where do transferred genes enter?

answers: opines
question: What do bacteria use as carbon and energy sources?

answers: end
question: What happens to infected plant cells?

answers: The Ti and Ri plasmids
question: What are endosymbionts of the bacteria?

context: Teeth (singular tooth) are small whitish structures found in the jaws (or mouths) of many vertebrates that are used to tear, scrape, milk and chew food. Teeth are not made of bone, but rather of tissues of varying density and hardness, such as enamel, dentine and cementum. Human teeth have a blood and nerve supply which enables proprioception. This is the ability of sensation when chewing, for example if we were to bite into something too hard for our teeth, such as a chipped plate mixed in food, our teeth send a message to our brain and we realise that it cannot be chewed, so we stop trying.
qas: answers: in the jaws (or mouths)
question: Where are teeth found?

answers: to tear, scrape, milk and chew food
question: What are teeth used for?

answers: enamel, dentine and cementum
question: What are teeth made out of?

answers: a blood and nerve supply
question: What in human teeth enables proprioception?

answers: our teeth send a message to our brain and we realise that it cannot be chewed, so we stop trying.
question: What happens when you bite something you cant chew?

context: The abomasum is the fourth and final stomach compartment in ruminants. It is a close equivalent of a monogastric stomach (e.g., those in humans or pigs), and digesta is processed here in much the same way. It serves primarily as a site for acid hydrolysis of microbial and dietary protein, preparing these protein sources for further digestion and absorption in the small intestine. Digesta is finally moved into the small intestine, where the digestion and absorption of nutrients occurs. Microbes produced in the reticulo-rumen are also digested in the small intestine.
qas: answers: The abomasum
question: What is the fourth and final stomach compartment in ruminants?

answers: a monogastric stomach
question: What is the abomasums close equivalent?

answers: a site for acid hydrolysis of microbial and dietary protein, preparing these protein sources for further digestion and absorption in the small intestine.
question: What does this site serve primarily as?

answers: the digestion and absorption of nutrients occurs
question: What happens to digesta when it moves to the small intestine?

answers: Microbes produced in the reticulo-rumen are also digested in the small intestine
question: What is also digested in the small intestine?

context: An earthworm's digestive system consists of a mouth, pharynx, esophagus, crop, gizzard, and intestine. The mouth is surrounded by strong lips, which act like a hand to grab pieces of dead grass, leaves, and weeds, with bits of soil to help chew. The lips break the food down into smaller pieces. In the pharynx, the food is lubricated by mucus secretions for easier passage. The esophagus adds calcium carbonate to neutralize the acids formed by food matter decay. Temporary storage occurs in the crop where food and calcium carbonate are mixed. The powerful muscles of the gizzard churn and mix the mass of food and dirt. When the churning is complete, the glands in the walls of the gizzard add enzymes to the thick paste, which helps chemically breakdown the organic matter. By peristalsis, the mixture is sent to the intestine where friendly bacteria continue chemical breakdown. This releases carbohydrates, protein, fat, and various vitamins and minerals for absorption into the body.
qas: answers: a mouth, pharynx, esophagus, crop, gizzard, and intestine.
question: What does a earthworms digestive systme consist of?

answers: dead grass, leaves, and weeds
question: What does an earthworm eat?

answers: The mouth is surrounded by strong lips
question: What helps the earthworm grab grass leaves and weeds?

answers: mucus
question: What is the food coated with for easier passage?

answers: The powerful muscles of the gizzard
question: What part of the earthworm helps churn and mix the dirt and food?

context: Digestion of some fats can begin in the mouth where lingual lipase breaks down some short chain lipids into diglycerides. However fats are mainly digested in the small intestine. The presence of fat in the small intestine produces hormones that stimulate the release of pancreatic lipase from the pancreas and bile from the liver which helps in the emulsification of fats for absorption of fatty acids. Complete digestion of one molecule of fat (a triglyceride) results a mixture of fatty acids, mono- and di-glycerides, as well as some undigested triglycerides, but no free glycerol molecules.
qas: answers: in the mouth
question: Where does the digestions of some fats start?

answers: the small intestine
question: Where are fats mainly digested?

answers: produces hormones that stimulate the release of pancreatic lipase from the pancreas and bile from the liver
question: What happens when there is a presence of fat in the small intestine?

answers: helps in the emulsification of fats for absorption of fatty acids
question: What does bile from the liver help do?

answers: a triglyceride
question: What is one molecule of fat?

context: Digestion is the breakdown of large insoluble food molecules into small water-soluble food molecules so that they can be absorbed into the watery blood plasma. In certain organisms, these smaller substances are absorbed through the small intestine into the blood stream. Digestion is a form of catabolism that is often divided into two processes based on how food is broken down: mechanical and chemical digestion. The term mechanical digestion refers to the physical breakdown of large pieces of food into smaller pieces which can subsequently be accessed by digestive enzymes. In chemical digestion, enzymes break down food into the small molecules the body can use.
qas: answers: the breakdown of large insoluble food molecules into small water-soluble food molecules so that they can be absorbed into the watery blood plasma
question: What is digestion?

answers: these smaller substances are absorbed through the small intestine into the blood stream
question: In some organisms, how are these molecules absorbed?

answers: mechanical and chemical digestion
question: What are the two ways that food is broken down?

answers: the physical breakdown of large pieces of food into smaller pieces which can subsequently be accessed by digestive enzymes
question: What is mechanical digestion?

answers: enzymes break down food into the small molecules the body can use
question: What is chemical digestion?

context: Different phases of digestion take place including: the cephalic phase , gastric phase, and intestinal phase. The cephalic phase occurs at the sight, thought and smell of food, which stimulate the cerebral cortex. Taste and smell stimuli are sent to the hypothalamus and medulla oblongata. After this it is routed through the vagus nerve and release of acetylcholine. Gastric secretion at this phase rises to 40% of maximum rate. Acidity in the stomach is not buffered by food at this point and thus acts to inhibit parietal (secretes acid) and G cell (secretes gastrin) activity via D cell secretion of somatostatin. The gastric phase takes 3 to 4 hours. It is stimulated by distension of the stomach, presence of food in stomach and decrease in pH. Distention activates long and myenteric reflexes. This activates the release of acetylcholine, which stimulates the release of more gastric juices. As protein enters the stomach, it binds to hydrogen ions, which raises the pH of the stomach. Inhibition of gastrin and gastric acid secretion is lifted. This triggers G cells to release gastrin, which in turn stimulates parietal cells to secrete gastric acid. Gastric acid is about 0.5% hydrochloric acid (HCl), which lowers the pH to the desired pH of 1-3. Acid release is also triggered by acetylcholine and histamine. The intestinal phase has two parts, the excitatory and the inhibitory. Partially digested food fills the duodenum. This triggers intestinal gastrin to be released. Enterogastric reflex inhibits vagal nuclei, activating sympathetic fibers causing the pyloric sphincter to tighten to prevent more food from entering, and inhibits local reflexes.
qas: answers: the cephalic phase , gastric phase, and intestinal phase
question: What are three digestions phases?

answers: at the sight, thought and smell of food, which stimulate the cerebral cortex
question: Where does the cephalic phase occur?

answers: the hypothalamus and medulla oblongata
question: Where are taste and smell stimuli sent to?

answers: 3 to 4 hours
question: How long does the gastric phase take?

answers: by distension of the stomach, presence of food in stomach and decrease in pH
question: How is the gastric phase stimulated to start?

context: In a channel transupport system, several proteins form a contiguous channel traversing the inner and outer membranes of the bacteria. It is a simple system, which consists of only three protein subunits: the ABC protein, membrane fusion protein (MFP), and outer membrane protein (OMP)[specify]. This secretion system transports various molecules, from ions, drugs, to proteins of various sizes (20 - 900 kDa). The molecules secreted vary in size from the small Escherichia coli peptide colicin V, (10 kDa) to the Pseudomonas fluorescens cell adhesion protein LapA of 900 kDa.
qas: answers: several proteins form a contiguous channel traversing the inner and outer membranes of the bacteria
question: What happens in a chennel transupport system? 

answers: the ABC protein, membrane fusion protein (MFP), and outer membrane protein (OMP)[specify]
question: What three protien subunites are in the chennel transupport system?

answers: various molecules, from ions, drugs, to proteins of various sizes
question: What does this secretion system transport?

context: In addition to the use of the multiprotein complexes listed above, Gram-negative bacteria possess another method for release of material: the formation of outer membrane vesicles. Portions of the outer membrane pinch off, forming spherical structures made of a lipid bilayer enclosing periplasmic materials. Vesicles from a number of bacterial species have been found to contain virulence factors, some have immunomodulatory effects, and some can directly adhere to and intoxicate host cells. While release of vesicles has been demonstrated as a general response to stress conditions, the process of loading cargo proteins seems to be selective.
qas: answers: the formation of outer membrane vesicles
question: What other method does Gram-negative bacters use to release material?

answers: , forming spherical structures made of a lipid bilayer enclosing periplasmic materials
question: What happens with the pinch off part of the outer membrane?

answers: response to stress conditions
question: What does the release of vesicles seem to demenstrate?

answers: some have immunomodulatory effects, and some can directly adhere to and intoxicate host cells
question: What virulence factors do some bacterial species have?

context: Underlying the process is muscle movement throughout the system through swallowing and peristalsis. Each step in digestion requires energy, and thus imposes an "overhead charge" on the energy made available from absorbed substances. Differences in that overhead cost are important influences on lifestyle, behavior, and even physical structures. Examples may be seen in humans, who differ considerably from other hominids (lack of hair, smaller jaws and musculature, different dentition, length of intestines, cooking, etc.).
qas: answers: swallowing and peristalsis
question: What muscle movements are used for digestion?

answers: energy
question: What does every stpe of digestion require?

answers: an "overhead charge"
question: What does needing energy to digest impose?

answers: lifestyle, behavior, and even physical structures
question: Over head charges influence what?

context: Digestion begins in the mouth with the secretion of saliva and its digestive enzymes. Food is formed into a bolus by the mechanical mastication and swallowed into the esophagus from where it enters the stomach through the action of peristalsis. Gastric juice contains hydrochloric acid and pepsin which would damage the walls of the stomach and mucus is secreted for protection. In the stomach further release of enzymes break down the food further and this is combined with the churning action of the stomach. The partially digested food enters the duodenum as a thick semi-liquid chyme. In the small intestine, the larger part of digestion takes place and this is helped by the secretions of bile, pancreatic juice and intestinal juice. The intestinal walls are lined with villi, and their epithelial cells is covered with numerous microvilli to improve the absorption of nutrients by increasing the surface area of the intestine.
qas: answers: in the mouth with the secretion of saliva and its digestive enzymes
question: Where does digestion begin?

answers: a bolus
question: What is food formed into before it is swallowed?

answers: the stomach
question: Where does food go after the esophagus?

answers: peristalsis
question: What is the action of food being moved into the stomach?

answers: hydrochloric acid and pepsin
question: What does gastric juice consist of?

context: Lactase is an enzyme that breaks down the disaccharide lactose to its component parts, glucose and galactose. Glucose and galactose can be absorbed by the small intestine. Approximately 65 percent of the adult population produce only small amounts of lactase and are unable to eat unfermented milk-based foods. This is commonly known as lactose intolerance. Lactose intolerance varies widely by ethnic heritage; more than 90 percent of peoples of east Asian descent are lactose intolerant, in contrast to about 5 percent of people of northern European descent.
qas: answers: an enzyme that breaks down the disaccharide lactose to its component parts
question: What is lactase?

answers: glucose and galactose
question: What are lactoses component parts?

answers: small intestine
question: Where are glucose and galactose absorbed?

answers: Approximately 65 percent
question: What percent of the population are unable to eat unfermented milk-based foods?

answers: lactose intolerance
question: What is knon as when you are  unable to eat unfermented milk-based foods?

context: After some time (typically 1–2 hours in humans, 4–6 hours in dogs, 3–4 hours in house cats),[citation needed] the resulting thick liquid is called chyme. When the pyloric sphincter valve opens, chyme enters the duodenum where it mixes with digestive enzymes from the pancreas and bile juice from the liver and then passes through the small intestine, in which digestion continues. When the chyme is fully digested, it is absorbed into the blood. 95% of absorption of nutrients occurs in the small intestine. Water and minerals are reabsorbed back into the blood in the colon (large intestine) where the pH is slightly acidic about 5.6 ~ 6.9. Some vitamins, such as biotin and vitamin K (K2MK7) produced by bacteria in the colon are also absorbed into the blood in the colon. Waste material is eliminated from the rectum during defecation.
qas: answers: chyme
question: What is the resulting thick liquid called?

answers: digestive enzymes from the pancreas and bile juice from the liver
question: What does chyme mix with in the duodenum?

answers: the small intestine
question: Where does hyme go after the duodenum?

answers: blood
question: Where is chyme absorbed into?

answers: the small intestine
question: Where does 95% of absobtion of nutrients occur?

context: In mammals, preparation for digestion begins with the cephalic phase in which saliva is produced in the mouth and digestive enzymes are produced in the stomach. Mechanical and chemical digestion begin in the mouth where food is chewed, and mixed with saliva to begin enzymatic processing of starches. The stomach continues to break food down mechanically and chemically through churning and mixing with both acids and enzymes. Absorption occurs in the stomach and gastrointestinal tract, and the process finishes with defecation.
qas: answers: the cephalic phase
question: What is the firs phase in preparation for digestion  in mammals?

answers: saliva is produced in the mouth and digestive enzymes are produced in the stomach
question: What is the cephalic phase?

answers: Mechanical and chemical digestion
question: What digestions begin in the mouth?

answers: The stomach continues to break food down mechanically and chemically through churning and mixing with both acids and enzymes
question: What happens in the stomach after the food is chewed and mixed with starches?

answers: in the stomach and gastrointestinal tract
question: Where does absorption occur?

context: Protein digestion occurs in the stomach and duodenum in which 3 main enzymes, pepsin secreted by the stomach and trypsin and chymotrypsin secreted by the pancreas, break down food proteins into polypeptides that are then broken down by various exopeptidases and dipeptidases into amino acids. The digestive enzymes however are mostly secreted as their inactive precursors, the zymogens. For example, trypsin is secreted by pancreas in the form of trypsinogen, which is activated in the duodenum by enterokinase to form trypsin. Trypsin then cleaves proteins to smaller polypeptides.
qas: answers: in the stomach and duodenum
question: Where does protein digestion occur?

answers: pepsin secreted by the stomach and trypsin and chymotrypsin
question: What are the three main enzymes that break down food?

answers: inactive precursors, the zymogens
question: What are digestive enzymes mostly secreted as?

answers: amino acids
question: What are dipeptidases broken down into?

answers: the pancreas
question: What organ secretes chymotrypsin?