Biochemistry

FIRST YEAR - FINAL TERM MR. Jan Jarrel Gillego 11/2021 - 01/2022
Digestive System

allows the body to eat only a few times each day and to
ingest more food than it can process at one time.

Secretion
 In a day, the digestive system secretes around 7 liters of
fluids.
 These fluids include saliva, mucus, hydrochloric acid,
enzymes, and bile.
 Saliva moistens dry food and contains salivary amylase, a
digestive enzyme that begins the digestion of carbohydrates.
 Mucus serves as a protective barrier and lubricant inside of
the GI tract.
 Hydrochloric acid helps to digest food chemically and
protects the body by killing bacteria present in our food.
 Enzymes are like tiny biochemical machines that
disassemble large macromolecules like proteins,
carbohydrates, and lipids into their smaller components.
 Finally, bile is used to emulsify large masses of lipids into
tiny globules for easy digestion.

D igestion of food into smaller pieces Digestion

I ngestion of food  Digestion is the process of turning large pieces of food into
mixingG and movement of food its component chemicals.
E xcretion of waste materials
 Mechanical digestion is the physical breakdown of large
S ecretion of fluids and digestive materials
pieces of food into smaller pieces.
absorpTion ion of nutrients
 This mode of digestion begins with the chewing of food by
the teeth and is continued through the muscular mixing of
Your Digestive System & How it Works food by the stomach and intestines.
What is the digestive system?  Bile produced by the liver is also used to mechanically break
 The digestive system is responsible for taking whole foods fats into smaller globules.
and turning them into energy and nutrients to allow the body  While food is being mechanically digested it is also being
to function, grow, and repair itself. The six primary chemically digested as larger and more complex molecules
processes of the digestive system include: are being broken down into smaller molecules that are easier
1. Digestion of food into smaller pieces to absorb.
2. Ingestion of food  Chemical digestion begins in the mouth with salivary
3. Mixing and movement of food and wastes through the amylase in saliva splitting complex carbohydrates into
body simple carbohydrates.
4. Excretion of wastes  The enzymes and acid in the stomach continue chemical
5. Secretion of fluids and digestive enzymes digestion, but the bulk of chemical digestion takes place in
6. Absorption of nutrients the small intestine thanks to the action of the pancreas.
 The pancreas secretes an incredibly strong digestive cocktail
known as pancreatic juice, which is capable of digesting
How does my digestive system work?
 Each part of your digestive system helps to move food and lipids, carbohydrates, proteins, and nucleic acids. By the
liquid through your GI tract, break food and liquid into time food has left the duodenum, it has been reduced to its
smaller parts, or both. chemical building blocks—fatty acids, amino acids,
 Once foods are broken into small enough parts, your body monosaccharides, and nucleotides.
can absorb and move the nutrients to where they are needed.
 Your large intestine absorbs water, and the waste products of Absorption
digestion become stool. Nerves and hormones help control  Once food has been reduced to its building blocks, it is
the digestive process. ready for the body to absorb.
 Absorption begins in the stomach with simple
molecules like water and alcohol being absorbed
Ingestion
 The first function of the digestive system is ingestion, or the directly into the bloodstream.
intake of food.  Most absorption takes place in the walls of the small
The mouth is responsible for this function, as it is the orifice intestine, which are densely folded to maximize the
through which all food enters the body. surface area in contact with digested food.
 The mouth and stomach are also responsible for the storage  Small blood and lymphatic vessels in the intestinal wall
of food as it is waiting to be digested. This storage capacity pick up the molecules and carry them to the rest of the
body.
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 Biochemistry
FIRST YEAR - FINAL TERM MR. Jan Jarrel Gillego 11/2021 - 01/2022
Digestive System

 The large intestine is also involved in the absorption

of water and vitamins B and K before feces leave the
body.

Processes of Digestion
 Food is the body’s source of fuel. The nutrients in food give
the body’s cells the energy they need to operate.
 Before food can be used it has to be mechanically broken
down into tiny pieces, then chemically broken down so
nutrients can be absorbed.
 In humans, proteins need to be broken down into amino
acids, starches into sugars, and fats into fatty acids and
glycerol.
 This mechanical and chemical breakdown encompasses the
process of digestion.
Excretion  Mechanical digestion: larger pieces of food get broken
 The final function of the digestive system is the excretion of down into smaller pieces while being prepared for chemical
waste in a process known as defecation. digestion; this process starts in the mouth and continues into
 Defecation removes indigestible substances from the body the stomach.
so that they do not accumulate inside the gut.  Chemical digestion: Several different enzymes break down
 The timing of defecation is controlled voluntarily by the macromolecules into smaller molecules that can be
conscious part of the brain, but must be accomplished on a absorbed. The parocess starts in the mouth and continues
regular basis to prevent a backup of indigestible materials. into the intestines.
 Saliva moistens the food, while the teeth masticate the food
and make it easier to swallow.
How does food move through my GI tract?
 To accomplish this moistening goal, the salivary glands
 Food moves through your GI tract by a process called
produce an estimated three liters of saliva per day.
peristalsis.
 The large, hollow organs of your GI tract contain a layer of
muscle that enables their walls to move.
 The movement pushes food and liquid through your GI tract
and mixes the contents within each organ.
 The muscle behind the food contracts and squeezes the food
forward, while the muscle in front of the food relaxes to
allow the food to move.

 Amylase, the digestive enzyme found in saliva, starts to

break down starch into simple sugars before the food even
leaves the mouth.
 The nervous pathway involved in salivary excretion requires
stimulation of receptors in the mouth, sensory impulses to
the brain stem, and parasympathetic impulses to salivary
glands.
 Once food is moistened and rolled and ready to swallow, it
is known as a bolus.

Swallowing and the Movement of Food

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 Biochemistry
FIRST YEAR - FINAL TERM MR. Jan Jarrel Gillego 11/2021 - 01/2022
Digestive System

 For swallowing to happen correctly a combination of 25 absorption in the small intestine.

muscles must all work together at the same time.  Stimulatory hormones such as gastrin and motilin help the
Swallowing occurs when the muscles in your tongue and stomach pump gastric juice and move chyme.
mouth move the bolus into your pharynx.  The complex network of hormones eventually prepares
 The pharynx, which is the passageway for food and air, is chyme for entry into the duodenum, the first segment of the
about five inches (5″) long—a remarkably small space. small intestine.
 A small flap of skin called the epiglottis closes over the
pharynx to prevent food from entering the trachea, which
Absorption in the Small Intestine
would cause choking. Instead, food is pushed into the
 During absorption, the nutrients that come from food (such
muscular tube called the esophagus.
as proteins, fats, carbohydrates, vitamins, and minerals) pass
through the wall of the small intestine and into the
bloodstream.
 In this way nutrients can be distributed throughout the rest of
the body.
 The small intestine increases surface area for absorption
through tiny interior projections, like small fingers, called
villi.

Waste Compaction in the Large Intestine

 In the large intestine there is resorption of water and
absorption of certain minerals as feces are formed. Feces are
the waste parts of the food that the body passes out through
the anus.

Organs of the Digestive System

 Waves of muscle movement, called peristalsis, move the
 The organs of the digestive system can be divided into
bolus down to the stomach.
upper and lower digestive tracts.
 The smooth muscles of the tubular digestive organs move
 The upper digestive tract consists of the esophagus,
the food efficiently along as it is broken down into easily
stomach, and the small intestine; the lower tract includes
absorbed ions and molecules.
all the large intestine, the rectum, and anus.
 While in the digestive tract, the food is really passing
through the body rather than being in the body.

The Upper Gastrointestinal Tract

 The upper gastrointestinal, or GI, tract is made up of three
main parts
 The esophagus.
 The stomach.
Large-scale Breakdown in the Stomach  The small intestine.
 Once the bolus reaches the stomach, gastric juices mix with
the partially digested food and continue the breakdown
process. The bolus is converted into a slimy material called The Lower Gastrointestinal Tract
chyme.  The lower GI tract contains the remainder of the system:
 The stomach is a muscular bag that maneuvers food  The large intestine
particles, mixing highly acidic gastric juice and powerful  The rectum
digestive enzymes with the chyme to prepare for nutrient  The anus

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 Biochemistry
FIRST YEAR - FINAL TERM MR. Jan Jarrel Gillego 11/2021 - 01/2022
Digestive System

 Now thoroughly digested, with its nutrients absorbed along

the path of the small intestine, what remains of our food gets
Food Breakdown and Absorption: The Upper GI Tract
passed into the lower GI tract.
 When we take a bite of food, the food material gets chewed
up and processed in the mouth, where saliva begins the
process of chemical and mechanical breakdown. The Waste Compaction and Removal: The Lower
chewing process is also known as mastication. Gastrointestinal Tract
 When we mix up food with saliva, the resulting mushy wad The Large Intestine (Colon)
is called a bolus. The bolus gets swallowed and begins its  Following nutrient absorption, the food waste reaches the
journey through the upper gastrointestinal tract. large intestine, or colon. The large intestine is responsible
for compacting waste material, removing water, and
producing feces —our solid-waste product.
The Esophagus  Accessory organs like the cecum and appendix, which are
 The upper GI tract begins with the esophagus, the long
remnants of our evolutionary past, serve as special pockets
muscular tube that carries food to the stomach.
at the beginning of the large intestine.
 The throat cavity in which our esophagus originates is
 The compacted and dried-out waste passes to the rectum,
known as the pharynx.
and out of the body through the anus. Healthy gut bacteria in
 As we swallow, the bolus moves down our esophagus, from
the large intestine also help to metabolize our waste as it
the pharynx to the stomach, through waves of muscle
finishes its journey.
movement known as peristalsis.
 The alimentary canal is made up of the oral cavity, pharynx,
 Next the bolus reaches the stomach itself.
esophagus, stomach, small intestines, and large intestines.
 In addition to the alimentary canal, there are several
The Stomach important accessory organs that help your body to digest
 The stomach is a muscular, hollow bag that is an important food but do not have food pass through them.
part of the upper GI tract. Many organisms have a variety of  Accessory parts
stomach types, with many segments or even multiple  Organs that are not in the digestive tract but help in
stomachs. the digestion of the digestive:
 As humans, we have only one stomach.  Teeth
 Here our bolus gets mixed with digestive acids, furthering  Tongue
breakdown of the bolus, and turning the bolus material into a  salivary glands
slimy mess called chyme. The chyme moves on into the  liver
small intestine, where nutrients are absorbed.  gallbladder
 pancreas
 To achieve the goal of providing energy and nutrients to the
body, six major functions take place in the digestive system:

Digestive System Anatomy

Mouth
 Food begins its journey through the digestive system in the
mouth, also known as the oral cavity. Inside the mouth are
many accessory organs that aid in the digestion of food—the
tongue, teeth, and salivary glands. Teeth chop food into
small pieces, which are moistened by saliva before the
tongue and other muscles push the food into the pharynx.

The Small Intestine

 The small intestine is an impressive digestive tube, spanning Mechanism of Swallowing
 Swallowing is a coordinated activity of the tongue, soft
an average of 20 feet in length.
palate, pharynx, and esophagus.
 The twists and turns of the small intestine, along with tiny
 Phases
interior projections known as villi, help to increase the
 Food is pushed into the pharynx by the tongue.
surface area for nutrient absorption.
(voluntary) - Tongue blocks the mouth
 This snaking tube is made up of three parts, in order from
 Soft palate closes off the nose
the stomach:
 Larynx (Adam's Apple) rises so the Epiglottis (a flap of
 The duodenum.
tissue) can close the opening of the trachea.
 The jejunum.
 the ileum.
 As the chyme makes its way through each segment of the Pharynx
small intestine, pancreatic juices from the pancreas start to  The pharynx, or throat, is a funnel-shaped tube connected to
break down proteins. Soapy bile from the liver, stored in the the posterior end of the mouth. The pharynx is responsible
gallbladder, gets squirted into the small intestine to help for the passing of masses of chewed 
emulsify—or break apart—fats.
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 Biochemistry
FIRST YEAR - FINAL TERM MR. Jan Jarrel Gillego 11/2021 - 01/2022
Digestive System

 The liver is a roughly triangular accessory organ of the

digestive system located to the right of the stomach, just
inferior to the diaphragm and superior to the small intestine.
 The liver weighs about 3 pounds and is the second largest
organ in the body.

Teeth
 The teeth are 32 small, hard organs found along the anterior
and lateral edges of the mouth. Each tooth is made of a
bone-like substance called dentin and covered in a layer of
enamel—the hardest substance in the body. Teeth are living
organs and contain blood vessels and nerves under the dentin  The liver has many different functions in the body, but the
in a soft region known as the pulp. The teeth are designed main function of the liver in digestion is the production of
for cutting and grinding food into smaller pieces. bile and its secretion into the small intestine.
 The gallbladder is a small, pear-shaped organ located just
posterior to the liver. The gallbladder is used to store and
Tongue
recycle excess bile from the small intestine so that it can be
 The tongue is located on the inferior portion of the mouth
reused for the digestion of subsequent meals.
just posterior and medial to the teeth. It is a small organ
made up of several pairs of muscles covered in a thin,
bumpy, skin-like layer. The outside of the tongue contains Liver
many rough papillae for gripping food as it is moved by the Is both an exocrine and endocrine gland?
tongue’s muscles. The taste buds on the surface of the  The liver has many functions some of which are important to
tongue detect taste molecules in food and connect to nerves digestion.
in the tongue to send taste information to the brain. The  The liver can detoxify various metabolites;
tongue also helps to push food toward the posterior part of synthesize proteins and produce biochemicals needed for
the mouth for swallowing. digestion.
 It regulates the storage of glycogen which it can form
from glucose (glycogenesis). The liver can also synthesize
Salivary Glands
glucose from certain amino acids. Its digestive functions are
 Surrounding the mouth are 3 sets of salivary glands. The
largely involved with the breaking down of carbohydrates.
salivary glands are accessory organs that produce a watery
 It also maintains protein metabolism in its synthesis and
secretion known as saliva. Saliva helps to moisten food and
degradation. In lipid metabolism it synthesizes cholesterol. 
begins the digestion of carbohydrates. The body also uses
 Fats are also produced in the process of lipogenesis. The
saliva to lubricate food as it passes through the mouth,
liver synthesizes the bulk of lipoproteins.
pharynx, and esophagus.
YOU CANNOT SWALLOW WHILE YOUR TONGUE IS  The liver is located in the upper right quadrant of the
OUT! abdomen and below the diaphragm to which it is attached at
You CANNOT breathe while your tongue is out! one part, This is to the right of the stomach and it overlies
the gall bladder.
 The liver produces bile, an important alkaline compound
Stomach which aids digestion.
 The stomach is a muscular sac that is located on the left side
of the abdominal cavity, just inferior to the diaphragm. In an
average person, the stomach is about the size of their two
fists placed next to each other.
 This major organ acts as a storage tank for food so that the
body has time to digest large meals properly.
 The stomach also contains hydrochloric acid and digestive
enzymes that continue the digestion of food that began in the
mouth.

 The liver plays a major role in carbohydrate, protein,

Liver and Gallbladder
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 Biochemistry
FIRST YEAR - FINAL TERM MR. Jan Jarrel Gillego 11/2021 - 01/2022
Digestive System

amino acid, and lipid metabolism.  The large intestine absorbs water and contains many
 The liver performs several roles in carbohydrate symbiotic bacteria that aid in the breaking down of wastes to
metabolism: The liver synthesizes and stores around 100 g extract some small amounts of nutrients. Feces in the large
of glycogen via glycogenesis, the formation of glycogen intestine exit the body through the anal canal.
from glucose.
 When needed, the liver releases glucose into the blood by
Common Digestive Disorders
performing glycogenolysis, the breakdown
Gastroesophageal Reflux Disease (GERD)
of glycogen into glucose.   If you have heartburn or acid reflux more than a couple of
 The liver is also responsible for gluconeogenesis, which is times a week, you may have Gastroesophageal Reflux
the synthesis of glucose from certain amino acids, lactate,
Disease, or GERD. The esophagus moves swallowed food
or glycerol. Adipose and liver cells produce glycerol down to your stomach. A ring of muscles—the lower
by breakdown of fat, which the liver uses for
esophageal sphincter (LES)—connects the stomach and
gluconeogenesis. esophagus. When the LES is weak, stomach acid can leak
 The heaviest organ in the body
back up into your esophagus and cause heartburn. This can
 Storehouse
cause serious damage to your esophagus over time. About
 Manufacturing Hub
20% of Americans suffer from GERD. You can treat GERD
 Processing Plant
with lifestyle changes, such as changing what and when you
eat, and eating smaller meals. Antacids or prescription-
Pancreas strength acid blockers can also help. 
 The pancreas is a large gland located just inferior and Peptic Ulcer Disease (PUD) and Gastritis
posterior to the stomach. It is about 6 inches long and shaped  PUD is an open sore in the lining of the stomach or upper
like short, lumpy snake with its “head” connected to the part of the small intestine. It affects over 15 million
duodenum and its “tail” pointing to the left wall of the Americans. Gastritis is inflammation of the stomach lining.
abdominal cavity. These two conditions have similar symptoms, including
 The pancreas secretes digestive enzymes into the small stomach pain and nausea, and similar causes. A bacterial
intestine to complete the chemical digestion of foods. infection—  H. pylori—is the most common cause of PUD
1. Proteases and often causes chronic gastritis. NSAIDs—including
 Digestion of proteins is initiated by pepsin in the aspirin, ibuprofen and naproxen—are another common
stomach, but the bulk of protein digestion is due to the cause. Antacids and proton pump inhibitors often help.
pancreatic proteases. Antibiotics treat  H. pylori infection. 
 Several proteases are synthesized in the pancreas and Stomach Flu
secreted into the lumen of the small intestine. The two  Stomach flu—or gastroenteritis—is an infection of the
major pancreatic proteases stomach and upper part of the small intestine. Common
are trypsin and chymotrypsin, which are synthesized symptoms are diarrhea, vomiting, stomach pain, and cramps.
and packaged into secretory vesicles as the inactive Rotavirus and norovirus, which affect millions of people
proenzymes trypsinogen and chymotrypsinogen. every year, are often the cause. Gastroenteritis often clears
2. Pancreatic Lipase up on its own, but you lose fluids through diarrhea and
 Synthesizes Lipids vomiting. Prevent dehydration by drinking water and
3. Amylase electrolyte drinks. 
The major dietary carbohydrate for many species is starch, a Constipation
storage form of glucose in plants. Amylase (technically  Constipation is difficult or infrequent passage of stool. If
alpha-amylase) is the enzyme that hydrolyses starch to you have bowel movements less than three times a week,
maltose (a glucose-glucose disaccharide), as well as the you likely are constipated. Chronic constipation affects
trisaccharide maltotriose and small branchpoints fragments about 63 million people in the United States. A common
called limit dextrins. The major source of amylase in all cause of constipation is not getting enough fiber in your diet.
species is pancreatic secretions, although amylase is also The main symptom of constipation is straining to go. In most
present in saliva of some animals, including humans. cases, increasing fiber, fluids, and exercise will solve this
4. Bicarbonate and Water condition. Use laxatives only as a temporary solution. 
 Epithelial cells in pancreatic ducts are the source of the Hemorrhoids
bicarbonate and water secreted by the pancreas.  Hemorrhoids are painful, swollen blood vessels in the anal
Bicarbonate is a base and critical to neutralizing the canal. Symptoms include pain, itching, and bright red blood
acid coming into the small intestine from the stomach. after a bowel movement. Constipation and pregnancy are
 In pancreatic duct cells, the bicarbonate is secreted into major causes. Hemorrhoids are common, with 75% of
the lumen of the duct and hence into pancreatic juice. people older than 45 having them. It helps to
avoid constipation by adding fiber and plenty of fluids to
your diet. Try hemorrhoid cream, suppositories, or a warm
Large Intestine bath to relieve pain and itchiness. It may feel a little
 The large intestine is a long, thick tube about 2.5 inches in embarrassing to talk about hemorrhoids, but don’t let that
diameter and about 5 feet long. stop you from seeking help if hemorrhoids persist. 
 It is located just inferior to the stomach and wraps around
the superior and lateral border of the small intestine.
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 Biochemistry
FIRST YEAR - FINAL TERM MR. Jan Jarrel Gillego 11/2021 - 01/2022
Digestive System

Gallstones
 The gallbladder is an organ attached to your intestine that
stores bile—a digestive juice. Bile can form small, hard
deposits called gallstones. About 20 million Americans have
gallstones, but not all of them are a problem. Some
gallstones don’t cause symptoms and go away on their own.
Others can cause severe pain or infection. You may also
have nausea, vomiting, and fever. Surgery is the usual
treatment for gallstones that cause these gallbladder attacks.