molecular phylogeny

MOLECULAR PHYLOGENY

Every living organism contains DNA, RNA, and proteins.

Closely related organisms generally have a high degree of agreement in the molecular structure of these substances, while the molecules of organisms distantly related usually show a pattern of dissimilarity.

Molecular phylogeny uses such data to build a "relationship tree" that shows the probable evolution of various organisms.
Molecular phylogenetics attempts to determine the rates and patterns of change occurring in DNA and proteins and to reconstruct the evolutionary history of genes and organisms.

Two general approaches may be taken to obtain this information.

In the first approach, scientists use DNA to study the evolution of an organism.

In the second approach, different organisms are used to study the evolution of DNA.

Whatever the approach, the general goal is to infer process from pattern: the processes of organismal evolution deduced from patterns of DNA variation and processes of molecular evolution inferred from the patterns of variations in the DNA itself.

Digestion in Humans

Digestive System

Digestion is the chemical breakdown of large food molecules into smaller molecules that can be used by cells. The breakdown occurs when certain specific enzymes are mixed with the food.
Enzymes involved in Digestion
The process of digestion produces glucose, amino acids, glycerol, and fatty acids.

The energy in glucose is used to produce ATP via the reactions of glycolysis, cellular respiration, and the electron transport system .

The body uses amino acids to construct proteins.

Glycerol and fatty acids can be converted to pyruvate and Acetyl CoA and then enter cellular respiration.
Mouth
Chewing breaks food into smaller particles so that chemical digestion can occur faster.
Enzymes
Salivary amylase breaks starch (a polysaccharide) down to maltose (a disaccharide).
Bicarbonate ions in saliva act as buffers, maintaining a pH between 6.5 and 7.5.
Mucins (mucous) lubricate and help hold chewed food together in a clump called a bolus.
The tongue contains chemical receptors in structures called taste buds.
The tongue is muscular and can move food. It pushes food to back where it is swallowed.
Pharynx
The respiratory and digestive passages meet in the pharynx.

They separate posterior to the pharynx to form the esophagus (leads to the stomach) and trachea (leads to the lungs).
Swallowing is accomplished by reflexes that close the opening to the trachea.
When swallowing, the epiglottis covers the trachea to prevent food from entering.
In the mouth, food is mixed with saliva and formed into a bolus.
Peristalsis refers to rhythmic contractions that move food in the gut. Peristalsis in the esophagus moves food from the mouth to the stomach.
Stomach
The stomach stores up to 2 liters of food.
Gastric glands within the stomach produce secretions called gastric juice.
The muscular walls of the stomach contract vigorously to mix food with gastric juice, producing a mixture called chyme.
Gastric juice
Pepsinogen is converted to pepsin, which digests proteins.
Pepsinogen production is stimulated by the presence of gastrin in the blood .
HCl
Hydrochloric acid (HCl) converts pepsinogen to pepsin which breaks down proteins to peptides. HCl maintains a pH in the stomach of approximately 2.0.
It also dissolves food and kills microorganisms.
Mucous protects the stomach from HCl and pepsin.
Secretion of Gastric Juice
Seeing, smelling, tasting, or thinking about food can result in the secretion of gastric juice.
Gastrin is a hormone that stimulates the stomach to secrete gastric juice.
An ulcer is an irritation due to gastric juice penetrating the mucous lining of the stomach or duodenum.
It is believed that ulcers are caused by the bacterium Helicobacter pylori, which, can thrive in the acid environment of the stomach. The presence of the bacteria on portions of the stomach lining prevents it from secreting mucous, making it susceptible to the digestive action of pepsin.
Duodenum
The duodenum is the first part of the small intestine.
Chyme enters through a sphincter.
It enters in tiny spurts.
At this point, proteins and carbohydrates are only partially digested and lipid digestion has not begun.
Pancreas
The pancreas acts as an exocrine gland by producing pancreatic juice which empties into the small intestine via a duct.
The pancreas also acts as an endocrine gland to produce insulin.

Pancreatic Juice
Pancreatic juice contains sodium bicarbonate which neutralizes the acidic material from the stomach.
Pancreatic amylase digests starch to maltose.
Trypsin and Chymotrypsin digest proteins to peptides.
Lipase digests fats to glycerol and fatty acids.
Liver
The liver produces bile which is stored in gallbladder and sent to the duodenum through a duct.
Bile emulsifies fats (separates it into small droplets) so they can mix with water and be acted upon by enzymes.
Other Functions of the Liver
1.The liver detoxifies blood from intestines that it receives via the hepatic portal vein.
2. The liver stores glucose as glycogen (animal starch) and breaks down glycogen to release glucose as needed.

This storage-release process maintains a constant glucose concentration in the blood (0.1%). If glycogen and glucose run short, proteins can be converted to glucose.
3. It produces blood proteins.
4. It destroys old red blood cells and converts hemoglobin from these cells to bilirubin and biliverdin which are components of bile.
5. Ammonia produced by the digestion of proteins is converted to a less toxic compound (urea) by the liver.
Hormones Involved in Digestion
The hormones listed below, like all hormones, reach their target cells by the circulatory system.
Gastrin
The presence of food in the stomach stimulates stretch receptors which relay this information to the medulla oblongata. The medulla stimulates endocrine cells in the stomach to secrete the hormone gastrin into the circulatory system. Gastrin stimulates the stomach to secrete gastric juice.
Secretin
Secretin is produced by cells of the duodenum.
It’s production is stimulated by acid chyme from stomach.
It stimulates the pancreas to produce sodium bicarbonate, which neutralizes the acidic chyme. It also stimulates the liver to secrete bile.
CCK (cholecystokinin)
CCK production is stimulated by the presence of food in the duodenum.
It stimulates the gallbladder to release bile and the pancreas to produce pancreatic enzymes.
GIP (Gastric Inhibitory Peptide)
Food in the duodenum stimulates certain endocrine cells to produce GIP.
It has the opposite effects of gastrin; it inhibits gastric glands in the stomach and it inhibits the mixing and churning movement of stomach muscles. This slows the rate of stomach emptying when the duodenum contains food.
Small Intestine
The small intestine is approximately 3 m long.
Like the stomach, it contains numerous ridges and furrows. In addition, there are numerous projections called villi that function to increase the surface area of the intestine. Individual villus cells have microvilli which greatly increase absorptive surface area.
The total absorptive surface area is equivalent to 500 or 600 square meters.
Each villus contains blood vessels and a lacteal (lymph vessel).
Peptidases and maltase are embedded within the plasma membrane of the microvilli.
Peptidases complete the digestion of peptides to amino acids.
Maltase completes the digestion of disaccharides.
Absorption
Absorption is an important function of the small intestine.
Active transport moves glucose and amino acids into the intestinal cells, then out where they are picked up by capillaries.
Glycerol and fatty acids produced by the digestion of fat enter the villi by diffusion and are reassembled into fat (triglycerides). They combine with proteins and are expelled by exocytosis. They move into the lacteals for transport via the lymphatic system.
Large Intestine
The large intestine is also called the colon.
It receives approximately 10 liters of water per day. 1.5 liters is from food and 8.5 liters is from secretions into the gut. 95% of this water is reabsorbed.
The large intestine also absorbs sodium and other ions but it excretes other metallic ions into the wastes.
If water is not absorbed, diarrhea can result, causing dehydration and ion loss.
It absorbs vitamin K produced by colon bacteria.
The last 20 cm of the large intestine is the rectum.
Feces is composed of approximately 75% water and 25% solids. One-third of the solids is intestinal bacteria, 2/3’s is undigested materials.
The cecum is a pouch at the junction of the small intestine and large intestine. In herbivorous mammals, it is large and houses bacteria capable of digesting cellulose. In human ancestors, the cecum was larger but has been reduced by evolutionary change to form the appendix.
Polyps
Polyps are small growths in the epithelial lining of the colon.
They can be benign or cancerous and can be removed individually.
A low-fat, high-fiber diet promotes regularity and is recommended as a protection against colon cancer.
Appendix
The appendix is attached to cecum.
Appendicitis is an infection. The appendix may swell and burst, leading to peritonitis (infection of the abdominal lining).
Summary of Digestive Enzymes
The digestive enzymes in the table below are summarized according to type of food that they digest.

role of liver in digestion

Liver:

An organ in the upper abdomen that aids in digestion and removes waste products and worn-out cells from the blood. The liver is the largest solid organ in the body. The liver weighs about three and a half pounds (1.6 kilograms). It measures about 8 inches (20 cm) horizontally (across) and 6.5 inches (17 cm) vertically (down) and is 4.5 inches (12 cm) thick.
Bile is a complex fluid containing water, electrolytes and a battery of organic molecules including bile acids, cholesterol, phospholipids and bilirubin that flows through the biliary tract into the small intestine.

There are two fundamentally important functions of bile in all species:
Bile contains bile acids, which are critical for digestion and absorption of fats and fat-soluble vitamins in the small intestine.
Many waste products including bilirubin, are eliminated from the body by secretion into bile and elimination in feces.
Adult humans produce 400 to 800 ml of bile daily, and other animals proportionately similar amounts.
In species with a gallbladder (man and most domestic animals except horses and rats), further modification of bile occurs in that organ. The gall bladder stores and concentrates bile during the fasting state. Typically, bile is concentrated five-fold in the gall bladder by absorption of water and small electrolytes - virtually all of the the organic molecules are retained.

Role of Bile Acids in Fat Digestion and Absorption
Emulsification of lipid aggregates: Bile acids have detergent action on particles of dietary fat which causes fat globules to break down or be emulsified into minute, microscopic droplets. Emulsification is not digestion per se, but is of importance because it greatly increases the surface area of fat, making it available for digestion by lipases, which cannot access the inside of lipid droplets.
Solubilization and transport of lipids in an aqueous environment: Bile acids are lipid carriers and are able to solubilize many lipids by forming micelles - aggregates of lipids such as fatty acids, cholesterol and monoglycerides - that remain suspended in water. Bile acids are also critical for transport and absorption of the fat-soluble vitamins.