Shivani+Sinha+Your+Inner+Fish

POST #1

“Let’s take a hypothetical humorless, quite unclown-like couple who have children. One of their sons was born with a genetic mutation that gave him a red rubber nose that squeaks. This son grows up and marries a lucky woman. He passes his mutated nose gene to his children, and they all have his red rubber nose that squeaks. Now, suppose one of his offspirings gets a mutation that causes him to have huge floppy feet. When this mutation passes to the next generation, all of his children are like him: they have a rubber nose that squeaks and huge floppy feet. Go one generation further. Imagine that one of these kids, the original couple’s great-grandchildren, has another mutation: orange curly hair. When this mutation passes to the //next// generation all of his children will have orange curly hair, a rubber nose that squeaks, and giant floppy feet. When you ask ‘Who is this bozo?’ you’ll be enquiring about each of our poor couple’s great-great-grandchildren” (Shubin 175)

This quote connects to our course curriculum in two different ways. The first is mutations. We learned about the different types of genetic mutations. A few types of mutations we learned about were the deletion of a gene, duplication of genes, inversion of genes, and translocation of genes. The deletion of a gene is when the genes of a chromosome are deleted and become permanently lost.
 * [[image:gene_deletion.gif caption="Deletion of Genes"]] ||
 * Deletion of Genes ||

The duplication of genes is when a set of genes is exhibited twice on the same chromosome.
 * [[image:gene_duplication.gif caption="Duplication of Genes"]] ||
 * Duplication of Genes ||

The inversion of genes is when the order of a set of genes is reversed,
 * [[image:gene_inversion.gif caption="Inversion of Genes"]] ||
 * Inversion of Genes ||

and the translocation of genes is when information from a chromosomes breaks and binds to a homologous chromosome.
 * [[image:gene_translocation.gif caption="Translocation of Genes"]] ||
 * Translocation of Genes ||

We also learned about mutations that occur at the DNA level during replication. The first type is deletion. Deletion is when certain nucleotides are deleted from the DNA sequence. Because of this, the protein coding process is affected, as the new codon may not code for the same amino acid. It also affects the other amino acids in the sequence, as the rest of the nucleotides will be out of place. The second kind is insertion. This is similar to deletion in the sense that it has the same effects. However, instead of nucleotides being deleted, they are inserted. These modifications in the sequence of nucleotides are known as frameshift mutations. The next type of mutation is inversion. This is when a set of nucleotides is reversed. This, however, does not have as major of an effect as it does not affect the rest of the nucleotide sequence. The last kind of mutation is substitution, which is when a certain nucleotide is replaced with another, not affecting the rest of the nucleotide sequence. (1)

Diseases can be derived from genetic mutation, which can subsequently be transmitted from parent to offspring. This is the second way this quote connects to the curriculum. In our course, we briefly studied sickle cell anemia, which causes the hemoglobin molecule in red blood cells to become deformed in the shape of sickles when exposed to low oxygen concentrations. These “sickled red blood cells” rupture, and the patient develops sickle cell anemia. This mutation can be transmitted over generations and leads to significant illness and discomfort in individuals.
 * [[image:sickle_cell_01.jpg caption="Sickled Red Blood Cells"]] ||
 * Sickled Red Blood Cells ||


 * [[image:chart.gif caption="Inheritance of Sickle Cell Disease From Parents who are Carriers (Sickle Cell Trait)"]] ||
 * Inheritance of Sickle Cell Disease From Parents who are Carriers (Sickle Cell Trait) ||

Above Image: [|http://www.nhlbi.nih.gov/health/dci/Diseases/Sca/SCA_WhatIs.html] Lower Image: [|http://www.dukehealth.org/health_library/advice_from_doctors/your_childs_health/sicklecelldisease] This quote also connects to evolution, one of the major themes of biology. Evolution is a complex process that results from the interaction of multiple factors. Genetic mutation is one such mechanism that may lead to the development of new genotypes and phenotypes as species evolve.

Works Cited: 1. "Genetic Mutations - Biology Online." //Life Science Reference - Biology Online//. Web. 28 May 2010. < [|http://www.biology-online.org/2/8_mutations.htm]>. 2. "Sickle Cell Anemia, What Is." //National Heart, Lung and Blood Institute//. Web. 28 May 2010. <[|http://www.nhlbi.nih.gov/health/dci/Diseases/Sca/SCA_WhatIs.html]>. 3. "Sickle Cell Disease." //DukeHealth.org//. Web. 28 May 2010. <[|http://www.dukehealth.org/health_library/advice_from_doctors/your_childs_health/sicklecelldisease]>.

Post #2 “We humans, like many other mammals, can rotate our thumb relative to our elbow. This simple function is very important for the use of our hands in everyday life. Imagine trying to eat, write, or throw a ball without being able to rotate your hand relative to your elbow. We can do this because one forearm bone, the radius, rotates along a pivot point at the elbow joint. The structure of the joint at the elbow is wonderfully designed for this function. At the end of our upper-arm bone, the humerus, lies a ball. The tip of the radius, which attaches here, forms a beautiful socket that fits on the ball. This ball-and-socket joint allows the rotation of our hand, called pronation and supination” (Shubin 42).

In class we learnt about different types of joints when talking about the skeletal system. Seven different movable joints include the ball-and-socket joint, the condyloid joint, the saddle joint, the pivot joint, the hinge joint, the ellipsoid joint, and the gliding joint.

The ball-and-socket joint is a joint in which the end of one bone is shaped like a ball and fits into a cup shaped receptacle on another bone to form a joint.Hip and shoulder joints are examples of ball and socket joint. //The ball and socket joint is the most movable of all the joints as it allows for maximum movement in three different planes (flexion and extension; abduction and adduction; rotation)// A joint that is very similar to the ball and socket joint and saddle joint is the ellipsoid joint, which allows for essentially the same type of movement, but to a lesser degree. Saddle joints are formed when the two bones making the joint both have complementary concave and convex surfaces. Thumb joint is the only saddle joint in the body. In a gliding (or plane) joint flat or relatively flat surfaces oppose each other allowing sliding or twisting without any circular movement. The joints formed between carpals of wrist and tarsals in ankles are examples of gliding joints. //The ellipsoid joint is a biaxial joint, allowing for movement in two different planes (flexion and extension; abduction and adduction). The saddle joint, like the ellipsoid joint must allow for movement in the same two planes; however, it also allows for some rotation. And lastly, gliding (plane) joints, are non-axial, as they do not function about an axis. They are shaped this way, however, because the bones must slide over each other. The picture shown below is of the hand. The carpals must slide over each other when this part of the body is moved to flexion, extension, radial deviation, or ulnar deviation.//

A condyloid joint is formed when the ovoid shaped end of a bone articulates a with a ellipsoid cavity of another bone. Such a joint allows angular motion. Examples of such joints are found between metacarpals and carpals in hand and tarsals and metatarsals in the foot. The joints between the phalanges in the fingers and toes are also condyloid joints. //This type of joint is mainly functional in one plane, extension and flexion. However, it does have minimal movement in the plane of rotation.// A pivot joint forms when a round or conical bony surface fits into a ring or tendon of another bone allowing rotational movement. The joint between the atlas and axis vertebra of the neck is an example of pivot joint. //The pivot joint is uniaxial, as it only allows for movement in the plane of rotation (along with pronation and supination).//

A hinge joint is formed when the convex surface of one bone fits into a concave depression of another bone. The elbow is an example of this type of joint. //The hinge joint, like the pivot joint is uniaxial, as it too only allows for movement in the plane of flexion and extension.//

This also relates to the theme of biology: structure to function. The structure of each joint is specialized for the type of movement carried out by each part of the body. The function of each of the above joints is written in italics after the joint descriptions.


 * //__ALL JOINT DESCRIPTIONS WERE TAKEN FROM SOURCE 1. PICTURES AND JOINT FUNCTIONS WERE TAKEN FROM SOURCE 2.__//**

Works Cited 1. "Joints." Web. 2 June 2010. . 2. "OVRT Resources for the Humanoid Animation Working Group." //Visualization and Virtual Reality for Manufacturing Home Page//. Web. 2 June 2010. .

Post #3 "New creatures with whole new capabilities came about: they got big, they moved around, and they developed new organs that helped them sense, eat, and digest their world" (Shubin 119).

Connection: This quote connects to our class discussions about body systems, and the different functions of the organs. For example, this quote specifically mentions eating and digestive mechanisms. In class, we very thoroughly covered the digestive system. The process of the digestive system starts when the food enters the mouth. In the mouth, teeth chew (mastication) and break down the food. This ultimately increases the surface area of the food, allowing for more room for digestive enzymes to start breaking food down. The enzyme amylase starts to break down carbohydrates, and the enzyme lipase stats to break down lipids. In the mouth, the food is then turned into a ball, known as the bolus, which then travels to the pharynx. The pharynx, also known as the throat, connects the mouth to the esophagus. The esophagus is the tube that ultimately brings food to the stomach from the pharynx. The esophagus, which is composed of smooth muscle, moves food to the stomach via involuntary contractions, known as peristalsis; peristalsis is responsible for moving food through the digestive tract. Located toward the end of the esophagus is a ring-shaped muscle, known as the lower esophageal sphincter. While this ring is normally closed and tense, it relaxes as food reaches it, allowing food to enter the stomach. It then closes again so that food toes not reenter the esophagus (regurgitation). The stomach serves as a holding container for the food. The stomach produces gastric acid, which includes hydrochloric acid. The secretion of these digestive juices is stimulated and regulated by the hormone gastrin. Gastric acid helps in digesting mainly large protein and fat molecules along with a few carbohydrates and alcohol. Furthermore, pepsin breaks down protein and works best in a low pH; it is activated and regulated by hydrochloric acid or itself (positive feedback). The stomach acids (hydrochloric acid) also helps in killing bacteria that may be present in the swallowed food by lowering the pH. The stomach also produces a lining of mucus to protect its walls because gastric acid is so acidic (pH 1-3). Furthermore, the stomach’s walls (mechanical churning) help in turning the bolus into chyme, which is like a semi-fluid mixture. Next is the liver. The liver serves as the body’s detoxifier, as it helps in breaking down toxins into less toxic substances. It not only breaks down toxins, but it also processes any consumed alcohol, breaks down medicines, and converts ammonia into urea. The liver also makes cholesterol and other important fats of the body. However, a very important function of the liver is producing bile, which is another digestive juice to be stored in the gall bladder. Because the bile is stored in the gall bladder, it becomes very concentrated, and therefore more powerful. When needed, the bile, along with the food exiting the stomach from the pyloric sphincter, enters the duodenum, which is the first segment of the small intestine. Here, the bile helps in breaking down fats and neutralizing acids. When food reaches the duodenum, it signals the pancreas to release digestive enzymes, such as pancreatic amylase (starch, glycogen, and carbohydrates), trypsin, chymotrypsin, and peptidases (proteins), and pancreatic lipase (fats). This is one of the functions of the pancreas; it is the source of powerful digestive enzymes. Its other function I to produce insulin and glucagon to maintain a balance of blood sugar levels in the body. These enzymes then enter the duodenum to help in neutralizing acid and breaking down fats, carbohydrates, and proteins into smaller molecules. Once the chyme has been further broken down in the duodenum, it moves into the next sections of the small intestine, the jejunum and ileum. The inner parts of the se two sections contain small, finger like extensions called villi (microvilli project from the villi). The villi and microvilli help to increase the surface area, as it is through here nutrients are absorbed into the blood stream. This concept also connects to the major theme of biology, structure to function, as this structure of the inside of the small intestine makes the absorption of nutrients more efficient. Furthermore, the capillaries located inside the villi have very thin walls to facilitate the diffusion of nutrients into the blood stream. As digestion finishes in the small intestine, all food and liquid is broken down into their nutrient components, such as vitamins and minerals, and absorbed. Unabsorbed nutrients then go to the large intestine. The large intestine is the last stage of digestion. Here, certain vitamins, water, and salts are reabsorbed and undigested minerals are processed. It also dries chyme and stores it as fecal matter until it is eliminated. The caecum is the first part of the large intestine; this part accepts the unabsorbed nutrients form the small intestine and sends it to the colon where it is turned into fecal matter. Fecal matter is then sent to the rectum where it remains until it moves to the anus and exits the body.

All of this majorly ties into the major theme of biology: regulation. There are many examples of regulation in the digestive system. Four examples include the production of gastrin, gastric inhibitory peptide (GIP), secretin, and cholecystokinin (CCK). The production of gastrin by the stomach’s lining can stimulate the secretion of gastric juices by gastric glands, and the contractions of smooth muscle in the stomach and small and large intestine, increasing gastric and intestinal motility. Furthermore, it can cause the relaxation of the pyloric sphincter, promoting gastric emptying into the small intestine. The lining of the duodenum produces GIP. It causes the inhibition of gastric juice secretion and gastric motility. This ultimately hinders digestion in the stomach and inhibits gastric emptying. The lining of the duodenum in the small intestine also produces secretin. This can stimulate the secretion of bicarbonate by the pancreas and the production of bile by the liver. Stimulating bicarbonate secretin will neutralize the acidity of chyme when released into the duodenum. The production of secretin inhibits the secretion of gastric juice and gastric motility, which, like GIP, hinders digestion in the stomach and inhibits gastric emptying. And lastly, the lining of the duodenum produces CCK, like GIP and secretin. This can cause the release of bile by the gall bladder and the secretion of pancreatic juice. Furthermore, it will cause the hepatopancreatic ampulla to relax. This will allow the bile and pancreatic juices to flow in to the duodenum.

__**//ALL INFORMATION TAKEN FROM SOURCE 1//**__ __Works Cited__ 1. Campbell, Neil A., and Jane B. Reece. //Biology//. San Francisco: Pearson, Benjamin Cummings, 2005. Print.

Post #4

"Something was missing. That something was enough oxygen on the earth to support bodies. When the earth's oxygen increased, bodies appeared everywhere. Life would never be the same" (Shubin 138).

This quote greatly relates to the process of respiration, as when oxygen became available to breathe on land, we developed organs to enable us to breathe out of the water. However, as I have already discussed respiration mechanisms on the macrobiology level as a commentary on Avery’s post, I will take this opportunity to connect this quote to cellular respiration, as the oxygen inhaled in respiration is brought to the cells to produce ATP.

The first step of cellular respiration, although anaerobic (not requiring oxygen), is glycolysis. It takes place in the cytoplasm of the mitochondria. In glycolysis, 1 molecule of glucose is converted into 2 molecules of G3P, and ultimately into 2 pyruvate. The net gain of glycolysis is 2 pyruvate, 2 ATP, 2 NADH, 2 H2O, and 2H. Phosphofructokinase (PFK) is an allosteric enzyme, which is used to catalyze the 3rd step of glycolysis. ATP acts as an allosteric inhibitor, as increased levels of ATP inhibit PFK to stop glycolysis; decreased levels will allow PFK to remain uninhibited, causing glycolysis to continue. The next step of cellular respiration is aerobic: the Krebs cycle, which takes place in the mitochondria. In the Krebs Cycle, a pyruvate from glycolysis binds with coenzyme A to form acetyl CoA. This then combines with oxaloacetate to form citric acid. Ultimately, ATP is generated via substrate-level phosphorylation. The net gain of 1 acetyl CoA is 3CO­2, 4 NADH, 1 FADH2, and 1 ATP. However, since 2 pyruvate (acetyl CoA) will cycle through, the net product will be 6 CO2, 8 NADH, 2 FADH2, and 2 ATP.

The last stage of cellular respiration is the electron transport chain/oxidative phosphorylation. In this aerobic process, taking place in the inner mitochondrial membrane, NADH releases electrons into cytochromes (integral proteins). Hydrogens are then pumped into the outer mitochondrial membrane, creating a proton gradient. Hydrogens are then pumped through ATP synthetase. This process generates energy to phosphorylate ADP into ATP. The final electron acceptor that drives this whole process is oxygen.

// __Works Cited__ // 1. Goldberg, Deborah T. //AP Biology//. Hauppauge, N.Y.: Barron's Educational Series, 2007. Print.
 * //__ALL INFORMATION TAKEN FROM SOURCE #1__//**

Post #5 "As we jog along a path, our muscles contract, our back, arms, and legs move, and our feet push against the ground to move us forward" (Shubin 124-125).

This quote connects to our class discussion involving the musculoskeletal system, specifically the contraction of muscles. Muscles are made up of the proteins myosin and actin, and are the most abundant tissues in animals. A muscle fiber is a bundle of myofibrils, which are composed of myofilaments (thin or thick). The thin filaments are the myosin, and the thick filaments are the actin. The basic contractile unit of the muscle is the sarcomere. Muscles are responsible for body movement, and the muscle fibers contract when stimulated by a nerve impulse. There are three different types of muscle. Skeletal muscle is responsible for the movement of bones. It is voluntary, attached to bones, striated (consisting of long fibers, each of which is a single muscle cell), and multinucleated. Tendons connect bone to muscle (and ligaments connect bone to bone). Furthermore, as muscles work by contracting, skeletal muscles work in antagonistic pairs. Cardiac Muscle is responsible for the beating of the heart. It is involuntary, striated, and auto-rhythmic (controlled by the pacemaker cells). And lastly, smooth muscle is responsible for the digestive system, arteries, and veins. It is involuntary, non-striated, and the first to evolve of these three. During muscle contraction, the length of the sarcomere is reduced as actin filaments slide over myosin. A motor neuron will cause a muscle fiber to contract when its depolarization causes the neurotransmitter acetylcholine to be released into the synapse of the neuromuscular junction. Acetylcholine released at the synaptic terminal diffuses across the synaptic cleft and binds to receptor proteins on the muscle fiber’s plasma membrane, triggering an action potential in the muscle fiber. This action potential is then propagated along the plasma membrane and down the T tubules. The action potential will also trigger the release of calcium ions from the sarcoplasmic reticulum. These calcium ions will bind to troponin in the thin filament, exposing the myosin-binding sites on actin. Myosin cross-bridges alternately attach to actin and detach (ATP powers this sliding of the filaments). The calcium ions are then removed by active transport into the sarcoplasmic reticulum after the action potential ends. And lastly, the tropomyosin blockage of myosin-binding sites is restored. Contraction ends, and the muscle fibers relax once again.

__**//ALL INFORMATION TAKEN FROM SOURCE #1//**__

Picture taken from Source #2

Works Cited: 1. Campbell, Neil A., and Jane B. Reece. //Biology//. San Francisco: Pearson, Benjamin Cummings, 2005. Print. 2. "Compendium Review: Movement." //Stephanie Rose//. Web. 14 June 2010. .