Thursday, December 20, 2007

Stage One: Glycolysis

Whats the point? To make ATP!!

Glycolysis literally means splitting two sugars. This name is appropriate because this is exactly what happens during the first stage of cellular respiration; glucose is digested.

Glycolysis is an ancient process. Bacteria where the first to do this.
Glycolysis is where energy transfer first evolved. It is a transfer of energy from organic molecules to inorganic molecules.

But its inefficient!
A working muscle use millions of molecules of ATP a second. Glycolysis only makes 2 ATP's.

Who were the first to do glucolysis?
Billions of years ago there was no free oxygen in the atmosphere.Oxygen had to be captured by organic molecules such as glucose.

All cells undergo glycolysis!

The Reaction:
1. Begins with one glucose molecule (six carbons)
2.Fructose-16bP takes off Phosphate from 2 ATP and place a phosphate on either side of the glucose.
3. The carbons pull apart due to oxygen's high electronegativity. This forms 2 pyruvates or two 3 carbon molecules.
4. 4 ATP's and 2NADH's (piggy bank) are formed. However 2ATP's were used to start the process (the match).
5. Net: 2ATP's and 2NADH's

Tuesday, December 18, 2007

What is the point? TO MAKE ATP

Guys today we learned how our body makes energy. Well what is the point? POINT IS TO MAKE ATP.

Energy is really important because we need it to reproduce, synthesis, to move, to grow, and to regulate our temperature.

The work of life is done by energy coupling, which is using exergonic reactions to fuel the endergonic reactions.

Whatever we eat, we have to digest or break it down to simpler molecules that can enter our cells and they can eventually use them. We need something in our body which helps to pass this energy around. And the best answer is ATP!!!.

ATP stands for Adenosine Triphospate. Where do we see Adenine before? In RNA and DNA.

ATP has three phosphate group attaches to an adenine and ribose.

First we start out with adenosine, and ribose, and when we attach one phosphate to this, this is named AMP or adenosine monophosphate, which means one phospate.

Then when we add another phosphate group to the adenine, ribose, and previous phosphate group, we make adenosine diphosphate, meaning two phosphates.

Third, we make ATP by adding another phosphate group, thus making adenine triphosphate.

Adding all these phosphates requires A LOT of energy and I mean A LOT.

BUT, the question is why does it require so much energy? Well lets see an example, remember when we hold magnets together towards the same poles, WHAT DO THEY DO? THEY REPEL EACH OTHER. This is the same reason for the phosphates. The phosphates are highly negative and do not want to be with another molecule which is also highly negative. This is due to the oxygen. AND WHAT IS OXYGEN? HIGHLY ELECTRONEGATIVE.

The phosphate bonds make ATP an excellent energy donor.


The word is PHOSPHORYLATION. This is when phosphate is taken off of ATP. This released phosphate can be transferred to other molecules. And enzyme that helps in this is kinase.

Building polymers from monomer is a perfect example of phosphorylation. The bonds holding the monomer have to be destabilized in order to make it a polymer.

The first step of cellular respiration is glycolysis. This is the breaking of glucose to make ATP. First the bonds of glucose have to be destabilized in order for it to be broken down. And whenever a carbon to carbon bond is broken, energy is released!!

Activators and Inhibitors

Hey guys, yesterday we finished our lecture on enzymes by talking about how activators and inhibitors affect enzyme activity. We also talked about allosteric regulation, cooperativity, metabolic pathways and how these pathways are efficient for the cell.

Enzyme activity is sensitive to the presence of specific substances that bind to the enzyme and cause conformational change in the enzyme (conformational change is the change in the shape of the molecule, in this case the active site of the enzyme). Through these substances, a cell is able to regulate which of its enzymes are active and which are inactive at a particular time. This allows the cell to increase its efficiency and to control changes in its characteristic during development.

The first type of substance that we will talk about is an activator which binds to the active site of the enzyme and increases the activity of the enzyme. Enzyme function is often assisted by additional chemical components known as cofactors and coenzymes.

Cofactors are non-protein, small inorganic compounds and ions. Inorganic compounds are compounds that do not have carbon to carbon bonds. These small molecules are usually metals and bind within the enzyme molecule. For example zinc is used by some enzymes to draw electrons away form their position in covalent bonds in the substrate, making the bonds less stable and easier to break the bonds between the substrate. *Remember glucose, it is stable and needs something to disrupt the bond well here the metals in the enzyme draw the electrons away from the substrate molecules, disrupting the bonds between the substrate.*

Coenzymes are nonprotein, organic molecules which are molecules that have carbon to carbon bonds. These molecules bind temporarily or permanently to the enzyme near its active site. Many vitamins are parts of coenzymes. In numerous ozidation reduction reactions that are catalyzed by enzymes, the electrons pass in pairs from the active site of the enzyme ot a coenzyme that serves as the electron acceptor. The coenzyme then trasfers the electrons to a different enzyme, which releases them to the substrates in another reaction. These electrons have energy with them. One of the most important coenzymes is the hydrogen acceptor nicotinamide adenine dinucleotide (NAD+).

Those were activators but there are also substances that bind to he an enzyme and decreases the activity of the enzyme and these substances are called inhibitors. There are four types of inhibition: competitive inhibition, noncompetitive inhibition, irreversible inhibition, and feedback inhibition.

competitive inhibitor

Competitive inhibitors compete with the substrate for the same active site, displacing a percentage of substrate molecules from the enzymes. One example of this type of inhibitors is the medicine penicillin. Penicillin blocks the enzyme bacteria use to build their cell wall. To overcome competitive inhibition is to increase the substrate concentration because if there is higher concentration of substrates than the inhibitor, then there would be more collisions between the enzyme and the substrate; the enzyme will more frequently collide with the substrate.

noncompetitive inhibitor

Noncompetitive inhibitors bind to the enzyme in a location other than the active site, changing the shape of the active site of the enzyme making the enzyme unable to bind to the substrate. Most noncompetitive inhibitors bind to a specific portion fo the enzyme called an allosteric site. A substance that binds ot an allosteric site and reduces enzyme activity si called an allosteric inhibitor. When this substance binds to this site, it causes a conformational change in the active site which is no longer a functional binding site.

Irreversible inhibitors are the same thing as competive and noncompetitive inhibitors, however irreversible inhibitors are inhibitors that permanently bind to the enzyme. So competitor would bind permanently to the active site while the allosteric (noncompetive) will permanently bind to the allosteric site of the enzyme.

Before we can talk about the last inhibitor, it is important if we get the understanding about metabolic pathways. Organisms contain thousands fo different kinds of enzymes that catalyze a wide variety fo reactions. Many of these reactions in a cell occur in sequences called metabolic or biochemical pathways. In such pathways, the product of one reaction becomes the substrate for the next reaction. Metabolic pathways creates organization and efficiency amongst the cell.

Now we can talk about feedback inhibition. Feedback inhibition is a process where the end production of a biochemical pathway acts as an inhibitor of an early reaction. Not only is it unnecessary to synthesize a compound when plenty is already present, but doing so would waste energy and raw materials. It is therefore advantageous for a cell to temporarily shut down biochemical pathways when their products are not needed and this is when feedback inhibition comes in. The end product of the pathway binds to an allosteric site on the enzyme that catalyzes the first reaction in the pathway, causing conformational change and preventing the enzyme from functioning properly.

For a better understanding of the biochemical pathway and the feedback inhibition please go to and go under enzymes and metabolism and click on the second biochemical pathway animations.

Allosteric regulation is conformational changes by regulatory molecules like inhibitors that keep enzyme in an inactive form and activators that keep the enzyme in an active form. Cooperativity is when a substrate acts as an activator because it causes a conformational change in the enzyme and this makes it easier for other substrates to bind to the enzyme.

Well I hope I had helped you out.

Tuesday, December 11, 2007

Metabolism and Enzymes

Metabolism and Enzymes!
Chemical Reactions:

Metabolism is a chemical reaction of life. Bonds forming and breaking between molecules are both involved.

Forming bonds are known as dehydration synthesis, and anabolic reactions. This synthesis requires an enzyme and the release of H2O, while bringing two molecules together.

This diagram shows the dehydration synthesis of sucrose. An enzyme combines Glucose and Frustose, while releasing H2O, to form the compound Sucrose.

Breaking bonds is known as hydrolysis, digestion and catabolic reastions. Breaking of bonds requires a different enzyme, and H2O, to breakdown a compound into two molecules.

This diagram shows Hydrolysis. An enzyme, as well as H2O, is used breakdown the compound into two seperate molecules.

Energy is present is both breaking and forming of bonds. Some reactions release energy, for example hydrolysis, the digesting of polymers. When reactions release energy, it is known as Exergonic.

While some reactions release energy, others require energy. Dehydration Synthesis, the building of polymers, is an example of a chemical reaction requiring energy. These chemical reactions are known as Endergonic.

Activation Energy:

Since reactions don't just happen spontaneously, since covalent bonds are stable, energy is needed to initiate a chemical reaction. This energy is known as Activation Energy. Sometimes the amount of energy needed to destabilize a bond is too much for life. An example of this is lighting a match to burn a piece of paper, like Ms. Foglia did in class.

When there is too much activaton energy in a reaction, a catalyst can be added to reduce the amount of activation energy used to start a reaction. For a cell to reduce energy, an enzyme is added. The enzyme acts as a catalyst for the cell. As Philmore said "Call in the ENZYMES!"

Wednesday, December 5, 2007

The Nervous System

Today in class we continued to learn about the NERVOUS SYSTEM.

Voltage-Gated Channels
Changes in charge across the membrane causes ion channels to open and close.
In response to depolarization, Na+ channels open quickly and close slowly. While K+ channels open slowly and close slowly in response to depolarization.A neuron has to re-set itself after every reaction for the next reaction. Na+ is moved back out while K+ is moved back in. One protein pumps both potassium and sodium out with the use of energy because both are moving against the concentration gradients.
The nerve re-sets itself by pumping 3 Na+ out and 2 K+ in, which is not an equal exchange. Active transport proteins in the membrane are responsible for pumping Na+ out and K+ in. These proteins require a great deal of energy, or ATP.
Action Potential Graph
1. Resting potential- voltage-gated ion channels are closed but some K+ pass through 2. Threshold Potential- an action potential is produced
3. Depolarization- voltage-gated sodium channels open and allow Na+ to diffuse
4. Na+ channels close and K+ channels open
5. Repolarization- diffusion of K+ out of the axon; resets charge gradient
6. Undershoot- K+ channels start to close
Myelin Sheath

Axons are lined with Schwann cells which act as insulators to ensure that signals go far. Signals travel from node to node to reach their destination. A loss of signal can cause Multiple Sclerosis, when the immune system attacks myelin sheath.

Due to the gaps between neurons, impulses have to jump the synapse as quickly as possible to get to other cells. A chemical charge is needed to jump the gaps, so chemicals stored in the vesicles release neurotransmitters. The diffusion of chemicals across the synpases carry the chemcial signal across the synapse.


-Acetylcholine: help in the contraction of muscles, transmit signals to skeletal muscle

-Epinephrine & Norepinephrine: fight or flight response

-Dopamine: help in getting people out of comas but too much of it can cause schizophrenia

-Serotonin: affects sleep, learning and attention

Our next sherpa will be Ashley Scavo.

Tuesday, December 4, 2007

Regulating The Internal Environment Part 2

~Maintaining Homeostasis~

Homesostasis in the body is maintained through a series of different actions trigured by different internal and external stimuli.

The Negative Feedback Loop is one of the most essential actions. It starts with a stimulis, sensors within the body monitor these changes and immdeiately send information to the corresponding intergrating sensor such as an organ or a gland. From there chemicals are released to return the condition to its normal state. Once the response is complete sensors stop sending information and the chemical is stopped, thus allowing the system to enter a state of rest until it must perform its' function again.

An example of this is the action your body goes through when you are threatened or excited. The pituitary gland releases a hormone that causes your adrenal glands to release adrenaline which allows your body to perform basic functions at a heightened level. Adrenaline effects your heartrate and general awareness, giving you abilities that you don't normally have.
The endocrine system also plays a large role in regulating homeostasis. Blood pressure and osmolarity are regulalted by the endocrine system, specifically the brain and kidneys. The pituitary gland monitors these conditions and when something happens to the levels of either osmolarity or BP then action is immediately taken.

-If blood osmolarity rises to high meaning it becomes hypertonic the pituitary gland trigures the release of an anti-diuretic hormone a.k.a. ADH. This increases the permeability of the collecting ducks in the kidneys allowing for increased water absorption. This dilutes the blood bringing it back down to a more stable level.

-If blood pressure drops too low renin is released which removes part of the protein angiotensinogen already found in the blood exposing its' reaction site allowing it to cause the kidneys to release aldosterone. This causes increased water and salt absorption replacing missing components of the blood so pressure is restored.

The other key system to maintaining homeostasis is the

Nervous System.

The most important cell of the nervous system is the neuron. The neurons in the body work very similar to a line of dominoes. A signal starts the reaction like knocking over the first one. A wave is then sent through each single cell until it reaches its predetermined destination. The only way it can occur again is if you reset the axons in a neuron or the lines of dominoes.

Nerve cell live in a sea of charged ions. Ions with negative charges (anions) are found more within the cell, and ions with positive charges (cations) are more common outside the cell. When a nerve is stimulated Sodium channels in the cell membrane open allowing the diffusion of positively charged ions into the cell. At this point the charge on the cell is reversed. Following the first wave another wave of channels is opened this time allowing cations to move out of the cell causing the repolarization of the nerve cell. This is the way messages are sent from anywhere in your body to your brain within milliseconds. After all channels have been closed again and the cell is stabalized it is ready to fire again.

Monday, December 3, 2007

Monday Dec. 3

Mammalian Kidney

-The 2 kidneys have 1,000,000 nephrons each inside them.
-The Nephron filter out urea and other solutes
-the blood leading to the kidneys is from the inferior vena cava
-an animals blood pressure forces the blood into the glomerulus forcing out the liquid and small solutes in the blood.
-too high of blood pressure in this region is hypertension which causes kidney damage
-the glomerulus is a ball of capilaries surrounded by the bowmans capsule which collects the liquid from the blood
-the bowmans capsule then leads to the loop of henle.
-the descending loop of henle reabsorbs h2o
-the ascending loop reabsorbs salts and pumps cl- that it followed by na+ due to unlike charge attraction.
-the collecting duct reabsorbs h2o and urea is passed through the bladder

-diffusion is used in the nephron whenever possible, water is never moved by active transport because it is unnecessary energy use

Whats left in the blood if all the liquid is squeezed out in the glomerulus?
-cells and proteins are too big to fit diffuse through the capillaries

Whats excreted?
-highly concentrated urea, excess h2o, excess solutes (salts and glucose)

Sunday, December 2, 2007

Regulating The Internal enviorment

Homeostasis is the tendency of the body to seek and maintain a condition of balance within its internal environment, even when faced with external changes. this includes cell growth ion balance temperature blood sugar levels energy production cell growth water balance and nutrients.

There are conformers and Regulators. Conformors change their internal conditions to what ever the external enviorment is. An example of a conformors are snakes.
Regulators maintain their interal conditions constant. Such as as body temperature, in humans the normal body temperatur is 98.6

Osmoregulation is the balance of fluids in order to maintain homeostasis.
Their are three conditions that are involved. For each of these conditions the kidney works in different ways.

Hypertonic is a solution with higher solute concentration (higher osmotic pressure) than another so water wants to move in.
Hypotonic is a solution with lower solute concentration (lower osmotic pressure) than another so water wants to move out of
Isotonic is solution with the same solute concentration (same osmotic pressure) as another no net movement of water.
fish that live in fresh water take up salt from the enviorment. Water will flow into the fish and the fish will excrete a low concentration urine to get rid of all of the extra water.
As for fish that live in salt water they tend to lose water and gain salt. They excrete salt from their gills. Water organisms excreteamonia they do not transform it.
Land animals need to conserve water and may need to conserve salt since they live in a dry enviormnent. When we digest foods we create waste products . when we consume nucleic acids we create amonia. Amonia is toxic an carcinogenic it is easily put into cells(soluble). Land animals change amonia into urea to make it less toxic and terrestrial. Uric acid is Eliminated in a pastelike form through the cloaca (mixed with feces) in birds and reptiles. Land animals must excrete it quickly, the longer that amonia is in our body the more problems we can encounter

Egg animals conserve as much water as possible. They create uric acid which is less soluble. it is not a liquid waste. To make something less soluble you make it bigger.
The kidney maintains homeostasis in the body by

removing waste products from the body
removing drugs form the body
balance the body's fluids
releases hormones that regulate blood pressure
produce an active form of vitamin D that promotes strong, healthy bones
control the production of red blood cells.

The kidney works in 4 steps

Filtration- body fluids are collected (blood).

Water and soluble material are removed.

Reabsorption- reabsorb needed substances back in the blood

Secretion- pump out unwanted substances to urine.

Excretion-remove excess substances and toxins from body.