Oceans Frozen 900 Ft. Global Warming You Say?

Over the last several years, biologists have been trying to figure out the chemical compositions of the primeval Earth (ancient Earth), as well as, when organic matter began to take control and produce life. When the Earth was first created, it was a giant hot ball of molten elements, that had a reducing atmosphere (meaning the atmosphere was composed of gases such as NH3-ammonia, CH4-methane, H2-elemental hydrogen, CO2-carbon dioxide, among others). In this case, life would have been very hard to get started, until better conditions arose. The important thing to realize was that it did, and the earth eventually cooled down -- maybe froze would be a better word. When looking at the carbon distribution in the Earth, biologists originally thought that it was mostly in the atmosphere as carbon dioxide (CO2), which would create the so called 'Greenhouse Effects' that are supposed to be causing global warming , today. When CO2 is in the atmosphere, it works as kind of a blanket to keep heat in. So, in the case of the Earth, the earth would have not cooled down as fast....OR DID IT? New theories are coming out saying that most of the carbon at this time was in fact not in the atmosphere as CO2, but in the ground as calcium carbonate (CaCO3). Due to the sun being about 70% as powerful as it is today, the earth with no greenhouse effects, would be super COLD! So cold that the whole world would have oceans that were frozen 900 + ft down! Sounds like it would be a challenge to ice fish, but at least it would have been safe to skate!

Evolution Lost

Is There a Limit to Evolution on Earth?

What are our limits to evolution? There are two theories concerning the growth of diversity amongst the planet. These 2 theories include diversity in an equilibrium or diversity that is rapidly expanding (occupying every possible niche, as well as, exploiting current ones in order to gain a better advantage). While the theory of equilibrium states that basically every niche has been occupied already and that in order for a new species to come on the scene, it must win out against a present species, this particular theory is not what we are concerned with in this blog. We are more so concerned with the expansion theory. In this theory, there is no noticeable (at least at the moment) ceiling for organisms diversifying or speciating in the world (meaning that more and more species can evolve and yet there still be more room on Earth). This could be a result of possible extinctions that have opened up the playing field OR that there is a constant arms race between members of the food chain -- or both! By arms race, I mean as the predators find ways of getting more energy, food, etc., the prey finds ways to survive while still be exploited by the predators. Many examples are available of this so called arms race, but nonetheless, when every avenue is exhausted to obtain energy to live, what is the last stronghold that organisms, possibly large or small, will try to take? Some scientists believe that if there is a limit to evolution and speciation is in fact, an expanding process, then individual organic molecules, such as carbon, might be the last frontier. This is a very mind opening thought! How long would this process take to get to such levels of energy scavenging? How densely populated will our earth be at this point? Will we even still exist by the time something like this can happen? It has yet to be seen, but you better believe, they are all possibilities!

Short Lesson on Meaning of Light Years

FOOD FOR THOUGHT: I am currently looking at Orion's Belt from my house right on the beach and due to the Turtle Law, all lights must be out. As a result, the stars are very noticeable. Apparently, this particular group of stars is 900 light years away. What that means is, that it takes us 900 years to see the light from these stars that we happen to be viewing right now, and vise verse. With that said, if there was some being living in a planet or other body near that star and they had a telescope to see what the earth looked like, they would be watching crazy battles during the Medieval period in Europe (William the Conqueror killing it!). They would see the start of the first crusade, the game of checkers invented, the Pueblo Indians in the southwest of North America were just getting started, and the city of Cusco, Peru being founded (all occurring around the year 1000 AD). Incredible!

Fangtooth in the Abyss

Glycolysis Broken Down

Glycolysis can be a pretty daunting concept to really get a firm understanding on, with so many different molecule derivatives involved. So here, I will be explaining this process in a step-by-step manner that hopefully, will help alleviate any frustrations. The main function of the glycolysis pathway, which occurs in the cytoplasm of cells, is to break down glucose into two 3-carbon molecules of pyruvate.

GLYCOLYTIC PATHWAY (STEP-BY-STEP)

1. Initially, Glucose (STARTING PRODUCT) is phosphorylated (given a molecule of phosphate) by ATP with the help of hexokinase (enzyme that facilitates phosphorylation), leading to the molecule, Glucose 6-phosphate.
2. Glucose 6-phosphate is rearranged by an enzyme known as Phosphoglucose isomerase, leading to the molecule Fructose 6-phosphate.
3. Following another phosphorylation, this time by the molecule Phosphofructokinase, Fructose 6-phosphate turns into Fructose 1,6-biphosphate. 
4. The 6 carbon molecule, Fructose 1,6-biphosphate is split into two 3-carbon molecules by an enzyme simply called an Isomerase. The resulting 2 molecules are as follows -- Dihydroxyacetone phosphate and Glyceraldehyde 3-phosphate (G3P). -- For the sake of keeping things simple, we are not going to worry about the Dihydroxyacetone phosphate because it is converted into G3P later in another reaction.
5. With that being said, we are left with one molecule to deal with (G3P), which undergoes oxidation, followed by yet another phosphorylation. This leads to the production of two NADH molecules, as well as, two 1,3-Bisphosphoglycerate (BPG) molecules. These reactions occur as a result of the enzyme, Glyceraldehyde 3-phosphate dehydrogenase.
6. Next, the enzyme phosphoglycerate kinase facilitates the removal of phosphate molecules by ADP, resulting in two molecules of 3-Phosphoglycerate (3PG). 
7. Conversion of 3PG by Phosphoglyceromutase, converts the 3PG into 2-Phosphoglycerate (2PG).
8. The enzyme Enolase removes a water molecule (H2O) from each 2PG molecule forming two Phosphoenolpyruvate (PEP) molecules. 
9. Finally, Pyruvate kinase facilitates the removal of two more phosphate molecules from PEP, producing two ATP molecules and two Pyruvate molecules (END PRODUCT).

FOLLOW THE CHART BELOW FOR AN OVERVIEW OF EACH MOLECULE. THIS PICTURE DOES NOT SHOW THE ENZYMES ASSOCIATED WITH EACH STEP; HOWEVER, THESE ARE MENTIONED ABOVE.

                                            


Please feel free to leave comments to let me know if you thought this blog was useful or if there is anything that I can improve upon. Thanks!

Animal Eukaryotic Cell Components: Structure and Function

I posted a picture of the eukaryotic animal cell earlier, but it was simply a labeled diagram. Here we will go into each of the major parts of the cell, as well as each organelle's function, not to mention the overall structure of the cell. As the name suggests, this type of cell can be found in all animals including fish, amphibians, reptiles, and mammals.

STRUCTURE OF THE CELL:

In the case of this cell, the eurkaryotic animal cell is encased by what is known as a plasma membrane, which keeps the cytoskeleton and various organelles inside. The inside of the cell has a gel-like matrix called the cytoplasm (the cytoplasm does not include organelles). 

COMPONENTS OF THE CELL: 

Nuclear Components

1. Nucleus: Spherical in shape and typically located in the middle of the cell (exceptions do occur), the nucleus is the source of all genetic information (before it is transcribed and translated), that leads to formation of nearly all the proteins that are in the eukaryotic cell. This organelle also has a double membrane around it. 
2. Nucleolus: A region surrounding the nucleus whose main function is in the synthesis of ribosomal RNA (also known as rRNA).
3. Nuclear envelope: Surface of the nucleus that contains two phospholipid bilayers, that are interspersed with holes, called nuclear pores. The outer most membrane of the nuclear envelope is continuous with the endoplasmic reticulum (ER).
4. Nuclear pores: Located where both of the phospholipid bilayers touch, these pores function in allowing small molecules to diffuse between the cytoplasm and nucleoplasm, while regulating the passage of proteins or RNA/RNA-protein complexes. 

Cytoplasmic Components

1. Actin filament: Long filaments that are about 7 nm in diameter and are made up of two globular alpha helices that wrap around each other. The main functions of these filaments in the cell concern with movement and range from contraction, pinching (during division), as well as, the formation of cellular extensions of the cell. These filaments can add or remove length through a process known as polymeration and depolymeration.
2. Microtubules: Hollow tubes ranging around 25 nm in diameter and composed of 13 protein protofilaments (each protofilament has subunits that alternate as alpha and beta tubulin subunits). Along with providing cellular movement, like the actin filaments, microtubules also help structure where the organelles are in the cell itself. 
3. Intermediate filament: These filaments are the most durable of all filaments, in terms of tensile strength and clock in at a diameter of 8-10 nm (intermediate in size between actin filaments and microtubules -- easy way to remember). The main function of these fibers is to provide structural stability to cells.

Remaining Organelles

1. Centriole: An organelle identical in structure to a basal body. It functions in dividing and organizing spindle fibers during the processes of mitosis and meiosis.
2. Lysosome: A membrane-bound vesicle that contains enzymes that break down worthless organelles and cell debris. These digestive enzymes are produced by the Golgi apparatus.
3. Plasma membrane: This membrane is composed of a phospholipid bilayer that surrounds the cytoplasm of the cell and can contain embedded proteins. The main functions of plasma membrane (PM) are to regulate what comes in and out of the cell, cell-to-cell recognition, adhesion and connection, and cell communication.
4. Ribosome: Small organelles found in the cytoplasm, as well as, the rough endoplasmic reticulum (rough ER) and are made up of RNA and proteins. They function as the site for protein and/or lipid synthesis. 
5. Endoplasmic reticulum (ER): This particular organelle is a network of internal membranes that function  in forming transport vesicles, lipid synthesis, and synthesis of membrane proteins. 
6. Golgi apparatus: A sack of flattened vesicles that receives transport vesicles from the ER and packages/modifies them for export of the cell. From that point, the Golgi apparatus secretes them into the cytoplasm. 
7. Mitochondria: Bacteria-like organelles that have a double membrane and are known as the 'power plants' because they provided energy to the cell via ATP and also are the sites of oxidative metabolism.

This is simply just a run through of the main components of an animal eukaryotic cell. If you have any question concerning details on any of these organelles/features, please don't hesitate to let me know by emailing me at holtzj@email.sc.edu. Thank you.

Enzymes: Structure, Function, Classification, and Specificity

Enzymes are proteins that vary widely in their particular structures, functions, and specificity; however, their general themes remain constant. More importantly, most of the biological reactions that occur, are governed by enzymes, making this an important topic to discuss.

STRUCTURE: 
The structure of enzymes normally is made up of individual proteins (strands of polypeptides -- which are themselves strands of amino acids that have been strung together), to form what is known as a globular protein. Each enzyme also has areas on it that look like a bite has been taken out of them, known as the active site. This is where the reactant binds to the enzyme, noncovalently. The bonding between the enzyme and the reactant, will be discussed later in the 'Specificity' section. It is important to realize that although each enzyme has an active site for which to bind the reactant, each reaction/binding requires a different shaped active site depending on that exact type of reaction.

                                   
FUNCTION:
The main function of any enzyme is to lower the energy of activation for a particular biological reaction, thus increasing the rate of that reaction. The amount of increase in the rate of the reaction can be up to thousands of trillions faster! The amazing part about enzymes is that they are able to help out reactions in such a huge fashion, yet, they are not consumed in the reaction and can immediately be used for another one. This trend will continue until a point called saturation kinetics is reached (will be discussed in a later blog), but briefly, it is a point where substrates are so numerous, that they must wait in line for an available enzyme to bind.

CLASSIFICATION: 
When classifying an enzyme, scientists use a nomenclature that simply uses a pre-fix that explains what the enzyme does. This can be a common word or a stem that relates to its function. At the end of the stem, the ending -ase is used to mean that it is an enzyme. For example, the word ligate means to bring things together. So when trying to name an enzyme that would bring perhaps, two proteins together (as is the case in DNA replication), scientists have named it 'ligase'. Here we will divide all enzymes into a total of 8 categories and along with their function.

1. oxidoreductase (oxidizes one molecule, while reducing another)
2. transferase (transfers a molecule)
3. hydrolase (breaks a hydrogen bond -- enzyme for word 'hydrolysis')
4. lyase (breaks up a molecule)
5. isomerase (changes structural arrangement of isomers)
6. ligase (brings molecules together)
7. kinase (adds a phosphate in process known as phosphorylation)
8. phosphotase (removes the aforementioned phosphate)

SPECIFICITY:
The bond between the active site on the enzyme and the substrate (on reactant) are highly specific. A good way to explain this is to look at the 'Lock and Key theory'. Basically, only a particular enzyme will bind to a particular substrate, allowing the enzymes to be more efficient (like a lock and key). Another theory is called the 'Induced Fit model', which says that the shape of both the enzyme and the substrate change upon binding, maintaining their specificity. Once the active site of the enzyme and the substrate come together, it is known as the enzyme-substrate complex.The take home message however, is that enzymes are very specific to what they're supposed to bind to, and unless there's a mutation in their genes during production, they don't mess up and stay highly consistent.

Enzyme Specificity Depiction

                                     
For the definitions to the bold-faced terms, check out the glossary. Also, soon to come on the subject, saturation kinetics, enzyme inhibition, and enzyme regulation. And don't forget, if you have any questions, please don't hesitate to email me at holtzj@email.sc.edu and I will do my best to assist you.

DIAGRAM OF CELL MODEL, LABELED.

Diagram of Cell

We will be defining the functions, as well as, the structures of the cell tomorrow morning. Please check back and give it a look Thanks!

Welcome to My Blog!

Welcome to my blog! The aim of creating this blog, is to share with the world the beauty of the biological world, in a more simplified, comprehensible view. I hope to make theories, concepts, etc., easy to understand and interpret. I also hope that at one point, this will be a blog that students ranging from middle school through college, can visit to learn and reinforce what they have previously learned. Throughout the next couple months, I will be experimenting with several topics in biology, as well as, biochemistry, to try and get a feel for this blog. Please, if you have any ideas concerning concepts that you would like a better all-around understanding on, don't hesitate to comment and/or request. Thank you.