Lab Time!!!

This week in AP Biology we did a photosynthesis lab. The first portion of out lab tested the different pigments in spinach leaves. The next portion of our lab tested the rate of photosynthesis in spinach leaves. 

The first lab where we tested for the different pigments showed four different pigments. There was chlorophyll a, chlorophyll b, xanthophyll, and carotene in the spinach leaves. We then tested for a constant that measured how far the chromatography solvent travelled divided by how far the pigment travelled. 

Part two of the lab tested the rate of photosynthesis in spinach leaves. At the first of the lab we took ten spinach leaf discs and put them in a syringe with a bicarbonate solution with dish soap. We them created a vacuum inside the syringe to compress the mesophyll cells so the leaf discs would sink. We then placed the discs into another bicarbonate solution. Every thirty seconds we checked for leaf discs that we're floating. This would mean the mesophyll cells had  air in them and that photosynthesis was occurring. 

The Food-Making Plant Process

               

 This week in AP Bio we went over Photosynthesis. Photosynthesis is an anabolic and endergonic process that plants use to produce food (glucose). The process is done in two reactions, the light reaction and the Calvin Cycle. The chemical equation of this process is:

6 CO₂ + 6 H₂O à C₆H₁₂O₆ + 6O₂

                The first reaction in Photosynthesis is the light reactions. In this reaction solar energy is converted into chemical energy in the thylakoid membrane. This starts with water being split, and because of this it provides a source of electrons and protons and gives off O₂ as a by-product. Light is then absorbed by chlorophyll which excites the electrons in a domino effect until finally the electrons are accepted by the primary electron acceptor. All of this takes place in photosystem two. The electrons are then passed via electron transport chain to photosystem one. The fall of the electrons to a lower energy level provides enough energy for the synthesis of ATP. As the electrons do through part of the electron transport chain a proton gradient of H⁺ is produced and which is often used in chemiosmosis. Light energy meanwhile is transferred by light harvesting complexes and is used to excite electrons in photosystem one until they are accepted by the primary electron transport. The electrons in photosystem’s one primary electron acceptor are then transferred through redox reactions to another electron transport chain, although this one does not produce a proton gradient. The electrons are then transferred to NADPH.

                The second reaction in Photosynthesis is the Calvin Cycle. The Calvin Cycle performs carbon fixation where it takes CO₂ from the air and it to the enzyme RuBP. Then through a series of reactions the ATP and NADPH produced by the light reactions are used up and recycled back. After all these reactions a sugar called G3P is produced which eventually is used to make glucose.

                 

FINALLY!!!

This week in AP Biology we reran our cellular respiration lab. We had tried to run it last week but unfortunately the lab went wrong. To begin the lab again we put the peas in water so they would germinate. Then, to prevent our lab going wrong from last time we hot glued the respirameters to the rubber cork they were supposed to be attached to. The next day in AP Biology we prepared for the lab even more. In the bottom of each test tube we placed a cotton ball and then put 1 mL of KOH solution on them. After that we placed a rayon ball which is considered a nonabsorbent cotton ball on top of them. The KOH solution attaches to the CO₂ released in cellular respiration that way in the experiment you are only measuring the amount of oxygen consumed. We finally ran our lab the next day after putting 10 germinating peas in test tubes 1 and 4 and then putting dry peas and beads of equal volume in test tubes 2 and 5 and glass beads of equal volume in test tubes 3 and 6. We placed the repirameters on top of the test tubes and put them in water baths of 10 and 25 degrees Celsius. After a five minute resting period we began to take measure on the respirameters of the amount of data consumed. Unfortunately our data was very irregular and did not make sense. We attributed this to the fact that we moved the test tubes while they were in the water baths which caused the red dye at the top of the respirameters to leak out. In the end though the germinating peas consumed the most oxygen in the 25 degree Celsius water bath. The colder temperatures affected the peas because it slowed down the process of cellular respiration. 

Oops!!!

This week in AP Biology we attempted to do two labs. Our first lab involved enzymes. In this lab we used hydrogen peroxide as a substrate and the enzyme in this lab would be peroxidase, an enzyme that is found in potatoes. In this lab we would dilute the hydrogen peroxide with water and add blended potato and water. When putting the two substances together the peroxidase in the potato would catalyze hydrogen peroxide into water and oxygen. We were going to see the rate of reaction of this catabolic reaction in different pHs, but unfortunately we prepared our different pH solutions too early and they began to mold. We now have to make more solutions of different pH and then we will be able to perform the lab. Our second lab dealt with cellular respiration. In this lab we were going to compare the amount of air produced by germinating peas, non-germinating peas and glass beads, and glass beads. We had six vials that we numbered one through six. In vial one we placed ten germinating peas. In vial two we put 10 non-germinating peas and a certain number of glass beads that made the volume of the germinating peas and non-germinating equal. In vial three we put only glass beads that equaled the volume of the germinating peas. We repeated this in vials four through six. After this was finished we placed vials one through three in a room temperature water bath and four through six in cool (10⁰C) water bath. The lab was not successful because the vials had repirometers on top of them and when the vials fell into the water the repirometers did also which screwed up the lab. This upcoming week in AP Biology we will restart the cellular respiration lab and will soon restart the enzyme lab.

                                      

The Rehash of Cellular Respiration

This week in AP Biology we expanded even more on the catabolic process that is cellular respiration. Cellular respiration can be broken down into three smaller processes. These processes are glycolysis, Citric Acid or Krebs’s Cycle, and Oxidative phosphorylation which is made up of the electron transport chain and chemiosmosis.

The first reaction that occurs is glycolysis in the cytoplasm in this reaction glucose is broken down from a six carbon molecule into two three carbon molecules called pyruvate if oxygen is present. The result of this is four molecules of ATP although we had to use two molecules of ATP to start giving us a net profit of two ATPs and two molecules NADH or FADH₂. If the process has to occur anaerobically rather than aerobically the glucose molecule is still broken down and the ATP is till produced, but lactic acid fermentation and alcohol fermentation may occur. In muscle cells when the muscle needs more energy than cellular respiration is giving out it performs lactic acid fermentation. When the glucose is broken down into pyruvate the pyruvate is then reduced by NADH and lactate is formed as a waste product.  The lactic acid builds up and can only be removed by exposure to oxygen. In certain prokaryotes and other anaerobic organisms alcohol fermentation is the source of energy. The pyruvate produced by glycolysis is changed into ethanol in alcohol fermentation.

After the glucose is broken down into two pyruvates the pyruvates must then be converted to acetyl CoA and diffuse across the mitochondria membrane before it can enter the Citric Acid Cycle. After the pyruvates are changed into acetyl CoA they enter the Citric Acid Cycle. The Citric Acid Cycle ends up reeasing the original six carbon atoms that were part of glycolysis at the begging as well as 3 NADH, 1 FADH₂, and 1 ATP for every turn. Since there are 2 acetyl CoAs the cycle has two turns giving it at the end 4NADH, 2 FADH₂, and 2 ATPs.

The energy held in the NADH and FADH₂ electron carriers is then used by the electron transport system. Unlike glycolysis and the Citric Acid Cycle which produces ATP through substrate level phosphorylation the electron transport chain and chemiosmosis produce ATP through oxidative phosphorylation. The electron carriers then deposit electrons to the electron transport chain. The loss of energy from the electrons is used to pump protons across the mitochondria’s inner membrane. Once the electrons are done they then combine with two hydrogen ions and oxygen to form water. The large concentration of protons or H⁺ ions then power the enzyme ATP synthase which starts pumping out ATP. This part of the process is called chemiosmosis. The end result of this can produce up to 26 or 28 ATPs.

Cellular Respiration

This week in AP Biology we learned about Cellular Respiration. Cellular Respiration is the process of taking food with 0₂ and creating ATP. Cellular Respiration takes place in and outside of the mitochondria. It can be performed both aerobically and anaerobically although, it is more productive aerobically. The equation for cellular respiration is C₆H₁₂O₆+6O₆ à 6CO₂+6H₂O.

There are three steps in cellular respiration they are glycolysis, The Krebs’s Cycle, and the electron transport chain. Glycolysis is taking glucose and breaking it down into two pyruvates. It occurs outside of the mitochondria in the cytoplasm. This produces two ATPs. After glycolysis the pyruvates are diffused across the mitochondria’s membrane where it is changed to acetyl CoA. From there the acetyl CoA enters the Krebs’s or citric acid cycle. This process produces 6 NADH, 2 FADH₂, and 2 ATPs. After the Krebs’s Cycle the NADH and FADH₂ go to the electron transport chain. There the NADH and FADH₂ release hydrogen atoms across the mitochondria’s membrane. When the outside of the mitochondria is saturated with hydrogen atoms it propels the enzyme ATP synthase to start producing ATP and it can produce up to thirty-four ATPs.

If cellular respiration occurs anaerobically it does not produce as much ATPs. Anaerobic respiration only has one step which is glycolysis. Lactic Acid Fermentation happens when muscle cells are placed under extreme pressure. The muscles cannot get enough oxygen so they start to perform cellular respiration anaerobically. This builds lactic acid in the cells and it can only go away by getting oxygen to the cells. When cellular respiration is performed anaerobically it is not as successful as when performed aerobically.

The O word!

This week in AP Biology we did a lab over osmosis. Last week we learned osmosis is a type of diffusion, but it only applies to water. The definition of osmosis is the diffusion of water across a selectively permeable membrane.

There are three terms often mentioned when dealing with osmosis and they are hypertonic, hypotonic, and isotonic. Hypertonic is the solution when comparing two solutions has the higher concentration gradient. When cells are placed in hypertonic solutions the water in the cell will rush out of the cell, and the cell will start to shrivel up. In plants this causes plasmolysis, which is when the plasma membrane detaches from the cell wall. Salt water is hypertonic to the cell in our bodies, so if you are ever dehydrated salt water will not hydrate you but will dehydrate you faster.  A hypotonic solution is the solution when comparing two solutions has the lower gradient concentration. Cell placed in a hypotonic solution will most likely bust because the water rushes into the cell because of osmosis, except in plant cells. The cells in plants like to be in a hypotonic solution because it keeps the cell turgid. An isotonic solution is when comparing two solutions and them having the same concentration gradient. This is how people want their cells to be at most times. In plant cells though, this is not the prime environment for the cells. Plant cells in an isotonic solution become flaccid which causes the plant to look wilted. 

 The lab we did was centered around these terms and how the solutions affect cells.

The Gatekeeper

  This week in AP Bio we learned about the gatekeeper of the cell. This guardian of the cell is called the plasma membrane. The plasma membrane is made of a phospho-lipid bi-layer and proteins. The phospho head of the bi-layer is hydrophillic, while the lipid tail is hydrophobic this characteristic of  is called amphipathic. The along with proteins embedded in membrane allows the cell to be selectively permeable. The function of the plasma membrane is to maintain homeostasis by controlling what goes in and out of the cell.
  There is two different ways the plasma membrane diffuses what goes in and out of the cell. One is passive transport that requires no energy; there is two types of passive transport diffusion and facilitated diffusion. Diffusion is when molecules move from a high concentration gradient to a low concentration gradient. Osmosis is also diffusion, but it is when water diffuses across the plasma membrane. Facilitated Diffusion is when molecules move from an are of high concentration to an area of low transportation using a transport protein. The other type of transport that the plasma membrane uses is active transport, and it does require energy. The molecules are moving from an area of low concentration to high concentration, and the cell uses energy from the mitochondria called ATP.
  When cells require to move large particles into or out of the cells they use endocytosis ans exocytosis. Endocytosis is when when the membrane is taking the particles into the cell by vesicles created by the membrane. Once the particles are taken to their destination the membrane is reabsorbed by the cell. There are three types of endocytosis. Phagocytosis although it is also called cell eating; it is when the vacuole or vesicle the material is contained in is sent to the lysosomes to be digestive. In pinocytosis, when the plasma membrane engulfs the materials is also takes in the extracellular fluid this is very important in red blood cells. The third type of endocytosis is receptor-mediator endocytosis it is when the cell binds itself to specific particles. Exocytosis is used when the cell is moving molecules out of the cell. The large particle exiting the cell is enveloped by a vesicle that is fused with the membrane once it's materials exit.
  Each of our cells have a surrounding plasma membrane, even prokaryote cells have one. Is is very crucial to all organisms in maintaining homeostasis.

The Endomembrane System!!!

  The Endomembrane System is very important in our cells. Eukaryotic cells are the only cells that have the endomembrane system. It consists of the the nuclear envelope, the endoplasmic reticulum (smooth and rough), the golgi apparatus, lysosomes, different types of vesicles and vacuoles, and the plasma membrane. The function of the Endomembrane System deals mostly with proteins. It includes the making, modification, sorting, and transport of proteins. All of the Endomembrane System is related by either physically touching or by vesicles transferring between the related organelles.
  Within the Endomembrane System there are many different organelles that have certain responsibilities in the cell. The nuclear envelope is a bi-layer membrane that encompasses the nucleus of cells. The endoplasmic reticulum is the place that proteins are synthesized and transported. Proteins are modified and also transported to other parts of the cell in the golgi apparatus. Lysosomes have a digestive enzyme that allows them to digest macromolecules in the cell. Vesicles are small bits of membranes that are used to transport substances in the cell. Vacuoles are used to store waste products and maintaining the shape of cells. The gatekeeper or plasma membrane of the the cell is used to regulates what enters and exit the cells.
  Endomembrane System consists of most of the membranes in the cells and has many different resposibilities in our cells that are imperative to our bodies.

   Pill Bugs or Roly Poly Ollies  

 This week in AP Biology we learned about pill bugs for our first big lab. Pill bugs also know as roly polys or pill bugs are very interesting creatures. Their scientific name is Armadillidiidae vulgare. Pill bugs are also part of the crustacean family, which is animals such as crabs and shrimps. Unlike its family members pill bugs can spend their entire life on earth. Pill bugs enjoy cool and dark places such as underneath a rock or in a basement. They can also be found in biomes all over the world. Pill bugs are a grey earthy color, but can be found in Europe with red dots giving them protection because other organisms associate them with black widow spiders. They have a an exoskeleton made up of chitin as we learned earlier is a carbohydrate. Pill bugs have seven jointed legs and two pairs of antennas but you can only see one. A pill bug's diet consists mostly of decomposing plants and animals. An interesting fact about pill bugs is that they have gills to breathe although they cannot live when submerged in water. Pill bugs get their nickname roly poly because of a defensive mechanism they have which they have that makes them roll up into a ball.
   Pill bugs are very interesting creatures they have odd quirks such as blue blood or drinking water with their anus.


P.S. (Roly Poly Ollies is my nickname for pill bugs)

Organelles in Animal Cells

Cells are the basis for the structure and function of all organisms. There are two different types of cells, eukaryotic and prokaryotic. Plants, animals, protists, and fungi are all made of eukaryotic cell, while bacteria and archea are made of prokaryotic cells. Cells are made of organelles that all have a specific job in cells. Animal cells and plant cells have different organelles in them. 

One type of organelle is the nucleus; it is used in storing genetic material that is later used in the reproduction of cells. Another type of organelle is the nucleolus of a cell. They are located inside the nucleus and are used for the production of ribosomes. Ribosomes are used in the synthesis of proteins. After ribosomes synthesize proteins they are then sent to the Rough Endoplasmic Reticulum where the proteins are created. Cell products such as proteins are sent to the Golgi apparatus to be modified, synthesized, and discharged from the cell. Lysosomes are digestive organelles in the cell. They use hydrolysis to break down macromolecules. Mitochondria in cells are the site of cellular respiration that creates ATP for the cell. The cytoskeletons of cells are used to transport materials in the cell and are important in the cell's structure. The plasma membrane of cells control what goes in and out through cells. Cytoplasm is the jelly like substance in cells it is also called cytosol. Centrioles help with cell division. All these organelles are what help cells to do their jobs, and without these organelles we would not be able to live.

Animal Cell

The BIG Four!!!!

This week in AP Biology we learned about macromolecules. There are four types of macromolecules, carbohydrates, lipids, proteins, and nucleic acids. They are the most important molecules of all living things. Carbohydrates, proteins, and nucleic acids are also organic compounds because of the elements involved in their makeup.

                Carbohydrates  are made up of carbon, hydrogen, and oxygen usually in a 1:2:1 ratio. The monomer of carbohydrates would be a monosaccharide coming from the Greek language in which monos means one and sacchar means sugar. Many of theses sugars put together will create polysaccharides. One type of polysaccharide is starch, which is used in plants to store glucose, a food source. Another polysaccharide is chitin, which is used by arthropods for their exoskeleton. Carbohydrates are very important in day to day life. 

                                                    

                One of the more unique macromolecules are lipids because they have no one true monomer. They are made up of carbon and hydrogen but also with a small amount of oxygen. Lipids are actually too small to be called macromolecules, but because of their inability to mix with water they are grouped together. Lipids have many forms and functions, but the three most important biologically, are fats, phospholipids, and steroids. A fat is consisted of glycerol and a fatty acid. Fats are used by animals to carry and store energy with them. Phosphlipids are made of two fatty acids bonded to a glycerol, and they are extremly important because they make up our cell membranes. Steroids are made of a carbon skeleton with four fused rings. Cholesterol and sex hormones are types of steroids. These are a few examples of lipids.

                                           

                 With every living thing depending on proteins you could probably say it was one of the most important macromolecules. It literally means in Greek "first" or "primary". The elements present in proteins are carbon, hydrogen, oxygen, nitrogen, and sulfur. The monomer of proteins are amino acids which when bonded together, by peptide bonds, create polypeptides. These polypeptides are what enzymes and insulin are made of. Proteins are very complex and important to our systems.

                                                            

                  The fourth macromolecule is called nucleic acids. Carbon, hydrogen, oxygen, nitrogen, and phosphorous are what create nucleic acids. A nucleotide is the building block or monomer of nucleic acids. Nucleotides are composed of a nitrogenous base, a pentose sugar, and one or more phosphate groups. On ethe nucleotides bond together they will create RNA or DNA. RNA is a nucleic acid that does various requirements in gene expression, while DNA store hereditary information. These are what nucleic acids compose and what their functions are.

                                                  

                   Macromolecules are complex and large molecules, that make up the critically important molecules of all living beings.