Blog Post #6 - Audrey Malone

     Our plant in the garden was initially growing and I had hope, but now it seems as though the broccoli plant sadly did not make it. Although other weeds and other plants have begun to grow throughout the garden and have greatly increased in biomass. The growth of the other plants is due to photosynthesis and the other plants cells dividing inside the plants allowing the garden to flourish. You can tell that the plants are receiving sunlight because they are growing using photosynthesis . During the process of photosynthesis the energy given from the sun is used to to convert carbon dioxide and water into a simple sugar, glucose. The process of photosynthesis begins as previously stated with the sun hitting the chlorophyll and as the leaves capture the sunlight. It's soon stored after in the covalent bonds of carbohydrate molecules. Later, the energy in the covalent bonds will be broken down in cellular respiration. Overall, photosynthesis is a multi step process that only needs sunlight, CO2, and water. You can also tell the plants are using cellular respiration because they are taking in the CO2 from the air and converting it into energy that is being used to grow all of the plants in the garden. Cellular respiration is the process in which energy is extracted to make ATP. ATP stands for adenosine triphosphate, it's a complicated organic chemical that provides energy. In the first stage of cellular respiration glucose is broken down in the cytoplasm of the cell. In stage 2 of cellular respiration pyruvate molecules are transported into the mitochondria of the cell. Therefore, moving on to the Krebs cycle. After, the Krebs cycle stage three occurs in which the energy in the energy carriers goes to an electron transport chain. While this step is happening ATP is being made.
    The enzymes Phosphoglycerate kinase and ribulose would be made when the plants RNA polymerase would become split and undoes the DNA because it would be using the process known as transcription and translation to make those proteins. As the RNA is copied it then gets sent through the messenger RNA or mRNA. After it would go to the tRNA which job is to transfer an amino acid to the correct codon. Lastly, when the tRNA reaches a stop codon it gets sent out as a competed protein. Proteins are fairly large (for a cell) complex molecules that are very important to the body in a plant or human. Proteins take on multiple important jobs they do almost all of the work in cells, and are required for structure and function in cells.

Blog Post #6 -Elena

1. How is your plant (or any plants in our garden, for that matter) getting bigger and adding biomass? Your explanation should correctly use the terms and concepts of cell division (mitosis), photosynthesis, and cellular respiration

Our plant is slowly adding biomass but it’s growth has stunted recently, most likely due to animals and insects. Other plants in the garden though, the weeds are growing very fast in biomass and have managed to take up most of the garden. This shows that the plants’s cells are dividing so that they are able to grow, they are also doing photosynthesis to get the nutrients they need to grow, the plants must also be doing cellular respiration because the plants are releasing oxygen and taking carbon dioxide in for photosynthesis and cellular respiration. 
During photosynthesis the plants are doing a chemical process that takes in sunlight and carbon dioxide and turns it into sugars that the plants cells can use for energy. Photosynthesis happens is when carbon dioxide enters the leaf through the stomata by diffusion. The water that is absorbed from the soil by the roots. The sunlight absorbed in the. Chlorophyll absorbs light energy, which is used to do photosynthesis. Photosynthesis is a process driven by energy, glucose molecules or other sugars, are constructed from water and carbon dioxide. The byproduct in the process is oxygen. 
Cellular respiration is basically the opposite of photosynthesis. The first step of cellular respiration is Glycolysis, where glucose undergoes chemical transformations, and in the end glucose gets converted into two molecules of pyruvate . In these reactions ATP is made, and NAD+ is converted into NADH. The second step of cellular respiration is Pyruvate oxidation, where each pyruvate goes into the mitochondrial matrix and is converted into a CoA. And Carbon Dioxide is released and NADPH is generated. The third step of cellular respiration the Citric acid cycle, where the acetyl CoA combines with a four carbon molecule and goes through a cycle of reactions, regenerating the four carbon starting molecule. ATP, NADH, and FADH2 is producaed, and carbon dioxide is released. The final step of cellular respiration is Oxidative phosphoryation, where the NADH and FADH2  deposits their electrons in the ecetron transport chain turning back into NAD+ and FAD. As the electrons are moving up the chan energy is beig released and used to pump protons to form a gradient. The protons then flow back into the matrix and through an enzyme called ATP synthase, making ATP. At the end of the transport chain oxygen takes the electrons and takes up protons to form water. 
Cell division is happening to create new cells. Cells in the plant go throught the stages of Prophase, Metaphase, Anaphase, Telophase, and Cytokenisis to duplicate.  In prophase the chromosomes get thicker and visable, and the nucleus dissapears. In Metaphase the chromosomes line up in the middle and the spindles grab ahold of the chromosomes. Anaphase is when the spindles help the chromosomes separate in half and move to opposite sides of the cell. Then in telophase the chomosomes have made it to the opposite sides of the cell and a nucleus has formed around the setts of chromosomes, and the cell starts to split in half. Finally in Cytokinesis, the cell splits in half, and the end relust is two new identical cells. 

1. Phosphoglycerate kinase (PKG) and ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) are two important enzymes used in photosynthesis. Describe how plants in the garden would make enzymes like these if a signal was sent to the nucleus to produce more of one of them. (Hint: enzymes belong to which category of biomolecule?)

Plants in the garden would make these enzymes when a RNA polymerase comes and undoes part of a DNA strand coping and transcribing it with RNA pairing bases to make a strand of RNA. Then after the DNA in put back together that new copied strip of RNA is taken to the ribosomes in the plant cell and there it is translated into amino acids which then build up into a protein or enzyme. 

Blog Post # 6 - Alia Latimer

Our plant itself, has either died, or lagged far behind the growth of it's surroundings. To be frank, I can't tell anymore. The plants in it's surroundings that we have come to know as weeds on the other hand are gaining biomass at a fast rate. They are very obviously in the ideal temperature, and getting the needed amount of resources to keep healthy. I can only imagine that although that change may seem effortless, thousands of millions of cells are hard at work to achieve this outcome. The cells are tirelessly replicating DNA and starting mitosis, over and over and over again. Through the five stages of cell division the DNA is unzipped , replicated, lined up, separated by the spindles, and a layer between the two sides takes form before finally separating. Any mistake during prophase, metaphase, anaphase, telophase, or cytokeinis could lead to the end of both the original cell and the one being made. This is a delicate and stressful process not unlike many of the other processes that the plant cells undergo. Under the sun the plant preforms photosynthesis to make sugars that feed into cellular respiration. The sunlight's energy is recepted in the thylakoids of the cloroplast, where it is used to create sugars and oxygen. Those sugars and oxygen in return are used in the mitocondria to produce energy , water, and carbon dioxide. Both the endless cycle repeated many times just to grow maybe a centimeter over the course of a week.
No doubt that on an even smaller level the plant is sending signals through out it's stock to make proteins, triggering the process of transcription as the DNA is unzipped and copied into RNA, then brought through the cytoplasm to the nucleus where the ribosomes and Ribosomal RNA await to use the trascript to assemble the series of amino acids. All the cells have the same genes, but the RNA of each cell only reads a small portion, in order to produce the different desired traits. RNA is really responsible for the bulk of the process of protein creation since it is the Messenger RNA that actually holds the transcript of the DNA, the transfer RNA that brings the messenger RNA to the ribosome, and the Ribosomal RNA that is responsible for using the transcript to assemble the series of amino acids that make up the protein. Like marionettes, pulled into the dance of a puppet master that never tires, they transcribe and translate, replicate and divide, just going and going until their gone. Tossed to the wind and replaced by one of it's copies, a disposable piece in the process of growth.

Blog Post #6 - Duaa Khan

1)Over the course of this experiment, our Broccolis have grown quite a bit especially within the past 6 months or so. Although they did have some difficulty striving for their lives, they overcame their struggles and were able to grow to their full potential. The main component that had tremendously helped our plants strive substantially was mitosis, also known as cell division. 

   Mitosis is a type of cell division in which one cell (the mother) divides to produce two new cells (the daughters) that are genetically identical to itself. In the context of the cell cycle, mitosis is the part of the division process in which the DNA of the cell's nucleus is split into two equal sets of chromosomes. The great majority of the cell divisions that happen in your body involve mitosis. During development and growth, mitosis populates an organism’s body with cells, and throughout an organism’s life, it replaces old, worn-out cells with new ones. For single-celled eukaryotes like yeast, mitotic divisions are actually a form of reproduction, adding new individuals to the population. In all of these cases, the “goal” of mitosis is to make sure that each daughter cell gets a perfect, full set of chromosomes. Cells with too few or too many chromosomes usually don’t function well: they may not survive, or they may even cause cancer. So, when cells undergo mitosis, they don’t just divide their DNA at random and toss it into piles for the two daughter cells. Instead, they split up their duplicated chromosomes in a carefully organized series of steps.

   Additionally, miosis is a type of cellular division in which animals or plants multiply their cell numbers. Mitosis produces two identical daughter cells in each division. There are some differences between mitosis in plants and animals. Plants for example do not have centrioles and they don't change their shape before division like animal cells do. Mitosis in plants happens in the meristems of the plant that are located at the tip of the stems and roots. These two areas are responsible for production.

   Plants perform photosynthesis because it generates the food and energy they need for growth and cellular respiration. It is important to note that not all plants photosynthesize. Some are parasites and simply attach themselves to other plants and feed from them. For plants to perform photosynthesis they require light energy from the sun, water and carbon dioxide. Water is absorbed from the soil into the cells of roots. The water passes from the root system to the xylem vessels in the stem until it reaches the leaves. Carbon dioxide is absorbed from the atmosphere through pores in the leaves called stomata. The leaves also contain chloroplasts which hold chlorophyll. The sun’s energy is captured by the chlorophyll.

   Cellular respiration is a metabolic pathway that breaks down glucose and produces ATP. The stages of cellular respiration include glycolysis, pyruvate oxidation, the citric acid or Krebs cycle, and oxidative phosphorylation.During cellular respiration, a glucose molecule is gradually broken down into carbon dioxide and water. Along the way, some ATP is produced directly in the reactions that transform glucose. Much more ATP, however, is produced later in a process called oxidative phosphorylation. Oxidative phosphorylation is powered by the movement of electrons through the electron transport chain, a series of proteins embedded in the inner membrane of the mitochondrion. These electrons come originally from glucose and are shuttled to the electron transport chain by electron carriers. Cellular respiration is what cells do to break up sugars to give energy they can use. This happens in all forms of life. Cellular respiration takes in food and uses it to create ATP, a chemical which the cell uses for energy. More specifically, cellular respiration is the process of breaking down sugar to the form of energy. This happens in all forms of life. Cellular respiration is the process that uses food molecules taken in by a cell to create ATP, a chemical which the cell uses as an energy-rich molecule to power all kinds of cell activities.

   Essentially, sugar (C6H12O6) is burned, or oxidized, down to CO2 and H2O, releasing energy (ATP) in the process. Why do cells need ATP? ALL cellular work -all the activities of life - requires energy, either from ATP or from related molecules. A lot of oxygen is required for this process! The sugar AND the oxygen are delivered to your cells via your bloodstream. This process occurs partially in the cytoplasm, and partially in the mitochondria. The mitochondria is another organelle in eukaryotic cells. like the chloroplast, the mitochondria has two lipid bilayers around it, and its own genome (indicating that it may be the result of endosymbiosis long ago). In some ways similar to the chloroplast, the mitochondria also has two main sites for the reactions: The matrix, a liquid part of the mitochondrion, and the cristae, the folded membranes in the mitochondrion. 1: Glycolysis ("splitting of sugar"): This step happens in the cytoplasm. One Glucose (C6H12O6) is broken down to 2 molecules of pyruvic acid. Results in the production of 2 ATPs for every glucose. But glucose is split into 2 molecules of pyruvate!). 2: Transition Reaction: Pyruvic Acid is shuttled into the mitochondria, where it is converted to a molecule called Acetyl CoA for further breakdown. 3: The Krebs Cycle, or Citric Acid Cycle: Occurs in the mitochondrial matrix, the liquid-y part of the mitochondria. In the presence of Oxygen gas (O2), all the hydrogens (H2) are stripped off the Acetyl CoA, two by two, to extract the electrons for making ATP, until there are no hydrogens left - and all that is left of the sugar is CO2 - a waste product - and H2O (exhale). The Krebs cycle results in the production of only ~4 ATPs, but produces a lot of NADH, which will go on to the next step. 4: The Electron Transport Chain and Chemiosmosis ("the big ATP payoff"). Occurs in the cristae of the mitochondria, the folded membranes inside the chloroplast. Electrons from Hydrogen are carried by NADH and passed down an electron transport chain to result in the production of ATP. Results in the production of ~32 ATPs for every glucose. The energy is used for a variety of reasons but mainly for growth. 

2)    The mechanism of transcription has parallels in that of DNA replication. As with DNA replication, partial unwinding of the double helix must occur before transcription can take place, and it is the RNA polymerase enzymes that catalyze this process. Unlike DNA replication, in which both strands are copied, only one strand is transcribed. The strand that contains the gene is called the sense strand, while the complementary strand is the antisense strand. The mRNA produced in transcription is a copy of the sense strand, but it is the antisense strand that is transcribed. Ribonucleotide triphosphate (NTPs) align along the antisense DNA strand, with Watson-Crick base pairing (A pairs with U). RNA polymerase joins the ribonucleotides together to form a pre-messenger RNA molecule that is complementary to a region of the antisense DNA strand. Transcription ends when the RNA polymerase enzyme reaches a triplet of bases that is read as a "stop" signal. The DNA molecule re-winds to re-form the double helix.