Three major themes this course

Reflecting back on the course, what are three major themes you would identify that connect the various topics discussed in this course – how are they connected to more than one topic, and how do they connect with what you knew before this course?  What knowledge have you gained with regards to these three themes you have identified?

1 Nucleic Acids
2 Thermodynamics
3 Photosynthesis

Nucleic Acids

Nucleic Acids can be related to most thing in biochemistry. They are very important and crucial for life. Nucleic Acids, RNA and DNA can be seen as storing units in the body for our hereditary information. DNA is composed of complementary bases such as A, G, C, T and RNA is composed of A, U, C, and T as complementary bases. RNA is helpful in that it helps the ribosome to translate the information in DNA into a protein. Nucleotides are made up of sugar-phosphate backbones, which they share, and their bases. There are only twenty amino acids that make up the sequences in our body, which can be very surprising. Nucleotide polymers join together to the monomer units by using oxygen on the phosophate, and a hydroxyl group on the sugar. Its really interesting to learn so much about nucleic acids and their role in replication, yet these simple nucleic acids are so essential and important to the body to produce every day functions.
Thermodynamics
This deals with the realtionship and converstions between heat and energy production. Almost anything that has to do with science can be connected to thermodynamics. Metabolic pathways that are occuring in the human body are using and producing energy. Energy production produces heat. For example, when going for a run your body is using and burning energy, where your muscles then give off heat. In past science classes the laws of thermodynamics which were  are laws in which govern the conversion of energy from one form of energy to another, the direction in which heat will flow, and the availability of energy to do work, for example the entropy of a closed system increases with time. Biological thermodynamics is the energy production in and between living organisms, structures and cells and the chemical reactions that allow these processes to take place. For example, the process of translation and transcription of genes require energy but is necessary for specific phenotypic traits and their functions to be expressed. Also the third law of thermodynamics was used alot in this biochemistry course, using Gibbs Free Energy, G= H-TS. Where H is enthalpy, T is temperature and S is entropy. Biological thermodynamics can be related to almost every chapter we have gone over in Microbiology and in any other science class taken in the past because there is always a necessity and production of heat, power and energy when talking about living things.

Photosynthesis
Only occurs in plant cells, in the plant leaves specifically. This is a way that plants obtain energy, by sunlight. Though, interestingly enough, very few algae can utilize sunlight for energy. Photosynthesis is the process of converting light energy to chemical energy for the cell to utilize it and/or store it in the bonds of sugar. Plants need not only sunlight but CO2 and H2O, to make sugar. From biochemistry I not only understand photosynthesis better but I understand the differences between plant cells, animal cells and bacterial cells. This process takes place in the chloroplasts of the plant cells, using chlorophyll, which is the green pigment that is involved in photosynthesis. Being able to physically see the differences in their structures and better understand their functions helps to give a better understanding of why plants need photosynthesis to occur. For example, if you have to distinguish a picture of an animal cell from a plant cell, being able to recognize the chloroplasts, like in class, helps to justify that is is a plant cell because animal cells do not have chloroplasts.

Lipid Metabolism

How would you explain the connection between glucose entering the body and energy created by the body to a friend, using your new biochemistry knowledge?

Overall, there are a set of specific chemical reactions that take place in the human body to sustain life, for example, the pathway of glycolysis. Glycolysis, in anaerobic conditions, produces lactic acid as its final product, which can cause plaque and bacteria build up in the mouth of humans etc. The body can tell what it will use for nutritious purposes and what is toxic to the body. There are many crucial steps in chemical reactions that take place in the body. Enzymes can be considered the main component of most metabolic pathways. Enzymes allow humans/organisms to catalyze reactions efficiently that require energy and would not occur by themselves, for example, by spontaneous reactions or by coupling reactions, which release energy.

For example, Ingested fat is taken in through the mouth, to the stomach, and into the small intestine, where it is broken down by bile. Long chain fatty acids are packed together in the small intestine and are taken up by the mucosal cells in the small intestine to be used for the synthesis of chylomicrons (composed of cholesterol, phospholipids, triacyglygerols, and apoproteins). Chylomicrons can then enter into the blood and be dispersed throughout the body for "fuel". This fuel helps the body’s cells to function properly and grow efficiently. This process of lipid metabolism and enzyme regulation of metabolic pathways also allows humans to be able to reproduce, respond to changes in the cells environment and/or receive signals from other cells in the body.

Thermodynamics/Carbohydrates

Thermodynamics is the study is heat, work, and power, which help biochemists to better understand the mechanisms of life and carbohydrate-lipid interaction. Carbohydrates main purpose is to store energy readily for our body, though they serve several biochemical functions. When viewing the process of thermodynamics and carbohydrate-lipid interaction, specific properties of carbohydrates in aqueous solutions can be detected, such as being able to notice the hydrophobic interaction which involves hydrocarbon tails of the lipid in aqueous dispersions. The importance of Carbohydrates structure is necessary for the body to perform its proper day to day functioning, such as providing energy through oxidation. Carbohydrates also play important roles in cell to cell communications and interaction, without them our body would not be able to properly function. Carbohydrates are essential to life. 


Our body is arranged in specific degrees of order, which are fashioned in a very complex way. Atoms in the body make up molecules which are arranged into cells, which make up organs, bones, muscles etc. Without the understanding of how thermodynamics and carbohydrates relate to the human body, we would not entirely comprehend why such things occur in the human body such as, muscle movement, ability to interpret information, digestions, and other cellular processes. Also with the ability to manipulate carbohydrates in the body and/or how they are transferred in the body, can be used to predict properties of other systems and enable for excessive advancement in the scientific/biochemistry field.

Medical Biochemistry

Medical Biochemistry website

http://www.topsite.com/goto/themedicalbiochemistrypage.org


This website is excellent for students and/or anyone who is interesting in learning more about biochemistry. It has very easy resourse tools and guides to help you better understand the basics of biochemistry, step by step. This website allows you to understand the biochemical, metabolic, and physiological processes at a push of a button. The home page is very straight forward, it gives you each section that you can chose to click on or skip. Fro example you can chose to learn about enzyme activity, living organisms, hormones, genes, etc. It has a very large variety of key information and processes that are somewhat straight forward and easy to learn.

This website it not only a helpful learning tool for students and teachers, but for anyone who is interested in learning more in a very easy and efficient way. The website has been around since 1996, which proves that it is a success for viewers, and is simple and fun to use.

Membranes (What knowledge have you connected with past knowledge?)

Membranes

In recent labs dealing with membranes I can not only better understand them but also physically can tell how they can be easy to manipulate and are strong. They are beneficial to use because they do not rip effortlessly and can undergo many different laboratory conditions, were as other things such as films or gels for example would not be able to stay intact. A cell would not be capable of performing many and/or all of its functions (mainly inside of the cell), if it wasn’t enclosed in a resilient external membrane. The membrane has multiple functions such as acting as a protection shield/selective barrier, only allowing certain things in and out of the cell, for example virus’s. Many proteins are allowed to move in and out of the membrane, depending on its size and shape, and the membrane and/or proteins are able to be dyed to better visualize specifics of the membrane and what it encompasses. In our recent lab, such as the Western Blot, we were able to manipulate and transfer proteins onto a membrane and add a blue like color to dye the protein bands on the membrane to be able to visualize the results, which then lets students better understand not only how the Western Block works but better understand the functions and purpose of the membrane in that specific lab.

Without the membrane the cell would appear nearly as a pile of mush, having no major function or importance. Membranes can be of all different sizes, thicknesses, and pore sizes depending on its purpose. A membrane is almost structured accordingly to what it is needed/used for, for example a plant membrane and human membrane appear much different due to them having different functions internally and externally. The membrane is not only the cells leading support system but also protects the cell from foreign substances/objects, which may be toxic and/or harmful to the cell, which could in turn lead to cell death.

Finding a protein using PDB explorer

GFP

The protein that I have chosen is the GFP protein, which stands for green fluorescent protein. This GFP protein is said to be found in the north pacific waters, in specific jellyfish. This jellyfish contains "bioluminescent protein, which is an aequorin." This protein itself is actually emits a blue color but this is where the GTP protein comes into play. The GTP protein then takes this bioluminescent protein and converts it to green light. It emits this color by absorbing the UV rays from the sun, through the water, into the jellyfish, which in turn emits its green fluorescent color, at a much lower intensity than the UV rays from the sun. If you were to look at this jellyfish not in the sunlight but rather inside under a regular lamp light it would appear to be a yellow color.

This GFP protein can be used in a number of ways, mostly because it is so easy to use. For example the GFP protein can be used as a marker protein in a therapeutic or cancer drug that you can be given to a patient with a certain disease and/or cancerous. Being able to track the path that this drug is traveling, being able to time its reaction rate (how quick the drug is being taken up by the cells) or see what isn't functioning appropriately. For example, if certain protein(s) aren’t binding or aren’t capable of binding proficiently to its specific receptor site, this would show researchers the location of where the cancer is being generated and could help supply answers to finding a cure.

GFP can also be used for studying abundant living cell types and making a slight mutation in the stability of the chromophore, or they can be used as biosensors, which sense ion or pH levels. It is a very unique, fast growing protein that is being used worldwide and is even being inserted into different animals such as rabbits, mice, frogs etc. GFP is a great tool for genetic engineering (it can fold on itself and glow) and its popularity of use is greater than ever.

What is Biochemistry?

What is biochemistry, and how does it differ from the fields of genetics, biology, chemistry, and molecular biology?

Biochemistry is the study of chemical reactions, structures and how living things are composed. Many science fields are tied into Biochemistry, such asOrganic Chemistry, which  allows us to better understand the composition of molecules. To me Biochemistry focuses on the medical field such as the study of pharmacology, and allows us to see the different mechanisms of drugs and how it acts on the body and using different concepts within the biochemistry field to help diagnose, asses and better understand specific diseases. Biochemistry can easily be tied into any field of science but there are the key factors in which each field of science focuses on, which sets them apart from one another.

Biochemistry differs from the field of genetics, biology, chemistry and molecular biology because many biochemists work in teams versus chemists, molecular biologists, geneticists, and biologists work on a wide range of things and usually work independently or with one other. You dont see many nobel prizes and awards to chemists and such to a group of ten people, it's usually to one individual or maybe a group of three. Also Biochemists are known to specialize in a particular field such as food research, air, drugs, water, waste...things to do with the environment and how they can better the earth as a whole. Biochemists mainly focus on the origins of life, the cell, and different ways you can minipulate these things, and seeing what effects will happen, in hopes to improve its function.

Molecular biology is comprised of chemistry, biology, and mostly genetics. Molecular biology deals with understanding how various systems of the cell function and are regulated. Genetics is the study of the molecular structure and function of genes, looking at how different genes are passed on from generation to generation.

To me Biochemists seem as though they are very highly educated eco-friendly researchers/scientist, "going green." They seem to focus on earthly things and how they can better the world. For example trying to find a safe way to get rid of toxic waste or cut down carbon emitions in the air. Especially in the era that we live in now, with this economy and polluted planet, I believe biochemistry is a more favored area of scientific research than it was 100 years ago.