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) Phosphorylation

2) Oxidation

3) Condensation and hydration

These 3 reactions are such a vital part of all the Biochemical pathways we have discussed in this course. Throughout the entire biochemical realm the reactions here are the common theme that are presented from beginning to end. For all the major biochemical structures from Amino Acids to Nucleic acids, they all travel through chemical reactions that rely on the 3 themes above at some point in their existence.  Entering this course I had been well versed on the science of the reactions needed for such important processes such as cellular respiration and electron transport. Glycolysis, metabolism, and enzymatic activity all have chemical reactions at its source.

   The connection of these chemical reactions touches all the prior knowledge up to this point. Genetics, biology, chemistry and organic chemistry all have shown me the vital importance of the processed to keep organic life in existence. What I have gained from the course is to further identify the importance of these themes and its strong connection to the process of organic reactions. The chemical reactions are the driving force to energy production (ATP) and without it we are left with nothing more than inability to action. Life truly is one large never ending recycle.

REDUCE

REUSE

RECYCLE

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?

The easiest way to explain to someone the process of glucose entering our body and energy created I would say is the explanation of cellular respiration. Cellular respiration is what cells do to break up sugars into a form that the cell can use as energy. 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. Regular cellular respiration is aerobic (requires oxygen). The aerobic process involves 3 parts:


Glycolysis
Citric Acid Cycle
Electron transport chain


Each of these parts has complexities all their own but all have the same product, ATP. Adenosine triphosphate is the main energy source for life and is continually needed and constantly created. 

What knowledge have you connected with past knowledge? #2

   This class has been an invaluable experience as I have been taking this class concurrently with Genetics. By taking this class in congress with Genetics has given me a vast advantage in the knowledge of of DNA replication. The biochemistry connection to all the processes within DNA transcription and translation have been an immediate connection to the Genetics I am experiencing along with Biochemistry. Being able to connect the concepts of Prokaryotic and Eukaryotic replication only expands the knowledge put forth by Genetics. The Biochemistry aspects of Translation and Transcription have further expanded on the concepts connected with Genetics. It takes it a step further by expanding on the specific proteins along the replications chains. IT shows that the G-C & A-T (and sometimes U) is just the beginning in a long process involving many proteins and enzymes that piece together and large picture of the overall DNA replications process.

Find an interesting biochemistry website and put its link in this entry, and describe what is found there.

   The website I came across was Metabolic Pathways of Biochemistry which is a informational site that is as an online reference for metabolism to many major biological pathways, primarily focused on human pathways. It shows carbohydrate, lipid, amino acid, & energy metabolism types. It also lists the free energy change for each step in the form of ΔG (kJ/mol). From glycolysis to oxidative phosphorylation, its all there and its also in 3D models! The particular pathway that grabbed my attention is the Citric Acid, tricarboxylic acid  (TCA) cycle, or Kreb's cycle depending on who you ask. This is a vital component for all all aerobic organisms to generate energy. This site is a wonderful online tool to quickly put forth the pathway to many of today's understood pathways for metabolism.

What knowledge have you connected with past knowledge?

   Biochemistry is full of rich connections to the past knowledge up to this point. It is a coming together of past education and placing it in such a way to fill in the details of the underlying mechanics and function. It is the integration of Organic Chemistry, Microbiology, Chemistry, and Biology ideals and placing it all together in the commonality of Biological Chemistry. From atomic structure to complex carbohydrates, it all touches upon the other schools of thought up to this point.

   Beginning with the comparison of Prokaryotes and Eukaryotes in Chapter 1 touches base with past knowledge of Microbiology and the separation of organelle and their functions. As we move forward to pH and pKa values in Chapter 2 touches upon the principles used in General Chemistry. Chapter 3 and Amino acids brings back the functionality of Organic Chemistry and its classifications of Carboxy groups and Amino groups with their backbone peptide structure. Chapter 4 and proteins gain more traction with Organic Chemistry and application of structure determination of function and its formula reactions.

   The one strong connection that stands out to me is Enzymatic activity. The combining of a Enzyme and substrate to for the E-S complex is a strong reminder of the ideals set forth in Biology. Enzymes and its catalysts are such a vital part of the homeostasis of all biological organisms.

Find a protein using PDB explorer–describe your protein, including what disease state or other real-world application it has. p53 (protein 53 or tumor protein 53)     p53 is a tumor suppressor protein encoded by the TP53 gene. p53 is crucial in many multicellular organisms for its function of regulation of the cell cycle by preventing cells from growing & dividing too fast or uncontrollably, which works as a tumor suppressor. The name p53 refers to its molecular mass which is 53-kilodalton (kDa). p53 tumor suppressor is a flexible molecule composed of 4 identical protein chains. For its role in preserving stability and preventing genome mutation, p53 has been described as "the guardian of the genome".    The cellular DNA faces many dangers including chemicals, viruses, radiation, and UV rays. p53 binds directly to DNA at chromosome 17 in humans. p53 serves a critical role in determining whether the DNA will be repaired, or the damaged cell will undergo apoptosis (self-destruction). If the DNA can be repaired, p53 activated genes which trigger DNA repairing proteins. p53 also arrests growth by holding the cell in the G1/S regulation point of its cell cycle. By holding its at this point, it allows the DNA repair proteins to fix the damage and continue its cell cycle. If the DNA cannot be repaired p53 suppresses cell division and signals for apoptosis. This prevents cells with mutated or damaged DNA from dividing, and prevents tumor development.    p53 has a central role in protecting your body from cancer. Cancer cells use two methods of mutations. They either cause uncontrolled growth and multiplication, or block the normal defense that protect against unnatural growth. Cancer changes the p53 protein and the TP53 gene by causing missense mutations that allow the cell to build with a p53 error. In this mutant the p53 is blocked and causes multiplication and uncontrolled growth, and the cell develops a tumor.

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


   Biochemistry is the study of the chemical processes that make up living things. It is the driving force behind all living matter. It is a multidisciplinary field that takes the ideas of other fields and breaks it down to its essence. It is the molecular nature of life processes. It primarily involves the structures of biological cellular components, and there functions on a molecular level. 


   Biochemistry differs from these other fields such as genetics, which is the study of the structure of genes and DNA specifically, where as Biochemistry deals with the chemistry of the entire cell the genes are in. Biology obviously lends itself to the beginning of the name, but biology is more of a grand scheme ideal which includes all of the processes involved in life, and biochemistry in the molecular make up specifically withing the biological cell. Chemistry is the foundation for all matter within the universe, living or not, the gives the groundwork for biochemistry to deal specifically with the chemical interactions of living matter. Molecular biology deal more specifically with the biological form of living matter, & Biochemistry explores more on function. 


    The field of biochemistry is forever linked to these other fields with research across the board linking the other disciplines. Biochemistry is the ideals of living matter and its function, but is tied within the disciplines of genetics and its genetic differences, & molecular biology with the building blocks of transcription, translation, and replication. Biochemistry is the chemistry behind all biological processes and synthesis of biological molecules.