Three Major Themes

Three major themes from the course are structure, function, and enzymes.
This course covered the structure of many different molecules.  We learned differences in structures of the amino acids, peptides, proteins, lipids, nucleic acids, etc.  Proteins alone have up to four different types of structural components. There can be different forms of molecules, molecules that have the same composition but are arranged differently.  For example left-handed amino acids are the active form found in eukaryotes.  If a right handed amino acid was found it would not be able to play its role.  We learned the difference types of bonds, such as polar bonds, covalent bonds, peptide bonds, hydrogen bonds.  The way things are bonded impacts what they do, or what they are capable of doing.
Function of the molecules and how they work as a team to keep organism alive.  Certain molecules may attract other molecules needed.  Other molecules proofread and repair damaged cells.  For example in Replication there are five different types of polymerase each with their own specific function.  For example in prokaryotes, polymerase I is involved in synthesis, proofreading, repair, and removal of RNA primers.  While pol III is the main polymerizing enzyme.  Each molecule found in organisms has a specific purpose.
Enzymes are important in aiding life processes that occur.  They help to speed up the reaction and can be inhibited or activated, depending on what surroundings are present.  For example phosphofructokinase, an enzyme in glycolysis is activated by AMP while it is inhibited by ATP.  There are different classes of enzymes such as kinases or isomerases.  Each class of enzyme aids a different type of reaction.  For example kinase reactions aid phosphorylations. 
These themes are connected because structure determines function, and enzymes aid in function.  A change in structure changes the task of the molecule.  Without the presence of a needed enzyme, a reaction may not occur, and the molecule will not perform its purpose.  All three themes are important in biochemistry, and were learned in other science courses.  This course has provided me with the knowledge to make these connections between the themes.  Biochemistry had brought all these themes together to give a better presentation of the overall picture.

Glucose, Energy Production, and Your Body In a Nutshell

Glucose is a carbohydrate that enters your body from the food you eat.  It can be stored in the muscle tissue as glycogen.  Glucose is used to produce energy by going through the glycolysis cycle.  Glycolysis is an anaerobic process, a process that does not require oxygen.  This allows for a faster production of energy than a aerobic process, a process that requires oxygen.  Think of a sprinter, a sprinter needs a smaller amount of energy fast compared to a long distance runner who needs more energy over a longer period of time.
The process of glycolysis  is a complicated ten step reaction that may contain foreign words for those who have not taken advanced chemistry courses.  Each reaction has its own enzyme, which helps to aid the reaction.  Glycolysis starts with glucose and ends with four molecules.  There are two molecules of pyruvate and two molecules of ATP (energy). Pyruvate will then continue on to other processes and generate 32 molecules of ATP.  Pyruvate can also synthesize glucose, through a process called gluconeogenesis.  Gluconeogensis is almost the exact reversal of glycolysis, however there are 3 irreversible reactions of glycolysis.  These reactions are different in gluconeogenesis and may require a different enzyme.

Connecting Knowledge with Past Knowledge Part 2

As we progress further into the semester I am able to make more connections from past courses.  As we get into the topic of DNA replication, most of the information is review from the Genetics course I have previously taken.  However in Genetics I learned the more general process of replication, transcription, and translation. In Biochemistry there is more detail on which specific binding occurs to continue the process.  The book goes into specific details and description of what type of bonds bind to the strands and proteins.  It goes into an in depth overview of these important science processes, which has lead to my better understanding of how and why these processes occurs.

For example in Transcription in Eukaryotes I knew of the different types of RNA polymerase and their roles in initiation.  However I did not know that there were six additional transcription factors found in the preinitiation complex. These include; TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH.  These general transcription factors are required for all promoters, and each has a different function.  This is just one example of how Biochemistry has given me a better understanding of the organization of transcription initiation, and how these factors allow the continuation of the rest of the process.  It has helped the process of transcription and translation to finally 'click' and I can now better understand.

This course has continued to allow me to make connections between the different branches of science, and help me get a better understanding of the overall picture.  By the end of this course I expect to have a deeper understanding, then I did before that will help me succeed in my scholastic and career goals.

Biochemistry on the Web

I have come across an interactive web site created by Wiley that explains the major concepts covered in Biochemistry.  It is based off the book Concepts in Biochemistry by Rodney Boyer. It offers interactive animations and tutorials in subjects such as protein folding, metabolism, DNA replication, etc.  It offers games, such as amino acid identification, to help make learning more enjoyable to the visitor.

It also offers Concept Reviews that help refresh basic topics such as pH and buffers, redox reactions, thermodynamics, logarithms, and elementary kinetics.  The information found here is important when trying to understand in depth biochemical concepts.

It offers Quizzes to test your knowledge and understanding.  The test taker gets immediate feedback on weather their answers were correct or not.  However these quizzes are based off the chapters in the book, Concepts in Biochemistry, and are not labeled by specific topic..

It highlights recent advances in the field of Biochemistry and explains how these advances solve real-world problems.  Some examples include AIDS therapies and DNA fingerprinting.  It gives students good answers to the question "Why is it important for me to know this?"

The site also provides web links for more information.  Overall the site is very informative and makes learning Biochemistry fun and interesting. 

To visit this website go to:
http://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htm

What knowledge have you connected with past knowlege?

I remember taking my first college science course, General Biology I and kept asking myself "Why do I need to know this?".  As I continue to take more in depth science classes, I now know the answer to my own question.  Each course goes beyond the basic knowledge I learned from my first college science class.  Even though each course covers a different subject, important information has come together to help me understand the overall picture.  Biochemistry continues to draw the overall picture.  It has helped me to see how chemistry and biology and other science topics are connected.

Before this course I had learned about the different pHs, but never quite understood the importance of pH.  I have learned that chemical processes that occur in the body are very sensitive to pH.  If the environment is not at the right hydrogen concentration, than the process may not occur.  Also relative to pH were pKa values, which I had never encountered until Organic Chemistry.  I know understand that any acid will act as a buffer in the +1 to -1 range of its pKa value.  This is important because a buffer resist change in pH, which allow chemical processes to occur.  Until this course I never made the connection between pH, pKa, and buffers.

The importance of sterochemistry has become relevant.  All amino acids that make up biologically active proteins are in the left handed form.  This is important to understand for structure determines function.  A slightest change in structure could effect a protein drastically.  By understanding the differences in structure, it has help me to put together the pieces of how it will effect a process.

 Through the beginning of the course til now I have been able to connect present knowledge with past knowledge  to help me better understand the overall picture.  Although I have already learned the information I need, it is coming together and I have a better understanding.   During the remaining course I believe that i will be able to make more connections and a deeper understanding of the importance of Biochemsity.

An Overview of the Protein Thrombin

       

         The protein thrombin is found in the blood of humans.  It is a serine protease like tyrpsin and chymotrypsin.  A serine protease is a protein cutting enzyme that uses a serine amino acid to perform the cleavage.  It has selective digestion, so that it does not digest other important proteins in the blood.
        Thrombin plays an important role in blood clotting.  When humans are wounded the body will build a temporary block to give the surrounding tissues a chance to repair the wound.  When the skin is cut and blood flows to cells that do not normally come in contact with blood, it signals the body.  These cells are called tissue factor.  Tissure factor will then activate Factor VII and Factor X.  These factors then activate thrombin, which translates the signal into action.  Thrombin clips a little piece of the large protein fibrinogen.  Fibrinogen assembles into large stringy networks that trap the blood cells forming a scab that blocks the wound.
         Since blood clotting can pose potential risks such as heart attack and strokes, it is carefully regulated. It's built as an inactive precursor that has several extra domains that are clipped off when activated. The thrombin molecule consists of calcium ions that bind to modified glutamate amino acids causing a positive charge and tether to the surfaces of blood vessels.  This prevents thrombin from spreading everywhere once activated.  The activation of thrombin only last several seconds to limit the clot to the area of damage.

To find out more information on thrombin please visit http://www.pdb.org/pdb/101/motm.do?momID=25

What is Biochemistry?

         According to Webster's 2002 dictionary biochemistry is the study of the chemistry of life processes in plants and animals. Biochemistry is a subsection under the wide subject of Science. Biology and chemistry are also subjects of science.  Biology covers a wide spectrum of topics on living things including origin, history, and characteristics.   Chemistry is all about reactions by which substances are produced or converted by.  Biochemistry combines these two subjects and shows how they work hand in hand with one another.  Overall biochemistry is the study of the complexity of life and the reactions that take place to allow organisms to live.
           Biochemistry differs from the other science fields in a variety of ways.  While there is some important biochemical features in Genetics, Genetics focuses on the difference in heredity and variability.  It studies how traits are passed on from generation to generation, and the causes of mutations.  Molecular biology overlaps all of these subjects (Biology,Chemistry, Genetics, and Biochemistry) and focuses on the interactions between various cell systems.  It studies how cell systems complete their own tasks, but also contribute to other cell system's tasks with feedback loops. Therefore all the subjects of Science overlap one another, but each subject focuses on a different aspect of science.