Looking back on the course, we have covered so many areas in science. Three main themes we discussed were Cycles, Transcription/Translation and Proteins. Many of the topics that were covered in this course were more entended and more intricate information on topics that were covered in many other science courses.
For example, when learning about cycles, we learned about Glycolysis, the Citric Acid Cycle, Gluconeogenesis, Beta Oxidation cycles, Photosynthesis, Cell Respiration and the Electron Transport Chain. All of these cycles I have covered in one or more previous science classes that I have taken. Including, but not limited to, Intro to Biology, Anatomy and Physiology and Organic Chemistry. In this course, we took a deeper look into each cycle, and I am able to understand them much better having reviewed and learned more about them. I really liked the fact that we were able to review things that may have already been learned in a previous course, because it really helps me understand it and refresh the cycles in my mind. It is going to help me be able to remember all of the cycles after I am completely out of school.
Transcription and Translation we have been learning about for what seems like forever. But, there has always been more to learn on these topics. While we learned about this throughout highschool and throughout different college science courses, I never got as in depth as we did in this course. I always had trouble distinguishing transcription from translation, even though it had been gone over hundreds of times. After this course, I am comfortable with the two and have a deeper understanding of what actually occurs during each. Pulling this into the Genetics course was great too! I was able to really concentrate on the two areas and apply them to more than one field at the same time.
Proteins are also things that have been talked about over the years. I just felt like this course helped to solidify the facts about them. This course helped bring things together for me. While learing about proteins as enzymes, which has been something we have all learned about at least once before this course, it has become more clear what an enzyme actually is and how proteins and enzymes relate to one another. Enzymes are needed to catalyze most reactions that occur in our bodies. This course helped to connect the need for proteins (as enzymes) for most of the reactions that we learned about to make them work,
I wish that there were more classes that sort of brought everything together like this one did. While we brought together different areas of science, we also were able to get more in depth into specific topics within. This course helped me solidify ideas, cycles, facts and much more. It helped me to connect what I have learned in other classes together, which made each topic make more sense and made it all seem a little more relavent.
Friday, May 14, 2010
Friday, April 23, 2010
How would you explain the connection between glucose entering the body and energy created by the body to a friend?
Glucose enters our body from the foods that we eat. Our food is digested and broken down into sugars which then enter the blood stream. This sugar (glucose) converts into pyruvate by a reaction pathway called Glycolysis. Our body makes ATP during Glycolysis. Using Glucose as the starting material we end up with 2 usable ATP (energy source). Using Glycogen as the starting material we end up with 3 usable ATP.
Glycolysis is a system of 10 steps starting with Glucose + ATP. Glucose gets a phosphate added onto it from the ATP. Then this glucose-phosphate molecule gets rearranged to give you a fructose-phosphate molecule. The fructose-phosphate molecule + ATP molecule to add another phosphate, giving a fructose-bisphosphate molecule. The fructose-bisphosphate molecule is then split into two molecules which are both then rearranged to give 2 G3P's (which we all learned about in high school). The -CHO group on the G3P is oxidized (lose electrons) then there is a transfer of phosphate from these new molecules to ADP creating 2 ATP! Molecules are then rearranged again in these new molecules that gave up their phosphate. Our bodies then remove a water molecule from the rearranged molecule. Water is then added to this molecule producing the pyruvate that we wanted and an inorganic phosphate. ADP reacts with the inorganic phosphate and gives us an ATP molecule and water.
After that long process (that actually happens very quickly) we are left with 2 ATP molecules that our bodies can use as energy!
The pyruvate that we made can be converted to lactate and sent to the liver. The liver then converts the lactate to glucose which can enter Glycolysis!
Glycolysis is a system of 10 steps starting with Glucose + ATP. Glucose gets a phosphate added onto it from the ATP. Then this glucose-phosphate molecule gets rearranged to give you a fructose-phosphate molecule. The fructose-phosphate molecule + ATP molecule to add another phosphate, giving a fructose-bisphosphate molecule. The fructose-bisphosphate molecule is then split into two molecules which are both then rearranged to give 2 G3P's (which we all learned about in high school). The -CHO group on the G3P is oxidized (lose electrons) then there is a transfer of phosphate from these new molecules to ADP creating 2 ATP! Molecules are then rearranged again in these new molecules that gave up their phosphate. Our bodies then remove a water molecule from the rearranged molecule. Water is then added to this molecule producing the pyruvate that we wanted and an inorganic phosphate. ADP reacts with the inorganic phosphate and gives us an ATP molecule and water.
After that long process (that actually happens very quickly) we are left with 2 ATP molecules that our bodies can use as energy!
The pyruvate that we made can be converted to lactate and sent to the liver. The liver then converts the lactate to glucose which can enter Glycolysis!
Questions from Glycogen Loading Presentation
Just wanted to take a minute to answer a few questions that were asked after my presentation.
1. How do we know how many carbs to take in? Does it vary from person to person?
-Yes, it does vary from person to person. They say that 55-60% of our caloric intake should be carbohydrates. This obviously is going to differ in the actual amount of carbs from person to person. Someone who consumes 3000 calories a day should have 1650-1800 of those calories come from carbohydrates, where someone who only consumed 1500 calories a day should only have 825-900 of those calories come from carbohydrates.
2. Do you think carb loading is worth it?
-Personally, I do not think that it works well enough to do. I also am not a person who runs marathons or anything like that. I was a cheerleader in high school and it was a tradition that we had a pasta party the Friday before our Sunday competition. While this is now just tradition, it sort of started off as a way to obtain more "energy" from the carbs in pasta. I think that even if I was training for the marathon, I still would not try carb loading. I do not think that it has a significant enough impact.
1. How do we know how many carbs to take in? Does it vary from person to person?
-Yes, it does vary from person to person. They say that 55-60% of our caloric intake should be carbohydrates. This obviously is going to differ in the actual amount of carbs from person to person. Someone who consumes 3000 calories a day should have 1650-1800 of those calories come from carbohydrates, where someone who only consumed 1500 calories a day should only have 825-900 of those calories come from carbohydrates.
2. Do you think carb loading is worth it?
-Personally, I do not think that it works well enough to do. I also am not a person who runs marathons or anything like that. I was a cheerleader in high school and it was a tradition that we had a pasta party the Friday before our Sunday competition. While this is now just tradition, it sort of started off as a way to obtain more "energy" from the carbs in pasta. I think that even if I was training for the marathon, I still would not try carb loading. I do not think that it has a significant enough impact.
Friday, April 9, 2010
What knowledge have you connected with past knowledge?
Since our last connecting knowledge blog, we have touched upon many things in class that most of us probably have had some sort of understanding of from previously taken classes. For example, in chapter 6 we talked about proteins as enzymes. Many of us have probably gone over the basics of enzymes in almost every science class we have taken. I learned about enzymes in general biology and learned about rate of reactions and thermodynamics in anatomy and a little bit in organic chemistry as well. I had already learned about exergonic/spontaneous and endergonic/nonspontaneous reactions as well as catalysis.
We covered catalysis in some detail in my anatomy course as we discussed the fact that our bodies cannot possibly survive without the use of catalysts. The reactions that happen in our body are far too slow on their own to sustain life, but with the use of catalysts the reactions become fast enough for us to live. I also learned about rates of reactions a lot in organic chemistry. We learned about reaction orders in organic as well.
I learned a little bit about lipids in my anatomy class including fatty acids and phospholipids. Hydrogenation was learned about in organic chemistry, which we now can connect more clearly with biology, as hydrogenated foods enter and affect our body. When talking about fatty acids and their carboxyl group being at the polar end and the hydrocarbon chain being at the nonpolar tail, that incorporates knowledge learned both in anatomy and organic chemistry. I learned about carboxyl groups and hydrocarbons in organic chemistry and polar and nonpolar ends in both organic and anatomy. I knew that molecules with double bonds were considered unsaturated, while molecules with single bonds were considered saturated from organic chemistry. I learned about phospholipids in anatomy and how they are used in our body. Waxes I learned a little bit about in general biology when talking about the waxes on plant leaves and stems. The waxes are used for plant protection as a type of skin.
I learned about peripheral, integral and transmembrane proteins in anatomy as well as passive (simple and facilitated) and active (primary and secondary) diffusion. The sodium potassium pump was covered extensively in anatomy. I'm sure we all knew the basics of DNA while coming into this class and I know that some of my classes have covered it fairly well, but there was still a lot that I had forgotten or just had never learned. Learning about eukaryotic versus prokaryotic DNA processes was new to me. I also knew the basics of transcription and translation from previous science classes (anatomy and general biology), but definitely needed to be taught again. I did not remember a lot of the differences and had never learned the prokaryotic and eukaryotic differences. I learned about codons previously but went into much more detail on both transcription and translation in this course than I ever have before.
As we get into metabolism, I have learned about catabolism and anabolism in anatomy and redox reactions in organic chemistry. We went through Glycolysis and the Krebs Cycle in anatomy, but I could use a refresher on those. I am getting more interested in the metabolism section because that seems to be the most interesting to me so far this semester. I have a basis of understanding some things that we will go over, so I am looking forward to going over those areas again. Once again I am able to see so many different science classes all interconnected and brought into one class.
We covered catalysis in some detail in my anatomy course as we discussed the fact that our bodies cannot possibly survive without the use of catalysts. The reactions that happen in our body are far too slow on their own to sustain life, but with the use of catalysts the reactions become fast enough for us to live. I also learned about rates of reactions a lot in organic chemistry. We learned about reaction orders in organic as well.
I learned a little bit about lipids in my anatomy class including fatty acids and phospholipids. Hydrogenation was learned about in organic chemistry, which we now can connect more clearly with biology, as hydrogenated foods enter and affect our body. When talking about fatty acids and their carboxyl group being at the polar end and the hydrocarbon chain being at the nonpolar tail, that incorporates knowledge learned both in anatomy and organic chemistry. I learned about carboxyl groups and hydrocarbons in organic chemistry and polar and nonpolar ends in both organic and anatomy. I knew that molecules with double bonds were considered unsaturated, while molecules with single bonds were considered saturated from organic chemistry. I learned about phospholipids in anatomy and how they are used in our body. Waxes I learned a little bit about in general biology when talking about the waxes on plant leaves and stems. The waxes are used for plant protection as a type of skin.
I learned about peripheral, integral and transmembrane proteins in anatomy as well as passive (simple and facilitated) and active (primary and secondary) diffusion. The sodium potassium pump was covered extensively in anatomy. I'm sure we all knew the basics of DNA while coming into this class and I know that some of my classes have covered it fairly well, but there was still a lot that I had forgotten or just had never learned. Learning about eukaryotic versus prokaryotic DNA processes was new to me. I also knew the basics of transcription and translation from previous science classes (anatomy and general biology), but definitely needed to be taught again. I did not remember a lot of the differences and had never learned the prokaryotic and eukaryotic differences. I learned about codons previously but went into much more detail on both transcription and translation in this course than I ever have before.
As we get into metabolism, I have learned about catabolism and anabolism in anatomy and redox reactions in organic chemistry. We went through Glycolysis and the Krebs Cycle in anatomy, but I could use a refresher on those. I am getting more interested in the metabolism section because that seems to be the most interesting to me so far this semester. I have a basis of understanding some things that we will go over, so I am looking forward to going over those areas again. Once again I am able to see so many different science classes all interconnected and brought into one class.
Monday, March 8, 2010
Find an interesting Biochemistry website and put its link in this entry, and describe briefly what is found there.
http://themedicalbiochemistrypage.org/
Copyright 1996-2010 Michael W. King, PhD
This website has a ton of information about many different aspects in Biochemistry. I was looking through the different pages and found so many topics that we have discussed in class, as well as other topics that relate to other classes I have taken. Some of the page topics include, Thermodynamics, Protein Structure and Analysis, Hemoglobin and Myoglobin, Enzyme Kinetics, Vitamins and Minerals, Glycolysis, Diabetes, Oxidative Phosphorylation, Sphingolipid Metabolism, Nucleotide Metabolism, Amino Acid Metabolism, DNA and RNA Metabolism, Protein Synthesis, Glycoproteins, Control of Gene Expression and The Cell Cycle. These pages all include a good amount of information about each topic, with pictures and diagrams to help explain the topic and processes. There was also a Diseases and Disorders page that caught my eye. This page has links to different diseases and defects. The last page that caught my eye, and I spent the most time reading, was the Muscle Biochemistry page. Muscles are interesting to me in general, so this page really caught my interest. It put together a lot of the information that I learned in Anatomy and Physiology with the Biochemistry aspect of muscles and how they function.
This page has a ton of information and I think is helpful as well. I would suggest taking a look at the abundance of topics that it presents.
Copyright 1996-2010 Michael W. King, PhD
This website has a ton of information about many different aspects in Biochemistry. I was looking through the different pages and found so many topics that we have discussed in class, as well as other topics that relate to other classes I have taken. Some of the page topics include, Thermodynamics, Protein Structure and Analysis, Hemoglobin and Myoglobin, Enzyme Kinetics, Vitamins and Minerals, Glycolysis, Diabetes, Oxidative Phosphorylation, Sphingolipid Metabolism, Nucleotide Metabolism, Amino Acid Metabolism, DNA and RNA Metabolism, Protein Synthesis, Glycoproteins, Control of Gene Expression and The Cell Cycle. These pages all include a good amount of information about each topic, with pictures and diagrams to help explain the topic and processes. There was also a Diseases and Disorders page that caught my eye. This page has links to different diseases and defects. The last page that caught my eye, and I spent the most time reading, was the Muscle Biochemistry page. Muscles are interesting to me in general, so this page really caught my interest. It put together a lot of the information that I learned in Anatomy and Physiology with the Biochemistry aspect of muscles and how they function.
This page has a ton of information and I think is helpful as well. I would suggest taking a look at the abundance of topics that it presents.
Thursday, February 25, 2010
What knowledge have you connected with past knowledge?
Biochemistry involves many other fields of science. Many of these fields have been studied by us previous to taking this course. We started talking about Animal versus Plant cells and their structure. We also talked about endosymbiosis, DNA and RNA along with Photosynthesis. These are all subjects that we learned in an intro to Biology course. This information was a nice review since I haven’t taken Biology in a few years.
We talked about functional groups, catalysis and energy processes. Bonds (especially hydrogen bonds), bond energies, hydrophobic versus hydrophilic molecules, proteins, fatty acid chains and pH (acids and bases, pKa and Ka, Henderson-Hasselbach equation) were also reviewed. We discussed different amino acids that are used in proteins and how they are bonded as well as titration curves. These are all topics that were covered in organic chemistry or general chemistry. This also was a nice review, since organic chemistry was not a strong class for me. We reviewed them in a way that was understandable and gave me a nice refresher of the material.
We then went deeper into amino acids and proteins beginning to expand more on the topic. We learned that Proline is actually an imino acid versus an amino acid and also learned about some uncommon amino acids that are modified amino acids. We went deeper into the ionization of amino acids and reviewed peptide bonding. The majority of the information we went over up to this point, I had touched upon at least briefly in another course, whether it was general Biology, General Chemistry, Organic Chemistry or Anatomy and Physiology. We took the information that was previously learned and either simply reviewed it or looked at it a little more and expanded our knowledge on the subject.
It wasn’t until we got to protein structure that I really began to learn something completely new. I had talked a little bit about protein structure in other courses, but did not actually learn the differences between primary, secondary, tertiary and quaternary structure until this course. Super secondary structures, motifs, and domains are completely new to me. A-helix and B-pleated sheets are a review from both Biology and Anatomy, but I had only learned about the involvement in DNA for the most part in previous courses. Proteins as Enzymes were a little bit of a review, but also included new information. I had learned about enzymes in General Chemistry, Anatomy and Organic Chemistry and knew that most enzymes are proteins but only some proteins are enzymes. I learned reaction orders in Organic Chemistry but did not really understand the concept until it was reviewed in this course.
I never realized how much one branch of science could really involve so many others. We are able to see all of the science courses that I took at my previous school, in Biochemistry. Not only is it a nice review, but it helps to know that all of the stuff we learned is actually useful in real life. All of the branches are intertwined and interrelated to one another.
We talked about functional groups, catalysis and energy processes. Bonds (especially hydrogen bonds), bond energies, hydrophobic versus hydrophilic molecules, proteins, fatty acid chains and pH (acids and bases, pKa and Ka, Henderson-Hasselbach equation) were also reviewed. We discussed different amino acids that are used in proteins and how they are bonded as well as titration curves. These are all topics that were covered in organic chemistry or general chemistry. This also was a nice review, since organic chemistry was not a strong class for me. We reviewed them in a way that was understandable and gave me a nice refresher of the material.
We then went deeper into amino acids and proteins beginning to expand more on the topic. We learned that Proline is actually an imino acid versus an amino acid and also learned about some uncommon amino acids that are modified amino acids. We went deeper into the ionization of amino acids and reviewed peptide bonding. The majority of the information we went over up to this point, I had touched upon at least briefly in another course, whether it was general Biology, General Chemistry, Organic Chemistry or Anatomy and Physiology. We took the information that was previously learned and either simply reviewed it or looked at it a little more and expanded our knowledge on the subject.
It wasn’t until we got to protein structure that I really began to learn something completely new. I had talked a little bit about protein structure in other courses, but did not actually learn the differences between primary, secondary, tertiary and quaternary structure until this course. Super secondary structures, motifs, and domains are completely new to me. A-helix and B-pleated sheets are a review from both Biology and Anatomy, but I had only learned about the involvement in DNA for the most part in previous courses. Proteins as Enzymes were a little bit of a review, but also included new information. I had learned about enzymes in General Chemistry, Anatomy and Organic Chemistry and knew that most enzymes are proteins but only some proteins are enzymes. I learned reaction orders in Organic Chemistry but did not really understand the concept until it was reviewed in this course.
I never realized how much one branch of science could really involve so many others. We are able to see all of the science courses that I took at my previous school, in Biochemistry. Not only is it a nice review, but it helps to know that all of the stuff we learned is actually useful in real life. All of the branches are intertwined and interrelated to one another.
Thursday, February 11, 2010
Find a protein using PDB explorer- describe your protein, including what disease state or other real-world application it has.
The protein I chose to look at in class was 1N5O. It is related to Breast cancer and is critical for BRCA1 tumore suppressor function. It is also involved with how BRTC mutations affect BRCA1 function. This is a rather small and sinple protein in comparison to others that were seen in class. Its secondary structure consisted of 6 alpha-helix (displayed as green crayons) and 8 beta-pleated sheets (displayed as tan flat sheets). There was no quaternary structure because there were no subunits within the protein. Viewing the protein in the "backbone" mode shows the backbone of the protein with no R groups. The "all atoms" mode shows the entire protein including the R groups.
Using the online technology that we learned about in class, we would be able to determine if any amino acid sequence is already part of a currently known protein or what other known proteins come close to the sequence. Looking at similar proteins, we may also be able to relate the function of a new amino acid sequence to one very similar to it.
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