Daily Newsletter: August 29, 2014 - Characteristics of Life

Daily Newsletter
August 29, 2014 

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Characteristics of Life

In order to have a meaningful discussion about living systems, we must first identify that which we will consider "living."  To do this, we identify characteristics that will allow us to differentiate between living and non-living objects.  To be effective, these characteristics must be see in all examples of life.

As a first principle, we will start with the cell theory:  All living organisms are composed of cells, and all cells come from pre-existing cells.  Thus, the cell is the basic unit of life.  One of our goals this semester is to gain an understanding of the cell, and build a working model of how a cell functions.  As a frame four this semester long discussion, let's first look at how the characteristics of life are revealed in a cell.

1. Homeostasis:  i.e., the same state.  This refers to the ability of a cell to maintain a constant 'internal' environment.  The environment around the cell can change (e.g., hot to cold, low salt to high salt), but the cell it self remains stable.  [Caveat:  All organisms have a range of environmental conditions where they can live; if you exceed the range, then the cell can not maintain homeostasis].  We shall see that the cell membrane is the defining structure of all cells, as it creates a boundary (inside vs. outside).  It is from this basic idea, and how we move things across the membrane, that we shall build the concept of homeostasis.
• A corollary characteristic is adaptation.   Cells can change in response to the environment.  For example, bacterial cells can change the phospholipids in their cell membrane as temperature changes.  One way this is done is by changing the amount of saturated fatty acids used in making phospholipids.  
• In order to adapt, you need to know how the environment changed.  This is done through systems of cellular receptors.  Stimulus (environmental change) ---> Receptor -----> Adaptation.  So cells also have the ability to Respond to Stimuli.  These stimuli could be physical factors (temperature or pH), or they could be chemical.  The thing to remember is that cells (and all life) have some type of Stimulus-Response (Receptor or Communication) system.
2. Growth:  It is easy to see a human growing from infant, through adolescence, to adulthood.  But what about cells?  We could look for the growth in size, but that can be difficult when looking at a single cell.  Instead for cells, we look at Cell Number (population size) and/or Biomass (e.g., the amount of carbon or maybe the dry weight of the population).  Growth is based on two other characteristics of life.
• Metabolism:  i.e.,  all chemical reactions in the body.  Often down played to just energy acquisition, metabolism also involves the acquisition of Carbon (needed for all biochemical compounds), other essential elements (like nitrogen), and the building of new biomolecules.  As cells make more biomolecules, they grow, and eventually divide.
• Reproduction:  reproduction is essentially the creation of new individual organisms, and is easily seen when a baby is born.  But reproduction has its basis in cellular action.  A cell, when given the correct stimulus, can divide.  Possibly it has grown too large, or it may have received a chemical signal to divide.  In either case, a cell will divide into two daughter cells.  Terms that will come up with reproduction are: binary fision, mitosis, meiosis, and cytokineses.
3. You may remember from other courses that Organization is often given as a characteristic.  Instead of talking about tissues and organs, I would remind you that living organisms are composed of cells.  If you have active, working cells, then you are living.  Doesn't matter if it is one cell or a million.

  

BOLO Microbiology Daily Newsletter February 4, 2014 - Metabolism & Growth

Microbiology Daily Newsletter

February 4, 2014 - Metabolism & Growth

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Metabolism and Growth are both essential characteristics of life, and are intimately related to each other.  You may recall that living systems require CHONPS (carbon, hydrogen, oxygen, nitrogen, phosphorous, and sulfur) to make biomolecules.  In addition, we need minerals, trace minerals, and energy in the form of reducing potential (i.e., electrons).  The acquisition of carbon and energy are the primary focus of central metabolism (glycolysis, citric acid cycle, etc...) and photosynthesis.  But what about the other needs?

Amino acids and nucleic acids both need nitrogen.  Nucleic acids need phosphorus in the form of phosphate groups.  Sulfur is needed to form disulfide bridges and a variety of thiols.  Phosphates become a prime regulator of protein function, and ions are needed to establish membrane potentials.  All of these are needed to increase the biomass (growth) of cells.

In looking at microorganisms you need to become accustomed to the metabolic needs and diversity of cells.  Though less than 1% of bacteria are culturable, these organisms have helped us understand the dynamic relationship between nutrition, metabolism and growth.  They have also provided researchers with known genes that can be used to understand potential functions from genetic analysis.

Today, your goal is to understand how variations in growth conditions can affect bacterial growth, both in terms of biomass accumulation and increases in population size (binary fission).

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Heterotrophy vs Autotrophy 

These two terms describe the acquisition of carbon. Heterotrophy is used to describe organisms that rely on organic carbon as building block. Autotrophy describes organisms that have the ability to fix carbon dioxide into an organic compound (carbon fixation means adding a CO₂ onto an existing organic carbon backbone; this makes the carbon biologically available).

Phototrophy vs Chemotrophy

These two terms describe the acquisition of energy in the form of reducing power.  Phototrophs have the ability to utilize photons to generate high energy electrons that can be used as reducing potential.  Chemotrophs utilize reduced compounds for reducing potential (i.e., energy).

The concept of chemotrophs can be further divided in to chemoorganotrophy, in which cells utilize reduced organic compounds for energy, and  chemolithotrophy, where cells utilize reduced inorganic compounds for energy.

Nitrogen

Molecular nitrogen is the most abundant gas in our atmosphere, but it is not very accessible by most biological organisms.  For nitrogen to become available, it needs to be reduced.  Atmospherically this is accomplished by electrical activity, but far more becomes available through biological means.  Nitrogen fixation is an important chemical pathway, and is the first step in the nitrogen cycle (the movement of nitrogen through ecosystems).  The diagram below provides an explanation of nitrogen fixation:

Plant Biotechnology Handbook by Niir Board.

Note the amount of redox reactions needed, and the requirement for Mo (Molybdenum) as a cofactor for the enzyme nitrogenase (looking at the nitrogenase cycle, how is molybdenum used?).  Notice also that Magnesium (Mg) is also needed during the reduction of molecular nitrogen.  Nitrogen has a number of biologically active states:  including NH₃, NH₄, NO₃, NO₂, and NO.  The movement of nitrogen through living systems is shown in the diagram below:

Nitrogen fixation.http://archive.bio.ed.ac.uk/jdeacon/microbes/nitrogen.htm

Can humans use raw NH₃?  How about bacteria?  Can all bacteria use NH₃, or only some?  These questions come to the heart of today's topic.  All bacteria need nitrogen, but they differ in how they acquire nitrogen.  Some can only harvest nitrogen from organic compounds, while others can make use of some of these other compounds.  Bacteria also have to give off nitrogen as waste, but how do they do it?  We convert ammonia to urea, but do bacteria need to make urea?  This also brings up another point about living in a community of different types of bacteria:  the waste of one cell, may be the food for another cell.

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Daily Challenge

What determines the metabolic diversity of a bacterial species?  What other conditions do you need to consider when growing bacteria?  How does central metabolism provide raw materials needed for growth?

BOLO Microbiology Daily Newsletter January 27, 2014 - Metabolism Basics

Microbiology Daily Newsletter

January 27, 2014 - Metabolism Basics

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Daily Topic: Metabolism Basics
Metabolism is something all students should be familiar with by this point, especially the catabolic processes of gycolysis and citric acid cycles.  Today, as a preparation for the work this week, we will do some reflection and clarification on catabolic metabolic processes.

1.  What is the purpose of metabolism?  If you say to gain energy, you are only half right.  Catabolism is going to have two outcomes:  energy harvesting and production of precursor metabolites.

The processes of glycolysis and citric acid cycle are going to release energy in the form of reducing potential, and many cells are built to harvest that reducing potential.  But the chemical intermediates of the two processes are also critical for building biomolecules.  We call these two processes "central metabolism" because we can build nearly every biomolecule from the precursor metabolites produced.

Cells have to maintain a balance between energy and precursors.  This is one reason why cells never reach the theoretical maximum yield of ATP production.

2.  What is the energy we harvest from these processes?  If your answer is ATP, then you need to reconsider.  ATP does not equal energy to a cell.  ATP is used to phosphorylate structures.  The -2 charge of phosphate will change the electrochemistry of any molecule it attaches to, and in the case of proteins, will induce a change of shape (conformation).  What then is the energy of cells?  Reducing Potential.  Those electrons moved during redox reactions constitute the real energy harvested during glycolysis and citric acid cycle.  It is the reducing potential we will use in electron transport chains to a proton motive force (an electrochemical gradient of hydrogen ions).

In the eukaryotic mitochondria, this proton motive force will be used to make ATP, but not so in bacteria.  Bacterial proton motive force can be used for active transport and flagellar movement directly.  ATP will still be made, as you need the ability to phosphorylate compounds and proteins, but bacteria will make less ATP than eukaryotic mitochondria.

3.  Why does it take 10 steps to break glucose into pyruvate?  During each step of glycolysis, you are inducing minor molecular changes that induce stress in the molecule.  Through these molecular alterations, the cell carefully extracts energy.  If there was a large change, you risk destabilizing the molecule and releasing energy as heat, which is dangerous to the cell.  The cell needs a series of controlled reactions to capture the most energy.

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Words of the Day:
There are four words that you need to know when dealing with metabolism.  The terms deal with how energy and carbon are acquired by a cell.

Energy Acquisition:  These terms deal with how the cell acquires reducing potential.

•      Phototroph
• The cell uses photons to raise the energy state of electrons.
• The cell then transfers these electrons to electron carriers and carbon.
• In essence, they produce reduced compounds from photons.
•      Chemotroph
• The cell uses reduced chemical compounds.
• The term can be divided into two subcategories:
• Chemolithotroph - use reduced inorganic compounds.
• Chemoorganotroph - use reduced organic compounds.

Carbon Acquisition:  This is how the cell acquires carbon for the production of biomolecules.

• Autotrophic
• The cell has the ability to take Carbon Dioxide and reduce it to form glucose or another sugar.
• The process is known as carbon fixation.
• The cell provides the organic structures needed by the cell.
• Heterotrophic
• The cell uses organic structures (or reduced carbon) from external sources (e.g., glucose, amino acids, lipids).
• These organic structures are converted to other biomolecules as needed.

Each organism is given a name based upon it's principle means of carbon and energy acquisition.  For example:

• Photoautotroph
• Photons used to raise energy states of carbon compounds.
• Cell can fix carbon
• Photoheterotroph
• Photons used to raise energy states of carbon compounds.
• Cells acquire organic structures from external sources.
• Chemolithoautotroph
• Reduced inorganic compounds primarily used for reducing potential.
• The cell can fix carbon.
• Chemoorganoheterotroph
• Reduced organic compounds primarily used for reducing potential.
• The cell acquires organic structures from external sources.

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Daily Challenge:  Reflection
What do you remember of metabolism?  Describe what you remember.  Does the information in this newsletter place metabolism into a new perspective for you?  How?  Do you remember the terms listed above?  Describe what you remember.  How do these terms help us to classify cells?  Reflect on this statement:  That the metabolic function of a cell is the most important aspect of a cell.

Daily Newsletter: September 28, 2012 - Metabolic Evolution & Scientific Articles

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Today you are going to look over a scientific article dealing with the evolution of metabolic processes. This is the first scientific article assigned, so I want to spend a little time going over how to read a scientific article.
One of the biggest struggles students have in science is reading scientific articles. These articles are dense, meaning they convey a great deal of information quickly. They are intended for experts, who have an understanding of the background, procedures and protocols. As a result, they are an obstacle when someone new to the field tries to figure out what the authors are saying in the paper.
Most people when they come to a scientific article start with the first line and then plow their way through. Novices become quickly overcome by the language, protocols and jargon, and just get frustrated. Experts rarely read the article from start to finish, but instead skip around. They use the break down of the article to focus their attention on what interests them.
All scientific articles start with an abstract. This is a summation of the paper, but be warned, this summation can be misleading. The purpose of the abstract is to provide a brief rundown of the paper so that people who are looking for an background or protocols can determine if the paper will be of use to them. WARNING: the abstract is for experts, not novices. More than one student has been burned by reading just the abstract and thinking they understood the paper.
While this may be heresy to some, skip the abstract. Don't read the abstract when you'rer assigned a paper. Remember, it is helpful to some one searching through articles. If you are assigned a paper by a teacher, skip the abstract. Instead, go right to the paper's introduction.
Scientific articles are generally broken down into section, with the most common being an introduction, methods, results and conclusion(discussion)*. The introduction holds the background for the paper, and generally includes why the author thinks the study is important. You can usually find the authors hypothesis and assumptions (research logic) here as well.
When you start reading the introduction, do not have a pencil or highlighter in hand. Just do a read through. If you don't understand something, skip it and go on. Just make it through once. On a note pad, write your first impressions. What stood out to you? Start a second read through, but this time have a highlighter, pen or pencil. Mark statements (does not have to be a full sentence) that you think are important. Write down any notes. Ultimately, your looking for a few things in the introduction:

1. Why does the author think this topic is important?
2. What has led to this current research?
3. What is the author's hypothesis?
4. New terms:
• Since your new to scientific papers, many of the terms will be new.
• To start, pick three that seem important to what the author is doing.
• Look them up and make a note of their definitions somewhere on your copy of the article. (a few words will do)

On your note pad, answer the questions above and make notes.
The METHODsection is one of the hardest to read for a novice, because the whole thing is filled with information on the exact procedures used. Unfortunately, this means you need to have background knowledge on how to do most of these procedures. But this is where we start to learn new techniques. On your first time through, just skim over the method section, but you need to come back to it (Just not immediately)
What to look for in the methods:
This ultimately depends on why you're reading the paper. Are you looking for a method? Are you trying to find an experimental protocol? Or are you trying to figure out how the author got their results? So the questions you ask could change depending upon your goals. The paper you have today has a non-standard arrangement, and the experimental protocol section is minimized (it is actually fleshed out in other sections). Generally though, you want to look to answer the following question:

1. How did the author set up the experiment?

• Did they use models systems? (Did they go to a location or did they attempt to replicate the system?)
• What controld did they use?
• How many replicates did they have?
• What experimental methods did they use?

Remember: Do not get bogged down trying to figure out their methods. It is OK if you can not fully answer the questions above. For your notes, pick one procedure that they used and look it up. Write down a one or two sentence description of what the procedure is used for and/or how it is done. It is important to remember that we learn procedures from reading scientific papers.
You should be able to trace the RESULTS back to particular methods used. A good author will provide you a story that leads from methods to results, and finally to a discussion about their conclusions. Results sections normally provide just the FACTS (evidence) that was generated from the methods. As the reader, you are looking to see if the results provide evidence supporting or refuting the authors hypothesis. Your also looking to see what the data says to you. Do the results tell you the same thing they "told" the author? i.e., the results will inform (be the foundation for) the author's conclusions. Based on the same evidence, do you reach the same conclusion? Why or why not? *NOTE: The article today combines results and discussions.
Again, you need to have a good background in the methods to understand and interpret results. So, your goal as a novice is to begin looking at the data to gain an understanding of what the data represents. This is about learning to read graphs and charts. Good authors will lead their reader through the data, but authors have different skills at conveying their data. For the paper today, take one graph, and see if you can figure out all that it is trying to convey. Read the results section, and find where the author discusses the graph. What are they trying to say? *NOTE: For today's paper, explain the results shown in Figure 1.
In the Discussion/Conclusion of the paper, the author attempts to tie together their results and present a logical case supporting their hypothesis. The emphasis here is on LOGICAL. How does the author support the hypothsis? What statements are made to demonstrate how the results support the hypothesis?
For the paper today, find a statement that you think shows where the author demonstrates the data supporting the hypothesis. Also, does the author address future directions for the research? Do they make specific claims?

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Reference

Huber, C., Kraus, F., Hanzlik, M., Eisenreich, W. and Wächtershäuser, G. (2012), Elements of Metabolic Evolution. Chem. Eur. J., 18: 2063–2080. doi: 10.1002/chem.201102914
Go to the GSU Library Homepage. Above the search box on the left, you will see a series of tabs. Click on the Journal tab. Type the word chemistry, and click GO. This will bring up a series of Chemistry Journals. You are looking for Chemistry : a European journal. Click on the Find It @ GSU button. You will need to sign-in if you are off campus; follow the sign-in proceedure.
You will then see a series of links that show the access GSU has to different versions. Click on the Full Text Online link. This will take you to the paper. You will have the option to open the paper as a PDF. This is the best way to get a copy to print or save. Open the paper and start to read and take notes.

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Daily Challenge

Read the article listed above. In the forum, write about the article. The specific information you need to add includes:

1. Why does the author think this topic is important?
2. What has led to this current research?
3. What is the author's hypothesis?
4. Three new terms.
5. How did the author set up the experiment?
6. New methods/protocolsa
7. Analysis of Figure 1.
8. How does the author link data to support hypothesis (conclusion)?
9. One specific claim or future direction for research.

Link to Forum

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Optional Challenge

Review of Lecture on September 28, 2012.
Link to Forum