All living things are able to perform metabolism in the acquisition of energy. In this chapter, we will identify some of the basic components of nutrition as they relate to the makeup of a cell. As we discussed in Chapter 2, cells have a selectively permeable membrane that governs what can enter and exit the cell.
Therefore, to bring necessary building blocks into the cytoplasm to meet metabolic needs, there will need to be transport mechanisms into the cell. We will review several strategies that unicellular organisms use to transport materials into the cell. We will then quickly distinguish between different strategies for acquiring nutrients, and then start a deeper discussion into bio- energetic principles.
We will be discussing the law of conservation of energy, the law of entropy, free energy available for work, and more, as we will discuss just because a reaction is spontaneous this does not tell us how fast the reaction will occur. In order to have reactions proceed in a biologically relevant time frame, it is necessary to use catalysts. Catalysts speed up the rate of reactions, and in cellular metabolism, our favorite catalyst is the enzyme.
But what is the ultimate goal of metabolism? We can boil metabolism down to a very simple idea. It involves... involves the movement of electrons.
Recall that covalent bonds are formed by the sharing of electrons. The energy of a glucose molecule, for example, is in the covalent bonds that form it. It is very important to appreciate that metabolism is a series of redox reactions that involve the donation and receiving of electrons through bond formation.
Once we are comfortable with this conversation, we can start to think about how to use the energy we will be ready to appraise some central metabolic pathways. While there are many variations, for this introductory look we will focus on the common pathway that many living cells share, glycolysis, the citric acid cycle, and the electron transfer chain. We will compare how these can be used with oxygen and without oxygen.
We will finish up with a short look at how and how biosynthesis pathways differ from these catabolic processes. We'll start this chapter with another definition, this time for nutrition. Overall, keep in mind that in this chapter we will be studying how organisms assimilate and use chemical substances. One thing we need to start off with is coming up with a classification scheme for our molecules.
One way to categorize molecules is by grouping them as either Inorganic or organic. These definitions do not determine the importance of the molecules in regards to life processes. These are strategies for breaking up how we discuss different structures.
For biologists, inorganic will not have both carbon and hydrogen, while organic will have both carbon and hydrogen somewhere in their structure. This definition does have some gray area among different groups of scientists. A biologist, chemist, organic chemist, and physicist may change these categories slightly. or place certain restrictions or exceptions to the definition. However, for our purposes, this is the line in the sand we will establish.
So if I'm talking about carbon dioxide, oxygen, water, or ammonia, where would I classify these? These are inorganic compounds. Does this mean they are unimportant or not used by organisms?
Of course not. All of these are very important to living organisms. Classifying them as inorganic simply tells us that we shouldn't expect to see both carbon and hydrogen in their structures.
So if I'm talking about methane or glucose, these would be organic. Glucose is obviously pretty commonly used by living organisms as a food source, but methane gas can actually be toxic and too high of concentrations. So again, organic doesn't necessarily translate to good or healthful. The designation is just telling us that we should expect to at least see both a carbon and a hydrogen somewhere in the structure.
When we start to think about what our organisms are going to need to assimilate to carry out life processes, it is helpful to start thinking about what physically builds up their structures. If you think back to the first few chapters, we can start to get a feel for what we will need, namely carbohydrates, lipids, nucleic acids, and proteins. Carbohydrates include sugars, such as glucose, but also the N-acetylglucosamine that builds the cell wall.
Lipids help to build the plasma membrane. Nucleic acids are the building blocks for DNA and RNA. and proteins are built of monomers of amino acids.
If you look at these structures, you will see at least carbon and hydrogen, so they are organic. But you will also see other component parts like oxygen, nitrogen, phosphates, and sulfur. Since these build the cell, we will obviously need large amounts of them.
Anything we need large amounts of in metabolism are called macronutrients. Be clear, this does not refer to the size of the molecules, but the amounts required. In your textbook, you are provided this diagram that shows the contribution of these atoms.
It should be noted that carbon is 50% of content of a cell, and that from a macromolecule standpoint, protein makes up 55% of the cell content. Hopefully this helps to drive home why these are macronutrients. The acronym used to help remember these is CHOMPS. However, while these are needed in large amounts, they are not the only thing a cell needs.
Things that are needed in small amounts are called micronutrients. Again, This does not refer to the size of the nutrient, but the relative amounts required by the cell to function. Additionally, this does not necessarily indicate importance. Micronutrients are very important.
You just don't need as large a volume of them as, say, carbon. This includes ions such as potassium, calcium, and sodium. We also see what are called prosthetic groups, or Inorganic metallic ions included in the micronutrients.
These will bind tightly with other macromolecules and help to activate or enhance things like enzymes. For example, iron is used so extensively in the electron transport chain that it has its own special subcategory when it's complexed with an enzyme, siderophores. Table 3.1 in your textbook shows you a list of trace elements, which is another name for micronutrients, and their associated function.
So we see iron and how it is part of the cytochromes that are found in the electron transport chain. We also see a number of other metallic ions like nickel, which is found in the enzyme urease. We have a test for urease production later in lab.
This table also shows you some coenzymes and cofactors. These tend to be organic substances that are non-proteins, but associate with enzymes and help them to function. This includes certain vitamins and electron carrier precursors.
And let us not forget that these will have to be transported into the cell, past the cell membrane. This is where the different types of integral proteins, and in some cases peripheral proteins, are used to create the proteins. will come into play. Not only is this how metabolites get moved into the cell, you can also see that this is some of the energy requirements of the cell.
First, be sure to differentiate between the two topics we are discussing here. We will start off talking about systems of transport that involves the energetics used to accomplish the task. Then we will talk about events that may occur in the system. involving that movement. These are two different things and you need to be careful when answering questions to use the correct terminology.
We'll start with the systems. The first system is the simple transport system. This is a This is how something like lactose, for example, is brought into the cell. In this system, a proton-motor force is used to bring in a substrate. So as the protons move down their gradient, they drag the substrate to be transported.
with it. Next we have group transport. This is more common in bacteria than eukaryotes.
Here we have direct phosphorylation during sugar uptake. The phosphate is transferred from a of phosphophenylpyruvate, or PEP, to the sugar being brought in. Keep an eye out during the opening steps of glycolysis.
The first step of much sugar metabolism involves phosphorylation, so this type of transport system actually helps to get the sugar ready to start being broken down. The last system we'll introduce is the ABC system. In this system, there is a protein intermediate that transfers energy.
to the substrate. So the substrate is not modified upon entry. So it's a more indirect phosphorylation. Much of these systems are used for vitamins and lipids.
In ABC transport, a periplasmic binding protein brings the substance to the integral protein transporter. On the other side, a peripheral protein provides energy to the integral protein. Now let's look at the type of events that might occur.
When one substrate is moved in a single direction, this is called a uniport event. When two substrates are moved in two different directions, this is called an antiport system. And when two substrates are moved in a single direction, this is a symport system.