Biology is the scientific study of life. Studying biology is an opportunity to ask exciting questions about the world that surrounds us. It is an opportunity to dig into some of humanity's deepest questions about our origins, our planet's history, and our connections to other living beings (big and small/extant or extinct). It is also an opportunity to dive into a world of practical problem solving and to think hard about possible solutions for improving health care, maintaining sustainable food supplies, and producing renewable energy technologies.
Studying biology helps us understand issues and address everyday problems. For instance, you can better understand how what you eat and the amount you exercise influence your health when you understand the biochemical reactions that describe how the food (matter) is transformed, how it and your body store energy, and how this energy can be transferred from the food to your muscles. Deciding whether or not to buy products labeled with terms like "antimicrobial" or "probiotic" can be easier if you understand what the microbes, which live in, on, and around us, do. Understanding the biochemical principles that describe the changes that happen to eggs as they cook can help us understand how similar physical processes may be central to the cellular stress response and some diseases. Your eye color can be better appreciated with an understanding of the genetic and biochemical mechanisms that link genetic information to physical traits.
Studying biology even helps us understand things that are "out of this world." For instance, understanding the requirements for life can help us look for life in places like Mars or deep in Earth’s crust. When we understand how to properly “rewire” cellular decision-making networks, we may finally be able to regenerate functional limbs or organs from someone’s own tissue, or reprogram diseased tissues back to health. There are many exciting opportunities. The key point is that mastering a few basic principles helps you understand and think more deeply about a wide array of topics. Keep this notion in mind throughout the course.
Biology: an interdisciplinary science
Questions in biology span size scales in excess of ten orders of magnitude, from the atomic makeup and chemical behavior of individual molecules to planetary-scale systems of interacting ecologies. Whatever the scale of interest, to develop a deep and functional understanding of biology, we must first appreciate biological concepts. This involves integrating important ideas and tools from across the spectrum of science, including chemistry, physics, and mathematics. Biology is truly an interdisciplinary science.
The potential impacts that can come from studying biology are broad
Some people may think studying biology is only about medicine—however, it can lead to or influence many different careers. Biology has applications that are both vast and wide-ranging. Applications include treating (human or other animal) patients, improving agricultural practices, developing new building materials, writing new energy policies, remedying global climate change, creating new works of art—the list goes on and on. For the curious, biology has plenty of unexplored mysteries.
As you study biology, appreciate its exciting questions and topics and be open-minded. Even though course topics may not always seem related at first, they likely are. Being open-minded helps you discover and appreciate the connections between the course’s topics and your interests. Discovering how seemingly different topics interrelate can give you a deeper appreciation for the things you enjoy and maybe even spark a new passion.
BIS2A—from molecules to cells
BIS2A focuses on the cell, one of the most fundamental units of life. Cells can be as simple as the disease-causing bacterium Mycoplasma genitalium, whose genome encodes just 525 genes (only 382 of which are essential for life), or as complex as a cell belonging to the multicellular plant Oryza sativa (rice), whose genome likely encodes ~51,000 genes. However, in spite of this diversity, all cells share some fundamental properties. In BIS2A, we explore basic problems that must be dealt with by all cells. We study the building blocks of cells, some of their key biochemical properties, how biological information is encoded and expressed in genetic material, and how all this combines to make a living system. We will also discuss some of the ways in which living systems exchange matter, energy, and information with their environment (including other living things). We focus primarily on core principles that are common to all life on Earth, and due to biology's large breadth, we put these ideas into a variety of contexts throughout the quarter.
Evolution and Natural Selection
Evolution and natural selection are core concepts in biology that are typically invoked to help explain the diversity of and relationships between life on Earth, both extant and extinct. Fortunately, in BIS2A, you need to understand and use only a few core ideas related to evolution and natural selection. We describe these below. You will expand your understanding and add details to these core concepts in BIS2B and BIS2C.
The first idea you need to grasp is that evolution can be simply defined as the development/change of something over time. In the automotive industry, the shapes and features of cars can be said to evolve (change in time). In fashion, it can be said that style evolves. In biology, life and, in particular, reproducing populations of organisms with different traits evolve.
The second thing to understand is that natural selection is a process by which nature filters organisms in a population. What is the filter? Here it becomes a little more complicated (but only a little). The simplest explanation is that the selective filter is just a combination of all living and nonliving factors in an environment, which influence how successfully an organism can reproduce. The factors that influence the ability of an organism to reproduce are known as selective pressures. A small but important complication is that these factors are not the same everywhere; they change in time and by location. Thus, the selective pressures that create the filter are constantly changing (sometimes rapidly, sometimes slowly), and organisms in the same reproducing population could experience different pressures at different times and in different locations.
The theory of evolution by natural selection puts these two ideas together; it stipulates that change in biology happens over time and that the variation in a population is constantly subjected to selection based on how differences in traits influence reproduction. But what are these characteristics or traits? What traits/features/functions can be subject to selection? The short answer is: just about anything associated with an organism for which variation exists in a population and for which this variation leads to a differential likelihood of generating offspring will probably be subject to filtering by natural selection. We also call these traits heritable phenotypes. Organisms in a population that have phenotypes, which enable them to pass the selective filter more efficiently than others, are said to have a selective advantage and/or greater fitness.
It is important to reiterate that while the phenotypes carried by individual organisms may be subject to selection, the process of evolution by natural selection both requires and acts on phenotypic variation within populations. If neither variation nor populations in which that variation can reside exist, there is no opportunity or need for selection. Everything is and stays the same.
Common misconceptions and a course specific note
Finally, we draw your attention to a critical point and common misconception among beginning students in biology. This misconception can arise when, for the sake of discussion, we decide to anthropomorphize nature by giving it an intellect. For example, we may try to build an example for evolution by natural selection by proposing that a surplus of a particular food exists in an environment and there is an organism close by that is starving. It would be correct to reason that if the organism could eat that food that this might give it a selective advantage over other organisms that cannot. If later we find an example of organisms that have the capability to eat that surplus food, it might be tempting to say that nature evolved to solve the problem the surplus food. The process of evolution by natural selection, however, happens randomly and without direction. That is, nature does NOT identify “problems” that are limiting fitness. Nature does NOT identify features that would make an organism more successful and then start creating diverse solutions that meet this need. The generation of variation is not guided. Variation happens and natural selection filters what works best. The observation that an organism exists that can eat the surplus food is not a reflection of nature actively solving a problem, but rather, a reflection of whatever processes that led to phenotypic variation in an ancestral population that created—among many other variants—a phenotype that increased fitness (possibly because the ancestral organisms were able to eat the surplus food).
This point of the preceding paragraph is particularly important to understand in the context of BIS2A because of the way we will be utilizing the Design Challenge to understand biology. While the Design Challenge is intended to help focus our attention on functions under selection and their relationship to determining fitness, it can be easy—if we aren’t attentive—to lapse into language that would suggest that nature purposefully designs solutions to solve specific problems. Always remember that we are looking retrospectively at what nature has selected and that we are attempting to understand why a specific phenotype may have been selected over many other possibilities. In doing so, we will be inferring or hypothesizing to the best of our ability (which is sometimes wrong) a sensible reason to explain why a phenotype might have provided a selective advantage. We are NOT saying that the phenotype evolved TO provide a specific selective advantage. The distinction between these two ideas may be subtle, but it is critical!
Note: possible discussion
What physical traits can you think of that give a selective advantage to certain species? Under what conditions would this trait grant those advantages? Under what conditions might that trait be a selective disadvantage?
Note: possible discussion
The great varieties of domesticated dog breeds from which we can choose for companionship are also the result of a process of evolution by selection. Likewise, the development of many very different looking crops—cabbage, brussel sprouts, kohlrabi, kale, broccoli and cauliflower—is also the result of evolution by selection. However, in these two cases the selection or filtering process is referred to artificial selection rather than natural selection. Discuss how artificial and natural selection are similar and different?
Note: possible discussion
How do environmental and political factors influence manufacturing processes such as automobile design? Fashion? Etc. What aspects are similar to the evolution of an organism, and what aspects are different?
Note: possible discussion
A related but slightly different misconception about evolution by natural selection is that this process leads to the creation of the most efficient solutions to problems. What is the problem with this notion?
General Approach to Biomolecule Types in BIS2A
Before you start
If necessary please review the Design Challenge module to review the Design Challenge rubric.
Some context and motivation
In BIS2A, we are concerned primarily with developing a functional understanding of a biological cell. In the context of a design problem, we might say that we want to solve the problem of building a cell. If we break this big task down into smaller problems, or alternatively, ask what types of things do we need to understand in order to do this, it would be reasonable to conclude that understanding what the cell is made of would be important. That said, it isn't sufficient to appreciate WHAT the cell is made of. We also need to understand the PROPERTIES of the materials that make up the cell. This requires us to dig into a little bit of chemistry—the science of the "stuff" (matter) that makes up the world we know.
This prospect of talking about molecular chemistry and thermodynamics makes some students of biology apprehensive. Hopefully, however, we will show that many of the vast number of biological processes that we care about arise directly from the chemical properties of the "stuff" that makes up life and that developing a functional understanding of some basic chemical concepts can be tremendously useful in thinking about how to solve problems in medicine, energy, and environment by attacking them at their core.
Importance of chemical composition
As a student in BIS2A, you will be asked to classify macromolecules into groups by looking at their chemical composition and, based on this composition, also infer some of the properties they might have. For example, carbohydrates typically have multiple hydroxyl groups. Hydroxyl groups are polar functional groups capable of forming hydrogen bonds. Therefore, some of the biologically relevant properties of various carbohydrates can be understood at some level by a balance between how they may tend to form hydrogen bonds with water, themselves or other molecules.
Linking structure to function
Each macromolecule plays a specific role in the overall functioning of a cell. The chemical properties and structure of a macromolecule will be directly related to its function. For example, the structure of a phospholipid can be broken down into two groups, a hydrophilic head group and a hydrophobic tail group. Each of these groups plays a role in not only the assembly of the cell membrane but also in the selectivity of substances that can/cannot cross the membrane.
The Structure of an atom
An atom is the smallest unit of matter that retains all of the chemical properties of an element. Elements are forms of matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions.
The chemistry discussed in BIS2A requires us to use a model for an atom. While there are more sophisticated models, the atomic model used in this course makes the simplifying assumption that the standard atom is composed of three subatomic particles, the proton, the neutron, and the electron. Protons and neutrons have a mass of approximately one atomic mass unit (a.m.u.). One atomic mass unit is approximately 1.660538921 x 10-27kg—roughly 1/12 of the mass of a carbon atom (see table below for more precise value). The mass of an electron is 0.000548597 a.m.u. or 9.1 x 10-31kg. Neutrons and protons reside at the center of the atom in a region call the nucleus while the electrons orbit around the nucleus in zones called orbitals, as illustrated below. The only exception to this description is the hydrogen (H) atom, which is composed of one proton and one electron with no neutrons. An atom is assigned an atomic number based on the number of protons in the nucleus. Neutral carbon (C), for instance has six neutrons, six protons, and six electrons. It has an atomic number of six and a mass of slightly more than 12 a.m.u.
|Charge||Mass (a.m.u.)||Mass (kg)||Location|
|Proton||+1||~1||1.6726 x 10-27||nucleus|
|Neutron||0||~1||1.6749 x 10-27||nucleus|
|Electron||–1||~0||9.1094 x 10-31||orbitals|
Table 1 reports the charge and location of three subatomic particles—the neutron, proton, and electron. Atomic mass unit = a.m.u. (a.k.a. dalton [Da])—this is defined as approximately one twelfth of the mass of a neutral carbon atom or 1.660538921 x 10−27 kg. This is roughly the mass of a proton or neutron.
Figure 2. Elements, such as helium depicted here, are made up of atoms. Atoms are made up of protons and neutrons located within the nucleus and electrons surrounding the nucleus in regions called orbitals. (Note: This figure depicts a Bohr model for an atom—we could use a new open source figure that depicts a more modern model for orbitals. If anyone finds one please forward it.)
By User: Yzmo (Own work) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/)], via Wikimedia Commons
Relative sizes and distribution of elements
The typical atom has a radius of one to two angstroms (Å). 1Å = 1 x 10-10m. The typical nucleus has a radius of 1 x 10-5Å or 10,000 smaller than the radius of the whole atom. By analogy, a typical large exercise ball has a radius of 0.85m. If this were an atom, the nucleus would have a radius about 1/2 to 1/10 of your thinnest hair. All of that extra volume is occupied by the electrons in regions called orbitals. For an ideal atom, orbitals are probabilistically defined regions in space around the nucleus in which an electron can be expected to be found.
For additional basic information on atomic structure click here.
For additional basic information on orbitals here.
For a review of atomic structure check out this Youtube video: atomic structure.
The properties of living and nonliving materials are determined to a large degree by the composition and organization of their constituent elements. Five elements are common to all living organisms: Oxygen (O), Carbon (C), Hydrogen (H), Phosphorous (P), and Nitrogen (N). Other elements like Sulfur (S), Calcium (Ca), Chloride (Cl), Sodium (Na), Iron (Fe), Cobalt (Co), Magnesium, Potassium (K), and several other trace elements are also necessary for life, but are typically found in far less abundance than the "top five" noted above. As a consequence, life's chemistry—and by extension the chemistry of relevance in BIS2A—largely focuses on common arrangements of and reactions between the "top five" core atoms of biology.
Figure 3. A table illustrating the abundance of elements in the human body. A pie chart illustrating the relationships in abundance between the four most common elements.
Credit: Data from Wikipedia (http://en.wikipedia.org/wiki/Abundan...mical_elements); chart created by Marc T. Facciotti
The Periodic Table
The different elements are organized and displayed in the periodic table. Devised by Russian chemist Dmitri Mendeleev (1834–1907) in 1869, the table groups elements that, due to some commonalities of their atomic structure, share certain chemical properties. The atomic structure of elements is responsible for their physical properties including whether they exist as gases, solids, or liquids under specific conditions and and their chemical reactivity, a term that refers to their ability to combine and to chemically bond with each other and other elements.
In the periodic table, shown below, the elements are organized and displayed according to their atomic number and are arranged in a series of rows and columns based on shared chemical and physical properties. In addition to providing the atomic number for each element, the periodic table also displays the element’s atomic mass. Looking at carbon, for example, its symbol (C) and name appear, as well as its atomic number of six (in the upper right-hand corner indicating the number of protons in the neutral nucleus) and its atomic mass of 12.11 (sum of the mass of electrons, protons, and neutrons).
A functional group may participate in a variety of chemical reactions. Some of the important functional groups in biological molecules are shown above: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl (not shown). These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids. Functional groups can sometimes be classified as having polar or nonpolar properties depending on their atomic composition and organization. The term polar describes something that has a property that is not symmetric about it—it can have different poles (more or less of something at different places). In the case of bonds and molecules, the property we care about is usually the distribution of electrons and therefore electric charge between the atoms. In a nonpolar bond or molecule, electrons and charge will be relatively evenly distributed. In a polar bond or molecule, electrons will tend to be more concentrated in some areas than others. An example of a nonpolar group is the methane molecule (see discussion in Bond Types Chapter for more detail). Among the polar functional groups is the carboxyl group found in amino acids, some amino acid side chains, and the fatty acids that form triglycerides and phospholipids.
Nonpolar functional groups
The methyl group is the only nonpolar functional group in our class list above. The methyl group consists of a carbon atom bound to three hydrogen atoms. In this class, we will treat these C-H bonds as effectively nonpolar covalent bonds (more on this in the Bond Types chapter). This means that methyl groups are unable to form hydrogen bonds and will not interact with polar compounds such as water.
The methyl groups highlighted above are found in a variety of biologically relevant compounds. In some cases, the compound can have a methyl group but still be a polar compound overall due to the presence of other functional groups with polar properties (see the discussion on polar functional groups below).
As we learn more about other functional groups, we will add to the list of nonpolar functional groups. Stay alert!
Polar functional groups
A hydroxyl (alcohol group) is an -OH group covalently bonded another atom. In biological molecules the hydroxyl group is often (but not always) found bound to a carbon atom, as depicted below. The oxygen atom is much more electronegative than either the hydrogen or the carbon, which will cause the electrons in the covalent bonds to spend more time around the oxygen than around the C or H. Therefore, the O-H and O-C bonds in the hydroxyl group will be polar covalent bonds. Figure 3 depicts the partial charges, δ+ and δ-, that are associated with the hydroxyl group.
Hydroxyl groups are very common in biological molecules. Hydroxyl groups appear on carbohydrates (A), on some amino acids (B), and on nucleic acids (C). Can you find any hydroxyl groups in the phospholipid in (D)?
Carboxylic acid is a combination of a carbonyl group and a hydroxyl group attached to the same carbon, resulting in new characteristics. The carboxyl group can ionize, which means it can act as an acid and release the hydrogen atom from the hydroxyl group as a free proton (H+). This results in a delocalized negative charge on the remaining oxygen atoms. Carboxyl groups can switch back and forth between protonated (R-COOH) and deprotonated (R-COO-) states depending on the pH of the solution.
The carboxyl group is very versatile. In its protonated state, it can form hydrogen bonds with other polar compounds. In its deprotonated state, it can form ionic bonds with other positively charged compounds. This will have several biological consequences that will be explored more when we discuss enzymes.
Can you identify all the carboxyl groups on the macromolecules shown above in Figure 5?
The amino group consists of a nitrogen atom attached by single bonds to hydrogen atoms. An organic compound that contains an amino group is called an amine. Like oxygen, nitrogen is also more electronegative than both carbon and hydrogen, which results in the amino group displaying some polar character.
Amino groups can also act as bases, which means that the nitrogen atom can bond to a fourth hydrogen atom, as shown in Figure 6. Once this occurs, the nitrogen atom gains a positive charge and can now participate in ionic bonds.
A phosphate group is a phosphorus atom covalently bound to four oxygen atoms and contains one P=O bond and three P-O− bonds. The oxygen atoms are more electronegative than the phosphorous atom, resulting in polar covalent bonds. Therefore, these oxygen atoms are able to form hydrogen bonds with nearby hydrogen atoms that also have a δ+(hydrogen atoms bound to another electronegative atom). Phosphate groups also contain a negative charge and can participate in ionic bonds.
Phosphate groups are common in nucleic acids and on phospholipids (the term "phospho" referring to the phosphate group on the lipid). In Figure 7 are images of a nucleotide, deoxyadenosine monphosphate (left), and a phosphoserine (right).
Figure 7. A nucleotide, deoxyadenosine monphosphate, is on the left, and phosphoserine is on the right. Each has a phosphate group circled in red.
Attribution: created by Marc T. Facciotti (own work)
You may also find it useful to start getting used to thinking about these molecules in three dimensions. The interactive figures below (try spinning the molecules) depict the two molecules above, deoxyadenosine monophosphate and phosphoserine as three dimensional models. Getting used to three dimensional representations of biomolecules and interacting with these models can help you start forming more detailed mental models of what biomolecules look like and how they might interact in "real life".