Life as we know it

We have briefly studied organic chemistry to understand the basis of Carbon-based life on our planet. Because Carbon has a valence of 4, we can understand the scientific rationalization of imagining Silicon-based life-forms in Science Fiction storylines. For an expanded view and understanding of Silicon versus Carbon life, please read this article at Treknews.

The study of life outside of Earth was referred to as exobiology. Now, the field of Astrobiology has emerged to consolidate fields of astronomy, astrogeology, molecular biology, ecology and chemistry in order to understand life within the universe. While Carbon is the basis of our Biology, we would imagine that life could arise in other forms given a different environment than ours. Life forms, as we know them, are predominantly composed of Hydrogen, Carbon, Oxygen, Nitrogen, Phosphorus and Sulfur. Given our brief introduction to chemistry towards the goal of understanding basic mechanisms of life, we can begin to understand other hypothetical biochemistries.

Not so hypothetical?

In 2010, Felisa Lauren Wolfe-Simon of the NASA Astrobiology Institute published a paper regarding and extremophile bacteria called GFAJ-1 from Mono Lake. Mono Lake is hypersaline (very salty) and basic in pH. The extreme conditions of the lake provided a unique environment on our planet that has given rise to specialized organisms. The paper published in the journal Science indicated that these bacteria could utilize Arsenic if starved of Phosphorus.

What’s the significance of this finding? Well, Arsenic is typically poisonous to life as we know it. Why would that be so? If we examine the location of Arsenic and Phosphorus on the periodic table, we see that they are in Group V. This means that they have a valence of 5. With 5 free electrons in the outer shell, we would suspect a similarity of reactivity and structure formation as we’ve already indicated between Carbon and Silicon. In our biology, we see that much of the Phosphorus in our body is a component of Phosphate, which is necessary for building our genetic material and for cellular energetics.

As we can see from the structures of Arsenate and Phosphate, they are similar. Because of this, Arsenate is highly toxic. Our cellular machinery recognizes it as something like Phosphate, but cannot utilize it the same way. If this newly identified bacteria could in fact utilize and incorporate Arsenate, it would represent a demonstrated hypothetical biochemistry that defied what was already known.

Nullify your hypothesis

In the scientific method, we fortify and rigorously test our hypotheses by attempting to nullify them in multiple ways. This methodology removes experimental biases from our interpretations. In the case of GFAJ-1, the outcome was so surprising and contrary to conventional biology that it attracted many scientists to carefully scrutinize the data that gave rise to the conclusion of Arsenate incorporation. At this time, criticism and analysis of the data have given rise to alternative interpretations and a second group has repeated the experiments without observing any Arsenic incorporation.

Your life

Some of you may be wondering how this plays any significant role in your life. Take a look at this topic from one of our nutrition classes at Citytech.

On February 17th, CNN published an online article about cancer treatment and argued towards prophylactically attacking cancer before the state or process of cancer arises. It originally contained an error.

A neutron is a sub-atomic particle. Sub-atomic indicates that it is smaller than an atom. We know that atoms build molecules and proteins are biologically important macromolecular polymers. We know that a proton is a sub-atomic particle that has an approximate mass of a neutron. From the context of the article, this is not where the error lies –proton in place of protein.

Some time after the article was published online, there was an edit to rectify the error:

New tools may also make it possible to detect diseases at a much earlier stage. The key is understanding how proteins — which are the building blocks of life — operate. Faulty proteins can be early indicators of a disease. The trouble is, tracing proteins is incredibly hard to do — they have to be examined at the level of a single neutron. About eight years ago Agus started another company called Applied Proteomics. He joined up with supercomputer guru Danny Hillis to create a system with the horsepower to catalogue hundreds of thousands of protein levels. The company is still a work in progress, but if it succeeds, it will provide an important diagnostic tool.

The passage now reads that proteins must be studied at the level of a single neutron. If a protein is a macromolecule and a neutron is a sub-atomic particle:

• What could that possibly mean to trace proteins at the level of the neutrons?

The passage then states that Applied Proteomics is cataloging hundreds of thousands of protein levels (in magenta). As a lay scientist:

• What are your interpretations of this last statement?
• How would you interpret the work of Applied Proteomics from this article?
• How would you interpret the work of Applied Proteomics from from their website?

As a scientist, I would remark that this statement is gibberish, especially in the context of the rest of the article. Often times, we come across improperly written statements. We understand that science is very technical, but understanding some basic concepts, we can identify the faults in improper statements. We can further attempt to clarify improper statements by seeking out additional information. Here, since the statements are so befuddling, we can then turn to the primary source of information –Applied Proteomics.

In the Biology Lab, we separated the dyes that are present in chocolate candies. We utilized the solubility in a solvent versus the retention on a stationary phase using paper chromatography. Please calculate the R_f:

Color	Distance (cm)		Rf
Red	Red 1.5
Green	Blue 7.5 Yellow 4.3
Orange	Red 1.4 Yellow 4.5
Yellow	Yellow 4.6
M&M Orange	Red 1.5 Yellow 4.6
M&M Red	Red 1.3
M&M Brown	Red 1.7 Yellow 3.1 Blue 7.1
M&M Green	Yellow 1.7 Blue 6.7
Solvent Front	Front 8.6

The mobile phase was a saltwater solution. What do we learn from the R_f of each food coloring dye assuming they are of equivalent mass and/or size?

Acids and Bases

We can call any compound that adds H⁺ ions (a free proton) into solution an acid. Along with this, we would expect that any compound that would decrease the concentration of free H⁺ of a solution as a base. pH is the power of H⁺ of a solution. We define this power as a molar concentration of H⁺ in solution. This concentration invariably ends up being a relatively small number (though great in absolute numbers) and is expressed as a decimal number. Because the range of the concentrations is so great, we express these numbers as logarithmic numbers to avoid writing many 0’s after the decimal and to facilitate communicating the concentration. Since these numbers are so (relatively) small, we use the negative logarithm to describe this concentration.

Mathematically defined, pH = -Log₁₀[H⁺]

The pH scale ranges so that anything below pH 7 is acidic and anything above pH 7 is alkaline. So a smaller number is more acidic. But didn’t we just state that something acidic contains more H⁺ ions? Remember, because we are dealing with a negative Logarithm, this means the concentration is higher.

Now you’re just talking crazy!

If we have a quantity that is 10², we know that translates into 100. Just as if we have a quantity of 10⁴, we know that translates into 10000. Just as it becomes inconvenient to keep writing all those 0’s, it’s really impractical to write many many 0’s after a decimal. It’s really hard to talk about too! So we likewise will express numbers like 0.0001 as 10^-4. A logarithm is the reverse function of an exponent. Therefore:

• Log₁₀(0.0001) = -4
• Log₁₀10^-4 = -4

So how do we define a solution that is pH 2? Well, we already decided that this solution is below pH 7 — making it an acid. But what does this mean in terms of H⁺ ion concentration?
Let’s work this out algebraically:

• pH = -Log₁₀[H⁺]               Let’s bring the (-) over to the other side
• -(pH) = Log₁₀[H⁺]            Now let’s reverse the Log → base 10
• 10^-(pH) = [H⁺]                    Plug in the pH → molar concentration of [H⁺]

As we can now see, a solution of pH 2 is acidic because the molar concentration of [H⁺] is 10^-2mole/L or 0.01M

You’re still talking crazy! That number is small!

It’s not a small number. Remember that a mole is 6.022 X 10²³. That’s a very large number! Think about it! A solution of pH 4 is acidic, but if we plug in the formula, we realize that this is equal to 0.0001M H⁺ – less than pH 2 at 0.01M!

But let’s compare it to the [H⁺] content of H₂O. Now I’m going to sound crazier! Water can be thought of as being in an equilibrium where some of the molecules are ionizing and deionizing. We can express this in 2 ways:

• H₂O ⇋ H⁺ + OH^–
• 2H₂O ⇋ H₃O⁺ + OH^–

So at any given point, a liter of H₂O at neutral pH (7) has 10^-7 moles of H⁺ ions. Incidentally, it also has 10^-7 moles of OH^– in solution. The second expression indicates the formation of a hydronium ion (H₃O⁺) instead of a free proton in solution. So something that is pH 2 is a stronger acid than pH 4, right? Nope. That just indicates the amount of free protons in solution. It is more acidic but acid strength means something else. When we talk about strong acids, it means that it is more likely to donate a proton to the solution because it is more likely to ionize. Let’s look at the following:

• HA ⇋ H⁺(aq) + A^–(aq)                               Where HA is an acid dissociating in solution

If this dissociation is very high, then we say that it is a strong acid. Similarly, a compound like NaOH readily dissociates completely in solution and provides OH^– ions that can readily remove H⁺ from solution –a strong base! We speak of dissociation in terms of rates and we express this as the acid dissociation constant, K_a. This is calculated using the concentrations of [H⁺] (proton), [A^–] (conjugate base) and [HA] (non-dissociated) at equilibrium:

• K_a = ([H⁺][A^–])/[HA]

Just like the orders of magnitude we have when discussing pH, the rates of dissociation are more conveniently communicated on a logarithmic scale.

• pK_a = -Log₁₀K_a

Think about it this way, if the concentration of the dissociated ions is very high, the numerator in the rate is very high → K_a is great. In other words, at equilibrium, the dissociation reaction looks more unidirectional than bi-directional as the compound is readily ionized:

• HA → H⁺(aq) + A^–(aq)

On this scale, we refer to anything with a pK_a < -2 as a strong acid since it will readily dissociate in solution. This form of the dissociation constant is extremely useful in estimating the pH of buffer solutions and for finding the equilibrium pH of the acid-base reaction (between the proton and the conjugate base). We can estimate the pH by utilizing the Henderson-Hasselbalch Equation:

• pH = pK_a + Log₁₀([A^–]/[HA])

Polar Covalent Bonds

H₂O is a polar covalent molecule. The Bonds between the H atoms and the O atom arise from sharing electrons. These shared electrons form to satisfy the octet rule. However, Oxygen is a “selfish” sharer. The electronegative aspect of Oxygen means that the electrons of the H₂O molecule preferentially associate near the Oxygen atom, creating partial charges. We indicate this by placing a δ- near the O and δ+’s near the H atoms. These partial charges make the H₂O polar. Because of this polarity, H₂O molecules arrange in a highly structured way.

These weak associations that arise from the polar:polar attractions are referred to as Hydrogen Bonds (H-bonds). While independently weak, the summation of all the H-bonds are very strong. These associations give rise to the special properties of water: surface tension, cohesion, adhesion, high specific heat capacity.

Surface Tension

Surface tension presents as an invisible film that encompasses the surface of water. The attractive forces arising from the intermolecular cohesion holds the surface of water together.

This water strider is not on top of the water because it is light. It has not broken through the surface of the water and is therefore, on top of the water.

Solutions

Water is an excellent solvent of other polar compounds. Table salt (NaCl) ionizes readily in water. The δ- O associate around Na⁺ while the δ+ H associate with the Cl^–. If NaCl is dissolved in H₂O, what do you think happens to the intermolecular interactions between water molecules? What do you think would happen to the H-bonds? Would you expect there to be a difference in the surface tension? How do you think this explains the difference of boiling or freezing?

Running on Water

Lizards of the genus Basiliscus have the nickname “Jesus Christ lizard” for their very special adaptation regarding water.

In the face of danger, these lizards run on their hind legs across water to escape predation. Their hind legs have long toes that help in increasing surface area to distribute their weight so they can propel themselves on the surface of the water. They do not sink because the surface tension of the water is not broken by the large surface covered by their feet. After about 4.5m, they lose sufficient momentum to propel themselves on the water surface and break through. H-bonds enable this adaptation.

What if?

The namesake of these lizards walked on water but was also able to turn water into wine. Wine is a solution of ethanol (11%) in water. Ethanol has a polar end and a non-polar end.

• How successful would the basilisk run on wine?
• Why?
• How could you test this without necessarily using a lizard?

Comparative Anatomy

Georges Cuvier was a French naturalist and zoologist who utilized the idea of comparative anatomy to establish the field of paleontology. He initially observed that features found in fossils could indicate shared function and relatedness between these features. He illustrated that African and Asian elephants represented 2 distinct species. Furthermore, he identified mammoth fossils as distinct separate species from living elephants.

Cuvier supported the idea of special creation to describe the origins of all life on Earth and harshly criticized transmutation as a means for various life forms to exist. Despite this, his use of comparative anatomy later provided crucial evidence that supported transmutation. Specifically, the ideas of homologous and analogous structures. With homologous structures, similar structures appear between similar species despite function and overall structure of those parts. With analogous structures, similar structures reflect a shared function due to the environment as opposed to a shared ancestry. This similarity of structure due to function and environment is referred to as convergence.

The similarity between the gross structure of the bodies of sharks and dolphins is related to the aquatic environment, but their fins are derived from disparate structures.

The case of 2 skulls

Two skulls are presented below. Both skulls have similar features.

Both skulls show very large teeth at the front of the mouth followed by a handful of flat grinding teeth in the rear of the mouth. Overall structure of these two skulls is very similar. To the untrained eye (and without any size reference) we could assume that they might even be from the same species.

1. Are these 2 skulls the same species of organism?
2. What are the supporting features that indicate that they belong to the same species?
3. If we look carefully at the dentition (teeth), do we learn about the the relatedness of the skulls?
4. What might we assume about diet by looking at the teeth from these skulls? Describe the teeth and identify what they would be used for.

What we notice immediately are the very large teeth at the front of the skulls. We might also notice further back in the mouth, the presence of very flat looking teeth.

Adaptation

The teeth from the 2 skulls indicate that they might be specialized for gnawing. In fact, the 2 skulls are clearly classifiable as rodents!

• Compare the 2 teeth in the front of your mouth (incisors) to the ones in the skulls
• While they are greatly different in size, do these teeth have a similar function?

As it turns out, the left skull actually belongs to a beaver and right skull belongs to a nutria.
Beavers are anthropomorphically characterized as industrious. They are large, semi-aquatic rodents that are known for their behavior of building dams in wetlands. Nutria are also semi-aquatic rodents, but they are smaller than beavers. While nutria have some similar features to beavers, nutria have long rat-like tails instead of the long flat paddled tail of the beaver.

Comparative anatomy using fossils is limited by the fact that soft tissue doesn’t fossilize readily. Looking at the living organisms, we can see that both species have webbed hind feet.

• Is this a common feature to all rodents?
• Swans also have webbed feet. Does this mean they are closely related?
• What does it mean if we decide that swans are not closely related?

Beavers occur naturally in the northern hemisphere while Nutria occur naturally in the southern hemisphere. Just like another invasive rodent species, nutria also exist in North America because they were introduced here.

• If beavers and nutria have similar structure and adaptations to a specific environment, would we expect them to compete?
• Would you expect the beaver to succeed in the natural environment of the nutria?

Magnification

Magnification is the process of enlarging the appearance of an object. We calculate the magnification of an object by indicating the fold change in size. So if something appears to be double the size of the real item, then it is obviously magnified 2X. Because there is a magnification by the eye-piece (ocular lens), as well as the objective lenses, our final magnification of an item is the product of those two lenses.

We can calculate that as:
Magnification_total = Magnification_objective X Magnification_ocular

Field of View (FOV)

In a microscope, we ordinarily observe things within a circular space (or field) as defined by the lenses. We refer to this observable area as the field of view (FOV). Understanding the size of the FOV is important because actual sizes of object can be calculated using the Magnification of the lenses. What are the effects of magnification on FOV?

In image 1, we can see a model of DNA on a table with a water bottle and a large area of the room. Image 2 displays less of the room in the background but the DNA model is larger in appearance because the magnification is greater. In image 3, we no longer see evidence of a door and the DNA model is much larger than before. In image 4, we no longer see the table the model and water bottle rest upon. While the last image is largest, we see less of the surrounding objects. We have higher magnification at the cost of field of view. FOV is inversely related to the magnification level.

Depth of field

We notice that when we observe 3 overlapping threads of different color under a microscope, we can focus on one thread at a time. Similarly, when we zoom in a great deal on the DNA model above, we notice that the print on the water bottle is not sharp.

We know that the water bottle is behind the DNA molecule. Under the microscope, the threads of differing color are also stacked on top of each other. We recognize that they are in different planes because they are three dimensional. Each thread has depth and do not occupy the same exact space. If we focus on the print of the water bottle on the image above, we would no longer see the lettering on the DNA molecule sharply. We refer to this concept as Depth of Field (DOF). Under the microscope, at a low magnification, we can make out fewer finer details. However, most items appear on the same plane in this case and or comparably sharp. But as we increase the magnification and see finer details, the distances between the various planes in view become more apparent. We can see a similar phenomenon at low magnification of the DNA model. At the low magnification, we may not be able to read the print on the water bottle, but the bottle and DNA molecule are of a similar distance from our view that the small difference in apparent depth is not as noticeable. We can still draw on other visual cues to know that the bottle is behind the model, but the sharpness of both items are equivalent.

Real biological examples

We can see the concepts of FOV and DOF in the following pictures.


In an even more extreme close-up (higher magnification), we would have difficulty focusing on both the eyes and beak since there is depth and distance between those features.

How do we use microscopes

In our lab, we look at some pond water. What do we see? Why is this significant? How does the microscope help us study these items? What is the utility of the the concepts of magnification, FOV and DOF when we use microscopes to study biological samples?