2.4. Atomic physics

Bohr atomic model was one of the first classic atomic models where the electrons orbit at specific distances from the atomic nucleus, like the planets orbit around the Sun.

This model can explain the reactivity and chemical bonds in certain elements, but it is just an approximate model because the electrons are not located in orbits but in atomic orbitals. 
These atomic orbitals are regions of space where the probability of finding an electron is greater according to the mathematical equations of quantum mechanics (Schrödinger equation). These atomic orbitals, with complex shapes, arise from the fact that electrons does not behave only as particles, but also as waves. Therefore, the term "orbit" in Bohr model is replaced by "atomic orbital" in this quantum-mechanic description.

Now, I will explain some concepts about quantum mechanics, but do not worry, I will try to do it in a simple and concise way.
Quantum mechanics establishes that to know an electron state in an atom (where that electron is in space), it is necessary to know the value of four quantum numbers, each one indicates a different property for that electron:

▣      Principal quantum number (n): indicates the orbital energy, the shell and the average distance between an electron and the nucleus. Its value goes from 1 to the shell containing the outermost electron of that atom, n = 1, 2, 3....

▣      Angular or azimuthal quantum number (l): describes the orbital shape. Its value depends on the former one (n), and it goes from 0 to n-1, l = 0, 1, 2,.....n-1.

l value	Type of orbital	Orbital shapes
1	s	Spherically shaped
2	p	Dumb-bell shaped
3	d	Most butterfly shaped
4	f	Exotic and complex

▣      Magnetic quantum number (m_l): characterises the orientation of the atomic orbital in space according to the axes X, Y and Z. It also depends on the former quantum number (l), the values ranges from –l to +l, with integer steps, including zero.

▣      Electron spin quantum number (m_s): unlike the others, it does not depend on another quantum number; m_s has just one of the two following values: +1/2 and -1/2. These two numbers tell us the two possible spin movements of an electron: clockwise and anticlockwise.

Name	Quantum number	Allowed values
Principal quantum number	n	1, 2, 3...
Angular or azimuthal quantum number	l	0, 1, 2, 3...n-1
Magnetic quantum number	ml	-l, (-l+1)...0...(l+1), l
Electron spin quantum number	ms	1/2, -1/2

So, the general idea you get from all this is that to describe an electron you need four properties that are indicated by four numbers, it is as if we would like to characterise an article of clothing with four features. Let’s say for example:

▶      Design (to know if it is a shirt, a scarf, a skirt, a pair of trousers…)

▶      Size (to know if it is an article of clothing for children, teenagers or adults)

▶      Color (blue, red, white…)

▶      Type of fabric (nylon, wool, cotton…)

Once we have all this information we can know what an article of clothing we are talking about. In the same way, once we know the four quantum numbers we can find out what electron we are referring to and where it is.

As we move forward along the periodic table the number of electrons in each element is increased by one unit in accordance with two principles, those are Pauli exclusion principle and Hund’s rule:

▣      The first one states that in the same atom, two electrons cannot have identical values for all four of their quantum numbers, in other words, two electrons cannot be in the same quantum state. If this principle were not true, the chemical behaviour of elements, and hence also nature, would be completely different from the way in which we know it.

▣      On the other hand, Hund’s rule states that in the same atomic orbital, electrons fill it in such a way that these electrons tend to be unpaired.
Making an analogy, we could say that electrons behave like people getting on a bus. You will have noticed that we prefer to sit without anyone next to us, and only when we do not have a chance to do it, it is when we sit next to someone else. Like electrons, in the same atomic orbital, we would rather be “unpaired” on a bus.

Let's consider the nitrogen atom which electron configuration^[1] is 1s²2s²2p³, whose electrons are arranged as follows:

As you can observe, the electrons in p orbital prefer to be unpaired, since all the orbitals in a shell (in our case, p orbitals in shell 2) must be occupied by, at least, one electron before a second electron is added. This fact, explained by Hund's rule, occurs so that the atom is more stable energetically.

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[1] It is the distribution of electrons of an atom in each energy level and atomic orbitals.

Source: McGraw-Hill, Física Raymond A. Serway, 1993.
            McGraw-Hill, Química Raymond Chang, 1992.

2.3. Chemical bonds

A chemical bond is defined as a force that joins two or more atoms from the same or different element to build more complex structures: molecules. Among the main bonds that form the biological macromolecules, which we will study in-depth later, we can find:

▣      Ionic bonds: between ions with opposite charges. An illustrative example of this kind of bond is represented by sodium chloride molecule (NaCl), commonly known as table salt. This molecule is formed by ionization^[1] of sodium atom (Na) and chlorine atom (Cl), and the attraction of resulting ions.

▣      Covalent bonds: the electrons are shared between atoms to form bonds and satisfy the octet rule^[2]. Within covalent bonds we can find two subtypes:

1.     Polar covalent bonds: the electrons are unequally shared by the atoms in such a way that they are more attracted by one of the nuclei than by the other (they have different electronegativity). Hence, one side of the molecule is slightly negative (δ-) and the other slightly positive (δ+). An example is water molecule where the oxygen atom is negative charged and the two hydrogen atoms are positive charged.

2.     Nonpolar covalent bonds: are formed by two atoms where the electrons are shared equally. Molecular oxygen (O₂) is an example where the electrons are distributed evenly.

▣      Hydrogen bonds: weak interactions between hydrogen atoms (slightly positive) and other atoms (usually nitrogen and oxygen) from the same or different molecule. They are in charge of zipping together the two strands of the DNA double helix molecule.

▣      Van der Waals interactions: weak interactions or attractions between molecules due to the fact that two or more of them depend on slight fluctuations of the electronic densities^[3], which are not always symmetrical around the atoms. This kind of interaction contributes with ionic, covalent and hydrogen bonds to the three-dimensional structure of proteins.

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[1] Process by ions are produced.
[2] It establishes that those atoms with eight electrons in their outermost shell or valence shell are more stable from an energetic point of view.
[3]  Probability of finding an electron in a certain region of space.

Source: OpenStax College, Biology. OpenStax College. 30 May 2013.

2.2. Some chemical definitions

Next, I would like to explain some basic definitions that I consider you should know to understand some concepts that we will see later. You may already know them as they are basic notions about chemistry that we all study at school, but I would like to brush up on them just in case:

▣      Atomic number: indicates the number of protons in an element. It helps us to distinguish elements from one another

▣      Mass number: is the addition of the number of protons and number of neutrons (electrons are ignored).

▣      Isotopes: those atoms of the same element that contain equal number of protons but unequal number of protons.

▣      Atomic mass: calculated from mass numbers of several isotopes that are from the same element. I’ll give you an example to clarify:

Gallium is a chemical element with two isotopes ⁶⁹Ga  and  ⁷¹Ga whose relative abundances are 60.2% and 39.8%, so the atomic mass is:

Gallium atomic mass = [ (69*60.2) + (71*39.8) ] / 100 = 69.7 u (being u: atomic mass unit, which is approximately the mass of one nucleon, either a single proton or neutron).

▣      Radioisotopes: those isotopes with a more stable electronic configuration by means of the emission of protons, neutrons and/or electrons.

▣      Periodic Table: table where the elements are organised according to their atomic number and distributed in rows and columns conforming to shared physical and chemical properties.

▣      Ions: those atoms that are more stable when they gain or lose electrons. In the first case, they are named anions or negative ions (e.g.: fluoride (F^-), sulfide (S^2-), and in the second they are called cations or positive anions (e.g.: sodium (Na⁺), lead (Pb²⁺)).

▣      Molecule: two or more atoms joined by chemical bonds.

▣      Chemical reaction: it occurs when two or more atoms are joined by bonds to form a molecule or when joined atoms are broken down.

▣      Reactives: substances used at the beginning of a chemical reaction, normally on the left side of the reaction.

▣      Products: subtances resulting from the end of a reaction, usually on the right side of a reaction.

▣      Electronegativity: tendency of an atom nucleus to attract electrons. It increases as we move to the top and right along the periodic table.

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[1] Partículas que constituyen el núcleo atómico: protones y neutrones.

Source: OpenStax College, Biology. OpenStax College. 30 May 2013.

2.1. Introduction to the atom. Its structure

Life, at its most fundamental level, is made up of matter that can be defined as any substance that takes up space and has mass.
We will begin our study of biology with the most basic element of matter: the atom, we will get to know its structure, types, properties and how they arrange, by means of bonds, to form configurations with a higher level of complexity, which are named molecules.
Atoms are the basic structural components of chemical elements, which can be described as unique forms of matter with specific physical and chemical properties that cannot be broken down (by ordinary chemical reactions) into smaller substances.

Elements are named by a capital letter or two letters, when the first one has already been taken by another element, these letters are called chemical symbols. Thus, for example: H is the chemical symbol for hydrogen and He is the chemical symbol for helium.
The four most common elements in living organisms, including human being, are oxygen (O), carbon (C), hydrogen (H) and nitrogen (N), whose percentages are:

Element	Percentage in living organisms
Oxygen	65%
Carbon	18%
Hydrogen	10%
Nitrogen	3%

As I have just mentioned, the structural components in elements are called atoms, which are the smallest units of matter that retain all the chemical properties of an element.
We can distinguish two different areas in an atom:

▣         The nucleus which is the centre of the atom made up of protons (p) and neutrons (n).

▣         The electrons (e^-) in orbit around the nucleus, this is the outermost region in an atom.

Protons and neutrons have, approximately, the same mass: 1.67*10^-24 g, but they differ in their electrical charges, whereas protons are positively charged, neutrons are uncharged. Electrons, however, have a very low mas: 9.11*10^-28 g, around 1/800 of an atomic mass unit^[1]. Therefore, their largest contribution is not to the atomic mass but to its charge, since this charge is equal to protons’ but with opposite sign (negative).

Interestingly, due to the tiny size of all these particles, most of the atomic volume is empty space ( > 99%), to give you an idea about what this means let’s imagine that our atom is a huge sphere around The Eiffel Tower (301 metres height), proportionally, the nucleus would be represented by a cherry stone and the electrons would be pinpoints around it. 

As a result of this enormous vacuum, you can wonder why solid objects are impenetrable and this is on account of the fact that the electronic shells repel (negatively charged) each other.

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[1] Atomic mass unit (u) or dalton (Da) is approximately the mass of one nucleon, either a single proton or neutron and is defined as one twelfth of an unbound neutral atom of carbon-12 and has a value of 1.660*10^-27 kg.

Source: OpenStax College, Biology. OpenStax College. 30 May 2013.

1.2. The scientific method

The scientific process normally begins with an observation (usually a problem that needs a solution) which leads to a question. Researchers, from this question, are going to follow the next steps:

▣      Proposing a hypothesis

Let’s remember that a hypothesis is a suggested explanation that can be tested. As several hypothesis can be capable of answering a single question (as we saw previously), several hypothesis can be proposed to solve a single problem. Once a hypothesis has been chosen, a prediction can be formulated with the following structure:  “If . . . then . . .”

    ▣      Hypothesis verification

Due to the fact that natural phenomena are not always as usual and flexible as we would like, observation is not often enough and researchers must carry out one or more experiments to get rid of one or more of the initial hypothesis.

Each experiment consists of:

▶      At least one variable which is any part of the experiment that can change during the same.

▶      At least one control group that contains the same features as the experimental group but they are not applied the hypothesis in study. By modifying variables, we can discover how they affect the experimental process and if the results of the experimental group are different from the control group such a difference is due to the hypothesis we are testing instead of external factors.

We can affirm, without a doubt, that the Italian physicist Galileo Galilei was the first one introducing experimentation in a systematic way in the world of natural sciences. Without experimentation, modern science would never have accomplished the advances we have today, that is why laboratories have become so essential for researchers.

Science, unlike general thinking, does not intend to prove anything because scientific knowledge, as time goes by, changes with new acquired knowledge. The objective is, hence, to test if the proposed hypothesis are refuted or disproved, which is general known as “falsifiable”.

The several steps in the scientific method can be represented as follows:

To clear up ideas I will give you a simple example:
Let's imagine you want to watch your favourite TV show but the television does not turn on (observation), so you wonder why (question).
The first idea you think of is there might have been a power cut (hypothesis), to check you do the following “experiment”: you switch on the lamps in your dining room and they light on (analyse the results), so the hypothesis is incorrect.
Then, you decide to look if your TV monitor is unplugged (second hypothesis), you do it (experiment) but the TV is plugged into the mains (analyse the results), this second hypothesis is also incorrect.
Thirdly, you check if the batteries in your remote control are used up (third hypothesis) and the “experiment” you do is to replace them with new ones, finally you manage to turn on the telly (analyse the results), so this last hypothesis was the correct one.

No doubt, this is a rather simplistic example of our daily life but allows us to know how science works with much more complex, significant and tough problems.

Source: OpenStax College, Biology. OpenStax College. 30 May 2013.

1.1. What is science? How it works

Science from the latin “scientia” (knowledge) can be defined as the knowledge that covers general trues or the way general laws work, especially developed and examined through the scientific method. Therefore, the scientific method plays a fundamental role in science and is a research method with very well defined steps, among them experimentation and observation.  

One of the most important aspects in this method is to check the proposed hypothesis through repeatable experiments, being a hypothesis a possible explanation about a fact that can be tested. At the same time, a hypothesis could become a verified theory, which are examined and verified through phenomena or observations. It should be pointed out that a well proposed hypothesis does not imply its validity, because that hypothesis could be false.

Let’s imagine, in a similar way like Galileo supposedly did, we are on the roof of a building and we would like to measure how long it takes a ball to get to the ground, we can formulate the following hypothesis:

▣      This time depends on what material the ball is made of.

▣      This time period is determined by the building height.

▣      This time interval depends on the ball mass.

▣      Finally, this time is subject to the look of the ball.

The first, second and third hypothesis can be true or false but they will always be verified designing several experiments. For instance, we can use balls made of diverse materials (iron, wood, plastic…), with different masses (50 g., 150 g.,    250 g…) or we could throw it from buildings with different heights. However, the last hypothesis is not valid, because appearance cannot be measured and therefore, cannot be tested in experiments.

The common goal in all sciences is to know. Scientists search to understand the world and the way it works, to do it they use two logical reasoning methods:

▣      Inductive reasoning: a logical reasoning that uses observations related to each other in order to achieve a general conclusion. From lots of observations, raw data (qualitative and quantitative) and an in-depth analysis, scientists deduce conclusions (inductions) based on evidences.

▣      Deductive reasoning: this kind of reasoning uses general principles or laws to predict specific results. In consequence, it is a thinking pattern that moves in the opposite direction to the former one. Starting from general principles, a scientist can extrapolate particular results which are valid as long as those general principles are also correct.

Both types of reasoning are used to allow the advance of scientific knowledge.

Fuente: OpenStax College, Biology. OpenStax College. 30 May 2013.

1. What is biology?

Biology is a field of study that we are completely familiar with because it is one of the main subject we all study when we were children at school. Anyway to lay the foundations, I would like to start from scratch giving you a brief definition about what biology is and its branches.
We can define biology as the science in charge of the study of living organisms, their interactions and their environment. The scope of biology is really large and it goes from submicroscope and microscope cell study to ecosystems and even the whole planet Earth.

Biology is included within the natural sciences which scope is the physical world, its phenomena and processes. A quite common division between these sciences establishes a differentiation between life sciences (mainly biology and medicine) and physical sciences which study the inert matter (physics, chemistry, astronomy and geology). Similarly, we can also find other interdisciplinary branches built on this division, like biophysics and biochemistry.
Natural sciences are, at times, known as “pure sciences” due to the fact that they are based on the use of quantitative data, whereas social sciences, to lead their research about the study of social and human behaviour, use qualitative assessments much more often.

Biology, as I said, on account of its really large scope of study is divided into several branches and subdisciplines. Thus, for example, the biologists who study anatomy are focused on the structure of an entire organism, physiologists research how these organisms work internally, botanists are specialized in the study of flora, zoologists explore fauna and so on…
But in this blog due to its own purpose, we will mainly focus on two aspects:

▣      Molecular Biology which is the study of the macromolecules that are the bricks of life and their interactions (molecules such as DNA, RNA and proteins).

▣      Cellular Biology whose study field is the cellular structure and its functions.

Source: OpenStax College, Biology. OpenStax College. 30 May 2013.