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Structures of Life: biological and general organic chemistry
All of life is composed of matter. Matter can be grouped into two forms. It can be in a pure form as one element, or in a compound.
Element - this is any matter that cannot be broken down into smaller, discrete forms by a chemical reaction. You've heard of elements like gold, iron, oxygen, and nitrogen.
Compound - this is any matter that is the combination of two or more elements. You know of compounds like water (hydrogen + two oxygens), table salt (sodium + chlorine), glass (silicon + oxygen), and chloroform (carbon, hydrogen, and chlorine).
Elements are listed in the periodic table, and there are 92 natural elements (Fig. 1). Four out of the 92 - carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) - are of great significance. Together they account for 96% of all mass in living things! These four elements plus 21 others are considered essential to life - including calcium, potassium, sodium, etc.
Many essential elements are only required in small quantities and are called trace elements, including iron, iodine, copper, and selenium.
Atoms and examples of chemistry in our daily life
Atoms make up elements, and atoms are given their unique properties by the specific amounts of subatomic particles they contain. Atoms used to be known as the smallest, indivisible units of elements, but we now know that is not the case. Atoms are divisible.
Atoms are made up of three subatomic particles - protons and neutrons in the nucleus of an atom (its center) and electrons orbiting around the nucleus. Protons are positively charged units of matter, neutrons have no charge, and electrons are negatively charged. Protons have mass, neutrons have about equal mass as protons, and electrons are essentially massless.
Electrons are described as "in orbit" around the nucleus of an atom, but it is also important to think of electrons as existing in levels known as shells. Electron shells are layers of energy that describe how far or how near a set of electrons sits to the nucleus of its atom (Fig. 2). Valence electrons sit on the valence shell (the outermost shell, farthest away from the nucleus), and have the highest amount of energy. These high-energy electrons are the most reactive and are the first electrons that take part in chemical reactions.
Elements are typically balanced and without a charge, with equal numbers of protons and electrons.
However, other forms of elements exist. These include ions and isotopes, distinguished by their relative proportions of protons, neutrons, and electrons.
Mass - this is a measure of matter. The mass of an object is the amount of matter that the object contains, with weight being considered the amount of force on a particular mass due to gravity.
Isotopes - are elements with different numbers of neutrons. For example, the element carbon has a mass number of 12 = 6 protons + 6 neutrons. But carbon has many isotopes, like carbon-11, which has 6 protons + 5 neutrons, and carbon-13, which has 6 protons + 7 neutrons.
Ions - are not electrochemically neutral; they have a charge. This is due to an unequal number of protons and electrons. Several ionic forms of the same element may exist, like Iron (Fe), with its two most common ions: Fe2+ and Fe3+. Ions can also be compounds, like the sulfate ion (SO42-) or the nitrate ion (NO3-).
Because ions are positively or negatively charged, bonds form when ions combine. Ionic bonds are one of 5 types of bonds we must know.
Types of Chemical Bonds
1. Ionic Bond
An ionic bond occurs when one compound donates or transfers its electrons to another compound. The receiving compound is always more electronegative than the donor compound.
Think of electronegativity as electron-attraction, or "electron-needing", so the receiving compound is more "electron-needing". The electron donor compound or atom will become a cation and have a positive charge. The electron receiver will become an anion, having a negative charge.
The overall ion will be net neutral because of the bond between the donor and receiver.
Anions = These are negatively charged ions, and are attracted to positively charged rods called anodes.
Cations = These are positively charged ions, and are attracted to negatively charged rods called cathodes.
Ionic bonds usually occur between metals (such as sodium, Na) and non-metals (such as chlorine, Cl), where the more electronegative non-metals draw electrons away from the electron-donating metals (Fig. 3).
The metals will become cations and the non-metal will become an anion and the two will be joined together by an ionic bond.
2. Covalent Bonds
Covalent bonds do not involve electron transfer, they involve electron sharing. Two electrons are shared between atoms or compounds, to make a covalent bond.
Covalent Polar Bonds
Polar covalent bonds are those that occur when the electrons are shared, but not equally.
In a polar covalent bond between two compounds, the more electronegative (electron-attracted) molecule will pull most of the electrons in the bond towards itself, and the less electronegative one will get less. Polar bonds occur when the bond between those two compounds is not shared equally.
The classic example of a covalent polar bond is water, but we will use ammonia as our example. Ammonia has the formula NH3 and all bonds in it are covalent. However, nitrogen is more electronegative than hydrogen, so nitrogen pulls electrons from these covalent bonds more than hydrogen does (Fig. 4).
Covalent Non-Polar Bond
Covalent non-polar bonds are shared equally between two atoms or compounds.
This can happen when the compound is composed of two of the same atom, like O2, or when a compound is made up of atoms with similar degrees of electronegativity (such as methane, CH4).
Ionic bonds are always between metals and non-metals, while covalent bonds are always between two (or more) non-metals. Remember that not all metals are obviously metallic, like gold or silver. For example, sodium and potassium are both metals!
3. Hydrogen Bonds
Hydrogen bonds are different from the bonds mentioned above because they occur between different molecules (intermolecular bonds), not within the same molecule (intramolecular bonds).
A hydrogen bond is a bond or interaction between a proton (hydrogen) in one molecule and an electronegative atom in another molecule.
Say there are two molecules of water, called Molecule A and Molecule B. The chemical formula for water is H2O, and Molecule A has two hydrogens bound covalently to its oxygen. The same situation is occurring in Molecule B.
Molecules A and B get close enough to interact. Then, a hydrogen from Molecule A makes a weak bond with the oxygen from Molecule B. This bond is a hydrogen bond, and while individually it is weak, the compounded effects of multiple hydrogen bonds can be quite strong.
4. Vander Waals Forces
Vander Waals forces are weak interactions between atoms or molecules, due to unequal distributions of electrons. These interactions can result in transient "hot spots" of negative and positive charges and are part of what gives large molecules their 3D shape.
Carbon and the role of chemistry in our daily life
Why single out carbon among other elements? Carbon is so important that it divides chemistry into two major groups - Organic Chemistry (the chemistry of carbon-containing compounds) and Inorganic Chemistry (the chemistry of non-carbon compounds). Carbon's importance is due to the following chemical properties:
- It has four valence electrons
- This means it can make up to four covalent bonds, and thus can be a part of large compounds
- It is usually electrochemically stable
- This allows it to form many different shapes and conformations comfortably, like rings, branches, and chains.
Carbon is the major contributor to the four major macromolecules of life: carbohydrates, proteins, lipids, and nucleic acids. Carbon forms the backbone of their chemical structures.
This carbon backbone combines with a series of other atoms and functional groups to create monomers (smaller, individual subunits of these organic compounds) which can be joined together to create polymers of these macromolecules.
For a more in-depth analysis of each macromolecule, click it!
Carbohydrates
Carbohydrates always have the following molecular setup: carbon, hydrogen, and oxygen, in a 1:2:1 ratio (Fig. 6). So for a six-carbon carbohydrate molecule, we'd have the following formula: C6H12O6. In fact, this is the formula for glucose!
Proteins
Proteins are made from amino acids, and there are 20 different amino acids. Each has a central carbon, with four things bound to it covalently - an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and an R-group (Fig. 7).
Whatever the R-group is, decides what the amino acid is!
Lipids
Lipids are a name for a heterogeneous group that includes steroids, fats (aka triglycerides), phospholipids, and oils. Lipids, like carbohydrates, are composed of hydrocarbons, but unlike carbohydrates, they don't have a fixed ratio.
Triglycerides are the most important fat in our diet, and also the major lipid in our bodies. They are highly hydrophobic because of their structure: a glycerol backbone + three fatty acid chains with long series of hydrocarbons (Fig. 8).
Nucleic Acids
DNA and RNA are the two nucleic acids, and they both contain three elements:
- Nitrogenous base
- Pentose sugar
- Phosphate group
A nitrogenous base is one of five ringed structures. You may have seen them before if you've ever read codes with lists of letters A, C, G, T or U. These letters signify the five different nitrogenous bases: adenosine, cytosine, guanine, thymidine and uracil.
A pentose sugar is a five-sided carbohydrate molecule.
Pent- means 5-sided shape!
Importance of inorganic chemistry in our daily life
If organic chemistry is largely hydrocarbons plus certain functional groups, what is inorganic chemistry comprised of?
Inorganic chemistry involves more ionic bonds, between metals and non-metals. The salt we eat, NaCl, is an inorganic compound. Although it has covalent bonds, by virtue of not having any carbon molecules, water is also an inorganic compound.
Inorganic chemistry is especially important in industry and manufacturing. Everything from pharmaceuticals, to technology, to beauty products to metalworking involves much inorganic chemistry, and the products produced from these industries are those we use in our daily lives.
A summary of the chemistry of life
All life is composed of matter, which includes elements and compounds. Compounds are created through different types of chemical bonds. The chemical reactions of life are dominated by the four most common elements in living things; carbon, hydrogen, oxygen, and nitrogen. Of these four, hydrocarbons are the most fundamental in organic chemistry. We can see hydrocarbons present in all four major macromolecules, carbohydrates - the major source of food and energy for living things, proteins - used to make everything from muscles to enzymes, lipids - required for cell membranes and to store energy as fat, and nucleic acids - which record and pass down our genetic material.The interplay of organic chemistry with inorganic chemistry that we see in acid-base neutralization reactions, in salt creation, in the oxidation and reduction of metals, allows for life as we know it to be produced and to continue.Chemistry of Life - Key takeaways
- The chemistry of life involves both organic and inorganic chemistry and is important in biology as well.
- There are four types of bonds: covalent, ionic, hydrogen, and Vander Waal's forces.
- Bonds can be either polar or non-polar, based on relative electronegativity.
- Organic chemistry always involves hydrocarbon compounds, whereas Inorganic chemistry often involves ionic bonds.
- Carbon is the backbone of the four major macromolecules of life - carbohydrates, proteins, lipids, and nucleic acids.
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Frequently Asked Questions about Chemistry of Life
What is the importance of chemistry in life?
Chemistry is important in life because certain molecules and reactions are common to all living things.
How does chemistry involved in our daily life?
The foods we eat are both built by and metabolized by chemical reactions. Also, chemistry is involved in protein formation, DNA formation, and fat creation.
Why is carbon so important to life and organic chemistry?
Carbon is a stable element that has four possible binding spots and is the backbone of all four of the major macromolecules of living things.
What are some examples of inorganic chemistry in life?
Neutralization reactions of acids and bases (such as taking tums for acid reflux) and the formation of salt in the ocean (sodium + chlorine forming sodium chloride) are two examples of inorganic chemistry in real life.
What are some examples of organic chemistry in life?
Organic chemistry is seen in saponification, the process of soap making. Also, in the creation of alcohol. Organic chemistry occurs in DNA creation as well.
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