[AP Biology 1.2] The Elements of Life
This section of the AP Biology curriculum is called The Elements of Life. This section focuses on the elements that are most essential to life on this planet, specifically carbon and its ability to form 4 covalent bonds. It also touches on nitrogen and phosphorus, two elements that are crucial in the formation of DNA, RNA, and proteins.
The following video summarizes the most important aspects of this topic!
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Resources for this Standard
The highly complex organization of living systems requires constant input of energy and the exchange of macromolecules.
Describe the composition of macromolecules required by living organisms
Organisms must exchange matter with the environment to grow, reproduce, and maintain organization.
Atoms and molecules from the environment are necessary to build new molecules–
- Carbon is used to build biological molecules such as carbohydrates, proteins, lipids, and nucleic acids. Carbon is used in storage compounds and cell formation in all organisms.
- Nitrogen is used to build proteins and nucleic acids. Phosphorus is used to build nucleic acids and certain lipids.
The Elements of Life Overview
The overarching theme of Unit 1.2 is “The Elements of Life.” Before getting into the complex macromolecules that organisms need to survive, we must first understand that there are several elements that all life is dependent on: Carbon, Hydrogen, Oxygen, Nitrogen, Sulfur, and Phosphorus. All life on Earth has very similar ratios of these elements – just one more piece of evidence that all life originated from a common ancestor.
In one of the most famous historical experiments ever conducted, Stanley Miller and Harold Urey were able to prove that the early atmosphere of Earth would be able to create the molecules of life without an actual organism. The team created a system in which water vapor was allowed to react with simple atmospheric compounds such as hydrogen gas, methane, and ammonia – while being subjected to powerful electrical shocks of an electrode to simulate lightning in the early atmosphere.
The scientists found that not only did these molecules combine in unique ways, but they started to create some of the same molecules produced by biological organisms – such as complex carbon-based molecule urea. Though this experiment was completed in 1953, more recent research has confirmed the results and have shown that even more complex molecules like RNA could have formed through natural reactions in Earth’s early atmosphere and oceans.
Of these, carbon is by far the most important. In fact, the entire field of Organic Chemistry is dedicated to studying the bonds between carbon and other atoms. The fact that complex, life-giving molecules can form simply by electrifying common atmospheric molecules is made possible by carbon – and its ability to form 4 covalent bonds to other molecules.
Carbon has the atomic number 6, meaning that it has 6 protons and 6 electrons. This means that carbon stores 2 electrons in the inner shell, and 4 electrons in the outer valence shell. Since the second electron shell of an atom can hold 8 electrons, carbon is constantly trying to fill up its outer valence shell by adding 4 more electrons. This means that carbon naturally forms 4 bonds with other atoms – whether that is 4 separate atoms or multiple bonds with a single atom. The valence shells of atoms like oxygen, nitrogen, or sulfur do not allow for this diversity.
In fact, the basis for all biological macromolecules is long carbon chains with attached hydrogens. We call these chains of carbon and hydrogen hydrocarbons. Hydrocarbons are naturally nonpolar and hydrophobic. However, by adding different atoms and functional groups to a carbon chain, it can take on a wide variety of other properties. For instance, saturated fat molecules consist of long hydrocarbon chains with a polar head group. These molecules store massive amounts of energy within the bonds, and they can be stored and manipulated within cells due to the polarity of their functional groups.
The fact that carbon can form 4 distinct bonds with other atoms also leads to the phenomenon of isomers. Isomers are molecules with the same elements, but a slightly different structure. Structural isomers contain all of the same atoms, but they are arranged in a slightly different order. Cis-trans isomers contain double-bonds. Since double bonds are rigid and cannot rotate, this leads to different forms of a molecule based on where the various functional groups are attached. If the functional groups fall on the same side of the double bond, the molecule is called the cis-isomer. If the functional groups are bonded on opposite sides of the double bond, they are known as trans-isomers. Lastly, enantiomers are molecules with the same atoms that are arranged like mirror images of each other when a carbon atom forms an asymmetric center. Enantiomers may be either L or D (L for levo or “left” and D for dextro or “right”).
The important thing about isomers is that they do not always function in similar ways. Consider the drug ibuprofen. The two enantiomers of ibuprofen have very different effects. One of the enantiomers is almost non-functional in humans, whereas the other arrangement makes the molecule 100-times more effective at treating inflammation. Given that most biological molecules have the potential to form many different isomers, biochemical processes have evolved to create very specific functional isomers. This is also why it is very difficult to design synthetic drugs that are as effective as their natural counterparts.
While carbon itself gives rise to the possibility of isomers, it is also very important what other molecules are attached to carbon in a biological molecule. In fact, there are several very common structures that get added to hydrocarbons that give molecules different properties. These are called functional groups – namely because they add specific functions to molecules that are needed for many complex biological reactions.
There are seven main functional groups used in biology that add specific properties to carbon chains. Hydroxyl groups (-OH) add polarity to a molecule, allowing it to interact with water and other polar molecules. Carbonyl groups (-C=O) allow a variety of bonds to be formed at the double-bonded oxygen molecule. Carboxyl groups (-COOH) form an acid in water, which allows the molecule to donate a hydrogen to complete a large variety of biochemical reactions.
Likewise, Amino groups (-NH2) act as a base because they can accept a hydrogen atom. Amino groups are crucial for forming proteins, as they allow for the bonds between amino acids to form into long chains that fold into functional proteins. Sulfhydryl groups (-SH) can form cross-links with other sulfhydryl groups – used by many protein molecules to create rigid 3-D formations. Methyl groups (-CH3) are not reactive, but they serve as tags on many biological molecules that help the cell recognize various substances.
Lastly, Phosphate groups (-OPO3-2) give carbon chains the ability to interact with water and release energy for other reactions. Phosphate groups allow molecules like ATP to provide energy to many different reactions that would not be possible otherwise. Phosphate is also critical in the formation of DNA and RNA, both of which have a sugar-phosphate backbone.