Organic Compounds

This section is intended for those who do not have a background in biology. It describes the four types of organic compounds in cells: carbohydrates, lipids, nucleic acids, and proteins.

Carbohydrates

Carbohydrates store energy in cells. They are constructed from carbon, hydrogen, and oxygen (C H O). Types of carbohydrates include starch, cellulose, and sugars.

Figure 6‑1. Sucrose (above) is a disaccharide (combination) of two monosaccharides: glucose is the ring on the left and fructose is the ring on the right side of the sucrose molecule.

Carbohydrates form from any of four sugar molecules: glucose, fructose, ribose, and deoxyribose. These sugars include rings of four or five carbons and oxygen, plus an additional carbon group and several hydroxyls (OH) and hydrogen atoms (H). Cells construct them from simpler three-carbon sugars (trioses). Glucose bonded to fructose is sucrose or table sugar (Figure 6‑1). Glucose has a ring of 5 carbons and oxygen and one extra attached carbon group.

Sugars that form long chains are polysaccharides. Cellulose, which is stronger than steel on a per weight basis, is a polysaccharide. Cellulose is the primary molecule in plant cells walls and gives plants the strength to form structures such as trunks and branches. As with carbohydrates, lipids include carbon, hydrogen, and oxygen. Unlike carbohydrates, lipids have more than 2 hydrogens for every oxygen. Lipids include fats (animals), oils (plants), and waxes. Lipids form the structure of cell membranes and form the waxy cuticle on leaves.

Lipids

Lipids include a range of compounds that are insoluble in water. They include fats (animals), oils (plants), waxes, vitamins, glycerides, and phospholipids. Glycerol (Figure 6‑2) provides the backbone to glycerides and phospholipids. They are three-carbon chains with 3 hydroxyls (OH) and 5 hydrogens.

Figure 6‑2. Three-carbon glycerol. Carbon is black, oxygen is red, and hydrogen is white. Credit: Benjah-bmm27. Public domain.

Fatty acids are straight chains of carbon and hydrogen atoms with a carboxyl group (COOH) at one end. Triglycerides have a glycerol backbone (Figure 6‑2) and three fatty acid tails and are the main component of plant oils and animal fats. When the body has excess energy, it makes triglycerides by the dehydration reaction (Figure 6-3) and stores the triglycerides in fat cells. The oils in algae and plants have triglycerides. To use triglycerides for biofuel in biodiesel, chemists break the glycerol backbone off the fatty acid tails, and the tails become the long carbon chains that provide energy in biodiesel or jet fuel.

Figure 6-3. Formation of triglycerides in blood by the dehydration reaction. Credit: OpenStax. Used here per CC SA 3.0.

Figure 6‑4. Membrane phospholipid with hydrophilic head and hydrophobic tail. Credit: OpenStax. Used here per CC BY-SA 4.0

Phospholipids have a glycerol backbone, a phosphate group, and two fatty acid tails (Figure 6‑4). They are of great interest to origin of life scientists because they are the structural unit of cellular membranes and were probably the structural unit of the first protocells.

Figure 6‑5. Phospholipid bilayer. Credit: OpenStax. Used here per CC BY-SA 4.0

The tails of phospholips are hydrophobic (hate water) and the heads are hydrophilic (like water) so they arrange themselves such that the tails point away from water and toward other tails. Thus, they naturally form a phospholipid bilayer (Figure 6‑5).

Figure 6‑6. Cross-section of spherical phospholipid bilayer vesicle (liposome). Not to scale. The membrane (phospholipid bilayer) is thin in comparison to the internal volume. Credit: SuperManu. Used here per CC BY-SA 3.0

Phospholipid bilayers naturally form vesicles, which are bubble-like structures (Figure 6‑6) with water on the inside and outside of the bilayers. Fatty acid vesicles are ideally suited to be cellular membranes, holding proteins and other molecules in their walls, and governing the passage of nutrients, protons, and other cellular compounds into and out of cells (Figure 6‑7). The fact that molecules arrange themselves into vesicles that perform all the functions of cellular membranes is amazing. Scientists know that these fatty acid vesicles formed naturally in the primitive solar system environment because they are found on meteorites.

Figure 6‑7. Phospholipid bilayer vesicle section as a cellular membrane. Credit: OpenStax. Used here per CC BY-SA 4.0

Proteins

Figure 6‑8. Amino acid with amino group (N-terminus) on left, and a carboxyl group (C-terminus) on right. R is a variable group, which can include different atoms and structures. Peptide bond forms by connection of N-terminus and C-terminus in amino acids. Credit: Yassine Mrabet. Public domain.

Proteins form extremely complex structures in cells. Their shapes and other features enable them to act like little machines. They are constructed from amino acids (Figure 6‑8). In addition to C H and O, amino acids include nitrogen, N. Amino acids have an amino group at one end and a carboxyl group at the other end. Protein chains form when the amino group nitrogen from one amino acid binds to the carboxyl group on another amino acid in a peptide bond. These bonds are strong and enable proteins to maintain their shape and structure.

Proteins perform many functions. Keratin protein forms strands, and is in hair, skin, and fingernails. Collagen protein is in ligaments and tendons. Proteins also form enzymes, which aid in chemical reactions in the cell. Proteins help us move: actin and myosin contract muscles, participate in cell movement and cell division, cytokinesis, and cell signaling. Hemoglobins transport oxygen in the body through the blood vessels, and lipoproteins transport fat in blood vessels. Insulin lowers blood sugar by signaling cells to remove sugar from blood vessels. Antibodies protect the body from pathogens. Proteins can regulate genes by cutting them or turning on and off genes.

Proteins are composed of various sequences of twenty amino acids: alanine, arginine, asparagine, aspartic acid (aspartate), cysteine, glutamine, glutamic acid (glutamate), glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine. Peptide bonds between nitrogen and carbon atoms bind amino acids in long chains that become proteins. The way that sequences of amino acids are arranged in proteins gives the proteins the shapes that are tailored to specific tasks within cells.

Proteins are like little machines in cells, and their shape enables them to accomplish their function. Proteins, such as ATP synthase (Figure 6‑19), have a specific shape. The shape is specifically designed for a task. Many diseases are caused by proteins with the wrong shape (mutation), which means they cannot perform their task in the cell.

Although amino acids form naturally in the environment, proteins do not form naturally in the environment. Their structural formation in cells is guided by RNA. Could such a complex structure evolve over time in biological cells from relatively simple proteins in protocells? How many algae cells were on the early earth? Algae cells divide two or three times per day. During a certain number of divisions, there is a mutation in DNA. It takes a cell 20 seconds to build a protein. With such frequent repetition and periodic mutation, many designs could be tested, and complex protein structures would evolve through natural selection.

Nucleic acids

RNA and DNA are nucleic acids, which are constructed from nucleotides (Figure 6‑9), which include a phosphate group, sugar, and nitrogenous base. They include C H O N and Phosphorus, P.

Nucleic acids carry the information in the cell. DNA stores the information, and RNA carries the information to the protein assembly machinery. There are four types of nitrogenous bases in DNA: adenine, thymine, guanine, and cytosine. The order in which they are arranged in the DNA or RNA strand is a code that governs the assembly of proteins. They bind across the DNA double helix at the nitrogenous base and form a base pair.

Figure 6‑9. Nucleotide (bottom) and two base pairs in DNA double helix (above). Credit: OpenStax. Used here per CC BY 4.0.

DNA has two strands (Figure 6-10), and RNA has one strand. RNA can also act like a protein and form a shape that accomplishes a specific task. This is why many scientists think that life began as RNA. It can hold information, but it can also accomplish tasks, as with proteins. For many decades, scientists had no idea how sugars, let alone nucleotides, might have formed naturally in the environment. It was a real bottleneck in origin of life research; however, the next section describes how Donald Sutherland’s laboratory found a pathway toward sugar and nucleotide formation in the environment.

Figure 6‑10. DNA and RNA nucleic acids. Credit: Sponk. Used here per CC BY-SA 3.0

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