Protein Chemistry

Lars Backman

• Editorial: De Gruyter
• Año: 2019
• ISBN:
  9783110566284
• Edición: 1
• Categoría: Biological Sciences
• Categoría: Biochemistry

This class-tested textbook gives an overview of the structure and functions of proteins and explains how amino acids form a defined structural entity with specific properties. The authors also introduce modern methods for purification and separation of proteins as well as different techniques for analyzing their structural and functional properties. A separate part of the book is devoted to enzymes and kinetics of enzymatic reactions.

1 The ballpark where it all occurs

The minimal functional unit of any living organism is the cell. Inside this confined space, the machinery required to produce everything necessary to survive (sustain life) is present. The presence of genetic material allows each cell to divide and thereby produce a progeny. Cells come in all shapes as well as sizes; some are extreme like some human neurons that can be close to a meter long but most are rather small, with diameters around 10 μm or less. The number of cells in an organism also differs, from a single cell in bacteria to some 10¹³–10¹⁴ cells in adult human (Figure 1.1).

Figure 1.1: Some typical cell shapes showing a bacteriophage, an endothelial cell, a nerve cell, a fibroblast and a red blood cell.

Irrespective of shape or size, all cells have certain common characteristics. They are all surrounded by a barrier, a membrane (sometimes called plasma membrane), separating the interior of the cell from the exterior. In the membrane, there are usually “doors” or “ports” that allow import as well as export of molecules and ions. Some molecules can diffuse through the membrane, whereas others require intricate systems to pass the barrier. There are receptors on the exterior surface of the membrane that accept external signals and transmit them across the membrane, to an internal acceptor, that in turn activates an intracellular process. Similar mechanisms are used to transmit signal the opposite way, from the inside of the cell to its outside. The transport across the membrane as well as all other processes occurring in the cell relay on proteins.

The number of proteins differs greatly from organism to organism. One of the smallest organisms, the parasite Mycoplasma genitalium (causes urethritis), contains 482 protein-coding genes, but only 382 of these genes are essential for survival. The genome of the endosymbiont Candidatus Carsonella ruddii is even smaller and codes for 182 proteins. This is in contrast to the human genome that consists of ca. 20,000 – 21,000 protein-coding genes that due to alternative splicing may give rise to many more proteins (more than one protein with different functions). The human genome also contains some 16,000–21,000 noncoding genes.

1.1 The tree of life

It is believed that life on Earth occurred about 3.7–4 billion years ago. In spite of tremendous efforts, the nature of the initial life is unknown, but it can be assumed that it was very simple. With time, functions were gained and evolved and life developed into something that constitutes the common ancestor to life of today.

This common ancestor gave rise to two branches in the tree of life. One branch that includes all bacteria and the other one that branched off with time into two separate branches: archaea and eukaryotes. During evolution, each of these three major groups have evolved and given rise to numerous organisms. It is estimated that there may be up to 10¹² different bacterial and archaeal species on Earth.

At the top of the tree of life, animals are located, thus being very recent inventions. For instance, the first human population diverged only about 300,000 years ago in Africa (Figure 1.2).

Figure 1.2: The tree of life.

1.2 Bacteria

Bacteria can be divided into three groups depending on their shape: spherical (coccus), rod-like (bacillus) and curved (vibrio, spirillum or spirochete). Although bacteria are unicellular, they may communicate with each other when forming biofilms through quorum sensing by using pheromones.

Bacteria are generally very small. The rod-shaped Escherichia coli is about 2 μm long and 0.5 μm in diameter. However, there are bacteria that are smaller and some are much larger.

Bacteria, like all other organisms, are surrounded by a membrane that controls the flow of molecules, prevents the loss of cell constituents and maintains proper intracellular milieu. The membrane is covered by a rigid cell wall or envelope, made of a peptidoglycan. In Gram-positive bacteria, the peptidoglycan is very thick and retains the Gram stain. The peptidoglycan layer in Gram-negative bacteria is very thin and therefore does not retain the Gram stain (Figure 1.3).

Figure 1.3: A typical bacterial cell.

The bacterial genome is localized to the nucleoid that often contains a single circular DNA molecule. The genome of E. coli consists of ca. 4,600,000 bp that under proper growth conditions are translated to proteins by more than 50,000 ribosomes. On the surface of the envelope, there are flagella and pili. Flagella allow the cell to swim in solution and pili provide adhesion points to the surface of animal cells.

1.3 Archaea

Archaea are the only organisms that inhabit extreme environments, such as hot springs, extremely acidic or alkaline waters. A well-studied archaeon is Halobacterium that thrives in extremely saline solution.

The shapes of archaea are similar to bacteria. Both archaea and bacteria move by means of flagella and divide by binary fission. The cell wall of archaea lacks peptidoglycan and the lipids of the membrane are different as they contain hydrocarbons rather than fatty acids that are linked to the glycerol moiety by ether bonds and not ester bonds as in bacterial and eukaryotic membrane lipids. It is also evident that metabolic pathways in archaea are distinct.

Based on genomic and biochemical studies, it is suggested that archaea are closer related to eukaryotes than to bacteria. In fact, it is not clear whether archaea and eukaryotes had a common ancestor or that the first eukaryote arose directly from an archaeon.

1.4 Eukaryotes

Eukaryotes are distinguished from bacteria and archaea by the presence of membrane-bounded organelles. In particular, the genetic material is contained within a distinct nucleus enclosed by a nuclear membrane or envelope. Eukaryotes can be classified as either animals, plants, fungi or protists. Any organism with a nucleus that are not animal, plant or fungus are classified as protists. Another classification separates eukaryotes into Excavate, Chromalveolata, Rhizaria, Archaeplastida and Unikonts. In this classification, animals and fungi, along with some protists, are placed into Unikonta and plants into Archaeplastida, whereas Excavate, Chromalveolata and Rhizaria include all other protists (Figure 1.4).

Figure 1.4: A general animal cell with cell organelles.

1.4.1 Nucleus

Most of the genetic material in a cell is contained in the cell nucleus. The nucleus is surrounded by the nuclear envelope that consists of the outer and inner nuclear membranes. In the envelope, there are nuclear pores that allow transport of molecules in both directions across the envelope. The nucleolus is a region of the genetic material that is particularly active and coding for ribosomal proteins and RNAs.

1.4.2 Endoplasmatic reticulum

The endoplasmatic reticulum or ER is an interconnected network of tubular membranes and flattened sacs, also called cisternae. The interior of the ER constitutes the lumen. As the ER is continuous with the outer nuclear membrane, the lumen and the volume between the two nuclear membranes are connected. The outer surface of the rough ER is studded with ribosomes, the site of protein synthesis. Proteins synthesized by ribosomes attached to the rough ER are generally destined for membranes or for export via the Golgi apparatus. Soluble proteins, present in the cytoplasm or in cell organelles, are often synthesized by free ribosomes.

The smooth ER has no ribosomes attached and is therefore not involved ...