Introduction to Biology through Information #5 [Cell Biology]

This time, we will delve into cells, the smallest structural units of life. Cells are separated from their environment by a cell membrane composed of a phospholipid bilayer. This allows the cell to isolate internal chemical reactions (metabolic networks) from the outside world and maintain a living state. Furthermore, cells only arise from other cells; from the perspective of the cell, biological inheritance, reproduction, and development are simply the repetition of cells dividing and fusing.

These characteristics of cells are closely related to life as an information carrier. If information is allowed to mix without restriction, it becomes disordered (or, to put it another way, entropy increases), so a boundary from the outside world or other information is necessary. It can be considered that the cell membrane is responsible for this. Cell division and inheritance are, of course, processes for transmitting information.

Homeostasis: Maintaining a living state

Let's dig a little deeper into cell metabolism and information. The maintenance of an internal state by a cell is called
homeostasis. In order to keep body temperature, pH, and chemical concentrations within a certain range, a series of information processing mechanisms work to receive external stimuli, read necessary genetic information from the genome, create proteins, and respond. While this is a different level of information than the sense in which genes transmit information, it can be considered that here, too, information—specifically, keeping essential variables for survival within a certain range—is being maintained over a long period.

Control of chemical reactions by enzymes

First, let's consider the control of chemical reactions to maintain homeostasis.
Enzymes are mainly composed of proteins and promote the production of specific products by binding to substrates and catalyzing chemical reactions. To maintain homeostasis, it is important to regulate intracellular metabolism and keep product concentrations constant. What is used here is feedback inhibition. In this mechanism, the final product of a metabolic pathway regulates the metabolic reaction by inhibiting the enzyme reaction at the initial stage of that pathway. In particular, when the initial enzyme is inhibited by binding to a site other than the active site, it is called allosteric inhibition. Generally, allosteric enzymes form complexes with multiple subunits and transition cooperatively between activated and inactivated states, thereby realizing reaction regulation through a non-linear relationship between substrate and reaction rate. It is interesting that this negative feedback, where a product suppresses its own production, is also used in control engineering, and that living organisms have implemented through evolution for hundreds of millions of years the same mechanism that humans would later devise.

Maintenance of homeostasis by cells and organelles

Living organisms are divided into prokaryotes and eukaryotes. The interior of a prokaryotic cell consists of a single compartment (it lacks membrane-bound organelles), and the DNA containing genetic information is localized in the cytoplasm as a nucleoid. On the other hand, eukaryotes, including us, have larger cells than prokaryotic cells and store genetic information within a nucleus covered by a nuclear membrane. Within the cytoplasm, there are organelles covered by biological membranes that perform diverse functions, creating a mechanism for specific enzyme reactions to proceed efficiently.

Below, we will explain the major organelles from the perspective of how they are involved in maintaining homeostasis, categorized by the maintenance of information itself, energy metabolism, and spatial control.

Maintenance of information

The nucleus is a structure covered by a double nuclear membrane that stores DNA. While the nucleus performs the replication of DNA, the medium of genetic information, and the transcription of mRNA, these pass through nuclear pores to function in the cytoplasm, so it can be said that the nucleus is an organ specialized for the retention and management of genetic information.

Ribosomes are composed of rRNA and ribosomal proteins. Based on the mRNA sequence transcribed in the nucleus, they link amino acids with peptide bonds for every triplet of bases (codon) to synthesize polypeptide chains. It can be said that they are protein synthesis machines that translate genetic information into physically functioning proteins.

Energy metabolism

Mitochondria perform catabolism, extracting chemical energy by oxidizing organic compounds and producing energy as ATP (adenosine triphosphate). When extracting energy from carbohydrates through cellular respiration, the glycolytic pathway first works in the cytoplasm, followed by the oxidation of pyruvate and substrate-level phosphorylation called the citric acid cycle in the mitochondrial matrix. Finally, mainly in the cristae of the mitochondria, the free energy released when electrons are transferred forms an electrochemical gradient across the membrane, and ATP synthesis occurs through oxidative phosphorylation using this. It is said that up to 34% of the energy stored in one molecule of glucose is converted into ATP by this process. ATP is also called the currency of energy within the cell, and because it is used in all metabolic reactions that consume energy essential for maintaining homeostasis, mitochondria are like power plants within the cell.

Chloroplasts are organelles for photosynthesis present in plant cells. They perform anabolism, receiving light energy with chlorophyll and converting it into chemical energy to synthesize organic compounds such as sugars. Photosynthesis is divided into the first stage, the light-dependent reaction, and the second stage, the Calvin cycle. In the light-dependent reaction that occurs in the thylakoid membrane of the chloroplast, light energy is converted into chemical energy such as ATP, and oxygen is released. In the Calvin cycle that occurs in the stroma of the chloroplast, reduction of carbon dioxide (carbon fixation) and synthesis of organic compounds (sugar synthesis) using chemical energy are performed. Since ATP production by catabolism in mitochondria is performed using the organic compounds synthesized here as materials, chloroplasts also contribute to energy production.

Spatial and environmental control

The endoplasmic reticulum is a network of membrane structures spreading through the cytoplasm, and there are two types: rough endoplasmic reticulum and smooth endoplasmic reticulum. The smooth endoplasmic reticulum performs lipid synthesis, such as steroid hormones, which are important for intercellular communication, and stores calcium, which is important for information transmission in muscle and nerve cells. The rough endoplasmic reticulum is responsible for sugar chain modification and transport of proteins synthesized by attached ribosomes. Also, the Golgi apparatus, which has a structure like stacked flat bags surrounded by membranes, also receives transport vesicles at the cis face, modifies and sorts proteins and lipids, and sends them from the trans face to the cell membrane and other organelles. As can be seen from the fact that blood types are determined by differences in sugar chains, chemical modifications such as sugar chain modification create further diversity in protein function (making information richer).

Lysosomes are mainly present in animal cells and contain hydrolytic enzymes inside to decompose unnecessary substances and waste products to extract nutrients, while also decomposing unnecessary proteins into reusable molecules. Vacuoles are mainly present in plant cells and fungi, and perform pH and pressure regulation and waste disposal. To reduce disorder in the cell and maintain order, it is important to destroy organs that no longer function and replace them with new ones. In that sense, waste disposal, along with pH and pressure regulation, works to maintain homeostasis.

The cytoskeleton is a proteinaceous fibrous structure that maintains the cell's shape and supports its internal structure. The cytoskeleton is divided into actin filaments, intermediate filaments, and microtubules. Intermediate filaments line the cell membrane and nuclear envelope. In addition to their structural support function, microtubules and actin filaments work with motor proteins to handle intracellular material transport. Furthermore, actin filaments contribute to the deformation and movement of the cell itself by forming contractile rings and lamellipodia. It can be said that these play a role in shaping the space within the cell for each protein and organelle to function properly, and in transporting them to those locations.

Information Replication and Cell Division

I mentioned in the previous article that DNA replication corresponds to copying information. However, even if information is replicated, if the cells that store it do not increase, single-celled organisms cannot multiply, and multicellular organisms cannot build their bodies. Therefore, after replicating chromosomal DNA, organisms must coordinate mitosis, which distributes the chromosomes into two and stores them in new nuclei, with cytokinesis, which separates the cytoplasm to include the new nuclei. However, when you think about it, in actual organisms, the cell growth rate changes depending on nutritional conditions, and if a mutation occurs in the DNA, it must be repaired before division, so these cell cycles must be precisely controlled.

The cell cycle is divided into four phases: the G1 phase, where cell growth and other cell-type-specific roles are performed; the S phase, where chromosomal DNA is replicated; the G2 phase, where preparations for cell division are made; and the M phase, where cell division occurs. Here, to ensure that somatic cell division occurs correctly, checkpoints are set, centered on molecules called cyclins and CDKs. This is as if exception handling, as shown in the Python-like pseudocode below, were implemented in the cell.

def cell_cycle():
    try:
        # G1/Sチェックポイント
        if not growth_signal_present():
            raise Exception("G1/Sチェックポイント失敗: 成長シグナルがありません")
        if not cell_has_grown_enough():
            raise Exception("G1/Sチェックポイント失敗: 細胞が十分に成長していません")

        # Sフェーズ：DNA複製
        replicate_dna()

        # G2/Mチェックポイント
        if not dna_replication_is_correct():
            raise Exception("G2/Mチェックポイント失敗: DNA複製エラーが見つかりました")

        # Mフェーズ：細胞分裂
        mitosis()

    except Exception as e:
        print(f"細胞周期が停止しました: {e}")
        # 修復またはアポトーシス(プログラムされた細胞死)
        repair_or_apoptosis()

In addition to somatic cell division, there is meiosis, which germ cells perform only once during the process of gamete formation. Organisms that usually have both sexes are diploid because they inherit one set of chromosomes from each parent, but if they were to form gametes through somatic cell division as is, the offspring would become tetraploid. Therefore, the gametes that produce the next generation become haploid through meiosis. The simplest way to produce haploid cells is to skip DNA replication and distribute the chromosomes, but in meiosis, after chromosomal DNA replication, the paternally derived homologous chromosomes and maternally derived homologous chromosomes pair up to become bivalent chromosomes, and the process goes through two stages: the homologous chromosomes separate, and then the sister chromatids within the homologous chromosomes separate.

Let's estimate how much genetic diversity occurs in gametes through meiosis. In this process, the separation of each homologous chromosome pair into gametes occurs independently, so in the case of humans with 23 homologous chromosomes, there are 2^23 combinations. Furthermore, it is said that recombination of paternally and maternally derived homologous chromosomes occurs through crossovers 1 to 3 times per chromosome pair between homologous chromosomes, which creates virtually infinite genetic diversity, and is the reason why even siblings have different genotypes and phenotypes.

References

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