2.12
Chemistry of the Cell
Cells are the basic building blocks of living organisms. They are composed mostly of water, organic molecules, and inorganic ions.
Water makes up around 70% of the cell. This aqueous environment in the cytoplasm is essential for the cell’s structure and for many of the reactions that occur within it.
Water is a highly polar molecule, so it will interact with other polar molecules and ions in the cell but not with the nonpolar ones.
The hydrophilic environment of the cytoplasm promotes the formation of proteins’ three-dimensional structures, with nonpolar amino acids at the core and polar ones at the surface.
In the case of membrane formation, polar head groups of phospholipids interact with water. In contrast, the nonpolar tails interact with each other creating a hydrophobic barrier to the outside of the cell.
The pH of biological fluids in the cell and its compartments is precisely buffered. The pH of the cytoplasm is around 7.2 and is regulated by molecules such as phosphate ions.
In contrast, the pH in the lysosomes, specialized cellular compartments, is around 5. This is because lysosomes contain enzymes that function optimally in acidic environments.
Organic molecules in the cell include carbohydrates, proteins, lipids, and nucleotides. All of these various macromolecules have a variety of roles.
Carbohydrates are a primary source of energy to power various metabolic processes; however, the cell can break down proteins and lipids for fuel as well.
Proteins can be enzymes that catalyze reactions, or they can contribute to cell structure.
Lipids are a significant component of cell membranes. Additionally, these macromolecules can covalently bond to each other to form conjugates such as glycoproteins and glycolipids, often found in cell membranes.
Nucleotides serve as the genetic material and also associate with proteins to form nucleoproteins that tightly package the DNA in a cell. The nucleotide ATP is also the source of energy for many cellular processes.
Inorganic ions critical to cell function include sodium, potassium, magnesium, calcium, phosphate, and chloride. Although these ions constitute less than 1% of the cell mass, they have diverse roles within the cell.
For example, ions such as calcium are used to relay biological signals throughout a cell, while magnesium is essential for many enzymes’ catalytic activity.
The cell is chemically composed of water, organic molecules and inorganic ions.
Water
The polarity of the water molecule and its resulting hydrogen bonding makes water a unique substance with special properties that are intimately tied to the processes of life. Life originally evolved in an aqueous environment, and most of an organism’s cellular chemistry and metabolism occur inside the aqueous contents of the cell’s cytoplasm. Special properties of water are its high heat capacity and heat of vaporization, its ability to dissolve polar molecules, its cohesive and adhesive properties, and its dissociation into ions that leads to the basis of pH. Understanding these characteristics of water helps to elucidate its importance in maintaining life.
One of water’s important properties is that it is a polar molecule: the hydrogen and oxygen within water molecules (H2O) form polar covalent bonds. While there is no net charge to a water molecule, water's polarity creates a slightly positive charge on hydrogen and a slightly negative charge on oxygen, contributing to water’s properties of attraction. Water generates charges because oxygen is more electronegative than hydrogen, making it more likely that a shared electron would be near the oxygen nucleus than the hydrogen nucleus, thus generating the partial negative charge near the oxygen.
As a result of water’s polarity, each water molecule attracts other water molecules because of the opposite charges between water molecules, forming hydrogen bonds. Water also attracts or is attracted to other polar molecules and ions. A polar substance that interacts readily with or dissolves in water is hydrophilic. In contrast, nonpolar molecules such as oils and fats do not interact well with water. These nonpolar compounds are hydrophobic.
Organic molecules
Proteins, carbohydrates, nucleic acids, and lipids are the four major classes of biological macromolecules—large molecules necessary for life that are built from smaller organic molecules. Macromolecules are composed of single units scientists call monomers that are joined by covalent bonds to form larger polymers. The polymer is more than the sum of its parts: it acquires new characteristics and leads to an osmotic pressure that is much lower than that formed by its ingredients. This is an important advantage in maintaining cellular osmotic conditions. A monomer joins with another monomer with water molecule release, leading to a covalent bond forming. Scientists call these dehydration or condensation reactions. When polymers break down into smaller units (monomers), they use a water molecule for each bond broken by these reactions. Such reactions are hydrolysis reactions. Dehydration and hydrolysis reactions are similar for all macromolecules, but each monomer and polymer reaction is specific to its class. Dehydration reactions typically require an investment of energy for new bond formation, while hydrolysis reactions typically release energy by breaking bonds.
Carbohydrates Carbohydrates are a group of macromolecules that are a vital energy source for the cell and provide structural support to plant cells, fungi, and all of the arthropods that include lobsters, crabs, shrimp, insects, and spiders. Carbohydrates can be classified into monosaccharides, disaccharides, and polysaccharides. Glucose storage, in the form of polymers like starch or glycogen, makes it slightly less accessible for metabolism; however, this prevents it from leaking out of the cell or creating a high osmotic pressure that could cause the cell to uptake excessive water.
Proteins Proteins are a class of macromolecules that perform a diverse range of functions for the cell. They help in metabolism by acting as enzymes, carriers, or hormones and provide structural support. The building blocks of proteins are amino acids.
Lipids Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, waxes, phospholipids, and steroids. Fats are a stored form of energy and are also known as triacylglycerols or triglycerides. Cholesterol is a type of steroid and is an important constituent of the plasma membrane, where it helps to maintain the membrane's fluid nature.
Nucleic acids Nucleic acids are molecules composed of nucleotides that direct cellular activities such as cell division and protein synthesis. There are two types of nucleic acids: DNA and RNA. DNA carries the cell's genetic blueprint and passes it on from parents to offspring. RNA is involved in protein synthesis and its regulation.
Inorganic ions
Inorganic ions constitute less than 1% of the cell mass but are critical to cell function. Those found in a cell include sodium, potassium, magnesium, calcium, phosphate, and chloride.
This text has been adapted from Openstax, Biology 2e, Unit 1: The Chemistry of Life.
Cells are the basic building blocks of living organisms. They are composed mostly of water, organic molecules, and inorganic ions.
Water makes up around 70% of the cell. This aqueous environment in the cytoplasm is essential for the cell’s structure and for many of the reactions that occur within it.
Water is a highly polar molecule, so it will interact with other polar molecules and ions in the cell but not with the nonpolar ones.
The hydrophilic environment of the cytoplasm promotes the formation of proteins’ three-dimensional structures, with nonpolar amino acids at the core and polar ones at the surface.
In the case of membrane formation, polar head groups of phospholipids interact with water. In contrast, the nonpolar tails interact with each other creating a hydrophobic barrier to the outside of the cell.
The pH of biological fluids in the cell and its compartments is precisely buffered. The pH of the cytoplasm is around 7.2 and is regulated by molecules such as phosphate ions.
In contrast, the pH in the lysosomes, specialized cellular compartments, is around 5. This is because lysosomes contain enzymes that function optimally in acidic environments.
Organic molecules in the cell include carbohydrates, proteins, lipids, and nucleotides. All of these various macromolecules have a variety of roles.
Carbohydrates are a primary source of energy to power various metabolic processes; however, the cell can break down proteins and lipids for fuel as well.
Proteins can be enzymes that catalyze reactions, or they can contribute to cell structure.
Lipids are a significant component of cell membranes. Additionally, these macromolecules can covalently bond to each other to form conjugates such as glycoproteins and glycolipids, often found in cell membranes.
Nucleotides serve as the genetic material and also associate with proteins to form nucleoproteins that tightly package the DNA in a cell. The nucleotide ATP is also the source of energy for many cellular processes.
Inorganic ions critical to cell function include sodium, potassium, magnesium, calcium, phosphate, and chloride. Although these ions constitute less than 1% of the cell mass, they have diverse roles within the cell.
For example, ions such as calcium are used to relay biological signals throughout a cell, while magnesium is essential for many enzymes’ catalytic activity.
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