Cells and Cell Biochemistry

Basic Chemical Structures

  • The human body is composed of a hierarchy of structures, from the whole organism down to individual chemical elements.
  • The smallest independent living structure is the cell.
  • Atoms, the basic building blocks of matter, will be examined, as well as how they interact to form new compounds in the body.
  • Although cells are the smallest living structures, they are made of smaller components: atoms.
  • Atoms of the same type form elements.
  • A compound is formed when two or more elements chemically combine (e.g., salt, NaCl, is a combination of sodium and chlorine).
  • Shorthand conventions use one or two letters of the atom's English or Latin name to represent atoms, elements, and compounds.
  • An atom is the smallest unit of matter retaining the chemical properties of its element.
  • Atoms consist of neutrons, protons, and electrons.
  • The combination of neutrons and protons in the nucleus creates different types of atoms.
  • Oxygen, carbon, hydrogen, and nitrogen make up approximately 96% of the body’s mass (Jenkins & Tortora, 2012).
  • Atoms are mostly empty space, with a central nucleus containing protons and neutrons, surrounded by a cloud of electrons (Figure 1).
  • Protons carry a positive charge, neutrons carry no charge, and electrons carry a negative charge.
  • Normally, the number of protons and electrons are equal, resulting in a neutral charge; however, this can change, leading to a positive or negative charge.

Chemical Bonding

  • Atoms may combine through chemical reactions to produce new compounds with different appearances and behaviors from their parent atoms.
  • Electrons have different energies and reside in different electron shells at varying distances from the nucleus.
  • The chemical activity of an atom is largely determined by the electrons in its outer energy level (Seeley et al., 2007).
  • When elements combine, they are held together by chemical bonds.
  • Strong bonds result in compounds less likely to participate in chemical activity than those with weaker bonds.

Ionic Bonds

  • Occur when an atom 'donates' an electron to another atom.
  • The atom donating the electron acquires a positive charge (cation).
  • The atom receiving the electron acquires a negative charge (anion).
  • Example: Sodium chloride (NaCl), where sodium donates an electron to chlorine, resulting in Na^+ and Cl^-, which attract each other (Figure 2).

Covalent Bonds

  • Atoms are bound together by sharing electrons.
  • One or more pairs of electrons are shared between the outer energy levels of the atoms.
  • Covalent bonds are stronger and more stable than ionic bonds, making them important in physiology (Waugh & Grant, 2006; Thibodeau & Patton, 2007) (Figure 3).

Organic and Inorganic Chemistry

  • Organic chemistry: Compounds that always contain carbon and usually hydrogen and/or oxygen; may also contain nitrogen and/or sulphur. Elements are usually bound by covalent bonds. Main organic compounds are carbohydrates, lipids, proteins, and nucleic acids, making up 38-43% of body mass (Jenkins & Tortora, 2012).
  • Inorganic chemistry: Substances that generally do not contain carbon and usually have simple structures. Water is the most important and abundant, making up 55-60% of adult body mass (Tortora & Derrickson, 2009).

pH Scale

  • Ranges from 0-14 and indicates the H^+ ion concentration of a solution, denoting acidity or alkalinity.
  • Pure water has a pH of 7 (neutral).
  • Solutions with pH < 7 are acidic; pH > 7 are alkaline.
  • The scale is logarithmic; each change of 1 represents a tenfold change in acidity or alkalinity.
  • Normal blood pH range: 7.35-7.45 (slightly alkaline).
  • Other body fluids have different pH values (e.g., gastric juice: 1.2-3.0; bile: 7.6-8.6) (Tortora & Derrickson, 2009).
  • Bodily mechanisms maintain stable blood pH to preserve homeostasis.

General Cell Characteristics

  • Cells are very small (7.5 micrometres - 150 micrometres).
  • Micrometre: 1/1000th of a millimetre.
  • The cell is the smallest functional unit of the body.
  • Tissues are collections of cells of the same type.
  • Living cell characteristics:
    • Movement and responsiveness.
    • Complexity.
    • Cellular organisation.
    • Growth and metabolism.
    • Reproduction.
    • Heredity and evolution.
    • Death.
  • A cell consists of three main components: the cell membrane, cytoplasm, and nucleus (Thibodeau & Patton, 2007).

Cell Membrane

  • Forms the external boundary of the cell, providing shape and protection.
  • Keeps cell contents stable and distinct from the external environment.
  • Selectively permeable, regulating molecule movement based on:
    • Molecule size.
    • Lipid solubility.
    • Presence of carrier molecules.
    • Electrical charge.
  • Composed of two layers of phospholipid molecules (phospholipid bilayer) with embedded proteins and sugar molecules (fluid mosaic model; Jenkins & Tortora, 2012).
  • Lipid-soluble substances (oxygen, carbon dioxide, steroids) pass readily through the bilayer.
  • Lipids act as barriers to other substances; proteins allow selective transport of water-soluble substances.
  • Integral proteins extend into or through the bilayer, forming pores for small water-soluble molecules.
  • Transport occurs via diffusion, facilitated diffusion, osmosis, active transport, and phagocytosis (Tortora & Derrickson, 2009); active transport and phagocytosis require energy.
  • Contains signal receptors for cell communication and adhesion molecules for tissue formation (Tortora & Derrickson, 2009).
  • Example: Thyroxine release is initiated by thyroid stimulating hormone binding to thyroid follicular cells.

Cytoplasm

  • Specialized living material within the cell membrane, mainly water (cytosol).
  • Contains sugars, proteins, ions, molecules, and enzymes for cellular activity.
  • Suspended in the cytoplasm are organelles, which vary in number and type by cell type and cooperate to maintain cellular homeostasis (Tortora & Derrickson, 2009).

Endoplasmic Reticulum (ER)

  • A network of interconnecting membranous canals extending from the nuclear membrane (Waugh & Grant, 2006; Seeley et al., 2007).
  • Transports proteins and other substances.
  • Serves as storage for substances like Ca^{2+} (Thibodeau & Patton, 2007).
    • Smooth ER: Manufactures fatty acids and steroids (e.g., oestrogen and testosterone).
    • Rough ER: Has ribosomes attached; the site of protein synthesis.

Ribosomes

  • Attached to rough ER and outer nuclear membrane or free in cytoplasm.
  • Composed of ribosomal RNA (rRNA) and protein.
  • Synthesizes enzymes and other protein compounds from amino acids (Waugh & Grant, 2006).

Mitochondria

  • Powerhouses of the cell; site of ATP (adenosine triphosphate) production.
  • ATP is the major energy source for cellular chemical reactions.
  • More active cells contain more mitochondria.
  • Originate maternally (only in the ovum).
  • Contain small amounts of DNA (Seeley et al., 2007; Tortora & Derrickson, 2009).

Golgi Apparatus

  • Made of 3-20 membranous sacs stacked near the nucleus.
  • Collects, modifies, and packages proteins and lipids from the ER.
  • Packages are known as secretory vesicles or granules.
  • Examples: Mucus-secreting cells and in the pancreas.
  • Vesicles are stored or transported out of the cell as needed.
  • Exocytosis: Contents of vesicles are transported outside the cell (Seeley et al., 2007).

Lysosomes

  • Small sacs formed from the Golgi apparatus, containing up to 60 digestive enzymes (Tortora & Derrickson, 2009).
  • Digest bacteria and damaged/worn-out cell components.
  • Endocytosis: Bacteria are drawn into the cell, forming a vesicle.
  • Lysosomes fuse with vesicles to release digestive enzymes.
  • Autolysis: Self-digestion of the cell by digestive enzymes after injury, trauma or death.
  • Recycle cytoplasmic contents; the liver recycles ≈50% weekly (Tortora & Derrickson, 2009).

Peroxisomes

  • Similar to lysosomes; abundant in kidneys and liver.
  • Break down fatty acids, amino acids, and hydrogen peroxide (H2O2).
  • Detoxify H2O2 by breaking it down into water (H2O) and oxygen (O2).

Proteasomes

  • Break down free proteins within the cytosol and nucleus.
  • Degrade proteins resulting from cell metabolism after their function is complete.
  • Contribute to homeostasis at the cellular level.
  • A typical cell contains many thousands (Tortora & Derrickson, 2009).

Centrosome

  • Consists of two centrioles, cylindrical organelles involved in separating duplicated chromosomes during cell division.

Cilia

  • Hair-like extensions on the free surfaces of some cells.
  • Move together in a wavelike motion, creating movement.
  • Example: Ciliated cells lining the respiratory tract move mucus toward the throat.
  • Found in the female reproductive tract to propel the ovum towards the uterus.
  • Damage leads to impaired function; respiratory cilia in smokers are damaged and cannot remove mucus, leading to retained sputum and possible infection.

Flagella

  • A single long projection extending from the cell surface.
  • Similar in structure to cilia, but longer and less numerous.
  • Propels the whole cell forward when active.
  • Only example in human anatomy: sperm cell.

Nucleus

  • Contains genes that control every organelle in the cytoplasm and cell reproduction.

  • Surrounded by a membrane, enclosing nucleoplasm.

  • Contains nucleoli and genetic material.

    • Nucleoli: Composed of DNA and RNA, synthesising and storing RNA which acts as a template for protein assembly.
    • Genetic Material: Mainly DNA (the blueprint of the body).
    • Chromatin: Genetic material when the cell is not reproducing.
    • Chromosomes: Formed from chromatin before cell reproduction.

  • Red blood cells lose their nucleus during maturation and cannot maintain themselves, surviving ≈120 days; bone marrow constantly produces new red blood cells.

Cell Differentiation

  • All cells originate from a single parent cell and undergo specialization/differentiation according to function.
  • Structure and function change, but they retain a full copy of genetic material.
  • Some portions of the genetic code are active, others inactive, depending on the cell type (Seeley et al., 2007).

Cell Types

  • Various types are produced as a result of cell differentiation.
  • Differ in appearance and function but contain the same basic components.
  • Similar cells form tissues, and tissues combine to form organs.

Other Concepts

Apoptosis

  • Programmed cell death during normal processes (Seeley et al, 2007).
  • Important during fetal development, maintains constant cell numbers in tissues, destroys dangerous cells such as virus-infected or cancerous cells, (Seeley et al, 2007).

Viruses

  • Not truly living organisms because they lack metabolism and can't reproduce without a host cell.
  • Described as active when able to invade host cells and replicate, and inert when this ability is lost (Elliot & Elliot, 2009).
  • Made of nucleic acid (DNA or RNA) surrounded by a protein coat.
  • Viruses increase in number through replication, using the host cell’s nucleic acid and protein synthesis mechanisms.

Virion

  • A complete virus particle, not a cell.

Capsid

  • The protein coat of a virus that protects the genome during transmission.