INTRODUCTION TO BIOCHEMISTRY AND THE CELL

Foundations of Biochemistry

• Biochemistry is defined as the scientific study of chemical processes within and relating to living organisms. It involves the exploration of the composition and structure of living cells, as well as the various reactions and processes that occur within those cells.

• Molecular scale components are essential to this field. A molecule is defined as a group of two or more atoms held together by chemical bonds. It represents the smallest basic unit of a pure substance that retains the specific physical and chemical traits of that unique substance.

• Chemical bonds consist of an enduring attraction between atoms, ions, or molecules that facilitates the formation of chemical compounds. There are several primary types of bonding mechanisms:

  • Ionic bonding: This involves the complete transfer of an electron from one atom to another (for example, from a sodium atom ($Na$) to a chlorine atom ($Cl$)).

  • Covalent bonding: This occurs when atoms share electrons to achieve stability.

  • Metallic bonding: In this state, ions are surrounded by a sea of free electrons.

  • Molecular bonding: This is characterized by a weak electrical attraction that binds molecules together.

Classification of Chemical Compounds

• Inorganic Molecules: These refer to chemical structures that typically do not contain both carbon and hydrogen atoms together. Common examples include:

  • Water: This is the most prevalent inorganic liquid on Earth; it is critical for supporting cell functions and general body chemistry.

  • Salts: These are ionic compounds that dissociate into charged particles ($ions$) when placed in water.

  • Acids and Bases: These substances are responsible for controlling the $pH$ balance of a system by either releasing or accepting hydrogen ions ($H^+$).

  • Simple Gases: These are basic molecules containing single elements or simple carbon forms that lack carbon-hydrogen chains. Specific examples explicitly mentioned include carbon dioxide ($CO^2$), ammonia ($NH^2$), and oxygen ($O^2$).

• Organic Molecules or Biomolecules: These are carbon-based chemical structures that typically contain carbon-hydrogen ($C-H$) bonds. They serve as the structural and functional foundation of all known life. Biomolecules are organic molecules produced by living organisms which are essential for life.

Comprehensive Comparison of Major Biomolecules

• Carbohydrates:

  • Monomers: Monosaccharides.

  • Primary Bonding: Joined by glycosidic bonds.

  • Elemental Composition: Carbon ($C$), Hydrogen ($H$), and Oxygen ($O$).

  • Functions: Serve as short-term energy sources, structural components, and reserve food storage.

  • Named Examples: Maltose, Glucose, Starch, Glycogen, and Cellulose.

• Proteins:

  • Monomers: Amino acids.

  • Primary Bonding: Joined by peptide bonds.

  • Elemental Composition: Carbon ($C$), Hydrogen ($H$), Oxygen ($O$), Nitrogen ($N$), and Sulfur ($S$).

  • Functions: Function as enzymes, structural materials, facilitators of movement, components of defense/immunity, hormones, and oxygen carriers.

  • Named Examples: Insulin, Collagen, and Myoglobin.

• Nucleic Acids:

  • Monomers: Nucleotides.

  • Primary Bonding: Joined by phosphodiester bonds.

  • Elemental Composition: Carbon ($C$), Hydrogen ($H$), Oxygen ($O$), Nitrogen ($N$), and Phosphorus ($P$).

  • Functions: Responsible for storing genetic information.

  • Named Examples: $DNA$ and $RNA$.

• Lipids:

  • Monomers: Fatty acids and glycerol.

  • Primary Bonding: Joined by ester bonds.

  • Elemental Composition: Carbon ($C$), Hydrogen ($H$), and Oxygen ($O$).

  • Functions: Serve as long-term energy sources, provide insulation, act as biological membrane components, and function as hormones.

  • Named Examples: Oils, Fats, and Waxes.

The Cell: Units and Functions

• The cell is established as the basic unit of life. While different cells may possess varying structures and specializations, they share several common characteristics.

• There are four primary categories of cell function:

  • Cell metabolism and energy use: This includes Anabolism (processes that build up molecules) and Catabolism (processes that break down molecules).

  • Synthesis of molecules: The creation of necessary chemical components.

  • Communication: The sending and receiving of signals.

  • Reproduction and inheritance: The process of cell regeneration.

Cellular Anatomy: Membranes and Genetic Structures

• Plasma Membrane:

  • This is the outermost layer of the cell, acting as a boundary that separates intracellular substances from extracellular substances.

  • It is selectively permeable, meaning it determines what moves into and out of the cell.

  • Composition: Primarily proteins and lipids with a small amount of carbohydrates.

  • Structure: It is organized as a phospholipid bilayer.

  • Properties: Components are divided into hydrophobic (water-repelling) and hydrophilic (water-loving) regions. Nonpolar regions reside in the interior, while polar regions face the surfaces.

  • Additional Features: Includes cholesterol, membrane channels, receptor molecules, and carbohydrate chains (often seen as part of the external surface).

• Nucleus:

  • A large, membrane-bound structure typically located near the cell center.

  • It is the location of Deoxyribonucleic Acid ($DNA$), which determines the structural and functional characteristics of the cell.

  • A gene is a specific region of a $DNA$ molecule that specifies an $RNA$ molecule.

  • The nucleus houses chromosomes, which are thread-like structures composed of $DNA$ and proteins carrying genetic information.

  • Humans possess $46$ chromosomes, with $23$ inherited from each parent.

  • Trisomy $21$ is a specific genetic condition characterized by an individual having an extra chromosome.

• Nucleoli:

  • These are diffuse bodies found inside the nucleus that lack a surrounding membrane.

  • Ribosomal Ribonucleic Acid ($rRNA$) is produced within the nucleolus to form large ribosomal units.

Cytoplasmic Elements and Organelles

• Cytoplasm: The material located outside of the nucleus but inside the plasma membrane.

• Ribosomes:

  • The primary site of protein synthesis.

  • They can be found attached to the Endoplasmic Reticulum or floating as Free Ribosomes.

• Endoplasmic Reticulum ($ER$):

  • A series of membranes forming sacs and tubules extending from the outer nuclear membrane into the cytoplasm.

  • Rough Endoplasmic Reticulum: Studded with ribosomes; serves as the site for protein production and modification.

  • Smooth Endoplasmic Reticulum: Lacks ribosomes; facilitates lipid synthesis and detoxification.

• Golgi Apparatus:

  • Acting as the packaging and distribution center, it modifies, packages, and distributes proteins and lipids from the $ER$.

  • It modifies proteins by attaching lipids or carbohydrates to them.

  • Materials are packaged into secretory vesicles that pinch off from the margins (specifically from the cisternae, moving from the cis face to the trans face and lumen).

  • The Golgi also participates in the formation of lysosomes.

• Secretory Vesicles:

  • Small, membrane-bound sacs that transport and store materials. They fuse with the cell membrane to release contents to the exterior.

• Lysosomes:

  • Membrane-bound vesicles containing hydrolytic enzymes used as intracellular digestive systems.

  • Autophagy is the specific process where lysosomes digest non-functional cell organelles.

• Peroxisomes:

  • Small membrane-bound vesicles containing enzymes to break down fatty acids and amino acids.

  • A byproduct of these reactions is hydrogen peroxide ($H_2O_2$), which can be toxic to the cell and is further broken down here.

• Proteasomes:

  • Large protein complexes with enzymes dedicated to digesting specific proteins.

• Mitochondria:

  • Referred to as the "powerhouse of the cell," they are the major energy source and the primary site for Adenosine Triphosphate ($ATP$) synthesis.

Cytoskeleton and Surface Structures

• The cytoskeleton consists of proteins that support the cell, anchor organelles, and allow for shape changes.

  • Centrosomes: The center of microtubule formation.

  • Microtubules: Hollow structures that support cytoplasm, assist in cell division, and form components of cilia and flagella. They influence the distribution of actin and intermediate filaments.

• Surface Projections:

  • Cilia: Slender protuberances that project from the cell body and move substances over the surface.

  • Flagella: Lash-like appendages that are longer than cilia; used to propel cells, such as sperm.

  • Microvilli: Much smaller than cilia and non-motile; they function to increase surface area to aid in absorption.

Distinctive Differences Between Prokaryotic and Eukaryotic Cells

• Biologic Distribution:

  • Eukaryotic: Found in animals and protozoa.

  • Prokaryotic: Found in all bacteria.

• Nuclear Membrane:

  • Eukaryotic: Present.

  • Prokaryotic: Absent.

• Membranous Structures:

  • Eukaryotic: Present.

  • Prokaryotic: Generally absent except for mesosomes and photosynthetic membranes.

• Microtubules:

  • Eukaryotic: Present.

  • Prokaryotic: Absent.

• Chromosomes:

  • Eukaryotic: Composed of both $DNA$ and protein.

  • Prokaryotic: Composed of $DNA$ alone.

• Flagella or Cilia:

  • Eukaryotic: When present, possess a complex structure.

  • Prokaryotic: When present, possess a simple structure; do not have cilia.

• Cell Wall:

  • Eukaryotic: Absent in animal cells.

  • Prokaryotic: Present with a complex chemical composition.

• Photosynthesis:

  • Eukaryotic: Absent (specifically in the context of the comparison chart provided).

  • Prokaryotic: Present within cyanobacteria.