MCB 150 Lecture Notes: Technology Intro, Domains of Life, and Carbohydrates

Technology Intro and Domains of Life

• Announcements:

  • Lecture 3 pre-lecture assignment due 1:00 PM Monday.

  • Lecture 3 post-lecture available after class on Monday and due at 1:00 PM on Tuesday.

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Linnaean System of Classification

• Originated in the 1700s by Carl Linnaeus, a Swedish botanist, physician, and zoologist. It's based on observable physical characteristics to categorize organisms.

• Key questions: Does the organism produce its own food (autotroph vs. heterotroph)? Is the organism capable of movement (motile vs. sessile)?

• Employed the Genus: species scheme, which is a binomial nomenclature system still fundamental in biological taxonomy today. The genus is capitalized and the species is in lowercase.

• Initially, only 2 kingdoms (animals & plants) were recognized, but this division proved insufficient to classify fungi, microbes, and other diverse life forms accurately, highlighting the need for more inclusive classification systems.

Advancements in Technology and Cell Examination

• Technological advancements, such as microscopy, enabled the examination of individual cell contents and structures at higher resolutions, leading to critical discoveries about cell types.

• Two basic types of cells were identified:

  • Eukaryotes: Cells containing a "kernel" (nucleus) enclosed by a nuclear membrane, along with other membrane-bound organelles. These are generally more complex cells.

  • Prokaryotes: Cells lacking a "kernel" (nucleus) or other membrane-bound organelles; their genetic material is typically found in a nucleoid region. These are generally smaller and less complex than eukaryotic cells.

Prokaryotic Cell

• Components:

  • Nucleoid: Typically consists of a single, circular chromosome, which is not enclosed by a membrane. It contains most of the cell’s genetic material.

  • Cytoplasmic membrane: Performs functions similar to internal membranes in eukaryotes, such as regulating the transport of materials and participating in metabolic processes.

  • Cell wall: Usually present and provides structural support and protection. Composition varies widely among different types of prokaryotes (e.g., peptidoglycan in bacteria).

Eukaryotic Cell

• Components:

  • Lysosome: Contains enzymes for breaking down cellular waste and debris.

  • Cytoplasmic membrane: Outer boundary of the cell, regulating the passage of substances in and out.

  • Golgi Apparatus: Modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles.

  • Endoplasmic reticulum: Network of membranes involved in the synthesis, modification, and transport of cellular materials (smooth and rough ER).

  • Mitochondrion: Powerhouse of the cell, responsible for ATP production through cellular respiration. Contains its own DNA.

  • Nucleus: Contains the cell's genetic material in the form of multiple linear chromosomes.

• Animal cell: Lacks cell walls and chloroplasts, which are present in plant cells. Plant cells also often contain a large central vacuole.

• The inside of the cell is separated into distinct compartments called organelles (representative, not exhaustive list), each performing specific functions to maintain cell viability and function.

Superkingdoms

• Until 1977, organisms were classified into 2 superkingdoms:

  • Prokaryotes: Characterized by the absence of a nuclear membrane and membrane-bound organelles. Included bacteria and archaea.

  • Eukaryotes: Characterized by the presence of a nuclear membrane and membrane-bound organelles, encompassing protists, fungi, plants, and animals.

• Physical/structural characteristics are useful for crude classifications, but understanding evolutionary relationships requires examining genomes and biochemical systems to reveal deeper connections.

Carl Woese and Ribosomal RNA

• In 1977, Carl Woese and co-workers revolutionized biological classification by comparing sequences in different species of small subunit ribosomal RNAs (SSU rRNA), which are essential for protein synthesis. This work revealed fundamental differences among prokaryotes.

Domains of Life

• Prokaryotes are actually two distinct groups of organisms:

  • (EU)BACTERIA: True bacteria like E. coli, found in diverse environments, including soil, water, and living organisms. They play roles in nutrient cycling and pathogenesis.

  • ARCHAEA: "Ancient" prokaryotes, often inhabiting extreme environments that resemble early Earth, such as high temperatures, pressures, acids, salts, and gases. They possess unique metabolic pathways.

• Archaeal rRNA sequences are more closely related to eukaryotic rRNA sequences than to bacterial rRNA sequences, indicating a closer evolutionary relationship between archaea and eukaryotes.

Revised Tree of Life

• Revised to include 3 DOMAINS rather than 2 superkingdoms:

  • Bacteria: One of the three domains of life, comprising prokaryotic organisms with distinct biochemical characteristics.

  • Archaea: Another domain of prokaryotic life, often found in extreme environments and more closely related to eukaryotes in certain molecular processes.

  • Eukarya: The domain encompassing all eukaryotic organisms, including protists, fungi, plants, and animals, characterized by cells with a nucleus and membrane-bound organelles.

• Despite physically resembling bacteria (both are prokaryotes), archaea are more similar to humans in most molecular processes than they are to E. coli, underscoring the importance of molecular analysis in understanding evolutionary relationships.

Comparison of Bacteria, Archaea, and Eukarya

Cell Theory

• No two species are identical structurally and biochemically, yet all are made of one or more cells, which serve as the fundamental units of life.

• Life requires a structural compartment separate from the external environment, enabling molecules to perform unique functions within a relatively constant internal environment (homeostasis).

• This "living compartment" is a cell, capable of carrying out all essential life processes.

Basic Tenets of Cell Theory

• Cells are the fundamental units of life, capable of independent existence and reproduction.

• All organisms are composed of one or more cells, emphasizing the universality of cellular organization.

• All cells come from pre-existing cells through cell division, rejecting spontaneous generation and highlighting the continuity of life.

Cell Size

• As cell size increases, the surface area-to-volume ratio decreases, which impacts the cell’s ability to efficiently exchange nutrients and waste with its environment.

Relative Size, Scale, and Resolution

• Resolution: The ability to distinguish the separation between two objects that are very close to each other. Higher resolution allows for finer details to be observed.

• Resolving power of light microscopes is 0.2 microns (\mum; 10^{-6} m), which limits the ability to see structures smaller than this using standard light microscopy.

Visualizing Sub-Cellular Objects

• Electron microscopy has a resolution of 0.5 nm (10^{-9} m), allowing for the visualization of subcellular objects and structures at a much higher level of detail than light microscopy.

• Denser material affects electrons more, causing greater scattering and resulting in darker areas in the image. This contrast helps in distinguishing different cellular components.

Cell Structure Overview

Approaching a Cell from the Outside

• Some cells (plants, most prokaryotes) have a relatively rigid cell wall providing shape and protection, mainly against mechanical stress and osmotic lysis.

• Every cell is surrounded by a Plasma Membrane:

  • Allows cells to maintain a constant internal environment (homeostasis) by regulating the movement of substances in and out.

  • Acts as a selectively permeable barrier, controlling which molecules can enter or exit the cell.

  • Is an interface for cells where information is received from adjacent cells and extracellular signals, allowing for cell communication and response to environmental cues.

  • Has molecules that are responsible for binding and adhering to adjacent cells, contributing to tissue formation and stability.

Macromolecules

• What composes the organelles, membranes, genomes, etc. of the cells we’ve examined? Understanding the macromolecules provides insight into the structure and function of cellular components.

• 4 major types of large biological polymers (macromolecules):

  • Proteins: Polymers of amino acids that perform a wide array of functions, including catalyzing reactions, transporting molecules, and providing structural support.

  • Nucleic Acids: Polymers of nucleotides (DNA and RNA) that store and transmit genetic information.

  • Carbohydrates (or Polysaccharides) [sugars]: Polymers of monosaccharides that serve as energy sources and structural components.

  • Lipids [fats]: Diverse group of hydrophobic molecules that include fats, oils, phospholipids, and steroids. They play roles in energy storage, membrane structure, and signaling.

Chemical Composition of a Bacterial Cell

• Approximate chemical composition of a bacterial cell:

Macromolecules (Polymers) and Monomers

• Macromolecules (Polymers) are made up of Monomers, which are the building blocks of biological polymers:

  • Proteins are composed of Amino Acids, linked together by peptide bonds.

  • Nucleic Acids are composed of Nucleotides, linked together by phosphodiester bonds to form DNA or RNA.

  • Polysaccharides are composed of Monosaccharides, linked together by glycosidic bonds.

  • (Membrane) Lipids are composed of Fatty Acids (and usually Glycerol), linked together by ester bonds in triglycerides.

Condensation and Hydrolysis

• Condensation (or Dehydration Synthesis):

  • Monomer in, water out: A chemical reaction where two molecules or subunits combine to form a larger molecule, with the simultaneous loss of a water molecule.

• Hydrolysis:

  • Water in, monomer out: A chemical reaction in which a molecule is cleaved into two or more smaller molecules by the addition of water. This breaks the bond between monomers.

Carbohydrates

Polysaccharides (Carbohydrates)

• Polysaccharides are made from condensation reactions bringing together monosaccharides, forming glycosidic bonds:

  • Uses: Storing energy, providing structural support (like in plant cell walls and exoskeletons), and playing a role in cell identification and recognition processes on the cell surface.

• “Carbohydrate” can refer either to the complex sugars (polysaccharides) or the simple sugars (monosaccharides), which are the basic building blocks.

  • General formula of a carbohydrate: Cn(H2O)_n with a backbone of H–C–OH, where n is the number of carbon atoms.

Standard Ring Structure of a Monosaccharide (Glucose)

• Standard Ring Structure of a Monosaccharide (Glucose)

Standard Conventions for Atoms in Ring Structures

• Within the ring itself, if you're not explicitly told otherwise, the atom is a Carbon (C). Carbons are implied at the corners of the ring structure.

• Within the ring itself, if an atom is not a Carbon, it needs to be specified (e.g., oxygen in the ring for most common monosaccharides).

• Above or below the ring, Carbons need to be specified; otherwise, it's assumed to be another type of atom (e.g., oxygen in a hydroxyl group).

• Above or below the ring, any atom that is not specifically identified is assumed to be a Hydrogen (H). These are often not drawn for simplicity but are understood to be present.

Monosaccharides

• Monosaccharides are typically found with 3, 5, or 6 carbons, categorized as trioses, pentoses, and hexoses, respectively.

• Glucose (C6H{12}O_6) is a hexose sugar and a primary source of energy in cells.

Circularization of Glucose

• α-glucose vs. β-glucose, which differ based on the orientation of the hydroxyl group on carbon 1. This difference impacts the structure and properties of resulting polysaccharides.

Isomers

• Some monosaccharides have identical formulas but different structures (called isomers), leading to variations in their chemical properties and biological functions:

  • Hexoses: 6-carbon sugars (C6H{12}O_6)

    • Glucose: The most common monosaccharide used for energy.

    • Galactose: A component of lactose, milk sugar.

    • Fructose: Found in fruits and honey; notably sweeter than glucose.

Other Monosaccharides

• Other monosaccharides have similar (but not identical) formulas, similar structures, and related functions, often playing specific roles in nucleic acids and energy transfer:

  • Deoxyribose: A 5-carbon sugar that is a component of DNA, lacking an oxygen atom on the 2' carbon compared to ribose.

  • Ribose: A 5-carbon sugar that is a component of RNA and is involved in energy transfer molecules like ATP.

Pentoses

• Monosaccharides are typically found with 3, 5, or 6 carbons such as Pentoses: 5-carbon sugars (C5H{10}O_5)

  • Ribose: A crucial component of RNA.

  • Ribulose: Involved in the Calvin cycle for carbon fixation in photosynthesis.

Disaccharide Formation

• Two monosaccharides can be brought together to form a very simple polysaccharide called a disaccharide via a covalent bond called a glycosidic linkage. This involves a condensation reaction.

• Note that the glucose molecule contributing its C1 is an alpha glucose, making the resulting glycosidic linkage an α-1,4 glycosidic linkage. The naming indicates the carbon atoms involved and the stereochemistry of the linkage.

• Cellobiose (not shown) is a disaccharide of beta glucose and another glucose connected via a β-1,4 glycosidic linkage. The β linkage results in different structural properties.

Examples of Disaccharides

• In maltose and cellobiose, both monosaccharides are glucose, but not all disaccharides have to be the same monomers:

  • Lactose (milk sugar) is a disaccharide of glucose and galactose, joined by a β-1,4-glycosidic bond.

  • Sucrose (table sugar) is a disaccharide of glucose and fructose, linked by an α-1,β-2-glycosidic bond.

Chemical Formula

• The chemical formula for a disaccharide of hexose sugars is C{12}H{22}O[11}

• Why does this differ from the general formula of Cn(H2O)_n? Because a molecule of water is removed during the formation of the glycosidic bond.

Terminology

• Some common terminology:

  • One monomer is a monosaccharide, the simplest form of a carbohydrate.

  • Two monomers are a disaccharide, formed by a glycosidic bond between two monosaccharides.

  • Several monomers are called an oligosaccharide (oligo = several), typically containing 3-10 monosaccharides.

  • Hundreds or thousands of monomers are a polysaccharide (poly = many), serving as energy storage or structural components.

Carbohydrate Modifications

• Carbohydrates can be modified, enhancing their roles in biological systems:

  • Linkage of oligosaccharides to other macromolecules: When covalently linked to membrane proteins or lipids (glycoproteins and glycolipids), carbohydrates act as identification and recognition molecules (chemical markers), as in blood typing. These modifications mediate cell-cell interactions.

  • Addition of chemical groups:

    • Fructose-1,6-bisphosphate: An intermediate in glycolysis.

    • Glucosamine: A component of cartilage.

    • Galactosamine: Found in certain glycoproteins and glycolipids.

Functions of Polysaccharides

• Polysaccharides serve as chemical sources of energy or structural compounds:

  • Cellulose: Provides structural support in plant cell walls.

  • Starches: Energy storage in plants.

  • Glycogen: Energy storage in animals.

Cellulose

• The most abundant carbon-containing (i.e., organic) compound on Earth, providing structural support to plant cell walls.

• Found in plant cell walls, providing rigidity and mechanical strength.

• Linear, unbranched polymer of glucose:

  • monomers covalently linked by β-1,4 glycosidic linkages, forming long, straight chains.

  • linear polymers held together by hydrogen bonding with neighboring strands, resulting in a strong, fibrous structure.

Starches

• Found chiefly in seeds, fruits, tubers, roots, and stems of plants; energy storage, mainly as amylose and amylopectin.

• Helical, unbranched or loosely branched polymers of glucose:

  • monomers within chains covalently linked by α-1,4 glycosidic linkages, forming a helical structure.

  • chains branch by connecting with other chains by α-1,6 glycosidic linkages, allowing for compact storage and quick release of glucose.