BIOLOGY FALL SEMESTER LECTURE NOTES TOPIC 1: CELL STRUCTURE AND EVOLUTION Understandings: ● Cell is the fundamental unit of life ● Cells have features that distinguish them from different taxonomic groups (as well as from other “life forms” like viruses. ● Structure of various cellular organelles ● Relationship between the structure and function of the cell ● Prokaryotic vs. Eukaryotic cells ● Origin of eukaryotic organelles ● Biological membranes Lecture 1: Cells and Cell Evolution ● What is a cell? ○ The smallest unit of life ○ Constitutes of basic building blocks of life ○ May be unicellular or multicellular ■ They may look simple (e.g., bacterial cells) or may be incredibly complicated (e.g., in unicellular organisms). ● Cell theory: ○ All living things are made up of cells. ○ Cells are the smallest unit of living things. ○ All cells arise from pre-existing cells. ○ Cells carry genetic material as DNA which is passed from parents to offspring. 1 ● ● Cells have multiple functions that link to the structure that they are formed in. ○ Structure of a cell is always related to its function. ○ Each cell performs a different function. E.g., transport, structural support etc. Cells vary hugely in size. ○ Viruses are the smallest ○ Largest cells are generally yeast. ■ Staining is used to look at and differentiate cells. ● Cells are prokaryotic or eukaryotic. ● Prokaryotic cells: ● ○ Lack a nucleus and membrane bound organelles ○ Belong to the kingdom Monera ○ Simple structure but ancient ○ Bacteria cells are prokaryotic ○ Reproduce asexually via binary fission Eukaryotic cells: ■ Have a nucleus that contains DNA ■ Compartmentalised by membrane bound organelles (each organelle has a specific role) 2 ■ More complex structure ■ Believed to have originated from prokaryotic cells (via endosymbiosis) ■ Eukaryotes can be divided into 4 distinct kingdoms: ● Plantae ● Animalia ● Fungi ● Protista Prokaryotic Cells Eukaryotic Cells DNA Circular & Naked Linear & bound to proteins Nucleus No Yes Organelles No Membrane-bound Ribosomes 70S 80S Reproduction Binary Fission Mitosis & Meiosis Chromosomes ● Haploid (single chromosome) Diploid ( Paired chromosomes) All living things are divided into 3 domains (or 5 kingdoms): ○ Archaea ■ Live in extreme (restricted) environments on earth believed to be similar to ancient environments (e.g., hot, salty, acidic etc.) ○ ■ Include methane-generating bacteria ■ Often called “extremophiles” Bacteria ■ Most diverse ■ Traditional bacteria (e.g., E. coli, Salmonella, Staphylococcus etc.) ■ Can be both beneficial and harmful to humans ■ Gram-positive and Gram-negative ■ Have different structural and biochemical differences - allows to differentiate disease-causing bacteria ○ Eukarya ■ ● Divided into 4 kingdoms: Plantae, Animalia, Fungi, Protista Archaea are more closely related to the Eukarya Classification of kingdoms 3 Monera Plantae Animalia Fungi Protista Nucleus No Yes Yes Yes Yes Unicellular/ Multicellular Unicellular (mostly) Multicellular (mostly) Multicellular (mostly) Unicellular and Multicellular Unicellular (mostly) Cell Wall Yes (peptidoglycan) Yes (cellulose) No Yes (chitin) Sometimes Nutrition Autotrophic/ Heterotrophic Autotrophic Heterotrophi c Heterotrophic Autotrophic / Heterotrophic Example Archaea Eubacteria Trees Flowers Insects Birds Yeasts Mushroom Protozoa Algae ● How did the earliest eukaryotic cells (“possessing a true nucleus” evolve? ○ ● Via the endosymbiosis theory Endosymbiosis Theory: ○ Endosymbiosis theory: states that some organelles were formed when an anaerobic prokaryote engulfed an aerobic prokaryote and formed a symbiotic relationship. ○ Mitochondria & chloroplast originated via this. ○ Steps: ■ Ancestor prokaryote which had several invaginations in the cytosol was present ■ These invaginations later formed certain cellular structures (like nuclear envelope, ER etc.) ■ A foreign prokaryote (e.g., an aerobic bacterium) was engulfed from the surrounding environment. ■ The uptake of the foreign aerobic bacterium allowed the cell to be able to do more functions. ■ This aerobic bacteria later became known as mitochondria. (Chloroplast was formed similarly). ■ The 2 main events that led to the formation of the very 1st eukaryotes were: 1) the uptake of the aerobic bacteria 2) uptake of the photosynthetic bacteria. ● Evidence for the endosymbiotic theory: ○ Evidence 1: Modern eukaryotes have a double membrane ■ 1st membrane is derived from the plasma membrane during the uptake (when 1 cell engulfed the other, it took that membrane and formed it around the other engulfed bacterium). ■ ○ 4 2nd membrane: belong to the host itself i.e., the ancestral prokaryote Evidence 2: Mitochondria & chloroplast have their own unique DNA ■ All the mitochondria and chloroplast have their own unique DNA which is different from the host DNA (its more “bacteria in character” than any other organism) ○ Evidence 3: Mitochondria & chloroplasts have their own ribosomes ■ They have their own ribosomes because they function more like a prokaryote. ■ They have their own DNA, Ribosomes because they need to survive so they make all the necessary proteins for function by themselves. ○ Evidence 4: Can replicate independently ■ Mitochondria & Chloroplasts have their own genes & can replicate independently of the nucleus via binary fission ● Bacteria cells: ○ ○ Features of Bacteria cells common to every prokaryotic cell: ■ No nucleus or membrane bound organelles ■ Circular naked DNA ■ 70S ribosomes Distinguishing features of bacteria: ■ Shape: Round, rod - like, spiral ■ Cell wall composition: Gram-positive (thick peptidoglycan layer) or Gram-negative (lipopolysaccharide layer) ● ■ Aerobic/Anaerobic: Anaerobic (obligate or facultative) or Aerobic ■ Nutrition: Autotrophic or heterotrophic Viruses: ○ Parasites ○ Not considered living because: ■ Not cellular ■ Cannot reproduce without a host ■ Have a protein coat that protects the genetic material inside but doesn't have any cell membrane or other organelles. 5 ■ Living things require energy. Outside of their host cell, viruses are inactive. They can only become active when they come in contact with the host cell. ○ Reproduce by invading a host and taking control of the host’s genome; getting the host to produce more virus particles. ○ Very small (nm in size) ○ Can only be viewed via an electron microscope ○ Diseases caused by viruses: AIDS, ebola, COVID, Herpes, Chickenpox, Influenza etc. ○ Bacteriophages: viruses that attack bacteria. ■ Phage therapy - a way to exploit virus-bacteria relationship for human benefit. ● Types of microscope to study cells: ○ Compound (Light) microscope: ■ ○ Transmission Electron Microscope (TEM): ■ ○ Shows a 3-D surface view Scanning Electron Microscope (SEM): ■ ○ Uses visible light to view the overall structure Shows the internal composition, 2-D image Stereo Microscope: ■ Looks at histology Lecture 2: Cell Structure ● 6 Plant vs Animal Cells (both are eukaryotic) Plant Cells Animal Cells Cell Wall Yes (cellulose) No Cell membrane Yes Yes Membrane-Bound organelles Yes Yes Plastids (chloroplast) Yes No Vacuole Yes (large, central) No (might have small temporary vacuoles) ● Plasmodesmata Yes No Centrioles No Yes (paired within centrosome) Cholesterol (in cell membrane) No Yes Shape Generally fixed, regular Amorphous Organelles - Structure and Function Organelles Nucleus Structure - Ribosomes - Endoplasmic Reticulum - Function Surrounded by a double membrane (nuclear envelope) Nuclear pores present in nuclear membrane Contain inner region called nucleolus - Two subunits made of RNA & protein 70S in prokaryotes & 80S in eukaryotes - System of membranes that connects the nucleus & plasma membrane. Can be ‘rough ER’ (studded with ribosomes) or ‘smooth ER’ (no ribosomes). - - - - Lysosomes Golgi 7 - - Stores DNA (genetic material) as chromatin which become visible as chromosomes during cell division. Nucleolus is the site of synthesis of rRNA Site of translation (polypeptide synthesis) Exported to the cytoplasm from the nucleolus. In cytoplasm: associated with mRNA & are involved in manufacture of proteins. rRER: allows translation of proteins destined for storage in vesicles sER: utilised primarily for lipid synthesis (including the cholesterols & phospholipids for membrane synthesis & repair) sER: enzymes also detoxify lipid-soluble drugs Membrane bound structures containing hydrolytic enzymes - Hydrolytic enzymes breakdown macromolecules. Inside has different pH to the rest of the cell which optimises the action of contained enzymes Flattened membrane sacs that - Involved in sorting, storing, Apparatus are associated with the ER and the cell membrane Mitochondrion - - modification & export of secretory products Materials are received by the cis face and undergoes changes as it passes from one membrane sac to another; eventually proteins & materials are released from the trans-face enclosed in vesicles. Double membrane structure (outer & inner membrane) Inner membrane folded into cristae Intermembrane space Mitochondrial matrix: space inside inner membrane Have their own DNA - Site of aerobic respiration Enzyme complexes involved in respiration are attached to inner membranes. Cytoskeleton - Made up of microfilaments, microtubules & intermediate filaments - Provides internal structure Involved in movement of organelles, chromosomes during cell division, orientation of wall fibres & mechanical support. Cell Walls - External outer covering made of cellulose - Provides support & mechanical strength ● Biological Membranes: ○ Regulate the transport of materials in and out of the cells by being selective ○ Are made up of phospholipids ○ Is semi-permeable ○ ■ Lipophilic, gases, small uncharged particles have high permeability ■ Charged particles, glucose, organic molecules have low permeability ■ Water moves through aquaporin channels Bilayer is held together by weak hydrophobic interactions between the phospholipid tails ○ Outer layer of the bilayer is hydrophilic (water-loving) while the inner layer is hydrophobic (water–hating) 8 ○ The lipid bilayer contains various proteins that sit on either side of the membrane or pass right through. ■ Membrane proteins accelerate the movement of substances across the membranes. ■ Can be either channel proteins (faster rate of transport) or carrier proteins (slower rate of transport) ○ Phospholipid Structure: ■ Hydrophilic (polar) head forming the outside of the outside of the membrane ■ 2 Hydrophobic (non-polar) fatty acid tails facing the inner side of the membrane ○ ○ ● Phospholipid bilayer components: ■ Phospholipids ■ Proteins (channel or carrier proteins) ■ Carbohydrates ■ Cholesterol Movement across the membrane occurs by: ■ Passive transport (no energy required) ■ Active transport (require expenditure of energy in form of ATP) ■ Facilitated diffusion How do the membranes become selective? ○ They become selective when they allow different molecules to pass through using facilitated diffusion. This is done through either protein channels or protein carriers. ○ Channel proteins: ■ Contain a pore via which ions move from one side of the membrane to other ○ ■ Ion-selective and may be gated ■ Only move molecules along a concentration gradient ■ Faster rate of transport than carrier proteins Carrier Proteins: ■ Bind a solute and undergo a conformational change to transport molecules across the membrane 9 ● ■ Only bind specific molecules via enzyme-substrate interaction ■ Move molecules against the concentration gradient in presence of ATP ■ Slower rate of transport than channel proteins Passive Transport: ○ Passive transport: movement of materials along a concentration gradient (high → low concentration) ○ Does not require ATP ○ 3 main types: ■ Simple diffusion: movement of small lipophilic molecules ■ Osmosis: movement of water molecules dependent on solute concentrations ■ Facilitated diffusion: movement of large charged molecules via membrane proteins ● Active transport ○ Active transport: uses ATP to move molecules from low concentration → high concentration ○ Active can be either primary or secondary ○ Primary Active transport: Uses direct energy to mediate transport ○ Secondary active transport: involves coupling the molecule with another to moving along an electrochemical gradient ● ■ Symport: movement of solutes in the same direction ■ Antiport: movement of 2 solutes in different directions Sodium-potassium Pump - primary active transport 1) 3 sodium ions move to intracellular sites on the sodium-potassium pump 2) A phosphate group is transferred to the pump via ATP hydrolysis 3) Pump undergoes a conformational change, translocating sodium across the membrane 4) The conformational change exposes 2 potassium binding sites on the extracellular surface of the pump 10 5) Phosphate group is released which returns the pump to the original conformation 6) This translocates potassium across the membrane completing the ion exchange 11
