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Unit 1: Cell Biology (Cell Introduction (Emergent Properties (In…

- - - - The cell theory states that:
        
        All living things are composed of cells (or cell products)
        
        The cell is the smallest unit of life
        
        Cells only arise from pre-existing cells
    - - Striated muscle fibres
        
        Muscle cells fuse to form fibres that may be very long (>300mm)
        
        Consequently, they have multiple nuclei despite being surrounded by a single, continuous plasma membrane
        
        Challenges the idea that cells always function as autonomous units
      - Aseptate fungal hyphae
        
        Fungi may have filamentous structures called hyphae, which are separated into cells by internal walls called septa
        
        Some fungi are not partitioned by septa and hence have a continuous cytoplasm along the length of the hyphae
        
        Challenges the idea that living structures are composed of discrete cells
      - Giant Algae
        
        Challenges the idea that larger organisms are always made of many microscopic cells
        
        Certain species of unicellular algae may grow to very large sizes (e.g. Acetabularia may exceed 7 cm in length)
  - - - Metabolism – Living things undertake essential chemical reactions
      - Reproduction – Living things produce offspring, either sexually or asexually
      - Sensitivity – Living things are responsive to internal and external stimuli
      - Homeostasis – Living things maintain a stable internal environment
      - Excretion – Living things exhibit the removal of waste products
      - Nutrition – Living things exchange materials and gases with the environment
      - Growth – Living things can move and change shape or size
    - - Scenedesmus (autotroph)
        
        Scenedesmus exchange gases and other essential materials via diffusion (nutrition / excretion)
        
        Chlorophyll pigments allow organic molecules to be produced via photosynthesis (metabolism)
        
        Daughter cells form as non-motile autospores via the internal asexual division of the parent cell (reproduction)
        
        Scenedesmus may exist as unicells or form colonies for protection (responsiveness)
      - Paramecium (heterotroph)
        
        Paramecia are surrounded by small hairs called cilia which allow it to move (responsiveness)
        
        Paramecia engulf food via a specialised membranous feeding groove called a cytostome (nutrition)
        
        Food particles are enclosed within small vacuoles that contain enzymes for digestion (metabolism)
        
        Solid wastes are removed via an anal pore, while liquid wastes are pumped out via contractile vacoules (excretion)
        
        Essential gases enter (e.g. O2) and exit (e.g. CO2) the cell via diffusion (homeostasis)
        
        Paramecia divide asexually (fission) although horizontal gene transfer can occur via conjugation (reproduction)
  - - - The rate of metabolism of a cell is a function of its mass / volume (larger cells need more energy to sustain essential functions)
      - The rate of material exchange is a function of its surface area (large membrane surface equates to more material movement)
    - - If metabolic rate exceeds the rate of exchange of vital materials and wastes (low SA:Vol ratio), the cell will eventually die
      - Hence growing cells tend to divide and remain small in order to maintain a high SA:Vol ratio suitable for survival
  - - - Mag = Image Size / Actual Size
    - - Actual Size = Image Size / Magnification
    - - Light microscopes use visible light and a combination of lenses to magnify images of mounted specimens
        
        Living specimens can be viewed in their natural colour, although stains may be applied to resolve specific structures
      - When attempting to draw microscopic structures, the following conventions should be followed:
        
        A title should be included to identify the specimen (e.g. name of organism, tissue or cell)
        
        A magnification or scale should be included to indicate relative size
        
        Identifiable structures should be clearly labelled (drawings should only reflect what is seen, not idealised versions)
  - - - Cells may be grouped together to form tissues
      - Organs are then formed from the functional grouping of multiple tissues
      - Organs that interact may form organ systems capable of carrying out specific body functions
      - Organ systems collectively carry out the life functions of the complete organism
    - - Muscle (Cell)
        
        Cardic (Tissue)
        
        Heart (Organ)
        
        Vascular (System)
        
        Human (Organism)
  - - - The process during development whereby newly formed cells become more specialized and distinct from one another as they mature.
      - All cells of an organism share an identical genome – each cell contains the entire set of genetic instructions for that organism
      - The activation of different instructions (genes) within a given cell by chemical signals will cause it to differentiate
    - - Within the nucleus of a eukaryotic cell, DNA is packaged with proteins to form chromatin
        
        Active genes are usually packaged in an expanded form called euchromatin that is accessible to transcriptional machinery
        
        Inactive genes are typically packaged in a more condensed form called heterochromatin (saves space, not transcribed)
      - Differentiated cells will have different regions of DNA packaged as euchromatin and heterochromatin according to their specific function
  - - - Self Renewal – They can continuously divide and replicate
      - Potency – They have the capacity to differentiate into specialised cell types
    - - There are four main types of stem cells present at various stages of human development:
        
        Totipotent – Can form any cell type, as well as extra-embryonic (placental) tissue (e.g. zygote)
        
        Pluripotent – Can form any cell type (e.g. embryonic stem cells)
        
        Multipotent – Can differentiate into a number of closely related cell types (e.g. haematopoeitic adult stem cells)
        
        Unipotent – Can not differentiate, but are capable of self renewal (e.g. progenitor cells, muscle stem cells)
    - - Necessary for embryonic development as they are an undifferentiated cell source from which all other cell types may be derived
      - Cell types that are not capable of self-renewal (e.g. amitotic nerve tissues) are considered to be non-stem cells
      - As these tissues cannot be regenerated or replaced, stem cells have become a viable therapeutic option when these tissues become damaged
  - - - The use of biochemical solutions to trigger the differentiation of stem cells into the desired cell type
      - Surgical implantation of cells into the patient’s own tissue
      - Suppression of host immune system to prevent rejection of cells (if stem cells are from foreign source)
      - Careful monitoring of new cells to ensure they do not become cancerous
    - - Stem cells can be derived from one of three sources:
        
        Embryos (may be specially created by therapeutic cloning)
        
        Umbilical cord blood or placenta of a new-born baby
        
        Certain adult tissues like the bone marrow (cells are not pluripotent)
      - The ethical considerations associated with the therapeutic use of stem cells will depend on the source
        
        Using multipotent adult tissue may be effective for certain conditions, but is limited in its scope of application
        
        Stem cells derived from umbilical cord blood need to be stored and preserved at cost, raising issues of availability and access
        
        The greatest yield of pluripotent stem cells comes from embryos, but requires the destruction of a potential living organism
      - Artificial Stem Cell Techniques
        
        Stem cells can be artificially generated via nuclear transfer or nuclear reprogramming
        
        Somatic Cell Nuclear Transfer (SCNT)
        
        Involves the creation of embryonic clones by fusing a diploid nucleus with an enucleated egg cell (therapeutic cloning)
        
        More embryos are created by this process than needed, raising ethical concerns about the exigency of excess embryos
        
        Advantages: Indistinguishable from embryo-derived cells
        
        Disadvantages: Involves ex vivo creation of embryos
        
        Nuclear Reprogramming
        
        Induce a change in the gene expression profile of a cell in order to transform it into a different cell type (transdifferentiation)
        
        Involves the use of oncogenic retroviruses and transgenes, increasing the risk of health consequences (i.e. cancer)
        
        Disadvantages: Uses oncogenic retroviruses and transgenes
        
        Advantages: Stem cells autologous to adult donor
  - - - Use lenses to bend light and magnify images by a factor of roughly 100-fold
      - Can be used to view living specimens in natural colour
      - Chemical dyes and fluorescent labelling may be applied to resolve specific structures
    - - Use electromagnets to focus electrons resulting in significantly greater magnifications and resolutions
      - Can be used to view dead specimens in monochrome (although false colour rendering may be applied)
      - Transmission electron microscopes (TEM) pass electrons through specimen to generate a cross-section
      - Scanning electron microscopes (SEM) scatter electrons over a surface to differentiate depth and map in 3D
- - - - Eubacteria – traditional bacteria including most known pathogenic forms (e.g. E. coli, S. aureus, etc.)
      - Archaebacteria – found in extreme environments like high temperatures, salt concentrations or pH (i.e. extremophiles)
    - - The circular DNA is copied in response to a replication signal
      - The two DNA loops attach to the membrane
      - The membrane elongates and pinches off (cytokinesis), forming two cells
    - - Cytoplasm – internal fluid component of the cell
      - Nucleoid – region of the cytoplasm where the DNA is located (DNA strand is circular and called a genophore)
      - Plasmids – autonomous circular DNA molecules that may be transferred between bacteria (horizontal gene transfer)
      - Ribosomes – complexes of RNA and protein that are responsible for polypeptide synthesis (prokaryote ribosome = 70S)
      - Cell membrane – Semi-permeable and selective barrier surrounding the cell
      - Cell wall – rigid outer covering made of peptidoglycan; maintains shape and prevents bursting (lysis)
      - Slime capsule – a thick polysaccharide layer used for protection against dessication (drying out) and phagocytosis
      - Flagella – Long, slender projections containing a motor protein that enables movement (singular: flagellum)
      - Pili – Hair-like extensions that enable adherence to surfaces (attachment pili) or mediate bacterial conjugation (sex pili)
  - - - Protista – unicellular organisms; or multicellular organisms without specialised tissue
      - Fungi – have a cell wall made of chitin and obtain nutrition via heterotrophic absorption
      - Plantae – have a cell wall made of cellulose and obtain nutrition autotrophically (via photosynthesis)
      - Animalia – no cell wall and obtain nutrition via heterotrophic ingestion
  - - - Ribocomes
        
        Structure: Two subunits made of RNA and protein; larger in eukaryotes (80S) than prokaryotes (70S)
        
        Function: Site of polypeptide synthesis (called translation)
      - Cytoskeleton
        
        Structure: A filamentous scaffolding within the cytoplasm (fluid portion of the cytoplasm is the cytosol)
        
        Function: Provides internal structure and mediates intracellular transport (less developed in prokaryotes)
      - Plasma membrane
        
        Structure: Phospholipid bilayer embedded with proteins (not an organelle per se, but a vital structure)
        
        Function: Sem-permeable and selective barrier surrounding the cell
    - - Nucleus
        
        Structure: Double membrane structure with pores; contains an inner region called a nucleolus
        
        Function: Stores genetic material (DNA) as chromatin; nucleolus is site of ribosome assembly
      - Endoplasmic Reticulum
        
        Structure: A membrane network that may be bare (smooth ER) or studded with ribosomes (rough ER)
        
        Function: Transports materials between organelles (smooth ER = lipids ; rough ER = proteins)
      - Golgi Apparatus
        
        Structure: An assembly of vesicles and folded membranes located near the cell membrane
        
        Function: Involved in the sorting, storing, modification and export of secretory products
      - Mitochondrion
        
        Structure: Double membrane structure, inner membrane highly folded into internal cristae
        
        Function: Site of aerobic respiration (ATP production)
      - Peroxisome
        
        Structure: Membranous sac containing a variety of catabolic enzymes
        
        Function: Catalyses breakdown of toxic substances (e.g. H2O2) and other metabolites
      - Centrosome
        
        Structure: Microtubule organising centre (contains paired centrioles in animal cells but not plant cells)
        
        Function: Radiating microtubules form spindle fibres and contribute to cell division (mitosis / meiosis)
    - - Chloroplast
        
        Structure: Double membrane structure with internal stacks of membranous discs (thylakoids)
        
        Function: Site of photosynthesis – manufactured organic molecules are stored in various plastids
      - Vacuole (large and central)
        
        Structure: Fluid-filled internal cavity surrounded by a membrane (tonoplast)
        
        Function: Maintains hydrostatic pressure (animal cells may have small, temporary vacuoles)
      - Cell Wall
        
        Structure: External outer covering made of cellulose (not an organelle, but a vital structure)
        
        Function: Provides support and mechanical strength; prevents excess water uptake
    - - Lysosome
        
        Structure: Membranous sacs filled with hydrolytic enzymes
        
        Function: Breakdown / hydrolysis of macromolecules (presence in plant cells is subject to debate)
  - - - DNA (composition and structure)
      - Organelles (types present and relative sizes)
      - Reproduction (mode differs according to chromosome structure)
      - Average size (exceptions may exist)
    - - DNA
        
        Naked
        
        Circular
        
        Usually no introns
      - Organelles
        
        No nucleus
        
        No membrane-bound
        
        70S ribosomes
      - Reproduction
        
        Binary fission
        
        Single chromosome (haploid)
      - Average Size
        
        Smaller (~1-5 µm)
    - - DNA
        
        Bound to protein
        
        Linear
        
        Usually no introns
      - Organelles
        
        Has a nucleus
        
        Membrane-bound
        
        80S ribosomes
      - Reproduction
        
        Mitosis and Meiosis
        
        Chromosomes paired (diploid or more)
      - Average Size
        
        Larger (~10-100 µm)
  - - - Mitochondria – Cells with many mitochondria typically undertake energy-consuming processes (e.g. neurons, muscle cells)
      - ER – Cells with extensive ER networks undertake secretory activities (e.g. plasma cells, exocrine gland cells)
      - Lysosomes – Cells rich in lysosomes tend to undertake digestive processes (e.g. phagocytes)
      - Chloroplasts – Cells with chloroplasts undergo photosynthesis (e.g. plant leaf tissue but not root tissue)
  - - - Eyepiece – The point through which the magnified image is observed (contains ocular lens)
      - Focus Mechanism – Responsible for resolving the image (may include both fine and coarse focus adjustments)
      - Revolving Nosepiece – Rotating device that allows for selection of objective lens
      - Objective Lens – Magnifies image of specimen (in conjunction with ocular lens)
      - Stage – Platform on which specimen is positioned (specimen is usually affixed to a glass slide)
      - Stage Clips – Holds specimen in place (some mechanical stages can be moved to reposition slide while viewing)
      - Iris Diaphragm – Regulates the intensity of light that is projected onto the slide
      - Light Source – Either external (redirected by mirrors) or internal (light bulb within the microscope base)
  - - - DNA stored within a nucleus
      - Larger ribosomes (80S in size)
      - A variety of membrane-bound organelles (e.g. mitochondria, ER, golgi apparatus)
    - - Presence or absence of specific sub-cellular structures
      - Composition of the plasma membrane
  - - - Lack a nucleus and membrane-bound organelles
      - Have circular DNA that is naked (not bound to protein)
      - Have smaller ribosomes (70S)
    - - Shape – Round (coccus), rod-like (bacillus), comma-shaped (vibrio) or spiral (spirilla / spirochete)
      - Cell wall composition – Gram-positive (thick peptidoglycan layer) or Gram-negative (lipopolysaccharide layer)
      - Gaseous requirements – Anaerobic (obligate or facultative) or aerobic
      - Nutritional patterns – Autotrophic (photosynthetic or chemosynthetic) or heterotrophic