Cells

Eukaryotic Cell Organelles

• Key organelles include the nucleus, endoplasmic reticulum (smooth and rough), Golgi apparatus, lysosomes, mitochondria, ribosomes, vacuoles, chloroplasts and cell walls.
• It is important to know the structure and function of these organelles.

Nucleus Structure and Function

• Key structures within the nucleus are the nuclear envelope, nuclear pores, nucleoplasm, chromosomes, and nucleolus.
• DNA replication and transcription occur in the nucleus.
• mRNA is created through transcription.
• The nucleolus is the site of rRNA production and ribosome assembly.
• The nucleus contains DNA, which is the genetic code for the cell.

Endoplasmic Reticulum (ER)

• There are two types: smooth ER (SER) and rough ER (RER).
• RER has ribosomes on its surface, while SER does not.
• RER is the site of protein synthesis due to the presence of ribosomes.
• SER synthesizes and stores lipids and carbohydrates.

Golgi Apparatus

• It is a folded membrane structure that modifies and packages molecules.
• Vesicles pinch off from the Golgi apparatus to transport modified molecules.
• Carbohydrates can be added to proteins to form glycoproteins.
• Involved in the production of secretory enzymes, transport and modification of lipids.
• Molecules are labeled with destinations by adding molecules that bind to receptors on target cells

Lysosomes

• They are bags of digestive enzymes involved in phagocytosis.
• Enzymes hydrolyze bacteria or viruses endocytosed by the cell
• Exocytosis releases the products outside the cell after digestion.

Mitochondria

• This is the site of aerobic respiration and ATP production.
• It has a double membrane: an outer membrane and a folded inner membrane forming cristae.
• Oxidative phosphorylation occurs in the inner membrane of the Mitochondria
• Mitochondria contain a loop of DNA similar to prokaryotic DNA, allowing them to code for respiratory enzymes.

Ribosomes

• Ribosomes are found in both prokaryotic and eukaryotic cells.
• Ribosomes are not membrane bound
• Eukaryotic cells contain larger 80S ribosomes, while prokaryotic cells, mitochondria, and chloroplasts have smaller 70S ribosomes.
• Ribosomes are the site of protein synthesis.

Vacuoles

• Vacuoles are found in plant cells, not animal cells.
• Surrounded by a single membrane called the tonoplast
• Vacuoles help maintain cell turgidity and provide support.
• They temporarily store sugars and amino acids.
• Pigments within vacuoles can color petals to attract pollinators.

Chloroplasts

• Chloroplasts are found in plants and are the site of photosynthesis.
• They are double-membrane organelles with thylakoid membranes that stack to form grana.
• Thylakoid membranes contain proteins and pigments like chlorophyll.
• Stroma surrounds the thylakoid membranes and contains enzymes for the light-independent reactions of photosynthesis.

Cell Walls

• Cell walls are found in plant and fungi cells, but not animal cells.
• They provide structural strength and prevent cell bursting due to osmosis.
• Cell walls are made of cellulose in plants and chitin in fungi.

Plasma Membrane

• Plasma membrane is found in all cells, and it controls what enters and exits the cell.
• Made of a phospholipid bilayer
• Membrane-bound organelles are also made of this phospholipid bilayer.

Prokaryotic Cells

• Prokaryotic cells are much smaller and lack membrane-bound organelles.
• They have 70S ribosomes and no nucleus; DNA is a single loop in the cytoplasm.
• Cell walls are made of murein.
• Additional loops of DNA called plasmids may be present.
• Some have a capsule to prevent desiccation and evade the immune system.
• Flagella may be present for movement.

Viruses

• Viruses are acellular and non-living.
• Structure includes genetic material, a capsid, and attachment proteins.
• Viruses replicate inside host cells, using the host cell's machinery to replicate their genetic material to produce more virions

Methods of Studying Cells

• Methods for studying cells have led to the discovery of internal cell structures.
• These methods include microscopy, cell fractionation, and ultracentrifugation.

Microscopy

• Magnification is how many times larger the image appears compared to the object.
• Resolution is the minimum distance between two objects to still view them separately.
• Optical microscopes use light, while electron microscopes use a beam of electrons.
• Resolution is determined by the wavelength of light in optical microscopes and the wavelength of the electron beam in electron microscopes.

Optical vs. Electron Microscopes

• Optical microscopes use a beam of light condensed by a lens.
• Electron microscopes use a beam of electrons condensed by electromagnets.
• Optical microscopes have poorer resolution due to the longer wavelength of light.
• Electron microscopes have higher resolving power because electrons have shorter wavelengths.
• Optical microscopes have lower magnification but can produce color images and view living samples.
• Electron microscopes produce black and white images and require samples to be in a vacuum, so living samples cannot be observed.

Transmission Electron Microscope (TEM)

• Requires extremely thin specimens.
• An electron beam is passed through the specimen; some parts absorb electrons and appear dark, while others appear lighter.
• TEM produces 2D images and allows for detailed observation of internal structures within small organelles.

Scanning Electron Microscope (SEM)

• Creates 3D images by beaming electrons onto the sample surface.
• Electrons are scattered differently depending on the surface contours.
• SEM does not require thin specimens.

Magnification Calculations

• The formula is IAM: Image size = Actual size x Magnification.
• It is important to ensure that image size and actual size are in the same units.

Eyepiece Graticule

• An eyepiece graticule is a scale on a glass disc inside the optical microscope used to measure specimens.
• The eyepiece graticule must be calibrated each time the objective lens is changed to determine the distance each division represents at the new magnification.

Cell Fractionation

• Used to isolate different organelles for further study.
• Cells are broken open in a cold, isotonic, and buffered solution.
  • Cold temperatures reduce enzyme activity.
  • Isotonic conditions prevent water movement into or out of organelles.
  • Buffered solutions prevent damage from acidity or alkalinity.
• There are two steps when performing Cell fractionation: homogenization and ultra centrifugation

Homogenization

• Method of breaking cells open; can be done using a blender.
• Breaks open the cells and releases the organelles without damaging them
• The solution must be cold isotonic and buffered
• It is important to filter the homogenate to remove large debris after breaking open the cells.

Ultracentrifugation

• Filtrate is spun at different speeds to separate organelles based on density.
• Centrifugal forces cause pellets to form at the bottom of the tube with the most dense organelles.
• The supernatant (liquid) is removed, and the process is repeated at increasing speeds.
• Nuclei are isolated first, followed by chloroplasts, mitochondria, lysosomes, ER, and ribosomes.

Cell Division

• Eukaryotic cells divide by mitosis or meiosis, prokaryotic cells replicate by binary fission.
• Viruses do not undergo cell division but replicate inside a host cell by injecting their genetic material which the host cell then uses to replicate the contents to produce more virions.

Cell Cycle

• Interphase, which includes G1, S, and G2 phases
• Mitosis (nuclear division)
• Cytokinesis (cytoplasmic division)

Interphase

• The longest cell cycle stage which includes all of G1, S & S2 stages
• Includes G1 (cell growth, organelle duplication), S (DNA replication), and G2 (further growth, preparation for mitosis, error checking).
• Error checking during the G2 phase will destroy the cell if there are errors.

Mitosis

• Consists of four key stages: prophase, metaphase, anaphase, and telophase (PMAT).
• There is only one round of division.
• Genetically identical diploid cells are created.
• Mitosis is used for growth and repair (e.g., clonal expansion of B cells).

Prophase

• Chromosomes condense and become visible.
• Centrioles move to opposite poles in animal cells, forming spindle fibers that attach to the centromeres and chromatids on the chromosomes.
• Plant cells have a spindle apparatus but lack centrioles.

Metaphase

• Chromosomes line up in single file along the equator.
• Spindle fibers attach to the centromere and chromatids.

Anaphase

• Spindle fibers retract, pulling on the centromere and chromatids.
• Centromeres divide, separating the chromatids, which are then called chromosomes, and pulled to opposite poles.
• This stage requires ATP from mitochondrial respiration.

Telophase

• Chromosomes are at each pole and become longer and thinner.
• Spindle fibers disintegrate, and the nucleus starts to reform.

Cytokinesis

• Cytoplasm divides to create two new genetically identical cells.

Mitotic Index

• Calculated by dividing the number of cells in mitosis by the total number of cells and multiplying by 100 (to get a percentage), which tells you how many cells are undergoing mitosis at any one time.

Prokaryotic Cell Division: Binary Fission

• Prokaryotic cells do not undergo mitosis.
• They reproduce via binary fission.
• The first step in binary fission is DNA replication:
  • Circular DNA and plasmids are replicated.
• The second step is cytoplasmic division:
  • Two daughter cells are formed.
  • Each daughter cell receives a single copy of the circular DNA.
  • The number of plasmids inherited can vary.

Viruses and Replication

• Viruses are non-living entities:
  • Thus, they do not undergo cell division.
• Viruses replicate by injecting their nucleic acid into a host cell.
  • The host cell then replicates the viral particles.

Plasma Membrane Structure: The Fluid Mosaic Model

• All cell and organelle membranes share the same basic structure.
• The structure is described by the fluid mosaic model:
  • Named because of the slight movement within the membrane.
  • Composed of various molecules:
    • Phospholipids.
    • Proteins.
    • Glycoproteins.
    • Glycolipids.

Phospholipid Bilayer

• The phospholipid bilayer forms the basic structure of the membrane.
• Phospholipids arrange themselves due to their amphipathic nature:
  • Hydrophilic heads:
    • Contain a negatively charged phosphate group.
    • Attracted to water.
  • Hydrophobic tails:
    • Repelled by water.
    • Can interact with lipids.
• Phospholipids orient with tails facing inward:
  • Heads face outward, interacting with water.

Cholesterol in the Membrane

• Cholesterol is present in some membranes.
• It restricts the lateral movement of other molecules.
• This reduces membrane fluidity at high temperatures:
  • Prevents leakage of water and dissolved ions.

Membrane Proteins: Peripheral and Integral

• Proteins are a major component of the membrane.
• They are embedded across the cell surface membrane.
• Peripheral proteins:
  • Located on the outer surface of the membrane.
  • Sometimes called extrinsic proteins.
  • Provide mechanical support.
  • Connect to proteins or lipids to form glycoproteins and glycolipids.
• Integral proteins:
  • Span the entire phospholipid bilayer.
  • Sometimes called intrinsic proteins.
• Carbohydrates bind to proteins and lipids to form glycoproteins and glycolipids:
  • Function in cell recognition and as receptors.

Function of Integral Membrane Proteins

• Integral proteins act as carrier proteins or protein channels.
• Protein channels:
  • Form water-filled tubes that allow water-soluble ions to diffuse across the membrane.
  • Selective, as channels only open in the presence of specific ions.
• Carrier proteins:
  • Bind to specific molecules.
  • Facilitate transport of larger molecules, like glucose and amino acids.
  • Binding causes the carrier protein to change shape.
  • The molecule is then released on the other side of the membrane.

Membrane Permeability

• Membranes are partially permeable.
• Only lipid-soluble substances and very small molecules can pass through by simple diffusion.
• Other molecules (water-soluble, polar, or large) require other transport mechanisms:
  • Facilitated diffusion.
  • Active transport.
  • Osmosis (for water).

Simple Diffusion

• Simple diffusion:
  • Net movement of molecules from an area of higher concentration to lower concentration.
  • Continues until equilibrium is reached.
  • Does not require ATP (passive process).
  • Driven by the kinetic energy of the molecules.
• Molecules must be lipid-soluble and small to diffuse across the membrane.

Facilitated Diffusion

• Facilitated diffusion:
  • Passive process (no ATP required).
  • Molecules move from higher to lower concentration.
  • Required for molecules that cannot directly diffuse through the phospholipids.
  • Occurs via protein channels or carrier proteins.
• Protein channels:
  • Water-filled tubes that allow water-soluble ions to diffuse through.
  • Selective, as channels only open in the presence of specific ions.
• Carrier proteins:
  • Bind to molecules like glucose.
  • Binding causes a change in the protein shape, allowing the molecule to be released on the other side.

Osmosis

• Osmosis:
  • Movement of water from an area of higher water potential to an area of lower water potential.
  • Occurs across a partially permeable membrane.
• Water potential:
  • The pressure created by water molecules.
  • Measured in kilopascals (kPa).
  • Represented by the symbol Ψ.
• Pure water has a water potential of zero (the highest possible value).
• Dissolving solutes in water reduces the water potential:
  • More solutes result in a more negative water potential.

Tonicity

• Isotonic:
  • The same water potential in the solution and the cell.
  • No net movement of water.
• Hypotonic:
  • The solution has a more positive (less negative) water potential than the cell.
  • Water moves into the cell.
• Hypertonic:
  • The solution has a more negative water potential than the cell.
  • Water moves out of the cell.

Effects of Tonicity on Animal Cells

• Isotonic solution:
  • No net water movement.
• Hypertonic solution:
  • Water moves out of the cell, causing it to shrivel (crenate).
• Hypotonic solution:
  • Water moves into the cell, potentially causing it to burst (lyse).

Active Transport

• Active transport:
  • Movement of substances from a lower concentration to a higher concentration.
  • Requires metabolic energy (ATP).
  • Involves carrier proteins.
• Process:
  • Molecule binds to a carrier protein with a complementary receptor shape.
  • ATP binds to the carrier protein.
  • ATP is hydrolyzed into ADP and inorganic phosphate (Pi).
  • Hydrolysis causes the carrier protein to change shape.
  • The molecule is released on the other side of the membrane.
  • Phosphate ion is released.
  • Carrier protein returns to its original shape.
  • The process can be repeated as long as ATP is available.

Co-transport

• Co-transport:
  • A type of active transport.
• Example: glucose or amino acid transport in the ileum with sodium ions.
  • Sodium ions are actively transported out of the epithelial cell into the capillaries.
  • This creates a lower concentration of sodium ions inside the epithelial cell.
  • Sodium ions diffuse down their concentration gradient from the ileum into the epithelial cell, through a co-transporter protein.
  • Glucose or amino acids also attach to the co-transporter protein and are transported into the epithelial cell against their concentration gradient.
  • Glucose then moves by facilitated diffusion from the epithelial cell into the blood.

Adaptations for Rapid Transport

• Cells can be adapted to increase the rate of transport across their membranes:
  • Increased surface area (e.g., microvilli).
  • Increased number of protein channels and carrier molecules.

Immunity: Identifying Self and Non-self

• The immune system identifies and destroys harmful foreign substances (non-self).
• Immune cells (lymphocytes) distinguish pathogens from body cells.
• Cells have specific molecules (usually proteins) on their surface, acting as identifiers.
• Non-self cells trigger an immune response.
• Surface molecules help identify:
  • Pathogens (bacteria, fungi, viruses).
  • Cells from other organisms (transplants).
  • Abnormal body cells (cancer cells).
  • Toxins released by pathogens.

Antigens and Immune Response

• An antigen is a molecule that generates an immune response.
• Antigens trigger lymphocytes.
• Antigens are usually proteins located on the cell surface.

Antigen Variability

• Pathogens' DNA can mutate frequently.
• Mutations in genes coding for antigens can change the antigen shape.
• Previous immunity may become ineffective due to this change.
• Memory cells in the blood recognize the old antigen shape, not the new one.
• Influenza virus mutates rapidly:
  • New flu vaccine created each year to account for these changes.

Immune Response: Overview

• If pathogens bypass physical and chemical barriers, white blood cells respond.
• White blood cells have specific and non-specific responses.
• Phagocytes (macrophages) provide a non-specific response.
• Lymphocytes provide a specific response.

Phagocytosis

• Phagocytosis:
  • A non-specific response by phagocytes (macrophages).
  • Macrophages are found in the blood and tissues.
• Stages:
  • Chemicals released by pathogens or abnormal cells attract phagocytes.
  • Phagocytes move towards the cell via chemotaxis.
  • Receptors on the phagocyte surface attach to chemicals or antigens on the pathogen.
  • The phagocyte engulfs the pathogen.
  • The engulfed pathogen is contained within a vesicle called a phagosome.
  • A lysosome fuses with the phagosome and releases lysozyme.
  • Lysozyme hydrolyzes and breaks down the pathogen.
  • Soluble products are absorbed and used by the phagocyte.
  • Waste and debris are released.

Specific Immune Response: T Lymphocytes (T Cells)

• T lymphocytes (T cells):
  • Made in the bone marrow but mature in the thymus.
  • Involved in the cell-mediated response.
• Cell-mediated response:
  • T cells respond to antigens on the surface of cells (antigen-presenting cells or APCs).
• Antigen-presenting cells (APCs):
  • Present non-self antigens on their surface.
  • Examples:
    • Infected body cells (present viral antigens).
    • Macrophages (present antigens from engulfed pathogens).
    • Transplanted organ cells (have different shaped antigens).
    • Cancer cells (have abnormal shaped self-antigens).

Cell-Mediated Response Process

• Phagocytes engulf and destroy pathogens, then present the antigens on their surface.
• Helper T cells have receptors that bind to the antigens on the APC.
• Binding activates the helper T cell to divide by mitosis.
• Cloned helper T cells differentiate into:
  • More helper T cells (activate B lymphocytes).
  • Stimulate macrophages to perform more phagocytosis.
  • Memory cells (for that specific antigen).
  • Cytotoxic T cells (killer cells).
• Cytotoxic T cells destroy infected or abnormal cells.
  • Release perforin, a protein that makes holes in the cell surface membrane.
  • This causes cell death by lysis (water influx) or shriveling (water outflux).
• Cytotoxic T cells are important in viral infections:
  • Body cells are sacrificed to prevent further viral replication.

B Lymphocytes (B Cells): Humoral Response

• B lymphocytes (B cells):
  • Made and mature in the bone marrow.
  • Involved in the humoral response.
• Humoral response:
  • Involves antibodies, which are soluble proteins transported in bodily fluids (humor).
  • Approximately 10 million different B cells, each with antibodies complementary to different antigens.
• Antigens in the blood bind to complementary antibodies on B cells.
• The B cell takes in the antigen by endocytosis and presents it on its surface.
• The B cell collides with a helper T cell and activates.
• Activated B cells undergo clonal expansion and differentiation:
  • Plasma cells.
  • Memory B cells.
• Plasma cells:
  • Make antibodies complementary to the antigen.
• Memory B cells:
  • Can rapidly divide into plasma cells upon reinfection.
  • Provide long-term immunity.

Memory B Cells

• Memory B cells:
  • Live for decades.
  • Cannot make antibodies directly.
  • Divide by mitosis and differentiate into plasma cells.
  • Result in rapid production of large numbers of antibodies upon reinfection.
  • Confer immunity to a particular disease.

Primary and Secondary Immune Response

• Primary response:
  • Occurs upon first exposure to an antigen.
  • Slower antibody production because of initial antigen-antibody binding process.
  • Fewer antibodies are produced.
  • Memory B cells are generated.
• Secondary response:
  • Occurs upon second exposure to the same antigen.
  • Rapid antibody production due to the presence of memory B cells.
  • Larger number of antibodies produced.

Antibody Structure

• Antibodies:
  • Quaternary structure proteins made of four polypeptide chains.
  • Variable region: binds to specific antigens.
  • Constant region: the same for different antibodies.
  • Heavy chains: longer polypeptide chains.
  • Light chains: shorter polypeptide chains.
  • Antigen-binding sites: located in the variable region.
  • Flexible, allowing binding to multiple antigens.

Antibody Function: Agglutination

• Antibodies can bind to multiple antigens, causing agglutination.
• Agglutination:
  • Clumping of antigens and antibodies.
  • Makes it easier for phagocytes to locate and destroy pathogens.

Active vs. Passive Immunity

• Active immunity:
  • Immunity is created by the individual's own immune system.
  • Follows exposure to a pathogen or antigen.
  • Can be natural (following infection) or artificial (following vaccination).
• Passive immunity:
  • Antibodies are introduced into the body.
  • The individual does not produce the antibodies themselves.
  • No creation of plasma or memory cells, so no long-term immunity.
  • Examples:
    • Antibodies passed from mother to fetus via placenta or breast milk.

Vaccines

• Vaccines:
  • Introduce small amounts of weakened or dead pathogens, or just their antigens, into the body.
  • Exposure to antigens activates B cells, causing clonal expansion and differentiation.
  • Plasma cells and memory B cells are produced.
• Memory B cells:
  • Stay in the blood for years.
  • Upon reinfection, they rapidly divide into plasma cells.
  • Large numbers of antibodies are created quickly.
  • Disease symptoms are reduced or eliminated.

Herd Immunity

• Herd immunity:
  • If a large proportion of a population is vaccinated, the pathogen cannot spread easily.
  • Provides protection for those who cannot be vaccinated:
    • Existing illnesses.
    • Lowered immunity.
    • Too young.
    • Pregnancy.

HIV Structure

• HIV Structure consists of:
  • Core which contains; RNA and reverse transcriptase
  • Capsid which is an outer protein coat
  • Envelope which is derived from the host cell membrane
  • Protein attachments that enable the virus to bind to host helper T cells

HIV Replication

• HIV replicates in helper T cells
• Step 1: Transported in the blood. Attaches to CD4 proteins on helper T cells
• Step 2: HIV protein capsule fuses with the helper T cell membrane, allowing the Rna and enzyme inside
• Step 3: HIV enzyme reverse transcriptase copies the viral RNA into a DNA copy
• Step 4: DNA moves to the helper T nucleus where RNA is transcribed where the cell starts to create viral proteins to create viral particles
• an HIV + person does not necessarily have AIDS
• the virus destroys helper T cells and this causes host is unable to produce an adequate immune response to other pathogens
• Immunodeficiency due to the virus is what leads to death

Monoclonal Antibodies

• Antibodies are proteins that bind with a complementary shape to a particular antigen
• Can be medically manipulated to:
  • Offer medical treatments and diagnosis
  • Used in tests (pregnancy, drugs, viral diseases)

Monoclonal Antibody Therapy

• Cancer treatment

Types

• Direct monoclonal antibody therapy
  • some cancers can be treated with monoclonal antibodies that have a binding site which is complementary to the antigens outside of cancer cells
  • Once the cancer cells are covered the chemicals cant bind and they cant divide and multiply uncontrollably
  • Since the binding sites are designed to only attach to cancer cells, normal cells should not be harmed
• Indirect monoclonal antibody therapy
  • Same process except cells contain drugs to fight the cancer
  • drug can destroy the cancer cells only
  • The drug is directly delivered to cancer cells reducing the harm to other cell tissues
  • This technique is sometimes referred to as a bullet drug

Medical Diagnosis use

• Pregnancy tests
• Viral drug and bacterial tests
• Viral flow tests use ELISA or ELIZA

ELISA (Enzyme-Linked Immunosorbent Assay)

• An immunoassay test that uses mobile and immobile antibodies
• Antibodies that are complementary in shape to the antigen being tested contains a colour dye attached to it
  • The test can confirm pregnancy through a HCG urine sample. The HCG urine sample comes into contact with HCG hormone bound antibodies resulting in a coloured blue line showing the test sample result
• Additional ELISA Test method
  • Sample placed in beaker and washed to remove unbound sample
  • Enzymes attach to an antibody that has been released
  • Substrate is then released and it produced a coloured product when an antibody with an attached enzyme is present
  • The presence of colour signifies the presence of the antigen and greater the colour intensity, the greater the indication of the antigen quantities

Ethics Surrounding Monoclonal Antibodies

• Debate about animal testing exists because tumours are injected into mice to allow for the production of antibodies
• Animals have to endure discomfort, harm and or death to the test subjects