Biophysics Lecture 1: The Cell

Biophysics: Lecture 1 "The Cell"

• All cells share common characteristics: a membrane, protoplasm (a thick fluid), organelles, and a control center with DNA.
• Cell types include prokaryotic and eukaryotic.
• Eukaryotic cells have a membrane-bound nucleus and many organelles. Examples include fungi, protists, plants, and animal cells.

Plasma Membrane "Phospholipid Bilayer"

• The plasma membrane is a phospholipid bilayer.
• It contains cell contents.
• It has a hydrophilic head and hydrophobic tails.
• The phospholipids arrange with their hydrophilic heads facing outward, and hydrophobic tails facing inward.

Membrane Proteins

• Membrane proteins include channels/transporters (moving molecules in one direction), receptors (recognizing chemicals), glycoproteins (identifying cell types), and enzymes (catalyzing substance production).

Cytoplasm

• The cytoplasm is a viscous fluid containing organelles and interconnected filaments/fibers.
• It's also called cytosol.

Nuclear Envelope

• Separates the nucleus from the rest of the cell.
• It has pores (10-50nm apart).
• The outer membrane is continuous with the Rough Endoplasmic Reticulum.

DNA

• Hereditary material.
• Chromosomes are originated from DNA.
• The nucleolus is involved in RNA synthesis, and forms ribosomes.

Endoplasmic Reticulum

• Helps move substances within cells.
• A network of interconnected membranes.
• Types:
  • Rough ER (RER): Has ribosomes attached, manufactures proteins.
  • Smooth ER (SER): No ribosomes, builds carbohydrates & lipids.

Golgi Apparatus

• Involved in plant cell wall synthesis.
• A packaging and shipping station for the cell.
• Responsible for vesicles used in endocytosis and exocytosis

Lysosomes

• Contain digestive enzymes.
• Aid in cell renewal; break down old cell parts; digest invaders.

Mitochondria

• The "powerhouse of the cell".
• Generates ATP (chemical energy source for the cell).
• Has its own DNA.
• Bound by a double membrane.
• Used in signaling, cellular differentiation, control of cell cycle and growth.
• Breaks down fuel molecules (glucose, fatty acids).

Lecture 2: "Plasma Membrane, Membrane Proteins & Transport Across the Plasma Membrane"

• Cell membranes are flexible, also known as the plasma membrane; a phospholipid bilayer that forms boundaries around the cells (provides a protective function).
• Membranes are responsible for bioelectricity (ion movement).
• Facilitates chemical communication (signaling) between cells.
• Controls the trafficking of molecules in and out of the cell.

Structure of Plasma Membrane

• Phospholipid arrangement: hydrophilic heads & hydrophobic tails arranged as heads-tail-tail-heads.
• Fluid Mosaic Model: A membrane is a mosaic of components (proteins, and other molecules). Most proteins and phospholipids are free to move within the membrane.

Membrane Proteins

• Integrins: Integrated within the phospholipid bilayer, strengthening the membrane.
• Integral Proteins: Transfer substances in and out of the cell.
• Glycoproteins: Carbohydrate chains on the surface, acting as recognition modules/fingerprints, and span the membrane transversely.

Intercellular Junction proteins

• Help cells stick together and communicate.
• Intercellular junctions form channels.
• Subunits are connexins, assembled to make connexons joining two cells.
• Connexons form gap junctions to allow small molecules between adjacent cells.
• Gap junctions have hemichannels, each has 12 units (each hemichannel with 6 units).

Simple Diffusion

• Movement of molecules from high to low concentration, without energy or carrier proteins.
• Concentration gradient is the driving force.

Facilitated diffusion

• Transport of small polar molecules and ions through passive transport proteins (no energy needed).
• Solute-specific proteins (e.g., glucose) facilitate diffusion into/out of cells.

Osmosis

• Diffusion of water across a selectively permeable membrane from high to low water concentration (higher water concentration to lower water concentration).
• Integral membrane proteins for facilitated transport.

Signal Transduction Proteins

• Bind hormones and other substances outside the cell.
• Binding triggers intracellular changes (signal transduction).
• Example: insulin binding to receptors, leading to glucose transport protein insertion into the membrane.

Transport Across the Membrane

• Active transport proteins require energy (e.g., Sodium-Potassium pump) to move substances across the membrane.
• Passive transport proteins do not require energy. Types: simple diffusion, facilitated diffusion, osmosis.

Lecture 3: "Active Transport"

• Bulk transport: a mode of active transport in which large molecules or small particles are transported across the plasma membrane using vesicles.
• Vesicles are used to transport large particles across the plasma membrane.
• Transport against concentration gradient (low to high concentration).
• Requires energy e.g. ATP (adenosine triphosphate)
• Protein Phosphorylation is when a molecule gains a phosphate, becoming phosphorylated; a molecule loses a phosphate, becoming de-phosphorylated.
• Protein Conformation: Spatial arrangement of protein changes affect the protein function.
• Types of Active Transport:
  • Exocytosis (outwards): materials are transported from inside to outside the cell within membrane-bound vesicles.
  • Endocytosis (inwards): particles are transferred into a cell by enclosing them within a vesicle made of plasma membrane. This includes Phagocytosis ("solid substances") and Pinocytosis ("liquid substances").
  • Receptor-mediated endocytosis; specific cellular uptake.

Lecture 4: "Generation of membrane potential"

• Cations are positively charged ions (e.g., K+, Na+, Ca2+). Anions are negatively charged ions (e.g., Cl-).
• Electrical gradient: difference in electrical charge across a membrane.
• Chemical gradient: difference in ion concentration across a membrane.
• Movement of ions across the cell membrane: ions move from higher to lower concentration; ions attract opposite charges and repel like charges; cell membrane permeability to ions determines their movement.
• Membrane potential/voltage results from unequal ion distribution across the membrane, creating a charge imbalance (inside more negative, outside more positive).
• Important for the generation of cellular activity, e.g. muscle contractions, nerve impulses.

Lecture 5 "Nernst Potential"

Factors defining the movement of ions across a cell membrane:

• Concentration Gradient: ions move from higher concentration to lower concentration
• Electrical Gradient: ions move from areas of like charge to different charges
• Ion Channel Number: permeability of the cell membrane to the ions define their movement across the membrane.
• Equilibrium Potential (Nernst Potential): the voltage across the cell membrane that balances out the difference in concentrations, across the membrane (no net movement of the given ion).
• Calculated using the Nernst equation (important information on factors which determine the Nernst value given is included in formula form in the notes).

Lecture 6 "Action Potential"

• Ion channels: transmembrane proteins that transport ions across cell membranes, grouped in gated and open channels.
• Gated Channels: open/close in response to certain stimuli (include voltage and ligand-gated ion channels).
• Ligand Channels: open when a specific ligand binds to it.
• Voltage Channels: open when voltage difference changes.
• Action Potential: a rapid rise and fall in membrane potential in a cell; action potentials must pass a threshold voltage in order for the action potential to happen, if it does not reach that threshold then it is known as failed initiation. Different states (amplitude); resting, depolarization, repolarization, hyperpolarization; characterized by differences in ion movement (ion flow) across the membrane.
• Action potentials have refractory periods: the time immediately after stimulation that another stimulus will not have the same effect.

Lecture 7 "Generation of Nerve Signal"

• Neurons: nerve cells sending messages throughout the body.
• Nerve Cell Structure:
  • Dendrites: receive information from other neurons and carry it to the cell body.
  • Cell body (soma): contains the cell nucleus.
  • Axon: transmits signals to other cells, can be myelinated or unmyelinated.
  • Nodes of Ranvier: areas of exposed axon in myelinated axons.
  • Schwann cells: form the myelin sheath surrounding axons in myelinated neurons, speeding up signal conduction in neurons.
• Synapse: space between two neurons where signals are transmitted (neurotransmitters released).
• Neurotransmitters: chemical substances that communicate between neurons.
• Synaptic Transmission Process: Neurotransmitters released from vesicles to receptors on postsynaptic neurons; the process (in brief) and their impact on neuron activity.
• Examples of neurotransmitters such as Acetylcholine, Serotonin, and Dopamine.

Lecture 8 "The mechanism of muscle contraction"

• Motor Unit: A group of muscle fibers controlled by one motor neuron. Different sizes/types of motor units.
• Synapse Between Neurons and Muscle Fibers: space between the neuron terminal and the muscle fiber where neurotransmitters diffuse.
• Muscle types: skeletal, smooth, and cardiac.
• Muscle Terminology: Sarco-, Myo-; related to Greek origin
• Sarcoplasmic reticulum, Sarcolema, Sarcoplasm, Myocyte

Muscle Structure and Contraction

• Myofibril structure describes parts of a muscle at a microscopic scale: Z discs, M lines, I Bands, and A Bands.
• Sliding Mechanism of Muscle Contraction details how actin and myosin filaments interact and slide over each other when a muscle contracts.
• Myosin head structure details (active binding sites).