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Cell Biology Lecture Notes

Cell Membrane Proteins

  • Integral Proteins:
    • Located within the transmembrane.
    • Can span from the outer to inner layer of the phospholipid bilayer.
  • Channel Proteins:
    • Transmembrane proteins with an open space inside.
    • Allow movement of substances in and out of the cell.
  • Transmembrane Protein Structure:
    • Cartoon representation: Blob-like.
    • Detailed representation: Long chain folded on itself.
    • Amphipathic: Contains both hydrophilic and hydrophobic sections.
      • Hydrophilic sections: Interact with extracellular and intracellular fluids.
      • Hydrophobic sections: Located within the membrane.
    • Cholesterol: Found in the hydrophobic regions, influences membrane fluidity.
  • Fluid Mosaic:
    • Describes the arrangement of proteins and lipids in the membrane.

Cell Junctions

  • Function: Connect adjacent cells.
  • Types:
    • Desmosomes
    • Tight junctions
    • Gap junctions
  • Integrins:
    • Transmembrane proteins.
    • Bind to specific proteins in the extracellular matrix.
    • Link to membrane proteins on adjacent cells, enabling cell-to-cell connection.

Desmosomes

  • Strong but spot-like junctions.
  • Involve cadherins (proteins) that extend into the extracellular space and connect with each other.
  • Contain a dense plaque (desmosome) for connection.
  • Allow space between cells, meaning substances can flow between them.

Tight Junctions

  • Extracellular surfaces are connected, but cells remain separate.
  • Prevent free flow between cells but provide physical connection.
  • Enable communication without allowing movement of substances between cells.

Gap Junctions

  • Protein channels physically link the cytosol of adjacent cells.
  • Allow for rapid communication and sharing of messengers between cells.
  • Prevent molecules from moving completely between cells due to the gap junction structure.

Nucleus

  • Function: Storage and transmission of genetic information.
  • Analogy: Head office of a factory.
  • Contains DNA associated with proteins, forming chromatin.
  • Chromatin condenses into chromosomes during cell division.
  • Surrounded by a nuclear envelope (a special membrane).
  • Nuclear pores in the envelope allow movement of substances in and out of the nucleus.
  • Nucleolus:
    • Dense, non-membrane-bound region.
    • Responsible for creating ribosomes.

Ribosomes

  • Protein factories of the cell.
  • Composed of protein and RNA.
  • Create new proteins.
  • Analogy: Physical workers in a factory.

Endoplasmic Reticulum (ER)

  • Analogy: Assembly line.
  • Two types:
    • Rough ER
    • Smooth ER

Rough Endoplasmic Reticulum

  • Has ribosomes on its surface (hence "rough").
  • Involved in packing proteins that are secreted or distributed to other organelles like golgi apparatus.

Smooth Endoplasmic Reticulum

  • No ribosomes attached.
  • Involved in lipid molecule synthesis, detoxification, and calcium storage and release.
  • Important for muscle cell function (specialized smooth ER).

Golgi Apparatus

  • Series of flattened membranous sacs.
  • Functions: Concentrates, modifies, and sorts proteins from the rough ER before distribution.
  • Analogy: Shipping and processing unit.
  • Packages proteins for secretion or transport to other organelles (e.g., mitochondria, smooth ER).

Endosomes

  • Vesicles and tubular structures between the plasma membrane and the Golgi apparatus.
  • Help in sorting, modifying, and directing traffic in cells.
  • Work with the Golgi apparatus to ensure proteins reach their destinations.

Mitochondria

  • Powerhouse of the cell.
  • Oval-shaped organelle with two membranes.
  • Function: Generates ATP using oxygen, producing CO_2 as a byproduct.
  • Has its own DNA, believed to be from ancient bacteria absorbed by cells.
  • Mitochondrial DNA is inherited maternally.

Lysosomes

  • Spherical or oval organelles surrounded by a single membrane.
  • Function: Break down bacteria and remove debris from cells.
  • Analogy: Recycling plant.
  • White blood cells have many lysosomes for their immune function.

Peroxisomes

  • Consume molecular oxygen and help in detoxification.
  • Less important compared to lysosomes.

Cytoskeleton

  • Filamentous network that maintains and changes cell shape, produces cell movement.
  • Three types:
    • Actin
    • Intermediate filaments
    • Microtubules
  • Intermediate filaments and microtubules maintain cell shape.
  • Analogy: Scaffolding during building construction.

Protein Synthesis: Transcription and Translation

  • Proteins are involved in all physiological processes.
  • Synthesis involves transcription and translation.
    • DNA \rightarrow RNA \rightarrow \text{Protein}
  • DNA:
    • Four bases code for proteins.
    • Bases arranged in 64 different three-letter combinations (codons).
    • Each codon specifies an amino acid.
      • Example: CCA, CCG, CCT, CCC all specify glycine.

Transcription

  • Creating RNA from DNA.
  • DNA as the original blueprint, RNA as a copy.
  • DNA binds with ribonucleotides paired with the DNA strand.
  • RNA has uracil (U) instead of thymine (T).
  • RNA cuts out non-coding regions (introns) and keeps coding regions (exons).
  • RNA breaks off, DNA re-helicalizes, and mature mRNA exits the nuclear envelope.

Translation

  • RNA passes into the cytoplasm and binds to a ribosome subunit.
  • Free amino acids link to corresponding tRNA.
  • Codons are associated with specific amino acids.
  • Amino acids are brought to the ribosome, and base pairs are shuttled off.
  • The chain is built as each codon is read and the appropriate amino acid is added.

Mutations

  • Changes in base pairs within a codon can lead to a different amino acid, altering protein function.
  • Caused by random chance, chemicals, or radiation.
  • Can result in impaired cell function or cell death or inconsequential changes.

Protein Degradation

  • Proteins degrade at different rates based on usage.
  • Proteins in high-strain areas degrade faster.
  • Proteins are attached to ubiquitin to signal degradation.

Ligand Binding

  • Ligand: Any molecule that binds to a protein.
  • Binding site: The location where the ligand binds.
  • Binding occurs due to electrical attractions between positive and negative charges.

Specificity

  • Ligand and binding site act as a key and keyhole.
  • Binding sites are specific to their ligands.

Affinity

  • High affinity: Correct shape and opposite charge.
  • Intermediate affinity: Correct shape but no charge or incorrect charge.
  • Low affinity: Incorrect shape and no opposite charge.
  • Saturation: The fraction of total binding sites that are occupied.

Allosteric Modulation

  • A protein has two binding sites:
    • Functional/Active site
    • Regulatory site
  • A modulator binds to the regulatory site, changing the shape of the functional site and causing higher affinity.

Covalent Modulation

  • Involves a chemical group of a protein cysteine.
  • Phosphorylation: Protein kinase breaking down ATP to add a phosphate group, altering the functional site affinity.