Cell and Molecular Biology Overview

Cell and Molecular Biology Overview

Importance of Cell and Molecular Biology

  • This course focuses on analyzing RNA-seq data, which studies the transcriptome (mRNA) of organisms.
  • Analyzing the transcriptome alone doesn't provide a complete understanding of how spaceflight affects an organism.
  • Understanding the protein encoded by the transcript is essential.
  • Understanding where the protein acts and how its action affects the cell's function is important.
    • Does it act in the cytoplasm?
    • Does it act in response to activation from another protein?
    • Is it part of a signal transduction cascade?
    • Is it a secreted protein affecting neighboring or distant cells?
  • The goal is to understand how up- or downregulation of a transcript affects the whole organism.

Cell Functions

  • Cells in animal and plant tissues have diverse functions:
    • Secreting soluble factors.
    • Electrical activity (neurons, muscle cells).
    • Immune cells destroying bacteria or viruses.
  • Cells have different maturity levels:
    • Fully differentiated/committed cells with tissue-specific functions.
    • Progenitor/undifferentiated cells (stem cells).

Stem Cells

  • Stem cells can differentiate into committed cells.
    • Adult stem cells differentiate into specific lineages.
    • Embryonic stem cells can become any cell type.

Cell Structure

  • Cellular components:
    • Mitochondria.
    • Cytoplasm.
    • Nucleus (with genetic material).
    • Golgi vesicles.
    • Secretory vesicles.
  • The cell membrane encloses the cell, separating it from external factors.

Cell Membrane

  • The cell membrane divides the cell from its external environment.
  • It is a bilayered structure composed of phospholipids with polar head groups and non-polar tail groups.
  • The hydrophobic tails are hidden from water, while polar groups interact with water inside and outside the cell.
  • Transmembrane proteins have both hydrophobic and hydrophilic domains.
    • They enable the passage of molecules into and out of the cell.
    • They facilitate attachment to the cell surface.

Membrane Proteins

  • Proteins anchored to the cell membrane serve as receptors.
  • Glycoproteins are proteins with attached carbohydrates.
  • Glycolipids are lipids with attached carbohydrates.
  • Transmembrane proteins form channels, allowing molecules to pass through.
    • These channels can act as pumps, maintaining the cell's internal chemistry.

Transmembrane Proteins and Information Transfer

  • Transmembrane proteins are crucial for transferring information from the external environment into the cell.
  • They form pores in the phospholipid bilayer, allowing inorganic ions to pass down concentration gradients (e.g., sodium, potassium, calcium).
    • This process doesn't require energy.
  • Other transmembrane proteins require energy to transport species against their concentration gradients.
    • Carrier proteins (ion pumps) bind the molecules to be transported.
  • Many proteins project into the extracellular space.
    • These serve as receptors for specific molecules, enabling cell anchoring to the extracellular matrix or for signal transduction cascades.
  • Carbohydrates projecting from the membrane are negatively charged, forming the cell glycocalyx.
    • This gives the cell a negatively charged characteristic on its exterior.

Plant Cell Structure

  • Plant cells share many organelles with animal cells but have:
    • A rigid cell wall.
    • Chloroplasts.
    • Large central vacuole.

Cell Wall

  • The cell wall provides semi-elastic support and a protective barrier.
  • It distinguishes plant cells from animal cells.
Functions of Cell Wall
  • Mechanical support.
  • Protection from mechanical injuries.
  • Permeability to water and solutes.
    • Water-filled channels allow diffusion of water and water-soluble substances.
  • Protection from pathogens.
  • Intercellular communication.
  • Osmotic pressure resistance (prevents bursting in hypotonic solutions).

Cytoskeleton

  • The cytoskeleton provides cell shape and enables motility.
  • It is a dynamic network of protein filaments in the cytoplasm.
  • Extends from the nucleus to the cell membrane.
  • Provides mechanical support and aids in motility.
Elements of Cytoskeleton
  • Actin microfilaments (approximately 8 nm in diameter).
  • Intermediate filaments (approximately 10 nm in diameter).
  • Microtubules (approximately 25 nm in diameter).
  • These protein-based structures can lengthen or shorten based on the cell's needs.
  • They can extend into pseudopodia, enabling cell migration towards chemical signals.
  • Microtubules are important for DNA separation during cell division.
  • Intermediate filaments attach to receptor proteins, translating external signals.

Chloroplasts

  • Chloroplasts are found only in plant cells.
  • They perform photosynthesis, converting light energy into chemical energy.
  • They have a double membrane (inner and outer).
  • Thylakoids contain chlorophyll.

Mitochondria

  • Mitochondria are the powerhouses of the cell.
  • Cells usually have multiple mitochondria.
  • They produce energy through oxidative phosphorylation.
  • They contain enzymes that break down glucose.
  • Unique structure: *Two phospholipid membranes (inner and outer).
    • Inner membrane is folded to increase surface area.
    • The outer membrane separates the matrix and inner membrane from the cytoplasm.
  • The matrix space contains enzymes that break down molecules like glucose.
  • Energy generation occurs at the inner membrane.
  • The end product of oxidative phosphorylation is ATP (adenosine triphosphate).
    • ATP is the energy currency of the cell.
    • ATP is hydrolyzed to ADP (adenosine diphosphate), releasing energy.
    • The energy is used to drive cellular processes and recycled back into ATP through phosphorylation.

Nucleus

  • The nucleus contains DNA, the genetic material.
  • It's the control center of the cell.
  • DNA is condensed into chromatin.
  • The nucleus is separated from the rest of the cell by the nuclear envelope, composed of two phospholipid membranes.
  • The outer membrane is contiguous with the endoplasmic reticulum and connected to the inner membrane by nuclear pores.
  • Nuclear pores allow specific molecules to enter the nucleus, enabling transcription.
  • The nucleolus is where ribosomes are assembled.
  • DNA is the template for genetic material.
  • mRNA contains genes, which are translated into proteins.
  • Gene expression occurs when DNA uncoils, is transcribed into mRNA, and then translated into protein.
  • When gene expression isn't occurring, DNA remains supercoiled.

Endoplasmic Reticulum (ER)

  • The ER is connected to the outer membrane of the nuclear envelope.
  • Protein synthesis occurs here.
  • It consists of flattened sheets of phospholipid membranes:
    • Rough ER: contains ribosomes on the external surface for protein synthesis.
    • Smooth ER: tubular structure without ribosomes.
  • Ribosomes have two subunits containing ribosomal RNA and associated proteins.
    • Globular structures catalyze mRNA-templated protein synthesis.
  • After formation, proteins are released into the ER lumen and directed to the smooth ER for packaging into phospholipid vesicles and transport to the Golgi apparatus.

Golgi Apparatus

  • The Golgi apparatus further modifies, sorts, and packages proteins for transport.
  • Proteins are targeted to specific organelles or released into the extracellular space.
  • This occurs via secretory vesicles, which bind with the plasma membrane to release proteins into the extracellular space.

Vesicles

  • Found throughout the cytoplasm, vesicles traffic from the ER to the Golgi or from the Golgi to a specific destination.
  • Proteins to be secreted are released via exocytosis (vesicle joins with the cell membrane).
  • Proteins gathered from other cells are taken up via endocytosis (infolding of the cell membrane).

Lysosomes

  • Lysosomes are vesicles containing enzymes that break down particles within endocytic vesicles.
  • This enables particle ingestion.
  • Granulocytes and neutrophils (immune cells) use this to digest foreign particles.

Cell Communication

Membrane Receptors

  • Membrane receptors enable interactions between a cell and its environment or between cells.
  • Outside-in signaling: cell signaling to other cells.
  • Inside-out signaling: cell secreting molecules or rearranging contacts, changing the extracellular environment.
  • Cell and extracellular matrix interactions are enabled by receptors on the cell surface, initiating or activating cell functions (e.g., spreading, migration, communication, differentiation, activation).

Cell Contacts

  • Tight junctions: Cells adhere to each other, allowing small molecules to pass between them.
  • Gap junctions: Small hydrophilic channels connecting different cell membranes.
  • Desmosomes: Mechanical attachment of different cells. *Belt desmosomes: broad bands.
    • Spot desmosomes: specific spots.

Types of Cell Membrane Receptors

  • Communication is critical for cells, both between cells and with the external environment.
  • Proteins bind to or are related to these receptors, which determines their function.
    • Some proteins inactivate receptors.
    • Others enable specific molecules to enter the cell.

Key Communication Around Membrane Receptors

*Cadherins: cell-to-cell contacts in the form of desmosomes, calcium-dependent homophilic binding (same to same).
* Cytoplasmic regions attach to intermediate filaments, linking intracellular and extracellular environments.
*Selectins: cell-to-cell contacts that enable binding in a heterophilic manner (different receptors bind each other).

  • Mucins: Cell-to-cell contacts; protein-based molecules with a sugar component that bind selectins in a heterophilic manner.
  • Integrins: Critical for cell-matrix interactions, linking extracellular matrix to intermediate filaments, enabling cell-to-extracellular matrix signaling.
Microgravity
  • In microgravity, changes to the mechanical environment surrounding cells affect integrins.
  • Integrins sense changes to the matrix (e.g., density), causing changes in mechanically sensitive cells.

Extracellular Matrix (ECM)

  • Crucial to cell survival, connecting a cell to its extracellular environment.
  • The ECM is dynamic, and these dynamics are altered under conditions like microgravity.
  • Fiber-reinforced matrix:
    *Fiber-forming elements: collagen, elastin.
    *Space-filling molecules: glycoproteins, proteoglycans.
  • The ECM is continuously remodeled; old components are digested, and new components are synthesized via enzymes.
Matrix Metalloproteinases (MMPs)
  • MMPs catalyze the degradation of the matrix by cleaving collagens and proteoglycans.
  • This is strictly regulated.
  • Tissue inhibitors of matrix metalloproteinases (TIMPs) prevent degradation from exceeding synthesis.
  • The balance between MMPs and TIMPs determines the extent of matrix degradation.

Impact on Cell Function

  • Cell-environment interaction affects cell function.
  • The localized microenvironment is critical to cell function, affecting distant tissues.
  • Signaling molecules circulate and cause changes to distant tissues.
  • Understanding these effects is important because they can affect cell survival, proliferation, and differentiation.
  • Different stiffness of the ECM can induce stem cells to differentiate into specific lineages.
    *If a mesenchymal stem cell is on a stiff matrix, it's more likely to form a bone cell.
    *If it's on a soft matrix, it's more likely to form a fat cell.
    *Receptor-ligand binding can change the function of committed cells, alter protein synthesis, and change the overall system balance.
  • The matrix environment affects cell migration.

Molecular Biology Overview

Central Dogma

  • The central dogma is:
    • \text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}
      *DNA is replicated, then transcribed into RNA, then RNA is translated into protein.
  • Proteins are the building blocks of the cell.
  • There is complexity to this process.
Expanded View of Central Dogma
  • Epigenetic modifications regulate gene expression at the DNA level.
  • MicroRNA formation regulates gene expression post-RNA production.
  • Regulatory sequences can affect splicing of transcripts.
  • Alterations occur to protein translation.
  • Post-translational modifications occur.
  • All affect cell biology.

Cellular Function Mechanisms

  • Cells have multiple mechanisms to carry out their function.
  • Mechanisms depend on what the cell needs to do and the environment.
  • Molecular mechanisms and pathways come together to create a functional cell.
  • It all starts with the central dogma: DNA replication, RNA transcription, and protein translation.

DNA Replication

  • DNA replication is well-known and well-understood, but new research emerges every year.
  • Positive and negative regulators are present in DNA replication.
  • For every known mechanism, there’s more being discovered.

Epigenetics

  • Epigenetics:
    • If twins have identical genes, why do they look different as they grow and have different responses to environmental factors?
  • How can the environment affect your DNA and gene expression?
    *DNA is packaged with histone proteins.
    *\text{DNA + Protein = Chromatin}
  • Histones enable regulation of gene expression, allowing different cells to use specific genes.
  • Histones are in octamers.
  • Epigenetic changes modify chemical tags attached to histones or DNA, which can cause lasting changes in gene expression and can be heritable.
Epigenetic Changes
  • DNA methylation: a methyl group is added to a cytosine residue in a CpG sequence.
  • Histone modification: an acetyl group or a methyl group is added directly to the histone tail.
  • These changes are maintained during development but can be affected by disease states, repressing or activating genes that should/shouldn't be.

Chromatin

  • DNA is packed into histone proteins, forming chromatin.
  • Histones regulate gene expression, allowing only specific genes to be expressed.
  • If DNA remains wrapped up in coils, not allowing unwinding from the histone, it can't be transcribed.

Effects of Epigenetic Changes

  • Disease progression, normal changes with aging.
  • Changes in acetylation of lymphocytes can lead to immune function disorders.
  • Epigenetic changes to somatic stem cells in bone marrow can cause bone loss, affecting muscle function and response to inflammation, and controlling skeletal muscle development.
  • Affects the cardiovascular system related to repair/regeneration, and aging of the cardiovascular system.

Epigenetic Changes and Diseases

  • Epigenetic changes can result in disease and affect aging.
  • If you have significant changes in acetylation of lymphocytes, then it can lead to immune function disorders.
  • If you have epigenetic changes to the somatic stem cells within the bone marrow, then it can cause bone loss, the same with muscle function, and it can affect the way that a muscle responds to inflammation and can control skeletal muscle development. The cardiovascular system can be related to repair and regeneration functions and also aging of the cardiovascular system.
  • Prader-Willi syndrome: deregulation of genes on the paternal side.
  • Cancers: changes in methylation patterns.
  • Leukemia: changes in methylation patterns.
  • Coffin-Lowry syndrome: changes to histone phosphorylation.

Epigenetics and Aging

  • Changes in chromatin contacts, different acetylation patterns change cell identity, causing functional tissues become dysfunctional and accelerate aging.

RNA Level

  • Transcriptomics: the study of all RNA in a cell, tissue, or organism.
  • Transcription creates RNA from DNA using RNA polymerase.
  • One of the main differences between DNA and RNA is that RNA is single-stranded while DNA is double-stranded.

Protein Synthesis

  • Translating mRNA into proteins.
  • mRNA is decoded, and an amino acid chain is created.
  • Folding the polypeptide into an active protein is essential.
  • Without protein folding, the protein is non-functional and can induce a disease state if incorrect.
Phases of Protein Synthesis
  • Initiation
  • Elongation
  • Termination
  • Occurs differently in eukaryotes and prokaryotes (eukaryotes outside the nucleus, prokaryotes inside the cytoplasm).