Cell and Molecular Biology Overview

Cell and Molecular Biology Overview

Introduction

  • The course focuses on analyzing data sets generated using RNA-seq, which examines the transcriptome (mRNA) of an organism.
  • Analyzing the transcriptome alone doesn't provide a complete understanding of how spaceflight affects an organism.
  • Understanding the protein a transcript encodes, where it acts, and how its action affects the cell is crucial.
  • Understanding how upregulation or downregulation of specific mRNA affects the overall organism is important.

Cell Functions

  • Cells have diverse functions in animal and plant tissues.
  • Some cells secrete soluble factors, others are electrically active (neurons, muscle cells), and some (immune cells) destroy invading bacteria or viruses.
  • Cells vary in maturity: fully differentiated/committed cells have tissue-specific functions, while undifferentiated progenitor cells (stem cells) are found throughout the body.
  • Stem cells can differentiate: adult stem cells commit to specific lineages, while embryonic stem cells can become any cell type.

Cell Structure

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

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.
  • Hydrophobic tails are hidden from water, while polar groups interact with water inside and outside the cell, due to thermodynamics.

Transmembrane Proteins

  • Located on the cell surface with hydrophobic and hydrophilic domains.
  • They enable the passage of substances into and out of the cell and facilitate attachment to the cell surface.
  • Proteins can be anchored onto the cell and act as receptors.
  • Examples: glycoproteins (protein with carbohydrate), glycolipids (lipid with carbohydrate).
  • Channels in the membrane act as pumps for specific molecules, maintaining cell chemistry.

Transmembrane Proteins and Information Transfer

  • Key for transferring information from the external environment into the cell.
  • They form small pores in the phospholipid bilayer, allowing inorganic ions to pass down concentration gradients (e.g., sodium, potassium, calcium).
  • This process doesn't require energy when ions travel down their concentration gradient.
  • Some transmembrane proteins require energy because they transport species against the concentration gradient.
  • Carrier proteins (ion pumps) physically bind molecules to be transported.
  • Many proteins project into the extracellular space and act as receptors for cell anchoring or signal transduction.
  • Carbohydrates projecting from the membrane are negatively charged, forming the negatively charged cell glycocalyx.

Plant Cells

  • Similar organelles to animal cells but also possess a rigid cell wall and chloroplasts.
  • The cell wall provides semi-elastic support and acts as a protective barrier against pathogens.
  • Chloroplasts are also present.

Cell Wall

  • Functions:
    • Mechanical support
    • Protection of inner components
    • Permeability to water and solutes via water-filled channels
    • Protection from pathogenic species
    • Intercellular communication
    • Osmotic pressure resistance to prevent bursting in hypotonic solutions

Cytoskeleton

  • Provides cell shape and enables cell motility.
  • Dynamic network of protein filaments in the cytoplasm, extending from the nucleus to the cell membrane.
  • Provides mechanical support and aids in motility.
  • Three major classes of elements:
    • Actin microfilaments (8 nm diameter)
    • Intermediate filaments (10 nm diameter)
    • Microtubules (25 nm diameter)
  • Protein-based structures can lengthen or shorten based on cell needs.
  • In cell migration, these structures extend into pseudopodia.
  • Microtubules play a role in DNA separation during cell division.
  • Intermediate filaments attach to receptor proteins, important for translating external signals.

Chloroplasts

  • Found only in plant cells.
  • Specialized organelles for photosynthesis (conversion of light energy to chemical energy).
  • Double membrane structure with inner and outer membranes.
  • Contain thylakoids, flattened sacs where chlorophyll is located.

Mitochondria

  • Powerhouses of the cell.
  • Produce energy through oxidative phosphorylation.
  • Contain enzymes that break down glucose.
  • Unique structure: inner and outer phospholipid membranes.
  • The inner membrane is folded to increase the surface area.
  • The matrix space contains enzymes that break down molecules.
  • Energy generation through redox reactions occurs at the inner membrane.
  • The end product of oxidative phosphorylation is adenosine triphosphate (ATP).
  • ATP is the energy currency of the cell, hydrolyzed to ADP (adenosine diphosphate) in an exothermic reaction that releases energy.
  • The energy from ATP hydrolysis drives cellular processes and is recycled back into ATP through phosphorylation.

Nucleus

  • Contains DNA (genetic material) and is the control center of the cell.
  • DNA is condensed into chromatin.
  • Separated from the rest of the cell by the nuclear envelope (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 and is translated into proteins.
  • Gene expression: DNA uncoils, is transcribed into mRNA, and then translated into protein.
  • When gene expression is not occurring, DNA remains supercoiled.

Endoplasmic Reticulum (ER)

  • Connected to the outer membrane of the nuclear envelope, the site of protein synthesis.
  • Long, flattened sheets of phospholipid membranes.
  • Two types:
    • Rough ER: contains ribosomes on the surface that synthesize proteins.
    • Smooth ER: tubular, lacks ribosomes.
  • Ribosomes consist of two subunits containing ribosomal RNA and associated proteins.
  • They catalyze the reaction where mRNA is used as a template to synthesize proteins.
  • After formation, proteins are released into the lumen of the ER and directed to the smooth ER for packaging into phospholipid vesicles for transport to the Golgi apparatus.

Golgi Apparatus

  • Proteins are further modified, sorted, and packaged for transport to their final destination (specific organelle or extracellular space).
  • This occurs via secretory vesicles, which contain the protein and bind with the plasma membrane to release the protein into the extracellular space.

Vesicles

  • Encapsulated by a phospholipid bilayer and found throughout the cytoplasm.
  • They traffic from the ER to the Golgi or from the Golgi to other destinations.
  • Secretion of protein via vesicle joining with the cell membrane is called exocytosis.
  • Uptake of particles from the extracellular environment via infolding of the cell membrane is called endocytosis.

Lysosomes

  • Vesicles that contain enzymes.
  • Break down particles within endocytic vesicles, enabling ingestion.
  • Used by granulocytes and neutrophils (immune cells) to digest foreign particles.

Membrane Receptors

  • Enable interactions between a cell and its extracellular environment or between cells.
  • Outside-in signaling: cell signaling to other cells or other cells signaling to one cell.
  • Inside-out signaling: cell secreting molecules or rearranging contacts.
  • Cell and extracellular matrix interactions are enabled by receptors on the cell surface.
  • These interactions can initiate or activate cell functions: cell spreading, migration, communication, differentiation, activation, etc.

Cell Contacts

  • Enable cell communication.
    • Tight junctions: cells adhere, allowing small molecules to pass.
    • Gap junctions: small hydrophilic channels connecting cell membranes.
    • Desmosomes: mechanical attachment of cells (belt desmosomes in broad bands or spot desmosomes in specific spots).

Cell Membrane Receptors

  • Critical for communication between cells and with the external environment.
  • When analyzing RNA-seq data sets, many proteins are related to these receptors, determining their function.
  • Some proteins can inactivate receptors, while others enable specific molecules to be brought into the cell.

Key Cell Communication via Membrane Receptors

  • Cadherins: cell-to-cell contacts in desmosomes, undergo calcium-dependent homophilic binding.
  • Selectins: cell-to-cell contacts enabling heterophilic binding.
  • Mucins: cell-to-cell contacts, protein-based molecule with sugar component binding selectin (heterophilic binding).
  • Integrins: critical for cell-matrix interactions, link extracellularly to intermediate filaments, directly couple the extracellular matrix to the cellular structure, enabling much cell-to-extracellular matrix signaling.

Microgravity and Integrins

  • Integrins sense changes to the matrix, such as density changes, causing changes to mechanically sensitive cells in microgravity.

Extracellular Matrix (ECM)

  • Crucial to cell survival.
  • Connects the cell to its extracellular environment, which is dynamic.
  • Dynamic changes in the ECM can be altered under conditions like microgravity.
  • It is a fiber-reinforced matrix with fiber-forming elements (collagen, elastin) and space-filling molecules (glycoproteins, proteoglycans).
  • The ECM is constantly remodeled; old components are digested, and new components are synthesized, catalyzed by enzymes.

Matrix Metalloproteinases (MMPs) and TIMPs

  • MMPs catalyze the degradation of the matrix by cleaving collagens and proteoglycans but are strictly regulated.
  • The degradation rate should not exceed the synthesis rate; otherwise, tissue breakdown can occur.
  • Tissue inhibitors of matrix metalloproteinases (TIMPs) regulate MMPs.
  • The balance between MMPs and TIMPs determines the extent of matrix degradation.

Why Is This Important?

  • The interaction between the cell and its environment affects cell function.
  • The microenvironment is critical to cell function.
  • The localized microenvironment around a tissue can be affected by both local and systemic events.
  • Signaling molecules are circulated and cause changes to distant tissues based on events in their microenvironments.
  • These effects can affect cell survival, proliferation, and differentiation. For example, different stiffness of ECM can induce stem cells to differentiate into specific lineages.
  • Protein synthesis, receptor-ligand binding in committed cells, and migration are also affected.

Central Dogma of Molecular Biology

  • DNA is replicated, then transcribed into RNA, and RNA is then translated into protein.
  • Protein forms the building blocks of the cell.
  • Epigenetic modifications regulate gene expression at the DNA level.
  • MicroRNA formation regulates gene expression following RNA production.

Expanded View of Central Dogma

  • Includes regulatory sequences affecting splicing of transcripts, alterations to the translation of proteins, and post-translational modifications.
  • All of these changes affect the biology of the cell.

Cellular Mechanisms and Pathways

  • Cells have multiple mechanisms for carrying out their function, dependent on cell type and environment.
  • Molecular mechanisms and pathways combine to create a functional cell, starting with DNA replication, RNA transcription, and translation into proteins.

DNA Replication

  • Well-known and well-understood mechanisms, but new research emerges every year.
  • Complexity is still being discovered despite DNA replication is well known.

Epigenetics

  • Spaceflight effects may be related to epigenetic changes.
  • Explains why identical twins can have different traits and responses to environmental factors as they age.
  • DNA is packaged with histone proteins to form chromatin.
  • These are wrapped up into nucleosomes.
  • Histones regulate gene expression, enabling different cells to use specific genes.
  • Epigenetic changes modify chemical tags attached to histones or DNA, causing changes in gene expression.
  • Changes can be heritable.

Epigenetic Changes

  • DNA methylation: a methyl group is added to a cytosine residue in a CpG sequence in the DNA.
  • Histone modification: an acetyl or methyl group is added to the histone tail at a specific point.
  • These changes are maintained during development but can be affected by disease states (causing genes or alterations to repress genes that are required or activate genes that should be repressed).

Histone Proteins and Chromatin

  • DNA is packed into histone proteins, forming chromatin.
  • Histone tails can be modified.
  • Histones regulate gene expression, allowing only specific genes to be expressed.

Effects of Epigenetic Changes

  • Disease progression and aging.
  • Significant changes in acetylation of lymphocytes can lead to immune function disorders.
  • Epigenetic changes to hematopoietic stem cells can cause bone loss.
  • Muscle function, the cardiovascular system, and aging are also affected.

Epigenetic Changes & Aging

  • Changes in chromatin contacts and acetylation patterns lead to dysfunctional tissues and accelerate aging.

RNA

  • Transcriptomics is the study of all RNA in a cell, tissue, or organism.
  • Transcription creates RNA from DNA using RNA polymerase.
  • RNA is single-stranded, while DNA is double-stranded.

Protein Synthesis

  • mRNA is translated into proteins, first decoding the mRNA.
  • Folding the polypeptide is essential for an active protein; incorrect folding can induce disease.
  • Three phases: initiation, elongation, and termination.
  • Occurs differently in eukaryotes (outside the nucleus) and prokaryotes (inside the cytoplasm).