Cell Biology: An Introduction

What is Cell Biology?

• Cell biology examines cells at various levels.
• Focus includes molecular composition and organization.
• Subcellular structure and organization are key aspects.
• The function of individual cellular components is studied.
• Cell differentiation and function are also examined.
• Studies communication between a cell and its environment.
• Cell replication is a key area of study.

Understanding Cells

• Modern cell biologists employ molecular genetics.
• Recombinant DNA and genetic engineering are utilized.
• Biochemistry provides essential tools and knowledge.
• Genomics and proteomics are incorporated.
• Systems biology is applied.
• Bioinformatics is crucial for data analysis.
• Advanced microscopy and imaging techniques are fundamental.

What is a Cell?

• The cell represents life's smallest unit.
• The plasma membrane separates the interior of a cell with order and structure from the non-living world.
• Nutrients, energy, and information are exchanged between the cell and its environment.

Universal Properties of Cells

• The cell delineates itself using the plasma membrane.
• The plasma membrane controls the exchange and communication with its non-living surroundings.
• The inside of a cell is ordered.
• Cells divide to form two new cells that ensure the continuation of life.
• DNA contains the genetic code stored chemically.
• The DNA code is replicated with fidelity.
• DNA encodes discrete units of information which are genes.
• Genes are transcribed into discrete RNA molecules.
• RNA is then translated into proteins, which are the workhorses of the cell.

Why Study Cell Biology?

• Understanding how cells function facilitates development of treatments for diseases.
• Treatments for cancer, like chemotherapy, radiotherapy, and surgery are possible
• Treatments for diabetes, like insulin and metformin among others are possible
• Treatments for infectious diseases (antibiotics, aseptic techniques) can be developed.
• Treatments for cystic fibrosis (antibiotics and other drugs) can be developed.
• Understanding cells can help make informed medical decisions.

Life's Chemical Information

• Life processes rely on chemical information.
• This information is stored, replicated, and interconverted.
• Much of this chemical information is "stored" as DNA.

Chemical Information Flow

• DNA synthesis (replication) creates more DNA.
• RNA synthesis (transcription) creates RNA from DNA.
• Protein synthesis (translation) creates proteins from RNA via amino acids.

DNA: The Code of Life

• The building blocks of DNA include phosphate, sugar, and a base to form a nucleotide.
• Nucleotides form a DNA strand.
• A new strand is templated by nucleotide monomers.
• DNA is a double-stranded molecule.
• The backbone consists of sugar-phosphate.
• Hydrogen bonds between base pairs stabilize the structure.
• DNA also forms a double helix.

DNA Replication

• DNA replication produces faithful copies of the living code, made of template and new strands.

Transcription

• Transcription converts the DNA code (gene) into RNA.
• Double-stranded DNA serves as an information archive.
• RNA molecules act as expendable information carriers.
• One strand is used as a template to direct RNA synthesis.
• Transcription provides a choice to either express or repress a gene.
• RNA facilitates information transfer.

Translation

• Translation involves ribosomes reading mRNA to synthesize proteins.

Ordered Living Organisms

• Living organisms are highly ordered and rich in endergonic compounds.
• Energy rich bonds within organic molecules contribute to this order.
• Metabolic pathways are interconnected and highly regulated.

Cellular Order and Energy

• Cells build order by converting simple molecules into complex ones, such as DNA.
• This process increases enthalpy and reduces entropy within the cell.
• Cells are not closed systems.
• Cells take in molecules from the external environment.
• Some molecules are burned for fuel and are coupled to other reactions.
• Fuel generates energy that is harnessed.

Catabolism and Anabolism

• Catabolic reactions release energy by being highly exergonic to increase disorder.
• Anabolic reactions are endergonic, storing energy and decreasing disorder.

Energy Currency

• Living cells use a common energy "currency" molecule.
• Food molecules provide energy.
• Energy is used to create a molecule needed by cells.
• Energy is used when oxidizing food and turning it into a more usable molecule.
• A molecule becomes available for cellular processes when it is used in catabolism.

ATP: The Energy Molecule

• Adenosine triphosphate (ATP) is the common energy "currency" molecule.
• ATP is carried by activated carrier molecules.
• ATP participates in phosphate transfer reactions to power cellular processes.

Cellular Diversity

• Cells vary greatly in structure and function across different organisms and within the same organism.

Prokaryotes vs. Eukaryotes

• A yeast cell is an example of a eukaryote that has membrane-bound organelles including a nucleus that sequesters DNA.
• E. coli is a prokaryote.
• Prokaryotic cells have a plasma membrane but no nucleus or other membrane bound organelles.

Prokaryotes and Eukaryotes Compared

• Prokaryotic cells lack a nucleus enclosing the genetic information (DNA).
• Prokaryotic cells lack other membrane-bound organelles.
• The plasma membrane is the only membrane structure in prokaryotic cells.
• Prokaryotes are mainly bacteria.
• Eukaryotic cells has genetic information (DNA) enclosed by the nucleus, which is a membrane-bound organelle.
• Eukaryotic cells contain various membrane-bound organelles with distinct functions.
• Eukaryotic cells has a cytoskeleton.
• Mitochondria and chloroplasts are organelles with their own genome.

Domains of Life

• Domains of life: Eukaryotes, Archaea, and Bacteria.

Last Universal Common Ancestor (LUCA)

• The last universal common ancestor of all living organisms was a common ancestor to Prokaryotes, Eukaryotes, and Archaebacteria.
• It lived about 3.5 million years ago.
• LUCA was a fairly complex cell.
• It had enzymes needed to synthesize cell membrane lipids.
• It had complex metabolic pathways and enzymes.
• It had translation (and ribosomes).

Eukaryotic Cell Evolution

• The origin of eukaryotic cells is still being studied.

Evolution of the Nucleus

• The nucleus likely evolved through membrane invagination.
• This created the nuclear envelope and endoplasmic reticulum.

Origin of Eukaryotic Cells

• Primordial eukaryotic cells may have been predatorial, consuming or eating other cells.
• White blood cells (neutrophils) eating red blood cells provide an example of phagocytosis.

Evolution of Eukaryotic Traits

• Primordial pre-eukaryotic cells may have been predatorial.
• The eating of cells is a process known as phagocytosis.
• Phagocytosis requires changes in cell shape driven by the cytoskeleton filaments.
• Nuclear enclosure would likely be advantageous to protect DNA from entanglement and breakage.

Origin of Mitochondria and Chloroplasts

• Predatorial eukaryotic cells may explain the origin of mitochondria and chloroplasts.

Unique Organelles

• Mitochondria and chloroplasts are unique among other organelles.
• They are energy organelles.
• Mitochondria and Chloroplasts are defined by a .
• They have their own genome.
• They have their own transfer RNAs, making them able to produce proteins independent of being directed by the cell where they reside (like cells).

Origin of Mitochondria

• Mitochondria originated from predation of oxidizing bacteria.
• The large cell gave the predator bacterium a symbiotic relationship providing food while the bacteria oxidized the food to release energy.
• The symbiotic relationship became permanent by loss of redundant genomes.

Origin of Chloroplasts

• The origin involves predation of photosynthetic bacteria (cyanobacteria).
• Cyanobacteria converted sunlight to food for a larger cell with mitochondria, which oxidized the food molecules to chemical energy.
• The symbiotic relationship became permanent by loss of redundant genomes.

Stages of Eukaryotic Cell Origin

• Stage 1: Ancestral pre-eukaryotic cells were likely predatorial, eating other cells by phagocytosis while evolving the nucleus to protect DNA molecules from damage.
• Stage 2: Predation of oxidizing bacteria led to endosymbiosis and eventually mitochondria.
• Stage 3: A line of mitochondria-containing eukaryotic cells may have internalized photosynthetic bacteria to become chloroplasts.

Summary: Prokaryotes and Eukaryotic cells

• Key differences exist between prokaryotes and eukaryotes concerning presence of a nucleus, mitochondira and/or chloroplasts, and various other membrane-bound organelles.
• Prokaryotes and eukaryotes evolved from a common ancestor.
• Organelles in eukaryotic cells have vital functions.

Molecules Inside Cells

• It is important to know types of molecules inside cells that contribute to survival of the cells.

Introduction to Cell Biology Topics

• Important topics include: Chemical information, DNA replication, Transcription and types of RNAs, Translation, Cellular Energy.
• Also important is understanding what Prokaryotes vs. eukaryotes are and the differences between them and studying the evolution of eukaryotic cells.
• Looking at the chemical composition of cells with small and Macromolecules including types and diversity (Shape determines function)
• Protein folding and structure, Amino acids and polypeptides, Ligand-protein interactions, kinases, phosphatase and GTPases.

Chemical Diversity of Cells

• The approximate chemical composition of a bacterial cell consists of the compounds Water, Inorganic ions, Sugars and precursors, Amino acids and precursors, Nucleotides and precursors, Fatty acids and precursors, Other small molecules, and Macromolecules (proteins, nucleic acids, and polysaccharides).

Macromolecules

• Macromolecules: polymers made of smaller repeated subunits.
• Examples: polysaccharide, protein, nucleic acid.
• Responsible for the complex shape, function, and regulation of cells.

Properties of Macromolecules

• Shape, size, and physical/chemical properties allow them to have specific functions.

Sugars and Polysaccharides

• Monosaccharides form polysaccharides via glycosidic bonds to allow energy to be stored, provide structural functions (cell walls), enable Cell signaling (cell-cell binding), and blood groups.

Nucleotides and Nucleic Acids

• Nucleotides, which consists of a triphosphate group, deoxyribose sugar and a nitrogenous base (adenine) are the monomers of nucleic acids.

• Five types of bases exist.

• Polymerization occurs through condensation reactions.

• DNA is the genetic code.

• RNA intermediates are important for information transfer with transcription, translation, gene regulation, and enzyme RNAs such as ribozymes.

Amino Acids and Proteins

• Proteins consist of of amino acids monomers, linked by peptide bonds.
• Play roles in structure, energy, information transfer and catalysis
• There are 20 different amino acids commonly found in proteins.

Macromolecular Complexity

• Macromolecules are responsible for the life's complexity.
• Covalent linkage and rearrangement of a few building blocks can create incredible diversity by changing:
  • Polymer Length
  • Linear sequence of Monomer Types
  • Covalent bonds between monomers, i.e., where on a molecule does one attach the next building block - important for polysaccharides
  • Conformation of a molecule, i.e., 3-D shape of a molecule

Protein Structure

• Proteins are experts at creating structural diversity from amino acids.
• Protein structure achieves a hierarchical structural order.
• Primary structure: the amino acid sequence in the polypeptide.
• Secondary structure: local folds of the polypeptide with a-helices and ẞ-sheets.
• Tertiary structure: the global, 3-D fold of the entire polypeptide.
• Quaternary structure: the positioning of all polypeptide chains needed to make a functional protein.

Primary Sequence

• The primary sequence affects look of the polypeptide chain.

Protein Folding

• Non-covalent interactions within the polypeptide chain are responsible for protein folding.

Tertiary Structure

• Secondary structures interact to form the three-dimensional structure (tertiary structure) of a protein.

Protein Interactions

• Proteins work by interacting with other molecules.
• Interacting molecules can be small molecules or macromolecules called ligands.
• Ligands bind to proteins through noncovalent bonds.
• Ligand binding specificity and strength (affinity) depends on type and number of non-covalent bonds.

Proteins Connections

• Proteins act like individual people.
• Proteins have their own "social network".
• Proteins need interactions with other molecules, including other proteins, for specific functions.

Summary: Intro to Cell Biology

• The cell is the unit of life.
• Cells have universal properties, indicating a common ancestor.
• Life depends on chemical information.
• DNA linear sequence stores information that is replicated, transcribed and eventually translated into protein.
• Cells harness energy to create order.
• The three cellular domains are: archaea, eubacteria (prokaryotes), and eukaryotes.
• Eukaryotic cells are internally complex with specialized compartments.
• These compartments are called organelles.
• Eukaryotic cells likely evolved because of predatorial lifestyle.
• Cells are built of common, though diverse, set of chemical groups.
• Macromolecules are responsible for immense chemical diversity.
• Proteins are "expert" folding molecules that determine function.