Cell Theory and Cell Types

• The Cell Theory states that cells are the fundamental units of life.
• All living organisms are composed of cells.
• Cells can only arise from pre-existing cells through cell division.
• Modern cells evolved from a common ancestor.
• Cells can reproduce, respond to the environment, harness energy, and evolve.
• Unicellular Organisms consist of single cells, such as bacteria, archaea, and amoeba.
• Multicellular Organisms can contain hundreds to trillions of cells such as mammals and plants.

Surface Area to Volume Ratio

• As an object's volume increases, its surface area also increases, but not at the same rate.
• Chemical activities, resource needs, and waste production increase faster than surface area.
• Large organisms are composed of many small cells to overcome limitations related to surface area.
• Cells can overcome surface area limitations by increasing membrane infoldings or increasing size in one dimension, such as nerve cells becoming thin and elongated.
• Cells can also increase the rate of substance transport across the membrane to help.
• The cell membrane acts as a selectively permeable barrier, preventing some substances from crossing while allowing others to enter and leave.
• By regulating transport, the cell membrane maintains a more or less constant internal environment, called homeostasis.
• The cell membrane serves as a boundary with the outside environment, facilitating communication with adjacent cells and receiving signals from the environment.
• Proteins protruding from the cell membrane are responsible for binding and adhering to adjacent cells.
• Overall the cell membrane contributes to cell shape.
• Cytoplasm refers to everything inside the cell, excluding the nucleus.
• Cytosol is the fluid not contained inside another compartment.

Organelles

• Organelles are membrane-enclosed compartments in eukaryotic cells that separate molecules and biochemical reactions, enabling regulation and efficiency.
• Examples of organelles include the nucleus and endoplasmic reticulum.
• Prokaryotic cells have diameters or lengths in the range of 1-10 μm.
• Eukaryotic cells range from 10-100 μm.

Prokaryotic Cells

• Bacteria and Archaea are Prokaryotic cells.
• The cell membrane encloses the cell, regulating material traffic and separating its interior from the external environment.
• The nucleoid is a region in the cell where DNA is located.
• Cytoplasm is material enclosed in the cell membrane.
• Ribosomes are complexes of RNA and proteins in the cytoplasm and are the sites of protein synthesis.
• The substances in the cytoplasm are in constant motion.
• A typical protein can move around the entire cell within a minute.
• Most prokaryotic cells have a cell wall located outside the cell membrane that supports the cell and determines its shape.
• Some bacteria have an outer membrane that encloses the peptidoglycan layer.
• Some bacteria have a capsule composed mostly of polysaccharides outside the cell wall protects from the immune system, drying out, and helps with attachment to other bacteria.
• Photosynthesizing bacteria contain molecules needed for photosynthesis, such as in Cynobacteria
• Other prokaryotes have internal membrane folds attached to the cell membrane that may function in cell division or energy-releasing reactions.
• Some prokaryotes swim by using flagella.
• Bacterial flagellum is made of flagellin.
• Pili are protein structures projecting from some bacterial cells used for adherence and exchanging genetic material.
• The cytoskeleton is a term for protein filaments that play roles in cell division, cell movement, and maintaining cell shapes.
• Prokaryotes have filamentous proteins that are homologous to eukaryotic cytoskeleton proteins.
• Eukaryotic Cell Compartmentalization is where Organelles carry out particular functions, which is important because it separates biochemical reactions from the rest of the cell.
• Lysosome hydrolyzing enzymes are kept away from other proteins in the cytoplasm.
• Lysosome pH is preserved.
• Organelle membranes separate charges for energy production, such as photosynthesis and respiration.
• Plant cells have a cell wall, plasmodesmata, and plastids (e.g., chloroplasts).
• Animal cells have a cell membrane, other cell junctions, and no plastids.

Nucleus

• The nucleus is the location of most of the cell's DNA.
• DNA replication occurs in the nucleus.
• The nucleus is the site where gene transcription is turned on or off.
• Nucleolus is the assembly of ribosomes from RNA and proteins.
• Nucleoplasm is everything in the nucleus except for the nucleolus.
• The nuclear envelope is an integrated structure composed of two membranes, perforated by nuclear pores, allowing only molecules less than 10 kDa to cross and has strict control of nuclear entry that is continuous with the ER.

Endomembrane System

• The endomembrane system includes the cell membrane, nuclear envelope, endoplasmic reticulum, Golgi apparatus, and lysosomes.
• Vesicles are tiny, membrane-surrounded droplets that shuttle substances between the components of the endomembrane system.
• The endoplasmic reticulum (ER) consists of interconnected membranes forming tubes and flattened sacs throughout the cytoplasm.
• Rough endoplasmic reticulum (RER) has ribosomes attached to the outer surface and is involved in protein synthesis.
• RER receives newly synthesized proteins into its lumen, segregating them away from the cytoplasm.
• The RER participates in transporting proteins to other locations in the cell.
• Within the RER, proteins can be chemically modified, such as by glycosylation, to alter their functions and be “tagged” for delivery to specific cellular destinations.
• Proteins are sent to other locations in the cell enclosed within vesicles that pinch off from the RER.
• Most membrane-bound proteins are made in the RER.
• Smooth ER (SER) lacks ribosomes, is more tubular, and is continuous with RER.
• Smooth endoplasmic reticulum is responsible for the chemical modification of small molecules that may be toxic to the cell.
• Glycogen degradation in animal cells occurs in the SER.
• Lipids and steroids, as well as polysaccharides in plant cells are synthesized in the SER.
• Calcium ions are stored for release to trigger numerous cell responses in the SER.
• The golgi apparatus consists of flattened membranous sacs called cisternae piled up like saucers and small membrane-enclosed vesicles.
• The golgi apparatus receives protein-containing vesicles from the RER.
• It modifies, concentrates, packages, and sorts proteins before they are sent to their cellular or extracellular destinations.
• It adds carbohydrates to proteins and modifies other carbohydrates that were attached to proteins in the RER.
• It is where some polysaccharides for the plant cell wall are synthesized
• It cuts certain large precursor proteins transferred from the RER into smaller, functional fragments.

Lysosomes

• Vesicles move from ER to cis-Golgi to medial-Golgi to trans-Golgi to the cell membrane or lysosome.
• Lysosomes are cellular "disposals," compartments for the breakdown of food, other cells, or foreign objects.
• Primary lysosomes originate from the Golgi apparatus and contain digestive enzymes.
• Macromolecules (proteins, polysaccharides, nucleic acids, and lipids) are hydrolyzed into their monomers in the lysosomes.
• Digestion products diffuse into the cytosol.
• Undigested materials are released via exocytosis.
• The interior of the lysosome is more acidic (pH 5) than the external cytoplasm (pH 7.2).
• Phagocytosis is where external particles are engulfed, fuse with primary lysosomes, undergo digestion, and digestion products diffuse into cytosol for recycling while undigested particles are excreted extracellularly.
• Mitochondria harvest chemical-bond energy from energy-rich molecules and release energy as ATP (adenosine triphosphate).
• Mitochondria reproduce and divide independently of the central nucleus.
• Range from 1 - >100,000 per cell.
• One membrane is smooth and permeable.
• The inner membrane is folded, called cristae, and is semi-permeable.
• The inner membrane has large protein complexes that participate in cellular respiration.
• The matrix contains molecules for respiration, DNA, and ribosomes for specific proteins.
• Chloroplasts divide independently of the cell nucleus.
• Chloroplasts contain the green pigment chlorophyll and are the sites of photosynthesis.
• Chloroplasts have two membranes and a series of internal membrane stacks.
• An individual unit is called a Thylakoid.
• A stack of thylakoids is a Granum.
• Membranes of the thylakoids contain chlorophyll and other pigments that harvest light energy for photosynthesis.
• Thylakoids of one granum may be connected to those of other grana.
• Chloroplast stroma contains DNA and ribosomes for chloroplast-specific proteins.
• Peroxisomes are organelles that accumulate toxic peroxide byproducts, such as hydrogen peroxide.
• Peroxides are safely broken down inside the peroxisomes without mixing with other parts of the cell.
• Glyoxysomes are found only in plants.
• Glyoxysomes are locations where stored lipids are converted into carbohydrates for transport to growing cells.
• Vacuoles occur in many eukaryotic cells, particularly those of plants, fungi, and protists.
• Vacuoles can take up more than 90% of the cell volume and grow as the cell grows.
• Water enters the vacuole due to dissolved substances, causing it to swell.
• A mature plant cell does not swell, but stiffens from increased water pressure, called turgor.
• Vacuoles contain some of the pigments in the petals and fruits of flowering plants, especially blue and pink ones.
• Pigments help attract animals that assist in pollination or seed dispersal.
• Vacuoles in seeds hydrolyze stored proteins into monomers, which are used as food by developing plant seedlings during germination.
• Vacuoles store toxic molecules and waste products.
• Stored materials deter some animals from eating the plants, which thus contributes to plant defense and survival.
• Tannins are an example.

Cytoskeleton

• The Cytoskeleton supports the cell and maintains its shape.
• It holds cell organelles and other particles in position within the cell.
• The Cytoskeleton moves organelles and other particles around in the cell.
• It is involved with movements of the cytoplasm, called cytoplasmic streaming.
• It interacts with extracellular structures, helping anchor the cell in place.
• Microfilaments are assembled from monomers of actin.
• Microfilaments can be single filaments, bundles, or in networks.
• Microfilaments are about 7 nm in diameter
• Microfilaments can be up to several micrometers long
• They help the entire cell or parts of the cell move
• They determine and stabilize cell shape
• Includes "Plus" and "Minus” ends.
• Actin polymerization is reversible.
• Elongate faster at the “Plus” end with more Actin added.
• Shorten with removal of Actin.
• Localized changes in cell shape.
• Cytoskeleton is involved in e.g. pinching of cell during division.
• Cytoskeleton forms cell extensions for movement for the Amoeba pseudopod.
• Cytoskeleton form a mesh network on inside of cell membrane that is Rigid, supports cell shape.
• These Cytoskeletal filaments are more permanent than the other two types and do not continually form and re-form.
• Intermediate Filaments and more permanent than the other two types that do not continually form and re-form.
• They anchor cell structures in place and Help maintain the positions of the nucleus and other organelles in the cell.
• Intermediate Filaments also resist tension
• They maintain rigidity in body surface tissues by connecting desmosomes.
• Microtubules are 25nm in diameter, several micrometers long. Assembled from they are dimers of α-tubulin and β-tubulin.
• Microtubules form rigid internal skeleton for some cells.
• Microtubules act as a framework along which motor proteins can move structures within the cell.

Motor Proteins

• Microtubules also include “Plus” end and "Minus" end
• Tubulin dimers can be rapidly added or subtracted at the "Plus" end, lengthening or shortening the microtubule.
• Some radiate from microtubule organizing center
• Microtubules don't move themselves, but by polymerizing and depolymerizing they can get to new parts of the cell.
• Microtubules act as a framework for the assembly of cellulose.
• Microtubules help orient the cellulose fibers of the cell wall.
• They are involved in the movement of chromosomes during cell division and serve as tracks for motor proteins.
• Motor proteins are associated with microtubules
• Kinesins move materials toward the "plus" end.
• Dyneins move materials toward the "minus" end.
• One function of motor proteins are the Movement of organelles like vesicles.
• Another function of motor proteins is the Movement of chromosomes during cell division and Kinesin walking.
• Dynein allows movement in cilia and flagella.
• The Plant Cell Wall provides support for the cell and plant by remaining rigid.
• It acts as a barrier to infection by fungi and organisms that cause plant diseases.
• It contributes to plant form by growing as the plant cells expand.
• Cellulose fibers are embedded in the Plant Cell Wall.
• It contains other complex polysaccharides and proteins.
• The middle lamella is the region between two adjacent cell walls
• Plasmodesmata are cell membrane-lined channels between adjacent cells which Extend through the cell walls.
• They connect cytoplasms of adjacent plant cells and permit the movement of water, ions, small molecules, RNA, and proteins.
• The animal cell extracellular matrix is where animal cells surrounded by, or in contact with, are extracellular matrix, containing:
• Protein Fibers such as collagen (most abundant protein in mammals, >25% of the protein in the human body).
• Matrix of glycoproteins termed proteoglycans
• Proteins that link protein fibers and proteoglycans together the animal extracellular matrix holds cells together in tissues and contributes to the physical properties of cellular aggregates called tissues
• Cartilage and bone are part of connective tissue and the Mineral component of bone is laid down on an organized extracellular matrix which helps filter materials passing between different tissues (e.g. kidneys).
• Extracellular matrix also orients cell movements during embryonic development and tissue repair, and plays a role in chemical signaling from one cell to another.
• The Theory of endosymbiosis is where Symbiosis means "living together".
• Some organelles-the mitochondria and the plastids-arose not by an infolding of the cell membrane but by one cell ingesting (but not digesting) another cell.
• The ingested cell lost its autonomy and some of its functions
• In endosymbiosis, Many of the ingested cell's genes were transferred to the host's DNA and Mitochondria and plastids in today's eukaryotic cells are the remnants of these symbionts.
• They Retain some specialized functions where the original chloroplast origin was most probably photosynthetic prokaryotes like cyanobacteria.
• Tests demonstrate that the drug cytochalasin B prevented microfilament formation from monomeric precursors, so complementary experiments show that the drug did not poison other cellular processes.
• Cytochalasin Tests determined that the Amoeboid cell movements are caused by the cytoskeleton through the addition of chemicals to test cell ability to move
• Some controls are:
• Cycloheximide - inhibits new protein synthesis
• Dinitrophenol - inhibits new ATP formation (energy)
• Colchicine - inhibits the polymerization of microtubules