cell theory:

1. all living things are composed of one or more cells

2. the cell is the basic unit of life

3. all cells are related by their descent from an ancestral cell

Eukaryotic cells:

• have membrane-bound organelles

• cytoplasm in the region between the plasma membrane and nucleus

• have a nucleus (serves as a site for DNA)

  • nucleus enclosed within a membranous nuclear envelope

• eukaryotic domain: includes plants, animals, fungi, and protists

  • can be as much as 100x larger than prokaryotic cells

procaryotic cells:

• cells may have a nucleoid (a region where DNA is stored but is not membrane-bound)

  • no nucleus

  • no membrane-bound organelles

    • cytoplasm bound by the plasma membrane

• archaea and bacteria domains

• ribosomes are not membrane enclosed

all cells:

• all cells on earth possess: (reflecting the common ancestry of all known life)

  • plasma membrane

  • cytosol

  • chromosomes (genome)

  • ribosomes

plasma membrane:

• a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell

• the general structure of a biological membrane is a double layer of phospholipids

  • the nonpolar nature of the interior of the lipid bilayer allows for small, nonpolar molecules to pass into and out of the cell with relative ease

    

Chromosomes are typically the lengths of DNA that contain genes

• a gene is a sections of DNA that codes for a protein

ribosomes are small cellular parts responsible for protein synthesis, based on the sequence of a strand of messenger RNA (mRNA) - mRNA sequence originate from the genome of a cell

• ribosomes are composed of ribosomal RNA (rRNA) and proteins

• composed of a small and large subunit

• all cells possess ribosomes, indicating the common ancestry of life on earth

Eukaryotic organelles:

• the endoplasmic reticulum exits in 2 forms: (endoplasmic reticulum - a network of membrane tubes within the cytoplasm of eukaryotic cells)

  • functions:

    • provides mechanical support

    • plays a role in intracellular transportation

  • smooth endoplasmic reticulum (smooth ER)

    • the site of cellular detoxification and lipid synthesis

    • does not have ribosomes attached

  • rough endoplasmic reticulum (rough ER)

    • has ribosomes fastened to its surface (attached to its membrane) and helps compartmentalize the cell

      • associated with packaging the newly synthesized proteins made by attached ribosomes for possible export from the cell (either out or inside membrane)

      • Functions:

        • carries out protein synthesis on ribosomes that are bound to its membrane

    

• golgi complex (golgi apparatus)

  • a series of membranous, flattened sacs (series of flattened membrane-bound sacs found in eukaryotic cells)

    • have incoming and secretory vesicles (membrane containers that help move material from one part of the cell to the next)

  • responsible for modifying newly-made proteins and packaging them for proper trafficking/distribution

    • involved in the correct folding and chemical modification of newly synthesized proteins and packaging proteins for trafficking

    • travels thru the golgi membranes (from short to long) and endures modification

    

• mitochondria

  • possess a double membrane

    • outer membrane is smooth

    • inner membrane is highly folded and convoluted (folds called cristae)

  • functions in production of ATP energy that eukaryotic cells can use for cell work

  • 

• lysosomes

  • membranous sacs containing hydrolytic enzymes for intracellular digestion and apoptosis (programmed cell death)

    • can be used to digest a variety of materials such as damaged cell parts or macromolecules

    • hydrolytic enzymes, contribute to cell function:

      • intracellular digestion

      • recycling of organic materials

      • programed cell death (apoptosis)

  • (membrane-enclosed sacs found in some eukaryotic cells that contain hydrolytic enzymes)

    

• vacuoles

  • membrane-bound sacs mostly used for storage (of nutrients, wastes, water)

  • membrane-bound sacs found in eukaryotic cells

    • in plants, vacuoles aid in retention of water for turgor pressure

      • turgor pressure - an internal cellular force, usually caused by water pushing up against the plasma membrane and cell wall

  • play a variety of roles from storage or water and other macromolecules to the release of waste from a cell

    • storage and release of water, macromolecules, and cellular waste products

      

• chloroplasts

  • found in eukaryotic cells such as photosynthetic algae and plants

  • posses a double outer membrane

  • perform photosynthesis

    • specialized for capturing energy from the sun and producing sugar for the organism

      

Plant vs animal cells:

• mitochondria vs chloroplast structure

  • the double-membrane structure of chloroplasts and mitochondria significantly increases surface are and efficiency

    • chloroplasts

      • specialized for photosynthesis (capturing energy from the sun to produce sugar)

      • contain stacks of membranous secs, called thylakoids

        • highly folded membrane compartments that are organized in stacks are called grana

        • folding of these internal membranes increases the efficiency of these reactions

        • light-dependent reactions occur here

        • stacks of thylakoids are referred to as grana

        • membranes contain chlorophyll pigments that comprise of the photosystems and electron transport proteins can be found between the photosystems, embedded in the thylakoid membrane

      • stroma is the fluid that fills the chloroplast

        • fluid between the inner chloroplast membrane and outside thylakoids

        • the carbon fixation (Calvin-Benson Cycle) reactions occur here

          

    • mitochondria

      • double membrane provides compartments for different metabolic reactions

      • capture energy from macromolecules

      • possess a highly-convoluted inner membrane, with folds called cristae

        • electron transport and ATP synthesis occur in the inner mitochondrial membrane

        • folding of the inner membrane increases the surface area, which allows for more ATP to be made

      • the fluid inside the inner and outer membrane is called the matrix

        • the Krebs cycle (citric acid cycle) reactions occur in the matrix

      • the space between the inner and outer membrane is the intermembrane space

        • 

surface area-to-volume

• biological systems must be able to efficiently:

  • obtain necessary recourses

  • eliminate wastes

  • acquire or dissipate thermal energy

  • exchange chemicals and energy with the surrounding environment

• the surface area to volume ratio of a cell is critical (SA:V)

  • small cells have greater surface area relative to volume

  • high surface area to volume ratios allow cells to have greater efficiency (more efficient exchange of materials with the environment)

  • as cells increase in volume, the relative surface area decreases and the demand for internal resources increases

    

• some cells possess highly convoluted membranes to increase surface area while minimally increasing volume

  • root hair cells on a plant root tissue increase surface area for water absorption

  • villi and microvilli on intestinal epithelial cells (in the small intestine) increase surface area for nutrient absorption

  • ex) tongue taste receptors

  • as organisms and/or cells increase in size, metabolic efficiency decreases, including efficiency in heat loss to the environment

  • as organisms increase in size, their SA:V ratio decreases, affecting properties like rate of heat exchange with the environment

    • ex: elephant ears

in addition to high surface area to volume ratio, many organisms possess beneficial adaptations to maximize exchange of materials with the environment

• gas exchange

  • the process by which gaseous molecules from the environment are absorbed by a cell while waste gases from the cell are released into the environment

    • ex) stomata in plant cells

cell membrane

• establishes a unique internal environment inside the cell (provide a boundary between the interior of the cell and the outside environment which allows the cell to control the transport of materials in and and of the cell)

• usually composed of a double layer of phospholipids and a variety of proteins

  • phospholipids are composed of a hydrophilic phosphate head and two hydrophobic fatty acid tails

    • phospholipids are amphipathic

      • hydrophilic phosphate head is polar

      • hydrophobic fatty acid tail is nonpolar

    • recall how phospholipids interact with water to form a bilayer

      • phospholipids spontaneously form a bi-layer in an aqueous environment

      • tails are located inside the bilayer

      • heads are exposed to the aqueous outside and aqueous inside environments

        

• proteins are scattered throughout the membrane

  • peripheral proteins are on the membrane’s exterior or interior surface

    • loosely bound to the surface of the membrane

    • hydrophilic with charged and polar side groups

  • integral proteins penetrate the membrane

    • span the membrane

    • hydrophilic with charged and polar side groups

    • hydrophobic with nonpolar side groups penetrate hydrophobic interior bilayer

    • ex) transmembrane proteins pass completely through the bilayer

  • many functions, examples include:

    • transport

    • cell-to-cell recognition

    • enzymatic activity

    • signal transduction

    • intercellular joining

    • attachment for extracellular matrix or cytoskeleton

• structured as a mosaic of protein molecules in a fluid bilayer of phospholipids

• fluid mosaic model - a moving phospholipid bilayer composed of varying types of molecules (proteins, steroids, carbohydrates)

  • the structure is not static and is held together primarily by hydrophobic interactions which are weaker than covalent bonds

  • most lipids and some proteins can shift and flow along the surface of the membrane or across the bilayer

  • cholesterol, a type of steroid, is randomly distributed and wedged between phospholipids in the cell membrane of eukaryotic cells

    • cholesterol regulates bilayer fluidity under different environmental conditions

  • diversity and location of the (molecules) carbohydrates and lipids enable them to function as markers

    • glycoproteins - one or more carbohydrate attached to a membrane protein

    • glycolipids - lipid with one or more carbohydrate attached

• other membrane components include steroids, glycoproteins, and glycolipids

  • membrane components are fluid and migrate throughout the structure

  • steroids can contribute to membrane fluidity

    • increased numbers of steroids increase fluidity

  • glycoproteins and glycolipids are useful in cellular identification

    • “glyco” refers to a carbohydrate chain attached to either a protein or lipid

cytoskeleton

• while not part of the membrane itself, it interacts with both the exterior and interior of the cell

cell walls

• composed of complex carbohydrates

  • plants - cellulose

    • polysaccharide

  • fungi - chitin

    • polysaccharide

  • prokaryotes - peptidoglycan

    • polymer consisting of sugar and amino acids

• as a structural boundary:

  • protects and maintains the shape of the cell

  • prevents against cellular rupture when internal water pressure is high

  • helps plants stand up against the force of gravity

• as a permeable barrier:

  • plasmodesmata - small holes between plant cells that allows the transfer of nutrients, waste, and ions

    • animal cells do not have cell walls

the cell membrane’s structure results in selective permeability

• selective permeability - the membrane’s ability to regulate the molecules/ions that are able to pass in and out of the intracellular environment

  • direct consequence of membrane structure

    

• the hydrophobic interior of the lipid bilayer makes it very unlikely that polar/large/charged molecules can cross

  • small nonpolar molecules cross with ease

    • ex) O2 , CO2, N2

  • small, polar molecules may cross, but very slowly

    • ex) H2O

    • small polar molecules, like H2O, can pass directly through the membrane in minimal amounts

    

• large/polar/charged (hydrophilic) substances require a transport protein to move through a cell membrane

  • the transport protein has a specific shape and polarity to accommodate a specific polar/charged/large substance

    

  • concentration gradient - when a solute is more concentrated in one area than another

    • a membrane separates two different concentrations of molecules

    • naturally will flow from high to low concentration in an attempt to create equilibrium

    • (Brownian motion - the random uncontrolled movement of particles in a fluid)

  • passive transport - the process by which molecules/ions diffuse across a membrane from high to low concentration

    • net movement of molecules from high concentration to low without metabolic energy, such as ATP, needed

    • plays a primary role in the import of materials and the export of wastes

    • diffusion is a natural phenomenon wherein particles spread out from high to low concentration

      • movement of molecules from high concentration to low concentration

      • small nonpolar molecules pass freely across cell membrane (N2, O2, CO2)

      • small amounts of very small polar molecules, like water, can diffuse across a cell membrane

    • because particles are moving with the concentration gradient, no energy input is required

      • gradient is the difference in concentrations between two different areas

        • a larger difference indicates a steeper gradient and a faster rate of diffusion

    • plays a significant role in absorption of nutrients and removal of wastes

      

  • active transport

    • moves molecules and/or ions against their concentration gradient (from low to high concentration)

      • therefore requires an energy input from the environment

      • active transport requires the direct input of energy (such as ATP) to move molecules from regions of low concentration to regions of high concentration

      

    

    • requires a transport protein, known as a pump, to shuttle molecules through the membrane against the gradient

      • pumps are a type of carrier protein

        • protein pumps are carrier proteins used in active transport

          • requires metabolic energy (such as ATP)

          • establishes and maintains concentration gradients

      • pumps require energy to…

        • move molecules against the concentration gradient

        • maintain concentration gradients, preventing the cell from reaching equilibrium

          • establishes and maintains concentration gradients

      • the energy usually supplied in the form of ATP

      • Na+/K+ ATPase (aka the sodium-potassium pump)

        • a useful active transport protein in maintaining ion gradients in animal cells

          • membrane potential is the voltage difference across the membrane

          • voltage is created by differences in the distribution of positive and negative ions across a membrane

          

          1. 1

          2. 2

          3. 3

          4. 4

          5. 5

          6. 6

        • Na+/K+ ATPase (Na+/K+ pump) contributes to the maintenance of the membrane potential

          • 3 Na+ pumped out

          • 2 K+ pumped in

    • cotransport - secondary active transport that uses the energy from an electrochemical gradient to transport two different ions across the membrane through a protein

      • symport - two different ions are transported in the same direction

      • antiport - two different ions are transported in opposite directions

    • the cell membrane allows for the creation of gradients

      • electrochemical gradient

        • type of concentration gradient

        • relies on membrane potential - electrical potential difference (voltage) across a membrane

      • membranes may become polarized by the movement of ions across the membrane

facilitated diffusion

• movement of molecules from high concentration to low concentration through transport proteins

  • allows for hydrophilic molecules and ions to pass through membranes

    • large and small polar molecules

    • large quantities of water can pass through aquaporins

    • charged ions, including Na+ and K+, require channel proteins

• speeds diffusion of large/polar/charged molecules by utilizing transport proteins

  • carrier protein - spans the membrane and change shape to move a target molecule from one side of the membrane to the other

  • channel protein - a hydrophilic tunnel spanning the membrane that allow specific target molecules to pass through

    • aquaporins are transport proteins specialized for the movement of water

      • large quantities of water move this way

    • ion channels are specialized for the movement of particular ions

      • ex) Na+ , Cl-

    • the movement of ions in one direction can create an electrochemical gradient across cell membrane

      • this creates a membrane potential, polarizing the membrane

      

Osmosis

• the diffusion of water through a selectively permeable membrane

  • differences in relative solute concentrations can facilitate osmosis

  • large quantities of water move via aquaporins

• Osmolarity - the total solute concentration in a solution

  • water has high solvency abilities

  • solute is the substance being dissolved

  • solvent is a substance that dissolves a solute

  • solution is a uniform mixture of one or more solutes dissolved in a solvent

    • (solvent + solute = solution)

• also defined as the passive transport of water from areas of high water concentration to low water concentration

  • water moves by osmosis into the area with a higher solute concentration

    • water concentrations and solute concentrations are inversely related

    • water would diffuse out of a hypotonic environment to a hypertonic environment

    • solutes diffuse along their own concentration gradients, from the hypertonic environment into the hypotonic environment

• water diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration until the solute concentration is equal on both sides

  

Tonicity

• the measurement of the relative concentrations of a solute between two solutions (inside and outside of the cell)

• internal cellular environments can be hypotonic, hypertonic, or isotonic to external environments

• the ability of a surrounding solution to cause a cell to gain or loose water

  • isotonic solution is one where solute concentration is the same as that inside the cell; no net water movement across the plasma membrane

    • equal concentrations of solute and solvent

    • when a cell is in an isotonic environment, a dynamic equilibrium exists with equal amounts of water moving in and out of the cell at equal rates

      • no net movement of water takes place

  • hypertonic solutions have a solute concentration greater than that inside the cell; cell loses water

    • more solute less solvent

  • hypotonic solutions have a solute concentration less than that inside the cell; cell gains water

    • less solute and more solvent

      

osmoregulation

• the ability of organisms to maintain water balance with their environment and control their internal solute concentration

  • contractive vacuole - an adaptation possessed by freshwater protists, Paramecia, to osmoregulate and maintain homeostasis

• in plant cells, osmoregulation maintains water balance and allows control of internal solute composition/water potential

  • environmental hypertonicity

    • less cellular solute and more cellular water

    • plasmolysis (water leaves the plant cell)

  • isotonic solution

    • equal solute and water

    • flaccid

  • environmental hypotonicity

    • more cellular solute and less cellular water

    • turgid (water rushing into cell)

• the cell wall helps maintain homeostasis for the plant in environmental hypotonicity

  • osmotic pressure is high outside of the plant cell due to environmental hypotonicity

  • water flows into the plant vacuoles via osmosis causing the vacuoles to expand and press against the cell wall

  • the cell wall expands until it begins to exert pressure back on the cell, this pressure is called turgor pressure

  • turgidity is the optimum state for a plant cell

• in animal cells, osmoregulation maintains water balance and allows control of internal solute composition/water potential

  • environmental hypertonicity

    • less cellular solute and more cellular water

    • shriveled

  • isotonic solution

    • equal solute equal water

    • normal

  • environmental hypotonicity

    • more cellular solute and less cellular water

    • lysed

• 

water potential

• measures the tendency of water to move by osmosis

  • calculated from pressure potential and solute potential

• a measurement that combines the effects of solute concentration and pressure

  • water potential of pure water in an open container is 0

    • no solute, no pressure

• solute potential and pressure potential contribute to the direction of water movement with regard to cells

• the more solute in a solution, the greater the interactions between the solutes and the polar water molecules

• formula for calculating water potential: Ѱ = Ѱ_P + Ѱ_s

  

• water flows from areas of high water potential to low water potential

  • the values of water potential can be positive, negative, or zero

  • the more negative the water potential, the more likely water will move into the area

    • Solute potential is represented by Ѱ_s and is always negative in value

    • Ѱ_s is determined by the ionization constant of the solute, the molar concentration of the solution, the temperature in Kelvin and the pressure constant, R

      • Ѱ_s = -iCRT

        • i = ionization constant

          • sucrose = 1, NaCl (salt) = 2

        • C = molar concentration

          • molarity (M) = moles of solute/volume of a solution

        • R = pressure constant

          • 0.0831 L Bars/mol K

        • T = temperature in kelvin

          • temperature in Celsius + 273 = kelvin

        • *the addition of solutes is equal to a more negative solution potential

    • Pressure potential is represented by Ѱ_p and is 0 bars in an open container at STP (standard temp and press.)

      • unit of pressure - bars

  • increasing the amount of solute in water will cause

    • an increase in solute potential

    • a decrease in water potential

  • increasing water potential will cause

    • an increase in pressure potential

  • decreasing pressure potential will cause

    • a decrease in water potential

  • in an open system, pressure potential is zero, so water potential is equal to solute potential

cells are capable of moving large quantities of substances into and out of the cytoplasm

• endocytosis - the process by which a cell can engulf extracellular material

  • in endocytosis, the cell uses energy to take in macromolecules and particulate matter by forming new vesicles derived from the plasma membrane

    • phagocytosis - endocytosis of solid particles (cell takes in large particles)

    • pinocytosis - endocytosis of liquid matter (cell takes in extracellular fluid containing dissolved substances)

    • receptor-mediated endocytosis - receptor proteins on the cell membrane are used to capture specific target molecules

• exocytosis - endocytosis in reverse; removes large cellular waste or release cellular products

  • internal vesicles use energy to fuse with the plasma membrane and secrete large macromolecules out of the cell

    • ex: proteins such as signaling proteins

    • ex: hormones

    • ex: waste

      

compartmentalization

• membranes and organelles isolate cellular functions, thereby increasing efficiency

  • prokaryotes isolate functions into cellular areas

  • compartmentalization reduces competition for space/resources/energy needed to perform cellular functions

    • membranes minimize competing interactions

  • compartmentalization in membrane-bound organelles also increases surface area which leads to higher efficiency

    • cellular compartments allow for various metabolic processes and specific enzymatic reactions to occur simultaneously, increasing the efficiency of the cell

      • ex: the hydrolytic enzymes of the lysosome function at an acidic environment

        • by having this compartmentalization, the inside of the lysosome can maintain a more acidic pH and allow for efficient hydrolysis to occur, while the rest of the cytoplasm can remain a more neutral environment

• Organelles possess structural features that suit the various chemical reactions they perform - membrane folding maximizes surface area for metabolic reactions to occur

  • Mitochondrial inner membranes are highly convoluted, and the increased surface area of the cristae allow for increased numbers of ETC proteins and ATP synthases, maximizing oxidative phosphorylation

  • Grana in chloroplasts also increase surface area for Photosystems and ETC proteins in the thylakoid membranes, thereby increasing photophosphorylation and NADPH in the light reactions

endosymbiont theory

• serves as the explanation for the origins of mitochondria and chloroplasts

  • Symbiosis describes a close, long-term, physical interaction between two different organisms

• states that an ancestral eukaryotic cell engulfed an ancestral mitochondrion, establishing a mutualistic relationship

  • Mutualism is a type of symbiosis where both parties benefit

    

• The ancestral eukaryote, after engulfing an ancestral mitochondrion, survived and reproduced often, establishing a lineage of eukaryotes that too possessed mitochondria

  • the nucleus and other membranes (e.g. ER) are theorized to have formed from the infoldings of the plasma membrane

  • mitochondria evolved from previously free living prokaryotic cells via endosymbiosis

    • a free-living aerobic prokaryote was engulfed by an anaerobic cell through endocytosis

    • the engulfed prokaryotic cell did not get digested by the engulfing cell; this arrangement became mutually beneficial

    • over time, the engulfed cell lost some of its independent functionality and became the mitochondria of the eukaryotic cell

  • chloroplast evolved from previously free-living prokaryotic cells via endosymbiosis

    • a free-living photosynthetic prokaryote was engulfed by another cell through endocytosis

    • the engulfed prokaryotic cell did not get digested by the engulfing cell; but rather each benefitted from the arrangement

    • over time, the engulfed cell lost some of its independent functionality and became the chloroplast of the eukaryotic cell

  • proof / evidence

    • both mitochondria and chloroplasts have double membranes, which function to regulate the passage of materials into and out of the cell and to maintain a stable internal environment

    • like prokaryotic cells; mitochondria and chloroplasts

      • both have their own circular DNA encoding genetic information and can reproduce by a similar process used by prokaryotes

      • both contain their own ribosomes that synthesize proteins

• comparison of compartmentalization of prokaryotic and eukaryotic cells

  • both have a plasma membrane

    • that separates their internal environment from their surrounding environment

  • prokaryotes have nucleoid region

    • internal regain that contains genetic material

  • eukaryotic cells have additional internal membranes and membrane-bound organelles that compartmentalize the cell

    • genetic materials is contained within a membrane-bound nucleus

• A descendant of this ancestral lineage later engulfed a photosynthetic prokaryote (an ancestral chloroplast) and also survived and reproduced often

  • The lineage produced by this second endosymbiosis lead to the plant cells extant on Earth

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