4.1: Studying Cells

• Cell -> tissue -> organ -> organ system

• Animal and plant cells are eukaryotic and bacterial are prokaryotic

• Microscope

  • The specimen that is right-side up and facing right on the microscope slide appears upside down and facing left because microscopes use two sets of lenses to magnify the image

  • Light microscope best for living organisms(to see individual cells, you would have to stain, but staining kills the cells)

  • Magnification - the process of enlarging an object

  • Resolving power - the ability to distinguish two adjacent structures as separate(higher resolution = good)

  • Scientists typically use electron microscopes

    • Use a beam of electrons instead of light, allowing higher magnification and higher resolving power

    • Cannot view living cells

• Antony van Leeuwenhoek observed movements of single-celled organisms or animalcules

  • Discovered bacteria and protozoa

• Unified cell theory - all living things are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells

4.3: Eukaryotic Cells

• Eukaryotic cells have a nucleus with a double membrane that encloses DNA unlike prokaryotic cells

  • Also, tend to be larger and have a variety of membrane-bound organelles

• Organelles are bound by membranes composed of phospholipid bilayers embedded with proteins to store hydrolytic enzymes and synthesize proteins

• The nucleolus in the nucleus is the site of ribosome assembly

  • Functional ribosomes are in the cytoplasm or attached to rough endoplasmic reticulum to synthesize proteins

• Golgi apparatus modifies and packages small molecules like lipids and proteins for distribution

• Mitochondria and chloroplasts capture energy

• Peroxisomes oxidize fatty acids and amino acids and break down hydrogen peroxide formed from these reactions, preventing it from going into the cytoplasm

• Vesicles and vacuoles store substances

  • Vacuole stores pigments, salts, minerals, nutrients, proteins, and degradation enzymes to maintain rigidity

  • Animal cells have centrosomes and lysosomes instead but lack cell walls

• Eukaryotic cells also have rod-shaped chromosomes unlike prokaryotes

• Plasma membrane

  • Phospholipid bilayer

  • Controls passage of molecules, ions, water, and oxygen(CO2 and ammonia leave the cell)

  • Plasma membranes of cells that absorb are folded into microvilli(inner part of the small intestine)

    • Celiac disease has an immune response to gluten, damaging microvilli

• Cytoplasm

  • Cytosol or cytoskeleton, various chemicals

  • Semi-solid consistency due to proteins and sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and ions

  • Metabolic reactions like protein synthesis take place

• Nucleus

  • Directs synthesis of ribosomes and proteins

  • The nuclear envelope covers the nucleus(phospholipid bilayer)

    • Punctuated with pores that control the passage of ions, molecules, and RNA

  • Nucleoplasm is a semi-solid fluid and has chromatin and nucleolus

  • Chromatin - unwound protein-chromosome complexes

  • Nucleolus clusters rRNA with associated proteins to assemble ribosomal subunits to transport out of pores

• Ribosomes

  • Receive orders of protein synthesis from DNA(mRNA) and mRNA travels to ribosomes, which translate code into a specific order of amino acids

• Mitochondria

  • Cellular respiration makes ATP with glucose

  • Mitochondria uses oxygen and produces CO2

  • Muscle cells have a high concentration of mitochondria

  • The inner layer has folds called cristae

• Peroxisomes can detoxify poisons in the body and glyoxysomes in plants convert stored fats into sugars

• Membranes of vesicles can fuse with plasma membranes or other membranes unlike that of vacuole

• Centrosome

  • The organizing center contains a pair of centrioles with nine triplets of microtubules

  • Replicates and pulls apart duplicated chromosomes

• Lysosome

  • Garbage disposal

  • Breakdown proteins, polysaccharides, lipids, nucleic acids, and old organelles

  • Enzymes are at lower pH, so more acidic than cytoplasm

• Chloroplast have stacked fluid-filled membranes called thylakoids(stacks are granum)

  • Fluid around grana is stroma

• Central vacuole

  • Key role in regulating cell’s concentration of water in changing conditions

  • If water concentration in soil lowers, water moves out of central vacuoles and cytoplasm, the central vacuole shrinks and leaves the cell wall unsupported

4.4: The Endomembrane System and Proteins

• Eukaryotic cells also have an endomembrane system that has the plasma membrane, nuclear envelope, lysosomes, vesicles, ER, and Golgi apparatus

• RER - protein synthesis and modification

• SER - synthesizes carbs, lipids, and steroids; detoxifies poisons; and stores calcium ions

• Lysosomes digest macromolecules and destroy pathogens

• Proteins in RER travel to the Golgi apparatus

  • If proteins are hydrolytic enzymes, they go to lysosomes

• ER

  • The endomembrane system is a group of membranes and organelles that work to modify, package, and transport

  • ER is a series of interconnected membranous sacs and tubules that modify proteins and synthesize lipids(performs in rough and smooth)

  • The hollow portion of tubules are lumen or cisternal space

  • Rough ER

    • Ribosomes transfer proteins to the lumen where they go through structural modifications like folding or side chains, which are incorporated into cellular membranes

    • Also makes phospholipids

    • It can also transport proteins or phospholipids through vesicles

  • Smooth ER

    • No ribosomes

    • Muscles cells, sarcoplasmic reticulum stores calcium ions to contract muscles

• Golgi apparatus

  • A series of flattened membranes where vesicles go before the final destination

  • The receiving side is called the cis face and the opposite is the trans face

  • Vesicles fuse with cis, empty contents, contents go through further modifications like the addition of short chains of sugar molecules, and then proteins are tagged with phosphate groups or other small molecules, and then they are put into secretory vesicles that bud from the trans face

  • Cells with a lot of secretory activity have more golgi like salivary glands

  • Plant cells - Golgi have the additional role of synthesizing polysaccharides for the cell wall and other parts of the cell

• Lysosomes

  • An example is a white blood cell called a macrophage

  • phagocytosis/endocytosis - section of the plasma membrane of the macrophage folds in and engulfs a pathogen

    • The invaginated section with the pathogen pinches itself off from the plasma membrane and becomes a vesicle that fuses with lysosome so hydrolytic enzymes can destroy the pathogen

4.5: Cytoskeleton

• All cells have cytoskeletons with different types of protein elements like microfilaments, intermediate filaments, and microtubules

• Provides rigidity and shape to the cell, facilitates cellular movement, anchors nucleus and other organelles in place, moves vesicles through the cell, and pulls replicated chromosomes to poles of a dividing cell

  • Protein elements are integral to the movement of centrioles, flagella, and cilia

• Microfilaments

  • Narrowest of protein fibers and function in cellular movement

  • Made of intertwined stands of a globular protein called actin, also known as actin filaments

  • Actin is powered by ATP to assemble its form, which serves as a track for the movement of myosin, a motor protein

    • Allowed actin to engage in cellular events requiring motion like cell division and cytoplasmic streaming, which is a circular movement of cell cytoplasm in plant cells

    • Actin and myosin filaments sliding against each other causes muscles to contract

  • Can depolymerize/disassemble and reform quickly, allowing a cell to change its shape and move

    • Blood cells make good use of this ability by moving to the site of an infection and phagocytizing the pathogen

• Intermediate filaments

  • Several strands of fibrous proteins that are wound together

  • Bear tension, maintaining the shape of the cell, and anchor cell structures in place

  • Most diverse with several types of fibrous proteins like keratin

• Microtubules

  • Small hollow tubes

  • Walls are made of polymerized dimers of alpha and beta tubulins, two globular proteins

  • Are the broadest components of the cytoskeleton

  • Help cells resist compression, provide a track of where vesicles move, and pull replicated chromosomes to opposite ends

  • It can also break and form quickly

  • Structural elements of flagella, cilia, centrioles

• Flagella and cilia

  • Flagella - long, hair-like structures that extend from the plasma membrane and are used to move an entire cell

    • Usually just one or two

  • Cilia usually extend along the entire surface of the plasma membrane(short, hair-like structures that are used to move cells or substances on the outer surface of the cell)

    • For example, cilia of cells lining the Fallopian tubes of the respiratory tract that trap matter and move it toward the nostrils

  • Flagella and cilia share a common structure of microtubules called a 9+2 array

    • A single flagellum or cilium is made of a ring of nine microtubule doublets, surrounding a single microtubule doublet in center

5.1: Components & Structure

• Integral proteins span the membrane and can transport materials into or out of cells(proteins can be hydrophilic or hydrophobic based on placement)

• Peripheral proteins are on the exterior and interior surfaces of membranes and can serve as enzymes, structural attachments for fibers of the cytoskeleton, and part of a cell’s recognition sites

  • Cell-specific proteins play a vital role in immune function, enable cells of a certain type to identify each other when forming a tissue, and allow hormones and other molecules to recognize target cells(proteins float throughout the membrane)

• Membrane can also transmit signals by integral proteins such as receptors

  • Proteins are both receivers of extracellular inputs and activators of intracellular processes

  • Receptors provide extracellular attachment sites for effectors like hormones and growth factors, also activating intracellular response cascades when effectors bound

• For a typical human cell in the plasma membrane, protein is 50%, lipids are 40% and carbs are 10%(varies with different cell membranes)

• Carbs are present only on the exterior surface of the plasma membrane and are attached to proteins, forming glycoproteins, or attached to lipids, forming glycolipids

• Phospholipids

  • Composed of amphiphilic, phospholipid molecules

  • Hydrophobic tails tend to be non-polar

  • Hydrophilic forms hydrogen bonds with water and other polar molecules on both the exterior and interior of the cell while the interior of the cell membrane is hydrophobic

  • Phospholipid molecule has a three-carbon glycerol backbone with 2 fatty acids attached to carbons 1 and 2 and a phosphate group attached to the 3rd carbon

  • Amphiphilic because the head has a polar/negative charge while the tail is non-polar(dual-loving)

    • Helps to form a lipid bilayer that separates the water and other materials

  • Phospholipids heated in an aqueous solution tend to form small spheres or droplets called micelles/liposomes

• Proteins

  • Single-pass integral membrane proteins usually have a hydrophobic transmembrane segment that has 20-25 amino acids

  • Some span only part of the membrane while others stretch from one side of the membrane to the other

  • Arrangement of regions of the protein tends to orient the protein alongside the phospholipids with the hydrophobic region of the protein adjacent to the tails of phospholipids and hydrophilic regions protruding from the membrane in contact with the cytosol

• Carbohydrates

  • They are always on the exterior and are bound to either proteins or lipids

  • Chains consist of 2-60 monosaccharide units

  • Form specialized sites on the cell surface that allow cells to recognize each other

  • Carbohydrate components of glycoproteins and glycolipids are called glycocalyx(highly hydrophilic and attracts large amounts of water to the surface of the cell, which allows interaction of the cell with its watery environment, embryonic development, cell identification, and cell-to-cell attachments)

• Membrane fluidity

  • If saturated fats are compressed by decreasing temps, they press in on each other, making a dense and rigid membrane

  • If unsaturated fats are compressed, the bends in their tails elbow adjacent molecules, maintaining space between phospholipids, allowing fluidity in the membrane at temps at which membranes with saturated phospholipid tails in their phospholipids would freeze

    • Important in a cold environment because cold tends to compress membranes composed largely of saturated fatty acids, making them less fluid and more susceptible to rupturing(organisms adapt to cold by changing proportions of unsaturated fatty acids)

  • Cholesterol tends to dampen the effects of temp on the membrane, functioning as a buffer that prevents lower temps from inhibiting fluidity and increased temps from increasing fluidity too much, meaning cholesterol extends the range of temp in which the membrane is fluid and functional

5.2: Passive Transport

• Water moves across plasma membranes through osmosis

  • The concentration gradient of water is inversely proportional to the concentration of solutes(water moves through channel proteins called aquaporins from higher water concentration to lower concentration)

  • Solute concentration in an out-of-cell influences osmosis

• Tonicity is how the extracellular concentration of solutes can change the volume of a cell by affecting osmosis

• Hypotonic - extracellular fluid has a lower concentration than the fluid inside the cell, water enters the cell, causing it to burst

  • Animal cells lyse

• Passive transport has substances moving from high concentrations to lower concentrations

• Polar substances have trouble passing through the lipid bilayer, so transport mechanisms are needed

• Diffusion

  • Molecules move randomly, at a rate that depends on how mass, their environment, and the amount of thermal energy they possess

  • Dynamic equilibrium is when there is no net movement(happens after diffusion)

  • More difference in concentration, more rapid diffusion

  • Heavy molecules move slowly

  • High temps increase energy and diffusion rate

  • Solvent density increases and diffusion rate decreases because they have a more difficult time getting through the denser medium

  • Polar has slower diffusion than non-polar

  • Greater distance to travel lowers diffusion rate because of upper limitation on cell size

• Facilitated transport

  • Move with the help of proteins because the protein being moved is polar, so proteins shield them

  • Channel proteins have a hydrophilic domain and channel that provides an opening through the membrane layers

    • Allows polar molecules to avoid the nonpolar central layer

  • The attachment of a particular ion can control the opening and closing of channels

  • When proteins are bound to ligands, they are saturated and the rate is at maximum(only a finite number of carrier proteins, so excess is excreted)

  • Channel proteins transport faster than carrier proteins

• Osmosis

  • More solutes = more water

  • Hemolysis - cell swelling and bursting

• Tonicity

  • How an extracellular solution can change the volume of the cell by affecting its osmosis

  • Low osmolality means more water molecules

  • Water moves to higher osmolality

  • Control osmosis through osmoregulation

  • The flow of water produces turgor pressure, which stiffens the cell walls of plants

  • Plasmolysis - When the plant is not watered, it becomes hypertonic, causing the cell membrane to detach from the wall and constrict the cytoplasm(lose turgor pressure and wilt)

  • Albumin is a major factor in controlling osmotic pressure

5.3: Active Transport

• Cell going against concentration gradient uses free energy from ATP and carrier proteins move that substance by acting like pumps

• Combined gradients that affect the movement of ions are concentration gradients and their electrical gradient(diff in charge across the membrane) are called electrochemical gradient

• The sodium-potassium pump maintains electrochemical gradients across the membranes of nerve cells in animals and is the primary active transport

• Concentration gradient is when the concentration of the substance inside the cell is greater than its concentration in the extracellular fluid or vice versa

• Electrochemical gradient

  • Because ions move and because cells contain proteins that don’t move and are mostly charged negatively, there is also an electrical gradient across the plasma membrane

  • The interior of cells has higher concentrations of potassium and lower concentrations of sodium than extracellular fluid, so NA tends to drive the electrical gradient into the cell, to the negatively charged interior

  • An electrical gradient of K also tends to drive it into the cell, but the concentration gradient of K drives K out of the cell

• ATP pumps work against electrochemical gradients

• Most of a cell’s energy is spent maintaining an imbalance of ions

• Primary active transport moves ions across a membrane and creates a diff in charge across that membrane, entirely depending on ATP

• Secondary active transport describes the movement of material that is due to the electrochemical gradient established by primary active transport that does not directly require ATP

• Carrier proteins

  • Transporters ions -> uniporters that carry one specific ion/molecule, symporters that carry two different ions in the same direction, and an antiporter that carries two different ions in different directions

    • Also found in facilitated diffusion and do not require ATP to work

• Secondary active transport

  • Uses the kinetic energy of sodium ions to bring other compounds against their concentration gradient

  • Sodium ion concentration build-up cause of primary active transport -> electrochemical gradient -> channel proteins exist and are open -> sodium ions move down its concentration gradient, moving other substances that are attached

  • The potential energy that is stored in hydrogen ions stored by secondary transport is translated into KE as ions move through ATP synthase, causing ADP to turn into ATP

5.4: Bulk Transport

• Receptor-mediated endocytosis is the uptake of substances by the cell targeted to a single type of substance that binds to a specific receptor protein on the external surface of the cell membrane before endocytosis

• Uptake and release of large molecules require energy

• Endocytosis is an active transport that moves particles into a cell(the plasma membrane of the cell invaginates, forming a pocket around the target particle)

  • Phagocytosis is the process by which large particles are taken in by a cell

  • A portion of the inward-facing surface becomes coated with clathrin, which stabilizes the portion, thereby extending from the body of the cell to surround the particle and enclose it

    • Clathrin disengages from the membrane and the vesicle merges with a lysosome for the breakdown of the material in the newly formed compartment(endosome)

    • The endosome merges with the membrane and releases contents into the extracellular fluid

  • Pinocytosis is where molecules and water are taken in, which the cell needs from the extracellular fluid, resulting in a smaller vesicle than phagocytosis does(does not merge with lysosome)

    • A variation of this is pinocytosis where it uses a coating protein called caveolin on the cytoplasmic membrane(cavities in the membrane that form vacuoles have membrane receptors and lipid rafts)

      • Used to bring small molecules into the cell and transport these molecules through the cell for their release on the other side of the cell(transcytosis)

  • Receptor-mediated endocytosis

    • Clathrin is attached to the cytoplasmic membrane(if the process is inefficient, the material will not be removed from the tissue fluids of blood, causing diseases like LDL deficiency)

• Exocytosis is the reverse process of moving material into a cell

  • Waste material is enveloped in a membrane and fuses with the interior of the membrane, opening the membranous envelope on the exterior of the cell