Unit 2: Cell Structure and Function

Cell Structure and Function

Cells

  • Cells: the basic structural and functional units of every organism

  • All cells:

  1. Are bound by a plasma membrane Contain cytosol Contain chromosomes Contain ribosomes

There are two types of cells: prokaryotes and eukaryotes

Prokaryotes Domains Bacteria and Archaea DNA is in the nucleoid region Generally smaller in size than eukaryotes Lack internal membrane bound organelles Have internal regions with specialized structures and functions

Eukaryotes Protists, fungi, animals, and plants DNA is in the nucleus Contain membrane bound organelles These membranes partition cell into specialized regions

Organelles

Organelles: membrane bound structures in eukaryotes Two classifications: Endomembrane organelles Nuclear envelope Endoplasmic reticulum Golgi complex Lysosomes Vesicles/Vacuoles Plasma membrane

Energy organelles Mitochondria Chloroplasts

Compartmentalization

  • Compartmentalization in organelles allows for different metabolic reactions to occur in different locations Increases surface area for reactions to occur Prevents interfering reactions from occuring in the same location

Unique Cell Components

Plants

Chloroplasts

  • Central vacuole

  • Cell wall

  • Plasmodesmata

Animals

  • Lysosomes

  • Centrosomes

  • Flagella

Endomembrane Organelles

Nucleus

  • Contains chromosomes (genetic information)

    • Enclosed by the nuclear envelope

      • Double membrane

    • Has pores

      • Pores regulate entry and exit of materials from the cell

Contains a nucleolus

  • Dense region of the nucleus where ribosomal RNA (rRNA) is synthesized

    • rRNA is combined with proteins to form large and small subunits of ribosomes

    • Subunits exit via nuclear pores

  • Assemble into ribosomes

    • Ribosomes translate messages found on mRNA into the primary structure of polypeptides

Review

In order for DNA to leave the nucleus, it must first be transcribed by RNA polymerase into messenger RNA (mRNA). The mRNA transcript must then be modified before leaving the nucleus to the cytoplasm. In the cytoplasm, the ribosomes decode the information in mRNA and form continuous chains of amino acids, thus forming a protein. This process of DNA → RNA → protein is known as transcription and translation and will be the main concepts covered in Unit 6.  

Ribosomes

  • Comprised of ribosomal RNA and protein

    • Function: synthesize proteins

Note: some texts do not classify ribosomes as organelles because they are not bound by a membrane

  • Can be found in two locations: 

  1. Cytosol 

    • Proteins produced here generally function only within the cytosol (i.e. enzymes)

    • Known as “free ribosomes”

  2. Bound to the endoplasmic reticulum or nuclear envelope

    • Proteins produced here can be secreted from the cell

      • Leave via transport vesicles

Endoplasmic Reticulum

  • A network of membranous sacs and tubes

    • Functions:

      • Synthesizes membranes

      • Compartmentalize the cell to keep proteins formed in the rough ER separate from those of free ribosomes

Two types: rough and smooth

  1. Rough ER

    • Contains ribosomes bound to the ER membrane

    • Allows for compartmentalization of cells

    • Helps carry out protein synthesis

  1. Smooth ER

  • Contains no ribosomes

  • Synthesizes lipids, metabolizes carbohydrates, and detoxifies the cell

Golgi Complex

Membrane bound structure.  Contains flattened membranous sacs called cisternae

  • Separate the sacs from the cytosol

  • Each cisternae is not connected

  • Has directionality

    • Cis face:

      • Receives vesicles from the ER

    • Trans face:

      • Sends vesicles back out into cytosol to other locations or to the plasma membrane for secretion

      • Functions:

        • Receives transport vesicles with materials from the ER

        • Modifies the materials

        • Sorts the materials

        • Adds molecular tags

        • Packages materials into new transport vesicles that exit the membrane via exocytosis

        • Ensures newly formed proteins are folded correctly and modified correctly to send to other parts of the cell or out of the cell.

Lysosomes

Membranous sac with hydrolytic enzymes

  • Function:

    • Hydrolyzes macromolecules in animal cells

    • Autophagy: lysosomes can recycle their own cell’s organic materials

      • Allows the cell to renew itself

      • Peroxisomes

        • Similar to lysosomes

        • Membrane bound metabolic compartment 

          • Catalyze reactions that produce H2O2

            • Enzymes in peroxisomes then break down H2O2 to water

Vacuoles

Large vesicles that stem from the ER and Golgi

  • Selective in transport

Types:

Food vacuole

  • Form via phagocytosis (cell eating) and then are digested by lysosomes

Contractile vacuole

  • Maintain water levels in cells

Central vacuole

  • Found in plants

    • Contains inorganic ions and water

    • Important for turgor pressure

Endomembrane System

Consists of a group of membrane-bound organelles and subcellular components

  • Endoplasmic reticulum (ER)

  • Golgi Complex

  • Lysosomes

  • Vacuoles 

  • Transport vehicles

  • Nuclear envelope

  • Plasma membrane

  • The endomembrane system organelles work together to:

    • Modify

    • Package

    • Transport the following throughout the cell:

      • Polysaccharides

      • Lipids

      • proteins

Energy Organelles

Endosymbiont Theory

  • Endosymbiont Theory: the theory that explains the similarities mitochondria and chloroplasts have to a prokaryote

    • Theory states that an early eukaryotic cell engulfed a prokaryotic cell

      • Prokaryotic cell became an endosymbiont (cell that lives in another cell)

        • Became one functional organism

        • Evidence:

        • Double Membrane: Organelles possess two membranes, suggesting an engulfed origin.

        • Ribosomes: They contain their own bacterial-type (70S) ribosomes.

        • Binary Fission: Organelles reproduce independently via binary fission, similar to bacteria.

        • Size: They are comparable in size to typical prokaryotes.

        • Circular DNA: They hold their own circular DNA, distinct from the nucleus.

        • Phylogenetics: Molecular sequencing links mitochondria to alphaproteobacteria and chloroplasts to cyanobacteria.

Mitochondria

Site of cellular respiration

  • Structure of the double membrane:

    • Outer membrane is smooth

    • Inner membrane has folds called cristae

      • Divides the mitochondria into two internal compartments and increases the surface area

      • The convoluted inner membrane forms folds that enable ATP to be synthesized more efficiently.

      • Intermembrane: space between inner and outer membrane

      • Mitochondrial matrix: enclosed by inner membrane

        • Location for the Krebs cycle

        • Contains: 

          • Enzymes that catalyze cellular respiration and produce ATP

          • Mitochondrial DNA

          • Ribosomes

The number of mitochondria in a cell correlates with metabolic activity

  • Cells with high metabolic activity have more mitochondria

    • Example: cells that move/contract

Chloroplast

  • Specialized organelles in photosynthetic organisms (plants and photosynthetic algae)

    • Site of photosynthesis

    • Contains the green pigment chlorophyll

  • Inside of its double membrane:

    • Thylakoids

      • Membranous sacs that can organize into stacks called grana

        • Light dependent reactions occur in grana

  • Stroma: fluid around thylakoids

    • Location for the Calvin cycle

    • Contains

      • Chloroplast DNA

      • Ribosomes

      • Enzymes

The Cytoskeleton

Cytoskeleton

  • A network of fibers throughout the cytoplasm

    • Give structural support (especially for animal cells) and mechanical support:

      • Anchor organelles

      • Allow for movement of vesicles and organelles and/or the whole cell

        • Movement occurs when the cytoskeleton interacts with motor proteins

There are 3 types of fibers in the cytoskeleton:

  1. Microtubules

  2. Microfilaments

  3. Intermediate filaments

Microtubules

Hollow rod-like structures made of the protein tubulin

  • Grow from the centrosome

    • Assist in microtubule assembly

Functions:

  • Serve as structural support (think: tracks) for the movement of organelles that are interacting with motor proteins

  • Assist in the separation of chromosomes during cell division

  • Cell motility (i.e., cilia and flagella)

Microfilaments

Thin solid rods made of the protein actin

Functions:

  • Maintain cell shape

    • Bear tension

  • Assist in muscle contraction and cell motility

    • Actin works with another protein called myosin to cause a contraction

  • Division of animal cells

    • Contractile ring of the cleavage furrow

Intermediate Filaments

  • Fibrous proteins made up of varying subunits

  • Permanent structural elements of cells

Functions:

  • Maintain cell shape

  • Anchor nucleus and organelles

  • Form the nuclear lamina

    • Lines the nuclear envelope

Cell Size

Cell Size

Cellular metabolism depends on cell size

Cellular waste must leave Dissipate thermal energy Nutrients and other resources/chemical materials must enter At a certain size, it begins to be too difficult for a cell to regulate what comes in and what goes out of the plasma membrane

Surface Area and Volume

The size of a cell will dictate the function

  • Cells need a high surface area-to-volume ratio to optimize the exchange of material through the plasma membrane

   A HIGH SA:V Ratio optimizes HOMEOSTASIS!!!

Formulas

  • Formulas for cuboidal cells

    • Total SA= height x width x number of sides x number of boxes (or SA = 6S2 if only 1 box)

    • Total V= height x width x length x number of boxes (or V = S3 if only one box)

    • SA to V ratio = SA/V

  • Formulas for spherical cells

    • SA = 4πr2

    • V =   4/3πr3 

    • SA:V ratio = SA/V

What Does This Mean for a Cell?

Cells tend to be small

  • Small cells have a high SA:V ratio

    • Optimizes exchange of materials at the plasma membrane

  • Larger cells have a lower SA:V ratio

    • Lose efficiency exchanging materials

      • The cellular demand for resources increases 

      • Rate of heat exchange decreases

Plasma Membranes and Membrane Permeability

Plasma Membrane

Phosphate group, Glycerol, Hydrophilic head, Hydrophobic tails

Separates internal cell environment from external environment

  • Comprised primarily of phospholipids

  • Phospholipids are amphipathic

    • Hydrophilic head and hydrophobic tails

    • Forms a bilayer

Selective permeability: The ability of membranes to regulate the substances that enter and exit Hydrophilic heads oriented TOWARD aqueous environments

Hydrophobic tails are facing inwards AWAY from aqueous environments

Fluid Mosaic Model

A model to describe the structure of cell membranes

  • Fluid: membrane is held together by weak hydrophobic interactions and can therefore move and shift

    • Temperature affects fluidity

    • Unsaturated hydrocarbon tails help maintain fluidity at low temps

      • Kinked tails prevent tight packing of phospholipids

  • Cholesterol helps maintain fluidity at high and low temps

    • High temp: reduces movement

    • Low temp: reduces tight packing of phospholipids

  • Mosaic: comprised of many macromolecules

Membrane Carbohydrates

Important for cell-to-cell recognition

  • Glycolipids

    • Carbohydrates bonded to lipids

  • Glycoproteins

    • Carbohydrates bonded to proteins

    • Most abundant

Plant Cells Have Walls

Plants have a cell wall that cover their plasma membranes

  • Extracellular structure (not found in animal cells)

    • Provides:

      • Shape/structure

      • Protection

      • Regulation of water intake

Membrane Transport and Facilitated Diffusion

Selective Permeability

Some substances can cross the membrane more easily than others

Easy passage across the membrane:

  • Small nonpolar, hydrophobic molecules

    • Examples:

      • Hydrocarbons

      • CO2, O2, N2

Difficult passage or protein assisted passage:

  • Hydrophilic, polar molecules, large molecules, ions

    • Examples:

      • Sugars, water

Transport Across a Membrane

There are two main types of transport across a membrane: passive and active

Passive Transport

  • Passive transport: transport of a molecule that does not require energy from the cell because a solute is moving with its concentration or electrochemical gradient

    • Involved in the import of materials and export of waste

    • Examples:

      • Diffusion

      • Osmosis

      • Facilitated 

diffusion

  • Diffusion: spontaneous process resulting from the constant motion of molecules

    • Substances move from a high to low concentration

      • Move DOWN the concentration gradient

Molecules diffuse directly across membrane

  • Different rates of diffusion for different molecules

Remember: even with diffusion the membrane is still selectively permeable

Osmosis: the diffusion of water down its concentration gradient across a selectively permeable membrane

  • Can also be thought of as the diffusion of water from areas of low solute concentration to areas of high solute concentration

  • Facilitated diffusion: diffusion of molecules through the membrane via transport proteins

    • Increases rate of diffusion for:

      • Small ions, water, carbohydrates

    • Two categories of transport proteins: channel and carrier

      • Each transport protein is specific for substances it can facilitate movement for

  • Why is facilitated diffusion passive transport and not active transport?

    • Facilitated diffusion is still passive transport because the substances the proteins are helping to move are moving DOWN their concentration gradient and NO energy is required

  • Channel proteins: provide a channel for molecules and ions to pass

    • Channel is hydrophilic

      • Many are gated channels

        • Only allow passage when there is a stimulus

      • Aquaporins: specific channel protein for water

Carrier proteins: undergo conformational changes for substances to pass

Active Transport

  • Active transport: transport of a molecule that requires energy because it moves a solute against its concentration gradient

    • Pumps

    • Cotransport

    • Exocytosis

    • Endocytosis

  • Active transport requires energy

    • Adenosine Triphosphate (ATP): Energy source used by cells 

    • ATP can transfer the terminal phosphate group to the transport protein, which changes the shape of the transport protein to better move a substance

Pumps: maintain membrane potential

  • Membrane potential: unequal concentrations of ions across the membrane results in an electrical charge (electrochemical gradient)

    • The cytoplasm is relatively negative in comparison to the extracellular fluid

    • Energy is stored in electrochemical gradients

Examples of pumps:

Electrogenic pumps: proteins that generate voltage across membranes, which can be used later as an energy source for cellular processes

  • Sodium potassium pump

    • Animal cells will regulate their relative concentrations of Na+ and K+

      • 3 Na+ get pumped out of the cell

      • 2  K+ get pumped into the cell

        • Results in a +1 net charge to the extracellular fluid

Sodium Potassium Pumps

Animal cells have a relatively high concentration of K+ inside the cell in comparison to outside the cell Animal cells have a relatively low concentration of Na+ inside the cell in comparison to outside the cell ATP phosphorylates the protein, which causes a conformational change In this shape, the protein has an affinity towards Na+  The new shape causes the affinity of the protein to be towards K+ When K+ binds to the protein, this phosphate group will be released Loss of the phosphate group causes the protein to return to its original shape

Active Transport

Examples of pumps:

  • Proton pump: integral membrane protein that builds up a proton gradient across the membrane

    • Used by plants, fungi, and bacteria

    • Pumps H+ out of the cell

  • Cotransport: the coupling of a favorable movement of one substance with an unfavorable movement of another substance

    • Uses the energy stored in electrochemical gradients (generated by pumps) to move substances against their concentration gradient

  • Favorable movement: downhill diffusion

  • Unfavorable movement: uphill transport

  • Plants use cotransport for sugars and amino acids

  • Example: sucrose-H+ cotransporter

    • Sucrose can travel into a plant cell against its concentration gradient ONLY if it is coupled with H+ that is diffusing down its electrochemical gradient

Transport of large molecules is done through exocytosis and endocytosis

Exocytosis: the secretion of molecules via vesicles that fuse to the plasma membrane

  • Vesicles can fuse to the membrane by forming a bilayer

    • Once fused, the contents of the vesicle are released to the extracellular fluid

    • Example: nerve cells releasing neurotransmitters

Endocytosis: the uptake of molecules from vesicles fused from the plasma membrane (think: opposite of exocytosis)

  • Phagocytosis

  • Pinocytosis

  • Receptor-mediated

Phagocytosis: when a cell engulfs particles to be later digested by lysosomes

  • Cell surrounds particle with pseudopodia

  • Packages particles into a food vacuole

    • Food vacuole fuses with a lysosome to be digested

Pinocytosis: nonspecific uptake of extracellular fluid containing dissolved molecules

  • Cell takes in dissolved molecules in a protein coated vesicle

    • Protein coat helps to mediate the transport of molecules

Receptor mediated endocytosis: specific uptake of molecules via solute binding to receptors on the plasma membrane

  • Allows the cell to take up large quantities of a specific substance

  • When solutes bind to the receptors, they cluster in a coated vesicle to be taken into the cell

Tonicity and Osmoregulation

Water Balance

Tonicity: the ability of an extracellular solution to cause a cell to gain or lose water

  • Depends on the concentration of solutes that cannot pass through the cell membrane

  • Cells can be in three types of solutions:

    • Isotonic

    • Hypertonic

    • Hypotonic

  • Osmoregulation: cells must be able to regulate their solute concentrations and maintain water balance

    • Animal cells will react differently than cells with cell walls, like plants, fungi, and some protists

Tonicity: Isotonic Solutions

Cells immersed in an isotonic solution have no net movement of water

  • The concentration of nonpenetrating solutes inside the cell is equal to that outside the cell.

    • Water diffuses into the cell at the same rate water moves out of the cell

Tonicity: Hypertonic Solutions

Cells immersed in a hypertonic solution lose water to their extracellular surroundings

  • The concentration of nonpenetrating solutes is higher outside of the cell

    • Water will move to the extracellular fluid

      • Cells shrivel and die

Plasmolysis: vacuole shrinks and the plasma membrane pulls away from the cell wall

Tonicity: Hypotonic Solutions

Cells immersed in a hypotonic solution gain water

  • The concentration of nonpenetrating solutes is lower outside of the cell

    • The cell will gain water 

      • Animal cells swell and lyse

      • Plant cells work optimally

Water Potential

Water potential: a physical property that predicts the direction water will flow

  • Includes the effects of solute concentration and  physical pressure

    • Water will flow from areas of:

      • High water potential to areas of low water potential

      • Low solute to areas of high solute concentration

      • High pressure to areas of low pressure

Water potential formula:

𝚿 = 𝚿s + 𝚿p

𝚿 - Greek letter “psi” represents water potential

  • Measured in megapascals (MPa) or bars

  • 1MPa = 10 bars

𝚿s - Solute potential (osmotic potential)

  • An increase in solutes causes binding to more free water

    • This reduces water potential

  • Expressed as a negative number

  • Pure water is 0 MPa

𝚿p - Pressure potential

  • The physical pressure on a solution

  • Can be + or - relative to atmospheric pressure

  • “Open air” means 𝚿p= 0 MPa

Calculating Solute Potential

Solute potential formula: 𝚿s = -iCRT

𝚿s - Solute potential

  • Measured MPa or bars

i - Ionization constant

  • Number of particles formed

    • If no ions are formed the ionization constant is 1 (ie sucrose)

C - Molar concentration

R - Pressure constant

  • 0.0831 liter bars/mol-K

  • 0.00831 liter MPA/mol K

T - Temperature in K

  • K = 273 + ℃