BISC 1111 GA 3

Prokaryotes

• do not have a true, membrane-enclosed nucleus

• have no membrane-bound organelles

  • instead have a nucleoid, a region where the DNA is concentrated

Eukaryotes

• membrane-bound organelles which compartmentalize their functions

• nucleus bound in a double membrane called the nuclear envelope

Prokaryotes vs eukaryotes

• Prokaryotes

  • Small cell size

  • Nucleoid (not enclosed)

  • Circular DNA

  • No membrane bound organelles

  • Unicellular

• Eukaryotes

  • Large cell size (relatively)

  • Nucleus (enclosed)

  • Linear DNA

  • Many membrane bound organelles

  • Multicellular or unicellular

Thiomargarita magnifica

• unicellular organism up to 2 cm in length

• 2 types of internal compartments: membrane enclosed “nucleoids” and a very large, water filled sac

What exactly needs to be compartmentalized?

• Eukaryotic cells have internal membranes which compartmentalize their functions

  • in other words, this separation of spaces within a cell allows for a division of labor amongst cell regions requiring different environmental conditions for specific metabolic processes

  • Eukaryotes comapartmentalize these various cell functions into vesicles called organelles and can move molecules from one compartment to another—something prokaryotes generally can’t

Selective permeability

• Phospholipids are ampipathic molecules, containing hydrophobic tails and hydrophilic heads 

• refers to its ability to differentiate between different types of molecules, only allowing some molecules through while blocking others

Membranes as “fluid mosaic”

• they are dynamic structures composed of (1) Phospholipids (2) Proteins (3) Carbohydrates (4) Cholesterol

Catabolic reactions

breaks down large macromolecules into smaller molecules and release energy in the process

Anabolic reactions

uses energy generated in catabolic reactions and raw materials gathered by the cell to synthesize larger biomolecules

Endomembrane system

• separates the cell into different compartments, or organelles, such as the nucleus, the endoplasmic reticulum (ER), the Golgi apparatus, and lysosomes

• selective permeability of lipid bilayers allows for unique conditions within each compartment

Endoplasmic reticulum

• accounts for more than half of the total membrane in many eukaryotic cells

• ER membrane is continuous within the nuclear envelope, allowing for RNAs exported from the nucleus to easily interact with ribosomes studded on the outer surface of the nuclear envelope and on the rough outer surface of the ER

Smooth ER

• synthesizes lipids

• detoxifies drugs and poisons

• stores calcium ions

Rough ER

• has bound ribosomes, which secrete glycoproteins (proteins covalently bonded to carbohydrates)

• distributes transport vesicles, secretory proteins surrounded by membranes

• is a membrane factory for the cell

Golgi apparatus

• consists of flattened membranous sacs called cisternae

• cis and trans faces

  • cis face is the region of the organelle facing towards the endoplasmic reticulum. as such, it serves to receive material from the ER

  • trans face, also known as the shipping face, is posterior to the cis face and points towards the plasma membrane of the cell

• folded proteins and lipids from the ER are transported to the cis face through transport vesicles

  • these products are modified, concentrated, and tagged

  • tagged products then sent into new vesicles that bud off the trans face to be transported to the appropriate destination

Lysosomes

• membranous sacs of hydrolytic or digestive enzymes made in the rough ER, which were then further refined in the golgi apparatus

• digestive enzymes only work well at relatively low pH, meaning that to do their job they must be contained within the compartment formed by the lysosome’s membrane

• most often used in phagocytosis and autophagy

• Some types of cells can engulf other cells by phagocytosis; ths forms a food vacuole (a lipid bilayer enclosed package of food brought in from outside the cell)

• also use enzymes to recycle the cell’s own organelles and macromolecules, a process called autophagy

Vacuoles

• large vesicles derived from ER and golgi apparatus with incredibly diverse functions

• In plants, some relatively small vacuoles may serve as storage containers for proteins or other important organic compounds (especially in cells of seeds)

• One of the most prominent features of a plant cell is the central vacuole, which serves s the cell’s main reservoir of inorganic ions like potassium or chloride

Transport across the cell membrane

• small molecules and water enter or leave the cell through the lipid bilayer or via transport proteins

• large molecules, such as polysaccharides and proteins, cross the membrane in bulk via vesicles

Exocytosis

• transport products out

• transport vesicles migrate to the membrane, fuse with it, and release their contents outside the cell

• very important process for cell signaling and communication

Endocytosis

• transport substances in

• molecules and large substances are taken into the cell via vesicles

• the membrane forms a pocket that deepens and pinches off forming a vesicle around the material for transport

Endocytosis: 3 main types

1. Phagocytosis

2. Pinocytosis

3. Receptor-mediated Endocytosis

Phagocytosis

cellular eating of a particle or even another organism

Pinocytosis

cellular drinking of the various solutes suspended in the extracellular fluid

Receptor-mediated endocytosis

a special case of pinocytosis that enables a cell to acquire large quantities of very specific substances from the extracellular fluid

How are the vesicles moving?

• any kind of cellular motility generally requires the interaction of motor proteins with elements of the cytoskeleton

• such an interaction requires the input of energy in the form of ATP

Mitochondria

the site of cellular respiration

• convoluted infoldings of the inner membrane, called cristae, allow a very large surface area for the work of the membrane bound enzymes that synthesize ATP during cellular respiration

Chloroplasts

the site of photosynthesis

• structure includes thylakoids, membranous sacs, stacked to form a granum

Endosymbiotic Theory

• the ancestor of modern eukaryotes engulfed” (“ate”) the ancestor of modern membrane-bound organelles

• instead of a standard exploitation interaction, this instead became mutualism

Evidence supporting endosymbiotic theory

1. Mitochondria and chloroplasts reproduce the same way as prokaryotes (divide by fission)

2. They have DNA and ribosomes similar to free-living prokaryotes

3. They have two membranes, inner one more like prokaryotes and the outer more like eukaryotes

Endosymbiotic events happened many times:

• Euglena: genus of single-celled flagellate eukaryotes that are conditionally both heterotrophic and autotrophic

• Euglena chloroplasts have 3 membranes, suggesting another endosymbiotic event

Fluid mosaic model

• depicts the membrane as a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids

• proteins are not randomly distributed in the membrane; they often form groups that carry out common functions

Fluidity of membranes

• membranes are held together mainly by weak hydrophobic interactions

• Most of the lipids and some proteins can move sideways within the membrane

• A lipid may flip-flop across the membrane, from one phospholipid layer to the other

Membranes must be fluid to work properly

• as temperatures cool, membranes switch from a fluid state to a solid state

• the temperature at which a membrane solidifies depends on the types of lipids

• membranes rich in unsaturated fats are more fluid than those rich in saturated fatty acids

Cholesterol

• a membrane component in animal cells that has variable effects on membrane fluidity at different temperatures

• plants use different but related sterol lipids to buffer membrane fludity

Role of cholesterol in membrane fluidity

Cholesterol reduces membrane fluidity at moderate temperatures by reducing phospholipid movement, but hinders solidification at low temperatures by disrupting packing

Patterns of protein folding in membrane proteins

• Integral proteins

  • a- helix - recognition, receptors

  • helical bundle - enzymes, transporters, receptors

  • B- barrel - transporters (channel proteins)

• Peripheral proteins

  • enzymes, anchorage, transporters (carriers)

Functions of cell-surface proteins:

• transport

• enzymatic activity

• signal transduction

• cell-cell recognition

• intercellular joining

• attachment to the cytoskeleton and extracellular matrix (ECM)

Glycolipids

carbohydrates bonded to lipids

Glycoproteins

carbohydrates bonded to proteins

GlycoRNA

discovered in 2019… not sure of function 100%—probably plays a role in immune system signaling

Synthesis & sidedness

• membranes have distinct inside and outside faces

• the composition and distribution of proteins, lipids, and associated carbohydrates is asymmetrical across the membrane

plasma membrane

• controls the exchange of materials between the cell and its surroundings

  • membranes exhibit selective permeability; some substances cross more easily than others

  • fluid mosaic model explains how membranes regulate molecular traffic across the membrane

Permeability of the lipid bilayer

• Hydrophobic molecules dissolve in the lipid bilayer and pass through the membrane rapidly

  • ex. Hydrocarbons, CO2 and O2 pass through easily

• Hydrophobic interior of the membrane impedes the passage of hydrophilic molecules

  • ex. Sugars, water and ions pass through slowly, if at all

Diffusion

the movement of particles of any substance so that they spread out evenly into the available space

• although each molecule moves randomly, diffusion of a population of molecules may be directional

• at dynamic equilibrium, as many molecules cross the membrane in one direction as in the other

Concentration gradient

• substances diffuse down this, the region along which the density of a chemical substance increases or decreases

• each substance moves down its own concentration gradient, unaffected by the concentrations of other substances

Passive transport

• diffusion of a substance across a biological membrane

  • because no energy is expended by the cell

• the concentration gradient represents potential energy that drives diffusion

• but the rate of diffusion also depends on membrane permeability ot the specific membrane

Osmosis

• the diffusion of free water (water molecules not clustered around another substance) across a selectively permeable membrane

• free water molecules diffuse across a membrane from the region of lower solute concentration to the region of higher solute concentration

Isotonic

if a solution’s solute concentration is the same as that inside the cell

Hypertonic

if a solution’s solute concentration outside the cell is greater than that inside the cell

Hypotonic

if a solution’s solute concentration outside the cell is less than that inside the cell

Transport proteins

hydrophilic and/or medium-large substances cross membranes passing through transport proteins

Channel proteins.

have a hydrophilic channel that certain molecules or ions can use as a tunnel

Carrier proteins.

bind to molecules and change shape to shuttle them across the membrane

Aquaporins

• channel proteins that greatly increase the rate of passage of water molecules (facilitate the diffusion of water)

• they are composed of four polypeptide subunits that each form a channel for the passage of water

• overall, up to 3 billion water molecules pass through per second

Facilitated diffusion

transport proteins speed the passive movement of molecules across the plasma membrane

• transport proteins include channel proteins and carrier proteins

Channel proteins

• provide corridors that allow a specific molecule or ion to cross the membrane

Ion channels

facilitate the transport of ions

Gated channels

ion channels that open or close in response to a stimulus

• ex. in nerve cells, potassium ion channels open in response to electrical stimulus

• other gated channels open in response to chemical stimulus—binding of a specific substance to the protein

Carrier proteins

• undergo a subtle shape change that moves the solute-binding site across the membrane

• this change in shape can be triggered by the binding and release if the transported molecule

• ones involved facilitated diffusion move substances down their concentration gradients; no energy input is required

Active transport

• requires energy, via ATP hydrolysis, to move substances against their concentration gradients. enables cells to maintain solute concentrations that differ from the environment

  • ex. concentration of potassium ions is higher and the concentration of sodium ions is lower inside animal cells than their surroundings

Sodium-potassium pump

• transfer of a phosphate group from ATP to this energizes the transport of K+ into the cell and Na+ out of the cell

MCQ: one where it asks where it is and everyone thought hydrolysis but its peptide bonds

A: peptide bond

Stanley Miller experiment–abiotic synthesis

• Stanley Miller’s classic experiment demonstrated the abiotic synthesis of organic compounds

• Experiments support the idea that abiotic synthesis of organic compounds, perhaps near volcanoes, could have been a stage in the origin of life

  • Organic compounds can be synthesized from inorganic compounds

Coconut question

• Hypothesis: Plants with different life-history strategies will have different macromolecule compositions. Plant seeds with higher fat to carb ratios will be from lineages that adapted to have longer seed dormancy periods before germination

• Carbs:

  • glucose - short-term energy storage

  • starch - long-term energy storage

• Lipids: higher proportion for longer dormancy period

  • stability at room temperature

  • high energy storage—twice as more dense in energy as carbs

  • Endosperm is rich in stored energy molecules, identity of which depends on plant’s life strategy

• Therefore, plants/seeds with long dormancy periods will have more fat as a proportion of their energy reserves, those who germinate immediately or do not disperse far have higher carb proportion

• Evolutionary strategy to have large energy quantity to germinate when conditions are favorable (coconut)

  • Coconuts can float at sea for years before making land fall to root and grow a new coconut plant. The fats stored within the coconut endosperm allow the seed embryo to not only survive the voyage, but also have enough energy to start growing rapidly once environmental conditions are right.

  • Coconut high in lipids, hard to find favorable conditions, could die if there were more carbs than lipids