mcdb 6 midterm 2 (week 4-7)

Light microscope (LM)

visible light is passed through a specimen and then through glass lenses

• lenses refract/bend the light to magnify image

• not able to see membrane organelles/sub-cellular structures (up to 200nm)

Electron Microscope (EM)

• Scanning electron microscope (SEM): focus beam of electrons onto the surface of specimen producing 3D images

• Transmission electron microscope (TEM): focus beam of electrons through a specimen to study internal structure of cells

size of plant and animal cells

10-100 μm

size of nuclei, bacteria, and mitochondria

1- 10 μm

3 important parameters of microscopy

• Magnification (ratio of image size to real size)

• Resolution (minimum distance between 2 distinguishable points)

• Contrast (difference in brightness between light and dark areas of image)

advances in light microscopy

• fluorescent markers label molecules to improve visualization of details

• confocal microscopy w/ sharpened images of tissues/cells

• improved resolution (as small as 10–20 nm)

Cell fractionation

breaks up the cells (sonication) and separates the components using centrifugation (based on size and weight)

• help correlate cell function with structure

Prokaryotic cells (Archaea/Bacteria)

• no nucleus/ membrane bound organelles

• DNA is an unbound region called nucleiod

• plasma membrane w/ cytoplasm inside and rigid cell wall on outside

• 1–5 μm

• divides by binary fission

Eukaryotic cells (animal, plant, fungi, and protist cells)

• DNA is in the nucleus (organelle bound by double membrane)

• larger than prokaryotic cells

• plasma membrane w/ cytoplasm inside

• 10–100 μm

Basic features of all cells

• plasma membrane

• semifluid substance (cytosol)

• chromosomes (carry genes)

• ribosomes (make proteins)

Plasma membrane

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

• double layer of phospholipids (bilayer)

• proteins embedded inside

What limits cell size?

Diffusion + metabolism (upper limits) —> ratio of surface area to volume is critical to facilitate exchange of materials (n² sa and n³ volume)

The nucleus

• contains most of cell’s genes

• nuclear envelope encloses nucleus

• double membrane (2 lipid bilayers)

• nuclear pores regulate entry/exit of molecules

• nuclear lamina to provide mechanical support of nucleus

• nucleolus on inside (site of rRNA synthesis)

Ribosomes

• complexes (not organelles) of rRNA and protein

• carry protein synthesis in cytosol (free) and outside of ER or in nuclear envelope (bound)

Endomembrane system components + function

• nuclear envelope, ER, Golgi, lysosomes, vacuoles, and PM (continuous or connected through vesicles)

• regulates protein traffic and performs metabolic functions

Endoplasmic Reticulum

• can account for more than half the total membrane in eukaryotic cells

• continuous with nuclear envelope

• Smooth ER + Rough ER

Smooth ER

• synthesis of lipids (cholesterol, sex hormones)

• metabolism of carbs (glycogen/cellulose)

• detoxification of drugs/poisons

• calcium ion storage

Rough ER

• has bound ribosomes (secrete glycoproteins)

• distributes transport vesicles

• membrane factory for cell

• site of protien synthesis: manufactures, packages, and transports proteins designated for cell membranes, other organelles, or secretion outside the cell

Golgi Apparatus

• shipping + receiving center (amazon)

• consists of flattened membranes sacs called cisternae (reservoir or pita bread)

• modifies products of ER

• manufactures macromolecules

• sorts/packages materials into transport vesicles

• cis + trans faces (receiving + shipping sides)

Lysosomes

• single membrane bound organelle found in many animal cells

• spherical (3D) vesicle containing hydrolytic enzymes (digest molecules)

  • enzymes work best in acidic environments

• involved in secretion, PM repair, and energy metabolism (reusing materials)

Phagocytosis

• when cells engulf another cell to form food vacuole

• lysosome fuses with the food vacuole + enzymes digest with molecules

Autophagy

recycling cells own organelles + macromolecules

• mechanism used by the lysosome to recycle the cells own dead or damaged organelles and macromolecules

Tay-Sachs Condition

inherited disease where lysosomes are unable to breakdown certain membrane glycolipids due to enzyme defect (glycolipids accumulate in brain cells —> death by 3-4 years old)

Vacuoles

vesicles derived from ER + golgi w/ inside solution differing from cytosol

• food vacuoles

• contractile vacuoles (found in freshwater protists to pump excess water out of

  cells)

• central vacuoles (found in mature plant cells to hold organic compounds and

  water)

Peroxisomes

• single membrane bound organelles that lack own genetic material

• produce hydrogen peroxide then convert it to water (detoxifying + oxidizing molecules)

Cellular respiration

A metabolic pathway breaking down glucose (C6H12O6) with oxygen to produce energy (ATP), water, and carbon dioxide

Endosymbiont theory

early ancestor of eukaryotic cells engulfed oxygen-using prokaryotic cell (bacteria) which formed endosymbiont relationship with the host. Host cell and bacteria merged into single eukaryotic cell with a mitochondrion. One of these cells might have later taken up photosynthetic prokaryote becoming the ancestor of cells that contain chloroplasts.

Sites of cellular respiration

mitochondria

Similarities between mitochondria/chloroplasts and bacteria

• enveloped by double membrane

• contain ribosomes and multiple circular DNA molecules (plasmids)

• grow and reproduce somewhat independently in cells

Mitochondria

• present in nearly all eukaryotic cells

• primary function to generate large quantities of energy in form of ATP

• contains smooth double membrane (outer membrane and inner membrane folded into cristae (large surface area for enzymes))

• inner membrane made out of inter membrane space and mitochondrial matrix

Chloroplasts

• site of photosynthesis (production of sugar + O2 while converting sunlight into ATP)

• contain green pigment chlorophyll and other enzymes for photosynthesis

The cytoskeleton

• network of fibers extending through cytoplasm

• organizes cells structures + activities

• helps support cell + maintain shape

• anchorage for organelles + molecules (very dynamic)

• interacts with motor proteins to produce motility

  • vesicles/organelles use motor protein feet to walk along tracks of cytoskeleton

Three main fibers of cytoskeleton

• microtubules: thickest

• intermediate filaments: diameters in middle range

• microfilaments/actin filaments: thinnest

Microtubules

• hollow dynamic rods constructed from tubulin, globular protein dimers

• shape + support of cell

• guide movement of organelles

• separate chromosomes during cell division

Microfilaments

• thin solid robs built from dynamic polymers (protein molecules of globular actin subunits)

• bears tension + resits pulling forces within cell

• function in cellular motility + interact with motor protein myosin

  • actin + myosin interact to cause muscle contraction, amoeboid movement of white blood cells, and cytoplasmic streaming in plant cells

• bundles of microfilaments make up core of microvilli of intestinal cells that increase cells surface area

Intermediate filaments

• only found in cells of some animals (like vertebrates)

• reinforce cell shape and fix organelles in place (anchor nucleus)

• formation of nuclear lamina

• more permanent cytoskeleton elements that other 2

Centrosomes

• in animal cells, microtubules grow out from a centrosome near the nucleus

• the centrosome is the “microtubule organizing center”

• centrosome has a pair of centrioles each with 9 triplets of microtubules arranged in a ring

Cilia and Flagella

• microtubules control the beating of cilia/flagella, which are microtubule-containing extensions projecting from some cells

• Flagella are limited to one or few per cell

• Cilia occur in large numbers on cell surfaces

• cilia and flagella differ in beating pattern

common structure of group of microtubules sheathed by the PM and a Basal body that anchors cilium or flagellum

Dynein

motor protein that “moves” flagella and cilia

• dynein arms alternately contact, move, and release the outer microtubules

• movements of the doublet arms cause cilium/flagellum to bend

  • nexin keeps doublets from sliding

Cell junctions

• plasmodesmata (plants); water, proteins, RNA can pass from cell to cell

• tight junctions (animals): form water tight seal between cells (caulking around a tub) (intestine/skin cells)

• desmosomes (animals): act like velcro + fasten cells together (heart muscle cells)

• gap junctions (animals): act like secret passageways + allow materials to pass between cells

Extracellular Matrix (ECM) of animal cells

• animal cells lack cell walls but are covered by elaborate ECM

• made up of glycoproteins (collagen, proteoglycans, fibronectin)

• ECM proteins bind to cell-surface receptor proteins in PM called integrins (membrane proteins with two subunits)

Role of membrane carbohydrates in cell cell recognition

• cells recognize each other by binding to surface molecules (often containing carbs) on extracellular surface of PM

• membrane carbs may be covalently bonded to lipids (forming glycolipids) or more commonly to proteins (glycoproteins)

Plasma membranes

• separate what inside of cell (cytoplasm) from outside

• selective permeability: certain molecules can passively diffuse across the membrane and larger molecules cannot (need active transport)

• made up of phospholipids (amphipathic: hydrophobic and hydrophilic regions)

  • stable boundary between two aqueous compartments

  • contain domains that reside within and outside of PM

Fluid Mosaic Model

mosaic of protein molecules bobbing in a fluid bilayer of phospholipids

• Mosaic model allows for proteins to shift/move in cell membrane due to the rearrangement of phospholipids

What determines/affects membrane fluidity

saturation of carbon molecules and cholesterol

• fluid = unsaturated (double bond/kinked) (like olive oil)

• viscous = saturated + packed together

• cholesterol = reduced fluidity at moderate temps but hinders solidification at low temps

As temps cool, membranes shift from fluid to solid state

What organelles make the plasma membrane + its components

The ER and the Golgi apparatus (components include proteins, lipids, and carbohydrates)

• more specifically: starts in the ER → golgi → vesicles → PM

Movement in and of a membrane

• most lipids and some proteins in a membrane can shift sideways

• movement of phospholipids is rapid and proteins move much slower

• some proteins move in directed manner, others anchored

• some proteins simply drift in membrane

What can/can’t pass through membranes

Easily pass

• small molecules (O2)

• hydrophobic/nonpolar molecules (still have to be small)

Cant easily pass

• polar molecules (sugars like glucose)

Characteristics of membrane proteins

• most membrane proteins are amphipathic

• determine most of the membranes specific functions

• integral proteins: penetrate hydrophobic interior of lipid bilayer (also called transmembrane proteins)

• peripheral proteins: loosely bound to surface of membrane (not actually embedded, could be hydrophilic)

Six major functions of membrane proteins

• transport

• enzymatic activity

• signal transduction (ex. from outside to inside cell)

• cell-cell recognition

• intercellular joining

• attachment to cytoskeleton + ECM

Transport proteins

• allow passage of hydrophilic substances across membrane (H2O, amino acids)

• specific for substance it moves

  • channel proteins have hydrophilic channel (aquaporins facilitate passage of water)

Carrier protiens

bind to molecules, change conformation (shape) and shuttle these molecules across the plasma membrane

Passive transport

no energy investment

• diffusion (osmosis; diffusion of water)

• facilitated diffusion (transport proteins; channel proteins, ion channels, carrier proteins)

Active transport

Requires energy (usually ATP) + moves substances against concentration gradient. Allows cells to maintain concentration gradients that differ from surroundings.

• sodium-potassium + proton pump (3 sodium “slots”, 2 potassium “slots”)

• sucrose-proton cotransporter

• bulk transport (exocytosis, endocytosis)

Ion Pumps

Sodium-potassium pump

• exchanges Na+ for K+ across PM in animal cells

• major electrogenic pump

  • generates voltage across a membrane (ions are charged)

• sodium fills 3 slots → phosphorylation in cytoplasm of ATP (one phosphate on pump) → sodium ions released → potassium molecules from outside bind to transport → dephosphorylation of pump → release of potassium molecules

Proton pump

• main electrogenic pump of plants, fungi, and bacteria

Diffusion

• tendency for molecules to spread out evenly in available space

• although molecules move randomly, it may be directional

• at dynamic equilibrium there are an even amount of molecules crossing the membrane in one direction as the other

• substances diffuse down their concentration gradient (more to less)

Facilitated diffusion

• transport proteins speed up passive movement across PM

• channel proteins provide corridors (aquaporins, ion channels)

• carrier proteins undergo subtle shape change to move solute across membrane

• no net energy input required!

Osmosis

diffusion of free water (solvent) across selectively permeable membrane from diluted solution (fewer solutes) to concentrated solution (more solutes)

• Flow of water is dependent on the solute concentration (not concentration of water)

Tonicity

ability of surrounding solution to cause cell to gain/lose water

• Isotonic: solute concentration same on either side: no net water movement

• Hypertonic: solute concentration greater outside PM than inside of cell (water will move outside)

• Hypotonic: solute concentration is greater inside cell (water will move in)

Osmoregulation

control of solute concentrations and water balance (necessary adaptation for life in such conditions)

• ex. contractile vacuole in paramecium caudatum

Water balance of plant cells

• rigid cell walls (cellulose) helps maintain water balance

• turgid (normal/very firm, hypotonic)

• flaccid (limp, isotonic)

• plasmolysis (lethal, hypertonic)

Cotransport

when a transport protein can couple the “downhill” diffusion of solute to “uphill” transport of second solute against its gradient

• proton pumps couple hydrogen ion gradient to drive active transport of nutrients (pumped out → low concentration → contransporter brings hydrogen ions back in cell along w sucrose/other)

Bulk transport

large molecules (polysaccharides/proteins) cross membrane in bulk using vesicles (requires energy!)

Exocytosis

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

• many secretory cells use exocytosis to export products (ex. hormones, proteins, etc.)

Endocytosis

cell takes in molecules/matter by forming new vesicles from PM (reversal of exocytosis + involves dif proteins)

• Phagocytosis (cellular eating)

• Pinocytosis (cellular drinking)

• Receptor mediated endocytosis (receptor recognizes molecules + forms vesicles to bring content into cell)

  • ex. cholesterol travels in LDLs (lipoprotiens which bind to receptors) + familial hypercholesterolemia (too much in blood) occurs when receptor proteins are defective or missing → atherosclerosis

Metabolism

getting energy from food to fuel all chemical reactions (sum of all chemical reactions needed for life)

• metabolism is an emergent property arising from orderly interactions between molecules (allows for fluctuations and adaptation to the environment)

Bioenergetics

study of how energy flows through living systems (environments and organisms)

Metabolic pathways

starts with primary molecule → ends with product (ex. ATP)

enzymes essential for each step

Catabolic pathways/catabolism

release energy by breaking down complex molecules into simpler compounds (DOWNHILL)

• energy is then available to do cellular work (ex. cellular respiration; glucose + organic fuels broken down into CO2 and H2O)

Anabolic pathways/anabolism

consume energy to build complex molecules from simpler ones (called biosynthetic pathways) (ex. proteins synthesized from simpler amino acids) (UPHILL)

Energy

capacity to cause change

• exists in various forms, some of which can perform work

Work

movement of matter against opposing forced (gravity/friction)

Forms of energy

• Kinetic energy: energy associated with motion

• Thermal energy: type of KE associated with random movement of atoms/molecules

  • Heat: transfer of thermal energy from one object to another (dif in temp)

• Light: energy that can be harnessed to perform work

• Potential energy: energy that matter possesses because of its location/structure

• Chemical energy: potential energy available for release in a chemical reaction

energy can be converted from one form to another

Thermodynamics

organisms are open systems

• First law: energy is neither created nor destroyed

• Second law: energy transfer/transformation increases entropy of the universe + some energy is lost to surroundings as heat

Entropy

measure of molecular disorder (dispersed energy in a system)

• heat increases disorder of the surroundings

• spontaneous processes require no energy input

• non spontaneous require energy supplied + lead to decrease in entropy

Free energy (Gibbs)

the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system (like a cell)

• ∆G = G final state - G initial state

Exergonic reactions

spontaneous reaction with net release of free energy (∆G < 0) (energy exiting)

• magnitude of ∆G represents max amount of work reaction can perform

Endergonic reactions

non spontaneous and absorb free energy from surroundings (∆G > 0) (energy entering)

• magnitude of ∆G represents quantity of energy required to drive reaction

Energy coupling

use of exergonic process to drive an endergonic one to do work (most energy coupling in cells mediated by ATP)

3 main kinds of work done by a cell

• Chemical (building biopolymer like protein/DNA)

• Transport (ex. sodium potassium pump)

• Mechanical (ex. protein motor walking on microtubule and carrying a vesicle)

Driven by ATP hydrolysis (energy released used for endergonic reactions)

ATP

Adenosine triphosphate: composed of a ribose (sugar), adenine (nitrogenous base), and 3 phosphate groups

• role in energy coupling (within the triphosphate group) and also used to make RNA (ribose backbone)

Hydrolysis of ATP

energy is released when terminal phosphate bond is broken (comes from chemical change to state of lower energy, not from bond itself) exergonic reaction

• triphosphate tail of ATP like a compressed spring (hydrolysis releases a lot of energy due to repulsive forces)

• ATP + H2O → ADP + Pi (ΔG = - 7.3 kcal/mol (- 30.5 kJ/mol))

How ATP drives transport + mechanical work

• leads to a change in a transport proteins shape that allows transport of solutes (negatively charged phosphates)

• ATP binds non covalently to motor proteins + then hydrolyzed —> shape change that walks the motor protein forward

Regeneration of ATP

• ATP is a renewable resource that is regenerated by addition of phosphate group to ADP

• energy to phosphorylate ADP comes from catabolic reactions in cell

• overall: coupled reactions are exergonic (ΔG < 0)