Cell Structures and Function

Structure determines form.

Form determines function.

Cells

Chapter 6

Overview: The Fundamental Units of Life

• All organisms are made of cells

• The cell is the simplest collection of matter that can live

• Structure is correlated function

• All cells are related by their descent from earlier cells

Fig. 6-1

Eukaryotic cells have internal membranes that compartmentalize their functions

• The basic structural and functional unit of every organism is one of two types of cells: prokaryotic or eukaryotic

• Only organisms of the domains Bacteria and Archaea consist of prokaryotic cells

• Protists, fungi, animals, and plants all consist of eukaryotic cells

Comparing Prokaryotic and Eukaryotic Cells

• Basic features of all cells:

– Plasma membrane

– Semifluid substance called cytosol (cytoplasm)

– DNA (chromosomes with genes)

– Ribosomes (make proteins)

• Prokaryotic cells are characterized by having

– No nucleus

– No membrane-bound organelles

– A single, circular chromosome

Fig. 6-6

Fimbriae

Nucleoid

Ribosomes

Plasma membrane

Cell wall

Capsule

Flagella

Bacterialchromosome

(a) A typical rod-shaped bacterium

(b) A thin section through the bacterium Bacillus coagulans (TEM)

0.5 µm

• Eukaryotic cells are characterized by having

– DNA in a nucleus that is bounded by a membranous nuclear envelope

– Membrane-bound organelles

• Eukaryotic cells are generally much larger than prokaryotic cells

• The logistics of carrying out cellular metabolism sets limits on the size of cells

• The surface area to volume ratio of a cell is critical

• As the surface area increases by a factor of n2, the volume increases by a factor of n3

• Small cells have a greater surface area relative to volume

Surface area increases whiletotal volume remains constant

5

11

6 150 750

125 1251

6 61.2

Total surface area

[Sum of the surface areas

(height width) of all boxes

sides number of boxes]

Total volume

[height width length number of boxes]

Surface-to-volume

(S-to-V) ratio

[surface area ÷ volume]

A Panoramic View of the Eukaryotic Cell

• A eukaryotic cell has internal membranes that partition the cell into organelles

• Plant and animal cells have most of the same organelles

ENDOPLASMIC RETICULUM (ER)

Smooth ERRough ERFlagellum

Centrosome

CYTOSKELETON:

Microfilaments

Intermediatefilaments

Microtubules

Microvilli

Peroxisome

MitochondrionLysosome

Golgiapparatus

Ribosomes

Plasma membrane

Nuclearenvelope

Nucleolus

Chromatin

NUCLEUS

NUCLEUS

Nuclear envelopeNucleolus

Chromatin

Rough endoplasmic reticulum

Smooth endoplasmic reticulum

Ribosomes

Central vacuole

Microfilaments

Intermediate filaments

Microtubules

CYTO-SKELETON

Chloroplast

PlasmodesmataWall of adjacent cell

Cell wall

Plasma membrane

Peroxisome

Mitochondrion

Golgiapparatus

The endomembrane system regulates protein traffic and performs metabolic functions in the eukaryotic cell

• Components of the endomembrane system:– Nuclear envelope

– Endoplasmic reticulum

– Golgi apparatus

– Lysosomes

– Vacuoles

– Plasma membrane

• These components are either continuous or connected via transfer by vesicles

The cytoskeleton is a network of fibers that organizes structures and activities in the eukaryote

• The cytoskeleton is a network of fibers extending throughout the cytoplasm

• It organizes the cell’s structures and activities, anchoring many organelles

• It is composed of three types of molecular structures:– Microtubules– Microfilaments– Intermediate filaments

The Extracellular Matrix (ECM) of Animal Cells

• Animal cells lack cell walls but are covered by an elaborate extracellular matrix (ECM)

• The ECM is made up of glycoproteins such as collagen, proteoglycans, and fibronectin

• ECM proteins bind to receptor proteins in the plasma membrane called integrins

• Functions of the ECM:– Support– Adhesion– Movement– Regulation

Collagen

Fibronectin

Plasma membrane

Proteoglycan complex

Integrins

CYTOPLASMMicro-filaments

EXTRACELLULAR FLUID

MEMBRANE STRUCTURE AND FUNCTION

Chapter 7

Plasma Membrane• Bilayer of phospholipids• Phospholipid

–The 2 tails are hydrophobic fatty acids–The head is a hydrophilic phosphate

group–The tails and head are connected by

glycerol• Cell membranes also contain proteins and

carbohydrates

Figure 8.1 Artificial membranes (cross sections)

Figure 8.4 The fluidity of membranes

• Held together by weak hydrophobic interactions

• Lipids and proteins can drift laterally within membrane

• Cholesterol regulates membrane fluidity (makes less fluid when it is warmer, more fluid when it is colder) and is only found in animal cells

• Unsaturated fatty acids have “kinks” at the double bonds causing them to not pack together closely – makes membrane more fluid

• Membrane proteins–Integral proteins - generally

transmembrane with hydrophobic regions

–Peripheral proteins - generally attached to membrane’s surface

• Cell-to-cell recognition –“Markers”- glycoproteins,

glycolipids, & oligosaccharides (short polysaccharides)

Figure 8.9 Some functions of membrane proteins

Figure 8.7 The structure of a transmembrane protein

Figure 8.6 The detailed structure of an animal cell’s plasma membrane, in cross section

TRAFFIC ACROSS MEMBRANE

• Selective Permeability - regulates the type and rate of molecular traffic into and out of cell–Nonpolar (hydrophobic) molecules

•dissolve in membrane•cross easily•ex. CO2 and O2

–Polar (hydrophilic) molecules•Small, uncharged pass through easily (ex. water)

•Larger, uncharged will not easily pass (ex. glucose)

•All ions, even small ones, have difficulty penetrating hydrophobic region (ex. Na+, H+)

• Passive Transport–Requires no energy–Diffusion - the net movement of a

substance down a concentration gradient (from high to low concentration)•Concentration gradient - regular, graded concentration change over a distance

•Net movement - the overall movement away from center of concentration

•Results from random molecular motion, although net movement may be directional

• Increases entropy (increases disorder)

•Decreases free energy (-ΔG) so it is a spontaneous process

•Rate of diffusion depends on permeability of membrane

•Water diffuses freely across most membranes

•Net movement stops at equilibrium

Figure 8.10 The diffusion of solutes across membranes

–Osmosis -diffusion of water•Water diffuses down its concentration gradient

•Direction is determined by total solute concentration, regardless of type or diversity of solutes in solutions

Figure 8.11 Osmosis

•Hypertonic - greater solute concentration

•Hypotonic - lower solute concentration

• Isotonic - same solute concentration•Water moves from hypotonic to hypertonic areas.

Figure 8.12 The water balance of living cells

•Effects of osmosis–In hypertonic solution: animal cells shrivel, plant cell are plasmolyzed (cell membrane pulls away from cell wall)

–In a hypotonic solution: animal cells are lysed (pop), plant cells are turgid (firm)

–In isotonic: animal cells normal, plant cells are flaccid (limp)

•Water potential (Ψ) is the measure of the tendency for a solution to take up water when separated from pure water by a selectively permeable membrane

•Water moves from high to low water potential

•Water potential depends on solute potential and pressure potential (in cells)

–Ψ = Ψp + Ψs

»Ψp is pressure potential»Ψs is solute potenial

–Water potential of pure water is zero so Ψs of any solution will always be negative

–Increasing solute, makes Ψs more negative

–Increasing Ψs decreases water potential.

–Pressure potential is influenced by water movement into and out of plant cells.

–Pressure potential is the physical pressure exerted on either side of a membrane.

–Increasing Ψp increases Ψ–A positive pressure potential means a

plant cell is turgid and a negative pressure means it is flaccid.

–Osmotic pressure is equal to, but opposite pressure potential.

–Ψp = 0 for things that are not cells (ex. lakes)

•Osmoregulation - controlling water balance–Contractile vacuoles pump out water (ex. Paramecium)

–Pumping out salts (ex. Bony fish)–Facilitated Diffusion - diffusion

across membrane with the help of transport proteins•Passive because solutes move down their concentration gradient and no energy is required

• Facilitated Diffusion Animation

Figure 8.13 The contractile vacuole of Paramecium: an evolutionary adaptation for osmoregulation

Figure 8.14 Two models for facilitated diffusion

• Transport proteins–Specific for the solutes that they

transport–Conformational change in protein allows

solute to be transferred to other side–Gated proteins - channel opens in

response to electrical or chemical signal–Ex. Aquaporins – channel proteins that

transport water via facilitated diffusion»Problems with aquaporins associated

with glaucoma, cataracts, and kidney diseases

• Active Transport - an energy requiring process during which a transport protein pumps a molecule across the membrane, against its concentration gradient (from low to high concentration)–Requires +ΔG–Helps cell maintain steep ionic

gradients across cell membrane–Uses ATP (energy)– Sodium Potassium Pump animation

Figure 8.15 The sodium-potassium pump: a specific case of active transport

–Ex. Sodium-potassium pump•Transport protein has binding sites for Na+ on interior side and sites for K+ on exterior side

•Na+ binds to protein and stimulates ATP to phosphorylize the protein thereby changing its shape

•This changed shape allows Na+ to be expelled outside of cell and allows K+ to bind on outside of protein

•K+ binding triggers release of phosphate from protein

•Loss of phosphate restores proteins original shape and expels K+ into cell

•Na+ K+ pump translocates 3 Na+

ions out of cell for every 2 K+ ions pumped into cell.

• Ion pumps generate voltage across membrane–Because anions and cations are

distributed unequally across cell membranes, all cells have voltages across their membranes (batteries)

–Membrane potential - voltage across membrane• ranges from -50 to -200 mv (the inside of the cell is more negative than the outside)

–That negative inside favors the passive transport of cations into the cell and anions out of cell.

–Electrochemical gradient - diffusion gradient resulting from combined effects of membrane potential and concentration gradient• Ions may not always diffuse down their concentration gradient, but always diffuse down their electrochemical gradient

–Electrogenic pump - a transport protein that generates voltage across membrane •Ex. Sodium potassium pump (in animals): 3 Na+ move out and only 2 K+ move in (net charge of +1 on outside of cell)

•Ex. Proton pump (in bacteria, fungi, and plants): actively transports H+ outside of cell

Figure 8.17 An electrogenic pump

Ion pump animation

• Cotransport - a process where a single ATP-powered pump actively transports one solute and indirectly drives the transport of other solutes against their concentration gradient

• Cotransport animation

Figure 8.18 Cotransport

–One example in plants: •An ATP driven proton pump sends H+ outside of the cell

•Then H+ diffuses back into cell via a specific transport protein

•As H+ diffuses, sucrose can ride the proton’s “coattails” and move into the cell (against its own concentration gradient).

–One example in humans:• If someone has severe diarrhea or

is badly dehydrated from running…–Give person solution high in

glucose and salt–Solutes transported to blood

causes water to move into blood from colon (rehydration)

–Cotransport involves Na+ and glucose so both needed

Figure 8.19 The three types of endocytosis in animal cells

• Exocytosis - process of exporting macromolecules (ex. proteins and polysaccharides) from a cell by fusion of vesicles with a cell membrane

• Endocytosis - process of importing macromolecules (ex. proteins and polysaccharides) into a cell by forming vesicles derived from the cell membrane

• Endo animation• More…

–Phagocytosis - endocytosis of solid particles

–Pinocytosis - endocytosis of fluid droplets

–Receptor-mediated endocytosis - a ligand binds to a receptor site in a coated pit and causes a vesicle to form and ingest material. This is more discriminating than pinocytosis.

TRANSPORT IN PLANTS

CHAPTER 36

Figure 36.1 An overview of transport in whole plants

OSMOSIS AND WATER POTENTIAL

• From high to low concentration = from hypotonic to hypertonic

• Water potential Ψ – from high to low water potential–Solute concentration and

pressure–Measured in megapascals (MPa)

• Plasmolyze – when a plant’s cell membrane pulls away from cell wall

• Turgor pressure – when a plant cell swells against its cell wall

• Turgid – plant cells that are “swelled” due to turgor pressure (healthy)

• Plants have aquaporins (as do animals).

Figure 36.4 Water relations of plant cells

Figure 36.5 A watered tomato plant regains its turgor

BULK FLOW• Movement of fluid driven by

PRESSURE• Occurs in both xylem (water carrying

cells/tube) and phloem (food carrying cells/tube), but how the pressure made is different–Xylem pressure due to

transpiration–Phloem pressure due to active

transport of sucrose

TRANSPORT OF XYLEM SAP

• Root pressure – accumulation of minerals lowers water potential so water moves into cortex (“center” tissue) from high to low water potential

• Can only move water upward a few meters

• Transpiration allows for xylem sap to be pulled upward very far!

Figure 36.9 Guttation

• Water evaporates from mesophyll cells in leaves through stomata (holes in leaves)

• Remaining water film on cells forms menisci

• The more concave the menisci become the more transpiration increases

• More evaporation = more transpiration

Figure 36.10 The generation of transpirational pull in a leaf

• This increases the water tension (negative pressure)

• Draws water upward and out of xylem through mesophyll like water in a syringe or straw

• Cohesion of water due to H bonding enables water to be pulled upward in narrow tracheids and vessels without water breaking apart

• Adhesion of water to hydrophilic walls of xylem help it to fight gravity

• This bulk-flow is solar-powered because sun is responsible for transpiration

Figure 36.11 Ascent of water in a tree

TRANSPIRATION CONTROL

• Must leave stomata open at some point to get CO2

• Guard cells open and close stomata–Flaccid guard cells close stomata–Turgid guard cells open stomata

Figure 36.12 An open (left) and closed (right) stoma of a spider plant (Chlorophytum colosum) leaf

Figure 36.12x Stomata on the underside of a leaf

Figure 36.13a The mechanism of stomatal opening and closing

• Guard cells become turgid by pumping out H+ (proton pump) which makes cell negative inside

• Then K+ comes in (attracted to negative inside)

• This decreases water potential inside so water moves into cell via osmosis

• Guard cells become flaccid when stomata close and K+ leaves causing water to leave cell

Figure 36.13b The mechanism of stomatal opening and closing

• In general, stomata open during day and close at night–Blue-light receptor in guard cell

signals proton pumps to start–Guard cells do photosynthesis and

some of that ATP runs proton pumps

–Low CO2 can signal opening–Internal clocks

ADAPTIONS TO REDUCE TRANSPIRATION

• C4 and CAM plants are better able to assimilate and use CO2

• Stomata in depressions on underside of leaf

• Some dessert plants shed leaves in driest months

TRANSLOCATION OF PHLOEM SAP

• Most prevalent solute is sucrose, but sap also includes amino acids, hormones, and minerals

• Moves both from root to shoot and from shoot to root

• General movement from sucrose source to sucrose sink

• Proton pumps (via cotransport) accumulate sucrose in phloem cells

• This reduces water potential and causes the uptake of water. This hydrostatic pressure forces sap to flow along tube.

• Pressure gradient reinforced by unloading of sucrose at sink.

• So building pressure at sucrose source and reduced pressure at sucrose sink causes sap to flow from the source to the sink.

• Xylem recycles water from source to sink.

Figure 36.17 Pressure flow in a sieve tube

Figure 36.18 Tapping phloem sap with the help of an aphid

Cell to Cell Communication

Chapter 11

Local and Long Distance Signaling

• Local signaling – influences cells in the nearby vicinity–Paracrine signaling – secreting cell releases

a regulator in the extracellular matrix–Synaptic signaling – nerve cell releases

neurotransmitter into a synapse (space between nerves)

• Long Distance signaling – can influence cells all over body–Hormone signaling – endocrine cells

secrete hormones into blood where they can reach any cell

Figure 11.3 Local and long-distance cell communication in animals

Figure 11.4 Communication by direct contact between cells

Cell junctions and cell-cell recognition

Three Stages of Cell Signaling

• Reception – target cell’s detection of a chemical signal–Signal is detected when it binds to a

receptor–Ligand – a signal molecule that binds to a

receptor• Transduction – binding of signal to receptor

stimulates a change in the receptor. –The changed receptor triggers a step or

many steps that lead to the cell response.• Response – end result – the cell response

Figure 11.5 Overview of cell signaling

Receptors

• Intracellular receptors – found in cytoplasm or on nucleus so signal must pass through cell membrane first–Testosterone receptor only found in

certain cells•An activated testosterone receptor acts as a transcription factor

•Transcription factors - turn on or turn off genes

Figure 11.10 Steroid hormone interacting with an intracellular receptor

• Cell Membrane Receptors – found in cell membrane–Three major types

•G-linked receptor•Receptor tyrosine kinase•Ligand-gated ion channel

Figure 11.6 The structure of a G-protein-linked receptor

Figure 11.7 The functioning of a G-protein-linked receptor

G Protein Animation

Figure 11.8 The structure and function of a tyrosine-kinase receptor

Figure 11.9 A ligand-gated ion-channel receptor

Transduction

• Signal transduction pathways – a chain of molecular interactions (like falling dominoes)

• Often involves protein phosphorylation and dephosphorylation–Protein kinases – enzymes that transfer

phosphate groups from ATP to a protein–Phosphorylation of protein often changes

protein from inactive to active form–Protein phosphatases – enzymes that

rapidly remove P (often turn off pathway)

Figure 11.11 A phosphorylation cascade

Second Messengers• Second messengers – small, nonprotein,

water-soluble molecules or ions that are part of signaling pathways

• Two most common second messengers–Ca2+

–cAMP or cyclic AMP (Cyclic adenosine monophosphate)

• Adenylyl cyclase – an enzyme in cell membranes that converts ATP into cAMP

• Phosphodiesterase – an enzyme that converts cAMP into AMP

Figure 11.12 Cyclic AMP

Figure 11.13 cAMP as a second messenger

Figure 11.16 Cytoplasmic response to a signal: the stimulation of glycogen breakdown by epinephrine

G Protein Animation for Epinephrine Ligand

Fine Tuning of Response

• Signal Amplification – number of activated products is much greater than in preceding step

• Specificity – different cells have different proteins so two cells can respond to same signal in different manner–Ex. epinephrine stimulates liver to break

down glycogen and heart cells to contract faster

• Scaffolding Proteins – large relay proteins to which several other relay proteins are attached

Figure 11.18 The specificity of cell signaling

Figure 11.19 A scaffolding protein

Apoptosis• Apoptosis - triggered by signals that

activate cell suicide • In C. elegans (small worm), death genes

called ced. When activated they stimulate death by activating proteases and nucleases.

• Very similar genes found in other animals including humans

• Apoptosis problems are associated with cancer, Parkinson’s, and alzheimer’s