Cell Structure and Biology

Advanced Placement Biology

Chapter 6

Mr. Knowles

Liberty Senior High School

Robert Hooke, 1665

Hooke’s First Microscope

History of the Cell• 1665- Robert Hooke described

cork as composed of cellulae (cell).• A few years later-Anton van

Leeuwenhoek described live cells.• 1838 and 1839- Schleiden and

Schwann developed the cell theory.

Schleiden and Schwann- Cell Theory

• All organisms are composed of cells or at least one.

• Cells are the smallest unit of life (a collection of metabolic processes + heredity).

• All cells come from other cells. None spontaneously arise.

• Different types of microscopes– Can be used to visualize different sized

cellular structures

Una

ide

d e

ye

1 m

0.1 nm

10 m

0.1 m

1 cm

1 mm

100 µm

10 µ m

1 µ m

100 nm

10 nm

1 nm

Length of somenerve and muscle cells

Chicken egg

Frog egg

Most plant and Animal cells

Smallest bacteria

Viruses

Ribosomes

Proteins

Lipids

Small molecules

Atoms

NucleusMost bacteriaMitochondrion

Lig

ht m

icro

sco

pe

Ele

ctro

n m

icro

sco

pe

Ele

ctro

n m

icro

sco

pe

Figure 6.2

Human height

Measurements1 centimeter (cm) = 102 meter (m) = 0.4 inch1 millimeter (mm) = 10–3 m1 micrometer (µm) = 10–3 mm = 10–6 m1 nanometer (nm) = 10–3 mm = 10–9 m

Use different methods for enhancing visualization of cellular structures

TECHNIQUE RESULT

Brightfield (unstained specimen). Passes light directly through specimen. Unless cell is naturally pigmented or artificially stained, image has little contrast. [Parts (a)–(d) show a human cheek epithelial cell.]

(a)

Brightfield (stained specimen). Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved).

(b)

Phase-contrast. Enhances contrast in unstained cells by amplifying variations in density within specimen; especially useful for examining living, unpigmented cells.

(c)

50 µm

Figure 6.3

Differential-interference-contrast (Nomarski). Like phase-contrast microscopy, it uses optical modifications to exaggerate differences indensity, making the image appear almost 3D.

Fluorescence. Shows the locations of specific molecules in the cell by tagging the molecules with fluorescent dyes or antibodies. These fluorescent substances absorb ultraviolet radiation and emit visible light, as shown here in a cell from an artery.

Confocal. Uses lasers and special optics for “optical sectioning” of fluorescently-stained specimens. Only a single plane of focus is illuminated; out-of-focus fluorescence above and below the plane is subtracted by a computer. A sharp image results, as seen in stained nervous tissue (top), where nerve cells are green, support cells are red, and regions of overlap are yellow. A standard fluorescence micrograph (bottom) of this relatively thick tissue is blurry.

50 µm

50 µm

(d)

(e)

(f)

• The scanning electron microscope (SEM)

– Provides for detailed study of the surface of a specimen

TECHNIQUE RESULTS

Scanning electron micro-scopy (SEM). Micrographs takenwith a scanning electron micro-scope show a 3D image of the surface of a specimen. This SEM shows the surface of a cell from a rabbit trachea (windpipe) covered with motile organelles called cilia. Beating of the cilia helps moveinhaled debris upward toward the throat.

(a)

Cilia

1 µm

Figure 6.4 (a)

• The transmission electron microscope (TEM)

– Provides for detailed study of the internal ultrastructure of cells

Transmission electron micro-scopy (TEM). A transmission electron microscope profiles a thin section of a specimen. Here we see a section through a tracheal cell, revealing its ultrastructure. In preparing the TEM, some cilia were cut along their lengths, creating longitudinal sections, while other cilia were cut straight across, creating cross sections.

(b)

Longitudinalsection ofcilium

Cross sectionof cilium

1 µm

Figure 6.4 (b)

Cell fractionation is used to isolate(fractionate) cell components, based on size and density.

First, cells are homogenized in a blender tobreak them up. The resulting mixture (cell homogenate) is thencentrifuged at various speeds and durations to fractionate the cellcomponents, forming a series of pellets.

• The process of cell fractionation

APPLICATION

TECHNIQUE

Figure 6.5

Tissuecells

Homogenization

Homogenate1000 g(1000 times theforce of gravity)

10 min Differential centrifugation

Supernatant pouredinto next tube

20,000 g20 min

Pellet rich innuclei andcellular debris

Pellet rich inmitochondria(and chloro-plasts if cellsare from a plant) Pellet rich in

“microsomes”(pieces of plasma mem-branes andcells’ internalmembranes)

Pellet rich inribosomes

150,000 g3 hr

80,000 g60 min

Figure 6.5

What’s the world’s largest living cell? Surface to Volume

Ratio

• A smaller cell– Has a higher surface to volume ratio, which

facilitates the exchange of materials into and out of the cell

Surface area increases whiletotal volume remains constant

5

1

1

Total surface area (height width number of sides number of boxes)

Total volume (height width length number of boxes)

Surface-to-volume ratio (surface area volume)

6

1

6

150

125

12

750

125

6

Figure 6.7

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

Pili: attachment structures onthe surface of some prokaryotes

Nucleoid: region where thecell’s DNA is located (notenclosed by a membrane)

Ribosomes: organelles thatsynthesize proteins

Plasma membrane: membraneenclosing the cytoplasm

Cell wall: rigid structure outsidethe plasma membrane

Capsule: jelly-like outer coatingof many prokaryotes

Flagella: locomotionorganelles ofsome bacteria

(a) A typical rod-shaped bacterium

0.5 µmBacterial

chromosome

Figure 6.6 A, B

Prokaryote vs. Eukaryote• Archaebacteria and Eubacteria.• Lack membrane-bound

organelles.• DNA in a nucleoid region.• Have plasma membrane.• Cell wall of peptidoglycan.• Use 70S ribosome.• Unique flagella-flagellin

protein.

• Animalia, Plantae, Protista, Fungi.

• Have true membrane-bound organelles.

• DNA in a nucleus.• Have plasma membrane.• Plants and some protists have

a cell wall of cellulose.• Use different ribosomes.

• Cell structure is correlated to cellular function

10 µm Figure 6.1

A Composite Eukaryotic Cell

• A animal cell:

Rough ER Smooth ER

Centrosome

CYTOSKELETON

Microfilaments

Microtubules

Microvilli

Peroxisome

Lysosome

Golgi apparatus

Ribosomes

In animal cells but not plant cells:LysosomesCentriolesFlagella (in some plant sperm)

Nucleolus

Chromatin

NUCLEUS

Flagelium

Intermediate filaments

ENDOPLASMIC RETICULUM (ER)

Mitochondrion

Nuclear envelope

Plasma membrane

Figure 6.9

• A plant cell:

In plant cells but not animal cells:ChloroplastsCentral vacuole and tonoplastCell wallPlasmodesmata

CYTOSKELETON

Ribosomes (small brwon dots)

Central vacuole

Microfilaments

Intermediate filaments

Microtubules

Rough endoplasmic reticulum

Smooth endoplasmic reticulum

ChromatinNUCLEUS

Nuclear envelope

Nucleolus

Chloroplast

PlasmodesmataWall of adjacent cell

Cell wall

Golgi apparatus

Peroxisome

Tonoplast

Centrosome

Plasma membrane

Mitochondrion

Figure 6.9

Corn Plant Cell

Show me some cell biology animation!

Other Differences Between Plant and

Animal Cells?

Click below for a good tutorial review of Prokaryotic,

Plant and Animal Cells

• The plasma membrane:– Functions as a selective barrier– Allows sufficient passage of nutrients

and waste

Carbohydrate side chain

Figure 6.8 A, B

Outside of cell

Inside of cell

Hydrophilicregion

Hydrophobicregion

Hydrophilicregion

(b) Structure of the plasma membrane

Phospholipid ProteinsTEM of a plasmamembrane. Theplasma membrane,here in a red bloodcell, appears as apair of dark bandsseparated by alight band.

(a)

0.1 µm

Plasma Membrane

Cytosol and Membranes

What is the function of organelles?

• To compartmentalize chemical reactions that may proceed simultaneously.

• To provide membranes on which to catalyze reactions.

Nuclear Envelope– Encloses the nucleus, separating its contents from the

cytoplasm

Figure 6.10

Nucleus

NucleusNucleolus

Chromatin

Nuclear envelope:Inner membrane

Outer membrane

Nuclear pore

Rough ER

Porecomplex

Surface of nuclear envelope.

Pore complexes (TEM). Nuclear lamina (TEM).

Close-up of nuclearenvelope

Ribosome

1 µm

1 µm

0.25 µm

EM of Nucleus

Nuclear Envelope

Nuclear Membrane

1. The Nucleus• Largest organelle, centralized in animal cells.• Stores and protects the cell’s genetic

information.• Surrounded by two phospholipid bilayer

membranes-nuclear envelope.• Where both layers are fused - nuclear pores

+ transport protein.

Nucleus and Nuclear Pore

What is the nuclear pore complex and what does it

do?

How is the ribosome assembled and what does

it do?

Do all cells have nuclei?

A REAL Fantastic Voyage to the Nucleus!

Organization of Nuclear DNA

Show me how DNA is packaged and organized!

Let’s take a look inside a cell!http://www.life.uiuc.edu/plan

tbio/cell/

The Nucleolus• Site within the nucleus of ribosomal

subunits are manufactured- rRNA + ribosomal proteins.

• Ribosomes leave the nucleus as subunits through the nuclear pore and are later reassembled.

• May be free (in the cytoplasm) or attached to the ER (rough ER).

The Nucleolus of an Algae Cell

– Carry out protein synthesis

ER

Ribosomes Cytosol

Free ribosomes

Bound ribosomes

Largesubunit

Smallsubunit

TEM showing ER and ribosomes Diagram of a ribosome

0.5 µm

Figure 6.11

Endoplasmic Reticulum (ER)

The Ribosome (40S and 60S)

Rough ER EM

Endoplasmic Reticulum (ER)• Means “little net within the cytoplasm”• Internal membrane system with a lipid

bilayer + proteins.• Weaved in sheets- forming channels.• Outer membrane of the nuclear envelope is

continuous with the ER membrane.• Some regions have embedded ribosomes.

The ER Membrane– Is continuous with the nuclear envelope

Smooth ER

Rough ER

ER lumen

Cisternae

RibosomesTransport vesicle

Smooth ER

Transitional ER

Rough ER 200 µm

Nuclearenvelope

Figure 6.12

The ER can Grow!

Two Types of (ER)1. Rough ER: heavily studded with ribosomes-

protein synthesis. Proteins have signal sequences which direct to a docking site on the surface of the ER.

2. Smooth ER: lack ribosomes; have enzymes embedded in membrane for carbohydrate and lipid synthesis.

3. Both secrete finished products in transport vesicles.

EM of Pancreas Cell + ER

Functions of Smooth ER

The smooth ER:

–Synthesizes lipids

–Metabolizes carbohydrates

–Stores calcium

–Detoxifies poison

The Golgi Complex• Flattened stacks of membranes in

the cytoplasm-cisternae.• Collection, packaging and

distribution of proteins and lipids.• Transport vesicles from RER and

SER fuse with the Golgi membrane.

Golgiapparatus

TEM of Golgi apparatus

cis face(“receiving” side ofGolgi apparatus)

Vesicles movefrom ER to Golgi Vesicles also

transport certainproteins back to ER

Vesicles coalesce toform new cis Golgi cisternae

Cisternalmaturation:Golgi cisternaemove in a cis-to-transdirection

Vesicles form andleave Golgi, carryingspecific proteins toother locations or tothe plasma mem-brane for secretion

Vesicles transport specificproteins backward to newerGolgi cisternae

Cisternae

trans face(“shipping” side ofGolgi apparatus)

0.1 0 µm16

5

2

3

4

Functions of the Golgi Apparatus

Figure 6.13

Transport of Proteins

Proteins Leaving the Golgi

The Golgi Complex• Proteins (from RER) may have short sugar chains

added--> glycoproteins.• Lipids (from SER) may have short sugar chains

added-->glycolipids.• Both collect at flattened ends-cisternae.• Cisternae membranes pinch off the glycoproteins and

glycolipids into secretory vesicles (liposomes).• Liposomes may fuse with plasma membane or

organelle membranes.

Show me some Golgi in action!

Lysosomes in Action!

Macrophages use Lysosomes

Lysosomes

Lysosomes carry out intracellular digestion by

– Phagocytosis

Figure 6.14 A(a) Phagocytosis: lysosome digesting food

1 µm

Lysosome containsactive hydrolyticenzymes

Food vacuole fuses with lysosome

Hydrolyticenzymes digestfood particles

Digestion

Food vacuole

Plasma membraneLysosome

Digestiveenzymes

Lysosome

Nucleus

Lysosomes• Membrane-bound organelle with digestive

enzymes.• Breakdown protein, nucleic acid, carbos,

lipids.• Digest old organelles and invading bacterial

cells.• Digestive enzymes only active at low pH.

Autophagy

Figure 6.14 B (b) Autophagy: lysosome breaking down damaged organelle

Lysosome containingtwo damaged organelles 1 µ m

Mitochondrionfragment

Peroxisomefragment

Lysosome fuses withvesicle containingdamaged organelle

Hydrolytic enzymesdigest organellecomponents

Vesicle containingdamaged mitochondrion

Digestion

Lysosome

Lysosomes• Inactive lysosomes-Primary Lysosomes, high

pH, enzymes are inactive.• Once fused with food vacuole- pump H+ into

compartment- active, Secondary Lysosomes.• Involved in normal cell death and programmed

cell death (apoptosis).• Ex. Tadpole tail tissue; webbing between human

fingers.

Peroxisomes: Oxidation• Peroxisomes:

– Produce hydrogen peroxide and convert it to water.

Chloroplast

Peroxisome

Mitochondrion

1 µmFigure 6.19

EM of Peroxisome

Plasma membrane expandsby fusion of vesicles; proteinsare secreted from cell

Transport vesicle carriesproteins to plasma membrane for secretion

Lysosome availablefor fusion with anothervesicle for digestion

4 5 6

Nuclear envelope isconnected to rough ER, which is also continuous

with smooth ER

Nucleus

Rough ER

Smooth ERcis Golgi

trans Golgi

Membranes and proteinsproduced by the ER flow in

the form of transport vesiclesto the Golgi

Nuclear envelop

Golgi pinches off transport Vesicles and other vesicles

that give rise to lysosomes and Vacuoles

1

3

2

Plasmamembrane

Relationships among organelles of the endomembrane system

Figure 6.16

Mitochondrion EM

EM of a Mitochondrion

Mitochondria

Let’s take a look inside a cell!http://www.life.uiuc.edu/plan

tbio/cell/

Mitochondrion (ia)• Rod-shaped organelle, 1-3 micrometers long.• Bounded by two membranes- outer is smooth;

inner is folded into continuous layers-cristae.• Two compartments- matrix-inside the inner

membrane and intermembrane space between the two membranes.

• Enzymes for oxidative metabolism are embedded in the inner membrane.

Mitochondria are enclosed by two membranes– A smooth outer membrane– An inner membrane folded into cristae

Mitochondrion

Intermembrane space

Outermembrane

Freeribosomesin the mitochondrialmatrix

MitochondrialDNA

Innermembrane

Cristae

Matrix

100 µmFigure 6.17

Mitochondria• Contain a circular piece of DNA for many of

the proteins in oxidative metabolism.• Also has its own rRNA and ribosomal

proteins--> own protein synthesis.• Involved in its own replication.• Circular DNA? Two membranes? Own Genes?

Own replication?• What does that sound like?

The Plastids

• Chloroplasts

• Leucoplasts

• Amyloplasts

• Chromoplasts

EM of Chloroplast

Chloroplast EM

Chloroplasts– Are found in leaves and other green organs of

plants and in algae.

Chloroplast

ChloroplastDNA

Ribosomes

Stroma

Inner and outermembranes

Thylakoid

1 µm

Granum

Figure 6.18

Chloroplasts• Algae and plants have organelles for photosynthesis.• Two membranes- outer and inner membranes.• A closed, stacked network of membranes-granum

(a).• Fluid-filled space around grana-stroma.• Disc-shaped structures-thylakoids.• Light-capturing enzymes are embedded on

thylakoids.

Chloroplasts• Have DNA which encode many enzymes

necessary for photosynthesis.• Do all plant cells have chloroplasts?• May lose internal structure-leucoplasts.• A leucoplast that stores starch-amyloplast.

Found in root cells.• A leucoplast that stores other pigments-

chromoplasts.

Centriole

Centriole• Barrel-shaped organelles in animals and

protists, NOT plants.

• Usually found in pairs around the nuclear membrane.

• Hollow cylinders made of microtubules (protein). Have their own DNA.

• Help move chromosome during cell division.

Some Other Organelles

• Central Vacuole or Tonoplast: in plants, for protein, water, and waste storage.

• Vesicles: in animals, usually smaller sacs used for storage and transport of materials.

Central Vacuoles– Are found in plant cells– Hold reserves of important organic

compounds and water

Central vacuole

Cytosol

Tonoplast

Centralvacuole

Nucleus

Cell wall

Chloroplast

5 µmFigure 6.15

Paramecium Contractile Vacuole

Laser Scissors and Tweezers!

Ovaetching and Gene Deletion with Lasers

The Cytoskeleton!

Cytoskeleton– Is a network of fibers extending throughout the

cytoplasmMicrotubule

0.25 µm MicrofilamentsFigure 6.20

• There are three main types of fibers that make up the cytoskeleton:

Table 6.1

Actin Filaments• Made of globular protein

monomers- actin• Actin monomers polymerize to

form actin filaments• Filaments are connected to

proteins within the plasma membrane.

How do you put actin together?

Actin Filaments

• Actin filaments are thinner, cause cellular movements like ameboid movements, cell pinching during division.

• Provide shape for the cell.

Actin that function in cellular motility– Contain the protein myosin in addition to actin

Actin filament

Myosin filament

Myosin motors in muscle cell contraction. (a)

Muscle cell

Myosin arm

Figure 6.27 A

Amoeboid Movement– Involves the contraction of actin and myosin

filamentsCortex (outer cytoplasm):gel with actin network

Inner cytoplasm: sol with actin subunits

Extendingpseudopodium

(b) Amoeboid movementFigure 6.27 B

Ameboid Movements

White Blood Cell + Bacteria

Actin forms Pseudopodia in Macrophages

Actin allows cells to grow- Root Hair Cell Growth

Actin permits cells to change shape- Fish cell ruffle and

fish cell lamellipodia.

What is cytoplasmic streaming?

Cytoplasmic Streaming– Is another form of locomotion created by

microfilamentsNonmovingcytoplasm (gel)

Chloroplast

Streamingcytoplasm(sol)

Parallel actinfilaments

Cell wall

(b) Cytoplasmic streaming in plant cellsFigure 6.27 C

So you want to see some actin in action?

Microtubules• 2 globular monomers- tubulin and

tubulin polymerize to form 13 protofilaments

• Filaments form wide, hollow tubes- microtubules.

• Form from nucleation centers (near nucleus) and radiate out.

Show me microtubulin and microtubles!

A Microtubule

Treadmilling of a Microtubule

Microtubules• Constantly polymerize and

depolymerize- GTP-binding at ends.

• Ends are + (away from center) or - (toward center).

• Cellular movements and intracellular movement of materials and organelles.

Show me REAL microtubular treadmilling!

Microtubules• Use specialized motor proteins to

move organelles along the microtubule.

• Kinesins- move organelles toward the + end (toward cell periphery)

• Dyneins- move them toward the - end (toward the center of cell)

How kinesins and dyneins work!

Microtubule and Motor Proteins

One more look at how a kinesin works!

How do kinesins work?

How do dyneins work?

A Working Model of Dynein Function

Microtubules and Motor Proteins Rearrange

Organelles

Microtubules are important in camouflage. They move

melanophores in fish epidermis.

Show me the microtubules!

Could a simple defect in a kinesin affect a whole

organism?

Wild-type Drosophila larva

Wild-type (Normal) Drosophila Movement

Mutant Kinesins in Drosophila (khc6 mutant)

EM of Intermediate Filaments

Intermediate Filaments

• Most durable protein filament- tough fibrous filaments of overlapping tetramers of protein (rope-like).

• Between actin and microtubules in size. Stable

• Ex. of Fibers- vimentin and keratin

Intermediate Filaments

• Anchored to proteins embedded into plasma membrane.

• Provide mechanical support to cell.

Growing Intermediate Filaments

Structural Support…that’s what I’m talking about!

Plant Cell Walls– Are made of cellulose fibers embedded in other

polysaccharides and protein– May have multiple layers

Central vacuoleof cell

Plasmamembrane

Secondarycell wall

Primarycell wall

Middlelamella

1 µm

Centralvacuoleof cell

Central vacuole

Cytosol

Plasma membrane

Plant cell walls

PlasmodesmataFigure 6.28

Plants: Plasmodesmata• Plasmodesmata

– Are channels that perforate plant cell walls

Interiorof cell

Interiorof cell

0.5 µm Plasmodesmata Plasma membranes

Cell walls

Figure 6.30

The Extracellular Matrix (ECM) of Animal Cells

• Animal cells– Lack cell walls– Are covered by an elaborate matrix, the ECM

The ECM– Is made up of glycoproteins and other

macromolecules

Collagen

Fibronectin

Plasmamembrane

EXTRACELLULAR FLUID

Micro-filaments

CYTOPLASM

Integrins

Polysaccharidemolecule

Carbo-hydrates

Proteoglycanmolecule

Coreprotein

Integrin

Figure 6.29

A proteoglycan complex

Types of Intercellular Junctions in animals

Tight junctions prevent fluid from moving across a layer of cells

Tight junction

0.5 µm

1 µm

Spacebetweencells

Plasma membranesof adjacent cells

Extracellularmatrix

Gap junction

Tight junctions

0.1 µm

Intermediatefilaments

Desmosome

Gapjunctions

At tight junctions, the membranes ofneighboring cells are very tightly pressedagainst each other, bound together byspecific proteins (purple). Forming continu-ous seals around the cells, tight junctionsprevent leakage of extracellular fluid acrossA layer of epithelial cells.

Desmosomes (also called anchoringjunctions) function like rivets, fastening cellsTogether into strong sheets. IntermediateFilaments made of sturdy keratin proteinsAnchor desmosomes in the cytoplasm.

Gap junctions (also called communicatingjunctions) provide cytoplasmic channels fromone cell to an adjacent cell. Gap junctions consist of special membrane proteins that surround a pore through which ions, sugars,amino acids, and other small molecules maypass. Gap junctions are necessary for commu-nication between cells in many types of tissues,including heart muscle and animal embryos.

TIGHT JUNCTIONS

DESMOSOMES

GAP JUNCTIONS

Figure 6.31

Cilia