NOTES: CH 6 – A Tour of the Cell. Overview: The Importance of Cells ● All organisms are made of...

NOTES: CH 6 – A Tour of the Cell

Overview: The Importance of Cells

● All organisms are made of cells

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

● Cell structure is correlated to cellular function

● All cells are related by their descent from earlier cells

Measurements1 centimeter (cm) = 10–2 meter (m) = 0.4 inch1 millimeter (mm) = 10–3 m1 micrometer (µm) = 10–3 mm = 10–6 m1 nanometer (nm) = 10–3 µm = 10–9 m

10 m

1 mHuman height

Length of somenerve andmuscle cells

Chicken egg

0.1 m

1 cm

Frog egg1 mm

100 µm

Most plant andanimal cells

10 µmNucleus

1 µm

Most bacteria

Mitochondrion

Smallest bacteria

Viruses100 nm

10 nmRibosomes

Proteins

Lipids

1 nmSmall molecules

Atoms0.1 nmU

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6.1 – Biologists use microscopes and the tools of biochemistry to study cells

Brightfield (unstained specimen)

50 µmBrightfield (stained specimen)

Phase-contrast

MICROSCOPES

1) Light Microscope

2) Electron Microscope (1950’s)

● Transmission Electron Microscope

● Scanning Electron Microscope

Light Microscope

● works by passing visible light through a thin section of specimen and then through glass lenses

● resolving power = 0.2 µm (size of small bacteria)

● max. magnification about 1000x

Electron Microscope (1950’s)

● uses electron beams which

have shorter wavelengths

of light

● resolving power = 0.2 nm

(most cell structures)

● magnification up to

40,000x

Electron Microscope1) Transmission Electron Microscope

-electrons transmitted through specimen are focused and image is magnified using electromagnets

-used to study internal cell structure

2) Scanning Electron Microscope

-electron beam scans the surface of a spec.

-useful for studying the surface of specimen in 3-D.

Disadvantages to EM…

● can only view dead cells (elaborate preparation)

● very expensive!

zooxanthellae cells cultured from coral

Aiptasia pulchella in a Scanning Electron

Microscope

WE CAN ALSO STUDY CELLS BY... ● Cell Fractionation =

disrupting cells to separate out cell organelles

● Centrifugation = spinning mixtures of cells and their parts at very high speeds; separates the components

6.2 – 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 (& are in the domain Eukarya)

Types of CELLS:

ALL CELLS:

● have a cell membrane

● have cytoplasm / cytosol

● have ribosomes (make

proteins)

● can reproduce & contain

genetic material (DNA /

chromatin / chromosomes)

CELLS CAN BE CLASSIFIED AS:

1) PROKARYOTES

2) EUKARYOTES

1) PROKARYOTES 2) EUKARYOTES

• oldest cells (3.5 billion years)

• single celled

• lack nucleus & membrane-bound organelles

• genetic material in a single, circular molecule (PLASMID) in region called NUCLEOID

• small (1-2 µm)

• Domains Bacteria and Archaea

• “newer” cells (1.5 billion years)

• single or multicellular

• have a “true” nucleus & membrane-bound organelles

• genetic material organized into CHROMOSOMES in NUCLEUS

• larger (2-1000 µm)

• Domain Eukarya, includes Kingdoms Protista, Fungi, Plantae, Animalia

A typicalrod-shapedbacterium

A thin section through thebacterium Bacilluscoagulans (TEM)

0.5 µm

Pili

Nucleoid

Ribosomes

Plasmamembrane

Cell wall

Capsule

Flagella

Bacterialchromosome

● although eukaryotic cells are larger than prokaryotes, there is a limit on cell size due to the logistics of carrying out cellular metabolism

Total surface area(height x width xnumber of sides xnumber of boxes)

6

125 125

150 750

1

11

5

1.2 66

Total volume(height x width x lengthX number of boxes)

Surface-to-volumeratio(surface area volume)

Surface area increases whileTotal volume remains constant

● The plasma membrane is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of the cell

● The general structure of

a biological membrane is

a double layer of

phospholipids

PLASMA MEMBRANE: the boundary of every cell

Hydrophilicregion

Hydrophobicregion

Carbohydrate side chain

Structure of the plasma membrane

Hydrophilicregion

Phospholipid Proteins

Outside of cell

Inside of cell 0.1 µm

TEM of a plasma membrane

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

Flagellum

Centrosome

CYTOSKELETON

Microfilaments

Intermediate filaments

Microtubules

Peroxisome

Microvilli

ENDOPLASMIC RETICULUM (ER

Rough ER Smooth ER

MitochondrionLysosome

Golgi apparatus

Ribosomes:

Plasma membrane

Nuclear envelope

NUCLEUS

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

Nucleolus

Chromatin

Roughendoplasmicreticulum

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

Smoothendoplasmicreticulum

Ribosomes(small brown dots)

Central vacuole

Microfilaments

IntermediatefilamentsMicrotubules

CYTOSKELETON

Chloroplast

Plasmodesmata

Wall of adjacent cell

Cell wall

Nuclearenvelope

Nucleolus

Chromatin

NUCLEUS

Centrosome

Golgiapparatus

Mitochondrion

Peroxisome

Plasmamembrane

6.3 - The eukaryotic cell’s genetic instructions are housed in the NUCLEUS and carried out by the ribosomes

● the nucleus contains most of the DNA in a eukaryotic cell

● ribosomes use the information from the DNA to make proteins

The Nucleus: Genetic Library of the Cell

● the nucleus contains most of the cell’s genes and is usually the most conspicuous organelle

● the nuclear envelope encloses the nucleus, separating it from the cytoplasm

● houses the information / instructions for cell functioning and maintenance …the “control center” of the cell

● averages 5 µm in diameter

Close-up of nuclearenvelope

Nucleus

Nucleolus

Chromatin

Nuclear envelope:Inner membraneOuter membrane

Nuclear pore

Porecomplex

Ribosome

Pore complexes (TEM) Nuclear lamina (TEM)

1 µm

Rough ER

Nucleus

1 µm

0.25 µm

Surface of nuclear envelope

NUCLEAR ENVELOPE ● double membrane which encloses

the nucleus

-each of the 2 membranes is a phospholipid bilayer w/specific proteins

-is perforated by pores which regulate molecular traffic into and out of the nucleus

-RNA and proteins enter or leave the nucleus through these pores

-breaks down prior to cell division

CHROMATIN ● fibrous, threadlike

complex of DNA and histone proteins which make up chromosomes in eukaryotic cells

CHROMOSOMES

● compacted, coiled up chromatin;

● visible under microscope;

● form just prior to cell division;

● human cells have 46 chromosomes (23 pairs)

NUCLEOLUS ● dense, spherical region in the nucleus

-visible in a nondividing cell-may be 2 or more per cell -packages ribosomal subunits from:1) rRNA: transcribed in nucleolus2) RNA produced elsewhere in nucleus-ribosomal subunits pass through nuclear pores to the cytoplasm where assembly into ribosomes is completed

RIBOSOMES

● cytoplasmic organelle; site of protein synthesis

-made of RNA and protein

-made in the nucleolus

-cells with high rates of protein synthesis have large numbers of nucleoli & ribosomes (e.g. human liver cells have millions)

● Ribosomes carry out protein synthesis in two locations:

-in the cytosol (free ribosomes)

-attached to the outside of the endoplasmic reticulum (ER) or the nuclear envelope (bound ribosomes)

RIBOSOMES

Ribosomes

0.5 µm

ER Cytosol

Endoplasmicreticulum (ER)

Free ribosomes

Bound ribosomes

Largesubunit

Smallsubunit

Diagram ofa ribosome

TEM showing ERand ribosomes

Cell Organelles (continued)

The Endomembrane System

**all structures are essentially compartments, closed off by their membranes from the cytoplasm

6.4 - The endomembrane system regulates protein traffic and performs metabolic functions in the 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 vesicles

The Endoplasmic Reticulum: Biosynthetic Factory

● The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells

● The ER membrane is continuous with the nuclear envelope

ENDOPLASMIC RETICULUM (ER): ● extensive network of tubules and sacs

● used for transport and/or modification of proteins;

● can be ROUGH (ribosomes) or SMOOTH (no ribosomes)

Rough ER: ● manufactures secretory

proteins and membranes ;● proteins made here may

be modified (i.e. folded into theirtertiary structure)

● usually closer in to nucleusthan smooth ER

Smooth ER:

● synthesizes lipids, phospholipids, steroids

● participates in carbohydrate metabolism

● detoxifies drugs and poisons

● stores calcium ions (for muscle

contraction)

Ribosomes

Smooth ER

Rough ER

ER lumen

Cisternae

Transport vesicle

Smooth ER Rough ER

Transitional ER

200 nm

Nuclearenvelope

● The Golgi apparatus consists of flattened membranous sacs called cisternae

● Functions of the Golgi apparatus:– Modifies products of the ER– Manufactures certain

macromolecules– Sorts and packages materials

into transport vesicles

The Golgi Apparatus: Shipping and Receiving Center

GOLGI APPARATUS:

● cis face (forming face; faces the rough ER) receives products by accepting transport vesicles from the rough ER

● trans face (maturing face; faces the

cell membrane) pinches off vesicles

from the Golgi and transports

molecules to other sites

trans face(“shipping” side ofGolgi apparatus) TEM of Golgi apparatus

0.1 µm

Golgi apparatus

cis face(“receiving” side ofGolgi apparatus)

Vesicles coalesce toform new cis Golgi cisternae Vesicles also

transport certainproteins back to ER

Vesicles movefrom ER to Golgi

Vesicles transport specificproteins backward to newerGolgi cisternae

Cisternalmaturation:Golgi cisternaemove in a cis-to-transdirection

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

Cisternae

Lysosomes: Digestive Compartments

● A lysosome is a membranous sac of hydrolytic enzymes

● Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids

● Lysosomes also use enzymes to recycle organelles and macromolecules, a process called autophagy

Phagocytosis: lysosome digesting food

1 µm

Plasmamembrane

Food vacuole

Lysosome

Nucleus

Digestiveenzymes

Digestion

Lysosome

Lysosome containsactive hydrolyticenzymes

Food vacuolefuses withlysosome

Hydrolyticenzymes digestfood particles

Autophagy: lysosome breaking down damaged organelle

1 µm

Vesicle containingdamaged mitochondrion

Mitochondrionfragment

Lysosome containingtwo damaged organelles

Digestion

Lysosome

Lysosome fuses withvesicle containingdamaged organelle

Peroxisomefragment

Hydrolytic enzymesdigest organellecomponents

LYSOSOMES ● probably pinch off from the trans face of Golgi;

● are responsible for intracellular digestion;

● recycle the cell’s own organic material;

● destroy cells

Other Membrane-Bound Organelles:1) Vacuoles

2) Peroxisomes

VESICLES / VACUOLES: ● membrane-enclosed sac

used for storage and/or transport animal cells, vacuoles are small and look like vesicles

**Vacuoles in plants have special characteristics:-plant cells have a LARGE central vacuole that stores water and water-soluble organic compounds and inorganic ions (K+ and Cl-);

PLANT VACUOLES…

● contain soluble pigments in some cells (red and blue

pigments in flowers);

● play a role in plant growth by absorbing water and

elongating the cell;

PLANT VACUOLES…

● help protect from predators by storing waste

products that may also be poisonous compounds

● Are surrounded by a membrane called the

TONOPLAST

● some fresh-water protists

have a contractile vacuole

that pumps excess water

from the cell

5 µm

Central vacuole

Cytosol

Tonoplast

Central vacuole

Nucleus

Cell wall

Chloroplast

The Endomembrane System: A Review

● The endomembrane system is a complex and dynamic player in the cell’s compartmental organization

Nuclear envelope

Nucleus

Rough ER

Smooth ER

Nuclear envelope

Nucleus

Rough ER

Smooth ER

Transport vesicle

cis Golgi

trans Golgi

Nuclear envelope

Nucleus

Rough ER

Smooth ER

Transport vesicle

cis Golgi

trans Golgi

Plasma membrane

6.5 - Mitochondria and chloroplasts change energy from one form to another

● Mitochondria are the sites of cellular respiration

● Chloroplasts, found only in plants and algae, are the sites of photosynthesis

● Mitochondria and chloroplasts are not part of the endomembrane system

● Peroxisomes are oxidative organelles

MITOCHONDRIA:

● sites of cellular respiration

● found in nearly all eukaryotic cells

● the # in cells varies and is related to the

cell’s metabolic activity

● inner membrane is convoluted

and contains proteins/enzymes

involved in cellular respiration

● inner membranes many

infoldings are called CRISTAE;

they increase the surface area

for cellular respiration

reactions to occur

● region within inner membrane is

the MITOCHONDRIAL MATRIX

Mitochondria in a human liver cell

Mitochondrion

Intermembrane space

Outer membrane

Inner membrane

Cristae

Matrix

100 nmMitochondrialDNA

Freeribosomes in themitochondrialmatrix

CHLOROPLASTS: (“the organelles that feed the world”)

● contain chlorophyll;● site of photosynthesis

(convert light energy into chemical energy;

● found in eukaryotic algae, leaves and other green plant organs;

● can change shape, move and divide

Chloroplasts: Capture of Light Energy

● Chloroplast structure includes:

-Thylakoids, membranous sacs

-Stroma, the internal fluid

Chloroplast

ChloroplastDNA

RibosomesStroma

Inner and outermembranes

Granum

Thylakoid1 µm

PEROXISOMES:

● contain special enzymes for specific metabolic pathways

● found in nearly all eukaryotic cells

● contain peroxide-producing enzymes

that transfer hydrogen ions to oxygen

producing hydrogen peroxide

● contain catalase enzyme which

converts / detoxifies hydrogen peroxide

to water

Chloroplast

Peroxisome

Mitochondrion

1 µm

6.6 - The cytoskeleton is a network of fibers that organizes structures and activities in the cell

● anchors and/or provides “tracks” for many organelles

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

Microtubule

Microfilaments0.25 µm

Components of the Cytoskeleton

● Microtubules are the thickest of the three components of the cytoskeleton

● Microfilaments, also called actin filaments, are the thinnest components

● Intermediate filaments are fibers with diameters in a middle range

Roles of the Cytoskeleton: Support, Motility, and Regulation

● the cytoskeleton helps to support the cell and maintain its shape

● it interacts with motor proteins to produce motility (movement)

● inside the cell, vesicles can travel along “monorails” provided by the cytoskeleton

● recent evidence suggests that the cytoskeleton may help regulate biochemical activities

Vesicle

Receptor formotor protein

Microtubuleof cytoskeleton

Motor protein(ATP powered)

ATP

0.25 µmMicrotubule Vesicles

Microtubules: ● straight, hollow rods made of protein called

TUBULIN;

● can serve as “tracks” to

guide organelle movement;

● involved in separation of chromosomes in cell

division; make up CENTRIOLES;

Cilia and Flagella● Microtubules control the beating of cilia and

flagella, locomotor appendages of some cells

● Cilia and flagella differ in their beating patterns

FLAGELLA and CILIA:

● FLAGELLA: longer than cilia; usually found singly or in pairs; used to propel a cell

● CILIA: shorter than flagella; usually present in great numbers; wavelike motion used to sweep extracellular material over/away from cell

5 µm

Direction of swimming

Motion of flagella

15 µm

Direction of organism’s movement

Motion of cilia

Direction ofactive stroke

Direction ofrecovery stroke

● Cilia and flagella share a common ultrastructure:

-A core of microtubules sheathed by the plasma membrane

-A basal body that anchors the cilium or flagellum

-A motor protein called DYNEIN, which drives the bending movements of a cilium or flagellum

0.5 µm

Microtubules

PlasmamembraneBasal body

Plasmamembrane

0.1 µm

Cross section of basal body

Triplet

Outer microtubuledoublet

0.1 µm

Dynein arms

Centralmicrotubule

Cross-linkingproteins insideouter doublets

Radialspoke

Dynein “walking”

Microtubuledoublets ATP

Dynein arm

Wavelike motion

Cross-linkingproteins insideouter doublets

ATP

Anchoragein cell

Effect of cross-linking proteins

Microfilaments:● can exist as single filaments or in bundles;

● formed from the protein ACTIN;

● help the cell (or parts of the cell) to contract;

● they stabilize cell shape;

● Involved in “pinching” contractions during cell division;

● Involved in forming “pseudopodia” that enable some cells to move.

YellowYellow: nucleus: nucleus

GreenGreen: microfilaments throughout : microfilaments throughout cytoplasmcytoplasm

Cortex (outer cytoplasm):gel with actin network

Amoeboid movement

Inner cytoplasm: solwith actin subunits

Extendingpseudopodium

Muscle cell

Actin filament

Myosin filamentMyosin arm

Myosin motors in muscle cell contraction

Nonmovingcytoplasm (gel)

Cytoplasmic streaming in plant cells

Chloroplast

Streamingcytoplasm(sol)

Cell wall

Parallel actinfilaments

Vacuole

Intermediate Filaments

● Intermediate filaments range in diameter from 8–12 nanometers, larger than microfilaments but smaller than microtubules

● They support cell shape and fix organelles in place

● Intermediate filaments are more permanent cytoskeleton fixtures than the other two classes

6.7 - Extracellular components and connections between cells help coordinate cellular activities

● Most cells synthesize and secrete materials that are external to the plasma membrane

● These extracellular structures include:– Cell walls of plants– The extracellular matrix (ECM) of animal cells– Intercellular junctions

Extracellular Structures:

● CELL WALL:

-semirigid structure

outside of cell membrane

of PLANT CELLS;

-consists of CELLULOSE

fibers + complex

polysaccharides

& proteins

-provides support, limits cell’s volume, and protects against fungi and/or microorganism infection.

Cell Walls of Plants

● Plant cell walls may have multiple layers:– Primary cell wall: relatively thin and flexible– Middle lamella: thin layer between primary walls

of adjacent cells– Secondary cell wall (in some cells): added

between the plasma membrane and the primary cell wall

● Plasmodesmata are channels between adjacent plant cells

Centralvacuole of cell

PlasmamembraneSecondarycell wall

Primarycell wall

Middlelamella

1 µm

Centralvacuole of cell

Central vacuoleCytosol

Plasma membrane

Plant cell walls

Plasmodesmata

The Extracellular Matrix (ECM) of Animal Cells:

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

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

Extracellular Structures:● EXTRACELLULAR MATRIX:

– fibrous proteins such as COLLAGEN and glycoproteins are secreted by and surround cells;

– it holds cells together in tissues;– helps filter materials passing between different

tissues;– orients cell movement during

development;– involved in cell-cell signalling.

EXTRACELLULAR FLUID ProteoglycancomplexCollagen

fiber

Fibronectin

Integrin Micro-filaments

CYTOPLASM

Plasmamembrane

Polysaccharidemolecule

Carbo-hydrates

Coreprotein

Proteoglycanmolecule

Proteoglycancomplex

Intercellular Junctions

● Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact

● Intercellular junctions facilitate this contact

Plants: Plasmodesmata● Plasmodesmata are channels that perforate

plant cell walls

● Through plasmodesmata, water and small solutes (and sometimes proteins and RNA) can pass from cell to cell

Interiorof cell

Interiorof cell

0.5 µm Plasmodesmata Plasma membranes

Cell walls

Animals: Tight Junctions, Desmosomes, and Gap Junctions

● At tight junctions, membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid

● Desmosomes (anchoring junctions) fasten cells together into strong sheets

● Gap junctions (communicating junctions) provide cytoplasmic channels between adjacent cells

Tight junctions preventfluid from moving across a layer of cells

Tight junction

0.5 µm

1 µm

0.1 µm

Gap junction

Extracellularmatrix

Spacebetweencells

Plasma membranesof adjacent cells

Intermediatefilaments

Tight junction

Desmosome

Gapjunctions

The Cell: A Living Unit Greater Than the Sum of Its Parts

● Cells rely on the integration of structures and organelles in order to function

● For example, a macrophage’s ability to destroy bacteria involves the whole cell, coordinating components such as the cytoskeleton, lysosomes, and plasma membrane

5 µ

m