Chapter 1 Intro to Cell

8/18/2019 Chapter 1 Intro to Cell

1/6

CHAPTER 1

INTRODUCTION TO THE S TUDYOF CELL& MOLECULARBIOLOGY

THE DISCOVERY OF CELLS

I. Robert Hooke (1665), English microscopist (at age 27, became curator of the Royal Society)A. Described chambers in cork; called them cells (cellulae) since they reminded him of cells occupied by monks

living in a monasteryB. Found them while trying to explain why cork stoppers could hold air in a bottle so effectivelyC. Was looking at empty cell walls, the remains of dead cells; no internal structure

II. Anton van Leeuwenhoek (1665-1675), Dutch seller of clothes & buttons in spare time, he was first todescribe living single cells; results were checked and confirmed by HookeA. Saw “animalcules” in pond water using the scopes of remarkable quality that he made B. Described various forms of bacteria from tooth scrapings & water in which pepper was soakedC. Eventually, became celebrity visited by Russia's Peter the Great & the queen of England

III. 1830s - full & widespread importance of cells realizedA. Matthias Schleiden, botanist (1838) - all plant tissues composed of cells; plant embryos arise from single cellB. Theodor Schwann, zoologist (1839) - same conclusion about animals; plants & animals similarC. Schwann then proposed first two tenets of Cell Theory

1. All organisms are composed of one or more cells. 2. The cell is the structural unit of life for all organisms.

D. However, the Schleiden-Schwann view of the origin of cells was less insightful since both agreed that cells couldarise from noncellular materials -> eventually disproved by others

E. Rudolf Virchow, German pathologist (1855) - added third tenet of Cell Theory derived from his cell divisionobservations; it ran counter to Schleiden-Schwann view of cell origins

1. Cells can arise only by division from a preexisting cell.

BASIC PROPERTIES OF CELLS

I. Life – most basic property of cells; they are the smallest units to exhibit this property; plant or animal cells can beremoved from organism & cultured in laboratoryA. Can grow and reproduce for a long time in culture, unlike their parts which soon deteriorateB. George Gey, Johns Hopkins Univ. (1951) - first human cell culture (HeLa cells); donor was Henrietta Lacks

(from her malignant tumor); still grown in laboratories todayC. Cultured cells are simpler to study than cells in body; cells grown in vitro (in culture, outside body) are essential

tool of cell & molecular biologists

II. Cells are highly complex and organizedA. Each level of structure in cells is consistent from cell to cell – each cell has consistent appearance in EM;

organelles have particular shape & location in individuals of a speciesB. Organelles have consistent macromolecular composition arranged in a predictable patternC. Cell structure similar organism to organism despite differences in higher anatomical features

III. Cells possess genetic program & the means to use it (a blueprint); encoded in collection of genesA. Blueprint for constructing cellular structures & ultimately organismsB. Directions for running cell activitiesC. Program for making more cells

IV. Cells are capable of producing more of themselves - mitosis and meiosisA. Contents of “mother” cell distributed to 2 “daughter” cells B. Before division, genetic material is faithfully copied; each daughter cell gets complete & equal share of genetic

informationC. Usually, daughter cells have roughly equal volume; during egg production, one cell gets most of cytoplasm &

half of genetic material

V. Cells acquire & utilize energy to develop & maintain complexity - photosynthesis & respirationA. Virtually all energy needed by life arrives from sunB. This energy is trapped by light-absorbing pigments in photosynthetic cellsC. Light energy turned to chemical energy by photosynthesis; stored in energy-rich carbohydratesD. Animals get energy prepackaged usually in form of glucoseE. Once in cell, glucose disassembled; most energy is stored as ATP & used to run cell activities

VI. Cells carry out many chemical reactions - sum total of chemical reactions in cells (metabolism); to do this, cellsrequire enzymes (molecules that greatly increase rate of chemical reactions)

VII. Cells engage in numerous mechanical activities based on dynamic, mechanical changes in cell:

A. Material moved from place to placeB. Structures assembled and disassembledC. Cells move from place to place


2/6

2 2

VIII. Cells able to respond to stimuli whether cells are uni- or multicellular - have receptors that sense environment &initiate responses (move away from object in path or toward nutrient source)

A. Most cells covered with receptors that interact in specific ways with substances in environment1. Receptors bind to hormones, growth factors, extracellular materials, surfaces of other cells2. Allow ways for external agents to evoke specific responses in target cells

B. Cells may respond to specific stimuli by:1. Altering metabolic activities2. Preparing for cell division3. Moving from one place to another, or

4. Even committing suicide

IX. Cells are capable of self-regulationA. Importance of regulatory mechanisms most evident when they break down

1. Failure of cell to correct error in DNA replication -> may lead to debilitating mutation2. Breakdown in growth control -> may lead to cancer cell & maybe death of whole organism

B. Example: Hans Driesch, German embryologist (1891) - separate first 2 or 4 cells in sea urchin embryo -> each produces normal embryo

TWO FUNDAMENTALLY DIFFERENT CLASSES OF CELLS:

PROKARYOTES AND EUKARYOTES

I. With advent of EM, 2 cell types were distinguished by size & types of internal structures (organelles); exhibited a largefundamental evolutionary discontinuity (no known intermediates)A. Prokaryotes ( pro - before; karyon - nucleus) – all bacteria, cyanobacteria (blue-green algae);

structurally simpler1. Prokaryotes now living very similar to those fossilized in >3.5 billion year old rocks (Australia, S.

Africa); sole life on planet for nearly 2 billion years before first eukaryoteB. Eukaryotes (eu - true) - structurally more complex; protists, fungi,

plants, animals

II. Similarities between prokaryotes and eukaryotes - reflect fact thateukaryotes almost certainly evolved from prokaryotic ancestorsA. Both types of cells share an identical genetic language

B. Both types of cells share a common set of metabolic pathways C. Both types of cells share common structural features - cell

membrane, cell walls (same function, different structure)

III. Characteristics that distinguish prokaryotic & eukaryotic cells - eukaryoticcells are internal much more complex (structurally and functionally)

A. Eukaryotes have membrane-bound nucleus with complex nuclearenvelope & other organelles

1. Prokaryotes have nucleoid (poorly demarcated cell region)[ nomembrane-bound organelles

B. Prokaryotes - relatively little DNA (0.25 - ~3 mm) coding for severalhundred to several thousand proteins (1 mm of DNA = ~3 x 106 base pairs)

1. Simplest eukaryotes (4.6 mm in yeast encoding ~6200 proteins)have slightly more DNA than prokaryotes; most eukaryotes have anorder of magnitude more DNA

C. Eukaryotic chromosomes numerous; contain linear DNA tightlyassociated with protein; prokaryotes have single, circular chromosome with DNA that is nearly naked

D. Cytoplasmic structures - eukaryotes have many; prokaryotes mostly devoid of such structures (except forinfolded bacterial mesosomes & cyanobacteria photosynthetic membranes)

1. Intracytoplasmic communication smaller issue in prokaryotes due to size (diffusion works); in eukaryotes,interconnected channels/vesicles transport stuff around cell & out of cell

2. Eukaryotes have cytoskeletal elements generally lacking in prokaryotes – cell contractility, movement,support

3. Ribosomes of prokaryotes smaller than those of eukaryotes (essentially same function)4. Both eukaryotes & prokaryotes may be surrounded by rigid, nonliving cell wall that protects,

but their chemical composition is very different5. Eukaryotes have more complex locomotor mechanisms – prokaryotes have rotating flagella; eukaryotes

have more complex flagella with different mechanism (also cilia & pseudopodia)

E. No mitosis or meiosis in prokaryotes (binary fission instead); prokaryotes proliferate faster (double in 20 - 40minutes; exchange genetic information via conjugation)

1. In eukaryotes, chromosomes are compacted & separated by mitotic spindle which allows each daughtercell to get equal genetic material

2. In prokaryotes, no chromosome compaction & no spindle; DNA copies separated by growth of interveningcell membrane


3/6

3 3

3. In conjugation, recipient almost never gets whole chromosome from donor; cell soon reverts to singlechromosome

F. Examples of some eukaryotic organelles and their functions – divide the cytoplasm into compartments withinwhich specialized activities take place

1. Mitochondria (plants & animals) – make chemical energy available to fuel cell activities2. Endoplasmic reticulum (plants & animals) – where many cell lipids & proteins are made3. Golgi complexes (plants & animals) – sorts, modifies, transports stuff to specific locations4. Variety of simple membrane-bound vesicles of varying dimensions plants & animals)

5. Chloroplasts (plants) – sites of photosynthesis6. Single large vacuole (plants) – occupies most of cell volume

IV. Prokaryotes not inferior - metabolically very sophisticated & highly evolvedA. Have remained on Earth more than 3 billion yearsB. They live on and in eukaryotic organisms, including humansC. Make almost everything they need; need only simple carbon (only 1 or 2 low MW organic compounds), nitrogen

source(s) & some inorganic ions; some live on only inorganic substances1. One species found in wells >1000 m below Earth's surface; live on basalt rock & H2 made by inorganic

reactions2. Even most versatile cells in human require a variety of organic compounds (vitamins, etc.)

D. Bacteria in our large intestine even make some essential dietary ingredients for us

Types of Prokaryotic Cells

I. Divided into two major groups or domains – Archaea & Bacteria

II. ARCHAEA (archaeons or archaebacteria) - groups of primitive bacteria (related DNA sequences); closest relatives offirst cells; live in extremely inhospitable environments (extremophiles)

A. Methanogens - capable of converting CO2 & H2 gases into methane (CH4) gasB. Halophiles - live in extremely salty environments (Dead Sea & Great Salt Lake)C. Acidophiles – acid-loving prokaryotes that live at pHs as low as 0D. Thermophiles - live at very high temperatures

1. Hyperthermophiles (ex.: Pyrolobus fumaril) - live in hydrothermal vents of ocean floor; reproduce attemperatures above 109°C & won't grow below 90°C

III. BACTERIA (eubacteria)A. Bacteria are present in every conceivable habitat on earth – permanent Antarctic ice shelf to driest African deserts

to internal confines of plants & animals, rock layers several km deep1. Some of these bacteria cut off from life on surface for >100,000,000 years

B. Example: Mycoplasma - smallest living cells (0.2 µm dia); only prokaryotes lacking cell wallC. Example: Cyanobacteria (formerly blue-green algae) - most complex; elaborate cytoplasmic

membrane arrays which are sites of photosynthesis; similar to membranes in chloroplasts1. Filled world with O2; need few resources to survive2. Some do N2 fixation - convert N2 gas into reduced nitrogen forms (e. g. NH3) used to make

amino acids & nucleotides

D. Those species capable of both photosynthesis & nitrogen fixation survive on barest resources – light, N2, CO2, H2O1. Not surprising that cyanobacteria are the first to colonize bare rocks left lifeless by volcano

IV. Prokaryotic diversity

A. To study prokaryotic diversity, cells can be concentrated, their DNA extracted & DNA sequences analyzed1. All organisms share certain genes (genes for rRNAs or some metabolic pathway enzymes)2. Sequences of these genes vary species to species3. Carefully analyze variety of sequences for particular gene in habitat -> tells you the number of species living

in the habitat

B. By carefully analyzing sequences in extracted DNA & comparing sequences to those in known organisms, onecan learn about phylogenetic relationships of these organisms1. Prokaryotes living in single Yellowstone National Park pool – 30% of sequences were from bacteria that could

not be grouped into any of the 14 known divisions in the domain Bacteria2. Based on such differences, the previously unidentified bacteria were put in 12 new divisions

C. Most habitats on earth teeming with previously unidentified prokaryotic life1. Archaea once thought to be restricted to harshest environments2. Now found to be common & abundant members of non-extreme habitats (oceans, lakes, soil)3. >90% of these organisms now thought to live in subsurface sediments well beneath oceans & upper soil layers;

not long ago, deeper sediments thought to be only sparsely populated4. Carbon sequestered in world's prokaryotes is roughly comparable to total carbon in plants


4/6

4 4

Types of Eukaryotic Cells

I. Unicellularity vs. multicellularity - most complex eukaryotic cells are among single-celled protistsA. Protists - must do everything an organism must do to survive; one evolutionary pathwayB. Multicellular organisms exhibit differentiation - different activities conducted by different types of specialized

cells

II. Example of multicellularity & differentiation - cellular slime mold Dictyostelium shows advantages provided bydivision of labor among cells

A. During most of life, they are independent amoebas, each a complete, self-sufficient organismB. If food scarce, stream toward each other & form sluglike aggregate (pseudoplasmodium or slug)

1. Slug migrates slowly over substratum leaving slime trail2. Previously single organisms now small part of larger, multicellular individual

C. Cells are no longer a homogeneous population1. Cells differentiate into prestalk cells of anterior third of slug and posterior prespore cells

D. Soon, slug stops moving, rounds up on substratum & extends upward into air1. Forms elongated fruiting body (sporangium)2. Sporangium has slender stalk supporting rounded mass of dormant, encapsulated spores3. Stalk (from prestalk cells) supports spore mass (from prespore cells) above substratum

4. Spores scatter and give rise to next generation of amoebas

III. Differentiation – process by which a relatively unspecialized cell becomes highly specializedA. Fertilized egg develops into many cell types (hundreds) in mature organism

1. Cells specialized for varied functions, have distinctive appearance, carry unique materials2. Cells have similar organelles but their number, appearance & location may differ & correlate with cell act.

B. Differentiation of each eukaryotic cell depends primarily on signals received from environment1. Signals, in turn, depend on position of cell within embryo2. As a result, different cell types acquire distinctive appearance & contain unique materials

C. Despite differences, various cells of multicellular plant or animal are made of similar organelles

1. Mitochondria are found in all cell types, but they may change shape (rounded or highly elongated &threadlike)2. Brown adipose cell (main function is generation of heat from chemical energy stored in fat); has numerous

fat droplets & lots of mitochondria where energy conversion occurs3. Plasma cell specialized for antibody production – have relatively small number of mitochondria but

extensive rough endoplasmic where protein synthesis occurs4. Number, appearance & location of organelles can be correlated with activities of particular cell type

IV. Cell & molecular biology research focuses on small number of representative or model organismsA. Saccharomycese cerevisiae, a budding yeastB. Arabadopsis thaliana – a mustard plantC. Caenorhabditis elegans – a nematodeD. Drosophila melanogaster – a fruit flyE. Mus musculus – a mouse

The Sizes of Cells and Their Components

I. Units of linear measure most often used to describe cell structuresA. Micrometers (µm; 10-6 m), nanometers (nm; 10-9 m)B. Ångstroms (Å; 10-10 m) – often used by molecular biologists for atomic dimensions although no longer formally

accepted in metric nomenclature); ~1 Å = diameter of H atom

II. Examples of dimensions of cells and cell componentsA. Typical globular protein (myoglobin) - ~ 4.5 nm x 3.5 nm x 2.5 nmB. Highly elongated proteins (collagen, myosin) - over 100 nm in lengthC. DNA - ~2 nm in widthD. Large molecular complexes (ribosomes, microtubules, microfilaments); 5 - 25 nm dia.E. Nuclei - about 10 µm diameter; mitochondria - about 2 µm in lengthF. Bacteria - 1 to 5 µm in length; eukaryotic cells - 10 to 30 µm in length

III. Why are most cells so small?A. Most eukaryotic cells have single nucleus with only 2 copies of most genes

1. Thus, cells can only produce limited number of mRNAs in a given amount of time2. The larger a cell's volume, the longer it takes to make the number of mRNAs the cell needs

B. As a cell increases in size, the surface area/volume ratio decreases1. If surface area/volume ratio gets too small, surface area not sufficient to take up substances needed to

support metabolism (oxygen, nutrients, etc.) or get rid of wastes


5/6

5 5

C. As cell gets larger, takes too long for diffusion to move substances in and out of active cell1. Time required for diffusion is proportional to the square of the distance traversed2. O2 required 100 µsec to diffuse 1 µm, but 10

6 times as long to diffuse 1 mm3. As cell becomes larger, distance from surface to interior gets larger; diffusion time to move things in & out

of metabolically active cell becomes prohibitively long

IV. How do large cells get around the surface area/volume problems? - examplesA. Ostrich egg & others - little living protoplasm spread over top of lots of inert yolk nutrientB. Giraffe (and other large animal) nerve cells - very long but very small diameter

C. Plant cell interior filled with large fluid-filled vacuole; needs no support, unlike cytoplasmD. Intestinal epithelium specialized for absorption with microvilli to increase surface area

Viruses

I. Pathogens smaller and, presumably, simpler than smallest bacteria; called viruses

A. Late 1800s - thought infectious diseases caused by bacteria but other agent soon found1. Sap from sick tobacco plant found to infect other plants while containing no bacteria2. Sap still infective if forced through filter with pores smaller than smallest known bacteria3. Infectious agent could not be grown in culture unless living plant cells also present

B. Wendell Stanley, Rockefeller Institute (1935) - tobacco mosaic virus (TMV), a rod-shaped particle wascrystallized & found to be infective; thought to be protein1. Now know it is a single RNA molecule surrounded by helical shell of protein subunits

C. Viruses responsible for many human diseases, some cancers - come in different shapes, sizes & constructions – AIDS, polio, influenza, cold sores, measles, a few types of cancers

II. Common virus properties - not considered living since need host to reproduce, metabolize, etc.

A. All are obligatory intracellular parasites (must reproduce in host cell [plant, animal, bacteria])1. Alone, they are unable to reproduce, metabolize or carry on other life-associated activities2. Thus, they are not considered to be organisms & not considered to be alive3. Once it has attached & passed through membrane, it can alter host cell activities

B. Outside of living cell, it exists as particle or virion, essentially a macromolecular package

C. Has genetic material (single/double stranded DNA or RNA); 3 or 4 genes up to several 1001. The fewer the genes, the more it relies on enzymes & other proteins encoded by host genes

D. Genetic material surrounded by protein capsule (capsid) usually made up of a specific number of subunits;efficient (need only a few genes to make capsid)1. Capsid subunits often organized into polyhedron with planar faces (ex.: 20-sided icosahedron) like adenovirus

which causes mammalian respiratory infections

E. Many animal viruses have capsid surrounded by lipid-containing outer envelope derived from modified host cell

membrane as virus buds from host cell surface (ex.: HIV)

F. Bacterial viruses (bacteriophages) are among most complex – T bacteriophages polyhedral head (containsDNA), cylindrical stalk (injects DNA) & tail fibers (attach to bacteria)1. Used in key experiments that revealed genetic material structure & properties

G. Viruses have surface proteins that bind to particular host cell surface component (specificity)1. HIV - glycoprotein of 120,000 dalton MW (gp120) interacts with specific protein (CD4) on surface of certain

white blood cells facilitating virus entry into host cell2. Viral & host protein interaction determines virus specificity, the hosts it can enter & infect

H. Most viruses have relatively narrow host range (certain cells of certain host like human cold & influenza viruses,

which are only able to infect human respiratory epithelium cells1. But some can have wide host range, infecting cells from a variety of organs or species - rabies infects variety

of mammalian host species (bats, dogs, humans)2. Host cell specificity change can have dramatic effect – 1918 influenza epidemic killed >20 million people;

flu strain may have been so virulent because it infected many cell types

III. Two basic types of viral infectionA. Lytic infection - virus usually arrests normal host activities, redirects cell to make new viral

nucleic acids & proteins that self-assemble into new virions1. Cell lyses to release new viral particles & infect neighboring cells

B. Formation of provirus - integrates its DNA into host DNA, but no immediate host cell death

IV. Effects of integrated provirus depend on type of virus & host cell - up to 1% of human DNA is DNA from provirusesthat infected our ancestors (now just genetic garbage transmitted passively)


6/6

6 6

A. Bacterial cells with provirus behave normally until exposed to some stimulus (e. g. UV radiation) that activatesdormant viral DNA1. Then cells make new virions & lyse releasing viral progeny - bacterial lambda () virus

B. Animal cells with provirus may make new viruses by cell surface budding without lysis – HIV1. Infected cell may stay alive for a period acting as a factory for production of new virions

C. Animal cells with provirus may lose growth & division control -> malignant (tumor viruses)

V. Viral origin A. Unlikely that viruses present before hosts since they need hosts for reproduction, etc.B. Since have same genetic language as hosts, they could not have arisen independently as primitive form after

other cells had evolvedC. Probably a degenerate form derived from more complex cellular organism - maybe evolved from small cell

chromosome fragments able to maintain a type of autonomous existence in cellD. Over time, these autonomous genetic elements acquired protein coat, became infective agentsE. Different viruses likely arose independently from various organisms (genes similar to host genes)

1. Corroboration – genes present in each group of viruses are different from those of other groups but similar togenes within host cells they infect

2. Difficult to find drugs not harmful to human host since viruses use host enzymes

VI. Viruses have virtues - research tool to study host DNA replication/gene expression, insect-killing viruses (pestcontrol), used to introduce foreign genes into human cells as treatment (gene therapy)

Viroids

I. T. O. Diener, U. S. Dept. of Agriculture (1971) - discovered an agent causing potato spindle-tuber disease; potatoesget gnarled, cracked

A. Infectious agent was small circular RNA lacking protein coat (viroids)B. Viroid traits

1. RNAs range from about 240 to 600 nucleotides (10% size of smaller viruses)2. No evidence that RNA codes for proteins; viroids use host enzymes & proteins completely; ex.: duplication of

viroid RNA in infected cell uses host RNA polymerase II

C. May cause disease by interfering with cell's normal path of gene expression (e. g. monopolize RNA polymerase IIto duplicate viroid RNA)

II. Viroid diseases can have serious effects on cropsA. Cadang-cadang - devastated coconut palm groves of PhilippinesB. Another has wreaked havoc on chrysanthemum industry in U. S.

Chapter 1 Intro to Cell

Documents

Transcript of Chapter 1 Intro to Cell