[PPT]Chapter Title - Personal Websites - Indiana University of ... 250 F17/Unit 1... · Web viewARCHAEA BACTERIA EUKARYA Green nonsulfur bacteria Mitochondrion Gram-positive bacteria

© 2015 Pearson Education, Inc.

Main Concept 1 Microbial Form and Function

Chapter 2 of Brock Microbiology text with some

examples taken from other chapters

Emphasis on prokaryotic microbes-not eukaryotes or

subcellular microbes


ARCHAEABACTERIA EUKARYA

Green nonsulfurbacteria

MitochondrionGram-positivebacteria

Proteobacteria

ChloroplastCyanobacteria

Green sulfurbacteria

Thermotoga

Thermodesulfobacterium

Aquifex

CrenarchaeotaThermoproteus

Pyrodictium

ThermococcusNitrosopumilus Pyrolobus

Methano-bacterium

EuryarchaeotaMethanosarcina

Thermoplasma

Methanopyrus

Extremehalophiles

Entamoebae Slimemolds

Animals

Fungi

Plants

Ciliates

Flagellates

Trichomonads

Microsporidia

Diplomonads

Macroorganisms

“Universal Tree” of Life-3 Domains

Only cellular systemsArchaea and Bacteria are prokaryotesEukarya are eukaryotes


I. A Note on Microscopy

Key technique for analyzing cell structure

Covered mainly in lab


Most Important Microscopic Test

The Gram stain

A differential staining technique

Most members of the Bacteria can be divided into two major groups called gram-positive and gram-negative

Gram-positive bacteria appear purple, and gram-negative bacteria appear red after staining



II. Cells of Bacteria and Archaea

• 2.5 Cell Morphology

• 2.6 Cell Size and the Significance of Being

Small


2.5 Cell Morphology

• Morphology = cell shape

• Major cell morphologies (Figure 2.11)• Coccus (pl. cocci): spherical or ovoid

• Rod: cylindrical shape (bacillus/bacilli)

• Spirillum: spiral shape

• Cells with unusual shapes• Spirochetes, appendaged bacteria, and filamentous

bacteria

• Many variations on basic morphological types

© 2015 Pearson Education, Inc. Figure 2.11

Coccus

Rod

Spirillum

Spirochete

Stalk Hypha

Filamentous bacteria

Budding and appendaged bacteria


2.5 Cell Morphology

Morphology is descriptive but typically does not

predict physiology, ecology, phylogeny, etc. of a

prokaryotic cell


Size range for prokaryotes: 0.2 µm to >700 µm

Most cultured rod-shaped bacteria are between 0.5 and 4.0 µm wide and < 15 µm long

Cellular organisms <0.15 µm in diameter are unlikely

Open oceans tend to contain small cells (0.2–0.4 µm in diameter)

Most prokaryotes are at the small end of the size range

2.6 Cell Size and the Significance of Being Small


Why are most prokaryotic cells small?

Explained by square-cube rule

As cells get larger their internal volume grows faster than their surface area (cube > square)

So in larger cells there is relatively less plasma membrane to bring in nutrients for the cytoplasm



Two prokaryotes notable for their large size

• Epulopiscium fishelsoni (Figure 2.12a and below)

• Thiomargarita namibiensis (Figure 2.12b)

2.6 Cell Size and the Significance of Being Small


How does a large prokaryote such as Thiomargarita survive?

https://microbewiki.kenyon.edu/index.php/Thiomargarita_namibiensis

Bacteria are generally small which is favourable for rapid growth and efficient nutrient uptake (Jorgensen 2010). Nutrients are able to diffuse faster and are more effectively taken up in smaller cells. The primary mechanism of nutrient uptake in T. namibiensis is through diffusion without usage of special transport systems (Schulz 2002). Despite the large size of the microbe, nutrients are still capable of efficient diffusion throughout the organism due to the large central vacuoles which limit the volume of the effective cytoplasm. The large size of T. namibiensis is a result of its storage compartments for soluble electron donors and acceptors (Schulz 2002). With this adaptation, this bacterium does not need to be in constant contact with nutrients and are still capable of surviving for long periods of time. The occasional exposure to substrates allows T. namibiensis to uptake essential nutrients for storage in the central vacuoles. This adaptation is necessary for its habitat in oceanic sediments where nutrients are only available through occasional sediment re-suspensions (Schulz 2002).


III. The Cytoplasmic Membrane and Transport(aka Plasma Membrane)

Three relevant sections of Chapter 2

• 2.7 Membrane Structure

• 2.8 Membrane Functions

• 2.9 Nutrient Transport


2.7 Membrane Structure

• Cytoplasmic membrane or plasma membrane• Thin structure that surrounds the cell

• Vital barrier that separates cytoplasm from environment

• Highly selective permeable barrier; enables

concentration of specific metabolites and excretion of

waste products



• Composition of membranes• Generic structure is phospholipid bilayer (Figure 2.14)

• Contain both hydrophobic and hydrophilic components

• Can exist in many different chemical forms as a result of

variation in the groups attached to the glycerol backbone

• Fatty acids or other lipids point inward to form

hydrophobic environment; hydrophilic portions remain

exposed to external environment or the cytoplasm


Fatty acids

Phosphate

Ethanolamine

Fatty acids

Hydrophilicregion

Hydrophobicregion

Hydrophilicregion

Glycerophosphates

Fatty acids

Glycerol



• Cytoplasmic membrane (Figure 2.15)

• 8–10 nm wide

• Embedded proteins (integral/peripheral)

• Stabilized by hydrogen bonds and hydrophobic

interactions

• Mg2+ and Ca2+ help stabilize membrane by forming ionic

bonds with negative charges on the phospholipids

• Somewhat fluid


Phospholipids

6–8 nm

Integralmembraneproteins

Hydrophilicgroups

Hydrophobicgroups

Phospholipidmolecule

Out

In



• Membrane proteins• Outer surface of cytoplasmic membrane can interact with a

variety of proteins that bind substrates or process large molecules for transport

• Inner surface of cytoplasmic membrane interacts with proteins involved in energy-yielding reactions and other important cellular functions

• Integral membrane proteins• Firmly embedded in the membrane

• Peripheral membrane proteins• One portion anchored in the membrane



Archaeal membranes depart from “standard” model

• Ether linkages in phospholipids of Archaea (Figure 2.16)

• Bacteria and Eukarya that have ester linkages in

phospholipids

• Archaeal lipids lack fatty acids; have isoprenes instead

• Major lipids are glycerol diethers and tetraethers

(Figure 2.17a and b)

• Can exist as lipid monolayers, bilayers, or mixture

(Figure 2.17)


Ester Ether

BacteriaEukarya

Archaea


Phytanyl

Glycerol dietherCH3 groups

Isoprene unit

Biphytanyl

Diglycerol tetraethers

Crenarchaeol

Out Out

In In

Glycerophosphates

Phytanyl

Membrane protein

Lipid monolayer

Biphytanyl orcrenarchaeol

Lipid bilayer


2.8 Membrane Function

• Permeability barrier (Figure 2.18)

• Polar and charged molecules must be transported

• Transport proteins accumulate solutes against the

concentration gradient

• Protein anchor

• Holds transport and other proteins in place

• Energy conservation

• Generation of proton motive force


Functions of the cytoplasmic membrane

Permeability barrier:Prevents leakage and functions as agateway for transport of nutrients into,and wastes out of, the cell

Protein anchor:Site of many proteins that participate intransport, bioenergetics, and chemotaxis

Energy conservation:Site of generation and dissipation of the proton motive force


2.9 Nutrient Transport

• Carrier-mediated transport systems bring in

nutrients (Figure 2.19)

• Show saturation effect

• Highly specific


Transporter saturated

Transport

Simple diffusion



• Three major classes of transport systems in

prokaryotes based on mechanics (Figure 2.20)

• Simple transport

• Group translocation

• ABC system

• All require energy in some form, usually proton

motive force or ATP


Out In

R~

2

3

Transportedsubstance

P

P

ATP ADP + Pi

Simple transport:Driven by the energyin the proton motiveForce (H+ gradient)

Group translocation:Chemical modificationof the transportedsubstance driven byphosphoenolpyruvate

ABC transporter: Bindingproteins are involvedand energy comesfrom ATP.

1



• Three types of transport events are possible

based on directions: uniport, symport, and

antiport (Figure 2.21)

• Uniporters transport in one direction across the

membrane

• Symporters function as co-transporters

• Antiporters transport a molecule across the membrane

while simultaneously transporting another molecule in

the opposite direction




• Simple transport-example:

• Lac permease of Escherichia coli

• Lactose is transported into E. coli by the simple

transporter lac permease, a symporter

• Activity of lac permease is energy-driven by proton motive

force



• Example of Group Transport: phosphotransferase

(PTS) system in E. coli (Figure 2.22)

• Type of group translocation: substance transported is

chemically modified during transport across the

membrane

• Best-studied system

• Moves glucose, fructose, mannose, others

• Five cytoplasmic proteins required

• Energy derived from phosphoenolpyruvate (PEP)


Nonspecific components Specific components

Cytoplasmicmembrane

OutGlucose

Directionof glucosetransport

Glucose 6_PP

InDirection of P transfer

PPyruvate

PE P

EnzI

HPr EnzIIa

EnzIIb

EnzIIc

P



• ABC (ATP-binding cassette) systems (Figure 2.23)

• >200 different systems identified in prokaryotes

• Often involved in uptake of organic compounds (e.g., sugars,

amino acids), inorganic nutrients (e.g., sulfate, phosphate),

and trace metals

• Typically display high substrate specificity

• Gram-negatives employ periplasmic substrate-binding

proteins and ATP-driven transport proteins

• Gram-positives employ fixed substrate-binding proteins and

ATP-driven transport proteins


Figure 2.23 (Gram -)


IV. Cell Walls of Bacteria and Archaea

• 2.10 Peptidoglycan

• 2.11 LPS: The Outer Membrane

• 2.12 Archaeal Cell Walls


2.10 Peptidoglycan-the Wonder Wall

• Gram-positives and gram-negatives have different

cell wall structure (Figure 2.24)

• Gram-negative cell wall

• Two layers: lipopolysaccharide (LPS) and

peptidoglycan

• Gram-positive cell wall

• One layer: peptidoglycan



2.10 Peptidoglycan

• Peptidoglycan (Figure 2.25)

• Rigid layer that provides strength to cell wall

• Polysaccharide composed of:

• N-acetylglucosamine and N-acetylmuramic acid

• Amino acids-vary

• Cross-linked for strength

• Different cross-linking in gram-negative bacteria and

gram-positive bacteria (Figure 2.26)


Peptidoglycan-(aka murein)a layer of sugars and amino acids linked together to form a chain-link type structure outside the cytoplasmic membrane.

NAG and NAM are the sugars


N-Acetylglucosamine N-Acetylmuramic acid

𝛃(1,4) 𝛃(1,4) 𝛃(1,4)

N-Acetyl group

Lysozyme-sensitivebondPeptide

cross-linksL-Alanine

D-Glutamic acid

Diaminopimelicacid

D-Alanine

Glyc

an te

trape

ptid

e

( M )( G )NAG and NAM

Non-proteinPeptide bond

Beta 1-4Glycoside inGram -)


Unusual amino acids

Targets for antibiotics:

Penicillin, Vancomycin: block cross-bridge formation

See: https://www.asm.org/index.php/antibiotics-that-inhibit-bacterial-peptidoglycan-synthesis


2.10 Peptidoglycan

• Gram-positive cell walls (Figure 2.27)

• Can contain up to 90% peptidoglycan

• Common to have teichoic acids (charged

carbohydrates) embedded in their cell wall for rigidity

• Wall teichoic acids-embedded in peptidoglycan only

• Lipoteichoic acids: extend to cytoplasmic membrane

and covalently bound to membrane lipids


Teichoic acid Peptidoglycan Lipoteichoicacid

Cytoplasmic membrane

Wall-associatedprotein


2.10 Peptidoglycan-not present in all microbes• Some Bacteria have cell walls with a different

chemical structure that is not really Gram + or –(Mycobacteria) they are called “acid-fast”

• Some prokaryotes lack cell walls• Mycoplasmas• Group of pathogenic bacteria

• Thermoplasma• Species of Archaea


2.11 LPS: The Outer Membrane

• Total cell wall contains ~10% peptidoglycan

• Most of cell wall composed of outer membrane,

aka lipopolysaccharide (LPS) layer• LPS consists of core polysaccharide and O-

polysaccharide and a membrane anchor (Lipid “A”)

(Figure 2.28)

• LPS replaces most of phospholipids in outer half of outer

membrane (Figure 2.29)

• Endotoxin: the toxic component of LPS



O-specificpolysaccharide

Core polysaccharide

Lipid A Protein

Lipopolysaccharide (LPS)

Phospholipid

PorinPorin

Lipoprotein

Outer membrane

Periplasm

Cytoplasmicmembrane

8 nm

Out

Cellwall

Outer membrane

Periplasm

Cytoplasmicmembrane

PeptidoglycanPeptidoglycan

In

Figure 2.29


2.11 LPS: The Outer Membrane

• Periplasm: space located between cytoplasmic

and outer membranes (Figure 2.29)

• ~15 nm wide

• Contents have gel-like consistency

• Houses many proteins

• Porins: channels for movement of hydrophilic

low-molecular-weight substances (Figure 2.29c)


2.12 Archaeal Cell Walls

• Most Archaea have cell walls, some do not

• Same functions as in Bacteria

• When present, Archaeal walls are built differently

than Bacterial cell wall

• Highly variable but two main types

• Pseudopeptidoglycan (pseudomurein) or

• “S-layers”



• Pseudomurein aka pseudopeptidoglycan

• Polysaccharide similar to peptidoglycan (Figure 2.30)

• Composed of N-acetylglucosamine and N-

acetylalosaminuronic acid (NAG and NAS)

• Beta 1-3 glycosides

• Found in cell walls of some Archaea including

Methanobacteria (methane producers)



• S-Layers (Surface Layer)• “Most common” cell wall type among Archaea

• Consist of protein, glycoprotein or sugar

• Paracrystalline structure (Figure 2.31)

• Network of proteins/glycoproteins attached to outer

surface of plasma membrane

• Has openings or “pores”






http://www.nature.com/nrmicro/journal/v13/n10/fig_tab/nrmicro3480_F1.html

Diagrams of wall structure

http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit1/prostruct/cw.html

More information on cell walls

Further reading if you want it

http://www.ucmp.berkeley.edu/archaea/archaea.html

More on the Archaea










V. Other Cell Surface Structures and Inclusions

• 2.13 Cell Surface Structures (Glycocalyx)

• 2.14 Cell Inclusions

• 2.15 Gas Vesicles

• 2.16 Endospores


2.13 Cell Surface Structures• Glycocalyx = capsules and slime layers• Polysaccharide layers, glycolipids, glycoproteins (Figure

2.32)

• May be thick or thin, rigid or flexible

• Assist in attachment to surfaces

• Protect against phagocytosis

• Resist desiccation

• External to cell

• In Gram + and –

• Not part of LPS outer membrane


2.13 Cell Surface Structures

• Capsules and slime layers• Slime layer = unorganized, loosely attached, aka “slime

wall”

• Capsule = more organized, tighter, harder to remove

Exact composition, function, appearance is species-specific


Cell Capsule



• Fimbriae• Filamentous protein structures for attachment

• curlin, adhesin

• Enable organisms to stick to surfaces or form pellicles

May enhance pathogenicity

Relatively thin and short



• Pilus (pili) • Filamentous protein structures

• Pilin

• Not much different from fimbriae but typically longer and

thicker-term usually reserved for appendage with

specific known function

• Such as sex pilus of E. coli. Facilitate genetic exchange

between cells (conjugation)

• Type IV pili involved in twitching motility (grappling hook

motility)



Sex pilus facilitates genetic exchange between cells

(conjugation)

Type IV pili involved in twitching motility (grappling hook

motility)


2.14 Cell Inclusions

• Inclusions visible in many prokaryotic cells

• Solid or semi-solid aggregates

• Mostly used for storage of vital nutrients

• Minerals, carbohydrates

• Not membrane-bound

• Aka storage granule


2.14 Cell Inclusions• Carbon storage polymers

• Poly-β-hydroxybutyric acid (PHB): lipid (Figure 2.35)

• Glycogen: glucose polymer

• Polyphosphates: accumulations of inorganic phosphate

(Figure 2.36a)

• Sulfur globules: composed of elemental sulfur (Figure

2.36b)

• Carbonate minerals: composed of barium, strontium, and

magnesium (Figure 2.37)


β-carbon

Polyhydroxyalkanoate


Polyphosphate

Sulfur


2.14 Cell Inclusions• Magnetosomes: magnetic storage inclusions (Figure 2.38)

• These inclusions do have a membrane to enclose iron

magnetite crystals

• Magnetosomes orient cell in Earth’s magnetic field

• Helps organisms know up from down


2.15 Gas Vesicles

• Gas vesicles• Confer buoyancy in

planktonic cells (Figure

2.39)

• Spindle-shaped, gas-filled

structures made of protein

(Figure 2.40)

• Impermeable to water


2.15 Gas Vesicles

• Molecular structure

of gas vesicles

• Gas vesicles are

composed of two

proteins, GvpA and

GvpC (Figure 2.41)

• Function by

decreasing cell

density


Photosynthetic bacteria like this cyanobacterium usually have internal membranes


Others-like this green sulfur bacterium-utilize membrane-boundVesicles to house photosynthetic apparatus


2.16 Endospores

• Endospores• Highly differentiated cells resistant to heat, harsh

chemicals, and radiation (Figure 2.42 )

• “Dormant” stage of bacterial life cycle (Figure 2.43) may

persist for decades in environment (soil)

• Ideal for dispersal via wind, water, or animal gut

• Present only in some gram-positive bacteria



Endospore Formation•Endospore forms inside mother cell•Core is dormant, inert, minimal but alive•Several tough layers form a resistant shell around core•Chemical makeup of each layer is different•Small acid-soluble spore proteins (SASP) contribute to resistance


YouTube version:

https://www.youtube.com/watch?v=7zCQLITFEb0

Note: dipicolinic acid




VI. Microbial Locomotion

• 2.17 Flagella and Swimming Motility

• 2.18 Gliding Motility

• 2.19 Chemotaxis and Other Taxes


2.17 Flagella and Swimming Motility

• Flagellum/flagella: extracellular structure that

assists in swimming

• Tend to be found on rods or spirals

• Cell may have 0, 1 or more

• Different arrangements: (a) peritrichous, (b) polar,

(c) lophotrichous (Figure 2.48) also amphitrichous

• Structurally very different from a eukaryotic flagellum




• Flagellar structure of Bacteria

• Consists of several components (Figure 2.51)

• Hollow filament composed of flagellin

• Move by rotation

• Hook region allows propeller action

• Powered by proton motive force


15–20 nm

Filament

Flagellin

LP

MS

HookOutermembrane(LPS)

L Ring

P Ring

Rod

PeptidoglycanPeriplasm

MS Ring

Basalbody

C Ring

Cytoplasmicmembrane

Fli proteins(motor switch)

Mot proteinMot protein

45 nm

Rod

MS Ring

C Ring

Mot protein

+ + + + + + + +

− − − − − − − −



• Flagellar structure of Archaea

• Archaellum

• More similar to bacterial pilus than flagellum

• Thinner, not hollow

• Probably powered by ATP

• No hook region

• Motility, recognition, attachment


14.20 Spirochetes and atypical flagella

• Treponema pallidum and Borrelia burgdorferii are notable

• Spirochaetes• Gram-negative, motile, and coiled (Figure 14.49)

• Widespread in aquatic environments and in animals

• Have endoflagella: located in the periplasm of the cell (Figure 14.50)


Endoflagellum

Protoplasmiccylinder

Outersheath

Endoflagellum (rigid,rotates, attached to oneend of protoplasmiccylinder)

Outer sheath(flexible)

Protoplasmic cylinder(rigid, generally helical)



2.18 Gliding Motility

• Gliding motility• Flagella-independent motility (Figure 2.56)

• Slower and smoother than swimming

• Movement typically occurs along long axis of cell

• Requires surface contact

• Mechanisms (not well understood)

• Excretion of polysaccharide slime

• Gliding-specific proteins

• Pili


2.19 Chemotaxis and Other Taxes

• Taxis: directed movement in response to chemical

or physical gradients

• Chemotaxis: response to chemicals

• Phototaxis: response to light

• Aerotaxis: response to oxygen

• Osmotaxis: response to ionic strength

• Hydrotaxis: response to water


2.19 Chemotaxis and Other Taxes

• Chemotaxis• Best studied in E. coli

• “Run and tumble” behavior (Figure 2.57)

• Attractants sensed by chemoreceptors

• http://web.biosci.utexas.edu/psaxena/

MicrobiologyAnimations/Animations/BacterialMotility/

PLAY_motility.html


• Flagella rotate clockwise = tumble

• Flagella rotate counterclockwise = straight line run

• Controlled by simple molecular clock system in

cell

• With no chemotaxis tumbles and runs alternate so

that no net movement occurs: random walk


• With chemotaxis, timing of clock is adjusted

• Runs are longer

• Produces net movement

• Chemotaxis works by controlling the rate of

switching between run and tumble-it re-sets clock

to favor run over tumble


Tumble

Run

Run

Attractant

No attractant present: Randomwalk

Attractant present: Directedmovement

Tumble

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[PPT]Chapter Title - Personal Websites - Indiana University of ... 250 F17/Unit 1... · Web viewARCHAEA BACTERIA EUKARYA Green nonsulfur bacteria Mitochondrion Gram-positive bacteria