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Diversity of Plants and Microorganisms > Prokaryote Cell Organisation > Flashcards

Prokaryote Cell Organisation Flashcards

1
Q

2 Domains of Prokaryotes

A

Two distinct ‘domains’ of Prokaryotes
- Bacteria
- Archaea

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2
Q

Sizes of Prokaryotes

A

Typically ~1 micrometre
= very high ratio of Surface area to Volume (SA:V)

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3
Q

Common shapes of prokaryotes

A
  1. Cocci (sing. Coccus)
    - Spherical
  2. Rods/bacilli (sing. bacillus)
    - n.b. some rods quite short
  3. Other shapes (examples)
    - Spirilla and “vibrios”
    - Filamentous
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4
Q

Colonies

A
  1. Chain colony (of cocci)
  2. Cluster (od cocci)
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5
Q

General features of Prokaryotes

A
  • Flagellum
  • Envelope
  • Cell membrane
  • Cytoplasm
  • Nucleoid
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6
Q

Typical features of Prokaryotes

A
  • Function-rich cell membrane
  • Rest of cell envelope usually complex, inc. cell wall
  • Other external (extracellular) features common (e.g. flagella; pili
  • Few internal structures/organelles; simple cytoskeleton
  • Small compact genome; usually one circular chromosome; in nucleoid
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7
Q

Cell membrane components

A

(= cytoplasmic membrane; plasma membrane; inner membrane)
- Phospholipid bilayer, rich in membrane proteins

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8
Q

Prokaryotic Cell Membrane

A

Remember: prokaryotes do NOT have..
- A complex endomembrane system
- or mitochondria

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9
Q

Some functions of the cell membrane

A
  1. Selective permeability: control movement of most molecules into and out of cytoplasm
  2. Forming proton (H+) gradient (& other ion gradients); harnessing the proton motive force (PMF)
  3. Detection of environmental signals
  4. Protein anchor, (some) structural support
  5. Attachment of chromosomes, especially during cell division
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10
Q

Transport across cell membrane

A
  • Small uncharged molecules: passive diffusion (e.g. oxygen, carbon dioxide)

Most charged/large molecules (including sugars, amino acids): require transport proteins
- facilitated diffusion
- Active transport against concentration gradients

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11
Q

Active transport across cell membrane, examples

A

1) Coupled transport
2) ATP-consuming
- e.g. ABC transporters

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12
Q

Examples of couple transport proteins

A
  1. Lac Permease (a symporter)
  2. Sodium-Proton Antiporter
    These transporters are powered directly by the Proton Motive Force
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13
Q

The rest of the cell envelope

A

Almost always includes the cell wall of **Peptidoglycan
From top to bottom:
- Outside
- Peptidoglycan cell wall
- Cell membrane
- Cytoplasm

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14
Q

Cell wall provides structural strength

A

e.g. resistance to osmotic pressure
- prevent cell bursts (lysis)

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15
Q

Peptidoglycan

A
  • Distinctive for bacteria. NOT in Archaea
  • Amino acids + sugars
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16
Q

Structure of Peptidoglycan

A
  • Glycan chains
  • Peptide cross-bridges
  • More a ‘cage’ than a ‘wall’
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17
Q

Glycans and Peptides

A

Glycans:
- Long linear chains of two alternating sugars:
N-acetyl glucosamine (G)
N-acetyl muramic acid (M)
Peptides:
- Each of a few amino acids. Cross-linked to connect the glycans

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18
Q

Penicillin method of action

A

Penicillin and many other antibiotics: block peptide cross-linking

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19
Q

Basic cell envelope architecture

A
  1. ‘Gram-positive’
    - Peptidoglycan wall usually thick
  2. ‘Gram-negative’
    - Thin peptidoglycan wall
    - + Outer membrane
    - More widespread
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20
Q

Gram-positive cell envelope

A

Many layers of peptidoglycan (often 20+)
- Thick peptidoglycan cell wall
- Teichoic acids
- Cell membrane

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21
Q

Gram-negative cell envelope

A
  • Outer membrane with Porin (outer leaflet, inner leaflet)
  • Peptidoglycan wall
  • Cell membrane (‘inner’ membrane)
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22
Q

Outer membrane composition

A

Very different composition to the cell membrane
- *Outer leaflet: mostly lipopolysaccharide (LPS)
- *Inner leaflet: contains major lipoproteins
- especially *Murein lipoprotein (Lpp), which chemically bonds to peptidoglycan cell wall

Outer membrane proteins
- e.g. Porins

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23
Q

Lipopolysaccharide (LPS)

A
  • ‘Lipid A’ + Polysaccharide
  • Outer portion is strain-specific ‘O-polysaccharide’
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24
Q

Porins

A
  • Aqueous channels
  • Allows passage of small molecules across the outer membrane
  • e.g. monosaccharides, amino acids, etc
  • (not whole proteins: too large)
    = outer membrane much more porous than cell membrane
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25
Q

Gram-negative cell wall

A

Between outer membrane and Cell membrane = Periplasm

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26
Q

Periplasm (periplasmic space)

A

Peri = ‘surround’ (compartment surrounding cell)
Compartment between cell membrane and outer membrane

Many distinct proteins:
- e.g. Enzymes involved in nutrient acquisition

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27
Q

ABC transporters

A
  • Solute-binding proteins are examples of periplasmic proteins
  • ABC transporters are active transport systems
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28
Q

Gram-positive cell envelope

A

Capsule and S-Layer (in some)
- Exterior to outer membrane

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29
Q

Extracellular layers

A
  • Common, but not universal
  • Usually not essential for cell viability
  • Often present only in some stages of life cycle

Examples:
- Capsules
- Protein ‘S-layers’

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30
Q

Capsules

A
  • Usually thick, but diffuse
  • Usually *polysaccharide

Some roles:
- Resistance to desiccation
- Protection from predation / immune system / viruses
- Adhesion to surfaces

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31
Q

External projections

A
  • Usually made of *protein
  • Extracellular; usually anchored to cell membrane, or outer membrane, or both

Examples:
- Bacterial flagella
- Pili

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32
Q

Bacterial Flagella

A
  • Thin, flexible, helical filaments:
  • Main function: swimming locomotion
  • Present in many bacterial groups
    • Often only expressed under some conditions
  • Many species are *peritrichous - many single flagella all over cell
    • e.g. Escherichia coli (E. coli)
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33
Q

Flagellum structure

A
  1. Filament
  2. Basal body
    - Ring of motor proteins in cell membrane, around *‘Rotor’
    - Flagellum rotates, powered by proton motive force (PMF)
34
Q

Flagellum function

A
  • Flagella can rotate clockwise and counter-clockwise (CCW)

In typical peritrichous cells:
- All CCW: Flagellar bundle formed; straight-line ‘run’
- 1+ Clockwise: no bundle, random ‘tumble’

35
Q

Swimming

A
  • Alternating runs and (random) tumbles -> ‘Random Walk’ through space
36
Q

Swimming with purpose

A
  • Random walk can be *biased by altering the *frequency of random tumbles in *response to a cue
  • e.g. Chemotaxis: move towards chemical attractant
37
Q

Pili

A
  • Many different sorts
  • Thin rods/tubes of protein
  • Typical roles:
  • *Adhesion (e.g. in genetic exchange & pathogenesis)
  • Locomotion (on surfaces)
38
Q

Cytoplasm

A

As in eukaryotes…
- Site of many enzymatic reactions
- Pools of small molecules
- Amino acids
- ATP
- Ions
- etc, etc, etc
- Site of protein synthesis (ribosomes)

39
Q

Prokaryotes: complex internal structures

A
  • Storage granule
  • Thylakoid membranes
  • Gas vesicles**
  • Carboxysome*
40
Q

Storage granules (energy/nutrient reserves)

A

Example:
- Poly-beta-hydroxybutyric acid (PHB) granules
- fatty acid polymer
- energy store: made under ‘excess carbon’ conditions

41
Q

Bacterial cytoskeleton: shape-determining proteins

A

Major shape-determining proteins:

“Z ring”; includes FtsZ
- Division plane (later)

-MreB
- Needed for elongation (growth) or rod-shaped cells
- Guides cell wall synthesis

42
Q

Prokaryotic DNA

A

Usually a single, circular chromosome
- but often with extrachromosomal ‘plasmids’

In a *‘Nucleoid’, not a separate nucleus
- Compaction via supercoiling, plus… DNA-binding proteins (not histones, in bacteria)

43
Q

Prokaryotic chromosome

A

Densely-packed with information:
- Most (~90%) of the DNA encodes proteins
- Intervening sequences (~introns) nearly absent
- Many genes in co-transcribed groups - *Operons

44
Q

Coupled transcription & translation

A

No sharp separation between nucleoid & cytoplasm allows couples transcription & translation

45
Q

Plasmids

A

*Extra-chromosomal genetic elements:
- Usually encode functions that change properties of the host cell, but are *not required for cell viability
- Often readily transferred between individual cells
- Some transferable between different species

46
Q

Plasmid Example: RK2

A
  • Encodes multiple antibiotic-resistance genes
  • “Promiscuous” (can be transferred between species)
47
Q

Chromosome replication

A
  • Usually one *origin of replication
  • Bidirectional: 2 replication forks
  • Complete when forks meet (at termination site)
  • Replication cycles overlap when cell generation time is shorter than DNA replication cycle
48
Q

Growth and Reproduction

A
  • Typically, cells grow, then divide evenly in two (binary fission)
    Division includes…
  • Replication of chromosome
  • Formation of septum (septation); at ‘Z ring’
49
Q

Bacterial population growth

A

Exponential growth equation:
Nt = N0 x 2^n
N0 = original number of cells;
n = number of generations
Some species can undergo binary fission every 20-30 minutes under optimal conditions

50
Q

The growth curve (in batch culture)

A
  • ‘Log phase’: period of exponential growth
  • Ended by nutrient limitation, or toxic buildup: culture enters ‘stationary phase’
51
Q

Differentiation

A

Different cell types in a few colonial forms
- (Heterocysts in some *Cyanobacteria)
More common: Alternate cell forms specialized for *dormancy and/or *dispersal. Examples…
- Akinetes (some Cyanobacteria)
- Spores** (some Actinobacteria)
- Endospores** (some Firmicutes)

52
Q

Organic vs Inorganic

A

Organic: C-H compounds
Inorganic: Others, including CO2, carbonates
Catabolism (breaking down) vs Anabolism (~biosynthesis)

53
Q

Organic carbon source for biomass

A

Convert (‘fix’) inorganic carbon (CO2): use existing organic molecules: autotroph + heterotroph

54
Q

4 Basic nutritional types of organisms

A
  1. Photoautotrophs
  2. Chemoautotrophs
  3. Photoheterotrophs
  4. Chemoheterotrophs
55
Q

Two types of Chemotrophs

A

Organotrophs
- Catabolism of *organic molecules
- Often just called ‘Heterotrophy’ but we will use ‘Organotrophy’ (clearer)

Lithotrophs
- Energy from oxidizing *inorganic molecules
e.g. sulfur, sulfide (H2S)

56
Q

Organism’s relationship with oxygen

A

Aerobes rely on oxygen (O2) as electron acceptor
- Obligate aerobes (need O2 fro growth)
- Microaerophiles (prefer low levels of O2)

Anaerobes do not use oxygen
- Aerotolerant anaerobes (tolerate but do not use O2)
- Obligate/strict Anaerobes (need very low O2 to live)

Facultative Anaerobes:
- Can use O2 but also grow in the absence of O2

57
Q

Humans respiration description

A

An ‘Aerobic Chemo-organo-heterotroph’
- Oxygen-dependent
- Energy from chemicals…
- Specifically, organic chemicals…
- And need existing organic carbon to make new biomass

58
Q

Input of catabolism is organotrophs

A
  • Simple sugars (and sugar acids): mostly from the break-down of polysaccharides (e.g. starch; cellulose; pectin, etc.)
59
Q

Energy realization in classic aerobic organotrophy

A

An oxidation-reduction (redox) reaction (i.e. transfer of electrons from a donor to acceptor)
- ‘Lots’ of energy because oxygen is a **strong acceptor

60
Q

Metabolic Diversity

A

Much of the metabolic diversity in prokaryotes is seen when oxygen and/or organic carbon is limited:

  • Fermentations
  • Anaerobic respiration
  • Lithotrophy
61
Q

Fermentations

A

~ Organotrophy, without external electron acceptor
- Substrates & products will be in ‘redox balance’
- No use of electron transport system

  • Often under anoxic (anaerobic) conditions

Low energy yields per molecule of substrate
- Large amounts of substrates converted
- Large amounts of end-products created

62
Q

Some fermentations (of glucose) and their end-products

A
  • ‘Lactic’ : 2 Lactate + 2H
  • ‘Heterolactic’ : Lactate + H + Ethanol + CO2
  • ‘Ethanolic’ : 2 Ethanol + 2 CO2
  • ‘Mixed-acid’ : various mixtures of organic acids & ethanol, CO2 & H2

Many fermentation end-products still energy-rich = Potential substrates (food) for other organisms

63
Q

Redox Reactions

A

Energy available from reaction depends on difference in reduction potential between electron acceptor and electron donor

  • Large positive value: lot of energy available
  • Large negative value: reaction instead needs a lot of energy to proceed
64
Q

Oxygen as acceptor

A
  • O2 an energetically valuable terminal electron acceptor (because E strongly positive)
  • But many other molecules could, in principle, be used as electron acceptors when oxygen is not available (e.e. during anoxia)
    Ex. Nitrate
65
Q

E. coli (facultative Anaerobe)

A

a) Under aerobic conditions: oxygen is electron accepetor
b) Under anoxia (e.g, after O2 used up) but if NO3 (nitrate) abundant, nitrate reduction

66
Q

Denitrification

A
  • Anaerobic respiration with Nitrate (NO3) as terminal electron acceptor, but reduced to N2 (not just NO2)
  • A major cause of loss if available nitrogen from ecosystems
67
Q

Sulfate Reduction

A
  • Anaerobic respiration by ‘sulphate-reducing bacteria’
  • An inorganic molecule (other than oxygen) used as an electron acceptor
68
Q

Lithotrophy

A
  • Where an inorganic molecule is used as the original *electron *donor (i.e. food!)

Needs a source of *reduced inorganic compounds…
- many metals/metal ions. Sulfur compounds, Nitrogen compounds, Hydrogen gas, etc. etc.

69
Q

Production of reduced inorganic compounds for lithotrophy

A

Produced by geological processes, or
Produced by other organisms:
- Anaerobic respiration (with low-reduction-potential electron acceptors)
- Fermentation

70
Q

Sulfer/sulfide oxidisers

A
  • Often at *interface between sulfide-rich anoxic layers and overlying aerobic zone
71
Q

Hydrogen (H2) in respiration

A

Strongly negative reduction potential
- Therefore an energy-rich ‘food’

Sources:
- Geological (e.g. Hydrothermal vents)
- Waste product of some fermentations

72
Q

Biosynthesis

A

Making new biomass
- the process of starting with basic organic molecules and making new organic compounds
- Requires organic carbon
- Requires Nitrogen for nitrogen-containing organic compounds

73
Q

Raw material for biosynthesis

A
  • Organotrophs in compost, surrounded by organic material
  • In hot springs, sulfur-oxidizing lithotroph, not much organic material, take CO2 from environment to make organic carbon, then organic material
74
Q

Autotrophy

A
  • Fixation of *inorganic carbon (usually CO2) to form *organic carbon: i.e. reduction of CO2
  • Most Phototrophs and most Lithotrophs are capable of autotrophy
  • Requires energy (generated via phototrophy or lithotrophy) including ‘reducing power’ (e.g. NADH)
75
Q

Carboxysomes

A

Crystalline aggragations of rubisCO
- the signature Calvin Cycle enzyme

76
Q

Lithoautotrophy

A

Some ecosystems are based in lithoautotrophy (not photoautotrophy) - energy comes from reduced inorganic molecules

77
Q

Nitrogen for biosynthesis

A

For biosynthesis of amino acids, nucleotides, vitamins etc.

Most prokaryotes can assimilate ammonium (NH4)
- many also assimilate nitrate (NO3)
- A very few require organic N (e.g. amino acids)

Some prokaryotes capable of ‘nitrogen fixation’ (atmospheric N2
-> NH4)

78
Q

Prokaryote ‘species’

A

In prokaryotes, no true sexual process
- So, ‘species’ based on operational criteria
- e.g. > 95% average nucleotide identity (ANI) of orthologs (~comparable genes)

79
Q

Number of prokaryote ‘species’

A

~15,000 named to date
Why so few?
1) Demanding rules to name a species (e.g. must be cultured!)
2) Prokaryote ‘species’ may contain much more genomic diversity than animal or plant species

80
Q

Patterns of prokaryote evolution

A

*Some groups distinguished by major cellular or physiological traits:
- e.g. Bacteria vs Archaea
- e.g. Spirochetes (periplasmic flagella)

But *many major traits appear in very distantly related organisms
- Much due to *horizontal (lateral) gene transfer

81
Q

Examined groups of Bacteria

A
  • Firmicutes
  • Actinobacteria
  • Proteobacteria
  • Cyanobacteria (& briefly, other photosynthesizers)
  • Spirochetes
    Some others
82
Q

Firmicutes

A

Diversity of Plants and Microorganisms (2 decks)

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