Prokaryote Cell Organisation Flashcards
1
Q
2 Domains of Prokaryotes
A
Two distinct ‘domains’ of Prokaryotes
- Bacteria
- Archaea
2
Q
Sizes of Prokaryotes
A
Typically ~1 micrometre
= very high ratio of Surface area to Volume (SA:V)
3
Q
Common shapes of prokaryotes
A
- Cocci (sing. Coccus)
- Spherical - Rods/bacilli (sing. bacillus)
- n.b. some rods quite short - Other shapes (examples)
- Spirilla and “vibrios”
- Filamentous
4
Q
Colonies
A
- Chain colony (of cocci)
- Cluster (od cocci)
5
Q
General features of Prokaryotes
A
- Flagellum
- Envelope
- Cell membrane
- Cytoplasm
- Nucleoid
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
7
Q
Cell membrane components
A
(= cytoplasmic membrane; plasma membrane; inner membrane)
- Phospholipid bilayer, rich in membrane proteins
8
Q
Prokaryotic Cell Membrane
A
Remember: prokaryotes do NOT have..
- A complex endomembrane system
- or mitochondria
9
Q
Some functions of the cell membrane
A
- Selective permeability: control movement of most molecules into and out of cytoplasm
- Forming proton (H+) gradient (& other ion gradients); harnessing the proton motive force (PMF)
- Detection of environmental signals
- Protein anchor, (some) structural support
- Attachment of chromosomes, especially during cell division
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
11
Q
Active transport across cell membrane, examples
A
1) Coupled transport
2) ATP-consuming
- e.g. ABC transporters
12
Q
Examples of couple transport proteins
A
- Lac Permease (a symporter)
- Sodium-Proton Antiporter
These transporters are powered directly by the Proton Motive Force
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
14
Q
Cell wall provides structural strength
A
e.g. resistance to osmotic pressure
- prevent cell bursts (lysis)
15
Q
Peptidoglycan
A
- Distinctive for bacteria. NOT in Archaea
- Amino acids + sugars
16
Q
Structure of Peptidoglycan
A
- Glycan chains
- Peptide cross-bridges
- More a ‘cage’ than a ‘wall’
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
18
Q
Penicillin method of action
A
Penicillin and many other antibiotics: block peptide cross-linking
19
Q
Basic cell envelope architecture
A
- ‘Gram-positive’
- Peptidoglycan wall usually thick - ‘Gram-negative’
- Thin peptidoglycan wall
- + Outer membrane
- More widespread
20
Q
Gram-positive cell envelope
A
Many layers of peptidoglycan (often 20+)
- Thick peptidoglycan cell wall
- Teichoic acids
- Cell membrane
21
Q
Gram-negative cell envelope
A
- Outer membrane with Porin (outer leaflet, inner leaflet)
- Peptidoglycan wall
- Cell membrane (‘inner’ membrane)
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
23
Q
Lipopolysaccharide (LPS)
A
- ‘Lipid A’ + Polysaccharide
- Outer portion is strain-specific ‘O-polysaccharide’
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
25
Gram-negative cell wall
Between outer membrane and Cell membrane = Periplasm
26
Periplasm (periplasmic space)
Peri = 'surround' (compartment surrounding cell)
Compartment between cell membrane and outer membrane
Many distinct proteins:
- e.g. Enzymes involved in nutrient acquisition
27
ABC transporters
- Solute-binding proteins are examples of *periplasmic proteins*
- ABC transporters are active transport systems
28
Gram-positive cell envelope
Capsule and S-Layer (in some)
- Exterior to outer membrane
29
Extracellular layers
- Common, but not universal
- Usually not essential for cell viability
- Often present only in some stages of life cycle
Examples:
- Capsules
- Protein 'S-layers'
30
Capsules
- Usually thick, but diffuse
- Usually *polysaccharide
Some roles:
- Resistance to desiccation
- Protection from predation / immune system / viruses
- Adhesion to surfaces
31
External projections
- Usually made of *protein
- Extracellular; usually anchored to cell membrane, or outer membrane, or both
Examples:
- Bacterial flagella
- Pili
32
Bacterial Flagella
- 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)
33
Flagellum structure
1. Filament
2. Basal body
- Ring of motor proteins in cell membrane, around *'Rotor'
- Flagellum rotates, powered by proton motive force (PMF)
34
Flagellum function
- 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
Swimming
- Alternating runs and (random) tumbles -> 'Random Walk' through space
36
Swimming with purpose
- 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
Pili
- Many different sorts
- Thin rods/tubes of protein
- Typical roles:
- *Adhesion (e.g. in genetic exchange & pathogenesis)
- Locomotion (on surfaces)
38
Cytoplasm
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
Prokaryotes: complex internal structures
- Storage granule
- Thylakoid membranes
- Gas vesicles**
- Carboxysome*
40
Storage granules (energy/nutrient reserves)
Example:
- Poly-beta-hydroxybutyric acid (PHB) granules
- fatty acid polymer
- energy store: made under 'excess carbon' conditions
41
Bacterial cytoskeleton: shape-determining proteins
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
Prokaryotic DNA
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
Prokaryotic chromosome
Densely-packed with information:
- Most (~90%) of the DNA encodes proteins
- Intervening sequences (~introns) nearly absent
- Many genes in co-transcribed groups - *Operons
44
Coupled transcription & translation
No sharp separation between nucleoid & cytoplasm allows couples transcription & translation
45
Plasmids
*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
Plasmid Example: RK2
- Encodes multiple antibiotic-resistance genes
- "Promiscuous" (can be transferred between species)
47
Chromosome replication
- 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
Growth and Reproduction
- Typically, cells grow, then divide evenly in two (binary fission)
Division includes...
- Replication of chromosome
- Formation of septum (septation); at 'Z ring'
49
Bacterial population growth
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
The growth curve (in batch culture)
- 'Log phase': period of exponential growth
- Ended by nutrient limitation, or toxic buildup: culture enters 'stationary phase'
51
Differentiation
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
Organic vs Inorganic
Organic: C-H compounds
Inorganic: Others, including CO2, carbonates
Catabolism (breaking down) vs Anabolism (~biosynthesis)
53
Organic carbon source for biomass
Convert ('fix') inorganic carbon (CO2): use existing organic molecules: autotroph + heterotroph
54
4 Basic nutritional types of organisms
1. Photoautotrophs
2. Chemoautotrophs
3. Photoheterotrophs
4. Chemoheterotrophs
55
Two types of Chemotrophs
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
Organism's relationship with oxygen
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
Humans respiration description
An 'Aerobic Chemo-organo-heterotroph'
- Oxygen-dependent
- Energy from chemicals...
- Specifically, organic chemicals...
- And need existing organic carbon to make new biomass
58
Input of catabolism is organotrophs
- Simple sugars (and sugar acids): mostly from the break-down of polysaccharides (e.g. starch; cellulose; pectin, etc.)
59
Energy realization in classic aerobic organotrophy
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
Metabolic Diversity
Much of the metabolic diversity in prokaryotes is seen when oxygen and/or organic carbon is limited:
- Fermentations
- Anaerobic respiration
- Lithotrophy
61
Fermentations
~ 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
Some fermentations (of glucose) and their end-products
- '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
Redox Reactions
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
Oxygen as acceptor
- 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
E. coli (facultative Anaerobe)
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
Denitrification
- 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
Sulfate Reduction
- Anaerobic respiration by 'sulphate-reducing bacteria'
- An inorganic molecule (other than oxygen) used as an electron acceptor
68
Lithotrophy
- 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
Production of reduced inorganic compounds for lithotrophy
Produced by geological processes, or
Produced by other organisms:
- Anaerobic respiration (with low-reduction-potential electron acceptors)
- Fermentation
70
Sulfer/sulfide oxidisers
- Often at *interface between sulfide-rich anoxic layers and overlying aerobic zone
71
Hydrogen (H2) in respiration
Strongly negative reduction potential
- Therefore an energy-rich 'food'
Sources:
- Geological (e.g. Hydrothermal vents)
- Waste product of some fermentations
72
Biosynthesis
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
Raw material for biosynthesis
- 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
Autotrophy
- 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
Carboxysomes
Crystalline aggragations of rubisCO
- the signature Calvin Cycle enzyme
76
Lithoautotrophy
Some ecosystems are based in lithoautotrophy (not photoautotrophy) - energy comes from reduced inorganic molecules
77
Nitrogen for biosynthesis
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
Prokaryote 'species'
In prokaryotes, no true sexual process
- So, 'species' based on operational criteria
- e.g. > 95% average nucleotide identity (ANI) of orthologs (~comparable genes)
79
Number of prokaryote 'species'
~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
Patterns of prokaryote evolution
*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
Examined groups of Bacteria
- Firmicutes
- Actinobacteria
- Proteobacteria
- Cyanobacteria (& briefly, other photosynthesizers)
- Spirochetes
Some others
82
Firmicutes
