Module 1 - The Cell Flashcards
(149 cards)
1
Q
What is the magnification of a microscope?
A
The capacity of as microscope to enlarge an object
2
Q
What is the resolution of a microscope?
A
The ability to distinguish two adjacent objects as distinct and separate
3
Q
What is the limiting factor in our ability to see small objects on a microscope?
A
Resolution
4
Q
What is the resolution limit of a light microscope?
A
0.2 um
5
Q
What are different ways of improving contrast in light microscopy?
A
Staining Phase contrast Differential interference contrast Dark Field Fluorescence
6
Q
Why are election microscopes able to magnify much larger than light microscopes?
A
Wavelength affects resolution. The wavelengths of electrons is much shorter than visible light.
7
Q
What is the spontaneous generation theory?
A
Organisms apparent on rotting food but not fresh food, arise spontaneously from non-living material
8
Q
How did Pasteur disprove spontaneous generation theory?
A
He created a flask with a bend in the tp, and heated a liquid to sterilise it. The dust & microbes were trapped in the bend of the flask and the liquid remained sterile indefinitely. He then tipped the flask so the liquid contacted the dust/microbes, and the liquid quickly putrefied.
9
Q
What are Koch’s postulates?
A
- The suspected pathogen must be present in all cases of the disease and absent from healthy animals 2. The suspected pathogen must be grown in pure culture 3. Cells from a pure culture of the suspected pathogen must cause disease in a healthy animal 4. The suspected pathogen must be resonated and shown to be the same as the original
10
Q
What is a pure culture?
A
A culture of a single species
11
Q
What is the purpose of Koch’s postulates?
A
Criteria for definitively linking a specific microorganism to a specific disease
12
Q
Why is ribosomal RNA (rRNA) used for phylogenetic analysis?
A
-Universally distributed -Functionally constant -Highly conserved -Adequate length to provide view of evolutionary relationship
13
Q
What are 3 properties of ALL microbial cells?
A
Metabolism Growth Evolution
14
Q
What are properties of SOME but NOT ALL microbial cells?
A
Differentiation Communication Genetic Exchange Motility
15
Q
What are the 2 lenses in a light microscope?
A
Ocular lens and objective lens
16
Q
What are basic dyes?
A
Positively charged dye that stain negatively charged cellular components like nucleic acids and surfaces of cells
17
Q
What 2 types of microscopy can be used without stains to view live specimens?
A
Phase-contrast and dark-field microscopy
18
Q
What colour do gram-positive and gram-negative microorganisms appear after gram staining?
A
Gram positive - purple-violet Gram negative - pink
19
Q
What microscopy can be used to generate a 3D image of a specimen?
A
Differential Interference Contrast (DIC) microscopy - 2 light beams, but no stain required Confocal Scanning Laser Microscopy (CSLM) - laser scanning of layers into computer generated image, often paired with fluorescent microscope
20
Q
What is the enrichment culture technique?
A
Microorganisms are isolated using highly selective media and incubation conditions that favour a particular metabolic group of organisms
21
Q
What is morphology?
A
Cell shape
22
Q
Name this morphology
A
Coccus (plural Cocci
23
Q
Name this morphology
A
Rod or bacillus
24
Q
Name this morphology
A
Spirillum (spirilla
25
Name this morphology
Spirochete
26
Name this Morphology
27
Name this Morphology
Filamentous
28
What is a chemolithotroph?
An organism that metabolises inorganic compounds for energy
29
What are sterols?
Rigid planar molecules that strengthen the membrane of eukaryotic cells
30
What are hopanoids?
Sterol-like substances that strengthen the cytoplasmic membrane of some bacteria
31
How are the cytoplasmic membranes of Archea different to bacteria and eukaryotes?
Bacteria and Eukarya have ester bonds between fatty acids and glycerol.
Archaea have ether bonds between glycerol and isoprene
32
What are the 3 major functions of the cytoplasmic membrane?
1. Cell's permeability barrier, preventing passive leakage in or out of cell
2. Anchors several proteins that catalyse key cell functions
3. in bacteria and archaea, plays a major role in energy conservation and consumption
33
What is peptidoglycan?
A rigid polysaccharide found in the cell walls of bacteria giving it structural strength. Not found in archaea or eukarya
34
What is lysozyme?
An enzyme that can weaken peptidoglycan in bacterial cell walls and cause cell lysis. Found in human tears, saliva and other secretions functioning as a line of defence against bacterial infection
35
Describe the cell wall structure of gram-positive bacteria
Up to 90% made of peptidoglycan, with teichoic and lipteichoic acids
36
Is this a gram-negative or gram-positive bacterial cell wall?
Gram positive
37
Is this a gram-negative or gram-positive bacterial cell wall?
Gram negative
38
Describe the cell wall structure of gram-negative bacteria
Only a small proportion is peptidoglycan. Mostly composed of the outer membrane. The lipopolysaccharide (LPS) layer.
39
What are the components of the LPS?
1. The lipid section
2. The polysaccharide section with 2 parts. The Core polysaccharide and the O-specific polysaccharide
Also Braun lipoproteins that connect peptidoglycan layer to LPS
40
What is endotoxin?
The toxic component of LPS, specifically Lipid A. They can cause violent symptoms in humans (ie salmonella)
41
What is the periplasm?
Space between the outer surface of the cytoplasmic membrane and the inner surface of the inner membrane
42
What is an endospore?
Highly differentiated cells, extremely resistant to environmental conditions. they function as survival units allowing the organism to survive. Dormant stage of bacterial life cycle, including periods away from a favourable host.
43
What are the steps of endosporulation?
Activation - when endospores are heated to sub lethal temp
Germination - very quick, signalled by loss of resistance to heat/chemicals and refractility
Outgrowth - visible swelling due to water uptake. Vegetative cell emerges from broken endospore
44
Why does the size of an organism matter?
Surface to volume ratio - ie diffusion distance for most inner part of a cell.
45
What are the limiting factors for size of an organism?
Upper limit determined by nutrient transport
Lower limit determine by essential components
46
What is meant by the fluid mosaic model of the cell membrane?
The membrane is not rigid, the proteins are free to move around (like fluid)
47
What is polar flagellation?
Flagella attached at one or both ends of a cell
48
What is iophotrichous and amphitrichous flagellation?
Iophotrichous - A type of polar flagellation where a tuft of flagella arise at one end of a cell
Amphitrichous - a type of polar flagellation where a tuft of flagella arise from both ends of a cell
49
What is peritrichous flagellation?
When flagella are attached all around the cell surface
50
What determines the speed of movement of flagella?
The strength of the proton motive force
51
What is the function of bacterial cell walls?
* Protection against osmotic lysis
* confers rigidity
* determines/maintains cell shape
52
How to penicillin and peptidoglycan layer interact?
Penicillins cleaves the cross link in peptidoglycan layer - inhibits synthesis in growing cells, little effect on cell wall of persisting bacteria
53
What types of organisms have peptidoglycan layer?
Only bacteria
54
What bacteria do not have cell walls?
Mycoplasma/acholeplasma
55
What is the difference between capsule and slime layers?
Capsule is an organised "halo" of tight matrix that excludes small particles.
Slime layer is more easily deformed and loosely attached
56
What are the functions of capsule/slime layers?
* Adhesion
* aggregation (biofilm)
* recognition
* avoid destruction by host
57
What are fimbriae and pili?
Thin filamentous protein structures that extend from cell with many different functions.
Fimbriae are many filaments, pili is only one.
58
What is chemotaxis?
Movement stimulated by specific chemicals
59
What is phototaxis?
Movement towards or away from light
60
What is endosymbiosis theory?
That mitochondria evolved from a bacterial invasion of a primitive eukaryotic cell
61
What is the evidence for endosymbiosis theory?
* The size and distribution in all eukaryotic cells
* Has circular DNA like a bacterial chromosome
* Mitochondrial ribosomes are 70S like bacteria
* Shared protein inhibitors with bacteria
62
Name each of these coccus arrangements
A) micrococcus - single
b) diplococcus - pairs
c) streptococcus - chains
d) staphylococcus - clumps in geometric arrangments
e) tetrad - in a plane of 4
f) sarcina - cube of 8
63
What is metabolism?
The sum of all biochemical pathways in the body. The sum of anabolism and catabolism
64
What are autotrophs?
Organisms that can synthesise their own organic compounds from CO2
65
What elements are essential for all microorganisms?
H, C, N, O, P, S, Se
66
What type of macromolecule makes up the greatest fraction of the dry weight of a cell?
Proteins - 55%
67
What is active transport?
The process by which cells accumulate solutes against the concentration gradient
68
What are the 3 basic mechanisms of active transport in the prokaryotic cell?
1. Simple transport - a transmembrane transport protein driven by proton notice force (symport or anti port)
2. Group translocation - chemical modification of the solute to be transported driven by energy-rich organic compound (ie Phosphoenolpyruvate)
3. ABC Transport - a periplasmic(gram -ve) or substrate (gram +ve) binding protein, transmembrane transport protein and ATP-hydrolising protein powered by ATP
69
What is glycolysis?
The catabolism pathway of glucose to pyruvate
70
What is a chemoorganotroph?
An organism that obtains its energy from oxidation of organic compounds
71
What is the most important micronutrient and why?
Iron - Fe
key component of electron transport chain & essential for respiration
72
What are growth factors?
Organic compounds vital for growth of microbes, needed in small amounts. Different requirements for different microorganisms.
Ie vitamins, essential amino acids etc
73
What is oxidation vs reduction?
Oxidation is REMOVAL of electron from substance
Reduction is ADDITION of an electron to a substance
OILRIG - Oxidised Is Loss, Reduction Is Gain
74
What is E0'?
E0' is Reduction Potential. Measured in Volts (V).
The tendency to donate or accept electrons.
Substances with more -ve E0' DONATES electrons to the substance with more +ve E0'.
75
What is fermentation?
Form of anaerobic catabolism where organic compounds both donate and accept electrons - no need for external electron acceptor.
76
What is the difference between fermentation and respiration in chemoorganotrophs?
* Fermentation - the organic compound is the electron donor AND the electron acceptor - closed system.
* Respiration - the organic compound is the electron donor and ANOTHER compound (organic or inorganic) is the electron acceptor. More energy yield from respiration.
77
What are the electron donor/acceptors in chemolithotrophic respiration?
Electron donor is inorganic molecule (ie H2, H2S, Fe2+, NH4+ etc).
Electron acceptors are other inorganic compounds or O2 (can be aerobic or inaerobic)
78
What is the ultimate different between aerobic and anaerobic respiration?
Difference in the electron ACCEPTORS (ie oxygen or otherwise)
79
What is the ultimate difference between chemoorganotrophy and chemolithotrophy?
Difference in electron DONORS (organic or inorganic)
80
What is the definition of growth in microbiology?
Increase in the number of cells
81
What type of growth is this an example of?
Binary fission
82
What is generation time?
The time required for 1 cell to form into 2 cells
83
What is budding cell division?
Cells that divide as a result of unequal cell growth. Unlike binary fission, results in 1 totally new daughter cell with parent cell retaining identity.
84
What is planktonic vs sessile growth?
Planktonic is suspended lifestyle (ie in water of a lake)
Sessile is attached to a surface
85
What is a biofilm?
Attached polysaccharide matrix with embedded bacterial cells. Multilayered biofilms of different organisms are microbial mats.
86
How can the number of microbial cells in a culture be measured?
* Hemocytometer - direct microscope counting using a special chamber and a grid
* turbidity - using spectrophotometer to measure optical density. Not an exact # cells but can measure growth over time
87
What are different classes of culture media?
1. Defined or simple media - exact composition is known. A precise amount of pure chemicals is added to distilled water.
2. Complex or Rich media - exact nutritional composition is unknown. Made from digests of microbial, animal or plant products.
3. Enriched medium - used for nutritionally demanding (fastidious) microbes
4. Selective medium - inhibits the growth of some microbes but not others
5. Differential medium - has indicator added which has colour change when particular reaction has occurred.
88
What is the equation to calculate the final number of cells after a period of time?
N = N02n
Where N0 is initial number of cells and n is how many generations
89
What is the equation to determine the number of generations?
n = [3.3(logN-logN0)]
Where N is final number of cells and N0 is initial number of cells
90
What is the equation for generation time?
G = t/n
where t is time and n is number of generations
91
Why does turbidity as a measure of culture growth become inaccurate at high optical densities?
Because dead cells still scatter light and contribute to turbidity, despite not being viable cells
92
What are the microbial growth phases?
* Lag phase
* Exponential phase
* stationary phase
* death phase
93
What is the instantaneous growth rate constant?
k.
Can be calculated by k = 0.693/g
Expression of the rate a population is growing at any instant, unit is h-1
94
What are the environmental factors that control microbial growth?
* Temperature
* Oxygen
* Ph
* Water
95
What is mesophilic?
Microbes with growth temperature range between 20-40° C. Capable of growth between 5 and 50°C
96
What is a psychrophile?
Microbes that thrive in cold environments with optimal growth temperature around 4°C. Able to grow below 0 but not above 20.
97
What is a thermophile?
Microbes with optimal temperature around 60° C (high). Unable to grow below 20°C
98
What is a hyperthermophile?
Microbes with very high optimal growth temperatures of around 88°C.
There is a subset of hyperthermophiles with higher again optimal temps around 106°C
99
How do protein structures contribute to the ability of microbes to survive at high and low temperatures?
Psychrophiles have more α-helix compared to β-sheets. They will have more structural flexibility and more glycine (glycine is very small therefore more loose structure)
Thermophiles have more ionic bonds, more hydrophobic interactions (highly hydrophobic interior)
100
How does membrane lipid composition contribute to ability of microorganism to survive high and low temps?
Unsaturated lipids have kink, can't line up therefore more fluid. So psychrophiles will have more unsaturated membrane lipids. Thermophiles will have more saturated membrane lipids to increase stability at high temperatures
101
What are facultative anaerobes?
Microbes that can survive under both aerobic or anaerobic, and will adjust their metabolism to suit. They can have a preference.
102
How are oxygen free radicals dangerous?
They are very reactive, they attach DNA, proteins and cell membranes
103
What protects the cell against oxidative stress?
Enzymatic antioxidants, and non-enzymatic free radical scavenging systems
104
Where in the cell are oxygen-derived free radicals produced in large amounts?
In eukaryotic cells - mitochondria
In prokaryotic cells - cell membrane
105
What is a neutrophile?
106
What is an acidophile and alkaliphile?
Acidophile is organism with optimal pH less than 5.5
Alkaliphile is organism with optimal pH greater than 8
107
What is the critical factor governing acidophily?
Stability of the cytoplasmic membrane
108
What is aw?
Water availability - ratio of vapour pressure of air in equilibrium with solution to vapour pressure of pure water.
Aw of 0 = no free water
aw of 1 = pure water
109
What is meant by positive water balance?
When a cell has a higher intracellular concentration of solutes than the environment therefore water moves into the cell by osmosis.
110
What is a halophile?
An organism that requires increased levels of NaCl in the environment for optimal growth (ie seawater)
111
What is halotolerant?
Organisms that can tolerate increased solute levels to an extent, but grow optimally without
112
What is a compatible solute?
A solute that can be used to increase solute concentration in the cell and increase osmotic potential, without interfering with biochemical processes
113
How can a cell compensate for being moved from an environment with high aw to low aw?
It can increase it's intracellular solute concentration to maintain osmotic potential by importing solutes from the environment, or synthesising solutes
114
What is the difference between sterilisation, disinfectant, antiseptic and pasteurisation?
* Sterilisation is removing ALL microorganisms from a surface
* Disinfectant is removing HARMFUL microorganisms from an inanimate object (chemically)
* Antiseptic is removing HARMFUL microorganisms from skin
* Pasteurisation is removing HARMFUL microorganisms from liquid
115
What are methods of physical anti microbial control?
* Autoclave (steam - high temps kill microbes)
* radiation (microwave, gamma, UV)
* Filtration
116
What are methods of chemical anti microbial control?
* Synthetic agents
* steriliants, disinfectants, antiseptics, sanitiser
117
What are methods for anti microbial control in vivo?
* Antibiotics (chemotherapeutic agents, naturally occurring antibiotics)
* can be bacteriostatic (inhibit growth), bacteriocidal (kill bacteria) or bacteriolytic (destroy cells)
* can be broad spectrum (all bacteria), narrow spectrum (gram -ve or +ve), or limited spectrum (1 type only)
118
What are 5 antibiotic modes of action?
1. Bacterial cell wall synthesis - peptidoglycan layer in bacteria but not human, required, disruption results in cell lysis
2. Interfere with protein synthesis - bind to prokaryotic ribosomal subunits and prevent translation
3. interfere with nucleic acid synthesis - can prevent RNA polymerase from transcribing or block enzymes for DNA replication
4. Inhibition of essential metabolic pathway - exploits differences in prokaryotes vs eukaryotes, inhibits key enzymes or can use competitive inhibition
5. Membrane inhibition/destruction - interfere with normal membrane function, cell wall of gram -ve is one point of attack
119
What are characteristics of clinical useful antibiotics?
* Wide spectrum of activity
* Non-toxic/non-allergenic to host
* Not impact normal flora of host
* Able to reach location of infection
* Inexpensive and easy to produce
* Chemically stable
* Unlikely to develop microbial resistance
120
What are 3 classes of antibiotics?
1. Synthetic anti microbial - synthetically produced compounds, either analogues of essential compounds or interfere with enzymes etc.
2. Naturally occurring - ie penicillins isolated from fungi etc. β-Lactam antibiotics most important of all time, target gram +ve crosslinking of peptidoglycan layer. Resistant bacteria produce β-lactamase.
3. Antibiotics from prokaryotes - effective against bacteria & produced by bacteria. Include tetracyclines, macrolides, platensimycin
121
What is a mutation?
A heritable change in the base sequence of the genome of an organism
122
What is a selectable mutation?
A genetic mutation that confers a clear advantage on the mutant strain under certain conditions
123
What is an auxotroph and prototroph?
A an auxotroph is a mutant strain with an additional nutritional requirement. A prototroph is the parental strain from which it was derived.
124
What is a spontaneous mutation?
A mutation that occurs without external intervention
125
What is an induced mutation?
Mutations caused by agents in the environment including made deliberately by humans. Can also include naturally occurring radiation etc.
126
What are silent, missense and nonsense mutations?
* Silent mutation is point mutation that doesn't result in a different amino acid in the polypeptide chain (makes no difference)
* Missense mutation is mutation that changes the amino acid in the polypeptide chain, therefore may impact function.
* Nonsense mutation is one that prematurely gives STOP codon and results in truncated polypeptide
127
What is a revertant and what are the 2 categories?
A strain in which the original phenotype that was changed by a mutation is restored.
* Same-site revertant restores activity at the same site as the original mutations (and is a true revertant if it restores the original sequence)
* second-site revertant restores wild-type phenotype by acting on a different location and compensating for the mutation (suppressor mutations)
128
What is a mutagen?
A biological, chemical or physical agent that increases the mutation rate
129
What is a virus?
An obligate intracellular parasite
130
What are 3 characteristics of viruses?
1. No metabolic activity of their own
2. cannot replicate on their own
3. hijack the machinery of host cells
131
What can viruses infect?
Any living things, and other viruses
132
What is a virion?
A complete viral particle as found outside of cells
133
What are the components of a virion?
Nucleic acid (genetic material)
Capsid (protein coat, made of capsomeres)
Other features ie Lipid envelope
134
What are the types of single stranded viral genomes?
* +sense - same base sequence to viral mRNA translated to proteins
* -sense
135
How can viral genome be classified?
* DNA vs RNA
* Double strand vs single strand
* + sense or -sense if single strand
* linear vs circular
* single molecule vs multiple molecules
136
What are some examples of capsid shapes?
* Helical
* Icosahedral
* Complex
137
What is a viral envelope?
A lipid layer enveloping the capsid. It is derived from the host cell and contains the viral proteins. (Ie Ebola)
Some viruses are naked ie no envelope (ie HPV)
138
Why do some viruses carry enzymes in their virions?
They can be important for infection or viral replication
139
What is viral specificity?
Each virus only has a limited host range - can only infect cells with receptors for viral proteins
140
What are the 5 steps of viral replication?
1. Attachment (Adsorption) - with cellular receptor, inducing conformational change that allows entry.
2. Penetration - entry/injection, in bacteriophage only genome enters, animals the whole virion enters & capsid then removed.
3. Synthesis - host machinery produces viral nucleic acid and proteins
4. Assembly - of newly synthesised material into complete virions (capsid with nucleic acid inside)
5. Release - of assembled virions. Can be destructive (lysis) or budding (enveloped viruses - how envelope is formed)
141
How does a temperate bacteriophage differ from a "standard" virus
As well as the lytic pathway, it can also have a lysogenic pathway where the viral genome is replicated along with the host without killing the cell.
It may switch between these pathways
142
What is transduction & the link to bacteriophages?
Sometimes during assembly, host DNA is packaged instead of viral genome. When that virion infects another bacterial cell, it injects the host DNA and homologous recombination can result. Note this is quite rare.
143
What are the different host cell fates of animal viruses?
* Lysis (virulent infection)
* Latent infection - virus is present but not actually replicating
* Persistent infection - slowly release virus without causing cell death
* Transformation - viral infection leads to cancerous/tumour-like cell
144
How can viruses be grown for study?
Plaque assay.
* Plate agar, virus & cells
* infected cells lyse
* each plaque = 1 infections particle
* calculate # viral particles in a solution (viral titre)
145
What type of virus is SARS-CoV-2?
ssRNA(+), linear, enveloped
146
What type of virus is Australian Bat Lyssavirus?
ssRNA (-), linear, enveloped
147
What kind of virus is HSV-1?
dsDNA, linear, enveloped
148
What type of virus is HIV?
SsRNA(+), [dsDNA] (retrovirus)
149
What are common targets for antivirals?
* Blocking attachment or entry (blocking protein/receptor interactions, or membrane fusion)
* Preventing uncoating (can't replicate if not uncoated)
* Preventing viral nucleic acid synthesis (nucleoside analogues/NRTIs which fuck up the chain, or NNRTI which blocks reverse transcriptase)
* Inhibit viral enzymes
* inhibit virion release
