MICROBIO 3 Flashcards
(114 cards)
1
Q
What happens when a polymerase incorporates a ddNTP during DNA synthesis?
A
The DNA chain is terminated
This is a key step in Sanger sequencing, leading to the generation of fragments of varying lengths.
2
Q
How is the identity of the terminal ddNTP determined in Sanger sequencing?
A
By capillary electrophoresis and fluorescence detection
3
Q
In pyrosequencing, what is released each time a new dNTP is inserted?
A
Pyrophosphate (PPi)
4
Q
What enzyme converts AMP + PPi into ATP in the pyrosequencing process?
A
Sulfurylase
5
Q
What does luciferase do in pyrosequencing?
A
Consumes ATP and emits light
6
Q
What separates DNA fragments by size in Sanger sequencing?
A
Capillary electrophoresis
7
Q
What is the role of apyrase during DNA synthesis in pyrosequencing?
A
Cleaves unused deoxyribonucleotides
8
Q
What are contigs in the context of DNA sequencing?
A
Consensus sequences formed from overlapping short sequences
9
Q
What does a computer scan for when identifying possible ORFs?
A
Start and stop codons
10
Q
What is the significance of a likely ribosomal-binding site (RBS) in ORF identification?
A
Increases the probability of a genuine ORF
11
Q
What does the heat map of gene expression indicate during nitrogen starvation?
A
Increased expression is shown in red; decreased expression in blue
12
Q
What do genes such as psbB and petF encode?
A
Key photosynthetic proteins
13
Q
What method is used to isolate total protein from a culture or environmental sample?
A
Fractionation into small peptides
14
Q
How are peptide fractions characterized in proteomics?
A
By mass spectrometry (MS)
15
Q
What does MALDI-TOF mass spectrometry measure?
A
Time of flight (TOF) based on mass/charge (m/z) ratio
16
Q
What can genomic sequencing trace in food safety and infectious disease?
A
The origin of strains or viruses
17
Q
What does systems biology integrate?
A
Genomics, transcriptomics, proteomics, metabolomics
18
Q
Define ‘omics’.
A
Broad discipline integrating methodologies to characterise and quantify large pools of biomolecules
19
Q
What is the genome?
A
The entire complement of genetic information
20
Q
What are some major omic themes?
A
- Genomics
- Transcriptomics
- Proteomics
- Metabolomics
- Metagenomics
21
Q
What is the first widely used method of DNA sequencing?
A
Dideoxy method (Sanger sequencing)
22
Q
What does genome annotation involve?
A
Converting raw sequence data into a list of genes and other functional sequences
23
Q
What does codon bias refer to?
A
Some codons are used more frequently than others
24
Q
What is the estimated minimum gene number for a viable cell?
A
250–300 genes
25
What characterizes small genomes in prokaryotes?
Typically around 112–140 kb and dependent on their host for nutrients
26
What is a major application of comparative genomics?
Searching for enzymes related to specific lifestyles
27
What is the largest known prokaryotic genome?
Sorangium cellulosum at 14.8 Mbp
28
What types of genes are most abundant in bacterial genomes?
Metabolic genes
29
True or False: Archaea have more genes for carbohydrate metabolism than Bacteria.
False
30
What is the function of BLAST in genomics?
Searching for similarity to ORFs in other genomes or conserved functional domains
31
What is the primary focus of gene content in Archaea compared to Bacteria?
Higher percentage of the genome is devoted to energy and coenzyme production
## Footnote
Archaea typically have fewer genes for carbohydrate metabolism and membrane functions than Bacteria.
32
What can skew conclusions about Archaea?
Presence of novel coenzymes in methanogenic Archaea and less overall study of Archaea
## Footnote
These factors can lead to misinterpretations in genomic analyses.
33
What is functional genomics?
Understanding gene expression, gene-product function, protein activity, and growth metabolites
## Footnote
It involves analyzing the entire complement of RNA, proteins, or metabolites produced under certain conditions.
34
What is a transcriptome?
Entire complement of RNA produced under certain conditions
## Footnote
It is a key component in functional genomics.
35
What is the significance of Paenibacillus strain LC231?
Displays resistance to 14 classes of antibiotics
## Footnote
It has 10 ORFs encoding resistance to 7 different antibiotic types.
36
What technique was used to detect function in antibiotic resistance genes?
Heterologous expression in Escherichia coli
## Footnote
This method allowed for the identification of five new antibiotic-resistance genes.
37
What is the mobilome?
Mobile genetic elements that can spread resistance to other species
## Footnote
It plays a crucial role in horizontal gene transfer.
38
What does metagenomics analyze?
Pooled DNA or RNA from environmental samples containing unisolated or unidentified organisms
## Footnote
It provides insights into the total gene content of a microbial community.
39
What is a metagenome?
Total gene content of a microbial community
## Footnote
It encompasses all genetic material from the community.
40
What are gene chips?
Outdated technology for analyzing gene expression
## Footnote
RNA-Seq analysis has largely replaced gene chips.
41
What does RNA-Seq analysis involve?
Conversion of all RNA into cDNA, followed by sequencing
## Footnote
It reveals which genes are transcribed and quantifies mRNA copies.
42
What is the primary method of choice for global studies of gene expression?
RNA-Seq analysis
## Footnote
It is preferred over microarrays for its accuracy.
43
What is proteomics?
Genome-wide study of the structure, function, and activity of an organism's proteins
## Footnote
It provides insights into protein modifications and interactions.
44
What is the interactome?
The complete set of interactions among cellular macromolecules
## Footnote
Typically depicted as network diagrams representing proteins and their interactions.
45
What does metabolomics study?
The complete set of metabolic intermediates and small molecules produced by an organism
## Footnote
It reflects the activity of enzymatic pathways.
46
What is the main function of the cytoplasmic membrane?
Selective permeability
## Footnote
It regulates the transport of nutrients in and waste products out.
47
What are the two types of membrane proteins?
* Integral membrane proteins
* Peripheral membrane proteins
## Footnote
Integral proteins are embedded, while peripheral proteins are loosely attached.
48
How do archaeal phospholipids differ from those in Bacteria and Eukarya?
Contain ether linkages instead of ester linkages
## Footnote
Archaeal lipids may have isoprenoid chains.
49
What are the three mechanisms of transport for nutrients into the cell?
* Simple transport
* Group translocation
* ABC (ATP-binding cassette) systems
## Footnote
These mechanisms involve various energy sources for transport.
50
What is active transport?
Accumulation of solutes against their concentration gradient
## Footnote
It requires energy input, often from ATP or proton motive force.
51
What type of transport involves chemical modification of the substrate?
Group translocation
## Footnote
An example is the phosphorylation of glucose during transport.
52
What drives the transport processes in cells?
Proton motive force
## Footnote
Proton motive force is the force generated by the proton gradient across a membrane, used to drive various transport mechanisms.
53
What are the two types of transport mechanisms mentioned?
* Symport
* Antiport
## Footnote
Symport involves cotransport of solute and H⁺ in the same direction, while antiport involves transport in opposite directions.
54
What is group translocation?
Transported substance is chemically modified
## Footnote
This process is often driven by energy-rich organic compounds such as phosphoenolpyruvate.
55
What are ABC transporter systems composed of?
* Periplasmic binding proteins
* Transmembrane channel
* ATP-hydrolysing component
## Footnote
ABC transporters are crucial for the uptake of various substrates across cellular membranes.
56
What structural feature must the cell wall withstand?
Osmotic/turgor pressure
## Footnote
This is essential to prevent cell lysis and maintain cell integrity.
57
How are bacteria classified based on their cell wall structure?
* Gram-positive
* Gram-negative
## Footnote
This classification is based on the differences in cell wall thickness and composition.
58
What does the Gram-positive cell envelope consist of?
Cytoplasmic membrane and a thick cell wall
## Footnote
The thick cell wall provides structural support and protection.
59
What characterizes the Gram-negative cell envelope?
Cytoplasmic membrane, thin cell wall, outer membrane, and periplasm
## Footnote
The periplasm is the space between the cytoplasmic and outer membranes.
60
What is the result of a Gram stain for Gram-positive bacteria?
Retain crystal violet (appear purple)
## Footnote
This is due to the thick peptidoglycan layer in their cell wall.
61
What is peptidoglycan?
A rigid polysaccharide layer providing strength
## Footnote
It is found in all bacteria but is absent in Archaea and Eukarya.
62
What constitutes the sugar backbone of peptidoglycan?
* N-acetylglucosamine (GlcNAc)
* N-acetylmuramic acid (MurNAc)
## Footnote
These sugars are joined by β-1,4 linkages.
63
What type of bonds link the peptide side chains in peptidoglycan?
Cross-links
## Footnote
These cross-links provide structural integrity to the cell wall.
64
What is the function of the outer membrane in Gram-negative bacteria?
Facilitates surface recognition and acts as a virulence factor
## Footnote
It also adds strength to the cell envelope.
65
What does LPS stand for?
Lipopolysaccharide
## Footnote
LPS is a major component of the outer membrane of Gram-negative bacteria.
66
What are the components of LPS?
* Lipid A
* Core polysaccharide
* O-specific polysaccharide
## Footnote
These components contribute to the structural integrity and function of the outer membrane.
67
What is the role of porins in the outer membrane?
Facilitate the transport of solutes
## Footnote
Porins are transmembrane proteins that form channels in the membrane.
68
What is unique about the archaeal cell envelope compared to bacteria?
Generally lack peptidoglycan and typically lack an outer membrane
## Footnote
Most Archaea have an S-layer instead.
69
What is pseudomurein?
Similar to peptidoglycan but composed of N-acetylglucosamine and N-acetyltalosaminuronic acid
## Footnote
It is linked by β-1,3 glycosidic bonds and is resistant to lysozyme and penicillin.
70
What are S-layers?
Paracrystalline arrays of protein or glycoprotein
## Footnote
They provide strength and protection and are the outermost layer if present.
71
What are the functions of capsules and slime layers?
* Assist in attachment to surfaces
* Contribute to biofilm development
* Enhance infectivity
* Prevent dehydration
## Footnote
These structures are made of sticky polysaccharides and vary in their attachment to the cell envelope.
72
What are fimbriae?
Short pili that mediate attachment
## Footnote
They are produced by all Gram-negative and many Gram-positive bacteria.
73
What is the role of conjugative pili?
Facilitate genetic exchange between cells
## Footnote
This process is known as conjugation.
74
What are gas vesicles used for?
Provide buoyancy
## Footnote
They allow certain bacteria to maintain their position in water columns.
75
What are the main types of inclusions found in cells?
* Energy reserves
* Carbon reservoirs
* Phosphorus reservoirs
* Specialized structures
## Footnote
Inclusions are often enclosed by a thin protein membrane to reduce osmotic stress.
76
What are gas vesicles?
Buoyant structures composed of two proteins that provide buoyancy to bacteria
## Footnote
Gas vesicles help cyanobacteria float in aquatic environments.
77
What is the function of magnetosomes?
Enable bacteria to orient within magnetic fields (magnetotaxis)
## Footnote
Magnetosomes consist of biomineralized magnetic iron oxides.
78
Define endospores.
Specialized, highly differentiated, dormant cells that are resistant to extreme conditions
## Footnote
Endospores serve as survival structures during unfavorable growth conditions.
79
What triggers endospore formation (sporulation)?
Nutrient limitation
## Footnote
Sporulation involves differentiation into a heat-resistant endospore.
80
Name the three steps involved in the germination process of endospores.
Activation, germination, and outgrowth
## Footnote
These steps convert dormant endospores back into vegetative cells.
81
What is the structure of a bacterial endospore?
Core, inner membrane, cortex, outer membrane, endospore coat, exosporium
## Footnote
The core contains small acid-soluble spore proteins (SASPs) that protect DNA.
82
What are the main components of a flagellum in Gram-negative bacteria?
Filament, hook, basal body (L, P, MS, C rings)
## Footnote
The basal body is embedded in the cell envelope and drives flagellar rotation.
83
True or False: Archaella are similar to bacterial flagella.
False
## Footnote
Archaella are protein structures more closely related to type IV pili and differ in composition and motility.
84
What is twitching motility?
Movement that requires type IV pili, where pili extend, attach to a surface, and retract to pull the cell forward
## Footnote
Twitching is slower than swimming and is seen in bacteria like Pseudomonas.
85
What is the difference between chemotaxis and phototaxis?
Chemotaxis: response to chemicals; Phototaxis: response to light
## Footnote
Both types of taxis direct movement to enhance resource acquisition or avoid harm.
86
What is the 'run and tumble' behaviour in bacteria?
Smooth forward motion followed by chaotic reorientation
## Footnote
This behaviour is used in chemotaxis to navigate toward attractants.
87
Fill in the blank: Endospores can remain dormant for _______ and convert rapidly back to vegetative cells when nutrients become available.
years
## Footnote
This characteristic allows endospores to survive in harsh conditions.
88
What are the two main types of motility in bacteria?
Swimming and surface motility
## Footnote
Surface motility includes twitching and gliding, which are typically slower than swimming.
89
What is the unique feature of archaella compared to bacterial flagella?
Smaller diameter and powered by ATP hydrolysis instead of the proton motive force
## Footnote
Archaella are not hollow and have fewer motor proteins.
90
Describe the structure of a bacterial flagellum.
Rigid, helical structure composed of flagellin, with a hook and basal body
## Footnote
The basal body is embedded in the cell envelope and is crucial for motility.
91
What is chemotaxis?
Movement of organisms in response to chemical stimuli
## Footnote
Chemotaxis can involve attraction to or repulsion from chemicals.
92
How do bacteria respond in the absence of an attractant?
Cells alternate between runs and tumbles, resulting in random swimming
93
What occurs in the presence of an attractant during chemotaxis?
Runs become biased towards the attractant gradient
94
What is the difference in behavior between polarly flagellated bacteria and peritrichously flagellated bacteria?
Polarly flagellated bacteria can swim backward by reversing flagellar rotation, while peritrichously flagellated bacteria tumble.
95
What is osmotaxis?
Response to ionic strength
96
What is hydrotaxis?
Response to water
97
What is aerotaxis?
Response to oxygen
98
What is phototaxis?
Response to light
99
What is scotophobotaxis?
Absence of light causes a cell to tumble and reorient towards light via biased random walk
100
What organelles are found in eukaryotic cells?
* Nucleus
* Mitochondria
* Golgi complex
* Lysosomes
* Endoplasmic reticula
* Microtubules
* Microfilaments
* Chloroplasts (in phototrophic eukaryotes)
101
What is the function of the nucleolus?
Site of ribosomal RNA synthesis
102
What is mitosis?
Nuclear division resulting in two diploid daughter cells
103
What is meiosis?
Specialized division converting diploid cells to haploid gametes
104
What occurs during the metaphase stage of mitosis?
Chromosomes align at the cell center
105
What is the role of mitochondria in eukaryotic cells?
Responsible for respiration and oxidative phosphorylation
106
What is the structure of mitochondria?
Enclosed by two membranes with inner membrane folds (cristae)
107
What is the function of chloroplasts?
Site of photosynthesis in phototrophic eukaryotes
108
What is the endosymbiotic origin of mitochondria and chloroplasts?
They descended from respiratory and phototrophic bacteria, respectively
109
What are microtubules?
Hollow tubes composed of α- and β-tubulin that maintain cell shape and facilitate motility
110
What are microfilaments?
Thin filaments composed of actin that support cell shape and motility
111
What is the function of the rough endoplasmic reticulum?
Studded with ribosomes; synthesizes glycoproteins and new membrane material
112
What is the role of lysosomes?
Contain digestive enzymes for recycling cellular components
113
What characterizes eukaryotic flagella?
Long, whip-like appendages with a '9+2' microtubule arrangement
114
What is the hypothesized origin of eukaryotes?
Symbiotic fusion between an archaeal host and a mitochondrial endosymbiont
