Unit 2 Flashcards
(113 cards)
1
Q
Cardinal conditions
A
the minimum, maximum and optimum growth conditions for an organism
2
Q
Optimum growth rates for:
A
Psychrophiles (≤ 15°C)
Mesophiles (20-45°C)
Thermophiles (45-80°C)
Hyperthermophiles (>80°C)
3
Q
Boiling water (100):
A
It kills vegetative cells and viruses but not endospores
4
Q
Autoclaving (121):
A
It kills vegetative cells, viruses, and bacterial endospores
5
Q
Dry heat sterilization
A
Like oven drying - requires a long time to kill endospores and is used for objects (e.g., glass petri plates)
6
Q
Flash pasteurization:
A
71°C for 15 sec, then rapid cooling. Used to reduce microbial numbers without altering flavor (milk, wine, beer); lengthens shelf life
7
Q
UHT (ultrahigh temperature) pasteurization
A
135°C for 1-2 sec, which is used to sterilize milk to enable storage at room temperature
8
Q
What is acidity used for?
A
Food preservation like canned tomatoes or salsa
9
Q
What are alkaline solutions used for?
A
Disinfection like bleach
10
Q
What is oxygens readily form
A
Reactive oxygen species (ROS)
11
Q
Ultraviolet (UV) radiation (220-300 nm)
A
It kills by damaging DNA (causes breaks) but is poor at penetrating many materials, such as glass and plastic
12
Q
Ionizing radiation (e.g., X-rays and gamma rays)
A
It has higher energy than UV radiation, so it penetrates materials well - used for sterilizing antibiotics, surgical supplies, food, plastic supplies, etc
13
Q
What are the five ways to control the growth of organisms?
A
Heat, pH, filtration, ionizing radiation, UV radiation
14
Q
Chemical antimicrobial agents
A
Chemicals that kill or inhibit the growth of microorganisms
15
Q
Disinfectants
A
Kill microbes on surfaces but do not sterilize them (e.g., detergents)
15
Q
Sterilization
A
Complete killing or removal of all organisms
15
Q
Antibiotics
A
Antimicrobial agents that are produced naturally by certain microorganisms - in addition to natural antibiotics, many other drugs are produced synthetically
15
Q
Cidal agents
A
Agents that kill microbes
16
Q
Lytic agent
A
Kill bacteria by lysing them
17
Q
Static agents
A
Agents that inhibit pathogen growth
18
Q
Minimum inhibitory concentration (MIC)
A
The lowest concentration of a chemical that
prevents the of growth of a specific microorganism
19
Q
Selective toxicity
A
The ability to kill or inhibit the growth of a pathogen while damaging the host as little as possible.
20
Q
What are the major causes of antibiotic resistance
A
Antibiotics are used as an additive to animal feed; antibiotics are overprescribed, antibiotics are improperly used
21
Q
Virion
A
The form of a virus that occurs extracellularly (outside a host cell) - allows the virus to travel from one host cell to another
22
Nucleic acid
Either RNA or DNA but not both
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Capsid (coat)
Protein shell surrounding the genome of a virus particle
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Nucleocapsid
Nucleic acid + capsid
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Envelope
A phospholipid bilayer membrane (from the host cell) is present in some viruses surrounding the capsid.
26
Virus
- A genetic element that can multiply only inside a living cell - have their own genome
- Particle composed of a protein capsid surrounding single-stranded DNA
27
Lytic pathway
Viral infection that leads to the virus replication and destruction of the host cell
28
Bacteriophages (phages)
Bacterial viruses
29
Capsomeres
Subunit of a virus capsid - composed of individual protein molecules that are often arranged in a highly repetitive pattern around the nucleic acid.
30
What are the two primary viral shapes?
Rod - has helical symmetry
Spherical: has icosahedral symmetry
31
Titer
A viral suspension that can be quantified to estimate the number of infectious virions present per volume of fluid.
32
Viral replication cycle steps
1. Attachment of the virion to the host cell
2. Penetration of the virion nucleic acid into the host cell
3. Synthesis of virus nucleic acid and protein by host cell
4. Assembly of capsids and packaging of viral genomes into new virions
5. Release of new virions from the cell and cell lysis
33
Plasmids
Circular or linear double-stranded DNA molecules that replicate independently from the chromosome - they are not essential for survival but often carry beneficial genes for functions like antibiotic resistance or special metabolic abilities
34
How is penetration different in animal viruses as compared to bacterial viruses?
The entire viral particle can penetrate an animal cell, while only the viral genome can penetrate a bacterial cell.
35
The Baltimore scheme used to classify viruses is based on ________.
The relationship of the viral genome to its mRNA
36
Viruses with a genome containing __________ primarily infect prokaryotic cells.
double-stranded DNA
37
Viroids are __________.
infectious RNA molecules that lack a protein component that are only in plants
38
Halophiles
The cell requires NaCl for growth
39
Halotolerant
Organisms can tolerate some level of NaCl but grow best in the absence of it
40
Osmophiles
Organisms able to live in environments high in sugar
41
Water activity
Measures of the degree of water availability
42
Quinolones
Synthetic antibacterial compounds disrupt bacterial metabolism preventing the supercoiling and packaging of DNA in the bacterial cell
43
3 ways cells can become antibiotic-resistant
1. modification of the drug target
2. formation of a biofilm
3. introduction of a resistance gene
44
Why is oxygen toxic to some organisms? Why are some anaerobes able to tolerate the presence of oxygen and others are not?
Oxygen is toxic to some organisms because it creates harmful molecules that damage cells. Some anaerobes can't protect themselves from these molecules, while others can because they have certain enzymes that break them down.
45
Describe several ways in which a virus is like a bacterium and several ways in which it differs from a bacterium.
- Viruses and bacteria cause infections and contain genetic material
- Bacteria are living organisms that can reproduce independently, while viruses are non-living and need a host to multiply. Bacteria have cellular structures like cell walls and ribosomes, but viruses lack these
46
How do you reduce antibiotic resistance?
- Taking a high concentration of an antibiotic
- Completing the antibiotic treatment program
- Using a narrow- rather than broad-spectrum antibiotic
47
Virulent virus
Viruses that lyses or kill the host cell
48
Temperate virus
Viruses that infect their host and establish a long-term stable relationship and don't cause host cell death
49
What are ways cells protect themselves from viruses
1. phage inclusion: enzymes modify viral DNA
2. Abortive infection: cell commits suicide
3. CRISPR: Cas system recognizes foreign DNA and degrades it
50
CSISPR
Functions to seek out and destroy foreign nucleic acid
- recognizes foreign DNA sequences that have previously entered the cell and directs the Cas proteins to destroy them
- DNA regions with repeated DNA sequences that are interspersed with short DNA sequences (“spacers”) acquired from infecting phages
50
Some bacteriophage possess an enzyme similar to ________, which makes a small hole in the bacterial cell wall, allowing the viral nucleic acid to enter.
Lysozyme
50
What is unusual about genetic information flow in retroviruses?
Their RNA genome is reverse-transcribed into DNA by the enzyme reverse transcriptase.
50
Retroviruses
Have single-stranded RNA but must turn it into DNA first using an enzyme called reverse transcriptase before making mRNA (only in animals)
51
Prions
Infectious agents whose extracellular form consists entirely of protein - only in animals
52
How does a prion differ from a viroid?
A prion is an infectious protein, while a viroid is an infectious RNA molecule. Viroids are composed of circular RNA and infect plants, whereas prions are protein-based and primarily affect animals
53
How does a prion differ from a virus?
A virus contains either DNA or RNA as genetic material. Viruses rely on their nucleic acid to replicate whereas prions propagate solely by protein misfolding.
54
What is the difference between a persistent and a latent viral infection?
In a persistent infection, the virus replicates within the host over an extended period without causing immediate cell death. In a latent infection, the virus integrates its genetic material into the host genome as a provirus and remains dormant
55
Early and late viral proteins are classified according to their relative...
Time of synthesis following host infection.
56
What do accessory proteins do?
Some help entry into or release from host cells
- Lysozyme: make holes in peptidoglycan
- Spike Proteins: enzyme breaks down connective tissue
57
Plaque
Zone of clearing that results from cell lysis - on agar
58
Most bacterial viruses are ssDNA or dsDNA?
dsDNA
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Early gene encode...
Proteins that promote phage genome replication
60
Lysogenic life cycle
Bacteriophages infect the genome and are replicated with the host chromosome
61
Prophage
A phage that is integrated into the host’s genome
62
Explain the three periods on the one-step growth curve of viral replication.
Eclipse period – period during which no infective virions are released
Rise period or maturation phase– period when infective virion numbers are increasing
Latent period: the shortest time necessary for viral reproduction
63
Transformation
Virus transforms host cells into tumor cells (e.g., HPV)
64
What is the central dogma of molecular biology?
The central dogma explains the flow of genetic information in cells:
1. Replication – DNA is duplicated.
2. Transcription – DNA’s information is copied into RNA.
3. Translation – mRNA is used to make proteins.
65
Define the terms complementary and antiparallel as they pertain to DNA?
Complementary: The way DNA bases pair up. Adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C).
Antiparallel: The two strands of DNA run in opposite directions. One strand runs from 5' to 3', and the other runs from 3' to 5'
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Operons
Clusters of genes that function together in specific pathways
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Transposable elements
Pieces of DNA that can move around the genome - are found in both prokaryotes and eukaryotes and can insert themselves into chromosomes, plasmids, or virus genomes. This movement of DNA contributes to genetic variation
68
R plasmids
Carry genes that provide resistance to antibiotics or other growth inhibitors - encode proteins that inactivate antibiotics or protect the bacterial cell in other ways
69
How large is the Escherichia coli genome in base pairs? How many genes does it contain?
4.6 million base pairs with 4,288 genes
70
Semiconservative Replication
Each new DNA double helix consists of one parental strand and one newly synthesized strand.
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DNA Polymerization
- DNA polymerases catalyze the addition of nucleotides to the growing DNA strand, requiring a free 3'-OH group on the DNA.
- The process always moves in the 5' to 3' direction, adding new nucleotides to the 3' end of the growing chain
72
Initiation of Replication
- The enzyme helicase unwinds the DNA double helix at the origin of replication
- When starting a new book, you first open the book (DNA helicase unwinds the helix), and then you start reading from the first page (primase creates a starting point or primer). Only then can the real reading (DNA replication) begin.
73
Leading and Lagging Strands
- Leading strand: Synthesized continuously in the 5' to 3' direction, with only one primer needed.
- Lagging strand: Synthesized discontinuously in short segments (Okazaki fragments), each needing its own RNA primer.
74
Do translation and transcription co-occur in prokaryotes or eukaryotes? Why is this beneficial
Prokaryotes - allows for rapid changes in gene expression and protein production and allows bacteria to grow rapidly and respond rapidly to changes in their environment
75
What are the two ways plasmids may replicate by
- Bidirectional Replication: within the cell
- Rolling Circle Replication: being transferred to new cell
75
What are the steps in transcription?
1. Initiation: RNA polymerase binds to the promoter
2. Elongation: RNA polymerase moves along the DNA, adding ribonucleotides to the growing RNA chain
3. Termination: Transcription stops when RNA polymerase encounters a termination signal.
76
Promotor
Sites on the DNA that RNA binds to for transcription to occur - sigma factor is responsible for recognizing the promoter
77
What is the role of messenger RNA (mRNA)? What are the other two classes of RNA?
A type of RNA that carries the genetic code from DNA to the ribosomes, where it serves as a template for protein synthesis.
- Ribosomal RNA (rRNA): This type forms the core structure of ribosomes
- Transfer RNA (tRNA): Brings the appropriate amino acids to the ribosome during protein synthesis
78
Polycistronic mRNA
A single RNA molecule that encodes multiple proteins - In bacteria, genes with related functions are grouped together in an operon and transcribed together as polycistronic mRNA, allowing for coordinated regulation of several genes at once
79
What type of structures lead to transcription termination in bacteria
- Stem-loop structures
- Rho-dependent termination
80
What three major components make up an archaeal promoter?
1. TATA Box:
2. B Recognition Element (BRE):
3. Initiator Element (INIT):
81
What steps take place in the processing of eukaryotic RNA?
1. Capping: A methylated guanine nucleotide is added to the 5’ end of the mRNA to protect it and facilitate translation initiation.
2. Splicing: Introns are removed, and exons are joined together.
3. Polyadenylation: The poly(A) tail, is added to the 3’ end of the mRNA. This stabilizes the mRNA and protects it from degradation.
82
What are start codons and stop codons?
- Start Codons: Signals the beginning of translation. The ribosome recognizes this codon to initiate protein synthesis.
- Stop Codons: Signals the termination of translation. The three stop codons are UAA, UAG, and UGA. When ribosomes encounter any of these codons, they release the newly synthesized polypeptide chain, ending the process.
83
Why is it essential for the ribosome to read “in frame”?
Ensure the sequence of codons corresponds to the intended sequence of amino acids.
84
What is codon bias?
Certain codons are used more than others for a given amino acid in the mRNA sequences.
85
Protein domain
A specific part of a protein that has a distinct structure and function. Helps a protein do many things at once
86
What is a transcription factor, and what are the two major types?
Proteins that control the rate of gene transcription by binding to specific DNA sequences
- activator proteins
- repressor proteins
87
What role do effectors have on transcription factors?
Effectors are small molecules that bind to transcription factors, altering their shape and enabling or preventing them from binding to DNA.
Inducers turn on transcription by helping activators.
Corepressors turn off transcription by helping repressors.
88
Enzyme Induction
It occurs when enzymes are produced only when their substrates (compounds they act on) are present.
89
Enzyme Repression
Occurs when the presence of a product, such as an amino acid, inhibits the production of enzymes responsible for synthesizing that product.
90
Regulon
A collection of operons regulated by the same regulatory protein allows for coordinated expression across multiple genes.
91
Two-Component Regulatory Systems
Components:
- Sensor Kinase: located in the cytoplasmic membrane, detects environmental signals and undergoes autophosphorylation at a specific histidine residue.
- Response Regulator: Typically a DNA-binding protein located in the cytoplasm. It can act as an activator or repressor of transcription. Regulates gene expression in response to the signal detected by the sensor kinase.
92
The two-component system relies on what initiates the response
phosphorylation
93
What does the two-component system use to reset
dephosphorylation
94
Quorum sensing
A regulatory mechanism that enables bacterial and archaeal populations to communicate and coordinate group behaviors based on their population density.
95
Distinguish between a mutation and a mutant.
A mutation is a change in the nucleotide sequence of the genome. A mutant is an organism (or virus) with a mutation in its genome.
96
Distinguish between screening and selection.
Screening is a process used to identify mutants that do not have a readily selectable advantage. Selection involves growing organisms under conditions where only mutants with a specific advantageous trait can survive, making the desired mutant easy to identify.
97
Auxotroph
An auxotroph is a mutant organism that has lost the ability to synthesize a particular compound (such as an amino acid) necessary for its growth. It requires that the compound be supplied in the growth medium.
98
Prototroph
A wild-type organism or strain that can synthesize all the compounds needed for its growth from basic nutrients.
99
Which protein in virtually all cells facilitates the pairing required for homologous recombination?
RecA protein
100
What is a merodiploid, and what is genetic complementation?
Merodiploid is a bacterial strain carrying two copies of a chromosomal segment. Genetic complementation occurs when a wild-type copy of a gene is introduced into a mutant strain, restoring the wild-type phenotype.
101
Competent
Cells that are able to take up DNA by
transformation
102
During natural competence, what cellular structure is used to bind DNA and take it to the cytoplasmic membrane?
Pili
103
Transduction
Mechanism of horizontal gene transfer in bacteria where there's transfer of bacterial DNA by viruses
- Generalized: is more random and less efficient in gene transfer - initiated during lytic cycle
- Specialized is more targeted but limited to specific regions of the genome - initiated during the lysogenic cycle
104
Homologous recombination
The process in which related DNA sequences from two different sources are exchanged
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Conjugation
The transfer of DNA with cell-to-cell contact
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Transformation
The uptake of free DNA from the environment
