Micro Exam 2 Flashcards
(177 cards)
1
Q
Small, circular chromosome, DNA organized in the cytoplasm
A
Bacterial Genome
2
Q
Larger, linear chromosomes, DNA stored in nucleus
A
Eukaryotic Genome
3
Q
What type of genome has more non-coding regions that must be excised?
A
Eukaryotic Genome
4
Q
Non-coding regions(not expressed)
A
Introns
5
Q
Coding regions(expressed)
A
Exons
6
Q
Can have chromosomes replicate and segregate during cell growth
A
Bacterial Genome
7
Q
Transferring DNA from parent cells to daughter cells
A
Vertical Gene Transfer
8
Q
Happens before cellular division
A
DNA replication
9
Q
Unwinds the double helix, forming a replication fork on both sides
A
DNA helicase
10
Q
Needs a DNA template and a primer. Synthesizes 5’ to 3’
A
DNA Polymerase
11
Q
Unwind the helix, add RNA primer, load enzyme for synthesis
A
Initiation
12
Q
Add in dNTP, release pyrophosphate, form a phosphodiester linkage
A
Elongation
13
Q
Occurs at Ter sites, replication is complete
A
Termination
14
Q
Continuous portion of the DNA
A
Leading strand
15
Q
Discontinuous portion of the DNA
A
Lagging strand
16
Q
Fork and replication are moving in the SAME direction
A
Leading strand
17
Q
Fork and replication are moving in the OPPOSITE direction
A
Lagging strand
18
Q
Order of strands from top to bottom
A
Coding (non-template strand)
Non-coding strand (template strand)
mRNA
19
Q
What strand is the mRNA complementary to?
A
Non-coding template strand
20
Q
Synthesizes short RNA strands (primers) that are complementary to template strand
A
Primase
21
Q
Joins Okazaki fragment
A
DNA Ligase
22
Q
Synthesizes RNA only in the 5’ to 3’ direction, needs DNA template, adds RNA bases
A
RNA polymerase
23
Q
Part of RNA polymerase, recognizes promoter and bind the DNA, prokaryotes only
A
Sigma factors
24
Q
Help turn specific genes on or off to slow down or speed up transcription via proteins, eukaryotic only
A
Transcription factors
25
Enzyme that catalyzes the peptide bond formation between amino acids, lines up with tRNA
Ribosomes
26
RNA consists of folded molecules which transport amino acids from the cytoplasm of the cell to a ribosome
tRNA
27
Molecule in cells that forms part of the protein-synthesizing organelle known as ribosome and that is exported to the cytoplasm to help translate mRNA into protein
rRNA
28
Sites in genomes where RNAP binds (starts)
Promoters
29
Sites where RNAP is released (ends)
Terminators
30
A collection of adjacent genes that are all transcribed into a single RNA and under the control of a single promoter
Operon
31
3 things Eukaryotes do post-transcriptional processing
-Add 5' cap
-Add ply A tail at the 3' end
-Splicing
32
Introns are removed before translation via this process
Splicing
33
What is on the anticodon?
tRNA
34
What is on the codon?
mRNA
35
Does the codon or anticodon have the amino acid codes?
Codon
36
Type of genome where transcription and translation are NOT in separate compartments, meaning translation can begin before mRNA is fully made
Bacterial genome
37
Type of genome where the ribosome recognizes the 5' cap structure and finds the AUG codon from there
Eukaryotic genome
38
The process used to control the timing, location, and amount in which genes are expressed
Gene regulation
39
Some microbes change or invert the DNA sequence to activate or disable a particular gene
Phase variation
40
Gene expression can be turned on or off via
DNA-binding proteins
41
Whether a regulatory protein can bind the DNA is often determined by the presence or absence of a...
Ligand
42
Example of DNA-binding proteins that regulate transcription
Repressor blocks transcription when bound to DNA but only when Fe2+ is available to help it bind OR activator promotes transcription when bound to DNA but only when the quorum-sensing signal is available to help it bind
43
Different sigma factors recognize different promoters, which express different genes
Alternate sigma factors
44
Two component system for sensing the environment
Sensor protein and response regulator
45
Membrane-bound, often a kinase (transfers phosphate)
Sensor protein
46
Activated by the sensor protein and regulates gene expression
Response regulator
47
2 Examples of the two component systems
-Quorum sensing
-Vancomycin resistance
48
Sensing signals (autoinducers) Chemical signaling molecules produced by bacteria to sense population density. As cells sense autoinducers, expression of the autoinducers increases (amplifies signal)
Quorum sensing
49
A heritable change in the DNA sequence
Mutation
50
Mutations due to normal cell processes, random and infrequent
Spontaneous mutation
51
Mutations where external factor (mutagen) increases the mutation rate (chemicals or radiation)
Induced mutation
52
Cell receives new DNA
Horizontal gene transfer
53
When do proofreading and mismatch repair occur?
During or right after DNA replication
54
This activity removes the most recent base if incorrect (proofreading)
3'-5' exonuclease
55
Two enzymes spot a mismatch, and another one finds the correct strand and cuts it all out. Missing nucleotides are replaced by DNA polymerase (small amount is removed)
Mismatch repair
56
Altered to a stop codon
Nonsense
57
One or more amino acids are changed
Missense
58
Damaged base is recognized and removed via DNA glycosylases, missing bases are replaced by DNA polymerase and ligase seals the nicks (large amount is removed)
Base excision repair
59
What enzyme makes base substitution errors?
Polymerases
60
Typical phenotype of strains isolated in nature
Wild type
61
"jumping genes" very large addition mutations that will likely knock out a gene
Transposons
62
Gene product is inactivated (missense or nonsense)
Null mutation/knock-out mutation
63
3 factors that determine whether a mutation becomes the predominant genotype in a population
-Environment
-Selective pressure
-Natural selection
64
One mechanism of change and vertical evolution
Mutations
65
In order for HGT to be passed vertically to daughter cells it must become part of the cell's genome via:
Have its own origin of replication OR be recombined or integrated into existing genome
66
Process of importing naked (free) DNA into bacteria
Transformation
67
The physiological state that allows cells to take up naked DNA via transformation
Competency
68
Forced competency
Chemical competent/heat shock or electric shock
69
Reasons for transformation:
Using DNA as food source
Take up similar DNA to fix mistakes
Obtain new genes from other bacteria (increase genetic diversity)
70
Are one or two DNA strands imported after transformation?
One DNA strand
71
Where does the DNA come from for transformation?
Dead cells
72
Mediated by direct contact between 2 cells
Conjugation
73
How does DNA get transferred to the other cell in conjugation?
Donor cell sends DNA through tube to recipient cells via plasmid (common) or chromosomal (rare) transfer
74
DNA sequence that contains the genes needed to facilitate conjugation
F (fertility) factor
75
Genotype strain containing the F factor for the donor cell
F+
76
Genotype strain containing the F factor for the recipient cell
F-
77
DNA sequence on the F factor that is cut (just one strand) in conjugation
oriT
78
What is the one strand of DNA helix that is transferred to the recipient cell in conjugation?
ssDNA
79
What is the result of conjugation in the two cells?
Both cells are F+ (donor DNA) cells
80
The structures that bring the donor in contact with the recipient and the bridge the DNA goes across (sex plus and bridge)
Mating pair formation (MPF)
81
Features of the genome and genes that help initiate transfer and replication of the F factor (oriT, nicking enzyme)
DNA transfer and replication (Dtr)
82
Genotype of strain containing the F factor in its chromosome Donor cell (rare) and recipient remains F- (does not receive full F factor)
Hfr
83
Virus mediated horizontal gene transfer (phage), infection cycle by virus can transfer DNA from one bacterial cell to another
Transduction
84
Phage accidentally adds bacterial DNA when packaging its genome into the protein capsid (packing mistake)
Generalized transduction
85
The phage genome gets into cell, initially integrates into a specific DNA sequence in the host genome (prophage). When excised out, phage DNA and some bacterial DNA is cut out, copied, and packaged. (Excision mistake)
Specialized transduction, ends up with a chunk of phage genome in the cell
86
Phage capsid (shell) filled with bacterial DNA
Transducing particle
87
What did Griffith experiment conclude?
That the genes that dictate how organisms develop are made up of DNA, not protein, RNA, lipids, etc.
88
What is needed for a bacterial cell to replicate and pass on newly acquired DNA from HGT to its daughter cells?
Donor DNA (single or double) and RecA to crossover
89
Process by which DNA is incorporated into the recipient cell's genome
Recombination
90
Requires that the two recombining molecules have long stretches of sequence homology/similarity
Generalized (homologous) Recombination
91
Short DNA sequence recognized by a special recombination enzyme
Site-specific Recombination
92
Bacterial protein that facilitates recombination
RecA
93
Those compounds a microbe cannot make itself but must gather from its immediate environment if the cell is to grow and divide
Essential nutrients
94
Obtain compounds from other organisms, use carbon
Heterotrophs
95
Make their own carbon compounds (CO2) via TSA cycle
Autotrophs
96
Rock eaters
Chemolithotrophs
97
Most chemolithotrophs are also...
Autotrophs
98
Light absorption and electron transfer
Photolysis
99
Why do plants need water for photosynthesis?
They use water and CO2 to release O2 as a byproduct
100
Uses an ETC, PMF, chemiosmosis, ATP Synthase to generate ATP energy
Photophosphorylation
101
Some bacteria can convert N2 gas to ammonium ions, which can be used for biosynthesis. Necessary for all life
Nitrogen fixation
102
Other bacteria transform ammonia to nitrate
Nitrificaiton
103
Other bacteria convert nitrate back to N2
Denitrification
104
No enzymes to detoxify ROS, must have NO O2
Obligate anaerobe
105
SOD + catalase, must have O2
Obligate aerobe
106
Low levels of SOD + catalase, prefer lower O2
Microaerophile
107
SOD + catalase, prefers O2, but has the option to grow without it
Facultative anaerobe
108
SOD, does not use O2, but can tolerate it
Aerotolerant anaerobe
109
Superoxide dismutase (SOD)
Breaks down oxygen radicals
110
Catalase
Enzymes that break down H2O2
111
Some microbes require growth factors that must be added to culture media before they will grow
Fastidious/auxotroph
112
Media where all the chemical components are known
Chemically defined media
113
Media where there are dead things in it
Complex media
114
Normal physiologic conditions
20-40C
Near-neutral pH
Salt concentration of 0.9%
Ample nutrients
115
-Above 80C
-pH above 9
-High salt
-Strict aerobe
-High pressure
Hyperthermophile
116
-50-80C
-pH 5-8
-High salt
-Facultative anaerobe
High pressure
Thermophile
117
-15-45C
-pH below 3
-High salt
-Microaerophile
-Barotolerant
Mesophile
118
-Below 15C
-pH below 3
-High salt
-Strict anaerobe
-Barotolerant
Psychrophile
119
Require elevated pressure to grow
Barophiles
120
Grow at elevated pressures to an extent (10-500atm)
Barotolerant
121
Can grow at mildly acidic pH, but do not thrive at very low pH
Acid tolerant microbes
122
pH adaptations
Maintain a neutral pH by pumping protons out of or into cell
123
Microbes that require high salt [ ]
Halophiles
124
Microbes that can deal with higher salt [ ] but not extreme
Halotolerant
125
The amount of time it takes for bacteria to double in size
Generation/doubling time
126
Parent cell divides into 2 daughter cells
Binary fission
127
Exponential growth
2-4-8-16-32-64...
128
Eukaryotic cellular division
Mitosis
129
Bacteria cellular division
Binary fission
130
Septum forms and cell divides
Septation
131
Bacteria are preparing their cell machinery for growth
Lag phase
132
Growth approximates an exponential curve
Log phase
133
Cells stop growing and shut down their growth machinery while turning on stress responses to help retain viability
Stationary phase
134
Cells begin to die at an exponential rate
Death Phase
135
Metabolites produced during active growth and metabolism
Primary metabolites
136
Metabolites not essential for rapid growth; often made for defense or survival (antibiotics or toxins)
Secondary metabolites
137
Direct methods of measuring cell growth
-Microscope count
-Cell-counting instruments
138
Indirect methods of measuring cell growth
-Measuring biomass
-Serial dilution
-Filtration
-Metabolic activity
139
Mass of bacteria that stick to and multiply on a surface
Biofilm
140
Free living cells in suspension
Planktonic
141
How do biofilms form?
Microcolonies form and cells secrete extracellular polymeric substances (EPS). Cells communicate via quorum sensing. Increase QS = # of cells increasing
142
Percent of infections that are in biofilm
70%
143
Purpose of biofilm
Protection, very resistant to antibiotics, facilitates movement of nutrients and wastes
144
Gram + bacteria producing a differentiated cell. Clostridium and bacillus
Endospore
145
Process cued by environmental conditions (starvation) to form endospores
Sporulation
146
Process where endospore returns to vegetative (normal) growth
Germination
147
2 guys who discovered endospores
Tyndall and Cohn
148
A complete virus particle
virion
149
Viruses that infect bacteria
phage
150
Goal of viruses
Direct host cell to express viral genes and proteins
151
Viruses finding new cells to infect via...
Transmission
152
Each virus species infects a particular group of host species
Host range
153
The range of tissue types a virus can infect
Tissue tropism
154
Viral components
-Nucleic acid
-Protein capsid/shell
-SOME have lipid bilayer envelope
155
-Nucleocapsid only
-More resistant to disinfectants
Naked viruses
156
-Nucleocapsid enclosed in lipid bilayer (from host)
-Contents between envelope and capsid
Enveloped viruses
157
Contents (proteins) that may be between the envelope and the capsid
Tegument
158
3 methods of viral attachment
-Spike proteins
-Tail fibers
-Fiber proteins
159
Radial symmetry, based on icosahedron
Icosahedral capsid
160
Helical capsid tube around the genome, generating a flexible filament
Helical/filamentous capsids
161
No symmetrical form, core wall contains genetic material
Complex/amorphous
162
Icosahedral head with genetic info with tail and tail fibers
Complex-tailed bacteriophages
163
Primary characteristic used to classify viruses
Genome
164
Secondary characteristics used to classify viruses
Envelope and shape
165
General scheme to viral replication
-Host recognition and attachment
-Genome entry
-Biosynthesis
-Assembly/maturation
-Release and transmission
166
Viruses quickly take over the host cell, make many copies, break the cell, and infect other cells
Lytic (productive)
167
Viruses sneak into the host's DNA, stay hidden, and wait. Later the can become active (switch to productive) and make copies and infect other cells
Lysogenic
168
Clearing on a lawn of bacteria on an agar plate
Plaque
169
NOT lytic. They don't directly kill the host. Often use host pili structure to exit
Filamentous phage
170
A phage genome that has integrated into the host genome
Prophage
171
Have the option to go latent in a pathway
Lysogen
172
Prophage genes can give the host new properties (new phenotype) even in the lysogenic state
Lysogenic conversion
173
Transduction that can happen if a mispackaging event happens, complex phage assembly is a complicated, step-by-step process
Generalized transduction
174
Transduction that happens when infection switches to the lytic pathway (end of lysogenic) and the prophage is excised out
Specialized transduction
175
Virus-host attachment triggers endoscope formation, might fuse with lysosome
Endocytosis
176
Envelope fuses with host plasma membrane
Fusion
177
Once in the host, capsid breaks down to release the genome
Uncoating
