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Year 3 > Micro Exam 2 > Flashcards

Micro Exam 2 Flashcards

1
Q

Small, circular chromosome, DNA organized in the cytoplasm

A

Bacterial Genome

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2
Q

Larger, linear chromosomes, DNA stored in nucleus

A

Eukaryotic Genome

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3
Q

What type of genome has more non-coding regions that must be excised?

A

Eukaryotic Genome

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4
Q

Non-coding regions(not expressed)

A

Introns

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5
Q

Coding regions(expressed)

A

Exons

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6
Q

Can have chromosomes replicate and segregate during cell growth

A

Bacterial Genome

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7
Q

Transferring DNA from parent cells to daughter cells

A

Vertical Gene Transfer

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8
Q

Happens before cellular division

A

DNA replication

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9
Q

Unwinds the double helix, forming a replication fork on both sides

A

DNA helicase

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10
Q

Needs a DNA template and a primer. Synthesizes 5’ to 3’

A

DNA Polymerase

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11
Q

Unwind the helix, add RNA primer, load enzyme for synthesis

A

Initiation

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12
Q

Add in dNTP, release pyrophosphate, form a phosphodiester linkage

A

Elongation

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13
Q

Occurs at Ter sites, replication is complete

A

Termination

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14
Q

Continuous portion of the DNA

A

Leading strand

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15
Q

Discontinuous portion of the DNA

A

Lagging strand

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16
Q

Fork and replication are moving in the SAME direction

A

Leading strand

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17
Q

Fork and replication are moving in the OPPOSITE direction

A

Lagging strand

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18
Q

Order of strands from top to bottom

A

Coding (non-template strand)
Non-coding strand (template strand)
mRNA

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19
Q

What strand is the mRNA complementary to?

A

Non-coding template strand

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20
Q

Synthesizes short RNA strands (primers) that are complementary to template strand

A

Primase

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21
Q

Joins Okazaki fragment

A

DNA Ligase

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22
Q

Synthesizes RNA only in the 5’ to 3’ direction, needs DNA template, adds RNA bases

A

RNA polymerase

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23
Q

Part of RNA polymerase, recognizes promoter and bind the DNA, prokaryotes only

A

Sigma factors

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24
Q

Help turn specific genes on or off to slow down or speed up transcription via proteins, eukaryotic only

A

Transcription factors

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25
Q

Enzyme that catalyzes the peptide bond formation between amino acids, lines up with tRNA

A

Ribosomes

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26
Q

RNA consists of folded molecules which transport amino acids from the cytoplasm of the cell to a ribosome

A

tRNA

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27
Q

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

A

rRNA

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28
Q

Sites in genomes where RNAP binds (starts)

A

Promoters

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29
Q

Sites where RNAP is released (ends)

A

Terminators

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30
Q

A collection of adjacent genes that are all transcribed into a single RNA and under the control of a single promoter

A

Operon

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31
Q

3 things Eukaryotes do post-transcriptional processing

A

-Add 5’ cap
-Add ply A tail at the 3’ end
-Splicing

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32
Q

Introns are removed before translation via this process

A

Splicing

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33
Q

What is on the anticodon?

A

tRNA

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34
Q

What is on the codon?

A

mRNA

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35
Q

Does the codon or anticodon have the amino acid codes?

A

Codon

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36
Q

Type of genome where transcription and translation are NOT in separate compartments, meaning translation can begin before mRNA is fully made

A

Bacterial genome

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37
Q

Type of genome where the ribosome recognizes the 5’ cap structure and finds the AUG codon from there

A

Eukaryotic genome

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38
Q

The process used to control the timing, location, and amount in which genes are expressed

A

Gene regulation

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39
Q

Some microbes change or invert the DNA sequence to activate or disable a particular gene

A

Phase variation

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40
Q

Gene expression can be turned on or off via

A

DNA-binding proteins

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41
Q

Whether a regulatory protein can bind the DNA is often determined by the presence or absence of a…

A

Ligand

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42
Q

Example of DNA-binding proteins that regulate transcription

A

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

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43
Q

Different sigma factors recognize different promoters, which express different genes

A

Alternate sigma factors

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44
Q

Two component system for sensing the environment

A

Sensor protein and response regulator

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45
Q

Membrane-bound, often a kinase (transfers phosphate)

A

Sensor protein

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46
Q

Activated by the sensor protein and regulates gene expression

A

Response regulator

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47
Q

2 Examples of the two component systems

A

-Quorum sensing
-Vancomycin resistance

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48
Q

Sensing signals (autoinducers) Chemical signaling molecules produced by bacteria to sense population density. As cells sense autoinducers, expression of the autoinducers increases (amplifies signal)

A

Quorum sensing

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49
Q

A heritable change in the DNA sequence

A

Mutation

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50
Q

Mutations due to normal cell processes, random and infrequent

A

Spontaneous mutation

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51
Q

Mutations where external factor (mutagen) increases the mutation rate (chemicals or radiation)

A

Induced mutation

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52
Q

Cell receives new DNA

A

Horizontal gene transfer

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53
Q

When do proofreading and mismatch repair occur?

A

During or right after DNA replication

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54
Q

This activity removes the most recent base if incorrect (proofreading)

A

3’-5’ exonuclease

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55
Q

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)

A

Mismatch repair

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56
Q

Altered to a stop codon

A

Nonsense

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57
Q

One or more amino acids are changed

A

Missense

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58
Q

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)

A

Base excision repair

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59
Q

What enzyme makes base substitution errors?

A

Polymerases

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60
Q

Typical phenotype of strains isolated in nature

A

Wild type

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61
Q

“jumping genes” very large addition mutations that will likely knock out a gene

A

Transposons

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62
Q

Gene product is inactivated (missense or nonsense)

A

Null mutation/knock-out mutation

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63
Q

3 factors that determine whether a mutation becomes the predominant genotype in a population

A

-Environment
-Selective pressure
-Natural selection

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64
Q

One mechanism of change and vertical evolution

A

Mutations

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65
Q

In order for HGT to be passed vertically to daughter cells it must become part of the cell’s genome via:

A

Have its own origin of replication OR be recombined or integrated into existing genome

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66
Q

Process of importing naked (free) DNA into bacteria

A

Transformation

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67
Q

The physiological state that allows cells to take up naked DNA via transformation

A

Competency

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68
Q

Forced competency

A

Chemical competent/heat shock or electric shock

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69
Q

Reasons for transformation:

A

Using DNA as food source
Take up similar DNA to fix mistakes
Obtain new genes from other bacteria (increase genetic diversity)

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70
Q

Are one or two DNA strands imported after transformation?

A

One DNA strand

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71
Q

Where does the DNA come from for transformation?

A

Dead cells

72
Q

Mediated by direct contact between 2 cells

A

Conjugation

73
Q

How does DNA get transferred to the other cell in conjugation?

A

Donor cell sends DNA through tube to recipient cells via plasmid (common) or chromosomal (rare) transfer

74
Q

DNA sequence that contains the genes needed to facilitate conjugation

A

F (fertility) factor

75
Q

Genotype strain containing the F factor for the donor cell

A

F+

76
Q

Genotype strain containing the F factor for the recipient cell

A

F-

77
Q

DNA sequence on the F factor that is cut (just one strand) in conjugation

A

oriT

78
Q

What is the one strand of DNA helix that is transferred to the recipient cell in conjugation?

A

ssDNA

79
Q

What is the result of conjugation in the two cells?

A

Both cells are F+ (donor DNA) cells

80
Q

The structures that bring the donor in contact with the recipient and the bridge the DNA goes across (sex plus and bridge)

A

Mating pair formation (MPF)

81
Q

Features of the genome and genes that help initiate transfer and replication of the F factor (oriT, nicking enzyme)

A

DNA transfer and replication (Dtr)

82
Q

Genotype of strain containing the F factor in its chromosome Donor cell (rare) and recipient remains F- (does not receive full F factor)

A

Hfr

83
Q

Virus mediated horizontal gene transfer (phage), infection cycle by virus can transfer DNA from one bacterial cell to another

A

Transduction

84
Q

Phage accidentally adds bacterial DNA when packaging its genome into the protein capsid (packing mistake)

A

Generalized transduction

85
Q

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)

A

Specialized transduction, ends up with a chunk of phage genome in the cell

86
Q

Phage capsid (shell) filled with bacterial DNA

A

Transducing particle

87
Q

What did Griffith experiment conclude?

A

That the genes that dictate how organisms develop are made up of DNA, not protein, RNA, lipids, etc.

88
Q

What is needed for a bacterial cell to replicate and pass on newly acquired DNA from HGT to its daughter cells?

A

Donor DNA (single or double) and RecA to crossover

89
Q

Process by which DNA is incorporated into the recipient cell’s genome

A

Recombination

90
Q

Requires that the two recombining molecules have long stretches of sequence homology/similarity

A

Generalized (homologous) Recombination

91
Q

Short DNA sequence recognized by a special recombination enzyme

A

Site-specific Recombination

92
Q

Bacterial protein that facilitates recombination

A

RecA

93
Q

Those compounds a microbe cannot make itself but must gather from its immediate environment if the cell is to grow and divide

A

Essential nutrients

94
Q

Obtain compounds from other organisms, use carbon

A

Heterotrophs

95
Q

Make their own carbon compounds (CO2) via TSA cycle

A

Autotrophs

96
Q

Rock eaters

A

Chemolithotrophs

97
Q

Most chemolithotrophs are also…

A

Autotrophs

98
Q

Light absorption and electron transfer

A

Photolysis

99
Q

Why do plants need water for photosynthesis?

A

They use water and CO2 to release O2 as a byproduct

100
Q

Uses an ETC, PMF, chemiosmosis, ATP Synthase to generate ATP energy

A

Photophosphorylation

101
Q

Some bacteria can convert N2 gas to ammonium ions, which can be used for biosynthesis. Necessary for all life

A

Nitrogen fixation

102
Q

Other bacteria transform ammonia to nitrate

A

Nitrificaiton

103
Q

Other bacteria convert nitrate back to N2

A

Denitrification

104
Q

No enzymes to detoxify ROS, must have NO O2

A

Obligate anaerobe

105
Q

SOD + catalase, must have O2

A

Obligate aerobe

106
Q

Low levels of SOD + catalase, prefer lower O2

A

Microaerophile

107
Q

SOD + catalase, prefers O2, but has the option to grow without it

A

Facultative anaerobe

108
Q

SOD, does not use O2, but can tolerate it

A

Aerotolerant anaerobe

109
Q

Superoxide dismutase (SOD)

A

Breaks down oxygen radicals

110
Q

Catalase

A

Enzymes that break down H2O2

111
Q

Some microbes require growth factors that must be added to culture media before they will grow

A

Fastidious/auxotroph

112
Q

Media where all the chemical components are known

A

Chemically defined media

113
Q

Media where there are dead things in it

A

Complex media

114
Q

Normal physiologic conditions

A

20-40C
Near-neutral pH
Salt concentration of 0.9%
Ample nutrients

115
Q

-Above 80C
-pH above 9
-High salt
-Strict aerobe
-High pressure

A

Hyperthermophile

116
Q

-50-80C
-pH 5-8
-High salt
-Facultative anaerobe
High pressure

A

Thermophile

117
Q

-15-45C
-pH below 3
-High salt
-Microaerophile
-Barotolerant

A

Mesophile

118
Q

-Below 15C
-pH below 3
-High salt
-Strict anaerobe
-Barotolerant

A

Psychrophile

119
Q

Require elevated pressure to grow

A

Barophiles

120
Q

Grow at elevated pressures to an extent (10-500atm)

A

Barotolerant

121
Q

Can grow at mildly acidic pH, but do not thrive at very low pH

A

Acid tolerant microbes

122
Q

pH adaptations

A

Maintain a neutral pH by pumping protons out of or into cell

123
Q

Microbes that require high salt [ ]

A

Halophiles

124
Q

Microbes that can deal with higher salt [ ] but not extreme

A

Halotolerant

125
Q

The amount of time it takes for bacteria to double in size

A

Generation/doubling time

126
Q

Parent cell divides into 2 daughter cells

A

Binary fission

127
Q

Exponential growth

A

2-4-8-16-32-64…

128
Q

Eukaryotic cellular division

A

Mitosis

129
Q

Bacteria cellular division

A

Binary fission

130
Q

Septum forms and cell divides

A

Septation

131
Q

Bacteria are preparing their cell machinery for growth

A

Lag phase

132
Q

Growth approximates an exponential curve

A

Log phase

133
Q

Cells stop growing and shut down their growth machinery while turning on stress responses to help retain viability

A

Stationary phase

134
Q

Cells begin to die at an exponential rate

A

Death Phase

135
Q

Metabolites produced during active growth and metabolism

A

Primary metabolites

136
Q

Metabolites not essential for rapid growth; often made for defense or survival (antibiotics or toxins)

A

Secondary metabolites

137
Q

Direct methods of measuring cell growth

A

-Microscope count
-Cell-counting instruments

138
Q

Indirect methods of measuring cell growth

A

-Measuring biomass
-Serial dilution
-Filtration
-Metabolic activity

139
Q

Mass of bacteria that stick to and multiply on a surface

A

Biofilm

140
Q

Free living cells in suspension

A

Planktonic

141
Q

How do biofilms form?

A

Microcolonies form and cells secrete extracellular polymeric substances (EPS). Cells communicate via quorum sensing. Increase QS = # of cells increasing

142
Q

Percent of infections that are in biofilm

A

70%

143
Q

Purpose of biofilm

A

Protection, very resistant to antibiotics, facilitates movement of nutrients and wastes

144
Q

Gram + bacteria producing a differentiated cell. Clostridium and bacillus

A

Endospore

145
Q

Process cued by environmental conditions (starvation) to form endospores

A

Sporulation

146
Q

Process where endospore returns to vegetative (normal) growth

A

Germination

147
Q

2 guys who discovered endospores

A

Tyndall and Cohn

148
Q

A complete virus particle

A

virion

149
Q

Viruses that infect bacteria

A

phage

150
Q

Goal of viruses

A

Direct host cell to express viral genes and proteins

151
Q

Viruses finding new cells to infect via…

A

Transmission

152
Q

Each virus species infects a particular group of host species

A

Host range

153
Q

The range of tissue types a virus can infect

A

Tissue tropism

154
Q

Viral components

A

-Nucleic acid
-Protein capsid/shell
-SOME have lipid bilayer envelope

155
Q

-Nucleocapsid only
-More resistant to disinfectants

A

Naked viruses

156
Q

-Nucleocapsid enclosed in lipid bilayer (from host)
-Contents between envelope and capsid

A

Enveloped viruses

157
Q

Contents (proteins) that may be between the envelope and the capsid

A

Tegument

158
Q

3 methods of viral attachment

A

-Spike proteins
-Tail fibers
-Fiber proteins

159
Q

Radial symmetry, based on icosahedron

A

Icosahedral capsid

160
Q

Helical capsid tube around the genome, generating a flexible filament

A

Helical/filamentous capsids

161
Q

No symmetrical form, core wall contains genetic material

A

Complex/amorphous

162
Q

Icosahedral head with genetic info with tail and tail fibers

A

Complex-tailed bacteriophages

163
Q

Primary characteristic used to classify viruses

A

Genome

164
Q

Secondary characteristics used to classify viruses

A

Envelope and shape

165
Q

General scheme to viral replication

A

-Host recognition and attachment
-Genome entry
-Biosynthesis
-Assembly/maturation
-Release and transmission

166
Q

Viruses quickly take over the host cell, make many copies, break the cell, and infect other cells

A

Lytic (productive)

167
Q

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

A

Lysogenic

168
Q

Clearing on a lawn of bacteria on an agar plate

A

Plaque

169
Q

NOT lytic. They don’t directly kill the host. Often use host pili structure to exit

A

Filamentous phage

170
Q

A phage genome that has integrated into the host genome

A

Prophage

171
Q

Have the option to go latent in a pathway

A

Lysogen

172
Q

Prophage genes can give the host new properties (new phenotype) even in the lysogenic state

A

Lysogenic conversion

173
Q

Transduction that can happen if a mispackaging event happens, complex phage assembly is a complicated, step-by-step process

A

Generalized transduction

174
Q

Transduction that happens when infection switches to the lytic pathway (end of lysogenic) and the prophage is excised out

A

Specialized transduction

175
Q

Virus-host attachment triggers endoscope formation, might fuse with lysosome

A

Endocytosis

176
Q

Envelope fuses with host plasma membrane

A

Fusion

177
Q

Once in the host, capsid breaks down to release the genome

A

Uncoating

Year 3 (7 decks)

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