Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BMSC 210 > Midterm #2 (lectures 12-21) > Flashcards

Midterm #2 (lectures 12-21) Flashcards

1
Q

What was Mendel’s primary contribution to genetics?

A

Documents patterns of heredity in pea plants

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
1
Q

Which experiment was the final confirmation that DNA is responsible for transformation, not protein?

A

Hershey and Chase experiment

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What was Griffith’s primary contribution to genetics?

A

“Transformation experiments” transform non-pathogenic bacteria strains to pathogenic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What was Chargaff’s primary contribution to genetics?

A

Discovers that A = T and C = G

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What was Watson and Crick’s primary contribution to genetics?

A

Proposed the double helix structure of DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What are the 4 components of the structure of DNA?

A
  1. Deoxynucleotides 5’-triphosphate
  2. Free hydroxyl group from ‘ end to the 3’ end
  3. Double helix
  4. Antiparallel, which is complimentary and reverse
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

How can the structure of DNA be denatured?

A

By heat or other chemicals

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

True of False: DNA provides structural function?

A

False

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

DNA is organized into into a _____, which is a genetic element where carrying genes essential for cellular function

A

chromosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the differences between prokaryote chromosomes and eukaryote chromosome?

A

Prokaryote: generally circular
Eukaryote: almost all linear

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

The chromosome is much _____ than the cell

A

bigger

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Because the chromosome is much bigger than the cell, how do bacteria/eukarya/archaea deal with this?

A

Bacteria: supercoil by topoisomerase
Eukarya: histone to wrap around proteins
Archaea: supercoil + histone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is extrachromosomal DNA?

A

Genes that are non-essential

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Where is extrachromosomal DNA found?

A

Plasmids, mitochondrion, and chloroplasts

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the central dogma?

A

DNA to RNA via transcription, and RNA to Protein via translation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the information functional unit?

A

Gene, which is made up of nucleic acid sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the 3 kinds of RNA?

A

Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What are the 3 kinds of DNA replication?

A
  1. Semi-conservative replication: results in two DNA molecules with one original strand and one new strand.
  2. Conservative replication: results in one molecule that consists of both original DNA strands and another molecule that consists of two new strands
  3. Dispersive replication: results in two DNA molecules where each individual strand is a patchwork of original and new DNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Which of the 3 DNA replication models is correct?

A

Semi-conservative

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the function of DNA polymerase I?

A

Removes RNA primer and replaces it with newly synthesized DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is the function of DNA polymerase II?

A

Main enzyme that adds nucleotides in the 5’ to 3’ direction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is the function of helicase?

A

Opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is the function of ligase?

A

Seals the gaps between the Okazaki fragments on the lagging strand to crease one continuous DNA strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is the function of primase?

A

Synthesizes RNA primers needed to start replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is the function of single-stranded binding proteins?

A

Bind to single-stranded DNA to prevent hydrogen bonding between DNA strands, reforming double-stranded DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is the function of topoisomerase II (DNA gyrase)?

A

Relaxes supercoiled chromosome to make DNA more accessible for the initiation of replication; helps relieve the stress on DNA when unwinding, by causing breaks and then resealing the DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What is the function of topoisomerase IV?

A

Introduced single-stranded break into concatenated chromosomes to release them from each other, and then reseals the DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is the structure and function of mRNA?

A

Structure: short, unstable, single-stranded
Function: serves as an intermediary between DNA and protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is the structure and function of rRNA?

A

Structure: longer, stable RNA molecules
Function: ensures the proper alignment of mRNA and ribosome during protein synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What is the structure and function of tRNA?

A

Structure: short, stable RNA
Function: carries the correct amino acid to the site of protein synthesis in the ribosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What is a sigma factor?

A

A protein needed for initiation of transcription in bacteria, enables specific binding of RNA polymerase to gene promoters

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What are promoter regions?

A

Where DNA polymerase initiates the process

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Th stronger the match, the stronger the sigma factor, the stronger the _______ will be

A

transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What are alternative sigma factors?

A

Response to different environments/stresses/signals

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

The more sigma factors you have, the more you can respond to the environment by modifying the sigma factor sequence, you are changing how ?

A

genes are expressed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What is an Open Reading Frame (ORF)?

A

Spans of DNA sequence between the start and stop codons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is the term polycistronic mean?

A

describes the situation in which two or more separate proteins are encoded on a single molecule of messenger RNA (mRNA). In prokaryotes, polycistronic expression is common

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What is an operon?

A

A cluster of genes that are transcribed together to give a single messenger RNA (mRNA) molecule, which therefore encodes multiple proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What are the 2 different ways of Termination of a specific sequence?

A
  1. Stem loop: GC-rich sequence, inverted loop, RNA pol pauses
  2. Rho-dependent: termination site, Rho cause RNA release
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Compare the promoters in bacteria vs archaea vs eukarya

A

Bacteria: sigma box, -10 and -35 box
Archaea: TATA box
Eukarya: Similar to archaea

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Compare the termination in bacteria vs archaea vs eukarya

A

Bacteria: stem loop and Rho
Archaea: Stem loop but no Rho
Eukarya: no loop, several factors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Compare the processing in bacteria vs archaea vs eukarya

A

Bacteria: absent
Archaea: some processing
Eukarya: exons and introns

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

Compare the cistonic in bacteria vs archaea vs eukarya

A

Bacteria: polycistronic
Archaea: polycistronic
Eukarya: monocistronic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Compare the chromosomes in bacteria vs archaea vs eukarya

A

Bacteria: single, circular; multiple linear, haploid, lack histone
Archaea: single, circular; multiple, histone
Eukarya: multiple, linear; haploid, multi, histone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

Compare the replication in bacteria vs archaea vs eukarya

A

Bacteria: single origin, replisome (gyrase)
Archaea: single, multiple, machinery similar to eukarya + gyrase
Eukarya: no gyrase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

Compare the transcription in bacteria vs archaea vs eukarya

A

Bacteria: protein + structure, unique machinery
Archaea: protein + structure, eukarya-like machinery
Eukarya: protein-termination, unique machinery

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What is the Wobble position?

A

3rd nucleic acid on the codon, can change but it is still the same amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

What is codon bias?

A

One bacteria may prefer one sequence compared to another, even if they give the same amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

To get a functional protein, you need ?

A
  1. Protein folding (spontaneous, requires assistance, misfolding)
  2. Chaperones (energy dependent process, folding and refolding, add cofactors, help secretion)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

Describe Type I gram-negative secretion system

A

ABC transporter
One step: cytoplasm to outside

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

Describe Type II gram-negative secretion system

A

Sec and Tat dependent
Two step: secrete from periplasm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

Describe Type V gram-negative secretion system

A

Autotransporter
Sec and Tat dependent
Two step: secrete from periplasm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

Describe Type III gram-negative secretion system

A

One step
Syringe-like
Bacterial pathogens
Inject proteins into eukaryotic cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

Describe Type IV gram-negative secretion system

A

One step
Pilus-like
Transfer DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

Describe Type VI gram-negative secretion system

A

One step
Spear-like
Bacteriophage tail
Pierce the membrane
Bacteria-bacteria competition

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

What is genetic regulation?

A

Control mRNA production through transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

What is post-transcription?

A

Control mRNA stability, and control translation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

What is post-translation?

A

Control protein activity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

What is the difference between genes that are constitutively expressed and genes that are expressed when needed?

A

Constitutively: essential function
Expressed when needed: under specific condition

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

What is the main function of effectors?

A

Change binding affinity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

Operon vs regulon

A

Operon: 1 promoter with many genes, polycistronic
Regulon: 1 regulator, many promoters. Disperse through the chromosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

What are regulatory RNAs?

A

RNA that are not translated, small RNA (sRNA)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

What is the intergenic region?

A

Low degree of complementary, needs a helper (protein)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

What are the 3 different mechanisms of RNA-based regulation?

A
  1. Affect mRNA stability (protect RNA from degradation, target RNA for degradation)
  2. Block RBD (block translation)
  3. Change the secondary structure
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

What is attenuation in terms of RNA-based regulation?

A

A secondary structure that in the mRNA that will allow translation or not based on the level and speed of translation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

What are riboswitches in terms of RNA-based regulation?

A

Secondary structures found in the RNA strand that will allow for transcription or translation to proceed. But they need a cofactor to bind to that structure or not to bind.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

What are the 2 ways to remove a protein?

A

Degradation and sequestration

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

What are the 2 parts of Two-component regulatory systems?

A

Sensor histidine kinase
Response regulator

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

How do two-component regulatory systems?

A

Stimuli induces autophosphorylation at the histidine residue. Transfer of phosphate to regulator, and has a feedback loop

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

What is Quorum Sensing?

A

a process of cell–cell communication that allows bacteria to share information about cell density and adjust gene expression accordingly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

How do bacteria acquire genetic diversity?

A

Vertical: new mutation
Horizontal: gene expression and acquisition, and selfish genetic elements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

What are mutations?

A

Changes in the nucleotide sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

What is a wild-type mutation?

A

Parental, isolated from nature

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

What is a mutant?

A

Carries change, has a different genotype

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

How do you increase the mutation rate?

A

Stresses and mutagens, which are naturally found in the environment

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

How do we determine mutagenic potential?

A

The Ames test: ability of a chemical to induce a revertant in an auxotroph. The higher the number of colonies, the higher the potential

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

What is a point mutation?

A

Substitution, deletion or insertion of a single base pair

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
77
Q

What is a silent mutation?

A

Substitution of a 3rd base of codon. There is no change in amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
78
Q

What is a missense mutation?

A

Substitution of 1st and 2nd base of codon. Amino acid change in protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
79
Q

What is a nonsense mutation?

A

Amino acid change to a stop codon. Causes an incomplete/truncated protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
80
Q

What is a frameshift mutation?

A

Single nucleotide inserted or removed, and causes a shift in the reading frame

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
81
Q

What is reversion?

A

A second mutation that can reverse the effect of a mutation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
82
Q

What is a revertant?

A

The phenotype is restored to the wild-type

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
83
Q

What is a true revertant?

A

Genotype is restored to the wild-type

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
84
Q

What is transformation?

A

Genetic transfer of free DNA to competent cells that are able to take said DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
85
Q

What is conjugation?

A

Genetic transfer requiring cell-cell contact. Plasmid encoded

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
86
Q

What is transduction?

A

Phages pick up host DNA and transfer into a new host

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
87
Q

What are the 2 kinds of transduction?

A
  1. Generalized: lytic phage/defective phage
  2. Specialized: temperate phage
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
88
Q

What is phage conversion?

A

Alteration of phenotype by prophages. Harmless bacteria can become pathogens

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
89
Q

What are 4 ways that prokaryotes defend themselves?

A

Mutation in receptors
Restriction enzymes
Phage exclusion
Programmed cell death

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
90
Q

What is CRISPR?

A

Cluster Regularly Interspaced Short Palindromic Repeats
Seek and destroy foreign nucleic acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
91
Q

What is genetic engineering?

A

Using in vitro techniques to alter genetic material in the lab

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
92
Q

What is a vector?

A

DNA molecule (often plasmid or virus) that is used as a vehicle to carry a particular DNA segment into a host cell as part of a cloning or recombinant DNA technique

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
93
Q

What is heterologous?

A

Expressing a gene in a different host

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
94
Q

What is a thermocycler?

A

Automated PCR machine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
95
Q

What is the proper order in the steps in PCR amplification:
1. Synthetic piece of DNA flanking sequence of interest to the reaction mixture is added
2. Heat and cool -repeat many similar cycles
3. Repeat 20-30x
4. DNA to be amplified is denatured by heating
5. Add DNA polymerase which extends primers using DNA

A

4, 1, 5, 2, 3

96
Q

PCR requires DNA ______ and artificial oligonucleotide _____ made of DNA and uses ______ DNA polymerase

A

polymerase, primers, thermostable

97
Q

Reverse Transcription PCR makes DNA from an mRNA _____, detects gene expression or produced intron-free eukaryotic gene for expression in bacteria, uses the enzyme reverse _______ to convert RNA into complementary DNA

A

template, transcriptase

98
Q

Agarose gel electrophoresis separates DNA molecules based on ___ and _____, nucleic acids migrate through the gel towards the ______ electrode, and ____molecules move _____ than large ones

A

size , charge, positive, small, faster

99
Q

Agarose gels can be stained with ? and DNA is visualized under ___ light

A

ethidium bromide, UV

100
Q

The same DNA cut with different _______ enzymes
will have different banding patterns on an agarose gel

A

restriction

101
Q

Nucleic acid hybridization is used to detect a certain nucleic acid sequence, from ___ different sources to give a hybrid, occurs usually with ______/_______ products.

A

2, colored, fluorescent

102
Q

What is a nucleic acid probe?

A

a single-stranded DNA or RNA fragment of known structure or function and is used to detect a target sequence of DNA in a sample

103
Q

How does a nucleic acid probe work?

A

DNA probes will bind to the gene of interest if it is present in the sample

104
Q

What is a southern blot?

A

Hybridization procedure where DNA is in the gel and probe is RNA or DNA

105
Q

What is a northern blot?

A

RNA is in the gel and the Probe is DNA or RNA

106
Q

What is FISH?

A

Fluorescent In Situ Hybridization, uses a fluorescent probe attached to oligonucleotide

107
Q

What is synthesized DNA used for?

A

For primers and probes, and site-directed mutagenesis

108
Q

What is cloning?

A

Movement of a gene from original source to small and manipulable genetic element (vector)

109
Q

What are the 2 main enzymes used for cloning?

A
  1. Restriction endonucleases
  2. DNA ligase: catalyzes the joining of two strands of DNA between the 5’ phosphate and 3’ OH
110
Q

What are two other enzymes used for cloning?

A

Reverse transcriptase: converts RNA into DNA
DNA polymerase: Mostly used for 5’to 3’ polymerizing activity. May also have 3’to 5’ and 5’ to 3’ exonuclease activity

111
Q

What are restriction endonucleases?

A

Recognize specific DNA sequences and cut DNA, widespread among bacteria but rare in eukaryotes

112
Q

What is the main function of Type II restriction endonucleases?

A

Cleave DNA within recognition sequence; most useful for specific DNA manipulation. Recognize inverted repeat sequences (palindromes)

113
Q

Molecules with complementary sticky ends can easily ____ or form
hydrogen bonds between complementary bases. Annealing step allows ______ of the single stranded overhangs

A

anneal, hybridization

114
Q

_____ by DNA ligase can rejoin the two sugar-phosphate backbones of DNA through covalent binding

A

Ligation

115
Q

Each restriction enzyme is partnered with a corresponding modification enzyme that shares the _____ recognition sequence

A

SAME

116
Q

What is the overall 7 steps in gene cloning:
1. Allows insertion of foreign DNA at a restriction site on a cloning vector by restriction enzymes/endonucleases
2. Isolation and fragmentation of source DNA
3. Expression of cloned gene and selection of gene product
4. Insertion of DNA fragment into cloning vector
5. Gene to be cloned can be amplified by polymerase chain reaction, synthesized by reverse transcriptase, or synthetic DNA made in vitro
6. Introduction of cloned DNA into host organism
7. Small, independently replicating genetic elements than can carry and replicate cloned DNA

A

2, 5, 4, 7, 1, 6, 3

117
Q

What is recombineering?

A

Allows foreign DNA to be inserted into
vectors/chromosome

118
Q

Biggest limitation of cloning is ?

A

modifications can only be
made at restriction enzyme sites

119
Q

Why plasmids as cloning vectors?

A

Small size; easy to isolate DNA, Independent origin of replication, Multiple copy number; get multiple copies of cloned gene per cell

120
Q

What is Blue-White screening?

A

Bacteria with cloning vector which may or may not
contain “insert” DNA. Blue colonies do not have vector with foreign DNA inserted, white colonies have foreign DNA inserted

121
Q

Plasmids specifically for cloning DNA products made by ___ in PCR, adds template-independent adenosine to 3’-end

A

Taq

122
Q

Linearized vectors containing overhanging thymidine allow _____ ____ and ____

A

base paring, ligation

123
Q

What are shuttle vectors?

A

It can propagate in two different host species. Therefore, DNA inserted into a shuttle vector can be tested or manipulated in two different cell types.

124
Q

If cells express the foreign gene expression might be detected using: ?

A

Antibodies, usually fluorescently labelled

125
Q

Ideal hosts should be: ?

A

Capable of rapid growth in inexpensive medium
Nonpathogenic
Capable of incorporating DNA
Genetically stable in culture
Equipped with appropriate enzymes

126
Q

What are expression vectors?

A

Allow experimenter to control the expression of cloned genes

127
Q

Obstacles in ways to express foreign genes include need for bacterial _____, _____ must be removed, codon usage/bias, post-translational ______

A

promoter, introns, modifications

128
Q

Recombinant proteins may cause problems like..?

A

Degradation by proteases, toxicity, insoluble inclusions

129
Q

What is site-directed mutagenesis?

A

Performed in viro and introduced mutations at a precise location, and can be used to assess the activity of a specific amino acid in a protein

130
Q

What are DNA cassettes/cartridges?

A

Synthetic fragments that can make more than a few base pair changes or replace sections of a gene via cassette mutagenesis

131
Q

What is gene disruption?

A

Inserts cassettes in middle of a gene, disrupting coding sequence

132
Q

What is a knockout mutation?

A

Loss of function if a gene in which cassette is inserted

133
Q

Gene ______ determine whether a gene is essential

A

knockouts

134
Q

What is a reporter gene?

A

Encodes protein, easy to detect and assay

135
Q

What are operon fusions?

A

Coding sequence with its own translational start site and signals are fused to transcriptional signals of another gene

136
Q

What are protein fusions?

A

Genes encoding two proteins are fused to share the same transcriptional and translational start and stop and yield one hybrid polypeptide

137
Q

What is a generation?

A

Refers to a successive major changes in sequencing technology

138
Q

The first generation of DNA sequencing used the ______ method

A

Sanger

139
Q

The Sanger method required that ?

A

Labeled dideoxynucleotides were added to a reaction so that the elongation of new DNA chains would terminate when the dideoxynucleotides were incorporated

140
Q

Second generation sequencing used similar chemistry, but ______ the reactions and improved ______ methods and computation so that more sequence information could be collected very rapidly

A

miniaturized, detection

141
Q

Third generation sequencing improved detection such that _____ molecules could be detected, thus even more _____ could be generated

A

single, sequence

142
Q

________ (second-generation) uses luciferase to detect incorporation of dNTPs

A

Pyrosequencing

143
Q

Describe 3rd Generation Nanopore Minion

A

When DNA molecules pass through or near the nanopore, there will be a change in the magnitude of the current in the nanopore, which is measured by a sensor

144
Q

What is annotation?

A

Converting raw sequence data into a list of genes present in the genome

145
Q

What are hypothetical proteins?

A

Uncharacterized ORFs; proteins that likely exist but whose function is currently unknown

146
Q

What is metagenomics?

A

Analyzes pooled DNA or RNA from environmental sample containing organisms which have not been isolated/identified

147
Q

What is the metagenome?

A

Total gene content of microbial community

148
Q

What is transcriptomics?

A

The study of the complete set of RNA transcripts that are produced from genomic DNA in cells or tissues

149
Q

What is the transcriptome?

A

The entire complement of RNA produced under a given set of growth conditions

150
Q

What are microarrays?

A

Small solid-state supports to which gene or portions of genes are fixed and arrayed spatially in a known pattern

151
Q

DNA segments/fragments on arrays are ______ with mRNA from cells grown under specific conditions and analyzed to determine
patterns of gene expression

A

hybridized

152
Q

Arrays are large and dense enough that the transcription pattern of an ____ genome can be analyzed

A

entire

153
Q

What kind of information can be derived from microarrays?

A

Global gene expression
Expression of specific groups of genes under different conditions
Expression of genes with unknown function, can yield clues to possible roles
Comparison of gene content in closely related organisms
Identification of specific organisms

154
Q

What is proteomics?

A

Study of the entire protein complement of a cell

155
Q

Proteins with >__% sequence similarity typically have similar functions; proteins with >__% sequence similarity almost certainly have similar functions

A

50, 70

156
Q

What are protein domains?

A

Distinct structural modules within proteins and have characteristic functions

157
Q

What are Interactomes?

A

Complete set of interactions among macromolecules, and the data expressed in the form of network diagrams

158
Q

What is metabolomics?

A

Study of the set of metabolites present within an organism, cell, or tissue

159
Q

What is the metabolome?

A

The complete set of metabolic intermediates and other small molecules produced in an organism

160
Q

What is systems biology?

A

Integration of different fields of “omics” research

161
Q

What is genetic drift?

A

The change in frequency of an existing gene variant in the population due to random chance, may cause gene variants to disappear completely and thereby reduce genetic variation

162
Q

Duplication and deletion has major evolutionary roles: ?

A

Govern genome size and content
Must classify genes based on shared ancestry for comparison

163
Q

What are Orthologs?

A

Genes which evolved from a common ancestral gene by speciation that usually have retained a similar function in different species

164
Q

What are Paralogs?

A

Genes related by duplication within the genome and often they acquire a new function

165
Q

What is a homolog?

A

Gene inherited in two species from a common ancestor. While homologous genes can be similar in sequence, similar sequences are not necessarily homologous

166
Q

How do duplication mutations increase
microbial fitness?

A

A duplication mutation creates a redundant copy of a gene sequence in the genome. The original gene copy retains its function, making it possible for the second copy to accumulate mutations freely without a loss of gene function in the cell so evolution can “experiment” with one copy of the gene

167
Q

What is horizontal gene transfer?

A

The transfer of genetic information between cells, as opposed to vertical inheritance from parental organism(s)

168
Q

What are the 3 mechanisms of horizontal gene transfer?

A

Transformation, transduction, and conjugation

169
Q

______ counters effect of deletions, preserving genes that benefit fitness

A

Selection

170
Q

What is the mobilome?

A

All kinds of transferrable elements, which includes plasmids, bacteriophage, transposons, integrations, etc

171
Q

Horizontally transferred genes typically do/do not encode core metabolic functions?

A

do not

172
Q

Comparative genomic analyses show entire genetic pathways (chromosomal/genomic islands) can be acquired via ?

A

horizontal gene transfer

173
Q

What is the core genome?

A

Consists of genome of genes shared by all the strains studied and probably encode functions related to the basic biology

174
Q

What is the pan-genome?

A

The sum of the core genome and the dispensable genome

175
Q

What is phylogeny?

A

The relationship of all organisms on the earth and assumes a common ancestor. It encompasses the genetic and genomic diversity of evolutionary lineages. Can be defined on the basis of genes or organisms

176
Q

More than 90 percent of characterized genera and
species come from four phyla: ?

A

Proteobacteria
Actinobacteria
Firmicutes
Bacteroidetes

177
Q

80+ phyla can be distinguished based on ____ ribosomal RNA

A

16S

178
Q

Place these categories into the proper order:
1. Phylum
2. Genus
3. Domain
4. Order
5. Class
6. Species
7. Family

A

3, 1, 5, 4, 7, 2, 6

179
Q

_______ largest and most metabolically diverse phylum

A

Proteobacteria

180
Q

______ make up the majority of known medically, industrially, and agriculturally significant bacteria

A

Proteobacteria

181
Q

_______ are all gram-negative

A

Proteobacteria

182
Q

________ have diverse energy generation mechanisms, diverse relationships with oxygen, and a variety of morphologies

A

Proteobacteria

183
Q

Proteobacteria is divided into six classes: ?

A

Alpha-, Beta-, Delta-, Gamma-, Epsilon-, Zeta-

184
Q

________ most are obligate aerobes or facultative aerobes, and many are oligotrophic

A

Alphaproteobacteria

185
Q

Describe Rickettsia

A

Alphaproteobacteria
Typhus; Rocky Mountain spotted fever
Ticks, fleas, lice, and mites
Unable to synthesize some metabolites, cell walls, host cell bursts and frees cells

186
Q

______ is the third-largest class of Proteobacteria and has much functional diversity

A

Betaproteobacteria

187
Q

Describe Neisseriales

A

Betaproteobacteria
Diverse chemoorganotrophs
Found from moist areas/oral cavity
Some pathogenic
Always cocci

188
Q

________ is the largest, most diverse class of Proteobacteria

A

Gammaproteobacteria

189
Q

_______ have diverse metabolic and ecological characteristics, known human pathogens, phototrophs, chemoorganotrophs,
chemolithotrophs, respiratory or fermentative metabolisms

A

Gammaproteobacteria

190
Q

Describe Enterobacteriales

A

Gammaproteobacteria
Facultative aerobic, gram-negative, nonsporulating
Oxidase -, catalase +
Two fermentation patterns

191
Q

What are the 2 fermentation patterns in enteric bacteria?

A
  1. Mixed-acid fermentation: acetic, lactic, and succinic acid formed in significant amounts; ethanol, CO2, and H2
  2. 2,3-butanediol fermentation: Butanediol,
    ethanol, more CO2 than H2, are main products; smaller amounts of acids formed
192
Q

What are the 4 types of Mixed-Acid fermenters?

A

Escherichia, Salmonella, Shigella, Proteus

193
Q

Describe Escherichia

A

Synthesize vitamins
Facultative aerobe that helps make large intestine anoxic
Some strains are pathogenic

194
Q

Describe Salmonella

A

Almost always pathogenic
Causes typhoid fever and gastroenteritis

195
Q

Describe Shigella

A

Typically pathogenic
Causes bacillary dysentery

196
Q

Describe Proteus

A

Genus containing highly motile cells
Frequent cause of urinary tract infections
Capable or swarming

197
Q

What are the 3 types of butanediol fermenters?

A

Enterobacter aerogenes, klebsiella, serratia

198
Q

Describe Enterobacter aerogenes

A

Gammaproteobacteria
Found in water, sewage, and intestinal tract
May cause urinary tract infection

199
Q

Describe Klebsiella

A

Gammaproteobacteria
Occasionally causes pneumonia
Most strains fix nitrogen

200
Q

Describe Serratia

A

Gammaproteobacteria
Forms red pyrrole-containing pigments called prodigiosins
May cause infection
Found in water, soil, and intestinal tracts

201
Q

Describe Pseudomonadales

A

Gammaproteobacteria
High antibiotic resistance
Aerobic respiratory chemoorganotrophs
Oxidase -, catalase +

202
Q

Describe Vibrionales

A

Gammaproteobacteria
Facultatively aerobic rods and curved rods that ferment
Cholera causes cholera in humans

203
Q

Describe Firmicutes

A

Endospore formers, lactic acid bacteria, others
Low G+C gram-positive bacteria

204
Q

Describe Tenericutes

A

Lack a cell wall, gram-positive

205
Q

Describe Actinobacteria

A

High G+C gram-positive bacteria

206
Q

Describe Lactobacillales

A

Firmicutes
Lactobacillus, streptococcus
Lactic acid bacteria: fermented
Widely used in food production
Aerotolerant anaerobes

207
Q

What is homofermentative?

A

Produce only lactic acid

208
Q

What is heterofermentative?

A

Produce ethanol, CO2, and lactate

209
Q

What are the 2 groups of streptococci?

A

Pyogenes and Viridans, and they are blood agar hemolysis diagnostic

210
Q

Describe Firmicutes: Nonsporulating Bacillales Clostridiales

A

Staphylococcus
Catalase +, gram-positive
Resistant to reduced water potential
Antibiotic resistant

211
Q

Describe Firmicutes: Sporulating Bacillales and Clostridiales

A

All endospore-forming bacteria are Bacillales or Clostridiales
Generally found in soils
Pathogenic species are saprophytic

212
Q

What does saccarolytic mean?

A

Ferment sugars

213
Q

What does proteolytic mean?

A

Ferment amino acids or amino acid pairs

214
Q

Describe Clostridium

A

Lacks a respiratory chai and obtains ATP by substrate level phosphorylation
Some are pathogenic, causing botulism, tetanus, gangrene, and gastroenteritis

215
Q

What are the 3 different methods of control?

A

Physical, mechanical removal, and chemical

216
Q

What is sterilization?

A

For inanimate items, completely eliminate all vegetative cells, endospores, and viruses

217
Q

What is disinfection?

A

For inanimate items, reduces or destroys microbial load using heat or chemicals

218
Q

What is sanitization?

A

For inanimate objects, reduces microbial load to a safe public health level using heat or chemicals

219
Q

What is antisepsis?

A

For living tissues, reduces microbial load using an antimicrobial chemicals

220
Q

What is degerming?

A

For living tissues, reduces microbial load using scrubbing and mild chemicals

221
Q

What are the 2 main physical methods of control?

A

Heat and radiation

222
Q

What is boiling?

A

Denatures proteins and alters membranes

223
Q

What is autoclaving?

A

Sterilizes at 121°C for 15 mins or more

224
Q

What is pasteurization?

A

HTST: heated at 72°C for 15s
UHT: heated at 13°8°C for +2s

225
Q

Which 6 physical methods of control reduce the population by killing?

A

Boiling, dry-heat oven, incineration, autoclave, pasteurization, high-pressure processing

226
Q

Which 6 physical methods of control control growth?

A

Refrigeration, freezing, Hyperbaric oxygen therapy, simple desiccation, reduce water activity, lyophilization

227
Q

What is the main example of mechanical removal controls?

A

Filters

228
Q

What are the 2 main chemical methods of control?

A

Gases and liquids

229
Q

What are the 2 divisions of gases?

A

Sterilization and disinfection

230
Q

What are the 2 divisions of liquid chemical controls?

A

Living and non-living

231
Q

What is bacteriostatic?

A

Stops growth, but does not kill

232
Q

What is bactericidal?

A

Kills bacteria

233
Q

What is bacteriolytic?

A

Lyses cells

234
Q

What is fungistatic/cidal?

A

Targets fungi

235
Q

What is viricistatic/dal?

A

Targets viruses

236
Q

What is sporocidal?

A

Kills spores

237
Q

Selective toxicity for chemotherapy is _____ for bacteria, _____ for virus and very ____ for eukaryotic pathogen

A

easier, harder, hard

BMSC 210 (3 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions