Midterm 2 Flashcards
Topic 3.1 - 5.2
1
Q
How do cells store their genetic information?
A
as DNA
2
Q
What happens in the first step of cell division?
A
DNA is copied via DNA replication
3
Q
What happens in transcription?
A
Genetic info from DNA is copied to RNA
4
Q
What’s mRNA
A
Messenger RNA
5
Q
What do open reading frames from mRNA get converted to via translation?
A
proteins
6
Q
rRNA
A
ribosomal RNA
7
Q
Are non-coding RNAs converted to protein?
A
No
8
Q
___ is a polymer comprised of strings of nucleotide monomers
A
DNA
9
Q
Comprised of 4 different nucleobases attached to a deoxyribose which carries a phosphate at the 5’ carbon.
A
Nucleotides
10
Q
What lacks a phosphate group?
A
Nucleosides
11
Q
Purines have a ____ interaction with ___ hydrogen bonds
A
weaker; 2
12
Q
C/G base pairs have a ____ interaction with __ hydrogen bonds
A
Stronger; 3
13
Q
_______ ________ is the key to DNA’s function: it enables identical copies to be made and genetic info to be converted to RNA/protein
A
Base Pairing
14
Q
DNA and ___ are chemically similar
A
RNA
15
Q
____ contains a 2’-hydroxyl group on its sugar (ribose)
A
RNA
16
Q
RNA is ____ chemically stable than DNA
A
less
17
Q
Structure of prokaryotic chromosomes
A
Genomes are smaller than ours but still huge – lots of structuring to fit inside a cell
18
Q
Uracil lacks a ______ group
A
methyl
19
Q
Prokaryotic chromosomes are usually ________ in shape
A
circular
20
Q
Which type of chromosome has extensive supercoiling & additional structuring layered on top?
A
prokaryotic chromosomes
21
Q
Many ________ are involved in prokaryotic chromosome structuring
A
proteins
22
Q
Name for the region of a cell containing the chromosome (not membrane bound)
A
Nucleoid
23
Q
Bacteria and archaea almost always have ___, circular chromosome
A
one
24
Q
Vibrio cholerae
A
bacterium with 2 chromosomes - one is ~3 Mbp, other 1Mbp
25
Streptomyces have ______ chromosomes
linear
26
__________ have multiple linear chromosomes
Eukaryotes
27
Which model yeast species has 16 chromosomes that vary in size?
Saccharomyces cerevisiae
28
__________ (and ________) generally have larger, less compact genomes than prokaryotes
eukaryotes, microbes
29
Do microbes have smaller/more compact genomes than higher eikaryotes?
Yes
30
Microbes have fewer ________/gene than higher eukaryotes such as plants
introns
31
What are introns?
non-coding gene segments removed during splicing
32
______ are segments of genetic material that encode a functional protein or RNA product
Genes
33
A typical prokaryotic genome is comprised of:
- 85-__% protein-coding genes
- 1-2% RNA genes - non-coding RNA
- __% non-coding DNA
90; 10
34
Genes can run in _____ direction and can _______
either; overlap
35
Genes are often organized into ___________-_______ clusters (the function of surrounding genes can offer insight into a gene's function.
functionally-related
36
Genes of a related function may be _________ around the chromosome
scattered
37
Can genes overlap on the genome to a certain extent?
Yes
38
______ can only live within the cells of another organism
Endosymbionts
39
__________ can have very small genomes and require another organism to live
parasites (they rely on host for many functions)
40
________ is a parasite that is very unlikely to live freely. It has a 0.5 Mb genome with ~500 genes
Mycoplasma
41
____-______ bacteria/archaea have larger genomes
Free-living
42
Some bacteria with complex life cycles have genomes as large as ~__Mb
15
43
_____ have the largest range in genome size and _______ have the shortest range in genome size
plants, mammals
44
In _________ genomes, as genome size increases, so does the number of genes
prokaryotic
45
Genes that encode specialized functions for adapting to different environments or operating in different lifestyles _____ in larger genomes
increase
46
The density of genes is _________
constant
47
- genes are present in all members
- usually conserved and important for biology of that lineage
Core genome
48
- all genes present in any member
- includes rare genes that encode highly specialized functions
Pan genome
49
Different lineages of Salmonella all share a ____ _______
Core Genome
50
Unique genes encode for ______ properties
unique
51
The ___ gene tells us the total repretiore of genes at the organisms disposal
pan
52
The _____ serovar is human adapted and encodes unique genes to help it infect & persist within humans
Typhi
53
Genomes of closely-related lineages often exhibit significant _______
synteny
54
Synteny
- the same genes in the same order
- homologous genes arranged in the same order in their genomes
55
Unique genes of a particular genome are often found in ______ of genes
blocks
(large blocks = genomic island)
(small blocks = genomic islet)
56
Genomic island and islets often represent ___________ acquired genes
horizontally
57
what is it that can allow a certain strain of an organism to hold genetic info to make a cell pathogenic and infect host cells
genetic islands
58
Bacteriophages
viruses that infect bacteria
59
A temperate phage is a type of bacteriophage that can integrate into bacterial genomes - called a _______. They can be ______ or _________.
prophage; stable; transient
60
Prophage content can ____ from strain to strain
vary
61
prophages can carry _____ _____ that have nothing to do with phage biology
cargo genes
62
Cargo genes can provide that bacterial host with useful ___ _____.
new genes
63
Many important bacterial toxins are encoded by _________
prophages
64
_______ are typically circular DNA molecules that are replicated in the cytoplasm
Plasmids
65
What do plasmids encode?
"non-essential" accessory genes - important under certain conditions such as antibiotic resistance genes
66
Plasmids vary in side from ~_ kbp to 1___, and they're typically less than _% the size of the genome
1; Mbp; 5
67
Plasmids can vary in copy number from _ to ___
1; >100
68
_______ contain genes to ensure their replication using host DNA replication machinery
Plasmids
69
__________ do not reproduce sexually, they use simple _____ ______ to produce genetically identical offspring
Prokaryotes; binary fission
70
Prokaryotes are not genetically _______. They mutate and exchange genes.
stagnant
71
What is a mutation
a heritable change in the DNA sequence of a genome. Includes substitution mutations, insertions, deletions -- any change
72
What is a mutant
an organism whose genome carries a mutation
73
_____-_____ strains isolate from nature and/or are used as the parental strain in a genetic study
wild-type
74
The term "wild-type" can also be applies to a _____ gene
single
75
Genotype
the complete genetic makeup of an organism
76
A __________ is an observable characteristic of an organism
phenotype
77
In prokaryotes, the mutant strain has a different ________ compared to the wild-type strain. It's common to test if the wild-type and mutant have differing __________.
genotype; phenotype
78
_______ mutation rate is ~ 10^-6 to 10^-7 per 1000 bp per round of replication for prokaryptes
Natural
79
Natural mutations happen when there are DNA _________ errors when copying genomic DNA
polymerase
80
Each round of replication will introduce a mutation to a given gene in one out of every ~_-__ million cells
1-10
81
In large bacterial populations there will likely be SOME genetic ______ in each gene
diversity
82
Most genomes are (almost) _______
identical
83
Acquiring _________ plays a major role in prokaryotic evolution
mutations
84
Horizontal gene transfer
Acquiring new genetic material from the environment (foreign DNA)
85
Foreign DNA can enter a prokaryotic cell in 3 major ways:
1) Transformation
2) Transduction
3) Conjugation
86
During gene transfer, inside the cell, DNA can:
1) Be degraded/lost
2) Replicate as a separate entity (plasma, phage)
3) Be integrated into the chromosome (recombination, transposition)
87
Process by which FREE DNA is incorporated into a recipient cell and brings about genetic change
Transformation
88
transformation can come from a variety of sources -- often _____ cells within their environments
lysed
89
DNA does not frequently cross the cell ________
membrane
90
A cell capable of taking up free DNA is said to be _________
competent
91
Some bacteria/archaea are _________ competent, others are not
naturally
92
In naturally competent organisms, how is competence regulated?
Tightly regulated
93
Can bacteria artificially be made competent in a lab setting?
Yes (DNA transfers)
94
How is DNA captured from the environment in competent organisms?
By pili, which retract, bringing DNA through the outer membrane of the cell
95
During transformation, one strand of DNA is typically _______ & the other strand passed through the _____________ membrane and into the cell via a multi-protein competence system
degraded; cytoplasmic
96
Transduction: ____________ infections
bacteriophage
97
What is a bacteriophage?
a virus that infects bacterium
98
What are virions holding?
a virus' DNA
99
_____ feature protein coats that protect DNA. They bind cells and inject DNA
Virions
100
Where phage DNA replicate and new particles are produced using host resources.
Lytic pathway
101
After viruses lyse a host cell, they're released to ______ ___ _____.
infect new cells
102
In a _________ _______, viral DNA is integrated into host DNA to create a prophage. This can be induced to trigger the lytic cycle.
lysogenic pathway
103
Some phages are purely _____ and only operate via a lytic pathway
lytic
104
Some phages are _________ and can operate via the lytic or the lysogenic pathway
temperate
105
What is transduction?
The process in which a virus (phage) transfers DNA from one cell to another
106
Generalized transduction:
- During the _____ cycle some host cell DNA is accidentally packaged into a viral particle
- This ___ injected into new cell in place of phage ___
lytic; DNA; DNA
107
Specialized Transduction:
- When a _______ is induced, its DNA is excised from genome & packaged into phage particles
- Sometimes some neighboring DNA is also packaged by mistake
- This DNA can then be _________ into a new cell by that phage particle
prophage; injected
108
What is conjugation?
Horizontal gene transfer that requires cell-cell contact
109
Typically _________ is mediated by plasmids called conjugative plasmids (the F plasmid has been a model)
conjugation
110
______ cell uses a conjugative pilus to grab a recipient cell
Donor
111
What is the specialized type IV secretion system used for?
In conjugation, this is used to replicate and transfer specific DNA from donor to recipient cell
112
Occasionally, the ____ __ ________ ______ can be used to transfer genomic DNA from one bacterium to another
type IV secretion system
113
What is genetic recombination?
Physical exchange of DNA between genetic elements
114
___________ _____________ is an important DNA repair mechanism used to repair double strand breaks and is important for horizontal gene transfer
Homologous recombination
115
Homologous recombination is important for ______ ______________ - deletions, duplications, inversions or segments of genomic DNA
genome rearrangements
116
What are transposable elements?
mobile genetic elements found in almost all species
117
_________ ________ contain a transposase gene flanked by ________ repeats
Transposable elements; inverted
118
Transposase enzymes are able to:
- recognize inverted repeats of ___ ________
- cleave that DNA to free "_________ ________"
- insert the transposable element into that DNA
- this process is called ___________
DNA sequences; transposable elements; transposition
119
Many transposable elements are _____________ - the move from one place to another. Others work via __________ mechanism - transposon remains and a copy is produced
conservative (cut and paste); replicative (copy and duplicate)
120
During evolution via horizontal gene transfer, much acquired DNA will ___ be evolutionarily useful and will ultimately be lost
not
121
What are these used for?
- transposon or recombination-mediated processes
- random processes/ errors during DNA replication or DNA repair
Evolution via horizontal gene transfer
122
During evolution, genes that provide a _________ __________ will be maintained and can outcompete parental strains that lack this new DNA
selective advantage
123
Microbial genomes contain a great deal of ____________-_________ DNA (we know from differences in GC content from related lineages)
horizontally-acquired
124
Horizontal gene transfer has a huge impact on _________ _______ via new virulence mechanisms and antibiotic resistance
infectious disease
125
Gene names are __ letters
4
126
The first 3 letters of gene names describe ________; and the fourth letter designates a _______ gene
function; specific
127
btuC is an example of a ____ _____
gene name (first three italicized)
128
BtuC is an example of a _______ _____
protein name (not italicized)
129
________ naming conventions vary, sometimes from species to species
Eukaryotic
130
A ___________ mutation relies on natural mutations that arise by random processes
Spontaneous
131
What are induced mutations?
When the organism is exposed to agents that increase the mutation rate. ex: UV light, chemicals interacting with DNA
132
_________ ________ mutations introduce a transposon which randomly inserts into the genome of the organism. It generally disrupts whatever gene it inserts into
Transposon insertion
133
_________ carries antibiotic resistance gene to isolate bacteria with a Tn insertion
Transposon
134
With selection, antibiotics can be used to identify the _______ if it grows and the parent doesn't
mutant
135
True or False:
Selection is highly efficient and can identify a single mutant with a desired phenotype out of millions of cells
True
136
It is easier to identify mutants that ____ _____ than parents by selection
grow better
137
You can identify mutants that grow worse that parents by using _______ _______
replica plating (plating the same colony on two different plates under two different conditions)
138
What is an example of mutants that require a specific nutrient to grow?
Auxotroph mutants
139
What does INseq stand for?
Transposon INsertion site sequencing
140
INseq is a useful modern _________ _________ tool
bacterial genetics
141
INseq is a large library of transposon (Tn) mutants. There are lots of different bacteria, each with ___ random __ ________.
One; Tn insertion
142
You can uncover the _________ of each Tn mutant in your library by sequencing the Tn insertion sites
frequency
143
The _____ __________ of DNA are being read during sequencing
input populations
144
To get an ______ _________, expose the mutant library to some sort of challenge
output population
145
What did Craig Venter do?
- didn't invent anything
- major name in DNA sequencing
- steered things in the right direction - computers are useful
146
DNA sequencing used to take ____ to accomplish, but is now much faster
years
147
Currently, all _________ isolates are typed by whole genome sequencing (WGS) as per PulseNet standardized protocol
Salmonella
148
DNA sequencing is now very accessible. It is $__ to sequence a complete genome
90
149
It takes __-__ days to sequence a complete genome
1-2
150
DNA ________ works by using short primers
polymerase
151
DNA sequencing was developed by Frederick _______ in the _____s (he got the Nobel prize for it)
Sanger; 1970s
152
DNA sequencing is based on DNA polymerase building a complementary strand using mostly ________ _____ and rare special _____ that lack a _____ and therefore cannot be elongated further
normal dNTPs; dNTPs; 3'OH
153
Special ddNTPs are each ________ a different way (different fluorophores)
labelled
154
Sanger sequencing uses __________ which are all a different colour
fluorophores
155
For Sanger sequencing, a _____ DNA primer is sequenced from a template strand but DNA polymerase is at the missing ____ in ddNTPs.
short; 3'OH group
156
What is an illumina image?
An image where each dot represents a cluster (DNA molecule being sequenced)
157
Reversibly terminated dNTPs used:
- Insert one labelled residue, take an image (A,C,T,G each a different ______ of fluorophore)
- Unblock the __' end so you can add another residue. Repeat.
- Each round, you ger an image of what residue is at each _______ for that position
colour; 3'; cluster
158
If we want to use genome sequencing tech to identify organisms them what do we need to know about them?
The organisms genome sequence
159
Genome sequencing can tell us:
- metabolic capabilities of an organism
- virulence genes, antibiotic resistance genes
- unusual mutations/phenotypes
- discover new genes
160
Genome sequencing provides a DNA ________ required for many studies/analyses
blueprint
161
What is the study of proteins called?
Proteomics
162
Genome sequencing can provide us with ________ & ___________ predictions for an organism
functional & metabolic
163
__________ is the study of the complete genetic content of an environmental sample, and can be done at the gene level
Metagenomics
164
When is it useful to use metagenomics to do massive sequencing of DNA purified from environmental samples to gather genomic information?
For organisms that cannot be cultured in the lab
165
Metagenomics can tell us about the ___________ of microbial communities and how that changes
composition
166
_____________ can be useful to understand which genes are being regulated/ turned on at one time
Transcriptomics
167
In transcriptomics, RNA can be converted to DNA using a process called _______ ___________, which can then be sequenced via next-generation methods
reverse transcription
168
Transcriptomics can be used to compare the expression of genes under different ________.
conditions
169
________ often relies on knowing the genomic DNA sequence, but doesn't use DNA sequencing
Proteomics
170
What does proteomics use to identify proteins/ protein levels?
mass spectrometry
171
Proteomics can tell you what _____ are present under which conditions
proteins
172
Does DNA do anything effective on its own?
No, it must be expressed and regulated
173
Transcription forms ___
Translation forms ________
RNA; protein
174
What are the three phases of transcription in bacteria?
1) Initiation
2) Transcription (elongation)
3) Termination
175
For DNA sequences to carry out functions, it must be converted to ____ via transcription
RNA
176
Transcriptional initiation is guided by DNA sequences called _______
promoters
177
What are promoters for transcription?
DNA sequences bound by factors that promote transcriptional initiation (residing upstream of genes)
178
The promoter is the key to ________ and informs transcription machinery of what to do
initiation
179
Binding of the ______ ________ and _________ ________ to the promoter region dictated if the promoter is active
sigma factors and regulatory proteins
180
Transcription uses an enzyme called ___ ___________
RNA polymerase
181
A ______ ________ is a special subunit of RNA polymerase that binds DNA as an essential step in initiating transcription
sigma factor
182
Different sigma factors produced under different conditions recognize different _________.
sequences
183
***The housekeeping sigma factor is called _____
RpoD
184
What does RpoD recognize?
Two sequences upstream of the transcriptional start site
185
RpoD
- What is the Upstream recognition sequence?
- What is the function?
- TTGACA
- For most genes, major house-keeping sigma factor for normal growth
186
RpoS
- What is the Upstream recognition sequence?
- What is the function?
- CCGGCG
- Stationary phase, plus oxidative and osmotic stress
187
The transcriptional start site is ~__ bp upstream from the +1 site, and the Pribnow box is ~10 bp upstream of it
35; 10
188
The __' end of a gene is considered upstream
5'
189
DNA has two strands, one is the coding strand and one is the _________ strand
template
190
Transcription only works in one direction, so RNAs are built from __' to __'
5' to 3'
191
RNA polymerase core enzyme is made up of __ subunits: alpha, beta, w, Holoenzyme includes sigma subunit
5
192
The _____ ______ binds the RNA polymerase (core enzyme) to the DNA strand then dissociates from the core enzyme
sigma factor
193
The ____ _______ creates a transcription bubble where DNA unwinds to expose the template for the formation of the RNA chain
core enzyme
194
____ are used as substrates to build the RNA chain one nucleotide at a time in the transcription bubble according to the DNA template strand
NTPs
195
Transcription continues until RNA polymerase encounters a ___________ __________. RNAP then dissociates from DNA, stops making RNA and releases transcript
transcriptional terminator
196
_________ __________ form when RNA hairpin structures form, followed by a string of "U" residues.
Intrinsic terminators
197
U residues act as a _____ ______ for RNAP - formation of hairpin forces RNAP off template
pause signal
198
What are rho-dependent terminators?
A protein called Rho binds RNA as it is being transcribed and causes RNA polymerase to dissociate after it encounters certain sequences
199
RNA that is converted to protein via translation
mRNA (messenger RNA)
200
RNA that's functional, used in translation process
tRNA (transfer RNA) and rRNA (ribosomal RNA)
201
~ __ % of RNA in cell is rRNA and tRNA
95
202
_____s contain both open reading frames (ORFs) and untranslated regions (UTR)
mRNAs
203
ORFs are translated to ________
protein
204
UTRs are parts of the mRNA transcript that are ____ translated into protein
not
205
What is the name for mRNAs that encode multiple ORFs?
polycistronic
206
Genes in an operon are ___________
cotranscribed
207
The ___ runs from the start codon through to the stop codon
ORF
208
Eukaryotic RNA polymerases are ____ ______ than of bacteria
more complex (12+ subunits)
209
Eukaryotic RNA polymerase requries ________ ______ to recognize promoters (they bind specific DNA sequences & recruit RNA polymerase)
transcription factors
210
Eukaryotes do not use ________ because each gene has its own promoter
operons
211
_________ RNA polymerase resembles RNA polymerase II from eukaryotes and has 11-13 subunits
Archaeal
212
Transcription in archaea is basically a less complex version of _________ transcription
eukaryotic
213
Proteins are ______________ that are comprised of polymers of amino acids connected by peptide bonds
polypeptides
214
Amino acids have an amino group on one side, an alpha-carbon in the middle (with R-group) and a ________ croup on the other side
carboxyl
215
_________ bonds hold proteins together by connecting the carboxylic acid group and the amino group of two amino acids
peptide
216
Proteins are ________ and run from their N-terminus to __-terminus
directional; C-terminus
217
The chain of amino acids in a protein is referred to as its ______ ________
primary structure
218
The most common secondary structures for proteins are ? And how are they formed?
alpha helices and beta sheets -- formed by hydrogen bonding in peptide backbone
219
There is great __________ diversity among proteins
structural
220
The ribosome uses tRNAs to convert the mRNA sequence into a _______ sequence
protein
221
tRNAs are ~__-__ bases long, extensively structured, and often contain ______ bases
70-90; modified
222
Each tRNA has a specific _________ that binds a particular three base codon for protein translation
anticodon
223
tRNA ___________ are the enzymes that "charge" tRNAs -- add the amino acid to the CCA and the 3' end
synthetases
224
Start codons encode for the first amino acid of a particular ___
ORF (N-terminal amino acid of a protein)
225
Translation typically begins at start codon ___ for all domains of life
AUG
226
In bacteria, start codon is translated to _-_____________ using a special tRNA
N-formylmethionine (fMet)
227
