Mod 3 Microbial Genetics Flashcards
1
Q
The study of heredity
A
Genetics
2
Q
Sum total of genetic material within a cell
A
Genome
3
Q
Genome of cells is made up of
A
DNA
4
Q
Genome of viruses is made up of
A
DNA or RNA
5
Q
mode of gene transfer in which DNA is taken up by cell and incorporated into it’s genome
A
Transformation
6
Q
units of DNA that contain the genetic information
A
Genes
7
Q
Gene Expression
A
begins with transcription, leading to translation and conformation
8
Q
Nucleoside
A
nitrogenous base + pentose sugar
9
Q
Nucleotide
A
nucleoside + phosphate groups
10
Q
In a eukaryotic cell the genome is made up of DNA information found in
A
The nucleus, chloroplasts, and mitochondria
11
Q
In a prokaryotic cell the genome is made up of DNA information found in
A
Plasmids
12
Q
Condensed, tightly wrapped form of the DNA molecule
A
Chromosome
13
Q
Shape of chromosomes for prokaryotic (eubacteria) cells
A
Single circular loops
14
Q
Shape of chromosomes for eukaryotic cells
A
Multiple and linear ( open on the ends)
15
Q
Two researchers who played a critical role in establishing that DNA is the genetic material
A
Fred Griffith (early 1900s) & Oswald Avery (mid 1900s)
16
Q
Discovered that non-pathogenic heat killed smooth strain and non-pathogenic rough cells combined to cause an infection
A
Fred Griffith
17
Q
Refined Griffith’s transformation experiments to show that DNA was the genetic material being transferred
A
Oswald Avery
18
Q
Two main themes of the Central Dogma of Biology
A
- DNA Replication
2. Gene Expression
19
Q
fundamental units of heredity that are responsible for a given trait
A
genes
20
Q
site on the chromosome that provides information for a certain cell function
A
genes
21
Q
genetic sequence of the DNA of a particular organism
A
Genotype
22
Q
physical expression of the genes; observable/measurable traits
A
Phenotype
23
Q
Genome size of a virus
A
4-5 genes
24
Q
Prokaryotic genome size - ex. E.coli
A
4,288 genes
25
Genome size of Human cells
31,000 genes
26
Two types of nucleic acids
DNA & RNA
27
Structure of a Nucleotide (3 parts)
1. Purine or pyrimidine base (nitrogen containing)
2. Ribose or deoxyribose (5 carbon sugar group)
1 & 2 } form Nucleoside of deoxynucleoside and
combine with
3. Phosphoric acid
28
Nucleoside =
nitrogenous base + pentose sugar
29
Nucleotide =
nucleoside + phosphate group
30
2 groups of Nitrogenous bases in DNA structure
Purines & Pyrimidines
31
Adenine & Guanine
Purines of DNA
32
Thymine & Cytosine
Pyrimidines of DNA
33
5 carbon sugar that is deoxygenated on carbon #2
Deoxyribose
34
alternate with pentose sugars to form the backbone of DNA structure
Phosphate groups
35
Individual nucleotide are connected together by ______ which are a type of ______.
phosphodiester bonds; covalent bond
36
two complementary strands of the repeating phosphate/pentose sugar + nitrogenous base structure form a
double helix
37
Describes that one strand of the double helix is situated in the 5'-> 3' while the other is 3' ->5'
Antiparallel
38
Base pairing rules
A with T: 2 hydrogen bonds
| G with C: 3 hydrogen bonds
39
Adenine only pairs with ____
Thymine
40
Guanine only pairs with ____
Cytosine
41
Nitrogenous base attaches to the
#1 Carbon
42
Phosphate groups attach to
3 & #5 Carbons
43
What is the complement to the following strand of DNA? 5' - TTGCTAAGG - 3'
3' - AACGATTCC - 5'
OR
5' - CCTTAGCAA - 3'
* Must denote orientation*
44
```
An organism with 1000 nucleotide base pairs in it's genome was found to contain 100 Adenine bases.
How many...
Thymine?
Guanine?
Cytosine?
```
```
Thymine = 100
Guanine = 900
Cytosine = 900
```
45
Pyrimidines of RNA
Cytosine & Uracil
46
Purines of RNA
Adenine & Guanine
47
Pentose sugar of RNA
Ribose Sugar
48
Consists of a single strand of nucleotides that can double back on itself and form a hairpin shape
RNA structure
49
3' - TACGTTCCATAG - 5'
| mRNa transcript of this DNA template is:
5' - AUGCAAGGUAUC - 3'
50
Three types of RNA
- ribosomal RNA (rRNA)
- transfer RNA (tRNA)
- messenger RNA (mRNA)
51
Coding RNA
messenger RNA (mRNA)
52
Non-coding RNA
ribosomal RNA & transfer RNA
53
Prokaryotic DNA is organized in one of two forms:
relaxed circle, or supercoiled DNA
54
Eukaryotic DNA wraps around these protein molecules to allow it to condense and take on a more closed form
Histones
55
Nucleosomes
coiled repeating units of DNA wrapped around histones
56
DNA Replication process
Parental DNA strands open and hydrogen bonds are broken to allow DNA Polymerase to read sequence and form a new daughter strand from the template
57
DNA Replicas are comprised of
1 Parental strand and 1 New daughter strand
58
Prokaryotic DNA Synthesis Process
DNA Polymerase Enzymes bind to the Origin of Replication and move away from each other (bidirectional) when they reach the Terminus the new circular chromosome has been created
59
Eukaryotic DNA Synthesis Process
Sets of DNA Polymerase enzymes bind to multiple origins of replication and move bidirectionally
60
The molecule of DNA that is read and interpreted to synthesis the new daughter strand is called
DNA template
61
DNA templates are always read in the _____ direction and synthesized in the _____ direction
3' - 5' ; 5' - 3'
62
DNA polymerase can't recognize the DNA template until a short strand of RNA primer is attached to it. This is synthesized by the enzyme_____
Primase
63
These are polymerized together to form a daughter stand of DNA
Deoxynucleotides
64
Binds to both sides of DNA at the Replication fork to catalyze synthesis of daughter strands
DNA Polymerase III
65
The enzyme opens up and breaks the hydrogen bonds between bases at the origin sites
DNA Helicase
66
Weak spots where Helicase can more easily break bonds
Adenine & Thymine (only 2 hydrogen bonds)
67
Bind to DNA to prevent reformation of hydrogen bonds until DNA Polymerase III can read and begin replication process
Single-stranded DNA binding proteins (SSBs)
68
ahead of the replication fork this enzyme unwinds DNA to relieve tension caused by Helicase to prevent "knots"
DNA Gyrase
69
Leading strand
the strand that is oriented in the 3' to 5' orientation
70
Lagging strand
has to get bent due to the fact that it is in the 5' to 3' orientation and is therefore synthesized discontinuously
71
Fragments formed on the lagging stand due to discontinuous synthesis
Okazaki fragments
72
works on lagging strand to remove primers and fills DNA gaps with correct nucleotides
DNA Polymerase I
73
enzyme that creates the covalent bonds to join Okazaki fragments to form a complete strand
DNA ligase
74
Has the ability to backup one base and remove a mismatched base
DNA polymerase III
75
DNA replication occurs faster in _____ with a rate of 750 to 1000 base pairs/ second
and slower in _______ at a rte of 50 - 100 base pairs per sec.
faster - prokaryotes
| slower - eukaryotes
76
the process of transcription, translation, & conformation to interpret the DNA code & produce functional protein
Gene Expression
77
small linear sequence of nucleotides with a fixed start & end point
Gene
78
a set of three nucleotides that codes for a single amino acid
Codon
79
T/F All genes code for proteins
False - tRNA & rRNA function as is
80
T/F One gene produces one polypeptide
True
81
the orientation in which a set of nucleotides are to be read
Reading Frame
82
Only one strand of DNA contains the gene. This strand is called the
Template Strand
83
This strand is interpreted by RNA polymerase to direct and create the RNA molecule (tRNA, mRNA, rRNA)
Template Strand
84
the complementary strand
Coding Strand
85
The _______ & the ________ are most important gene regions in the transcription steps.
Promotor; terminator
86
The ________ & the ________ are most important in directing translation
leader; trailer
87
This region of the gene contains the information that directs the synthesis of the polypeptides
Coding
88
sequence of bases that is located at the start of the 3' end of a gene
Promoter
89
Region important for enhancing the binding of RNA polymerase
Promoter
90
Two sites recognized by RNA polymerase as weak areas for binding
- 10 promoter (Pribnow Box)
| - 35 promoter
91
This region is not transcribed or translated
Promoter
92
Starts with the +1 nucleotide in the mRNA
Leader region
93
Contained in the leader region and helps alignment of mRNA with the 16s rRNA ribosome
Shine-Delgarno Sequence
94
always starts in the DNA sequence with TAC
Coding region
95
Universal start codon sequence
AUG
96
Stop codons
UGA,
UAG,
UAA
97
Required for expression of coding region
Trailer sequence
98
Required for stopping the transcription process
Terminator sequence
99
mRNA molecule is a transcription of these regions
Leader, Coding, Trailer
100
Through translation the mRNA molecule is used to create a
polypeptide
101
3 Steps of Transcription
Initiation
Elongation
Termination
102
Formation of the transcription bubble occurs during
Initiation
103
Once RNA polymerase has bound to the promotor and it opens and begins unwinding we have formed the
Transcription Bubble
104
RNA polymerase transcribes the DNA template. This step is
Elongation
105
RNA polymerase reads the template in the orientation _______ and synthesizes RNA in the orientation ________
3' - 5' ; 5' - 3'
106
Eukaryotic transcription takes place in
the nucleus
107
"important" information in genes
Exons
108
"non-important" information in genes
Introns
109
Eukaryotic Promotors
TATA box (-30) & CAAT box (-50-100)
110
take up space and segment exons; must be removed from transcript for ribosome to read and produce the correct protein
Introns
111
Added to the 5' side as posttranscriptional modification to protect it from enzymatic digestion
7 -methylguanosine nucleotide (guanine cap)
112
Added to the 3' side in posttranscriptionl modification to protect it from enzymatic digestion
200 adenine nucleotides - Poly-A tail
113
3 Posttranscriptional modifications in Eukaryotic transcription
1. Guanine cap added
2. Poly A tail added
3. Introns cut out and exons connected together
114
Enzymes that forms lariat and removes introns
Splicesomes
115
Posttranscriptional modifications are only seen in _______ organisms
Eukaryotic
116
Translation occurs by reading
codon sequences
117
more that one codon can code for the same amino acid called
Code degeneracy
118
of possible codons
64
119
61 codons that code for specific amino acids
sense codons
120
3 codons that are stop codons
Nonsense
121
The universal start codon is ____ and codes for ____
AUG; methionine
122
3rd position of the codon can vary without changing the correct amino acid - 1st & 2nd are most important
Wobble Effect
123
This type of RNA is the transcript template with the codon sequence
mRNA
124
This type of RNA carries specific amino acids to the ribosomes for protein synthesis
tRNA
125
RNA that is a component of the ribosomes and either catalyzes transpeptidation reactions or aligns the mRNA to the Shine-Delgarno sequence
rRNA
126
In ________ transcription and translation can occur simultaneously but in ______ they are separated by the ______.
Prokayotes; Eukaryotes; nuclear membrane
127
Numerous ribosomes can synthesis on one mRNA strand called a
polyribosome
128
the end of the tRNA molecule that contains the amino acid
Acceptor end
129
If the acceptor end has an amino acid attached it is called
charged tRNA
130
The end of tRNA that is exposed to recognize/bind the mRNA codon
Anticodon
131
Two subunits of ribosome
30S & 50S
132
found in the 30S subunit of ribosome and is the complement to the shine-delgarno sequence - recognizes it for alignment
16S rRNA
133
found in the 50S subunit of ribosome and has enzymatic activity to form peptide bonds between amino acids
23S rRNA
134
Process of Initiation
1. 30S subunit binds to mRNA
2. Special initiator tRNA carries methionine binds to 30S subunit
3. 50S subunit binds the 30S-mRNA-tRNA complex
135
3 important sites on Ribosome
A site, P site, E site
136
site that accepts incoming tRNA
A site
137
site that contains tRNA with polypeptide chain and donates it to the tRNA in A site when bond is formed
P site
138
site where tRNAs are released
E site
139
Elongation of the polypeptide chain is terminated when
A stop codon enters the A site
140
WHich region contains he shine-delgarno sequence
Leader
141
WHich gene region is important for RNA polymerase binding and activity?
Promoter
142
List all the Purines
Adenine & Guanine
143
List all the Pyrimidines
Thymine, Cytosine, & Uracil
144
Genes that are expressed continuously
constitutive genes
145
housekeeping genes
produced all the time and play a central routine role in the maintenance of the. cell
146
encode for enzymes that are expressed in specific situation - can be turned on/off
Inducible genes
147
the effector molecule that increases the expression of the inducible gene
inducer
148
Regulatory proteins of transcription
repressor proteins & activator proteins
149
proteins that bind to specific sites on the DNA to inhibit or enhance RNA polymerase binding
Regulatory proteins
150
Repressor proteins bind to
operator regions
151
activator proteins bind to
areas upstream of the promotor
152
Polycistronic
In an open reading frame there is more than one gene that is produced
153
Prokaryotic genomes encode for more than one gene so are
polycistronic
154
Eukaryotic genomes are
monocistronic
155
the sequence of bases coding for a cistron
Operon
156
regulates an organism to only work to catabolize lactose when it is present
Lac Operon
157
there is always a low level of basal transcription occurring because
operons are leaky
158
When lac(i) is present it binds to the operator region as a
repressor
159
structural genes of the lac operon
lacZ, lacY, lacA
160
functions of B-galactosidase
- breaks lactose down to glucose & galactose
| - converts lactose to allolactose
161
produces B-galactosidase
lacZ gene
162
function of lactose permease
transport lactose from outside to inside the cell
163
produces lactose permease
lacY gene
164
this turns on the lac operon
allolactose
165
galactoside transacetylase without a known function
lacA
166
not part of the lac operon but is important in controlling it
lacI
167
when there is no lactose present
the lac operon gene is not turned on
168
When lactose is present _____ is formed by B-galactosidase.
allolactose
169
Allolactose binds to the _______ releasing it from the operator and allows for expression of the lac operon.
repressor protein
170
When a cell uses all the lactose in the environment there is not more production of allolactose so
the repressor protein is opened and freed to attach back to the operator
171
These operons are biosynthetic/ anabolic pathways
Argenine Operon & Tryptophan Operon
172
Argenine acts as a co-repressor meaning
it binds to the inactive repressor to bind to operator to block RNA polymerase activity
173
the end product from the Argenine operon is
enzymes that help in the synthesis of Argenine
174
Repressor of argenine operon is formed in _______ and requires ________ as a co-repressor.
and inactive state; argenine
175
Genes of the trp operon are
enzymes used to synthesize Tryptophan
176
molecules that are used to regulate this operon work by bending the DNA at the promotor region preventing it from binding
Arabinose Operon
177
These regulate the Arabinose operon by binding to different sites on and around the operator to bend the molecule
AraC molecules
178
AraC molecules have open ends that bind to _____ when there is no Arabinose in the environment.
eachother
179
A change in phenotype due to a change in genotype
mutation
180
An organism that is in it's natural, nonmutated characteristic
wild type
181
An organism that has a mutation
mutant strain
182
mutation that creates a mutant from a wild type strain
forward mutation
183
mutation that reverts a mutant strain back to a wild type strain
reversion (back) mutation
184
Two categories of mutation causes
spontaneous mutations & induced mutations
185
a random change in the DNA due to errors in replication without a known cause
Spontaneous mutations
186
mutations that result from exposure to known mutagens
Induced mutations
187
Categories of Mutations
```
Point
Missense
Nonsense
Silent
Frameshift
```
188
mutation category - substitution of a base occurs
Point mutation
189
mutation category - causes change in a single amino acid
Missense mutation
190
mutation category - changes a normal codon into a stop codon which truncates a polypeptide
Nonsense mutation
191
mutation category - changes a base but does not alter the phenotype of the cell
Silent mutation
192
mutation category - when the reading frame of the mRNA is shifted. Occurs when 1 or 2 bases are added or deleted
Frameshift mutation
193
Used as a repair mechanism by proofreading and exonuclease activity
DNA polymerase
194
repair that occurs by removing distorted bases or entire nucleotides that cause a distortion
Excision repair
195
repair that occurs by repairing altered bases without removing them
Direct repair
196
uses the enzyme photolyase to split thymine dimers apart using visible light
Photoreactivation
197
This repair requires the cell to have a copy of the molecule that needs to be repaired to use as a "blueprint" for repair
Recombinatorial Repair
198
A mutant organism that requires an essential macromolecule be provided to it because it can't make it
Auxotrophs
199
method used to indirectly select auxotrophic mutants through selective media
Replica plating
200
Selection of mutants that can grow in an adverse condition or environmental stress
Direct Selection
201
What is the Ames test?
a test for carcinogens; a mutational reversion assay
202
Indicator organism in the Ames test that is a mutant strain of Salmonella typhimurium
Auxotroph Histidine
203
transfer of DNA from one cell to another cell
Horizontal Gene Transfer
204
transfer or DNA by direct cell to cell contact
Conjugation
205
requires formation of the sex pilus for DNA transfer
Conjugation
206
This is used to transfer plasmids of pieces of chromosomal DNA
Conjugation
207
methods of creating genetic variation
Horizontal Gene Transfer, Transformation, Transduction, Transposition
208
DNA segments that shift from site to site
Transposons
209
Genetic variation that occurs when pieces of DNA move and integrate into different sites in the chromosomes
Transposition
210
Genetic variation that occurs when DNA is transferred from cell to cell by bacterial phage
Transduction
211
AKA Jumping Genes
Transposons
212
Using a plate with antibiotic on it and growing a culture is a _______ method for isolating _______.
direct; antibiotic resistant mutations
213
An Ames test is performed and the plate results in no growth - this means
the chemical being tested is not a carcinogen - does not have the ability to revert mutation
214
requires one cell to be an F+. cell and another to be F- to build a conjugation tube/ sex pilus
Horizontal Gene transfer
215
Competent cells pick up DNA fragments from the environment and incorporate it into it's DNA; demonstrated in Griffith's experiments
Transformation
216
When phage takes up information from one host cell and carries it to infect another cell _______ occurs.
Transduction
