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Microbiology > Lecture 5 Bacterial Genome Replication, expression, and regulation 1 > Flashcards

Lecture 5 Bacterial Genome Replication, expression, and regulation 1 Flashcards

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Biology 101 flashcards
1
Q

All DNA present in a cell or virus

A

Genome

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2
Q

Bacteria and Archaea generally have ___ set(s) of DNA

A

1 (haploid-1N)

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3
Q

Eukaryotes have ___ set(s) of DNA

A

2 (diploid-2N)

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4
Q

Specific set of genes an organism possesses

A

Genotype

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5
Q

Collection of observable characteristics

A

Phenotype

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6
Q

Griffith in 1928 observed the change of non-virulent organisms into virulent ones as a result of ______

A

transformation

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7
Q

MacLeod and McCarty in 1944 showed that the transforming particle in Griffith’s experiments was ___

A

DNA

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8
Q

Explain how Hersey and Chase experimented to show DNA as a genetic material in 1952

A
  • They used bacteriophage T2 infection as a model
  • They labeled DNA with 32P (radioactive marker)
  • They labeled the protein coat with 35S(radioactive marker)
  • Their experiment showed that only DNA entered the cell but both new DNA and protein coats were synthesized in new viruses thus indicating DNA had genetic information for both of these viral components
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9
Q

DNA and RNA are polymers of nucleotides linked together by ______

A

phosphodiester bonds

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10
Q

DNA is transcribed into

A
  • tRNA, mRNA, rRNA, snRNA
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11
Q

what are the forms of RNA

A

tRNA, mRNA, rRNA, microRNA, siRNA, snRNA

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12
Q

___ and ___ grooves form when the 2 DNA strands twist around each other

A

major and minor

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13
Q

Most RNA molecules are ____ stranded but some are _____

A

single, double stranded

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14
Q

Proteins are polymers of ____ linked by ____ bonds

A

amino acids, peptide

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15
Q

amino acids have a ___ carbon, ____ group, ___ group, and ___ chain

A

central carbon, carboxyl group (c-terminus), Amino group (N-terminus), and side chain

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16
Q

what determines the properties of the amino acids

A

the side chain

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17
Q

DNA replication is semi-conservative meaning what

A

each daughter cell obtains one old and one new strand

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18
Q

DNA in most bacteria is ____

A

circular

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19
Q

The portion of the genome that contains an origin that is replicated as a unit

A

replicon

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20
Q

Because the bacterial chromosome is a single replicon

A

The forks meet on the other side and two separate chromosomes are released

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21
Q

DNA in bacteria has _____ replication from a single origin

A

Bidirectional

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22
Q

the replication of Bacteria, such as E. coli, consists at least _____ proteins

A

30

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23
Q

The two replication forks in bacterial DNA replication proceed bidirectionally until they meet a site called the

A

replication termination site (ter)

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24
Q

What serve as DNA polymerase substrates

A

deoxynucleoside triphosphates: dATP, dTTP, dCTP, dGTP

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25
Q

What are incorporated into the growing DNA chain

A

deoxynucleoside monophosphates: dNMPs: dAMP, dTMP, dCMP, dGMP

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26
Q

For DNA polymerase to catalyze the synthesis of DNA it needs what 3 things

A
  • A template (which is read in the 3’ to 5’ direction
  • a primer (to provide a free 3’-hydroxyl group to which nucleotides can be added
  • dNTPs
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27
Q

function of DnaA in E. coli

A

initiation of replication; binds origin of replication (oriC)

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28
Q

function of DnaB in E. coli

A

Helicase (5’–>3’) ; breaks hydrogen bonds holding two strands of double helix together ; promotes DNA primase activity; involved in promise assembly

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29
Q

function of DNA gyrase in E. coli

A

Relieves supercoiling of DNA produced as DNA strands are separated by helicases; separates daughter molecules in final stages of replication

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30
Q

Function of SSB (single stranded binding) proteins

A

Bind single-stranded DNA after strands are separated by helicases

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31
Q

Function of DnaC in E. coli

A

Helicase loader, helps direct DnaB protein (helicase) to DNA template

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32
Q

function of DNA primase

A

Synthesis of RNA; component of primosome

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33
Q

Function of DNA polymerase III holoenzyme

A

complex of about 20 polypeptides; catalyzes most of the DNA synthesis that occurs during DNA replication; has 3’—>5’ exonuclease (proofreading) activity

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34
Q

Function of DNA polymerase I

A

Removes RNA primers; fills gaps in DNA formed by removal of RNA primer

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35
Q

Functions of Ribonuclease H in E. coli

A

Removes RNA primers

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36
Q

Functions of DNA ligase

A

Selas nicked DNA, joining DNA fragments together

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37
Q

Function of Tus in E. coli

A

Termination of replication

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38
Q

What is the function of Topoisomerase IV in E. coli

A

Separation of chromosomes upon completion of DNA replication

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39
Q

E. coli has ____ different DNA polymerases

A

5

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40
Q

DNA polymerase III holoenzyme is a multifunctional enzyme composed of ___ different proteins

A

10

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41
Q

Polymerase III has ____ core enzymes

A

2 (some evidence suggests 3)

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42
Q

What are the functions of the 2 core enzymes in DNA polymerase III

A
  • catalyze DNA synthesis (alpha subunit)

- Proofreading for fidelity (epsilon subunit)

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43
Q

what is the function of the tau dimer in DNA polymerase III holoenzyme

A

clamp loader, each subunit is attached to a core enzyme

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44
Q

_____ unwinds DNA strands

A

Helicases (DnaB)

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45
Q

Keeps strands apart for replication to occur

A

single stranded binding proteins (SSB)

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46
Q

Breaks one strand of DNA to relieve tension from rapid unwinding of double helix and prevents super coiling

A

Topoisomerases

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47
Q

_____ is an important topoisomerase in E. coli that is not only important during DNA replication but also for introducing negative supercoiling in the bacterial chromosome that helps compact it

A

DNA gyrase

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48
Q

synthesizes short complementary strands of RNA (about 10 nucleotides) to serve as primers needed by DNA polymerase

A

Primase (this is an RNA polymerase), which means that it can initiate RNA synthesis without an existing 3’-OH

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49
Q

The complex of primase and its accessory proteins is called the

A

primosome

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50
Q

Bacterial initiator protein ____ is responsible for triggering DNA replication

A

DnaA

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51
Q

DnaA proteins bind regions in ____ throughout the cell cycle, to initiate replication

A

OriC

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52
Q

After most of the lagging strand has been synthesized by the formation of Okazaki fragments. DNA polymerase ____ removes the RNA primers.

A

I

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53
Q

unlike DNA polymerase III DNA polymerase I has the ability to snip off nucleotides one at a time starting at the

A

5’ end while moving toward the 3’ end of the RNA primer

5’ to 3’ exonuclease activity

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54
Q

In the lagging strand at the end of each okazaki fragment the B clamp loader

A

is discarded and a new one is added

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55
Q

DNA ligase forms a phosphodiester bond between _________ of the growing strand and the ______ of an okazaki fragment

A

3’-hydroxyl, 5’-phosphate

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56
Q

DNA polymerase III has removes mismatched bases by _____ activity

A

3’-to-5’ exonuclease activity

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57
Q

Replication of E. coli stops when the replisome reaches _______ on DNA

A

termination site (ter)

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58
Q

____ form when the two circular daughter chromosomes do not separate after replication (interlocked)

A

Catenanes

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59
Q

____ is when Two chromosomes joined together to form a single chromosome that is twice as long

A

dimerized chromosome

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60
Q

Dimerized chromosomes are resolved by

A

XerCD recombinase (these catalyze an intramolecular cross-over that separates the two chromosomes

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61
Q

Catenanes arise from the activity of ______ during chromosome replication. Accordingly, they are resolved by _____

A

topoisomerases, topoisomerases

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62
Q

dimerized chromosomes arise from ______ that can occur during chromosome replication between daughter chromosomes

A

recombination events

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63
Q

how can bacteria solve the linear chromosome problem

A
  • disguise their ends

- An enzyme telomere resolvase (ResT) forms hairpin ends for each daughter molecule

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64
Q

a basic unit of genetic information

A

Gene

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65
Q

codons are found in ____ and code for a single amino acid

A

mRNA

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66
Q

_____ strand of DNA directs RNA synthesis

A

template strand (read in the 3’-to-5’ direction)

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67
Q

____ DNA strand is the same nucleotide sequence as mRNA

A

coding strand (complementary DNA strand)

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68
Q

____ is the binding site in a gene for RNA polymerase

A

promoter

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69
Q

The promotor is neither transcribed nor translated; it functions

A

strictly to orient RNA polymerase so it is a specific distance from the first DNA nucleotide that will serve as a template for RNA synthesis

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70
Q

The transcription start site represents the

A

first nucleotide in the mRNA synthesized from the gene (note that this site does not necessarily code for amino acids)

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71
Q

What is the important sequence in the leader region ( point that is transcribed into mRNA but is not translated into amino acids) in bacteria that initiates translation

A

Shine-Dalgarno sequence

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72
Q

The coding region typically begins with the template DNA sequence _____

A

3’-TAC-5’ (this is transcribed into 5’-AUG-3’ which codes for the first amino acid)

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73
Q

3’-AUG-5’ on mRNA codes for

A

N-Formylmethione (start codon)

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74
Q

The coding region ends with

A

a stop codon immediately followed by a trailer (which is transcribed but not translated and prepares the RNA polymerase to detach), and then a terminator which makes the RNA polymerase detach

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75
Q

DNA sequences that code for tRNA and rRNA are considered ____

A

genes

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76
Q

Can genes coding for tRNA may code for more than a single tRNA molecule or type of tRNA

A

yes

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77
Q

genes coding for rRNA are transcribed as

A

single, large precursor

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78
Q

spacers between the coding region of both, tRNA and rRNA, are removed after _____, some by the use of special ribonuclease called _____

A

transcription, ribozymes

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79
Q

_____ carries amino acids during protein synthesis

A

tRNA

80
Q

RNA has a complementary sequence to the ____ DNA

A

template

81
Q

______ mRNA is often found in bacteria and archaea, while humans only have _____ mRNA

A

polycistronic, monocistronic

82
Q

_______ has no catalytic activity but helps RNA polymerase holoenzyme recognize the promotor and initiate trancription

A

sigma factor

83
Q

Transcription involves three separate processes

A
  • initiation
  • elongation
  • termination
84
Q

RNA polymerase is composed of ____ chains and catalyzes RNA synthesis

A

5

85
Q

RNA polymerase RNA is

A

core enzyme + sigma factor (note that only the haloenzme can begin transcription)

86
Q

bacterial promotors have two characteristic features, which are

A

a sequence of six bases about 35 base pairs before (upstream) the transcription starting point and a TATAAT sequence called the Pribnow box (about 10 base pairs before the starting site)

87
Q

The Pribnow box is usually about _______ upstream of the transcriptional start site

A

10 base pairs upstream

88
Q

sigma factor70 recognizes what consensus sequences

A

promotors having -10 and -35 sequences

89
Q

what are consensus sequences

A

the promotor (ex. -10 and -35) that are recognized by a specific sigma factor (different sigmas mean different initiation sites)

90
Q

After binding, RAN polymerase unwinds the DNA and a transcription bubble is produced, inside the bubble is

A

RNA:DNA hybrid

91
Q

Some Transcription terminators require the aid of the ____ factor for termination

A

rho

92
Q

There are how many codons

A

64

93
Q

how many sense codons are there (codons that specify amino acids)

A

61

94
Q

how many stop (nonsense) codons are there

A

3

95
Q

RNA polymerase specifically binds to what part of the promotor sequence

A

Pribnow box

96
Q

The Sine-Dalgarno sequence is in what region of what strand and marks what process

A

Leader of mRNA, signals the start of translation

97
Q

What DNA sequence marks the start of transcription

A

3’-TAC-5’ this produces the codon AUG which codes for N-formylmethionine, a modified amino acid used to initiate protein synthesis in bacteria

98
Q

DNA sequences that code for tRNA and rRNA are considered ____

A

genes

99
Q

genes coding for tRNA may code for __________

A

more than a single tRNA molecule or type of tRNA

100
Q

genes coding for rRNA are transcribed as

A

single, large precursor

101
Q

Site where RNA polymerase binds to initiate transcription, is not transcribed, and has specific sequence before transcription starting point and a Pribnow box which contains consensus sequence

A

Promoter

102
Q

Transcription termination

A
  • occurs when core RNA polymerase dissociates from template DNA
  • DNA sequence mark the end of gene in the trailer and the terminator
  • soem terminators require the aid of the rho factor for termination
103
Q

Code degeneracy

A

up to six different codons can code for a single amino acid

104
Q

The ____ position of a codon is less important than the ___ or ___

A

3rd, is less important than the 1st or 2nd

105
Q

some microbes incorporate two rare amino acids into polypeptides

A
  • selenocysteine

- pyrrolysine

106
Q

Is it true that some protist can use a single stop codon and have the other two code for amino acids

A

yes

107
Q

what is the direction of translation

A

N terminus to C terminus

108
Q

what is the site of translation

A

Ribosome

109
Q

complex of mRNA with several ribosomes

A

polyribosome

110
Q

coupled transcription/translation in _____

A

bacteria/archaea

111
Q

attachment of amino acids to tRNA is catalyzed by _____

A

aminoacyl tRAN syntheses (at least 20)

112
Q

The bacterial ribosome

A
  • 70S ribosome= 30S and 50S subunits

- Translational domain on both subunits is responsible for translation

113
Q

_____ rRNA ribosomal binding site (RBS) binds to shine dalgarno site on mRNA for protein synthesis

A

16S

114
Q

what rRNA binds protein needed for initiation of translation and amino acyl-t-RNA

A

16S rRNA ribosomal binding site (RBS)

115
Q

Ribozyme catalyzes peptide bond formation at what rRNA

A

23S rRNA

116
Q

Bacterial initiator tRNA

A

N-formylmethionine-tRNA

117
Q

Archaea and eukaryote initiator tRNA

A

Methionine-tRNA

118
Q

in bateria initiation of translation begins when

A
  • initiator codon binds 16S rRNA in 30S subunit

- Shine Dalgarno sequence of mRNA is aligned with 16S rRNA

119
Q

_____ initiation factors (IF) in bacteria are required for the formation of the initiation complex of translation

A

3 (note that the reaction is catalyzed by GTP)

120
Q

Sequential addition of amino acids to growing polypeptide

A

Elongation cycle

121
Q

The elongation of the polypeptide chain consists of three phases what are they

A
  • aminoacyl-tRNA binding
  • transpeptidation reaction
  • translocation
122
Q

Binds initiator tRNA or tRNA attached to growing polypeptide (peptidyl-tRNA)

A

Peptidyl (donor; P ) site

123
Q

Binds incoming aminoacyl-tRNA

A

aminoacyl (acceptor; A) site

124
Q

briefly binds empty tRNA before it leaves ribosome

A

exit (E) site

125
Q

Transpeptidation reaction is catalyzed by

A

peptidyl transferase of 23S rRNA

126
Q

In transpeptidation reaction the amino group of the ____ site amino acid reacts with the carboxyl group of the C-terminal amino acid on the ____ site tRNA. Thus the peptide chain is

A

A, P, the peptide chain is transferred from P site to A site

127
Q

What are the 3 simultaneous evens in the final phase of elongation cycle- Translocation

A
  • peptidyl-tRNA moves from A site to P site
  • ribosome moves down one codon
  • empty tRNA leaves P site
    (note that this requires GTP hydrolysis)
128
Q

what are the three stop (nonsense) codons

A

UAA, UAG, UGA

129
Q

_____ aid in the recognition of stop codons

A

release factors (RFs)

130
Q

How many Release factors are in prokaryotes

A

3

131
Q

how many release factors are in eukaryotes

A

1

132
Q

Protein function depends on 3-D shape and this occurs as a post translational event including

A
  • requires folding
  • association with other proteins
  • delivered to proper sub cellular or extracellular site.
133
Q

Proteins that aid the folding of nascent polypeptides

A

molecular chaperones

134
Q

Functions of molecular chaperones

A
  • proteins that aid the folding of nascent polypeptides
  • protect cells form thermal damage
  • aid in transport of proteins across membranes
135
Q

movement of proteins from cytoplasm to plasma membrane or periplasmic space

A

Translocation (include transport proteins, ETC proteins, proteins involved in chemotaxis and cell wall synthesis, enzymes)

136
Q

Movement of proteins from the cytoplasm to external environment

A

Secretion

137
Q

major pathway for all bacteria for transporting proteins across the plasma membrane

A

Sec-dependent pathway

138
Q

Gram-negative bacteria common translocation and secretion systems

A
  • Proteins can be transported across the outer membrane by several different mechanisms, some of which bypass the Sec system, by moving proteins directly from the cytoplasm to the outside of the cell.
  • may use sec-dependent pathway b
  • also must cross the outer membrane using Types I, II, III,IV, V systems
139
Q

all common translocation and secretion pathways require

A

energy

140
Q

The sec-dependent pathway is also called the

A

General dependent pathway

141
Q

The sec-dependent pathway is ____ conserved in all domains

A

Highly

142
Q

posttranlational Proteins secreted by sec-dependent pathway are synthesized as preproteins having amino-terminal _____, which function is

A

Signal peptide, which is recognized and bound by chaperone proteins (SecB) this helps delay protein folding

143
Q

______, ______, and ______ form a channel in the membrane for the sec-dependent pathway

A
  • secY
  • secE
  • secG
144
Q

_____ translocates preprotein through the plasma membrane

A

secA

145
Q

in the sec pathway When the preprotein emerges through the plasma membrane a signal peptidase

A

removes the signal peptide and thus allows folding to take place

146
Q

Type I secretion systems

A
  • related to ABC transport systems
  • Gram-positive/Gram-negative bacteria, and archaea
  • Secretion of toxins, proteases, other proteins
147
Q

Type I secretion systems are involved in the secretion of

A

toxins, proteases, and other proteins

148
Q

What is the Tat system

A
  • protein translocation system in bacteria and some archaea
  • moves across plasma membrane
  • Tat pathway translocated folded proteins with “twin” arginine residues in their signal sequence
  • Works with Type II secretion system (in gram negative bacteria it uses Type II secretion system to transport proteins across the outer membrane)
149
Q

how is the Tat system distinguished from the sec pathway

A

by the nature of the protein transported. The sec pathway translocates unfolded proteins; the Tat pathway translocates folded proteins. furthermore the TAT pathway only moves proteins that feature two, or “twin” arginine residues in their signal sequence (note tat stands for twin arginine translocase)

150
Q

Type IV secretion system secretes ______ and ____ and is found in

A
  • secretes proteins and secretes DNA from donor to recipient bacterium during conjugation
  • found in both Gram-positive and Gram-negative
151
Q

how many protein secretion systems are there in gram-negative bacteria. which ones are also found in gram-positive

A

6, Type I and IV are also found in gram-postive (note that the ones unique to gram-negative II,III, and V secrete virulence factors)

152
Q

what is the function of Type II secretion pathway

A

transports proteins across the outer membrane that were first translocated across plasma membrane by sec-dependent pathway

153
Q

Does Type I secretion pathway bypass the Sec pathway

A

yes it spans the periplasmic and outer-membrane

154
Q

Type ___, ____, and ___ systems are able to transport proteins without help form the sec system (thus are sec independent)

A

Type I, III, and VI

155
Q

Type III secretion pathway forms ______ and transports

A

injectisomes (needles) that deliver virulence factors and proteins

156
Q

Why are type V secretion pathway called auto transporters

A

because after using the sec pathway to get across the periplasmic membrane they are able to form a pore and transport themselves through the outer membrane

157
Q

what type of secretion pathway is similar to bacteriophage

A

Type VI

158
Q

What are the two approaches to regulation of protein

A
  • Regulation of gene expression (transcription initiation, elongation, and translation)
  • Alter activity of enzymes and proteins (post translational)
159
Q

what are constitutive genes

A

are housekeeping genes that are expressed continuously by the cell

160
Q

What are inducible genes

A

genes that code for inducible enzymes needed only in certain environments

161
Q

Beta-galatosidase reaction catalyzes

A

lactose hydrolysis into galactose and glucose

162
Q

____ enzymes are present only when their substrate is available

A

inducer

163
Q

enzymes that function in biosynthetic pathways are products of

A

repressible genes

164
Q

many enzymes that function in catabolic pathways are ____ enzymes

A

inducible

165
Q

Inhibiting transcription is ____ control

A

negative

166
Q

promoting transcription is _____ control

A

positive

167
Q

in bacteria repressor proteins attache to a region called the _____, which usually overlaps or is downstream of the promotor

A

operator

168
Q

Activator proteins attach to ________, and these are often upstream of the promoter

A

Activator-binding sites

169
Q

what is the function of corepressors

A

they activate aporepressors

170
Q

enzymes of a catabolic pathway are only needed (increased mRNA synthesis) when the

A

preferred substrate is available

171
Q

The lactose operon is a ______ transcriptional control of inducible genes

A

negative

172
Q

The lac operon contains ____ structural genes controlled by the ____, which binds the operator

A

3, lac repressor (lacl) (enzymes are not normally produced unless lactose is present)

173
Q

tetramers of lac repressor form and bind to ____ operator sites

A

3 (O1, O2, O3)

174
Q

Lac repressor bends DNA and prevents _____ from accessing promoter

A

RNA polymerase

175
Q

Presence of ____ binds to lac repressor ( thus meaning it is no longer bound to operator)

A

allolactose

176
Q

what is the secondary regulatory protein of the lac operon

A

catabolite activator protein (CAP)

177
Q

CAP regulates the lac operon in response to the presence or absence

A

of glucose.

178
Q

The highest levels of transcription of the lac operon occur when lactose is ____ and Glucose is

A

available and glucose is not

179
Q

The lowest levels of transcription of the lac operon occur when lactose is ____ and glucose is

A

not available, and glucose is

180
Q

what do the genes of the lac operon produce

A
  • beta-galactosidase
  • Beta-galactoside permease (note this is the protein responsible for lactose uptake)
  • Beta-galatoside transacetylase
181
Q

what is the main function of catabolite activator protein (CAP)

A

is an activator of the lac operon that is responsible for maintaining glucose levels

182
Q

The tryptophan (trp) operon consists of ____ structural genes which code for enzymes needed to synthesize tryptophan

A

5

183
Q

Negative transcriptional control of repressible genes of the tryptophan operon is controlled by

A

tryptophan repressor

184
Q

is tryptophan repressor active when tryptophan levels are low

A

no

185
Q

What is the corepressor for the tryptophan repressor

A

Trypotphan (increased levels lead to activation of trp repressor)

186
Q

The arbinose operon has transcriptional control by a protein that acts

A

both positive and negatively

187
Q

the area operon encodes enzymes needed for catabolism of

A

arbinose to xyluose 5-phosphate (an intermediate of the pentose phosphate pathway)

188
Q

The ara operon is regulated by ____, which can interact with three different regulatory sequences: ___, ____ , and ____

A

AraC, araO2, araO1, and araI

189
Q

The activity of AraC on the Arabinose (ara) operon depends on ___ . explain

A

Activity depends on environmental conditions. When arabinose is present it inactivates AraC and can actually open the DNA fro transcription. When arabinose is absent then AraC blocks the promotor and RNA synthase

190
Q

what is attenuation

A

Termination of transcription within the leader region (leader peptide)

191
Q

The ability to attenuate transcription is based on what two things

A
  • the nature of the leader and the fact that transcription and translation are coupled in bacteria
192
Q

attenuation was first demonstrated with

A

trp operon

193
Q

attenuation occurs through _____

A

stem-loop structures in the mRNA depending on trp level

194
Q

regulation by ______ is a specialized form of transcription attenuation that involves mRNA folding but not ribosome behavior

A

riboswitches (sensory RNAs)

195
Q

explain how riboswitches regulate transcription

A

if the leader of mRNA (the riboswitch) is folded one way than transcription continues if it is folded another way then it is terminated. (note that the mRNA folding pattern is determined by binding an effector molecule directly to the mRNA- a capability previously thought confined to proteins

196
Q

Controlling transcription with riboswitches is an important method used by _______ to regulate amino acid-related genes

A

Gram-positive bacteria

Microbiology (16 decks)

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