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

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Flashcards in Lecture 5 Bacterial Genome Replication, expression, and regulation 1 Deck (196):
1

All DNA present in a cell or virus

Genome

2

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

1 (haploid-1N)

3

Eukaryotes have ___ set(s) of DNA

2 (diploid-2N)

4

Specific set of genes an organism possesses

Genotype

5

Collection of observable characteristics

Phenotype

6

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

transformation

7

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

DNA

8

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

- 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

9

DNA and RNA are polymers of nucleotides linked together by ______

phosphodiester bonds

10

DNA is transcribed into

- tRNA, mRNA, rRNA, snRNA

11

what are the forms of RNA

tRNA, mRNA, rRNA, microRNA, siRNA, snRNA

12

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

major and minor

13

Most RNA molecules are ____ stranded but some are _____

single, double stranded

14

Proteins are polymers of ____ linked by ____ bonds

amino acids, peptide

15

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

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

16

what determines the properties of the amino acids

the side chain

17

DNA replication is semi-conservative meaning what

each daughter cell obtains one old and one new strand

18

DNA in most bacteria is ____

circular

19

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

replicon

20

Because the bacterial chromosome is a single replicon

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

21

DNA in bacteria has _____ replication from a single origin

Bidirectional

22

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

30

23

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

replication termination site (ter)

24

What serve as DNA polymerase substrates

deoxynucleoside triphosphates: dATP, dTTP, dCTP, dGTP

25

What are incorporated into the growing DNA chain

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

26

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

- 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

27

function of DnaA in E. coli

initiation of replication; binds origin of replication (oriC)

28

function of DnaB in E. coli

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

29

function of DNA gyrase in E. coli

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

30

Function of SSB (single stranded binding) proteins

Bind single-stranded DNA after strands are separated by helicases

31

Function of DnaC in E. coli

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

32

function of DNA primase

Synthesis of RNA; component of primosome

33

Function of DNA polymerase III holoenzyme

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

34

Function of DNA polymerase I

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

35

Functions of Ribonuclease H in E. coli

Removes RNA primers

36

Functions of DNA ligase

Selas nicked DNA, joining DNA fragments together

37

Function of Tus in E. coli

Termination of replication

38

What is the function of Topoisomerase IV in E. coli

Separation of chromosomes upon completion of DNA replication

39

E. coli has ____ different DNA polymerases

5

40

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

10

41

Polymerase III has ____ core enzymes

2 (some evidence suggests 3)

42

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

- catalyze DNA synthesis (alpha subunit)
- Proofreading for fidelity (epsilon subunit)

43

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

clamp loader, each subunit is attached to a core enzyme

44

_____ unwinds DNA strands

Helicases (DnaB)

45

Keeps strands apart for replication to occur

single stranded binding proteins (SSB)

46

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

Topoisomerases

47

_____ 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

DNA gyrase

48

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

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

49

The complex of primase and its accessory proteins is called the

primosome

50

Bacterial initiator protein ____ is responsible for triggering DNA replication

DnaA

51

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

OriC

52

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

I

53

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

5' end while moving toward the 3' end of the RNA primer
(5' to 3' exonuclease activity)

54

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

is discarded and a new one is added

55

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

3'-hydroxyl, 5'-phosphate

56

DNA polymerase III has removes mismatched bases by _____ activity

3'-to-5' exonuclease activity

57

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

termination site (ter)

58

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

Catenanes

59

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

dimerized chromosome

60

Dimerized chromosomes are resolved by

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

61

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

topoisomerases, topoisomerases

62

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

recombination events

63

how can bacteria solve the linear chromosome problem

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

64

a basic unit of genetic information

Gene

65

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

mRNA

66

_____ strand of DNA directs RNA synthesis

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

67

____ DNA strand is the same nucleotide sequence as mRNA

coding strand (complementary DNA strand)

68

____ is the binding site in a gene for RNA polymerase

promoter

69

The promotor is neither transcribed nor translated; it functions

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

70

The transcription start site represents the

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

71

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

Shine-Dalgarno sequence

72

The coding region typically begins with the template DNA sequence _____

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

73

3'-AUG-5' on mRNA codes for

N-Formylmethione (start codon)

74

The coding region ends with

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

75

DNA sequences that code for tRNA and rRNA are considered ____

genes

76

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

yes

77

genes coding for rRNA are transcribed as

single, large precursor

78

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

transcription, ribozymes

79

_____ carries amino acids during protein synthesis

tRNA

80

RNA has a complementary sequence to the ____ DNA

template

81

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

polycistronic, monocistronic

82

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

sigma factor

83

Transcription involves three separate processes

- initiation
- elongation
- termination

84

RNA polymerase is composed of ____ chains and catalyzes RNA synthesis

5

85

RNA polymerase RNA is

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

86

bacterial promotors have two characteristic features, which are

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

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

10 base pairs upstream

88

sigma factor70 recognizes what consensus sequences

promotors having -10 and -35 sequences

89

what are consensus sequences

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

90

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

RNA:DNA hybrid

91

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

rho

92

There are how many codons

64

93

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

61

94

how many stop (nonsense) codons are there

3

95

RNA polymerase specifically binds to what part of the promotor sequence

Pribnow box

96

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

Leader of mRNA, signals the start of translation

97

What DNA sequence marks the start of transcription

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

DNA sequences that code for tRNA and rRNA are considered ____

genes

99

genes coding for tRNA may code for __________

more than a single tRNA molecule or type of tRNA

100

genes coding for rRNA are transcribed as

single, large precursor

101

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

Promoter

102

Transcription termination

- 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

Code degeneracy

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

104

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

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

105

some microbes incorporate two rare amino acids into polypeptides

- selenocysteine
- pyrrolysine

106

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

yes

107

what is the direction of translation

N terminus to C terminus

108

what is the site of translation

Ribosome

109

complex of mRNA with several ribosomes

polyribosome

110

coupled transcription/translation in _____

bacteria/archaea

111

attachment of amino acids to tRNA is catalyzed by _____

aminoacyl tRAN syntheses (at least 20)

112

The bacterial ribosome

- 70S ribosome= 30S and 50S subunits
- Translational domain on both subunits is responsible for translation

113

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

16S

114

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

16S rRNA ribosomal binding site (RBS)

115

Ribozyme catalyzes peptide bond formation at what rRNA

23S rRNA

116

Bacterial initiator tRNA

N-formylmethionine-tRNA

117

Archaea and eukaryote initiator tRNA

Methionine-tRNA

118

in bateria initiation of translation begins when

- initiator codon binds 16S rRNA in 30S subunit
- Shine Dalgarno sequence of mRNA is aligned with 16S rRNA

119

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

3 (note that the reaction is catalyzed by GTP)

120

Sequential addition of amino acids to growing polypeptide

Elongation cycle

121

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

- aminoacyl-tRNA binding
- transpeptidation reaction
- translocation

122

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

Peptidyl (donor; P ) site

123

Binds incoming aminoacyl-tRNA

aminoacyl (acceptor; A) site

124

briefly binds empty tRNA before it leaves ribosome

exit (E) site

125

Transpeptidation reaction is catalyzed by

peptidyl transferase of 23S rRNA

126

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

127

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

- 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

what are the three stop (nonsense) codons

UAA, UAG, UGA

129

_____ aid in the recognition of stop codons

release factors (RFs)

130

How many Release factors are in prokaryotes

3

131

how many release factors are in eukaryotes

1

132

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

- requires folding
- association with other proteins
- delivered to proper sub cellular or extracellular site.

133

Proteins that aid the folding of nascent polypeptides

molecular chaperones

134

Functions of molecular chaperones

- proteins that aid the folding of nascent polypeptides
- protect cells form thermal damage
- aid in transport of proteins across membranes

135

movement of proteins from cytoplasm to plasma membrane or periplasmic space

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

136

Movement of proteins from the cytoplasm to external environment

Secretion

137

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

Sec-dependent pathway

138

Gram-negative bacteria common translocation and secretion systems

- 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

all common translocation and secretion pathways require

energy

140

The sec-dependent pathway is also called the

General dependent pathway

141

The sec-dependent pathway is ____ conserved in all domains

Highly

142

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

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

143

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

- secY
- secE
- secG

144

_____ translocates preprotein through the plasma membrane

secA

145

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

removes the signal peptide and thus allows folding to take place

146

Type I secretion systems

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

147

Type I secretion systems are involved in the secretion of

toxins, proteases, and other proteins

148

What is the Tat system

- 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

how is the Tat system distinguished from the sec pathway

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

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

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

151

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

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

what is the function of Type II secretion pathway

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

153

Does Type I secretion pathway bypass the Sec pathway

yes it spans the periplasmic and outer-membrane

154

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

Type I, III, and VI

155

Type III secretion pathway forms ______ and transports

injectisomes (needles) that deliver virulence factors and proteins

156

Why are type V secretion pathway called auto transporters

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

what type of secretion pathway is similar to bacteriophage

Type VI

158

What are the two approaches to regulation of protein

- Regulation of gene expression (transcription initiation, elongation, and translation)
- Alter activity of enzymes and proteins (post translational)

159

what are constitutive genes

are housekeeping genes that are expressed continuously by the cell

160

What are inducible genes

genes that code for inducible enzymes needed only in certain environments

161

Beta-galatosidase reaction catalyzes

lactose hydrolysis into galactose and glucose

162

____ enzymes are present only when their substrate is available

inducer

163

enzymes that function in biosynthetic pathways are products of

repressible genes

164

many enzymes that function in catabolic pathways are ____ enzymes

inducible

165

Inhibiting transcription is ____ control

negative

166

promoting transcription is _____ control

positive

167

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

operator

168

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

Activator-binding sites

169

what is the function of corepressors

they activate aporepressors

170

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

preferred substrate is available

171

The lactose operon is a ______ transcriptional control of inducible genes

negative

172

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

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

173

tetramers of lac repressor form and bind to ____ operator sites

3 (O1, O2, O3)

174

Lac repressor bends DNA and prevents _____ from accessing promoter

RNA polymerase

175

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

allolactose

176

what is the secondary regulatory protein of the lac operon

catabolite activator protein (CAP)

177

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

of glucose.

178

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

available and glucose is not

179

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

not available, and glucose is

180

what do the genes of the lac operon produce

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

181

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

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

182

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

5

183

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

tryptophan repressor

184

is tryptophan repressor active when tryptophan levels are low

no

185

What is the corepressor for the tryptophan repressor

Trypotphan (increased levels lead to activation of trp repressor)

186

The arbinose operon has transcriptional control by a protein that acts

both positive and negatively

187

the area operon encodes enzymes needed for catabolism of

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

188

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

AraC, araO2, araO1, and araI

189

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

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

what is attenuation

Termination of transcription within the leader region (leader peptide)

191

The ability to attenuate transcription is based on what two things

- the nature of the leader and the fact that transcription and translation are coupled in bacteria

192

attenuation was first demonstrated with

trp operon

193

attenuation occurs through _____

stem-loop structures in the mRNA depending on trp level

194

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

riboswitches (sensory RNAs)

195

explain how riboswitches regulate transcription

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

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

Gram-positive bacteria