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Biology 2051 > Exam 2 > Flashcards

Exam 2 Flashcards

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1
Q

making a copy of the DNA

A

replication

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2
Q

synthesis of RNA from DNA

A

transcription

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3
Q

synthesis of proteins from mRNA

A

translation

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4
Q

How do bacteria make more cells? How do eukaryotes go through cells?

A

Bacteria - replicating and dividing

Eukaryotes - mitosis and meiosis

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5
Q

Where are linear chromosomes found?

A

Eukaryotic cells and some viruses

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6
Q

What is the shape of bacterial and archaeal chromosomes?

A

Circular

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7
Q

How many chromosomes are found in a bacterial cell? How many are found in eukarya?

A

Bacteria - one

Eukarya - 46

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8
Q

How many base pairs are in archaea, and what genes are included in the chromosomes?

A

4.6 million base pairs

Includes necessary genes for everyday circumstances

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9
Q

How many base pairs are in bacteria, and what genes are included in the chromosome?

A

94 thousand base pairs

There are no housekeeping genes, just genes for special circumstances

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10
Q

What are the main parts of the structure of DNA?

A
  • Hydrogen bonds connecting nucleotides
  • antiparallel strands
  • sugar phosphate backbone/phosphodiester bonds
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11
Q

Why are hydrogen bonds good for connecting nucleotides?

A

They are strong but can come apart in heat which is useful to translation and transcription

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12
Q

What is the difference in structure between DNA and RNA

A

RNA: 2’ Carbon connects to an oxygen

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13
Q

What carbons are involved in connecting each deoxyribose to phosphate in DNA?

A

5’ and 3’

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14
Q

How is eukarya DNA stored?

A

DNA is coiled around histones because the cell only needs access to certain parts of the DNA at a time.

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15
Q

How is archaea DNA stored?

A

Some archaea use histone proteins, but most supercoil their DNA

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16
Q

How is bacterial DNA stored?

A

DNA is supercoiled which allows the cell to access only the needed DNA/loops

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17
Q

What do bacteria and archaea use to supercoil DNA?

A

DNA gyrase

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18
Q

What are the size dimensions of an E. coli chromosome?

A
  1. 6 million base pairs, 0.34 nm per base pair

1. 56 mm long chromosome packs into a 2 micrometer by 0.8 micrometer cell

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19
Q

Where are bacterial and archaea chromosomes located?

A

nucleoid

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20
Q

Where are the eukaryotic chromosomes located?

A

nucleus

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21
Q

Status of plasmids in bacteria and archaea

A

Extrachromosomal plasmids

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22
Q

Status of plasmids in eukarya

A

Plasmids are rare; mitochondrion and chloroplast have their own DNA

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23
Q

Which domain has chromosomes with transposable elements?

A

all

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24
Q

The largest plasmids (Archaea) are so large they might turn out to be small chromosomes

A

Halobacterium and Halococcus

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25
Q

RNA translated into protein

A

mRNA

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26
Q

RNA that carries amino acids to be put into proteins

A

tRNA

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27
Q

brings together mRNA and tRNAs for protein synthesis

A

rRNA

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28
Q

DNA sequence upstream of transcription start site

A

promoter

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29
Q

adds ribonucleotides complementary to the DNA molecule

A

RNA polymerase

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30
Q

sequence where transcription stops

A

terminator

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31
Q

How many genes are transcribed at a time in eukaryotes

A

one

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32
Q

takes the introns out of the strand so that the eons can exit the nucleus and have a cap/tail added in the cytoplasm

A

splisozome

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33
Q

line on RNA polymerase in eukaryotes to help bind to promoter

A

transcription factors

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34
Q

what binds transcription factors in eukaryotes

A

TATA box

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35
Q

in this, TFB lines RNA polymerase at the starts. It also has a TATA box, and TBP is the TATA binding protein

A

Archaea

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36
Q

In only bacteria, this binds to promoter then RNA polymerase starts transcription

A

Sigma factor

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37
Q

What does RNA polymerase read when transcribing DNA

A

Reads the 3 to 5 strand

Makes a 5 to 3 strand

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38
Q

How many RNA polymerases can read the DNA at once in bacterial transcription

A

there can be multiple RNA polymerases to amplify the signal

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39
Q

Describe bacterial transcription

A

Sigma recognizes promoter and initiation site. Transcription begins; sigma released. RNA chain grows. Termination site reached; chain growth stops. Polymerase and RNA released.

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40
Q

What is the difference in genome of a prokaryote compared to a eukaryote

A

Prokaryotes

  • do not have intervening sequence
  • no nucleus so no cap or tail
  • the RNA is already mature
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41
Q

What makes prokaryotes able to cotranscribed multiple genes

A

polycistronic mRNA

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42
Q

Two ways to terminate transcription in bacteria

A

Rho-dependent & Intrinsic/Hairpin

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43
Q

How does Rho-dependent termination work in bacteria

A

Rho binds to RNA moving towards RNA polymerase - DNA complex. Rho removes RNA polymerase when RNA polymerase reaches the Rho-dependent termination site

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44
Q

How do intrinsic terminators work in bacteria

A

Inverted repeats in DNA sequence forming a stem-loop (hairpin) structure after transcription

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45
Q

How does termination work in eukarya and archaea

A

AAUAA signals endonuclease cleavage

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46
Q

RNA polymerase of bacteria

A

one with 4 subunits

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47
Q

RNA polymerase of archaea

A

one with 8 subunits similar to Eukarya RNA polymerase II

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48
Q

RNA polymerase of eukarya

A

3, each with over 12 subunits, RNA polymerase II transcribes mRNA

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49
Q

Promoter Recognition Sequences in Bacteria

A
  • 35 sequence (TTGACA)

- 10 sequence (Pribnow box, TATAAT)

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50
Q

Only exist in prokaryotes. Several genes cotranscribed. Encode proteins or rRNA that are used together.

A

Operon

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51
Q

What types of operons are in E. coli?

A

amino acid and sugar operons to make amino acids and break down sugars, respectively

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52
Q

involves enzyme repression and induction

A

negative control of transcription

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53
Q

occurs when a sufficient product is present to stop synthesis of enzymes no longer needed

A

enzyme repression

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54
Q

Arg operon is an example of enzyme repression. How does it work?

A

In the absence of arginine, the repressor is not bound to the operator.
In the presence of arginine, arginine binds to the repressor allowing the repressor to bind to the operator to block transcription.
Arginine acts as a corepressor

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55
Q

occurs when the substrate is present to make enzymes needed to use substrate

A

enzyme induction

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56
Q

Lac operon is an example of enzyme induction. How does it work?

A

Int he absence of lactose, the lac repressor binds to the operator to block transcription. In the presence of lactose, the allolactose binds to the repressor to move the repressor off of the operator to allow transcription

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57
Q

activation of transcription controlled by binding of activator protein when inducer is present

A

positive control of transcription

58
Q

Why is catabolite repression an example of positive control of transcription

A

It regulates if an activator protein can bind or not, which is why it’s under positive control. Glucose, lactose, maltose are all catabolites that break down molecules to make ATP.

59
Q

Describe the “glucose effect” of catabolite repression

A

Glucose can repress another catabolite’s use. When the cells run out of glucose they switch, transcribe the lac operon, and start growing on the lactose. Always use glucose first because it is the simplest/easiest. Diauxic growth - when it finishes using glucose, the cell stops growing and looks for something available like lactose.

60
Q

Overall regulation of the lac system

A

Activation: Binding of CRP to cAMP recruits RNA polymerase to start transcription.
Repression: The inducer (allolactose) separates from the repressor to activate it. The active repress binds to the operator and blocks transcription

61
Q

Regulation of the lac system

A

POSITIVE CONTROL: In the absence of glucose, there is sufficient cAMP to bind to CRP. CRP is an activator protein and when bound by cAMP can bind to the activator binding site in the promoter of the lac operon.
NEGATIVE CONTROL: In the presence of lactose, lactose is taken into the cell and converted to allolactose. Allolactose binds to the lac repressor removing the lac repressor from the lac operator.

62
Q

Regulation of the mal operon - positive control

A

In the absence of maltose, there is no activation of the mal operon.
Activation - in the presence of maltose (inducer), maltose binds to the maltose activator protein to bind to the activator binding site to activate transcription.

63
Q

more than one operon under the control of a single regulatory protein (ex. Maltose and arginine in E. coli)

A

regulon

64
Q

Control of transcription in Archaea by repressor proteins like NrpR

A

NrpR blocks TFB and TBP binding - no transcription.
NrpR binds alpha-ketoglutarate. This releases the NrpR from the DNA.
When NrpR is released TBP and TFP can bind - transcription proceeds

65
Q

How does the 2 component regulatory system work?

A

The sensor kinase detects the environmental signal and autophosphorylates. The phosphoric group on the sensor kinase is then transferred to a response regulator that can bind to DNA and affect transcription

66
Q

How does the multi component phosphorylation transfer system regulate sporulation

A

Sensor kinases recognize signals and become autophosphorylated. Changes phosphorylation of sporulation factors in the cell. Sigma factor is inactive when bound to a sporulation factor. Signal from endospore activates sigma factor, early endospore genes are transcribed. Signal from mother cell triggers synthesis of sigma factor in endospore and pro-sigmaK in the mother cell. Signal from endospore activates sigma factor.

67
Q

mRNA sequence of three nucleotides

A

Codon

68
Q

What does AUG code for in bacteria

A

formyl methionine

69
Q

What does AUG code for in archaea and eukarya

A

methionine

70
Q

Where is the open reading frame

A

from start codon to stop codon

71
Q

What is the region before the start codon

A

5’ untranslated region

72
Q

How many total codons exist?

A

64

73
Q

What decides where a peptide can be in a cell?

A

Amino acids decide based on their characteristics (acid, basic, polar, non polar..)

74
Q

What is the alternate amino acid that UGA codes for if there is a recognition sequence downstream of the mRNAt that forms a stem loop

A

selenocysteine

75
Q

What is the alternate amino acid UAG can code for

A

pyrrolysine

76
Q

Attached to the amino acid corresponding to the codon. Has anticodon sequence that temporarily base pairs with mRNA codon during translation

A

Aminoacyl Transfer RNA (tRNA)

77
Q

Brings together mRNA and tRNA for protein synthesis

A

Ribosome

78
Q

How does the ribosome move along the mRNA

A

one codon at a time

79
Q

Overall size of the ribosome in bacteria and archaea

A

70S

80
Q

Overall size of the ribosome in eukarya

A

80S

81
Q

Ribosomal rRNA in bacteria and archaea

A

16S

23S and 5S

82
Q

Ribosomal rRNA in eukarya

A

18S

28S, 5.8S, 5S

83
Q

Total ribosomal proteins in bacteria? Archaea? Eukarya?

A

Bacteria: 56
Archaea: 67
Eukarya: 78

84
Q

How many proteins are common to all domains

A

34

85
Q

How many proteins are unique to bacteria

A

22

86
Q

How many proteins are unique to archaea and eukarya

A

33 proteins are common too archaea and eukarya

11 proteins are unique to eukarya

87
Q

Explain translation (APE)

A

Acceptance Site
P site: where the tRNA that was used will be so they can attach the first amino acid to the next one
Exit Site: empty tRNA leaves through here
Release factor comes in and dislodges the ribosome at a stop codon

88
Q

Helps add the large subunit covalently to the small subunit

A

GTP

89
Q

What is required to move each tRNA

A

i molecule of GTP

90
Q

Translation in a prokaryotic cell

A

1 or more genes to 1 mRNA to one protein per gene in DNA. Each region is translated to create one polypeptide per coding region.

91
Q

Translation in a eukaryotic cell

A

1 gene to 1 mRNA to 1 protein

92
Q

several ribosomes can translate a single mRNA molecule simultaneously

A

polysome

93
Q

Cells of this species can divide in six minutes because transcription and translation happen back to back

A

Vibrio

94
Q

What is the main benefit of the quickness of division in vibrio cells

A

allows cell to respond to changes in the environment very fast

95
Q

Induced mutations

A

Physical and Chemical

96
Q

Spontaneous mutations

A

Errors by DNA polymerase in DNA replication. No control.

97
Q

penetrates tissues, causes formation of ions that can break covalent bonds

A

ionizing radiation

98
Q

low levels of ionizing radiation create

A

point mutations

99
Q

high levels of ionizing radiation create

A

large chromosomal mutations

100
Q

Difference between gamma and UV radiation

A

Gamma: will kill you
UV: will only affect your skin tissues

101
Q

can survive exposure to gamma radiation that would kill humans

A

Deinococcus radiodurans

102
Q

is found in soils and seeps up. If it is released into the air, it gets diluted. Responsible for 20,000 lung cancer deaths each year

A

Radon

103
Q

Common intercalating agent used to stain DNA in gel electrophoresis. When bound to DNA, it fluoresces orange under UV light

A

Ethidium Bromide

104
Q

Insert between bases in one or both strands that cause the helix to relax; inserts space in the strand and causes a frame shift mutation.

A

intercalating agent

105
Q

Allows us to determine if a chemical is a mutagen, carcinogen, etc.

A

Ames test

106
Q

What is the procedure for doing the Ames test?

A

Bacteria is plated on agar plate, and a disc is put in the middle of the plate. No histidine (essential amino acid) is on the plate. Control only has the water on the disk but the test disk has the chemical.If the chemical is a mutagen there will be more revertants around the disk indicating the increase mutation rate

107
Q

Wild-type salmonella strain that had a mutation making it capable of making histidine

A

His-Plus

108
Q

a change in one or a few base pairs that can occur anywhere in the genome and can affect gene expression

A

point mutations

109
Q

New codon results in an amino acid that can result in a faulty protein. Most common when the first nucleotide is the one altered, but also common when the 2nd nucleotide is altered

A

Missense

110
Q

New codon that is a stop codon. Results in a truncated protein (shorter).

A

Nonsense

111
Q

New codon, but it codes for the same amino acid. Most common when 3rd nucleotide is the one altered

A

Silent

112
Q

Three types of base-pair substitutions

A

Missense, Nonsense, Silent

113
Q

A shift in the open reading frame caused by insertions or deletions. In most cases it will affect the regions around insertion or deletion location.

A

Frame shift mutation

114
Q

Shift in the +1 direction

A

Insertion

115
Q

Shift in the -1 direction

A

Deletion

116
Q

2 classes based on how the mutation affects phenotype

A

Forward & Reverse

117
Q

Functional to nonfunctional/or new function

A

Forward mutation

118
Q

Nonfunctional/new reverts back to functional

A

Reverse mutation

119
Q

Wild-type is chemotactic (run and change direction in response to chemical). Mutants don’t tend to change direction in response to chemical

A

Vibrio anguillarum

120
Q

Wild-type have a smooth appearance. The mutants are rough.

A

Mycobacterium smegmatis

121
Q

Mobile genetic element. DNA segment that can move from one position to another in the genome by non homologous recombination. Cause mutation by insertional mutagenesis.

A

Transposable elements

122
Q

2 forms of transposable elements

A

autonomous and nonatonomous

123
Q

Has transposase gene so they can transpose by themselves. Insertion results in mutable allele that is unstable

A

Autonomous transposable elements

124
Q

Cannot transpose by themselves because they lack a transposase gene. Insertions are stable because they can’t move.

A

Nonatonomous transposable elements

125
Q

Transposable element insertion into reading frame of gene results in loss of function mutation, typically complete loss of function

A

null mutation

126
Q

How would a transposable element insertion result in an altered gene expression?

A

Transposable element promoter affect nearby genes

127
Q

Classes of Transposable Elements

A

Those that move as DNA

Those that move as RNA and then convert to DNA for integration

128
Q

What types of transposable elements move as DNA?

A

Bacterial insertion sequences (IS) elements and transposons (Tn)

129
Q

What types of transposable elements move as RNA?

A

Yeast (Ty) transposons

130
Q

Characteristics of Insertion Sequences

A

IS1, IS2, etc.
768bp - 5000+ bp in length
Have inverted repeats at the ends
Contains transposase gene that codes for the transposase enzyme that IS1 needs to move

131
Q

2 types of transposons (Tn)

A

Composite (Tn10) and Non-Composite (Tn3)

132
Q

Contains antibiotic resistance genes. Have IS element at each end that contain transposase genes needed for Tn to move. Conservative transposition. Transpositions result in target site duplications on either side of the transposons.

A

Composite (Tn10)

133
Q

Contains antibiotic resistance genes. Contain transposase gene. No IS elements. Replication transpositions (makes copy of itself, keeps doubling). . Transposon results in target site duplication on either side of the transposon.

A

Non-Composite (Tn3)

134
Q

Ty that codes for gag structural protein

A

TyA

135
Q

Ty that codes for pol polyprotein

A

TyB

136
Q

Progenitors of retroviruses like HIV

A

Transposons in yeast (Ty)

137
Q

Replication error rates for humans

A

10^-5

138
Q

Replication error rates for bacteria

A

10^-6

139
Q

DNA virus replication error rates

A

10^-4

140
Q

RNA virus replication error rates

A

10^-3

141
Q

Mechanism of the SOS Response

A

DNA damage activates RecA which activates LexA protease activity. (The repressor LexA is self-cleaved, degrading it allows for transcription of many genes including several DNA polymerases needed to repair the damage.)
When the damage is repaired rica is inactivated and newly made LexA represses DNA repair genes

Biology 2051 (7 decks)

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