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Cell Bio Exam 2 > Lecture 6 - From DNA to Proteins > Flashcards

Lecture 6 - From DNA to Proteins Flashcards

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Biology 101 flashcards
1
Q

what does an ames test show?

A

it is a standard test in biotechnology that reveals mutagenic potential of the compounds by reverting histidine-auxotrophic phenotype of S. typhimurium

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2
Q

what are some examples of exogenous sources?

A

radiation, chemicals

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3
Q

what are some examples of endogenous sources?

A

replication errors, spontaneous hydrolysis

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4
Q

DNA damage may result in what?

A

mutations in somatic cells and germline cells

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5
Q

what are the types of DNA damage?

A
  • oxidation (most frequent source of DNA damage)
  • alkylation (addition of alkyl groups to bases)
  • deamination (loss and/or substitution of amino groups at the bases)
  • depurination/depyrimidination of bases
  • formation of base dimers & more complex heterocycles induced by ionizing radiation and carcinogens
  • single & double stranded DNA breaks
  • mismatch (replication error)
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6
Q

what is deamination?

A

it is when cytosine is converted to uracil

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7
Q

what happens during depurination?

A

removes guanine or adenine from DNA

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8
Q

what is radiation a significant source of?

A

DNA damage that frequently causes various DNA modifications depending on the radiation energy

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9
Q

what are examples of ionizing radiation?

A

X-rays, UV light, and gamma rays

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10
Q

how does ionizing radiation cause significantly more damage?

A

in the form of ring openings, it causes fragmentation of bases and breakage of phosphodiester bonds (i.e. single and double stranded breaks)

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11
Q

how does UV light affect the DNA bases?

A

it induces the condensation of 2 ethylene groups into cyclobutane ring. which can occur in the cell between 2 adjacent pyrimidine bases (typically thymines)

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12
Q

what happens during alkylation of DNA?

A

adds a methyl group to guanine to yield O6-methylguanine

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13
Q

what is mistaken DNA alkylation caused by?

A
  • alkylating agents normally present in the cell (such as S-adenosyl-methionine = a donor of methyl group for many intracellular reactions)
  • toxins called alkylating agents such as nitrogen mustard
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14
Q

what does O6-methylguanine base-pair with?

A

CANNOT pair with cytosine, must pair with THYMINE

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15
Q

what does the formation of O6-methylguanine result in?

A

inherited mutation

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16
Q

what is the most frequent source of mutagenic alterations in DNA?

A

DNA oxidative damage

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17
Q

what are reactive oxygen species (ROS) and how do they arise?

A

ROS such as hydrogen peroxide, hydroxyl and superoxide radicals; they arise during ionizing irradiation and as byproducts of oxidative metabolism

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18
Q

what is the most detected product of DNA oxidation?

A

8-oxo-2’-deoxyguanosince (8-oxo-G)

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19
Q

what is used to measure the oxidative stress in cells and tissues?

A

accumulation of 8-oxo-G

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20
Q

what are the types of DNA repair?

A
  • base excision repair
  • nucleotide excision repair
  • mismatch repair
  • homologous recombination
  • non-homologous end joining
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21
Q

how does methylation of DNA work?

A

specific methylases distinguishes “old” strand from the “new” one

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22
Q

what do proteins of mismatch repair complex recognize?

A

recognize unpaired (‘melted”) part of double-stranded DNA as both nucleotides are ‘natural’

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23
Q

what is the driving force of evolution?

A

DNA mutagenesis

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24
Q

the DNA repair system has not evolved to protect what?

A

the individuals after reproductive age

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25
Q

what are conserved or invariant nucleotide sequences?

A

those that encode for important genes or traits preserved in evolution

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26
Q

which type of sequences often indicate regions that encode for obsolete functions?

A

variable sequences

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27
Q

what is the evolutionary clock?

A

number and type of nucleotide substitutions accumulated over time in variable sequences

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28
Q

what was used as an original model system to study gene expression and its regulation?

A

bacteriophages

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29
Q

what do gene readout start with?

A

the synthesis of single-stranded RNA copy using double-stranded DNA as a template

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30
Q

the amount of genetic information released from each gene may be significantly amplified thru what?

A

thru increased rates of transcription and/or translation

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31
Q

what direction does the extension of the RNA strand go during synthesis?

A

5’ to 3’ direction; the 3’ end extends

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32
Q

during transcription, which RNA strand is complementary to one of DNA strands?

A

the nascent RNA strand

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33
Q

what is the coding strand?

A

the opposite to the template strand in double-stranded DNA helix

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34
Q

if the coding strand of DNA is:
5’ ATTGGTACTCC 3’
what would be the template strand and what would be the RNA strand?

A

template strand:
3’ TAACCATGAGG 5’
RNA strand:
5’ AUUGGUACUCC 3’

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35
Q

how are stem loops formed?

A

only in RNA since it is a single strand; the bases in the single strand seek stability by forming base pairs between bases on the same strand

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36
Q

how are RNA secondary structures stabilized?

A

by non-conventional (non-canonical) pairs, such as G-A and C-U

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37
Q

in order to synthesize RNA, what must RNA polymerase do?

A

it has to separate (melt) the strands first, making one strand available for readout

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38
Q

what direction does RNA polymerase move?

A

it moves along the double strand in the direction that the template strand is read from 3’ to 5’ direction
- this ensures that RNA as antiparallel strand is synthesized in 5’ to 3’ direction

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39
Q

describe the RNA-DNA hybrid

A
  • thermodynamically more stable than the corresponding DNA-DNA hybrid in double-stranded DNA of the same size and sequence
  • provides great stability to the moving transcription machinery that does not dissociate from DNA when it stops
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40
Q

what do messenger RNAs (mRNAs) do?

A

code for proteins

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41
Q

what so ribosomal proteins (rRNA) do?

A

forms the core of the ribosome’s structure and catalyze protein synthesis

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42
Q

what does microRNAs (miRNAs) do?

A

regulate gene expression

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43
Q

what do transfer RNAs (tRNAs) do?

A

serve as adaptors between mRNA and amino acids during protein synthesis

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44
Q

what are other noncoding RNAs do?

A

are used in RNA splicing, gene regulation, telomere maintenance, and many other processes

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45
Q

what is the paradox of transcription in prokaryotes?

A

the same enzyme should have high affinity to a particular DNA sequence in order to initiate transcription at a very specific place
- at the same time, the very same enzyme has to be tightly bound to the DNA during elongation of transcription regardless the sequence

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46
Q

how does the paradox of transcription in prokaryotes get solved?

A

by a special protein called sigma factor

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47
Q

does the sigma factor get released at first attempt? why or why not?

A

no, normally DNA polymerase will make many attempts to escape promoter by synthesizing short, abortive RNA products

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48
Q

what do sigma factors in bacteria cells allow?

A

allow switching transcription from housekeeping genes to a set of specialized genes using the same RNA polymerase core enzyme

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49
Q

what is the transcription terminator in prokaryotes?

A

a sequence that encodes a stem-loop in RNA followed by a polyU tract

50
Q

bacteria has ___ RNA polymerase, while eukaryotes have a set of ___ nuclear enzymes?

A

one; 3

51
Q

what does the basic eukaryotic transcription factor TBP (TATA-binding protein) insert?

A

inserts aromatic amino acid radicals (phenylalanines) between base pairs and changes its conformation so that the residues work like levers to bend (kink) DNA at the promoter

52
Q

what are RNA-degrading enzymes (RNAses) for?

A

ensure that RNA copies are always fresh, and do not have unwanted modifications that may accumulate over time

53
Q

what are the most important steps of eukaryotic mRNA processing?

A

capping, polyadenylation, and splicing

54
Q

what is capping?

A

it is the covalent attachment of 7-methylguanosince to 5’ triphosphate
- starts right after the transcript emerges from RNA polymerase

55
Q

what is the function of poly-A-polymerase?

A

it adds a poly-A-tail at the 3’ end in non-template manner

- before this addition, the 3’ untranslated region (3’-UTR) is trimmed

56
Q

protein-encoding genes are interrupted by non-coding sequences called what?

A

introns

57
Q

what are exons?

A

the coding regions in genes

58
Q

what does splicing involve?

A

immature, newly synthesized eukaryotic mRNA gets the introns out and the exons fused (spliced) together

59
Q

some introns require assistance from what?

A

small nuclear RNA (snRNA) protein complexes (snRNPs or “snurps”)

60
Q

what greatly increases the variety of products that can be obtained from the same gene?

A

alternative splicing

61
Q

what are the differences in how prokaryotes and eukaryotes handle their mRNAs?

A
  • all steps of mRNA processing in eukaryotes occur simultaneously and start as soon as the corresponding parts of mRNA emerge from the transcription complex
  • translation of bacterial mRNAs may occur simultaneously with their synthesis, as long as the 5’ end emerges
62
Q

what is a codon?

A

a sequence of 3 nucleotides (triplets of nucleotides) from 5’ to 3’ end that encode for amino acid

63
Q

what is degeneracy of genetic code?

A

a result of simple mathematical probability to have just sufficient code variations for each amino acid out of 20
- also provides additional protection from mutations

64
Q

what are the designated codons that translate for start and stop sites?

A
  • ALWAYS starts with AUG (methionine)
  • stop codons do not encode for any amino acids; synthesis of polypeptide chain is interrupted once it hits any of the 3 stop codons
65
Q

what is the open reading frame (ORF)?

A

linear sequence of codons that encode the polypeptide sequence, from the start codon to the termination codon

66
Q

which 2 non-coding RNA types are the most important?

A

tRNAs and rRNAs

67
Q

what is an anticodon?

A

a triplet of nucleotides that is complementary to RNA codon in antiparallel orientation

68
Q

what is aminoacyl tRNA synthetase (transferase)?

A

enzyme that covalently attaches correct amino acid to the 3’ end of corresponding tRNA

69
Q

what does aminoacyl-tRNA synthase create for translation?

A

aminoacyl-tRNA adapter

70
Q

the energy of ATP hydrolysis is used to create what?

A

the high-energy bond between acyl group of amino acid and tRNA which is later used as an energy source for the synthesis of polypeptide bonds (aka translation)

71
Q

where does the translation of all eukaryotic mRNAs occur?

A

in the cytosol

72
Q

where does the synthesis of rRNA, trimming of rRNA, and assembly of large and small ribosomal subunits occur?

A

in the nucleoli

73
Q

how many sites does a ribosome have that permits the recognition of RNA template and tRNA binding?

A
  • E site = exit
  • P site = peptidyl-tRNA
  • A site = aminoacyl-tRNA
74
Q

what happens during the initiation of translation?

A
  • requires protein translation initiation factors that recognize a ribosome binding site (RBS), which is a specific nucleotide sequence that includes initiation codon ATG
75
Q

what is the ribosome binding site (RBS) called in eukaryotes?

A

Kozak consensus

76
Q

what is the RBS called in prokaryotes?

A

Shine-Dalgarno

77
Q

what causes the termination of translation?

A
  • protein release factor binds termination codon

- promotes dissociation of ribosomes on 2 subunits that are recycled

78
Q

how is the termination of translation different in eukaryotes vs prokaryotes?

A
  • in eukaryotes, a single mature mRNA encodes for a single polypeptide
  • in prokaryotes, a single mRNA may encode several polypeptides with their own sites for translation initiation AND termination
79
Q

what is ubiquitin?

A

a small protein that marks other soluble cytosolic proteins for degradation by proteasome

80
Q

what is proteasome?

A

a large protein-degrading complex that utilize short-lived and misfolded proteins

81
Q

what can reprogram any differentiated cell into a pluripotent cell that has embryonic stem cell-like properties?

A

artificial expression of a set of 4 genes (each of which encodes for a transcription regulator protein)

82
Q

what may provide clues on how the development of late onset diseases may be triggered?

A

induced pluripotent stem cells (IPSCs)

83
Q

how would patient-specific cells differentiated from IPSCs may be compared with similar cells?

A

they would be isolated from healthy subjects in regard to how they respond to stimuli, stress conditions, and treatment in vitro

84
Q

what are the 3 different control regulation steps that happen during gene expression?

A

1) transcriptional control
2) mRNA degradation control
3) translation control

85
Q

when is transcription control exerted?

A

at the level of transcription initiation; either permitting or preventing the binding of RNA polymerase at the promoter region

86
Q

what is the leucine zipper?

A

a crisscrossed helical element that is found in a number of transcription regulators that is capable of accessing the DNA major groove along the double helix
- is so tightly structured that the distance between amino acid residues that interact w base pairs is strictly maintained

87
Q

what roles do the zinc fingers and helix-turn-helix motifs perform?

A

orienting recognition elements so that they bind certain base pairs at the promoter DNA

88
Q

what is another example of transcription activator?

A

homeodomains

89
Q

what do many transcription regulators bind to DNA as?

A

dimers

90
Q

in bacterial chromosomes, how are genes fixated and expressed?

A

clustered and often expressed together

91
Q

what is an operon?

A

a set of genes expressed from a single promoter

- typical for BACTERIA

92
Q

what are bacteria incapable of storing?

A

large amounts of polysaccharides

93
Q

what is a constitutive promoter?

A

one that works all the time as long as RNA polymerase is available

94
Q

what is a promoter that is inducible?

A

they are transcriptional switches that control operons to allow transcription from those promoters only at certain conditions
- so that the cell can respond to the changes in their environment very efficiently

95
Q

what are operators?

A

regulatory elements that control the activity of promoters by suppression

96
Q

where are operators located?

A
  • either adjacent to the basic promoter sequence

- or overlaps with the promoter

97
Q

how are bacteria capable of turning off corresponding anabolic genes?

A

by using allosterically regulated transcription repressors

98
Q

what is a repressor?

A

a special regulatory protein

99
Q

where do the promoter sequences located on DNA?

A

typically on -35 and -10

100
Q

describe the example of the bacteria E. coli using transcriptional repressors

A
  • E. coli can either synthesize tryptophan or uptake it from surroundings
  • in presence of imported tryptophan, bacteria DO need enzymes to synthesize it & corresponding operon that encodes for the set of tryptophan-synthesized enzymes is turned OFF w/ a repressor
  • repressor binds tryptophan in such a conformation locks the access of RNA polymerase
101
Q

in the absence of imported tryptophan, what happens?

A

the repressor cannot bind to the operator DNA, and the block is removed

102
Q

what are transcriptional activators/activator proteins for?

A

it recruits RNA polymerase to the promoter and ensures productive transcription

103
Q

what does the Lac operon in E. coli control?

A

the set of genes that utilize lactose by breaking it down to galactose and glucose when it is available from the extracellular sources

104
Q

what happens when glucose is available. versus lactose?

A

bacteria prefers glucose and will then turn off the transcription of lac operon off

105
Q

what happens when there is an absence of glucose?

A
  • bacteria makes cAMP (which allosterically activates CAP)
106
Q

what is CAP?

A

the lac operon activator that activates a number of genes allowing bacteria to use various alternative sources (including lactose)

107
Q

what happens if lactose is absent?

A

lac operon specific repressor binds operator and turns the operon off

108
Q

what happens in the presence of lactose?

A

its byproduct allolactose binds repressor and removes the transcription block

109
Q

what is the MOST complex molecular process in eukaryotes?

A

transcription regulation

110
Q

what are enhancers?

A

distant DNA elements that recruit activator proteins and thus permit transcription

111
Q

how is coordinated expression of certain genes achieved in eukaryotes?

A

by bringing together RNA loops from different parts of chromosomes

112
Q

how is transcription usually activated in eukaryotes?

A

thru the loosening of chromatin

113
Q

what are 2 things that can be inherited by the daughter chromosome?

A
  1. histone

2. DNA modifications

114
Q

how can sequence-specific binding protein repress the translation of some mRNAs?

A

by keeping the ribosome from binding to the ribosome-binding sequence on mRNA through the stabilization of double-standard (stem-loop) structures that encompass ribosomal binding site (RBS)
- thus makes RBS inaccessible to ribosome assembly as it would require single-stranded unfolded mRNA

115
Q

what do MicroRNAs (miRNAs) do in eukaryotic cells?

A

direct the destruction of target mRNA; regulate gene expression by targeting complementary RNA molecules for destruction`

116
Q

what is silencing?

A

negative regulation of transcription that controls gene expression of the level of mRNA stability

117
Q

why are small interference RNAs (siRNAs) produced?

A

they are produced in response to foreign double-stranded RNAs

118
Q

where can double-stranded RNA (dsRNA) come from?

A

either normally of viral origin or from transposones

119
Q

what are transposones?

A

mobile elements that can move from one part of the genome to another interfering with normal genome activity

120
Q

what is artificial RNAi used for?

A

to downregulate (or silence) specific genes in cultured cells and model organisms

Cell Bio Exam 2 (4 decks)

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