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Intro Molecular Biology > Midterm 2 > Flashcards

Midterm 2 Flashcards

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1
Q

When did scientists show that the information in DNA can be copied into RNA and then into protein?

A

1950s

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2
Q

How is the genetic code redundant?

A

64 codons that give only 20 amino acids, where the last nucleotide in a codon is different (first two usually all give the same amino acid).

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3
Q

Translation

A

The conversion of information in RNA into protein.

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4
Q

Genetic code

A

The correspondence between nucleotides in a mRNA and the amino acid sequence of a protein.

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5
Q

Codon

A

Group of three consecutive nucleotides in RNA that specify an amino acid.

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6
Q

Reading frames

A

The portion of a mRNA that is translated.

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7
Q

How many ORF are there? How many give the correct protein?

A

3 ORF with ONLY 1 giving the correct protein.

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8
Q

How did researchers create a cell-free system for protein synthesis?

A

Broke open E.coli cells and centrifuged where lighter components were needed for protein synthesis. They applied radioactive amino acids that would result in radiolabeled proteins. Another centrifuge done again and the radioactive layer of proteins at the top were assessed.

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9
Q

What does translation depend on?

A

Adaptor molecules

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10
Q

What do adpator molecules bind to?

A

Bind to a codon at one site on their surface and to an amino acid at another site.

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11
Q

What is the appearance of a tRNA?

A

Folded, double-helical structure formed by base-paired regions to give a cloverleaf

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12
Q

What additional forming of the cloverleaf tRNA form?

A

Compact, L-shaped structure held together by additional hyrdogen bonds between different regions of the molecule.

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13
Q

Anticodon

A

A region on the tRNA that contains a set of three consecutive nucleotides that bind by base pairing to the complementary codon in the mRNA/

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14
Q

What is the importance of the 3’ end of the tRNA?

A

Site where the amino acid that matches the codon is covalently attached.

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15
Q

Wobble base-pairing

A

Only the first two positions of the codon match while the third position doesn’t bind explaining the difference in the third nucleotide in amino acids.

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16
Q

aminoacyl-tRNA synthetases

A

Enzymes that recognize and attach the correct amino acid to tRNAs.

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17
Q

What part do aminoacyl-tRNA synthetases recognize?

A

Specific nucleotides in both the anticodon and the amino-acid accepting arm of the correct tRNA.

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18
Q

Charging

A

The process of the synthetase attaching the amino acid to its corresponding tRNA.

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19
Q

What energy is used in the synthetase-catalyzed reaction?

A

Hydrolysis of ATP

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20
Q

What energy is used to link the amino acid to the chain of polypetides?

A

The high-energy bond between the charged tRNA and the amino acid.

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21
Q

Ribosome

A

A large complex of small proteins (ribosomal) and RNA molecules known as ribosomal RNAs (rRNAs).

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22
Q

What is the purpose of a ribosome?

A

Allow the translation of mRNA into protein by moving along the mRNA, holding the tRNAs, and linking the amino acids to form a chain.

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23
Q

What are the subunits of a ribosome?

A

Small and large subunit.

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24
Q

What does the small ribosomal subunit do?

A

Matches the tRNAs to the codons of the mRNA.

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25
Q

What does the large ribosomal subunit do?

A

Catalyzes the formation of peptide bonds that link the amino acids in a polypeptide chain.

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26
Q

Where does the subunits of the ribosome bind to the mRNA?

A

5’ end

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27
Q

What happens to the subunits of the ribosome when protein synthesis is done?

A

Separate

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28
Q

Compare the speed of eukaryotic ribosome versus bacterial ones.

A

Eukaryotic - 2 amino acids to a polypeptide chain per second.
Bacterial - 20 amino acids per second.

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29
Q

What are the three sites on tRNA?

A

A (aminoacyl-tRNA), P (peptidyl-tRNA), and E (exit) site.

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30
Q

Explain the process of translation from the three sites on the ribosome.

A
  1. Initiator charged tRNA enters the P site, base pairing with the complementary codon on the mRNA.
  2. Next charged tRNA enters the A site and its amino acid is linked to the peptide chain at P site (through the carboxyl end joined by a peptide bond to free amino group in A site).
  3. Large ribosome shifts forward, moving the initiator tRNA to E site, ejecting it.
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31
Q

What way are new proteins synthesized?

A

Amino to its carboxyl end.

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32
Q

How many small ribosome sites can be occupied at a time?

A

Two

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33
Q

How much RNA makes ribosome?

A

2/3 by weight

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34
Q

What is responsible for the ribosomes structure and its ability to catalyze protein synthesis?

A

rRNAs

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35
Q

Where are rRNAs located in the ribosome?

A

Form a highly compact core

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36
Q

Where are ribosomal proteins located in a ribosome?

A

Located on the surface where they fill in the gaps of the folded RNA.

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37
Q

What is the role of ribosomal proteins?

A

To fold and stabilize the RNA core

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38
Q

What is the catalytic site for peptide bond formation formed by?

A

The 23S rRNA of the large subunit, which is a peptidyl transferase.

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39
Q

Ribozymes

A

RNA molecules that have catalytic activity.

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40
Q

What is the methionine removed by?

A

A specific protease

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41
Q

What is needed for the initiation of protein synthesis in eukaryotes?

A

Proteins known as translation initiation factors.

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42
Q

Why is an initiator tRNA molecule added first?

A

Only adaptor capable of binding tightly to the P site in absence of the large ribosomal subunit.

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43
Q

When are the initiation factors released? Why?

A

When the AUG is recognized to allow for the large ribosomal subunit to bind and complete protein assembly.

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44
Q

What do bacterial mRNA have to tell the ribosome where to bind?

A

Specific ribosome-binding sequences that are up to six nucleotides long and located a few nucleotides upstream of an AUG.

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45
Q

Polycistronic

A

The ability of bacterial mRNA to encode several different proteins from the same mRNA molecule.

46
Q

What is the end of translation signified by?

A

A stop codon, UAA, UAG, and UGA.

47
Q

What do release factors do?

A

Proteins that bind to the stop codon and alter the activity of peptidyl transferase, allowing the addition of an H2O to peptidyl tRNA instead of an amino acid, thus releasing the chain.

48
Q

What do chaperone proteins do?

A

Fold proteins correctly in the cell.

49
Q

When do chaperone proteins attach to a protein?

A

As they emerge from the ribosome.

50
Q

Polysomes

A

Ribosomes that bind to the 5’ end of mRNA as it’s being translated.

51
Q

How far apart is each ribosome attached to a mRNA molecule?

A

80 nucleotides apart.

52
Q

What is the importance of polysomes?

A

Allow more protein molecules to be made at a given time.

53
Q

When do polysomes attach to bacterial mRNA?

A

Ribosomes attach to free end before transcription of RNA is complete, following closely behind RNA polymerase.

54
Q

What is a fundamental feature of all life in terms of mRNA?

A

Ability to translate mRNAs into functional proteins.

55
Q

What are functions of proteolytic pathways?

A

Degrade proteins with short lifetimes and remove proteins that are damaged or misfolded.

56
Q

Proteasomes

A

Large protein machines that break down proteins.

57
Q

What is the structure of a proteasome?

A

Central cylinder with an active site in an inner chamber and ends stoppered by a large protein complex (at least 10 subunits).

58
Q

How do proteasomes work?

A

Protein stoppers bind to the damaged proteins and unfold the proteins, threading them into the inner chamber. Proteases chop them into short peptides and released from either end.

59
Q

How are ubiquitin chains added?

A

A certain amino acid sequence on one that needs it (short-lived) or signals exposed from misfolding/damage.

60
Q

What does the final concentration of a protein depend on?

A

Rate at which each of the steps are carried out.

61
Q

What must proteasomes recognize in eukaryotic damaged proteins?

A

Covalent attachment of a ubiquitin chain.

62
Q

What may happen to a protein once released?

A

Post-translational modifications like covalent phosphorylation, binding of cofactors, or association with other protein subunits.

63
Q

What is the sequence of -10 (3’ to 5’)?

A

ATATAA

64
Q

What is the sequence of -35 (3’ to 5’)?

A

AACTGT

65
Q

What does the RNA transcript form to stall RNA polymerase?

A

Hairpin loop (done by G + Cs binding with other G + Cs to form hydrogen bonds), thus transcription is done (RHO independent factor).

66
Q

What are transcription factors?

A

Proteins that act directly with DNA

67
Q

General transcription factors

A

Those involved in binding directly to DNA, thus initiating transcription.

68
Q

What do general transcription factors require?

A

Special transcription factors.

69
Q

Where did the idea of genes being switched on and off come from?

A

E.coli and its adaptable changes in the composition of their growth medium.

70
Q

Transcription regulators

A

Proteins that bind to DNA and control gene transcription.

71
Q

What are regulatory DNA sequences used for?

A

To switch a gene on or off.

72
Q

What is the composition of a regulatory DNA sequence in a bacteria versus eukaryotes?

A
  1. Short as 10 nucleotide pairs in bacteria
  2. 10,000 nucleotide pairs in eukaryotes
73
Q

What is the purpose of regulatory DNA sequences in a bacteria?

A

Respond to a single signal

74
Q

What is the purpose of regulatory DNA sequences in an eukaryotic cell?

A

Microprocessors, integrating information from multiple signals.

75
Q

What is the purpose of transcription regulators?

A

Binds to a regulatory DNA sequence to act as a switch to control transcription.

76
Q

How many DNA sequences does a single transcriptional regulator recognize?

A

ONLY one

77
Q

How do proteins recognize a specific nucleotide sequence?

A

Surface of the protein fits tightly against the surface features of a DNA double helix.

78
Q

How does the protein make contact with a nucleotide sequence?

A

Protein inserts itself into the major groove of the helix to make contacts with nucleotide pairs here.

79
Q

How many molecular contacts are formed at a protein-DNA interface?

A

10-20 contacts

80
Q

Are protein-DNA interactions strong?

A

The most tightest and specific molecular interactions.

81
Q

What do transcription regulators bind to DNA as?

A

Dimers

82
Q

What is the purpose of dimers?

A

Doubles the area of contact with DNA, thus increasing the strength and specificity of the protein-DNA interaction.

83
Q

Homeodomain

A

An area in eukaryotes where proteins make interactions with DNA.

84
Q

How do bacteria regulate the expression of their genes?

A

According to the food sources that are available.

85
Q

What is an operon?

A

A cluster of genes on a chromosome that are transcribed from a single promoter as one long mRNA molecule.

86
Q

Explain what happens when tryptophan concentrations are low.

A

The operon is transcribed and mRNA is translated, thus the enzymes will produce tryp.

87
Q

What happens when tryptophan concentrations are high?

A

The production of the operon stops.

88
Q

What does the transcription regulator bind to in the operon?

A

Operator

89
Q

What happens when the regulator binds to the operator in the tryptophan operon?

A

Blocks the access of the RNA polymerase to the promoters, thus preventing transcription, known as the tryptophan repressor (works with excessive amounts of tryp).

90
Q

Why is a tryptophan repressor an allosteric protein?

A

The binding of tryp causes a change in its structure so that the protein can bind to the operator sequence.

91
Q

How is the tryp repressor protein always present in the cell?

A

Gene that encodes it is transcribed at a low level.

92
Q

Transcriptional repressor protein

A

Switches genes off

93
Q

Transcriptional activator protein

A

Switch genes on

94
Q

Where do transcriptonal activators bind to? What does this help?

A

Promoters where they position RNA polymerase to start transcription.

95
Q

What do activator proteins bind to? WHat do they help with?

A

The promoters to allow RNA polymerase to bind and start transcription.

96
Q

Explain activator proteins in the lac operon.

A

CAP activator proteins bind to cAMP when there is an absence of glucose, allowing it to bind to the promoter thus proteins to digest lactose can be made (lactose is PRESENT).

97
Q

How does the Lac repressor work?

A

Binds to the operator when there is an absence of lactose.

98
Q

What circuits are controlled by transcription regulatory devices in eukaryotes?

A

Allow a fertilized egg to form the tissues and organs of a multicellular organism.

99
Q

Enhancers

A

DNA sites that eukaryotic gene activators bind to to increase the rate of transcription.

100
Q

Where do activator proteins bind to in eukaryotes?

A

Either upstream or downstream from a gene’s promoter.

101
Q

What happens to the DNA between the enhancer and the pronmotor?

A

The DNA loops to allow the activator proteins to influence the direct events at the promoter.

102
Q

What do proteins on the DNA help with in terms of transcription regulators?

A

Additional proteins that link the distantly bound transcription regulators to proteins, RNA polymerase and general transcription factors, at the promoter.

103
Q

What does the large complex of Mediator do (transcriptional regulator)?

A

Proteins function by adding in the assembly of the general transcription factors and RNA polymerase to form a larger transcription complex at the promoter.

104
Q

What do eukaryotic repressors do?

A

Decreases transcription by preventing the assembly of a large transcription complex at the promoter.

105
Q

What do eukaryotic transcriptional regulators attract? Purpose?

A

Attract proteins that modify chromatin structure so that affect the accessibility of the promoter to the general transcription factors and RNA polymerase.

106
Q

What are three descriptions of the amino acid reading frame?

A

Redundant (same amino acid produced from different codons), universal (same codes used throughout species) and continuous (always read constantly in groups of three).

107
Q

Why can nucleosomes inhibit transcription?

A

If they are positioned over the promoter than they block physically block the assembly of the general transcription factors or RNA polymerase.

108
Q

What did chromatin packaging evolve?

A

Prevent leaky gene expression by blocking the initiation of transcription in the absence of proper activator proteins.

109
Q

What is a gene activator that uses chromatin modifying?

A

The recruitment of histone acetyl transferases.

110
Q

How do histone acetyl transferases help with chromatin modification?

A

Allows the attachment of acetyl groups to lysines in the tail of histone proteins, thus giving them a greater accessibility to DNA and attract protein that promote transcription

111
Q

How can gene repressor proteins modify chromatin?

A

Repressors attract histone deacetylases where they remove acetyl groups from histone tails, thus making them less accessible to DNA, thus transcription initiation won’t occur.

Intro Molecular Biology (5 decks)

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