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Applied Biochem > How Genes Direct The Production Of Proteins- Exam III > Flashcards

How Genes Direct The Production Of Proteins- Exam III Flashcards

1
Q

Cell achieve their specialized function based upon the expression of ______ and any subsequent _____ of the resulting proteins.

A

Specific genes; post-translational modifications

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2
Q

What is degraded quicker DNA or RNA? Why?

A

RNA because of nucleophilic attack of the ribose moiety

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3
Q

What degrades RNA very quickly?

A

Ribonuclease

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4
Q

In both prokaryotes and eukaryotes, you can have adjacent genes that get transcribed in:

A

Opposite directions

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5
Q

A segment of DNA that is transcribed into RNA and its associated transcriptional control regions

A

Gene

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6
Q

The transcriptional control regions of genes and RNA

A

Promotor regions

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7
Q

The type of RNA that is translated into proteins

A

Messenger RNA (mRNA)

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8
Q

The type of RNA that are important for the transfer of amino acids to the growing peptide chain.

A

Transfer RNA (tRNA)

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9
Q

What is the most abundant form of RNA?

A

Ribosomal RNA (rRNA)

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10
Q

Form of RNA that encodes ribosomal proteins

A

Ribosomal RNA (rRNA)

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11
Q

What form of RNA blocks the translation on specific mRNAs and thereby regulate gene expression?

A

microRNA (miRNA)

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12
Q

What form of RNA turns off gene expression by directing the selective degradation of mRNAs

A

Small interfering RNAs (siRNAs)

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13
Q

What form of RNA that process and chemically modify rRNAs

A

Small nucleolar RNAs (snoRNAs)

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14
Q

What form of RNAs modify snoRNAs and snRNAs?

A

Small cajal RNAs (scaRNAs)

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15
Q

Involved in telomere synthesis, X-chromosome interaction, and protein transport into the ER

A

Other non coding RNAs

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16
Q

Abundance of rRNA in the cell

A

~80%

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17
Q

abundance of tRNA in the cell:

A

~15%

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18
Q

Abundance of mRNA inside the cell:

A

3-5%

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19
Q

All RNAs have to be transcribed from a:

A

Gene in the genome

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20
Q

In eukaryotic organisms, most protein coding genes are transcribed by:

A

RNA polymerase II

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21
Q

When you see RNA polymerase II think:

A

Protein coding

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22
Q

Transcription always starts at a _____ point in the DNA and requires unwinding of the DNA to create the proper single-stranded template

A

Specific

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23
Q

Gene expression is regulated by numerous transcription factors that interact with ______ in DNA or proteins bound to these regions.

A

Promotor elements

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24
Q

The presence/absence of specific factors is an obligatory first step in the initiation of ______ binding.

A

RNA polymerase

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25
Q

An important sequence of the 5’ side (start site) of transcription

A

TATA Box

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26
Q

Transcription starts at what base:

A

Base 1

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27
Q

TATA box is rich in:

A

Thymidine and adenine residues

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28
Q

The TATA box will bind a very important transcription factor, (a dimer) called:

A

TBP & TFIID

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29
Q

The dimer that TATA box binds to is composed of:

A

TBP & TFIID

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30
Q

The TATA box localizes the dimer to position itself relative to the start site of transcription through the binding of the _____ to the TATA box

A

TBP

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31
Q

Once the TATA Box bind TBP what happens:

A

TFIID will bind and correctly position itself

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32
Q

Once the TBP and TFIID factors are positioned properly, _____ will come in and position itself.

A

TFIIB

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33
Q

The binding and positioning of TFIIB leads to the recruitment of:

A

A bunch of other factors

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34
Q

Once the TATA box has bound TBP and TBP allows for the correct positioning of TFIID, and TFIID allows for the correct positioning of TFIIB, and TFIIB recruits all the other important guys, this will allow for the:

A

Proper binding of RNA polymerase II

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35
Q

It’s important that RNA polymerase II positions itself:

A

Around the DNA molecule in the proper place

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36
Q

The RNA polymerase II should be bound on the DNA so that the start site of transcription occurs at:

A

Nucleotide 1

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37
Q

The TATA is located:

A

Left of the start site of transcription (-15 to -25 ) 5’ to the start site

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38
Q

Once the RNA polymerase II has bound there is a ____ that wraps around the DNA

A

CTD- (cytoplasmic tail domain)

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39
Q

A couple of _____ reactions occur on the cytoplasmic tail domain of the RNA polymerase II

A

Phosphorylation

40
Q

The phosphorylation reactions on the CTD of the RNA polymerase II leads to:

A

The disassembly of a lot of the general transcription factors

41
Q

When we have disassembly of most of the general transcription factors, caused by phosphorylation reactions on CTD, this allows for ____ activity and a _____ that is ready to go.

A

Helicase activity, and RNA polymerase ready to go

42
Q

Inside the binding pocket or the RNA polymerase, what is functioning?

A

Helicase

43
Q

The RNA polymerase is adding ______ to the growing RNA transcript through the uptake channel.

A

Ribonucleoside triphosphates

44
Q

On the growing mRNA transcript, the 5’ _____ is connecting to the 3’ ____

A

5’ Phosphate to 3’ hydroxyl

45
Q

RNA is not just a ____ molecule because it can fold back on itself and base pair

A

Linear molecule

46
Q

Key transcription factor TFIID is made of:

A

TBP subunit + TAF subunit

47
Q

The TBP subunit recognizes:

A

TATA box

48
Q

the TAF subunit recognizes other ____ sequences near the transcription start point and regulates DNA-binding by_____.

A

DNA sequences; by TBP

49
Q

TFIIB recognizes the _____ element in promoters

A

BRE

50
Q

The TFIIB accurately positions:

A

RNA polymerase II

51
Q

What element is important for accurately positioning the RNA polymerase at the transcriptional start site

A

BRE element

52
Q

All of the RNA polymerases have a preference for the types of genes that they bind-

RNA Polymerase I:

RNA Polymerase II:

RNA Polymerase III:

A

RNA polymerase I- rRNA genes
RNA polymerase II- protein coding genes, snoRNA genes, miRNA genes, siRNAgenes and most snRNA genes
RNA polymerase III- tRNA genes

53
Q

Processing events of mRNA include:

A

Capping, Splicing, Editing, Polyadenylation, Transport

54
Q

Capping:

A

Guanasine cap added to 5’ end

55
Q

In protein coding genes, poly-A tail added to the 3’ end

A

Polyadenylation

56
Q

Transport of mRNA involves the movement out of the _____ and into the _____.

A

Nucleus ——> cytoplasm

57
Q

Linear coding sequence is made of all of the _____ joined

A

Exons

58
Q

In mRNA processing the 5’ and 3’ untranslated region gets:

A

Kept in the linear sequence

59
Q

splicing occurs by a complex of RNA and protein molecules collectively known as the

A

Splicesome

60
Q

The spliceosome is made up of:

A

SnRNAs in a complex with 7 protein subunits

61
Q

The spliceosome made of the snRNAs in a complex with the 7 protein subunits come together and form a:

A

SNP

62
Q

What are the snRNAs involve din splicing?

A

U1, U2, U4, U5 and U6

63
Q

The snRNAs of the spliceosome provide proper:

A

Base pairing with the mRNA

64
Q

Splicing will join the ___ end of exon 1 to the ____ end of exon 2 and the ____ end of exon 2 to the ______ end of exon 3

A

3’ end of exon 1 to 5’ end of exon 2 and the 3’ end of exon 2 to the 5’ end of exon 3

65
Q

Splicing involves the formation of a ____ structure.

A

Lariat

66
Q

In splicing, a particular ____ residue in the intron sequence that undergoes a nucleophilic attack at the junction between the intron and the exon.

A

Adenosine

67
Q

What is more important for splicing, the sequence of nucleotides in the exon or intron? Why?

A

The sequences in the intron because this determines where the splicing will occur

68
Q

We estimate about _____ proteins in the human proteome

A

~250,000

69
Q

The tropomyosin gene can be spliced to form what types of mRNA based on the splicing resulting in different isoforms of the mRNA

A

Striated muscle mRNA
smooth muscle mRNA
Fibroblast mRNA (x2)
Brain mRNA

70
Q

The 5’ cap and splicing of the primary mRNA transcript occur as soon as the ______ emerges from the RNA polymerase

A

HnRNA

71
Q

The poly A tail added to the 3’ end occurs by a set of RNA-binding proteins and processing enzymes after it _____ from the RNA polymerase

A

Completely emerges

72
Q

The mature mRNA means that the mRNA has been:

A

Spliced, capped and poly tail added

73
Q

The mature mRNA gets transported from the nucleus to the _____ and to the ____ where protein synthesis can take place.

A

Cytoplasm and to the ER

74
Q

Small non coding RNAs that are about 21-25 nucleotides long

A

MicroRNA (miRNA)

75
Q

What type of RNA binds to the 3’UTR region of target mRNA to form an RNA-inducing silencing complex (RISC)

A

MiRNA

76
Q

MiRNA bind to the 3’UTR of mRNA to form an:

A

RNA-inducing silencing complex (RISC)

77
Q

The RISC (RNA-inducing silencing complex) formed by the miRNA :

A

Suppresses protein synthesis and or induces mRNA degredation

78
Q

What suppresses protein synthesis or mRNA degradation?

A

RNA-inducing silencing complex (RISC)

79
Q

Each miRNA can target ______ different mRNAs

A

Many

80
Q

MicroRNA genes are transcribed by:

A

RNA polymerase II

81
Q

These miRNAs are formed by: A miRNA gene gets transcribed through RNA polymerase II and they make an initial transcript that makes a hairpin double stranded molecule which is exported out of the nucleus and into the cytoplasm where a specific enzyme called ____ clips the bubble formed to create a mature miRNA that then binds to a bunch of proteins that make up a complex that up a ____ complex, and this complex binds to the mRNA at the 3’ untranslated region to form the ______.

A

Dicer; argonaute complex; RISC

82
Q

3 bases code for:

A

A single amino acid

83
Q

3 base sequence is known as a _____ in the mRNA

A

Codon

84
Q

The genetic code is _____ for all organisms

A

Universal

85
Q

Important features of the genetic code: (4)

A
  1. Commaless
  2. Degenerate
  3. 3rd base less specific
  4. 3 stop codons that do not code for amino acids
86
Q

The commaless feature of the genetic code means that the code is read from beginning to end so the _____ is critical.

A

Reading frame

87
Q

The degeneracy of the genetic code means:

A

More than one codon can make the same amino acid

88
Q

The third base rule of the genetic code means:

A

The 3rd base is less specific than the first 2 (wobble position)

89
Q

The 3 base genetic code allows for ____ possible codons.

A

64

90
Q

AUG codes for:

A

Methionine

91
Q

What are the 3 stop codons:

A

UAA UAG UGA

92
Q

Roberts Syndrome severity can be as simple as ______ or as harsh as ______.

A

Craniofacial abnormality to lethal embryology

93
Q

Roberts syndrome is a _____ mutation of ______

A

Homozygous mutation of ESCO2

94
Q

ESCO2 in Roberts syndrome encodes for an:

A

Acetyltransferase

95
Q

The ESCO2 in Roberts syndrome encodes acetyltransferase which is important for the formation of _____ that binds to chromosomes and creates cohesion between sister chromatids.

A

Cohesion complex

96
Q

The changes in the level of ESCO2 result in changes in the level of :

A

Ribosomal gene transcription.

Applied Biochem (18 decks)

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