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MCB 701 > Sorci-Thomas fix > Flashcards

Sorci-Thomas fix Flashcards

1
Q

mRNA

A

messenger RNA; codes for proteins

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2
Q

rRNA

A

ribosmal RNA; forms the basic pattern and structure of the ribosome - catalyzes protein synthesis

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3
Q

tRNA

A

transfer RNA; carries amino acids to ribosome during translation

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4
Q

snRNA

A

small nuclear RNA; functions in a variety of nuclear processes, including pre-mRNA splicing

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5
Q

snoRNA

A

small nucleolar RNA; used to process and chemically modify rRNA

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6
Q

scaRNA

A

small cajal RNA; used to modify snoRNA and snRNA

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7
Q

miRNA

A

micro RNA; regulates gene expression by blocking translation of selective mRNA

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8
Q

siRNA

A

small interfering RNA; turns off gene expression by directing degradation of selective mRNA and establishing compact chromatin structures

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9
Q

RNA Polymerase I

A

most rRNA gene

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10
Q

RNA Polymerase II

A

all protein-coding genes; snoRNA, miRNA, and siRNA genes; and most snRNA genes

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11
Q

RNA Polymerase III

A

tRNA genes; some rRNA, snRNA genes, and genes for other small RNAs

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12
Q

CTD

A

C-terminal domain; A 52 tandem repeat of 7 amino acid chain tethered to an RNAP II that keeps proteins needed in transcription process available until needed.

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13
Q

TFIID

A

Recognizes TATA box and other DNA sequences at the transcription start site; regulates DNA binding by TBP

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14
Q

TIFFB

A

Recognizes BRE element in promoters; accurately positions RNAP II at the transcription start site

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15
Q

TFIIF

A

Stabilizes RNAP II interaction with TBP and TFIIB; helps attract TFIIE and TFIIF

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16
Q

TFIIE

A

Attracts and regulates TFIIH

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17
Q

TFIIH

A

Unwinds DNA at the transcription start site; phosphorylates Ser5 of RNAP II CTD; releases RNAP II from the promoter

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18
Q

Enhancer site

A

Site that attracts an enhancer protein; enhancer protein - can be either be at the 3’ or 5’ end of the gene - promotes the rate of transcirption. may help keep the complex together

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19
Q

RNA Polymerase II Mechanics

A

1: TFIID binds to TATA box at TBP (TATA binding protein) location
2: Remaining transcription factors and RNAP II assemble at promoter
3: TFIIH hydrolyzes ATP to pry apart DNA to expose template strand
4: RNAP II remains at promoter and synthesizes short lengths of RNA until conformational changes allow it to move away from the promoter
* Eukaryotic mRNA requires further processing

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20
Q

Consensus sequence

A

Key sequences with a little variability that attract binding elements (e.g. TATA box)

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21
Q

Splicing

A

In eukaryotes. removal of noncoding intron sequences on an mRNA to bring exons together. ~ 75% of genes can be spliced in multiple ways; allows for different varieties of the same protein to be produced in different tissues.

Mostly occurs during transcription

Intronic adenine attacks 5’ splice site and cuts sugar backbone and forms a covalent link with the 5’ end of the cut site (forming a lariat); 3’ end of cut site attacks the start site of the next exon, releasing the intron.

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22
Q

5’ Capping

A

A 7-methyl guanosine attached to the 5’ end of an mRNA transcript via 5’-5’ triphosphate linkage; allows the ribosome to differentiate the ends of the transcript

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23
Q

Spliceosome

A

A complex made up of 7 snRNPs (U1, U2 U2AF, U4, U5, U6, BBP) that recognize nucleotide splicing sequences and participate in the chemistry of splicing

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24
Q

Splicosome Mechanics

A
  • U1 Forms base pairs with 5’ splice site
  • BBP and U2AF recognize and pairs to branch-point site
  • U2 displaces U2AF/BBP at branch-point site
  • U4/U6 form base pair interactions and with U5 creates active site of spliceosome and positions appropriate portions of pre-mRNA for first splice reaction
  • Other Rna/RNA rearrangements and break apart U4/U6 complex and U6 carries 3’ end of one exon to the 5’ end of the next exon
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25
Q

Exon skipping

A

Not all exons in a pre-mRNA are incorporated into the complete mRNA

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26
Q

Cajal bodies

A

Proposed sites where snRNP and snoRNP undergo final modifications

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27
Q

Nuclear transport receptors

A

Escorts mRNA from nucleus to cytosol through nuclear pore complex; For mRNA export, specific nuclear transport receptors must be in place; Re-enters nucleus after transport for future use

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28
Q

Eukaryotic Ribosome Initiation

A

eIF2 loads initiator tRNA-methionine complex onto the P-site of the small ribosomal subunit

Small ribosomal subunit binds to the 5’ end of mRNA and moves in the 3’ direction until it reaches an AUG sequence

Initiation factors disassociate from the small subunit to allow the large subunit to attach

Protein synthesis proceeds

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29
Q

EF-G

A

Binds to ribosome A-site and moves ribosome one codon in 3’ direction

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30
Q

Ribosome translation

A

Aminoacyl-tRNA binds to vacant A-site and spent t-RNA dissociates from E-site

Ribosome forms peptide bond between amino acids at the P- and A- sites, releasing the amino acid from the P-site tRNA

Large ribosomal subunit shifts one codon in the 3’ direction, leaving the tRNAs in hybrid sites

Small ribosomal subunit follows large subunit and resets with an empty A-site

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31
Q

Helix Turn Helix

A

A transcription factor that is constructed from two α-helices connected by a short chain of amino acids. C-terminal helix is the recognition helix and fits into the major groove of DNA sequences.

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32
Q

EF-Tu

A

Binds GTP and aminoacyl-tRNA and shuttles aminoacyl-tRNA inot the A-site

Checks codon/anticodon pairing

Increases translation accuracy and helps move the reaction forward

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33
Q

Nuclear pore complex

A

Aqueous channels in the nuclear membrane that directly connect the nucleoplasm and cytoplasm

Allows small molecules to directly diffuse through (<50kD), and requires larger molecules to pass through via nuclear transport receptors - these proofread the molecule to make sure it is export-ready.

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34
Q

Poly-A tail

A

After transcription cleavage, PAP (polyA polymerase) adds ~200 nucleotides to the 3’ end

Does not require template to add sequences; is not encoded directly by the genome

PAP assemble to to determine polyA tail length

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35
Q

Helix loop helix motif

A

A dimer made up of two α helix monomers that connect via a loop structure. Each monomer interacts with the major groove and dimerizes another monomer. makes specific contacts with the DNA

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36
Q

The levels of gene expression

A 
Transcription proteins into the nucleus
Assembly of transcription machinery at start sites
Post-transcriptional modification
Capping
Proofreading
Export
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37
Q

Footprinting

A

A method used to locate the site at which a protein interacts with DNA

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38
Q

Gene control regions

A

The whole repertoire of DNA that is involved in regulating and initiating transcription.

includes promoter regions and regulatory sequences; can be either adjacent or distant from one another

39
Q

Ribosomal Initiation

A

EMPTY

40
Q

Ribosome sites

A

A-site: Aminoacyl-tRNA entry site

P-site: Site of peptide formation; peptide is transfered from tRNA to amino acid in A-site

E-site: tRNA exit site

41
Q

Exon skipping

A

Not all exons from pre-mRNA are incorporated into the mRNA; this allows for protein variation in different tissues

42
Q

Gene activator proteins

A

EMPTY

43
Q

CHIP Assay

A

Chromatin immunoprecipitation assay

provides a way to determine sites that a given gene regulatory protein occupies under certain conditions in vivo.

44
Q

Affinity Chromatography

A

Used to determine a protein that interacts with a specific sequence

Stage 1: Multiple sequences are attached to column matrix; proteins are washed through to determine the proteins that interact with DNA

Stage 2: Column matrix only has one type of sequence attached to it. DNA binding proteins washed through to determine which proteins will interact with that specific protein

45
Q

Regulation of gene regulatory proteins

A 
Synthesized only when needed
Ligand binding activation
Covalent modification
Forming a complex with another protein
Unmasking of an inhibitor
Stimulation of nuclear entry
Release from a membrane bilayer
46
Q

Epigenetic Inheritance Mechanisms

A

EMPTY

47
Q

Gel mobility shift Assay

A

EMPTY

48
Q

Leucine Zipper

A

A transcription factor made up of two α helices form a coilded coil and are held together by Leu side chains that extend from each helix; grips the DNA like a clothespin at the major groove; acts like an enhancer, but is not an enhancer

49
Q

Frameshift/Point mutations

A

EMPTY

50
Q

DNA Methylation

A

EMPTY

51
Q

Imprinting

A

EMPTY

52
Q

Repressor protein mechanisms

A 
Competitive DNA binding
Masking the activation surface
Direct interaction with general transcription factors
Chromatin remodeling complexes
Histone deacetylases
Histone methyl transferases
53
Q

Positive and Negative Control of Splicing Regulation

A

EMPTY

54
Q

Mechanisms of translational control (eukaryotes)

A

EMPTY

55
Q

General order of events that lead to transcription initiation

A

Gene activator protein binds to chromatin
Chromatin remodeling
Covalent histone modification
Additional activator proteins bind to gene regulatory protein
Assembly of pre-initiation complex at the promoter
Transcription initiation

56
Q

Four most important ways to locally alter chromatin

A

Covalent histone modifications
Nucleosome removal
Nucleosome remodeling
Nucleosome replacement

57
Q

Zinc Finger

A

A structural element that holds an α helix and β sheet together; often found in tandem clusters so that the can contact the major groove of DNA

58
Q

mRNA catabolism

A

EMPTY

59
Q

Mechanisms of translational control (bacteria)

A

EMPTY

60
Q

Post transcriptional controls

A

EMPTY

61
Q

Transcription Initiation

A

EMPTY

62
Q

cleavage, polyadenylation, termination

A

EMPTY

63
Q

Protein aggregation

A

EMPTY

64
Q

Histone Modification

A

EMPTY

65
Q

Gene Activator Proteins

A

EMPTY

66
Q

Protein synthesis

A

EMPTY

67
Q

Protein folding

A

EMPTY

68
Q

DNA to Protein Pathway

A

EMPTY

69
Q

Capping, elongation, splicing

A

EMPTY

70
Q

Post Translational Control

A

EMPTY

71
Q

miRNA processing

A

EMPTY

72
Q

Protein folding chaperones

A

EMPTY

73
Q

Positive Feedback Loop

A

EMPTY

74
Q

Post-transcriptional quality control

A

EMPTY

75
Q

Ubiquitin

A

EMPTY

76
Q

Aggregation

A

EMPTY

77
Q

Protein degradation

A

EMPTY

78
Q

mRNA degradation

A

EMPTY

79
Q

Internal Ribosome Entry Sites (IRES)

A

EMPTY

80
Q

TATA box

A

Short sequence primarily made up of T and A, located ~25 nucleotides upstream of start site; not the only site, but most important for RNAP II

81
Q

Promoter sequence/protein

A

Typically at the 5’ start site of transcription; fixes the start site and assembles the transcription proteins

82
Q

Initiation Factor phosphorylation

A

EMPTY

83
Q

Ubiquination

A

EMPTY

84
Q

hsp60

A

EMPTY

85
Q

Degradation signal

A

EMPTY

86
Q

Export

A

EMPTY

87
Q

Important sites for genome splicing

A

EMPTY

88
Q

hsp70

A

EMPTY

89
Q

Cryptic splice site

A

Nucleotide sequences within the RNA that resemble the splicing signals in the intron; can lead to incorrect splices.

90
Q

Transcription factors

A 
Proteins that regulate the type of behavior a genome expresses. Can be in many different conformations:
Helix turn helix
Helix loop helix
Leucine Zipper
Zinc finger
91
Q

Phylogenetic footprinting

A

Comparing the genomes of closely related species to identify consensus sequences - these are probably regulatory sequences that control gene expression (as these sequences will not probably change very much over time)

92
Q

Regulatory sequence

A

Binding sites for gene regulatory proteins; these affect the rate of transcription initiation

93
Q

Promoter sequence

A

The sequence of DNA where the general transcription factors and polymerase assemble

94
Q

Repressor protein methods

A 
Competitive DNA binding
Masking
Direct interaction
Recruitment of chromatin remodeling components
Deacetylase recruitment
histone methyl transferase

MCB 701 (5 decks)

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