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MCB 701 > Sorci-Thomas fix > Flashcards

Sorci-Thomas fix Flashcards

(94 cards)

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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
Exon skipping
Not all exons in a pre-mRNA are incorporated into the complete mRNA
26
Cajal bodies
Proposed sites where snRNP and snoRNP undergo final modifications
27
Nuclear transport receptors
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
28
Eukaryotic Ribosome Initiation
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
29
EF-G
Binds to ribosome A-site and moves ribosome one codon in 3' direction
30
Ribosome translation
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
31
Helix Turn Helix
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.
32
EF-Tu
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
33
Nuclear pore complex
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.
34
Poly-A tail
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
35
Helix loop helix motif
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
36
The levels of gene expression
``` Transcription proteins into the nucleus Assembly of transcription machinery at start sites Post-transcriptional modification Capping Proofreading Export ```
37
Footprinting
A method used to locate the site at which a protein interacts with DNA
38
Gene control regions
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
Ribosomal Initiation
EMPTY
40
Ribosome sites
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
Exon skipping
Not all exons from pre-mRNA are incorporated into the mRNA; this allows for protein variation in different tissues
42
Gene activator proteins
EMPTY
43
CHIP Assay
Chromatin immunoprecipitation assay provides a way to determine sites that a given gene regulatory protein occupies under certain conditions in vivo.
44
Affinity Chromatography
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
Regulation of gene regulatory proteins
``` 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
Epigenetic Inheritance Mechanisms
EMPTY
47
Gel mobility shift Assay
EMPTY
48
Leucine Zipper
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
Frameshift/Point mutations
EMPTY
50
DNA Methylation
EMPTY
51
Imprinting
EMPTY
52
Repressor protein mechanisms
``` Competitive DNA binding Masking the activation surface Direct interaction with general transcription factors Chromatin remodeling complexes Histone deacetylases Histone methyl transferases ```
53
Positive and Negative Control of Splicing Regulation
EMPTY
54
Mechanisms of translational control (eukaryotes)
EMPTY
55
General order of events that lead to transcription initiation
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
Four most important ways to locally alter chromatin
Covalent histone modifications Nucleosome removal Nucleosome remodeling Nucleosome replacement
57
Zinc Finger
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
mRNA catabolism
EMPTY
59
Mechanisms of translational control (bacteria)
EMPTY
60
Post transcriptional controls
EMPTY
61
Transcription Initiation
EMPTY
62
cleavage, polyadenylation, termination
EMPTY
63
Protein aggregation
EMPTY
64
Histone Modification
EMPTY
65
Gene Activator Proteins
EMPTY
66
Protein synthesis
EMPTY
67
Protein folding
EMPTY
68
DNA to Protein Pathway
EMPTY
69
Capping, elongation, splicing
EMPTY
70
Post Translational Control
EMPTY
71
miRNA processing
EMPTY
72
Protein folding chaperones
EMPTY
73
Positive Feedback Loop
EMPTY
74
Post-transcriptional quality control
EMPTY
75
Ubiquitin
EMPTY
76
Aggregation
EMPTY
77
Protein degradation
EMPTY
78
mRNA degradation
EMPTY
79
Internal Ribosome Entry Sites (IRES)
EMPTY
80
TATA box
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
Promoter sequence/protein
Typically at the 5' start site of transcription; fixes the start site and assembles the transcription proteins
82
Initiation Factor phosphorylation
EMPTY
83
Ubiquination
EMPTY
84
hsp60
EMPTY
85
Degradation signal
EMPTY
86
Export
EMPTY
87
Important sites for genome splicing
EMPTY
88
hsp70
EMPTY
89
Cryptic splice site
Nucleotide sequences within the RNA that resemble the splicing signals in the intron; can lead to incorrect splices.
90
Transcription factors
``` 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
Phylogenetic footprinting
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
Regulatory sequence
Binding sites for gene regulatory proteins; these affect the rate of transcription initiation
93
Promoter sequence
The sequence of DNA where the general transcription factors and polymerase assemble
94
Repressor protein methods
``` Competitive DNA binding Masking Direct interaction Recruitment of chromatin remodeling components Deacetylase recruitment histone methyl transferase ```

MCB 701 (5 decks)

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