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BMSC 220 > Topic 6 > Flashcards

Topic 6 Flashcards

1
Q

Regulating ____________ is one of the fundamental ways in which cells can modify their activities

A

gene expression

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2
Q

changes in gene expression are involved in…

A
  • response of cells to their environment
  • regulation of cell cycle
  • distinct activities and coordination of different cell types
  • cell differentiation and development
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3
Q

RNA polymerases

A

the principal enzyme responsible for RNA synthesis

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4
Q

Unlike DNA polymerase, RNA polymerase do not require ….

A

a primer sequence to initiate RNA synthesis

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5
Q

genes are regulated by….

A

“dimmer switches” known as promoters

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6
Q

promoters

A

DNA sequence with which RNA polymerase and other proteins interact to initiate and regulate rate of transcription

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7
Q

transcription

A

RNA synthesis using a DNA template (a copy)

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8
Q

translation

A

protein synthesis using an mRNA template (translating)

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9
Q

mRNA

A

RNA molecules that serve as templates for protein synthesis (RNA polymerase II)

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10
Q

rRNA

A

a component of ribosomes (RNA polymerase I, Polymerase III)

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11
Q

tRNA

A

serves as adaptor molecules that align amino acids along the mRNA template (RNA polymerase III)

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12
Q

make up well over 90% of total RNA by mass in any cell

A

rRNA and tRNA

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13
Q

regulatory mechanisms

A

ensure correct gene is transcribed in the correct cell type at the correct time and in correct amount

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14
Q

DNA sequence element

A

term used to denote a specific short sequence of DNA base pairs within a gene promoter

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15
Q

Cis-acting DNA sequences

A

aka promoter and enhancer elements; regulate expression of genes

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16
Q

basal or core promoter

A

ex. TATA box, initiator (Ing) DNA sequence

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17
Q

upstream promoter and enhancers

A

same functionally; transcriptional regulatory sequences that can be located at a significant distance from promoter; binding sites for gene specific transcription factors

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18
Q

enhancers can be…

A

upstream and downstream

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19
Q

usually only one _______, but could be multiple _________________

A

TATA box, CAT and GC boxes

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20
Q

SV40 enhancer

A

can function in any orientation and in any position relative to core promoter

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21
Q

plasmid DNA

A

a method by which to introduce recombinant DNA into a cell

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22
Q

reporter gene

A

a gene that encodes an easily assayed enzyme or other protein and can be used to replace the normal gene sequence adjacent to a gene promoter

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23
Q

Other methods of incorporating altered DNA sequences into a genome:

A

retrovirus/lentivirus and CRISPR/Cas9

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24
Q

transcription factors

A

proteins that are required for RNA polymerase II to initiate transcription

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25
general transcription factors
involved in initiation of transcriptionand are part of general transcription machinery
26
gene specific transcription factors
not part of general machinery; proteins that exhibit DNA sequence-specific binding properties, direct activity of the general transcription factors and modulate activity of basal transcription complex
27
general transcription factors and RNA polymerase II are thought to assemble in...
a step-wise manner around the basal promoter region
28
the complex formed from a general transcription factor and RNA polymerase II
transcription initiation complex aka pre initiation complex aka basal transcription complex
29
TATA box
a regulatory DNA sequence found in promoters transcribed by RNA pol. II
30
TATA-binding protein or TBP
a basal transcription factor that binds directly to the TATA box
31
TBP-associated factors or TAFs
proteins associated with TBP in the general transcription factor (TFIID)
32
TFIIB associates with TFIID at the...... followed by recruitment of ............ and TFIIF
core promoter, RNA polymerase
33
After polymerase II joins promoter, ..... and ..... complete formation of initiation complex
TFIIE and TFIIH
34
How do gene-specific transcription factors work?
by either modifying the rate of transcription initiation by the basal transcription complex and/or rate of basal transcription complex assembly
35
Similar to TBP, recognition and binding sites of most transcription factors consist of......
short DNA sequences
36
which transcription factor recognizes the DNA sequence GGGCGG (GC box)
SP1
37
which transcription factor recognizes the DNA sequence CCAAT(CAT box)
CBTF
38
What specifies the amount of transcriptional initiation by RNA pol. II
combo of transcription factors interacting at a specific gene's promoter/enhancer sequence at one point in time
39
immunoglobin heavy chain enhancer
contains nine functional sequence elements
40
DNA-affinity chromatography
a method used to isolate transcription factors based on their binding to specific DNA sequences in order to study them further
41
steroid hormone receptors
transcription factors that regulate gene transcription in response to hormones
42
homeodomain proteins
contains a helix-turn-helix DNA binding domain and play critical roles in regulation of gene expression during embryonic development
43
transcription factors can function as either...
transcriptional activators and transcriptional repressors
44
2 general mechanisms of action of transcriptional activators
- interact with mediators and general transcription factors | - interact with coactivators, which modify chromatin structure
45
mediator
a large protein complex that binds to pre initiation complex and plays a key role in linking general transcription factors to gene specific transcription factors that regulate gene expression
46
How do transcription factors bound to distant enhancers interact with proteins in the RNA pol/mediator complex at the core promoter?
DNA looping
47
Release of RNA pol from basal complex to initiate transcription requires what....
phosphorylation and helices activities of TFIIH
48
gene expression is regulated by...
repressors and transcriptional activators
49
transcriptional repressors function by
- blocking binding of transcription activator to DNA sequence element - repress mediator activity - interaction with co-repressors
50
co-repressors
modify chromatin structure into a non-permissive state
51
example of gene activation and repression
control of lac operon
52
chromatin
decondensed state
53
chromatin remodeling
moving, removal and/or addition of histones
54
histone code
- histone tail acetylation and deacetylation | - other histone modification
55
histone modification can be stably inherited through...
epigenetic mechanisms
56
Chromatin remodelling factors
- slide nucleosomes along DNA - change conformation of the nucleosomes - eject the histone from DNA
57
histone acetylation
modification of histones by addition of acetyl groups to specific lysine residues in histone tails; result in transcriptionally permissive chromatin
58
histone deacetylation
gives rise to non-permissive chromatin state
59
DNA methylation
- prevent movement of transposon | - inactivate genes involved in development and differentiation
60
methylation patterns
-can be reversed but also passed to daughter cells as epigenetic inheritance
61
genomic imprinting
only of of two parental alleles of some genes is expresses during embryonic development
62
polyadenylation
adding a poly-A tail to pre-mRNA
63
what is added to 5' end in the beginning
7-methylguanosine cap
64
spliceosomes
large complexes composed of proteins and RNAs; multiple snRNP complexes
65
snRNAs
small nuclear RNAs that range in size to form the RNA component of spliceosome
66
types of snRNAs
U1, U2, U4, U5, U6
67
snRNPs
small nuclear ribonucleoprotein particles; complexes of snRNAs with proteins that play central roles in splicing process
68
types of snRNPs
U1, U2, U3, U5, U4/U6
69
actual splicing reaction is catalyzed by..
U6
70
alternative splicing
generation of different mRNAs by varying the pattern of pre-mRNA splicing to create multiple different, but related, proteins from same gene; some exons are removed with the introns
71
Each human gene yields and average show many alternatively spliced mRNAs?
6; but some can produce thousands
72
SR splicing factors
SR proteins; bind to exon sequence to direct where a spliceosome forms; make final choice of exons that will appear in any one cell type for alternatively spliced mRNA
73
DSCAM gene
contains four sets of alternative exons, each being incorporated into the spliced mRNA
74
Why is DSCAM mRNA important to neurons during embryonic development?
cell surface adhesion molecule important in allowing neurons to find their target cells
75
alternative splicing of DSCAMmeans...
different forms of a cell surface
76
pre-rRNA
primary transcript cleaved to form individual ribosomal RNAs (28S, 18S, 5.8S)
77
Extensive processing of pre-rRNA takes place...
before they can be assembled for use in protein synthesis
78
pre-tRNAs
transcribed as a group and are cleaved into individual tRNA molecules
79
5' end of eukaryotic tRNA is cleaved by...
RNase P
80
3' end of eukaryotic tRNAis cleaved by...
conventional RNase and has the sequence CCA added to end to facilitate binding to amino acids

BMSC 220 (12 decks)

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