eukaryotic transcription

Question 1

messenger RNA (mRNA)

Answer 1

encodes the AA sequence for a protein; primary transcript of a gene undergoes RNA processing to generate a mature mRNA that can be used by the ribosome

Question 2

transfer RNA (tRNA)

Answer 2

delivers an amino acid to the ribosome

Question 3

ribosomal RNAs (rRNA)

Answer 3

components of a ribosome

Question 4

small nuclear RNA (snRNA)

Answer 4

components of the spliceosome, the enzyme that catalyzes removal of introns during RNA processing

Question 5

microRNA (miRNA) and small interfering (siRNA)

Answer 5

act on mature mRNAs to decrease translation of the mRNA

Question 6

small nucleolar RNAs (snoRNA)

Answer 6

small RNA molecules that guide posttranscriptional base modifications in tRNAs, rRNAs, and snRNAs

Question 7

long non-coding RNA (lncRNA)

Answer 7

RNA molecules that do not encode protein; some lncRNAs influence gene expression

Question 8

eukaryotic genes stand alone in single transcription units. each gene has its own ___________ and __________

Answer 8

promoters and terminators

Question 9

the genes are organized with ___________ structure
- _____ code for sequence that will be included in a mature mRNA
- ______ sequences will be eliminated during RNA processing
- a _______________ includes both introns and exon sequences

Answer 9

intro-exon; exons; introns; primary transcript

Question 10

___________ is a light staining material
- the level of staining suggests a more open chromatin structure
- the genes in _______ are available for transcription

Answer 10

euchromatin

Question 11

___________ is the dark staining matter in a nucleus
- the level of staining reflects a condensed chromatin structure
- the DNA contains silenced genes and many types of repetitive DNA

Answer 11

heterchromatin

Question 12

constitutive heterchromatin

Answer 12

always in heterochromatin state; telomeres (no genes so nothing to express

Question 13

facultative heterchromatin

Answer 13

differs between cell types; can revert to euchromatin under certain stimuli

Question 14

the ___________ is the basic unit of chromatin

Answer 14

nucleosome

Question 15

DNA-histone core contacts are ___________________
- ______________ and ___________ occur between the positively charged ______________ and the negatively charged ________________ of DNA

Answer 15

sequence independent; electrostatic interactions and H-bonds; histone proteins; sugar-phosphate backbone of DNA

Question 16

a _______________ contains two copies each of histones ____, _____, ___, and ____
- disordered histone tails interact with other nucleosomes

Answer 16

histone core; H2A, H2B, H3, and H4

Question 17

_____________ locks DNA to the nucleosome

Answer 17

Histone H1

Question 18

chromatin structure is a product of the combined actions of _____________, such as _________________ and _____________, and trans-acting _____________________ that bind to epigenetic marks or to DNA

Answer 18

epigenetic marks; histone modifications; DNA methylation; transcription factors

Question 19

condensed chromatin is “closed” and viewed as transcriptionally silent
- inaccessible to most activators and chromatin remodeling complexes
- accessible only by ___________________________

Answer 19

pioneering transcription factors

Question 20

____________ means above genetics. the mediators of epigenetics are covalent modifications of the chromatin or DNA that do NOT affect the DNA sequence of bases (just affects access)

Answer 20

epigenetics

Question 21

the ___________ provide areas for interaction between ______________

Answer 21

histone tails; nucleosomes

Question 22

hypermethylation

Answer 22

often associated with closed chromatin (heterochromatin)

Question 23

histone acetylation

Answer 23

is found in areas of open chromatin (euchromatin)

Question 24

the histone tails include the N termini of histones ___ and ____, plus both the N and C termini of ____ and ____.

Answer 24

H3 and H4; H2A and H2B

Question 25

histone acetyltransferase (HAT)

Answer 25

acetylates lysine in the histone tails (euchromatin region)

Question 26

histone deacetylase (HDAC)

Answer 26

removes acetyl groups from the histone tails (not as accessible so transcription turns off; in euchromatin region)

Question 27

histone methyltransferase (HMT)

Answer 27

methylates lysine and arginine (lot harder to reverse; heterochromatin regions)

Question 28

the actions of HATs and HDACs oppose each other so acetylation of histone tails is _____________

Answer 28

readily reversible

Question 29

acetylation... - reduces the electrostatic attraction between nucleosomes and with DNA - favors recruitment of a _______________ - highly associated with transcriptional activation

Answer 29

neutralizes the positive charge on lysine in histone tails chromatin remodeling complex

Question 30

methylation ... - effect on transcription depends on location of amino acid and # of methyl groups - H3K4/H3K36/H3K79 (activation) - H3K9/H3K27/H4K20 (silencing)

Answer 30

retains the positive charge on lysine/arginine in histone tails

Question 31

hypermethylation (DNA) of a CpG island near a promoter ______________________

Answer 31

silences that promoter

Question 32

cytosine in the sequence CG is called a "CpG" and can be methylated by ______________________ at many sites within the genome - some promoter proximal regions of genes have a cluster of CG's in the sequence called a __________

Answer 32

DNA methyltransferase (DNMT); CpG island

Question 33

once chromatin structure is open, transcription factors (___________) bind specifically to sites in DNA to facilitate transcription. In eukaryotes, most gene regulation is positive, because activators are required to recruit ___________________ to a _____________

Answer 33

activators; RNA polymerase II; promoter

Question 34

_____________________ is recruited to a gene locus by a transcription factor and then acetylates surrounding histones.

Answer 34

histone acetyltransferase (HAT) -> favors DNA accessibility

Question 35

__________________ like _______ manipulate nucleosomes.

Answer 35

chromatin remodeling complexes; SWI/SNF

Question 36

______ is recruited to local sites in the genome - ______ either binds to acetylated histone or is recruited to a gene by protein-protein interactions with a _____________________

Answer 36

SWI/SNF; SWI/SNF; pioneering transcription factor

Question 37

chromatin remodeling complexes alter chromatin structure by: - chromatin remodeling "spreads" to surrounding area of the genome changing the accessibility of the DNA for activator proteins

Answer 37

unwrapping DNA from nucleosomes repositioning nucleosomes evicting nucleosomes

Question 38

the combined actions of _______ and ______________________ together lead to open chromatin structure

Answer 38

HATs and chromatin remodeling complexes

Question 39

the transcription start site is devoid of _________________ to make room for assembly of the _____________________________. - ______ bind near promoters and act to maintain open chromatin structure

Answer 39

nucleosomes; transcription preinitiation complex; HATS

Question 40

RNA polymerase II

Answer 40

makes mRNA and some small RNAs

Question 41

RNA polymerase I

Answer 41

synthesizes ribosomal rRNA

Question 42

RNA polymerase III

Answer 42

generates tRNA and other small RNAs

Question 43

if there is no _______ subunit, then it cannot locate and bind to promoters

Answer 43

sigma

Question 44

mammalian genes have ______________ elements, but also ____________ at distant locations along the chromosome. they are binding sites for transcription factors.

Answer 44

promoter proximal; enhancers

Question 45

______________ are sequence specific DNA binding proteins. These proteins typically have a modular design with a ________________ and _______________

Answer 45

transcription factors; DNA binding domain (DBD); activation domain (AD)

Question 46

the DBD is designed to position a _____________ into the major groove forming chemical bonds with the base pairs.

Answer 46

recognition helix

Question 47

recognition helix

Answer 47

amino acids that interact with base pairs

Question 48

_____________ major structural features: two anti-parallel B strands and an a helix; Zn coordinated by 2 cys and 2 his; a conserved phe/tyr and leu - _________ can be used to recognize many different DNA sequences

Answer 48

classical zinc-finger motif; Zn fingers

Question 49

the recognition helix AAs facing the DNA major groove can be different for each of the Zn fingers. therefore...

Answer 49

each Zn finger recognizes a different sequence of bases

Question 50

nuclear receptor transcription factors bind DNA as _________ - both subunits contribute one recognition helix - each subunit has two Zn fingers: only the first Zn finger has a recognition helix and the second is a structural feature that supports the recognition helix

Answer 50

dimers

Question 51

the level of transcription of a gene depends on the occupancy of its ____________ regulatory elements by _______________. Binding of several activators to a gene is required. The coordinate action between factors is referred to as __________________. The same gene may be subject to different regulatory mechanisms in different cell types.

Answer 51

cis-acting; transcription factors; combinatorial control

Question 52

before initiation of transcription, what must happen?

Answer 52

a very large protein complex must be assembled on the cis-acting regulatory elements of a gene

Question 53

transcription factor GR is a nuclear receptor that acts as an ____________ for many mammalian genes - GR binds to _________________ located at promoter-proximal sites or in enhancers

Answer 53

activator; hormone response element

Question 54

_____________ contain clusters of the recognition sequences for several different transcription factors; together these transcription factors account for ____________ function - also relies on DNA bending by ____________________ proteins

Answer 54

enhancers; enhancer; high mobility group (HMG)

Question 55

although some transcription factors directly interact with the preinitiation complex, __________ provides the primary means of communication between ___________ and the ____________________

Answer 55

mediator; activators; preinitiation complex

Question 56

transcription preinitation complex - ______ (complex) binds at the promoter - _______ may join the complex (creates docking site) - _______ binds to DNA and TBP (creates docking site) - _____________ joins the complex by binding to TFIIB - ____ and _____ enter the complex in succession - ______ is a complex with two distinct functions: _________________________________ & _____________________________________

Answer 56

TFIID; TFIIA; TFIIB; TFIIF/RNA pol II; TFIIE and TFIIH; TFIIH; DNA helicase to generate transcription bubble and protein kinase that phosphorylated the RNA pol II CTD to initiate transcription

Question 57

________ is a complex made up of _______ and many _____ proteins

Answer 57

TFIID; TBP; TAF

Question 58

_______________ locates and binds to TATA boxes in eukaryotic promoters - TATA boxes are present in only about 10% of promoters - TBP is an example of a minor groove DNA binding protein

Answer 58

TATA binding protein (TBP)

Question 59

________________ methylates H3K9->H3K9me3 - provides a docking site for _________________

Answer 59

histone methyltransferase (HMT); heterochromatin protein (HP1)