Control of Gene Expression

Question 1

Controlling gene expression can often be achieved by controlling _______ _______

Answer 1

transcription initiation

Question 2

_______ _______ bind to DNA, modulating the binding of RNA polymerase to the promoter

Answer 2

Regulatory proteins

Question 3

_______ organisms regulate gene expression in responds to their environment

Answer 3

Prokaryotic

Question 4

_______ cells regulate gene expression to maintain a constant internal environment (_______ ) in the organism

Answer 4

Eukaryotic, homeostasis

Question 5

Regulatory proteins gain access to the bases of DNA at the _______ _______

Answer 5

major groove

Question 6

Regulatory proteins possess DNA-binding _______

Answer 6

motifs

Question 7

Regulatory proteins either block transcription by preventing _______ _______ to bind, or stimulate transcription by facilitating it to bind to the _______

Answer 7

RNA polymerase, promoter

Question 8

Within the major groove, nucleotides’ _______ _______ donors and acceptors are accessible. There is a unique pattern of accessibility for each base pair combination which enables _______ to read the sequence without _______ DNA

Answer 8

hydrogen bond, proteins, unwinding

Question 9

DNA-binding _______ are regions of _______ proteins which bind to DNA

Answer 9

motifs, regulatory

Question 10

The _______-_______-_______ motif is two α-helical segments linked by a nonhelical segment. The _______ is a special class of this and is critical in Eukaryotic development

Answer 10

Helix-turn-helix, Homeodomain

Question 11

The _______ _______ motif has several forms, and uses zinc atoms to coordinate DNA binding

Answer 11

Zinc finger

Question 12

The _______ _______ motif is a dimerization motif in which a region in one subunit interacts with a similar region on another subunit forming a zipper-like connection

Answer 12

Leucine zipper

Question 13

In Prokaryotic regulation, Transcription inititiation can be _______ or _______ controlled

Answer 13

positively, negatively

Question 14

_______ control of prokaryotic transcription initiation increases frequency. _______ enhance binding of RNA polymerase to the _______

Answer 14

Positive, Activators, promoter

Question 15

_______ control of Prokaryotic transcription initiation decreases frequency. _______ bind to regulatory sites on DNA called _______ that prevent or decrease initiation frequency

Answer 15

Negative, Repressors, operators

Question 16

_______ molecules can act on both repressors and activators

Answer 16

Effector

Question 17

Prokaryotic cells often respond to their _______ by changes in gene expression. Genes involved in the same metabolic pathway are organized in _______.

Answer 17

environment, operons

Question 18

_______ occurs when the presence of a substrate (a specific substance) triggers the production of enzymes needed to produce it

Answer 18

Induction

Question 19

_______ means the cell is capable of making an enzyme but doesn’t

Answer 19

Repression

Question 20

The _______ _______ encodes proteins necessary for the use of lactose as an energy source

Answer 20

lac operon

Question 21

β-galactosidase is known as _______, permease as _______, and transacetylase as _______. The gene for the lac repressor (_______) is linked to the rest of the lac operon

Answer 21

lacZ, lacY, lacA, lacl

Question 22

The lac operon is _______ regulated by a _______ protein.

Answer 22

negatively, repressor

Question 23

The lac repressor binds to the _______ to block transcription. In the presence of lactose, an inducer molecule (_______) binds to the repressor protein. The repressor can no longer bind to the _______ and transcription proceeds

Answer 23

operator, allolactose, operator

Question 24

_______ _______ is a mechanism for the preferential use of glucose in the presence of other sugars.

Answer 24

Glucose repression

Question 25

_______ _______ _______ (CAP) is an allosteric protein with cAMP as effector

Answer 25

Catabolic activator protein

Question 26

The level of _______ in cells is reduced in the presence of glucose so that no stimulation of transcription from _______-responsive operons takes place.

Answer 26

cAMP, CAP

Question 27

_______ _______ - The presence of glucose inhibits the transport of lactose into the cell, EVEN IF there is lactose present

Answer 27

Inducer exclusion

Question 28

The _______ _______ encodes genes for the biosynthesis of tryptophan

Answer 28

trp operon

Question 29

The trp operon is not expressed when the cell contains sufficient amounts of _______

Answer 29

tryptophan

Question 30

The trp _______ is a helix-turn-helix protein that binds to the operator site adjacent to the trp _______

Answer 30

repressor, promoter

Question 31

The trp operon is negatively regulated by the trp _______ protein. This protein binds to the _______ to block transcription. This binding process requires a _______ which is tryptophan.

Answer 31

repressor, operator, corepressor

Question 32

When tryptophan levels fall, the repressor can't bind to the operator, so the operon is _______ (versus being induced).

Answer 32

derepressed

Question 33

Tryptophan binding increases the _______ between the two recognition helices, allowing the repressor to fit into two adjacent portions of the _______ _______ in DNA

Answer 33

distance, major groove

Question 34

In Eukaryotic regulation, the control of _______ is more complex. The major differences from prokaryotes is that Eukaryotes have DNA organized into _______ which complicates the protein-DNA interaction. Also, Eukaryotic transcription occurs in the _______ while translation occurs in the _______.

Answer 34

transcription, chromatin, nucleus, cytoplasm

Question 35

_______ transcription factors are named TF + roman numeral + letter. The roman numeral indicates which _______ _______ the TF interacts with.

Answer 35

General, RNA Polymerase

Question 36

General TF's are necessary for the assembly of a transcription _______ and the recruitment of RNA Pol II to a _______

Answer 36

apparatus, promoter

Question 37

TFIID recognizes _______ _______ sequences

Answer 37

TATA box

Question 37

The initiation complex formed by _______ _______ _______ can initiate synthesis at a _______ level

Answer 37

General transcription factors, basal

Question 38

_______ _______ _______ act in a tissue- or time- dependent manner to stimulate higher levels of transcription than the basal level

Answer 38

Specific transcription factors

Question 39

Each specific TF consists of a _______-_______ domain and a separate _______ domain that interacts with the transcription apparatus. These domains are _______ in the protein

Answer 39

DNA-binding, activating, independent

Question 40

_______ form the binding sites for general TFs.

Answer 40

Promoters

Question 41

General TFs mediate the binding of RNA polymerase II to the _______

Answer 41

promoter

Question 42

_______ are the binding site of the specific TFs

Answer 42

Enhancers

Question 43

Specific TF's act over large distances by bending DNA to form a loop to position the _______ closer to the _______

Answer 43

Enhancer, promoter

Question 44

Coactivators and mediators are required for the function of _______ _______

Answer 44

transcription factors

Question 45

The number of _______ is small compared to the number of TFs because one can be used with multiple TFs

Answer 45

coactivators

Question 46

The _______ is essential to some but not all TFs.

Answer 46

mediator

Question 47

Virtually all genes transcribed by _______ _______ _______ need the same suite of general TFs to assemble an _______ _______

Answer 47

initiation complex

Question 48

The ultimate level of transcription depends on the _______ _______ _______ that together make up the _______ _______

Answer 48

specific transcription factors, transcription complex

Question 49

In the Eukaryotic _______ structure, DNA is wound around histone proteins to form nucleosomes.

Answer 49

chromatin

Question 50

DNA is wound around _______ proteins to form _______ in the Eukaryotic chromatin structure

Answer 50

histone, nucleosomes

Question 51

_______ and _______ complicate the process of transcription by restricting the access of the transcription machinery to the DNA

Answer 51

Nucleosomes, histones

Question 52

Alterations in _______ structure are though to be the basis for epigenetics.

Answer 52

chromatin

Question 53

_______ alterations must persist in the absence of the initiating stimulus, and must be inherited through _______ _______.

Answer 53

Epigenetic, cell division

Question 54

_______ _______: High levels of it is correlated with inactive genes, and allele-specific gene expression in genomic imprinting is at least partially due to it.

Answer 54

DNA methylation

Question 55

Mammalian females inactivate one _______ _______ as a form of dosage compensation.

Answer 55

X chromosome

Question 56

There are four possible _______ that can be modified

Answer 56

histones

Question 57

_______, _______, and _______ are all possible histone modifications

Answer 57

Acetylation, methylation, phosphorylation

Question 58

In general, the histone modification _______ is correlated with active sites of transcription.

Answer 58

acetylation

Question 59

Some transcription coactivators have been shown to be _______ _______ (HATs). Transcription is increased by removing higher order _______ structure that would prevent transcription

Answer 59

Histone acetylases, chromatin

Question 60

Gene expressions can be controlled after transcription with: _______ RNA's (miRNA and siRNA), _______ splicing, RNA _______, or _______ degredation

Answer 60

Small, alternative, editing, mRNA

Question 61

_______-_______ mutant alters developmental timing in C. elegans

Answer 61

lin-4

Question 62

lin-4 does not encode a protein product, instead it encodes two _______ _______ molecules

Answer 62

small RNA

Question 63

lin-4 RNA acts as a transcriptional _______ of an mRNA

Answer 63

repressor

Question 64

miRNA production begins with RNA pol II producing a transcript called the _______-_______

Answer 64

pri-miRNA

Question 65

miRNA folds back on itself to form a _______-and-_______ structure which is cleaved by _______ to form pre-miRNA

Answer 65

stem, loop, Drosha

Question 66

pre-miRNA is exported from the nucleus and cleaved by _______ to produce a short double stranded RNA containing the miRNA

Answer 66

Dicer

Question 67

miRNA is loaded into a protein complex called an _______ _______ _______ _______ (RISC)

Answer 67

RNA induced silencing complex

Question 68

RISC includes the RNA-binding protein _______, which interacts with the miRNA

Answer 68

Ago

Question 69

RISC is targeted to repress the expression of genes based on the sequence complementary to the _______. This complementary region is usually in the ___ untranslated region of genes

Answer 69

miRNA, 3'

Question 70

_______ _______ refers to small RNA gene silencing, and involves the production of _______

Answer 70

RNA interference, siRNAs

Question 71

Production of siRNA is similar to miRNAs, but siRNAs arise from a _______ double-stranded RNA. _______ cuts yield of multiple siRNAs which are loaded into _______. The target _______ is then cleaved by the siRNA

Answer 71

long, Dicer, RISC, mRNA

Question 72

_______ represses genes different from its origin

Answer 72

miRNA

Question 73

_______ tends to repress genes they were derived from

Answer 73

siRNA

Question 74

The editing of mature _______ transcripts can produce altered versions that are not truly encoded in the genome

Answer 74

mRNA

Question 75

In mammals, RNA editing involves the chemical modification of a base to change its _______-_______ properties

Answer 75

base-pairing