Regulation of Gene Expression

Question 1

Does a gene contain introns, exons, UTRs, and transcriptional control regions?

Answer 1

YES - ALL of these components (even non-coding)

Question 2

Are DNA binding proteins reading the direct sequence?

Answer 2

NO; just reading their ability to interact with certain constituents

Question 3

Why are the minor and major grooves of a DNA strand significant?

Answer 3

the grooves provide access to components of the nucleotide bases (located in the core)

Question 4

Patterns of DNA ____ are important for the control of gene expression.

Answer 4

methylation

Question 5

What does WISE bind to to prevent Wnt binding?

Answer 5

Lrp5/6

Question 6

Initially, the activation of tooth development involves which two layers?

Answer 6

ectoderm and the mesenchyme

Question 7

The majority of DNA binding protein motifs function as ___ or ___.

Answer 7

dimers; tandem clusters

Question 8

Do both X-chromosomes and Y-chromosomes undergo recombination?

Answer 8

NO; Y-chromosomes do not undergo recombination

Question 9

How is beta-catenin kept at low levels inside the cell?

Answer 9

it is part of a degradation complex

Question 10

What contributes to the structure of the major and minor grooves?

Answer 10

C:G and A:T and how the keto- and hydrogen groups are arranged

Question 11

Why are there so many levels of seemingly redundant controls in gene expression?

Answer 11

because gene expression is a tightly regulated process where the gene needs to be activated or deactivated at VERY specific times

Question 12

___ and ___ and ___ are gene regulatory proteins that assist in the unwinding of DNA for transcriptional activity.

Answer 12

Mediators; DNA binding proteins; chromatin remodeling proteins

Question 13

___ is when your goal is to sequence every base in the organism’s genetic code and put it in the correct order.

Answer 13

Genome sequencing

Question 14

At what level of control do microRNAs operate at?

Answer 14

RNA degradation control

Question 15

What are the levels of gene expression control?

Answer 15

Transcriptional machinery
Intracellular hormone-receptor complexes
Intracellular second messengers
Gene + class specific transcription factors
Regulatory sequences

Question 16

What level of control is DNA to RNA transcript?

Answer 16

transcriptional control

Question 17

A _____ is when the gene products that are being produced regulate the expression of other genes.

Answer 17

hierarchical gene cluster of regulation

Question 18

Why was identifying genes on the Y-chromosome generally more difficult than identifying genes on the X-chromosome?

Answer 18

Y-chromosomes do not undergo recombination

Question 19

At what level of control does the inactivation or activation of proteins occur?

Answer 19

post-translationally

Question 20

What is chromatin remodeling?

Answer 20

the opening up of the condensed DNA structure

Question 21

What level of control is the synthesis of protein from mRNA?

Answer 21

translation control

Question 22

What does Wnt do in the Wnt/b-catenein pathway?

Answer 22

it binds to Lrp5/6, allowing the transcription of Tcf (transcription factor)
*potential to cause cancer if transcription allowed

Question 23

What do the sFRPs bind to to prevent Wnt binding?

Answer 23

Wnt

Question 24

What do leucine zippers promote?

Answer 24

DNA binding and dimerization

Question 25

What type of modification level would the phosphorylation of pre-peptide hormones be at?

Answer 25

post-translational

Question 26

What does Frizzled bind to to prevent Wnt binding?

Answer 26

Wnt

Question 27

A ____ protein motif consists of 2 alpha-helices joined by a short stretch of amino acids.

Answer 27

helix-turn-helix

Question 28

What are the 5 families of signal proteins present in animal growth and development?

Answer 28

``` RTK (EGF, FGF) TGF-beta (BMP, nodal) Wnt Hedgehog Notch ```

Question 29

Prior to DNA sequencing, what was used to explore where a certain gene resided?

Answer 29

genetic linkage analysis

Question 30

What is the first order of condensation of DNA?

Answer 30

the "beads on a string" nucleosome structure

Question 31

What level of control is the creation of new mRNA?

Answer 31

RNA processing control

Question 32

What genetic material in the body undergoes recombination?

Answer 32

autosomes and X-chromsomes (because in females we have 2 X chromosomes)

Question 33

What is a segment of DNA called that is transcribed into RNA and its associated transcriptional control regions?

Answer 33

A gene

Question 34

What proteins would regulate gene expression by increasing the level of transcription?

Answer 34

activators and coactivators

Question 35

Beta-catenin levels are normally kept at very ___ levels inside the cell.

Answer 35

low

Question 36

Which DNA binding protein motif contains two leucine-rich proteins with alpha-helices and form a Y-shaped coil structure?

Answer 36

Leucine Zipper (both protein and DNA binding)

Question 37

What level of control is the maturation of mRNA into the cytosol?

Answer 37

RNA transport and localization control

Question 38

What is the first step in the activation of transcription at a specific promoter?

Answer 38

a gene activator protein binds to chromatin OR an inhibitor is removed from the complex

Question 39

What level of control is the activation or inactivation of proteins?

Answer 39

protein activity control

Question 40

A _____ protein motif is common in transcription factors and consists of alpha-helices bound by looping amino acid stretch.

Answer 40

helix-loop-helix

Question 41

At what level of control does the protein assembly complex, ribosomes, and charge tRNAs operate at?

Answer 41

translational control (post-transcriptional)

Question 42

Genes involved in tooth development are ___ and ___ restricted in their pattern of expression in order to result in the correct placement of the teeth and jaws.

Answer 42

spatially; regionally

Question 43

____ sequences are valuable in consumer gene sequencing (23andme, etc.).

Answer 43

Specific target

Question 44

Human gene names are ___ and ___; mouse gene names are ___ and ___.

Answer 44

capitalized and italicized; lowercase and italicized

Question 45

What level of control is the inactivation of mRNA?

Answer 45

mRNA degradation control (microRNA)

Question 46

What prevents DNA from folding up on itself or binding inappropriately after uncoiling?

Answer 46

histone modification enzymes

Question 47

What provides the proper hydrogen donors and acceptors and methyl groups to allow the receptor to bind to a certain region?

Answer 47

nuclear response element sequences

Question 48

Beta-catenin is considered a ____ of transcription because it _______.

Answer 48

coactivator; cannot transcribe itself, but allows Tcf to

Question 49

How is DNA read?

Answer 49

using DNA binding protein motifs, potential interactions (H and O), and nuclear response elements

Question 50

Why can we have these great distances between regulatory sequences and the start site of transcription in eukaryotes?

Answer 50

loops can actually place the regulatory sequences and start site right on top of each other

Question 51

What type of sequencing aims to only sequence the protein-coding regions called exons?

Answer 51

Exomic sequencing

Question 52

These enzymes function to modify DNA proteins associated with DNA.

Answer 52

histone acetylase and deacetylase

Question 53

Which DNA binding protein motif is distinguished by the presence of a bound zinc ion?

Answer 53

Zinc Finger Motifs

Question 54

In negative regulation, bound Lrp5/6 + Dkk1 + Kremen get ____ in the cytoplasm.

Answer 54

degraded (so Wnt cannot bind or do anything)

Question 55

When Wnt comes and binds to the Lrp5/6 + Frizzled complex, what happens?

Answer 55

beta-catenin is NO LONGER degraded and translocated into the nucleus where it binds with Tcf (transcription factors)

Question 56

DNA ____ a rigid linear structure.

Answer 56

IS NOT

Question 57

____ and ____ of histones turns the genes in DNA "off" and "on," either allowing access for the transcription factors or blocking DNA access.

Answer 57

Methylation; demethylation

Question 58

There are multiple levels of control in gene expression. What are they?

Answer 58

``` transcriptional control RNA processing control RNA transport/localization control mRNA degradation control translation control protein activity control ```

Question 59

Can DNA regulatory sequences be found in the 5' or 3' ends or in introns?

Answer 59

YES

Question 60

A scientist wants to investigate which genes are being expressed in a certain tissue at this time. What type of sequencing would she use to determine the genes being expressed?

Answer 60

Transcriptomic sequencing (mRNA)

Question 61

What gene regulatory proteins would decrease or block gene transcription?

Answer 61

repressors and corepressors

Question 62

_____ binds to Lrp5/6 and prevents Wnt from binding.

Answer 62

Sclerostin

Question 63

The protein signaling that occurs back and forth between the ectoderm and the mesenchyme in early tooth development is called ____.

Answer 63

reciprocal induction

Question 64

What does the protein recognize and react with in the major and minor grooves of DNA?

Answer 64

potential interactions; whether or not there are hydrogen bond acceptors or donators or hydrogen atoms or methyl groups (NOT BASES)

Question 65

In prokaryotes, the DNA regulatory sequences are located ____ to the RNA polymerase II binding site; in eukaryotes, DNA regulatory sequences can be located ___ relative to start site of transcription.

Answer 65

very closely; great distances away

Question 66

What proteins prevent Wnt from binding and also regulate the Wnt/b-catenin pathway?

Answer 66

Sclerostin, sFRPs, WISE, (Dkk1 + Kremen), Frizzled

Question 67

What are transcription factors searching for using their side chains?

Answer 67

potential interactions that may be had between hydrogen and oxygen atoms

Question 68

In DNA, what reacts with the side chains of amino acids?

Answer 68

base moieties, such as the hydrogen and keto-groups

Question 69

Summarize the activation of transcription at a specific promoter.

Answer 69

gene activator protein >> histone modification >> activator proteins bound to gene regulatory region >> RNA polymerase >> assembly of initiation complex >> transcription initiation