Gebelein 1

Question 1

_____ are a gene profiling technique where cDNA is hybridized to a plate with complementary oligos to assess gene expression levels.

Answer 1

Microarrays

Question 2

A classic gene profiling technique, the _____ blot, uses a labeled probe to detect a specific transcript.

Answer 2

Northern

Question 3

_____ is a gene profiling technique where mRNA is converted to cDNA and amplified with PCR to measure gene expression.

Answer 3

qPCR

Question 4

_____ is a powerful gene profiling technique that involves isolating mRNA, converting it to cDNA, and sequencing it.

Answer 4

RNA sequencing

Question 5

Single-cell RNA sequencing allows researchers to analyze gene expression at the _____ level.

Answer 5

individual cell

Question 6

One advantage of RNA-seq over microarrays is that it allows for the analysis of sequence _____, such as mutations.

Answer 6

changes

Question 7

Eukaryotic gene expression can be controlled at _____ steps.

Answer 7

six

Question 8

RNA _____, which encompasses splicing, localization, and degradation, represents a key control point in gene expression.

Answer 8

processing

Question 9

_____ are DNA sequences that can recruit sequence-specific transcription factors to enhance or inhibit the activity of RNA polymerase at the promoter.

Answer 9

Enhancers

Question 10

_____ are DNA sequences responsible for recruiting the RNA polymerase machinery and initiating transcription.

Answer 10

Promoters

Question 11

_____ function as boundaries on a chromosome, preventing interactions between DNA sequences located on opposite sides.

Answer 11

Insulators

Question 12

Proteins that bind to specific DNA sequences (TFBSs) to regulate transcription are known as _____.

Answer 12

Sequence-specific TFs

Question 13

Proteins that bind to specific DNA sequences (TFBSs) to regulate transcription are known as _____.

Answer 13

Sequence-specific TFs

Question 14

General TFs, together with RNA polymerase II, are core proteins essential for the synthesis of all _______.

Answer 14

mRNAs

Question 15

_____ are proteins that package DNA into structural units called nucleosomes.

Answer 15

Histones

Question 16

Modifications to histones can alter their ability to bind to _____.

Answer 16

DNA

Question 17

Regulatory proteins known as _____ are recruited by transcription factors to either activate or repress transcription, often through modifications to histones or the RNA pol II enzyme.

Answer 17

co-activators/co-repressors

Question 18

_____ assays are one method used by researchers to assess for promoter activity in cells.

Answer 18

Reporter

Question 19

_____ and _____ are two approaches used to determine which transcription factor binds to a particular DNA sequence.

Answer 19

Biochemical, bioinformatic

Question 20

The initial crucial step in transcriptional regulation is the recognition and ________ of a pre-initiation complex (PIC) at promoter sequences.

Answer 20

recruitment

Question 21

The second step in transcriptional regulation, _____, encompasses the “melting” of DNA to form an open complex and the phosphorylation of Ser-5 on the CTD of RNA polymerase II.

Answer 21

transcription initiation

Question 22

_____ involves the phosphorylation of the CTD at both Ser2 and Ser5.

Answer 22

Transcription elongation

Question 23

Key components involved in promoter recognition and PIC formation include: _____, general transcription factors (TFIID, TFIIA, TFIIB, TFIIE, TFIIF, TFIIH), and core promoter sequences.

Answer 23

RNA polymerase II (RNA-polII)

Question 24

Scientists utilized _____ genetics and biochemical fractionation coupled with protein complex _____ to initially identify and investigate the key “trans” players in transcription.

Answer 24

yeast, purification

Question 25

While the biochemical definition of the PIC excludes the _____ complex, it is important to note that the _______ is essential for general transcription in vivo.

Answer 25

mediator

Question 26

The composition of some ________ TFs, such as TFIID and the Mediator, can vary among cell types due to the expression of distinct subunits.

Answer 26

“general”

Question 27

_____ is a technique used to identify “protected” (bound) DNA sequences by detecting regions where protein binding shields DNA from nuclease digestion.

Answer 27

DNA footprinting

Question 28

_____ is a technique employed to study the interactions between proteins and DNA within a cellular context.

Answer 28

Chromatin Immunoprecipitation (ChIP)

Question 29

Compared to footprinting with a nuclease, ChIP offers _____ resolution.

Answer 29

lower

Question 30

Two variations of the ChIP technique are _____ and _____.

Answer 30

ChIP-PCR, ChIP-seq

Question 31

_____ combines ChIP with exonuclease digestion, enabling the identification of protected DNA regions in vivo with enhanced precision.

Answer 31

ChIP-Exo

Question 32

A crucial DNA-binding component of the TFIID complex, the _____ (TBP), plays a vital role in transcription initiation.

Answer 32

TATA Binding Protein

Question 33

TBP binds to the _____ groove of DNA, resulting in both a local distortion of the DNA path and partial unwinding of the DNA helix.

Answer 33

minor

Question 34

_____ possesses both helicase activity, essential for unwinding the DNA double helix to create the transcription bubble during initiation, and kinase activity, responsible for phosphorylating the CTD of Pol II.

Answer 34

TFIIH

Question 35

The _____ complex plays a crucial role in recruiting the super elongation complex (SEC) after the release of PolII from the PIC, marking a key step in the transition from transcription initiation to elongation.

Answer 35

Mediator

Question 36

What is gene regulation?

Answer 36

The “controlled” making of gene products required for cellular function.

Question 37

Mammalian DNA contains around ________ genes.

Answer 37

20,000

Question 38

What are the major control points in gene regulation?

Answer 38

Transcription, RNA processing, Translation, Post-translational modifications and degradation

Question 39

What are cis-regulatory modules?

Answer 39

DNA sequences that are required for and/or alter the process of transcription.

Question 40

What are promoters?

Answer 40

DNA sequences that recruit the RNA polymerase machinery and initiate transcription

Question 41

What are enhancers?

Answer 41

DNA sequences that recruit sequence-specific transcription factors that ”enhance” or ”inhibit” the activity of RNA polymerase at the promoter.

Question 42

True or False: Enhancers must be near promoters.

Answer 42

False, they can be distant from promoters

Question 43

What are insulators?

Answer 43

DNA sequences that recruit “architectural” proteins to create barriers along the chromosome. In general, DNA sequences on opposite sides of the insulator
do not physically associate with each other.

Question 44

Areas between insulator sequences are often called ___________.

Answer 44

Topological associated domains (TADs)

Question 45

What are transcription factor proteins?

Answer 45

Proteins that regulate the
process of transcription

Question 46

What are the core proteins required for all mRNA synthesis?

Answer 46

General” TFs and RNA polII

Question 47

What are sequence-specific TFs?

Answer 47

Proteins that bind specific DNA
binding sites (TFBSs) to aid or inhibit transcription. Can
bind either promoters or enhancers.

Question 48

What are co-activators/co-repressors?

Answer 48

Regulatory proteins
recruited by TFs to either promote or inhibit transcription,
often by modifying histones or the RNA polII enzyme.