Chapter 8

Question 1

What is the central dogma?

Answer 1

DNA –> RNA –> Protein

Question 2

How does RNA differ from DNA?

Answer 2

Ribose sugar, uracil instead of thymine, single-stranded, less stable, catalytic.

Question 3

Describe the Central Dogma in detail

Answer 3

DNA Replication copies DNA
Transcription converts DNA into pre-mRNA.
RNA processing modifies pre-mRNA into mature mRNA.
Translation uses mRNA to build proteins.

Question 4

Name six classes of RNA and their functions.

Answer 4

mRNA (codes proteins)
tRNA (brings amino acids)
rRNA (ribosome structure)
snRNA (splicing)
miRNA (regulates translation)
siRNA (defense).

Question 5

In which direction is RNA synthesized?

Answer 5

5’ –> 3’

Question 6

What are the two prokaryotic promoter regions?

Answer 6

-35 and -10

Question 7

What does sigma factor do?

Answer 7

Binds promoter, melts DNA, positions RNA polymerase.

Question 8

Name two types of transcription termination in prokaryotes.

Answer 8

Intrinsic (hairpin + U-rich) and rho-dependent.

Question 9

What are the three main eukaryotic promoter elements?

Answer 9

TATA box (-25), CAAT box (-80), GC-rich box (-90).

Question 10

What is added to the 5′ end of RNA during processing?

Answer 10

7-methylguanosine cap.

Question 11

What is added to the 3′ end of RNA during processing?

Answer 11

Poly(A) tail

Question 12

What removes introns?

Answer 12

Spliceosome (snRNAs + proteins).

Question 13

What is alternative splicing?

Answer 13

Different exon combinations → multiple proteins from one gene.

Question 14

Which snRNA binds the branch-point A?

Answer 14

U2

Question 15

What does Dicer do?

Answer 15

Cuts dsRNA into siRNAs.

Question 16

What is RISC?

Answer 16

RNA-induced silencing complex; uses siRNA to degrade target RNA.

Question 17

How does miRNA regulate gene expression?

Answer 17

Partial complementarity inhibits translation; perfect complementarity cleaves RNA.

Question 18

What is the main purpose of RNA interference?

Answer 18

Destroy viral RNA and regulate gene expression.

Question 19

Which proteins bind ESEs?

Answer 19

SR proteins (rich in Arginine and Serine).

Question 20

During which stage of transcription does splicing occur?

Answer 20

Elongation

Question 21

What is the difference between strong and weak splice sites?

Answer 21

Strong match consensus; weak deviate and need enhancers.

Question 22

What enzyme produces siRNA from double-stranded RNA?

Answer 22

Dicer

Question 23

What complex does siRNA form to degrade target RNA?

Answer 23

RISC (RNA-induced silencing complex)

Question 24

What chemical reaction unzips siRNA in RISC?

Answer 24

Hydrolysis

Question 25

Where do siRNAs come from?

Answer 25

They are processed from double-stranded RNA, often from viruses or experimental triggers.

Question 26

How is miRNA different from siRNA?

Answer 26

miRNA is genome-encoded and processed from hairpin precursors; siRNA comes from external dsRNA.

Question 27

Which polymerase transcribes miRNA?

Answer 27

RNA Polymerase II

Question 28

What does Dicer do to miRNA precursors?

Answer 28

Trims hairpin RNA into 22 nt fragments.

Question 29

List the steps of RNA Interference

Answer 29

dsRNA recognized by Dicer → cut into siRNAs. siRNAs form RISC complex. RISC unzips siRNA and binds target RNA. Target RNA is degraded.

Question 30

What is the difference in complementarity requirements for miRNA vs siRNA?

Answer 30

siRNA requires perfect complementarity; miRNA often works with partial complementarity

Question 31

What does the spliceosome do?

Answer 31

Remove introns and join exons in pre-mRNA

Question 32

Which snRNA binds the 5′ splice site?

Answer 32

U1

Question 33

What proteins help splice weak sites?

Answer 33

SR Proteins (rich in Serine and Arginine)

Question 34

List RNAi steps briefly

Answer 34

dsRNA → Dicer → siRNA → RISC → mRNA degradation.

Question 35

What is an enhancer and how does it influence transcription?

Answer 35

A DNA sequence that increases transcription efficiency by recruiting activator proteins; can be located upstream, downstream, or within introns.

Question 36

How can you experimentally confirm a sequence act as an enhancer?

Answer 36

Use a reporter gene assay (e.g., GFP or luciferase) to test tissue-specific expression.

Question 37

Which enzymes modify histones to regulate chromatin structure?

Answer 37

HAT (Histone Acetyltransferase): Adds acetyl groups → opens chromatin. HDAC (Histone Deacetylase): Removes acetyl groups → closes chromatin.

Question 38

What is the role of SWI/SNF proteins?

Answer 38

Remodel nucleosomes to expose promoter regions for transcription initiation.

Question 39

What does DNase I hypersensitivity indicate?

Answer 39

Regions of open chromatin accessible to transcription factors and regulatory proteins.

Question 40

What is the role of the CTD during transcription?

Answer 40

Coordinates RNA processing events (capping, splicing, polyadenylation) during elongation.

Question 41

What is RNA interference and its purpose?

Answer 41

A gene-silencing mechanism triggered by dsRNA; involves Dicer and RISC to degrade or inhibit target mRNA.

Question 42

What is Dicer’s function in RNA interference?

Answer 42

Cleaves dsRNA or hairpin RNA into ~22 bp fragments for incorporation into RISC.