Gene Expression

Question 1

• is the process wherein genetic information from DNA is transferred into RNA.
• It is the first step in the expression of the
  genetic information stored in the genome:
  from gene to gene product (frequently a
  protein).

Answer 1

Transcription

Question 2

It became very rapidly clear in the 50s that
DNA could not be directly converted into
protein, and there had to be an intermediate
step.
● This unstable product was identified as

Answer 2

RNA

Question 3

● It is a single-stranded molecule that
contains Uracil instead of Thymine.
● It uses ribose sugar instead of
deoxyribose

Answer 3

RNA

Question 4

Three major classes of RNA:
They participate in protein synthesis and are synthesized from DNA by transcription

Answer 4

1. Ribosomal RNA, rRNA
2. Transfer RNA, tRNA
3. Messenger RNA, mRNA

Question 5

Other forms of RNA:

Answer 5

• small nuclear RNA (snRNA).
• small nucleolar RNA (snoRNA).
• microRNA (miRNA). ~22 nt RNA molecules that regulate the expression of mRNA molecules.
• long non-coding RNA (lncRNA).
• siRNA – RNA interference&raquo_space;> 2006 Nobel Prize Andrew Z. Fire & Craig C. Mello

Question 6

(snRNA).

Answer 6

small nuclear RNA

Question 7

(snoRNA).

Answer 7

small nucleolar RNA

Question 8

(miRNA). ~22 nt RNA molecules that regulate the expression of mRNA molecules.

Answer 8

microRNA

Question 9

(lncRNA).

Answer 9

long non-coding RNA

Question 10

siRNA –&raquo_space;> 2006 Nobel Prize Andrew Z. Fire & Craig C. Mello

Answer 10

RNA interference

Question 11

is a segment (or segments) of the DNA with a distinct
sequence of nucleotides that is transcribed and translated into a
protein product that contributes to the expression of a specific
phenotype/function

Answer 11

gene

Question 12

The sequences after the transcription initiation site towards the 3’ end of the template strand are called

Answer 12

upstream elements

Question 13

while those sequences before the transcription termination site towards the 5’ end are
called the

Answer 13

downstream elements

Question 14

The CORE enzyme has five subunits (~400 kDa)

Answer 14

β’, β, α, αCTD, ω

Question 15

: largest subunit, encoded by rpoC.
Contains part of the active center responsible for RNA synthesis

Answer 15

β’

Question 16

: second-largest subunit, encoded by rpoB.
Contains the rest of the active center responsible for RNA synthesis.

Answer 16

β

Question 17

: third-largest subunit and is present in two copies per molecule of
RNA pol, αI and αII. Each α contains two domains: αNTD (N-Terminal
domain) and αCTD (C-terminal domain). αNTD required for assembly
of RNA pol

Answer 17

α

Question 18

required for interaction with the promoter, non-sequence/non
specific interactions at most promoters and sequence-specific
interactions at upstream-element-containing promoters. α interacts
with regulatory factors.

Answer 18

αCTD

Question 19

: smallest subunit. ω facilitates assembly of RNAP and stabilizes
RNAP

Answer 19

ω

Question 20

TREU OR FALSE
RNA polymerases in some living organisms
are evolutionary relate

Answer 20

False: all

Question 21

EVENTS IN TRSNCRIPTION:
the RNA polymerase, together with any
initiation factors required, binds to the promoter, the DNA
sequence where transcription starts.
● Once formed, the promoter-polymerase complex
undergoes structural changes required for initiation to
proceed.
● The DNA will then unwind around the point where
transcription will start.
● The base pairs are disrupted, producing a “transcription
bubble” of single-stranded DNA.
● The new ribonucleotide is added to the 3’ end of the
growing strand since transcription always occurs in a 5’
to-3’ direction.

Answer 21

Initiation

Question 22

TRUE OR FALSE
Only one RNA strand acts as a template on which the RNA strand is built.

Answer 22

False: DNA

Question 23

This strand is called the template strand or
?

Answer 23

antisense strand or non-coding strand.

Question 24

The other strand to where the code being copied is located is called the non-template strand or?

Answer 24

the sense strand or the coding strand.

Question 25

The -10 region is located 10 nucleotide (nt) upstream of the transcription start site and is known as the Blank

Answer 25

Pribnow-Schaller box.

Question 26

The -35 region is located at 35 nt upstream of
the transcription start site.
● Many prokaryotes share a common or similar sequence
at their -35 and -10 regions.
● These shared sequences are called Blank

Answer 26

consensus sequences.

Question 27

At -25 is the sequence Blank

Answer 27

TATA (TATA box)

Question 28

at -80 is the sequence Blank

Answer 28

CAAT (CAAT box)

Question 29

In prokaryotes, the initiation
factor is called the Blank

Answer 29

sigma factor/s

Question 30

In eukaryotes, the initiation factor is called
a Blank.

Answer 30

transcription factor (TF)

Question 31

True or False
TATA-binding protein is also part of TFIIA
that binds the TATA-box.

Answer 31

False: TFIID

Question 32

During Blank, the enzyme performs an impressive
range of tasks in addition to the catalysis of mRNA
synthesis.
● It unwinds the DNA in front and reanneals it behind, it
dissociates the growing mRNA chain from the
template as it moves along, and it performs
proofreading functions.
● Recall that during replication, in contrast, several
different enzymes are required to catalyze a similar
range of functions.

Answer 32

elongation

Question 33

● Once the polymerase has finished
transcribing the protein-coding region or the
gene, it must stop and release the mRNA
product as well as dissociate from the DNA.
● In some cells, specific and well
characterized sequences signal termination
of transcription.
● In others, it is less clear what triggers the
enzyme to stop transcribing and detaching
itself from the template.

Answer 33

Termination

Question 34

occurs when the termination sequence forms a GC stem-loop in the nascent RNA, which causes RNA pol to pause.

Answer 34

Rho-independent termination

Question 35

the “hot pursuit” model
for rho action suggests that Rho binds to a nascent
RNA chain

Answer 35

Rho-dependent termination

Question 37

This process involves the addition of a modified
guanine base to the 5’ end of the RNA.

Answer 37

Capping

Question 38

A Blank is added to the 5’ end of
the growing transcript by a 5’-to-5’ phosphate
linkage.

Answer 38

7-methylguanosine cap

Question 39

Unlike prokaryotes, eukaryotic genes have noncoding DNA sequences called Blank inserted between the coding sequences called Blank.

Answer 39

introns, exons

Question 40

Thus, the final stage of RNA processing after the termination of transcription is the removal of introns (noncoding sequences) and joining of the exons (coding sequences) together.
● This process is called Blank

Answer 40

splicing

Question 41

• occurs in introns that form a ribozyme, performing the functions of the spliceosome by RNA alone

Answer 41

Self-splicing

Question 41

This process is called splicing which is carried out in a series of reactions catalyzed by the Blank, a
ribonucleoprotein complex.

Answer 41

spliceosome

Question 42

• occurs within same pre-mRNA molecule

Answer 42

Cis-splicing

Question 43

• uses two separate pre-mRNA molecules to form a chimeric non-colinear RNA

Answer 43

Trans-splicing

Question 44

Single-stranded RNA that is complementary to
a mRNA transcribed within a cell.
* These are long noncoding RNA (lncRNA).

Answer 44

Antisense RNA

Question 45

True or False
This effect could occur in trans. i.e. the
antisense RNA needs to be produced
from the same gene as the sense RNA.

Answer 45

False: does not need

Question 46

Won the Nobel Prize in Physiology or Medicine 2006 for their discovery of RNA interference gene silencing by double-stranded RNA

Answer 46

Andrew Z. Fire and Craig C. Mello

Question 47

True or False
The RNAi process is Found in eukaryotes and prokaryotes.

Answer 47

False: only found in eukaryotes.

Question 48

True or False
Canonical RNAi is triggered by some form of short dsRNA.

Answer 48

False: long dsRNA.

Question 49

can originate from various sources including viruses and their replication intermediates or base pairing if RNAs transcribed in the genome (either as an intramolecular duplex (hairpin dsRNA), or by base pairing RNAs transcribed in cis (convergent transcription) or in trans (from interspersed
elements, pseudogenes etc.).

Answer 49

dsRNA

Question 50

– where one strand of siRNA duplex is selected and loaded onto an Argonaute

Answer 50

loading

Question 51

– cleavage of long dsRNA into siRNA duplexes by RNase III Dicer

Answer 51

dicing

Question 52

protein from AGO subfamily

Answer 52

Argonaute

Question 53

True or False
In all species, RNAi also involves an RNA-dependent RNA polymerase
(RdRp), which may generate initial substrates or participate in amplification of
the response by converting cognate RNAs into dsRNA.

Answer 53

False: some species

Question 54

Won the Nobel Prize in Physiology or Medicine 2024 for the discovery of microRNA and its role in post-transcriptional gene regulation

Answer 54

Victor Ambros and Gary Ruvkun

Question 55

True or False
miRNAs are genome-encoded.

Answer 55

True

Question 56

The key bridge between AGO and proteins mediating deadenylation and decapping is Blank.

Answer 56

GW182 protein