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1
Q

Biosynthesis of RNA is called

A

transcription

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2
Q

Protein synthesis is called

A

translation

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3
Q

When DNA is used as a template to produce RNA, that is what you call

A

transcription

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4
Q

RNA–>DNA is what you call

A

reverse transcription

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5
Q

The central dogma of molecular biology:

A

Information contained in DNA molecules is expressed in
the structure of proteins

 because DNA is the genetic material, and it provides
information contained in the DNA molecule per se
and is expressed through the central dogma of
molecular biology

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6
Q

TRUE OR FALSE

gene expression is the turning on/ turning point or activation of a gene

A

TRUE

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7
Q

How many parent strand is used in DNA replication

A

only one parent strand

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8
Q

DNA template will serve as a template as is to produce the needed RNA and that process is called

A

transcription

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9
Q

Order of types of RNA used in transcription

A

mRNA
tRNA
rRNA
(miRNA, siRNA, snRNA)

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10
Q

primer and primase enzyme is important in

A

DNA replication?

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11
Q

a primer is NOT needed for

A

RNA synthesis (transcription)

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12
Q

the reaction proceeds

from the ___ direction

A

5’ to 3’ direction

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13
Q

The process in which information encoded in a DNA
molecule (coming from the parent strand) is copied into
mRNA molecules

A

Transcription

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14
Q

Transcription takes place in the

A

nucleus

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15
Q

While DNA replication takes place in

A

Cytoplasm

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16
Q

transcription starts when the DNA double Helix

A

begins to unwind near the gene to be transcribed

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17
Q

TRUE OR FALSE

during transcriptions, ribonucleotides are
involved not deoxyribonucleotides

A

true

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18
Q

deoxyribonucleotides – involved in

A

DNA replication

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19
Q

is usually synthesized using a DNA template in the

process called transcription

A

RNA

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20
Q

The enzyme that catalyzes the process (transcription) is a

A

DNA dependent RNA polymerase

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21
Q

The ribonucleotides has

A

ribose, pyrimidine, purine base,

and must also contain phosphate

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22
Q

There are 4 ribonucleotides triphosphates:

A

ATP, GTP, CTP, and UTP – these are required along with

magnesium ion during the process of transcription

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23
Q

TRUE OR FALSE

A primer is needed in transcription

A

FALSE
 Again, A primer is not needed but in the DNA
template, it is required

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24
Q

these are required along with

magnesium ion during the process of transcription

A

4 ribonucleotides triphosphates: ATP, GTP, CTP, and UTP

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25
Q

For the case of biosynthesis, the RNA chain grows from

A

the 5’ to the 3’ end – same for transcription

The 5’ remains its triphosphate group

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26
Q

TRUE OR FALSE
The DNA uses one strand as a template for RNA
synthesis

A

TRUE

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27
Q

The base sequence of the DNA contains signal for:

A

 initiation
 followed by propagation / elongation
 then transcription of RNA synthesis –

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28
Q

as template strand for RNA synthesis, the RNA
product sequence matches the other strand of RNA
which is called

A

coding strand

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29
Q

enzymes called ___ catalyze

transcription

A

Polymerase

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30
Q

Poly I:
Poly II:
Poly III:

A

Poly I: rRNA formation
Poly II: mRNA formation
Poly III: tRNA formation

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31
Q

the locus of

termination of transcription.

A

termination site

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32
Q

The coding strand is the

A

3’ during the replication process

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33
Q

Enzymes that play major role here:

A 
o Helicase
o RNA polymerase
 Poly I – for rRNA formation
 Poly II – for mRNA formation
 Poly III – for tRNA formation
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34
Q

You would observe here a bubble. This serves as the

A

initiation site

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35
Q

this is where the

nucleotide would come in one after the other.

A

termination site

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36
Q

catalyzed also by RNA
Polymerase, which is about 470,000 Daltons (molecular
mass) with five (5) types of subunits

A

 Prokaryotic transcription

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37
Q

five (5) types of subunits in prokaryotic transcription

A 
o Two (2) Alpha (α),
o Beta (β)
o Beta-1/Beta prime (β’)
o Sigma (σ)
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38
Q

RNA polymerase moves along the template strand of DNA

and produces a complementary strand:

A

RNA sequence that

matches the coding strand of the DNA

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39
Q

RNA polymerase now recognizes specific DNA sequence
and these are called the

would tell the polymerase which DNA should
be transcribed. It promotes transcription

A

promoters

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40
Q

this region affects the binding to the DNA

A

promoter region

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41
Q

is loosely bound to RNA
polymerase and is involved in promoter recognition at the
recognition site

A

sigma (σ) subunit

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42
Q

Transcription can be further subdivided into (3) three parts:

A

oInitiation
o Elongation
o Termination
o *Other books may include propagation

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43
Q

In Prokaryotes the ____ make up
the core of the enzyme and are very much responsible for
the enzymatic activity that catalyze nucleotide incorporation

A

subunits of RNA polymerase

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44
Q

So which of the DNA strand is used for transcription?

A

To make any particular RNA product later on, the RNA
polymerase reach one of the DNA strands
(From 3 prime to 5 prime), and produce the RNA from
5 prime to 3 prime.

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45
Q

The other strand of DNA is now what you call the

(yung color green near sa cursor ni Doc)

A

coding strand

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46
Q

Its sequence matches that of the RNA that is

produced.

A

coding strand

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47
Q

In eukaryotes, the opposite strand is

often used to produce ____ which function in gene expression

A

small interfering non-coding RNA

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48
Q

In eukaryotes. Three kinds of polymerases catalyze

transcription.

A

 RNA polymerase I (pol I) catalyzes the formation of
most of the rRNA.
 Pol II catalyzes mRNA formation.
 Pol III catalyzes tRNA formation as well as ribosomal
subunit.

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49
Q

what

is the molecular mass of rRNA polymerase

A

about 470,000 Daltons.

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50
Q

A eukaryotic gene has two parts

A

structural gene

regulatory gene

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51
Q

gene that is transcribed into
RNA;

is made of exons
(coding region) and introns (non-coding
region and often times being removed or
spliced).

A

structural gene

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52
Q

gene that controls transcription;

not transcribed but
has control elements, one of which is the promoter.

A

regulatory gene

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53
Q

provides

the regulatory mechanism. called promoter

A

regulatory gene

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54
Q

is unique to each gene.

A

promoter

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55
Q

here is always a sequence of bases on the

DNA strand called an

A

initiation signal
(other
books call is as transcription initiation
site).

56
Q

Promoters also contain

A

consensus sequence such as TATA box

57
Q

which the nucleotides T and A are repeated many

times.

A

consensus sequence–TATA box– of promoters

58
Q

a DNA sequence near the
transcription start site or TSS (Campbell and
Farrell) that is bound by RNA polymerase
during transcription-initiation process

59
Q

Promoter is a DNA sequence near the ____ tha tis bound by RNA polymerase
during transcription-initiation process

A

transcription start site or TSS

60
Q

a promoter is a DNA sequence near the
transcription start site or TSS (Campbell and
Farrell) that is bound by ___ during transcription-initiation process

A

RNA polymerase

61
Q

These are DNA sequence farther

away from the start site.

62
Q

A regulatory gene that controls transcription;
the regulatory gene that is not transcribed but
has control elements, one of which is the

A

promoter

enhancers??

63
Q

They bind proteins
and these are called transcription factors and
stimulate transcription above the base on
effects during the process of transcription

64
Q

stimulate transcription above the base on

effects during the process of transcription

65
Q

It serves as the promoter region and

becomes the initiation site

66
Q

The promoters and key elements are

sequences at regions (2)

A

-34 region and -10 regions

67
Q

The latter is called the TATA

box or

A 
PRIBNO box (also called the
Goldberg-Hogness box)
68
Q

In eukaryotic transcription, RNA
polymerase binds to promoters as
well but there is no

A

sigma (σ) subunit

Although there is a specific
subunit specified, but it is involved in
the promoter-recognition site

69
Q

A TATA box lies approximately

A

26 base pairs

upstream

70
Q

All three RNA polymerases interact with their

promoter regions via

A

via transcription factors

that are binding proteins

71
Q

How does RNA polymerase know where to begin transcription?

In prokaryotes, RNA
polymerase is directed to the
gene to be transcribed by the
interactions between the

A

polymerase sigma subunit (σ) and sequences of DNA near the site (promoter region).

72
Q 
After initiation
has taken place, RNA
polymerase zips up the
complementary bases in a
process called
A

elongation or

propagation

73
Q

involves formation of a phosphate ester bonds
between each ribose and the next phosphate
group.

A

Elongation

74
Q

the 5’  3’ direction

A. Elongation
B. Propagation
C. Initiation

A

A. Elongation

75
Q

At the end of each gene is a

A

termination sequence

76
Q

4 principal control mechanisms for prokaryotic

transcription

A

 Sigma (σ) factors
 Enhancers and Silencers
 Operons
 Transcription attenuation

77
Q

o Accounts for what are up regulated or down regulated,
expressed, unexpressed, overexpressed

A. Sigma Factors
B. Enhancers and Silencers
C. Operons
D. Transcription attenuation

A

B. Enhancers and Silencers

78
Q

o The alternative sigma factors can direct RNA polymerase
to different promoters altering the choice of RNA product

A. Sigma Factors
B. Enhancers and Silencers
C. Operons
D. Transcription attenuation

A

A. Sigma Factors

79
Q

o Controls transcription after it has begun by adjusting level
of transcription base on the quantity of a related
metabolite

A. Sigma Factors
B. Enhancers and Silencers
C. Operons
D. Transcription attenuation

A

D. Transcription attenuation

80
Q

o DNA sequences found upstream of promoters that
stimulate or reduce transcription, respectively
o These sequences bind to specific proteins called
transcription factors

A. Sigma Factors
B. Enhancers and Silencers
C. Operons
D. Transcription attenuation

A

B. Enhancers and Silencers

81
Q

a good example of this is the Trp-Operon

 Based on the level of tryptophan
 Affects transcription of genes that produce the
enzyme that make tryptophan

A. Sigma Factors
B. Enhancers and Silencers
C. Operons
D. Transcription attenuation

A

D. Transcription attenuation

82
Q

An example is
o Lactose operon (lac-operon) from Escherichia coli
 Common operon produce beta-galactosidase and
other enzymes involved in metabolism of lactose
 Galactose – sugar that differs from glucose in carbon
4 (-OH groups point at different directions)

A. Sigma Factors
B. Enhancers and Silencers
C. Operons
D. Transcription attenuation

A

C. Operons

83
Q

 Genes involved in common metabolic process that
are controlled as a group
 With an operon, a regulatory gene produces either an
inducer or repressor of the operon
 Metabolites act as co-inducers or co-repressors to
affect transcription of structural genes

A

o Tryptophan operon (Trp-operon)

84
Q

o Tryptophan operon (Trp-operon) is involved in

A. Sigma Factors
B. Enhancers and Silencers
C. Operons
D. Transcription attenuation

A

C. Operons

D. Transcription attenuation

85
Q

3 types of RNA polymerases in Eukaryotic Transcription

and other elements

A

Poly 1 - rRNA
Poly II - mRNA
Poly III - tRNA

TATA box
o Resides in the -25 region
o Important promoter element

6 general
transcription factors involved in forming initiation complex

Enhancers and Silencers

86
Q

Element in eukaryotic transcription

o Resides in the -25 region
o Important promoter element

A

 TATA box

87
Q

TRUE OR FALSE
Organization of promoters and enhancers are more
complicated in prokaryotes

A

FALSE

Organization of promoters and enhancers are more
complicated in eukaryotes

88
Q

TRUE OR FALSE
o Many control mechanisms are based on response
elements

89
Q
  • react to metabolic signals like heat, heavy

metals, and cyclic AMP (cAMP) molecules

90
Q

TRUE OR FALSE
In prokaryotic transcription

There is the involvement of small noncoding RNA

A

FALSE

In eukaryotic transcription

91
Q

Element of eukaryotic transcription that

o Creates a new layer of transcription control
o Binds to template strand and cause inhibition of
transcription

A

small noncoding RNA

92
Q

TRUE OR FALSE

The RNA products of transcription are not necessarily
functional RNAs.

93
Q

RNA products of transcription are made functional by

A

post-transcription

modification.

94
Q

 Transcribed mRNA is capped at

95
Q

Inhibition of transcription is the role of the

A

small noncoding RNA

96
Q 
are proteins that bind to DNA and
often have recognizable structural motifs that exhibit the
following: 
Helix-turn-helix
zinc finger
basic region leucine finger/zipper
A

Transcription factors

97
Q

transcription factors bound to DNA are structural motifs that exhibit the
following:

A

Helix-turn-helix (major structural motif capable of binding
DNA)

zinc finger (small protein structural motif that is
characterized by the coordination of one or more zinc
ions (Zn2+) to stabilize the fold)

basic refion leucine finger/zipper

98
Q

many RNA molecules are modified often extensively before

they arrive at their final form through

A

Post-transcription

modification

99
Q

TRUE OR FALSE

there are several modifications that are common with tRNA
and rRNA

100
Q

messenger RNA (mRNA) is modified by putting a cap on the

A

5’ end and the polyA tail on the 3’ end

101
Q

The 5’ end acquires a:

The 3’ end acquires a:

A

The 5’ end acquires a: methylated guanine (7-mG-cap).

The 3’ end acquires a: polyA tail that may contain from 100 to 200 adenine residues

102
Q

TRUE OR FALSE

Once the two ends are capped, the exons are spliced out

A

FALSE

Once the two ends are capped, the introns are spliced out

103
Q

mRNA is also modified by the removal of intervening

sequences called

104
Q

splicing of introns depends on a separate type of RNA called the

A

small nuclear ribonucleoproteins (snRNPs)

105
Q

alternative splicing of mRNA helps account the fact that

A

there are more proteins produced in eukaryotes than

these are separated genes

106
Q

different types of post-transcription modification:

A

o capping
o methylation
o formation/addition of polyA tail
o splicing

107
Q

o DNA coding strand consists of the following:

A

 Promoter region

 Repeating units of the Gene: Exon 1, Intron, Exon 2,
Intron, Exon 3, Intron, Exon 4, Intron

108
Q

towards the initiation site, it consists of two (2) very

important regions:

A

 TATA box (also called Data Region, GoldbergHogness box, or Pribnow box)
 Initiation site

109
Q

mRNA will aid the transcription by

A

producing a new
transcript
 coupled with several modification/processing such as
the capping, methylation, polyA addition, splicing)

110
Q

After a series of processing, from the mRNA

Transcript, it is now converted into a

A

mature mRNA

111
Q

consists of 100-200 polynucleotides

 Introns are spliced/removed that is why only exons
are seen

112
Q

types of RNA that participate in translation

A

mRNA, rRNA, and tRNA

tRNA is a VIP in translation

113
Q

Protein synthesis takes place on

114
Q

the sites for protein synthesis

115
Q

DNA replication takes place in the

116
Q

Transcription takes place in the

117
Q

TRUE OR FALSE

A ribosome dissociates into a larger and a smaller body.

118
Q

In higher organisms, including humans, the larger body if ribosome is
called a

the smaller body is called a __
ribosome

119
Q

The 5’ end of the mature mRNA is bonded to the __

ribosome and this unit then joined to the __ ribosome.

A

The 5’ end of the mature mRNA is bonded to the 40S

ribosome and this unit then joined to the 60S ribosome.

120
Q

Together the 40S and 60S ribosomes form a unit on which

A

mRNA is stretched out.

121
Q

Triplets of bases on mRNA are called

122
Q
  • start codon

Cannot initiate translation without this

A

AUG (methionine)

123
Q

The 20 amino acids are then brought to the mRNA-ribosome

complex, each amino acid by its own particular

124
Q

TRUE OR FALSE

A

Each tRNA is specific for only one amino acid.

125
Q

Each cell carries at least 20 specific enzymes, each

A

specific

for one amino acid.

126
Q

Each enzyme recognizes how many tRNA

A

only one tRNA.

127
Q

The enzyme bonds the activated amino acid to the 3’terminal

-OH group of the appropriate tRNA by what bond

A

an ester bond.

128
Q

At the opposite end of the tRNA molecule is a

A

codon

recognition site.

129
Q

The codon recognition site is a sequence of three bases

called

130
Q

This triplet of bases aligns itself in what fashion

A

complementary

to the codon triplet on mRNA

131
Q

If mRNA is polyU what is formed

132
Q

the triplet UUU,

therefore, must code for

133
Q

If mRNA is poly —ACACAC— what is formed

A

poly(Thr-His)

134
Q

ACA must code for

135
Q

CAC must code for

Biochemistry Lecture (8 decks)

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