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Biochemistry Lecture > Nucleic acids > Flashcards

Nucleic acids Flashcards

1
Q

From the end of the 19th century, biologists suspected that
the transmission of hereditary information took place in the
nucleus, more specifically in structures called

A

chromosomes.

genes
within the chromosomes.

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2
Q

The hereditary information was though to reside in

A

genes

within the chromosomes.

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3
Q

the basic unit of heredity

o made up of DNA

A

Genes

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4
Q

is a structure in the nucleus of a cell that

conveys information

A

DNA

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5
Q

act as instructions to make proteins

through the process of protein synthesis

A

DNA

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6
Q

Transcription

A

from DNA to RNA

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7
Q

Chromosomes are made up largely of proteins called (2)

A

histones and nucleic acids.

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8
Q

there are four (4) types of histones:

A

H1, H2A & H2B,

H3, H4

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9
Q

there are three (3) levels of structures for nucleic acids:

A

Primary structure
Secondary Structure
Tertiary structure

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10
Q

level of structures for nucleic acids:

pertains to the order of bases in the polynucleotide (several nucleotide units) sequence

A

Primary structure

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11
Q

level of structures for nucleic acids: pertains to the three-dimensional
conformation of the backbone

A

Secondary Structure

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12
Q

level of structures for nucleic acids: pertains to the supercoiling of the molecule

A

Tertiary structure

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13
Q

By the ___, it became clear that deoxyribonucleic acids

(DNA) carry the hereditary information.

A

1940s

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14
Q

DNA is a substance (initially called___) containing nitrogen and phosphorous from cell nuclei

A

Nuclein

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15
Q

key molecule of heredity

A

DNA (carrier of genetic code)

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16
Q

TRUE OR FALSE: each gene

controls the manufacture of one protein

A

True

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17
Q

 Led to the discover of the molecular structure of DNA

A

the

double helix.

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18
Q

the double helix.

was discovered by

A

Watson & Crick in 1953

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19
Q

two principal kinds of nucleic acids in cells:

A 
Ribonucleic acids (RNA)
o Deoxyribonucleic acids (DNA)
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20
Q 
Deoxyribonucleic acids (DNA)
 first founded by
A

Friedrich Miescher in 1869

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21
Q

completed Friedrich Miescher model in
February 1953, which is now accepted as the first
correct model of the double-helix

A

Watson and Crick

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22
Q

Both RNA and DNA are polymers built from monomers called

A

nucleotides

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23
Q

Nucleotide is composed of:

A

four (4) different nitrogenous bases (A, T, C, G)
 Adenine
 Thymine
 Cytosine
 Guanine
o five-carbon sugar: ribose & deoxyribose (D-ribose)
o phosphate molecules (coming from phosphoric acid)

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24
Q

five (5) different nitrogenous bases

A 
Adenine
 Thymine
 Cytosine
 Guanine
Uracil
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25
Q

five-carbon sugar:

A

ribose & deoxyribose

D-ribose & 2-deoxy-D-ribose

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26
Q

phosphate molecules comes from

A

phosphoric acid

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27
Q

DNA and RNA differ in

A

secondary and tertiary structures.

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28
Q

TRUE OR FALSE: The interaction of nucleic acids with other classes of
biomolecules such as proteins would form complexes,
which is similar to the interactions of the subunits in an
oligomeric (short chain) protein.

A

True
a good example would be the RNA and the proteins in ribosomes

RNA is involved in protein synthesis

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29
Q

two types of bases

A

PURINE / PYRIMIDINE BASES

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30
Q

Double ring aromatic compound found in both DNA and RNA (counterclockwise counting)

A

Purines

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31
Q

single ring aromatic compounds

clockwise counting

A

PYRIMIDINE

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32
Q

IUPAC name of Adenine

A

6-Aminopurine

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33
Q

IUPAC name of Guanine

A

2-Amino-6-oxypurine

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34
Q

IUPAC name of Cytosine (counterpart of thymine)

A

2-Oxy-4-

aminopyrimidine

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35
Q

IUPAC name of Thymine

A

2,4-Dioxy-5-methylpyrimidine

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36
Q

Lookalike of uracil except for the presence of

methyl group at position 5

A

Thymine

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37
Q

IUPAC name of Uracil

A

2,4-Dioxypyrimidine

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38
Q

A compound that consists of D-ribose or 2-deoxy-D-ribose

bonded to a purine or pyrimidine base by a B-N-glycosidic

A

NUCLEOSIDES

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39
Q

Consists of a base and a sugar covalently linked

A

NUCLEOSIDES

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40
Q

Base forming a glycosidic linkage with sugar

A

NUCLEOSIDES

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41
Q

Attachment with sugar:
Position 9:
Position 1:

A

Position 9: for Purines
Forms an N-9-C-1 glycosidic linkage with the sugar
(ribose and deoxyribose)

Position 1: for Pyrimidines
Forms an N-1-C-1 glycosidic linkage with the sugar
(ribose and deoxyribose)

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42
Q

Two types of glycosidic bonds (links the bases to the

sugar moiety)

A

 N,C, glycosidic bond (since both are 1)

 N-9-C-1 glycosidic bond

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43
Q

MAJOR DIFFERENCE BETWEEN DNA AND RNA
double-stranded:
single-stranded:

A

double-stranded: DNA

single-stranded: RNA

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44
Q

MAJOR DIFFERENCE BETWEEN DNA AND RNA
responsible for genetic information transmission :

A transmits genetic codes that are necessary
for protein creation (or synthesis):

A

responsible for genetic information transmission : DNA

A transmits genetic codes that are necessary
for protein creation (or synthesis): RNA

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45
Q

Uracil is the only base present in

A

RNA

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46
Q

MAJOR DIFFERENCE BETWEEN DNA AND RNA
found in the cytoplasm, nucleus, and in the ribosome:

located in the nucleus and mitochondria:

A

found in the cytoplasm, nucleus, and in the ribosome: RNA

located in the nucleus and mitochondria: DNA

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47
Q

type of RNA needed for protein synthesis

A

Ribosomal RNA (rRNA)

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48
Q

MAJOR DIFFERENCE BETWEEN DNA AND RNA
molecular weight is 2-6 million:

molecular weight is 25,000- 2 million (depending on the type):

A

molecular weight is 2-6 million: DNA

molecular weight is 25,000- 2 million (depending on the type): RNA

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49
Q

TRUE OR FALSE: RNA (alkaline condition) is more stable molecule than DNA

A

FALSE

Has something to do with the structure of the sugar
moiety
 Deoxyribose is more stable
 Due to presence of hydroxyl group at Carbon 2 of the RIBOSE. The presence of OH makes the structure less stable

Hence, DNA is more stable, and it should be because
DNA is very much responsible in replication, and it is
the first step in the Central Dogma of Molecular Biology.

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50
Q

Major requirement for DNA is that should be very
stable, and it has something to do with the
presence of

A

two deoxy sugars in DNA.

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51
Q

TRUE OR FALSE:

RNA is vulnerable to UV damage than DNA

A

FALSE

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52
Q

THREE DIFFERENT DNA TYPES

A

A-DNA
B-DNA
Z-DNA

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53
Q

o Right-handed double helix similar to the B-DNA
o Stouter than B-DNA
o For every turn of amino acid polynucleotide, this would
have more compared to the B-DNA

A

A-DNA

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54
Q

o Most common DNA conformation and is right-handed

A

B-DNA

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55
Q

o Left-handed DNA where the double helix winds to the
left in a zigzag pattern
o Slender compared to A-DNA

A

Z-DNA

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56
Q

A compound that consists of D-ribose or 2-deoxy-D-ribose
bonded to a purine or pyrimidine base by a β-N-glycosidic
bond.

A

NUCLEOSIDES

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57
Q

 a five-carbon sugar
 naming is 2-deoxy, wherein there is an OH
 just the mere presence of hydroxyl radical makes it less stable because this can undergo another
reaction

A

D-ribose / Ribose

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58
Q

because OH at anomeric carbon (position 1) is

going up so this becomes

A

β-D-riboside

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59
Q

Ending of nucleoside is

A

-ine (Uridine, Thymidine)

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60
Q

Uridine will only be present in

A

RNA

The counter part of that
in DNA would be Thymidine. So instead of Uracil, you
attach Thymidine, and the sugar will also change. The
sugar would be β-D-deoxy-ribose.

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61
Q

A nucleoside in which a molecule of phosphoric acid is
esterifies with an -OH of the monosaccharide, most
commonly either at 3’ or 5’ -OH.

A

NUCLEOTIDES

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62
Q

Base + Sugar + Phosphate group

A

NUCLEOTIDES

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63
Q

Esterified at Carbon 5 (yellow) or at Carbon 3 (green)

position to attach, so you form now a polynucleotide

A

NUCLEOTIDES

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64
Q

one phosphate:
two phosphate:
three phosphate:

A

one phosphate: AMP or adenosine monophosphate

two phosphate: ADP or adenosine
diphosphate

three phosphate: ATP or adenosine
triphosphate

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65
Q

energy currency that will be produced in metabolism

A

AMP,ADP, ATP

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66
Q

common currency which energy gained

from food is converted and stored

A

ATP

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67
Q

repeated linkages, where the three
prime or five prime are phosphodiester bond (additional
linkages aside from glycosidic linkage/bond). — this
forms sugar phosphate backbone repeats in order
to come up with

A

Polynucleotide

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68
Q

DNA or RNA? :

When nucleotide are joined by a phosphodiester bond
they form a sugar phosphate molecule or backbone

A

Both

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69
Q

this is the genetic

information that ultimately leads to the RNA or protein

A

The sequence of bases (Primary, Secondary, tertiary)

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70
Q

When we talk of RNA or protein synthesis: the first

amino acid that would be coded (start codon) is the

A

(methionine) — used to synthesize proteins

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71
Q

Leslie Orgel is the father of the ___, established a world theory of the origin of life

A

RNA

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72
Q

present in all biological cells, an important macromolecule
principally involved in protein synthesis of proteins, carrying
the messenger instructions from DNA (transcription RNA to
DNA, translation/protein synthesis RNA to RNA)), which
itself contains the genetic instructions required for the
development and maintenance of life

A

RNA

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73
Q

For nucleic acids, this is the sequence of
nucleotides, beginning with a nucleotide that has the free
five prime terminus.

A

PRIMARY (1”) STRUCTURE

o The strand is read from the 5’ end to the 3’ end
o Thus, the sequence AGT means that adenine (A) is
the base at the 5’ terminus and Thymine (T) is the
base at 3’ terminus

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74
Q

TRUE OR FALSE:
The secondary structure of the DNA structure IS constant and this
serves as the sugar phosphate backbone and this is
constant depending on the sugar that is present

A

TRUE

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75
Q

The ordered arrangement

of nucleic acid strands.

A

Secondary structure

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76
Q

what structure was

proposed by James Watson and Francis Crick in 1953.

A

Secondary structure

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77
Q

A type of 2° structure of DNA in which two
polynucleotide strands are coiled around each other in a
screw-like fashion in an anti-parallel.

A

Double helix

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78
Q

type of seondary structure that resembles a ladder but the hydrogen bonding that bonds the bases makes them antiparallel

A

Double helix

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79
Q

the three-dimensional conformation of

the backbone of the DNA

A

Secondary structure

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80
Q

Chargaff’s rule:

A

complementary base pairing
C can bind with G ; G with C

T can bind A (vice versa)

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81
Q

A DNA double helical structure has two grooves:

A

minor

groove and major groove (large groove)

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82
Q

Type of DNA:
o Stout
o Would normally contain 11 base pairs which is why it
appears to be stout

A

A-DNA

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83
Q

Type of DNA:

The principal form of DNA that occurs in nature

A

B-DNA

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84
Q

Type of DNA:
o The helix winds upward to the right
o Would normally contain about 10 base pairs

A

B-DNA

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85
Q

A complete turn of the helix would span 10 base.

The distance per turn of helix is:

The distance between individual base pairs would be:

A

34 angstroms or 3.4 nanometer

3.4 angstroms or 0.34 nm apart

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86
Q

in B-DNA
The inside diameter is:

the outside diameter is :

A

The inside diameter is: 1.5nm or 11 angstroms

the outside diameter is :
20 angstroms or 2.0 nm

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87
Q

TRUE OR FALSE
Phosphate has a negative charge (-3) and it imparts negativity. It has negative phosphate charge along the entire length of each strand which will elicit a certain
behavior

A

True

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88
Q

o Left-handed
o Winds the direction of the fingers of the left-handed
o Thin or slender and elongated in contrast to the A-DNA

A

Z-DNA

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89
Q

o Would normally have less base pairs per turn of the helix

A

Z-DNA

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90
Q

Important in the structure as it would impart stability

A

Base Pairing

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91
Q

BASE PAIRING:
two hydrogen bonds form what pair

three hydrogen bonds form what pair

A

A and T pair

G and C pair

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92
Q

Which would be more stable? Which would require

more energy to break?

A

G and C pair

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93
Q

TRUE OR FALSE:
Sugar phosphate backbone are always at the inner
sides/ region of the double helical structure

A

FALSE
always at the outer
sides/ region of the double helical structure

It forms the double helical structure in its anti-parallel
direction

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94
Q

• DNA is coiled around proteins called

A

HISTONES

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95
Q

Coiling refers to what type of structure

A

Tertiary structure

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96
Q

rich in the basic amino acids Lys and Arg,

whose side chains have a positive charge.

A

Histones

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97
Q

The negatively-charged DNA molecules and positively charged

histones attract one another and form units called

A

nucleosomes (11 nm size)

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98
Q

A core of eight histone molecules around

which the DNA helix is wrapped

A

Nucleosome (11nm size)

There are 4 types of histones and 2 strands consisting
of the DNA double helical structure forming 8 histone
molecules where the DNA helix is wrapped.

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99
Q

Nucleosomes are further condensed into

A

Chromatin

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100
Q

are organized into loops, and the loops into the bands that provide the superstructure
of chromosomes.

A

Chromatin fibers

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101
Q

OTHER SUPERSTRUCTURES:

Six nucleosomes per turn

A

Slenoid (30nm)

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102
Q

OTHER SUPERSTRUCTURES:

50 turns per loop

A

Loops (250nm)

103
Q

OTHER SUPERSTRUCTURES:

18 loops

A

Miniband (840nm)

104
Q

OTHER SUPERSTRUCTURES:

Stacked minibands

A

Chromosome (840nm)

105
Q

TRUE OR FALSE:
Exceptional fidelity refers to A partners with T, and C only
pairs with G, and vice versa. Thus, their amounts are equal.
(Chargaff’s rule)

A

true

106
Q

replication yields two molecules of this that is identical to the original one, ensuring transmission of genetic information to daughter cells with exceptional fidelity

A

Replication

107
Q

The sequence of bases in DNA is recorded as a sequence of complementary bases in single-stranded mRNA molecule

A

Transcription

108
Q

Three-base codons on the mRNA corresponding to specific amino acids direct the sequence of building a protein. These codons are recognized by tRNAs carrying the appropriate amino acids. Ribosomes are the machinery for protein synthesis

A

Translation

109
Q

Type of RNA:
Small

Transports amino
acids to site of protein
synthesis

A

Transfer

RNA (tRNA)

110
Q

Type of RNA:
Several kinds, variable in size

Combines with
proteins to form
ribosomes, the site of
protein synthesis

A

Ribosomal RNA

rRNA

111
Q

Type of RNA:
variable in size

Directs amino acid
sequence of proteins

A

Messenger RNA
(mRNA)

carry the genetic information from
the DNA in the nucleus directly to the cytoplasm, where most of the
protein is synthesized.

112
Q

Type of RNA:
small

Processes initial
mRNA to its mature
form in eukaryotes

This process is often referred to as splicing, and it is an active area of research.

A

Small nuclear

RNA (snRNA)

113
Q

Type of RNA:
Small

Affects gene
expression; used by
scientists to knock out
a gene being studied

A

Small interfering

RNA (siRNA)

114
Q

Type of RNA:
Small

Affects gene
expression, important
in growth and development

A

Micro RNA (miRNA)

115
Q

Type of RNA:
variable in size

Involved in activating
or silencing specific
genes

A

Long non-coding

RNA (lncRNA)

116
Q

Type of RNA:
Small

Protects animal
genomes against
transposons

A

Piwi-associated RNA

117
Q

Type of RNA:
Variable in size

Acts as miRNA
sponge, controlling
the effects of miRNA

A

Circular RNA

Created by
alternative splicing of introns

118
Q

The smallest kind of the three RNAs

A

Transfer RNA (tRNA)

119
Q

A single stranded polynucleotide chain between 73-94
nucleotide residues

Carries an amino acid at its 3’ end

A

Transfer RNA (tRNA)

120
Q

Anticodon loop contains the

A

tRNA – trinucleotide
sequence that is complementary to the codons that will be
found in the messenger RNA

121
Q

In prokaryotes, ribosomes assume a __ shape upon

undergoing lysis and fractionation

A

70S (Svedberg)

122
Q

In eukaryotes, there are two ribosomal subunits that are

both made up of __ and ___

A

2/3 RNA and 1/3 proteins

30S subunit can be dissociated by sodium dodecyl
sulfate (SDS, a detergent), forming 16S rRNA + 21
proteins

50S subunit dissociates into 23S rRNA + 5S rRNA + 34
proteins

123
Q

a unit that measures how

fast molecules move in a centrifuge

A

Svedberg (S)

124
Q

Segment of DNA that carries a base sequence that directs

the synthesis of a particular protein, tRNA, or mRNA

A

Genes

125
Q

Bacterial genes:

Higher organisms:

A

Bacterial genes: Continuous

Higher organisms: Discontinuous

126
Q

Section of DNA/ A gene that codes for a protein or RNA

A

Exons

127
Q

A gene that Does not code for anything functional

A

Introns

128
Q

transcription and translation in prokaryotes

A

DNA-dependent RNA polymerase will transcribe DNA of genes A, B, and C hwich then comes up with an mRNA
Ribosomes will translate this mRNA into proteins A,B,C

129
Q

Exons are joined together in a mature mRNA strand by

A

removing or splicing introns out of the equation since they

are noncoding, intervening sequences

130
Q

intervening sequences in gene

A

Introns

131
Q

The DNA in the chromosomes carries out two functions:

A

o It reproduces itself. This process is called replication.
 DNA to DNA
o It supplies the information necessary to make all the RNA
and proteins in the body, including enzymes.
 DNA to RNA (Transcription) to proteins (Translation)

132
Q

Replication begins at a point in the DNA called the origin of
replication or

A

Replication fork

133
Q

(the point at which new DNA

strands are formed)

A

Replication fork

134
Q

the protein whose
binding prepares for the start of DNA replication in
eukaryotes

A

Replication activator protein (RAP)

135
Q
  • DNA to DNA through the action of

DNA polymerase

A

DNA replication

136
Q

RNA back to DNA

A

Reverse Transcription

137
Q

DNA to RNA

A

Transcription

138
Q

When RNA is converted to proteins
(amino acids) through the actions of or facilitated by
ribosomes (site of protein synthesis)

A

Translation

There is the participation of ribosomes and mRNA

139
Q

a double helical structure that consists of the 3’

and 5’ strands in a spiral that are antiparallel

A

DNA

140
Q

TRUE OR FALSE Base pairing can be seen and are stabilized by the
Hydrogen bonding

A

TRUE

3 H-bond stabilize the C-G base pair
 2 H-bond stabilize the A-T base pair

141
Q

What type of replication happens When a cell divides into two, each of the two cells have
retained one of the original template strand and one of
the new strand (daughter strand)

A

Semiconservative type of replication

142
Q

Two cells have retained one of the original template
strand and one of the new strand that will combine
with the leading strand.

A

Semiconservative Replication

143
Q

One of the other parent strand (lagging strand),
another new strand will partner with this one
(complementary base pairing)

A

Semiconservative Replication

144
Q

From a single parent strand, form two new daughter

strand and that is what you call

A

l semiconservative

replication.

145
Q

When DNA molecules are replicated, the strands are

separated at

A

Origin of replication / replication fork

146
Q

Synthesis occurs in both directions in the point of replication along the replication ofrl that’s why we call it

Occurs only in prokaryotes

A

bidirectional

147
Q

it is semi discontinuous
DNA replication wherein all synthesis of nucleotide
chains occurs in what
direction from the perspective of the chain being
synthesized

A

5’ to 3’

direction

148
Q

The three hydroxyl group at the end of the growing

chain acts a

A

Nucleophile

this is a form of
nucleophilic attack with the removal of water

It attacks phosphorous adjacent to the sugar in the
nucleotide that is to be added to the growing chain,
leading to the elimination of the pyrophosphate group and the formation of a new phosphodiester bond
(green part), that is how you increase the DNA

149
Q

This enzyme will continuously add bases

A

DNA polymerase III

150
Q

DNA polymerase synthesizes one

strand ____ and the other one ____

A

Continuously

Discontinuously

that’s why we say semiconservative and semi
discontinuous type of DNA replication

151
Q

Lagging

strand

A

Complementary strand
3”
synthesize discontinuously

semi discontinuous replication

152
Q

Leading strand

A

5”

Synthesize continuously

153
Q

Okazaki fragment is formed in the

A

lagging strand

154
Q

small pieces of DNA that are formed discontinuously, and which are later
joined together by the enzyme and that is the DNA
ligase, contrary to its name ligase, which is to ligate,
it joins the fragments together

A

Okazaki fragment

155
Q

TRUE OR FALSE

Reaction of DNA synthesis involves nucleophilic attack
of the three hydroxyl group of one nucleotide on the
phosphate of the incoming nucleotide triphosphate

A

true

156
Q

How many DNA polymerase exists in e.coli (gram negative coli) and most commonly used bacteria (and prokaryotes in general)

A

5 DNA polymerase

157
Q

Polymerase that is the principal enzyme responsible for
synthesis of new DNA or daughter strand of DNA –
multisubunit enzyme

A

Polymerase 3

158
Q

Polymerase that is involved in proofreading and repair

processes

A

Polymerase 1,2

159
Q

TRUE OR FALSE

not all DNA requires RNA primer

A

FALSE

All DNA requires RNA primer

160
Q

DNA in prokaryotes are ____: 2 replication forks that

advance in opposite direction (to the right and left reference point is the origin of replication)

A

bidirectional

161
Q

Types of replications:

A

o Semiconservative replication (standard)
o Semidiscontinous replication
o Bidirectional
 Present in prokaryotes

162
Q

enzyme that
introduces a swivel point in advance to the
movement of the replication fork/ helix destabilizing protein

A

DNA gyrase

163
Q

enzyme that
binds at the replication fork and it will
unwind since its twisted

A

 Alpha-Helixase

164
Q

o Promotes unwinding, exposing the single stranded
region of the protein (SSB) of the template DNA
o These are stabilized in the DNA binding protein

A

 Alpha-Helixase

165
Q

enzyme that
catalyzes the synthesis of an
RNA primer – all synthesis requires a RNA primar
(important in DNA replication)

A

primase

166
Q

enzyme that

Synthesis of the 2 strands, 2 newly synthesized strand is catalyzed by

A

polymerase 3

167
Q

enzyme that
removes the primer which also replaces
the primer with deoxynucleotide (sugar present is
deoxyribose)

A

Polymerase 1

168
Q

enzyme that

joins or seals the gap/nics

A

DNA ligase

169
Q

This
reaction eliminates some of the positive charges on
histones and weakens the strength of the DNAhistone interaction

A

process of acetylation-deacetylation of lysine residue on histones

In first step of replication –opening up the superstructure of the chromosomes

170
Q

proteins attached to nucleic acids

A

histones

171
Q

Opening up the superstructure of the

chromosome would require

A

acetylation and

deacetylation of the lysine residue of histone

172
Q

This is the first step that

happens during DNA replication

A

the DNA-histone interaction.

acetylation and
deacetylation of the lysine residue of histone

173
Q

Enzyme that
relaxes the supercoiling, since it is twisted (double
helical), by breaking the strands.

A

Tropoisomerases / DNA gyrases

174
Q

2nd step of DNA replication

A

Relaxation of Higher-Order Structures of DNA.
Tropoisomerases(also called gyrases) temporarily
introduce either single-or double strand breaks in DNA

175
Q

3rd step of DNA replication

A

Replication of DNA molecules starts with the unwinding of
the double helix which can occur at either end or in the
middle.

176
Q

Special unwinding proteins (enzymes) that attach themselves to one DNA strand and cause the separation of the double helix.

A

Helicases

177
Q

Enzyme that
induces the negative supercoils in the
DNA to compensate for the positive supercoils that would
form because of strand separation

relaxes the supercoiling,

A

DNA gyrase / Tropoisomerase

178
Q

Enzyme that

induce strand separation causing unwinding of the strands

A

Helicases

179
Q

Enzyme that
protects the
single-stranded regions from nucleases. ito yung nagseset
ng signal para ma-retain yung unwinding so that the DNA
replication will take place. Marerelax ngayon yung single
stranded parent strand

A

Single-stranded binding proteins (SSB)

180
Q

Enzyme that
links pieces of newly found DNA together. It plays a role in the Okazaki fragments. DNA ligase seals the remaining nicks of gap

A

DNA ligase

181
Q

Enzyme that
primes the synthesis of the lagging strand by the
formation of a primer.

A

Primase

182
Q

Enzyme that
removes primer

(Replaces the primer with deoxyribonucleotide)

A

polymerase 1

183
Q

Enzyme that
helps in the synthesis of new strands;
this enzyme catalyzes the synthesis of new strands.

A

polymerase 3

184
Q

The primer and the protein at the

replication fork, as a whole is called

A

primosome

185
Q

The primer and the protein at the
replication fork, as a whole, are now called primosome,
and that the entire complex including the DNA
polymerases, we have 1 and 3 playing very important role.
The entire complex is called

A

Replisome

186
Q

are short—4 to 15 nucleotides long—RNA
oligonucleotides synthesized from ribonucleoside
triphosphates. They are needed to initiate the
primase-catalyzed synthesis of both daughter
strands.

A

Primers/primase

187
Q

The enzyme enables complementary
base pairing with high specificity. While bases are
being hydrogen bonded to their partners,
polymerases join the nucleotide backbones.

A

DNA polymerase

188
Q

fragments consist of about 200 nucleotides each, named

A

Okazaki fragments

189
Q

TRUE OR FALSE
Along the lagging strand 3’—>5”, the enzymes can
synthesize long fragments

A

FALSE
Along the lagging strand 3’—>5”, the enzymes can
synthesize only short fragments

190
Q

The Okazaki fragments and any nicks remaining are

eventually joined by

A

DNA ligase.

191
Q

How do you add now the nucleotides from a growing

DNA chain?

A

at the carbon 3 position ( wherein
there is a hydroxyl group in the deoxyribose)
 To increase the growing chain of DNA, the nucleotide will be acting
as a nucleophile. And through nucleophilic attack, it will
attach at the phosphate group (carbon 5 of the
CH2OH)

Then you form now the product which is
pyrophosphate and you will have a newly synthesized
phosphodiester bond.

192
Q

Process involved in DNA amplification

A

through PCR

We can now
increase the amount of DNA. That is why you can now
perform different DNA manufacturing.

You can isolate DNa from the hair or any other tissues
as long as it is still active (not burned, not denatured)
 As long as you still have the intact protein, you can still
produce millions of copies of a certain/ selected DNA
fragment that can be made within few hours with a high
precision machine (through PCR).

193
Q

In using PCR to amplify DNA, what must be known

A

the sequence of a gene / sequenced segment bordering

194
Q

are polynucleotides consisting of

12 to 16 nucleotides

A

Primers

When added to the target DNA
segment, they hybridize with the end of each strand of the
gene (Kase nagkakaron ng complementary base pairing)

195
Q

What happens in PCR – DNA amplification

A

You have here the targeted sequence, then you have to
complement the DNA sequence with a primer that can
help synthesize only that sequence.

: Heating to 95°C to unwind the double helix.
There is the presence of taq DNA Polymerase

dATP, dTTP,
dGTP, and dCTP (d = deoxy), which are nucleotides,
and the participation of the four bases are also present.

Then, it is cooled to 70°C and primer is added. This
produces two new daughter strands.

Cycle 1 is repeated forming four new
daughter strands from one parent strand (the targeted
sequence). DNA replication proceeds from four duplex
of DNA molecule. Each will dissociate into two forming
8 duplex.

After cycle 3, there will be 16 duplexes. This
is how DNA is amplified from a small sample (blood,
hair, semen, etc.)

196
Q

Enzyme used in PCR that can tolerate high temperatures since it is isolated from a hieat-tolerant bacteria

A

taq DNA polymerase

197
Q

TRUE OR FALSE
DNA replication in eukaryotes is similar to DNA replication
in prokaryotes.

A

TRUE

198
Q

Difference in DNA replication of eukaryotes and prokaryotes

A

the process of histones.

Histones are complex to eukaryotic DNA

Different proteins are used, and the system is more
complex than prokaryotes

Replication is controlled that it occurs only once during a
cell division cycle

199
Q

Cell division cycle:

preparation of cell to divide

A

G1 phase

200
Q

Cell division cycle:

organizes and condenses the genetic material

A

G2 phase

201
Q

Cell division cycle:

where DNA replication occurs

A

o S phase

202
Q

Cell division cycle:

complete cell division

A

M Phase

203
Q

what are the o 5 DNA polymerases

A 
α (alpha), 
β (beta), 
γ (gamma), 
θ (theta), and 
ε (epsilon)
204
Q

Type of DNA polymerase:

the principal synthesizer of DNA and
is equivalent to Polymerase III in prokaryotes

A

Polymerase γ

205
Q

Viability of cells depend on them

they can can
detect, recognize, and remove mutations from DNA

A

DNA repair enzymes

206
Q

Due to these, there can be mutations when it

comes to base pairing

A

Due to wear and tear

207
Q

TRUE OR FALSE

Polymerases never make mistakes when it comes to proofreading the bases and codons

A

FALSE

Sometimes in the proofreading of bases and codons, the
polymerases may commit mistakes resulting int
spontaneous mutation

208
Q

Mutation that is the Result of error in natural or biological processes

o It is a natural occurrence

A

spontaneous mutation

209
Q

Common spontaneous mutations are due to

A

depurination and deamination –
(removal of amine groups) of the pyrimidine and purine
bases

210
Q

Two types of Mutation

A

Spontaneous Mutation

Induced Mutation

211
Q

Mutation that is Due to external agents in the environment causing changes
in DNA structures

A

Induced Mutation

212
Q

External agents that causes induced mutation

A

Physical agents: heat, UV irradiation

Chemical Agents: benzo-a-pyrene (an intercalating
agent from charred portions of broiled meat or fish that
can insert itself in DNA base pairing)

High-oxidizing agents such as hydrogen peroxide,
superoxide anion(free radical), hydroxyl radicals and peroxyl radicals

Aflaxtoxins, Acridine orange stain, mushrooms, alcohol
o most chemicals used in the laboratory like Acridine
orange, Benzo[a]pyrene

213
Q

MUTAGEN – agents that may cause damage to the bases

A

High-oxidizing agents such as hydrogen peroxide,
superoxide anion(free radical), hydroxyl radicals and
peroxyl radicals

214
Q

MUTAGEN –
an intercalating
agent from charred portions of broiled meat or fish that
can insert itself in DNA base pairing

A

benzo-a-pyrene (Chemical agent)

215
Q

MUTAGEN:

toxin present in moldy peanuts

A

Aflaxtoxins

216
Q

TRUE OR FALSE :
There are cases when mutations may be reversed back
and structures go back to their native conformation, which makes them unstable

A

true

217
Q

Cause of spontaneous mutation:

more common and a kind of intervention
of the glycosidic bond linkage due to chemical instability
of the purine and the pyrimidine bases

A

depurination

218
Q

Cause of spontaneous mutation:

Errors in copying or internal chemical reactions can create damage internally

A

deamination

deamination of cytosine turns into uracil, which create a mismatch

former C-G base pair becomes U-G mispairing that must be removed
error must be detected by DNA polymerase

219
Q

most common base repairs means

A

BER, base excision repair.

220
Q

there are two pathways by which the BER exist and by

which DNA is repaired:

A

Specific DNA ???

Synthesis step – Enzyme DNA

221
Q

BER pathway: What enzyme
recognizes the damaged base and catalyzes
the hydrolysis of β-glycosidic bond between
that base and the sugar deoxyribose) thereby
releasing the damaged base completing the
excision (acts like a scissor)

sugar phosphate backbone is still intact

A

Glycolase

222
Q

BER pathway: What Enzyme?

inserts the correct nucleotide, cytidine
(becomes automatic repair system; detection
that there is a mutation and instantaneously
repaired through insertion of correct
nucleotide)

A

DNA Polymerase (Pol III)

223
Q

types of gene mutation

A 
Point mutation
Missense mutation
Silent mutation
Nonsense mutation
Frameshift mutation
Transversion
224
Q

Type of gene mutation:

 affects a single base pair
(as in the case of
hemoglobin-S where only
position 6 amino acid is
affected)
 may cause silent,
missense, or nonsense
mutation
 ex. Covid-19 delta variant
A

Point mutation

225
Q

Type of gene mutation:

 if the mRNA codon codes
for a different amino acid
 may retain function
depending on the
chemistry of the new
amino acid and its
location in the protein
A

Missense mutation

226
Q

Type of gene mutation:

 if the mRNA codon codes
for the same amino acid
 occurs when the change
of a single DNA
nucleotide within a
protein-coding portion of a gene does not affect the
sequence of amino acids
A

Silent mutation

227
Q

Type of gene mutation:

 if the mRNA codon
becomes a stop codon
 produce truncated and
frequently nonfunctional
proteins
A

Nonsense mutation

228
Q

Type of gene mutation:

 results from an insertion
or deletion of nucleotide/s
that is not a multiple of
three
 change in reading frame
alters every amino acid
after the point of the
mutation and results in a
nonfunctional protein
A

Frameshift mutation

229
Q

Type of gene mutation:

 refers to a purine being
replaced by a pyrimidine
or vice versa

A

Transversion

230
Q

BER pathway: what enzyme
at the AP site (apurinic or apyrimidinic site)
created in this way, the backbone is cleaved
by this enzyme

A

endonuclease

231
Q

BER pathway: what enzyme
liberates the
sugar-phosphate unit of the damaged site

A

exonuclease

232
Q

BER pathway: what enzyme
seals the backbone
to complete the repair

A

DNA ligase

233
Q

The information that determines external characteristics
(red hair, blue eyes) and internal characteristics (blood group,
hereditary diseases) was thought to reside in

A

genes

234
Q

TRUE OR FALSE:
not all genes lead to the production of
protein

A

TRUE

We now know that not all genes lead to the production of
protein, but all genes do lead to the production of another type of nucleic acid,
called ribonucleic acid (RNA).

235
Q

TRUE OR FALSE:

Both DNA and RNA are polymers

A

TRUE

236
Q

The bases found in DNA and RNA are

A

heterocyclic aromatic amines

237
Q

When phosphoric acid froms a phosphate ester bond with a nucleoside

A

nucleotide

238
Q

Polymers composed

of nucleotides

A

Nucleic acids

239
Q

The backbone in DNA consists

of alternating

A

deoxyribose and phosphate groups

240
Q

the bases form this type of interaction which stabilizes the double helix

A

bases are hydrophobic and forms hydrophobic interaction to stabilize the double helix

241
Q

A/T could not fit with G/C because

A

it forms much weaker hydrogen bonding

a pyrimidine must always opposite a purine

242
Q

distinguishing feature of the B-DNA

A

major and minor groove

243
Q

arise because the two strands are not

equally spaced around the helix

A

major and minor groove

Interactions of proteins and drugs with the
major and minor grooves of DNA serve as an active area of research.

244
Q

the force of attraction that exists between nucleosome (DNA-histone)

A

electrostatic (ionic) forces

245
Q

An RNA that consists of a chain of nucleotides
whose sequence is exactly complementary to that of one of the
strands of the DNA

A

mRNA

246
Q

Small spherical
bodies in the cell made of protein
and RNA; the site of protein
synthesis

A

Ribosomes

247
Q

Type of RNA that inhibits translation of mRNA into protein and promote the degradation of mRNA

can also stimulate
protein production in cells when the cell cycle has been arrested.

A

miRNA

248
Q

type of RNA that is used to eliminate expression of an undesirable
gene, such as one that causes uncontrolled cell growth or one that
came from a virus by degrading that specific mRNA molecule to control the gene activity

A

siRNA

249
Q

type of RNA that is
subtle control mechanism for miRNA’s own control
of transcription

A

Circular RNA

250
Q

Replication begins at a point in the DNA called an

The point
on the DNA where replication proceeds is called the

A

Origin of replication

Replication fork

251
Q

Primer is made up of

A

RNA

252
Q

These

assemblies of enzyme “factories” go by the name of

A

Replisomes

Complex of DNA polymerase and primer and proteins in replication fork

they
contain key enzymes such as polymerases, helicases, and primases

253
Q

Enzyme that is also involved in the

untangling of the replicated chromosomes, before cell division can occur.

A

Topoisomerase / gyrase

254
Q

Enzyme that hydrolyzes ATP as the DNA strand

moves through. The energy of the hydrolysis promotes this movement.

A

Helicase

Biochemistry Lecture (8 decks)

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