Nucleic acids Flashcards
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
chromosomes.
genes
within the chromosomes.
The hereditary information was though to reside in
genes
within the chromosomes.
the basic unit of heredity
o made up of DNA
Genes
is a structure in the nucleus of a cell that
conveys information
DNA
act as instructions to make proteins
through the process of protein synthesis
DNA
Transcription
from DNA to RNA
Chromosomes are made up largely of proteins called (2)
histones and nucleic acids.
there are four (4) types of histones:
H1, H2A & H2B,
H3, H4
there are three (3) levels of structures for nucleic acids:
Primary structure
Secondary Structure
Tertiary structure
level of structures for nucleic acids:
pertains to the order of bases in the polynucleotide (several nucleotide units) sequence
Primary structure
level of structures for nucleic acids: pertains to the three-dimensional
conformation of the backbone
Secondary Structure
level of structures for nucleic acids: pertains to the supercoiling of the molecule
Tertiary structure
By the ___, it became clear that deoxyribonucleic acids
(DNA) carry the hereditary information.
1940s
DNA is a substance (initially called___) containing nitrogen and phosphorous from cell nuclei
Nuclein
key molecule of heredity
DNA (carrier of genetic code)
TRUE OR FALSE: each gene
controls the manufacture of one protein
True
Led to the discover of the molecular structure of DNA
the
double helix.
the double helix.
was discovered by
Watson & Crick in 1953
two principal kinds of nucleic acids in cells:
Ribonucleic acids (RNA) o Deoxyribonucleic acids (DNA)
Deoxyribonucleic acids (DNA) first founded by
Friedrich Miescher in 1869
completed Friedrich Miescher model in
February 1953, which is now accepted as the first
correct model of the double-helix
Watson and Crick
Both RNA and DNA are polymers built from monomers called
nucleotides
Nucleotide is composed of:
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)
five (5) different nitrogenous bases
Adenine Thymine Cytosine Guanine Uracil
five-carbon sugar:
ribose & deoxyribose
D-ribose & 2-deoxy-D-ribose
phosphate molecules comes from
phosphoric acid
DNA and RNA differ in
secondary and tertiary structures.
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.
True
a good example would be the RNA and the proteins in ribosomes
RNA is involved in protein synthesis
two types of bases
PURINE / PYRIMIDINE BASES
Double ring aromatic compound found in both DNA and RNA (counterclockwise counting)
Purines
single ring aromatic compounds
clockwise counting
PYRIMIDINE
IUPAC name of Adenine
6-Aminopurine
IUPAC name of Guanine
2-Amino-6-oxypurine
IUPAC name of Cytosine (counterpart of thymine)
2-Oxy-4-
aminopyrimidine
IUPAC name of Thymine
2,4-Dioxy-5-methylpyrimidine
Lookalike of uracil except for the presence of
methyl group at position 5
Thymine
IUPAC name of Uracil
2,4-Dioxypyrimidine
A compound that consists of D-ribose or 2-deoxy-D-ribose
bonded to a purine or pyrimidine base by a B-N-glycosidic
NUCLEOSIDES
Consists of a base and a sugar covalently linked
NUCLEOSIDES
Base forming a glycosidic linkage with sugar
NUCLEOSIDES
Attachment with sugar:
Position 9:
Position 1:
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)
Two types of glycosidic bonds (links the bases to the
sugar moiety)
N,C, glycosidic bond (since both are 1)
N-9-C-1 glycosidic bond
MAJOR DIFFERENCE BETWEEN DNA AND RNA
double-stranded:
single-stranded:
double-stranded: DNA
single-stranded: RNA
MAJOR DIFFERENCE BETWEEN DNA AND RNA
responsible for genetic information transmission :
A transmits genetic codes that are necessary
for protein creation (or synthesis):
responsible for genetic information transmission : DNA
A transmits genetic codes that are necessary
for protein creation (or synthesis): RNA
Uracil is the only base present in
RNA
MAJOR DIFFERENCE BETWEEN DNA AND RNA
found in the cytoplasm, nucleus, and in the ribosome:
located in the nucleus and mitochondria:
found in the cytoplasm, nucleus, and in the ribosome: RNA
located in the nucleus and mitochondria: DNA
type of RNA needed for protein synthesis
Ribosomal RNA (rRNA)
MAJOR DIFFERENCE BETWEEN DNA AND RNA
molecular weight is 2-6 million:
molecular weight is 25,000- 2 million (depending on the type):
molecular weight is 2-6 million: DNA
molecular weight is 25,000- 2 million (depending on the type): RNA
TRUE OR FALSE: RNA (alkaline condition) is more stable molecule than DNA
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.
Major requirement for DNA is that should be very
stable, and it has something to do with the
presence of
two deoxy sugars in DNA.
TRUE OR FALSE:
RNA is vulnerable to UV damage than DNA
FALSE
THREE DIFFERENT DNA TYPES
A-DNA
B-DNA
Z-DNA
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-DNA
o Most common DNA conformation and is right-handed
B-DNA
o Left-handed DNA where the double helix winds to the
left in a zigzag pattern
o Slender compared to A-DNA
Z-DNA
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.
NUCLEOSIDES
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
D-ribose / Ribose
because OH at anomeric carbon (position 1) is
going up so this becomes
β-D-riboside
Ending of nucleoside is
-ine (Uridine, Thymidine)
Uridine will only be present in
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.
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.
NUCLEOTIDES
Base + Sugar + Phosphate group
NUCLEOTIDES
Esterified at Carbon 5 (yellow) or at Carbon 3 (green)
position to attach, so you form now a polynucleotide
NUCLEOTIDES
one phosphate:
two phosphate:
three phosphate:
one phosphate: AMP or adenosine monophosphate
two phosphate: ADP or adenosine
diphosphate
three phosphate: ATP or adenosine
triphosphate
energy currency that will be produced in metabolism
AMP,ADP, ATP
common currency which energy gained
from food is converted and stored
ATP
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
Polynucleotide
DNA or RNA? :
When nucleotide are joined by a phosphodiester bond
they form a sugar phosphate molecule or backbone
Both
this is the genetic
information that ultimately leads to the RNA or protein
The sequence of bases (Primary, Secondary, tertiary)
When we talk of RNA or protein synthesis: the first
amino acid that would be coded (start codon) is the
(methionine) — used to synthesize proteins
Leslie Orgel is the father of the ___, established a world theory of the origin of life
RNA
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
RNA
For nucleic acids, this is the sequence of
nucleotides, beginning with a nucleotide that has the free
five prime terminus.
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
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
TRUE
The ordered arrangement
of nucleic acid strands.
Secondary structure
what structure was
proposed by James Watson and Francis Crick in 1953.
Secondary structure
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.
Double helix
type of seondary structure that resembles a ladder but the hydrogen bonding that bonds the bases makes them antiparallel
Double helix
the three-dimensional conformation of
the backbone of the DNA
Secondary structure
Chargaff’s rule:
complementary base pairing
C can bind with G ; G with C
T can bind A (vice versa)
A DNA double helical structure has two grooves:
minor
groove and major groove (large groove)
Type of DNA:
o Stout
o Would normally contain 11 base pairs which is why it
appears to be stout
A-DNA
Type of DNA:
The principal form of DNA that occurs in nature
B-DNA
Type of DNA:
o The helix winds upward to the right
o Would normally contain about 10 base pairs
B-DNA
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:
34 angstroms or 3.4 nanometer
3.4 angstroms or 0.34 nm apart
in B-DNA
The inside diameter is:
the outside diameter is :
The inside diameter is: 1.5nm or 11 angstroms
the outside diameter is :
20 angstroms or 2.0 nm
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
True
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
Z-DNA
o Would normally have less base pairs per turn of the helix
Z-DNA
Important in the structure as it would impart stability
Base Pairing
BASE PAIRING:
two hydrogen bonds form what pair
three hydrogen bonds form what pair
A and T pair
G and C pair
Which would be more stable? Which would require
more energy to break?
G and C pair
TRUE OR FALSE:
Sugar phosphate backbone are always at the inner
sides/ region of the double helical structure
FALSE
always at the outer
sides/ region of the double helical structure
It forms the double helical structure in its anti-parallel
direction
• DNA is coiled around proteins called
HISTONES
Coiling refers to what type of structure
Tertiary structure
rich in the basic amino acids Lys and Arg,
whose side chains have a positive charge.
Histones
The negatively-charged DNA molecules and positively charged
histones attract one another and form units called
nucleosomes (11 nm size)
A core of eight histone molecules around
which the DNA helix is wrapped
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.
Nucleosomes are further condensed into
Chromatin
are organized into loops, and the loops into the bands that provide the superstructure
of chromosomes.
Chromatin fibers
OTHER SUPERSTRUCTURES:
Six nucleosomes per turn
Slenoid (30nm)
OTHER SUPERSTRUCTURES:
50 turns per loop
Loops (250nm)
OTHER SUPERSTRUCTURES:
18 loops
Miniband (840nm)
OTHER SUPERSTRUCTURES:
Stacked minibands
Chromosome (840nm)
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)
true
replication yields two molecules of this that is identical to the original one, ensuring transmission of genetic information to daughter cells with exceptional fidelity
Replication
The sequence of bases in DNA is recorded as a sequence of complementary bases in single-stranded mRNA molecule
Transcription
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
Translation
Type of RNA:
Small
Transports amino
acids to site of protein
synthesis
Transfer
RNA (tRNA)
Type of RNA:
Several kinds, variable in size
Combines with
proteins to form
ribosomes, the site of
protein synthesis
Ribosomal RNA
rRNA
Type of RNA:
variable in size
Directs amino acid
sequence of proteins
Messenger RNA
(mRNA)
carry the genetic information from
the DNA in the nucleus directly to the cytoplasm, where most of the
protein is synthesized.
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.
Small nuclear
RNA (snRNA)
Type of RNA:
Small
Affects gene
expression; used by
scientists to knock out
a gene being studied
Small interfering
RNA (siRNA)
Type of RNA:
Small
Affects gene
expression, important
in growth and development
Micro RNA (miRNA)
Type of RNA:
variable in size
Involved in activating
or silencing specific
genes
Long non-coding
RNA (lncRNA)
Type of RNA:
Small
Protects animal
genomes against
transposons
Piwi-associated RNA
Type of RNA:
Variable in size
Acts as miRNA
sponge, controlling
the effects of miRNA
Circular RNA
Created by
alternative splicing of introns
The smallest kind of the three RNAs
Transfer RNA (tRNA)
A single stranded polynucleotide chain between 73-94
nucleotide residues
Carries an amino acid at its 3’ end
Transfer RNA (tRNA)
Anticodon loop contains the
tRNA – trinucleotide
sequence that is complementary to the codons that will be
found in the messenger RNA
In prokaryotes, ribosomes assume a __ shape upon
undergoing lysis and fractionation
70S (Svedberg)
In eukaryotes, there are two ribosomal subunits that are
both made up of __ and ___
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
a unit that measures how
fast molecules move in a centrifuge
Svedberg (S)
Segment of DNA that carries a base sequence that directs
the synthesis of a particular protein, tRNA, or mRNA
Genes
Bacterial genes:
Higher organisms:
Bacterial genes: Continuous
Higher organisms: Discontinuous
Section of DNA/ A gene that codes for a protein or RNA
Exons
A gene that Does not code for anything functional
Introns
transcription and translation in prokaryotes
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
Exons are joined together in a mature mRNA strand by
removing or splicing introns out of the equation since they
are noncoding, intervening sequences
intervening sequences in gene
Introns
The DNA in the chromosomes carries out two functions:
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)
Replication begins at a point in the DNA called the origin of
replication or
Replication fork
(the point at which new DNA
strands are formed)
Replication fork
the protein whose
binding prepares for the start of DNA replication in
eukaryotes
Replication activator protein (RAP)
- DNA to DNA through the action of
DNA polymerase
DNA replication
RNA back to DNA
Reverse Transcription
DNA to RNA
Transcription
When RNA is converted to proteins
(amino acids) through the actions of or facilitated by
ribosomes (site of protein synthesis)
Translation
There is the participation of ribosomes and mRNA
a double helical structure that consists of the 3’
and 5’ strands in a spiral that are antiparallel
DNA
TRUE OR FALSE Base pairing can be seen and are stabilized by the
Hydrogen bonding
TRUE
3 H-bond stabilize the C-G base pair
2 H-bond stabilize the A-T base pair
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)
Semiconservative type of replication
Two cells have retained one of the original template
strand and one of the new strand that will combine
with the leading strand.
Semiconservative Replication
One of the other parent strand (lagging strand),
another new strand will partner with this one
(complementary base pairing)
Semiconservative Replication
From a single parent strand, form two new daughter
strand and that is what you call
l semiconservative
replication.
When DNA molecules are replicated, the strands are
separated at
Origin of replication / replication fork
Synthesis occurs in both directions in the point of replication along the replication ofrl that’s why we call it
Occurs only in prokaryotes
bidirectional
it is semi discontinuous
DNA replication wherein all synthesis of nucleotide
chains occurs in what
direction from the perspective of the chain being
synthesized
5’ to 3’
direction
The three hydroxyl group at the end of the growing
chain acts 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
This enzyme will continuously add bases
DNA polymerase III
DNA polymerase synthesizes one
strand ____ and the other one ____
Continuously
Discontinuously
that’s why we say semiconservative and semi
discontinuous type of DNA replication
Lagging
strand
Complementary strand
3”
synthesize discontinuously
semi discontinuous replication
Leading strand
5”
Synthesize continuously
Okazaki fragment is formed in the
lagging strand
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
Okazaki fragment
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
true
How many DNA polymerase exists in e.coli (gram negative coli) and most commonly used bacteria (and prokaryotes in general)
5 DNA polymerase
Polymerase that is the principal enzyme responsible for
synthesis of new DNA or daughter strand of DNA –
multisubunit enzyme
Polymerase 3
Polymerase that is involved in proofreading and repair
processes
Polymerase 1,2
TRUE OR FALSE
not all DNA requires RNA primer
FALSE
All DNA requires RNA primer
DNA in prokaryotes are ____: 2 replication forks that
advance in opposite direction (to the right and left reference point is the origin of replication)
bidirectional
Types of replications:
o Semiconservative replication (standard)
o Semidiscontinous replication
o Bidirectional
Present in prokaryotes
enzyme that
introduces a swivel point in advance to the
movement of the replication fork/ helix destabilizing protein
DNA gyrase
enzyme that
binds at the replication fork and it will
unwind since its twisted
Alpha-Helixase
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
Alpha-Helixase
enzyme that
catalyzes the synthesis of an
RNA primer – all synthesis requires a RNA primar
(important in DNA replication)
primase
enzyme that
Synthesis of the 2 strands, 2 newly synthesized strand is catalyzed by
polymerase 3
enzyme that
removes the primer which also replaces
the primer with deoxynucleotide (sugar present is
deoxyribose)
Polymerase 1
enzyme that
joins or seals the gap/nics
DNA ligase
This
reaction eliminates some of the positive charges on
histones and weakens the strength of the DNAhistone interaction
process of acetylation-deacetylation of lysine residue on histones
In first step of replication –opening up the superstructure of the chromosomes
proteins attached to nucleic acids
histones
Opening up the superstructure of the
chromosome would require
acetylation and
deacetylation of the lysine residue of histone
This is the first step that
happens during DNA replication
the DNA-histone interaction.
acetylation and
deacetylation of the lysine residue of histone
Enzyme that
relaxes the supercoiling, since it is twisted (double
helical), by breaking the strands.
Tropoisomerases / DNA gyrases
2nd step of DNA replication
Relaxation of Higher-Order Structures of DNA.
Tropoisomerases(also called gyrases) temporarily
introduce either single-or double strand breaks in DNA
3rd step of DNA replication
Replication of DNA molecules starts with the unwinding of
the double helix which can occur at either end or in the
middle.
Special unwinding proteins (enzymes) that attach themselves to one DNA strand and cause the separation of the double helix.
Helicases
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,
DNA gyrase / Tropoisomerase
Enzyme that
induce strand separation causing unwinding of the strands
Helicases
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
Single-stranded binding proteins (SSB)
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
DNA ligase
Enzyme that
primes the synthesis of the lagging strand by the
formation of a primer.
Primase
Enzyme that
removes primer
(Replaces the primer with deoxyribonucleotide)
polymerase 1
Enzyme that
helps in the synthesis of new strands;
this enzyme catalyzes the synthesis of new strands.
polymerase 3
The primer and the protein at the
replication fork, as a whole is called
primosome
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
Replisome
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.
Primers/primase
The enzyme enables complementary
base pairing with high specificity. While bases are
being hydrogen bonded to their partners,
polymerases join the nucleotide backbones.
DNA polymerase
fragments consist of about 200 nucleotides each, named
Okazaki fragments
TRUE OR FALSE
Along the lagging strand 3’—>5”, the enzymes can
synthesize long fragments
FALSE
Along the lagging strand 3’—>5”, the enzymes can
synthesize only short fragments
The Okazaki fragments and any nicks remaining are
eventually joined by
DNA ligase.
How do you add now the nucleotides from a growing
DNA chain?
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.
Process involved in DNA amplification
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).
In using PCR to amplify DNA, what must be known
the sequence of a gene / sequenced segment bordering
are polynucleotides consisting of
12 to 16 nucleotides
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)
What happens in PCR – DNA amplification
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.)
Enzyme used in PCR that can tolerate high temperatures since it is isolated from a hieat-tolerant bacteria
taq DNA polymerase
TRUE OR FALSE
DNA replication in eukaryotes is similar to DNA replication
in prokaryotes.
TRUE
Difference in DNA replication of eukaryotes and prokaryotes
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
Cell division cycle:
preparation of cell to divide
G1 phase
Cell division cycle:
organizes and condenses the genetic material
G2 phase
Cell division cycle:
where DNA replication occurs
o S phase
Cell division cycle:
complete cell division
M Phase
what are the o 5 DNA polymerases
α (alpha), β (beta), γ (gamma), θ (theta), and ε (epsilon)
Type of DNA polymerase:
the principal synthesizer of DNA and
is equivalent to Polymerase III in prokaryotes
Polymerase γ
Viability of cells depend on them
they can can
detect, recognize, and remove mutations from DNA
DNA repair enzymes
Due to these, there can be mutations when it
comes to base pairing
Due to wear and tear
TRUE OR FALSE
Polymerases never make mistakes when it comes to proofreading the bases and codons
FALSE
Sometimes in the proofreading of bases and codons, the
polymerases may commit mistakes resulting int
spontaneous mutation
Mutation that is the Result of error in natural or biological processes
o It is a natural occurrence
spontaneous mutation
Common spontaneous mutations are due to
depurination and deamination –
(removal of amine groups) of the pyrimidine and purine
bases
Two types of Mutation
Spontaneous Mutation
Induced Mutation
Mutation that is Due to external agents in the environment causing changes
in DNA structures
Induced Mutation
External agents that causes induced mutation
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
MUTAGEN – agents that may cause damage to the bases
High-oxidizing agents such as hydrogen peroxide,
superoxide anion(free radical), hydroxyl radicals and
peroxyl radicals
MUTAGEN –
an intercalating
agent from charred portions of broiled meat or fish that
can insert itself in DNA base pairing
benzo-a-pyrene (Chemical agent)
MUTAGEN:
toxin present in moldy peanuts
Aflaxtoxins
TRUE OR FALSE :
There are cases when mutations may be reversed back
and structures go back to their native conformation, which makes them unstable
true
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
depurination
Cause of spontaneous mutation:
Errors in copying or internal chemical reactions can create damage internally
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
most common base repairs means
BER, base excision repair.
there are two pathways by which the BER exist and by
which DNA is repaired:
Specific DNA ???
Synthesis step – Enzyme DNA
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
Glycolase
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)
DNA Polymerase (Pol III)
types of gene mutation
Point mutation Missense mutation Silent mutation Nonsense mutation Frameshift mutation Transversion
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
Point mutation
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
Missense mutation
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
Silent mutation
Type of gene mutation:
if the mRNA codon becomes a stop codon produce truncated and frequently nonfunctional proteins
Nonsense mutation
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
Frameshift mutation
Type of gene mutation:
refers to a purine being
replaced by a pyrimidine
or vice versa
Transversion
BER pathway: what enzyme
at the AP site (apurinic or apyrimidinic site)
created in this way, the backbone is cleaved
by this enzyme
endonuclease
BER pathway: what enzyme
liberates the
sugar-phosphate unit of the damaged site
exonuclease
BER pathway: what enzyme
seals the backbone
to complete the repair
DNA ligase
The information that determines external characteristics
(red hair, blue eyes) and internal characteristics (blood group,
hereditary diseases) was thought to reside in
genes
TRUE OR FALSE:
not all genes lead to the production of
protein
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).
TRUE OR FALSE:
Both DNA and RNA are polymers
TRUE
The bases found in DNA and RNA are
heterocyclic aromatic amines
When phosphoric acid froms a phosphate ester bond with a nucleoside
nucleotide
Polymers composed
of nucleotides
Nucleic acids
The backbone in DNA consists
of alternating
deoxyribose and phosphate groups
the bases form this type of interaction which stabilizes the double helix
bases are hydrophobic and forms hydrophobic interaction to stabilize the double helix
A/T could not fit with G/C because
it forms much weaker hydrogen bonding
a pyrimidine must always opposite a purine
distinguishing feature of the B-DNA
major and minor groove
arise because the two strands are not
equally spaced around the helix
major and minor groove
Interactions of proteins and drugs with the
major and minor grooves of DNA serve as an active area of research.
the force of attraction that exists between nucleosome (DNA-histone)
electrostatic (ionic) forces
An RNA that consists of a chain of nucleotides
whose sequence is exactly complementary to that of one of the
strands of the DNA
mRNA
Small spherical
bodies in the cell made of protein
and RNA; the site of protein
synthesis
Ribosomes
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.
miRNA
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
siRNA
type of RNA that is
subtle control mechanism for miRNA’s own control
of transcription
Circular RNA
Replication begins at a point in the DNA called an
The point
on the DNA where replication proceeds is called the
Origin of replication
Replication fork
Primer is made up of
RNA
These
assemblies of enzyme “factories” go by the name of
Replisomes
Complex of DNA polymerase and primer and proteins in replication fork
they
contain key enzymes such as polymerases, helicases, and primases
Enzyme that is also involved in the
untangling of the replicated chromosomes, before cell division can occur.
Topoisomerase / gyrase
Enzyme that hydrolyzes ATP as the DNA strand
moves through. The energy of the hydrolysis promotes this movement.
Helicase
