DNA replication involves unwinding the double helix at the replication fork, synthesizing new strands in a semi-conservative manner, and joining fragments. It is semi-conservative, with each parental strand serving as a template for a new daughter strand. Replication is bidirectional and occurs continuously on the leading strand but discontinuously on the lagging strand, which is synthesized in fragments called Okazaki fragments. The process involves initiation at the origin of replication, unwinding and stabilizing the strands, primer formation, strand elongation, fragment joining, and termination.
DNA replication is the process by which DNA makes a copy of itself during cell division.The separation of the two single strands of DNA creates a 'Y' shape called a replication 'fork'. The two separated strands will act as templates for making the new strands of DNA.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
DNA replication is the process by which DNA makes a copy of itself during cell division.The separation of the two single strands of DNA creates a 'Y' shape called a replication 'fork'. The two separated strands will act as templates for making the new strands of DNA.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
2. How does DNA Replicate?
• The data collected by Meselson and Stahl were consistent with
the SEMICONSERVATIVE model of replication.
– Remember, this was the model that was suggested by the
complementary structure of DNA molecules.
– The real beauty of the Meselson-Stahl experiment was the fact that
they could distinguish among all possible models.
Conservative Semiconservative Dispersive
3. Features of DNA Replication
• DNA replication is semi-conservative
– Each strand of template DNA is being copied.
• DNA replication is bidirectional
– Bidirectional replication involves two replication forks,
which move in opposite directions
• DNA replication is semi-discontinuous
– The leading strand copies continuously
– The lagging strand copies in segments (Okazaki
fragments) which must be joined
4. Steps in DNA Replication
• Replication involves 3 stages:
- initiation
- elongation
- termination
• Replication begins at site called origin of
replication
- 1 in prokaryotes
- numerous in eukaryotes
5. • Opening DNA double helix
– initiating replication
– unwinding duplex
– stabilizing single strands
– relieve torque
• Building a primer
• Assembling complementary strands
• Removing the primer
• Joining Okazaki fragments
Replication Process
6. Overview
1. An initiator protein binds to and separates the strands at the
replication origin
2. Helicase separates the strands at the replication fork
3. Gyrase relieves supercoiling as it develops
4. Primase creates a short RNA primer
5. DNA polymerase III extends the strand
6. DNA polymerase I replaces the RNA primer with DNA
7. Ligase repairs missing phosphodiester bonds between fragments
7. Replication as a process
• Double-stranded DNA unwinds.
The junction of the unwound
molecules is a replication fork.
A new strand is formed by pairing
complementary bases with the
old strand.
Two strands are made.
Each has one new and one old
DNA strand.
8. The process of DNA Replication
• Unwinding of DNA with helicase: Unwinding
a portion of the DNA double helix using energy
derived from ATP
• Binding Single-stranded proteins :Keeps the
unwound DNA strands from re-annealing
• Gyrases: Eliminates super coiling that
accompanies unwinding removes torsion strain
by opening double helix.
9.
10. The process of DNA Replication
• RNA Primase: Attaches RNA primers (5-15 bp) on
to DNA template to initiate DNA synthesis. Initiation
of okazaki fragment on lagging strand by primosome-
a protein complex contain DNA primase and DNA
helicase.
• DNA Polymerase delta (ð): Binds to the 5' - 3'
strand in order to bring nucleotides and create the
daughter leading strand.
11. The process of DNA Replication
• DNA Polymerase epsilon (å): Binds to the 3' - 5'
strand in order to create discontinuous segments starting
from different RNA primers.
Exonuclease (DNA Polymerase I): Finds and
removes the RNA Primers
DNA Ligase: Adds phosphate in the remaining gaps of
the phosphate - sugar backbone
Nucleases: Remove wrong nucleotides from the
daughter strand
12. Initiation
• Initiator protein (Dna A) is responsible for
intial step in unwinding the helix, binds to the
origin and separates strands
13. A eukaryotic chromosome have hundreds or even
thousands of replication origins
Replication begins at specific sites
where the two parental strands
separate and form replication
bubbles.
The bubbles expand laterally, as
DNA replication proceeds in both
directions.
Eventually, the replication
bubbles fuse, and synthesis of
the daughter strands is
complete.
1
2
3
Origin of replication
Bubble
Parental (template) strand
Daughter (new) strand
Replication fork
Two daughter DNA molecules
In eukaryotes, DNA replication begins at many sites along the giant
DNA molecule of each chromosome. In this micrograph, three replication
bubbles are visible along the DNA of
a cultured Chinese hamster cell (TEM).
(b)
(a)
0.25 µm
14. Replication fork
1. As the strands of DNA
unwind, an area of
replication called the
replication fork is
created
2. As nucleotides are
added, the replication
fork moves down the
parental strand
3. Replication is completed
when the replication
fork reaches the end of
the parent strand
17. DNA polymerases
• Add nucleotides against a DNA template to the 3' end of
the growing strand (5’3’ growth)
Requirements
1. A template
2. Deoxyribonucleoside
triphosphates which
serve both as the
source for the
nucleotide and as
the energy source
3. A primer
18. Primase
• DNA polymerase needs a primer
• Short bits of RNA serve as the primer
• The primer is added by a DNA-dependent RNA
polymerase called primase
• RNA polymerases are different from DNA
polymerases as they can initiate a new strand
based on a template strand
19. Primer
• Only one primer is needed for synthesis of
the leading strand
– But for synthesis of the lagging strand, each
Okazaki fragment must be primed separately
20. Type I Topoisomerases
• One strand is
“nicked,” allowing
the remaining intact
phosphate backbone
to twist under
torsion
• The nicked strand is
then rejoined
• No net energy
expenditure
21. DNA polymerase I
(α in eukaryotes)
• Does all the stuff DNA poly III does
– 5‘3' polymerase
– 3‘5' exonuclease
• Also a 5‘3' exonuclease
– removes damaged bases
– removes primers
• Slower than DNA poly III. abundant
22. DNA polymerase III
(δ in eukaryotes)
The main polymerase in bacteria consists of 10 peptide sub
units
5‘3' polymerase
3‘5' exonuclease for proof reading
23. Elongation of DNA Replication
• DNA polymerase binds to 3'-end of RNA primer
- makes DNA in 5' --> 3' direction
- slides along template strand in 3' --> 5'
direction
• Elongation can occur continuously on one of the
template strands as helix opens in front of it
- strand with continuous replication is called
leading strand
24. Termination of DNA Replication
• RNA primers removed from newly
synthesized DNA molecules and replaced
by DNA
• DNA ligase seals gaps between these
fragments
27. Figure 16.16
Overall direction of replication
Leading
strand
Lagging
strand
Lagging
strand
Leading
strand
OVERVIEW
Leading
strand
Replication fork
DNA pol III
Primase
Primer
DNA pol III Lagging
strand
DNA pol I
Parental DNA
5
3
4
3
2
Origin of replication
DNA ligase
1
5
3
Helicase unwinds the
parental double helix.
1
Molecules of single-
strand binding protein
stabilize the unwound
template strands.
2 The leading strand is
synthesized continuously in the
5 3 direction by DNA pol III.
3
Primase begins synthesis
of RNA primer for fifth
Okazaki fragment.
4
DNA pol III is completing synthesis of
the fourth fragment, when it reaches the
RNA primer on the third fragment, it will
dissociate, move to the replication fork,
and add DNA nucleotides to the 3 end
of the fifth fragment primer.
5
DNA pol I removes the primer from the 5 end
of the second fragment, replacing it with DNA
nucleotides that it adds one by one to the 3 end
of the third fragment. The replacement of the
last RNA nucleotide with DNA leaves the sugar-
phosphate backbone with a free 3 end.
6
DNA ligase bonds
the 3 end of the
second fragment to
the 5 end of the first
fragment.
7
A summary of DNA replication