The document discusses DNA replication in bacteriophages and eukaryotes. In bacteriophages, rolling circle replication produces long concatemers that are then cleaved by an endonuclease into individual linear genomes. Eukaryotic replication differs from prokaryotes in that eukaryotes have multiple chromosomes, linear chromosomes with telomeres, and nucleosomes. Telomeres are replicated by the reverse transcription of an RNA template by telomerase. Nucleosomes are replicated through the addition of new histone proteins to accommodate the packaging of two genomes.
The current presentation talks about the mechanism of eukaryotic replication with emphasis on replicative control along various phases of Cell Cycle. The current presentation also gives a detailed insight on Hefick's limit and the functionality of telomerase.
DNA replication is a semiconservative process. It means that each strand acts as a template for the synthesis of a new complementary strand. Therefore, this process takes us from one parent molecule to two daughter molecules, with each newly formed double helix containing one new and one old strand.
The current presentation talks about the mechanism of eukaryotic replication with emphasis on replicative control along various phases of Cell Cycle. The current presentation also gives a detailed insight on Hefick's limit and the functionality of telomerase.
DNA replication is a semiconservative process. It means that each strand acts as a template for the synthesis of a new complementary strand. Therefore, this process takes us from one parent molecule to two daughter molecules, with each newly formed double helix containing one new and one old strand.
DNA organization or Genetic makeup in Prokaryotic and Eukaryotic SystemsBir Bahadur Thapa
DNA organization or Genetic makeup in Prokaryotic and Eukaryotic Systems!! It is prepared under the syllabus of Tribhuwan University, Nepal, MSc. 3rd Semester as a lecture class!!
1.) What does “exonuclease” activity mean Which enzyme important fo.pdfnaveenkumar29100
1.) What does “exonuclease” activity mean? Which enzyme important for DNA polymerization
has both 5’ – 3’ AND 3’ – 5’ exonuclease activity? Which is important for proofreading
function?
2.) How are the site(s) where replication begin(s) is/are characterized as in both prokaryotes and
eukaryotes? What is beneficial about this? Are the sites the same in prokaryotes and eukaryotes?
3.) Arrange the following proteins in the proper order in which they participate in DNA
replication.
1 = Primase
2 = Helicase
3 = Single-strand binding proteins
4 = DNA polymerase I
5 =DNA polymerase III
4.) When does DNA replicate in the cell cycle of eukaryotes and prokaryotes?
5.) Why are Okazaki fragments only found on the lagging strand, but not on the leading strand of
DNA?
6.) What protein transports the histones of Nucleosomes into the nucleus?
7.) Describe the differences between Topoisomerase I and Topoisomerase II.
8.) During DNA replication, ___________ adds an RNA primer to naked template strands of
DNA. Why is this necessary during replication? What fills the gap after removal of this RNA
primer?
9.) What is the problem with the ends of linear eukaryotic chromosomes? How does telomerase
help the issue?
Solution
1. Exonuclease activity means that enzymes work by cleaving nucleotides one at a time from the
end (exo) of a polynucleotide chain. A hydrolyzing reaction breaks phosphodiester bonds at
either the 3’ or the 5’ ends.
DNA polymerase I is the enzyme important for DNA polymerization and has both 5’ – 3’ and 3’
– 5’ exonuclease activity, which is used in editing and proofreading DNA for errors. The 3\' to 5\'
can remove only one mononucleotide at a time, whereas the 5\' to 3\' activity can remove up to
10 nucleotides at a time.
2. Sites from which the process of replication starts are different in prokaryotes and Eukaryotes.
Prokaryotes have only one origin of replication per DNA molecule, whereas in ekaryotes, there
are multiple sites for origin of replication.
To initiate DNA replication in Eukaryotes, multiple replicative proteins assemble on and
dissociate from these replicative origins. DNA double helix is unwound and an initial priming
event by DNA polymerase occurs on the leading strand.To initiate the process of DNA
replication, multiple replicative proteins assemble on and dissociate from these replicative
origins. The individual factors work together to direct the formation of the pre-replication
complex (pre-RC), a key intermediate in the replication initiation process.
In case of prokaryotes, Helicase separates the DNA to form a replication fork at the origin of
replication where DNA replication begins. Replication forks extend bi-directionally as
replication continues. The initiation of DNA replication is mediated by DnaA, a protein that
binds to a region of the origin known as the DnaA box. E. coli, has 4 DnaA boxes, each of which
contains a highly conserved 9 bp consensus sequence 5\' - TTATCCACA - 3\'.
3. Enzymes that participate in DNa.
DNA replication is the most important process central dogma in the molecular genetics. So i hope this power point presentation useful to the students of B.Sc Agriculture and M.Sc Genetics and Plant Breeding.
The material of a talk that I prepared to give in the online camel conference of Oman. Unfortunately, I had a death in the family the day before the conference and the material was presented by my friend Dr. Mohammed Alabri from Oman. The material is in Arabic and focused for camel breeders.
The material of a two days workshop that I gave at Sultan Qaboos University in Oman about the importance of livestock biobanks and how to establish an organized one. The workshop was given in Arabic.
A presentation as a webinar for the Winn Feline Foundation that focuses on recent findings related to the signatures of selection in the domestic cat genome
This was my presentation at the Plant and Animal Genome Conference 2019 in San Diego. My talk was a presentation of the thesis project of my student Mona Abdi. The focus of the presentation and project was the genomic signatures of selection in the domestic cat breeds.
This is a my lecture about camels title "Journey around the camel". The lecture was in Arabic and is related to a book under preparation with the same title. This part of the journey around the camel introduces the major camel breeds in the Arabian Peninsula and their external phenotypes and groupings.
This lecture covers some nice stories about the origins of the words "genome" and the derived word "genomics". the lecture also introduces viral, bacterial, and eukaryotic genomes.
This lecture covers key findings to the development of genomics as a field. This first part covers briefly Mendel to knowing that DNA is the genetic material by Hershey and Chase
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
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.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
3. AIMS
• Understand the replication in bacteriophage and
the benefits of such replication method for the
virus.
• Understand the DNA replication in eukaryotes
and how it differs from that of prokaryotes.
• Learn the names of the enzymes in the
replication of eukaryotic genome and their
equivalent in prokaryotes.
• Understand how the differences in the replication
of eukaryotic DNA is fixed.
4. Replication in phages
• Bacteriophage (lambda λ): has a
linear genome (ds DNA) enclosed a
protein body.
• The linear genome contains sticky
ends/overhang (single strand DNA
on each end).
In phage body In host cell
5. Replication in phages
• The sticky ends are complementary to each
other.
• When the linear DNA of a phage is injected
into a host cell, the sticky ends complement
each other to make a circular DNA.
In phage body In host cell
6. Rolling circle replication
1. Generate a nick (cut) in one
of the strands at Ori.
2. The 5’ end is displaced with
SSB.
3. The free 3’ end of the nick
acts as a primer for DNA
polymerase.
7. Rolling circle replication
4. The single stand segment
of the circular DNA acts as a
template (what kind?).
5. Displaced single strand
DNA rolls out as a free
tongue as the replication go
forward.
6. This rolls multiple times
which generates many copies
of the linear phage genome
all as a single molecule.
8. Replication in phages
Result of the rolling circle replication is
multiple copies of the virus DNA in one linear
molecule called concatemer.
Concatemer
Cos sequence
9. Replication in phages
• An Endonuclease comes to cut the
concatemer into multiple genomes.
• The endonuclease binds to a specific sequence
called Cos sequence and cuts DNA generating
sticky ends.
• Each linear genome gets packaged into a
protein body to make the progeny of phages.
Concatemer
Cos sequence
10. Finishing phage genome
Endonuclease cuts the concatemer at the Cos
sequence to generate multiple linear copies of the
genome
Endonuclease cut sites
12. Replication in Eukaryotes
Prokaryotes Eukaryotes
1. Single chromosome
2. Circular chromosome
3. Chromosomes with
NO ends
4. Small genome
5. No nucleosomes
1. Multiple chromosomes
2. Linear chromosomes
3. Chromosomes with ends
4. Large genome
5. Nucleosome packaging
13. Replication in Eukaryotes
Difference #1: prokaryotes have a single origin of
replication but eukaryotes have many.
• Many chromosomes ➔ need many origins of
replication.
• Large genome ➔ need many origins of
replication.
14. Replication in Eukaryotes
Why many Oris in Eukaryotes?
• E.coli genome is ~5Mb and the replication rate is
very fast (1000bp/s).
• Human genome is ~3Gb and replication rate is
slower (100 bp/s). To solve this (many replicons).
Ori
Replicon Replicon
One
Replicon
15. Initiation of replication
• DNA replication in eukaryotes start at a sequence
called autonomously replication sequence
(ARS).
What is the equivalent in prokaryotes?
• Initiation protein in eukaryotes is a multiunit
complex called origin recognition complex
(ORC).
What is the equivalent in prokaryotes?
17. Replication in Eukaryotes
Differences in the names of the enzymes
Prokaryotes Eukaryotes
Primase
DNA Pol III
Pol I
Ligase
Pol (α) alpha
Pol (ε) epsilon
Pol (δ) delta
Eukaryotic Ligase
18. Replication in Eukaryotes
Difference #2: circular chromosome in prokaryote
and linear chromosomes in eukaryotes.
Eukaryotic chromosomes are linear and have ends
called telomeres.
19. Replication in Eukaryotes
New
Replication
Remove primers
5’
5’
Overhang
Overhang
DNA Pol can not add nucleotides without
3’OH
If this does not get fixed chromosomes will
get shorter every time DNA is replicated
20. Solution: Telomere replication
• End of the chromosome (telomere) has a
specific sequence of repeats.
• Telomere repeat sequence in human is 5’
TTAGGG 3’.
• A specific enzyme called Telomerase
recognizes the repeat sequence (How?)
• Telomerase is an enzyme composed of:
• Protein (polymerase)
• RNA (template)
21. Solution: Telomere replication
• The RNA part of the telomerase is
complementary to the repeat sequence of the
telomere and acts as a template to regenerate
the ends of the chromosomes.
• The addition of repeat sequences happens
multiple times to extend the telomeres.
23. Some Terms
• The process of making DNA from DNA template
is called Replication.
• The process of making RNA from DNA template
is called Transcription.
• The process of making DNA from RNA template
is called Reverse Transcription.
So what is the process in which telomerase
acts?
24. Nucleosome replication
• Nucleosomes are parts of DNA condensation in
eukaryotes.
• 8 histone (octamer) proteins make a one
nucleosome.
• H2A/H2B make one dimer while H3/H4 make the
second dimer.
How many dimers in a single nucleosome?
Difference #3: eukaryotic DNA is wrapped around
nucleosomes.
25. Nucleosome replication
• When replicating DNA the histones are removed
to allow for the replication of DNA.
• When replication is done double the amount of
nucleosomes needs to added to the old and
newly replicated DNA.
So we need more histones, what do we do?
26. Nucleosome replication
• More histone proteins are made to
accommodate the organization of two
genomes.
• Nucleosomes are made of new and old dimers.
• On each genome different combination of
dimers are generated:
New/new New/old Old/old
28. To study
Histone chaperone
Telomere
Telomerase
Pol (α)
Pol (ε)
Pol (δ)
Rolling circle replication
Cos sequence
Endonuclease
Concatemer
H2A/H2B dimer
H3/H4 dimer
Replication
Transcription
Reverse Transcription
Replicon
ARS
ORC
29. Expectations
• You know the replication process in bacteriophage.
• You know that replication process in prokaryotes is
similar to that of eukaryotes with some differences.
• You know the differences between eukaryotic and
prokaryotic replication process and link this to the
differenced in genome characteristics.
• You know the differences in enzyme names.
• You know how the ends of chromosomes are
replicated.
• You know how nucleosomes are replicated.
