1. DNA repair is a collection of processes by which cells identify and correct damage to DNA molecules to maintain the integrity of the genome.
2. There are several pathways of DNA repair including base excision repair, nucleotide excision repair, mismatch repair, non-homologous end joining, and homologous recombination.
3. Defects in DNA repair pathways can lead to increased mutations, cancer, and cell death if damage is left unrepaired.
N-terminal tails of histones are the most accessible regions for modifications. These post-translational modification (PTM) of histones is a crucial step in epigenetic regulation of a gene.
N-terminal tails of histones are the most accessible regions for modifications. These post-translational modification (PTM) of histones is a crucial step in epigenetic regulation of a gene.
Each day the genome is subjected to thousands of DNA damaging events from diverse sources which can have potentially deleterious consequences. In order to maintain genome integrity eukaryotic cells have evolved a highly complex and multifaceted response network called the DNA damage response, or ?DDR?....
Each day the genome is subjected to thousands of DNA damaging events from diverse sources which can have potentially deleterious consequences. In order to maintain genome integrity eukaryotic cells have evolved a highly complex and multifaceted response network called the DNA damage response, or ?DDR?
Each day the genome is subjected to thousands of DNA damaging events from diverse sources which can have potentially deleterious consequences. In order to maintain genome integrity eukaryotic cells have evolved a highly complex and multifaceted response network called the DNA damage response, or ?DDR?....
Each day the genome is subjected to thousands of DNA damaging events from div...semualkaira
Each day the genome is subjected to thousands of DNA damaging events from diverse sources which can have potentially deleterious consequences. In order to maintain genome integrity eukaryotic cells have evolved a highly complex and multifaceted response network called the DNA damage response, or ?DDR?..
Each day the genome is subjected to thousands of DNA damaging events from diverse sources which can have potentially deleterious consequences. In order to maintain genome integrity eukaryotic cells have evolved a highly complex and multifaceted response network called the DNA damage response
Describe the repair mechanisms used during DNA replication.Soluti.pdfkellenaowardstrigl34
Describe the repair mechanisms used during DNA replication.
Solution
DNA like any other molecule can undergo a variety of chemical reactions. Because DNA
uniquely serves as a permanent copy of the cell genome, however, changes in its structure are of
much greater consequence than are alterations in other cell components, i.e RNA’s and Proteins.
Mutations can consider the incorporation of incorrect bases during DNA replication. And also,
various chemical changes occur in DNA either spontaneously or as a result of exposure to
chemicals or radiation. Such damage to DNA can block replication or transcription, and can
result in a high frequency of mutations—consequences that are unacceptable from the standpoint
of cell reproduction.
To maintain the integrity of their genomes, cells have therefore had to evolve mechanisms to
repair damaged DNA. DNA repair mechanism can be divided into two general classes: (1) direct
reversal of the chemical reaction responsible for DNA damage, and (2) removal of the damaged
bases followed by their replacement with newly synthesized DNA. The rate of DNA repair is
dependent on many factors, including the cell type, the age of the cell, and the extracellular
environment. A cell that has accumulated a large amount of DNA damage, or one that no longer
effectively repairs damage incurred to its DNA, can enter one of three possible states:
1. an irreversible state of dormancy, known as senescence
2. cell suicide, also known as apoptosis or programmed cell death
3. unregulated cell division, which can lead to the formation of a tumor that is cancerous
The DNA repair ability of a cell is vital to the integrity of its genome and thus to the normal
functionality of that organism.
Direct reversal
Cells are known to eliminate three types of damage to their DNA by chemically reversing it.
These mechanisms do not require a template,the types of damage they counteract can occur in
only one of the four bases. Such direct reversal mechanisms are specific to the type of damage
incurred and do not involve breakage of the phosphodiester backbone. The formation of
pyrimidine dimers upon irradiation with UV light results in an abnormal covalent bond between
adjacent pyrimidine bases. The photo reactivation process directly reverses this damage by the
action of the enzyme photolyase, whose activation is obligately dependent on energy absorbed
from blue/UV light (300–500 nm wavelength) to promote catalysis.
The second type of damage, methylation of guanine bases, is directly reversed by the protein
methyl guanine methyl transferase (MGMT),
The third type of DNA damage reversed by cells is certain methylation of the bases cytosine and
adenine.
Excision Repair mechanisms
Single strand damage:
When only one of the two strands of a double helix has a defect, the other strand can be used as a
template to guide the correction of the damaged strand. In order to repair damage to one of the
two paired molecules of DNA, there exist a number of excis.
Introduction
Enzyme involve of DNA repair
Types of DNA repair
direct DNA repair
excision repair system
mismatch repair system
Conclusion
Reference
DNA polymerase –a class of enzyme to all synthesize 5’ to 3’ direction of nucleotides.
DNA polymerase I – a class of enzyme 1st isolated by Escherichia coli, and function is removes of RNA primers ,during DNA replication.
Helicase- any of a group of enzyme that unwind the two strand of DNA to facilitate DNA replication.
Exonuclease – an enzyme capable of cutting phosphodiester bonds between nucleotides located at an end of a DNA strand .
Endonuclease – an enzyme capable of cleaving phosphodiester bonds between nucleotide located internally in a DNA strand .
DNA ligase – a enzyme that fill the gap of nucleotides.
Title: Sense of Smell
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the primary categories of smells and the concept of odor blindness.
Explain the structure and location of the olfactory membrane and mucosa, including the types and roles of cells involved in olfaction.
Describe the pathway and mechanisms of olfactory signal transmission from the olfactory receptors to the brain.
Illustrate the biochemical cascade triggered by odorant binding to olfactory receptors, including the role of G-proteins and second messengers in generating an action potential.
Identify different types of olfactory disorders such as anosmia, hyposmia, hyperosmia, and dysosmia, including their potential causes.
Key Topics:
Olfactory Genes:
3% of the human genome accounts for olfactory genes.
400 genes for odorant receptors.
Olfactory Membrane:
Located in the superior part of the nasal cavity.
Medially: Folds downward along the superior septum.
Laterally: Folds over the superior turbinate and upper surface of the middle turbinate.
Total surface area: 5-10 square centimeters.
Olfactory Mucosa:
Olfactory Cells: Bipolar nerve cells derived from the CNS (100 million), with 4-25 olfactory cilia per cell.
Sustentacular Cells: Produce mucus and maintain ionic and molecular environment.
Basal Cells: Replace worn-out olfactory cells with an average lifespan of 1-2 months.
Bowman’s Gland: Secretes mucus.
Stimulation of Olfactory Cells:
Odorant dissolves in mucus and attaches to receptors on olfactory cilia.
Involves a cascade effect through G-proteins and second messengers, leading to depolarization and action potential generation in the olfactory nerve.
Quality of a Good Odorant:
Small (3-20 Carbon atoms), volatile, water-soluble, and lipid-soluble.
Facilitated by odorant-binding proteins in mucus.
Membrane Potential and Action Potential:
Resting membrane potential: -55mV.
Action potential frequency in the olfactory nerve increases with odorant strength.
Adaptation Towards the Sense of Smell:
Rapid adaptation within the first second, with further slow adaptation.
Psychological adaptation greater than receptor adaptation, involving feedback inhibition from the central nervous system.
Primary Sensations of Smell:
Camphoraceous, Musky, Floral, Pepperminty, Ethereal, Pungent, Putrid.
Odor Detection Threshold:
Examples: Hydrogen sulfide (0.0005 ppm), Methyl-mercaptan (0.002 ppm).
Some toxic substances are odorless at lethal concentrations.
Characteristics of Smell:
Odor blindness for single substances due to lack of appropriate receptor protein.
Behavioral and emotional influences of smell.
Transmission of Olfactory Signals:
From olfactory cells to glomeruli in the olfactory bulb, involving lateral inhibition.
Primitive, less old, and new olfactory systems with different path
Ethanol (CH3CH2OH), or beverage alcohol, is a two-carbon alcohol
that is rapidly distributed in the body and brain. Ethanol alters many
neurochemical systems and has rewarding and addictive properties. It
is the oldest recreational drug and likely contributes to more morbidity,
mortality, and public health costs than all illicit drugs combined. The
5th edition of the Diagnostic and Statistical Manual of Mental Disorders
(DSM-5) integrates alcohol abuse and alcohol dependence into a single
disorder called alcohol use disorder (AUD), with mild, moderate,
and severe subclassifications (American Psychiatric Association, 2013).
In the DSM-5, all types of substance abuse and dependence have been
combined into a single substance use disorder (SUD) on a continuum
from mild to severe. A diagnosis of AUD requires that at least two of
the 11 DSM-5 behaviors be present within a 12-month period (mild
AUD: 2–3 criteria; moderate AUD: 4–5 criteria; severe AUD: 6–11 criteria).
The four main behavioral effects of AUD are impaired control over
drinking, negative social consequences, risky use, and altered physiological
effects (tolerance, withdrawal). This chapter presents an overview
of the prevalence and harmful consequences of AUD in the U.S.,
the systemic nature of the disease, neurocircuitry and stages of AUD,
comorbidities, fetal alcohol spectrum disorders, genetic risk factors, and
pharmacotherapies for AUD.
MANAGEMENT OF ATRIOVENTRICULAR CONDUCTION BLOCK.pdfJim Jacob Roy
Cardiac conduction defects can occur due to various causes.
Atrioventricular conduction blocks ( AV blocks ) are classified into 3 types.
This document describes the acute management of AV block.
Couples presenting to the infertility clinic- Do they really have infertility...Sujoy Dasgupta
Dr Sujoy Dasgupta presented the study on "Couples presenting to the infertility clinic- Do they really have infertility? – The unexplored stories of non-consummation" in the 13th Congress of the Asia Pacific Initiative on Reproduction (ASPIRE 2024) at Manila on 24 May, 2024.
Pulmonary Thromboembolism - etilogy, types, medical- Surgical and nursing man...VarunMahajani
Disruption of blood supply to lung alveoli due to blockage of one or more pulmonary blood vessels is called as Pulmonary thromboembolism. In this presentation we will discuss its causes, types and its management in depth.
These lecture slides, by Dr Sidra Arshad, offer a quick overview of physiological basis of a normal electrocardiogram.
Learning objectives:
1. Define an electrocardiogram (ECG) and electrocardiography
2. Describe how dipoles generated by the heart produce the waveforms of the ECG
3. Describe the components of a normal electrocardiogram of a typical bipolar leads (limb II)
4. Differentiate between intervals and segments
5. Enlist some common indications for obtaining an ECG
Study Resources:
1. Chapter 11, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 9, Human Physiology - From Cells to Systems, Lauralee Sherwood, 9th edition
3. Chapter 29, Ganong’s Review of Medical Physiology, 26th edition
4. Electrocardiogram, StatPearls - https://www.ncbi.nlm.nih.gov/books/NBK549803/
5. ECG in Medical Practice by ABM Abdullah, 4th edition
6. ECG Basics, http://www.nataliescasebook.com/tag/e-c-g-basics
The prostate is an exocrine gland of the male mammalian reproductive system
It is a walnut-sized gland that forms part of the male reproductive system and is located in front of the rectum and just below the urinary bladder
Function is to store and secrete a clear, slightly alkaline fluid that constitutes 10-30% of the volume of the seminal fluid that along with the spermatozoa, constitutes semen
A healthy human prostate measures (4cm-vertical, by 3cm-horizontal, 2cm ant-post ).
It surrounds the urethra just below the urinary bladder. It has anterior, median, posterior and two lateral lobes
It’s work is regulated by androgens which are responsible for male sex characteristics
Generalised disease of the prostate due to hormonal derangement which leads to non malignant enlargement of the gland (increase in the number of epithelial cells and stromal tissue)to cause compression of the urethra leading to symptoms (LUTS
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Lung Cancer: Artificial Intelligence, Synergetics, Complex System Analysis, S...Oleg Kshivets
RESULTS: Overall life span (LS) was 2252.1±1742.5 days and cumulative 5-year survival (5YS) reached 73.2%, 10 years – 64.8%, 20 years – 42.5%. 513 LCP lived more than 5 years (LS=3124.6±1525.6 days), 148 LCP – more than 10 years (LS=5054.4±1504.1 days).199 LCP died because of LC (LS=562.7±374.5 days). 5YS of LCP after bi/lobectomies was significantly superior in comparison with LCP after pneumonectomies (78.1% vs.63.7%, P=0.00001 by log-rank test). AT significantly improved 5YS (66.3% vs. 34.8%) (P=0.00000 by log-rank test) only for LCP with N1-2. Cox modeling displayed that 5YS of LCP significantly depended on: phase transition (PT) early-invasive LC in terms of synergetics, PT N0—N12, cell ratio factors (ratio between cancer cells- CC and blood cells subpopulations), G1-3, histology, glucose, AT, blood cell circuit, prothrombin index, heparin tolerance, recalcification time (P=0.000-0.038). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and PT early-invasive LC (rank=1), PT N0—N12 (rank=2), thrombocytes/CC (3), erythrocytes/CC (4), eosinophils/CC (5), healthy cells/CC (6), lymphocytes/CC (7), segmented neutrophils/CC (8), stick neutrophils/CC (9), monocytes/CC (10); leucocytes/CC (11). Correct prediction of 5YS was 100% by neural networks computing (area under ROC curve=1.0; error=0.0).
CONCLUSIONS: 5YS of LCP after radical procedures significantly depended on: 1) PT early-invasive cancer; 2) PT N0--N12; 3) cell ratio factors; 4) blood cell circuit; 5) biochemical factors; 6) hemostasis system; 7) AT; 8) LC characteristics; 9) LC cell dynamics; 10) surgery type: lobectomy/pneumonectomy; 11) anthropometric data. Optimal diagnosis and treatment strategies for LC are: 1) screening and early detection of LC; 2) availability of experienced thoracic surgeons because of complexity of radical procedures; 3) aggressive en block surgery and adequate lymph node dissection for completeness; 4) precise prediction; 5) adjuvant chemoimmunoradiotherapy for LCP with unfavorable prognosis.
2. DNA damage, if not repaired, may affect
replication and transcription, leading to
mutation or cell death
DNA repair is a collection of processes by
which a cell identifies and corrects damage
to the DNA molecules that encode its
genome.
What is DNA repair?
3. Efficient DNA replication
DNA replication is highly efficient process
Replication error rate is only 1 defect in 10 8 nucleotides
DNA repair rate is 99%
Unrepaired error rate is only 1 in 10 10
nucleotides
Human genome=6.4x10 9 base pairs
4. DNA
damage
Activation of cell cycle check
points
DNA repair
SOS
Response (synthesis of repair enzymes
Trans lesion synthesis/ bypas-Photoreactivation
-Demethylation
MMR BER NER HR NHEJ
FAILURE
Senescence
Apoptosis Mutation
If excess damage
If excess damage
No effect
Cancer
Death
5. TYPE OF DAMAGE DAMAGE MECH. REPAIR
MECH.
Single Base Alteration Depurination BER
Deamination BER
Alkylation BER
Base Analogue Incorporation BER
Mismatch Base MMR
Double Base Alteration Pyrimidine dimer NER
Purine dimer NER
Chain Break Single stranded break HR,NHEJ
Double stranded break HR,NHEJ
Cross linking Between DNA-DNA HR
Between DNA-Protein ?
Polymerase slippage Replication error in
microsettelite
MMR & NER
7. DNA
damage
Activation of cell cycle check
points
DNA repair
SOS
Response (synthesis of repair enzymes
Trans lesion synthesis/ bypas-Photoreactivation
-Demethylation
MMR BER NER HR NHEJ
FAILURE
Senescence
Apoptosis Mutation
If excess damage
If excess damage
No effect
Cancer
Death
8. SOS response
SOS repair occurs when cells are
overwhelmed by UV damage - this allows
the cell to survive but at the cost of
mutagenesis.
SOS response only triggered when other
repair systems are overwhelmed by amount
of damage so that unrepaired DNA
accumulates in the cell.
9.
10.
11. DNA
damage
Activation of cell cycle check
points
DNA repair
SOS
Response (synthesis of repair enzymes
Trans lesion synthesis/ bypas-Photoreactivation
-Demethylation
MMR BER NER HR NHEJ
FAILURE
Senescence
Apoptosis Mutation
If excess damage
If excess damage
No effect
Cancer
Death
12. Direct reversal of DNA damage
Photoreactivation (the enzyme DNA photolyase
captures energy from light )
It is found in plants and some prokaryotes
15. DNA
damage
Activation of cell cycle check
points
DNA repair
SOS
Response (synthesis of repair enzymes
Trans lesion synthesis/ bypas-Photoreactivation
-Demethylation
MMR BER NER HR NHEJ
FAILURE
Senescence
Apoptosis Mutation
If excess damage
If excess damage
No effect
Cancer
Death
16. Mismatch repair(MMR)
• MMR system is an excision/resynthesis system that
can be divided into 4 phases:
• (i) recognition of a mismatch by MutS proteins
• (ii) recruitment of repair enzymes
• (iii) excision of the incorrect sequence,
• (iv) resynthesis by DNA polymerase using the
parental strand as a template.
17. When MMR is implicated?
When a mismatch base is
encountered
When DNA polymerase slippage
forms loop type defect
During replication,
18. In prokaryotes like E.coli…
Mut proteins
Mut S Mut L Mut H
Scans DNA and
recognize the
mismatch base
on daughter strand
-Links Mut S and Mut H
-Activates Mut H
-Binds the complex to
hemi methylated GATC
sequence
-Helicase activity
19.
20. Clinical importance
hereditary nonpolyposis colon cancer ( HNPCC )
Faulty mismatch repair
Mutation in gene hMSH2 and hMLH1
Defective mismatch repair mechanism
Autosomal dominant
carcinoma
21.
22. In eukaryotes-
MutS homologs: Msh2/Msh6 (MutSα)
Msh2/Msh3 (MutSβ)
MutL homologs: MLH1 and PMS2(MutLα)
MLH1 and PMS1(MutLβ)
MLH1 and MLH3(MutLγ)
23. TYPE OF DAMAGE DAMAGE MECH. REPAIR
MECH.
Single Base Alteration Depurination BER
Deamination BER
Alkylation BER
Base Analogue Incorporation BER
Mismatch Base MMR
Double Base Alteration Pyrimidine dimer NER
Purine dimer NER
Chain Break Single stranded break HR,NHEJ
Double stranded break HR,NHEJ
Cross linking Between DNA-DNA HR
Between DNA-Protein ?
Polymerase slippage Replication error in
microsettelite
MMR & NER
24. Microsatellite instability (MSI)
It is a condition manifested by damaged DNA due to
defects in the normal DNA repair process.
Microsatellites are repeated sequences of DNA
A dinucleotide repeat of CA, is most common
DNA polymerase slips out from these sequences
while replication and forms loop
This is corrected by MMR and NER mechanism
25. Defect in MMR will result in increase or decrease length
Microsatellites
It will cause DNA mutation
26.
27. TYPE OF DAMAGE DAMAGE MECH. REPAIR
MECH.
Single Base Alteration Depurination BER
Deamination BER
Alkylation BER
Base Analogue Incorporation BER
Mismatch Base MMR
Double Base Alteration Pyrimidine dimer NER
Purine dimer NER
Chain Break Single stranded break HR,NHEJ
Double stranded break HR,NHEJ
Cross linking Between DNA-DNA HR
Between DNA-Protein ?
Polymerase slippage Replication error in
microsettelite
MMR & NER
28. Base excision repair
Variety of DNA glycosylases, for different types of
damaged bases.
They scan the genome and flips out the wrong base
AP endonuclease recognizes sites with a missing
base; cleaves sugar-phosphate backbone.
(Deoxyribose phosphate lyase) removes the sugar-
phosphate lacking the base.
29.
30. Nucleotide Excision Repair
Used for repair of DNA adducts
EXAMPLES: thymine-thymine dimers
Produced by chemical and UV radiation damage
31. Nucleotide Excision repair in E.coli
1.UvrA and UvrB scan DNA to identify a distortion
2. UvrA leaves the complex ,and UvrB melts DNA
locally around the distortion
3. UvrC forms a complex with UvrB and creates nicks
to the 5’ side of the lesion
4. DNA helicase UvrD releases the single stranded
fragment from the duplex, and DNA Pol I and ligase
repair and seal the gap
32.
33. Nucleotide excision repair in eukaryotes
Two major pathways
Global genome repair Transcription coupled repair
34. Type of protein Function
DDB1 ,DDB2(XPE)
XPC
Recognize damage
XPG -- Stabilizes TFIIH
-- Endonuclease activity
XPD
(subunit of TFIIH)
Act as helicase
XPB
(subunit of TFIIH)
Act as ATPase
XPA Involved in damage
verification
XPF endonuclease
35.
36. Clinical Importance
Xeroderma pigmentosum is an autosomal recessive
genetic disease .
The clinical syndrome include marked sensitivity to
sunlight ( UV rays ) with subsequent formation of
multiple skin cancers & premature death .
The risk of developing skin cancer is increased 1000
to 2000 fold.
Cells cultured from patients with xeroderma
pigmentosum exhibit low activity for the nucleotide
excision repair process
37. TYPE OF DAMAGE DAMAGE MECH. REPAIR
MECH.
Single Base Alteration Depurination BER
Deamination BER
Alkylation BER
Base Analogue Incorporation BER
Mismatch Base MMR
Double Base Alteration Pyrimidine dimer NER
Purine dimer NER
Chain Break Single stranded break HR,NHEJ
Double stranded break HR,NHEJ
Cross linking Between DNA-DNA HR
Between DNA-Protein ?
Polymerase slippage Replication error in
microsettelite
MMR & NER
40. Two proteins are involved in the non homologous
rejoining of a DNA break .
Ku protein, a hetero dimer with two subunits
bind to free DNA ends & has latent ATP
dependent helicase activity .
The DNA bound Ku hetero dimer recruits an unusual
DNA dependent Protein kinase
( DNA – PK )
41. DNA – PK has a binding site for DNA free ends
It allows the approximation of the 2 separated ends .
The free end DNA/Ku/DNA – PK complex activates the
kinase activity in the later.
DNA – PK reciprocally phosphorylates Ku .
42. DNA – PK then dissociates from the DNA & Ku,
resulting in activation of the Ku helicase.
This results in unwinding of the 2 ends.
The unwound approximated DNA forms base pairs.
The extra nucleotide tails are removed by an
exonuclease & the gaps are filled and closed by DNA
ligase .
43. Homologous recombination
Double strand break
MRN complex binds to DNA on either side of the break
Various proteins will trim back 5’ ends
Production of 3’ overhangs on ssDNA
RPA will cover ssDNA & prevents its own winding
Rad 51 produce nucleoprotein on ss DNA
44. Strand invasion in identical duplex
D-loop formation between 3’ overhang and
homologous chromosome
DNA polymerase will extend it
Holiday junction formation
DSBR pathway SDSA pathway
Cross over product Non cross over product
45.
46.
47.
48. DNA
damage
Activation of cell cycle check
points
DNA repair
SOS
Response (synthesis of repair enzymes
Trans lesion synthesis/ bypas-Photoreactivation
-Demethylation
MMR BER NER HR NHEJ
FAILURE
Senescence
Apoptosis Mutation
If excess damage
If excess damage
No effect
Cancer
Death
49. Trans lesion DNA synthesis
Occurs when the above repairs are not
efficient enough
Prevents cell from having un-replicated
chromosome at the cost of some point
mutation
enables replication to proceed across
DNA damage