This document provides information about DNA replication, transcription, and repair. It discusses the key components and processes of DNA replication including initiation, priming, elongation, and termination. It describes the central dogma of molecular biology involving the flow of genetic information from DNA to RNA to protein. The document also summarizes the main types of DNA repair including mismatch repair, base excision repair, nucleotide excision repair, nonhomologous end joining, and recombination repair.
The slide presenting the Importance of genetic code and discusses how does the genetic code deduced that brings in the entire understanding of Genetic today.
The slide presenting the Importance of genetic code and discusses how does the genetic code deduced that brings in the entire understanding of Genetic today.
Nucleic Acids
DNA
Eukaryotic Chromosomes
The Histones
Deoxynucleic acid ( DNA )
Importance of Nucleotides
Base pairing
Denaturation and Renaturation
Determination GC content
Prokaryotic DNA synthesis
Prokaryotic DNA Replication
Transcription
Coding Strand and Template Strand
Steps of RNA synthesize
A powerpoint presentation for Mrs. Tabor's 7th grade science students. I have a FITB note sheet to accompany this presentation and would be happy to email it to you. Contact stabor@belgradeschools.com
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.
Title: Sense of Taste
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 structure and function of taste buds.
Describe the relationship between the taste threshold and taste index of common substances.
Explain the chemical basis and signal transduction of taste perception for each type of primary taste sensation.
Recognize different abnormalities of taste perception and their causes.
Key Topics:
Significance of Taste Sensation:
Differentiation between pleasant and harmful food
Influence on behavior
Selection of food based on metabolic needs
Receptors of Taste:
Taste buds on the tongue
Influence of sense of smell, texture of food, and pain stimulation (e.g., by pepper)
Primary and Secondary Taste Sensations:
Primary taste sensations: Sweet, Sour, Salty, Bitter, Umami
Chemical basis and signal transduction mechanisms for each taste
Taste Threshold and Index:
Taste threshold values for Sweet (sucrose), Salty (NaCl), Sour (HCl), and Bitter (Quinine)
Taste index relationship: Inversely proportional to taste threshold
Taste Blindness:
Inability to taste certain substances, particularly thiourea compounds
Example: Phenylthiocarbamide
Structure and Function of Taste Buds:
Composition: Epithelial cells, Sustentacular/Supporting cells, Taste cells, Basal cells
Features: Taste pores, Taste hairs/microvilli, and Taste nerve fibers
Location of Taste Buds:
Found in papillae of the tongue (Fungiform, Circumvallate, Foliate)
Also present on the palate, tonsillar pillars, epiglottis, and proximal esophagus
Mechanism of Taste Stimulation:
Interaction of taste substances with receptors on microvilli
Signal transduction pathways for Umami, Sweet, Bitter, Sour, and Salty tastes
Taste Sensitivity and Adaptation:
Decrease in sensitivity with age
Rapid adaptation of taste sensation
Role of Saliva in Taste:
Dissolution of tastants to reach receptors
Washing away the stimulus
Taste Preferences and Aversions:
Mechanisms behind taste preference and aversion
Influence of receptors and neural pathways
Impact of Sensory Nerve Damage:
Degeneration of taste buds if the sensory nerve fiber is cut
Abnormalities of Taste Detection:
Conditions: Ageusia, Hypogeusia, Dysgeusia (parageusia)
Causes: Nerve damage, neurological disorders, infections, poor oral hygiene, adverse drug effects, deficiencies, aging, tobacco use, altered neurotransmitter levels
Neurotransmitters and Taste Threshold:
Effects of serotonin (5-HT) and norepinephrine (NE) on taste sensitivity
Supertasters:
25% of the population with heightened sensitivity to taste, especially bitterness
Increased number of fungiform papillae
Recomendações da OMS sobre cuidados maternos e neonatais para uma experiência pós-natal positiva.
Em consonância com os ODS – Objetivos do Desenvolvimento Sustentável e a Estratégia Global para a Saúde das Mulheres, Crianças e Adolescentes, e aplicando uma abordagem baseada nos direitos humanos, os esforços de cuidados pós-natais devem expandir-se para além da cobertura e da simples sobrevivência, de modo a incluir cuidados de qualidade.
Estas diretrizes visam melhorar a qualidade dos cuidados pós-natais essenciais e de rotina prestados às mulheres e aos recém-nascidos, com o objetivo final de melhorar a saúde e o bem-estar materno e neonatal.
Uma “experiência pós-natal positiva” é um resultado importante para todas as mulheres que dão à luz e para os seus recém-nascidos, estabelecendo as bases para a melhoria da saúde e do bem-estar a curto e longo prazo. Uma experiência pós-natal positiva é definida como aquela em que as mulheres, pessoas que gestam, os recém-nascidos, os casais, os pais, os cuidadores e as famílias recebem informação consistente, garantia e apoio de profissionais de saúde motivados; e onde um sistema de saúde flexível e com recursos reconheça as necessidades das mulheres e dos bebês e respeite o seu contexto cultural.
Estas diretrizes consolidadas apresentam algumas recomendações novas e já bem fundamentadas sobre cuidados pós-natais de rotina para mulheres e neonatos que recebem cuidados no pós-parto em unidades de saúde ou na comunidade, independentemente dos recursos disponíveis.
É fornecido um conjunto abrangente de recomendações para cuidados durante o período puerperal, com ênfase nos cuidados essenciais que todas as mulheres e recém-nascidos devem receber, e com a devida atenção à qualidade dos cuidados; isto é, a entrega e a experiência do cuidado recebido. Estas diretrizes atualizam e ampliam as recomendações da OMS de 2014 sobre cuidados pós-natais da mãe e do recém-nascido e complementam as atuais diretrizes da OMS sobre a gestão de complicações pós-natais.
O estabelecimento da amamentação e o manejo das principais intercorrências é contemplada.
Recomendamos muito.
Vamos discutir essas recomendações no nosso curso de pós-graduação em Aleitamento no Instituto Ciclos.
Esta publicação só está disponível em inglês até o momento.
Prof. Marcus Renato de Carvalho
www.agostodourado.com
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
Knee anatomy and clinical tests 2024.pdfvimalpl1234
This includes all relevant anatomy and clinical tests compiled from standard textbooks, Campbell,netter etc..It is comprehensive and best suited for orthopaedicians and orthopaedic residents.
Acute scrotum is a general term referring to an emergency condition affecting the contents or the wall of the scrotum.
There are a number of conditions that present acutely, predominantly with pain and/or swelling
A careful and detailed history and examination, and in some cases, investigations allow differentiation between these diagnoses. A prompt diagnosis is essential as the patient may require urgent surgical intervention
Testicular torsion refers to twisting of the spermatic cord, causing ischaemia of the testicle.
Testicular torsion results from inadequate fixation of the testis to the tunica vaginalis producing ischemia from reduced arterial inflow and venous outflow obstruction.
The prevalence of testicular torsion in adult patients hospitalized with acute scrotal pain is approximately 25 to 50 percent
New Directions in Targeted Therapeutic Approaches for Older Adults With Mantl...i3 Health
i3 Health is pleased to make the speaker slides from this activity available for use as a non-accredited self-study or teaching resource.
This slide deck presented by Dr. Kami Maddocks, Professor-Clinical in the Division of Hematology and
Associate Division Director for Ambulatory Operations
The Ohio State University Comprehensive Cancer Center, will provide insight into new directions in targeted therapeutic approaches for older adults with mantle cell lymphoma.
STATEMENT OF NEED
Mantle cell lymphoma (MCL) is a rare, aggressive B-cell non-Hodgkin lymphoma (NHL) accounting for 5% to 7% of all lymphomas. Its prognosis ranges from indolent disease that does not require treatment for years to very aggressive disease, which is associated with poor survival (Silkenstedt et al, 2021). Typically, MCL is diagnosed at advanced stage and in older patients who cannot tolerate intensive therapy (NCCN, 2022). Although recent advances have slightly increased remission rates, recurrence and relapse remain very common, leading to a median overall survival between 3 and 6 years (LLS, 2021). Though there are several effective options, progress is still needed towards establishing an accepted frontline approach for MCL (Castellino et al, 2022). Treatment selection and management of MCL are complicated by the heterogeneity of prognosis, advanced age and comorbidities of patients, and lack of an established standard approach for treatment, making it vital that clinicians be familiar with the latest research and advances in this area. In this activity chaired by Michael Wang, MD, Professor in the Department of Lymphoma & Myeloma at MD Anderson Cancer Center, expert faculty will discuss prognostic factors informing treatment, the promising results of recent trials in new therapeutic approaches, and the implications of treatment resistance in therapeutic selection for MCL.
Target Audience
Hematology/oncology fellows, attending faculty, and other health care professionals involved in the treatment of patients with mantle cell lymphoma (MCL).
Learning Objectives
1.) Identify clinical and biological prognostic factors that can guide treatment decision making for older adults with MCL
2.) Evaluate emerging data on targeted therapeutic approaches for treatment-naive and relapsed/refractory MCL and their applicability to older adults
3.) Assess mechanisms of resistance to targeted therapies for MCL and their implications for treatment selection
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
- Video recording of this lecture in English language: https://youtu.be/lK81BzxMqdo
- Video recording of this lecture in Arabic language: https://youtu.be/Ve4P0COk9OI
- Link to download the book free: https://nephrotube.blogspot.com/p/nephrotube-nephrology-books.html
- Link to NephroTube website: www.NephroTube.com
- Link to NephroTube social media accounts: https://nephrotube.blogspot.com/p/join-nephrotube-on-social-media.html
These simplified slides by Dr. Sidra Arshad present an overview of the non-respiratory functions of the respiratory tract.
Learning objectives:
1. Enlist the non-respiratory functions of the respiratory tract
2. Briefly explain how these functions are carried out
3. Discuss the significance of dead space
4. Differentiate between minute ventilation and alveolar ventilation
5. Describe the cough and sneeze reflexes
Study Resources:
1. Chapter 39, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 34, Ganong’s Review of Medical Physiology, 26th edition
3. Chapter 17, Human Physiology by Lauralee Sherwood, 9th edition
4. Non-respiratory functions of the lungs https://academic.oup.com/bjaed/article/13/3/98/278874
Ozempic: Preoperative Management of Patients on GLP-1 Receptor Agonists Saeid Safari
Preoperative Management of Patients on GLP-1 Receptor Agonists like Ozempic and Semiglutide
ASA GUIDELINE
NYSORA Guideline
2 Case Reports of Gastric Ultrasound
263778731218 Abortion Clinic /Pills In Harare ,sisternakatoto
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ARTIFICIAL INTELLIGENCE IN HEALTHCARE.pdfAnujkumaranit
Artificial intelligence (AI) refers to the simulation of human intelligence processes by machines, especially computer systems. It encompasses tasks such as learning, reasoning, problem-solving, perception, and language understanding. AI technologies are revolutionizing various fields, from healthcare to finance, by enabling machines to perform tasks that typically require human intelligence.
1. MM
Androu Waheeb
Most pictures from MM lecture series given in RCSI-Bahrain
2. MM – DNA
Androu Waheeb
Most pictures from MM lecture series given in RCSI-Bahrain
3. BASE
NUCLEOTIDES
PO4 CH2
• Building blocks of DNA O
• Made up of SUGAR
• Pentose sugar
• Nitrogen base (1’)
OH
• Phosphate group (5’)
• Link to form sugar phosphate backbone of DNA
• Phosphodiester bond b/w 3’ OH and 5’ PO 4
• Covalent bond
4. NUCLEOTIDE BASES
• 2 kinds of bases each with 2 types
• Purine
• Adenine (A)
• Guanine (G)
• Pyramidines
• Thymine (T)
• Cytosine (C)
• Bases form hydrogen bonds to hold both strands
• Bonds are complimentary and specific: purine with pyrimidine
• A - - T (2 H bonds)
• G - - - C (3 H bonds)
• Hence both strands are complementary (reflections of each other)
5. DNA – STRAND STRUCTURE
• Made up of nucleotides
• 2 strands
• Each strand is made of
• Sugar phosphate backbone on outside (because it is hydrophilic)
• Formed by phosphodiester bonds b/w 3’ OH and 5’ PO4
• Bases protrude on inside of helix (because they are hydrophobic and H bond
together)
• Anti-parallel direction
• Direction marked by free 5’ PO4 or 3’ OH group on the end
• The 5’ of one strand is in front of the 3’ of the other
• Complementary
• One strand has the information
6. DNA – HELIX STRUCTURE
• 2 strands make a helix
• Double helix
• Wound around common axis
• Right handed helix
• Diameter = 20 A = 2 nm
• Bases separated by 3.4 A and 30 o rotation
• Helix has 2 groovs
• Major Groove (22 A wide)
• Bases more exposed proteins bind DNA sequences here
• Minor Groove (12 A wide)
7. DNA – BONDS
• Order of collective strength
• Covalent bond
• Phosphodiester bonds
• Van der waals forces
• Between bases on same strand
• Hydrogen bond
• Between bases on different strands
8. DNA – MACROSTRUCTURE
• 2 strands wrapped in double helix
• Double helix wrapped around histones beads on string
• = sequence of nucleosomes (DNA + Histones)
• Beads on string loops into a solenoid
• Solenoid loops on itself supported by scaffold proteins
looped domains (interphase)
• Looped domains loops around itself
• This is packed into a chromosome (metaphase)
9. DNA MACROSTRUCTURE – DEFINITIONS
• Chromatin
• DNA + protein
• Chromosome
• compacted chromatin
• Chromatid
• 1 of a duplicate of chromosome strands formed in cell division and separated in the
last phase to become individual chromosomes
• Duplication occurs in mitosis
• Nucleosome
• Sequence of DNA wrapped around one histone complex
10. NUCLEOSOMES
• DNA + Histones
• Nucleosome involves 2 sets of 4 subtypes of histones
• 2x H2A
• 2x H2B
• 2x H3
• 2x H4
• Histones interact with DNA because they have a lot of +ve amino acids (Lysine) which
interacts with –ve DNA
• H1 attaches to linker DNA b/w neucleosomes
11. CHROMATIN – CLASSIFICATION
• 2 kinds
• Euchromatin
• Readily accessible DNA
• Acetylation of bases relaxation of DNA into euchromatin
• Heterochromatin
• Supercoiled and compacted
• Not accessible
• Methylation compaction of DNA into heterochromatin
• Some areas of DNA always in heterochromatin form
12. CHROMOSOME – STRUCTURE
• Compacted chromatin
• Has centromere
• Holds chromatids together
• Attaches to mitotic spindles
• Attaches to homologous chromosome
• Has telomere
• Repetitive DNA
• Protects ends of chromosomes
• Has 2 arms
• Longer arm (p)
• Shorter arm (q)
13. CHROMOSOME – PROCESSING
• Banding
• Stain with Gimensa stain light and dark bands
• Dark bands (G bands) are heterochromatin
• Light bands (R bands) are euchromatin
• Karyotyping
• Representing all chromosomes by
• Number
• Type
• Shape
14. DNA – PROCESSES
• Denaturation
• Separating DNA strands
• Involved breaking of H bonds
• Starts in A - - T rich areas
• Causes:
• Temperature (melting)
• Melting Temperature: temperature at which 50% of DNA is denatured
• High pH
• Low salt
• Renaturation (annealing)
• Occurs if heat denatured DNA is cooled
15. DNA – MODIFICATION
• Methylation
• Chemical modification
• Adding methyl group to C
• Makes DNA inactive
• Makes structure inaccessible to proteins
• Mutations
• DNA sequence changed by mutagens damages DNA
• Mutagens
• Radiation (X-ray / UV)
• chemicals
16. DNA – FUNCTION
• Stores genetic information
• 1 gene = information for 1 protein / RNA + its regulatory information
• Gene is made of many codons
• 1 codon = 3 nucleotides = information for 1 amino acid
• Sequence of codons = sequence of amino acids in protein
• Genome = sum total of all DNA in organism
• Humans: 23 pairs of chromosomes, one pair is sexual
• Human Genome Project = identify all genes of human genome
17. MM – CENTRAL DOGMA
Androu Waheeb
Most pictures from MM lecture series given in RCSI-Bahrain
18. CENTRAL DOGMA (FLOW OF GENETIC INFO)
Replication
DNA Transcription RNA Translation PROTEIN Function
• Problem in flow
• Cancer
• Chronic illness
• Mutation
19. UNIQUE PROCESSES
Reverse Transcription
RNA (Viruses) DNA
RNA Replication (Viruses &
RNA Plants) RNA
Protein Replication (Prions)
Protein Protein
20. MM – REPLICATION
Androu Waheeb
Most pictures from MM lecture series given in RCSI-Bahrain
21. DNA REPLICATION
Replication
DNA Transcription RNA Translation PROTEIN Function
• Problem in flow
• Cancer
RNA • Chronic illness
primer
• Mutation
22. DNA REPLICATION – REQUIREMENTS
• Enzymes (Replisome)
• Helicase
• Primase
• Polymerase: elongates primer replicating DNA
• Topoisomerase
• Ligase: connects loose ends of DNA fragments
• Proteins
• ssBP (single stranded binding proteins)
• Sliding clamp
• Encircles DNA and binds polymerase increase processivity
• dNTPs + Mg2+
• Single stranded template strand
• Semiconservative
24. DNA REPLICATION – PROCESS
• Initiation
• Starts at origin of replication (Ori)
• Eukaryotes: many sites many replication forks
• Prokaryotes: one site one replication fork
• AT rich sequence
• Separation of both strands
• DNA Helicase unwinds helix
• Requires ATP
• ssBP bind to exposed bases to prevent reannealing
• Topoisomerase
• Uncoils supercoiled part of DNA
25. DNA REPLICATION – PROCESS
• Priming
• Primase RNA Primer
• In eukaryotes it is a/w DNA pol a
• Elongation
• DNA polymerase elongates primer
• Requires free 3’ OH group
• Specific directionality
• Reads: 3’ to 5’
• Makes new: 5’ to 3’
• Prokaryotes: DNA pol III
• a/w Sliding Clamp
• Eukaryotes: started by DNA pol a and continued by d
• Pol d a/w Proliferating Cell Nuclear Antigen (PCNA)
26. DNA REPLICATION – PRO: PROCESS
• DNA Polymerase can only elongate in 5’ to 3’ direction
• Both strands replicated simultaneously
• Semidiscontinuous Replication
• Leading strand
• Replicated continuously
• Lagging strand
• Replicated discontinuously in fragments (Okazaki Fragments)
• Primase makes new primer at regular intervals
• DNA Pol elongates it in 5’ to 3’ direction (NEW)
• DNA Pol blocked when near new primer
27. DNA Polymerase – Classification
POC Prokaryote Eukaryote
DNA Pol I II III α β ε δ γ
Locates nick Elongates Initiates repl’n
b/w OF, primer, Completes
a/w Primase
Functio Removes RNA catalyzing on pol a Mitochon-
ahead, Repair Extends Repair Repair drial DNA
n Replace with PDEB
replicating
primer by Leading and Replication
DNA, Replace short piece of Lagging
primer DNA DNA
Proofre
ading
YES N/A YES
x YES
Polyme
5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’
rase
Exonu
clease
3’ 5’ 3’ 5’ 3’ 5’
High:
x 3’ 5’
Proces Sliding
Moder High:
sivity Clamp ate PCNA
28. DNA REPLICATION – PROCESS
• Depriming
• Prokaryotes: Replacement of RNA primer by DNA pol I
• Locates nick b/w OF Removes RNA ahead Adds DNA
• Eukaryotes:
• Rnase H1 removes RNA FEN1 removes last RNA and proofreads forward 15
bp DNA pol d copies into DNA
• Ligating
• Ligase connect loose ends of DNA
29. DNA REPLICATION – PRO: PROCESS
• Termination
• Have termination sequences opposite to Ori
• Proteins bind sequence
• Prevent helicase unwinding
• Dissociation of replisome
• Eukaryotes
• Terminate when replication forks collide
• End of lagging strand (3’) filled with telomeres
• TTAGGG tandem repeats
• Synthesized by telomerase
• RNA template for telomere
• Normally in rapidly diving cells ex. Gametes
• Function declines as cell develops
Telomere shortens DNA damage stop division
• Absence senescence; enhanced Cancer
30. DNA REPLICATION – PRO/EUK DIFFERENCES
POC PRO EUK
Initiation 1 Ori 1 fork Many Oris many forks
Elongation DNA pol III DNA pol a d
RNA removed by Rnase H1 FEN
Depriming Replased by DNA Pol I
1 removes last 5’ RNA and
proofreads 15 bp after DNA Pol d
makes DNA
Termination sequences bind Terminate when replication forks
Termination protein dislocate Helicase end
replication
meet
End of 3’ end filled with telomeres
31. DNA REPLICATION – NOTES
• Need to disassemble nucleosomes and reassemble
• Random distribution of histones
32. MM – DNA ERRORS, DAMAGE, AND REPAIR
Androu Waheeb
Most pictures from MM lecture series given in RCSI-Bahrain
33. DNA REPLICATION – ERRORS
• Errors cause mutation if not repaired
• Errors prevented
• Substrate specificity
• DNA Pol only catalyzes reaction between complementary bases
• Proofreading
• Errors repaired
34. DNA DAMAGE
• Constant
• Agents
• Radiation
• Chemicals
• Cell repairs damage
• Causes mutations if not repaired
• Insertion
• Deletion
• Substitution
35. DNA REPAIR
• 5 ways
• Mismatch repair
• Base excision repair
• Nucleotide excision repair
• Nonhomologous End Joining
• Recombination Repair
36. DNA REPAIR – MISMATCH REPAIR
• Process
• Mismatch
• Kink
• MutS binds
• MutL recruited
• DNA forms loop
• MutH breaks daughter strand (parent methylated)
• UvrD unwinds DNA
• Exonuclease removes DNA
• DNA pol makes DNA
• Ligase joins ends
• Defect HNPC (Heriditary Non Polyposis Cancer)
37. DNA REPAIR – BASE EXCISION REPAIR
• Process
• Base lost chemically
• Removed by DNA glycosylase
• AP endonuuclease cuts backbone
• Exonuclease removes base
• DNA Pol makes DNA
• Ligase joins ends
38. DNA REPAIR – NUCLEOTIDE EXCISION REPAIR
• Process
• Kink in chain
• UvrABC endonuclease cleaves both sides
• UvrD removes sequence
• DNA Pol makes DNA
• DNA Ligase joins ends
• Defect Xeroderma Pigmentosum (AR)
• Photosensitivity
• Sking CA
39. DNA REPAIR – NHEJ
• Process
• Double stranded break
• Ku protein senses break
• Holds both strands
• Ends are aligned, trimmed, or filled
• DNA Ligase joins strands
• Causes mutations
• Deficiency CA and Immunodeficiency Syndrome
40. DNA REPAIR – RECOMBINATION REPAIR
• Process
• Double stranded break
• Recombination
• Uses info of homologous chromosome to repair
• Defect Breast CA
• Ex. BRCA 1 and BRCA 2
41. MM – TRANSCRIPTION
Androu Waheeb
Most pictures from MM lecture series given in RCSI-Bahrain
42. TRANSCRIPTION
Replication
DNA Transcription RNA Translation PROTEIN Function
• Problem in flow
• Cancer
• Chronic illness
• Mutation
45. TRANSCRIPTION – REQUIREMENTS
• Promoter on DNA
• Conserved sequence
• TATAAT
• RNA Polymerase
• No primer required
• 4 subunits
• α
• β: Binds NTPs + Catalyze bond formation
• β’: Binds DNA template
• σ: recognizes promoter sequence
• RNTPs : A, G, C, U
46. TRANSCRIPTION – PROCESS
• Initiation
• RNAP binds promoter sequence ( σ)
• Unwinds Promoter
• Elongation
• σ dissociates
• RNA Polymerase reads ONE strand in 3’ 5’
• make unbranched RNA in 5’ 3’ direction
• RNA = Complementary strand
• Transcription bubble that moves along strand
• Termination
• Transcription of terminator sequence (3’UTR) RNAP dissociate
47. TRANSCRIPTION – TERMINATION
• Terminator sequences
• Hairpin loop
• GC rich
• hairpin structure (stem and loop structure)
• Followed by poly-U
• weak hybridization b/w DNA and RNA
• RNAP pauses RNAP dissociates
48. TRANSCRIPTION – PRODUCTS
• Always RNA, usually single stranded, unbranched
• tRNA
• Involved in translation
• tRNA genes
• Not translated
• rRNA
• ribosomes for translation
• rRNA genes
• Not translated
• mRNA
• Translated protein
• Protein coding genes
49. TRANSCRIPTION – EUKARYOTES
• 5 differences
• Require regulatory proteins to expose promoters
• DNA Packaging
• RNA processing & exporting
• Nucleus
• translation and transcription not simultaneous
• Has 4 RNA Polymerases
• RNAP I rRNA (Nucleolus)
• RNAP II mRNA precursors (Nucleoplasm)
• RNAP III tRNA and 5S rRNA (Nucleoplasm)
• Mitochondrial RNA Pol mtRNAs (Mitochondrion)
• More extensive transcription control
• Post-transcriptional mRNA processing
50. TRANSLATION (EUKS) – MRNA PROCESSING
1o
DNA RNA
Modified
Pol II
Transcript
• Sum total of 1 o transcripts = heterogeneous nuclear RNA (hnRNA)
• Modification
• 5’ Cap
• Splicing
• 3’ poly(A) tail
51. TRANSCRIPTION (EUKS) – 5’ CAPPING
• 7-methyl-guanosine residue
• 5’ tp 5’ triphosphate link
• Guanyltransferase
• Cap binds proteins
• protect mRNA from nuclease
• Guides mRNA export through nuclear pore
• Initiation of transcription
54. TRANSCRIPTION (EUKS) – 3’ TAIL
• Process
• Polyadenylation signal sequence from termination sequence (AAUAAA)
• Recruit endonuclease
• Cleave 20 bases downstream of sequence
• Poly(A) polymerase adds 40-250 A to cleaved end
• Function
• Bind PABP (Poly-A Binding Protein)
• Stabilize molecule
• Protects against 3’ exonuclease
• Facilitates export of mRNA
• Shortened in cytosol
55. TRANSCRIPTION (EUKS) – VARIABILITY
• Can make more proteins than genes encode
• Alternative Splicing
• 1o Transcript splice variants (may be tissue specific)
• process
• Retains / skips exons
• Retains / skips introns
• Shift splice site different exon size
• RNA Editing
• 1o Transcript introduce new stop codon
• Done by enzymes
• Ex: deamination of C to U by Apolipoprotein B Deaminase
57. TRANSCRIPTION – MEDICAL USES
• Antibiotics can stop transcription
• Rifampicin
• Binds β sub-unit of prokaryotic RNAP prevents elongation
• Actinomycin D
• Binds DNA prevents unwinding prevents initiation
58. MM – GENES
Androu Waheeb
Most pictures from MM lecture series given in RCSI-Bahrain
59. GENES
• 1 gene = information for 1 protein
• Has promoter and terminator sequence (consensus sequence)
• Composed of sequence of codons
[+1]
Upstream Downstream
-4-3 -2 P-1 CODING REIGON T
RNA
5' 3'
60. GENES – GENETIC CODE
• 1 codon code 1 amino acid in protein sequence
• 1 codon = 3 base pairs
• Simple math
• Code cracked by trial of all possible codes
• Code is
• Degenerate
• 1 amino acid more than 1 codon
• Differ in 3 rd base
• Non-overlapping (read in triplets from mRNA)
• Open Reading Frames
61. TRANSLATION – OPEN READING FRAMES
• Open Reading Frame
Reading frame 1
• Read in non-overlapping triplets A U G U U U AAA U G G U G A
• Determined by start codon location start Phe Lys Trp Stop
• Only one ORF has useful informatiaon Reading frame 2
A U G U U U AAA U G G U G A
Cys Leu Asn Gly
Reading frame 3
A U G U U U AAA U G G U G A
Val Stop Start Val
62. MM – REGULATION OF EXPRESSION
Androu Waheeb
Most pictures from MM lecture series given in RCSI-Bahrain
64. EXPRESSION REGULATION – GENERAL
• Only express what's required
• Cancer
• Inefficient
• Cellular specialization
• Done by transcription factors
• Protein binds promoter and enhancer gene expression
DNA Many bases
5’ 3’
Enhancer Promoter
Transcribed Region
- TF binding site
65. EXPRESSION REGULATION – TYPES
• Constitutive
• Always on
• Proteins always required Balance b/w protein synthesis and half life
• Regulated by tf that are always on
• Inducible
• Need to be turned on
Nucleus
• Respond to environment
• Ex GF
• Regulated by inducible tf
• Signal transduction activate tf
68. EXPRESSION REGULATION (EUK) – CHROMATIN
STRUCTURE
• Remodel to gain access
• Tight chromatin no access for tf to bind
• Req unwinding acetylation
• Histones have tails interact with neighboring DNA chromatin structure
• Tails have + Lys interact with neighboring DNA condense DNA
• Histone Deacetylases (HDACs)
• Acetylated tails have – charge looser structure exposure
• Histone Acetyl Transferases (HATs)
69. EXPRESSION REGULATION (EUK) –
TRANSCRIPTION INITIATION
• Most imp
• Depends on
• Strength of promoter
• Enhancer element
• Interaction with other bound factors
• 2 types of promoters
• Basal promoter
• Enhancer element Coding sequence
70. EXPRESSION REGULATION (EUK) – BASAL
PROMOTER
• Essential
• Close to start site
• Function
• Locates start of gene
• Induces low level of transcription
• Higher if more tf binding sites
• Binds basal tf RNA pol II binds transcription
• 2 types
• TATA box
• strong (binds all alone)
• TFIID and TBP RNA pol II pre-initiation complex
• Closer to start site of transcription
• CCAT box
• weak (requires co-activators to bind)
• Farther from start site
71. EXPRESSION REGULATION (EUK) – ENHANCER
ELEMENT
• Function
• Binds specific transcription factors
• Enhances expression
• Allows tissue specificity
72. EXPRESSION REGULATION (EUK) – TFS
• Protein bind promoter regulate transcription
• 3 domains
• DNA binding domain
• Dimerization Domain
• Transactivation domain
• Drives transcription
• If TF found in tissue expression
• Tissue specificity
• Activated by environmental cues
• Expression
• Active
• Bind ligand
• Bind inhibitor
• Localization
• Phosphorylation
76. EXPRESSION REGULATION (EUK) – MRNA
STABILITY
• Determined by 3’UTR
• Protector factors bind it
• Degraded by endonuclease
• Ex TfR on transferrin mRNA
• Makes transferrin
• Transports Fe
• Has Iron responsive element in 3’ UTR: binds IRBP protective
• Fe Low: TfR stable
• Fe High: TfR unstable
• Ex poly(A) tail
• Binds PABP protection
78. MM – TRANSLATION
Androu Waheeb
Most pictures from MM lecture series given in RCSI-Bahrain
79. TRANSLATION
Replication
DNA Transcription RNA Translation PROTEIN Function
• Problem in flow
• Cancer
• Chronic illness
• Mutation
80. TRANSLATION – GENERAL
• mRNA codons code for amino acid protein
• Eukaryotes and prokaryotes
• Eukaryotes
• Processed mRNA exported from nucleus
• Translation in cytoplasm OR RER
• Prokaryotes
• Translation co-transcriptional
• 1 ribosome 1 mRNA
• 1 mRNA Many ribosomes = polyribosome
81. TRANSLATION - REQUIREMENTS
• mRNA
• template
• tRNA
• Carries amino acids to mRNA
• Specific
• rRNA
• Structural AND functional role in ribosome
• Ribosomal Proteins
• Protein factors: All GTPases
rRNA Proteins Ribosomes
82. TRANSLATION REQ’S – TRNA
• Clover leaf structure
• One amino acid binding arm
• One anti-codon arm
• Has wobble pos’n efficiency
• 20 tRNA for 20 amino acids
• Amino acid bound by aminoacyl-tRNA-synthase
• Needs ATP
• Bound tRNA = charged tRNA
• Specific to amino acid
• Done by shape of tRNA
• recognition by diff synthase
84. TRANSLATION REQ’S – RIBOSOME
• Made of 2 subunits
• Named after sedimentation coefficient
• Each subunit made of rRNA + Protein
• 2 kinds
• Eukaryotes
• 80 S made of 40 S and 60 S
• Prokaryotes
• 70 S made of 30 S and 50 S
• Function: translation of mRNA using tRNA
• Clinical: Chloramphinecol binds 50S --| peptidyl transferase --| translation
85. TRANSLATION REQ’S – RIBOSOME
• Has 3 sites
• A (Aminoacyl) site
• Binds new tRNA
• P (Peptidyl) site
• Has the protein being formed
• E (Exit) site
• Deacylated tRNA
• Has 2 centres
• Peptidyl transferase centre
• Where peptide bond formation catalyzed
• Decoding centre
• Ensures only complementary anti-codon tRNA are added
87. TRANSLATION – INITIATION
• General
• Start Codon: AUG Met
• Inserted by initiator tRNA
• Euk: embedded in Kozak Sequence
• Start codon recognition sequence
• GCC AUG
• efficent recognition
• Process
• 5’ cap recognition
• Assembly of initiation complex = 40 S + Met-tRNA
• Scan mRNA 5’ 3’ (ATP)
• Recognition of start codon
• assembly of complete ribosome
• Initiation complex at P site
88. TRANSLATION – ELONGATION
• EF1-GTP
• Entry of aminoacyl-tRNA into A site EF1
• GTP hydrolyzed and Ef1 released
• Peptide bond forms b/w aa’s
• Peptidyltransferase EF
2
• Chain moves from P to A site
• Ribosome moves 1 codon
• Driven by EF2 + GTP
• Hydrolysis
• tRNA moved from A to P
• Empty tRNA moves P E released recycled
90. TRANSLATION – TERMINATION
• Ribosome Stop Codon (A)
• Recognised by tripeptide in release factor
• Release factor (RF1) binds to A site
• GTP hydrolysis
• disassembly of the tRNA-ribosome-mRNA complex and
• release of nascent polypeptide
91. POST-TRANSLATIONAL EVENTS
• Protein folding
• required structure for function
• 1o (sequence of aa) 2o (a helix/b sheets) 3o (3D) 4o structure (multinumeric)
• Post-translational modifications
• modify function and position
• Example
• Glycosylation: secreted
• Fatty acyl groups: membrane anchors
• Protein targeting
• moves protein to location
92. POST-TRANSLATIONAL EVENTS – TARGETING
• Short sequences of aa target protein to location
• Secreted
• Nuclear
• Nuclear Localization Sequence (NLS)
• Recognized by proteins in nuclear pores
93. POST-TRANSLATIONAL TARGETING –
SECRETORY PROTEINS
• Made in RER
• Signal sequence at N end
• Hydrophobic
• binds RER membrane
• moves protein through RER membrane
• signal sequence cleaved
• concentrated internally
• move into Golgi in transport vesicles
• move to Plasma membrane in secretory vesicles
• Secretory vesicle fuses with membrane protein expelled
95. MM – BIOTECHNOLOGY
Androu Waheeb
Most pictures from MM lecture series given in RCSI-Bahrain
96. BIOTECH – ISOLATION OF DNA
• Tissue Sample
• Homogenize Tissue
Detergent
• Lyse Cells
High Salt
• Precipitate Protein
Centrifuge
• Remove Protein
Salt + Alcohol
• Precipitate DNA
Water / Buffer
• Redissolve DNA
-80 o C
• Store DNA (Stable)
97. BIOTECH – ISOLATION OF RNA
• Problems • Tissue Sample
• RNA is unstable
• Homogenize Tissue
• Degraded by RNA nucleases Chaotropic
• RNA nucleases are stable solution • Lyse Cells
• Chaotropic Solution High Salt
• Precipitate Protein
• Salts
Centrifuge
• Denature proteins • Remove Protein
• Ex. Guanidium hypochloride
Salt + Alcohol
• Convert to DNA and store DNA • Precipitate RNA
Water / Buffer
• Redissolve RNA
Stringent
Conditions • Store RNA
98. BIOTECH – ISOLATION OF MRNA
• Isolate RNA
• Isolate with poly(T) resin
• Binds to poly(A) tail
99. BIOTECH – CDNA SYNTHESIS
• cDNA = Complimentary DNA = made from mRNA
• Isolate RNA
• Isolate mRNA
Reverse Transcriptase +
RNase H • cDNA - - mRNA
Hydrolyze rest of RNA
• ss cDNA
Terminal deoxynucleotidyl
transferase • Poly C Cap
Ligate Poly G adaptor
• Primed cDNA
DNA Polymerase + dNTPs
• ds DNA
100. BIOTECH – RECOMBINATION
• Recombination: manipulation of DNA
• Uses
• DNA sequencing
• Diagnosis
• Gene-therapy
• Protein production
• Research
102. BIOTECH RECOMBINATION – RESTRICTION
ENDONUCLEASES
• Enzyme
• Cleaves both DNA strands at specific site
• Recognition sites
• Pallindromic
• Read same both ways
• 2 types
• Leaves blunt ends
• Leaves sticky ends
• Advantage in DNA addition
103. BIOTECH – RESTRICTION MAPPING
• Identifies different DNA
• Cut DNA into restriction fragments with Restriction Endonucleases
• Different sequences have diff # of restriction sites
• Different fragment sizes
• Separate by electrophoresis
• Separate different fragments based on size
• Different sequence = different restriction map
• Too many fragment size combinations smear
104. BIOTECH RECOMBINATION – CLONING
• Fragment of DNA Vector Introduced into cells Replicated Copy DNA
• Vector must have
• Ori
• Selectable marker
• Multiple cloning sites
106. BIOTECH – HYBRIDIZATION
• ss complementary DNA sequences at 50-60oC anneal autonomously
• Attach probe labeled with fluorescent or radioactive tag
RNA
• Differentiates different DNA
• 3 kinds
• Southern
• DNA
• Northern
• RNA
• Western
DNA
107. BIOTECH HYBRIDIZATION – S. BLOTTING
• DNA
Restriction Endonuclease
• Fragmented DNA
Gel Electrophoresis
• Separate fragments
Alkaline Solution
• Denatures DNA
Transfer to blotting
membrane
Add unrelated DNA
• Blocks blotting membrane
Add probe
• Hybridises with
complementary DNA
Wash + Visualise
108. BIOTECH HYBRIDIZATION – S. BLOTTING
• Detects variations in DNA
sequences involving the
restriction site
• Create different size
restriction fragment
• Diff in length = RFLP
(Restriction Fragment
Length polymorphism)
• Use: DNA Fingerprinting
• Ex. SCA
109. BIOTECH HYBRIDIZATION – N. BLOTTING
• Identifies RNA presence
•
•
Hybridize RNA with DNA probe
Same process as Northern
RNA
DNA
110. BIOTECH – REVERSE HYBRIDIZATION
• Reverse N. Blot
• DNA probe on a chip
• RNA fluorescently labeled and added
• Expressed DNA will hybridize with RNA labelling identification
111. BIOTECH HYBRIDIZATION – ARRAY
HYBRIDIZATION
• Deposit many DNA samples into hybridization matrix
• Probe all simultaneously
• Use microarrays
• Cloned DNA fragments spotted onto slide
• Oligos made in situ to probe
• Hybridize with target
• Target is labeled
• Wash after exposure
• If see label target there
113. BIOTECH – GENE AMPLIFICATION (PCR)
• Exponential increase in copies of target
• Requirements
• Template
• dNTP + Mg
• 2 Oligonucleotide primers
• Designed artificially
• Know some of the required sequence
• Mark borders of gene to be amplified
• Thermostable Polymerase (taq)
• Thermal Cycler
115. BIOTECH – PCR PRODUCTS
• Amplified amount of target DNA
• Analyze sample
• After Amplification
• Real Time
• Add probe oligonucleotide with fluorescent reporter and quencher
• Quencher stops reporter when close
• Taq pol had 5’ 3’ exonuclease
• When amplifying, it removes tag tag away from quencher tag fluoresces
116. BIOTECH – DNA SEQUENCING
• Sanger dideoxy chain termination method controlled interruption of polymerization
• ddNTP’s don’t have 3’ and 2’ OH group No phosphodiester bond Chain termination
• Process
• 4 reaction beakers
• Each has
• Template
• Primer
• dNTP + Mg
• DNA pol
• 1 kind of ddNTPs
• Allow replication strand stops at each position with the ddNTP
• Electrophorese to separate
• Polyacrylamide gel separates diff of 1 nucleotide
117. BIOTECH – DNA SEQUENCING
Automated Fluorescence
DNA sequencing
118. BIOTECH – AUTOMATION
• Automated Flouresceent DNA sequencing
• High throughput DNA sequencing
• Mass spectrometer
• DNA Chip
• Allows synthesis of oligonucleotides in situ to probe target
• Add 1 nucleotide at a time
• Other high througput methods
• Real Time PCR
• Pyrosequencing