- The document summarizes purine and pyrimidine nucleotide metabolism. It describes the biosynthesis and degradation pathways of purines and pyrimidines, and their regulation. Key enzymes and cofactors like tetrahydrofolate and PRPP are discussed.
- Inhibitors of nucleotide metabolism are important targets for cancer chemotherapy drugs. Drugs like methotrexate and fluorouracil inhibit key enzymes to selectively target rapidly dividing cancer cells.
- The metabolism of purines and pyrimidines provides the essential building blocks for nucleic acid synthesis and is tightly regulated through feedback inhibition at multiple steps in the pathways. Proper regulation is crucial as nucleotides are required for cell growth and proliferation.
The slide has some brief introduction to nucleotide chemistry, History, General features of nucleotides, Nomenclature, Individual properties of bases, Classification
and Synthetic analogues of biomedical importance.
Nucleic acid metabolism is an important topic in metabolism paper which will be useful for B.Sc., M.sc ., Biochemistry ,Biotechnology,Microbiology and Medical Students
The slide has some brief introduction to nucleotide chemistry, History, General features of nucleotides, Nomenclature, Individual properties of bases, Classification
and Synthetic analogues of biomedical importance.
Nucleic acid metabolism is an important topic in metabolism paper which will be useful for B.Sc., M.sc ., Biochemistry ,Biotechnology,Microbiology and Medical Students
De novo and salvage pathway of nucleotides synthesis.pptx✨M.A kawish Ⓜ️
This slides explains Metabolism topic "De novo and salvage pathway of nucleotides synthesis. In which synthesis of Purines and pyrimidines synthesis has been occurred. In last there is a difference between these two pathways.
This is a continuation of the earlier slide with a name "Nucleotides". Please refer to the previous mentioned slide before moving to this slide for a better overall concept on nucleotides and nucleic acids.
Nucleotide Biosynthesis involves 2 processes. one is Denovo synthesis and other is Salvage pathway. An outline of both the processes has given in this presentation.
BIOSYNTHESIS OF PHOSPHOLIPIDS
Phospholipids:-
These are compounds containing, in addition to fatty acid and glycerol, phosphoric acid, nitrogenous bases, and another substituent. Polar compounds composed of alcohol attached by phosphodiester bridge to either diacylglycerol or sphingosine.
Amphipathic in nature has a hydrophilic head (phosphate +alcohol
eg., serine, ethanolamine, and choline) and a long, hydrophobic tail
(fatty acids or derivatives ).
- CLASSIFICATION OF PHOSPHOLIPIDS:-
- Glycerophospholipids
- Spingophospholipids or Sphingomyelin
- SYNTHESIS OF PHOSPHOLIPIDS
- FUNCTIONS OF PHOSPHOLIPIDS
- FUNCTIONS OF SPHINGOLIPIDS
introduction of Purine and Pyrimidine metabolism, biosynthesis and degradation of nucleotides, biological functions and metabolic disorders, chemical analogues and therapeutic drugs, uric acid metabolism
Digestion of proteins, absorption of amino acids, synthesis of amino acids, catabolism of amino acids and synthesis of specialised non-protein compounds from amino acids for undergraduates
De novo and salvage pathway of nucleotides synthesis.pptx✨M.A kawish Ⓜ️
This slides explains Metabolism topic "De novo and salvage pathway of nucleotides synthesis. In which synthesis of Purines and pyrimidines synthesis has been occurred. In last there is a difference between these two pathways.
This is a continuation of the earlier slide with a name "Nucleotides". Please refer to the previous mentioned slide before moving to this slide for a better overall concept on nucleotides and nucleic acids.
Nucleotide Biosynthesis involves 2 processes. one is Denovo synthesis and other is Salvage pathway. An outline of both the processes has given in this presentation.
BIOSYNTHESIS OF PHOSPHOLIPIDS
Phospholipids:-
These are compounds containing, in addition to fatty acid and glycerol, phosphoric acid, nitrogenous bases, and another substituent. Polar compounds composed of alcohol attached by phosphodiester bridge to either diacylglycerol or sphingosine.
Amphipathic in nature has a hydrophilic head (phosphate +alcohol
eg., serine, ethanolamine, and choline) and a long, hydrophobic tail
(fatty acids or derivatives ).
- CLASSIFICATION OF PHOSPHOLIPIDS:-
- Glycerophospholipids
- Spingophospholipids or Sphingomyelin
- SYNTHESIS OF PHOSPHOLIPIDS
- FUNCTIONS OF PHOSPHOLIPIDS
- FUNCTIONS OF SPHINGOLIPIDS
introduction of Purine and Pyrimidine metabolism, biosynthesis and degradation of nucleotides, biological functions and metabolic disorders, chemical analogues and therapeutic drugs, uric acid metabolism
Digestion of proteins, absorption of amino acids, synthesis of amino acids, catabolism of amino acids and synthesis of specialised non-protein compounds from amino acids for undergraduates
Slideshow is from the University of Michigan Medical School's M1 Renal sequence
View additional course materials on Open.Michigan:
openmi.ch/med-M1Renal
DNA replication, repair and recombination NotesYi Fan Chen
DNA, replication, repair and recombination Notes based on Molecular biology of the cell. Biology Elite: biologyelite.weebly.com, please use together with the presentation
Lecture 1 part.1 Structure and Function of Nucleic AcidDrQuratulAin5
This presentation is the part of Molecular Biology and Genetic course that would describe you about structure and function of nucleic acid and there types
nucleotide chemistry & metabolism will help to students to gain knowledge about molecular basics & drugs used in certain cancer therapies , viral disorders etc.
This presentation deals with Thiamine Pyrophosphate (TPP), Pyridoxal Phosphate (PLP) and Coenzyme- A .
A brief description about Vitamins and Co enzymes. Then synthesis and application of PLP, TTP and Co-enzyme A
GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
Guy Korland, CEO and Co-founder of FalkorDB, will review two articles on the integration of language models with knowledge graphs.
1. Unifying Large Language Models and Knowledge Graphs: A Roadmap.
https://arxiv.org/abs/2306.08302
2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs:
https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/
Generating a custom Ruby SDK for your web service or Rails API using Smithyg2nightmarescribd
Have you ever wanted a Ruby client API to communicate with your web service? Smithy is a protocol-agnostic language for defining services and SDKs. Smithy Ruby is an implementation of Smithy that generates a Ruby SDK using a Smithy model. In this talk, we will explore Smithy and Smithy Ruby to learn how to generate custom feature-rich SDKs that can communicate with any web service, such as a Rails JSON API.
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
Do you want to learn how to model and simulate an electrical network from scratch in under an hour?
Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)!
During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
- For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.
Neuro-symbolic is not enough, we need neuro-*semantic*Frank van Harmelen
Neuro-symbolic (NeSy) AI is on the rise. However, simply machine learning on just any symbolic structure is not sufficient to really harvest the gains of NeSy. These will only be gained when the symbolic structures have an actual semantics. I give an operational definition of semantics as “predictable inference”.
All of this illustrated with link prediction over knowledge graphs, but the argument is general.
Slack (or Teams) Automation for Bonterra Impact Management (fka Social Soluti...Jeffrey Haguewood
Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
We believe integration and automation are essential to user experience and the promise of efficient work through technology. Automation is the critical ingredient to realizing that full vision. We develop integration products and services for Bonterra Case Management software to support the deployment of automations for a variety of use cases.
This video focuses on the notifications, alerts, and approval requests using Slack for Bonterra Impact Management. The solutions covered in this webinar can also be deployed for Microsoft Teams.
Interested in deploying notification automations for Bonterra Impact Management? Contact us at sales@sidekicksolutionsllc.com to discuss next steps.
Accelerate your Kubernetes clusters with Varnish CachingThijs Feryn
A presentation about the usage and availability of Varnish on Kubernetes. This talk explores the capabilities of Varnish caching and shows how to use the Varnish Helm chart to deploy it to Kubernetes.
This presentation was delivered at K8SUG Singapore. See https://feryn.eu/presentations/accelerate-your-kubernetes-clusters-with-varnish-caching-k8sug-singapore-28-2024 for more details.
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024
https://alandix.com/academic/papers/synergy2024-epistemic/
As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.
Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. What’s changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
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However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks.
In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
De-mystifying Zero to One: Design Informed Techniques for Greenfield Innovati...
Synthesis of nucleotides_11
1. Metabolism of purine and pyrimidine nucleotides Department of Biochemistry 2011 (E.T.)
2.
3. Significance of folic acid for synthesis of bases Folát Green food, liver, food yeast, egg yelow The effective form in organism of human is tetrahydrofolate N N O H N N C H 2 N H 2 N C O N H C H C H 2 C H 2 C O O - C O O - H
4. (dihydro)folate reductase (catalyzes the both reactions in animals and some microorganisms) folate tetrahydrofolate dihydrofolate NADPH + H + NADP NADP NADPH + H + N N O H N H 2 N C O N H C H C H 2 C H 2 C O O - C O O - H C H 2 N N H Formation of tetrahydrofolate + +
5. Methotrexate (anticancer drug) Inhibitors of (dihydro)folate reductase: Trimethoprim (bacteriostatics) it inhibits bacterial dihydrofolate reductase N N
6. N-5,N-10- methylen H 4 F – synthesis of thymine N-10-formyl H 4 F – synthesis of purine 5 10 1 3 Using of tetrahydrofolate in synthesis of purines and pyrimidines N N O H N H 2 N C O N H C H C H 2 C H 2 C O O - C O O - C H 2 N N H C H 2 N N O H N H 2 N C O N H C H C H 2 C H 2 C O O - C O O - C H 2 N N H C H O H
7. Significance of glutamine for biosynthesis of purines and pyrimidines - It is donor of amino group Why the cells with high mitotic rate consume high amounts of glutamine?
8. Required for synthesis of: purine nucleotides pyrimidine nukleotides NAD + , NADP + PRPP – phosphoribosyl diphosphate Activated pentose
9. Ribose-5P + ATP PRPP + AMP PRPP-synthase Synthesis of phosphoribosyl diphosphate (PRPP) (kinase)
10. Differences in purine and pyrimidine synthesis Purines Synthesis starts with PRPP, purine ring is built step-by-step with C-1 of PRPP as a primer Pyrimidines The pyrimidine ring is synthetized before ribose is added
11.
12.
13. Comparision of carbamoyl phosphate synthetases inhibition: UTP activation: ATP activation: N-acetylglutamate Regulation glutamin ammonia Source of nitrogen synthesis of pyrimidine synthesis of urea Metabolic pathway cytoplasma mitochondria Localization in the cell Carbamoyl phosphate synthetase II Carbamoyl phosphate synthetase I Enzyme typ
14. Steps in pyrimidine biosynthesis - in detail Carbamoyl aspartate dihydroorotate orotate Orotidine monophophate PRPP Uridine monophosphate
15. ATP Biosynthesis of UTP a CTP Phosphorylation using ATP UMP UDP ADP ATP ADP + P glutamin glutamate CTP ATP ADP UTP
16. Formation of dTMP (methylation) H 4 F is required for methylation The methyl donor is methylen-H 4 folate which becomes oxidized during transfer.
17. UDP dUDP dUMP TMP Methylene –H 4 F DHF serine Thymidylátsynthasa (enzym závislý na folátu) Dihydrofolátreduktasa glycin Formation of dTMP NADPH NADP Methylene group bonded to H 4 F is during the transfer to dUMP reduced to methyl group H 4 F
18. UDP dUDP dUMP TMP Thymidylate synthase (folate dependent enzyme) Dihydrofolate reductase Formation of TMP NADP After release of methylene H 4 F becomes oxidized to H 2 F Methylene –H 4 F H 2 F serin H 4 F glycin NADPH
19. N N O H N H 2 N C O N H C H C H 2 C H 2 C O O - C O O - C H 2 N N H C H 2 N N O H N H 2 N C O N H C H C H 2 C H 2 C O O - C O O - C H 2 N H N NADPH + H + NADP + CH 2 CH 2 -H 4 F H 2 F H 4 F H H H H Dihydrofolate reductase
20. (Dihydro)folate reductase reduces dihydrofolate (H 2 F) back to tetrahydrofolate (H 4 F) Why metotrexate (amethopterine) functions as antineoplastic agent?
21.
22. Dihydrofolate reductase - target of anti-tumour therapy . Aminopterin (4-amino-dihydrofolate) and methotrexate (amethopterin, 4-amino-10-methyl-dihydrofolate) are anti-folate drugs - potent competitive inhibitors of dihydrofolate reductase. They bind the enzyme 1000x more tightly than folate, they function as competitive inhibitors.
23. Also thymidylate synthase can be inhibited Cytostatic effect – cell division is stopped Fluorouracil is converted in vivo into fluorodeoxyuridylate It irreversibly inhibits thymidylate synthase (suicide inhibition) All antineoplastic drugs are toxic not only for cancer cells but for all rapidly dividing cells, including those in bone marrow, intstinal mucosa and hair bulbs. Therefore, bone marrow depression, diarrhea, and hair loss are common side effects of cancer chemotherapy.
24. Formation of pyrimidine nucleotides by salvage pathway (using of free bases for the synthesis) Thymine Deoxyribose-1- phosphate P i Thymidine 1. Relatively non-specific pyrimidine nucleoside phosphorylase converts the pyrimidine bases to their nucleosides Uracil or Cytosine Ribose-1-phosphate P i Uridine Nebo Cytidine
25.
26.
27. Degradation of pyrimidine nucleotides Free bases are converted to: NH 3 , CO 2 , -alanine, ( -aminoisobutyrate) Soluble metabolites – excretion in urine deamination reduction -alanin -aminoisobutyrate from thymine Dephosphorylation and cleavage of nucleosides.
28. Ribose-5-phosphate 3 glycin HCO 3 - aspartate formyl-H 4 F glutamine 1 PRPP formyl-H 4 F 2 4 6 7 8 Biosynthesis of purine nucleotides (multienzyme complex) Inosine-5-P (IMP) 5 cytoplasma Mainly in liver N H N O N N C C C
29. Biosynthesis of IMP in more details Gln Glu Inosine monophosphate ATP, glycin ADP Formyl-THF THF Glu Gln H 2 O CO 2 asp formylTHF THF H 2 O fosforibosylamin PRPP
30. Inosine-5-P (IMP) Serves as the branchpoint from which adenine and guanine nucleotides can be produced aspartate, GTP amination AMP oxidation amination GMP Glutamine, ATP XMP mycofenolic acid N N O N N H ribose-5-P
31.
32. Synthesis of AMP and GMP (more detailed) IMP Asp GTP GDP + Pi fumarate AMP NAD + NADH + H + ATP AMP + PPi XMP GMP Gln Glu H 2 O N N O N N R i b o se H P N N N C H C H 2 C O O C O O N N R i b o se P - - N N N H 2 N N R i b o se P N N O O N N R i b o se H P N N O H 2 N N N R i b o se H P H H
33.
34. Synthesis of purine nucleotides by salvage pathway Extrahepatal tissues Recyclation of free bases Purine + PRPP purine nucleotide monphosphate + PP Phosphoribosyltransferases: Adenine phosphoribosyltransferase Hypoxantine phosphoribosyltransferase Recyclation of purine bases by phosphoribosyltransferase
35. Formation of purine nucleotides by the action of phosphoribosyl transferases
36.
37. Synthesis of nucleoside diphosphates and nukleoside triphosphates Nucleoside monophosphate Nucleoside diphosphate Nucleoside triphosphate ATP ADP ATP ADP kinases
38.
39. Formation od 2-deoxyribonucleotides (purine and pyrimidine) Nucleoside diphosphate 2-deoxynucleoside diphosphate reduction Thioredoxin, thioredoxin reductase and NADPH are required H Thioredoxin reductase is selenoenzyme deoxygenation
42. Degradation of purine nucleotides AMP,GMP, IMP,XMP 5-nucleotidase guanosine, inosine, xantosine + P i nukleosidfosforylasa Adenosine + P i , guanin, hypoxantin, xantin + riboso-1-P adenosindeaminasa inosin nukleosidfosforylasa odštěpení fosfátu In liver
43. AMP,GMP, IMP,XMP 5-nucleotidase guanosine, inosine, xantosine + P i nucleoside phosphorylase Adenosine + P i , guanine, hypoxantine, xantine + ribose-1-P Adenosine deaminase inosine nucleoside phosphorylase Degradation of purine nucleotides
44. Adenosine deaminase deficiency Enzyme deficiency acummulation of adenosine in cells (esp. lymphocytes) conversion to AMP,dAMP, ADP by cellular kinases. Inhibition of ribonucleotide reduktase Synthesis of other nucleotides drops Cells cannot make DNA and devide. One of the causes severe combined immunodeficiency disease (SCID).
45. hypoxantine xantine Uric acid Xantine oxidase guanin guanase Final product of human purine degradation (400-600 mg /day) Inhibition by oxypurinol Degradationof purine bases
46.
47. Allopurinol – in the body is converted to oxypurinol - competitive inhibitor of xantinoxidase Treatment of gout : oxypurinol inhibits xantine oxidase More soluble xantine and hypoxantine are accumulated. Hypoxantine can be „salvaged“ in patients with normal level of hypoxantine phosphoribosyltransferase.
49. Replication of DNA Each of the two parental strands serves as a template for the synthesis of complementary strand Bases in the new strand are attached on the principle of complementarity to the bases in the template strand Location: nucleus
50. Non protein substrates necessary for replication template Mateřské strand of DNA Initiation of replication primer RNA cofactor Mg 2+ High energy substrate dATP, dCTP, dGTP, dTTP Function Compound
51. Enzymes and other proteins involved in replication (different for prokaryotes and eukaryotes) Catalyzes joining of DNA fragments DNA-ligase catalyzes joining of nucleotides to 3´-terminal of the growing chain DNA-dependent DNA polymerases RNA primer formation RNA polymerase (primase) Unwinding enzyme ( ATP is required) Helicase Function Enzyme
52. Enzymy a pomocné proteiny pro syntézu DNA (pokračování) prevents this DNA polymerase from dissociating from the template DNA strand Sliding clamp Function Enzym enable s replication at the 3´-ends of linear chromosomes (not present in all cells) Telomerase Hydrolyzes RNA from RNA-DNA hybrids RNA-nuclease Relieve torsional strain on parental duplex caused by unwinding Topoisomerase prevention of reannealing SSB-proteins
53. The all DNA polymerases attach nucleotides on 3´-end of a growing chain (new DNA is formed in the direction 5´ 3´) Chemical reaction of DNA synthesis Synthetic process is catalyzed by DNA-polymerases Already formed strand (DNA or RNA) reacts with deoxyribonucleoside triphosphate (dNTP) Diphosphate is released and dNMP is attached by ester bond
54. Formation of a bond between new deoxynucleotide and the chain of DNA during elongation dNTP-2 reacts with 3´-terminal of the growing chain 3´-terminal of the growing chain
55. Chain elongation dNTP3 + PPi Ester bond is formed between the 3´-OH group of growing chain and 5´-phosphate of entering nucleotide 5´ 3´ Diphosphate is released (complexed with Mg 2+ ions).
56. Some anticancer and antiviral drugs are nucleotides missing the 3‘ OH. Such "dideoxy" nucleotides shut down replication after being incorporated into the strand. Fast-replicating DNA in cancer cells or viruses is inactivated by these drugs. Significance of 3‘OH group
57.
58.
59. Ori-binding proteins Origin (rich in A,T sequences) Denaturation in A,T site Replication starts in the origine and continues untill both forks meets Initiation in prokaryotes
60. Nuclear DNA is replicated only in the S phase of the cell cycle , mitosis takes place after the replication of all DNA sequences has been completed. Two gaps in time separate the two processes. Eukaryotic DNA replication synthetic phase - replication of DNA (6 – 8 h) preparation for mitosis - G 2 (2 – 6 h) G 1 ( ~ 10 h) or G 0 (variable quiescence phase) M mitosis and cell division (1 h) S
61.
62. Eukaryotic DNA replication 3´ 5´ Direction of replication origin Replicon ( replication eye or bubble ) joining of replicons Replication forks
63. Unwinding protein (ATP-dependent) (helicase) ATP ADP Proteins stabilizing single strand structure (ssb-proteins single strain binding) Proteins that are involved in unwinding and prevention of reannealing 3´ 5´
64.
65. DNA polymerase initially adds a deoxyribonucleotide to the 3´-hydroxyl group of the primer and then continues adding deoxyribonucleotides to the 3´-end 3´ 5´ Primer RNA New DNA
66. RNA primer is subsequently removed by the action of exonuclease and the gap is filled by by DNA polymerase Degraded RNA 3´ 5´
67. Synthesis of DNA proceeds always in 5´ 3´ direction The synthesis of new DNA along the A parental strand occurs without problems 3´ Parental chain A (leading strand) Parental chain B (lagging strand) How will occur the synthesis among the B chain? 5´ 5´
68. The lagging strand is synthetized discontinuously – Okazaki fragments are formed Okazaki fragments Okazaki fragments are synthesized 5´ 3´ direction 3´ 5´ 5´ 3´ RNA primer new DNA
69. Okazaki fragments 3´ 5´ 5´ 3´ As replication progress, the RNA primers are removed from Okazaki fragments. DNA polymerase fills the gaps produced by removal of the primers.DNA ligase will join the fragments of DNA Lagging strand – replication occurs discontinuously in direction away from the fork
70. *The main enzyme of replication Prokaryotic DNA-polymerases 3´->5´ Replication, proofreading and editing DNA polymerase III* 3´->5´ DNA repair DNA polymerase II 5´ ->3´ and 3´->5´ Filling if gap after removal RNA primer, DNA repair, removal of RNA primers DNA polymerase I Exonuclease activity Polymerase activity (for all enzymes 5´ -> 3´) Polymerase
71. * At least 9 polymerases is known **major replicative enzyme Eukaryotic DNA-polymerases 3´->5´ replication DNA polymerase 3´->5´ replication, DNA repair DNA polymerase ** 3´->5´ replication in mitochondria DNA polymerase no DNA repair DNA polymerase no replication, DNA repair DNA polymerase Exonuclease activity Polymerase activity (for all enzymes 5´ -> 3´) Polymerase*
72. Topoisomerase (Topology od DNA = tridimensional structure of DNA) Topoisomerase regulates the formation of superhelices These enzymes catalyze the concerted breakage and rejoining of DNA strands, producing a DNA that is more or less superhelical than the original The precise regulation of the cellular level of DNA superhelicity is important to facilitate protein interaction with DNA DNA topoisomerases have many functions (at replication, transcription, repairs, etc.) http://www.youtube.com/watch?v=EYGrElVyHnU positive negative supercoiling
73. Supercoiling at unwinding double helix DNA Positive supercoiling Negative supercoiling DNA topoisomerases have many functions (at replication, transcripti, repair, …)
74. Make a transient single-strand break in negatively supercoiled DNA double helix. Passage of the unbroken strand through the gap eliminates one supercoil from DNA. Energy is not required. Present in prokaryotes and eukaryotes. Topoisomerase I Topoisomerase II It binds to double helix DNA and cleave both strands. It can relax supercoiled DNA or introduce supercoil into DNA. Present in prokaryotes and eukaryotes. Requires ATP cleavage energy. .
75. Action of topoisomerase I Interuption of phosphodiester bond followed by rotation around the second strand and closing the break by ligation
76. Inhibitors of human topoisomerase prevent replication Antineoplastic drugs Examples of topoisomerase inhibitors camptothecine – plant product antracyclines (daunorubicine) -bacterial products podophyllotoxines-plant product
79. Telomeres As DNA replication approaches the end of chromosome, a problem develop with lagging strand. Either primase cannot lay down a primer at very end of the chromosome, or after DNA replication is complete, the RNA at the end is degraded. Consequently, the newly synthesized strand is shorter at the 5´end, and there is 3´-overhang in DNA strand being replicated. Lagging strand RNA primer 3´overhang 5´terminal Template strand B Telomers are special sequences at the ends of chromosomes Tandem repeats od species-specific oligonucleotides, G-rich (in human TTAGGG up to 1000x) They protect the ends of chromosomes against nuclease activities. telomeric DNA
80.
81. Telomerase action Replicating leading strand is not included in the scheme RNA template RNA-primer Telomerase action Lagging strand 5´-ending strand is extended by normal lagging strand synthesis replicated strand complementary to the 3´-end of the chromosome 5´- 3´- pol
82. ? Does the length of telomers correlate with the age of the cell and its replication capacity? The inability to replicate telomeres has been linked to cell aging and death Many somatic cells do not express telomerase – when placed in culture, they survive a fixed number of population doublings, enter senescence and then die. Analysis has shown significant telomere shortening in those cells. In contrast, stem cells do express telomerase and appear to have an infinite lifetime in culture. Therefore research is focused on understanding of the role of telomeres in aging, growth and cancer
83. It is estimated that the number of damaging interventions into the DNA structure in the human cell is about: 10 4 -10 6 /day In addult human (10 12 cells) it results in 10 16 -10 18 repair processes per day. DNA damage and repair
84. DNA damage and repair Spontaneous and temporary Tautomer formation Chemicals (derivateves of psoralene, mitomycine C) Cross-linkages Ionizing radiation, chemicals (bleomycine) Strand breaks UV radiation Formation of dimers Intercalating drugs (acridines) Deletion-insertion Spontaneous deamination Non-correct base Ionizing radiation, alkylating agents Altered base Depurination (10 4 purines/day) Missing base Cause of damage Type of damage
85. All cells are able to recognize damaged DNA and possess highly efficient mechanisms to repair modified or damaged DNA. DNA repair enzymes: Specific glycosylases can eliminate altered bases by hydrolysis of the N -glycosidic bond between the base and deoxyribose; specific endonucleases cause break s in the strand , 5´ - 3´ exonucleases excise one or more nucleotides from the strand DNA polymerase fills in the gap , DNA ligase rejoins the DNA strand. The two major repair pathways are b ase excision repair and nucleotide excision repair .
86. Examples: Base excision repair Cytosine has been deaminated to uracil: Uracil N-glycosylase removes the base, an AP site (apyrimidinic site) exists - the ribose phosphate backbone is intact, the base is missing. The gap is filled in by insertion of cytidine phosphate by DNA polymerase and the corrected strand resealed by DNA ligase . AP endonuclease splits the phosphodiester bond adjacent to the missing base, the residual deoxyribose unit is excised by exonuclease (or deoxyribose phosphodiesterase). 5´- ATGC C GCATTGA 3´- TACGGCGTAACT 5´- ATGC U GCATTGA 3´- TACGGCGTAACT 5´- ATGCCGCATTGA 3´- TACGGCGTAACT 5´- ATGC GCATTGA 3´- TACGGCGTAACT 5´- ATGC GCATTGA 3´- TACGGCGTAACT
87. Nucleotide excision repair Thymine dimer has been formed by UV radiation: DNA polymerase carries out the repair synthesis. The distortion induced by the pyrimidine dimer is recognized by the multisubunit complex. Endonuclease called excinuclease cuts the strand at (not closely adjacent) phosphodiester bonds on the dimer's 5´- and 3´-sides, and The 3´-end of the newly synthesized DNA stretch and the original part of the DNA chain are joined by DNA ligase. 5´- ATGCCGCA TT GATAG 3´- TACGGCGTAACTATC 5´- ATGCCGCA TT GATAG 3´- TACGGCGTAACTATC 5´- AT AG 3´- TACGGCGTAACTATC 5´- AT GCCGCATTGAT AG 3´- TACGGCGTAACTATC 5´- ATGCCGCATTGATAG 3´- TACGGCGTAACTATC exonuclease catalyzes excision of the oligonucleotide.