Лекции „Обмяна на веществата (Метаболитни процеси) Организатори: ими-бан и Биомат Форум; лектор: Светослав Марков Лекция 1 ими, зала 164, 26. 11. 2015, 16 17 ч. Съдържание



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Курс лекции „Обмяна на веществата (Метаболитни процеси)”

Организатори: ИМИ-БАН и Биомат Форум; лектор: Светослав Марков



Лекция 1 ИМИ, зала 164, 26.11.2015, 16 – 17 ч.

Съдържание

А. Мотивация: управление на обмяната на веществата

Б. Основни понятия



Метаболизъм (в клетка) >10^13

https://bg.wikipedia.org/wiki/Клетка

https://bg.wikipedia.org/wiki/Метаболизъм

https://bg.wikipedia.org/wiki/Метаболитен_път

Ензими и белтъци, аминокиселини

https://bg.wikipedia.org/wiki/Ензим

https://bg.wikipedia.org/wiki/Белтък

https://bg.wikipedia.org/wiki/Аминокиселина

https://en.wikipedia.org/wiki/Essential_amino_acid

Каршиков, А., Белтъчна структура - анимация MPG

Нуклеотиди, ДНК, РНК

https://bg.wikipedia.org/wiki/Нуклеотид

https://bg.wikipedia.org/wiki/Дезоксирибонуклеинова_киселина

https://bg.wikipedia.org/wiki/Рибонуклеинова_киселина

Рибозоми

https://bg.wikipedia.org/wiki/Рибозома

Метаболитни пътеки и мрежи

https://bg.wikipedia.org/wiki/Метаболитен_път

Лекция 2 ИМИ, зала 164, 21.01.2016, 15 – 16:30 ч.

Съдържание

В. Генна експресия Централна догма в молекулярната биология

Преговор


https://bg.wikipedia.org/wiki/Клетка

https://bg.wikipedia.org/wiki/Генна_експресия

https://bg.wikipedia.org/wiki/Централна_догма_в_молекулярната_биология

Видове белтъци според техните функции



https://bg.wikipedia.org/wiki/Ензим

https://bg.wikipedia.org/wiki/Рецептор

https://bg.wikipedia.org/wiki/Йонен_канал

https://bg.wikipedia.org/wiki/Хормон

Белтъчни структури (органели)



https://bg.wikipedia.org/wiki/Калиево-натриева_помпа

https://bg.wikipedia.org/wiki/Антитяло

https://bg.wikipedia.org/wiki/Рибозома

https://bg.wikipedia.org/wiki/Лизозома

https://bg.wikipedia.org/wiki/хранене

Известни режими на хранене и диети

http://www.hisarlaka.com/dieti/1586-dietata-na-petya-raeva.html

Кleta4no hranene

https://www.zdravoslovno.com/blog/barbara-wren

http://e-zdrave.eu/index.php?route=product/category&path=53_54

http://www.alloe.net/publikacii/kleta4no%20hranene.pdf

Gabriel method



http://www.thegabrielmethod.com/

http://www.dietsinreview.com/diets/the-gabriel-method/

Paleo Diet



https://en.wikipedia.org/wiki/Paleolithic_diet

English version

Lecture course “Metabolic processes”

Contents


  1. Motivation: Management of metabolic processes and diseases– some examples

Metabolic management of brain cancer

http://www.sciencedirect.com/science/article/pii/S0005272810006857

Metabolic Processes of osteoarthritis

http://www.limbrel.com/hcp-metabolic-processes.php

http://www.genome.jp/kegg/

  1. Preliminaries: Basic knowledge

Metabolism (in the cell) >10^13 cells in humans

https://en.wikipedia.org/wiki/Cell_(biology)

https://en.wikipedia.org/wiki/Eukaryote

https://en.wikipedia.org/wiki/Metabolism

https://en.wikipedia.org/wiki/Metabolic_pathway

http://www.metabolicvisualizer.org/

http://www.wikipathways.org/index.php/WikiPathways

Enzymes & proteins

https://en.wikipedia.org/wiki/Enzyme

https://en.wikipedia.org/wiki/Enzyme#Metabolism

https://en.wikipedia.org/wiki/Protein

https://en.wikipedia.org/wiki/Amino_acid

http://highered.mheducation.com/sites/0072943696/student_view0/chapter2/animation__protein_denaturation.html

https://www.youtube.com/watch?v=qBRFIMcxZNM

http://www.bcconline.com/biol10rs/Pearson-Animations/protein_structure.swf

https://en.wikipedia.org/wiki/Essential_amino_acid

Karshikoff, A., Protein structucture animation MPG



Nucleotides

https://en.wikipedia.org/wiki/Nucleotide

https://en.wikipedia.org/wiki/Transcription_%28genetics%29

https://en.wikipedia.org/wiki/Messenger_RNA

https://en.wikipedia.org/wiki/Translation_%28biology%29

Signalling pathways

https://www.google.bg/?gfe_rd=cr&ei=sv1SVoe9BbCz8weotaLACA&gws_rd=ssl#q=signalling+pathways+ppt

https://www.google.bg/?gfe_rd=cr&ei=sv1SVoe9BbCz8weotaLACA&gws_rd=ssl#q=signalling+pathways+ppt

Gene expression

https://en.wikipedia.org/wiki/Gene_expression

Ribosomes

https://en.wikipedia.org/wiki/Ribosome

https://www.dnalc.org/view/16933-3D-Animation-of-DNA-to-RNA-to-Protein.html

https://www.dnalc.org/view/15501-Translation-RNA-to-protein-3D-animation-with-basic-narration.html

  1. Biomathematics perspective

Enzyme kinetics

https://en.wikipedia.org/wiki/Enzyme_kinetics

The law of mass action

https://en.wikipedia.org/wiki/Law_of_mass_action

Cato M. Guldberg and Peter Waage between 1864 and 1879 in

The law of Victor Henri

https://en.wikipedia.org/wiki/Victor_Henri

http://www.biomath.bg/s%20markov%20publications/A2014-BMC-Stanko-Gergana.pdf

http://www.biomath.bg/s%20markov%20publications/A20015-MATCOM-Stanko-michaelis.pdf

Bacterial growth

http://www.biomath.bg/s%20markov%20publications/A2015-MathChem_Hausdorff_Dist.pdf

http://www.biomath.bg/s%20markov%20publications/A2013-Biomath-cell-growth.pdf

  1. Management of metabolic processes

Some examples of diseases

https://en.wikipedia.org/wiki/Proteopathy

protein misfolding and disease; the role of chaperones

https://en.wikipedia.org/wiki/Post-translational_modification

Metabolic management of brain cancer

http://www.sciencedirect.com/science/article/pii/S0005272810006857

Metabolic Processes of osteoarthritis

http://www.limbrel.com/hcp-metabolic-processes.php

The microvascular system:

https://en.wikipedia.org/wiki/Capillary

http://cshperspectives.cshlp.org/content/early/2014/10/23/cshperspect.a016345

http://ndt.oxfordjournals.org/content/early/2010/10/08/ndt.gfq635.full

Diabetis

http://www.eufic.org/article/en/diet-related-diseases/obesity/expid/basics-obesity-overweight/

https://cspinet.org/new/pdf/cdc_briefing_book_fy10.pdf

https://en.wikipedia.org/wiki/Metabolic_acidosis

Thyroid diseases

https://en.wikipedia.org/wiki/Thyroid_disease

Glaucoma

https://en.wikipedia.org/wiki/Glaucoma

Management of metabolic processes – some analogues

A state. A home (kitchen). Potato pilling. Robots in war.

Nutrition

https://en.wikipedia.org/wiki/Nutrition

Management of metabolic processes – some known regimes and diets discussed

Familiar nutritional and dieting regimes

Separate nutrition

http://dietsindetails.com/article_separated_nutrition.html

http://joyoflosingweight.com/nutrition/47-separate-nutrition.html

Separate nutrition: optimization of the work of body systems? Article in Russian


Konyshev VA, Vasilevskaia LS

http://www.ncbi.nlm.nih.gov/pubmed/1514251

Fasting

https://en.wikipedia.org/wiki/Fasting

http://jeune-et-randonnee.pagesperso-orange.fr/devries.pdf

http://www.ncbi.nlm.nih.gov/pubmed/24434759

http://news.nationalpost.com/health/therapeutic-fasting-741073

http://nutritionstudies.org/fasting-effective-ancient-therapy-todays-health-concerns/

one day fasting (in joga)



The diet of Petya Raeva

http://www.hisarlaka.com/dieti/1586-dietata-na-petya-raeva.html

Cell nutrition

https://www.zdravoslovno.com/blog/barbara-wren

http://e-zdrave.eu/index.php?route=product/category&path=53_54

http://www.alloe.net/publikacii/kleta4no%20hranene.pdf

Gabriel method



http://www.thegabrielmethod.com/

http://www.dietsinreview.com/diets/the-gabriel-method/

Paleo Diet



https://en.wikipedia.org/wiki/Paleolithic_diet

  1. Personal experience and results


http://www.biomath.bg/S_Markov.php#Publications
http://www.biomath.bg/s%20markov%20publications/A2013-Biomath-cell-growth.pdf
http://www.biomath.bg/s%20markov%20publications/A20015-MATCOM-Stanko-michaelis.pdf


  1. People, books, history


Victor Henri
J. Murray
R. Tsanev

7. Proteopathy
https://en.wikipedia.org/wiki/Proteopathy
CHRISTOPHER M. DOBSON, Protein misfolding, evolution and disease, TIBS 24, 1999
 Reynaud, E. (2010) Protein Misfolding and Degenerative Diseases. Nature Education 3(9):28
http://www.nature.com/scitable/topicpage/protein-misfolding-and-degenerative-diseases-14434929

References and Recommended Reading


Anfinsen, C. B. The formation and stabilization of protein structure. Biochemical Journal 128, 737–749 (1972)

Beadle, G. W. & Tatum, E. L. Genetic control of biochemical reactions in Neurospora. PNAS 27, 499–506 (1941)

Chiti, F. & Dobson, C. M. Protein misfolding, functional amyloid, and human disease. Annual Review of Biochemistry 75, 333–366 (2006)

Dill, K. A. & Chan, H. S. From Levinthal to pathways to funnels. Nature Structural Biology 4, 10–19 (1997)

Dobson, C. M. Protein folding and misfolding. Nature 426, 884–890 (2003) doi:10.1038/nature02261

Dobson, C. M. Protein misfolding diseases: Getting out of shape. Nature 418, 729–730 (2002) doi:10.1038/418729a

Ellis, J. Proteins as molecular chaperones. Nature 328, 378–379 (1987) doi:10.1038/328378a0

Fändrich, M. & Dobson, C. M. The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation The EMBO Journal 21, 5682-5690 (2002).

Finkel, T. Radical medicine: Treating ageing to cure disease. Nature Reviews Molecular Cell Biology 6, 971–976 (2005)

Gamow, G. & Ycas, M. Statistical correlation of protein and ribonucleic acid composition. PNAS 41, 1011–1019 (1955)

Kaufman, R. J., et al. The unfolded protein response in nutrient sensing and differation. Nature Reviews Molecular Cell Biology 3, 411-421 (2002)

Laskey, R. A. et al. Nucleosomes are assembled by an acidic protein which binds histones and transfers them to DNA. Nature 275, 416–420 (1978) doi:10.1038/275416a0

Levinthal, C. Are there pathways for protein folding? Journal de Chimie Physique et de Physico-Chimie Biologique 65, 44–45 (1968)

Lin, M. Y. & Beal, M. F. Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases. Nature 443, 787–795 (2006)


V. Markov
Ivan Mitov, 130th anniversary of Prof. Dr. Vladimir Markov, Biomath 2 (2013), 1312312,

http://dx.doi.org/10.11145/j.biomath.2013.12.312
https://www.google.bg/?gfe_rd=cr&ei=sv1SVoe9BbCz8weotaLACA&gws_rd=ssl#q=nestor+markov&start=10
N. Markov
http://www.sustz.com/Proceeding09/Papers/Social%20studies/History/N_KANEV.pdf
https://bg.wikipedia.org/wiki/%D0%9D%D0%B5%D1%81%D1%82%D0%BE%D1%80_%D0%9C%D0%B0%D1%80%D0%BA%D0%BE%D0%B2

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