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poslední aktualizace Wednesday, 02-Oct-2019 15:52:39 CEST
stránky od 1.9.2011 navštívilo:

Materiály k přednáškám a cvičením (F1190, F5351, F8390, F8380) a praktikům (F5370)
Program Semináře biofyziky a biofyzikální chemie F7790 pro podzimní semestr 2019/20
 


 

F1190


otázky ke zkoušce

 
Biofyzikalni laborator @UFKL

 
Otázky ke zkoušce F1190
  • Nakreslete proteinovou páteř (alespoň pořadí tří aminokyselin) a nakreslete úhly φ a ψ.
  • Napište reakci, při níž vzniká peptidová vazba a popište základní charakteristiky peptidové vazby.
  • Jaké typy aminokyselin (podle chemického charakteru postranních řetězců) se běžně vyskytují v živých organismech. Nakreslete alespoň 5 aminokyselin.
  • Popište α-helix a β-skládaný list a jejich úlohu v terciární struktuře proteinu.
  • Popište, čeho se týkal Anfinsenův experiment.
  • Nakreslete a popište jednu purinovou a jednu pyrimidinovou bázi nukleových kyselin. Popište základní stavební jednotky řetězce nukleových kyselin, uveďte příklady párování bází ve dvojšroubovicích, triplexech nebo kvadruplexech.
  • Popište dvoujšroubovici DNA - velký žlábek, malý žlábek, konformace cukrů, torzní úhly, náboj na cukr-fosfátové páteři, proti-ionty. Kdo jsou objevitelé struktury DNA, jaké znáte alternativní modely?
  • Seřaďte následující sloučeniny podle stoupajícího bodu varu. Odůvodněte pořadí. Pro informaci: body varu jsou: 36, 69, 103, 138, 163, 186 °C.
    n-hexan
    n-pentan
    kyselina n-butanová
    kyselina n-pentanová
    n-pentanal
    n-pentanol
  • a) Jaký je rozdíl v molekulové stavbě mezi nasycenými a nenasycenými mastnými kyselinami?
    b) Jaký je STRUKTURNÍ rozdíl ve stavbě molekul trans-nenasycených a cis-nenasycených mastných kyselin?
    c) Jak se rozdíl z b) projevuje ve stavbě molekulové mřížky a jaký má tento rozdíl vliv na bod varu?
    d) Jaký mají vliv cis-nenasycené a trans-nenasycené kyseliny na lidské zdraví?
  • Popište model tekuté mozaiky. Vysvětlete lipid, monovrstva, dvojvrstva, funkci cholesterolu.
  • Popište fungování Na+/K+ pumpy a její úlohu v buňce.
  • Nakreslete a popište eukaryotní a prokaryotní buňku a stručně popište nejvýznamější rozdíl(y).
  • Při glykolýze je glukóza oxidována pomocí dvou ekvivalentů NAD+, přičemž vznikají dva ekvivalenty pyruvátu, CH3-CO-COO-.
    a) Určete oxidační čísla všech atomů v molekulách glukózy a pyruvátu.
    b) Formulujte rovnice pro oxidaci glukózy na pyruvát a pro redukci NAD+ na NADH.
    c) Napište celkovou rovnici pro oxidaci glukózy na pyruvát pomocí NAD+.
    (Pokud tato otázka bude položena při kolokviu, dostanete vzorec NAD+ (bez oxidačních čísel) jako přílohu. Ten tedy nemusíte znát zpaměti. Nutno ale vědět, kde a jak v molekule nastává redukce.)
  • Vypočtěte meziatomové vzdálenosti N-H, CA-HA, N-CA, CA-C a C=O, pokud znáte:
       ATOM     22  N   ILE A   2      10.475  -0.321   0.272
       ATOM     23  CA  ILE A   2       9.106  -0.195   0.826
       ATOM     24  C   ILE A   2       9.162  -0.298   2.352
       ATOM     25  O   ILE A   2       9.595  -1.341   2.800
       ATOM     30  H   ILE A   2      10.688  -1.266  -0.104
       ATOM     31  HA  ILE A   2       8.723   0.766   0.555
      
  • Nejrozšířenější formou Lennard-Jonesova potenciálu je V = Ar-12 – Br-6 (tzv. potenciál 6-12). Jiná používaná forma vyjadřuje repulzivní energii členem závislým na r-9, tedy V = Cr-9 – Dr-6 (tzv. potenciál 6-9). Předpokládejte, že pro pár atomů A a B znáte parametry pro párový potenciál prvního typu, a potřebujete potenciál nahradit potenciálem druhého typu tak, aby výsledná křívka V = f(r) měla minimum stejné hloubky Vmin = ε pro stejný odstup rmin-. Vypočítejte parametry A a B potenciálu 6-9 pomocí paremetrů C a D potenciálu 6-9.
  • Nakreslete Lewisův vzorec (zohledňující vazebné i nevazebné elektronové páry) pro následující sloučeniny nebo jonty: OH-, H2O, H2O2, N2, HCl, HCN, CH3COOH.
  • Vysvětlete vodíkovou vazbu, typické vzdálenosti a energie.
 

 

 

 

F5351



 

 

F8390



 

F7790

Biofyzikalni laborator @UFKL

 
Semináře CC060, C8010 a F7790 se v jarním semestru 2020 konají v níže uvedených datech (zatím) od 14.00 do 16.00 v místnosti 205 budovy A11 na Univerzitním kampusu Bohunice (UKB).

Obecná doporučení, jak se chovat (nejen) na semináři:
General recommendations how to behave (not only) during the seminar:
 
All I Really Need To Know I Learned In Kindergarten by Robert Fulghum:
Robert Fulghum: Všechno, co opravdu potřebuju znát, jsem se naučil v mateřské školce
 

As of attendance: MU study and examination regulations Section 9, paragraph 2: Full-time students are required to attend teaching activities with the exception of lectures and consultations.
Paragraph 6: A student has the right to a minimum of one unexcused absence per semester from compulsory teaching activities in a given course; this does not apply to intensive courses or specially scheduled courses (section 9, subsection 4). In case a student utilizes the right described in the first sentence, he/she must meet in-term assessment requirements or other conditions associated with teaching activities in a given course, if so prescribed. A higher number of absences may be stipulated by the teacher if so permitted by teaching and study-related conditions.
Paragraph 7: A student is obliged to provide a written excuse letter to the faculty Office for Studies justifying his/her absence within five workdays of the teaching activity he/she was absent from.
 
Na téma docházky: Studijní a zkušební řád Masarykovy univerzity Čl. 9, odst. 2: Účast ve výuce je pro studenty prezenční formy studia povinná s výjimkou přednášek a konzultací.
Čl. 9, odst. 6: Studenti mají během jednoho semestru právo na minimálně jednu neomluvenou absenci v povinné výuce daného předmětu; toto neplatí v případě předmětů, které vyžadují blokovou výuku nebo výuku se zvláštním časovým průběhem (čl. 9 odst. 4). Pokud student využije právo uvedené ve větě první, musí splnit požadavky průběžných kontrol nebo jiné podmínky výuky předmětu, pokud jsou pro daný předmět předepsány. Vyučující může stanovit i vyšší počet absencí, pokud to umožňují podmínky výuky a studia daného předmětu.
Čl. 9, odst. 7: Student je povinen písemně omluvit na studijním oddělení fakulty svou neúčast do 5 pracovních dnů od termínu konání výuky, jež je omlouvána.
 
Prezentace by měly splňovat následující kriteria:
The presentations should follow these criterions:
  • neměly by být kratší 20 minut a delší 30 minut
    shouldn't be shorter 20 minutes and longer 30 minutes
  • měly by být srozumitelné širšímu vědeckému publiku
    should be comprehensible to wider audience
  • měly by obsahovat:
    should include:
    • stručné představení přednášejícího
      short intro of the presenter (the host of the seminar - Žídek / Kubíček - will also introduce the presenter before the presentation)
    • úvod do problematiky
      Introduction
    • popis problému, způsob jeho řešení a cíle
      Description of the problem, aims of the study and your approach to solve your project
    • výsledky
      Results
    • závěr
      Conclusion
  • jsou vedeny v anglickém jazyce
    by default, all lectures are in English
  • přednášející se dostaví v dostatečném předstihu před zahájením semináře a zkontroluje, že veškerá audiovizuální technika funguje a je kompatibilní s připravenou přednáškou
    the presenter is responsible for checking the room and AV-devices being compatible with her/his presentation and make sure that everything is ready to start on time

 
To book your seminar, select available slots: Doodle planning
The doodle planning is to ease planning, provide flexibility and aviod overlaps during the time when the organizers of the seminars do not have access to computer. The selected slots will be then confirmed and listed below.
1 October 8
Thursday
SPEAKER: prof. Lukáš Žídek, Ph.D.; Mgr. Karel Kubíček, Ph.D.
TOPIC: Introductory seminar
WHERE: Google Meet
WHEN: @2PM s.t.
LSSS: Life Sciences Seminars in 2020 are cancelled because of the COVID-19 pandemic.
2 October 15
Thursday
SPEAKER:
TOPIC:
SPEAKER:
TOPIC:
WHERE: Google Meet
WHEN: @2PM s.t.
Instructions to connect: Open Google Meet in your browser (you can find it in Information System, External Servises, G Suite, Meet; it should be sufficient to have a regular .mail.muni.cz account, no extra software or account is needed) Connect to the "ncbr" meeting (I open the meeting shortly before 14:00) Switch off your camera and microphone during the presentation to improve quality of the connection If you have any questions/comments during discussion after the presentation, turn on your microphone to let us know that you wish to ask If anything is unclear, send me an email.
3 November 19
Thursday
SPEAKER: Rahul Deb (Vácha Lab)
TOPIC: Computational Design of Transmembrane Pore-Forming Antimicrobial Peptides
Abstract: Increasing incidences of antibiotic resistance in bacteria represent a global health challenge. Development of new and non-conventional anti-infective therapeutics is needed. Antimicrobial peptides, which can kill bacteria by forming leaky pores in the bacterial cytoplasmic membrane, have potentials to become a novel class of antibiotics. However, de novo design and optimization of peptide pores remain challenging due to the missing guiding rules. Here, we use computer simulation and fluorescent dye leakage experiments to investigate the ability of amphiphilic, α-helical peptides to form and stabilize leaky transmembrane pores. By simulating more than a hundred model peptides, we determine the positions in the sequence which are suitable for pore-stabilizing intermolecular stacking and salt bridge interactions. Based on the findings from simulations, we propose the guidelines for designing stable barrel-stave pore-forming peptides. Designed peptides are verified to form leaky pores by in vitro calcein leakage assay using large unilamellar vesicles. Peptides exhibit a broad spectrum of bactericidal activity against both Gram-negative and Gram-positive bacteria including the ESKAPE pathogens and cause low toxicity to human cells. Our novel sequence patterns with the identified role of individual residues open doors to develop variable transmembrane pores with a wide range of applications including the antimicrobial therapeutics. Increasing incidences of antibiotic resistance ...
WHERE: Google Meet
WHEN: @2PM s.t.
4 December 3
Thursday
SPEAKER: Aliaksei Chareshneu (Koča lab)
TOPIC: NACHRDB: Solving the puzzle of structure-function relationships in nicotinic acetylcholine receptors (nAChRs)
Abstract: The nicotinic acetylcholine receptor (nAChR) is an evolutionary ancient allosteric membrane protein mediating synaptic transmission. This prototypic pentameric ligand-gated ion channel (pLGIC) is expressed in many tissues and species, being involved in a wide range of physiological processes (motor control, attention, learning), pathophysiological processess (myasthenia gravis, snake & cone snail envenomation, Parkinson & Alzheimer diseases, schizophrenia, epilepsy) and addictions (alcohol, tobacco). Recently, potential nAChR implication in COVID-19 pathogenesis became a new emerging research direction. Since nAChR biochemical isolation in 1970, extensive studies produced over 5000 publications with huge amounts of structural-functional data. However, the cumulative residue-level knowledge on nAChRs, spanning 50 years of research, is not systematically accessible. The multitude of receptor types, residue numbering schemes, and methods used, together with diverse terminology and scattered nature of existing findings make it harder to summarize the current knowledge and apply it efficiently to promote further discoveries. There is no single resource providing an access to and visualization of such extensive information. Bridging this gap, we developed NACHRDB (https://crocodile.ncbr.muni.cz/Apps/NAChRDB/) – an interactive web platform providing fast access to relevant structural-functional information on nAChRs and facilitating its interpretation through integration of residue-level functional annotations with 3D visualization and sequence alignment. Besides, NACHRDB contains predictions of residues, potentially relevant for nAChR allostery, derived from computational analyses based on atomic charges’ and channel lining profiles. NACHRDB can help to reveal gaps in current knowledge and guide the further studies on nAChRs, contributing to the clarification of allosteric regulation of this important receptor channel family. The nicotinic acetylcholine receptor (nAChR) is ...
WHERE: Google Meet
WHEN: @2PM s.t.
5 December 10
Thursday
SPEAKER: Ivo Durník (Koča lab)
TOPIC: DNA Damage and Repair
Abstract: Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical properties of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structures suggests the role of DNA bending, the theoretical support is not fully convincing. Here, we present a computational study focused on a base-pair opening into the minor groove, a specific base-pair motion observed upon interaction with MutS. Propensities for the opening were evaluated in terms of two base-pair parameters: Opening and Shear. We tested all possible base pairs in anti/anti, anti/syn and syn/anti orientations and found clear discrimination between mismatches and canonical base-pairs only for the opening into the minor groove. Besides, the discrimination gap was also confirmed in hotspot and coldspot sequences, indicating that the opening could play a more significant role in the mismatch recognition than previously recognized. Our findings can be helpful for a better understanding of sequence-dependent mutability. Further, detailed structural characterization of mismatches can serve for designing anti-cancer drugs targeting mismatched base pairs. Mismatch repair is a highly conserved cellular ...
WHERE: Google Meet
WHEN: @2PM s.t.
6 December 17
Thursday
SPEAKER: Pavlína Pokorná (Šponer lab)
TOPIC: Role of Structural Dynamics in Biomolecular Recognition – a case of HP1 chromodomain.
Abstract: Molecular dynamics (MD) simulations enable studies of structural dynamics with a detailed spatial and temporal resolution, unreachable for any experimental technique. In my talk, I will show how MD technique can be used to unravel the key role of structural dynamics in biomolecular recognition and binding. I will use a case of a well-established methyl-lysine reader – chromodomain of HP1 protein, as an example. HP1 is a multifunctional protein found at chromosomes, shown to bind specific regions of lysine-methylated histone tails. The ARKS amino-acid motif (with methylated K) was originally proposed to be recognized and bound by HP1 chromodomain but not all sequences bearing this motif bind and biding sequence with unusual ATKA motif was later found to bind as well. My MD simulations, based on experimental structures with peptides containing the ARKS motif, show that a larger segment, up to 11 amino-acids, is read by HP1. I will show how very different sequences can bind to the HP1 chromodomain in a very similar manner thanks to the ability of different amino-acid positions to form mutually replaceable interactions and thus substitute for each other. This mutual amino-acid replaceability allows for biding of the ATKA motif, for which I predict the recognition pattern, while it also increases sequence flexibility of the read histone tail segments. Link to the : published work Molecular dynamics (MD) simulations enable ...
WHERE: Google Meet
WHEN: @2PM s.t.

SPEAKER: Klaudia Mráziková (Šponer lab)
Contribution postponed to January 7, 2021 TOPIC: UUCG RNA tetraloop as a force-field challenge
Abstract: UUCG tetraloop is an important stem-loop RNA structure. It is stabilized by molecular interactions like hydrogen bonds, base-base stacking, and sugar-base stacking. The performance of molecular mechanical (MM) force fields used in molecular dynamics simulations is unsatisfactory for UUCG tetraloop. Quantum mechanical (QM) methods are highly accurate computational methods often used to validate or improve MM force fields. Here, I will talk about the force field deficiencies in describing molecular interactions of UUCG tetraloop, revealed by quantum mechanical/molecular mechanical (QM/MM) and QM calculations. This work indicates that the poor behavior of the UUCG tetraloop in the simulations is complex and cannot be attributed to one dominant and straightforwardly correctable factor. Published here UUCG tetraloop is an important stem-loop ...
7 January 7
Thursday
SPEAKER: Klaudia Mráziková
TOPIC:Vide Ultra
Klaudia Mrazikova's talk is uploaded. Please go to IS, study material for CB060 (regardless of what course you enrolled), Homework vaults (Odevzdavarny), talks and watch the record. Link to the: presentation (about 25'46''). We will only have the on-line discussion of the talk, starting at 14:00.
WHERE: Google Meet
WHEN: @2PM s.t.
8 January 14
Thursday
SPEAKER: Aleš Obrdrlík, Ph.D.
TOPIC: Investigating functions of RNA binding proteins in gene expression control
Abstract: Co and post-transcriptional control of gene expression at the level of mRNAs is found in all higher eukaryotes. Herein, RNA binding proteins (RBPs) play an essential role at any level of the mRNA life cycle. In fact, roles of RBPs in mRNA processing, mRNA translation, mRNA surveillance and decay and their impact on cellular homeostasis and development, have been in the focus of life science for more than 40 years. During the last decade, this complex scientific challenge has been expanded even more by the re-discovery of chemical RNA modifications and their potential role in the control of gene expression.
This seminar will cover my research as a postdoctoral fellow at EMBL Heidelberg and will provide a conceptual over-view and insights into preliminary data of my current research activity at CEITEC, in the group of Dr. Stepanka Vanacova.
I will present a new method for isolation of protein complexes and associated RNA-targets (ipaRt), which I have developed to explore transcriptome-wide binding landscapes of the RNA binding Exon-Junction-Complex (EJC) in adult Drosophila melanogaster. I will discuss obtained insights into the regulation of EJC RNA assembly in the fly and conclusions about the functional divergence of EJC during eukaryotic evolution.
Investigating the regulation of m6A RNA modification in mammalian cells, I will present my current work on the mammalian RNA de-methylases FTO and ALKBH5. I will introduce synthetic lethality screening assay, which I utilize to explore genome-wide interactions of the mammalian de-methylases and will present recent results from my screen on FTO.
Co and post-transcriptional control of gene expression ...
WHERE: Google Meet
WHEN: @2PM s.t.


     

     
    ========

    F1190

    Úvod do biofyziky

    F5351

    Základy molekulární biofyziky

    F5370

    Biofyzikální praktikum UFKL

    F6342

    Základy lékařské biofyziky

    F8380

    Základy molekulového modelování a bioinformatiky

    F9600

    Spektroskopické studium biopolymerů

    F9601

    Optické studium jednotlivých molekul

    F9602

    Interakce elektromag. pole se živou hmotou

    F9603

    Od diagnózy k léku

    FA601

    Fotosyntéza

    FA602

    Strukturní biologie: biofyzikální aspekty

    FA603

    Elektronová mikroskopie v biologii

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