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Structure and Properties of Biopolymers - MB140P37
Title: Struktura a vlastnosti inf. biopolymerů
Czech title: Struktura a vlastnosti inf. biopolymerů
Guaranteed by: Department of Genetics and Microbiology (31-140)
Faculty: Faculty of Science
Actual: from 2022 to 2023
Semester: summer
E-Credits: 5
Examination process: summer s.:combined
Hours per week, examination: summer s.:3/2, Ex [HT]
Capacity: 250
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Level: basic
Explanation: Přihlašovací údaje do Moodle se dozvíte na první přednášce.Pokud bude výuka probíhat online, bude využit systém Zoomhttps://cuni-cz.zoom.us/j/97168520616
Additional information: http://dl2.cuni.cz/course/view.php?id=260
Note: enabled for web enrollment
Guarantor: doc. RNDr. Radovan Fišer, Ph.D.
Teacher(s): doc. RNDr. Radovan Fišer, Ph.D.
Annotation -
Last update: doc. RNDr. Radovan Fišer, Ph.D. (02.02.2021)
The lecture (in Czech) is focused
(a) on description of molecular structures of biopolymers (proteins and nucleic acids) and their subunits, including conformational polymorphism, polymorphism of sequences, special structures and topology of nucleic acids,
(b) properties of biopolymers, which are important for their function, determination of their concentration, isolation, separation, sequencing, denaturation, reassociation, degradation, modification and analysis and
(c) basic methods exploited for separation and analysis of biopolymers especially those which are important in connection with genetic engineering - techniques.
The lecture is an extension of the lecture "Molecular biology" and complementary to "Genetic engineering". Moodle and PyMOL tools are used during the course. If the lessons take place online, the Zoom system will be used (the link will be sent to enrolled students by e-mail).

Literature -
Last update: doc. RNDr. Radovan Fišer, Ph.D. (02.02.2021)

The course materials will be updated in the moodle environment https://dl2.cuni.cz/

Online lectures and exercises will take place using the Zoom system. Students will have recordings of lectures available.


Literature (in Czech):
Voet P. a Voet J.G. (překlad Kotyk et al 1994) Biochemie, nakladatelství AVČR ACADEMIA, Praha
(Vybrané kapitoly týkající se NA+proteinů a jejich stavebních jednotek)

Vondrejs et al. Genové inženýrství I. II. III. IV.
(Vybrané kapitoly týkající se metod pro separaci a analýzu NA+ proteinů založených na vlastnostech biopolymerů)

Vacík a kol. : Přehled středoškolské chemie SPN 1999 str. 64-106


Software:
PyMOL http://www.pymol.org/

On-line sources:
http://www.umass.edu/molvis/workshop/ 
http://www.proteopedia.org/
https://fold.it
Requirements to the exam -
Last update: doc. RNDr. Radovan Fišer, Ph.D. (25.10.2019)
 
Please note, the lectures are given in Czech language only.
The exam takes the form of a test on the following topics:

1) Formulas, names and abbreviations of subunits and precursors of nucleic acids derived from major bases (+ pseudouridine, dideoxyNTP). Spatial arrangement and properties of these structures, keto-enol, amino-imino tautomers, atom numbering and torsion angle marking, base analogs, mutability, hydration, hydrogen bridges, Watson-Crick base pairs.

2) Coded amino acids-names, three-letter abbreviations, dissociation and association patterns, approximate values of pKa groups and their names, acidic, basic neutral amino acids, polar and non-polar, aromatic, containing S, -OH and various other groups. Chirality, hydrogen bridges and hydration, peptide and isopeptide bond- mesomerism.

3) Basic concepts, formulas and small tasks to solve around the structure and properties of biopolymers.

4) Small tasks about using and applying methods for analysis and separation of biopolymers.

 

A total of 3 optional tests are written during the exercises, the results of which are reflected in the final grade.

 
There are no substitute dates for ongoing tests. The resulting mark "excellent" can be achieved even without continuous tests.
The tutorial is supplemented by tasks assigned in the Moodle environment. Solving these tasks is not necessary, but is appropriate. Some exam questions will follow up on the Moodle tasks.

The result will show the following results:

A = 1st optional test -> max. 7 points
B = 2nd optional test -> max. 7 points
C = 3rd optional test -> max. 7 points
Z = Test result -> 0 - 100 points

If Z is> 60, then:
The sum of points X = A + B + C + Z

If Z <60, then:
The sum of points X = Z

Marking:
X> 90 => grade 1
X ∊ (75-90) => grade 2
X ∊ (60-75) => grade 3
X <60 => failed

This means that who does not pass the test will not help him / her. Others may improve grades due to optional tests.
 
Syllabus -
Last update: doc. RNDr. Radovan Fišer, Ph.D. (02.02.2021)

Please note, the lectures are given in Czech language only.

The lecture will be recorded by the teacher (sound + projected image). These materials will be accessible online.

TOPICS:

Structure and properties of DNA, RNA and their subunits

Conformational polymorphism, sequence polymorphism, structural anomalies and DNA topology
Electron microscopy of nucleic acids
Denaturation and reassociation analysis of nucleic acids, reassociation probes and matrices (microarrays)


Structure and properties of proteins and their subunits

Determination of molar mass of protein molecules
Protein mass spectrometry

Overview of separation and purification techniques

Sedimentation analysis of biopolymers, moving interface method, differential, isokinetic and isopycnic centrifugation
Electrophoretic analysis and separation of biopolymers including pulse electrophoresis
Chromatography

Determination of concentration of information biopolymers (spectrophotometry, fluorimetry and colorimetry)

DNA, RNA and protein sequencing

Details of quantitative polymerase chain reaction (Real-time PCR or qPCR)

Determination of structure and interactions of DNA, RNA and proteins (basics of MS, NMR, X-ray diffraction)

Methods of monitoring gene expression, resp. representation of various RNAs or proteins in biological objects

Much of the practical exercises use PyMOL. It is advisable to carry your own notebook with you (the teacher announces in advance when it is needed).
 
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