The aim of studying and bibliography

The main aim of study: Introduction to the biochemistry: characterisation of key bioactive molecules and process.

The general information about the module: Students will be presented with importance and characterisation of important chemical molecules and will learn about the transformation of those molecules by living organisms.

others: Zasoby internetowe, aktualne publikacje naukowe z zakresu biochemii.

Bibliography required to complete the module

Bibliography used during lectures

1	Berg J.M., Tymoczko J.L., Stryer L.	Biochemia	Wydawnictwo Naukowe PWN, Warszawa.	2011
2	Doonan S.	Białka i peptydy	Wydawnictwo Naukowe PWN.	2008
3	Nelson D.L., Cox M.M.	Lehninger Principles of Biochemistry	W. H. Freeman and Company.	2008

Bibliography used during classes/laboratories/others

1

Kłyszejko-Stefanowicz L., red.

Ćwiczenia z biochemii.

Wydawnictwo Naukowe PWN, Warszawa.

2013

Bibliography to self-study

1	Hames D.B., Hooper N.M.	Biochemia: krótkie wykłady	Wydawnictwo Naukowe PWN, Warszawa.	2010
2	Tymoczko J.L., Berg J.M., Stryer L.	Biochemia: krótki kurs	Wydawnictwo Naukowe PWN, Warszawa.	2013
3	Turner P.C. et al.	Krótkie wykłady: Biologia Molekularna	Wydawnictwo Naukowe PWN, Warszawa.	2002

Basic requirements in category knowledge/skills/social competences

Formal requirements: Registration for the semester.

Basic requirements in category knowledge: Basic knowledge of cell biology and general, inorganic and organic chemistry

Basic requirements in category skills: Ability to independently search and interpret scientific information. Ability to work in laboratory under the supervision.

Basic requirements in category social competences: Ability to work as a part of a team during search and interpretation of scientific information. Ability to work in a team as a part of laboratory exercises under the supervision.

Module outcomes

MEK	The student who completed the module	Types of classes / teaching methods leading to achieving a given outcome of teaching	Methods of verifying every mentioned outcome of teaching	Relationships with KEK	Relationships with PRK
01	Student understands the structure and function of living things.	lecture	examination	K_W05+++ K_U06++ K_K01+++	P6S_KK P6S_KR P6S_UU P6S_WG
02	Student knows the chemical nature of the main classes of biological compounds, such as: amino acids, peptides, proteins, polysaccharides, lipids, nucleotides and nucleic acids	lectures, laboratory exercises	exam, admittance test	K_W05+++ K_U06++ K_K01+++	P6S_KK P6S_KR P6S_UU P6S_WG
03	Understands principles of spatial organization of multi-molecular compounds, such as proteins, polysaccharides and nucleic acids.	lecture, laboratory exercises	exam, written colloquium	K_W05+++ K_U06++ K_K01+++	P6S_KK P6S_KR P6S_UU P6S_WG
04	Understands relationship between protein structure and function, the example of myoglobin and hemoglobin	lectures	exam	K_W05+++ K_U06++ K_K01+++	P6S_KK P6S_KR P6S_UU P6S_WG
05	Knows units of enzyme activity and the standard enzyme classification	lecture, laboratory exercises	examination, admittance test	K_W05+++ K_U09++ K_K01+++	P6S_KK P6S_KR P6S_UO P6S_UW P6S_WG
06	Knows fundamentals of classical enzyme kinetics	lecture, laboratory exercises	exam, written colloquium	K_W05+++ K_U06++ K_K01+++	P6S_KK P6S_KR P6S_UU P6S_WG
07	Is able to describe and characterise basic kindes of enzyme regulation	lecture	examination	K_W05+++ K_U06++ K_K01+++	P6S_KK P6S_KR P6S_UU P6S_WG
08	Knows structure of cell membrane and membrane transport types	lecture	exam	K_W05+++ K_U06++ K_K01+++	P6S_KK P6S_KR P6S_UU P6S_WG
09	Knows basic intracellular signaling pathways	lectures	exam	K_W05+++ K_U06++ K_K01+++	P6S_KK P6S_KR P6S_UU P6S_WG
10	Knows mechanisms of replication, transcription, and translation in procaryotes and eucaryotes	lecture	examination	K_W05+++ K_U06++ K_K01+++	P6S_KK P6S_KR P6S_UU P6S_WG
11	Knows complexity and interdependence of metabolic pathways in living organisms	lecture	examination	K_W05+++ K_U06++ K_K01+++	P6S_KK P6S_KR P6S_UU P6S_WG
12	Knows basic transformations and metabolic pathways in plant and animal cells.	lectures	exam	K_W05+++ K_U06++ K_K01+++	P6S_KK P6S_KR P6S_UU P6S_WG
13	Is able to isolate compound of interest from the biological material	laboratory exercises	observation, written report	K_W14+++ K_U09++ K_K01+++ K_K03+++	P6S_KK P6S_KR P6S_UO P6S_UW P6S_WG
14	Is able to identify compound of interest	laboratory exercises	observation, written report	K_W14+++ K_U09++ K_K01+++ K_K03+++	P6S_KK P6S_KR P6S_UO P6S_UW P6S_WG
15	Knows a basic methods in studies of macromolecules	laboratory exercises	observation, written report	K_W14+++ K_U09++ K_U15++ K_K01+++ K_K03+++	P6S_KK P6S_KR P6S_UO P6S_UW P6S_WG
16	Knows how to work in a group and individually	laboratory exercises	observation	K_K03+++	P6S_KR
17	Is responsible for occupational health	laboratory exercises	observation	K_K03+++	P6S_KR
18	Understands the need of improving skills and knowledge resulting from the constantly expanding knowledge	lecture, laboratory exercises	exam, written colloquium, written report	K_K01+++	P6S_KK P6S_KR

Attention: Depending on the epidemic situation, verification of the achieved learning outcomes specified in the study program, in particular credits and examinations at the end of specific classes, can be implemented remotely (real-time meetings).

The syllabus of the module

Sem.	TK	The content	realized in	MEK
3	TK01	Biochemistry - the molecular logic of living organisms.	W01-02	MEK01 MEK11 MEK18
3	TK02	Structure and properties of amino acids. Proteins: a hierarchical organization of structure. Basic aspects of the protein structure and function. Myoglobin and hemoglobin.	W03-08	MEK02 MEK03 MEK04 MEK18
3	TK03	Introduction to enzymes. Factors affecting enzyme activity. Enzyme kinetics and inhibition. Control of enzyme activity.	W09-12	MEK05 MEK06 MEK07 MEK18
3	TK04	Carbohydrates: monosaccharide, oligosaccharide and polysaccharides structures. Glycoproteins.	W13-14	MEK02 MEK03 MEK18
3	TK05	Lipids. Structure of cell membranes. Mechanisms of transport across cell membranes.	W15-20	MEK02 MEK08 MEK18
3	TK06	Membrane receptors and sygnal transduction in cell.	W21-22	MEK09 MEK18
3	TK07	Transduction of genetic information in cell. DNA structure and replication. RNA synthesis and splicing. Protein synthesis.	W23-30	MEK02 MEK03 MEK10 MEK18
3	TK08	Identification of amino acids and proteins by specific colour reactions and TLC method.	L01-05	MEK02 MEK03 MEK14 MEK16 MEK17 MEK18
3	TK09	Determination of protein concentration.	L06-10	MEK03 MEK15 MEK16 MEK17 MEK18
3	TK10	Identification of simple sugars and polisaccharides by colour reactions. Hydrolysis of sucrose.	L11-15	MEK02 MEK03 MEK14 MEK16 MEK17 MEK18
3	TK11	Separation of amylose and amylopectin from potato starch. Hydrolysis of starch.	L16-20	MEK02 MEK03 MEK13 MEK14 MEK16 MEK17 MEK18
3	TK12	Isolation of cholesterol from a chicken egg yolk. Identification of cholesterol by Salkowski method.	L21-25	MEK02 MEK13 MEK14 MEK16 MEK17 MEK18
3	TK13	Determination of nitrate(III) levels in meat products with the Grieass reagent.	L26-30	MEK13 MEK14 MEK16 MEK17 MEK18
4	TK01	Metabolism: organisation and basic ideas.	W01-02	MEK01 MEK11 MEK18
4	TK02	Carbohydrate metabolism: glycolysis and gluconeogenesis.	W03-07	MEK11 MEK12 MEK18
4	TK03	Cellular respiration and energetics: citric acid cycle, oxidative phosphorylation, photosynthesis.	L08-15	MEK11 MEK12 MEK18
4	TK04	Isolation and determination of superoxide dismutase (SOD) activity from the yeast Saccharomyces cerevisiae.	L01-05	MEK05 MEK13 MEK15 MEK16 MEK17 MEK18
4	TK05	Identification of superoxide dismutase by native gel electrophoresis and negative staining.	L06-10	MEK14 MEK15 MEK16 MEK17 MEK18
4	TK06	Native gel electrophoresis and identification of LDH isoenzymes.	L11-15	MEK14 MEK15 MEK16 MEK17 MEK18
4	TK07	Isolation of macromolecules by gel filtration.	L16-20	MEK15 MEK16 MEK17 MEK18
4	TK08	Separation of lysozyme from chicken egg by ion-exchange chromatography.	L21-25	MEK13 MEK14 MEK15 MEK16 MEK17 MEK18
4	TK09	Identification of lysozyme by SDS-PAGE electrophoresis.	L26-30	MEK14 MEK15 MEK16 MEK17 MEK18

The student's effort

The type of classes	The work before classes	The participation in classes	The work after classes
Lecture (sem. 3)		contact hours: 15.00 hours/sem.	complementing/reading through notes: 5.00 hours/sem. Studying the recommended bibliography: 5.00 hours/sem.
Laboratory (sem. 3)	The preparation for a Laboratory: 5.00 hours/sem. The preparation for a test: 10.00 hours/sem.	contact hours: 30.00 hours/sem.	Finishing/Making the report: 5.00 hours/sem.
Advice (sem. 3)
Exam (sem. 3)	The preparation for an Exam: 10.00 hours/sem.	The written exam: 2.00 hours/sem.
Lecture (sem. 4)		contact hours: 30.00 hours/sem.	complementing/reading through notes: 5.00 hours/sem. Studying the recommended bibliography: 15.00 hours/sem.
Laboratory (sem. 4)	The preparation for a Laboratory: 5.00 hours/sem. The preparation for a test: 10.00 hours/sem.	contact hours: 30.00 hours/sem.	Finishing/Making the report: 5.00 hours/sem.
Advice (sem. 4)
Exam (sem. 4)	The preparation for an Exam: 25.00 hours/sem.	The written exam: 2.00 hours/sem.

The way of giving the component module grades and the final grade

The type of classes	The way of giving the final grade
Lecture	The grade is issued in a manner appropriate to the number of points received during the exam
Laboratory	The grade is issued on the basis of the average grade of 5 tests. Test points: 3 points -[3], 3.5 points - [3,5], 4 points - [4], 4.5 points - [4,5], 5 points - [5]
The final grade	The final grade is the average of the grade of lectures and a final evaluation labs (50/50). The average may be drawn only if both grades are positive
Lecture	The grade is issued in a manner appropriate to the number of points received during the exam
Laboratory	The grade is issued on the basis of the average grade of 3 tests. Test points: 3 points -[3], 3.5 points - [3,5], 4 points - [4], 4.5 points - [4,5], 5 points - [5]
The final grade	The final grade is the average of the grade of lectures and a final evaluation labs (50/50). The average may be drawn only if both grades are positive

Sample problems

Required during the exam/when receiving the credit
(-)

Realized during classes/laboratories/projects
(-)

Others
(-)

Can a student use any teaching aids during the exam/when receiving the credit : no

The contents of the module are associated with the research profile: yes

1	A. Kołodziej; Z. Krupa; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman	Untargeted metabolomics of bladder tissue using liquid chromatography and quadrupole time-of-flight mass spectrometry for cancer biomarker detection	2024
2	B. Guratowska; A. Kuźniar; J. Nizioł; A. Nowak; M. Okrasa; T. Ruman; M. Ryngajłło; J. Szulc	Uncontrolled Post-Industrial Landfill—Source of Metals, Potential Toxic Compounds, Dust, and Pathogens in Environment—A Case Study	2024
3	M. Misiorek; N. Pieńkowska; M. Siorek; Ż. Szymaszek; M. Twardowska; Ł. Uram; S. Wołowiec	Repurposed Drugs Celecoxib and Fmoc-L-Leucine Alone and in Combination as Temozolomide-Resistant Antiglioma Agents—Comparative Studies on Normal and Immortalized Cell Lines, and on C. elegans	2024
4	V. Copie; A. Kołodziej; Z. Krupa; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman; B. Tripet	Metabolomic profiling of human bladder tissue extracts	2024
5	Z. Krupa; M. Misiorek; J. Nizioł; T. Ruman	Infrared Laser-Based Selected Reaction Monitoring Mass Spectrometry Imaging of Banana (Musa spp.) Tissue—New Method for Detection and Spatial Localization of Metabolites in Food	2024
6	A. Arendowski; A. Kołodziej; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman	Monoisotopic silver nanoparticles-based mass spectrometry imaging of human bladder cancer tissue: Biomarker discovery	2023
7	A. Kołodziej; A. Nieczaj; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman	Untargeted urinary metabolomics for bladder cancer biomarker screening with ultrahigh-resolution mass spectrometry	2023
8	A. Kołodziej; Z. Krupa; J. Nizioł; A. Płaza-Altamer; T. Ruman	Infrared pulsed fiber laser-produced gold and silver-109 nanoparticles for laser desorption/ionization mass spectrometry of steroid hormones	2023
9	M. Dudek; B. Gutarowska; M. Komar; J. Nizioł; P. Nowicka-Krawczyk; T. Ruman	Biodeterioration potential of algae on building materials - Model study	2023
10	S. Kuberski; A. Kuźniar; J. Nizioł; A. Nowak; I. Nowak; M. Okrasa; T. Ruman; B. Szponar; J. Szulc	Biological and chemical contamination of illegal, uncontrolled refuse storage areas in Poland	2023
11	V. Copie; A. Kołodziej; A. Nieczaj; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman; B. Tripet	Targeted and untargeted urinary metabolic profiling of bladder cancer	2023
12	A. Kołodziej; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman	Untargeted ultra-high-resolution mass spectrometry metabolomic profiling of blood serum in bladder cancer	2022
13	A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman	Infrared pulsed fiber laser-produced silver-109 nanoparticles for laser desorption/ionization mass spectrometry of 3-hydroxycarboxylic acids	2022
14	A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman	Infrared pulsed fiber laser-produced silver-109-nanoparticles for laser desorption/ionization mass spectrometry of amino acids	2022
15	A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman	Infrared pulsed fiber laser-produced silver-109-nanoparticles for laser desorption/ionization mass spectrometry of carboxylic acids	2022
16	A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman	Laser Ablation Synthesis in Solution and Nebulization of Silver-109 Nanoparticles for Mass Spectrometry and Mass Spectrometry Imaging	2022
17	A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman	Laser generated gold nanoparticles for mass spectrometry of low molecular weight compounds	2022
18	A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman	Obrazowanie tkanek za pomocą spektrometrii mas z laserową desorpcją/jonizacją	2022
19	B. Gutarowska; M. Komar; P. Konca; J. Nizioł; P. Nowicka-Krawczyk; T. Ruman	Metabolomic analysis of photosynthetic biofilms on building façades in temperate climate zones	2022
20	B. Gutarowska; T. Ruman; J. Szulc	Metagenomika i metabolomika – nowoczesne metody systemowe w identyfikacji mikroorganizmów oraz metabolitów odpowiedzialnych za niszczenie obiektów zabytkowych	2022
21	S. Kuberski; J. Nizioł; A. Nowak; M. Okrasa; T. Ruman; J. Szulc	Assessment of Physicochemical, Microbiological and Toxicological Hazards at an Illegal Landfill in Central Poland	2022
22	V. Copie; A. Kołodziej; J. Nizioł; K. Nogueira; L. Nogueira; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman; B. Tripet	Metabolomic and elemental profiling of blood serum in bladder cancer	2022
23	A. Arendowski; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; T. Ruman	Serum and urine analysis with gold nanoparticle-assisted laser desorption/ionization mass spectrometry for renal cell carcinoma metabolic biomarkers discovery	2021
24	A. Arendowski; V. Copie; J. Nizioł; K. Nogueira; L. Nogueira; K. Ossoliński; T. Ruman; B. Tripet	Metabolomic and elemental profiling of human tissue in kidney cancer	2021
25	A. Arendowski; V. Copie; J. Nizioł; K. Ossoliński; T. Ruman; B. Tripet	Nuclear magnetic resonance and surface-assisted laser desorption/ionization mass spectrometry-based metabolome profiling of urine samples from kidney cancer patients	2021
26	A. Kołodziej; T. Ruman; J. Szulc	Silver-109/Silver/Gold Nanoparticle-Enhanced Target Surface-Assisted Laser Desorption/Ionisation Mass Spectrometry—The New Methods for an Assessment of Mycotoxin Concentration on Building Materials	2021
27	B. Gutarowska; K. Majchrzycka; J. Nizioł; A. Nowak; M. Okrasa; T. Ruman; M. Sulyok; B. Szponar; J. Szulc	Microbiological and Toxicological Hazards in Sewage Treatment Plant Bioaerosol and Dust	2021
28	I. Beech; A. Drążkowska; B. Guratowska; J. Karbowska-Berent; T. Ruman; J. Sunner; J. Szulc	Metabolomics and metagenomics analysis of 18th century archaeological silk	2021
29	M. Misiorek; J. Nizioł; T. Ruman	Zastosowanie spektometrii mas do obrazowania rozmieszczenia flawonoidów w owocu truskawki	2021
30	A. Arendowski; J. Nizioł; K. Ossoliński; T. Ruman	Gold nanostructures - assisted laser desorption/ionization mass spectrometry for kidney cancer blood serum biomarker screening	2020
31	A. Arendowski; J. Nizioł; K. Ossoliński; T. Ruman	Screening of Urinary Renal Cancer Metabolic Biomarkers with Gold Nanoparticles-assisted Laser Desorption/Ionization Mass Spectrometry	2020
32	A. Arendowski; V. Copie; J. Nizioł; K. Ossoliński; T. Ruman; B. Tripet	Nuclear magnetic resonance and surface-assisted laser desorption/ionization mass spectrometry-based serum metabolomics of kidney cancer	2020
33	A. Filipowicz-Rachwał; J. Markowicz; M. Misiorek; Ł. Uram; E. Wałajtys-Rode; S. Wołowiec	Celecoxib substituted biotinylated poly(amidoamine) G3 dendrimer as potential treatment for temozolomide resistant glioma therapy and anti-nematode agent	2020
34	A. Kołodziej; J. Nizioł; T. Ruman	Gold and silver nanoparticles-based laser desorption/ionization mass spectrometry method for detection and quantification of carboxylic acids	2020
35	B. Guratowska; J. Karbowska-Berent; T. Kozielec; T. Ruman; J. Szulc	Analyses of microorganisms and metabolites diversity on historic photographs using innovative methods	2020
36	B. Gutarowska; A. Jachowicz; S. Kowalska; W. Machnowski; T. Ruman; A. Steglinska; J. Szulc	Beeswax-Modified Textiles: Method of Preparation and Assessment of Antimicrobial Properties	2020
37	B. Gutarowska; I. Jablonskaja; E. Jabłońska; J. Karbowska-Berent; T. Ruman; J. Szulc	Metabolomics and metagenomics characteristic of historic beeswax seals	2020
38	E. Chmiel; A. Czerniecka-Kubicka; M. Misiorek; M. Pyda; P. Tutka; Ł. Uram; M. Walczak; S. Wołowiec	Stepwise glucoheptoamidation of poly(amidoamine) dendrimer G3 to tune physicochemical properties of the potential drug carrier: in vitro tests for cytisine conjugates	2020
39	I. Beech; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza; T. Ruman; J. Sunner	Localization of Metabolites of Human Kidney Tissue with Infrared Laser-Based Selected Reaction Monitoring Mass Spectrometry Imaging and Silver-109 Nanoparticle-Based Surface Assisted Laser Desorption/Ionization Mass Spectrometry Imaging	2020
40	T. Ruman; J. Szulc	Laser Ablation Remote-Electrospray Ionisation Mass Spectrometry (LARESI MSI) Imaging—New Method for Detection and Spatial Localization of Metabolites and Mycotoxins Produced by Moulds	2020
41	A. Arendowski; J. Kucharz; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; T. Ruman; P. Wiechno	Mass spectrometry-based metabolomic profiling of prostate cancer-a pilot study	2019
42	A. Filipowicz-Rachwał; J. Markowicz; M. Misiorek; M. Pichla; Ł. Uram; E. Wałajtys-Rode; S. Wołowiec	The Effect of Biotinylated PAMAM G3 Dendrimers Conjugated with COX-2 Inhibitor (celecoxib) and PPARγ Agonist (Fmoc-L-Leucine) on Human Normal Fibroblasts, Immortalized Keratinocytes and Glioma Cells in Vitro	2019
43	A. Filipowicz-Rachwał; M. Misiorek; Ł. Uram; E. Wałajtys-Rode; A. Winiarz; S. Wołowiec	Synthesis and Different Effects of Biotinylated PAMAM G3 Dendrimer Substituted with Nimesulide in Human Normal Fibroblasts and Squamous Carcinoma Cells	2019
44	J. Cebulski; M. Kus-Liśkiewicz; T. Ruman; M. Stompor; D. Szmuc; K. Szmuc; Ł. Szyller; S. Wołowiec; I. Zawlik	Silver nanoparticles deposited on calcium hydrogenphosphate - silver phosphate matrix; biological activity of the composite	2019
45	M. Misiorek; J. Nizioł; T. Ruman	Mass spectrometry imaging of low molecular weight metabolites in strawberry fruit (Fragaria x ananassa Duch.) cv. Primoris with 109Ag nanoparticle enhanced target	2019