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General Biochemistry
2nd year of study - Farmacy
Questions which you may have
Why should I learn General Biochemistry?
Where can I use this knowledge?
How teaching will be organized?
Which literature?
Why should I attend lectures?
What is seminar?
What is organization of practical training?
How can I get credit?
What I must know to pass exam and how
the exam will be organized?
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Organization
Lectures
Prof. Wsl, Prof. Kvasnikov, Prof. Drata, dr. karydov, dr. Novotn

Seminars
1
st
seminar: Basic calculations in the biochemistry (dr. Brtkov)
2nd a 3rd seminar: metabolic pathways (Prof. Kvasnikov)

Practical training (on Fridays)
Mgr. Brtkov
Mgr. Matoukov
Mrs. Pakostov

Information on www.faf.cuni.cz
Information for students
Study materials
Department of Biochemical Sciences General Biochemistry

Consultation
Anytime after confirmation (tel. 495 067 370;
e-mail: Vladimir.Wsol@faf.cuni.cz)
List of lectures General Biochemistry
Summer semester 2012/2013
18. 2. Introduction to Biochemistry prof. Wsl

20. 2. Amino Acids, Peptides, Proteins prof. Drata

25. 2. Enzymes and Enzyme Kinetics prof. Drata

27. 2. Part I Review prof. Drata

4. 3. Thermodynamics + Introduction to Metabolism prof. Wsl

6. 3. Citric Acid Cycle, PD Complex prof. Wsl

11. 3. Metabolism of Carbohydrates I dr. karydov

13. 3. Metabolism of Carbohydrates II dr. karydov

18. 3. Glycogen Metabolism dr. karydov

20. 3. Part II Review prof. Wsl

25. 3. Lipid Metabolism I dr. karydov

27. 3. Lipid Metabolism II dr. karydov

1.4. Easter

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List of lectures General Biochemistry
Summer semester 2012/2013
3. 4. Amino Acids Metabolism I prof. Kvasnikov

8. 4. Amino Acid Metabolism II prof. Kvasnikov

10. 4. Part III Review prof. Kvasnikov

15. 4. Nucleotides, Metabolism of Nucleotides doc. imnek

17. 4. Heme and Hemoglobin prof. Drata

22. 4. Mitochondrion, Transport in Organism prof. Wsl

24. 4. Respiratory chain, Oxidative Phosphorylation prof. Wsl

29. 4. Metabolic Interrelationship prof. Wsl

6. 5. Cell-Cell Signalling I dr. Novotn

13. 5. Cell-Cell Signalling II dr. Novotn

15. 5. Basics of Xenobiochemistry prof. Wsl

20. 5. Test Example with Discussion prof. Wsl

Seminars

1st Seminar Basic calculations in the biochemistry
March exact date will be updated

2nd Seminar Metabolism of nutrients and their
interrelationship
Will be updated

3rd Seminar Catabolic and anabolic pathways
(carbohydrates, proteins and lipids), their
interrelationships
Will be updated


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Practical Exercises
Qualitative and quantitative determination of
amino acids.
Properties of protein solutions.
Protein assay.
Dialysis and gel filtration.
Identification of sugars.
Qualitative analysis of urine.
Measurement of enzyme activity.
Enzyme kinetics.
Influence of modulators on enzyme activity.
Effect of pH on enzyme activity.

Study literature
Champe PC., Harvey RA., Ferrier DR.
Biochemistry
Devlin TM.
Textbook of Biochemistry
Mathews CK. and Van Holde KE.
Biochemistry
Stryer L.
Biochemistry
Nelson DL. and Cox MM.
Lehninger Principles of Biochemistry
Michal G.
Biochemical Pathways


5
6
7
Why attend lectures.?
Biochemistry is huge
Lectures show a requisite extent
Lectures emphasize important things

Biochemistry is difficult
Lectures can explain what is difficult
to understand

We should understand the context
and relationships
and these are hard readable from
books

Seminar tests
Who will get 24 and more points (it
means more than 80 %)

He/she doesnt have to write test before
exam (validity is just for one term!!!)

He/she can take pre-exam


8
SOME OF THEM
Essential Structures
Amino Acids
C
H
N H
2
H
COOH C
H
N H
2
CH
3
COOH
C
H
N H
2
COOH
CH
C H
3
CH
3
C
H
N H
2
COOH
CH
2
CH
C H
3 CH
3
C
H
N H
2
COOH
CH
C H
2
CH
3
CH
3
C
H
N H
2
CH
2
COOH
N
H
C
H
N H
2
COOH
CH
2
CH
2
S
CH
3
C
H
N H
2
CH
2
COOH
C H
2
C H
2
CH
2
CH
N COOH
H H
C
H
COOH N H
2
CH
2
OH
C
H
COOH N H
2
CH
C H
3
OH
C
H
COOH N H
2
CH
2
OH
C
H
COOH N H
2
CH
2
C
O NH
2
C
H
COOH N H
2
CH
2
CH
2
C
O NH
2
C
H
COOH N H
2
CH
2
COOH
C
H
COOH N H
2
CH
2
CH
2
COOH
C
H
COOH N H
2
CH
2
CH
2
CH
2
NH
C
N H
2
NH
2
C
H
COOH N H
2
CH
2
CH
2
CH
2
CH
2
NH
2
C
H
COOH N H
2
CH
2
N H
NH
C
H
COOH N H
2
CH
2
SH
Glycine Alanine
Valine Leucine Isoleucine
Tryptophan
Methionine
Phenylalanine Proline
+
Serine
Threonine
Tyrosine
Asparagine Glutamine Aspartate Glutamate
+
Arginine Lysine Histidine
+
Cysteine
9
Carbohydrates
Ribose
Ribulose
xylulose
Small organic molecules
C
O
N H
2
OPO
3
CH
2
C H
COO
NH
3
+
CH
2
NH
3
+
CH
2
C
O
NH
2
N H
2
C H
3
C
O
COO
C H
3
C
O
SCoA
C
H
2
C
O
COO OOC C COO C
H
2
C
H
2
OOC
O
C
O
SCoA C
H
2
C
H
2
OOC C
H
2
COO C
O
C H
3
COO C
C H
H
OOC
2-
Carbamoyl phosphate
-
Ornithine Urea
Pyruvate
-
Acetyl CoA
Oxaloacetate
- -
-Ketoglutarate
- -
Succinyl CoA
- - -
-
Acetoacetate Fumarate
10
Metabolites of AAs
O H C
H
2
C
H
2
O H
NH
3
+
O H C
H
C
H
2
O H
NH
3
+
OH
O H C
H
C
H
2
O H
N
H
OH
CH
3
N
H
C
H
2
C
H
2
O H
NH
3
+
C
H
2
C
H
2
N
N
H
NH
3
+
Dopamine Norepinephrine
Epinephrine
Serotonin
Histamine
11
Cholesterol
CH
3
CH
3
HC CH
2
O
CH
3
CH
2
CH
2
CH
CH
3
CH
3
O
C R
3-hydroxy-3-methyl-glutaryl CoA
CH
2
-O-CO-R
1
CH R -CO-O-
CH
2
OPO
3
Phosphatidate (phosphatidic acid)
2
2 -
12
CH
2
OH
CHOH
CH
2
OH
glycerol
CH2 O H CHO H
CH
2
COH
CHOH
CH
2
OH
glyceraldehyde
CH
2
OH
CO
CH
2
OH
CH2 O H CHO H
dihydroxyacetone