1. BIOCHEMISTRY
Textbook: “A Text Book of Biochemistry”, by Zhao Baochang, etc, 2004.
Books for reference:
“Biochemistry”, by L. Stryer, 6th edition, W.H. Freeman and Company, 2006.
“Instant Notes in Biochemistry”, by B.D. Hames & N.M. Hooper, 2nd edition, BIOS Scientific Publishers Limited, 2000.

2. Important Concepts
Biochemistry is the study of the molecular composition of living cells, the chemical reactions of biological compounds, and the regulation of these reactions.
Major components in body include water (55%), protein (19%), fat (19%), inorganic matter (7%), carbohydrate (<1%), and nucleic acid (<1%).
Metabolism refers to all the chemical reactions of a living organism.

3. Why to study?
Biochemistry is one of the basic courses that can help you to understand the physiological and pathological processes in the body at molecular levels, and more importantly, to use the knowledge to .
Biochemistry is also a powerful tool in life-scientific studies—prepares you to be a good scientist.

4. How to study?
Classroom study: it is impossible for a lecturer to give all details of the knowledge in a limited lecturing-time, but it is important for the students to catch the main points during the class.
Your study should not be limited to classroom and textbook, but be anyway that helps you understand well the concepts and the principles of biochemistry, such as discussions between teacher-students and among students, lab study, scientific journals...

5. Chapter 1. Structures and Functions of Nucleic Acids
Nucleic Acids include deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The genes of all cells and many viruses are made up of DNA, while RNA serves as the machinery of protein synthesis.
The flow of genetic information:
DNA RNA Protein
translation
transcription

6. 1. Composition of nucleic acids
DNA: Adenine(A), Guanine(G),
Thymine(T), Cytosine(C)
RNA: Adenine(A), Guanine(G),
Uracil(U), Cytosine(C)
DNA: deoxyribose
RNA: ribose
1) Phosphate
2) Bases
3) Pentoses

7. Structures of bases Purine Guanine(G) Adenine(A)
Pyrimidine Cytosine(C) uracil(U) Thymine(T)

8. Structures of pentoses
Deoxyribose ribose

9. 2. Nucleosides and nucleotides
1) Nucleoside: base-pentose
Deoxyadenosine Adenosine

10. 2) Nucleotide: base-pentose-phosphate
Deoxyadenosine
monophosphate (dAMP)
Adenosine
monophosphate (AMP)

11. A) Deoxyribonucleotides
3) Common nucleotides:
A) Deoxyribonucleotides
dAMP
dADP
dATP

12. B) Ribonucleotides
AMP
ADP
ATP

13. Names of nucleoside and nucleotides
Base Ribonucleoside Ribonucleotide
In RNA:
adenine Adenosine Adenosine-5’-monophosphate
guanine Guanosine Guanosine -5’-monophosphate
cytosine Cytidine Cytidine -5’-monophosphate
uracil Uridine Uridine -5’-monophosphate
In DNA:
adenine deoxyadenosine deoxyadenosine-5’-monophosphate
guanine deoxyguanosine deoxyguanosine-5’-monophosphate
cytosine deoxycytidine deoxycytidine-5’-monophosphate
thymine deoxythymidine deoxythymidine-5’-monophosphate

14. Abbreviated names of nucleoside mono-, di-, tri- phosphates
Base NMP NDP NTP
Ribonucleotides:
A AMP ADP ATP
G GMP GDP GTP
C CMP CDP CTP
U UMP UDP UTP
Deoxyribonucleotides:
A dAMP dADP dATP
G dGMP dGDP dGTP
C dCMP dCDP dCTP
T dTMP dTDP dTTP

15. Ultraviolet absorption spectra of ribonucleotides

16. Ultraviolet absorption of nucleotides is due to the optical property of the bases. The wavelength at 260nm is often used to quantitatively analyze bases, nucleosides, nucleotides, or nucleic acids.

17. 3. Primary structure of nucleic acids
Nucleotides are linked by 3’,5’- phosphodiester bonds to form oligo- or poly- nucleotides.
RNA: polynucleotide chains
DNA: polydeoxynucleotide chains

18. 3’,5’- phosphodiesters
5’- end
3’,5’- phosphodiesters
3’- end

19. Direction: 5’  3’

20. 2) Primary structure of nucleic acids refers to the nucleotide sequence of the polynucleotide chain. The primary structure of a DNA chain may be expressed as:
A C T G C T
5’ P P P P P P OH 3’
Or: ’ pApCpTpGpCpT 3’
Or: ’ ACTGCT 3’

21. 4. Stereo structures of DNA
The secondary structure of DNA
Watson-Crick model: DNA double helix.
The two polynucleotide chains are coiled around a common axis in opposite directions.
The bases are on the inside of the helix, forming hydrogen bonds between the two chains by A-T and G-C complementary pairing.
The phosphate and deoxyribose are on the outside as the backbones. The base sequence carries the genetic information.

22. Minor groove
Major groove
The DNA double helix

23. Double helical structure of DNA
34Å
Minor groove
Major groove

24. The DNA base pairs

25. 2) The higher-level structures of DNA
Prokaryotic DNA: is circular double stranded and may be further folded into loops or supercoils with or without DNA binding proteins.
Eukaryotic DNA: is complexed with a histone octamer to form a nucleosome.

26. Histones
Five main types of histones: H1, H2a, H2b, H3 and H4. They are basic DNA-binding proteins.
The histone octamer consists of 8 histones: two molecules of each H2a, H2b, H3 and H4, serving as a core of nucleosome.

27. Prokaryotic DNA loops

28. Structure of nucleosome

29. Formation of chromosome

30. About DNA
DNA is of paramount importance for storing, expressing and transmitting genetic information.
Growth, reproduction and hereditary characteristics depend on DNA.
DNA contains the information that directs the development of an organism.
DNA is able to replicate each time a cell divides and also have the information that is to be selectively expressed.

31. 5. RNA Structure
Most RNA molecules are single-stranded polymer chains consisting of ribonucleotides linked by 3’5’ phosphodiester bonds. However, some regions of RNA can form double-stranded structures by A-U and G-C base pairing within the single chain itself.

32. RNA and DNA structures

33. RNAs in the mammalian cell
RNA Function
rRNA ribosomal RNA component of ribosome
mRNA messenger RNA template for Pr. Synthesis
tRNA transfer RNA transporter of amino acids
HnRNA heterogeneous precursor of mRNA
nuclear RNA
SnRNA small nuclear RNA splicing of HnRNA
SnoRNA small nucleolar RNA processing of rRNA
ScRNA small cytoplasmic RNA signal-peptide recognition

34. 1) Structure of mRNA The structural characteristics of mRNA:
A cap structure at the 5’ end: protects the 5’ end from degradation by nuclease and helps in the initiation of protein synthesis.
A polyA tail at the 3’ end: is not encoded by DNA but added after transcription. The polyA tail protects the 3’end from nuclease digestion and stabilizes the mRNA.

35. c) A coding sequence at the center: encodes the amino acid sequence of a polypeptide. One mRNA only encodes one polypeptide chain in mammalian cell, but may encode several polypeptides in bacteria.
Cap
Non-coding
Coding sequence
Non-coding
polyA tail 5’ 3’

36. The cap structure of mRNA

37. 2) Structure of tRNA
Secondary structure of tRNA: a cloverleaf structure containing an anticodon arm, a DHU arm, a TC arm, and an amino acid acceptor stem.
Tertiary structure of tRNA: at the level of secondary structure the molecule further folds to form a “L” shape 3-d structure.

38. Secondary structure of tRNA

39. Tertiary structure of tRNA

40. 3) Structure of rRNA
A ribosome consists of a small and a large subunit, each of which contains proteins and rRNAs forming a site for protein synthesis.
Types of rRNA:
prokaryotes eukaryotes
Small subunit S S
rRNA S S
Large subunit S S
rRNA S, 5S S, 5.8S, 5S

41. Types of rRNA

42. b) Secondary structure of rRNA: complex, different in size, composition, and 3-d structure.

43. About RNA
mRNA participates in the process of selective expression of genetic information stored in DNA.
tRNA serves as carrier of genetic information to the site of protein synthesis.
rRNA is an essential component of ribosomes.

44. 6. Properties of nucleic acids
Denaturation and renaturation
Denaturation: due to the action of some physical (heat etc.) or chemical (organic solvents etc.) factors the native structure of a nucleic acid molecule can be changed, resulting in loss of its biological functions and showing several physical changes (increase in viscosity and in absorbance of UV light).

45. Renaturation: when the denaturing factors are removed, the denatured nucleic acid molecules may restore their native structures with recovery of their biological functions and physical properties.
Melting temperature (Tm) of DNA: the temperature at which 50% of the maximum optical density is reached.

46. Melting curve

47. 2) Hybridization: a process of association through base-pairing between two polynucleotide chains that are complementary in base sequence to each other.
Hybridization can occur between DNA- DNA, RNA-RNA, or DNA-RNA polynucleotide chains of different origins.
Hybridization is a powerful technique that can be used for probing specific genes.

48. Principles of nucleic acid hybridization