BIOCHEMISTRY

Textbook: “A Text Book of Biochemistry”, by Zhao Baochang, etc, 2004.

Books for reference:

1. “Biochemistry”, by L. Stryer, 6th edition, W.H. Freeman and Company, 2006.

2. “Instant Notes in Biochemistry”, by B.D. Hames & N.M. Hooper, 2nd edition, BIOS Scientific Publishers Limited, 2000.

Important Concepts

1. Biochemistry is the study of the molecular composition of living cells, the chemical reactions of biological compounds, and the regulation of these reactions.

2. Major components in body include water (55%), protein (19%), fat (19%), inorganic matter (7%), carbohydrate (<1%), and nucleic acid (<1%).

3. Metabolism refers to all the chemical reactions of a living organism.

Why to study?

1. 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 .

2. Biochemistry is also a powerful tool in life-scientific studies—prepares you to be a good scientist.

How to study?

1. 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.

2. 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...

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 Proteintranscription translation

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

2) Bases

3) Pentoses

1) Phosphate

Structures of bases

Purine Guanine(G) Adenine(A)

Pyrimidine Cytosine(C) uracil(U) Thymine(T)

Structures of pentoses

Deoxyribose ribose

2. Nucleosides and nucleotides

1) Nucleoside: base-pentose

Deoxyadenosine Adenosine

2) Nucleotide: base-pentose-phosphate

O

Deoxyadenosine monophosphate (dAMP)

Adenosine monophosphate (AMP)

3) Common nucleotides:

A) Deoxyribonucleotides

dAMP

dATP

dADP

HO

B) Ribonucleotides

AMP

ATP

ADP

Names of nucleoside and nucleotidesBase 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

Abbreviated names of nucleoside

mono-, di-, tri- phosphatesBase NMP NDP NTPRibonucleotides:A AMP ADP ATPG GMP GDP GTP C CMP CDP CTP U UMP UDP UTP

Deoxyribonucleotides:A dAMP dADP dATPG dGMP dGDP dGTP C dCMP dCDP dCTP T dTMP dTDP dTTP

Ultraviolet absorption spectra of ribonucleotides

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.

3. Primary structure of nucleic acids

1) Nucleotides are linked by 3’,5’- phosphodiester bonds to form oligo- or poly- nucleotides.

RNA: polynucleotide chains

DNA: polydeoxynucleotide chains

3’,5’- phosphodiesters

O

H

H

H

CH2 Base

O

H

O

P-O O

O

H

H

H

CH2 Base

O

H

O

P

O-

-O O

O

H

H

H

CH2 Base

OH

H

O

P-O O

3’,5’- phosphodiesters

5’- end

3’- end

Direction: 5’ 3’

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: 5’ pApCpTpGpCpT 3’

Or: 5’ ACTGCT 3’

4. Stereo structures of DNA

1) The secondary structure of DNA

Watson-Crick model: DNA double helix.• The two polynucleotide chains are coiled around a com

mon 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.

The DNA double helix

Minor groove

Major groove

Double helical structure of DNA

Minor groove

Major groove

34Å

The DNA base pairs

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.

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.

Prokaryotic DNA loops

Structure of nucleosome

Formation of chromosome

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.

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.

RNA and DNA structures

RNAs in the mammalian cellRNA 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

1) Structure of mRNA

The structural characteristics of mRNA:

a) A cap structure at the 5’ end: protects the 5’ end from degradation by nuclease and helps in the initiation of protein synthesis.

b) 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.

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

5’ 3’

Non-coding Coding sequence polyA tailNon-coding

The cap structure of mRNA

2) Structure of tRNA

a) Secondary structure of tRNA: a cloverleaf structure containing an anticodon arm, a DHU arm, a TC arm, and an amino acid acceptor stem.

b) Tertiary structure of tRNA: at the level of secondary structure the molecule further folds to form a “L” shape 3-d structure.

Secondary structure of tRNA

Tertiary structure of tRNA

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 30S 40S

rRNA 16S 18S

Large subunit 50S 60S

rRNA 23S, 5S 28S, 5.8S, 5S

Types of rRNA

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

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.

6. Properties of nucleic acids

1) 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).

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.

Melting curve

30 50 70 90

1.4

1.3

1.2

1.1

1.0

Rel

ativ

e op

tical

den

sity

(26

0nm

)

Tm

Temperature (oC)

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.

Principles of nucleic acid hybridization