BIOCHEMISTRY (Mrs Hang)

CONTENT:

I. Amino Acids, Peptides, Proteins

1. Amino Acids
2. Peptides and Proteins
3. Working with Proteins
4. The structure of Proteins: Primary Structure
II. The three-dimensional structure of protein
1. Protein Structure: Overview
2. Protein Secondary Structure
3. Protein Teriary Structure
4. Protein Denaturation and Folding
III. Nucleotides and Nucleic Acids
1. Basic Concepts
2. Nucleic Acid Structure
3. Nucleic Acid Chemistry
4. Functions of Nucleotides
I.Amino Acids, Peptides, Proteins:
1. Amino Acids:
o Structure:

o Chiral centre (bond to 4 different groups)

-> Nguyên tử có 1 chiral centre sẽ có Enantiomer (đồng phân quang học- Stereoisomers that are
nonsuperposable mirror images of each other)

NOTE:

-The aa residues in protein are exclusively L stereoisomers

-The D-aa : in small peptide in cell wall or in antibacterial ( not in protein)

  Classification (depends on R group):

R group aa Characteristics
Nonpolar, aliphatic Glycine, Alanine, Proline, Valine, Hydrophobic-> often residue inside the
Leucine, Isoleucine, Methionine protein
Aromatic Tyrosine, Phenylalanine, -Hydrophobic
Tryptophan -Absorb UV light (280nm) -> UV detecter
to define the presentation and the
concentration
Polar, uncharged Serine, Threonine, Cysteine, Hydrophilic
Asparagine, Glutamine
Positively charged Lysine, Arginine, Histidine Hydrophilic, act as base
Negatively charged Aspartate, Glutamate Hydrophilic, act as acid
CH3-O-H

 Titration curve

HA <-> A- +H+
Cân bằng

A*H:HA=Ka
Pk1 pkr pk2
Positive aa: +2 -> +1 -> 0 -> -1 pI=(pKr +pK2):2
Negative aa: +1 -> 0 -> -1 -> -2 pI=(pK1 + pKr) :2

pI (isoelectric point): net charged of aa = 0

NOTE: Với aa có nhiều hơn 1 nhóm -NH2 hoặc -COOH thì pI sẽ là trung bình cộng của pK chuyển
từ dạng có net charged = +1 đến 0 và pK chuyển từ dạng có net charged = 0 đến -1

 Post-translational modification:
 One of the reasons for more than 300 aa found in organism
Some common modification:

+ Phosphorylation Note: cách nhớ ý nghĩa của các biến đổi:

 + Methylation Hậu tố -ation nghĩa là gắn thêm vào
+ Acetylation ->các biến đổi này là gắn thêm các nhóm hoặc các chất
+ Hydroxylation như phosphate, methyl, lipid,…
+ Lipidation
+ Ubiquitination

 Functions of amino acids:

+ building blocks of proteins
+ precursors for many biologically active molecules, such as neurotransmitters ,local mediators ,
energy-related metabolites…
+ energy source during prolonged fasting, diabetes…(convert into Glucose)
+ regulators of gene expression and cellular signalling
 Essential and conditional essential aa
+ Essential: our body cannot produce Isoleucine Leucine Lysine Methionine Phenylalanine
Threonine Tryptophan Valine Histidine Asparagine

2. Peptide and protein:

 Multisubunit:
Protein that compose of more than one polypeptide chain
 Oligomeric : at least 2 chains in multisubunit protein are identical (protomer)
 Conjugated protein:
Protein that contains permanantly associated chemical components (prosthetic group) in
addition to aa
aa -> peptide -> polypeptide -> cuộn thành protein
-> cuộn lại gắn thêm vơi snhieeuf chuỗi polypeptide -> multisubunit
-> cuộn lại gắn với các (kim loại, lipid, vitamin….) -> conjugated protein

Class Prosthetic group

Lipoprotein Lipid
Glycoprotein Carbohydrate
 Phosphoprotein Phosphate
Hemoprotein Heme (iron porphyrin)
Metalloprotein Metal

3. Working with protein:

Key terms:
Term Definition
Crude extract a solution released when breaking open the cell
Fractionation The process of separating the proteins or other
components of a complex molecular mixture into
fractions based on differences in properties such
as solubility, net charge, molecular weight, or
function.
Dialysis Removal of small molecules from a solution of a
macromolecule by their diffusion through a
semipermeable membrane into a suitably
buffered solution.

- Column chromatography:
a. Ion-exchange chromatography:
 Principle:
Exploits different in the sign and magnitude of the net electric charge of protein at a given pH
 Mechanism:
 b. Size-exclusion chromatography:
 Principle:
Separate according to size:
+ Large protein emerge from the column sooner than small ones
 Mechanism:

c. Affinity chromatography:
 Principle:
Different bindind affinity of the different proteins to the stationary phase
 Mechanism:
4. Primary structure of protein:

- Definition:
A description of all covalent bonds linking amino acid residues in a protein: peptide and
disulfide bonds

- Sequencing short polypeptide:

 Polypeptide: (N- ) aa1-aa2-…..
B1: thả P -> P-aa1-aa2-…..
B2: CF3COOH -> P-aa1 + aa2-aa3-…..

- Sequencing large
protein:
1. Breaking the
disulfit bonds
2. Cleaving
peptide bonds
3. Sequencing the
peptides
4. Order the
peptide
fragment
5. Locating the
disulfit bond

A-B-C-R-X-E-F-K-T-V

-> A-B-C-R + X-E-F-K +T-V

II.The three-dimensional structure of protein
1. Overview:
Key terms:

conformation A spatial arrangement of substituent groups

that are free to assume different positions
in space, without breaking any bonds,
because of the freedom of bond rotation.
native conformation The biologically active conformation of a
macromolecule.
solvation layer The solvent interface of any chemical
compound or biomolecule that constitutes
the solute
Weak bonds:

- Hydrogen bond

- Hydrophobic interaction

- Van-der-waals

- Ionic bond

- Stabilizing the comformation:

Most of the structural patterns reflect 2 rules:

(1) Hydrophobic residues are largely buried in the protein interior, away from water
 Reduce the ordered water in forming solvation layer

(2) The number of hydrogen bonds and ionic interactions within the protein is maximized
D-H ---- A- (H2O)
a-a-a-a-a-a-a-a-a-a-a-a-a-a
- Peptide bond:
2. Protein secondary structure:
- Definition:
The local spatial arrangement of the main-chain atoms in a segment of a polymer
(polypeptide or polynucleotide) chain.

a. Alpha-helix:
a1-a2-a3-a4
Polypeptide : 80 aa -> tạo ra đc 1 chuỗi alpha helix dài bn A 0
- Five types of constraints affect the stability of an α helix:

(1) the intrinsic propensity of an amino acid residue to form an α helix;

(2) the interactions between R groups, particularly those spaced three

(or four) residues apart;

(3) the bulkiness of adjacent R groups: many adjacent long block of

negatively charged or positive charged R group prevent formation of the α
helix

(4) the occurrence of Pro and Gly residues;

(5) interactions between amino acid residues at the ends of the helical
segment and the electric dipole inherent to the α helix.

b. Beta-Sheet:

Ala- val- pro

Pro- val- ala

c. Beta-turn:
- β turns: connect the ends of two adjacent segments of an antiparallel β sheet
- Gly and Pro residues often occur in β turns
- 2 common types:

3. Tertiary and Quaternary structure:

a. Definition:

Term Definition
tertiary structure overall three-dimensional arrangement of all
atoms in a protein
quaternary structure the arrangement of two or more separate
polypeptide chains, or subunits, which may
be identical or different.
fibrous proteins Insoluble proteins that serve a protective or
structural role; contain polypeptide chains
that generally share a common secondary
structure, beta sheet
globular proteins Soluble proteins with a globular (somewhat
rounded) shape
Motif (flod) Any distinct folding pattern for elements of
secondary structure, observed in one more
more proteins. 
domain A distinct structural unit of a polypeptide;
domains may have separate functions and
may fold as independent, compact units.
intrinsically disordered proteins Proteins, or segments of proteins, that lack a
definable three-dimensional structure in
solution
multimer A protein consisting of multiple monomers.
Alpha helix- Zn -alpha helix
 4. Protein denaturation and folding:
a. Denaturation:
- Definition: Partial or complete unfolding of the specific native conformation of a
polypeptide chain, protein, or nucleic acid such that the function of the molecule is lost.
- Denaturing agents
+ pH; changes in charge
+ Miscible solvents; to disrupt hydrophobic interaction
+ Urea, guanidine hydrochloride; to disrupt hydrophobic interaction
+ Detergent; to disrupt hydrophobic interaction
- Renaturation: Regaining of native conformation (structure) (only in some protein)
b. Folding:
- Some proteins can fold themselves => the aa sequence determine their tertiary structure
- Some proteins undergo assisted folding=> required Chaperones
- Chaperones: Any of several classes of proteins or protein complexes that catalyze the
accurate folding of proteins in all cells.
 2 classes:
+ Molecular chaperones: proteins that facilitating correct folding pathway: Hsp70 and
Hsp40 in eukaryotes; DnaK and DnaJ in prokaryotes
+ Chaperonins: a complex of proteins that functions in protein folding: GroES/GroEL in
bacteria; Hsp60 in eukaryotes.

I. Nucleotides and Nucleic Acids:

1. Basic concept:
- Nucleotides characteristic components:

(1) a nitrogenous (nitrogen-containing) base (derivatives of purine or pyrimidine)

(2) A pentose

(3) a phosphate

- Nucleoside: is nucleotide without phosphate group -> compose of ribose and base
NOTE: cách nhớ tên:

Phần base + osine = tên của Nucleoside

Phần base + ylate = tên của Nucleotide

- DNA

- Differences in DNA and RNA

DNA RNA
pentose Deoxyribose (deoxy in C-2) ribose
Purine A, G A,G
Pyrimidine T,C T,U
Unit Deoxyribosenucleotide ribosenucleotide

- Alkaline hydrolysis
+ RNA being hydrolysis in alkal environment
+ Don’t happen in DNA
2. Nucleic Acid structure:
- Double helix:

+ the two antiparallel polynucleotide chains of

double-helical DNA are not identical

+ they are complementary to each other

(Chargaff’s rule)

- Unusual structure:
(1) A,B,Z form:
(2) Palindrone
Đọc từ 5’-3’ của 2 mạch sẽ giống nhau

(3) Miror repeat

Đọc từ 5’-3’ và đọc từ 3’-5’ trên cùng 1 mạch sẽ giống nhau

(4) Hairpin
Trong cùng 1 mạch có 2 đoạn bổ sung cho nhau

(5) Cruciform
 Tương tự Hairpin nhưng mà ở 2 mạch

3. Nucleic Acid Chemical:

- Denaturation:
The loss of H bond between base pairs due to heat or chemical

G-C: 3 H , A-T:2 H -> chuỗi %G-C càng lớn thì càng cần nhiều nhiều nhiệt để phá vỡ
RNA-RNA > RNA-DNA > DNA-DNA

- Annealing: the reverse process of denaturation (occur when slowly colling down)
- DNA hybrization:
The single DNA stands of 2 diffenrent initial sample can form duplexes ( create H bond
between Nu of 2 stands) if they are similarity
- Nonenzymatic transformation:
(1) Deamination: -NH2 group of base turn into ketone
(2) Depurination: hydrolysis seperating the base from nucleotide
(3) Formation of pyrimidine dimers induced by UV light: UV light lead to the formation of
covalent bond between 2 adjacent thymines.
(4) Reagents cause DNA dâmges
+ NaNO2, NaNO3 : promote Deamination
+ Alkylating reagent: Alter base into uncommon form
Base -> common: A-T và G-C
-> uncommon: G’-T và A’-C
Initial: G-C -> G’-C -> G’-T và G-C -> G-T và G-C -> G-C và A-T và G-C và G-C
4. Other functions:

Functions Example
Nucleotides Carry Chemical Energy in Cells ATP
Component of enzyme cofactors Adenine nucleotide in CoA (coenzyme A)
Regulatory Molecules cAMP, cGMP,ppGpp