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Chapter 1. Protein. Contents. 1. Chemical components 2. Molecular structures 3. Structure-function relationship 4. Physical and chemical properties 5. Exploration of proteins. What are proteins?.

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chapter 1

Chapter 1


  • 1. Chemical components
  • 2. Molecular structures
  • 3. Structure-function relationship
  • 4. Physical and chemical properties
  • 5. Exploration of proteins
what are proteins
What are proteins?

Proteins are macromolecules composed of amino acids linked together through peptide bonds.


Element components of


  • major elements

C, H, O, N, S.

  • trace elements

P, Fe, Cu, Zn, I, …

The average nitrogen content in proteins is about 16%.

The protein quantity can be estimated.

protein in 100g sample = N per gram x 6.25 x 100


The basic building blocks of proteins

Amino Acids

only 20 types of amino acids are used for protein synthesis in biological systems.

L-α-Amino acid

a classification of amino acids
A Classification of Amino Acids
  • Amino acids are grouped as

(1) non-polar, hydrophobic;

(2) polar, neutral;

(3) acidic;

(4) basic.

special amino acids
Special amino acids
  • Gly
  • Pro
  • Cys

optically inactive

Having a ring structure and imino group

active thiol groups to form disulfide bond


A peptide isa compound of amino acids linked together by peptide bonds.

peptide bond
peptide bond

A peptide bond is a covalent bond formed between the carboxyl group of one AA and the amino group of its next AA with the elimination of one H2O molecule.

biologically active peptides
Biologically active peptides

Glutathione (GSH)

As a reductant to protect nucleic acids and proteins

Peptide hormones

Neuropeptides responsible for signal transduction

section 2 molecular structures of proteins
Section 2Molecular Structures of Proteins

Primary Structure


Tertiary Structure

Spatial structure

Quaternary Structure

primary structure
Primary Structure

The primary structure of proteins is defined as a linear sequence of amino acidsjoined together by peptide bonds.

Peptide bonds and disulfide bonds are responsible for maintaining the primary structure.

secondary structure
Secondary Structure

The secondary structure of a protein is defined as a local spatial structure of a certain peptide segment, that is, the relative positions of backbone atoms of this peptide segment.

H-bonds are responsible for stabilizing the secondary structure.

Repeating units of Ca-C(=O)-N(-H)-Ca constitute the backbone of peptide chain.

Six atoms, Ca-C(=O)-N(-H)-Ca, constitute a planer peptide unit.

four common types of secondary structure
Four common types of secondary structure
  • α-helix
  • β-pleated sheet
  • β-turn
  • random coil

When several local peptides of defined secondary structures are close enough in space, they are able to form a particular structure---Motif.

Zinc finger

HLH (helix-loop-helix)

HTH (helix-turn-helix)

tertiary structure
Tertiary Structure
  • The tertiary structure is defined as the three-dimensional arrangement of all atoms of a protein.
five types of interactions stabilize the protein tertiary structure
Five types of interactions stabilize the protein tertiary structure.
  • •hydrophobic interaction
  • •ionic interaction
  • •hydrogen bond
  • •van der Waals interaction
  • •disulfide bond

Large polypeptides may be organized into structurally close but functionally independent units---Domain


Chaperones are large, multisubunit proteins that promote protein foldings

quaternary structure
Quaternary Structure

The quaternary structure is defined as the spatial arrangement of multiple subunits of a protein.

These subunits are associated through H-bonds, ionic interactions, and hydrophobic interactions.

protein classification
Protein classification
  • Constituents

simple protein

conjugated protein = protein +

prosthetic groups

Overall shape

Globular protein long/short < 10

Fibrous proteinlong/short > 10

section 3 structure function relationship of proteins
Section 3 Structure-Function Relationship of Proteins
  • Relationship between primary structure and function

Primary structure is the fundamental to the spatial structures and biological functions of proteins.

  • Proteins having similar amino acid sequences demonstrate the functional similarity.
  • The alternation of key AAs in a protein will cause the lose of its biological functions.
relationship between spatial structure and function
Relationship between spatial structure and function
  • A particular spatial structure of a protein is strongly correlated with its specific biological functions.

1.The denatured protein remains its primary structure, but no biological function.

2. Allosteric change of hemoglobin by O2

isoelectric point pi
isoelectric point (pI)
  • The pH at which the protein has zero net-charge is referred to as isoelectric point (pI)
2 colloid property
2. Colloid property

Hydration shell and electric repulsion make proteins stable in solution.

3 protein denaturation renaturation precipitation and coagulation
3 Protein denaturationrenaturation, precipitation and coagulation
  • The process in which a protein loses its native conformation under the treatment of denaturants is referred to as protein denaturation.


sterilization, lyophilization

4 uv absorption
4 UV absorption
  • Trp, Tyr, and Phe have aromatic groups of resonance double bonds.
  • Proteins have a strong absorption at 280nm
5 coloring reactions
5 Coloring reactions
  • Biuret reaction
  • Ninhydrinreaction
section 5 exploration of protein
Section 5 Exploration of Protein
  • Isolation and purification

• Centrifugation

• Dialysis

• Precipitation

• Chromatography

• Electrophoresis

protein sequence determination
Protein Sequence Determination
  • Edman degradation
  • Deduction from DNA sequence
structure determination
Structure Determination
  • Circular dichroism spectroscopy
  • X-ray crystallography
  • Nuclear magnetic resonance spectroscopy
  • Computer simulation