chapter 1
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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?
Proteins are macromolecules composed of amino acids linked together through peptide bonds.
Section 1 Chemical Components of
Proteins
major elements C, H, O, N, S. trace elements P, Fe, Cu, Zn, I, …
Element components of proteins
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
only 20 types of amino acids are used for protein synthesis in biological systems.
L-α-Amino acid
The basic building blocks of proteins
Amino Acids
L-α-Amino acid
COOH
C HH2N
R
¹² ͬ²¿ ·Ö¦Á
²à Á´
A Classification of Amino Acids Amino acids are grouped as (1) non-polar, hydrophobic; (2) polar, neutral; (3) acidic; (4) basic.
Special amino acids
Gly
Pro
Cys
optically inactive
Having a ring structure and imino group
active thiol groups to form disulfide bond
Peptide
A peptide is a compound of amino acids linked together by peptide bonds.
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 activepeptides
Glutathione (GSH) As a reductant to protect nucleic acid
s and proteinsPeptide hormones Neuropeptides responsible for signal
transduction
Section 2 Molecular Structures of Proteins
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
Spatial structure
Primary Structure The primary structure of proteins is def
ined as a linear sequence of amino acids joined together by peptide bonds.
Peptide bonds and disulfide bonds are responsible for maintaining the primary 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
α-helix β-pleated sheet β-turn random coil
Motif
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
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. • hydrophobic interaction • ionic interaction • hydrogen bond • van der Waals interaction
• disulfide bond
Domain
Large polypeptides may be organized into structurally close but functionally independent units---Domain
Chaperon
Chaperones are large, multisubunit proteins that promote protein foldings
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.
From primary to quaternary structure
Protein classification Constituents simple protein conjugated protein = protein + prosthetic
groups
Overall shape Globular protein long/short < 10 Fibrous protein long/short > 10
Section 3 Structure-Function Relationship of Proteins Relationship between primary structu
re and function Primary structure is the fundamental t
o the spatial structures and biological functions of proteins.
Example
1. Proteins having similar amino acid sequences demonstrate the functional similarity.
2. The alternation of key AAs in a protein will cause the lose of its biological functions.
Relationship between spatial structure and function
A particular spatial structure of a protein is strongly correlated with its specific biological functions.
Example
1.The denatured protein remains its primary structure, but no biological function.
2. Allosteric change of hemoglobin by O2
Section 4 Physical and Chemical Properties of Proteins
1. Amphoteric
isoelectric point (pI) The pH at which the protein has zer
o net-charge is referred to as isoelectric point (pI)
2. Colloid property
Hydration shell and electric repulsion make proteins stable in solution.
3 Protein denaturation renaturation, precipitation and coagulation The process in which a protein loses
its native conformation under the treatment of denaturants is referred to as protein denaturation.
• Applicationssterilization, lyophilization
4 UV absorption
Trp, Tyr, and Phe have aromatic groups of resonance double bonds.
Proteins have a strong absorption at 280nm
5 Coloring reactions
Biuret reaction Ninhydrin reaction
Section 5 Exploration of Protein
Isolation and purification• Centrifugation• Dialysis• Precipitation• Chromatography• Electrophoresis
Protein Sequence Determination
Edman degradation Deduction from DNA sequence
StructureDetermination
Circular dichroism spectroscopy X-ray crystallography Nuclear magnetic resonance spectr
oscopy Computer simulation
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