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Protein-2

In biochemistry, proteins are an important class of biological macromolecules in organisms. They are composed of amino acids connected by peptide bonds and have complex structures and diverse functions. It introduces protein molecular structure, protein physical and chemical properties, peptides and other knowledge points in detail.

Edited at 2024-12-01 17:24:29

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Protein-2

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Protein-2

peptide

peptide bond

Found in protein and peptide molecules, an amide bond formed by the condensation of the α-carboxyl group of one amino acid with the α-amino group of another amino acid

peptide unit

There is a P-π conjugation effect between the lone pair of electrons in the nitrogen unit and the π electrons in the C=O bond -> conjugation can occur

There is a certain degree of double bond nature between the double bonds and they cannot rotate freely.

peptide plane

The six atoms of the peptide unit are all in the same plane

Peptide units are almost all trans structures, and the conformation can be rotated

Peptide/Amino Acid Residues

Classification

2-Dipeptide

2-10-oligopeptide

10-50-Peptides

>50-Protein

active peptide

Peptide substances with special physiological functions

Plays an important role in metabolic regulation, nerve conduction, cell differentiation, growth and development, immune defense, reproductive regulation, free radical scavenging & tumorigenesis, etc.

Classification

endogenous active peptides

exogenous active peptides

The products of limited digestion of food proteins are directly absorbed and participate in feeding, digestion, metabolism, and endocrine regulation.

Reduced Glutathione/GSH

Glutamic acid, cysteine, glycine - an acidic tripeptide connected by isopeptide bonds & peptide bonds, containing sulfhydryl groups as the main functional group

Reducing, important antioxidant

Carnosine & Anserine

dipeptide

Antioxidant, involved in scavenging reactive oxygen species

protein molecular structure

Classification

basic structure

Primary structure-amino acid sequence

The entire amino acid sequence of one or more peptide chains that constitute a protein molecule, including the positions of possible disulfide bonds, but excluding other spatial structures other than the α-carbon configuration.

Main chemical bonds - peptide bonds/disulfide bonds

Function

The primary structure of a protein is its spatial basis

Proteins with similar primary structures have similar functions

The primary structure of homologous proteins contains biological evolution information

Changing the primary structure of a protein can directly affect its function

spatial conformation

Classification

Secondary structure - peptide conformation - describes the local spatial structure of the main chain atoms

The spatial layout of the main chain atoms of a local peptide segment of a protein (containing 3-30 amino acid residues), that is, the main chain conformation, excluding side chain conformation and the spatial layout between peptide segments.

Classification

alpha helix

right hand helix

Each helix contains 3.6 amino acid residues and has a pitch of 0.54nm.

Amino acid side chains extend to the outside of the helix and are stabilized by hydrogen bonds.

beta sheet

The main chain conformation of local peptide segments of the protein forms a zigzag fold

Parallel combinations form group pleat structures - parallel/anti-parallel

β-turn

A rigid peptide segment used to connect other secondary structures in protein molecules

Contains four amino acid residues - proline appears most frequently in the second position of the residue, and glycine appears most frequently in the third position

ring

random curl

Chemical Bonding: Hydrogen Bonding

Tertiary structure - subunit conformation - describes the spatial structure of all atoms

The spatial arrangement of all atoms contained in a protein molecule or one of its subunits, excluding its structural relationship with other molecules or subunits

Chemical bonds: non-covalent bonds such as hydrophobic interactions, ionic bonds, hydrogen bonds, van der Waals forces, and a small amount of covalent bonds such as disulfide bonds

Classification

Myoglobin - stores and transports oxygen within cells

Ribonuclease-hydrolyzes ribonucleic acid

Motif/motif - a recognizable structural unit formed by the further aggregation and combination of two adjacent ends or segments of the same or different secondary structures

Helix-loop-helix - Motif structure with chelated Ca2

Zinc finger – a motif structure that chelates Zn2

Structural domain - a structural unit with a compact, independent, stable and specific function formed by a peptide chain in the tertiary structure

Quaternary structure - tetramer conformation - describes the interrelationships between subunits

The number, type, spatial layout of all subunits contained in a multi-subunit protein & the mutual binding and interaction between subunits, but does not include the tertiary structure of the subunits

Classification (whether it contains quaternary structure)

monomeric protein

multi-subunit protein

Number of subunits contained - dimer, trimer, tetramer

Types of subunits included - homomeric proteins, heteromeric proteins

Proto[polymer] - a structural unit in the quaternary structure with spatial symmetry, which can be regarded as a homopolymer

Function

Conformation determines function, allostery changes activity

Conformational classification - globular proteins/fibrillar proteins

Physiological function—active protein [substance]/structural protein [substance]

Allosteric proteins and allosteric effects

Synergistic effect - binding of one site to a ligand causes a conformational change in the protein, which in turn affects the affinity or binding speed of other sites to their respective ligands.

Positive synergistic effect - leading to enhanced affinity and faster binding

Negative synergy - leading to decreased affinity and slower binding

synergistic effect - synergistic effect produced by the same ligand

Heterotropic effect - the synergistic effect produced by different ligands

Protein physical and chemical properties

General properties

UV absorption characteristics

The peptide bond structure contained has strong absorption of ultraviolet light below 220nm.

The tryptophan and tyrosine contained in it have strong absorption of 280nm ultraviolet rays

Color reaction - ninhydrin reaction, biuret reaction

N-terminal reaction

Amphoteric ionization and isoelectric point

Macromolecule properties

Colloidal properties

Its stabilizing factor is the repulsion of like charges. Hydration film

Sedimentation - The particles of protein are denser than water and have a tendency to settle under the influence of gravity in solution.

Sedimentation coefficient

Protein denaturation and renaturation

Many proteins are composed of more than one peptide chain. Each peptide chain contains its tertiary structure and is called a subunit of the protein. This type of protein is called a multi-subunit protein.