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01139630 生物化学

说在前面：全英文的生物化学难点在有很多专业名词的生词，且许多酶和反应的名字非常易混，不好记忆。可以先用中文记忆逻辑关系，再记英文词汇（逃

我这里的章节不会按照老师的ppt进行，而是按照知识的自然顺序。

Fall semester: Zengyi Chang, Yongmei Qin

Spring semester: Junyu Xiao, Xiao-Wei Chen, Chengqi Yi

Chapter 1 Introduction

1. Foundations of Biochemistry

Cell structure

  • cytoplasm
  • plasma membrane
  • ribosomes
  • nucleoid
  • cytoplasm
  • plasma membrane
  • ribosomes
  • nucleus
  • nuclear membrane
  • membrane-bounded organelles

macromolecules: proteins, polysaccharides, nucleic acids, lipids

Biomolecules are compounds of carbon

  • The four single bonds around a carbon have a characteristic tetrahedral arrangement
  • It is able to link into linear, branched or cyclic structures, to which all kinds of functional groups (e.g., alcohol, amino, carboxyl) can be attached
  • C-C single bonds are free to rotate
  • C=C double bonds are shorter and do not allow free rotation. The two carbons and atoms attached to them all lie in the same rigid plane

区分概念：Conformation (构象) and Configuration (构型)

  • the spatial arrangement of substituent groups that without breaking any bonds, are free to assume different positions in space because of the freedom of rotation about single bonds
  • Conformational changes in protein are common and functionally important

  • the isomers can not be interconverted unless covalent bonds are broken. Configuration is conferred by the presence of double bonds(1) or chiral centers(2)

    1. cis顺式 trans反式
    2. D / L

  • Chiral molecules: A carbon atom with four different substituents which is asymmetric （opposite： achiral molecule）

  • Function of biomolecules are stereospecific

  • Enantiomers (对映异构物) and Diasteromers (⾮对映异构物)

common fuctional groups

biochemistryEN1

from Lehninger Biochemistry

  • The chemical personality of a molecule is determined by its functional groups

2. Water

hydrogen bonds

  • Hydrogen bond readily occurs between an electronegative atom and a hydrogen covalently bonded to another electronegative atom (always O or N), when they are ~0.3 nm (3 angstrom) apart
  • Hydrogen bonds are “weak” bonds, but The “weakness” of hydrogen bonds are important to biological system. eg. DNA

Water are solvent

  • Hydrophilic(亲水的): soluble in water
  • Hydrophobic(疏水的): not soluble in water
  • Amphipathic (or amphiphilic)(两亲的): part of the compound likes water and part of the compound repels water

Chapter 2 Proteins

1. Amino acids

History

A class of compounds, synthesized by plants and vital for animal health, was first identified in the 18th century

  • The compounds we now know as proteins were observed to coagulate or flocculate when treated with heat or acid. Early examples included egg-white albumin, serum albumin, fibrin, and wheat gluten, as documented by Fourcroy and others in the 18th century.
  • By the early 19th century, it was recognized that these nitrogen-containing compounds were essential for animal survival.
  • In 1838, Mulder and Berzelius introduced the term "protein"—from the Greek prōteios, meaning "primary" or "holding first place"—to designate this class of substances
  • It was initially believed that proteins from plants could be directly incorporated into animal tissues.
  • Later in the 19th century, digestion studies revealed that proteins are in fact composed of amino acids.

basic structure

All standard amino acids are α-amino acids, sharing a common core structure:

  • central α-carbon atom
  • a primary amino group (–NH₂)
  • a hydrogen atom (–H)
  • carboxyl group (–COOH)
  • distinctive side chain (R group)

BIochemistryEN2

from Lehninger Biochemistry

Each standard amino acid has a unique combination of properties

Nearly all proteins are composed of L-amino acids

  • Jacobus van 't Hoff and Joseph Le Bel independently proposed in 1874 the tetrahedral geometry of carbon atoms, explaining chirality and optical activity.
  • Emil Fischer established the D/L naming system in 1900s, using D- and L-glyceraldehyde（甘油醛） as reference standards.
  • All amino acids they tested from proteins could be chemically correlated to L-glyceraldehyde.
  • In 1951, Johannes Martin Bijvoet et al confirmed the L-configuration of amino acids via X-ray crystallography.
  • D-amino acids were in 1950s through the chemical analysis of hydrolyzed bacterial cell walls (Peptidoglycan).

Two cysteine residues in peptide chains can form a covalent disulfide bond between them

  • Disulfide bonds, intrachain or interchain, are common structural features in secreted proteins（分泌蛋白） and peptides, as well as in proteins from thermophilic archaea（热塑性古生菌）
  • In contrast, they are uncommon in the cytosolic proteins（胞内蛋白） of eukaryotic and bacterial cells owing to the reducing intracellular environment

Some uncommon amino acids are generated in proteins through post-translational modifications

Certain uncommon amino acids are biosynthesized in proteins through reversible post-translational modifications

  • Phosphorylation(on Ser, Thr, Tyr)
  • Methylation (on Arg)
  • Acetylation (on Lys)
  • Methylation(on Glu)
  • Adenylylation (on Tyr)

properties

  • absorption of near-UV light (280 nm)
  • Free amino acids are capable of acting as diprotic or triprotic acids
  • At physiological pH (~7.4), amino acids predominantly exist as zwitterions
  • Both the α-carboxyl and the α-amino groups become more acidic due to the effects of neighboring chemical groups
  • characteristic isoelectric point (pI)