Chapter 1 Cells and macromolecules RNA Protein DNA Prokaryotic cell Eukaryotic cell

Other macromolecules unrelated to MB course Polysaccharides lipids Complex macromolecules including these molecules

1.1 Cellular classification (Eubacteria, Archea, Eukaryotes, Cellular differentiation) 1.2 Subcellular organelles (Nuclei, mitochondria and chloroplasts, endoplasmic reticulum, microbodies, organelle isolation) 1.3 Macromolecules (protein and nucleic acids, polysaccarides, lipids, complex macromolecules) 1.4 Large macromolecular Assemblies (protein complex, nucleoprotein, membranes, noncovalent interactions)

1.1 Cellular classification Classifying organisms according to cell types Eukaryotic cell Prokaryotic cell

重点 Prokaryotes （原核生物）(Simplest living cells) Eukaryotes （真核生物） Eubacteria （真细菌） Archaea （古细菌） Structural features 1-10 mm, no distinct subcellular organelles, pili, flagella 10-100 mm, Organelles Biochemistry rRNA molecules are different among these kingdoms (rRNA based phylogeny, Fig. S2) Ester linkage（酯键）(link) Ether linkage （醚键） Ester linkage（酯键） Energy production, metabolism Replication, transcription and translation Differentiation (link) Formation of spores Embryonic cell differentiation 重点

Phylogenetic tree determined by rRNA sequence comparisons Fig. S2

重点 (鞭毛) (类核) (纤毛) 典型原核细胞示意图

Cell wall: to prevent cell lysis in environments of low osmolarity Plasma membrane: lipid bilayer and embedded proteins for small molecule exchange Genetic materials: nucleiod (single and circular chromosome), plasmid Ribosmes: protein synthesis machinery Pili: to allow the cell to attach to other cells and surface Flagella: cell movement

重点 典型真核细胞示意图

Cytoskeletal Fiber： Controls the shape and movement of the cell Organizes some metabolic functions

Cellular differentiation (细胞分化) Definition: The daughter cells change their patterns of gene expression to become functionally different from the parent cell after cell division. The main molecular reason: change of the genes being transcribed, but not that of the DNA content. Regulated by developmental control genes, mutations in these genes result in abnormal body plans.

Cross with Cell Biology Course For example Spore formation among prokaryotes and lower eukaryotes Embryonic cell differentiate into highly specialized cells among higher eukaryotes.

Cell differentiation in yeast (酵母） Mating: n + n  2n Spore formation: 2n  n + n Cell differentiation in yeast (酵母）

Differentiation is regulated by developmental control genes Embryonic cell differentiation in Xenopus (爪蟾属)：from a single cell to an adult tadpole Differentiation is regulated by developmental control genes Fig. S4

1.2 Subcellular organelles Nuclei mitochondria and chloroplasts, Cross with Cell Biology 1.2 Subcellular organelles Nuclei mitochondria and chloroplasts, endoplasmic reticulum, microbodies, organelle isolation

DNA replicationRNA transcription & processing  Ribosome assembly （核） DNA replicationRNA transcription & processing  Ribosome assembly

DNA replication, RNA transcription, protein synthesis （线粒体） Main function: cellular respiration/ATP production via oxidative phosphorylation DNA replication, RNA transcription, protein synthesis Nuclear-encoded Mitochonrial proteins: synthesis and transportation

（叶绿体） A plant specific organelle （类囊体） （基粒） Photosynthesis, the light-dependent assimilation of CO2 and H2O to form carbohydrates and O2 DNA replication, RNA transcription, protein synthesis Nuclear-encoded chloroplast proteins: synthesis and transportation

(内质网) Protein synthesis （酯类代谢） （药物的氧化和解毒） drug oxidation and detoxificatin （酯类代谢） （药物的氧化和解毒）

Microbodies (lysosomes, peroxisomes and glycoxysomes) （溶酶体，过氧化物酶体，醛氧化酶体） Glyoxysomes are specialized plant peroxisomes which carry out the reactions of glyoxylate cycle（乙醛酸循环）.

Organelle isolation: centrifugation (离心) Density gradient centrifugation Rate zonal (velocity) centrifugation Equilibrium centrifugation Differential (speed) centrifugation: Sedimentation coefficient (s) Density gradients: to prevent convective mixing of the components after separation and to ensure linear sedimentation rates of the components Supporting materials: sucrose (蔗糖）, Ficoll, cesdium chloride （氯化铯）

1.3 Macromolecules Protein (Section B) Nucleic acids (Section C) Polysaccharides Lipids Complex macromolecules MB course (X), Biochemistry () Immunology ()

Polysaccharides are polymers of simple sugars covalently linked by glycosidic bonds.

Lipids: individual lipids are not strictly macromolecules, large lipid molecules are built up from small monomeric units and involved in many macromolecule assembly Triglycerides (甘油三酯)

Complex macromolecules (复合大分子） Covalent or noncovalent associations of more than one major classes of large biomolecules which greatly increases the functionality or structural capabilities of the complex. Nulceoprotein: nucleic acids + protein (Section A4) Glycoprotein: carbohydrate + protein Lipoprotein: Lipid + protein

生物大分子间相互作用的化学力 生物大分子的基本结构是靠共价键结合的，但是生物学功能的执行是靠生物大分子之间的相互作用来实现的。如：①蛋白质与DNA的相互作用；②蛋白质与RNA的相互作用；②蛋白质与蛋白质的相互作用。 生物大分子间相互作用的化学力 1 扩散作用 (Diffusion) 2 专一性相互作用 结构基序，离子键，氢键，范德华力

生物大分子内部相互作用的化学键 1、共价键 (Covalent bond)：成键原子间通过电子对共享形成的。键 能一般在200KJ/mol以上。 磷酸二酯键、肽键、二硫键，－S－S－ 2、弱键（非共价键 noncovalent bond）：小于20KJ/mol。 （1）氢键 (Hydrogen bond) （2）盐键（离子键）静电作用力 (Ionic bond) （3）范德华力（短程力）(Van der Waals force) （4）疏水作用 (Hydrophobic interaction) 3、配位键一般在250KJ/mol以上

Large macromolecular Assemblies Noncovalent interactions 1.4 Large macromolecular Assemblies Protein complexes Nucleoprotein Membranes Noncovalent interactions

重点 protein complexes (cilia and flagella) Noncovalent interaction Long polymers of tubulin (microfilament) actin and myosin, components of muscle fibers as well keratin Fig.1. Schematic diagram showing the (a) cross-sectional and (b) surface pattern of tubulin a and b subunits in a microtubule Noncovalent interaction

associations of nucleic acids and protein 重点 Nulceoprotein (1) associations of nucleic acids and protein Ribosome: ribosomal proteins ＋ rRNAs Crystal structure of 50S rRNA

重点 Nulceoprotein (2) deoxyribonucleoprotein consisting of DNA & histones to form a repeating unit called nucleosome Chromatin (染色质): Viruses: Telomerase (端粒酶) : Ribonuclease P： protein capsid + RNA or DNA replicating the ends of eukaryotic chromosomes. RNA acts as the replication template, and protein catalyzes the reaction tRNA maturation. Protein ＋ P RNA

Noncovalent interactions The force of macromolecule assembly 重点 Noncovalent interactions The force of macromolecule assembly Charge-charge interactions (salt bridges): charged molecules Charge-dipole, dipole-dipole: either or both of the participants is a dipole . Dispersion interactions: non-poplar molecule van der Waals forces: noncovalent associations between uncharged molecules. *Hydrogen bonds (dipole-dipole): nucleic acids *Hydrophobic interaction: proteins

(uncharged molecules) (偶极) (uncharged molecules)