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1、Obligatory course for biology students Prerequisite: General biology, Biochemistry Molecular Biology Prokaryotic Cell (does not have nucleus) Archaebacteria and eubacteria *Archea: Methnogens (anaerobic) Extreme halophiles (dead sea) Extreme thermophiles (hot spring, geysers) Eukaryotic Cell (contai
2、n a nucleus) Protista, fungi, animals and plants Cells: Cytoplasm: proteins, ribosome, metabolites and ions Plasma membrane: phospholipid bilyer, associated proteins and carbohydrates DNAs, mtDNA Basic Cellular ComponentsBasic Cellular Components Prokaryotic cells Prokaryotic cells BacteriaBacteria:
3、 Gram-negative- Cell wall (3 layers: Periplasmic space; peptidoglycan; outer membrane) Gram-positive-Cell wall (thicker peptidoglycan layer) *Quite sensitive to lysozyme and penicillin Capsule and slime:Capsule and slime: The hydrophilic gel surrounding the cell wall in most bacteria Flagella:Flagel
4、la: Long, rigid protein roads, facilitating the movement of motile bacteria FimbriaeFimbriae and and pilipili: : Short hair-like structure and attach other cells (essential infecting other organisms) Spores:Spores: A small, often unicelluar, reproductive unit of plants, algae, fungi, protoza, and ba
5、cteria Organization of Eukaryotic CellsOrganization of Eukaryotic Cells Endoplasmic reticulum BiomembraneBiomembrane NucleusNucleus Nuclear envelope Nucleolus Nucleoplasm Chromosome and Chromosome and karyotypekaryotype Long arm: q (for queue) Short arm: p (for petit) GimsaGimsa ( (QuinacrineQuinacr
6、ine) ) Dark band: G band or G + band (AT rich) Light band: R band or G band (GC rich) Organelles in the CytoplasmOrganelles in the Cytoplasm (The membrane-bound structure in a cell) Mitochondria Chloroplasts Endoplasmic reticulum Golgi apparatus Peroxisomes Lysosomes Vacuoles Glyoxisomes Mitochondri
7、aMitochondria Size: 1.5-2.0 in length, 0.5-1.0 um in diameter Approx the same as E. coli Maternal inheritance Many copies: occupying of the cytoplasmic volume Role: produce ATP Encode: proteins and RNAs mtDNA ChloroplastsChloroplasts Thylakoloids 类囊体 Chlorophylls: located on the Thylakoloid membrane
8、 to absorb light for photosynthesis Light 2H2O-O2 + 4H + +4e- H+ +ADP 3- + Pi 2- -ATP 4- + H2O Endoplasmic reticulumEndoplasmic reticulum Rough ER: process newly synthesized peptides from ribosome Smooth ER: involved in the synthesis and metabolism of lipids GolgiGolgi apparatus apparatus Major site
9、 for sorting and modifications of proteins and lipids rough ER-transport vesicles-Golgi-Glycoproteins PeroxisomesPeroxisomes Peroxisome: contain enzymes for degrading amino acids and fatty aids Catalase 2H202-2H20 +02 LysosomesLysosomes Lysosomes : 1) nuclease for degrading DNA and RNA 2) Protease f
10、or degrading proteins and other enzymes for degrading polysacchrides and lipids 3) lysosomes exist only in animal cells (plant -vacuoles for degrading macromolecules) GlyoxisomesGlyoxisomes 乙醛酸循环体乙醛酸循环体 Found mainly in plant seeds Fatty acids-Acetyl CoA Microbodies: Peroxisomes +Glyoxisomes VirusesV
11、iruses Baltimore Classification Structure Life Cycles The life cycle of Viruses 1 ) Attachment: viral surface protein-host cell receptor e.g: HIV GP120 - CD4 glutamatic acids Basic: lysine, arginine & histidine Aromatic: tyrosine, tryptophan and phenylalanine Sulfur: cysteine, methionine Uncharged h
12、ydrophilic: serine, threonine, asparagine, glutamine Inactive hydrophobic: glycine, alanine, valine, leucine, isoleucine Special structure: proline Salt bridge: interaction between + & - R groups, important stabilizing force in proteins Disufide bonds: strong force for stabilizing the globular struc
13、ture Methionine: synthesis of all peptide chains starts from methionine Proline: the only amino acid has its R group and amino group directly connected- often located at the turn of a peptide in the 3-D structure of a protein PeptidePeptide is a chain of amino acids linked together by peptide bonds.
14、 PolypeptidesPolypeptides usually refer to long peptides whereas oligopeptidesoligopeptides are short peptides ( pI pH pI Protein structure Charge 1: Ion-exchange chromatography Column + anions + + Sample mixture Protein binding Column + proteins Column + anions Ion displacing Purified protein Prote
15、in structure + Charge 2: Electrophoresis Protein migrate at different position depending on their net charge Protein structure Charge 3: Isoelectric focusing A protein will stop moving at position corresponding to its isoelectric point (pI) in a pH gradient gel. Protein structure 3. Hydrophobicity:
16、hydrophobic interaction chromatography Similar to ion-exchange chromatography except that column material contains aromatic or aliphatic alkyl groups Protein structure 4. Affinity chromatography Enzyme-substrate binding Receptor-ligand binding Antibody-antigen binding Protein structure 5. Recombinan
17、t techniques: Clone the interested protein encoding gene in an expression vector with a purification tag added at the 5- or 3 end of the gene Protein overexpression in a cell Protein purification with affinity chromatography. Protein structure Mass Determination Gel filtration chromatography and SDS
18、-PAGE Comparing of the unknown protein with a proper standard Popular SDS-PAGE: cheap and easy with a 5-10% error SDS: sodium dodecyl sulfate, makes the proteins negatively charged and the overall charge of a protein is dependent on its mass. Protein structure Mass spectrometry: Molecules are vapori
19、zed and ionized, and the degree of deflection (mass-dependent) of the ions in an electromagnetic field is measured extremely accurate, but expensive MALDI can measure the mass of proteins smaller than 100 KDa Helpful to detect post-translational modification Protein sequencing: relying on the protei
20、n data base Protein sequencing : Determine the primary structure of a protein Specific enzyme/chemical cleavage: Trypsin cleaves after lysine (K) or arginine (R) V8 proteease cleaves after glutamic acid (E) Cyanogen bromide cleaves after methionine (M) Edaman degradation: Performed in an automated p
21、rotein sequencer Determine the sequence of a polypeptide from N- terminal amino acid one by one. Expensive and laborious Protein structure Most protein sequences are deduced from the DNA/cDNA sequence Direct sequencing: determine the N-terminal sequences or some limited internal sequence constructio
22、n of an oligonulceotide or antibody probe fishing the gene or cDNA Protein structure X-ray crystallography and NMR Determing the tertiary structure (3-D) of a protein X-ray crystallography: Measuring the pattern of diffraction of a beam of X-rays as it pass through a crystal. The first hand data obt
23、ained is electron density map, the crystal structure is then deduced. A very powerful tool in understanding protein tertiary structure Many proteins have been crystallized and analyzed Protein structure Measuring the relaxation of protons after they have been excited by radio frequencies in a strong
24、 magnetic field Measure protein structure in liquid but not in crystal Protein measured can not be larger than 30 KDa NMR Nucleotide: pentose +base + phosphate Nucleoside: pentose +base BaseBase A, C, G, T exist in DNA A, C, G, U exist in RNA The nucleic acid chainThe nucleic acid chain DNA 3D struc
25、tureDNA 3D structure DNA 3D structureDNA 3D structure RNA StructureRNA Structure Gene TranscriptionGene Transcription 1 Overview of Gene Expression2 Overview of Transcription 3 Genes Regulatory Elements4 Transcription Mechanism in Prokaryotes 5 Transcription Mechanism in Eukaryotes 6 Motif Structure of Transcription Factors 7 Histone Acetylation and DNA methylation 8 Regulation of Transcription Factors 9 Transcription of RNA Genes10 Genome Replication of Viruses antisense Exon skipping
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