Introduction to Cell biology

1. Introduction to Cell biology

2. Hierarchical organisation of the structure of living systems organisms organs tissues cells Nucleus, mitochondria, Golgi apparat, etc Ribosomes, chromosomes, cytoskeleton, membranes, etc polysaccharides triacylglycerols nucleic acids proteins monosaccharides phospolipids nucleotides N-containing bases Ribose Fatty acids, glycerol, cholin aminoacids

3. Cells as seen before the cell theory Anton van Leeuwenhoek, XVII. century: algae, bacteria, sperm cells, etc.

4. Robert Hooke 1665: „cell”: unit in dead samples of cork.

5. The cell theoryCell as the central unit of biological organization • Cells are the basic units of life. • All living organisms are made up of cells. • Only living cells can produce new cells. • Matthias Schleiden 1838 Theodor Schwann 1835 • plants are made up of cells animals are made up of cells

6. Rudolf Virchow 1858: • „Every animal appears • as the sum of vital units, • each of which bears in itself • the complete characteristics • of life”

7. Louis Pasteur 1865 : „Spontaneous generation” of life ruled out experimentally „There is now no circumstance known in which it can be affirmed that microscopic beings came into the world without germs, without parents similar to themselves."

8. Tranzitions from non-living towards living: I. Prions: molecules resembling ion channels, causing serious illnesses

9. Tranzitions from non-living towards living: II. Viruses Viruses have no metabolism and can not reproduce by themselves. They contain genetic material (either RNA or DNA) and proteins. After infection they use the machinery of the host cell to produce more viruses. Highly simplified structure of a virus

10. The HIV virus

11. Prokaryotic and eukaryotic cells Diagram EM 1 mm 1 mm

12. I. (BIO)CHEMICAL FOUNDATIONS

13. The most important groups of organic molecules: Proteins composed of amino acids Lipids composed of glycerol and fatty acids Carbohydrates: mono-, oligo- and polysaccharides Nucleic acids: DNA, RNAs

14. I./1. PROTEINS • Classification of proteins: • Enzymes • Receptors • Transport proteins • Storage proteins (casein in milk, ferritin /iron/) • Contractile proteins • Structural proteins • Immune proteins • Regulatory proteins • Others (e.g. antifreeze proteins)

15. Amino acids: General chemical structure: NH2-knk,,-COOH Peptide bound: NH2-knk,,-COOH + NH2-knk,,-COOH i NH2-knk,,-CONH-knk,,-COOH + H2O 20 different amino acids in unlimited amount in any possible variations may form unlimited number of various peptide chains

16. Primary structure Primary structure or sequence: linear arrangement of the amino acids that constitute the polypeptide chain Sequencing: to determine the order of amino acids of a protein. Sequence motive: a specific amino acid arrangement that appears in several different proteins and play the same role in these proteins. Examples: DNA binding motive signal sequence (transport of the protein to a given organelle) sequence for phosphorylation ligand-binding sequences (e.g. ATP, growth hormons)

17. Secondary structure Local organisation (folding) of parts of a polypeptide chain. Most important secondary structure elements: a-helix and b-sheet ( L. Pauling, early 1950s) In the rodlike a-helix the polypeptide backbone is folded into a spiral that is held in place by hydrogen bonds.

18. The b sheet consists of laterally packed b strands (extended polypeptide structures). b sheets are stabilized by hydrogen bonds between the strands. The compact structure of the proteins is ensured by turns (compact, U-shaped elements stabilized by H-bonds) and loops (long, loose bends) between the a-helical and b-sheet structures.

19. a-Helix b strands Loops and turns An example: Ribonuclease

20. Tertiary and quaternary structure Tertiary structure: Three-dimensional arrangement of all amino acids, which results in mainly from hydrophobic interactions between nonpolar amino acid side-chains. These interactions hold helices, strands and coils together. The highest level of organisation for monomeric proteins. Quaternary structure: number and relative positions of subunits in multimeric proteins. Determination of the three-dimensional structure of proteins: x-ray crystallography nuclear magnetic resonance (NMR)

21. An example: Haemoglobin

22. Membrane lipids (polar) Storage lipids (apolar) Phospholipids Glycolipids Triacylglycerol Glycero- phospholipids Sphingolipids I./2. LIPIDS AND THEIR COMPONENTS

23. Triacylglycerols Serve for storage (lipid droplets in fat cells) and isolation.

24. Membrane lipids

25. Cholesterol In addition to the phospholipids, it occurs in biological membranes – exclusively in eukaryotes. Stabilizes the membranes.

26. I./3. CARBOHYDRATES The most abundant biomolecules on the earth. Essential components of foodstuff (sugar) Forms of occurence in living systems: monosaccharides (e.g. glucose) oligosaccharides (e.g. saccharose, lactose) polysaccharides (e.g. glycogene, starch) Occurrence in complex macromolecules: with lipids (e.g.glycolipides) with proteins (glycoproteins and proteoglycans) within nucleic acids (constituents of RNA and DNA)

27. Some monosaccharides Glycogene: polysaccharide

28. I./4. NUCLEIC ACIDS BASE PHOSPHATE SUGAR Nucleic acids are the information-storing molecules of the cells. They are linear polymers of nucleotides connected by phosphodiester bonds. A nucleotide is composed of an organic base a pentose (five-carbon sugar) a phosphate group

29. The base components of nucleic acids adenine uracil cytosine thymine guanine N-containing (heterocyclic) ring molecules: purines ( a pair of fused ring) and pyrimidines ( a single ring). cytosine (C), adenine (A) & guanine (G): in RNA and DNA thymine (T): in DNA uracil (U): in RNA

30. Chemical structure of nucleic acids DNA or RNA strand formation: polymerization (condensation) of nucleotides, by forming phosphodiester bonds. Nucleic acid sequence with one-letter codes: e.g. A-C-T-T-C-G-G beginning with 5’end In RNA the sugar component is ribose (one OH more)

31. RNA The RNA molecule is most often single-stranded. Intramolecular basepairs are forming frequently (e.g. tRNA), resulting in formation of secondary structure elements. Further organization of secondary structures lead to the appearance of tertiary structure.

32. A considerable fraction of RNA occurs in great complexes together with proteins (e.g. ribosomes) • RNA can have catalytic activity (ribozymes). • RNA is the genetic material in several viruses (polio, influenza, rota, HIV, etc).

33. DNA: its native state is a righthanded double helix of two antiparallel chains The bases of the two chains ( one running 5’ 3’, the other one 3’5’) are held in precise register by H-bonds. Base-pair complementarity A is paired with T G is paired with C thymine cytosine H-bonds guanine adenine sugar-phosphate backbone

34. Space-filling model of the DNA double helix

35. Nobel Prize 1962 James Dewey Watson Harvard University Cambridge, MA, USA Francis Harry Compton Crick Institute of Molecular Biology Cambridge, United Kingdom „for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material”

36. General principles of nucleic acid polymerization • Both DNA and RNA chains are produced in cells by copying a preexisting DNA strand (template) according to the rules of Watson-Crick DNA pairing /A-T, G-C, A-U/. • Nucleic acid growth is in one direction: from the 5’ (phosphate) end to the 3’ (hydroxyl) end. • Special enzymes (polymerases) are necessary to produce DNA or RNA. • DNA double helix synthesis by base-pair copying requires the unwinding of the original duplex. A single stranded region (growing fork) is formed.

37. I.4.1. Cellular processes involving nucleic acids Gene expression DNA RNA Protein Trans- cription Trans- lation Repli-cation Cell division DNA

38. The central dogma of genetics retroviruses DNA – RNA – Protein DNA stores the information RNA is the messenger (sometimes stores information, sometimes acts as an enzyme) Proteins are structural units and working molecules.

39. The genetic code: organisation and transformation DNA RNA Protein 4 Bases A G C T 4 Bases A G C U 20 amino- acids Organisation in triplets 1 triplet (codon) = 1 code word 64 code words More than one codon for each amino acid. The code is redundant.

40. The genetic code (RNA to amino acids) The genetic code is (almost) universal: the meaning of each codon is the same in most known organism. Unusual codon usage occurs in mitochondria, chloroplasts and several archaebacteria.

41. Reading frames __GCUUGUUAACGAAUUA Leu--Val--Tyr--Glu--Leu __GCUUGUUAACGAAUUA Ala--Cys--Leu--Arg--Ile The genetic code is commaless! Thus: 5’___ GCUUGUUAACGAAUUA__ mRNA

42. I.4.2. Gene and genome Gene: The nucleotide sequence needed to produce a functionally competent „working molecule” (RNA or protein Genome: The totality of the genes of a given organism.

43. Genome Sequence Projects Since 1995 the following complete genom sequences became available: Prokaryotes: More than 30 Bakterial species (several disease-causing ones), some Archaebakteria Eukaryotes: Saccharomyces cerevisae (baker’s yeast) Caenorhabditis elegans (worm) Drosophila melanogaster (fruitfly) Arabidopsis thaliana (plant) Mus musculus (mouse) Homo sapiens

45. The human genome • the sequence of the human genom contains 3,3 billion bases, organised in 24 chromosomes (22, X,Y) • 30 000 to 40 000 genes • 233 genes are evidently of bacterial origin • 98 % of the sequence is „nonfunctional” • the genetic identity of the human beings is 99.9 % • Nature, 15. February 2001/Science, 16. February 2001

46. 1.4.3. Gene expression Gene expression: the entire cellular process whereby the information encoded in a particular gene is decoded to a particular protein. Molecular processes involved in gene expression: transcription und translation. During transcription an RNA (messenger RNA, mRNA) is synthesized, which contains the genetic information of the DNA as a complementary sequence. The procedure is catalyzed by DNA dependent RNA polymerases. During translation the nucleotide sequence of the mRNA is converted to amino acid sequence of a protein. Besides the mRNA, ribosomes and tRNAs numerous enzymes and regulator proteins play important roles in this procedure.

47. Organization of genes in DNA in prokaryotes and eukaryotes lac operon P O Promoter region Z Y A Operator region Prokaryotes: Protein-coding regions, organized in operons, are closely spaced along the DNA sequence. Example: the lac operon of E. coli (Jacob and Monod, 1960s) Transcription control region

48. Eukaryotes: a considerable amount of DNA is untranslated Transcribed regions of most of the genes is composed of several exons (translated from mRNA) and introns (eliminated from mRNA before translation). Example: human beta globin gene: 50 90 130 222 850 126 132 Untranslated regions Exons Introns

49. Main features of gene expression in prokaryotes and eukaryotes P O Z Y A start site for RNA synthesis transcription 5’ 3’ Z Y A Polycistronic mRNA start sites for protein synthesis translation Proteins Z Y A Prokaryotes Example: lac operon RNA polymerase

50. Eukaryotes: • Trancription occurs in the nucleus, translation in the cytoplasm. • Primary RNAs undergo processing within the nucleus:  addition of 5’cap  polyadenilation  splicing (removal of introns) • mRNAs are monocistronic. • Besides the nucleus, DNA occurs also in mitochondria and chloroplasts.