Chapter 2 Genes and Chromosomes

1. Chapter 2 Genes and Chromosomes

2. 2.1 DNA & DNA Structure

3. 1. Nucleoside and Nucleotide (1) Components：pentose, base, phosphate group

4. Base Pentose In DNA or RNA, a pentose is associated with only one phosphate group, but a cellular free nucleotide (such as ATP) may contain more than one phosphate group.  If all phosphate groups are removed, a nucleotide becomes a nucleoside.

5. (2) Bases in DNA or RNA Adenine(A) Cytosine(C) Guanine(G) Thymine(T) Uracil(U). A, C, G and T  exist in DNA; A, C, G and U  exist in RNA. Albrecht Kossel

6. 2. Nucleic Acid Chain condensation reaction, phosphodiester bond, DNA polymerase 连接反应 (ligation reaction)

7. Synthesis of a nucleic acid chain always proceeds from 5’ to 3’.

8. 3. DNA Structure (1) DNA Primary Structure The primary structure of DNA is the sequence itself - the order of nucleotides in the deoxyribonucleic acid polymer. Question 3 Why is DNA sequence important?

9. (2) DNA Secondary Structure Right-handed or left-handed Helix Diameter           Base Inclination      Bp / helical turn   Helix pitch   Major groove Minor groove

10. 10 bp/turn B-form

11. Pitch Handedness Base Inclination A B Z

12. Animation

13. (3) DNA Supercoil

14. 4. DNA denaturation and renaturation Denaturation: dsDNA → ssDNA Renaturation: ssDNA → dsDNA

15. 2.2 Gene & Genome

16. 1. Concepts of Gene (1) Gene= In molecular terms, it is the entire DNA sequence includingexons, introns, and noncoding transcription-control regionsnecessary for production of a functional protein or RNA. exons introns noncoding transcription-control regions

17. (2) Regulatory Gene A DNA sequence or a gene that functions to control the expression of other genes. (3) Structural Gene A DNA sequence or a gene that codes the production of RNA, a specific protein or peptide. (4) Gene Cluster It is a group of adjacent genes that are identical or related.

18. (5) Gene Family A group of related genes having similar DNA sequence evolved from a single ancestral. These genes make similar products and may or may not be located in the same region of a chromosome. Question: What is different between gene cluster or gene family?

19. 2. Genome (1) Genome Complete collection of a cell or an organism’s genetic information as linked genes in a long strand of DNA. (2) Genomics The branch of genetics that studies organisms in terms of their genomes (their full DNA sequences).

20. (3) Functional genomics The branch of genomics that determines the biological function of the genes and their resulting proteins, and the role played by the proteins in the organisms’ biochemical processes. (4) Structural genomics The branch of genomics that determines the three-dimensional structures of proteins.

21. 3. Size of genome(1) Prokaryotic cell vs Eukaryotic cell(2) Size ↔ Evolution ?

22. 4. Model Organisms • Bacteria (E. coli, several others) • Yeast (Saccharomyces cerevisiae) • Plant (Arabidopsis thaliana) • Caenorhabditis elegans • Fruit fly • Zebrafish • Mouse • Human ………

23. Question Why do we choose these organisms as models? Animation

24. 2.3 Features of Genomes

25. 1. Features of Prokaryotic Genomes (1) Relatively small -- size, content (2) Simple structure (3) Transcription unit concept….. (4) Overlapping gene concept….. Now, it is also found in eukaryotic genomes…..

26. 2. Genomes of Prokaryotes Most of them: double-helix , circular Small number: single strand, DNA  Scaffold:loops, supercoiled

27. (1) E.coli Genome • 4.6 million bp • 90% of genome encodes protein • 4288 genes. • almost no repeated DNA

29. (2) Phage genome λ phage genome Regulatory genes Replication genes– 2 genes Lysis genes– 3 genes Recombination genes– 10 genes Head– 10 genes Tail– 12 genes

30. 3. Features of Eukaryotic Genomes (1) Big size, big content (2) Repeat sequence (3) Single cistron (4) Gene uncontinuous (intron and exon) (5) Pseudogene (6) mtDNA & ctDNA

31. 4. Genome of Eukaryotes (1) Human Genome nuclear genome + mitochondrial genome

33. Information derived from the HGP ► less than 2% of the human genome codes for proteins ► almost all (99.9%) nucleotide bases are exactly the same in all people ► ("junk DNA") make up at least 50% • ► 24% important for translation • ► Repetitive elements • Satellites (regular, mini-, micro-) • Transposons • Retrotransposons • Parasites

34. Question Is the junk DNA real junk?

35. HGP Goals Now • To identify the function of the human genome • To understandhow and why genes can cause diseases • To speed up the use of genetic information in biomedical research and put it to work

37. (2) Other Genomes of Eukaryotes

38.  Yeast genome  Mouse genome  Drosophila genome  C. elegans genome  Arabidopsis thaliana genome

39. 2.4 Nucleosome and Chromosomes

40. 1. Histones and Non-histones 2. Nucleosome (1) concept  ~200 bp of DNA  Histone contains 5 kinds : H1, H2A, H2B, H3, H4 (2) packing

41. 3. DNA Coiling into a chromosome (1) Packing ratio (2) Packing levels solenoid chromatin fiber chromatid chromosome

43. 2.5 DNA Replication

44. 1. Semiconservative Replication (1) Models of DNA Replication

45. What is semiconservative replication? Each strand acts as a template for a new double helix. The established model of DNA replication in which each double-stranded molecule is composed of one parental strand and one newly polymerized strand. Two requirements: ● DNA template ● Free 3' -OH group

46. (2) Replication elements Origin, Ori  Replicon  Replication fork Bidirection

48. 2. The Enzymology of DNA Replication substrate, polymerase, DNA template, primer, enzymes, proteins ……

49. (1) Topoisomerase(2) Helicase(4) Primase(5) DNA Polymerase III(6) DNA polymerase I(7) DNA ligase

50. 3. Features of DNA Replication in Prokaryores (1) Replication Ori in E.coli (2) Initiation of DNA replication in E.coli