1. A Biology Primer Part II: DNA, RNA, replication, and reproduction Vasileios Hatzivassiloglou University of Texas at Dallas

2. Last time we covered Biological classification Organisms, tissues, cells and organelles Main cell functions and the role that proteins play Primary structure of proteins as a sequence of amino acids

3. Protein manifestation Amino-acid sequence provides primary structure (one dimensional) Specifies protein’s native state in the physical world Actual form of protein folding affected by other things as well – a major bioinformatics problem

4. Protein secondary structure Alpha-helix is the main secondary structure (local folding) Scale: 0.5 nm wide, 1.5 nm long per amino acid Connection every four amino acids

5. Tertiary structure and beyond

6. Example protein structure

7. Significance for biology Three-dimensional folding affects what the protein can do Predicting three-dimensional structure from amino acid sequence enables understanding of protein function Statistical and rule-based (including grammar-based models)

8. Deoxyribonucleic acid (DNA) Another macromolecule (polymer) found in the nucleus of cells Contains all genetic information Consists of connected nucleotides Each nucleotide is connected via infrastructure consisting of a phosphate and a sugar molecule (deoxyribose) The structural blocks are the nucleotides or bases

9. DNA Bases Only four bases –Adenine (A) –Cytocine (C) –Guanine (G) –Thymine (T) One-dimensional structure Chemical properties impose ordering (like proteins) from 5’ end to 3’ end

10. DNA base pairing Hydrogen bonds between A-T and C-G (order matters)

11. DNA in three dimensions Famous double helix Can be “unzipped” Anti-parallel configuration between the two strands (5’-to-3’ with 3’-to-5’)

12. The Double Helix

13. DNA size Measured in bases (kb or Mb) In bacteria, one circular helix In more complex organisms, organized into chromosomes (each one helix) E. coli: one helix, 4.6 Mb Yeast: 15 Mb Humans: 23 double chromosomes, smallest has 50 Mb, total 3 Gb

14. DNA information content Different types of regions: –Regions that code for a protein (genes) –Regions that regulate when the gene is expressed as a protein, typically nearby –Regions that we don’t know what their function is (“junk” DNA)

15. Number of genes Varies by complexity of organism E. Coli: about 4,000 Yeast: about 6,000 C. Elegans (1mm worm): about 13,000 Humans: about 32,000 (thought to be 100,000) Genes packed and uniformly distributed in prokaryotes, not so in eukaryotes Only 3-10% of human DNA is “useful”

16. The genome Total gene content for an organism Genes will vary from individual to individual, but will be substantially identical (99.9% in humans)

17. Ribonucleic acid (RNA) Very similar chemically to DNA Differences: –the base uracil (U) replaces thymine (T). Similar chemically, both bond with adenine (A). –the sugar ribose replaces deoxyribose –generally single-stranded –partially self-hybridizes (thus forming three dimensional structure)

18. RNA function Can pack the same information as DNA Serves as an intermediate stage during gene expression Carries information around the cell Is part of certain cell structures (ribosomes)

19. Major biological processes Replication (from DNA to DNA) –occurs during cell division both internally and when the organism is reproducing Gene expression (from DNA to protein via RNA) –may occur once or often

20. Reproduction Three main mechanisms –In single-cell organisms, one cell division (binary fission) is enough –Asexual reproduction can do the same on a larger scale (many cells), e.g., plants that grow from cuttings –Sexual reproduction is used by the majority of complex organisms

21. Cell division Simpler in prokaryotic organisms (single- cell) A parent cell produces two identical or nearly identical daughter cells (exponential growth) Mutations can occur here (especially in bacteria)

22. Phases of a cell’s life Growth (G1) Replication (S) Growth (G2) Division (M) Repeat until eventual apoptosis (cell death)

23. Replication The DNA double helix is “unzipped” into two single complementary strands by an enzymatic protein (DNA polymerase) Each DNA strand attracts the corresponding base from a “soup” of free nucleotides The two strands join together (with the same hydrogen bonds between A-T and C-G)

24. DNA replication

25. Complications in replication Replication can only occur in the 5’-to-3’ direction (can only add to the 3’ end) One strand is replicated normally The other strand is replicated in short pieces Another protein (DNA ligase) puts the fragments together Errors can occur!

26. Binary fission

27. Cytokinesis Actual division of the cell Cytosol and organelles are distributed about equally Slightly different process in animals (via cleavage) and plants (via cell plate)

28. Cleavage in animal cells Cleavage furrow formed by actin and myosin

29. Diploid vs. haploid Diploid cells contain paired chromosomes from father and mother (homologues) Haploid cells have only one chromosome of each kind Organisms can be diploid (humans), haploid (fungi), or alternate between the two stages (marine algae)

30. How organisms reproduce In asexual reproduction, a single cell division is enough In sexual reproduction, two haploid cells join together to form the new organism –Haploid organisms can just join –Diploid organisms must produce special haploid cells (germ cells)

31. Division in diploid eukaryotes DNA replication (S, synthesis phase) Cell division (M, mitosis) for somatic cells Special double division (M, meiosis) division for germ cells or gametes

32. Mitosis Breakdown of nuclear membrane Chromosomes duplicate creating sister chromatids attached at the centromere Chromosomes separate and each is guided towards one area of the cell Cytokinesis occurs

33. Mitosis