A Biology Primer Part II: DNA, RNA, replication, and reproduction

1. A Biology PrimerPart 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