Phys 214. Planets and Life

1. Phys 214. Planets and Life Dr. Cristina Buzea Department of Physics Room 259 E-mail: cristi@physics.queensu.ca (Please use PHYS214 in e-mail subject) Lecture 15. DNA and heredity. Induced pluripotent stem cells. February 11th, 2008

2. Contents • Textbook pages 165-166, 171-178 • DNA and heredity • How is heredity encoded in DNA • DNA replication • Genes and genomes • Induced pluripotent stem cells • Classification of life • Microscopic life • News - changes in the calendar • Quizzes: 25 February, 10 March, 24 March • Assignments - 3 March, 17 March • (Note that I removed an assignment).

3. DNA and heredity All life on Earth encode hereditary info in DNA & RNA (some viruses). DNA (Deoxyribonucleic acid) double helix = 2 phosphate deoxyribose backbones RNA (Ribonucleic acid) a single strand – a single backbone of ribose – bases exposed The basic molecular building blocks of DNA and RNA are the bases - nucleotides. Of the many possible nucleotides, the DNA used in living organisms on Earth uses only four. The four DNA bases: A - adenine, G - guanine, T - thymine, C - cytosine The only possible pairing between bases: A-T, and C-G Instead of thymine, RNA uses the nucleotide base uracil. RNA is very important – carries out genetic instructions – messenger RNA (mRNA), transfer RNA (tRNA) collects amino acids, ribosomal RNA (rRNA) building proteins in ribosomes.

4. How is heredity encoded in the DNA DNA determines the structure and function of the cells. The operating instructions are contained in the arrangement of bases (A,T,C,G). Gene = the instructions that represent an individual function (e.g. how to build a protein). Gene - long strand of DNA that contains: 1) a promoter (controls the activity of a gene), and 2) coding sequence (determines what the gene produces) exon 3) non-coding sequence - intron (can regulate the conditions of gene expression {process in which the information encoded in a gene is converted into a form useful for the cell.}). Genome = the complete set of genetic information that makes up an organism. Chromosome National Institute of Health Cell stained with flourescent dyes undergoing chromosome duplication. The material stained red is the cell membrane, light blue - chromosomes. http://publications.nigms.nih.gov/moleculestomeds/images/newtcells

5. How is heredity encoded in the DNA The genetic code. 3 DNA bases in a row and four to choose from = 43 = 64 larger than the 20 amino acids used to built proteins (20) – redundant ACC and ACA represent the same amino acid The codes for many amino acids depend on the first 2 bases of the three (probably early life used a two-base language. A strand of DNA has a long unbroken sequence of bases: e.g. ACTCATTCAAGC. Set of rules of how to read the sequence – break in words, where to start and stop. Genetic code = set of rules for reading DNA = the same in nearly all living organisms on Earth. Genetic words consist of three DNA bases in a row; For protein building each word is either a particular amino acid or a “start” “stop reading” instruction.

6. How is heredity encoded in the DNA The genetic code the same in nearly all living organisms on Earth! Variations in the genetic code found in mitochondria – organelle in eukaryote cells that contain their own DNA! (symbiotic relationship between microorganisms that lead to lateral gene transfer) Genetic code is like a language – everyone spoke the same language -> common ancestor Mitochondrion (up) scanning electron microscope image (SEM) (down) transmission electron microscope image (TEM)

7. DNA replication DNA is copied via a process called replication. • DNA double helix -> (2) unzip -> (3) each strand serve as template for a new strand, according to the base pairing rule -> (4) Two identical copies of the original DNA (going to the dividing cell) The two strands making up the double helix of DNA are said to be complementary (not identical). DNA replication very fast. Three billion base sequence in human genome – in a few hours.

8. How is heredity encoded in the DNA Diagram of the "typical" eukaryotic protein-coding gene. Promoters and enhancers determine what portions of the DNA will be transcribed into the precursor mRNA (pre-mRNA). The pre-mRNA is then spliced into messenger RNA (mRNA) which is later translated into protein. DNA is enclosed in the cell nucleus and never gets out. The information is sent out by messenger RNA (mRNA). Gene expression = process in which the information encoded in a gene is converted into a form useful for the cell (mRNA or proteins). • Transcription - process of converting a sequence of nucleotides in a section of DNA to a sequence of nucleotides in RNA, as a precursor to protein synthesis . • Translation - process of converting a sequence of nucleotides in messenger RNA into a protein (in ribosomes)

9. Mutations and evolution Many enzymes involved in DNA replication - errors less than one per billion base copied. Mutation = any change in the base sequence of an organism’s DNA (attachment of the wrong base, extra base in a gene, a base deleted, entire sequence duplicated or eliminated). Some mutations are benign: ACC changes into ACA – code for the same amino acid = the instructions for the same protein made by the gene Mutations that add or delete a base within a gene have the most detrimental effect on protein structure (no punctuation or spacing between words). Sickle-celldisease = mutation in the gene that makes hemoglobin Some mutations are beneficial leading to evolution. Lateral gene transfer = transfer of genes from one organism to another. Bacterial resistance to antibiotics Genetic engineering (insulin produced by bacteria that have been inserted with human gene for insulin) Lateral gene transfer leads to faster speciation (appearance of a new species) than individual mutations (later on this subject).

10. How is heredity encoded in the DNA DNA is packaged in chromosomes. Chromosomes contain: - a single continuous piece of DNA (which contains many genes) - DNA-bound proteins (serve to package the DNA and control its functions). Chromosomes vary between different organisms: - eukaryotic cells (with nucleus) - DNA molecule -large linear chromosomes - prokaryotic cells (without nucleus) - smaller circular chromosomes (plasmid). A scheme of a condensed (metaphase) chromosome. (1) Chromatid - one of the two identical parts of the chromosome after S phase. (2) Centromere - the point where the two chromatids touch, and where the microtubules attach. (3) Short arm. (4) Long arm.

11. How is heredity encoded in the DNA

12. How is heredity encoded in the DNA

13. Genes and genome Eukaryotes - no clear relationship between genome sizes and complexity. The latest estimate in the number of genes in the human genome - under 3 billion base pairs and about 20,000–25,000 genes [Pennisi 2007 Science 316 (5828): 1113]. Amoeba -over 670 billion base pairs (200 times > human genome). Rice – has 37,000 genes. Every member of a species has the same basic genome, with some variation between individuals. In general – every cell in a living organism contains the same set of genes as other types of cells of the same organism. (muscle cells, brain differ because they express or use different portions of the full set of genes. One cell contains the set of instructions to build an entire organism or any type of cell. Cloning = process by which a single cell from a living organism is used to grow an entirely new organism with an identical set of genes. Amoeba http://www.dr-ralf-wagner.de/ Storing operating instructions is essential for life to exist! Extraterrestrial life may not use DNA to store information but will very likely use a molecule with a similar function.

14. Induced pluripotent stem cells Every cell in a living organism contains the same set of genes as other types of cells of the same organism! Example: induced pluripotent stem cells how our genetic material expressed in all of our adult somatic cells (any cells forming the body of an organism, as opposed to germline cells) can be utilized to generate any other tissue or treat disease. Stem cells = retain the ability to renew themselves and can differentiate into a wide range of specialized cell types (brain, muscles, etc). Embryonic stem cells (ES) - found in blastocysts (embryo) There is a great deal of controversy in our scientific community in how should research on embryonic stem cell research should be directed. There is not only lack of consensus on how to pursue scientific questions using ES cells, lack of funding from governments, but also, lack of clear laws given the ethical dilemma that ES cells use implies.

15. Induced pluripotent stem cells After Shinya Yamanaka from Kyoto University first demonstrated that he could reprogram adult somatic cells in something that look like an embryonic stem cell, a surge of disbelief and awe was followed by an incredible interest into finding what Shinya called induced Pluripotent Stem cells or iPS. Pluripotent = ability to develop into multiple cell types including nervous system, skin, muscle, and skeleton.

16. Induced pluripotent stem cells Enucleated = A cell with its nucleus removed Induced Pluripotent Stem Cells Embryonic Stem Cells Hallmark of ES cell programming (embryo)

17. Induced pluripotent stem cells Yamanaka’s group was the first to demonstrate that a handful of genes, namely, Oct3/4, Sox2, c-Myc, and Klf4 (Takahashi and Yamanaka, Cell 2007) were required to re-program mouse embryonic fibroblast (MEF) and adult mouse tail-tip fibroblast to what they called induced Pluripotent Stem cells (iPS). iPS generated were indistinguishable from Embryonic Stem cells (ES) in morphology, proliferation, gene expression and the ability to give rise to teratoma formation (tumor consisting of different types of tissue). Teratoma formation is a proof of principle towards demonstrating that any somatic adult cell can become, upon the re-expression of the right genes, pluripotent.

18. Induced pluripotent stem cells

19. Induced pluripotent stem cells Fibroblast iPS

20. Induced pluripotent stem cells

21. Induced pluripotent stem cells Derivation of autologous (self) iPS cells from hS/hS mice and correction of the sickle allele by gene targeting

22. Induced pluripotent stem cells

23. Classification of life • Old classification - two kingdoms - plants & animals • Main difference between plant and animal cells: plant cells have a cell wall that helps protect the cell membrane, while animal cells do not. • This classification does not work for microorganisms. • Modern classification based on cell biochemistry, including genetics.

24. Microscopic life From a microscopic structural point of view, cells on Earth come in two types: 1. Without a nucleus - prokaryotes. 2. With a nucleus - eukaryotes. Cell nucleus - an internal membrane that effectively walls off the genetic material (DNA) from the rest of the cell. All prokaryotes are unicellular (bacteria). Eukaryotes can be: - unicellular (amoeba) - or multicellular (humans, plants, animals). All multicellular organisms are eukaryotes. E. Coli

25. Microscopic life - the dominant form of life on Earth Helicobacter Pylori Much of microscopic life is harmful: E. Coli, Salmonella (food poisoning), Chlamydia pneumonia (heart disease, Alzheimer’s disease), Helicobacter pylori (gastric ulcer ), nanobacteria (kidney stones), streptococcal bacteria (pediatric obsessive-compulsive disorder) C. Buzea et al. Biointerphases 2 (2007) MR17 Not all bacteria are harmful, some are crucial for our survival. - intestinal bacteria provide vitamins - cycling carbon (decomposing) organic matter, soil, and atmosphere - fermentation cheese, genetic engineering, antibiotics • Just because there are small, single-cell organisms are not a minor form of life! Microbes are the dominant form of life on Earth! Total mass of microbes in the oceans is about 5,000 times larger that of all humans! Streptomyces bacteria that produce the antibiotic streptomycin

26. Next lecture • Phylogenetic tree • Metabolism, ATP, carbon and energy sources, water