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Cell Structure Review and Introduction to DNA

Cell Structure Review and Introduction to DNA. Did you know?. 100 years ago we did not know why some children had brown eyes and some blue 75 years ago we did know the structure of dextrose 50 years ago we did not know the correct number of chromosomes

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Cell Structure Review and Introduction to DNA

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  1. Cell Structure Review and Introduction to DNA

  2. Did you know? • 100 years ago we did not know why some children had brown eyes and some blue • 75 years ago we did know the structure of dextrose • 50 years ago we did not know the correct number of chromosomes • 25 years ago we did not know any of the genes linked to cancer • What is one you know of? • BRCA breast cancer gene

  3. Eukaryotes Nucleus Membrane-bound organelles Microtubules are the building blocks for a flagella Cell membranes can contain cholesterol Cell size is usually bigger Introns in the DNA Prokaryotes No nucleus No membrane-bound organelles Flagella is the building block No cholesterol in cell membranes Cell size is usually smaller Usually no introns Differences Between Eukaryote and Prokaryote Cell

  4. Eukaryotes

  5. Sources of DNA • How are Eukaryotes and Prokaryotes different? • Eukaryotes • DNA is in the nucleus • Prokaryotes have no nucleus, so where is the DNA? • Floating in the cytoplasm, which is usually attached to the cell membrane. • Bacteria contain 1 long circular DNA molecule, super coiled. • E. coli contains 1 chromosome w/4000 genes and 4.6 million base pairs (bp) • R Plasmids: bacteria with small ring of DNA floating in cytoplasm and these contain the antibiotic resistance genes • Genes are turned “on” or “off” easily

  6. Eukaryotic DNA • DNA packaged into chromosomes • Each single DNA may contain several million nucleotides and many thousands of genes • Humans have 46 chromosomes per cell with about 3 billion base pairs making up about 40,000 genes

  7. Historical Figures in Molecular Biology (visit DNAi.org) • Miescher • Griffith • Avery, McCarty and MacLeod • Chargaff • Wilkins, Franklin, Watson & Crick

  8. Key people in genetics and DNA • Gregor Mendel: heredity passed down from parents; relationship between phenotype and genotype • Schleiden and Schwann’s “cell theory” explained fertilization of sperm and egg to make zygote • 1905 discovered sex chromosomes existed; years later realized there are more chromosomes that are responsible for traits • Watson and Crick: 3D structure of DNA in 1953 • DNA actually discovered in 1869, by 1900 understood that it was composed of 5C sugar, phosphate, and 5 types of nitrogen rich bases (ATCGU), 1920s we understood that RNA and DNA were different

  9. N N C O C C N C N N C N C C C N N C Key Historical People • Erwin Chargaff • determined percents of purines and pyrimidines present • Rosalind Franklin • X-ray diffraction technique was key to understanding the helix structure

  10. Role of X-Ray Crystallography • X-rays diffracted by the regularly arranged atoms of a simple crystal (Max von Laue) • Pauling, Franklin, Wilkins, Watson and Crick were all working diligently to discover the structure of DNA

  11. What Nucleotides are involved? • What are the 4 nucleotides of DNA? • Adenine, thymine, guanine, cytosine • What pairs with what? • Adenine and Thymine • Cytosine and Guanine

  12. Complementary Base Pairing DNA consists of two polynucleotide chains wound around each other to form a double helix. The two chains are held together by complementary base pairing; that is, specific bonding between A and T bases and between G and C bases on the two strands Two antiparallel DNA polynucleotide chains held together by complementary base pairing. To make a stable double helix, the two strands of DNA are antiparallel; that is, the 5’ - 3' direction of one strand runs opposite to the other strand. The two DNA chains are held together by complementary base pairing between A and T bases and between G and C bases. The helix has a right hand twist.

  13. In a DNA polynucleotide chain, nucleotides are joined by phosphodiester bonds formed between the 5' carbon of one sugar and the 3' carbon of the next sugar. A freephosphate defines the 5' end of the chain and a free hydroxyl group defines the 3' end of the chain.

  14. Basics to DNA Structure • Rails of ladder: run in opposite directions (anti-parallel) • Contains alternating units of deoxyribose sugar and phosphate • Each rung composed of a base pair held together by weak hydrogen bonds • 10 base pairs per turn • 34 A total so 3.4 A between pairs

  15. DNA Replication • DNA helicase • Single-strand binding proteins • Primase • DNA polymerase • DNA ligase • Okazaki fragments

  16. So why is DNA replication so important to us? • DNA is the carrier of genetic information for all living organisms • Through the process of replication, the entire genome is copied and passed down to each new cell made in the body. • Replication is also the way genetic information is passed from parents to offspring.

  17. Replication • DNA polymerase can only directly synthesize new DNA in the 5' to 3' direction • Chargaff’s Rule for determining how many nucleotides are present: • In double-stranded DNA, G = C, and A = T. • If C = 21, then G = 21 and G + C is 42. Therefore A + T = 100 - 42 = 58, and T = 58/2 = 29 percent. • A/T, G/C, and (A+G)/(C+T) are all equal to 1 • Semiconservative Replication: making 2 daughter stands from a single parent strand • Therefore DNA replication takes place prior to cell division

  18. DNA Helicase and SSB • DNA Helicase is an enzyme which begins the unzipping process. Also prevents DNA from rebinding. • Problem is that it creates a knotted up mess of DNA • Topoisomerase cuts one strand of unwound and allows it to unwind and then reseals it. It prevents damage to the DNA by allowing it to swivel. • Once DNA is unzipped the base pairs of each single stand will begin forming helix structure • SSB (single strand binding proteins) are formed to block this action; prevent recombining

  19. Getting Replication Started

  20. Replication Bubble The DNA begins to split from many points along the strands and separate from that point, creatinga bubble-like area.

  21. Replication Fork When referring to the replication of DNA in a singular direction, the original DNA splits in two, forming two prongs, which resemble a fork.

  22. Primase and DNA Polymerase • Primase is an RNA polymerase which does not need a primer to initiate synthesis • RNase H comes into remove the RNA primer made by primase before DNA is replicated • DNA polymerase III can only add nucleotides onto the 3’ end of an existing DNA fragment so if this is the case then where does the first piece of DNA come from?

  23. Okazaki fragments and DNA Ligase • DNA synthesis is always 5’ to 3’ • Leading strand is synthesized and the lagging strand has small fragments formed which are later joined together. • Fragments are called Okazaki fragments after the scientist who discovered this process. • Polymerase I removes RNA primer and replaces it with DNA nucleotides in Okazaki fragments • DNA ligase is the enzyme which joins the Okazaki fragments together

  24. DNA Replication

  25. Checking your knowledge • What are the two strands of DNA called after they unzip? • Leading and lagging • What enzyme is used for unzipping? • DNA helicase • What direction does DNA replicate? • Actually both, 5’ to 3’ easy, continuous and self correcting; 3’to 5’ takes longer, more chance of error and requires DNA polymerase and DNA ligase

  26. Checking your knowledge • What are the fragments formed during replication called and what strand are they formed on? • Okazawki fragments; lagging 3’ to 5’ strand • What 3 enzymes are required for DNA replication? • DNA helicase, DNA polymerase, topoisomerase

  27. RNA: how is it different from DNA? • Pentose sugar is ribose instead of deoxyribose • Uracil replaces Thymine • RNA is single stranded

  28. What is transcription? Where does it occur? • Transcription: the process of deciphering a DNA nucleotide code and converting into into an RNA nucleotide code; RNA carries genetic message to a ribosome for translation into a protein. • Proteins do the work of cells and give cells and organisms their unique characteristics.

  29. Transcription occurs in 5’ to 3’ direction Note: single strand of RNA

  30. Transcription Initiation Transcription factors bind to the TATA box which guide the RNA Polymerase to the starting point of the gene.

  31. Transcription Elongation RNA Polymerase continues to assemble RNA nucleotides in a complementary fashion to the 3’5’ template strand

  32. Transcription Termination Once the RNA Polymerase hits the termination sequence, it releases from the template and the RNAS transcript floats away.

  33. RNA Processing Slicesome cuts out the intron sequences and joins the exons to make the final mRNA Poly A tails are added to the 3’ end Methylated G cap added to the 5’ end

  34. More essential terms • Intron: region on a gene that is transcribed into a mRNA molecule but not expressed in a protein; spacer DNA • Exon: region of a gene that directly codes for a protein, it is the region of the gene that is expressed

  35. Eukaryote

  36. Some essential terms • Operon: section of prokaryotic DNA consisting of one or more genes and their controlling elements. • Promoter: the region at the beginning of a gene where RNA polymerase binds; the promoter promotes the recruitment of RNA polymerase and other factors required for transformation • Operator: region on an operon that can either turn on or off expression of a set of genes depending on the binding of a regulatory molecule • Genetic engineers use promoter and operator regions to turn on / off the production of certain genes

  37. Lac Operon

  38. Codon Chart

  39. Translation

  40. Translation Initiation Initiator tRNA binds to the AUG codon of the mRNA. This tRNA has an anticodon of UAC and carries Met amino acid so all translated products start with the Met amino acid

  41. Translation Elongation A site – tRNA enters with its new amino acid P site – growing amino acid chain is linked to newly arriving amino acid by a peptide bond E site – tRNA leaves without its amino acid

  42. Translation Termination When stop codon appears in A site, there is no tRNA to bind so a release factor binds instead This causes the polypeptide chain to release Finally, it also causes the ribosome subunits to disassociate and translation is terminated

  43. Amino Acids and Proteins

  44. Mutations • Occur when DNA Polymerase makes a mistake or environmental factors cause an alteration in the DNA sequence • Mutations can be harmful, beneficial, or neutral

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