Chapter 8 DNA and RNA

1. Chapter 8DNA and RNA Biology 100

2. Structure of DNA • Deoxyribonucleic Acid (DNA) serves as the memory/blueprint for proteins in the cell. • The building block of DNA (and RNA) is the nucleotide: • What composes the nucleotide? • Phosphate Group • 5C deoxyribose sugar (ribose sugar for RNA) • Nitrogenous base • Two important functions of DNA • Pass genetic info • Control synthesis of a protein

3. Structure of DNA • There are 4 different bases in DNA • Adenine (A) and guanine (G) have double rings. These are known as Purines. • Thymine (T) and cytosine (C) have single rings. These are Pyrimidines. • On a single strand, the phosphate group of one nucleotide forms a covalent bond with the sugar of the next.

4. Structure of DNA • The base pairs of DNA are: • Thymine pairs with Adenine • Guanine pairs with Cytosine • Give the complementary strand: A T C G G T C A C T G G T A G C C A G T G A C C

5. Structure of DNA • Rosalind Franklin suggested that the structure of DNA was a helix. • In1953, James Watson and Francis Crick took some of Rosalind’s x-ray diffraction images of DNA and correctly determined that it was a double helix. • Using Tinker toys, they made their model of DNA. • The final structure of DNA: • Sugar-phosphate bond on the outside, and the nitrogen bases on the inside, connected by hydrogen bonds.

6. Structure of DNA • DNA has bases pair up in groups of two. Guanine will pair with Cytosine, and Adenine will pair with Thymine. • This is known as base complementarity. • DNA resembles a ladder with the sides of the ladder formed by the sugar-phosphate backbones. The rungs are the complementary bases held together by hydrogen bonds. • The ladder is twisted like a spiral helix, known as the double helix.

7. DNA Replication • Cells constantly grow and divide, so DNA needs to be copied for each new cell. • First, DNA helicase unwinds the DNA double helix for about 1,000 nucleotides and forms a replication bubble.

8. DNA Replication • Then, DNA polymerase assembles a complementary new strand on each old one, using free DNA nucleotides, building two strands in opposite directions.

9. DNA Replication • DNA ligase attaches one new strand to the previously replicated segment, and helicase unwinds another section.

10. DNA Replication • After replication, there are two molecules of identical DNA. • Each DNA will have one strand from the original DNA molecules (the parent strand), and one from the replicated DNA (daughter strand). • This makes the strand semiconservative. • DNA Replication

11. DNA Replication • Once every 10,000 bases, DNA polymerase adds the wrong nucleotide. • Before proceeding to the next nucleotide, it proofreads the copy against the parental strand and corrects the error most of the time. • The actual error rate is about 1 or 2 errors per billion nucleotides. • If each human diploid cell contains 6.2 billion nucleotides, are any two cells actually identical?

12. Why is the DNA code important? • The order of the nitrogenous bases in DNA is the genetic information that codes for proteins. • Proteins help provide the cell with structure. Enzymes are also made of proteins, which help carry out chemical reactions. • A gene is a section of the DNA double helix with information for synthesizing a specific protein.

13. RNA • Ribonucleic Acid (RNA)is the other type of nucleic acid used in protein production. • RNA is single-stranded, and has ribose as it’s 5C sugar. • In RNA, the base pairs are: • Uracil with Adenine • Guanine with Cytosine • Find the complementary strand: A C U G G U A C U G A C C A U G

14. Cell Differentiation • All cells will use the information in their DNA to produce the same “house-keeping” proteins. • But differentiated cells will express (“turn on”) genes that have the information for proteins which support their specific activities. • In the end, only a small fraction of genes are expressed in any particular cell type.

15. Cell Differentiation • Different differentiated cells also like to vary in the level of expression, how much of a protein is synthesized. • Individual cells vary their level of expression of a gene over time as demand for their protein product increases and decreases.

16. Adult Stem Cells • In most cases, once a cell have become differentiated, it is locked into that path and cannot be transformed into another cell type. • In contrast, stem cells are unspecialized cells that renew themselves in this undifferentiated form. • Under appropriate conditions, some cells differentiate to fulfill specific needs that an organism has. • Stem cells in bone marrow (adult stem cells) specialize into any role that blood cells undertake in the body. • These stem cells are multipotent - capable of many roles, but not all.

17. Adult Stem Cells • Recent research has indicated that some adult stem cells may be even more flexible than previously thought, perhaps close to pluripotent. • They may not only be able to differentiate into the specialized cells characteristic of their tissues, but they may also be able to specialize into other cell types.

18. Fetal Stem Cells • Embryonic (fetal) stem cells are pluripotent. • Cultured cells can be induced to specialize into all types of adult cells. • They are typically obtained from an early developmental stage, the blastocyst. • Embryonic stem cells are also available in umbilical cord blood.

19. Stem Cells • After extracting undifferentiated cells from a blastocyst, cells are cultured on feeder plates. • If the embryonic stem cells are allowed to clump together, they can spontaneously differentiate. • By including specific molecules into the cultures or otherwise changing conditions, the clumps can be directed to differentiate into specific cell types.

20. Bone Marrow • Individuals may suffer deficiencies in red or white blood cells caused by cancer, anemia, inherited genetic diseases, or immune-system disorders. • Typically, healthy bone marrow, containing blood-forming stem cells, is extracted from a donor. • The bone marrow is introduced into the recipient’s blood. • The new stem cells repopulate the bone marrow and restore the population of blood cells.

21. Potential Application of Stem Cells • Type-1 Diabetes • In type 1 (juvenile) diabetes, the immune system attacks insulin-producing cells in the pancreas, leading to diabetes = elevated glucose levels. • New stem cells may be able to replace to the lost cells. • Heart Disease • If cardiac muscle cells are deprived of oxygen because of blocked arteries, they die and are replaced by scar tissue. • Stem cells may allow regeneration of cardiac tissue if they can differentiate into muscles cells and integrate into the heart.

22. Potential Application of Stem Cells • In individuals with Parkinson’s disease, neurons which produce the neurotransmitter dopamine die, leading to uncoordinated movements. • Preliminary studies indicate that neural stem cells can be injected into the brains of Parkinson’s patients, reducing disease symptoms

23. Potential Application of Stem Cells • A patient’s DNA is extracted and injected into an enucleated egg. • A similar technique was used to produce the first cloned mammal, the sheep Dolly, in 1996. • The embryonic stem cells would then induced to develop into a specific tissue needed by the patient.

24. Protein Synthesis • Also known as the central dogma of gene expression. • Protein synthesis occurs in two steps, transcription and translation. • In transcription, a gene, a region of information contained in the order of nucleotides in DNA, is copied as RNA. • In translation, information on mRNA is used to direct the order with which amino acids are linked together to form polypeptides at the ribosomes.

25. How information is stored in DNA • The genetic code is a language in which all “words” are three letters long (triplets) and combinations of the nitrogen bases. • The letters: A,T,C,G in DNA or A,U,C,G in RNA, are the alphabet. • As triplets, 43 combinations = 64 “words” • There are 20 amino acids commonly used in proteins. Each “word” is a code for an amino acid. • 64 words are more than enough to specify 20 amino acids • Each word, a unique combination of three nucleotides, is called a codon.

26. Genetic Code • Each codon indicates only one amino acid. • There is more than one codon for most amino acids. Except for tryptophan or methionine, each amino acids has 2-6 possible codons. • The 3rd position, the wobble position is less critical in dictating specific amino acids.

27. Genetic Code • AUG is the start codon (Methionine), which tells the mRNA to begin translation. If AUG is not found, translation will not begin. • There are three stop codons (UAA, UAG, UGA) the protein will be released.

28. Genetic Code • During translation, codons are read without pause or skipping from the start codon to the stop codon. • The start codon establishes the reading frame, the blocks of 3 nucleotides that will translated. • Any nucleotide is part of only one triplet, they do not overlap.

29. Codons • Which codon is it? • UUU • Phenylalanine • UGA • Stop • AUG • Methionine (Start) • GAA • Glutamic Acid

30. Types of RNA • Messenger RNA (mRNA) has the specific information necessary to place amino acids in the correct order to build the right polypeptide. • Simply put, it is the template to guide the synthesis of a chain of amino acids that form a protein.

31. Types of RNA • Transfer RNA (tRNA) molecules carry specific amino acids from the cytoplasm to the ribosome. • Each tRNA has an amino acid binding siteto which a specific amino acid is attached. • Each tRNA has an anti-codon region, an area complementary to the codon on mRNA.

32. Types of RNA • Ribosomal RNA (rRNA) combines with proteins to form ribosomes. • The rRNA and protein molecules combine to form large ribosomal subunits and small ribosomal subunits in the nucleolus.

33. Transcription • Transcription occurs in three parts: • Initiation, the key enzyme, RNA polymerase, finds the correct region of DNA to begin the process. • Elongation, the DNA double helix unwinds a bit and RNA polymerase makes a RNA copy of the DNA template. • Termination, the RNA polymerase reaches the end of the gene and releases the RNA molecule.

34. Synthesis of RNA • A gene consists of several sections. • The promotor sequence is the site where transcription factor proteins and RNA polymerase bind initially. • The core of the gene consists of the protein code, the information required for synthesizing a protein. • The termination sequence indicates the end of the gene, the end for transcription.

35. Transcription - Initiation • In eukaryotes, proteins called transcription factorsbind to the promotor region. • They assist the binding of RNA polymerase to the correct spot.

36. Translation - Elongation • Once RNA polymerase binds, the DNA double helix begins to unwind. • One strand has the information for the gene, the coding strand. • RNA polymerase copies the coding strand as an RNA strand.

37. Transcription - Termination • Elongation continues until RNA polymerase reaches a specific DNA sequence called a terminator. • At this point the new RNA strand is either released or cut free.

38. Translation of Proteins • Translation also has three stages: • In initiation, mRNA, tRNA, and the small and large ribosomal subunits are brought together. • In elongation, the information on the mRNA is used to order tRNA carrying the correct amino acids. • At termination, the components, including the new polypeptide, separate.

39. Translation - Initiation • Initiation starts when mRNA binds to the small ribosomal subunit. • The initiator tRNA, carrying the amino acid methionine, binds because of its complementary anticodon to the start codon. • Next, the large ribosomal subunit connects to this complex.

40. Translation - Elongation • The next tRNA with the correct amino acid slip into place. • The ribosome catalyzes a peptide bond between amino acids. • The old tRNA is released. • The whole complex: mRNA and tRNA with growing polypeptide, slides down the ribosome by 3 nucleotides (translocation).

41. Translation - Elongation • The next tRNA with an anticodon matching the next codon slips into place. • This cycle of tRNA positioning, peptide bond formation, old tRNA release, moving of the mRNA + tRNA + polypeptide continues.

42. Translation - Termination • When the process reaches the stop codon, a release factor protein enters the ribosome. • The release factor breaks the bond between the last tRNA and the polypeptide. • The polypeptide floats away • The mRNA is released. • Protein Synthesis

43. Control of Protein Synthesis • As part of differentiation, cells turn some genes off and others on. • Plus, they can control how quickly/often a gene is transcribed and how often a mRNA from that gene is translated. • If a section of chromosome is tightly coiled (like during mitosis), transcription factors and RNA polymerase cannot access the promotor sequence. • Any genes in these regions are turned off.

44. Control of Protein Synthesis • If acetyl groups (-COCH3) are attached to histone proteins at a section of DNA, transcription occurs more easily. • If methyl groups (-CH3) are attached to the DNA itself, the methylated genes are turned off. • Enzymes actively control which sections of a chromosome have methylation and acetylation

45. Control of Protein Synthesis • Without activated transcription factors, a gene will be transcribed, but at a low level. • If activated transcription factors are present, RNA polymerase can bind more easily to the promotor. • Transcription occurs faster. • Often activated transcription factors will enhance transcription of several genes whose proteins will work together in the cell.

46. Control of Protein Synthesis • Some genes are transcribed more often because of the presence of enhancer DNA regions. • Activators that bind to the enhancer region make it easier to transcription factors and RNA polymerase to bind to the promotor. • Other DNA regions, called silencers, decrease the rate of transcription.

47. Control of Protein Synthesis • Once a mRNA has finished transcription of one polypeptide, it is available to produce another. • Eventually, the mRNA will be degraded, but the rate of degradation is under active control. • The mRNA that is translated into a protein which assists iron absorption is degraded much faster when the cell has abundant supplies of iron.

48. Protein Synthesis • In bacteria, one gene is transcribed into one mRNA which is translated into one protein. • In eukaryotes, one gene can produce several different proteins. • Eukaryotic gene include exons which have information for proteins and introns which do not. • The introns are removed during post-transcriptional processing. • The exons are joined together.

49. Protein Synthesis • In alternative splicing, some sections of the original mRNA are removed in some versions, but other sections are removed in other versions. • The result is that the same gene can produce two different proteins. • Alternative splicing is behind the observation that the 20,000 genes in the human genome lead to 80,000 to 100,000 different proteins.

50. In fruit flies, the gene for sex determination contains two possible stop signs. • In some individuals, the first stop codon is removed. • The protein that is translated from this splicing leads to the development of a female fruit fly. • If the first stop codon is not spliced, no functional protein is transcribed. • The fruit fly develops as a male