1. מבנה הקשר הפוספודיאסטרי 1) קשר '3 – '5 פוספו די-אסטרי 2) כיווניות
3) קצה ‘5
קצה ‘3
4) במעלה או
במורד הזרם
(upstream or
downstream)

2. זיווגי בסיסים - basepairing
בסיס משלים

3. מבנה הסליל הכפול dsDNA *הסליל מפותל סביב ציר מרכזי *הבסיסים פונים
למרכז הציר

4. dsDNA
קשרים תוך מולקולרים לחיזוק המבנה בסלילי

6. Helix axis
DNA road

8. מגרעת

9. Groove
חריץ/מסילה

13. A:T and G:C
כיווניות
קשר פוספו
A = 10-10

14. A = 10-10 Mili (m) = 10-3 Micro (m) = 10-6 Nano (n) = 10-9
Pico (p) = 10-12
Fenta (f) = 10-15
A = 10-10

15. שאלת תירגול: מדוע בחרת ללמוד רפואה
1. אני מעוניין לעזור לאנושות
2. הנושא מעניין
3. קידום אישי
4. המשפחה לחצה
יש לך 30 שניות לענות תשובה!

16. דנטורציה ורנטורציה
And Denaturation

19. דנטורציה ורנטורציה של DNA

20. דנטורציה

23. ספקטרופוטומטר

25. DNA Denatures at High Temperatures

26. חד-גדילי
דו-גדילי

28. 1. לאדם 2. לחיידק 3. אין מספיק מידע 4. לשניהם Tm זהה
שאלה: אורך הגנום ההומני הוא 3 טרליון זווגי בסיסים, לעומתו אורך הגנום של חיידק ה-e. coli הוא 1.5 מיליון זיווגי בסיסים. הגנום ההומני מורכב מ-47% זיווגי בסיסים של GC ולעומתו הגנום של החיידק בעל 52% של GC. למי טמפרטורת Tm יותר גבוה?
1. לאדם
2. לחיידק
3. אין מספיק מידע
4. לשניהם Tm זהה

29. רנטורציה

30. Less complex DNA renatures faster
For an equal mass/vol:

32. Over 40% of the human genome corresponds to interspersed repeats
Census of human repeats
Over 40% of the human genome corresponds to interspersed repeats
IHGSC. Nature (2001)

34. Types of DNA in each kinetic component
Human genomic DNA

35. מיקרוסטליט
1.4 M

36. Humans (H. sapiens) and bonobos (P
Humans (H. sapiens) and bonobos (P. paniscus) share a cryptic microsatellite element in the 5' regulatory region of AVPR1A, which is absent in the chimpanzee (P. troglodytes).

38. פטריות
אצות
30-40,000 genes

40. Fundamental properties of genes
Genes are heritable units, arranged linearly along chromosomes.
Complementation analysis of a large number of mutants defines genes that determine a function.
E.g., biosynthetic pathway or DNA replication.
Genetic techniques in microorganisms were used to determine the fine structure of a gene.
Genes encode polypeptides
Codons are triplets of nucleotides that encode an amino acid.

42. מבנה הכרומוזום בשלב חלוקת התא
Gene 3
גן – אזור ב-ד.נ.א מימנו מתורגמת מולקולת ר.נ.א בעלת פעילות ביולוגית

43. אינטרונים נמצאים רק באוקריוטים
אינטרונים – רצפים שמוסרים בגרעין ולא נשארים במולקולת הרנא הבוגר
אקסונים – רצפים שנשארים במולקולת הרנא הבשלה
אינטרונים נמצאים רק באוקריוטים

44. אקסון – רצף שנשאר ברנא לאחר העיבוד ועובר לציטופלזמה
אינטרון – רצף המוסר מהרנא בגרעין
פרומוטר
אקסון
אינטרון

46. מהם הכרומוזומים? 1. אתרי עיגון של הדנא בגרעין 2. מבנה הגרעין
3. מיכלי אריזה של הדנא
4. מיכלי אריזה של החלבונים

47. Human genome 2.91 billion base pairs 21,000 protein coding genes
(~32,000 non-coding genes)
1.5% exons (127 nucleotides)
24% introns (~3,000 nucleotides)
75% intergenic (no genes)
Average size of a gene is 27,894 bases
Contains an average of 8.8 exons
Titin contains 234 exons.

48. List of 68 eukaryotes, 141 bacteria, and 17 archaea at
Sample genomes
Species
Size
Genes
Genes/Mb
H.sapiens
3,200Mb
35,000 11
D.melanogaster
137Mb
13.338 97
C.elegans
85.5Mb
18,266
214
A.thaliana
115Mb
25,800
224
S.cerevisiae
15Mb
6,144
410
E.coli
4.6Mb
4,300
934
 List of 68 eukaryotes, 141 bacteria, and 17 archaea at

49. What does the Genome tell us?
Estimated number of genes ~32,000
Only 1 to 1.5% of the genome encodes proteins
75% of the genome is not transcribed
46% is repetitive DNA
JUNK DNA –the fodder/history of evolution
Recombination
Diversity
“genomic” disease

51. We humans are 99.9% identical at the DNA sequence level
There are still ~3 million nucleotide differences among us called SNPs (60,000 within the exons)---that presumably account for differences in disease susceptibility, drug responses, etc.
Polymorphic variation between and within populations
Implications for concepts of “race,” “individuality”

52. 21,000

55. Duchenne Muscular Dystrophy
ניוון שרירים
MOLECULAR BIOLOGY OF THE DISEASE
Duchenne Muscular Dystrophy is one of more than twenty different types of muscular dystrophy. The Duchenne type affects only boys and is known to result from a defect in a single important protein in muscle fibers called Dystrophin. The muscle fiber will break down if the Dystrophin is missing and is unable to function properly. As a result, the reduction in the number of good muscle fibers and the whole muscle becomes weak.

56. כמה מחלות גנטיות יכולות להיות?
1. לא יותר מ-100
2. כ-1000 מחלות
3. כ מחלות
4. כמספר הגנים.

60. Summary DNA, Chromosome Centromere, telomere, replication origin
Nucleosome, Chromatin,
Histone: H1, H2A, H2B, H3, H4
Histone octamer, DNA packaging
DNA binding proteins, Histone modifications

61. The Global Structure of Chromosomes
Some rare cases of interphase chromosomes, certain features maybe universal
Representative forms forming typical interphase chromosome
Chromosome at mitosis

62. Lampbrush chromosomes (amphibian oocyte, immature eggs)

63. A model for the structure of a lampbrush chromosome
Chromomeres: highly condensed and in general not expressed until unfolding

64. A polytene chromosome from Drosophila salivary gland
Dark bands and interbands

65. Electron Microscope image of Drosophila polytene chromosome

66. Folding and refolding at a time course of 22 hours
Chromosome puffs
Folding and refolding at a time course of 22 hours

67. RNA synthesis in Chromosome puffs
Red: newly synthesized BrUTP; Blue: old ones diffused

68. RNA synthesis in Chromosome puffs

69. RNA synthesis in Chromosome puffs

70. Model of RNA synthesis in Chromosome puffs

71. A model for the structure of an interphase chromosome

72. Position Effects on Gene Expression Heterochromatin: condensed
Euchromatin: loose

73. Speculative Model for the heterochromatin at the ends of yeast chromosomes
Sir: Silent information regulator binding to unacetylated histone tails

74. Speculative Model for the heterochromatin at the ends of yeast chromosomes
DNA-binding proteins recognize DNA sequence close to telomere, recruit Sir proteins and cause histone tail modification, forming heterochromatin

75. Two speculative models for how the tight packaging of DNA in heterochromatin can be inherited during chromosome replication

77. The specialized nucleosome formed on centromeres
Also belongs to heterochromatin

78. The structure of a human centromere Alpha satellite DNA sequence
Kinetochore inner plate
Kinetochore outer plate
Spindle microtubules

79. The plasticity of human centromere formation

81. A typical mitotic chromosome at metaphase

82. SEM of a region near one end of a typical mitotic chromosome

83. EM of a mitotic chromosome

84. דנטורציה ורנטורציה של DNA

85. פטריות
אצות
30-40,000 genes

87. Condensin plays important roles
Chromatin Packing
Condensin plays important roles

88. The SMC (Structural Maintenance of Chromosomes) proteins in condensins

89. Selective localization of two interphase chromosomes
Chromosome 18 (red) and 19 (turquoise)

90. Specific regions of interphase chromosomes in close proximity to the nuclear envelope
Two different regions of chromosome 2 (yellow and magenta) close to the nuclear envelop (green)

91. Summary
Chromosomes are decondensed during interphase and hard to visualize
Lampbrush chromosomes of vertebrate oocytes and polytene chromosomes in the giant secretory cells of insects are exceptions, revealing the global organization of chromosome
Gene expression needs the decondensation of chromosome loops
Euchromatin and heterochromatin
Telomere and centromere are general heterochromatin
Chromosomes are spatially organized and deposited in nucleus
Mitotic chromosomes are condensed and organized.

93. DNA Molecules are highly condensed in chromosomes
Nucleosomes of interphase under electron microscope
Nucleosome: basic level of chromosome/chromatin organization
Chromatin: protein-DNA complex
Histone: DNA binding protein
A: diameter 30 nm; B: further unfolding, beads on a string conformation

95. חרוזים ע"ג חוט

96. Histone היסטונים

97. HDAC
HDAC activity
HAT

98. מבנה הנוקלאוזום

99. Structure of the nucleosome
How can you control attachment to histones?

100. Nucleosome Structures
Histone octamer
2 H2A
2 H2B
2 H3
2 H4

101. The bending of DNA in a nucleosome
1. Flexibility of DNAs: A-T riched minor groove inside and G-C riched groove outside
2. DNA bound protein can also help

102. X-ray diffraction analyses of crystals
Structure of a nucleosome core particle

103. Structural Organization of the Core Histones

104. The Assembly of the Core Histones

105. Notice the long tails of the octamer
מה המשמעות של זנבות ההיסטונים?

106. Nucleosomes
What is the problem in organizing DNA?

107. Higher order structure of nucleosomes
A solenoid is a coil of insulated or enameled wire wound on a rod-shaped form made of solid iron, solid steel, or powdered iron

108. Irregularities in the 30-nm fiber
Flexible linker, DNA binding proteins
Structural modulators: H1 histone, ATP-driven Chromatin remodeling machine, covalent modification of histone tails

109. H2A
H2B H3 H4

110. The function of Histone H1

111. The function of Histone tails

112. Chromatin Remodeling

113. Histones binding to DNA

114. Cyclic Diagram for nucleosome formation and disruption

115. אריזה של דנא עם חלבונים נקראת כרומטין
Covalent Modification of core histone tails
Acetylation of lysines (K)
Mythylation of lysines
Phosphorylation of serines (S)
Histone acetyl transferase (HAT)
Histone deacetylase (HDAC)
HDAC activity
אפיגנטיקה
Acetylation
Mythylation

116. שאלה: איזה מבין ההיסטונים עובר הכי הרבה מודיפיקציות?
H2a
H2b H3 H4

118. נוקלאוזום במבט על
Protein Gel

120. Histone 3D

121. Zigzag model of the 30-nm chromatin fiber

122. מנוקלאוזום לסלנואיד
solenoid

123. פיגום

124. מבנה הכרומוזום

125. מבנה הכרומוזום בשלב המטפזי

126. אופן אריזת הDNA
בתא: מהנוקלאוזום
לכרומוזום.

130. Histon assembly movie
DNA to chromatin

131. אופן אריזת הDNA
בתא: מהנוקלאוזום
לכרומוזום.

132. אריזה של דנא עם חלבונים נקראת כרומטין
Covalent Modification of core histone tails
Acetylation of lysines (K)
Mythylation of lysines
Phosphorylation of serines (S)
Histone acetyl transferase (HAT)
Histone deacetylase (HDAC)
HDAC activity
אפיגנטיקה
Acetylation
Mythylation

133. Spreading of heterochromatin in flies (and humans!)
כרומטין: אופן האריזה של הדנא עם חלבונים
Spreading of heterochromatin in flies (and humans!)
K9 of H3
(H3K9me)
epigenetics is the study of changes in gene expression or cellular phenotype, caused by mechanisms other than changes in the underlying DNA sequence.

134. Spreading of silenced chromatin on a homeotic gene
E(z) (SET)
K27 of H3
H3K27me
Polycomb
Polycomb
Polycomb
Polycomb-complexed chromatin

135. Heterochromatin vs. euchromatin
adapted from Jenuwein & Allis (2001) Science 293, 1074

136. DNA Methylation & the Epigenetic Code
Paula Vertino, Henry Stewart Talks

137. DNA Methylation & Histone Modifications Form the Epigenetic Code
Paula Vertino, Henry Stewart Talks

138. Methylation of Cytosine in DNA
פרופ' חיים סידר
CpG methylation
Paula Vertino, Henry Stewart Talks

139. 5-Methyl Cytosine in DNA
Paula Vertino, Henry Stewart Talks

140. Cytosine Methylation Maintains Inactive-Condensed Chromatin State
Transcription factors
RNA polymerase
Transcription
Acetylation
DNA methyltransferase
5-methyl-C
Methyl-CpG
Binding proteins
and associated
co-repressors
Histone deacetylase
Transcription blocked
Deacetylation X
Chromatin compaction
Transcriptional silencing
Alex Meissner, Henry Stewart Talks

141. 5-Methyl Cytosine is Found in Heterochromatic Regions
John Greally, Henry Stewart Talks

142. Structure & Epigenetics of Euchromatin versus HeterochromatinMe
Paula Vertino, Henry Stewart Talks

143. Critical CpG Sequences in CpG Islands Near Promoters
פרופ' חיים סידר
Alex Meissner, Henry Stewart Talks

144. Organization of the Epigenome
Paula Vertino, Henry Stewart Talks

145. Epigenetic Imprinting
Marisa Bartolomei, Henry Stewart Talks

146. Epigenetic Imprinting of H19 & Igf2 Loci
Marisa Bartolomei, Henry Stewart Talks

147. Insulator Model for the Imprinting of H19 & Igf2 Loci
Marisa Bartolomei, Henry Stewart Talks

148. Methylation Changes During Development
Marisa Bartolomei, Henry Stewart Talks

149. Demethylation of the Paternal Genome
Adrien Bird, Henry Stewart Talks

150. Methylation Changes During Development
Paula Vertino, Henry Stewart Talks

151. Methylation Changes During Development
Paula Vertino, Henry Stewart Talks

152. Methylation Changes During Development
Paula Vertino, Henry Stewart Talks

153. מבנה של כרומוזום במיקרוסקופ אלקטרוני
מבנה של כרומוזום במיקרוסקופ אלקטרוני

154. 4 46 Human 32 Yeast 42 Macaque 40 Mouse 38 Cat 48 Potato 26 Frog 20
Total number of chromosomes/somatic (body) cell 4
Penicillin mold 46
Human 32
Yeast 42
Macaque 40
Mouse 38
Cat 48
Potato 26
Frog 20
Algae 16
Planaria
Corn 8
Fruit fly
Species
There is no connection between the number of chromosomes and the genome size, gene content, or any other feature of genomes. It is and essentially independent characteristic.
Dog 78

155. Myrmecia pilosula Smallest number of chromosomes known in a eukaryote:
1 pair (2 total per somatic cell)
Myrmecia pilosula

156. Ophioglossum reticulatum, a fern
Largest number of chromosomes known in a eukaryote:
630 pairs (1260 total per somatic cell)
Ophioglossum reticulatum, a fern

157. שרך

158. Chromatine compartment

159. Cockayne syndrome group B (CSB) cells that fail to express CSB protein which causes profound neurological and developmental defects
צביעת DAPI של הDNA- עם סמן לגן (נקודה לבנה)

160. Chromosome fragility

161. Chromosomal fragile sites are loci that are especially prone to forming gaps or breaks on metaphase chromosomes when cells are cultured under conditions that inhibit DNA replication or repair. The relationship of "rare" folate sensitive fragile sites with (CCG)n expansion and, in some cases, genetic disease is well established.

162. Fragile X syndrome
What is Fragile X syndrome?  Fragile X syndrome is the most common inherited cause of mental impairment, affecting approximately 1 in 2,000 males and 1 in 4,000 females worldwide.
Cytogenetic analysis of metaphase spreads demonstrates the presence of the fragile site in less than 60% of cells in most affected individuals.).
In 1991, the fragile X gene (FMR1) was characterized and found to contain a tandem repeated trinucleotide sequence (CGG) near its 5' end. The mutation responsible for fragile X syndrome involves expansion of this repeat segment. The number of CGG repeats in the FMR1 genes of the normal population varies from six to approximately 50. There are two main categories of mutation, premutations of approximately 50 to 200 repeats and full mutations of more than approximately 200 repeats. There is no clear boundary between the upper limit of normal and the lower limit of the premutation range. For this reason, alleles with approximately copies of the repeat are said to be in the "grey zone." Some alleles in this size range are unstable and expand from generation to generation, while others are stably inherited. A premutation is susceptible to expansion after passage through a female meiosis. The larger the size of a woman's premutation, the more the risk of expansion to a full mutation in her offspring. .

164. חלוקת התא

165. Mitosis animation