Y1 Biology 131 Syllabus - Academic Year

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1 Y1 Biology 131 Syllabus - Academic Year Monday 28/11/2016 DNA Packaging Week 11 Tuesday 29/11/2016 Regulation of gene expression Wednesday 22/9/2014 Cell cycle Sunday 4/12/2016 Tutorial Monday 5/12/2016 Regulation of cell cycle Week 12 Tuesday 6/12/2016 Protein trafficking Wednesday 7/12/2016 Introduction to intracellular signaling المولد النبوي - Birthday Sunday 11/12/2016 Prophet s Week 13 Monday 12/12/2016 Cell death /apoptosis Tuesday 13/12/2016 Review session

2 DNA packaging Dr. Sarray sameh, Ph.D

3 Why DNA packaging is required and how DNA is packaged into chromosomes? - If stretched end to end, a DNA is about 3 meters long and it has to be packed in a nucleus which is only a few micrometers in diameter: the DNA must be tightly compacted to fit. This occurs through an elaborate, multilevel system of DNA packing. There are various orders of packaging: First order of packaging: nucleosomes Second order of packaging: solenoid fiber Looped domain Chromosome

4 DNA compaction -The compaction of linear DNA in eukaryotic chromosomes involves interactions between DNA and proteins: Histones proteines -The combination of DNA and histones proteins : Chromatin During interphase of the cell cycle, chromatin fibers are usually highly extended within the nucleus. During mitosis, the chromatin condenses to form chromosomes. 2 types: heterochromatin & euchromatin

Basic protein;their positively charged amino

negatively charged DNA (phosphate group).

types of histones: Histones proteins NUCLEOSOME *

two of each make up the octamer The DNA is

5 Basic protein;their positively charged amino acids ( lysine and arginine) bind tightly to negatively charged DNA (phosphate group). Responsible for the first level of DNA packing 5 types of histones: Histones proteins NUCLEOSOME * H2A, H2B, H3 and H4: are the core histones; and two of each make up the octamer The DNA is wrapped around histones * H1 is the linker histone: binds to DNA Nucleosome

6 In electron micrographs, nucleosomes has the appearance of beads on a string. Each bead is a nucleosome, Nucleosomes as beads on a string. Regularly spaced nucleosomes consist of core histone proteins bound to DNA.

7 - The beaded string seems to remain essentially intact throughout the cell cycle. - Histones leave the DNA only transiently during DNA replication. - They stay with the DNA during transcription: By changing shape and position, nucleosomes allow RNA-synthesizing polymerases to move along the DNA.

8 Levels of DNA packing - 1 st level: nucleosome - 2 nd level: solenoid fiber - 3 rd level: looped domain - 4 th level: chromosome

9 1 st level: Nucleosome Solenoid fiber Looped domain chromatid chromosome

First level of packing: nucleosome -Nucleosome: fundamental repeating subunits: DNA wrapped twice around an octamer of core histones (2 of each)+h1 -The

10 First level of packing: nucleosome -Nucleosome: fundamental repeating subunits: DNA wrapped twice around an octamer of core histones (2 of each)+h1 -The DNA that is between each histone octamer is called the linker DNA -Nucleosome diameter: 11nm This structure shortens the DNA length about seven fold!!!!

11 2nd level: Solenoid Fiber

fiber is organized in a stacked spiral of nucleosome -The

12 Second level of packing: Solenoid fiber - 6 nucleosome aggregate together forms solenoid - H1 stabilizes the structure -Solenoid fiber is organized in a stacked spiral of nucleosome -The solenoid fiber shortens the total length of DNA about, seven fold more

3 rd level of packing: formation of loop domains

organize the chromosomes within the nucleus.

13 3 rd level of packing: formation of loop domains making up a 300-nm fiber - Involves interaction between 30nm fiber and the nuclear matrix -The loops are attached to the nuclear matrix to organize the chromosomes within the nucleus. loops Matrix protein /scaffold associated chromatin loop domains

Fourth level of packing: Chromosome (super solenoid structure) - Final level of packaging - Occurs during mitosis: The looped domains themselves coil and fold forming the characteristic metaphase

14 Fourth level of packing: Chromosome (super solenoid structure) - Final level of packaging - Occurs during mitosis: The looped domains themselves coil and fold forming the characteristic metaphase chromosome -2 multiprotein complexes help to form and organize metaphase chromosomes: * condensin (role in condensation) and * cohesin (role in sister chromatid alignement) 700 nm 1,400 nm (d) Metaphase chromosome

regulatory proteins and RNA polymerase to bind with DNA sequence and initiate transcription Heterochromatin Tightly compacted

16 Heterochromatin vs Euchromatin The compaction level of interphase chromosomes is not completely uniform: Euchromatin: it is lightly packed form of DNA 92% of human genome is euchromatic Transcriptionnaly active: its unfolded structure allows the gene regulatory proteins and RNA polymerase to bind with DNA sequence and initiate transcription Heterochromatin Tightly compacted regions of chromosomes e.g; Centromere and telomere both are heterochromatin Transcriptionally inactive less accessible to transcription factors

18 Modifications in Histones Histones can be changed to alter DNA packing (increase & decrease). There are 3 main types of modifications: /decrease These modifications can lead to regulation of Gene expression: Acetylation and phosphorylation make the histone more negative which weakens the packing ability of histones due to the repelling of negative-negative charges:easy access for gene transcription. Methylation of histones can either increase or decrease transcription of genes, depending on which amino acids in the histones are methylated, and how many methyl groups are attached: Methylation events that weaken chemical attractions increase transcription; However, if histones becomes more hydrophobic so it will enable the histone to more tightly pack (turn off the gene transcription)

19 Exemples of methylation: Methylation of histone H4 on Arginine amino acid at the 4th position, opens the chromatin structure leading to transcriptional activation Methylation of H3 on lysines residues at the 4 th and 79 th position, opens the chromatin structure leading to transcriptional activation * Methylation of histone H3 on lysines residues at the 9 th and 27 th position condenses the chromatin structure leading to transcriptional inactivation

20 THE END!

as enzyme Functions: Structural: role in the shape of chromosome Regulatory: by promoting gene expression

21 Non- Histones proteins They are all the proteins associated with the DNA apart from the histones. They are Acidic in nature (negative charge) and likely to bind the positively charged histones Mostly act as enzyme Functions: Structural: role in the shape of chromosome Regulatory: by promoting gene expression Enzymatic: many enzymatic activities associated with chromatin (nucleases, polymerases..are all nonhistone proteine)

Chromosome structure - Each chromosome contains many origins of replication that are interspersed about

-Each chromosome contain a centromere that forms a recognition site for the kinetochore protein.

22 Chromosome structure - Each chromosome contains many origins of replication that are interspersed about base pairs. -Each chromosome contain a centromere that forms a recognition site for the kinetochore protein. It is the region where sister chromatids are connected and split chromosome into 2 arms: p arm (petit), q arm (long arm). -Telomeres contain specialized sequences (TTAGGG) located at both ends of the chromosome. - Genes are interspersed throughout the chromosome - Repetitive sequences are commonly found near centromeric and telomeric region but they may be interspersed throughout the chromosome.

NUCLEUS. Fig. 2. Various stages in the condensation of chromatin

NUCLEUS. Fig. 2. Various stages in the condensation of chromatin NUCLEUS Animal cells contain DNA in nucleus (contains ~ 98% of cell DNA) and mitochondrion. Both compartments are surrounded by an envelope (double membrane). Nuclear DNA represents some linear molecules