NOTES - Week 2 - nucleus, mitochondria, chromosomes, structure of chromatin.

Question 1

Conclusion you can draw from these pictures.

Answer 1

Shows the big size of the nucleus in a cell and from the right we can see that vast majority of nucleic acids are in the nucleus. DAPI able to bind with nucleic acids region that is rich with Adenine and Thynine- thats why we see nucleic acids!

Question 2

Explain the nucleus

It is what?

It can be said that it is what? And why?

What molecules does it contain?

What do you know about the amount of nucleus in a cell? Examples?

Answer 2

Most prominent membrane-bounded organelle.

“Controlling center of the cell” dvs contain nessecary info for survival and normal function of the cell.

Contains linear DNA molecules

Few cells that don’t have nucleus → highly specialised cells = RBC with only goal is to transport oxygen.
Also some have multiple nucleus.

Nucleus: generally important in cells because of function but not necessary for survival → means that stem cells need to have….

Question 3

Explain the picture

Hints: what can you see, understand the arrows,

Answer 3

Electromicroscopy of nucleus

Clearly see membrane-bounded organelle.

On zoom in we can see pore complexes on aoom membranebounded organelle.

Question 4

Name all the red parts

Explain the red box name that is bounded with the yellow net. What it is.

Tell me about the nuclear envelpope, what it is and what it contains. Also its functions.

Answer 4

Outer membrane: continuation of rough ER
Perinuclear space: between inner and outer membrane. Cont. of rough ER lumen

Lamina - specifik protein

Nuclear envelope function: physically separates nucleus from cytoplasma in Eukaryotes cells.
Functionally: separates 2 processes..
1. Copy of info (mRNA synthesis) from
2. Protein synthesis (occurs in cytoplasma/membrane of Rough ER)

obs separated by time and space

Question 5

Outer nuclear membrane
Inner nuclear membrane
Perinuclear space

Size difference

Answer 5

OM and IM. Same by structure and thickness. Small differences. 7-8 nm thick

PS: 10-30 nm wide

Question 6

Not a question - just look at the image and point out the things you know

Question 7

What is NPC?

What does it consist of?

Answer 7

Large complicated protein complex which forms a channel - transport pathway.

Consists of proteins called nucleoporins (NUPS aka noobs) = involed in selecting molecules that are passing trough.

NPC responsible for protected exchange of components between nucleus and cytoplasma.

NPC density depends on function.

Question 8

Schematic repr. of NPC

Answer 8

8 groups of Nups = spokes

Question 9

What does the central transporter do?
It’s surrounded by..?

What assists the active transport macromolecules have.
- tell me more about what they do

What binds importing molecules and what binds exporting molecules.

Answer 9

Question 10

Explain LINC

Answer 10

Question 11

Nuclear lamina

Answer 11

Question 12

2 types of lamina

Answer 12

Isoforms meaning
same gene but by changing parts - acquire different isoforms

Question 13

What does nuclear lamina form

hint: appearance

Answer 13

Question 14

What is lamina involved in?

Answer 14

Question 15

What are laminopathies?

Answer 15

Question 16

What is phenotypes

Answer 16

Different changes to the protein coding genes will lead to different disorder phenotypes. All linked with disfunction of lamina and LINC both protein complexes.

Question 17

What is the nucleoplasm

Answer 17

Question 18

What are non-histone proteins

Answer 18

Question 19

What are histones?

Contains:
Contribute to?
What form

Answer 19

Aminoacids makes it postive

H1 DNA linkers-

Hjäölper att ske transkription även om dem är så tajta

Question 20

Fill in red boxes

Answer 20

Question 21

Majority of DNA is packed where?

What are nucleosomes

Histone octamere wrap around?

Linker DNA?

Chromatosome?

Answer 21

Chromatin är histoner packat runt DNA
nucelosome- packed twice

Question 22

Name all parts of the picture

What is this structure called

Answer 22

Chromatin fiber

Question 23

Explain this picture

Answer 23

The chromatin fibers forms a kind of loops. The loops are held together by red lines (scaffold proteins)

Scaffold proteins give structure to chromatin. By these loops = spiral structure

Question 24

From DNA to metaphase chromosome?
8 steps (general understanding of order)

Answer 24

1. DNA simplest level of chromatin
2. Nucleosome
   DNA bound with histones ( + - charge)
3. Nucleosome 8 histones, 1,65x wraps around
4. Chromatosome: nucleosome + H1 histone
5. 30nm fiber
6. loops avg 300 nm
7. Compressed
8. supertight coiling

Question 25

What is Chromatin?

Answer 25

Question 26

What is TAD and chromosomal territories? State of euchromatin and heterochromatin in interphase!!!!

Answer 26

**Topologically Association Domains (TADs):** ▪ chromatine in further organized into TADs, ▪ regions within which DNA interactions are **more frequent** than with regions outside the TAD ▪ these domains **facilitate regulatory elements**, like enhancers, to interact more easily with their target gene ▪ each **chromosome is divided** into TADs ▪ TADs with **repressed transcriptional** activity tend to be associated with nuclear lamina, while **active TADs** tend to reside more in in the nuclear interior Repressed = heterochromatin Active tads = euchromatin INTERPHASE CHROMATIN!!!!!!!!!!!!!

Question 27

Eurochromatin Heterochromatin Difference?

Answer 27

Question 28

More details about heterochromatin

Answer 28

Heterochromatin consist of **constitutive** heterochromatin and **facultative** heterochromatin: **Constitutive heterochromatin** - contains highly repetitive sequences of genetically inactive DNA (satellite DNA). Serves as a structural element of the chromosome. In humans, chromosomes abundant with heterochromatic regions are chromosomes 1, 9, 16, 19, and Y chromosome. It is **stable** during all stages of development in all tissues. --------------------------- **Facultative heterochromatin** - the chromatin which become heterochromatic in certain cells and tissues e.g., it makes up the inactive X chromosome in female somatic cells **(Barr body).** Facultative heterochromatin is **reversible** - may at time lose its condensed state and become transcriptional active.

Question 29

Use the words methylated, hypo-acetylated, and genetic recombination in context of this lecture

Answer 29

Question 30

Functions of heterochromatin

Answer 30

- Centromere function - Organisation of nuclear domains - Gene repression (epigenetic replication)

Question 31

Metephase chromosome

Answer 31

1/2 Metaphase chromosome The tight coiling of the 250 nm fibre produces the chromatid of a chromosome. ■During the S phase (interphase) of the cell cycle replication of DNA take place and two identical chromatids are produced. ■Chromosomes (metaphase chromosomes mitotic chromosomes) can be observed during the cell division. 2/2

Question 32

Fill in the gaps and explain what they are.

Answer 32

Question 33

What are sister chromatides What is Centromere

Answer 33

Question 34

What is Kinotochore And what it is needed for, What is Satelittes What is Secondary constriction?

Answer 34

Question 35

Name all the different parts of the chromosome! Think of association

Answer 35

Question 36

What is NOR The ends of linear DNA *(((it contains what repeated nucleotide sequence))))*

Answer 36

Question 37

Explain this

Answer 37

Represents structure of the telomeres. 6 nucleotide repetition will go (full varv) T-loop

Question 38

Functions of telomeres

Answer 38

Question 39

What is ICFS? Short about symptoms? Explain Molecular mechanism ICFS

Answer 39

Immunodeficiency – centromeric instability – Facial anomalies syndrome (ICF) Symtoms in name!

Question 40

What does she say in this slide?

Answer 40

Karyotype pictures: strange shape of chromosome - with stretched centromeric parts of it = result of un/low methylated centromerc regions of chromosome During cell division - this strange shape with centromeres in between

Question 41

Set of chromosomes

Answer 41

Number, size and shapes of the metaphase chromosomes constitute the karyotype, which is distinctive for each species

Question 42

(not important) A common misconception about humans and amount of chromosomes we have compared to our intelligence

Answer 42

Numbers characteristics for each species karyotype, not the size of the genome = not intelligence

Question 43

Describe the human karyotype Somatic and germ cells have.. What determines sex linked characteristics

Answer 43

Question 44

What are the short regions of homology between the X and Y chromosome What type of chromosomes are we talking about?

Answer 44

Sex chromosomes, but not all regions are sex-linked regions. They are called PS... because they behave in a .... (Look at the pic)

Question 45

Compare male and female chromosomes

Answer 45

Question 46

What to extract for info from this picture

Answer 46

Schematic repr. of how barr body looks like Microscopic slide (stain with specific dye) → barr body is dot One chromosome heterochromatic → darker in microscope

Question 47

OBS not normal karyotype

Answer 47

47. 2. 48. Usually only 1 chromosome will be randomly staying active and all the rest will be inactivated 45, 0 turner syndrom. Deletion of x chromosomes. no barrbodies visible. 46, 0 male, only 1 x chromosome = no barr bodies visible.

Question 48

Be able to undestand this image!

Question 49

What conclusion can be drawn for this picture

Answer 49

Short list of chromosome groups by size. A largest. G smallest Description based on position of centromere

Question 50

**The nucleolus** What exists here? structure?

Answer 50

Question 51

Prokaryotic chromosome What is nucleoid

Answer 51

Nucleoid is a place in prokaryotic cells where most of the genetic information is stored

Question 52

Size difference between stretched DNA of prokary. and cell What helps maintain the nucleoid structure

Answer 52

Question 53

What can be seen of these 2 pictures

Answer 53

Left: Schematic rep. chromosome is already supercoiled and (+ binding proteins) will bend DNA to fit into the cell Right: electromicroscopy, see the areas that rep. DNA chromosome supercoiled binded together with enzymes (who takes part in formation of nucleoid and enzymes which are involved in gene expression of the DNA)

Question 54

Mitochondria 7.30 lecture 2 part 3 Cristae and matrix location?

Answer 54

Mitochondria and chloroplasts likely evolved from engulfed prokaryotes that once lived as independent organisms. At some point, a eukaryotic cell engulfed an aerobic prokaryote, which then formed an endosymbiotic relationship with the host eukaryote, gradually developing into a mitochondrion. Self replecating means that it can replicate independently from cell cycle mitochrondria has lot of similiarities with prokaryotes.

Question 55

What is mitochondria composed of?

Answer 55

Question 56

What is mtDNA

Answer 56

Question 57

Features and functions of mitochondria

Answer 57

Question 58

Summary lecture 2 obs more in answer

Answer 58