Nuclear Structure

Question 1

chromatin

Answer 1

• organization of cell’s genetic material into long DNA protein fibers
• consists of ~3x10^9 base pairs of DNA plus histone and non-histone proteins

Question 2

chromosomes

Answer 2

• highly folded, coiled chromatin that appears as discrete, dense structures during mitosis

Question 3

How is chromatin organized within the cell during interphase?

Answer 3

• chromatin disperses into tangle of fibers confined to a central position in cell and surrounded by double membrane (nucleus)

Question 4

nuclear matrix

Answer 4

• consists of network of non-histone proteins

- provides structural scaffold for chromatin and helps regulate its genetic activity

Question 5

nuclear lamina

Answer 5

• periphery of nuclear matrix

- fibrous layer constructed of lamins

Question 6

lamins

Answer 6

• intermediate filament type proteins that construct nuclear lamina

Question 7

nuclear envelope

Answer 7

• consists of two phospholipid membranes penetrated by nuclear pore complexes
• outer part is continuous with rough ER
• inner membrane supported by intermediate filaments attached to inner surface (nuclear lamina)

Question 8

nuclear pore complexes (NPC)

Answer 8

• large macromolecular complexes that have 8-fold symmetry
• undergo complete breakdown and reformation at each cell division
• penetrate nuclear envelope
• selectively transport proteins and RNA molecules in both directions between the nucleus and cytoplasm (all pores are the same, but can select for dif things)

Question 9

nucleolus

Answer 9

• dense nuclear region containing chromatin whose DNA specifies the major ribosomal RNA’s
• primary site of ribosomal production and assembly

Question 10

looped domains

Answer 10

• organization of interphase chromatin
• attach to specific points on nuclear matrix
• can contain several genes and be temple active or inactive depending on cell type
• take very distant parts of DNA and bring them together
• regulation all within given chromosome

Question 11

template inactive

Answer 11

• majority of chromatin

Question 12

temple active

Answer 12

• minority of chromatin

Question 13

heterochromatin

Answer 13

• small amount of inactive chromatin in a given nucleus that appears highly condensed morphologically

Question 14

euchromatin

Answer 14

• large amount of chromatin that appears in dispersed form

- both active and inactive chromatin

Question 15

nucleosome

Answer 15

• subunit of chromatin
• consists of two copies each of histone proteins H2A, H2B, H3, and H4, wrapped in 146 base pairs of DNA
• one copy of H1 associated with (20-50 base pair DNA linker connecting adjacent subunits)

Question 16

What is the hierarchy of chromatin organization?

Answer 16

• no clear organization
• 11 nm and 30 nm present due to sample preparation
• TEM shows that many intermediate forms found (of differing diameters), so organization is much more random than previously thought

Question 17

gene

Answer 17

• transcriptional unit of DNA

- contains 10 nucleosomes or more worth of DNA, including exons and introns

Question 18

exons

Answer 18

• expressed sequences encoding protein domains

- not expressed equally in every cell

Question 19

introns

Answer 19

• intervening sequences

Question 20

conformation of nucleosomes associated with active genes

Answer 20

• different than conformation of nucleosomes associated with inactive genes
• due to secondary modifications of the histones and differences in associated non-histones

Question 21

semi-conservative replication of DNA

Answer 21

• replicated DNA contains one new strand and one template strand
• use of same DNA polymerase for oppositely oriented templates implies discontinuous synthesis of one of the new strands

Question 22

phosphorylation of nuclear lamins

Answer 22

• happens prior to mitosis

- leads to disassembly of the nuclear lamina and nuclear envelope

Question 23

dephosphorylation of nuclear lamins

Answer 23

• happens after cytokinesis

- nucleus reassembles in each daughter cell

Question 24

alternative splicing

Answer 24

• leads to many-fold different proteins than would be expected
• occurs by various routes
• important for function of nuclear pore

Question 25

default pathway of alternative splicing

Answer 25

• alternative splicing by mutually exclusive exon use

- uses ubiquitously present splicing factors such as ASF/SF2

Question 26

non-default pathway of alternative splicing

Answer 26

• alternative splicing by mutually exclusive exon use

- uses a regulated splicing factor such as hnRNPA1

Question 27

use of mutually exclusive exon alternative splicing for fibroblast growth factor receptor 2 (FGFR2)

Answer 27

• default pathway: found in epithelial cells

- non-default pathway: found in mesenchymal cells

Question 28

housekeeping genes

Answer 28

• expressed in every cell

Question 29

constitutive heterochromatin

Answer 29

• contain same regions of genetically inactive, highly repetitive sequences of DNA
• generally found in the same regions of chromosomes when compared to other cells (near centromeres and telomeres)

Question 30

facultative heterochromatin

Answer 30

• also condensed and not involved in transcription process

- not repetitive and has inconsistent nuclear and chromosomal localization when compared with other cells

Question 31

How do the different domains of the nucleus remain separate from one another?

Answer 31

• like an oil-water interaction between dif parts of chromatin
• some domains are more hydrophobic or hydrophilic
• repel each other

Question 32

protein scaffolds

Answer 32

• DNA organizes around them

Question 33

Completely unwound, how long is the DNA that exists in any one cell?

Answer 33

• 6 feet long (an IMMENSE amount of DNA)

Question 34

How does preparation influence chromatin structure?

Answer 34

• can cause chromatin to organize in certain forms that don’t exist in living nucleus
• chromosomes actually form and can be demonstrated in live cells

Question 35

Hutchinson-GIlford Progeria Syndrome is an example of disruption in what nuclear structure?

Answer 35

• disruption of nuclear lamina caused by mutations in lamin proteins or wash proteins
• causes wrinkled nuclear lamina that lacks integrity

Question 36

lamin mutation of progeria

Answer 36

• 50 amino acid deletion (important sequence deleted)
• modification and processing of gene but no upstream cleavage
• mutated prelamin called progerin

Question 37

wash mutation of progeria

Answer 37

• wash proteins interact with lamins to maintain structurally integrity of nucleus
• wash mutants do not interact with lamins, leading to mess up nuclear lamina

Question 38

What is the relationship between perturbed nuclear shape and aging?

Answer 38

• if nucleus is misshapen, processes that normally get corrected for are not corrected
• blocks occur at expression, repair, and replication
• errors propagate
• leads to earlier signs of aging (cancer)

Question 39

What is the structure of nuclear pore complexes?

Answer 39

• 8 fold symmetry
• membrane continuous around edges
• nuclear cage formed in nucleus
• in cytoplasm, pore interacting with intermediate filament proteins
• conformationally flexible to allow material in/out

Question 40

T-antigen with normal nuclear import signal

Answer 40

• T-antigen made fluorescent

- allowed into nucleus

Question 41

T-antigen with mutated nuclear import signal

Answer 41

• only cytoplasm has T-antigen

Question 42

factors attached to proteins that allow for trafficking through nuclear pore

Answer 42

• nucleo-localization sequence (involved in transport of tRNA out of nucleus)
• shuttle proteins (snRNA’s accompany spliced RNA into cytoplasm)
• ribosomal proteins