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BIO 200 > Unit 3 : Nuclear Structure & Function > Flashcards

Unit 3 : Nuclear Structure & Function Flashcards

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Biology 101 flashcards
1
Q

Nuclear Envelope

A

double membrane shrouding contents of nucleus

inner + outer membrane with perinuclear space between

outer membrane continuous with ER

perinuclear space continuous with ER lumen

cytoplasm and nucleoplasm connected through nuclear pores

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2
Q

Nuclear Lamina

A

directly under inner membrane of envelope

meshwork of intermediate filaments

support nuclear envelope - keeps nucleus from being torn apart during normal cell processes

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3
Q

Chromatin

A

Interphase DNA

attached to nuclear envelope via lamina

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4
Q

During mitosis

A

nuclear lamina breaks down nuclear envelope so chromosomes released
>nuclear laminas phosphorylated
> conformational change in lamins and causes
destabilization of the nuclear lamina, which
results in its breakdown

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5
Q

Interphase Chromatin level of stabilization

A

Highly organized due to presence of sub-cellular regions in nucleus

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6
Q

Nucleolus

A

Prominent sub-cellular regions in the nucleus

visible by TEM

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7
Q

Function of nucleolus

A

synthesize all of the ribosomes the cell needs to continue to function

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8
Q

Ribosomes

A

ribonucleoproteins

made up of proteins + RNA

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9
Q

Nucleolus organizer regions

A

rDNA regions

regions around where nucleolus forms

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10
Q

Nuclear Pores

A

control the transport of macromolecules in and out of the nucleus

only way to access the nucleus

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11
Q

Nuclear Import/ Export happens via the Nuclear Pores

A

2 possible mechanisms depending on size of molecule

    1) Very small molecules - diffuse through the center 
        of the pore without help

    2) Molecules that are larger than the diffusion limit 
         - require the input of energy to facilitate 
         transport ( GTP used )
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12
Q

Diameter of nuclear pores

A

passage of material by free diffusion is about 9 nm

molecules larger than 9nm strictly controlled

molecules that are too big are not allowed to pass

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13
Q

What goes in nuclear pores ?

A

Histone proteins
Polymerases
Transcription factors
Ribosomal proteins

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14
Q

What goes out of nuclear pores ?

A

Ribosomal subunits
mRNA - protein complexes
fully processed spliced transcripts

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15
Q

Protein targeting to nucleus

A

there is a specific signal that is used by the cell to identify what can enter the nucleus, what can exit

proteins that have business in the nucleus must contain within their amino acid sequences signals that are recognized by the system

All proteins that must enter a membrane-bound organelle will be specifically targeted there by some mechanism encoded in the primary sequence of the protein

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16
Q

Targeting signals

A

First - every protein that is sent (targeted) to a specific site within the cell must have a destination-specific code associated with it

Second - there must be some sort of specific receptor for destination

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17
Q

differences in the final destination of proteins

A

consequence of targeting signals contained within the primary amino acid sequence of the protein itself

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18
Q

consensus sequences

A

they show the most common amino acid sequences that are used for a specific type of protein targeting

1 ) If one lines up the amino acid sequences of a number of proteins that are targeted to a particular organelle - they all contain this sequence or something very similar to it

2 ) some amount of variation in the signal that is used to enter a specific organelle but we are disregarding this

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19
Q

Import into the Nucleus

A

Targeting Signal: KKKRK
or
‘-Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val-‘

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20
Q

KKKRK

A

internal targeting sequence

must also be on the surface of the 3D protein

proteins are imported into the nucleus after translation, in a folded state

occurrence of this targeting sequence in a protein is said to be both necessary and sufficient

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21
Q

Steps of Nuclear Import

A

1 ) NLS is first recognized on the protein to be imported - KKKRK

2 ) NLS region on the surface of the nuclear protein binds to a soluble cytosolic NIR and forms a protein-receptor complex

3 ) The protein-receptor complex binds to the cytosolic fibril of the nuclear pore –> GTP-driven reaction results in a change in the configuration of the pore –> translocation (movement) of the protein complex through the pore and into the nucleus.

4 ) Once inside the nucleus, the nuclear import receptor dissociates from the nuclear protein and returned to the cytosol.

5 ) NLS remains part of the nuclear protein

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22
Q

Export of Proteins from the Nucleus

A

protein contains a nuclear export signal that binds with a receptor –> binds to the nuclear pore –> nuclear export receptor and the protein dissociate after transport –> export of ribosomal subunits through nuclear pores works through a more complex similar process

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23
Q

DNA packing in Interphase Nucleus

A

DNA will be packed up so tightly that it cannot be accessed and read

When gene expression is required - specific regions of the packed DNA will be loosened so that transcription factors and other expression machinery can bind to the DNA and transcribe it

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24
Q

Packed DNA called

A

chromatin

30nm fiber - average diameter of chromatin measured by TEM

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25
Q

Chromatin is formed from

A

DNA and Histones

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26
Q

Chromatin can be remodeled and regulated by

A

non-histone chromatin-associated proteins

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27
Q

Non-histone chromatin-associated proteins

A

heterogeneous group that interact with DNA and/or histones

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28
Q

Histones

A

set of basic proteins that interact strongly with DNA
overall + charge due to basic amino acid side
chains

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29
Q

Core histones

A

H2A H2B H3 H4

interact strongly with each other and with DNA to form nucleosome

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30
Q

H1

A

unique histone that binds to outside of nucleosome

helps pack nucleosomes together to pack DNA tightly

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31
Q

Nucleosome core particle

A

DNA + core histones

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32
Q

Linker DNA

A

DNA between each nucleosome core particle

33
Q

Nucleosome

A

Nucleosome core particle + Linker DNA

34
Q

histone tails

A

important in the regulation of chromosome structure including euchromatin to heterochromatin

35
Q

First level of packing

A

Beads-on-a-string

36
Q

Beads-on-a-string

A

call it the 10 or 11nm fiber

it is not really seen in a live cell

result of experimental manipulation to remove the H1 histone and unpack the DNA

37
Q

Second level of Packing

A

Chromatin

38
Q

Chromatin

A

11nm fiber is further condensed into the 30nm fiber through interaction with Histone H1

30nm chromatin fiber is the naturally occurring level organization of chromatin in the interphase nucleus

39
Q

Upper levels of Chromatin packing

A

non-histone scaffolding proteins further pack 30nm in interphase

help make large chromosomal loops of DNA with genes exposed at ends of loops

40
Q

Separating DNA and histone proteins

A

ionic salt washes

41
Q

ionic salt washes

A

dissociates chromatin due to non-covalent interactions between DNA and proteins

42
Q

Summary of Nuclease Digestion Experiment

A

1 ) Lightly digest chromatin with nuclease

2) Remove all associated proteins
3) Separate DNA molecules by size using gel electrophoresis

43
Q

key idea is to lightly digest chromatin with an enzyme that selectively digests

A

exposed DNA only

44
Q

enzyme that selectively digests is

A

micrococcal nuclease

45
Q

Key idea

A

micrococcal nuclease can be used to determine what DNA is tightly bound to proteins thus ‘protected’ from cutting by nuclease

All unprotected DNA will eventually be destroyed if the nuclease is left to digest for long enough

46
Q

Key assumptions of this experiment

A

If there is a repeating protein structure that associates with the DNA there will be protected pieces of DNA left after nuclease digestion

These pieces of DNA will have a standard size if they are bound to the same type of structural complex

47
Q

Gel Electrophoresis of DNA fragments

A

Used to separate DNA (or RNA)

Gel made of agarose

DNA already - charged so no SDS required

result is a banding pattern on a gel that tells use about relative size and abundance of each DNA fragment

48
Q

SDS-PAGE

A

Used to separate proteins.

gel is made of polyacrylamide

Prior to electrophoresis - proteins must be pre-treated with SDS and heat to denature and coat them with a uniform negative charge

End result is a banding pattern on a gel that tells use about relative size and abundance of each protein

49
Q

Transcriptional control

A

when and how often genes are transcribed

50
Q

RNA processing control

A

which combinations of introns/exons are produced so different proteins can be made from the same gene

51
Q

Once the processed mRNA leaves the nucleus

A

the cell continues to regulate the gene products by controlling

when and how translation happens
when the mRNA is degraded
what kinds of post-translational modifications take place
when the protein is tagged for destruction

52
Q

Control of Chromatin Structure

A

Controls Access to Genes

53
Q

Interphase chromatin / 30nm divided into

A

Constitutive Heterochromatin

Facultative Heterochromatin

54
Q

Constitutive Heterochromatin

A

heterochromatin is always condensed

happens in structural areas centromeres and telomeres

no genes to be found in areas with constitutive heterochromatin

55
Q

Facultative Heterochromatin

A

heterochromatin that is not always condensed

Genes within facultative heterochromatin have been shut down temporarily by restricting access to the DNA - very important way that the cell controls gene transcription

Mutations in the genes that help regions of the chromosome transition between euchromatin and heterochromatin can be quite serious, and often result in cancer

56
Q

Modification of Chromatin & Histones

A

Controls Access to Genes in DNA

57
Q

allow or restrict access to genes controlled by

A

1 ) Histone modifying enzymes

2 ) Chromatin remodeling complexes

58
Q

Histone Modifying Enzymes

A

chemically alter the histones of the nucleosome core

tails are modified by the addition of a variety of chemical functional groups the most common modifications include acetylation (Ac), methylation (M) and/or phosphorylation (P)

59
Q

what determines what happens to a particular stretch of chromatin at any given time

A

pattern of these modifications

60
Q

Chromatin Remodeling Complexes

A

Modification of the histone tails commonly results in formation of specific binding sites for enzymes which then bind to the entire nucleosome complex and ‘shift’ the DNA that is wrapped around it so DNA can be re-positioned - process is absolutely essential for genes to be exposed and expressed

61
Q

evidence to suggest that during mitosis many of the chromatin remodeling complexes are

A

inactivated - so heterochromatin can be formed efficiently without any chance DNA loosens again

62
Q

Transcription Factors Control Transcription at the Gene Level

A

required to allow the RNA polymerase to bind to the DNA for initiation

can enhance or inhibit transcription

63
Q

The Structure of a Eukaryotic Gene - Review

A

The coding strand

The template strand

64
Q

key DNA sequences in this transcription unit that should be highlighted

A 
5' flanking sequence
Enhancer region
Promoter region
Transcription start site
Transcription stop site
3' flanking sequence
Translation start site
Translation stop sight
65
Q

Transcription Factors control

A

when and how Transcription Happens

66
Q

Activators (protein) bind

A

Enhancer regions

67
Q

Repressors (protein) bind

A

Suppressor regions

68
Q

Co-factors

A

work together with other regulators to change the transcriptional response

69
Q

Chromatin remodeling complexes

A

bind to nucleosomes and help promote the transition between euchromatin & heterochromatin

70
Q

Transcription Factors and Chromatin Remodeling Complexes Work Together to

A

control Eukaryotic Gene Expression

71
Q

Fig 8-11

A

On the left, the activator acts as a binding site for a histone modifying enzyme

On the right, the activator creates a binding site for a chromatin remodeling complex

72
Q

General Principles of Transcript Processing

A

All transcripts are processed (mRNA, rRNA, tRNA) in the nucleus before they are transported to the cytoplasm

Processing is carried out by proteins (and RNA) that bind to and modify the transcripts

Virtually all processing signals are encoded into the primary sequence of the RNA transcripts themselves

Processing may include any of the following modifications:

1) Addition of sequences (e.g. 5’ cap and polyA tail in mRNA)
2) Cleavage of the transcript into several pieces (rRNA)
3) Removal of some sequences (all classes of RNA)
4) Splicing (i.e. removal of sequences by cleavage, followed be re-joining of remaining RNA fragments back together)

73
Q

three different RNA polymerases in the nucleus

A

Polymerase I
Polymerase II
Polymerase III

74
Q

3 major processing events that happen with mRNA

A

RNA capping

Polyadenylation

Splicing

75
Q

snRNPs

A

small nuclear RiboNucleoProteins

enzymes that contain a small RNA molecule that is complementary to the recognition sequences in the RNA transcript

come together to form a large complex called the spliceosome

76
Q

Summary of the Process of RNA Splicing

A

the formation of the spliceosome begins when the RNA portions of the snRNPs recognize the intron/exon junctions and base pair with them

snRNPs arrive and interact to bring them together and form the complete spliceosome

The second cut in the transcript occurs at the right edge of the intron and the two exons are joined together

77
Q

promoter choice

A

some genes will have two or even more promoters, each of which leads to the production of a different initial exon

78
Q

trans-splicing

A

exons from 2 separate gene transcripts are spliced together to produce a completely new mRNA

BIO 200 (2 decks)

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