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BIOL 200 > unit three > Flashcards

unit three Flashcards

1
Q

what does the presence of a nucleus do for the eukaryote?

A
  1. separation of transcription and transition (major role)
  2. protection of coding material (minor role)
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2
Q

what are chromosome territories?

A

interphase chromosomes are spatially organized

chromosomes are not all tangled together - they are distinct regions of the nucleus

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3
Q

what are the components of the nucelus?

A

nuclear envelope - double membrane (2 lipid bilayers)
nuclear pores - allow passage in and out of the cell
chromatin (condensed) have diff degrees of packaging

cisternae show that the nucleus is continuous with the ER

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4
Q

how can you tell the difference between heterochromatin and euchromatin in microscope images?

A

euchromatin will be lighter in colour

heterochromatin will be darker in colour because it is more densely packed

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5
Q

what is the nuclear lamina?

A

meshwork of special class of intermediate filament proteins called lamins

help anchor interphase chromatin

aids in disassembly and reassembly of the nuclear envelope during cell division

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6
Q

what is phosphorylation?

A

covalent attachment of a phosphate group

a mechanism that cells use to regulate function

the addition of a phosphate group (large negative group) changes the conformation of the protein

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7
Q

is the nucleolus a membrane bound organelle?

A

no but it has a diff density than the surrounding environment

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8
Q

what is the nucleolus?

A

a specialized chromosomal region of the nucleus

it is a site of rRNA synthesis (rRNA is transcribed in here) and assembly of ribosomal subunits made from rRNA and ribosomal proteins

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9
Q

what are nucleolus organizers?

A

pairs of chromosomes in the human genome that contain rRNA encoding regions (5 pairs)

the nucleolus develops from them

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10
Q

where do ribosomal subunits (large and small) come together during translation?

A

the cytoplasm

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11
Q

what do heterochromatin and euchromatin describe?

A

the degree of DNA packing along a single interphase chromosome

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12
Q

describe heterochromatin

A

densely staining regions

about 10% of an interphase chromosome

concentrated around centromere and telomeres of chromosomes

not many active genes included in heterochromatin (tend to be silent)

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13
Q

describe euchromatin

A

lightly staining regions

contains less condensed DNA

genes within this region are actively being transcribed

not as tightly packed so they are more accessible to transcriptional machinery

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14
Q

what kind of molecules should be imported into the nucleus?

A

any enzymes required for:

DNA replication, transcription, gene regulation, mRNA processing, DNA structure (ex. histones), ribosome assembly

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15
Q

what kind of molecules should be exported out of the nucleus?

A

assembled ribosomal subunit

mRNA

tRNA

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16
Q

what kind of structural cues could the nuclear pore use to differentiate?

A

molecular shapes

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17
Q

is the act of viral particles passing through the nuclear pore active or passive?

A

active process

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18
Q

what are the two mechanisms for nuclear transport?

A

diffusion and active transport

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19
Q

describe diffusion

A

ions and small molecules

molecules 5 kDa or 9 nm in diameter can pass freely and non-selectively through the nuclear pore complex (NPC)

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20
Q

describe active transport

A

energy required to transport larger molecules into nucleus

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21
Q

what are the two requirements for targeting nuclear proteins to specific locations?

A
  1. a specific signal sequence in the transported protein (encoded within the protein)
  2. a specific protein receptor that recognizes and binds to that signal sequence
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22
Q

what is the process of import into the nucleus called?

A

nuclear localization signal (NLS)

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23
Q

what is the process of export out of the nucleus called?

A

nuclear export signal (NES)

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24
Q

what is the nuclear transport receptor?

A

bind to the nuclear signal sequence and can dock onto proteins of the nuclear pore (NIR and NER)

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25
Q

describe the process of entering and exiting the nucleus

A

the transported protein contains a targeting signal in its primary amino acid sequence - the NLS or NES goes off and the NIR or NER binds

26
Q

what is the role of GTP?

A

active transport also requires energy - powered through GTP through a GTP binding protein

the hydrolysis of GTP is required and provides the energy to allow for nuclear import

27
Q

what requirements are common to other targeted proteins?

A
  1. targeting signals are encoded within proteins
  2. targeting signals direct the protein to a specific organelle
  3. targeting signal must be present for protein to leave the cytosol compartment
28
Q

what happens to proteins with no targeting signals?

A

they remain in the cytoplasm

29
Q

how can one identify the amino acids that code for targeting signals within a protein?

A

KKKRK - nuclear localization sequence

30
Q

what is loss-of-functions experiments?

A

remove the system and observe what happens (eg. deletion and mutation)

this type of experiment asks if the component removed is necessary

31
Q

what are gain of function experiments?

A

add a component that is not normally present and observe what happens

this experiment asks if the component added is sufficient

is the component added enough to perform the function

32
Q

how are proteins exported?

A

in a similar way to the way that import happens

ie. nuclear export protein signal (NES) in protein is bound by protein receptor, which aids in active export of protein out of the nuclear pore

33
Q

how is RNA exported?

A

mature RNA ready for export MUST be bound by proteins

NES is an amino acid signal, which means that RNA cannot possess it (though it may code for translation of an NES)

34
Q

what are the four requirements of DNA and the nucleus?

A
  1. nucleus needs to be functionally organized
  2. DNA needs to be compacted to fit
  3. Need to accurately divide chromosomes during cell division
  4. DNA needs to be accessible
35
Q

describe chromosome territories

A

interphase chromosomes are spatially organized

chromosomes are not all tangled together - they are distinct

specific regions of the chromosomes are attached to either the nuclear envelope or the nuclear lamins

36
Q

what does it mean by the nucleus needs to be functionally organized?

A
  • the chromosomes are spatially organized
  • the nucleolus is another functionally distinct region inside the nucleus
  • the structure varies along a single interphase chromosome (euchromatin and heterochromatin are not static)
37
Q

in a living eukaryotic cell, what is the most common arrangement for chromatin?

A

in the interphase nucleus, it is the 30 nm fiber

38
Q

what are the levels of packing for DNA?

A
  1. naked DNA (2 nm): just the double helix, no proteins
  2. nucleosomes (10-11): beads on a string structure - DNA is wound around the nucleosomes - bound up with histones; only seen experimentally
  3. chromatin (30 nm) - transcriptionally active; interphase chromatin can form higher-ordered loops of the 30 nm fiber
  4. Chromatin condensation: beyond the 30 nm loops, additional folding only happens when chromatin condenses into chromosomes during mitosis
39
Q

what are nucleosomes?

A

DNA + 8 core histone proteins

(H2A, H2B, H3, H4) * 2

40
Q

how is the histone octamer complex formed?

A

it is a complex comprising two copies of four polypeptides that form primarily due to hydrophobic interactions between their tertiary structures

41
Q

what is the biochemical approach to understand histone/ DNA structure?

A

if DNA is wound up with histone core, the nuclease won’t be able to get at the DNA

only the exposed linkers will be digested

nuclease digestion occurs then gel electrophoresis

42
Q

what is brief nuclease digest vs. extended nuclease digest?

A

brief: random cuts made in linker DNA

extended: all exposed linker DNA digested

43
Q

how do we separate the DNA from the histones?

A

wash with a high salt solution

44
Q

what is the difference between 10 nm fiber and the 30 nm fiber?

A

the 10-11 nm fiber does not have H1 histone bound to it while the 30 nm fiber does

45
Q

what is H1 histone?

A

linker histone - binds linker DNA

pulls nucleosomes together into the 30 nm fiber

46
Q

is chromatin only made of histone proteins and DNA?

A

No there are other proteins that help to bend the fiber even more

47
Q

what are loops of 30 nm chromatin formed from?

A

formed by non-histone chromatin proteins that form a scaffold

48
Q

describe mitotic chromosomes

A

after DNA replication, 2 copies of each chromosome

it is poorly understood how mitotic chromosomes become so compact

10 000 fold shorter than its length

49
Q

what are the 3 imp DNA sequences in the eukaryotic chromosome that are required to go through the cell cycle?

A
  1. telomere: repeating sequence at the end
  2. replication origin: can be more than one; where DNA pol goes to replicate
  3. centromere: attachment to mitotic spindle
50
Q

can histones dissociate from DNA?

A

Yes, histones are not permanently bound. they must dissociate because we want to regulate DNA packing

51
Q

what are the methods to change the level of DNA packing?

A

a) histone modification of tails
b) chromatin remodeling complexes
c) transcription regulators binding

52
Q

how do changes in histone modifications lead to changes in chromatin structure?

A

they change the affinity between the histone octamer and the DNA

they help recruit other proteins to chromatin

53
Q

describe histone mod of tails

A

histone tails can be modified and interact to compact chromatin into heterochromatin

reversible mod: acetylation (removes charge - losen), methylation, and phosphorylation

54
Q

describe chromatin remodeling complex

A

density of interphase chromatin is regulated by recruiting chromatin remodeling complexes

the complex binds histones/ DNA to slide the nucleosome, revealing more free DNA

the chromatin remodeling complex can slide nucleosomes so that the DNA wrapped around the nucleosome can now be accessed by the transcription machinery

55
Q

describe transcription regulators binding

A

transcription regulators can further destabilize nucleosomes & create open DNA regions (unpack DNA) and increase access of transcription machinery

inactive genes: nucleosomes are packed in tightly
active genes need access: nucleosome destabilization/ displacement

56
Q

what are the 3 major ways in which expression is controlled in the nucleus?

A
  1. chromatin remodelling as a way to control access to genes
  2. the extensive use of transcription factors by eukaryotes to control expression
  3. RNA modification prior to nuclear export
57
Q

what are the 2 major parts of a transcription unit?

A

regulatory region and transcribed region

58
Q

what accounts for the differences in gene expression in different cell types?

A

transcription factors can have + and - control over gene expression

different genes transcribed at different rates

same gene transcribed at different rates in different tissue

same gene transcribed at different rates at different times during development in the same tissue

59
Q

what must happen before transcription can occur?

A

binding of RNA pol

eukaryotes: the promoter is recognized by several general transcription factors

prokaryotes: the promoter is recognized by a subunit of bacterial polymerase (sigma factor)

60
Q

what is the general transcriptional machinery in eukaryotic genes?

A

TBP = TATA binding protein
general transcription factors bind to the basal promoter and recruit RNA pol

61
Q

how do DNA-binding proteins (TF) specifically recognize the correct binding site on DNA?

A

they make specific non-covalent interactions with the sides of the base-pairs in the major or minor groove of that sequence

62
Q

what determines when and how much RNA is transcribed from a gene?

A

the interplay between all of the regulatory sequences and the regulatory proteins that bind them

BIOL 200 (3 decks)

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