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BIO 200 MIDTERM 1 > UNIT 3 > Flashcards

UNIT 3 Flashcards

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1
Q

Components of a nucleus

A

nucleus envelope, nuclear pores, chromatin, nucleolus and cisternae

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2
Q

Nuclear envelope

A

the outer nuclear membrane is continuos with the rough endoplasmic reticulum and has ribosomes attached

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3
Q

Nuclear lamina

A
  • provides structural support to the nucleus
  • plays an important role in DNA replication, transcription and gene regulation
  • helps in disassembly and re-assembly of the nuclear envelope during cell division
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4
Q

How does phosphorylation
regulate disassembly/reassembly
of the nuclear envelope & nuclear pores?

A

phosphorylation helps break down the nuclear structures for division, and dephosphorylation helps rebuild them afterward.

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5
Q

Nucleolus

A
  • A specialized chromosomal region of the nucleus
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6
Q

The nucleolus is responsible for:

A
  • Producing ribosomal RNA (rRNA): It makes the RNA needed for ribosomes.
  • Assembling ribosomes: It combines rRNA with proteins to form ribosomal subunits.
  • Processing rRNA: It modifies the rRNA into its final form for use in protein synthesis.
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7
Q

Ribosomes are made of rRNA and protein

A
  • rRNA Production: rRNA is produced in the nucleolus of the nucleus.
  • Protein Production: Ribosomal proteins are made in the cytoplasm and then transported back into the nucleus.
  • Assembly: In the nucleolus, rRNA and ribosomal proteins come together to form large and small ribosomal subunits.
  • Export: These subunits are exported separately to the cytoplasm, where they combine to form functional ribosomes for protein synthesis.
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8
Q

Nucleoli and the cell cycle

A

In interphase, the
nucleolus organizing
centers (NOCs) come together
to form a nucleolus

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9
Q

Does the number of nucleoli in a human cell depend on the cell cycle?

A

true

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10
Q

In mitosis…

A

the nucleolus fragments and disappears

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11
Q

In telophase..

A

the tips of the 10 chromosomes reform 10 small nucleoli which then fuse into a single nucleolus

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12
Q

Nuclear pores

A

gateways in the nuclear envelope that control what enters and exits the nucleus

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13
Q

What goes in the cell?…

A

proteins needed for DNA replication, transcription, gene regulation, mRNA processing, DNA structure and ribosomal subunit assembly

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14
Q

What goes out?…

A

Assembled ribosomal subunits, mRNA and tRNA

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15
Q

How does stuff get in & out of the nucleus?

A

occurs through bidirectional movement via nuclear pore complexes

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16
Q

Two mechanisms for nuclear import

A

Free diffusion and Active transport

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17
Q

Free diffusion

A

Ions and small macromolecules (9nm in diameter) can pass freely and non-selectively through the nuclear pore complex

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18
Q

Active transport

A

to transport larger molecules (>9nm) into and out of the nucleus

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19
Q

Histones

A
  • small + charged proteins that bind to negatively charged DNA
  • they help package DNA into chromatin -> form nucleosomes
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19
Q

Lamins

A
  • type of intermediate filament protein that form the nuclear lamina.
    -They provide structural support to the nucleus, help anchor chromatin, and are involved in organizing the nuclear envelope during cell division.
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19
Q

RNA Polymerase

A

enzyme that synthesizes RNA from a DNA template.
- essential for transcription

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20
Q

What do histones, lamins and polymerase have in common?

A

they contribute to the organization and integrity of the nucleus, impacting DNA packaging, transcription and overall gene regulation

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21
Q

Two requirements for
targeting proteins to
specific locations

A
  1. A specific signal
    sequence in the
    transported protein.
  2. A specific protein
    receptor that recognizes
    that signal sequence.
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22
Q

Active nuclear transport

A
  • refers to the processes that occur at the nuclear membrane
  • type of active transport
  • transported protein contains a targeting signal in its primary amino acid sequence
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23
Q

Nuclear transport receptor

A

They recognize and bind to specific sequences within the proteins that signal they need to be transported.

24
Q

Proteins with no localization signal in their primary sequence will end up localized in…

A

CYTOSOL

25
Q

Key ideas about protein targeting

A
  • targeting signals are encoded within proteins
  • targeting signals direct the protein to a specific organelle
  • targeting signal must be present for protein to leave the cytosol compartment
26
Q

Signal sequence to import into nucleus

A

K-K-K-R-K

27
Q

Components needed for import/export from the nucleus?

A
  1. Cargo proteins (eg. KKKRK)
  2. Receptor proteins (recognizes signal sequence & binds cargo protein)
  3. Nuclear Pore complex
28
Q

How might one identify & study a targeting sequence?

A
  • Remove parts of the protein and see if it can still be
    targeted to its final location
  • Deletions
  • Partial digestion
  • Mutate amino acids and see which changes affect
    targeting
  • Fuse different regions of the protein to a cytosolic
    protein and see if location of the cytosolic protein is
    affected
29
Q

Loss of function experiments

A

Remove from the system and observe what happens
e.g. deletion, mutation
* This type of experiment asks if the component removed is necessary

30
Q

Gain of function experiments

A

Add a component that is not normally present and observe what happens. This type of experiment asks if the component added is sufficient

31
Q

Export from the nucleus

A
  1. When a protein has an NES, it can be recognized and bound by a nuclear transport receptor.
  2. Mature RNA ready to export must be bound by proteins (RNA does not have an amino acid)
32
Q

How to fit 2m of DNA into a tiny space

A
  1. chromatin needs to be functionally organized
  2. DNA needs to be compacted to fit
  3. Need to accurately divide chromosomes up during cell division
    4.DNA still needs to be accesible
33
Q

Types of chromatin

A

euchromatin and heterochromatin

34
Q

Heterochromatin

A
  • densely staining regions
  • 10% of an interphase chromosome
  • concentrated around centromere & telomeres of chromosomes
35
Q

Euchromatin

A
  • lightly staining regions
  • contains less condensed DNA
  • Genes within this region are actively being transcribed
36
Q

Levels of DNA packing in the nucleus

A
  1. Naked DNA
  2. Beads on a string form DNA -> nucleosomes (10-11nm)
  3. Interphase chromatin
37
Q

Nucleosome core histone

A

The nucleosome core is made up of eight histone proteins, which include two copies each of four different histones: H2A, H2B, H3, and H4. This octamer forms the core around which DNA wraps.

38
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.

39
Q

What kind of interactions allows for DNA to
wrap around the histone octamer?

A

hydrogen bonds and ionic bonds

40
Q

Steps in assembling the histone octamer

A

1.Histones are synthesized and imported into the nucleus.
2. H3-H4 dimers form first, then H2A-H2B dimers.
3. The H3-H4 tetramer is the first to bind to DNA.
4. H2A-H2B dimers join to complete the histone octamer.
5. DNA wraps around the histone octamer, forming nucleosomes.
6. Linker histone H1 binds to DNA to organize and compact the nucleosome structure.

41
Q

Difference between 10nm fiber and the 30 nm fiber?

A

the 10-11 nm fiber does not have h1 histone bound to it while the 30nm fiber does

42
Q

Why is there extreme packaging during cell division?

A

so that we dont have cells missing bits of DNA

43
Q

Chromatin is only made up of histone proteins and DNA
TRUE/FALSE

A

FALSE

44
Q

When is heterochromatin formed?

A

when chromatin becomes tightly packed and inactive

45
Q

Formation of heterochromatin

A

happens through:
1. histone modifications like methylation
2. proteins like HP1 bind to modified histones making structure more compact
3. DNA methylation silence genes
5. chromatin becomes less accessible and gene expression is turned off in these regions.

46
Q

Histones bind tightly to the DNA so that DNA cannot move?

A

False because DNA needs to be accesible

47
Q

Methods to change the level of DNA packing

A
  1. Chromatin remodeling complexes
  2. Histone modifications
  3. Binding of transcription regulators
48
Q

Chromatin remodeling complexes

A

they physically move nucleosomes closer or farther apart so that some regions of DNA can be more accesible

49
Q

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

A

can lead to alterations in chromatin structure

50
Q

Histone modification of tails

A
  • Acetylation: Loosens DNA, making it easier for genes to be expressed.
  • Methylation: Can either activate or silence genes.
  • Phosphorylation: Involved in processes like DNA repair or preparing chromosomes for division.
51
Q

3 Major ways gene expression is controlled in the nucleus

A
  1. Chromatin remodeling as a way to control access to
    genes.
  2. Extensive use of transcription regulators by eukaryotes to control expression.
  3. RNA modification prior to nuclear export.
51
Q

Transcription regulators can further destabilize nucleosomes and create open DNA regions

A

Inactive Genes: Nucleosomes are tightly packed, preventing access to DNA and keeping genes turned off.

Transcription Regulators: These proteins destabilize or move nucleosomes, creating open DNA regions.

Active Genes: For a gene to be expressed, nucleosomes need to be less packed, allowing access for the transcription machinery.

52
Q

Anatomy of transcription unit

A

consists of regulatory region and transcribed region

53
Q

how is transcription regulated

A

Transcription Factors: Proteins that bind to specific DNA sequences (promoters and enhancers) to enhance or inhibit transcription.

Chromatin Structure: Modifications to histones and chromatin remodeling complexes can make DNA more or less accessible for transcription.

Epigenetic Modifications: Chemical changes to DNA (like methylation) and histones that can affect gene expression without altering the DNA sequence.

RNA Processing: Alternative splicing and modification of mRNA can influence which genes are expressed.

54
Q

Where does protein synthesis happen?

A

in the cytosol

55
Q

Different RNAs are processed in unique ways: After transcription…

A

mRNA: pre-mRNA is processed into mRNA -> exported to the cytosol for translation.

tRNA: Pre-tRNA is processed into -> tRNA, which becomes charged with an amino acid in the cytosol, ready for translation.

rRNA: Pre-rRNA is processed into -> rRNA, which combines with ribosomal proteins to form ribosomal subunits that function in the cytosol.

56
Q

These modifications are crucial for mRNA stability and function in protein synthesis…

A

5’ Cap: Added shortly after RNA synthesis begins, this cap consists of a modified guanine with a methyl group

3’ Poly-A Tail: A sequence in the pre-mRNA signals for cleavage, followed by the addition of a series of adenine nucleotides

57
Q

Purpose of 5’ capping

A
  • to protect from nuclease degradation
  • helps in binding protein for export from nucleus
  • helps in ribosome recognition & binding
    ( to initiate translation in the cytoplasm )
58
Q

Purpose of 3’-poly a tail

A
  • helps in stabilizing the transcript
  • helps translation termination
59
Q

Only the properly processed mRNA’s can exit the nucleus?

A

TRUE

BIO 200 MIDTERM 1 (3 decks)

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