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Immunology > Lecture 15 > Flashcards

Lecture 15 Flashcards

1
Q

The human genomic DNA is in how many chromosomes?

A

46 chromosomes or 23 pairs

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2
Q

What does packaging DNA do?

A

Protects it from damage and contributes to regulation of replication & transcription

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3
Q

Why is it important to package DNA so small?

A

To be able to fit into the nucelus

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4
Q

What stages are in interphase?

A
  • G1, S, G2

- G0 for non-dividing cells

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5
Q

During interphase, what form does DNA take?

A

DNA is present as chromatin

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6
Q

What is the appearance of chromatin?

A
  • Appears amorphous and randomly distributed

- It is “uncondensed”

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7
Q

What does the S phase of interphase stand for?

A

Synthesis

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8
Q

What happens to the chromosomes during S phase?

A

Each chromosome is replicated, resulting 2 sister chromatids that remain associated

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9
Q

What are the stages of mitosis?

A

Prophase, metaphase, anaphase, telophase

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10
Q

What occurs during prophase of mitosis?

A

The chromosomes become more compact, forming condensed chrmosomes

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11
Q

How does the shape of chromosomes change after cell division?

A

Once cell division is complete the chromosomes again become uncondensed and the cycle repeats.

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12
Q

Is chromosome or chromatin more condensed?

A

DNA is more condensed in chromosomes than in chromatin but chromatin DNA is still condensed and has multiple levels of organization.

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13
Q

What happens in interphase of mitosis?

A

DNA replicates

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14
Q

What happens in prophase of mitosis?

A
  • Chromosomes condense, the spindle forms, and the nuclear envelope disintegrates
  • Each chromosome has two chromatids
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15
Q

What happens in metaphase of mitosis?

A

Each chromosome aligns independently at the metaphase plate

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16
Q

What happens in anaphase of mitosis?

A

Chromatids separate

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17
Q

What happens in telophase and cytokinesis of mitosis?

A

The nuclear envelope reforms and the cell now divides (cytokinesis)

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18
Q

After cell division a typical eukaryotic cell contains how many copies of each chromosome

A
  • 2 copies of each chromosome (is diploid)
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19
Q

When does the synthesis of histones occur?

A

Late in the 1st “gap phase” (G1)

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20
Q

Fxn of histones?

A

Package and order DNA into structured units

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21
Q

During histone synthesis the cell enters what phase in order for what process to begin?

A

The cell enters S phase and DNA replication begins

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22
Q

Which strand(s) are histones and non-histone proteins deposited onto to produce chromatin?

A

Both the template and daughter DNA molecules to produce chromatin

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23
Q

When DNA replication is complete which phase does the cell enter?

A

2nd gap phase, G2

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24
Q

At the end of G2 the cell is ready to enter what?

A

Mitosis where it will divide, distributing one copy of each chromosome to each daughter cell

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25
Q

What does chromatin consist of?

A

DNA + histones + non-histone proteins

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26
Q

What is heterochromatin?

A

Condensed chromosome

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27
Q

What is the nucleus?

A

Membrane-bound organelle in eukaryotic cells that contains the genetic material

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28
Q

What is on the nuclear envelope’s inner and outer membrane?

A

Nuclear pores

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29
Q

What are nuclear pores

A

Elaborate gates that control transport of small and large molecules to/from the nucleus

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30
Q

The nuclear membrane is continuous with ___

A

The endoplasmic reticulum

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31
Q

What is the nuclear lamina

A

The inner surface of the nuclear envelope

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32
Q

What is the nuclear lamina lined with?

A

Proteins called nuclear lamins

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33
Q

What do nuclear lamins form?

A

Intermediate filaments that also extend across the cytoplasm to provide structural support

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34
Q

How do chromatin and nuclear RNAs attach to the nuclear membrane?

A

Via the lamins

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35
Q

What is the fxn of endoplasmic reticulum?

A

Shares nuclear membrane

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36
Q

What is the nuclear pore complex?

A

Highly complex proteinaceous pore that regulates the entry/exit of proteins, and exit of mRNA (proteins are made in the cytoplasm from mRNA – some are transported back into the nucleus)

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37
Q

Fxn of nuclear lamina

A

Provides structural rigidity to nucleus and, site of attachment for chromatin

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38
Q

Fxn of nuclear matrix

A

Diffuse nuclear scaffold consisting of proteins that attach chromosomes to the nuclear envelope or other structures in the nucleus

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39
Q

Fxn of nucleolus?

A

A ribosome-producing sub-compartment of the nucleus

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40
Q

What is nucleoplasm?

A

Chromatin/chromosome-containing region

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41
Q

What is chromatin?

A

Chromosomal material – protein-DNA complex

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42
Q

What does chromatin consist of?

A

fibres containing ~equal masses of DNA and protein, along with a small amount of RNA

43
Q

DNA in chromatin is tightly associated with what proteins? Their fxn?

A
  • Histones

- Protect and package the DNA and regulate replication and transcription by limiting its access

44
Q

What is the 1st lvl of chromatin packaging?

A

Nucleosomes

45
Q

What occurs in 1st lvl of chromatin packing?

A
  • Histones package and order the DNA into structured units called nucleosomes
  • Nucleosomes are packaged into higher order structure
  • Chromatin also contains non-histone protein
46
Q

What are nucleosomes?

A

Fundamental unit of chromatin aka beads-on-a-strings

47
Q

What are the major protein component of chromatin

A

Histones

48
Q

How does the charge of histones affect DNA?

A

Histones are small, very basic proteins that contain ~25% lysine’s and arginines to neutralize the highly charged DNA

49
Q

What does the assembly of histones with DNA require?

A

Molecular chaperones

50
Q

What are the 5 types of histones?

A
  • H2A
  • H2B
  • H3
  • H4
  • H1
51
Q

What are the core histones? Purpose?

A
  • H2A, H2B, H3, H4

- 2 copies of each form an octamer (8 subunits). The DNA is wrapped around the histone core to form the nucleosome

52
Q

What is the fxn of H1

A

Clamps DNA wrapped around nucleosome

53
Q

How do histones compare between species?

A

Histones are very highly conserved. For example, H4 is 98% identical between cows and peas

54
Q

The DNA in the nucleosome is ~2 loops
of ___ supercoil
secured to the histone core by histone
protein H1.

A
  • Negative supercoil (under wound) (note: negative supercoil

even though the coil is left-handed.)

55
Q

What is the linker DNA?

A

DNA between histone wrapped nucleosome

56
Q

What is link DNA digested by?

A

Nuclease

57
Q

What does a nucleosome include?

A

~200 nucleotide pairs of DNA and core histones

58
Q

How are nucleosomes dissociated?

A
  • Dissociation with high concentration of salt

- This disrupts the electrostatic interactions between the histone proteins and the DNA

59
Q

What is the second level of chromatin organization?

A
  • 11nm chromatin fibers coil to form 30nm chromatin fibers or solenoids
  • provides ~100-fold compaction of DNA
60
Q

Chromatin in interphase and non-dividing cells are in what level of chromatin organization?

A
  • 2nd level of chromatin organization (30nm fiber)
61
Q

What is the role of histone H1 in compaction to the 30nm fiber?

A

H1 holds the DNA on the histone core and is necessary for the formation of the 30nm fiber.

62
Q

Where is H1 located in the 30nm fiber?

A
  • the interior
63
Q

RNA synthesis (transcription) occurs during interphase when chromosomes are in the 30nm fibers. Protein complexes must associate with the DNA and scan along it, opening up the duplex to synthesize daughter strands & make RNA. Thus what happen for this to occur?

A
  • Regions of tightly packed DNA in the 30nm fiber must become partially dissociated to be accessible to the DNA replication and transcription machinery… this is accomplished using histone modifying enzymes and chromatin remodelling proteins
64
Q

When the 30nm fiber further compacts to form condensed chromosomes what is the overall compaction?

A

10,000 fold

65
Q

What is the nuclear scaffold made of?

A
  • Mainly H1

- Topo II

66
Q

Why is Topo II needed in the nuclear scaffold?

A

Required to supercoil the DNA during chromatin assembly

67
Q

Further looping/coiling of solenoid DNA into highly compacted, transcriptional silent form of chromatin called?

A

Heterochromatin

68
Q

When does heterochromatin formation occur?

A

During mitosis

69
Q

Histone 2A and 2B form a ____ dimer through an interaction known as the ___

A
  • Head to tail dimer

- Handshake

70
Q

2 H3/H4 dimers associate to form what?

A

A tetramer

71
Q

2 H3/H4 dimers associate with 2 H2A/H2B to form what?

A

An octamer

72
Q

Nucleosome core particle is consisted of what two things?

A

Histone core + 146 bp DNA

73
Q

DNA wraps tightly around histone octamer with exactly how many and what type of turn?

A

1.65 turns of negative supercoil

74
Q

In nucleosomes, what do (positively charged) histones interact with in DNA that explains the histone’s lack of sequence specificity?

A

Histones interact primarily with the sugar-phosphate backbones

75
Q

What interactions does the exposed DNA surfaces in nucleosomes allow for?

A

Interactions between DNA surfaces and DNA binding proteins

76
Q

How much of the DNA surface is exposed and available to interact with the DNA binding proteins in the 11 nm fiber?

A

70%

77
Q

What protrudes from the octamers (core histone)?

A

N-terminal tails (rmb histone core is an octamer made from H2A, H2B etc… so the tails are H2A tail, H2B tail etc.)

78
Q

What is the charge on the N-terminal tails of the histone protein and why?

A

Positively charged due to many Lys and Arg residues

79
Q

How does the N-terminal histone tails help mediate assembly of 30nm fiber?

A

Histone tails pack nucleosomes into 30nm fiber cause positively charged N-termini bind negatively charged sugar-phosphate backbone on DNA of neighbouring nucleosomes

80
Q

What holds the 30nm fiber?

A
  • Histone H1 proteins, which “pull” the nucleosomes together

- N-terminal tails

81
Q

Where can gene transcription (RNA synthesis) not occur?

A

In the solenoid

82
Q

What are the 3 possible covalent modifications on histone tails?

A
  • Phosphorylation of series (-PO4)
  • Irreversible methylation of lysine’s (-CH3)
  • Reversible acetylation of lysine’s (C=O - CH3)
83
Q

Histones are modified in the assembled nucleosomes in order to regulate what two things?

A
  • Chromosome structure (compaction)

- Gene activity (i.e. transcription)

84
Q

Do nuclear enzymes add or remove modifications?

A

They do both

85
Q

What is histone acetylation?

A

Reversible modification of lysine’s in the N-terminal regions of the core histones

86
Q

Results from histone acetylation?

A
  • Loss of positive charge reduces binding to DNA and destabilizes chromatin
  • Acetylated regions attract proteins that can either cause further compaction or can facilitate access to DNA
87
Q

What reverses histone acetylation?

A

Deacetylases

88
Q

Where do covalent modifications occur in histones?

A

On specific residues in the N-terminus of the histones

89
Q

What is the patterns of modification called?

A

Histone code

90
Q

What recognizes the histone code?

A

Enzymes that alter the structure of chromatin e.g. modifications associated with transcriptional activation would be recognized by enzymes that make the chromatin more accessible to the transcriptionally machine, same for replicate machinery

91
Q

What does chromatin remodelling alter?

A
  • The accessibility of DNA to DNA-binding proteins
  • change nucleosome structure to change the positionsof nucleosomes on the DNA (translocation) orto change the structure of DNA within the nucleosomes so that DNA is not as tightly associated with the histone core
92
Q

How can chromatin become “remodelled” (2 things)

A
  1. enzymes that covalently modify histones e.g. histone acetyltransferases, deacetylases etc.
  2. the work of chromatin remodelling complexes
93
Q

What do chromatin remodelling complexes do?

A

Work to inc or dec its accessibility to proteins in the cell, particularly those involved in gene expression, replication and repair, thus chromatin structure is dynamic

94
Q

Do chromatin remodeling complexes require energy?

A

Yes they hydrolyze ATP to remodel or translocate nucleosomes

95
Q

How is DNA replication during interphase done

A

As the replication fork approaches a stretch of chromatin, nucleosomes on the parental duplex are displaced and new ones (containing both re-cycled and new histones) are re-formed on the newly synthesized daughter duplexes.

96
Q

What are 5 non-histone DNA binding proteins used during replication?

A

DNA polymerases, ssDNA binding proteins, Topo I and II, helicase, primase etc.

97
Q

What are 2 non-histone DNA binding proteins used during transcription?

A

RNA polymerases, transcription factors (activators and suppressors)

98
Q

What are 2 non-histone DNA binding proteins used during RNA processing?

A

factors for ribosomal assembly (ribosomal proteins), nuclear RNPs (ribonucleoproteins) involved in mRNA processing

99
Q

What are 4 other non-histone DNA binding proteins?

A

Telomere associated proteins, centromere associated proteins, scaffolding proteins, recombination proteins

100
Q

Chromosomes must be replicated, and the sister chromatids separated to allow one complete copy to be passed on to each daughter cell. This process is controlled by what three DNA sequences within the chromosome? All three sequences are necessary for a functional chromosome.

A

the replication origin (many), the centromere and the telomere (two)

101
Q

What is the replication origin?

A
  • the location at which DNA duplication beings
  • eukaryotic chromosomes contain many origins or replication to ensure that the entire chromosome can be replicated rapidly
102
Q

What is centromere?

A
  • attachment site for mitotic spindle (via a protein complex called a kinetochore)
  • allows for one copy of each duplicated and condensed chromosome to be pulled to each daughter cell during cell division
103
Q

What is a telomere?

A
  • formed at the end of chromosomes
  • contain sequence repeats that enable the ends of chromosomes to be efficiently replicated
  • protect the ends of chromosomes from nucleases and from being recognized as “breaks” in need of repair

Immunology (14 decks)

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