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Biochem 524 > Chapter 4 - DNA, Chromosomes and Genomes > Flashcards

Chapter 4 - DNA, Chromosomes and Genomes Flashcards

1
Q

What is the only nonhomologous chromosome?

A

Sex chromosomes in males

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2
Q

Transposable elements

A

Mobile pieces of DNA that have gradually inserted themselves in the chromosomes over evolutionary time and usually multiplying in the genome

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3
Q

Number of protein coding genes

A

About 21,000

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4
Q

Interphase

A

Genes expressed, chromosomes replicated

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5
Q

Sister chromatids

A

Two replicas remaining together as a pair

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6
Q

Mitotic chromosomes

A

Highly condensed chromosomes in diving cells

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7
Q

Replication Origen

A

The location at which duplication of the DNA begins

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8
Q

Centromere

A

Allows one copy of each duplicated and condensed chromosome to be pulled apart into each new daughter cells

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9
Q

Kinetochores

A

Protein complex that forms at centromere and attaches the duplicated chromosomes to the mitotic spindle

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10
Q

Chromatin

A

Complex that includes protein and nuclear DNA

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11
Q

Nucleosome

A

First and most basic level of chromosome compaction - caused by histones

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12
Q

Diameter/width of chromatin when at first level compaction

A

30nm

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13
Q

Nucleosome core particle compostion

A

A complex of eight histone proteins

2 molecules of each:
H2A, H2B, H3, H4

  1. H2A and H2B form a dimer
  2. H3-H4 dimers bind to make H3-H4 tetramer
  3. The tetramer binds with two H2 dimers
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14
Q

Turn number of DNA on histone complex

A

1.7

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15
Q

Histone fold

A

Structural motif, found in common within all histone proteins, formed from three α helices connected by three loops.

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16
Q

Common amino acids in each core of histones

A

Lysine and arginine

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17
Q

Homologous chromosomes

A

The maternal and paternal pair of chromosomes

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18
Q

Histone core consists of

A
  1. Made of two H2A-H2B dimers and two H3-H4 dimers
  2. H3-H4 dimers are bounded together to form a tetramer
  3. H2A-H2B dimers bind to the H3-H4 tetramer but not to each other
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19
Q

What two amino acids make up the majority of residues on the histones? Why?

A

20-24%

  1. Lysine
  2. Arginine
  3. Both are positively charged amino acids so make the histones positively charged and better at associating with the negatively charged DNA
20
Q

Turns around histone

A

1.7

21
Q

How many hydrogen bonds former between histone and DNA?

A

142

22
Q

Bending of DNA

A
  1. Bending of DNA is not smooth and many kinks are seen.

2. Bending requires substantial compression of minor groove

23
Q

What are histone tails for?

A

Histone tails go through modification that then control critical aspects of chromatin structure and function.

24
Q

Evolutionary history of histones

A
  1. Highly conserved
  2. Histones of pea and cow differ at only two points (2nd and 102nd)!
  3. Such high conservation suggest that minor changes in amino acid is deleterious for cells.
25
Q

Nucleotide preference histones

A

Histones prefer AA, TT and TA nucleotides in minor groove inside but prefers G-C in the the outer minor grooves

26
Q

How cells loosen DNA-histone contacts

A

Through chromatin remodeling complexes

  1. Include subunit that hydrolysis ATP.
  2. This subunit binds to both the protein core and DNA strand of Nucleosome
  3. Using energy from ATP, complex moves DNA relative to histone core.
  4. Complex also temporarily changes Nucleosome structure so DNA binds less tightly
  5. Through various cycles of ATP hydrolysis, remodeling complexes can catalyze histone sliding.
  6. Some remodeling complexes can remove completely or partial parts (H2A-H2B) of Nucleosome
27
Q

What causes Nucleosomes to stack so tightly?

A

Two factors:

  1. Histone tails (especially H4 tail)
  2. Linker histone (H1) - binds to each nucleosome
28
Q

Most common nucleosome stacking model

A

Zigzag

29
Q

Epigenetic inheritance

A

Cell memory based on inherited chromatin structure rather than change in DNA

30
Q

Position effect

A

The phenomenon where a piece of euchromatic can be translocation to heterochromatin.
(Often silences normally active genes)

31
Q

When are major histones synthesized?

A

During S-phase behind replication fork

32
Q

When are histone variants made?

A

Throughout interphase

33
Q

How many histone modification coordinate sets are there in mammalian cells?

A

15

34
Q

Histone code

A

The modifications of histones and their interactions with Nucleosome

35
Q

What protein complex recognizes specific combination of histone modifications? What does this protein do?

A
  1. Reader complex

2. Once specific histone modifications found, will attract proteins to execute appropriate biological function

36
Q

Position effect variegation

A

Look up properly

37
Q

HATs

A

Histone acetyl transferase

38
Q

HDACs

A

Histone deacetylase complexes

39
Q

What does histone modification usually depend on?

A

Transcription regulatory protein or transcription factors

40
Q

What effect does acetylation of lysines on N-tail have on chromatin structure?

A

Loosens chromatin structure because it removes positive charge on lysine weakening the association with DNA

41
Q

What affect does trimethylation of a specific lysine on H3 tail have on chromatin structure?

A

Attracts heterochromatin-specific protein HP1 that contributes to spread of heterochromatin

42
Q

How does the chromatin modification spread across the chromosome?

A
  1. Modifying enzymes mark one or few neighboring nucleosomes.
  2. Reader protein recognizes these marks and binds to them tightly
  3. This activates an attached writer enzyme that is positioned near on an adjacent nucleosome.
  4. Writer enzyme marks adjacent nucleosome.
  5. Causes a chain reaction of writer-reader cycles along the chromosome
  6. NOTE: much more complex - also has ATP dependent remodeling protein that work in concert with reader and writer all part of the same complex.
43
Q

What stops modification chain reactions down the chromosome?

A

Barrier proteins.

  1. The tethering of a region of chromatin to a large fixed site, such as nuclear pore complex, can form a barrier that stops heterochromatin spread.
  2. Tight binding of barrier proteins to nucleosomes can make them heterochromatin resistant.
  3. By recruiting a group of highly active histone-modifying enzymes, barriers can erase histone marks.
44
Q

Example of third kind of histone modifying barrier enzymes

A

A potent acetylation of lysine 9 on histone H3 will compete with lysine 9 methylation preventing the HP1 from binding and therefore prevent heterochromatin formation.

45
Q

Centromere-specific variant H3 histone during mitosis

A

Centromere protein-A (CENP-A) - needed with additional proteins to form the kinetochore.

46
Q

What do centromeres largely consist of?

A

Alpha satellite DNA (repeated sequences)

Biochem 524 (6 decks)

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