Chapter 4 - DNA, Chromosomes and Genomes

Question 1

What is the only nonhomologous chromosome?

Answer 1

Sex chromosomes in males

Question 2

Transposable elements

Answer 2

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

Question 3

Number of protein coding genes

Answer 3

About 21,000

Question 4

Interphase

Answer 4

Genes expressed, chromosomes replicated

Question 5

Sister chromatids

Answer 5

Two replicas remaining together as a pair

Question 6

Mitotic chromosomes

Answer 6

Highly condensed chromosomes in diving cells

Question 7

Replication Origen

Answer 7

The location at which duplication of the DNA begins

Question 8

Centromere

Answer 8

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

Question 9

Kinetochores

Answer 9

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

Question 10

Chromatin

Answer 10

Complex that includes protein and nuclear DNA

Question 11

Nucleosome

Answer 11

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

Question 12

Diameter/width of chromatin when at first level compaction

Answer 12

30nm

Question 13

Nucleosome core particle compostion

Answer 13

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

Question 14

Turn number of DNA on histone complex

Answer 14

1.7

Question 15

Histone fold

Answer 15

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

Question 16

Common amino acids in each core of histones

Answer 16

Lysine and arginine

Question 17

Homologous chromosomes

Answer 17

The maternal and paternal pair of chromosomes

Question 18

Histone core consists of

Answer 18

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

Question 19

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

Answer 19

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

Question 20

Turns around histone

Answer 20

1.7

Question 21

How many hydrogen bonds former between histone and DNA?

Answer 21

142

Question 22

Bending of DNA

Answer 22

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

2. Bending requires substantial compression of minor groove

Question 23

What are histone tails for?

Answer 23

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

Question 24

Evolutionary history of histones

Answer 24

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.

Question 25

Nucleotide preference histones

Answer 25

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

Question 26

How cells loosen DNA-histone contacts

Answer 26

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

Question 27

What causes Nucleosomes to stack so tightly?

Answer 27

Two factors: 1. Histone tails (especially H4 tail) 2. Linker histone (H1) - binds to each nucleosome

Question 28

Most common nucleosome stacking model

Answer 28

Zigzag

Question 29

Epigenetic inheritance

Answer 29

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

Question 30

Position effect

Answer 30

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

Question 31

When are major histones synthesized?

Answer 31

During S-phase behind replication fork

Question 32

When are histone variants made?

Answer 32

Throughout interphase

Question 33

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

Answer 33

15

Question 34

Histone code

Answer 34

The modifications of histones and their interactions with Nucleosome

Question 35

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

Answer 35

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

Question 36

Position effect variegation

Answer 36

Look up properly

Question 37

HATs

Answer 37

Histone acetyl transferase

Question 38

HDACs

Answer 38

Histone deacetylase complexes

Question 39

What does histone modification usually depend on?

Answer 39

Transcription regulatory protein or transcription factors

Question 40

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

Answer 40

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

Question 41

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

Answer 41

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

Question 42

How does the chromatin modification spread across the chromosome?

Answer 42

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.

Question 43

What stops modification chain reactions down the chromosome?

Answer 43

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.

Question 44

Example of third kind of histone modifying barrier enzymes

Answer 44

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.

Question 45

Centromere-specific variant H3 histone during mitosis

Answer 45

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

Question 46

What do centromeres largely consist of?

Answer 46

Alpha satellite DNA (repeated sequences)