Lecture 9

Question 1

Chromatin

Answer 1

Complex of DNA and proteins that makes up the chromosome

Question 2

Nucleosome

Answer 2

DNA + histone; octamers with two copies each of H2A, H2B, H3, and H4

Histones have many + residues to interact with - DNA phosphate backbone

147 bp per nucleosome; 1 and 2/3 turns around protein core

Question 3

Linker DNA

Answer 3

10-90 bp between nucleosomes in beads-on-a-string structure

Question 4

30nm fiber

Answer 4

Two-start helix with H1 histone

Question 5

Histone tail

Answer 5

Flexible N-terminal tails in all histones and C-terminal tails in H2A and H2B

Question 6

Histone modifications (4)

Answer 6

Methylation, acetylation, ubiquitination, phosphorylation

Question 7

Histone acetylation

Answer 7

Neutralizes lysine +,

HATs - histone acetyltransferases

HDACs - histone deacetylases

Question 8

Histone methylation

Answer 8

Maintains lysine + (prevents easy acetylation; can be trimethylated)

HMTs - histone methyltransferases

KDM - histone lysine (K) demethylase

Question 9

Euchromatin vs. heterochromatin re: DNA transcription

Answer 9

Euchromatin - looser DNA => more accessible to transcription enzymes => greater gene expression

Heterochromatin - tightly packed DNA => less accessible to transcription enzymes => less gene expression

Question 10

Histone code

Answer 10

Euchromatin - H3K4 trimethylated, K9 K14 K18 K27 acetylated, S10 phosphorylated

Heterochromatin - H3K9 and H3K27 trimethylated

Read by heterochromatin protein 1 (HP1) and TFIID

Question 11

X chromosome inactivation

Answer 11

Creation of Barr body. e.g. Calico cat with different fur pattern in clone

Question 12

Heterochromatin protein 1

Answer 12

Recognizes H3K9 trimethylation at chromodomain

Chromoshadow domain induces further trimethylation of nearby H3K9s

End result: Heterochromatin

Boundary element on chromatin prevents further trimethylation

Question 13

TFIID

Answer 13

Recognizes H3K9 acetylation at bromodomain

H3K9 acetylation also attracts TAFII, which attaches to promoter

End result: Transcription

Question 14

Fragile X syndrome (*)

Answer 14

Methyl CpG binding protein 2 (MeCP2) recognizes methylated C (*DNA methylation)

MeCP2 recruits HDAC and HMT

Question 15

Induced pluripotent stem cells

Answer 15

Induction by unwrapping previously wrapped genes (heterochromatin -> euchromatin)

Question 16

Chromatin immunoprecipitation (ChIP)

5 steps and purpose

Answer 16

Determine bead DNA and string DNA; also determine state of transition to iPS cell

1) Isolate and shear chromatin mechanically
2) Apply antibodies for acetylated histone tails
3) Immunoprecipitate a la column chromatography
4) Release precipitated DNA from histones
5) PCR and compare to genome to locate sequence

Question 17

Giemsa stain

Answer 17

Stain applied to chromatin; absorbing parts are G bands, others are R bands; useful for karyotyping

Question 18

Philadelphia chromosome

Answer 18

Short chromosome 22 from translocation of piece to chromosome 7; associated with chronic myeloid leukemia

Question 19

Elements for inheritance and replication of chromosomes (3)

Answer 19

Autonomously replicating sequences (ARS; origins of replication)

Centromere for reliable mitotic segregation (CEN)

Telomeres (TEL)