Chapter 4

Question 1

Define chromosomes

Answer 1

Structure composed of a DNA molecule (in eukaryotes linear, in prokaryotes circular) and associated proteins, and which carries part of or all of the hereditary information of an organism.

Question 2

Define chromatin

Answer 2

Complex of DNA, histones and non-histone proteins found in the nucleus of a eukaryotic cell.

Question 3

Define nucleosomes

Answer 3

Bead-like structure in eukaryotic chromatin composed a short length (147bp) of DNA wrapped around a core of 8 histones (normally H2A, H2B, H3 and H4), as well as linker DNA (the DNA between the histone complexes).

Question 4

Define Karyotype

Answer 4

The full set of chromosomes of a cell arranged by size, shape and number

Question 5

Defines genes

Answer 5

Region of DNA that is transcribed as a single unit and carries information for a discrete hereditary characteristic, either a protein or an RNA molecule.

Question 6

How many genes does yeast have?

Answer 6

~6600 genes

Question 7

How many genes do humans have?

Answer 7

~30.000 genes (21.000 coding genes)

Question 8

Why can the different between genome size and amount of genes vary so much between two organisms?

Answer 8

A lot of intergenic DNA in the human genome. Intergenic DNA has many functions such as regulating gene expression and large-scale organization of chromatin. Also, repetitive sequences scattered throughout the genome, as wells as, transposable elements.

Question 9

What is transposable elements/jumping genes/transposons?

Answer 9

Sequences of DNA that “jumps” from one location in the genome to another., with the risk of destroying or altering the genes activity.

Question 10

How many chromosomes does humans have?

Answer 10

22 autosome chromosomes (not sex chromosomes)

Question 11

What is the differences between male and female chromosomes?

Answer 11

Females have 23 pairs of X chromosomes and males have 24 different X and Y chromosomes

Question 12

4) List three specialized DNA sequences and their function that act to ensure that the number and morphology of chromosomes are constant from one generation to the next.

Answer 12

Telomers – repetitive nucleotide sequences at the end of eukaryotic DNA which in most cells are shortened during replication. Shortening of the telomers act as buffer preserving important genetic information during cell division. Furthermore, telomers protect DNA ends from repair mechanisms which would otherwise falsely recognize these as double stranded breaks.

Centromers – Sequences where kinetochore complexes assemble during cell division, and pull apart sister chromatids.

Origin of replication – Sequences from where replication is initiated.

Question 13

Describe level of DNA condensation and interaction

- 10 nm fiber (bead-on-a-string)

Answer 13

Hydrogen bonds, salt bridges and hydrophobic interactions maintain DNA to histone interaction.

Question 14

Describe level of DNA condensation and interaction

- 30 nm fiber

Answer 14

Interaction between histone tails (which can be modified by post translational modification of histone tails), as well as, the linker histone H1 maintains the zig-zag organization of the 30nm fiber.

Question 15

Describe level of DNA condensation and interaction

- Chromatin looping (“700nm fiber”)

Answer 15

Highly condensed chromatin (M phase). Held together by Cohesin (holds sister chromatids together) and Condensin (structural proteins).

Question 16

Define epigenetic inheritance

Answer 16

Inheritance of any feature from one generation to another that does not result from changes in the sequence of DNA

Question 17

Define heterochromatin

Answer 17

Region of an interphase chromosome that is highly condensed

Question 18

Define Euchromatin

Answer 18

Region of an interphase chromosome that is less condensed

Question 19

In what type of chromatin are actively expressed genes most often found?

Answer 19

Euchromatin, as this is less condensed compared to heterochromatin.

Question 20

What is the histone code?

Answer 20

Post-translational modification (PTM) can occur at numerous amino acid residues of histone in a nucleosome. The histone code is the specific set of PTM on a nucleosome. Each combination of modifications is thought to lead to a specific biological outcome.

Question 21

Why does the cell have histone variants?

Answer 21

The presence of different histone variants in nucleosomes leads to different biological outcome. Histone variants can therefore used by the cell to specify the function of the nucleosome.

Question 22

Protein groups and their control of nucleosomal modification

Define transcription factors

Answer 22

Interacts sequence-specifically with DNA and can recruit writers or erasers

Question 23

Protein groups and their control of nucleosomal modification

Define readers

Answer 23

Reads histone and DNA modifications and can recruit writers or erasers

Question 24

Protein groups and their control of nucleosomal modification

Define writers

Answer 24

Adds histone or DNA modifications

Question 25

Protein groups and their control of nucleosomal modification Define Erasers

Answer 25

Removes histone or DNA modifications

Question 26

Protein groups and their control of nucleosomal modification Define Barrier

Answer 26

Shields or counteracts the spreading of histone or DNA modifications

Question 27

Protein groups and their control of nucleosomal modification Define Chromatin remodeling complexes

Answer 27

Moves histones relative to DNA at the cost of ATP

Question 28

Protein groups and their control of nucleosomal modification Define Histone chaperones

Answer 28

Replaces histones within the histone core of nucleosomes, thereby binding and regulation nucleosome assembly

Question 29

Defines a promoter

Answer 29

Region of DNA that initiates transcription of a particular gene.

Question 30

Defines an enhancer

Answer 30

Small region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur.

Question 31

Define transcription factor

Answer 31

Protein that controls the rate of transcription of genetic information by binding to a specific DNA sequence. Regulates genes expression. Help recruit cofactors and other proteins

Question 32

Define motif

Answer 32

A protein sequence motif, or pattern, can be broadly defined as a set of conserved amino acid residues that are important for protein function and are located within a certain distance from each other

Question 33

Define histone methylation

Answer 33

Associated with inactive chromatin

Question 34

Define histone acetylation

Answer 34

Associated with active cromatin

Question 35

Provide evidence that transcription factor/DNA interactions are dynamic

Answer 35

- GFP tagged Glucorticoid Receptoer (GR) and mCherry tagges Estrogen Recepter (ER) are two receptors which recognize the same DNA motif. - The receptors only transiently occupied DNA - When both were activated and present, both receptors were able to bind to the same motif. - One receptor did not block for the other to bind, showing that the process is dynamic.

Question 36

Provide evidence that transcription factor/DNA interactions are dynamic

Answer 36

- GFP tagged Glucorticoid Receptoer (GR) and mCherry tagges Estrogen Recepter (ER) are two receptors which recognize the same DNA motif. - The receptors only transiently occupied DNA - When both were activated and present, both receptors were able to bind to the same motif. - One receptor did not block for the other to bind, (they seemed to enhance each other) showing that the process is dynamic. Shows TFs are not competitive

Question 37

14) How do inactive and active chromatin regions differ in condensation and localization within in the nucleus?

Answer 37

Active - less condensed (euchromatin), histone marks indicating active chromatin (acetylation), chromatin is further away from nuclear envelope compared to inactive chromatin. Inactive - condensed (heterchromatin), histone modifications indicative of inactive chromatin (methylation), chromatin is closer to nuclear envelope compared to active chromatin.

Question 38

14) How do inactive and active chromatin regions differ in condensation and localization within in the nucleus?

Answer 38

Active - less condensed (euchromatin), histone marks indicating active chromatin (acetylation), chromatin is further away from nuclear envelope compared to inactive chromatin. Inactive - condensed (heterchromatin), histone modifications indicative of inactive chromatin (methylation), chromatin is closer to nuclear envelope compared to active chromatin.

Question 39

How is cellular identity pass on from parent cell to daughter cell?

Answer 39

Chromatin structures can be epigenetically inherited in the daughter cells by different mechanisms Histone marks are maintained by reuse of histones after the replication fork by spreading of existing marks. Histones already have modifications specific from the parent cell, and these histones are inherited by the daughter cells to form new chromatin structures. All the existing proteins from the cytoplasm and nucleus is divided into two, wherein TF’s specific to the cell identity are already present, and will therefore influence the chromatin structure in the daughter cell. Methylation of the DNA is catalyzed post cell division by DNA maintenance methylases.