Week 1 (Chromosones & Genomes)

Question 1

Define pseudogene

Answer 1

A gene with a DNA sequence closely resembling that of a functional gene but containing many mutations that prevents its proper expression or function

Question 2

What are exons? What are introns?

Answer 2

the coding sequences in genes noncoding sequences in genes

Question 3

What are the highly condensed chromosomes in a dividing cell are known as?

Answer 3

mitotic chromosomes

Question 4

What is the cell cycle?

Answer 4

provides for a temporal separation between the duplication of chromosomes and their segregation into two daughter cells

Question 5

What happens during interphase?

Answer 5

During interphase, the cell is actively expressing its genes and is therefore synthesizing proteins. Also, during interphase and before cell division, the DNA is replicated and each chromosome is duplicated to produce two closely paired sister DNA molecules (called sister chromatids)

Question 6

What happens during M phase of the cell cycle?

Answer 6

when mitosis occurs and the nucleus is divided into two daughter nuclei. During this stage, the chromosomes condense, the nuclear envelope breaks down, and the mitotic spindle forms from microtubules and other proteins. The condensed mitotic chromosomes are captured by the mitotic spindle, and one complete set of chromosomes is then pulled to each end of the cell by separating the members of each sister-chromatid pair. A nuclear envelope re-forms around each chromosome set, and in the final step of m phase, the cell divides to produce two daughter cells

Question 7

What is the function of centromeres?

Answer 7

allows one copy of each duplicated and condensed chromosome to be pulled into each daughter cell when a cell divides.

Question 8

What is a kinetochore?

Answer 8

A protein complex that forms at the centromere and attaches the duplicated chromosomes to the mitotic spindle, allowing them to be pulled apart

Question 9

What are telomeres?

Answer 9

The ends of chromosomes. They contain repeated nucleotide sequences that enable the ends of chromosomes to be efficiently replicated.

Question 10

What other function do telomeres perform?

Answer 10

the repeated telomere DNA sequences, together with the regions adjoining them, form structures that protect the end of the chromosome from being mistaken by the cell for a broken DNA molecule in need of repair

Question 11

Why do chromosomes decondense?

Answer 11

Gene expression DNA repair Replication

Question 12

What are the 2 types of proteins that bind to the DNA to form eukaryotic chromosomes?

Answer 12

1. Histones 2. Non-histone chromosomal protein

Question 13

What is chromatin?

Answer 13

Consists of DNA bound to both histone and non-histone proteins. It is the complex of both type of protein with the nuclear DNA of Eukaryotic cells

Question 14

What is the nucleosome?

Answer 14

A protein-DNA complex DNA wound around a histone core The formation of nucleosomes converts a DNA molecule into a chromatin

Question 15

What is responsible for the nucleosome?

Answer 15

Histones are responsible for the first and most basic level of chromosome packing, the nucleosome. Each individual nucleosome core particle consists of a complex of eight histone proteins

Question 16

What is the histone Octamer?

Answer 16

A complex of 8 histone proteins It forms a protein core around which the double-stranded DNA is wound

Question 17

What is linker DNA

Answer 17

separates each nucleosome core particle from the next

Question 18

What is a histone fold What is it formed by?

Answer 18

A structural motif Formed from three α helices connected by two loops

Question 19

How do histones bind together to create a compact octamer core?

Answer 19

the histone folds first bind to each other to form H3–H4 and H2A–H2B dimers, and the H3–H4 dimers combine to form tetramers. An H3–H4 tetramer then further combines with two H2A–H2B dimers to form the compact octamer core

Question 20

How many hydrogen bonds are formed between and the histone core in each nucleosome?

Answer 20

142

Question 21

What is a ‘handshake?’

Answer 21

Reactions by which histones form dimers

Question 22

What problems would be caused if nucleosomes remained fixed in place

Answer 22

1. This would pose problems for genetic readout mechanisms, which in principle require easy access to many specific DNA sequences

2. It would also hinder the rapid passage of the DNA transcription and replication machinery through chromatin

Question 23

What is nucelosome sliding?

Answer 23

This subunit binds both to the protein core of the nucleosome and to the double-stranded DNA that winds around it. By using the energy of ATP hydrolysis to move this DNA relative to the core, the protein complex changes the structure of a nucleosome temporarily, making the DNA less tightly bound to the histone core. Through repeated cycles of ATP hydrolysis that pull the nucleosome core along the DNA double helix, the remodeling complexes can catalyze nucleosome sliding. In this way, they can reposition nucleosomes to expose specific regions of DNA, thereby making them available to other proteins in the cell

Question 24

What are remodelling complexes able to do?

Answer 24

Remove either all or part of the nucleosome core from a nucleosome—catalyzing either an exchange of its H2A–H2B histones, or the complete removal of the octameric core from the DNA

Question 25

What are chromatin remodelling complexes?

Answer 25

Most are large protein complexes that can contain 10 or more subunits, some of which bind to specific modifications on histones.

They act locally to influence chromatin structure

Question 26

Why is the arrangement of nucleosomes said to be dynamic?

Answer 26

1. The exact positions of nucleosomes along a stretch of DNA depend mainly on the presence and nature of other proteins bound to the DNA.
2. Due to the presence of ATP-dependent chromatin remodeling complexes, the arrangement of nucleosomes on DNA can be highly dynamic, changing rapidly according to the needs of the cell.

Question 27

What is the most imporatant influence on nucleosome positioning?

Answer 27

1. The presence of other tightly bound proteins on the DNA.
2. Some bound proteins favor the formation of a nucleosome adjacent to them.
3. Others create obstacles that force the nucleosomes to move elsewhere.

Question 28

What is linker histone? (H1)

Answer 28

It is larger than the individual core histones and it has been considerably less well conserved during evolution. A single histone H1 molecule binds to each nucleosome, contacting both DNA and protein, and changing the path of the DNA as it exits from the nucleosome. This change in the exit path of DNA is thought to help compact nucleosomal DNA

Question 29

What causes nucleosomes to stack so tightly on each other?

Answer 29

1. Nucleosome-to- nucleosome linkages that involve histone tails, most notably the H4 tail, constitute one important factor
2. Additional histone that is often present in a 1-to-1 ratio with nucleosome cores, known as histone H1

Question 30

What are histone tails?

Answer 30

histone tails, one from each histone protein, that extend from each nucleosome

Question 31

What are the function of histone tails?

Answer 31

Thought to be involved in interactions between nucleosomes that help to pack them together

Question 32

What is the function of topoisomerase II

Answer 32

They are required for higher level chromatin condensation. It disentangles DNA from different chromosomes permitting ech chromosome to fold into a discrete compact structure