centromere
One copy of all the genetic information encoded in a cell or virus. In a eukaryote, this generally constitutes one copy of all the genetic information in the nucleus. Separate genomes are found in certain organelles, particularly mitochondria and chloropl
telomere
Specialized nucleic acid structure found at the ends of linear eukaryotic chromosomes.
plasmid
An extrachromosomal, independently replicating, small circular DNA molecule; commonly employed in genetic engineering.
DNA supercoiling
The coiling of DNA upon itself, generally as a result of bending, underwinding, or overwinding of the DNA helix.
relaxed DNA
Any DNA that exists in its most stable and unstrained structure, typically the B form under most cellular conditions.
closed-circular DNA
A continuous double-stranded DNA molecule with no free 3' or 5' ends.
topoisomer
molecule
Different forms of a covalently closed, circular DNA
type I or II topoisomerase
Enzymes that introduce positive or negative supercoils in closed, circular duplex DNA by cleaving one of the two DNA strands, passing the intact strand through the break, and ligating the broken ends.
chromatin
A filamentous complex of DNA, histones, and other proteins, constituting the eukaryotic chromosome.
histone
The family of basic proteins that associate tightly with DNA in the chromosomes of all eukaryotic cells.
nucleosome
In eukaryotes, the structural unit for packaging chromatin; consists of a DNA strand wound around a histone core.
core histones
The four histone proteins (H2A, H2B, H3, and H4) that form the octameric core of a nucleosome.
histone tail
The flexible, disordered N-terminal ends of the histone proteins that comprise the histone core. These ends protrude from the nucleosome and contact adjacent nucleosomes.
chromosomal scaffold
Proteinaceous residue after extraction of histones from chromosomes.
chromatin remodeling complex
A class of enzymes with ATPase activity that move, eject, or restructure histones.
ChIP-Seq
Chromatin immunoprecipitation followed by DNA sequencing.
epigenetic inheritance
Inherited characteristic acquired by means that do not involve the nucleotide sequence of the parental chromosomes; for example, covalent modifications of histones.
histone acetyltransferase (HAT)
Any of a family of enzymes that transfer an acetyl group from acetyl-CoA to the �-amino group of specific Lys residues on histone tails.
histone code
Hypothetical code in which successive covalent modifications of histone tails and DNA trigger chromatin remodeling and transcriptional activation events.
True
True or False. Specific proteins are used to condense bacterial DNA.
c. karyotype
A ___________ shows an individual cell's metaphase chromosomes arranged in pairs and sorted by size.
b. chromatin
Five major histone classes interact with DNA in eukaryotic ___________.
X-ray crystallography
_____________ is a technique that provides high-resolution images of nucleosome core particles.
structural maintenance of chromosomes proteins
What are SMC proteins?
fluorescent in situ hybridization
FISH stands for:
Five
________ major histone classes interact with DNA in eukaryotic chromatin.
zigzag
Nucleosomes fold into a three-dimensional structure in which the linker DNA has a _____________ pattern.
solenoid
A structure called a ________ becomes visible after histones are depleted by treating chromosomes with 2 M NaCl.
telomere
The ___________, which is present at either end of the chromosome, is needed for stability.
microtubule
The centromere is the site of ___________ attachment.
beads on a string
Term used to describe the structure of chromatin:
Down syndrome
Chromosomal defect in which individuals have three copies of chromosome 21:
negatively
DNA is ___________ charged.
They can modify the N-terminal tails of histones.
Which of the following is NOT a way chromatin remodeling complexes affect nucleosomes?
octameric
The core particle of nucleosomes consists of a(n)____________ protein complex.
False. In living cells, nucleosomes are packed upon one another to generate regular arrays in which the DNA is more highly condensed, usually in the form of a 30-nm fiber. The beads-on-a-string form of chromatin is usually observed only after the 30-nm fi
In the living cell, chromatin usually adopts the extended 'beads-on-a-string' form.
True. All the core histones are rich in lysine and arginine, which have basic - positively charged - side chains that can neutralize the negatively charged DNA backbone
The four core histones are relatively small proteins with a very high proportion of positively charged amino acids; the positive charge helps the his-tones bind tightly to DNA, regardless of its nucleotide sequence.
False. By using the energy of ATP hydrolysis, chromatin remodeling complexes can catalyze the movement of nucleosomes along DNA, or even between segments of DNA.
Nucleosomes bind DNA so tightly that they cannot move from the positions where they are first assembled.
The number of molecules of DNA in a human cell depends on the type of cell and its stage in the cell cycle. For the vast majority of somatic cells, there are 46 molecules of DNA (chromosomes) per cell prior to replication. After replication, but before co
Consider the following statement: A human cell contains 46 molecules of DNA in its nucleus. Do you agree with it? Why or why not?
By comparing the normal chromosomes 9 and 22 with their abnormal counterparts, it would appear that the bottom portion of chromosome 22 has been translocated to the bottom of chromosome 9. The presence of two X chromosomes indicates that this patient is f
An abnormal human karyotype is shown in Figure 8-1. This particular karyotype is found in the cancer cells of more than 90% of patients with chronic myelogenous leukemia. Arrows indicate two abnormal chromosomes. Describe the event that led to this abnorm
Replication origins are the specialized sequences that control the beginning of DNA replication, the process that allows chromosomes to be duplicated. Centromeres are the specialized sequences that permit one copy each of the duplicated chromosomes to be
List the three specialized DNA sequences and their functions that act to ensure that the number and morphology of chromosomes are constant from one generation of a cell to the next.
The essence of your proposed cure is that telomerase is essential for cancer cells and that its inhibition would ultimately stop their growth. The troubling aspect of the rival company's observations is that mice lacking telomerase still get cancers, indi
Early in development, most human cells turn off expression of an essential component of telomerase, the enzyme responsible for addition of telomere repeat sequences (5'-TTAGGG) to the ends of chromosomes. Thus, as our cells proliferate their telomeres get
In contrast to most proteins, which accumulate amino acid changes over evolutionary time, the functions of histone proteins must involve nearly all of their amino acids, so that a change in any position is deleterious to the cell. Histone proteins are exq
Histone proteins are among the most highly conserved proteins in eukaryotes. Histone H4 proteins from a pea and a cow, for example, differ in only 2 of 102 amino acids. However, comparison of the two gene sequences shows many more differences. These obser
The packing ratio within a nucleosome core is 4.5 [(146 bp X 0.34 nm/bp)/(11 nm) = 4.5]..
A single nucleosome is 11 nm long and contains 146 bp of DNA (0.34 nm/bp). What packing ratio (DNA length to nucleosome length) has been achieved by wrapping DNA around the histone octamer?
If there are an additional 54 bp of linker DNA, then the packing ratio for 'beads-on-a-string' DNA is 2.3 [(200 bp X 0.34 nm/bp)/(11 nm + {54 bp X 0.34 nm/bp}) = 2.3].
Assuming that there are an additional 54 bp of extended DNA in the linker between nucleosomes, how condensed is 'beads-on-a-string' DNA relative to fully extended DNA?
Adenylation
Which of the following is NOT typically a modification of histones?
There are 14 bands visible in the reproduction of the gel shown in Figure 8-2, suggesting that S. cerevisiae has 14 chromosomes. From other studies, it is known that two chromosomes of very nearly the same length are present in the third band from the top
Q8.28 One way to demonstrate that a chromosome contains a single DNA molecule is to use a technique called pulsed-field gel electrophoresis, which can separate DNA molecules up to 107 bp in length. Ordinary gel electrophoresis cannot separate such long mo
These results argue strongly that the SWI/SNF complex slides nucleosomes along the DNA in an ATP-dependent manner. Two key observations support this model. First, incubation with SWI/SNF causes the nucleosome to disappear from the small fragment released
Moving nucleosomes out of the way is important for turning genes on. In yeast the 11-subunit SWI/SNF complex, which is the founding member of the ATP-dependent chromatin remodeling complexes, is required for both activating and repressing gene transcripti
In trans.
A histone modification that attracts other proteins such as a transcription factor is said to be acting:
The enzymes responsible can create histone variants.
Which of the following is NOT true about histone modification and the enzymes that create
them?
ChIP-Seq
Which of the following methods can be used to determine the position of nucleosomes in the genome?
Immunoprecipitationofnucleosome-DNAcomplexeswithhistoneantibody.
which of the following is a step in a ChIP-Seq assay?
Have variant patterns of modifications as a result of the structural differences in their
terminal sequences.
Histone variants:
Maturation of RNA
Which of the following is NOT affected by the presence of epigenetic marks?
Gcn5 is a transcriptional activator that implies that the acetylase activity may account for the activator's regulatory function. Ultimately Gcn5 was shown to have histone acetylase (HAT) activity.
When the gene that encodes the histones acetylase (HAT) was isolated, it was shown to have homology to the yeast protein, Gcn5. Why was this an exciting find?