Chapter 10 Molecular Structure of Chromosomes and Transposable Elements

10.1, 10.2, 10.3, 10.4

Chromosomes

The structures within living cells that contain the genetic material.

Genome

The entire complement of genetic material in an organism or species.

For prokaryotes, the genome is typically…

a single circular chromosome.

For eukaryotes, genetic material is found…

in different cellular compartments.

Chromosomal sequences facilitate four important processes to fulfill their role at the molecular level:

synthesis of RNA and cellular proteins, the replication of chromosomes, the proper segregation of chromosomes, and the compaction of chromosomes so that they fit within living cells.

Transposable element (TE)

a short segment of DNA that can be inserted in multiple locations within chromosomal DNA.

In most species, the chromosomal DNA…

is a circular molecule, though some species have linear chromosomes.

Most prokaryotic species contain…

a single type of chromosome, but it may present in multiple copies.

A typical chromosome is…

a few million base pairs in length. Protein-coding genes account for the majority of the chromosomal DNA.

Several thousand different genes are interspersed throughout the chromosome. The majority of the chromosomal DNA are…

protein-coding genes

Protein-coding genes

genes that carry the information to produce mRNA and that code the amino acid sequence of polypeptides.

Several thousand different genes are interspersed throughout the chromosome. The short regions between adjacent genes are called…

intergenic regions.

Intergenic regions

in a chromosome, a nontranscribed region of DNA that lies between two adjacent genes.

bacterial chromosomes usually have…

one origin of replication

At least one of replication is required to…

to initiate DNA replication.

These sequences are found in multiple copies and are usually interspersed within the intergenic regions throughout the chromosome.

repetitive sequences

repetitive sequences

short DNA sequences that occur many times within a species’ genome. Some of these sequences are transposable elements that can move throughout the genome.

the Role of repetitive sequences in a variety of genetic processes:

DNA folding, gene regulation, and genetic recombination.

nucleoid

a darkly staining region that contains the genetic material of mitochondria, chloroplasts, or bacteria.

To fit within the bacterial cell, the chromosomal DNA…

…must be compacted about a 1000-fold. The mechanism is not entirely understood, and it may vary among different bacterial species. It is generally thought to involve the formation of loop domains called microdomains.

microdomains

a loop of DNA that is found in a bacterial chromosome and is typically 10 kbp in length.

the number of loops varies according to…

…the size of the bacterial chromosome and the species.

the lengths and boundaries of these microdomains are thought to be dynamic, changing…

…in response to environmental conditions.

To form micro and macro (which is not discussed in slides) domains, bacteria use a set of DNA-binding proteins called [blank] that facilitate chromosome compaction and organization.

nucleoid-associated proteins (NAPS)

nucleoid-associated proteins (NAPS)

a set of DNA-binding proteins found in bacteria that facilitate chromosome compaction and organization.

Because the two strands within DNA already coil around each other, the formation of additional coils due to twisting forces is referred to as [blank]

DNA supercoiling

DNA supercoiling can be either [blank] (overwinding) or [blank] (underwinding)

positive or negative

the different conformations of DNA are called [blank]

topoisomers

the chromosomal DNA in bacteria is [blank] supercoiled

negatively supercoiled

Benefits of negative supercoiled DNA:

promotes DNA strand separation in smaller regions and enhances replication and transcription which require DNA strand separation.

the control of supercoiling in bacteria is accomplished by two main enzymes. The competing action of these two enzymes governs the overall supercoiling of bacterial DNA…

DNA gyrase (also termed DNA topoisomerase ll) and DNA topoisomerase l

DNA gyrase (or DNA topoisomerase ll) roles:

introduces negative supercoils using energy from ATP, relaxed positive supercoils when they occur, can untangle intertwined DNA molecules

DNA topoisomerase l roles:

relaxes negative supercoils

the ability of gyrase to introduce negative supercoils into DNA is…

…crucial for bacteria to survive.

blocking the function of gyrase is a way to…

…cure or alleviate bacterial diseases.

two main classes of drugs inhibit gyrase and other bacterial topoisomerases, thereby blocking bacterial cell growth:

quinolones and coumarins

quinolones and coumarins do not inhibit…

…eukaryotic topoisomerases, which are structurally different from their bacterial counterparts.

properties of eukaryotic chromosomes:

usually linear, 1 or more sets composed of several different chromosomes, tens of millions to hundreds of millions of base pairs in length, hundreds to several thousand different genes per chromosome.

properties of eukaryotic chromosomes cont:

genes of higher eukaryotes have non-coding intervening sequences called introns, multiple origins of replication per chromosome, a single centromere, specialized regions at each end called telomeres that play a role in DNA replication and chromosomal stability.

introns (or intervening sequence)

a segment of RNA that is removed during RNA splicing.

centromeres

a segment of a eukaryotic chromosome that provides an attachment site for the kinetochore.

kinetochore

a protein complex bound to a centromere of a chromosome during meiosis and mitosis.

telomeres

specialized repeated sequences of DNA found at the ends of eukaryotic chromosomes. they prevent chromosomal rearrangements such as translocations and they prevent chromosome shortening.

different eukaryotic species vary dramatically in…

…the size of their genomes.

sequence complexity

refers to the number of times a particular base sequence appears throughout the genome of a species.

the three main types of repetitive sequences

unique or non-repetitive, moderately repetitive, and highly repetitive.

unique or non-repetitive sequences

sequences found once or a few times in the genome. Protein-coding genes are typically unique sequences of DNA. In humans make up roughly 41% of the genome (protein-coding regions: 2%, introns: 24%, and unique regions that are not found within genes: 15%).

moderately repetitive sequences

base sequences that are found a few hundred to several thousand times in a genome.

Transposition

Involves the integration of small segments of the DNA into a new location in the genome. This can occur at many different locations within the genome.

These small, mobile DNA segments are termed

Transposable elements (TEs)