Chapter 12 DNA organization in chromosomes

• a single nucleic acid molecule
• largely devoid of associated proteins
• much smaller than eukaryotic chromosomes
• single or double-stranded DNA or RNA
• viral can be circular or linear molecules
• material is inert until released into host cell

• bacterial chromosomes are circular, double stranded DNA compacted into nucleoid region
• bacterial chromosomes can be readily replicated and transcribed

DNA in bacteria may be associated with these proteins

• compacts DNA
• most circular DNA molecules in bacteria are slightly underwound and supercoiled

• cut one or both DNA strands and wind or unwind the helix before resealing the ends
• found in eukaryotes along with supercoiled DNA

DNA replication and transcription

• very large eukaryotic chromosomes that can be visualized by light microscopy
• these chromosomes are unusual and not usually found in eukaryotic cells

• found in various tissues in the larvae of some flies and several species of protozoans and plants
• have distinctive banding patterns
• represent paired homologs
• composed of large numbers of identical DNA strands

distinctive banding patterns

the DNA of the paired homologs of polytene chromosomes undergoes many rounds of replication without strand separation or cytoplasmic dividsion

occurs in polytene chromosomes where the DNA has uncoiled that are visible manifestations of a high level of gene activity (transcription that produces RNA)

• chromosomes are large and have extensive DNA looping
• found in most vertebrate oocytes as well as spermatocytes of some insects
• found in the diplotene stage of prophase I of meiosis
• lampbrush loops are similar to puffs in polytene chromosomes and are sites of geen activity

• eukaryotic chromosomes complexed into a nucleoprotein structure
• during interphase, chromatin is dispersed throughout nucleus
• during cell division, chromatin condenses and becomes visible as chromosomes
• bound up in nucleosomes with a positive charged proteins called histones or nonhistones

positive charged proteins

H1,H2A,H2B,H3, and H4

• electronic microscopic observations of chromatin have revealed its fibers are composed of a linear array of spherical particles (nucleosomes)
• concensed several times to form the intact chromatids

relax its compact structure and expose regions of DNA to regulatory proteins

• unstructured tails that are not packed into the folded histone domains with the nucleosome but protrude from them
• provide potential targets along the chromatin fiber for chemical modifications that may include acetylation, methylation, phosphorylation

uncoiled and active

• condensed areas and are inactive because they either lack genes or contain genes that are repressed
• telomere maintains chromosome integrity
• centromere is involved in chromosome movement

only the centromeres (heterochromatin are stained)

due to differential staining along the length of each chromosome

• heterogeneity and complexity of the chromosome
• unique banding pattern allows the distinction of identical-sized chromosomes and centromere placement
• precision allows homologs to be distinguished from one another, including translocated segments

• sequences are repeated many times within eukaryotic chromosomes
• there are a number of categories of repetitive DNA

• highly repetitive and consists of short repeated sequences
• found in the heterochromatic regions of chromosomes
• not found in prokaryotes

• primary constrictions along eukaryotic chromosomes
• mediate chromosomal migration during mitosis and meiosis

region that bind to the spindle fibers during cell division

sequences consist of short tandem repeats that contribute to the stability and integrity of the chromosome

• variable number tandem repeats (VNTRs)
• minisatellites
• Microsatellites (short tandem repeats, STRs)

dispersed throughout the genome rather than tandemly repeated and constitute over 1/3 of the human genome

transposable elements are generated via an RNA intermediate

• large number of single-copy noncoding regions
• these are DNA sequences that have undergone significant mutational alterations (inserations and deletions) and are not transcribed