Chapter 10
What anchor the bases of loops?
-DNA binding proteins
How does it do this?
-DNA binds to A subunits (lower jaws) -DNA wraps around the A subunits in a right-handed direction -B subunits clamp onto DNA -DNA held in lower jaws is cut -DNA held in upper jaws is released and passes downward through the opening in the cut DNA (uses 2 ATP molecules) -cut DNA is ligated back together and the DNA is released from the gyrase
Describe how renaturation experiments are undertaken
-DNA is broken up into pieces containing several hundred base pairs -DNA is then denatured into single-stranded pieces by heat treatment -when the temperature is lowered, the pieces of DNA that are complementary can re-associate, or renature, with each other to form double-stranded molecules
What other histone is found in most eukaryotic cells? What is its role?
-H1, aka the "linker histone" -binds to DNA in the linker region between nucleosomes and may help to compact adjacent nucleosomes
How many nucleoids does a cell have?
-a cell may have have one or several nucleoids
What do they contain?
-a combination of viral and host cell molecules
What is a genome?
-a complete set of genetic material in a particular compartment -genome may be present in multiple copies within a compartment, and within a cell
What are nucleosomes?
-a double-stranded segment of DNA wrapped around an octamer of histone proteins -the repeating structural unit within eukaryotic chromatin
How long is a typical bacterial chromosome?
-a few million base pairs (bp) in length
What does each of the histone proteins consist of?
-a globular domain and a flexible, charge amino terminus -contain a large number of lysine and arginine amino acids
What is a kinetochore?
-a group of cellular proteins that linke the centromere to the spindle apparatus during mitosis and meiosis, ensuring the proper segregation of chromosomes to each daughter cell
What genomes do mammals have?
-a nuclear genome and a mitochondrial genome
What is cohesin?
-a protein complex that facilitates the alignment of sister chromatids -found along the entire length of the chromatid after S phase until the middle of prophase
What does the rate of renaturation of complementary DNA strands provide?
-a way to distinguish between unique, moderately repetitive, and highly repetitive sequences -renaturation rate depends on the concentration of its complementary partner
What are four possible types of DNA supercoiling?
-a. a left handed twist (underwinding) that produces fewer turns -b. a left handed twist (underwinding) that produces a negative supercoil -c. a right handed twist (overwinding) that produces more turns -d. a right handed twist (overwinding) that produces a positive supercoil
How does cohesin work? (describe the mechanics)
-after S phase is completed, many cohesin complexes bind along each chromatid, thereby facilitating their attachment to each other -during the middle of prophase, cohesin is released from the chromosome arms, but some cohesin remains in the centromeric regions -at anaphase, the remaining cohesin complexes are rapidly degraded by separase, which promotes sister chromatid separation
What are the key features of eukaryotic chromosomes?
-are usuallly linear -is tens of millions to hundreds of millions of base pairs in length -occur in sets; many species are diploid and therefore contain 2 sets of chromosomes -genes are interspersed throughout the chromosome -each chromosome contains many origins of replication -each chromosome contains a centromere that forms a recognition site for kinetochore proteins -telomeres contain specialized sequences located at both ends of the linear chromosome -repetitive sequences are commonly found near centromeric and telomeric regions
How many chromosomes do bacterial cells usually contain? How many copies are found?
-bacterial cells usually contain a single type of chromosome -the chromosome be present in multiple copies -bacteria may have one to four identical chromosomes per cell -the number of copies varies depending upon the bacterial species
How much does the loop structure compact the circular chromosome by?
-by about 10-fold
What are capsids built from?
-capsids are build from protein subunits called capsomeres
What are chromosomes?
-cellular structures that contain genetic material -are associated with proteins
What is the structure of DNA gyrase?
-contains four subunits (two A and two B)
What are viral envelopes derived from?
-derived from the host cell's membrane
What does each octamer of histone proteins contain?
-eight histone subunits -two copies of each of the four histone proteins: H2A, H2B, H3, and H4 (also known as the core histones)
What does strand separation enhance?
-enhances genetic activities such as replication and transcription that require DNA strands to be separated
In addition to chromosomes, what might bacterial cells also have?
-extrachromosomal DNA, or plasmids
How is a viral membrane obtained?
-from the host cell when the virus buds through the plasma membrane
What do chromosomes carry?
-genes necessary for the survival of the organism
How do viral envelopes help viruses?
-help them to infect hosts
What is it responsible for?
-introducing negative supercoils (or relaxing positive supercoils) using the energy of ATP
How is chromosomal DNA in living bacteria supercoiled?
-it is negatively supercoiled -one negative supercoil occurs per 40 turns of the double helix
Describe the denaturation rate of a genome that is not very complex
-it will be fast because it contains a good deal of highly repetitive DNA
Describe the denaturation rate of a genome that is very complex-
-it will be slow because it contains a good deal of unique DNA
What are the two levels of bacterial DNA compaction?
-loop domains -supercoiling
How many origins of replication do mammals usually have?
-many -approximately 200
Descrive the basic features of viral genomes
-may consist of DNA or RNA; consequently known as DNA viruses or RNA viruses -may be single-stranded or double-stranded -vary in size from several thousand to more than a hundred thousand nucleotides in length
What is a viral envelope?
-membranous envelopes that surround the capsides of some viruses
In what shape is bacterial DNA typically found?
-most, but not all, bacterial species contain circular chromosomal DNA
Which of these are topoisomers of each other?
-only b and d are topoisomers -the DNA conformations a and d are unstable comformations and do not occur in living cells
How many origins of replication do bacteria use?
-only one
What is their role?
-play a role in the proper segregation of chromosomes during mitosis and meiosis
What are the functions of telomeres?
-prevent chromosomal rearrangements such as translocations -prevent chromosome shortening by protecting chromosomes from digestion by exonucleases as well as coordinate a special form of telomeric DNA replication
What are histone proteins?
-proteins involved in forming the nucleosome structure of eukaryotic chromatin
What are centromeres?
-segment of eukaryotic chromosomal DNA that provides at attachment site for the kinetochore -most eukaryotes contain a single centromere
What are loop domains?
-segments of chromosomal DNA folded into a structure that resembles a loop
What is an origin of replication?
-sequence that is a few hundred nucleotides in length -functions as an initiation site for the assembly of several proteins required for DNA replication
What are viruses?
-small infectious particles that contain nucleic acid as their genetic material -are surrounded by a protein coat and in some cases a membranous envelope -depend upon living host cells in order to reproduce
What are telomeres?
-specialized regions at the end of linear chromosomes
What does the majority of bacterial DNA consist of?
-structural genes that encode proteins -short intergenic regions
What is chromatin?
-the DNA-protein complex that is found within eukaryotic chromosomes -can change its shape and composition during the life of a cell
Where in the cell is the nucleoid found?
-the bacterial nucleoid is not a separate cellular compartment -the bacterial nucleoid is in direct contact with the cytoplasm of the cell
What is a nucleus?
-the cellular compartment within eukaryotic cells where chromosomes are located
What is DNA supercoiling?
-the formation of additional coils in DNA due to twisting forces
What is a viral genome?
-the genetic material that a virus contains -also known as "viral chromosome"
How many loops are typically present within a bacterial chromosome?
-the number of loops varies according to the size of the bacterial chromosome and the species
What is a capsid?
-the protein shell that encloses a viral genome
In order to serve this function, what four important processes must chromosomes facilitate?
-the synthesis of RNA and cellular proteins -the replication of chromosomes -the proper segregation of chromosomes -the compaction of chromosomes so that they can fit within the living cell
What is the role of the nucleosome?
-to aid DNA compaction
What is the primary function of chromosomes?
-to store and pass on the information necessary to produce the characteristics of an organism
How many copies of the nuclear genome do human somatic cells have?
-two copies
What is the net result of this action?
-two negative supercoils have been introduced into the DNA molecule
What genomes do plants have?
-typically, a nuclear, mitochondrial, and a chloroplast genome
How does bacterial DNA become supercoiled?
-using the enzyme DNA gyrase (bacteria)/topoisomerase II (eukaryotes)
Where are chromosomes found within bacteria?
-within a region of the cell known as the nucleoid
Describe the six layers of DNA compaction
1. Naked DNA helix - 2 nm 2. Nucleosomes ("beads on a string") - 11 nm 3. 30 nm fiber - 30 nm 4. Radial loop domains - 300 nm 5. Further compaction of radial loops - 700 nm 6. Metaphase chromosome - 1400 nm
What important consequences does negative supercoiling have?
1. makes DNA much more compact, helping to decrease the size of the bacterial chromosome 2. affects DNA function by creating tension on the DNA strands that may be released by DNA strand separation
