BIOL 300 - Chapter 7

what is the issue with packaging DNA into phages/bacterial cells/nuclei?

DNA length exceeds dimensions of the compartment its meant to be stored in, so it needs to be greatly compressed

what is the order of compaction for DNA?

double helix > nucleosome (w 8 histone proteins) > chromatosome (nucleosome plus H1 histone) > 30nm fiber > 250nm fiber > chromatid

why is DNA packaging necessary?

way to organize and control DNA that is highly regulated and repeatable. DNA is also unaccessible when compacted so its protected, and its easier to divide during mitosis

what are the two restrictions for virus DNA packaging?

packaging is predetermined by genome size, and it must all fit within protein coat assembled by proteins

what is the first strategy for virus genome packaging?

genome packaging is coupled with protein shell assembly - shell is assembled around nucleic acid, condensing the DNA/RNA with protein-nucleic acid interactions

what is the second strategy for genome packaging?

genome is inserted and condensed after an empty protein shell is constructed - shell is made, and genome is inserted afterwards, being condensed as it enters

what is the nucleation center?

site that initiates growth of new microtubules needed for cell shape, transport, and division

what are NAPs?

nucleoid-associated proteins.- proteins that help stabilize supercoiling in viruses and organizes nucleoid

how do NAPs affect spatial arrangement of DNA?

are able to bend, wrap, or bridge DNA to compact it

how many supercoiled domains does protein binding isolate DNA into?

~400

how compact is the mitotic chromosome?

most condensed form - responsible for the iconic X shape

how compact is the interphase chromosome?

less condensed than the mitotic chromosome

what is the H-NS protein?

histone like nucleoid-structuring protein - manages genome evolution, DNA condensation, and transcription. has preference for AT rich DNA and helps NAP influence gene promoter activity and nucleoid structure

what is the HU protein?

helps organize and compact bacterial DNA - binds DNA and has a high affinity for distorted DNA regions

what is the ploidy of cells in metaphase?

tetraploid - 4 chromosome copies

what are mitotic chromosomes made up of?

2 centromeres (attach to spindle via kinetochore, and connect chromosomes), 4 telomeres (prevents chromosome fusion), 4 arms

how is chromosome packaging reproducible?

order of genes on mitotic chromosomes are in the same order as on relaxed, linear DNA

what is the chromosome scaffold?

facilitates condensation of chromatin into visible chromosomes at metaphase, and acts as skeleton for DNA folds to be put on

what is involved in Giemsa staining?

proteolytic digestion and giemsa dye (binds to AT seq)

what are G-bands?

darker bands on chromosomes with Giemsa staining - it’s where genes are NOT, just represents higher density of AT seq

what are Interbands?

lighter bands on chromosomes with Giemsa staining - its where genes ARE

what is the significance of Giemsa staining?

acts as a low resolution map that can identify each chromosome (and defects like trisomy), and can identify chromosome abnormality

what is the purpose of low resolution chromosome maps?

can identify a gene’s cytogenic location using a numbering system based on banding pattern

how do chromosomes look inside interphase chromatin?

different chromosomes can’t be distinguished, since they’re loosely packed and not all are packed the same way

what is euchromatin?

less densely packed form of DNA packaging (represented by lighter staining) - dispersed across nucleoplasm, most transcriptionally active

what is heterochromatin?

more condensed form of DNA, similar to mitotic chromosome (represented by darker staining) - doesnt change much through cell cycle and is located at nuclear periphery and surrounding nucleolus, least transcriptionally active

how are chromatin states dynamic?

euchromatin can be condensed and decondensed as needed throughout the cell cycle - some chromatin can transition between euchromatin and heterochromatin to control gene transcription

what are the two types of heterochromatin in interphase?

constitutive and facultative

what is constitutive heterochromatin?

heterochromatin that’s compaction state never changes regardless of surroundings; contains very little genes (such as centromere, telomere, and repetitive/noncoding seq)

what is facultative heterochromatin?

heterochromatin that has the ability to convert to euchromatin - has silenced genes or genes that are differentially expressed, and is molecularly distinct

how do interphase chromatin territories work?

3D space is occupied by individual chromosomes and aren’t tangled, but also has an area of interaction for active genes from several chromosomes to cluster

what is a polytene chromosome?

amplified form of interphase chromosomes in insects that arise through many rounds of DNA replication without separation of daughter chromatids

what is endoreduplication?

biological process where a cell replicates its DNA multiple times without undergoing mitosis or cell division, resulting in a polyploid cell with multiple copies of its genome within a single nucleus

what are puffs in polytene chromosomes?

transcriptionally active sites that are inducible

what makes up centromeric chromatin?

DNA, centromeric histone variant, kinetochore

what does the DNA in centromeric chromatin consist of?

satellite repeat DNA sequences (function unclear but doesnt seem to determine centromere formation)

what does the histone variant in centromeric chromatin consist of?

H3(CENH3), which is the determinant of establishing a functional centromere

what is a kinetochore?

protein complex that allows for attachment of centromere to spindle

what is an acentric fragment as a centromere defect?

fragment of chromosome that lacks a centromere and is lost at cell division

what happens if a chromosome has two centromeres?

translocation and joining can occur

what is a telomere?

region at the end of chromosomes that are vulnerable to exonucleases that are protected by DNA sequences meant to be destroyed

what are the two problems that occur at the end of DNA ends?

sticky ends and end replication issues

what are sticky ends?

DNA ends that are recognized as a double strand break, which triggers end joining DNA repair and prevents telomeres from being placed down (makes DNA less stable)

what are the end replication issues related with DNA ends?

DNA polymerase can’t reach the 5’ end when synthesizing DNA, so DNA is shortened every time replication occurs which therefore shortens telomeres until none are left

what is cell “immortality” (in theory)?

when cell telomeres are always kept the length they were when the cell was created, so it can divide an infinite amount of times

in what is telomerase highly expressed?

germ cells, stem cells, and cancer cells (why they multiply so fast and consistently)

what is the telomere sequence?

minisatellite and microsatellite sequences repeated (these are tandem repeats)