Lecture 8 Flashcards
chromosomes condense for cell division to –
prevent breaking themselves
cell nucleus provides separate environments for
gene transcription and regulation
heterochromatin contains specially condensed region of DNA =
gene silencing
each chromosomes in a eukaryotic cell consists of a single, enormously long linear – along with proteins that fold and pack it
DNA molecule
T/F: in addition to packaging proteins, chromosomes are also associated with many other proteins and RNA molecules
true
the complex of DNA and tightly bound protein is called
chromatin
except for – and a few highly specialized cell types that cannot multiply and either lack DNA altogether (RBC) or have replicated with DNA w/o completing cell division (megakaryocytes) each human cell nucleus contains two copies of each chromosome, one inherited from mom and one from dad
gametes
maternal and paternal chromosomes of a pair are called
homologous chromosomes
the only non homologous chromosome pairs are the
sex chromosomes
Each human cell contains – chromosomes
46 (22 common + sex chromosome)
labeled DNA can only form base pairs or – to the chromosomes from which it was derived
hybridize
karyotypes help determine
abnormalities and translocations
karyotype
display of all chromosomes at mitosis
A short strand of nucleic acid tagged with fluorescent dye serves as a – that picks out its complementary DNA sequences, lighting up the target chromosomes at any site where it bind
probe
chromosome painting is most frequently done at – when chromosomes are especially compacted and easy to visualize
mitosis
stain chromosome with dyes that reveal a striking and reproducible pattern of bands along each –
mitotic chromosome
banding patterns of mitotic chromosomes presumably reflect – in chromatin structure
variations
human genome have a lot of – between genes that you can play with later
DNA interspersed
majority of human genes consist of a long string of alternating exons and introns with most of the gene consisting of –
introns
the majority of genes from an organism with concise genomes
lack introns
regulatory DNA is also much more – in organisms with concise genomes
compressed
regulatory DNA are – to exons and introns
upstream
exon carry info for protein, – of human genome
1.5%
– are spliced out before making proteins
introns
most pseudogenes arise from
duplication fo a functional gene followed by mutations
nucleotide pairs in human genome
3.2 billion
number of genes coding for proteins in human genome
21,000
number of no coding RNA genes in human genome
9000
percentage of DNA in other highly conserved sequences in human genome
3.5%
number of pseudogenes in human genome
20,000+
– provides a temporal separation between the duplication of chromosomes and their segregation into two daughter cells
cell cycle
each chromosome is composed of – after gene duplication
two sister chromatids
during the long – of the cell cycle, genes are expressed
interphase
In M phase, the – attaches the duplicated chromosomes to the mitotic spindle (microtubules) so that a copy of the entire genome is distributed to each daughter cell during mitosis
centromere
– attaches the centromere to the spindle
kinetochore
– form special caps at each chromosome end
telomere
chromosome’s basic functions are controlled by three types of specialized – each of which binds specific proteins that guide the machinery that replicates and segregates chromosomes
nucleotide sequences in the DNA
one type of nucleotide sequence acts as a – the location at which duplication of the DNA begins
DNA replication origin
although not as condensed as mitotic chromosomes, the DNA or human interphase chromosomes is still
tightly packed
chromosome structure is – (packaging of chromosomes is accomplished in a way that allows rapid, localized, on-demand access to DNA)
dynamic
chromatin =
1/3 DNA + 1/3 histone + 1/3 non-histone proteins
basic unit of eukaryotic chromosome structure
nucleosome
nucleosome core particle =
147 nucleotide pairs wrapped 1.7 times around the histone core
– digests linker DNA of the beads-on-a-string form of chromatin
nuclease
after dissociation with high concentration of salt the released nucelosome core particle –>
octameric histone core + 147 nucleotide pair DNA double helix
each of the core histones contain an – which is subject to several forms of covalent modification and a –
N-terminus tail and histone fold region
the histone fold contains
3 alpha helices
N-terminus of core histones is important for modification which helps –
gene expression
polypeptides of histones form a dimer through –
handshake interaction
All eight N-terminal tails of the histones protrude from the –
disc shaped core structure
the conformations of the histone N-terminus tails are – and serve as binding sites for other sets of proteins
highly flexible
histone compact and protect DNA which helps in
gene regulation
142 hydrogen bonds are formed between – and – in each nucleosome
DNA and the histone core
interface between DNA backbone and histone core also have
salt linkages and hydrophobic interactions
more than 1/5 of the amino acids in each of the core histones are either
Lys or Arg
interface between DNA backbone and histone core in a nucleosome have nonspecific binding every – nucleotides
200
preferred on minor groove outside
G-C
preferred on minor groove inside
A-T
T/F: several kinks are seen in the path of DNA around the histone due to the nonuniform surface of the core
true
T/F: as a reflection of their fundamental role in DNA function through controlling chromatin structure, the histones are among the most highly conserved eukaryotic proteins
true
The – is compressed on the inside of the turn as DNA makes 1.7 turns around the histone core
minor groove
nucleosome sliding is catalyzed by
ATP-dependent chromatin remodeling complexes
Using the energy of ATP hydrolysis, the chromatin remodeling complex is though to – the DNA of its bound nucleosome core
push on
ATP dependent chromatin remodeling complexes can also remove – and exchange –
remove entire nucleosome core and exchange histone dimers
a zig-zag model for the 30 nm –
chromatin fiber
single histone H1 changes the path of the DNA as it exits from the nucleosome which is thought to help –
compact nucleosomal DNA
H1 core region constrains an additional – of DNA where it exits from the nucleosome core and is important for compacting chromatin
20 nucleotide pairs
histone H1 is present in a – ration with nucleosome cores
1-to-1
two types of chromatin in the interphase nuclei of many eukaryotic cells
heterochromatin and euchromatin
descriptor for compact chromatin domains that share the common feature of being unusually resistant to gene expression
heterochromatin
when euchromatin are converted to heterochromatic state, their genes are generally – as a result
switched off
through chromosome breakage and rejoining, a piece of chromosome that is normally euchromatic can be – into the neighboring heterochromatin
translocated
to express a gene you need a – upstream
promoter
white gene in fruit fly controls – and is named after the mutation
eye pigment production
wild-type flies with normal white gene have – eyes
red eyes
in flies with a normal white gene has been moved near a region of heterochromatin, the eyes are – with both red and white patches
mottled
early in development, when the heterochromatin is first formed, it spreads into neighboring euchromatin to – in different embryonic cells
different extents
in each cell, once the heterochromatic condition is established on a piece of chromatin, it tends to be – by all of that cell’s progeny
stably inherited
heterochromatin is normally prevented from spreading into adjacent regions of euchromatin by
barrier DNA sequences
histone tails can be modified and regulate – associated with them
gene expression
histone tails are thought to be involved in interactions between nucleosomes that help to –
pack them together
methylated histone –>
change binding site for other proteins
methylation of histones can be
silencing or activating
acetylated histone =
turn on gene
acetylation
lysine
methylation
lysine and arginine
phosphorylation
serine
lysine can be methylated or acetylated but
not both at the same time
three different levels of – can be recognized by different binding proteins and thus have different significance for the cell
lysine methylation
acetylation removes – on lysine
plus charge
serine phosphorylation – to a histone
adds a negative charge
the H3 tail can be marked by different sets of modification that act in – to convey a specific meaning
combination
reading a histone mark generally involves the – at other sites on the nucleosome along with the indicated H3 tail recognition
joint recognition marks
covalent modifications and – act in concert to control chromatin function
histone variants
histone variants are inserted into nucleosome at specific sites on chromosomes by – that act in concert with histone chaperone
chromatin remodeling complex
reader complex =
protein modules that bind to specific histone modifications on nucleosome + scaffold protein
covalent modification on histone tail
mark
only a specific combination of marks will cause the – to bind to chromatin and attract the additional protein complexes needed to catalyze a biological function
reader complex
T/F: only need one regulatory protein to bind to reader writer complex for the whole thing to open up
true
a complex of – proteins spread specific chromatin modifications along a chromosome
reader and writer
enzyme that creates a specific modification on one or more of the four nucleosomal histones
writer
After its recruitment to a specific site on a chromosome by – the writer collaborates with a reader protein to spread its mark from nucleosome to nucleosome by means of the indicated reader-writer complex
transcription regulatory protein
the reader must recognize the – that the writer produces
same histone modification mark
the binding of the reader – the writer
activates
reader-writer complex also works with – which reposition the modified nucleosome
ATP-dependent chromatin remodeling complex
– block the spread of reader-writer complexes and separate neighboring chromatin domains
barrier DNA sequences
T/F: combinations of barrier action may function at any one site
true
the – of a region of chromatin to a large fixes site, such as the nuclear pore, can form a barrier that stops the spread of heterochromatin
tethering
the – of barrier proteins to a group of nucleosomes can make this chromatin resistant to heterochromatin spreading
tight binding
by recruiting a group of highly active – barriers can erase the histone marks that are required for heterochromatin to spread
histone-modifying enzymes
chromatin structures can be – following DNA replication
inherited
after chromosome duplication some of the specialized chromatin components like new heterochromatin proteins are added to regions with –
modified histones
activating chromatin structures can be inherited –
epigenetically
T/F: all 30,000 genes in genome are turned on in every cell
false
nucleus from the region where the MyoD gene is normally turned on is inserted into an enucleated egg –> progeny cell nuclei abnormally express the MyoD protein in – of the “nuclear transplant embryo” that forms
non-muscle regions
abnormal expression of MyoD protein can be attributed to the maintenance of the MyoD promoter region in its – through many cycles of cell division that produce the blastula stage embryo
active chromatin state
inherited chromatin state underlies the – observed
epigenetic memory
