Week 3 Flashcards
1KB
1000 base pairs
cross-talk
over time, some genes from mitochondrial and chloroplast sequences have migrated to the nucleus
why do organisms across the tree of life have such noticeable differences in size?
as complexity increases, there seems to be a trend toward larger genomes
what is included in the DNA that we have?
- 50% of the genome is made up of repetitive DNA
- 50% is unique sequences
- less than 1% of your genome encodes proteins
label a diagram for the percentage of the human genome and their functions
describe the necessity of packaging of DNA in the cell in prokaryotes
- in a non-packaged state, even the small prokaryotic genome would occupy a considerable portion of the cell volume
- DNA is condensed through folding and twisting and is complexed with proteins
- this forms the prokaryotic nucleioid
the chromosome solution
method of getting eukaryotic genome packed into cell
fluorescence in situ hybridisation (FISH)
- heat up chromosomes
- DNA helix will loosen a bit
- mix in a probe (short sequence of DNA) that is complementary to some of the sequence on the chromosome
- fluorescent dye is stuck onto the probe
- some of the strands will find their complementary sequence and bind there
describe the constitution of a chromosome
- each chromosome contains a single, long, linear DNA molecule and associated proteins called chromatin
- chromatin is tightly packaged, but dynamic as the DNA must remain accessible for transcription, replication and repair
draw interphase chromatin
draw M phase chromatin
centromere and sequencing
difficult area to sequence as it is very compact
telomeres and sequencing
compact so hard to sequence
levels of organisation of chromatin
- short region of DNA double helix
- ‘beads on a ring’ form of chromatin (double wrapped around nucleosome with some linker DNA)
- chromatin fibre of packed nucleosomes (30nm fibre)
- chromatin fiber folded into loops
- entire mitotic chromosome
describe the types and arrangement of histone proteins
- small proteins - rich in lysine and arginine
- positive charge neutralizes negative charge of DNA
- four core histone proteins (H2A, H2B, H3 & H4)
- pair of each in octamer core
- one linker histone (H1)
- H2A and H2B form a dimer, H3 & H4 form a dimer
- each core histone protein has a tail that can be covalently modified (reversibly) to be methylated, phosphorylated, acetylated; this is important for regulation of nucleosomes and how compact the DNA is
H1
acts as a paper clip and changes the trajectory of the linker DNA so it is bent and compacted better
how are chromatin loops made
sequence-specific clamp proteins and cohesions are involved in forming chromatin loops
how are chromatin loops altered during mitosis?
as cells enter mitosis, condensins replace
most cohesins to form double loops of
chromatin to generate compact chromosome
each DNA molecule has been packaged into a mitotic chromosome that is ——- times shorter than its extended length
10,000
function of chromatin re-modeling complexes an histone modifying enzymes
proteins that work together to make changes in chromatin structure and alter access to DNA for replication or transcription, so that the DNA is in a state where the cell can actually use it.
heterochromatin
highly condensed chromatin
- meiotic and mitotic chromosomes
- centromeres and telomeres
- time spent highly condensed varies (constitutive vs facultative)
heterochromatic regions of interphase chromosomes are areas where gene expression is
suppressed
euchromatin
relatively non-condensed chromatin
- degree of condensation varies
- level of activity varies (ie quiescent vs active)
active euchromatic regions of interphase chromosomes are areas where genes tend to be
expressed
constitutive heterochromatin
highly condensed pretty much all the time (eg centromeres/telomeres)
facultative heterochromatin
easier to decondense; genes that may need attention sometimes, like regulatory sequences
quiescent euchromatin
a level of condensation that is not as loose as active euchromatin but not as tight as heterochromatin
active euchromatin
genes are being expressed (transcribed)
heterochromatic vs euchromatic
a continuum that is dynamic
what is the degree of chromatin condensation controlled by?
localised covalent modification of histones, the presence of chromatin remodelling complexes, and RNA polymerase (transcription) complexes model the reversible switching from euchromatic to heterochromatic regions along chromosomes
how are interphase chromosomes arranged in the nucleus?
- discrete regions
- these regions can vary from cell to cell
gene off -> gene on
- homologous chromosomes detected by hybridisation techniques
- part of the chromosome is loosened so specially marked gene is moved to loosely compacted area of chromosome
is DNA replication conservative or semi-conservative? describe both
conservative: daughter cells have both parental DNA strands in one daughter cell and both of the newly synthesised strands in the other cell
semi-conservative: two daughter cells each have one parental DNA strand and one newly synthesised strand
why is conservative DNA replication problematic?
- if there is a mistake in the newly synthesised strands, there is no other strand to rectify this
what is the direction of DNA replication?
there are three main models that occur in nature, but we will focus on bidirectional growth from one starting point - DNA is growing in two directions from every point of origin. Bacteria and eukaryotes use this methods
describe the start of DNA replication
- double helix is opened with the aid of initiator proteins at the replication origin
- single stranded DNA templates are thus ready for DNA synthesis
where does DNA replication start?
always starts from the same location on DNA
What are some of the characteristics of the
sequences at replication origins?
Easy to open, A-T rich
Recognized by initiator proteins that bind to the DNA
how many origins of replications do origins have?
bacteria have a single one, eukaryotes have multiple (DNA is a lot bigger, so this is more effective)
Rolling Circle Replication
bidirectional; only applies to circular genomes
what happens at DNA replication forks?
5’ to 3’ direction (rule of DNA polymerase) growth in DNA. Okazaki fragments are formed in the lagging strand. The replication fork is asymmetrical - leading strand (5’ to 3’) replicated continuously, lagging (3’ to 5’) replicated discontinuously
