Lecture 5: Flashcards
What kind of chromosomes are easy to see in FISH, with familiar down syndrome
Mitotic chromosomes (G2)
What kind of chromosomes are difficult to see with FISH, because the probes recognize ends of the chromosome in the domain–rather than at centromere
G1
In the Philadelphia Chromosome, probes are placed on either side of the…
break point
In the Philadelphia Chromosome, if the probes are on opposite sides of the centromere—what happens to the signal?
(G1) signals would not overlap
RNA folded up to 3D structure to have…
enzymatic activity
H-N bonds or H-O bonds are longer?
H-N
Longer RNA molecules can…
fold back and H bond with themselves
The earliest natural selection would have been for an RNA enzyme that can catalyze its own…
replication
RNA would ____ a cell to exist. It’s replication would only occur when ___ are available
not need, RNA nucleotides
Some naturally occurring lipids spontaneously
form….
double-membrane spheres if the lipid
concentrations are high enough
It has been proposed that the road to life began in…
pools of fresh water on volcanic islands that contained RNA nucleotides and lipids
Would provide enclosed spaces that the virus can dump its content into and replicate its RNA
Double membrane spheres
RNA splicing has proteins bound to it to make it more ___. Proteins largely but not entirely ___
efficient, replaced RNA
These RNA enzymes are thought to be ___ from before proteins were recruited
holdovers
What came along after proteins
DNA
DNA and RNA have how many phosphates?
3
Why can’t RNA form a B helix?
RNA cannot make a compact shape because O is too bulky on 2nd Carbon
ability to synthesize DNA using RNA as a template
Reverse Transcriptase
The bacterial chromosome, although in contact with cytoplasm, remains where?
in a domain
Supercoiling destabilizes what in the genome?
A/T rich
Stress as a result of negative supercoiling the DNA can cause ____ to come apart more easily
A/T rich regions
What regions in supercoiled DNA strand are A/T rich?
At origins of replication and at gene promotors (open complex formed easier)
What does not use supercoiling?
Eukaryotes
Can replicate themselves without replicating the genome
Transposable elements
Alu elements are long or short
short
E.coli F factor is an example of an..
invasion
What transposon cannot replicate? What can?
Simple, can= retro and replicative
Transposons can destroy a gene, causing an….
insertion mutation
What enzyme catalyzes excision and insertion in transposition
transposase
2 transposons of the same kind next to each other make up a…
Composite transposons
Recognizes IR’s and cuts and pastes
Transposase gene
Resolvase role in replicative transposition
Catalyzes recombination between 2 elements, causing co-integrant to form two separate structures (each with a copy of TE)
A cointegrant is made up of
plasmid and a bacterial chromosome
Transposons aid in the spread of…
antibiotic resistance genes
Most common transposition in humans
retro
Retrotransposition found in…
eukaryotes
What transposons are autonomous?
Eukaryotic and retro
Retrotransposition intermeditae
Reverse transcriptase
Retroelements use what in their transposition mechanism
RNA intermediates (RNA poly. 3)
The movement of retro-elements also requires two key enzymes…
Reverse transcriptase and integrase
Inserts double stranded DNA into genome
Integrase
Makes DNA copy of RNA and encodes for integrase
Reverse transcriptase
Transposons are ___ when they contain all the information necessary for transposition to occur
autonomous
Encode their own reverse transcriptase and their own integrase
Autonomous
Transposons are ___ when they lack a gene that is necessary for transposition to occur
nonautonomous
Majority of human transposons are…
autonomous
Have signal sequences to encode themselves but don’t encode for the proteins (reverse transcriptase or integrase)
autonomous
Alu elements are autonomous or non
non
Must abundant transposon
alu elements
Non-LTR retrotransposon or LTR retrotransposon are most abundant
Non LTR
Non-LTR retrotransposon have no…
repeats at the ends (ensure of how they replicate)
LTR retrotransposition are found? How long?
retroviruses, few hundred nucleotides long
Like viral counterparts, they encoded viral related proteins that are needed for the transposition process
LTR retrotransposition
Humans only have dead…
LTR retrotransposition
The organization of retroelements can be
variable
RNA viruses that make a DNA copy that integrates into the host’s genome
Retroviruses
Humans dont have genuine ____ but they do have ___ that resemble ___
LTR transposons, ERVs, LTR transposons
What makes up 1/3 of the human genome and are the most common retroelements in humans
LINE-1 and SINEs
Length of LINE-1 vs SINEs
LINE-1: Up to 6 kb
SINEs: less than 500 bp
Example of a SINE
Alu
Present in more than 1,000,000 copies in the human genome
Alu
Found in around 900,000 copies per genome
LINE-1
Most successful: LINE-1 vs SINEs
LINE 1
There are no LTRs in LINE-1 or SINE
LINE-1
What family of retroelements doesn’t share any sequence similarities with viruses
Alu
Alu family is derived from a…
single ancestral gene: 7SL RNA gene
A part of a RNA-protein complex that transports proteins carrying a specific sequence to the ER (while still being synthesized)
7SL RNA gene
A single retroelement can be copied into how many RNA transcripts in retrotransposition? What does this tell us?
many, they can accumulate rapidly in genome
The original interpretation of retroelements is that they…
exist because they can
Retroelements are similar to…
parasites
They can proliferate within the host as long as they do not harm the host to the extend that they significantly disrupt survival
Parasites, selfish DNA theory
slower dividing organisms= ___ TE
more
Gene duplication involves ____, located where?
LINE-1 elements, Y chromosome or part of immune system
LINE-1 elements help with ___
natural selection because of gene duplication
Bacterial retroelements can carry
antibiotic resistance genes
Retroelements may cause ___ through recombination
greater genetic variability
Retroelements offer what?
evolutionary advantage
A TE known as P element has expanded throughout the
fruit fly population worldwide, only strains found unless lab stocks were collected before 1950s
TE can ___ enter the genome and ___
rapidly, proliferate
Many transposons in humans are shut down and don’t multiply very often because…
cells recognize their repetitive nature
TE can alter what in gene expression?
can donate promoters and enhancers that alter gene function
Can spread from a TE and silence a nearby gene
Heterochromatin
Heterochromatin: stable or unstable
unstable
Can spread and contract influencing nearby genes differently in different people
heterochromatin
If a transposable element loses its heterochromatin, this can cause…
expose DNA sequences that alter gene expression
What can promote TE replication
radiation, stress
Transposition: regulated or non-regulated
tightly regulated because it is usually harmful
Eukaryotic cells were broken open and the DNA was seen in a bead on a string form known as….
nucleosomes
The proteins in nucleosomes are called….
histones
Histone proteins charge
basic, positively charged AA (Lysine and arginine)
Histone proteins bind with the
negative charged phosphates on DNA backbone
Have a globular domain and flexible charged amino terminus or tail
histones
What makes up a nucleosome
8 histones + DNA
What are the core histone types? How many make up an octamer?
H2A, H2B, H3, H4; two of each
What is the linker histone? Binds what?
H1, linker DNA but not as tightly as core histones
A nucleosome is composed of DNA wrapped around the octamer of __
histone proteins
___ bp of DNA make ___ turns around the octamer
146, 1.65
The nucleosome “beads on a string” structure ___ DNA legnth about ___
shortens, seven fold
In real life, the DNA is ___ in relation to the histones
larger
All beads on a string nucleosome images were obtained in conditions where a protein called ___ was missing from the chromatin
H1(get stretched out of bead)
In conditions were a histone H1 is in the chromatin, a ___ chromatin fiber is seen: ___ nm in diameter. This is seen where?
thicker, 30 nm, in the cell
In conditions where the 30 nm fiber is partially disrupted, you see a structure that looks like a….
zig zag
30 nm fibers are organized into ___. Two proteins responsible for this are _____
loops, CTCF and SMC proteins
The proteins (CTCF and SMC) in the loops are located at the
base
In ___ the chromosomal DNA is even more highly compacted
metaphase
DNA cannot go…
back and forth
When not condensed in mitosis, where are chromosomes in the cell
take up territories
The compaction level of ___ chromosomes is not completely uniform
interphase
Heterochromatin vs. Euchromatin
Hetero:
- less condensed chromosome regions
- transcriptionally active
Euch:
- tighly compacted
- transcriptionally inactive
Can be expressed with right transcription factors: hereo or euchromatin
euchromatin
Repressive, not expressed: Hetero or euchromatin
hetero
What type of chromatin is located in regions where 30 nm fiber forms radial loop domains
euchromatin
What type of chromatin is located in radial loop domains, compacted even more
heterochromatin
Two types of heterochromatin?
Constitutive vs faculative
What type of heterochromatin: regions that are always heterochromatic
constitutive
What type of heterochromatin: regions that interconvert between euchromatin and heterochromain
Facultative heterochromatin
Examples of constitutive heterchromatin
around centromeres, telomeres, and TE
Examples of facultative heterchromatin
cannot be expressed, Barr body (X inactive chromosomes)
Facultative heterochromatin regulates…
gene expression
Using ___, heterochromatin can be seen as dark staining regions in the ___ nucleus
electron microscopy, interphase
Much of the heterochromain is localized….
to the periphery of nucleus and nucleolus
Nuclear periphery moves around heterchromatin, helping to
maintain it
Nuclear lamina helps to…
maintain heterochromatin
A large proportion of heterochromatin associates with the ___ at the ___
nuclear lamina, at nuclear periphery
Relationship between age and heterochromatin
as people age, less heterochromatin
A mutation in the nuclear lamina comprises the maintenance of heterochromatin and causes pre-mature aging
Hutchinson-Gilford progeria
What is defective in Hutchinson-Gilford progeria
Lamin A
In Hutchinson-Gilford progeria, the person loses heterochromatin ___ faster
10x
