Lecture 4: DNA/RNA, chromosomes and transposable elements Flashcards
The heterozygote exhibits a phenotype that’s intermediate between the corresponding homozygotes
Incomplete dominance
used much more when discussing human diseased
Haploinsufficiency
Explain the process of floruescent hybridization?
- Mitotic chromosomes are headed up, strands separate, and H bonds are broken.
- Mix in probe and cool down DNA
- When you reneal the DNA, one copy outcompetes another strand—can see probe in genome
shows the DNA sequence genome by taking DNA sequence and adding fluroescent chemicals
flourescent hybridization?
Result of Translocation producing Philadelphia Chromosome detected using
FISH
What procedure was used for reciprocal translocation
FISH
Why do translocations occur so much between 9 and 22 chromosomes?
Domains are close by in the nucleus
Shows the different domains in the nucleus, every chromosome colored differently
Spectral Karyotyping
Allodiploid vs. allotetraploid
allodiploid are sterile, no tetrads in meiosis I
allotetraploid have twice as many chromosomes, viable and fertile
Fused haploid radish and haploid cabbage produced…
allodiploid
Fused diploid radish and diploid cabbage produce…
allotetraploid
Synaptonemal complex gets broken, two chromosomes of each species moving to opposite poles in: allotetraploid or allodiploid
allotetraploid
How many metacentric, submetacentric, and acrocentric chromosomes do humans have?
metacentric: 1
acro: 5
submet: most
In Robertsonian Translocations the long arms of two ___ chromosomes have fused.
acrocentric
One example of a Robertsonian translocation is
Familial Down Syndrome (14 and 21)
Any chromosome, not X or Y, will give rise to a ____ if embryo has one chromosome or 3 copies (besides trisomy 21)
miscarriage
In DNA or RNA, no phosphate present on sugar is known as
nucleoside
The RNA nucleotides that are precursors to RNA polymers have….
3 phosphates
Two RNA nucleotides can ___ undergo the reaction shown below because it i
thermodynamically favored
spontaneously
If you mix RNA precursors, what do you get?
pyrophosphate (2 phosphates released) and RNA dinucleotide
In the backbone of RNA, the 5’ end has no ____ and the 3’ end has what attached to the 1st C and 3rd C?
5’= no nucleotide
3’ 1st C: base attached
3’ 3rd C: phosphate and another nucleotide attached
RNA most stable in what envrionment
acidic
In the RNA world, you just need what for RNA to self replicate
RNA nucleotide
RNA can act as___ in the rna world
Polymerases
Hydrogen bonds in RNA are only located when….
strands are opposite in direction
The 3D structure of RNA is needed for…
catalytic activity
Why did the RNA World recruit protein?
protein has greater catalytic potential than RNA
Proteins are synthesized by…
RNA
The enzyme that attaches amino acids to a growing amino acid chain is called the
ribosome
In bacteria and eukaryotes: what’s the ratio of RNA and protein in the ribosome
60% rna, 40% ribosome
The amino acids are Brought to the enzyme by
trna
The amino acid sequence is coded in the
mrna
determines the template of amino acids
mrna
If you get rid of proteins and are left with RNA, what happens to the enzymatic activity? If you get rid of RNA and are left with proteins, what happens to the activity?
can still get activity, vs. get nothing if RNA not present
As volcanic activity diminshed, there would have been a strong selection for the inclusion of ___ which is a much more stable molecule for storing information
DNA
Scientists propose that an ancestral RNA molecule had the ability to synthesize DNA using RNA as a template: what enzyme
Reverse Transcriptase
Enzyme evolution of proteins outcompetes….
RNA
What enzyme is very abundant in the RNA world
RNA polymerase
There needs to be an RNA enzyme that synthesizes DNA using…
RNA template
DNA vs RNA nucleotides
DNA: A, G, C, T
RNA: A, G, C, U
Differences in deoxyribose and ribose
deoxyribose has an H, ribose has an extra O on C 2
DNA is more stable than rna because
extra O
Uracil vs. thymine
uracil lacks a methyl
connects the 5’ carbon of one nucleotide to the 3’ carbon of another
phosphate
The nucleotide strands have direction from
5 to 3
The phosphates and sugar
molecules form the…
backbone of nucleic acid strand
Link the 1st Carbon and base (ex. Guanine) in DNA or RNA dinucleotide
glycosidic bond
Links phosphate to O of the next molecule in a DNA or RNA dinucleotide
phosphodiester bonds
RNA nucleotides originate?
arise spontaneously
The two RNA nucleotides vs. RNA dinucleotide energy levels
two individual RNA nucleotides: higher energy
RNA dinucleotide: lower energy
When an RNA dinucleotide is formed, what is released?
pyrophosphate
RNA polymerase needs how many templates
1
RNA genome diseases with no DNA were the….
1st to exist
RNA vs proteins: hydrophilic or hydrophobic
RNA: hydrophilic
protein: hydrophilic or hydrophobic
How many nucleotides make up an amino acid
3
They tried to build models of DNA using the available
information for DNA structure
Watson and crick
What are the base pairs that are equally abundant?
a and t, g and c
Watson and crick dna double helix led them to discover
that A could hydrogen bond to T and G could hydrogen bond to C
What was linkage was proposed by w and c
phosphodiester
People knew the nucleotide structure before W&C, but not the ___ structure because people….
DNA, purified an enzyme (DNAase) and when DNA was exposed to DNAase, produced 4 nucleotide precursors
The dna strands are…
antiparallel and right handed
There are ____ nucleotides in each strand per complete ___° turn of
the helix.
10, 360 degrees
The dna bases are oriented so that they are…
flat and facing each other
The DNA helix is called a…
B helix (more stable than RNA A helix)
What is the advantage of the B helix vs. A helix
Oxygen at the 2nd carbon on the A helix is too bulky
C nucleotides would H bond ___ with G nucleotide
3 times
a more stable molecule for storing information
DNA
Scientists propose that an ancestral RNA molecule had the ability to synthesize DNA using RNA as a template
Reverse Transcriptase
The bacterial chromosome is found in a region of the cell called the
nucleoid
Domain in the cell with DNA of bacteria
nucleoid
Shape of bacterial chromosomes
ciricular
Unlike eukaryotes, the nucleoid is….
not bounded by membrane, in contact with cytoplasm
Each bacterial cell can have 1 or more…
chromosomes
One origin of replication in…
bacterial chromoosmes
Most bacterial species contain how many chromosomes
1 single type
Genes are closely spaced together in
bacterial chromosomes
There are how many repetitive sequences in a bacterial chromosomes
few
Bacterial chromosomal DNA is compacted about ____ by ____
1000 fold by proteins into loops
When bacterial chromosomal dna is compacted, the involves the formation of….
loop domains
After loop domains are formed in bacterial chromosomal dna, what occurs to further compact the chromosome? Who does it? Requires what?
DNA supercoiling by gyrase/topoisomerase II (needs energy)
Promoter of bacterial genes
A/T rich
The chromosomal DNA in bacteria is
negatively supercoiled
In E. coli, there is ___ negative supercoil per __ turns of the double helix
1, 40
Negative supercoiling has two major effects…
- Helps in the compaction of the chromosome
- Creates tension that may be released by DNA strand separation
origins of replication in bacterial chromosomal dna are rich in..
A/T rich (less H bonds than G/c)
Supercoiling helps separate strands because of
stress
Introduces negative supercoils using energy from ATP
DNA gyrase
relax positive supercoils that arise during DNA replication and transcription
DNA gyrase
Relaxes negative supercoils when there are too many
DNA topoisomerase I
The competing action of these two enzymes governs the overall supercoiling of bacterial DNA. What enzymes?
DNA topoisomerase I and DNA gyrase
The ability of gyrase to introduce negative
supercoils into DNA is crucial for…
bacteria to surivive
Blocking the function of what enzyme is a way to cure bacterial diseases
DNA gyrase
Two main classes of drugs inhibit gyrase but not eukaryotic topoisomerases
- Quinolones
- Coumarins
An example of a quinolone is
Cipro (antibotic that kills bacteria)
Three types of DNA sequences are
required for chromosomal replication and
segregation. what are they?
Origins of replication hundreds or thousands along the chromosome. Human genome has 50,000-100,000 origins.
Centromeres
Telomeres
in eukaryotic chromosomes, genes are located where?
between the centromeric and telomeric regions along the entire chromosome
A single eukaryotic chromosome has how many genes
usually has a few hundred to several thousand genes
Eukaryotic chromosomes are what shape? Occur in?
linear, sets (many species are diploid)
each chromosome contains a ___ that forms a recognition site for kineticore proteins
centromere
Contain specialized sequences located at both ends of a linear chromosome
telomeres
In eukaryotic chromosomes, repetitive sequences are commonly found…
by centromere and telomere
Found in two copies (one from mom and one from dad) Includes structural genes as well as intergenic areas
In humans, make up roughly 40% of the genome
Unique or non-repetitive sequences (genes)
Found a few hundred to a few thousand times
Includes:
Genes for rRNA and histones Origins of replication
Some Transposable elements
Moderately repetitive DNA sequences
Found tens of thousands to millions of times
Each copy is relatively short (a few nucleotides to several hundred in length)
Some sequences are interspersed throughout the genome
Highly repetitive DNA sequences
Highly repetitive DNA sequences in eukaryotes are dominated by ____
transposable elements
Were viruses at one point, stayed in the genome, make DNA copies of RNA genome and insert copies into the genome
ERV elements
Examples of Highly repetitive DNA sequences
Alu transposable elements in humans (11% of human DNA)
LINE-1 transposable elements in humans (20% of human DNA) ERV elements (Endogenous RetroViruses) (8% of human DNA)
What two eukarytoic genomes can tolerate ploidys
Amphibians and plants
Causes for Differences in Eukaryotic Genome Size?
DIfferences in number of genome duplications (ploidy) and in the accumulation of repetitive sequences
transposable elements probably occur in the genomes of…
all species
Relationship between transposable elements and fast/slow dividing organisms in various species
Slower dividing organisms have an increase in transposable elements
involves the integration of small
segments of DNA called transposable elements
(TEs) or transposons into the chromosome
Transposition
DNA sequences that make copies of themselves
transposable elements
Most transposable elements come from
Line 1 transposon and Alu transposon
Three general types of transposition pathways
have been identified
- Simple transposition
- Replicative transposition
- Retrotransposition (including LINE-1 and Alu)
are small circular independently replicating minichromosomes found in bacteria and yeast
Plasmids
Plasmids ___ essential for life in bacteria or yeast
not essential
The best understood bacterial plasmid is the
E coli F factor
What did the e coli f factor do??
encodes proteins causing tubes to come off of bacteria. If another bacteria comes along, it can fuse with membrane and plasmid can fuse through the tube into other bacteria
Plasmids are useful in studying
transposable elements
Simple transposition is a mechanism called
cut and paste
Simple transposition is found in
bacteria and eukaryotes
Simple transolocation mechanism steps…
when it moves to another site, it makes a staggered cut, and it inserts somewhere else
The enzyme ‘Transposase’ catalyzes the
Excision and Insertion in…
simple transposition
converts single to double stranded dna
dna polymerase
dna base sequence targets are in the same direction and are repeated at both ends of the element
simple transposition
simple transposons in eukaryotes are….
dervived from homology and not functional/active
What type of transposition confers a selective advantage
composite transposons
contain additional genes that aren’t necessary for transposition, two copies of simple transposon on either side of gene
composite transposons
what transposition can move genes around
composite
Created by two transposons flanking the additional genes
and behaving as one transposon. Transposon sequence may then be
lost turning them into….
composite transposons
What transposition has one more gene, known as resolvase, not in eukaryotes and only in bacteria?
replicative
This mechanism involves replication of the TE and insertion of the copy into another chromosomal location
Replicative transposition
gene is found between the inverted repeats in Replicative Transposition
resolvase
In replicative transposition, Insertion into the genome causes a short target sequence at the site of insertion to be duplicated to form…
Direct Repeats
Replicative Transposition Requires what enzymes?
transposase and resolvase
Replicative transposition has been studied in several bacterial transposons and in…
phage u (Mu)
The net result of replicative transposition is that a….
TE occurs at a new site and the TE remains in its original location
In replicative transposition, there are what on the target sequence in the plasmid?
staggered cuts by transposase
Makes cuts at on the target sequence and transposable element and the strands are exchanged and ligated together in what? By what?
replicative transposition, transposase
the product of replicative transposition is…
a cointegrant
Replicative transposons can also give rise to
composite transposons
large circular chromosome, plasmid inserted into chromosome by transposon
cointegrant
Some transposons encode a ____, gives a specific homologous recombination to give plasmid and chromosome with transposon
resolvase
Catalyzes the recombination between two elements of a cointegrant, turning the cointegrant into 2 separate structures, each with a transposable element
resolvase
Retrotransposition is found in
eukaryotes
Transposon is copied into RNA, RNA copied in double stranded DNA, then DNA inserts itself elsewhere
retrotransposition
RNA intermediate in retrotransposition
Reverse transcriptase
