Genes And Chromosomes Flashcards
What accounts for the non coding sequence in humans?
Regulatory sequences]
Unknown function
- repetitive DNA (not in bacteria)
- unique sequence
What are regulatory sequences?
Signal defining the start or end of a gene
Influence transcription and translation
Introns (not in bacteria)
Invitation points for replication
What percent human DNA codes for protein?
~1.5%
59% is repetitive DNA
24% regulatory gens
15% unknown
What kind of genes have introns?
Eukaryotic genes have introns
Prokaryotic genes do not
Eukaryotic genes are monoistronic, what does it mean?
One gene/mRNA
Alternative splicing may result in multiple mRNAs per gene
Prokaryotic genes may be polycistronic, what does this mean?
Multiple genes/mRNA
Usually with related function
What is a plasmid in bacteria?
Independent circular DNA
Replicate autonomously
Have horizontal gene transfer in bacteria
DNA in a bacteria (in the nucleoid) is attached to what?
A core protein and RNA
What protein core is seen in bacterial DNA?
HU: a histone-like protein that bends DNA in a tight circle
What is RNAse?
An enzyme that degrades RNA
What are some examples of genes that are repeated in the human genome?
Histone genes
rRN genes
What are the characteristics of highly repeated sequences?
Almost always the same Short repeated units Repeated in Tandem in clusters >100k repeats 3% of the human genome
What are the characteristics of moderately repeated genes?
Diverge considerably
Larger repeated units
Dispersed throughout our genome
42% of the human genome
What is highly repeated DNA referred as? Why?
Satellite DNA because it separates from the bulk of the genomic DNA in ultracentrifugation
-like a satellite of a larger body
What are the 3 classes of satellites?
Satellite
Minisatellite
Micro satellite
Where are satellites usually found?
Centromeres where spindles attach (kinetochore)
Where are mimisatellites found?
Telomeric repeats
What are minisatellites used for?
DNA markers in DNA fingerprinting and allele tracking
Which of the satellites are polymorphic?
Minisatellite
Micro satellite
What are microsatellites also known as?
Short tandem repeats (STR)
What satellites can be used for DNA markers in DNA fingerprinting and allele tracking?
Mini and micro satellites
What is a telomere?
A special class of minisatellites Repeat ~1500 times at the end of all chromosomes
Vertebrate telomeres repeat sequence:TTAGGG
What are the 2 clases of interspersed repeats? (Moderately repeated DNA)s
SINEs
LINEs
What are SINEs?
Short interpersed nuclear elements
What are some characteristics of SINEs?
~300 bp, with > a million copies throughout the genome
~13% of the genome
All elements re most common
What are Alu elements?
Most abundant sequence in the human genome
Often play a role in unequal crossing over, leading to chromosomal deletions and duplications, or inversions
What are LINEs?
Long interspersed nuclear elements
What are some characteristics of LINEs?
L1 elements: ~6000bp long
~21% of the nuclear genome
What are SINEs and LINEs evolutionary remnants of?
Retrotransposons
What are retrotransposons?
“Jumping genes”
DNA fragments that can copy themselves to new locations
99.9% are inactive. A small number remain active and can cause gene mutations after transposition
What do class 1 transposons do?
Use a “copy and paste” mechanism
Transcription to RNA
reverse transcription to DNA
LINEs carry genes for what?
Reverse transcriptase and an endonuclease (for reintegration)
What do class II transposons do?
Use a “cut and paste” mechanism
Require an enzyme called a transposase
How do prokaryote package their DNA?
Use supercoiling
Coating with positively charged polyamines (spearmint or spermidine)
How do Eukaryotes package their DNA?
Wrapping around small, positively charged proteins called histones
Compaction into chromatin
How many base pairs are there in the double helix per turn?
10.5 by per turn
When DNA is overwound what develops?
Positive supercoils
When DNA is under wound what develops?
Negative supercoils
This restores the normal Watson and crick structure
What increases the tendency toward strand separation?
Negative supercoils
Under winding typically precedes strand separation
What occurs in front of strand separation such re replication and transcription?
Positive supercoils
What occurs in front of eukaryotic replication forks?
Positive supercoils
What typed of DNA is easier to separate?
It takes less energy to separate underwound DNA than to separate normal relaxed DNA
What is linking number?
The number of times one strand crosses the other
Is a method for quantitatively describing supercoiling
In DNA
Lk= length of DNA in bp/ Number of bp per turn
If you have 2100 bp in a DNA circle and you have relaxed DNA (10.5 be per turn), what is the linking number?
Lk=2100/10.5=200
How is Lk increased or decreased?
Negative supercoiling decreases Lk
Positive supercoiling increases Lk
What are topoisomerases?
Enzymes that alter supercoiling
-relieves torsional stress by removing or creating supercoils
What do type I topoisomerases do?
Nick DNA (cut one strand)
Don’t require energy
What do type 2 Topoisomerase do?
Cut both strands of DNA
Require ATP
How many topoisomerase do bacteria have?
4
2 of each type I and type 2
What is gyrase?
A special topoisomerase found in bacteria with unique properties
By how much does type 1 topoisomerase change Lk by?
They change Lk by 1
What is the reaction mechanism of type 1 of topoisomerase?
- A hydroxyl in a tyrosine (Y) in the enzyme attacks a phosphodiester bond on one strand
- The cleaved strand rotates around the other strand
- The cleaved strand is religated
How many super oils do type 2 topoisomerase remove and by how much do they change Lk?
Removes 2 supercoils at a time and change Lk by 2
Where is type 2 topoisomerase activated at?
Regions where 2 double strands cross over each other
What is the reaction mechanism for type 2 topoisomerase?
- The enzyme binds to one double-strand (called G segment, for gate)
- It then binds 2 ATP molecules, undergoes a structural transition, and cleaves both strands of the G segment
- The second double-strand (T segment, for transport) moves through the break
- The G segment is re-ligated and ATP hydrolysis resets the enzyme
What does gyrase introduce to DNA?
Introduces negative supercoils using energy from ATP hydrolysis
What is the function of DNA gyrase?
The negative supercoils introduced neutralize the positive supercoils introduced by strand unwinding during DNA replication
What are some examples of type 2 topoisomerase (gyrase) inhibitors (antibiotics).
Quinolones: -1. Fluoroquinolones, -2. Nalidixic Acid, -3. Ciprofloxacin
What is the major for of chromatic during interphase?
Euchromatin
What is the major form of chromatin during mitosis and meiosis?
Heterochromatin
Where is heterochromatin found during interphase?
Nuclear periphery
-Genes are unavailable for transcription and silent
What is the basic unit of a chromatin?
Nucleosomes
~1.8 turns of DNA (146bp) about a histone octamer
What is a histone octamer found in a nucleosome?
2 of each: H2A H2B H3 H4
What does Histone H1 bind to?
Binds the linker DNA DNA facilitates higher level of packaging (30nm fiber or solenoid fiber)
What does a nucleosome look like?
“Beads-on-a-string” or the 10nm Fiber
How does Nuclease break down chromatin and naked DNA?
Chromatin produces DNA fragments 146 by in length
Naked DNA is completely broken down into nucleotides
What are the four core proteins found in the same protein family?
H2A
H2B
H3
H4
What kind of charge do histones carry?
They are positively charged because they are rich in Lysine and Arginine
How do core histones attach to DNA?
They behind very strongly to the negatively charged phosphate groups of DNA through ionic interactions (mainly in minor groove)
What are the parts of a nucleosome?
Hydrophobic core (C-terminal alpha-helical domains)
N-terminal tails (flexible, rich in Lys and Arg)
How can the tails of nucleosome be modified?
The basic residues in the tail can be modified by acetylation or methylation
(Example of epigenetics)
How can you neutralize histones ?
Acetylation of Lys or Arg neutralizes their positive charge
What is histone acetylation associated with?
Euchromatin
Active gene expression
What is Histone deacetylation associated with?
Heterochromatin
Gene silencing
What are the enzymes involved in Histone acetylation?
Histone acetyltransferase (HATS) add acetylation groups
Histone Deacetylases (HDACs) remove acetylation groups
Where can methylation occur in a histone?
Methyl groups can be added to Lys and Arg residues in their tails
What are the effects of histone methylation?
W/ Eu/heterochromatin
Depends on which specific reside in the various histones is methylated
Mediated by other proteins that bind these methylation
What are some examples of histone methylation?
H3K9-trimethylation is associated with heterochromatin and gene silencing
H3K4-trimethylation is associated with euchromatin and gene expression
What kind of supercoil do histones introduce?
Negative supercoiling
What are some examples of Eukaryotic topoisomerase inhibitors (chemotherapeutics)?
Type I topoisomerse inhibitors : Irinotecan, topotecan
Type II topoisomerase inhibitors: amsacrine, etoposide, doxorubicin*, daunorubicin
