Final-Genes Flashcards
Alveolates- ciliates
What is nuclear dimorphism?
Having 2 DIFFERENT KINDS of nuclei
Ciliates
What is the Macronucleus
REALLY large genes, are expressed and NOT inherited
“Soma” = body
Ciliates
What is the Micronucleus?
REALLY small, NOT Expressed and inherited
“Germ line” sperm/egg
Ciliates
What is the ciliate life cycle
Conjucation (tube between cells), meoisis in the MICRO nuclei (4- 3 degraded = 1, haploid) MITOSIS makes 2 identical nuclei, exchange and fuse, mitosis twice (4 nuclei) develop into MACRO from MICRO, old MACRO degrades, cells seperate
Ciliates
MACRO vs MICRO who has more genome?
MACRO has more DNA (amplification) but has LESS Information because mostly duplicated/deletions
Ciliates
What are the 3 steps of changing MICRO into MACRO?
FAD
- Fragmentation: genome broken up into a lot of chromosomes 2. Amplification 3. Deletion
Ciliates
What are pointers?
Once IES is eliminated there is one present at junction
1-2 bases
Ciliates
What is epigenetic?
Something that is inherited, but is not in the genome
Ciliates
When is the Micronucleus transcribed in Tetrahymena
During Meiosis
Ciliates- Tetrahymena
What is a scanRNA?
Micronucleus transcripts are processesed into short pieces of DNA
30 Bp fragments
Ciliates- Tetrahymena
MIC to MAC
Scan RNAS leave the MICRO and go to old parental MACRO, scan the genome for an identical sequence, find a match and bind, if they bind they are degraded, if not they are not. Remaining scanRNAS go to developing zygotic MACRO and scan again- binds to IES and gets deleted (recombination)
Ciliates- Oxytricha
MIC to MAC
Transcribes whole genome in parental MAC, scanRNAS move to developing MAC, scanRNA base pairs with DNA and LOOPS are removed (IES)
Transcription STARTS in parental MAC
Ciliates
MIC to MAC
Tetrahymena VS oxytricha
In Tetra: ScanRNAS bind to IES (part that is deleted) In Oxy: Coming from a genome that IES is already deleted (Parental MAC) forms loops
OPPOSITE information to eachother
Ciliates- Oxytricha
What are the implications
Acquire mutations as they do Mitosis
Occurs in one genome but not other
CELL FIXES DNA TO MATCH RNA
Ciliates
Why dont mutations acquire in Tetra?
If there would be a mismatch, it is deleted anyways, scanRNAS come from MIC
Excavata
What is the nuclear genome expression of Trypanosomes?
Packed blocks of genomes on the same side, no promotors
Use histones instead of promoters- at the start of each block
Excavata- Trypanosomes
How do Ribosomes jump down to the next gene with giant mRNA?
Trans-splicing
Excavata- Trypanosomes
How are polycisteronic messages broken up?
Splice leaders at each junction point, breaks up so gene is attached to RNA with a cap - poly AAA tails added and now can be monocystronic message
Excavata- Trypanosomes
How do trypanosomes control how much of a sequence is translated?
Half life: How long the mRNA lasts in the cell
Excavata- Trypanosomes
Where are trypanosomes genes expressed?
In the Mitochondria
Excavata- Trypanosomes
What is the name of Trypanosomes genome?
K-DNA
Excavata- Trypanosomes
What are the 2 types of DNA ?
Mini circles: connected in a chain Maxi circles: interweved in
MANY MINI, FEW MAXI
Excavata- Trypanosomes
Maxi circles
Large pieces of DNA that are broken (full of deletions/mutations) that get fixed by Mini circles
Excavata- Trypanosomes
Mini circles
Encode GuideRNA that has information to fix transcripts of broken genes (rna editing)
Excavata- Trypanosomes
WHY do trypanosomes break the essential dogma?
DNA (info) –> RNA (copy) –> Proteins (translated copy)
DNA (info from maxi) –> RNA (more info from mini after transcriptions) –> protein
Excavata- Trypanosomes
HOW does RNA editing in trypanosomes work?
Inserts or deletes U’s, 3’ to 5’ (opposite)
Accounts for 50% of base pairs
Excavata- Trypanosomes
How many different mini circles are there?
5000, each has conserved regions and guideRNA
Excavata- Trypanosomes
What are the 3 parts of GuideRNA?
**1. Anchor sequence 2. Editing zone 3. Poly-U tail **
Excavata- Trypanosomes
How do GuideRNAS edit?
Anchor sequence binds to RNA (cant edit here), editing zone breaks backbone of RNA and inserts UU, poly UU tail binds to anything
Excavata- Trypanosomes
Why does it go 3’ to 5’?
Each guide RNA makes the anchor sequence for the next guide RNA
Excavata- Trypanosomes
Why are there so many guide RNAs?
Need to bind, edit and fall off
Excavata- Trypanosomes
How do Trypanosomes keep track of what has been edited with so many chromosomes and copies to replicate?
the “nick”
Semi conservitive replication: one strand has nicks other does not
Excavata- Trypanosomes
Parts of DNA replication: Primease
Enzyme that makes RNA primer for DNA replication
Excavata- Trypanosomes
Parts of DNA replication: Single stranded endonuclease
Deletes primer
Excavata- Trypanosomes
Parts of DNA replication: PolyB
Fills in after RNA primer gets deleted
Excavata- Trypanosomes
Parts of DNA replication: TOPO II
Breaks strands, twists and sticks them back together
Pulls minicircles through
Excavata- Trypanosomes
How does the cell know it is done DNA replication?
Every molecule has nicks- cell knows its done and all nicks are repaired quickly
Define complexity:
More steps in a system
NOT better/worse
2 examples of complexity
- Ciliate genomes 2. Trypanosomes editing
WHY
What is a possible explanation for the complexity?
More recombination possibilities, acquiring change may help with evolving, control of expression
Constructive neutral evolution
The thing that fixes the problem evolved before the problem and allows it to happen
Example of constructive neutral evolution in fungus
RNA stem loops
TRNA binds to stem and strengthens it- weakens selection on the base pairs against mutations , mutations that would have been deleterious are now neutral
System worked well by itself now has 2 essential parts for the same
INCREASED complexity and didnt change function
Example of constructive neutral evolution in fungus
What happens after the first mutation
System is driven forward, a lot of mutations can follow the first one because protein is there
Order of events: protein bound first and allowed mutation to happen
If reversed: cell would die
OTHER examples of systems that evolved constructive neutral evolution
ribosome, spliceosomes, protein-protein interactions
Constructive neutral evolution
Trypanosomes:
GuideRNA existence allowed the gene to get messed up
Opens the floodgates to high number of deletions in genome b/c easy fix
Constructive neutral evolution
Ciliate genomes:
IES are transposoons, MIC doesnt get expressed and when new MAC develops- recognizes as IES and deletes
MIC/MAC development supresses deleterious effect
