Final-Genes Flashcards by Jessica Kasapi

Alveolates- ciliates

What is nuclear dimorphism?

Having 2 DIFFERENT KINDS of nuclei

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Ciliates

What is the Macronucleus

REALLY large genes, are expressed and NOT inherited

“Soma” = body

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Ciliates

What is the Micronucleus?

REALLY small, NOT Expressed and inherited

“Germ line” sperm/egg

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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

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Ciliates

MACRO vs MICRO who has more genome?

MACRO has more DNA (amplification) but has LESS Information because mostly duplicated/deletions

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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

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Ciliates

What are pointers?

Once IES is eliminated there is one present at junction

1-2 bases

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Ciliates

What is epigenetic?

Something that is inherited, but is not in the genome

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Ciliates

When is the Micronucleus transcribed in Tetrahymena

During Meiosis

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Ciliates- Tetrahymena

What is a scanRNA?

Micronucleus transcripts are processesed into short pieces of DNA

30 Bp fragments

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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)

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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

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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

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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

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Ciliates

Why dont mutations acquire in Tetra?

If there would be a mismatch, it is deleted anyways, scanRNAS come from MIC

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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

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Excavata- Trypanosomes

How do Ribosomes jump down to the next gene with giant mRNA?

Trans-splicing

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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

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Excavata- Trypanosomes

How do trypanosomes control how much of a sequence is translated?

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Half life: How long the mRNA lasts in the cell

Excavata- Trypanosomes

Where are trypanosomes genes expressed?

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In the Mitochondria

Excavata- Trypanosomes

What is the name of Trypanosomes genome?

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K-DNA

Excavata- Trypanosomes

What are the 2 types of DNA ?

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Mini circles: connected in a chain Maxi circles: interweved in

MANY MINI, FEW MAXI

Excavata- Trypanosomes

Maxi circles

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Large pieces of DNA that are broken (full of deletions/mutations) that get fixed by Mini circles

Excavata- Trypanosomes

Mini circles

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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

1. 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 ## Footnote 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 ## Footnote 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

Final-Genes Flashcards

(46 cards)