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micro > Final-Genes > Flashcards

Final-Genes Flashcards

1
Q

Alveolates- ciliates

What is nuclear dimorphism?

A

Having 2 DIFFERENT KINDS of nuclei

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2
Q

Ciliates

What is the Macronucleus

A

REALLY large genes, are expressed and NOT inherited

“Soma” = body

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3
Q

Ciliates

What is the Micronucleus?

A

REALLY small, NOT Expressed and inherited

“Germ line” sperm/egg

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4
Q

Ciliates

What is the ciliate life cycle

A

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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5
Q

Ciliates

MACRO vs MICRO who has more genome?

A

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

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6
Q

Ciliates

What are the 3 steps of changing MICRO into MACRO?

FAD

A
  1. Fragmentation: genome broken up into a lot of chromosomes 2. Amplification 3. Deletion
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7
Q

Ciliates

What are pointers?

A

Once IES is eliminated there is one present at junction

1-2 bases

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8
Q

Ciliates

What is epigenetic?

A

Something that is inherited, but is not in the genome

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9
Q

Ciliates

When is the Micronucleus transcribed in Tetrahymena

A

During Meiosis

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10
Q

Ciliates- Tetrahymena

What is a scanRNA?

A

Micronucleus transcripts are processesed into short pieces of DNA

30 Bp fragments

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11
Q

Ciliates- Tetrahymena

MIC to MAC

A

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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12
Q

Ciliates- Oxytricha

MIC to MAC

A

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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13
Q

Ciliates

MIC to MAC

Tetrahymena VS oxytricha

A

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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14
Q

Ciliates- Oxytricha

What are the implications

A

Acquire mutations as they do Mitosis

Occurs in one genome but not other

CELL FIXES DNA TO MATCH RNA

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15
Q

Ciliates

Why dont mutations acquire in Tetra?

A

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

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16
Q

Excavata

What is the nuclear genome expression of Trypanosomes?

A

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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17
Q

Excavata- Trypanosomes

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

A

Trans-splicing

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18
Q

Excavata- Trypanosomes

How are polycisteronic messages broken up?

A

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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19
Q

Excavata- Trypanosomes

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

A

Half life: How long the mRNA lasts in the cell

20
Q

Excavata- Trypanosomes

Where are trypanosomes genes expressed?

A

In the Mitochondria

21
Q

Excavata- Trypanosomes

What is the name of Trypanosomes genome?

A

K-DNA

22
Q

Excavata- Trypanosomes

What are the 2 types of DNA ?

A

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

MANY MINI, FEW MAXI

23
Q

Excavata- Trypanosomes

Maxi circles

A

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

24
Q

Excavata- Trypanosomes

Mini circles

A

Encode GuideRNA that has information to fix transcripts of broken genes (rna editing)

25
Q

Excavata- Trypanosomes

WHY do trypanosomes break the essential dogma?

DNA (info) –> RNA (copy) –> Proteins (translated copy)

A

DNA (info from maxi) –> RNA (more info from mini after transcriptions) –> protein

26
Q

Excavata- Trypanosomes

HOW does RNA editing in trypanosomes work?

A

Inserts or deletes U’s, 3’ to 5’ (opposite)

Accounts for 50% of base pairs

27
Q

Excavata- Trypanosomes

How many different mini circles are there?

A

5000, each has conserved regions and guideRNA

28
Q

Excavata- Trypanosomes

What are the 3 parts of GuideRNA?

A

**1. Anchor sequence 2. Editing zone 3. Poly-U tail **

29
Q

Excavata- Trypanosomes

How do GuideRNAS edit?

A

Anchor sequence binds to RNA (cant edit here), editing zone breaks backbone of RNA and inserts UU, poly UU tail binds to anything

30
Q

Excavata- Trypanosomes

Why does it go 3’ to 5’?

A

Each guide RNA makes the anchor sequence for the next guide RNA

31
Q

Excavata- Trypanosomes

Why are there so many guide RNAs?

A

Need to bind, edit and fall off

32
Q

Excavata- Trypanosomes

How do Trypanosomes keep track of what has been edited with so many chromosomes and copies to replicate?

A

the “nick”

Semi conservitive replication: one strand has nicks other does not

33
Q

Excavata- Trypanosomes

Parts of DNA replication: Primease

A

Enzyme that makes RNA primer for DNA replication

34
Q

Excavata- Trypanosomes

Parts of DNA replication: Single stranded endonuclease

A

Deletes primer

35
Q

Excavata- Trypanosomes

Parts of DNA replication: PolyB

A

Fills in after RNA primer gets deleted

36
Q

Excavata- Trypanosomes

Parts of DNA replication: TOPO II

A

Breaks strands, twists and sticks them back together

Pulls minicircles through

37
Q

Excavata- Trypanosomes

How does the cell know it is done DNA replication?

A

Every molecule has nicks- cell knows its done and all nicks are repaired quickly

38
Q

Define complexity:

A

More steps in a system

NOT better/worse

39
Q

2 examples of complexity

A
  1. Ciliate genomes 2. Trypanosomes editing
40
Q

WHY

What is a possible explanation for the complexity?

A

More recombination possibilities, acquiring change may help with evolving, control of expression

41
Q

Constructive neutral evolution

A

The thing that fixes the problem evolved before the problem and allows it to happen

42
Q

Example of constructive neutral evolution in fungus

RNA stem loops

A

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

43
Q

Example of constructive neutral evolution in fungus

What happens after the first mutation

A

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

44
Q

OTHER examples of systems that evolved constructive neutral evolution

A

ribosome, spliceosomes, protein-protein interactions

45
Q

Constructive neutral evolution

Trypanosomes:

A

GuideRNA existence allowed the gene to get messed up

Opens the floodgates to high number of deletions in genome b/c easy fix

46
Q

Constructive neutral evolution

Ciliate genomes:

A

IES are transposoons, MIC doesnt get expressed and when new MAC develops- recognizes as IES and deletes

MIC/MAC development supresses deleterious effect

micro (8 decks)

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