Week 1 - Gene Expression and Rearrangement Flashcards
What is the goldfish memory experiment
creation of memories –> turn light on, on one side of tank and when fish goes there it gets shocked
- shock teaches the fish to swim away from light to voice shock (creates memory)
- puromycin used –> stop fish from developing memory
What does puromycin do?
inhibits protein synthesis in eukaryotes
HIV causes ____ which is a ______
AIDS, retrovirus
What is gene expression?
process where information stored in a genome is transformed to yield functional products
Bacterial Characteristics
- mRNAs polycistronic transcripts (encode 1+ protein)
- transcription and translation are coupled
–> un-compartmented, no organelles - 1 RNAP transcribes all genes
- mRNA primary transcript generally not spliced
- Bare DNA (not wrapped within a nucleosome)
Eukaryotic Characteristics
- mRNAs monocistronic
- compartmented, nucleus cytoplasm, etc.
- packaged DNA within nucleosome (4 histones )
- nucleosome + DNA = chromatin
- transcription and translation are NOT coupled
- multiple RNAP mol, often 3, 4 and 5 in plants
- transcript in nucleus is highly processed
- translation occurs in cytoplasm
Role of RNAP2 ?
transcribes most protein coding genes
Role of RNAP1 ?
transcribes rRNA genes
Role of RNAP3 ?
transcribes tRNA and some small RNA genes
What are we discussing when referring RNA populations?
Transcriptome
How to know what level gene expression is regulated at?
- need to use some basic Molecular biology
1. Is the transcript present or not?
Reg. of gene expression:
1. Is the transcript present or not?
transcript detection/accumulation
Reg. of gene expression:
What is the structure of the transcript?
transcript analysis/sequencing
Reg. of gene expression:
Is the protein expressed?
Protein detection/antibody or activty
Humoral response to pathogens
production of antibodies that recognize and destroy the pathogen
- produced by b-cells in our immune system
- clonal expansion of b-cells that produce specific antigens on the pathogen
- antibody bind to antigen and x bacteria targeted for destruction
(antibody made up of 2 heavy chain and 2 light chains)
Cellular response to pathogens
- t-cells have receptors that recognize the invading pathogen
what does salmonella in salmonella enterica express?
- salmonella expresses b-protein
salmonella promoter
- can transcribe an operon with two coding regions
1. encodes flagellin B protein
2 encodes FjiA
FjiA
- repressor of the transcription of the gene that encodes FjiC protein
FjiC
- when FjiC is expressed, the promoter for FjiC is facing opposite direction of FjiB and A such that FjiA and B are not expressed
what is the the central gene regulatory event of salmonella?
orientation of the promoter relative to the expression of flagellin A and B
no expression of FjiA and B = __________
expression of FjiC
What are hixL and hixR ?
similar sequences that are inverted relative to one another
- cis-acting elements required for inversion
- binding sites for hin recombinase (trans acting factor)
hin recombinase
- binds to hixL or hixR –> will bring both together to promote site specific recombination between hixR and hixL such that the site is now inverted
- promoter now away from coding region of FjiB and repressor
IGH locus
genes that encodes heavy chains of immunoglobulins
- on 14th chromosome
- variable region (vH), organized region (dH), jH and constant region (cH)
- none of these regions are transcribed until after rearrangement
what occurs after IGH transcription?
when transcribed, there’s production of protein giving heavy chain portion of antibody
- consequence: missing sections of locus
RAG1 and RAG2
(recombination activating gene 1/2)
- randomly choose one of the RRS elements next to the DH or Vh domain in IGH locus
- RRS (cis) - recombination signal seq
- RAGs induce DS breaks next door to RRS –> loop lost bound to RRS seq
- vH and dH domains with a double stranded break
what repairs vH and dH DS DNA break?
non-homologous end joining (NHEJ)
macronucleus (MAC)
expressed DNA
800n
somatic nucleus
- transcribed
- 800 copies of 2-5% of the germ-line genome (MIC)
micronucleus (MIC)
germ-line 2n
- not transcribed
- 95% of MIC eliminated, 5% remains and nano chromosomes
- DNA segments need to be eliminated and descrambled as they are in different orientation before getting put into nano chromosomes
nanochromosomes
- every gene is on nano chromosomes
- transcribed –> order of elements is preserved in transcript
- DNA info is preserved in the mRNAA that’s expressed from macronucleus
- has telomeres at the end
old MAC
will disappear and as new MAC develops
Developing MAC
DNA elimination and descrambling
descrambling
mRNA from old MAC info. is used to help descramble information in the MIC
