Week 1 - Gene Expression and Rearrangement

Question 1

What is the goldfish memory experiment

Answer 1

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

Question 2

What does puromycin do?

Answer 2

inhibits protein synthesis in eukaryotes

Question 3

HIV causes ____ which is a ______

Answer 3

AIDS, retrovirus

Question 4

What is gene expression?

Answer 4

process where information stored in a genome is transformed to yield functional products

Question 5

Bacterial Characteristics

Answer 5

• 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)

Question 6

Eukaryotic Characteristics

Answer 6

• 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

Question 7

Role of RNAP2 ?

Answer 7

transcribes most protein coding genes

Question 8

Role of RNAP1 ?

Answer 8

transcribes rRNA genes

Question 9

Role of RNAP3 ?

Answer 9

transcribes tRNA and some small RNA genes

Question 10

What are we discussing when referring RNA populations?

Answer 10

Transcriptome

Question 11

How to know what level gene expression is regulated at?

Answer 11

• need to use some basic Molecular biology
  1. Is the transcript present or not?

Question 12

Reg. of gene expression:
1. Is the transcript present or not?

Answer 12

transcript detection/accumulation

Question 13

Reg. of gene expression:
What is the structure of the transcript?

Answer 13

transcript analysis/sequencing

Question 14

Reg. of gene expression:
Is the protein expressed?

Answer 14

Protein detection/antibody or activty

Question 15

Humoral response to pathogens

Answer 15

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)

Question 16

Cellular response to pathogens

Answer 16

• t-cells have receptors that recognize the invading pathogen

Question 17

what does salmonella in salmonella enterica express?

Answer 17

• salmonella expresses b-protein

Question 18

salmonella promoter

Answer 18

• can transcribe an operon with two coding regions
  1. encodes flagellin B protein
  2 encodes FjiA

Question 19

FjiA

Answer 19

• repressor of the transcription of the gene that encodes FjiC protein

Question 20

FjiC

Answer 20

• when FjiC is expressed, the promoter for FjiC is facing opposite direction of FjiB and A such that FjiA and B are not expressed

Question 21

what is the the central gene regulatory event of salmonella?

Answer 21

orientation of the promoter relative to the expression of flagellin A and B

Question 22

no expression of FjiA and B = __________

Answer 22

expression of FjiC

Question 23

What are hixL and hixR ?

Answer 23

similar sequences that are inverted relative to one another
- cis-acting elements required for inversion
- binding sites for hin recombinase (trans acting factor)

Question 24

hin recombinase

Answer 24

• 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

Question 25

IGH locus

Answer 25

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

Question 26

what occurs after IGH transcription?

Answer 26

when transcribed, there's production of protein giving heavy chain portion of antibody - consequence: missing sections of locus

Question 27

RAG1 and RAG2 (recombination activating gene 1/2)

Answer 27

- 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

Question 28

what repairs vH and dH DS DNA break?

Answer 28

non-homologous end joining (NHEJ)

Question 29

macronucleus (MAC)

Answer 29

expressed DNA

Question 30

800n

Answer 30

somatic nucleus - transcribed - 800 copies of 2-5% of the germ-line genome (MIC)

Question 31

micronucleus (MIC)

Answer 31

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

Question 32

nanochromosomes

Answer 32

- 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

Question 33

old MAC

Answer 33

will disappear and as new MAC develops

Question 34

Developing MAC

Answer 34

DNA elimination and descrambling

Question 35

descrambling

Answer 35

mRNA from old MAC info. is used to help descramble information in the MIC