chapter 18: gene regulation steps 2-5

Question 1

what happens during processing control (step 2)

Answer 1

regulates production of mature mRNA molecules from precursor RNA

Question 2

what is a regulation process that includes splicing

Answer 2

alternative splicing: differs per protein, some introns with part of exon is removed, in others they dont

Question 3

what is the disease associated with alternative splicing

Answer 3

hutching gilford: caused by a single base error in an intron. U is mutated on a Lamin A gene
-U1 cant bind which leads to the intron not being removed

Question 4

describe the IPEX syndrome (step 2 processing control)

Answer 4

-no proper processing leads to autoimmune disease
-DNA has a mutation that passes on to RNA which does not allow Poly A proteins to bind
-this causes RNA to degrade quickly and translation elongation is not triggered.
-no FOX P3 protein: which is necessary for T reg cells

Question 5

what happens when T regulatory proteins are not made? describe components and effects (IPEX syndrome)

Answer 5

-T reg cells: release chem signals to regulate cytotoxic and helper t cells. Without them liver and kidney cells are destroyed.
*dont want cytotoxic and helper cells on forever, can harm the body.

components:
-MHCI: turn on cytotoxic t cells
-MHCII: trigger helper T cells
-Cytotoxic t cells: kill own cell in body, sacrifice to eliminate bacteria
-helper t cells: activate b cells when they encounter bacteria, trigger inflammation

1. macrophage engulfs bacteria into phagosome
2. phagosome fuses with lysosome: phagolysosome
3. bacteria pieces are placed on MHC
   4.MHCI: if other cells are infected with the same bacteria, cytotoxic kills them
4. MHCII: helper t cells help b cells activate.

Question 6

what is myotonic dystrophy? and what occurs?

Answer 6

demonstrates importance for proper intron removal in RNA splicing
- muscle Lind-like protein (MBLN-1), gene in DNA has a CTG region repeated too many times
-proteins bind to the repeated region and shield U2 SnURP from binding to the A branch point
-U1 SnURP interacts with U2 on another exon branch point= removes an extra exon, which does not allow a functional protein

Question 7

the eIF2 system is control in which step?

Answer 7

translational control, step 3

Question 8

describe what occurs in the eIF2 system

Answer 8

1. eIF-alpha Kinase: activated by stress on a cell like viral attack, exposure to toxins, etc. phosphorylates eIF- alpha
2. eIF -alpha-P: sticks to eIF2-beta, making it inactive
3. eIF2-B: active state, enzyme brings first methionine with tRNA in translation initiation

Question 9

when is the eIF2 system relevant

Answer 9

-when a virus enters the cell to make virus proteins by inserting genetic info into

Question 10

what are the characteristics of miRNA (mRNA degradation)

Answer 10

-do not get used for protein production
-get transcribed by an RNA poly II
-have a G cap and poly A tail
-fold into a stem leaf structure
-found in the nucleus
-located between protein-coding regions, considered “junk DNA”
-play roles in ensuring proper levels of RNA’s and LNCR
-built during transcription regulation

Question 11

what happens to miRNA before they leave the nucleus

Answer 11

-drosha protein: modifies miRNA, removes the G cap and poly A tail
* miRNA is cut into precursor miRNA, removal allows miRNA to leave nucleus and enter the cytolplasm

Question 12

what happens to miRNA in the cytoplasm

Answer 12

-Dicer protein: cuts ends on each side of pre-miRNA. makes 3’ overhangs.
-binds to argonant protein: pulls off one strand mi RNA. includes around 21 bases
-forms RISC: RNA induced silencing complex; will match and degrade mRNA.
*Translation of mRNA is inhibited.

Question 13

how is Alzheimer’s an example of mRNA degradation by miRNA

Answer 13

-bace 1 enzyme: generates B-amyloid proteins, more amyloid increases chance of misfolded B amyloids. stabilized by LNCR
-misfolded-B amyloids: detected in plaques, deformed brain tissue.
-LNCR needs to be chewed up by a specific RISC complex, if miRNA is not functioning properly, it is not chewed up again.
-if it is not chewed up, it leads to too many stabilized Bace 1 enzymes which leads to high levels of misfolded amyloid proteins

Question 14

what is siRNA (mRNA degradation)

Answer 14

-human manipulated, specific to gene
-not delivered to the nucleus
1. take LNCR
2. insert into cell through transfection: into a phospholipid bilayer bubble
3. fuse
4. dicer cuts
5. Ago 1 separates strands
6. RISC complex is formed and chews LNCR specific

Question 15

why is protein degradation beneficial?

Answer 15

-breakdown of proteins allows amino acids to be broken out of polypeptide chains and form other proteins

Question 16

what is ubiquitin

Answer 16

small protein, very common
1. bind to enzyme and tags it with 70 a.a
2. triggers ubiquitination further= U chain made
3. U chain is fed into proteasomes: use active enzymes called proteases, they degrade proteins to short peptides and single a.a
4. secondary active transport is used to bring aa into cells

Question 17

what happens to the size of the genes used in southern blot:

Answer 17

-size differences will be seen, due to restriction enzymes

Question 18

northern blot

Answer 18

finds RNA
-cell is opened and contents are inserted into a column, poly A stick to T’s inside, everything else runs through and then it is placed into an elution buffer and RNA drips out.
-all RNA is the same size
-uses the same probe as southern
-exposes into pH or temp difference and compares how the gene is turned on for transcription regulation

Question 19

western blot

Answer 19

-tests whether or not RNA is translated into a protein
-open the cell and isolate proteins
-run gell in acrylimide
-blot: saturated buffer (filter paper), gel, nitro cellular membrane, saturated buffer, inside a chamber with charge which pulls the protein up
-dicer needs to be purified:
1. size exclusion column separates and collects proteins, largest run through first, separate dicer from similar sized proteins, add similar sized proteins into an ion exchange column, pick + charge ion system, + charge proteins run faster, (-) dicer takes longer. collect by separating.
2. take dicer and inject into a bunny: dicer sticks to cells and mass produce, and release antibody, label antibodies.
*radioactive antibodies as a probe.