gene regulation

Question 1

What is epigenetics

Answer 1

the study of how cells control gene activity without changing the DNA sequence.

Question 2

How do are cells, that have identical genes, appear and function so differently?

Answer 2

• Different gene expression

Question 3

What are the main protein components of a Chromosome?

Answer 3

Histones: bind to Dna and give chromosomes shape and help activity of genes
8 histones come together to make a nucleosome

Question 4

What structural similarities do these four proteins share

Answer 4

Each histone has
- 3 alpha regions
- N terminal tail (where regulation occurs as post-translational modifications) and c terminal tail

Question 5

How do they interact with the DNA?

Answer 5

DNA can make two full warp around H3\H4 tetramer
H2.H2B tetramer comes in
Tails of histones stick out

Question 6

In what region on the proteins do these modifications mainly occur?

Answer 6

Histone tails are the sites of active post-translational modifications

Question 7

acetylation

Answer 7

removes positive charge on lysine

Question 8

Methylation

Answer 8

methyl groups added to lysine side chains (larger positive charges)

Question 9

Phosphorylation

Answer 9

makes tails of serine, threonine and tyrosine negative.

Question 10

How do these proteins and DNA interact to give Chromosomes more condensed or relaxed states?

Answer 10

Histone acetyltransferase: relax the structure of chromosomes Histone De-acetylase: more condensed

Question 11

How do HAT’s and HDAC’s alter gene expressio

Answer 11

HAT- by transferring acetyl groups to specific lysine
HDAC: removes acetyl groups from lysine to compact

Question 12

chromatin remodeling limited to only acetylation of Histones?

Answer 12

no, Mainence Methyltransferase

DNA polymerase and methylation reproduce genome

Question 13

What is the general model for methylation?

Answer 13

Addition of methyl group to DNA, proteins, or other molecules that can affect how cells act in the body
Methylation can turn off genes

Question 14

methylation a permanent or transient way to turn off genes?

Answer 14

A temporary way to turn off genes.

Question 15

reverse methylation

Answer 15

DNA methyltransferase inhibited

Question 16

other factors that can influence DNA methylation levels?

Answer 16

nutrition

Question 17

What exactly is a gene

Answer 17

Portion of DNA that is transcribed, has a promoter, a promoter-proximal element, and enhancers

Question 18

PPE and enhancer

Answer 18

PPE: located near the promoter
Enhancer: located further away from gene

Question 19

What is the difference between General and Specific Transcription Factors?

Answer 19

General: all genes have them in order to proceed with transcription
Specific: ex: PPE/ enhancer , specific for a particular gene

Question 20

What is the “Combination Lock” model for Transcriptional Regulation?

Answer 20

Where co activations work with enhancer, PPE, and promoter region to initiate transcription

Question 21

how Transcription Factors can bind and affect DNA at other points. what causes different gene expression

Answer 21

Enhancers can still be accessed on tightly packed DNA. These enhancers are transcription regulators. They recruit HAT proteins, not other transcription factors. Specific TF can bind and They can recruit HAT’s to relax condensed Chromatin allowing Transcription.

Different types of enhancers is what causes a different gene expression

Question 22

Coordination can be enhanced/repressed with other signaling molecules

Answer 22

Just transcription factors can translate and will have slow rate of transcription

If a specific transcription factor binds with a specific signaling molecule, it can bind to multiple genes. Combination with a specific along with a common factor, it can amp up the rate of transcription

Question 23

“Master TF” can cause the expression of multiple genes – MyoD

Answer 23

• A cell that doesn’t know what it is, will not express genes. They are off
• Reason: earlier gene, gene for MyoD, a specific transcription factor, is off.
• gene is necessary to turn muscle genes on.
• As cell becomes muscle cell, one of genes will start expressing, the myoD gene,
• Low level of expression to create MyoD protein
• As cell continues to actually becomes muscle cell, MyoD will be a transcription factor for itself.
• MyoD will come back and bind to MyoD gene and upregulate more MyoD
• Also a transcription factor for other genes, upregulate to make different transcription factors. (make more myosin

Question 24

a. What is microRNA (miRNA) and how does it inhibit gene expression?

Answer 24

• miRNA: very small (22 bp) and interacts with a protein to form a miRNA protein complex.
• Goes out into cytoplasm and looks for mRNA that has a complementary sequence and can hybridize to mRNA, it can degrade mRNA strand.
• The more its complemented, the faster itll degrade. If its not that complement, itll inhibit the message.
• Depending on how long the message is in the cytoplasm, control how much of gene product is made.

Question 25

How do the specific structures of Ferratin or Transferrin mRNA’s up or down regulate their gene expression in conditions of high or low [Iron] in a cell?

Answer 25

• bind to hairpin structure of mRNA that encodes for either transferrin ( can make a transmembrane ion that can bring FE into cell) or ferritin(storage FE)
• ferritin: in lack of iorn, ferritin is blocked (located at 5’ end and can not translate the mRNA strand) in lots of iron, iron, will bind to aconitase, causing change, fall off the mRNA and allow translation to happen.
• Transferrin: in lack of iron, located at 3’ end, can encode for receptor to bring in more FE , lots of iron, same will happen, but once it falls off hairpin, exonucleases can degrade mRNA of making transferrin receptor

Question 26

What is the basic mechanism for most protein degradation in Eukaryotes?

Answer 26

Ubiquitin: protein that can tag other proteins for degradation. Damage, unfolded, . Stick ubiquitin onto proteins. 4 units on protein will be a strong signal for degredation

Question 27

. Defects in this system are thought to be involved in what two health issues?

Answer 27

Cancer and Alzheimer’s