The Central Dogma

Question 1

What is true of cells and their expression of genes?

Answer 1

Often, cells are always expressing genes, but at different amounts and rates, due to a difference in the ability of specific transcription factors.

Question 2

What are 5 general places to regulate gene expression?

Answer 2

Chromatin remodeling, transcription factor regulation, mRNA splicing/maturation, destruction of mRNAs, or protein level phosphorylation

Question 3

Nucleosome

Answer 3

Histone octamer surrounded by DNA

Question 4

Inactive genes [methyl/acetyl]

Answer 4

Methylated DNA in promoter, and methylated, deacetylated histones

Question 5

Active genes

Answer 5

acetylated, non-methylated histones

Question 6

What do acetyl groups do to histones?

Answer 6

It spreads them apart, unwinding the DNA

Question 7

Promoter

Answer 7

sequence that starts the sequence of an active gene

Question 8

What are CpG islands?

Answer 8

They are places where a transcription factor binds and activates a promoter to transcribe the active gene

Question 9

Where is DNA methylation high?

Answer 9

In primordial germ cells, right before fertilization, and at the embryo stage.

Question 10

General transcription factors

Answer 10

bind to gene promoters and organize the transcriptional machinery

Question 11

Regulatory transcription factors

Answer 11

bind to enhancers to make transcription more or less efficient

Question 12

Where is the TATA box located?

Answer 12

In the promoter sequence.

Question 13

What must be true before RNA polymerase can bind to the gene?

Answer 13

Several General transcription factors must be present

Question 14

How to regulatory transcription factors interact with enhancers?

Answer 14

They can create a 3d complex such as the mediator complex which more easily allow RNA polymerase to bind.

Question 15

Where in relation are enhancers located to the active gene?

Answer 15

Usually far away

Question 16

What are two properties of regulatory transcription factor binding that promotes differentiation and variation?

Answer 16

Combinations of transcription factors, and cascades can induce variability

Question 17

How do transcription factors ensure differential gene expression?

Answer 17

Specific tissues have specific transcription factors that activate tissue specific enhancer sequences

Question 18

MyoD1 [explanation, sufficiency/necessity]

Answer 18

Can induce differentiation into muscle. is sufficient, but not necessary, as this works with myf5 as well

Question 19

What is the technical name of something that promotes differentiation into muscle?

Answer 19

myogenic factors

Question 20

Pax6

Answer 20

induces differentiation into eye tissue

Question 21

How can you study transcriptional regulation without changing the gene’s natural function?

Answer 21

Fuse the regulatory DNA associated with a gene to a “reporter” e.g GFP

Question 22

Splicing

Answer 22

taking specific exons out of the nRNA , can make many combinations.

Question 23

5’ cap

Answer 23

translatability

Question 24

3’-UTR

Answer 24

mRNA localization, regulation of translation

Question 25

poly A tail

Answer 25

mRNA stability, translation

Question 26

Polyadenylation element

Answer 26

AAUAAA catalyze addition of As to the tail.

Question 27

Where do RNAs usually end up in the Oocyte?

Answer 27

In the vegetable pole

Question 28

What is nanos mRNA

Answer 28

mRNA that is being currently translated

Question 29

What section of mRNAs attach to microtuble motors?

Answer 29

The 3’-UTR region

Question 30

Which direction do kinesins travel?

Answer 30

Toward the posterior end of the cell [Positive]

Question 31

Which direction do dyneins move?

Answer 31

Toward the anterior end of the cell [Negative]

Question 32

What do bicoid mRNAs attach to? [which motor]

Answer 32

Dyneins

Question 33

What do oskar mRNAs attach to? [which motor]

Answer 33

Kinesins

Question 34

What are two ways that mRNA translatability can be affected?

Answer 34

The Maskin/CPEB/4E complex, and the Bicoid/Caudal complex.

Question 35

How is the Maskin/CPEB/4E complex changed after fertilization?

Answer 35

CPEB is phosphorylated, poly(A)polymerase is recruited, building As which can bind poly(A) binding protein(PABP), which can finally initiate translational cofactors at the 5’ end.

Question 36

The maternal to zygotic transition varies in time between species [true/false]

Answer 36

true

Question 37

What is the name of small RNAs that regulate mRNAs?

Answer 37

micro RNAs, [miRNAs]

Question 38

First stage of a microRNA

Answer 38

pri-miRNA (primary micro RNA)

Question 39

Pri-miRNA is processed to ____ by ____ in the second step

Answer 39

Pri-miRNA is processed to pre-miRNA by Drosha

Question 40

Pre-miRNA is processed by ____ into short double stranded RNA duplexes.

Answer 40

Dicer

Question 41

RISC choices

Answer 41

if the mRNAs match, then the mRNA is destroyed. If the match is inexact, translation is blocked.

Question 42

Degradation of proteins is marked by ____ to be sent to the ____ for destruction

Answer 42

Degradation of proteins is marked by ubiquitins to be sent to the proteasome for destruction

Question 43

What famous signaling pathway that we have been studying uses proteasome?

Answer 43

Wnt B catenin signaling. In the absence of Wnt signaling, GSK-3, and APC add ubiquitins to Beta catenin, destroying it.