Gene Expession

Question 1

Where do transcription factors bind to on small stretches of DNA?

Answer 1

The minor and major groove

Question 2

How can gene transcription be activated at a distance?

Answer 2

DNA looping

Question 3

What are the conserved signalling pathways?

Answer 3

Notch, wnt, hedgehog, TGFb family, RTK family

Question 4

Why do cells have the same genes yet express different phenotypes?

Answer 4

they all have the same but are expressing different genes, i.e some of the genes re turned off some are on regulated by transcription factors

Question 5

How are genes switched on?

Answer 5

activator proteins binding to the promoter region of a gene to begin transcription

Question 6

What would happen to the lac operon gene in the following circumstances:
1. +glucose, +lactose
2. +glucose, -lactose
3. -glucose, -lactose
4. -glucose, +lactose

Answer 6

1. operon is off, glucose is used as food source
2. lac repressor binds, operon is off and glucose used as food source
3. repressor is bound, activator is bound, operon is off
4. activator is bound, operon is on, lactose can be used

Question 7

What is a cis regulatory sequence?

Answer 7

a little bit of DNA where transcription factors bind, that’s on the sae molecule that the gene is on

Question 8

what are examples of homeodomain proteins

Answer 8

hox genes, nanog and Pitx1

Question 9

Where do homeotic mutations occur

Answer 9

in the homeodomain protein transcription factor

Question 10

What is a helix-loop-helix protein and an example

Answer 10

made up of a short alpha helix connected by a loop to a second, longer alpha helix. binds as a dimer to interact with DNA. such as MyoD

Question 11

Explain how the cis-regulatory sequences of the eve gene cause a stripe pattern

Answer 11

each of the 7 regulatory segments is responsible for one of the 7 stripes. such as eve stripe 2 - regulated by 2 activator proteins and 2 repressor proteins.

Question 12

What is the difference in Pitx1 expression between marine and freshwater fish

Answer 12

Pitx1 expression results in a pelvic spine in stickleback fish, caused by changes in cis-regulatory sequences meaning that in freshwater fish, the TF cannot bind and the pelvic spine isn’t formed

Question 13

Give the chain of events from an external signal to the result in developmental processes

Answer 13

external signal -> TF -> genes -> proteins -> cell properties -> developmental processes

Question 14

What is the basis of the notch signalling pathway?

Answer 14

activated by ligand on neighbouring cells, contact-dependent, NOTCH receptor interacts with logan’s and some is cleaved off. moves to nucleus and targets CSL pathway. involved in lateral inhibition and somite formation

Question 15

What is the basis of the Wnt signalling pathway?

Answer 15

binds to frizzled receptor, paracrine signalling, moves to nucleus, signalling prevents the degradation of beta catenin TF. when signalling is present the TF can enter the nucleus and alter transcription. used in limb development, tissue regeneration

Question 16

What is the basis of hedgehog signalling?

Answer 16

binds to patched receptor, stops smoothened proteins working which translocates Ci protein to nucleus. with no hedgehog signalling, Ci is cleaved and repressed genes. involved in limb development, facial morphogenesis

Question 17

What is the basis of the TGF beta family

Answer 17

extracellular TGF binds to receptors, activates SMAD proteins and phosporylates them to trans locate TF to nucleus. involved in bone formation and early vertebrate patterning

Question 18

What is the basis of the RTK family

Answer 18

fibroblast and epidermal growth factors interact with RTKs which phosphorylase tyrosine residues, results in a cascade with phosphorylates the nuclear TF. maintains the mesoderm and involved in cell proliferation and limb patterning

Question 19

What 3 mechanisms result in signalling specificity?

Answer 19

gene duplication, the response of the cell depending on the accumulation of other signals it recieves at the same time, cells with different TFs, proteins, RNA and chromatin states respond differently

Question 20

What are the 2 mechanisms cells can use to maintain a differentiated state?

Answer 20

• autoactivated expression
• trithorax and polycomb groups stamping the chromatin to give a heritable record

Question 21

What is the polycomb group responsible for?

Answer 21

structural development and stating what cells in certain locations will develop into. maintains hox gene repression/switching off genes

Question 22

What is the trithorax group responsible for?

Answer 22

maintaining hox gene expression

Question 23

What are the two types of chromatin

Answer 23

heterochromatin - condensed, restricts gene expression, inherited by daughter cells
euchromatin - looser

Question 24

How is heterochromatin involved in early X chromosome development

Answer 24

one of the 2 X chromosomes is inactivated and becomes heterochromatin so will not express genes as TF’s cannot bind - therefore only 1 X chromosome will be expressing genes

Question 25

What is the structure of chromatin

Answer 25

repeating nucleosome units (DNA helix wrapped around histones - histone tails can extend out from the core histones) with non-histone proteins attached. chromatin ins 30nm thread.

Question 26

How can histone tails be modified

Answer 26

methylation, acetylation and phosphorylation - changes histones and DNA to express things differently. modification is reversible

Question 27

How can chromatin be modified

Answer 27

changing the histone variant

Question 28

How can TF’s cause changes in chromatin structure

Answer 28

nucleosome sliding, nucleosome removal, histone replacement and histone modification - all alter spaces for TF to bind more easily

Question 29

How do embryonic stem cells remain in their state

Answer 29

by autoactivation and cross activation to maintain TF expression