Regulation of Gene Expression

Question 0

What distinguishes higher organisms isn’t a difference of genes, but rather a difference in the …

Answer 0

regulation of genes

Question 1

Because all nucleated cells contain the same DNA, the difference in cell phenotype must be based on _______

Answer 1

differential regulation of gene expression

Question 2

Think of 6 ways eukaryotic gene expression can be controlled.

Answer 2

1) DNA structure
2) Frequency
3) Splicing
4) where mRNAs go
5) which mRNAs are translated
6) rate of mRNA degredation
7) control of proteins

Question 3

Just know that increasing the number of gene copies can increase expression. More copies, more expression.

Answer 3

Gene Copy Number

Question 4

Euchromatin __________

Answer 4

Transcriptionally active; loose chromatin

Question 5

Heterochromatin____________

Answer 5

compact chromatin (SILENCING genes), transcriptionally inactive

Question 6

Acetylation of Histones=

Answer 6

euchromatin, active transcription

Question 7

Deacetylation of histones=

Answer 7

Heterochromatin, inactive transcription

Question 8

Regulatory regions near transcription initiation contain short stretches of DNA called ______ and gene regulatory proteins, _______, that recognize and bind to these stretches for gene regulation

Answer 8

DNA- cis-acting

protein- trans-acting

Question 9

The _____ groove of the DNA helix is accessible for regulatory proteins to bind to for regulation

Answer 9

Major

*** proteins can bend DNA and change the structure of DNA for gene regulatioin

Question 10

Gene regulatory proteins contain specific structural motifs that recognize DNA sequences. Numerous contacts are made to ensure that the interaction between protein and DNA is strong.

Answer 10

Cool.

Question 11

Motif __________ is one of the most simplest and common motifs.

Answer 11

Helix-turn-helix

Question 12

Motif– _________ proteins are a special subclass of helix-turn-helix proteins that are key Regulators of animal development (embryonic)

Answer 12

Homeodomain proteins

***** important

Question 13

Motif- another important group of regulatory proteins is ________ proteins because they have zinc atoms and they look like fingers.

Answer 13

Zinc Finger Motif…..pretty obvious

Question 14

Motif- This dimer grips DNA like a clothespin on a clothesline. It’s called the _______ motif

Answer 14

Leucine Zipper

Question 15

Motif– _______ motifs can create both homodimers and heterodimes

Answer 15

Helix-Loop-Helix

Question 16

Many regulatory proteins can bind as heterodimers. Heterodimerization increases….

Answer 16

the variety of DNA sequences recognized

Question 17

In bacteria, gene switches allow for the expression of genes to be dependent on the available food in the environment. “Gene switches in action”.

Answer 17

Awesome.

Question 18

Explain the E.Coli tryptophan operator. ie. What happens when tryptophan is present in the cells environment?

Answer 18

• the 5 genes needed to produce tryptophan are next to each other and are controlled by one operator
• when tryptophan is present in environment, expression of 5 genes no longer needed–> production needs to be shut off
• tryptophan activates tryptophan repressor protein which attaches to the operator, blocking the binding of the promoter
• NEGATIVE CONTROL

Question 19

Activator proteins can ….

Answer 19

assist in the binding of RNA poly to help promote transcription

Question 20

Negative regulation:

Answer 20

bound repressor protein prevents transcription

Question 21

Positive regulation:

Answer 21

bound activator protein promotes transcription

Question 22

______can bind regulatory protein to remove it from DNA or bind to allow regulatory protein to bind to DNA– for both repressor protein or activator protein

Answer 22

ligands

Question 23

Go study lac operon

Answer 23

Quick quesiton: what if there was a mutation of the enzyme that converts Lactose into Allolactose…?

Question 24

Regulation in eukaryotes is very complex. Regulatory regions can be very long, and unlike prokaryotes, RNA poly cannot initiate transcription on its own; it must have __________ proteins that assemble at the promoter for transcription to occur

Answer 24

basal transcription factor proteins

Question 25

Regulatory sites that are distant from the promoter are called ______. These sequences loop to join the promoter

Answer 25

enhancers ***can also repress

Question 26

Many gene regulatory proteins consist of two domains: a _____ that recognizes specific DNA and an _____ that accelerates transcription

Answer 26

structural motif; activation domain

Question 27

Transcriptional synergy:

Answer 27

multiple activators can have a greater than additive effect on gene transcription

Question 28

Don't forget how important opening and closing chromatin is for gene regulation. Histone acetylases and histone deacetlyases.....

Answer 28

Acetlyation opens=transcription active | Deacetylation closes= transcription inactive

Question 29

Competitive DNA binding: gene ____ proteins can compete with gene activator proteins for the same regulatory DNA sequence.

Answer 29

Gene Repressor Proteins

Question 30

Masking the activation surface: repressor proteins can....

Answer 30

bind the activation site of the activator protein thereby preventing activation of transcription

Question 31

Direct interaction with the general transcription factors: the repressor blocks assembly of the....

Answer 31

general transcription factors

Question 32

Recruitment of chromatin remodeling complexes: repressor proteins recruit chromatin remodeling proteins which essentially...

Answer 32

closes up the DNA, silencing the promoter

Question 33

Recruitment of histone deacetylases: the repressor attracts histone deacetylases to the ______

Answer 33

promoter

Question 34

gene regulatory proteins often assemble into complexes on DNA. An example is the ______; a group of proteins that form together on an enhancer to regulate transcription at a distant site

Answer 34

Enhanceosome

Question 35

Insulators are....

Answer 35

DNA sequences that prevent regulatory proteins from influencing distant genes (like non related genes)

Question 36

Insulator sequences both prevent the spread of ______ and directionally block the action of _____

Answer 36

heterochromatin; enhancers

Question 37

An example of a gene that would be coordinated by a single protein is ________

Answer 37

human glucacorticoid receptor protein, which makes things like cortisol *** Rapid change wanted in gene expression

Question 38

Chromosome-wide alterations in chromatin structure ( and ultimately gene expression) can be _____

Answer 38

inherited

Question 39

Epigenetics is defined as ________, ________ changes in the genome (no changes in the sequence) that regulate gene expression, most often resulting in _______. It can be influenced by the environment

Answer 39

heritable, reversible; gene silencing

Question 40

_______is a classic example of epigenetics, which is involved in imprinting, development, X-inactivation, and diseases

Answer 40

DNA methylation

Question 41

Explain X inactivation

Answer 41

Female= 2X chromosome only one can be active, the other becomes bar-body of heterochromatin-->silenced chromosomes<-- which is mediated by noncoding RNA called XIST

Question 42

What are four mechanisms that produce epigenetic form of inheritance:

Answer 42

1- positive feedback 2- histone modification (production of heterochromatin) 3- DNA methylation ---leads to heterochromatin 4- Protein aggregation state, conformational change to aggregate state

Question 43

The inactivation of the X chromosome in inherited, meaning...

Answer 43

the progeny cells of the early embryo will have the same X silenced --> clonal inheritance

Question 44

The "5th most common base" is _______. | When something gets methylated, it is maintained in progeny cells of replication.

Answer 44

5-methylcytosine

Question 45

Imprinting is differential expression of gene allele depending on _________

Answer 45

parental origin

Question 46

The purpose of imprinting is to control....

Answer 46

gene dosage= only one allele is expressed as the other allele is imprinted and silent

Question 47

Imprint is created in the _______ cells

Answer 47

parental germ cells ***paternal or maternal

Question 48

The mechanism of gene silencing for imprinting is....which leads to....

Answer 48

5-cytosine DNA methylation which leads to chromatin condenstation

Question 49

Read through mouse slides about imprinting....Male sticks with male, female with female?

Answer 49

ok.

Question 50

Silencing of tumor suppressor genes is common in cancer. Think about it.

Answer 50

Tumor suppressor gene methylated probably....heterochromatin...silenced....gene doesn't express tumor suppressor protein.

Question 51

Transcription of genes can be increased by extracellular signals that induce signal transduction cascades. Examples:

Answer 51

hormones | growth factors

Question 52

Splicing can be regulated by ____, _____, _____ and _______

Answer 52

tissue stage of development age disease

Question 53

Abnormal splicing of mRNA can give rise to proteins with oncogenic properities

Answer 53

bummer

Question 54

Gene expression can be regulated by nuclear transport. How is that?

Answer 54

mRNA is regulated by signal-mediated transport through the nuclear pore grated channel -only fully processed mRNAS can be transported

Question 55

The ____ protein of HIV transports unspliced HIV mRNA from nucleus to cytoplasm, skipping regulation by nuclear transportation

Answer 55

Rev Protein

Question 56

The amount of mRNA in the cell is due to ____ and ____ of mRNA

Answer 56

the rates of synthesis and decay

Question 57

To control the amount of mRNA, the _______ can be tightly regulated. Increase ______, decrease mRNA, decrease expression.

Answer 57

rate of degradation for both blanks

Question 58

Two ways metabolism is regulated in cells:

Answer 58

1- amount of DNA | 2- amount of protein translated

Question 59

If there's a question about antisense mRNAS just pick answer with .....

Answer 59

circadian clock

Question 60

_______ and _____ are short RNAs that are used to silence viral gene expression

Answer 60

microRNA and short interfering RNA (siRNA)

Question 61

Low iron (Fe) requires that cell to shut off _____

Answer 61

Ferritin production

Question 62

Ferritin does what?

Answer 62

Ferritin binds and sequesters intracellular iron. Therefore in a low Fe state, ferritin would need to be shut off

Question 63

in state of low Fe, Ferritin is inhibited by..

Answer 63

IRE-BP protein that inhibits ferritin translation

Question 64

Transferrin receptors do what?

Answer 64

import iron across the plasma membrane of a cell

Question 65

Ferritin and Transferrin are both mediated by the same iron-responsive regulatory protein _____ , that dissociates from mRNA when it binds Fe.

Answer 65

Aconitase ***** but both ferritin and transferrin are regulated differently

Question 66

Binding of aconitase to the 5' end of ferritin receptor mRNA blocks..... So: -Fe starvation -Fe excess

Answer 66

blocks translation initiaiton Fe starvation: not bound by Fe so translation blocked, therefore ferritin can't sequester Fe Fe excess: Fe binds aconitase, releasing it from ferritin hair loop, allowing for translation of ferritin gene--Fe going to be sequestered

Question 67

Binding of aconitase to the 3' end of transferrin receptor mRNA.... - Fe starvation - Fe excess

Answer 67

... stabilizes mRNA by preventing endonucleases from cleaving/degrading mRNA - Fe starvation: aconitase binds mRNA hairpin, allowing for Transferrin translation--> uptake of Fe into cell - Fe excess: aconitase bound by Fe, released from mRNA, leaving hairpin free for degredation --> transferrin receptor gene not translated

Question 68

glycosylation:

Answer 68

addition of a carbohydrate to protein

Question 69

phosphorylation:

Answer 69

kinases add proteins to make them active/inactive dephosphorylation: removes p (phosphatases)

Question 70

Lipid modification:

Answer 70

addition of lipid to protein

Question 71

Cleavage of protein:

Answer 71

unmasks functional group of protein

Question 72

Circadian clock runs on 24 hour clock that....

Answer 72

produces Tim and Per proteins that repress own transcription in nucleus on 24 hours cycle. Light degrades Tim

Question 73

you can also degrade and allosterically regulated proteins

Answer 73

Last card.