Lecture 15

Question 1

different cell types of a multicellular organism contain _______

Answer 1

the same DNA

Question 2

is the DNA sequence in the neutron the same as the DNA sequence found within a liver cell?

Answer 2

yes, it is the expression of different collection of genes in a cell type that cause large variations in size, shape, behaviour and function

Question 3

what are house keeping genes

Answer 3

• genes that are common to all cells of a multicellular organism

Question 4

example of house keeping genes

Answer 4

• ribosomal proteins
• RNA polymerases
• cytoskeleton proteins

Question 5

gene expression

Answer 5

• cells can alter their pattern of gene expression in response to extracellular signals

for example: cortisol
- in liver cells, tyrosine aminotransferase increases
- in fat cells, tyrosine aminotransferase decreases
- in other cells there is no affect

Question 6

how do we regulate gene expression

Answer 6

• regulation can occur at various steps, but control over transcription (step 1) is very important

Question 7

how can transcription be turned “of” or “on”

Answer 7

• transcription is control by regulatory DNA sequences
• the operator of the trp opera is a regulatory DNA sequence that controls transcription of tryptophan production and related products by being bound by a repressor protein

Question 8

transcriptional regulators (give examples)

Answer 8

• bind to regulatory DNA sequences to promote or repress gene expression
• tryptophan repressor is a transcriptional regulator, but more specifically it is a transcriptional repressor because it inhibits transcription
• CAP is a regulatory activator because its binding to regulatory DNA sequences promotes gene expression

Question 9

how to transcriptional regulators bind

Answer 9

• often insert into the major groove of DNA where specific amino acids can interact with specific base pairs
• or bind as dimers which increases the area of contact with DNA which increases strength and specificity of protein-DNA interaction

Question 10

what are operons

Answer 10

• genes that encode proteins that are all involved in the same process
• bacteria usually cluster genes into operons

Question 11

how are operons controlled

Answer 11

• they are controlled by a single promoter

Question 12

what is the significance of the tryptophan operon?

Answer 12

• when tryptophan levels are low, RNA polymerase binds to the promoter and begins transcription of products involved in tryptophan production
• when tryptophan levels are high, tryptophan binds to the tryptophan repressor which allows it to bind to the operator. This binding prevents RNA polymerase from binding

Question 13

give an example of a transcriptional regulator that is controlled by multiple transcriptional regulators

Answer 13

Lac operon:
- encodes for proteins that are involved in lactose metabolism
- E. coli can used glucose or lactose as a carbon source, but it prefers glucose

Question 14

What is negative regulation of the lac operon

Answer 14

• the lac repressor can bind to the operator and prevent transcription
• when lactose is present, the lac repressor does not bind to the operator
• when lactose is absent, the lac repressor binds to the operator and prevents transcription

Question 15

what is produced when lactose is present

Answer 15

• allolactose

Question 16

what is the positive regulation if the lac operon

Answer 16

• the transcriptional activator, CAP, can bind to regulatory DNA sequences to promote transcription of Lac operon
• helps RNA polymerase bind
• CAP only binds with high level cAMP
• levels of cAMP are inversely proportional to levels of glucose

Question 17

when will lac operon be highly expressed

Answer 17

• no glucose
• high lactose

Question 18

what do the controls ensure

Answer 18

• the controls ensure that the lac operon is expresses when lactose is present and no glucose is present
• this makes sense for E. coli because it prefers glucose over lactose

Question 19

how do transcriptional activators interact with the promoter

Answer 19

• by “looping” the DNA

Question 20

What is the enhancer and mediator in eukaryotic transcriptional regulation

Answer 20

• enhancer: binding site for activator proteins –> promotes transcription
• repressors do the opposite
• mediator: a complex of proteins that serves as an intermediate between regulatory proteins and the transcription complex

Question 21

how do eukaryotes deal with higher levels of chromatin condensation when regulating gene expression

Answer 21

1. chromatin-remodelling complexes
2. covalently modify histone proteins
   ex. histone acetyltransferases promote the acetylation of lysine, allowing greater accessibility of DNA
   - histone deacetylases remove acetyl groups and reverse this affect

Question 22

what is cell memory

Answer 22

changes in gene expression are remembered by a cell

Question 23

what is combinatorial control

Answer 23

the way groups of transcription regulators work together

Question 24

instead of clustering genes into operons like bacteria, what do eukaryotes do to control multiple genes at the same time

Answer 24

• eukaryotes use combinatorial control to make single transcription regulator control multiple genes simultaneously

Question 25

combinatorial control example

Answer 25

- imagine each lock represented a gene and you need to express the gene you need all transcription regulators - all the genes have all the transcription activators except for one (the triangle) - when the triangle is present all genes can be expressed at the same time - same thing can happen with transcription repressors

Question 26

list epigenetic mechanisms behind cell memory

Answer 26

- cells can ensure their daughters "remember" what kind of cell they were 1. positive feedback loops 2. DNA methylation 3. histone modification

Question 27

what do epigenetic mechanisms do?

Answer 27

- they alter gene expression without changing the nucleotide sequence of the DNA - they are forms of epigenetic inheritance

Question 28

Describe the effects that a single transcriptional regulator can have on development

Answer 28

- can trigger formation of entire organs - for example Ey can give rise to an entire eye in the middle of a leg

Question 29

How does positive feedback loops aid in cell memory

Answer 29

- it ensures that all future progeny will also be same cell type

Question 30

How is DNA methylation a method behind cell memory

Answer 30

- because DNA methylation can affect gene expression and DNA methylation patterns are passed down to progeny cells

Question 31

How is histone modification aid in cell memory

Answer 31

- histone modification can affect gene expression - histone modification can be inherited by daughter chromosome

Question 32

post transcriptional controls

Answer 32

- gene expression can be controlled by regulating translation initiation examples: - represser protein binds and prevent mRNA from binding to the ribosome - mRNA is usually found with AUG blocked until the temperature rises

Question 33

What are regulatory RNAs

Answer 33

noncoding RNAs with the ability to regulate gene expression - microRNAs (miRNAs) - small interfering RNAs (siRNAs) - long noncoding RNAs

Question 34

How do long noncoding mRNAs regulate gene expression

Answer 34

- may coat the chromosome, causing the association of chromatin-remolding complexes to form heterochromatin

Question 35

What are micro RNAs

Answer 35

- 22 nucleotides in length - complexes with proteins to create the RNA-induced silencing complex (RISC) as a single strand - the miRNA binds to the complementary sequences on target mRNA and causes the degradation of that mRNA by nucleases within RISC

Question 36

What are small interfering RNAs

Answer 36

- defines mechanism against foreign RNA (this is know as RNA interference) - the foreign dsRNA is cleaved by dicer resulting in siRNA - siRNAs bind to the RISC, but only one strand remains bound - the bound RNA binds to complementary RNA which causes its degradation by nucleases within RISC