Selected Section 3 Material

Question 1

Operon

Answer 1

A cluster of genes under a single promoter

Question 2

How do multiple genes transcribed together get turned into multiple proteins?

Answer 2

• Firstly, this only occurs in bacteria. Eukaryotes have a promoter for each gene.
• Even though all the genes in a promoter get transcribed together, they don’t get translated together because each gene has its own rbs (ribosomal binding site) and its own start and stop codons, so they can each be translated by a separate polymerase
• Prokaryotes use an rbs instead of a poly A tail and a 5’ cap b/c they only have one type of RNA polymerase

Question 3

What are the proteins used in the lac operon and digesting lactose?

Answer 3

• The Lac Y gene on the lac operon codes for lactose permease, which will then go exist on the cell membrane to bring lactose into the cell
• Lac Z gene codes for beta-galactosidase, which metabolizes (essentially cuts, in this case) lactose into glucose and galactose, and the glucose can then enter glycolysis to produce ATP

Question 4

How do prokaryotes organize the genes in their operators and why?

Answer 4

• Prokaryotes often organize genes that are in the same metabolic pathway under the same promoter to make it easier to do things more quickly and to be able to control regulation of an entire metabolic pathway with only one promoter

Question 5

k

Answer 5

Remember: bacteria have CORE promoter (general promoter, contains -10 region and -35 region?) and CAP site (gene specific element?)
Eukaryotes have a CORE promoter (TATA box, general promoter), proximal promoter elements, and enhancers

Question 6

cis-regulatory elements

Answer 6

DNA sequences that can function to regulate DNA sequences, like CORE promoter, PPEs, and Enhancers
- Trans-regulatory elements are proteins and things that bind to the DNA to influence transcription, so aren’t actually part of the DNA. These are transcription factors

Question 7

CORE Promoter in Eukaryotes

Answer 7

• Also called the TATA box
• Determines where transcription starts (TSS) and the direction in which transcription takes place
• Recruits TFIID and Pol II, but WITH HELP
• Doesn’t have much transcriptional activity, however, which is why it needs PPEs and Enhancers for a good amount of transcription to occur

Question 8

PPEs/ Enhancers

Answer 8

• Are cis-regulatory elements
• Control level of gene expression with TFs
• Can control where (in which cell type) and when (under which conditions) transcription occurs. This is b/c the TFs activate them, and the TFs are only present in certain cell types and/or conditions

Question 9

Why are TFs considered to be “modular?”

Answer 9

• Because the activation domain and DNA binding domain can function independently of one another
• Because it is modular, we can build artificial transcription factors by linking different DBDs to different ADs (ADs are general, so they aren’t gene specific)

Question 10

Transregulatory elements

Answer 10

Another term for transcription factors

Question 11

DNA Binding Domain

Answer 11

• Has binding specificity, which is determined by its interactions with the bases
• Has binding affinity (how tightly it can bind) which is determined by its interaction with the entire DNA monomer

Question 12

Activation Domain

Answer 12

• Promotes TFII and Pol II recruitment to CORE promoter
• Can recruit Pol II in one of three ways:
  1. Multiple AD domains of various TFs recruit a large protein complex called a mediator which recruits TFII and Pol II
  2. AD recruits some other binding partner to help recruit TFII and/or Pol II
  3. AD recruits TFII and/or Pol II itself
• Also helps in chromatin remodeling by…

Question 13

nucleosome

Answer 13

• About 150 bp of DNA wrapped around 8 histones (that make up the histone complex we typically refer to just as the histone)
• The 8 histones are 2 H2A, 2H2B, 2 H3, and 2 H4

Question 14

Chromatin Remodeling complexes

Answer 14

• A type of helicase
• Are able to remodel the DNA to make a CORE promoter or some other transcriptional element functional
• Require ATP
• Allow transitions between euchromatin states to happen fast
• Do NOT have specific binding domains

Question 15

Histone methylation

Answer 15

• Methylation at K4 of H3 promotes the euchromatin state by being able to bind to chromodomains that are transcriptional activators
• Methylation of K27 and K9 of H3 promotes the heterochromatin state by being able to bind to chromodomains that are transcriptional repressors

Question 16

Mechanisms of heterochromatin spreading

Answer 16

• At telomeres, there are many proteins, including Sir2, and these proteins can attach to the histones near the telomeres
• Sir2 is a histone deacetylase and promotes the spreading of nucleosome deacetylation
• Sir2 removes acetyl groups from neighboring histones
• Since Sir2 prefers to bind to deacetylated histones, these newly deacetylated histones will recruit more Sir2 to deacetylation their neighbors, and the chain continues
• When methylation occurs on K9, this causes a protein called HP1 to be recruited
• HP1 binds to the methylation w/ its chromodomain and it promotes the aggregation of histones to form heterochromatin regions, as well as recruiting more methyl transferases to neighboring histones

Question 17

Glucorticoid

Answer 17

Anti-inflammatory drug/hormone

• Binds to its receptor, which happens to be TF
• The TF has three domains: LBD, DBD, and Repressor domain