Study your flashcards anywhere!

Download the official Cram app for free >

  • Shuffle
    Toggle On
    Toggle Off
  • Alphabetize
    Toggle On
    Toggle Off
  • Front First
    Toggle On
    Toggle Off
  • Both Sides
    Toggle On
    Toggle Off
  • Read
    Toggle On
    Toggle Off

How to study your flashcards.

Right/Left arrow keys: Navigate between flashcards.right arrow keyleft arrow key

Up/Down arrow keys: Flip the card between the front and back.down keyup key

H key: Show hint (3rd side).h key

A key: Read text to speech.a key


Play button


Play button




Click to flip

95 Cards in this Set

  • Front
  • Back
What is an excellent example of gene expression regulation in prokaryotes?
The Lac Operon
What is the Lac Operon?
An operon required for the transport and metabolism of lactose in E. coli and other enteric bacteria.
What does the Lac operon consist of?
-3 structural genes
-A promoter
-An operator
-A regulator gene
What is the promoter?
The nucleotide sequence that serves as a recogn motif for RNA Polymerase
What is the operator?
The nucleotide sequence that binds the repressor protein.
What is the regulatory gene in the Lac Operon??
The LacI gene, which encodes a REPRESSOR PROTEIN.
In prokaryotes, where is gene regulation primarily exerted?
At the level of TRANSCRIPTION.
What are Inducers?
Proteins which bind the Repressor protein and weaken its affinity for the Operator.
What are 2 inducers for the Lac Operon?
-Allolactose (byproduct of Beta-galactosidase
-IPTG (gratuitous inducer)
What causes the expression of the REPRESSOR gene?
It is upstream of the Lac Operon promoter, so it has its OWN promoter.
What results when Repressor protein is bound to Operator?
Transcription of the 3 structural genes is prevented.
What are the 3 genes encoded by the Lac Operon?
1) LacZ - B-galactosidase
2) LacY - B-galactoside permease
3) LacA - B-galactoside transacetylase
What does B-galactoseidase do?
-Intracellular enzyme that cleaves the disaccharide lactose -> glucose/galactose.
What does B-galactoside permease do?
-Membrane bound transport protein that pumps lactose into the cell
What does B-galactoside transacetylase do?
-Transfers an acetyl group from acetyl-CoA to B-galctosides.
What type of expression is exhibited by the Lac I gene?
Constitutive expression - the Repressor protein is always around, because Bacteria prefer to utilize glucose.
How does Repressor inhibit Lac operon gene expression?
-What is essential for this?
When bound to Operator it inhibits RNAP from binding the Promotor sequence.
-Lac levels MUST BE LOW.
What happens when Lactose becomes available to E.coli?
-Allolactose (lactose byproduct) binds Repressor
-Conformational change reduces affinity for Operator
-RNAP can now transcribe genes
What is an important characteristic of the Operator site on lac operon?
It exhibits palindromic sequences - opposite in each direction.
What is the significance of the palindromic nature of the Operator site?
The protein that binds it (Repressor) must do so as a DIMER.
What is the mechanism of the Repressor protein?
It binds DNA within the region that would be protected by RNA Pol; this excludes RNAP from binding.
-Does Repressor bind Operator specifically or nonspcfcly?
-So where on DNA helix does it bind?
-Very Specifically - an ARG residue binds a G-C base pair.
-Repressor binds within the major groove.
Resulting from the specific binding btwn Operator and Repressor, in what 2 ways could the bond affinity be altered?
1. Altering the Arg residue (to a neutral AA like Lys)
2. Mutate GC bp to AT
Does the DNAP protected site on Lac operon have palindromic symmetry?
No. :-)
What is the very start of what makes enterics prefer Glucose as a carbon source?
When Glucose=high, cAMP=low

When cAMP=high, Glucose=low
Why is cAMP important with respect to Glucose preference?
cAMP must be complexed to CAP in order for CAP to bind the promoter on lac operon.
What is CAP?
Catabolite Activator Protein
What does CAP do?
When bound to cAMP, it binds the Promoter on lac operon.
What is the result of CAP-cAMP binding lac operon's Promoter region?
It turns on the promoter and allows RNAP to bind and transcribe!
So what 3 conditions are essential for lactose utilization?
-Glucose must be low
-Lactose must be present
-cAMP must be high
If CAP binds the promoter region, doesn't it get in the way of RNAP binding?
No; it binds a region just adjacent to the promoter.
How exactly does CAP-DNA interaction facilitate RNAP binding?
B/c it shows 2-fold rotational symmetry, CAP-cAMP binding provides more sites for RNAP to interact w/ DNA.
In addition to facilitating RNAP binding to Promoter site, what does CAP do?
Upregulate RNA Polymerase.
What is the consensus sequence for the bacterial -10 Promoter?
What is the effect of:
Glucose is high so cAMP is low; no CAP can bind to allow RNAP binding to promoter.
What is the effect of:
-Glu is high, cAMP is low, so no CAP is bound.
-No Lac present, so no inducer to loosen repressor.
What is the effect of:
-cAMP is high so CAP can bind
-Lac is not present so no inducer to loosen repressor.
What is the effect of:
-Glu is low, cAMP is high, CAP can bind to allow RNAP to bind Promoter (TATAAT)
-Lac is present, Inducer is present to loosen Repressor
-RNAP can bind and transcribe
What are 2 types of Negative Regulation via Ligands?
1. Ligand binding repressor removes it and turns gene on.
2. Ligand binding repressor keeps it on the gene; removal of ligand turns gene on.
What is negative regulation?
The repression of genes via a repressor protein - a ligand can be used as either an inducer or helper.
What is positive regulation?
The activation of a gene via binding of an activator protein
What type of regulation is exhibited by CAP?
Positive - where binding of the ligand (cAMP) facilitates binding of the regulatory protein and turns the gene on.
What type of regulation is exhibited by LacI?
Negative - ligand binding causes repressor to unbind.
What are 2 major differences between Euk and Prok gene expression?
1. Proks are polycistronic, Euks are monocistronic.
2. Txn/Tsln in Proks is coupled; in Euks, uncoupled.
How is the SPACING (dstnc from reg protein-binding sites to Promoter regions) different btwn Euks/Proks?
Prokaryotes: CAP must be very close - addition of even 5 nt can result in failure to txn.
Euks - distance is not as important - may be 500-1000s of nt btwn them.
List 4 major areas of Eukaryotic Gene expression:
1. Basal Txn Machinery
2. Regulating Proteins (activators/repressors)
3. Coactivators (mediators)
4. Insulators
What is the basal transcriptional machinery made of?
-General Transcription factors
-TATA binding protein
How is it that Regulating proteins can act at a distance from the promoter?
DNA can wrap around to bring them within close proximity.
What are Coactivators?
Mediating proteins that link the basal txn apparatus to upstream regulatory proteins.
What are insulators?
Sequences of DNA that protect the basal txn machinery to prevent the regulatory proteins from talking to a different polymerase on adjacent genes.
What is the order of assembly of the basal txn machinery?
(6 steps)
1. TBP - TATAA binding protein
2. Other factors
3. Unphosphorylated RNAP II
4. Lose some factors
5. Phosphorylate CTD of RNAPII
6. Txnl elongation occurs!
What is the CTD of RNA Pol II?
C-terminal domain - its phosphorylation is essential for activity.
What are the 4 major types of Transcription Factors in eukaryotes?
1. Helix-turn-helix proteins
2. Zinc finger proteins
3. Leucine zipper proteins
4. Helix-loop-helix proteins
What is the structural feature of a helix-turn-helix protein?
2 alpha helices, separated by B-turn "Recognition helix" which fits into major groove.
What is the structural feature of a Zinc finger protein?
Zinc finger proteins contain ZINC bound to Cys and His side chains.
What is the structural feature of leucine zipper proteins?
2 alpha helices:
-one w/ basic residues for DNA binding
-one w/ regularly spaced Leu for dimerization.
What is the structural feature of helix-loop-helix proteins?
DNA-binding alpha helix, 2 dimerization helices separated by nonhelical loops.
What are 2 examples of helix-turn-helix proteins?
1. Homeodomain proteins (regulators in embryonic devo)
2. Most Prokaryotic repressors
What are good examples of Zinc finger proteins?
Steroid and Thyroid hormone receptors
What are some examples of Leucine zipper proteins?
-C/EBP (gene activator in liver)
-c-Myc, c-Fox, c-Jun (growth regulators, protooncogene products)
What are 3 areas of trnscrption that euk proteins involved?
1. DNA binding
2. Protein-protein interaction
3. Transcriptional activation
How do helix-turn-helix proteins interact with DNA?
They bind palindromic sequences as a dimer by fitting into the major groove.
What exactly on the helix-turn-helix proteins binds the major groove?
2 alpha helices.
Describe the Zinc Finger Motif
-2 Cys and 2 His bind Zinc in a tetrahedral coordination.
-Holds an alpha helix so that its basic Arginine residues optimally bind major groove.
What are 2 examples of the zinc finger motif again?
-Steroid hormone receptors
-Thyroid hormone receptors
Describe the Leucine zipper motif
-Leucine zippers are a dimer of basic proteins - result of protein-protein interaction.
-The dimer binds a palindromic DNA sequence, for its regulatory function.
What does the leucine zipper consist of?
A heptad repeat of leucine resideus - which allows interaction of 2 alpha helices.
Explain the concept of Helix-loop-helix proteins:
Amphipathic molecules that BIND another protein to make a dimer; The DNA-binding dimer is often heterodimeric.
Again, give 3 examples of helix-loop-helix proteins:
How exactly do transcription factors regulate gene expression?
TF's have different domains:
-DNA binding domains
-Protein-protein or ligand binding domains
Give 3 examples of characteristic activation domains in TF's:
1. Acidic domains
2. Glutamine-rich domains
3. Proline-rich domains
How could the activity of a putative activator be studied?
By fusing it to a known DNA binding domain (tether)
What is the difference between euchromatin and heterochromatin?
Heterochromatin = highly condensed.
Euchromatin = relatively diffuse
Which type of chromatin is more active; euchromatin or hetero?
Where in chickens is the globin gene more active, and how would you know?
More active in blood cells, not in the oviduct; can tell because it is nuclease sensitive.
Where in chickens is the ovalbumin gene more active?
Active in the oviduct, not in blood cells.
How does methylation affect chromatin?
Methylation causes condensing and deactivation of genes.
List 4 possible ways that Negative TF's may act:
1. Bind DNA to block a POS factor from binding.
2. Bind a POS TF to prevint it from binding - or speed its degradation
3. Inhibit binding/assembly of preinitiation complex
4. Recruit histone deacetylase
What is the term for
-Highly condensed chromatin
-Relatively diffuse chromatin
Condensed = herochromatin

Diffuse = euchromatin
What is the activity level of heterochromatin?
Transcriptionally Inactive
What type of protein is H1 generally described as?
A linker protein - it binds the linker regions of nucleosomal DNA.
Which kind of chromatin are H1 proteins generally associated with?
Condensed - Heterochromatin - they hold it together.
How do Methylation and Acetylation change chromatin?
Acetylation opens it up; Methylation closes it down.
What 3 chemical modifications are associated with active chromatin?
-Sensitivity to nuclease
What is a syndrome associated with histone modification?
Why is it that methylated DNA is generally inactive?
Proteins recognize the methyls, and prevent binding of transcription factors.
So what is associated with cancerous tissue?
Hypomethylated DNA
What are insulators?
sequences that can block enhancer promoter interaction
What are insulators important in?
Gene therapy - blocking aberrant activation of genes.
How are insulators proposed to work?
By providing a binding site for proteins (CCCTC-binding factor) which lead to the recruitment of chromatin remodeling enzymes.
What is a disease that has been associated with loss of insulator sequences?
Myotonic muscular dystrophy
What is the problem in myotonic muscular dystrophy?
Insulator sequence loss results in aberrent activation of the DMPK gene by a nearby enhancer.
What is a Barr Body?
The inactive X chromosome in female somatic cells.
How do cells know which X chromosome to turn off?
They don't; it's random
What is seen in women heterozygous for anhidrotic ectodermal dysplasia?
Patches of skin w/out sweat glands(mutant active), and Patches of normal skin (mutant inactive).