genetics exam #3 content updated

structural genes

encode proteins that do the cell’s work

ex: lacZ, lacY, lacA

regulatory genes

encode products that control other genes

ex: lacI → repressor

constitutive genes

always on/being transcribed

ex: lacI

negative control

regulatory protein is a repressor → turns genes off

positive control

regulatory protein is an activator → turns gene on (stimulates transcription)

what are the different levels of gene expression?

• transcription (most common(

• mRNA

• translation

• protein

DNA-binding proteins

proteins that interact with the DNA molecule to regulate gene expression, replicate genetic material, or repair cellular damage.

motif of the proteins (their characteristic structure) fits the major groove of the DNA helix, H-bonding to bases

example of classical bacterial motif

helix-turn-helix

example of eukaryotic motifs

zinc finger, leucine zipper, homeodomain

what are the features of an operon and what do they do?

1. promoter: where RNA polymerase binds

2. operator: repressor binds to this

3. structural genes: encode enzymes

4. regulatory gene: outside the operon and regulates structural genes

negative inducible operon

gene normally off

inducer inactivates the repressor, turning the gene on.

ex: lac

negative repressible operon

gene normally on

corepressor activates repressor, turning the gene off

ex: trp

positive inducible operon

gene normally off

inducer activates activator

ex: cAMP

positive repressible operon

gene normally on

molecule inactivates activator

explain the lac operon structure

lac operon has three structural genes (lacZ, lacY, lacA). upstream is the promoter and then the operator, where the repressor protein binds.

the lacI gene (regulatory gene) makes the repressor protein and it’s always made (constitutive)

lac operon is off by default

explain what happens to lac operon when lactose is present

1. lactose(inducer) gets converted to allolactose, which binds the repressor protein

2. repressor protein changes shape, so it gets lets go of operator

3. with operator unblocked, RNA polymerase can now bind freely to the promoter and transcribe all the structural genes into a single mRNA strand.

cis-acting elements regarding operons

DNA sequences that regulate the expression of genes located on the same piece of DNA. cannot diffuse to other chromosomes or DNA strands.

in the lac operon, the cis elements are the promoter, operator, and cap-binding site

trans-acting elements regarding operons

molecules encoded by regulatory genes that are diffusible -< can regulate target DNA sequences regardless of their location

in the lac operon, the lac repressor protein (lacI gene product) can bind to any operator within the cell.

what does lacI- mutation do?

repressor protein nonfunctional, so the operon is always on.

trans, recessive

what does lacI^s mutation do?

binds the operator, but can’t respond to allolactose, so the operon is never induced

trans, dominant

what does lacO^c mutation do?

operator is mutated so the repressor can’t bind, so the operon is always on

cis because it only affects the gene on the same DNA

what does lacP- mutation do?

promoter is broken, so RNA polymerase cannot bind and no transcription occurs even if allolactose is present

cis

catobolite repression and what does it result from?

when glucose is available, bacterial genes that participate in the metabolism of other sugars are turned off because metabolism of glucose is preferable, since it requires less energy,

results from positive control in response to glucose. (transcription is turned on in response to low glucose)

explain catabolite repression with the lac operon

1. when lactose is present, the repressor protein is removed from the operon and transcription is active. Even with the repressor protein gone, transcription is week unless CAP-cAMP is bound near the promoter. This speeds up the transcription.

2. When glucose is low, CAP-cAMP is high, encouraging the transcription of the structural genes.

3. however, if glucose is high, CAP-cAMP will be low, and thus lac operon won’t turn on.

4. cell will metabolize glucose instead b/c it''s easier

what does trp operon do?

makes the enzymes that synthesize tryptophan

• trp operon is a negative repressible operon. it has 5 structural genes that produce the components of 3 enzymes.

• the enzymes convert a precursor molecule to tryptophan

• when tryptophan is low, the trp repressor is normally inactive and it can’t bind to the operator

• when tryptophan is high, tryptophan binds to the trp repressor, activating it. the trp repressor then binds to the operator and shuts transcription of the structural genes off → no more tryptophan synthesized

attenuation

regulatory mechanism in trp operon that causes premature transcription termination when tryptophan levels are high

works with the operon to make sure that tryptophan isn’t being synthesized when it’s already at high levels

bacterial enhancers

have binding sites for proteins that increase transcription at promoters that are from the enhancer

what are the main types of enhancers (3)?

1. antisense RNA

2. riboswitches

3. ribozymes

enhancer: antisense RNA definition

controls gene expression by binding to sequences on mRNA and inhibiting its translation

enhancer: riboswitches definition

sequence on mRNA molecule where regulatory molecules can bind and affect gene expression by influencing the formation of secondary structures in the mRNA

enhancer: ribozyme definition

RNA catalyst that can break sugar-phosphate backbone of RNA, preventing translation of mRNA.

methods of gene regulation found ONLY in bacteria, not eukaryotes

• genes are organized into operons that are transcribed into a single mRNA cluster

  • transcription and translation occur at the same time

methods of gene regulation found ONLY in eukaryotes, not bacteria

• no operons. eukaryotes have their own promoters and are transcribed separately

• chromatin structure affects gene expression

• transcription and translation are separated in time and space

what are the levels of control of gene expression in eukaryotes?

1. chromatin

2. transcription factors

3. RNA-level control

heterochromatin

condensed, transcription off

euchromatin

open, transcription on

CpG when DNA is condensed (heterochromatin-like)

CpG is methylated and has deacetylated histones

CpG when DNA is open (heterochromatin-like)

unmethylated and histones carry acetyl groups that spread the nucleosomes apart, exposing a stretch of bare DNA transcription can bind → turns on gene