Gene Regulation Flashcards
What 3 mechanisms do cells use to regulate metabolic flow?
- ) By changing substrate concentration availability
- ) By changing the relative activity or efficiency of enzymes.
- ) By changing the quantity of enzyme present (The regulation of gene expression is important here.)
How is regulation of gene expression illustrated in differentiation?
By changing the quantity of an enzyme present, the behaviors of liver cells, brain cells, and skin cells all differ even though they all contain the same genetic makeup.
How does substrate availability impact enzyme activity?
- ) For many enzymes, affinity for a substrate (Km) is close to physiological concentration so the rate of utilization is responsive to changes in concentration.
- ) The availability of metal ions and cofactors may impact enzyme activity.
- ) The enzyme is affected by immediate environment.
- ) Enzymes are often compartmentalized and found only in certain organelles.
- ) Sometimes enzymes that catalyze a sequence of reactions are organized as part of a macromolecular complex.
What two mechanisms are used to alter enzyme activity?
Allosteric Regulation and Covalent Modification
What is Allosteric Regulation?
What is an example of Allosteric Regulation?
- ) The catalytic activity of regulatory enzymes is modulated by allosteric effectors. The effector binds to an allosteric (regulatory) site on the enzyme and causes a conformational change that impacts the catalytic activity of the enzyme.
- ) Negative feedback = End products block pathway.
What is Covalent Modification?
Interconvertible enzymes exist in 2 forms, active and inactive, depending on whether or not the enzyme has been covalently modified by the attachment a some group. Enzymes are either activated or deactivated by phosphorylation.
What Covalent Modification involves Activation by Proteolysis?
Some enzymes and hormones are initially synthesized in an inactive form. Protease action then removes part of the molecule to produce the active form.
Proinsulin –> Insulin, Protrypsin –> Trypsin,
(Remember: Proteolysis is permanent.)
In what 3 ways do prokaryotes regulate enzyme levels by controlling their rate of synthesis?
- ) Constitutive enzymes are made in fixed amounts. They are required in fairly constant amounts at all times and are often referred to as “Housekeeping genes.”
- ) Some enzymes are only useful for the catabolism of certain nutrients only when that nutrient is present. These enzymes are made at only a low basal level. (Ex. Galactosidase is only made when lactose is present.)
- ) Some enzymes are used for biosynthesis of metabolites (amino acids) and are made when the end product is not present. If the end product is available, the synthesis of these enzymes is repressed. (Ex. Enzymes involved in tryptophan biosynthesis.)
What is the Lactose (Lac) Operon of E. coli?
The system consists of 3 enzymes: galactosidase, galactoside permease, and galactoside acetylase. When E. coli is growing where glucose is present, these enzymes are only at low level. When glucose and lactose are present, the enzymes are still at low level. When only lactose is present, they are all expressed in equal amounts (either high or low). The structural genes (coding for the amino acid sequence of the enzymes) are physically associated with regulatory genes to form the operon.
How is the Lac Operon of E. coli an example of Induction?
- ) In glucose, repressor binds to operator to block transcription. (This is negative control.)
- ) In lactose, the inducer binds to the repressor to release it from the operator and allow the RNA polymerase to proceed. Since glucose is low, cAMP will be high. cAMP binds to the CAP protein which then binds the CAP binding site, helping the RNA polymerase bind the promoter. (This is positive control.) The 3 enzymes are produced from one long polycistronic message (ZYA).
- ) In both, the inducer releases the repressor from the operator, but since glucose is present, cAMP will be low. With no cAMP-CAP complex, RNA polymerase will not be able to bind. (The effect of glucose is catabolite repression.)
How is the Jacob and Monod Model an example of Repression-Derepression?
Regulation by enzyme repression and derepression is usually used in anabolic pathways in which presence of the end product represses the enzyme and absence of the end product derepresses the enzyme.
(The tryptophan biosynthesis pathway is regulated in this way.)
How does the Jacob and Monod Model differ from the Lac Operon?
In the Jacob and Monod Model, the repressor is always present but is inactive (has no affinity for the operator) unless it is complexed with the corepressor (end product). Thus, if the end product is not available, the repressor does not bind to the operator and the enzymes are derepressed and are all made from a polycistronic message (ABC). If the end product is available, the repressor-corepressor complex binds to the operator and inhibits transcription by blocking the RNA polymerase after it binds the promoter site.
What is Attenuation?
Attenuation is regulation by premature termination of mRNA synthesis.
At what level is regulation occurring in the induction or repression of the Jacob-Monod Model and in Attenuation?
In the Jacob-Monod Model, regulation is at variable initiation. In Attenuation, regulation occurs at variable termination. In both cases. regulation is at the transcriptional level.
What is the mechanism of action for Attenuation?
In high amino acid concentrations, mRNA synthesis is terminated prematurely so that the biosynthetic enzymes are not made. In low amino acid concentration, mRNA synthesis is completed so that the biosynthetic enzymes are made. (This is coordinate expression.)
In Attenuation, what determines whether the mRNA transcript is terminated early or completed?
Whether the mRNA transcript is terminated early or completed depends on which of the several possible secondary structures form at the 5’ end of nascent mRNA. The formation of the secondary structure depends on the rate of movement of the first ribosome to translate the message.
In Attenuation, what is the function of the leader peptide?
The 5’ ends of these mRNA encode a short polypeptide called a leader peptide that contains seven codons for the amino acid (Histidine) being controlled by the operon. If Histidine is plentiful, ribosomes translate this region quickly, which results in a long leader peptide and formation of an attenuator stem between 3 and 4 that codes for stop. If Histidine is depleted, the ribosomes stall during translation and the attenuator stem forms between 2 and 3 and a polycistronic message signals transcription to continue.
What type of DNA sequence is found in prokaryotes?
Prokaryotes have a single copy of unique DNA.
What type of DNA sequence is found in eukaryotes?
Eukaryotes have a single copy (one copy per haploid genome, genes for most enzymes) that is either mostly reiterated (several to hundreds of copies of rRNA genes) or highly reiterated (thousands to millions of copies of human Alu sequences).
What are the 2 types of chromatin?
Heterochromatin = condensed, inactive Euchromatin = open structure, transcriptionally active, subject to DNase I cutting
What are the definitions of Constitutive, Induction, Repression-Derepression, and Attenuation?
Constitutive - Always needed so always present (Housekeeping genes)
Induction - Turned on in response to environment (Lac operon)
Repression-Derepression - Turned off by presence of molecule then turned back on in absence of molecule
Attenuation - Determines premature termination of mRNA synthesis
What is the difference between prokaryotes and eukaryotes in reference to DNA size?
Humans have 1000 times more DNA but only 5 times more genes so differences are in gene regulation.
What is the difference between prokaryotes and eukaryotes in reference to where DNA is made and how it is packaged?
E. coli make their DNA in chromosome and plasmid then package it as supercoiled DNA in a circular genome.
Humans make their DNA in nucleus and mitochondria then package it as linear nuclear DNA in chromatin.
What is the difference between prokaryotes and eukaryotes in reference to where genes are found, how they are regulated and by what kind of message?
E. coli has genes in operons and regulates them based on what is in the environment using a polycistronic (all genes in a row) message.
Human genes are usually scattered (sometimes in families) and regulate them based on what is in the environment as well as stage of differentiation using monocistronic (not clustered) messages.
What is the difference between prokaryotes in reference to presence of introns, usefulness of DNA, and gene copies?
E. coli does not have introns but most of its DNA is useful and genes are mostly in single copy.
Humans have introns but there is a lot of useless DNA and genes are in a reiterated single copy.
How is Hemoglobin an example of how eukaryotic genes are sometimes organized into families?
Different Hb genes expressed during different stages of development: Zeta2Epsilon2 in embryo, Alpha2Gamma2 in fetus, Alpha2Beta2 + Alpha2Delta2 in Adult
Alpha, and Zeta genes are on chromosome 16.
Beta, Delta, Gamma, and Epsilon genes on chromosome 11.
What are 2 examples of PoC 1: Specific chromosomes or regions may be inactivated during development?
- ) One X chromosome in each female mammalian cell is inactivated by condensation to heterochromatin (Lyon hypothesis, Barr bodies, Calico cats).
- ) DNA methylation turns off genes.
What is an example of PoC 2: Specific chromosomal regions may be activated by translocation?
Genes for the variable and constant regions of antibody molecules may be joined by translocation before they are activated.
What is an example of PoC 3: Specific chromosomal material may be lost during development?
The human red blood cell loses its entire nucleus.
What is an example of PoC 4: Gene reiteration - the presence of many identical genes permits the corresponding transcripts to be made a high rate?
Xenopus has about 900 rRNA genes in each cell.
What are 2 examples of PoC 5: Gene amplification?
- ) rRNA genes in the Xenopus oocyte are multiplied 1000-fold.
- ) Tumor cells can sometimes become resistant to Methotrexate by amplification of DHFR genes.
What are 3 examples of PoC 6: Specific genes can be activated for transcription?
- ) Different tissues contain differing quantities of mRNAs.
- ) Sometimes due to transcription factors (Ex. Steroid hormones exert their effects by interacting with TFs.)
- ) Sometimes due to aceylation of histones (Acetylation of histones determines how open/closed DNA, thus regulating access to information.)
What is an example of PoC 7: Primary transcripts may require processing (Alternative Splicing) to produce the active mature mRNA (Ex. Membrane-bound vs. secreted immunoglobulins)?
Different tissues contain differing quantities of mRNAs.
What are 2 examples of PoC 8: mRNA must be transported from the nucleus to the cytoplasm?
- ) Different tissues contain differing quantities of mRNAs.
- ) Cancer cells take advantage of this. There is no RNA restricted to nucleus in cancer so end up with uncontrolled translation into proteins.
What are 2 examples of PoC 9: Rate of mRNA degradation?
- ) Hemoglobin mRNA has a half-life of 100 days while the HeLa cell mRNA has a half-life of several hours.
- ) Iron regulates the half-life of human transferrin receptor mRNA.
What are 2 examples of PoC 10: mRNA in the cytoplasm may be masked in an inactive form?
- ) Maternal mRNA in eggs remains inactive until after fertilization.
- ) Iron regulates whether or not human ferritin mRNA is translated.
What are 2 examples of PoC 11: Rate of translation?
- ) The alpha and beta chains of Hemoglobin are translated at different rates.
- ) Heme regulates initiation of translation.
What is an example of PoC 12: The post-translational fate of a protein may depend on the class of ribosomes on which it is synthesized?
Proteins to be secreted or incorporated into the membrane are synthesized on ribosomes bound to the rough endoplasmic reticulum.
What is an example of PoC 13: Protein modification?
Proinsulin is cleaved to form active Insulin.
What are 2 examples of PoC 14: Protein degradation rate?
IgG antibody half-life = 25 days.
IgE antibody half-life = 25 days.