Chapter 13: Regulation of Gene Expression

pg 237

The operons are present in which kind of organisms?

Prokaryotes

What does the operon model explain?

Gene regulation in prokaryotes

What are the four elements of an operon?

Regulator gene, promoter, operator, and structural genes

What is the function of the regulator gene of an operon?

On the outside of operon, codes for a DNA-binding protein that acts as a repressor (controls whether operon is active or not)

What does a regulatory protein do?

It induces or inhibits the expression of a gene

What does a repressor protein do?

It suppresses the transcription of a gene and controls whether an operon is active or not

What is the function of the promoter of an operon?

Sequence of DNA where RNA polymerase first attaches to begin transcription of grouped genes

In simple terms, what is the function of the promoter?

It signals the start of the operon and location where transcription begins

What is the function of the operon of the promoter?

The short portion of DNA where an active repressor binds

What happens when the active repressor binds to the operator?

RNA polymerase cannot attach to the promoter and transcription cannot occur

What does the operator control?

The transcription of structural genes

What is the function of the structural genes of an operon?

They code for enzymes and proteins that are involved in the metabolic pathway of an operon

What are the two kinds of operons seen on prokaryotes?

Trp and Lac

What is unique about the trp operon? (think in terms of the repressor and operator)

The regulator codes for a repressor that ordinarily is unable to attach to the operator.

Knowing the unique factor of the trp operon, what is RNA polymerase able to do?

RNA polymerase can bind to the promoter, and the structural genes of the operon are ordinarily expressed

What is produced from the RNA polymerase binding to the promotor in a trp operon?

5 different enzymes that are part of an anabolic pathway for the synthesis of the amino acid tryptophan

What happens when tryptophan is absent in a trp operon?

1. The regulator gene codes for a repressor protein that is normally inactive
2. RNA polymerase attaches to the promoter and the structural genes are expressed
3. The enzymes needed to synthesize tryptophan are produced

What happens when tryptophan is present in a trp operon?

1. Tryptophan binds to the repressor and changes its shape
2. The changing in shapes allows the now active repressor to operator to prevent RNA polymerase from binding to the promoter
3. The structural genes are not produced

When are structural genes produced in a trp operon? When tryptophan is present or absent?

Absent

When tryptophan is present, why is the trp operon unit said to be a repressible operon?

Since RNA cannot bind to the promoter, the structural genes are not expressed and are inhibited. In other words, it represses the expression of genes in this operon.

If there is no need for certain proteins or enzymes, in what state are the genes used to make them in? (Are they active or inactive?)

Inactive

What happens when E. Coli is denied glucose and given lactose instead?

The cell immediately begins to make the three enzymes needed for lactose metabolism

What are the functions of the three enzymes that are needed to break down lactose?

1. One gene is for an enzyme (B-galactpsidase) and breaks down lactose to glucose and galactose
2. One codes for a permease that facilitates the entry of lactose into the cell
3. One codes for an enzyme (transacetylase), which has an accessory function in lactose metabolism

What happens when lactose in absent in the lac operon?

1. The regulator gene codes for a repressor that is normally active
2. The repressor binds to the operator and RNA polymerase cannot attach to the promoter and the structural genes are not produced

What happens when lactose is present in the lac operon?

1. Lactose binds to the active repressor (this changes its shape and the repressor becomes inactive)
2. Since there was a change in shape, the repressor cannot bind to the operator
3. RNA polymerase binds to the promoter and the structural genes are expressed

In which operon is the repressor usually inactive?

trp

In which operon is the repressor usually active?

lac

When lactose is present, why is the lac operon described as an inducible operon?

Since the presence of lactose brings about the expression of genes, it is called an inducer. Therefore, the lac operon can be described as an inducible operon

Why are inducible operons usually found in catabolic pathways that break down a nutrient?

Because the enzymes need to be active only when the nutrient is present (in a lac operon)

Which molecules accumulates when glucose is absent?

Cyclic AMP (cAMP)

How does the E. Coli bacterium ensure that the lactose operon is maximally turned on only when glucose is absent?

1. cAMP binds to a molecule called a catabolite activator protein (CAP)
2. The cAMpP/CAP complex binds to the CAP binding site next to the lac promoter
3. When CAP binds to DNA, the DNA bends and exposes the promoter to RNA polymerase
4. RNA polymerase binds to the promoter → the genes are then transcribed and leads to their expression

When glucose is present, in what states are cAMP, CAP, and the lac operon in?

* There is little cAMP in the cell
* CAP is inactive
* The Lac Operon doesn’t function maximally

How is the CAP protein’s regulation of the lac operon an example of positive control?

Because when this molecule is active, it promotes the activity of an operon

How is the use of repressors an example of negative control?

When repressors are active, they shut down an operon

When is the lac operon maximally active?

When glucose is absent and lactose is present

What happens when glucose and lactose are both present in the lac operon?

The cell will preferentially metabolize glucose

What are the different cell types in eukaryotes determined by?

Different genes that are actively expressed in each cell

What are the five primary levels of control in a eukaryotic cell?

1. Chromatin structure
2. Transcriptional control
3. Posttranscriptional control
4. Translational control
5. Posttranslational control

Define chromatin structure

One method of epigenetic inheritance

Define epigenetic inheritance

The transmission of genetic information outside the coding sequences of a gene

Define transcriptional control

The degree to which a gene is transcribed into mRNA determines the amount of gene product

Define posttranscriptional control

Involves mRNA processing and how fast mRNA leaves the nucleus

Define translational control

Occurs in the cytoplasm and affects when translation begins and how long it will continue for

Define posttranslational control

Takes place in the cytoplasm and occurs after protein synthesis

What would happen to DNA without histones?

It would not fit inside the nucleus

Active genes are associated with which kind of chromatin?

Euchromatin (loosely packed chromatin)

Inactive genes contains which kind of protein?

Heterochromatin (tightly packed chromatin)

What does a nucleosome consist of?

A portion of DNA wrapped around a group of histones

Histones have tails. What are those tails comprised of?

Strings of amino acids that extend beyond the main portion of a nucleosome

In heterochromatin, what happens to the tail of the histone?

It tends to bear methyl groups (-CH3)

In euchromatin, what happens to the tail of the histone?

It tends to be acetylated and have attached acetyl groups (-COCH3)

When does euchromatin become genetically active?

When histones no longer bar access to DNA

What occurs when the DNA in euchromatin is transcribed?

A chromatin remodeling complex pushes aside the histone portion of a nucleosome so that access to the DNA is not barred and transcription can begin

What occurs after the chromatin remodeling complex allows access to DNA and transcription has finally begun?

Many decondensed loops radiate from the central axis of the chromosome (named lampbrush because feathery appearance resembles the brushes that were used to clean kerosene lamps)

What are chromatin remodeling complexes also capable of?

They may affect gene expression by adding acetyl or methyl groups to histone tails

Why are genes within heterochromatin seldom or never transcribed?

Because highly condensed heterochromatin is inaccessible to RNA polymerase

What is a barr body?

An inactive X chromosome

Why does one of the X chromosomes in the cells of female embryos undergo inactivation?

To compensate for the fact that females have two X chromosomes and that males have one. This allows both males and females to produce the same amount of gene product from a single X chromosome

What occurs in epigenetic inheritance?

Variations in the pattern of inheritance is not due to changes in the sequence of the DNA nucleotides

What occurs in genomic imprinting?

Either the mother’s or father’s gene (not both) is methylated during gamete formation

In genomic imprinting, what would happen if an allele is highly methylated?

The gene will not be expressed

What is the term “epigenetic inheritance” broadly used for?

Other inheritance patterns that do not depend on the genes themselves

What does epigenetic inheritance explain?

Unusual inheritance patterns

Transcriptional control contains the participation of which elements?

Transcription factors, activators, and repressor

Transcription in eukaryotes is controlled by what kind of proteins?

DNA-binding

What are transcription factors?

Proteins that help regulate transcription by assisting the binding of the RNA polymerase to the promoter

Transcription cannot begin without the assistance of which DNA-binding protein?

A Transcription activator

Where do transcription activators bind to?

Enhancers (are found some distance from the promoter)

What brings the transcription activators that are attached to the enhancers into contact with the transcription factor complex?

A hairpin loop in the DNA

What do transcription factors bind to?

The promoter

Which molecules are always present in the nucleus of a cell, but will most likely have to be activated in some way before they bind to the DNA?

Transcription factors, activators, and repressors

When does activation of a molecule occur?

When it is phosphorylated by a kinase

What does a kinase do?

Adds a phosphate group to molecules

What does a phosphatase do?

Removes a phosphate group

What are phosphatase and kinases?

Signaling proteins involved in a growth regulatory network that reaches from receptors in the plasma membrane to the genes in the nucleus

What does posttranscriptional control include?

Alternative mRNA splicing and controlling the speed with which mRNA leaves the nucleus

What occurs during pre-mRNA splicing in posttranscriptional control?

Introns (noncoding regions) are excised and exons (expressed regions) are joined together to form an mRNA

What does alternative pre-mRNA splicing allow for?

For complex organisms to recombine their genes in novel ways to create the great variety of proteins found in these organisms

How is further posttranscriptional control of gene expression achieved?

By modifying the speed of transport of mRNA from the nucleus into the cytoplasm

if only 1.5% of DNA is used to code for protein, what is the rest of it used for?

The rest is used to form small RNAs (sRNAs)

How are sRNAs made?

Double-stranded RNA (dsRNA) is diced up by enzymes in the cell to form sRNAs

What is the first way that sRNAs have been found to regulate gene expression?

Have been known to alter compaction of DNA so that some genes are inaccessible to the transcription machinery of the cell

What is the second way that sRNAs have been found to regulate gene expression?

sRNAs are the source of microRNAs (miRNAs), which are small snippets of RNA that can bind to and dampen the translation of mRNA in the cytoplasm

What are miRNAs?

Small snippets of RNA that can bind to and dampen the translation of mRNA in the cytoplasm

What is the third and final way that sRNAs have been found to regulate gene expression?

sRNAs are the source of small interfering RNAs (siRNAs) that join with enzyme RISC (RNA-induced silencing complex) to form an active silencing complex. This activated complex targets specific mRNAs in the cell for breakdown, preventing them from being expressed

What is RNA inference?

When both miRNA and siRNA molecules interfere with the normal gene expression pathways

When does translational control begin?

When the processed mRNA molecule reaches the cytoplasm and before there is a protein product

What is attributed to the 5’ end caps and 4’ poly-A tails of mRNAs?

The long life of mRNAs that code for hemoglobin in mammalian red blood cells

When does posttranslational control begin?

Once a protein has been synthesized and has become active

What does posttranslational control represent?

The last chance a cell has for influencing gene expression

What is regulated by the use of proteases?

How long a protein remains active in a cell

What is a protease?

Enzymes that break down proteins

How do proteases protect the cell?

They are typically confined to the lysosomes or special structures called proteaomes

What must happens for a protein to enter a proteasome?

It has to be tagged with a signaling protein that is recognized by the proteasome cap

What happens when the proteasome cap recognizes the tag?

It opens and allows the protein to enter the core of the structure, where it is digested to peptide fragments

What are germ-line mutations?

Mutations that occur in sex cells and can be passed to subsequent generations

What are somatic mutations?

Mutations that occur in body cells, and therefore, they only affect a small number of cells in a tissue

Which mutation (germ-line or somatic) can lead to the development of cancer?

Somatic

What are spontaneous mutations?

Mutations that arise as a result of abnormalities in normal biological processes

What are induced mutations?

Mutations that may result from exposure to toxic chemicals or radiation, which can induce (cause) changes in the base sequence of DNA