Chapter 17 - Regulation and Mutations   

The genes that are expressed and the quantities at which those genes are expressed define an organism's phenotype.

• Gene expression regulation is critical in determining an organism's phenotype.
• The interaction of regulatory proteins with regulatory regions in the genome can control genes.
• Regulatory proteins are proteins that have the ability to activate or deactivate genes by binding to certain nucleotide sequences.
• Regulatory sequences are the nucleotide sequences to which these regulatory proteins bind.

Gene expression may be affected by mutations in the DNA.

• This chapter will go over how genes are controlled (in prokaryotes and eukaryotes) and the many sorts of mutations that can impact an organism's phenotype.
• Promoters are noncoding regulatory regions that act as RNA polymerase binding sites.
• Operators are noncoding regulatory regions that act as repressor protein binding sites (a type of regulatory protein).

Structural genes are coding sequences that include the genetic code for the proteins needed to carry out the operon's function.

• Inducible operons and repressible operons are the two types of bacterial operons that you must grasp for the AP Biology test.
• Consider what would be most beneficial to the bacterium in its environment when deciding whether to switch an operon "on" or "off."
• If the purpose of an operon is to digest a molecule, it is beneficial to the bacteria to switch "off" the operon if the molecule is not present and to turn "on" the operon if the molecule is present.
• ^^If the purpose of an operon is to synthesis a molecule, it is beneficial to turn the operon "on" if the molecule is not present but favorable to switch the operon "off" if the molecule is present.^^

Inducible operons often have a catabolic function (digesting molecules) and are switched off in the absence of the proper inducer molecule.

• In an inducible operon, the repressor protein attaches to the operator region, preventing RNA polymerase from transcribing the operon.
• When an inducer molecule is present, the inducer attaches to the repressor protein, causing it to change form and no longer be able to connect to the opera.
• When an inducer molecule is present, the inducer attaches to the repressor protein, causing it to change form and no longer be able to connect to the operator sequence.
• This enables RNA polymerase to start transcribing the operon.
• The lac operon is a famous example of an inducible operon.

The lac operon's role is to create the proteins needed to digest the sugar lactose.

• %%If no lactose is present, the lac repressor protein binds to the operator, preventing RNA polymerase from transcribing the operon.%%

Lactose acts as the lac operon's inducer molecule.

• Lactose binds to the lac repressor protein, altering its structure so that it can no longer bind to the operator sequence.
• This permits RNA polymerase to transcribe the genes for the lactose-digesting proteins.
• After all of the lactose has been digested, the repressor may bind to the operator sequence once more, thereby shutting down the operon.
• This sort of feedback system permits the cell to produce the proteins required for lactose digestion only when they are required, therefore conserving vital cell resources.

When glucose levels fall, cAMP levels rise in the cell.

• cAMP binds to the catabolite activator protein (CAP), causing it to bind at a CAP binding site close to the promoter.
• This enhances RNA polymerase's affinity for the promoter, hence promoting transcription.
• When glucose, another fuel supply for bacteria, is unavailable, transcription of the lac operon increases, allowing the cell to survive.
• %%When glucose, another food source for the bacteria, is missing, transcription of the lac operon increases, allowing the cell to use the energy in lactose more efficiently.%%
• Repressible operons often have an anabolic function (synthesizing molecules) and are activated until the operon's output is abundant in the cell.
• An example of a repressible operon is the trp operon.

The trp operon's job is to create the enzymes required to manufacture the amino acid tryptophan.

• The amino acid tryptophan acts as a corepressor in the trp operon.
• @@The trp repressor protein cannot bind to the operator sequence on its own; it must first be coupled to the amino acid tryptophan before it can bind to the operator sequence.@@
• As a result, if no tryptophan is available, the trp repressor will not bind to the operator and RNA polymerase will be able to transcribe the operon. In eukaryotes, epigenetic alterations can also impact gene expression.

Epigenetic alterations are reversible modifications to the nucleotides of the DNA sequence, such as nucleotide methylation (adding a methyl group).

• Because a methylated nucleotide is far less likely to be translated, the cell may alter gene expression by varying the degree of methylation in distinct genes.
• The histone proteins that surround DNA when it is packed into chromosomes can also be epigenetically changed by adding acetyl groups (acetylation).
• When histone proteins are acetylated, DNA becomes more loosely coiled around the histone proteins, making it more accessible to enzymes.

Euchromatin is DNA that is more loosely coiled around histone proteins, making it more accessible to RNA polymerase and resulting in higher gene expression in the euchromatin.

• Hete is formed when DNA in chromosomes is firmly coiled around histone proteins.
• An organism's phenotype is defined not only by which genes are expressed but also by the levels at which those genes are expressed.
• A skin cell that expresses higher quantities of the melanin protein, for example, will look darker in color than a skin cell that expresses lesser levels of the melanin protein.

The timing of transcription factor expression throughout development is crucial for the generation of specialized tissues and organs from a single-celled zygote.

• Flaws in the timing of these genes' expression can lead to errors in an organism's body plan or architecture.
• The Hox genes, a family of genes that code for transcription factors, were found in Drosophila flies.
• During development, the Hox gene, which codes for antennapedia, regulates the creation of legs in Drosophila.

Mutations in this gene, or expression of this gene at an inopportune moment, can result in legs not developing or legs growing in the incorrect body segment.

• Because of the genetic code's redundancy, certain mutations have no effect on the amino acid sequence of a protein.
• Mutations can occur as a result of environmental stimuli such as chemicals or radiation, or as a result of random mistakes in DNA replication.
• Errors in mitosis or meiosis can also result in mutations.
• Aneuploidy can occur when homologous chromosomes fail to split during meiosis (an incorrect number of chromosomes).
• In animals, aneuploidies can be deadly or cause infertility or other problems.
• Aneuploidies that result in polyploids (an full additional set of chromosomes) in plants, on the other hand, might provide a benefit to the plant, making it more likely to survive.
• Mutations in the genome can also be passed down from generation to generation.

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