CONTROLLING DNA

So we know how, but what about the when and how much? After studying DNA, and the mechanism of translation and transcription, have you asked yourself how all of this gets controlled? How does the cell know how much it has to create and when to do so?

Eukaryotic control of gene expression If you think carefully about it, each cell in the body is designed to specialize in one function However, each of these cells contain the whole genome

Control at the DNA level By modifying DNA or using proteins that attach themselves to DNA, gene production (and therefore protein production) can be halted by stopping transcription

Silencing DNA in Eukaryotes DNA METHYLATION attaches methyl groups (CH 3 ) groups to DNA Although methyl groups can be present in active DNA, inactive DNA is much higher in the number of methyl groups present on the DNA strand This method is usually used for long term gene silencing

Organization of DNA and regulation Recall that the production of mRNA requires a large group of proteins called an TRANSCRIPTION INITIATION COMPLEX These proteins bind to sequences on DNA before the gene that is to be transcribed For example, PROMOTER REGIONS that RNA polymerase binds to is an example of a CONTROL ELEMENT

Prokaryotic DNA regulation For example, tryptophan is an amino acid that can be synthesized by bacteria when the environment cannot provide it Therefore, the genes that code for the enzyme necessary for tryptophan production are grouped together and controlled together This is the basis of an operon: a group of related genes controlled by a single promoter and an OPERATOR: a sequence that binds a supressor to shut off transcription

Tryptophan (trp) operon In E.coli, the trp operon is composed of 5 genes (trp A-E) Upstream to these genes is a promoter and an operon

Negative feedback When trypotphan is present, it binds to the repressor activating it This makes tryptophan a COREPRESSOR that is needed to shut down trp transcription This repressor then binds to the operator, which is located downstream from the promoter chp13/ html chp13/ html

lac Operon Another example of an operon is the control of the genes that produce the enzymes necessary for the metabolism of lactose Lactose can be used as an alternative energy source for bacteria if glucose is not readily available (this is also a regulatory process found in E.coli – if you drink milk, the E.coli in your gut can use the lactose for energy)

Repressible vs. Inducible Operons The trp operon is said to be a REPRESSIBLE operon since the presence of tryptophan shuts off the transcription of the

Active repressor The lac operon has a regulatory gene lacI that produces a protein that acts as an active repressor This will allow the transcription of the lac genes

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Differences The logic behind these controls is based on the preservation of energy Since tryptophan is an essential amino acid, it is in high demand – and therefore, keeping its gene active is essential – but if it is readily available it makes sense to shut down the cell machinery and save the energy required to power the pathway

Postranscriptional control: mRNA RNA processing can also be used to control protein expression mRNA lifespan can help to control how long a piece of mRNA remains stable and intact – this will limit the amount of protein that can be produced from this mRNA

Postranscriptional control: Controlling Translation The production of heme – a necessary protein in hemoglobin – is regulated by a translation inhibitor When heme is low, a regulatory protein inactivates a translation inhibitor allowing for the translation of the mRNA

When DNA is uncontrollable

Problems with DNA Ultimately, mutations in DNA can cause problems in the production of necessary proteins for DNA production Mutations can be caused by chemicals, radiation, or viruses that interfere with the DNA molecule Silent mutations Missense mutation Nonsense mutations

Types of DNA mutation DNA mutations can occur in a few different ways: – Point mutation – Frame shift mutation – Deletion – Insertion – Inversion – DNA expression mutation – Translocation The following examples are taken from: shtml shtml

Point mutation The change in one base pair Original: The fat cat ate the wee rat. Point Mutation: The fat hat ate the wee rat.

Frame shift mutation This usually results in a useless or shortened protein An example of a frame-shift mutation using our sample sentence is when the 't' from cat is removed, but we keep the original letter spacing: Original: The fat cat ate the wee rat. Frame Shift: The fat caa tet hew eer at

Deletion The removal of base pairs from a DNA sequence Original: The fat cat ate the wee rat. Deletion:The fat ate the wee rat.

Insertion The insertion of additional base pairs Original: The fat cat ate the wee rat. Insertion: The fat cat xlw ate the wee rat.

Inversion The reversal of sections of genes Original: The fat cat ate the wee rat. Inversion: The fat tar eew eht eta tac.

Note that deletions, insertions and point mutations can cause frame shift mutations, changing how the DNA is read

Point mutations can cause problems when the mutation create an alternate codon that results in changing an amino acid in the primary protein structure This can affect the folding of the protein, changing the structure and therefore the function

DNA expression mutation These mutations change the way that DNA is expressed – normally quiet genes may suddenly become very active These mutations can be the cause of cancer if growth stimulating genes are affected Translocation or transposition of genes Gene amplification can cause A point mutation can

Translocation Occurs when groups of base pairs are shifted from one part of the genome to another This can happen at the chromosomal level where entire sections of chromosomes are broken off and reattached to other areas This can cause major problems since so much DNA has been shifted

Eukaryotes and Prokaryotes Prokaryotes have circular genomes, eukaryotes have linear genomes Eukaryotes usually have much larger genomes