Anatomy and Function of a Gene: Dissection Through Mutation I

Genes with one common allele are _________, while genes with several common alleles in natural population are ________.

Define wild type allele in terms of monomorphic genes

Define wild type allele in terms of polymorphic genes

A mutation that changes a ____ _____ allele of a gene (regardless of definition) to a _______ allele is called a forward mutation. The resulting novel mutant allele can be either _______ or _______ to the original ______ ______ allele

How do geneticists diagram forward mutations?

Mutations can also cause a novel mutant allele to revert back to the _____ ______ in a process known as _______ mutation or ________

How do geneticists diagram reverse mutations?

Mendel originally defined genes by the visible phenotypic effects (yellow or green, round or wrinkled) of their _______ _______. In fact, the only way he knew that genes existed at all was because alternative alleles for seven particular pea genes had arisen through ________ mutations

Mutations can occur in ______ cells or in ______ cells. The mutations in Mendel's pea plants were heritable because they occurred in the _____ cells of the plants and were thus transmitted through ______.

Close to a century later, knowledge of DNA structure clarified that such mutations are _______ changes in DNA base sequence. DNA thus carries the potential for genetic changes in the same place it carries genetic information aka:

When does a substitution occur?
What is the result in the daughter double helix?

Substitutions can be subdivided into ________ and ________

transitions
transversions

deletion
insertion

Deletions and insertions can be as small as a _______ base pair or as large as _______ (millions of base pairs).

Large deletions and insertions are only some of the complex mutations that can reorganize genomes by changing either (3):

A _____ fraction of the mutations in a genome actually alter the nucleotide sequences of genes in a way that affects gene _______

By changing one allele to another, these (function altering) mutations modify the _______ or _______ of a gene's protein product, and the modification in protein _______ or _______ influences _________.

All other mutations either alter genes in ways that do not affect their ______ or change the _____ between genes

Mutations that modify gene function happen so _______ that geneticists must examine a very large number of individuals from a formerly ________ population to detect the new ________that reflect these mutations

Rates of spontaneous mutations (2-story)

Mutation rates in euks (4) compared to that of proks (3)

Detecting revertants (5-story)
Hint: Gene function is easy to disrupt but hard to restore

It actually makes sense that sperm carry more mutations than oocytes. (explain)

Human females are born with essentially all of the _____ ______ they will ever produce. It has been estimated that the germ-line cells of a female zygote need to undergo only ____ rounds of mitotic cell divisions to produce all of these oocytes. Male germ-line, on the other hand, undergo mitosis ______ throughout life

Why is it difficult to study the events that produce mutations and how do researchers overcome such difficulty

In one study, investigators spread wild-type bacteria on the surface of ______ containing sufficient nutrients for growth as well as a large amount of a bacteria-killing substance, such as an _______ or ________.

Although _____ of the bacterial cells died, a few showed _________ to the bactericidal substance and continued to ______ and ______. The descendants of a single resistant bacterium, produced by many rounds of ______ ______, formed a mound of genetically _______ cells called a colony

In 1934, Salvador Luria and Max Delbrück devised an experiment to examine the origin of _______ _______

What was Salvador Luria and Max Delbrück's reasoning with regards to the origin of the mutations that were causing the resistance?

The mutation conferring resistance can, in theory, arise at any _______ during the growth of the culture. If it happens early, the cell in which it occurs will produce _____ _____ progeny prior to petri plating; if it happens later, there will be far ______ _____  progeny when the time for plating arrives

After plating, these numerical differences will show up as _________ in the numbers of resistant colonies growing in the different petri plates

What were the results of the fluctuation test? (3-story)

Replica plating

Researchers used another technique known as _____ _____ to demonstrate even more directly that the mutations conferring bacterial resistance occur _______ the cells encounter the bactericide that selects for their resitance

These key experiments showed that bacterial resistance to phages and other batericides is the result of ________, and these ________ do not arise in particular genes as a directed response to _________ change

Instead, mutations (in resistant colonies) occur ________ as a result of _______ processes that can happen at _____ time and hit the genome at _____ place

Once such random changes occur however, they usually remain ______. If the resistant mutants of the Luria and Delbrück experiment, for example, were grown for many generations in medium that did not contain bacteriophages, they would nevertheless remain _______ to this bactericidal virus

Replica plating verifies that bacterial resistance is the result of preexsiting mutations
Part a (3-Story) and Part b (2-story)

The creation of a heritable mutation is the outcome of several competing process: ______, ______, and _______

First, of course, a _______ event must occur to alter the DNA. Two different kinds of events initiate DNA changes. Name them

Just after being made, DNA changes are not yet actual mutations but only potential mutations. (why?)

These DNA repair machines are engaged in a continual race with _____ ________. If repair of damaged DNA or misincorporated nucleotides occurs ______ the next round of ____ _______, then the sequence is corrected and no mutation will result

However, if the repair enzymes do not correct the problem _______ the next round of ____ _______, the mutation becomes _______ established in both strands of the double helix and a _______ mutation is the outcome

Chemical and physical assaults on DNA are quite ________. Geneticists estimate, for example, that the ________ of a purine base, A or G, from the deoxyribose-phosphate backbone occurs _____ times an hour in every human cell

Depurination

Why does the DNA replication process introduce a random base opposite the apurinic site? What is the result?

Deamination

Deaminiation can change cytosine (C) to _______, the nitrogenous base found in RNA but not in DNA

Why is it that deamination followed by replication may alter a C-G base pair to a T-A pair in future generation of DNA molecules? What kind of mutation is this?

Other assaults include naturally occurring radiation such as ______ ______ and _______ which break the sugar phosphate backbone

Ultraviolet light is another possible source of assault which causes adjacent _______ residues to become chemically linked into _______-______ _______

In the image, _______ damage is done to _____ of the four bases. If not repaired before DNA replication, all of these changes alter the info of the DNA molecule ________

If the cellular machinery for some reason incorporates an incorrect base during replication, for instance, a C opposite an A instead of the expected T, what happens during the next replication cycle?

Careful measurements of the fidelity of replication in vivo, in both bacteria and human cells, show that such errors are exceedingly _____

The replication machinery ________ errors through successive stages of correction. In the test tube, DNA polymerases replicate DNA with an error rate of about one mistake in every _____ bases copied

This rate is about ______ fold worse than that achieved by the cell. Even so, it is impressively low and is only attained because polymerase molecules provide, along with their ________ function, a _______/_______ function in the form of a _______ that is activated whenever the polymerase makes a ________

This nuclease portion of the polymerase molecule called the _______ ___________,recognizes a mispaired bases and _______ it,  allowing the polymerase to copy the nucleotide ________ on the next try

Without its nuclease portion, DNA polymerase would have an error rate of one mistake in every ____ bases copied, so its editing function improves the fidelity of replication _____ fold

DNA polymerase in vivo is part of a replication system including many other proteins that collectively improve on the error rate another 10-fold, bringing it to within about 100-fold of the fidelity attained by the cell. The 100-fold higher accuracy of the cell depends on a back up system called ______ ______ ________ repair. What does it do?

Tautomerization

Tautomerization is a reason _____ _______ can make mistakes. Each of the four bases has two _______, similar chemical forms that _________ continually

The _______ between the tautomers is such that each base is almost ______ in the form in  which A pairs with T and G pairs with C.

If, by chance, a base in the template strand is in its rare tautomeric form when DNA polymers arrives, what happens?

If the misincorporated nucleotide is not corrected by mismatch repair before the next round of replication, a ______ mutation occurs

In 1992, molecular geneticists discovered a completely unexpected type of mutation in humans: the excessive amplication of a _____ base triplet normally repeated on a few to 50 times in succession. If, for example, a normal allele of a gene carries five consecutive repetitions of the base triplet ________, an abnormal allele could carry _____ repeats in a row

Repeats of several other trinucleotides (CAG, CTG, GCC, and GAA) can also be ________, such that the number of repeats often ______ or _______ in different cells of a single individual

Instability can also occur during gamete production, resulting in changes in ______ _____ from one generation to the next

Unstable trinucleotide repeats have now been found within about 20 different human genes, all associated with ___________ diseases. In all cases, an expansion of the repeats beyond a _____ ______ results in a disease-causing allele. State two examples

A general feature of both groups of trinucleotide repeat diseases is that the _____ _______ at a particular location, the higher the probability that _______ and _______ will occur

Pre-mutation alleles

Why do some alleles with intermediate numbers of trinucleotide repeats behave as so called pre-mutation alleles

For example, in fragile X syndrome, individuals with pre-mutation alleles have ______ phenotypes, but the expanded repeat number  means that such __________ alleles are highly likely to expand or contract during ________

Carriers of pre-mutation alleles thus have a _____ probability of giving new diseases (with ________ numbers of repeats) to their children

The approximately 20 known neurogenerative diseases caused by genes with unstable trinucleotide (triplet) repeats fall into two categories (name them)

In polyQ disease genes, the repeated triplet is always _____, while in non-polyQ disease genes, __________ repeat may be either CGG, CTG, GCC or GAA.

The two types of triplet repeat diseases are distinguished by the effect of the repeat sequence on gene function. How does this work in both disease types?

Huntington disease is a ______ disease; and fragile X syndrome, is a ______ disease

Each CAG specifies that the amino acid _______ (Q) should be added to the HD protein, so the normal protein 6-28 Q amino acids in a row in its so-called ______ region.

An HD allele with ___ or more repeats encodes a mutant HD protein with an _______ polyQ region that is ______ to nerve cells. Proteins encoded by pre-mutation alleles function _______, but have an ______ repeat number

Why are polyQ disease alleles like ___ called gain of function mutants

Typical for many gain of function mutants, polyQ disease alleles show ________ inheritance (why?)

The disease is caused by expansion of CGG repeat region in an ______ gene called FMR-1 (Fragile X mental retardation-1)

The CGGs of FMR-1 are located in a region of the gene outside of the ORF called the _______

Normal FMR-1⁺ genes have 6-55 CGG repeats; expansion of the repeat number to ______ CGGs or more results in an FMR-1 disease allele that is ______ to produce the FMR-1 protein

Without FMR-1 protein, nerve cells cannot properly form connections called _______. A common feature to all non-polyQ diseases is that the triplets are located in a part of the gene ______ of the ORF. The expanded repeats in non-polyQ disease genes generally prevent ______ production, and so non-polyQ disease genes are ______ of function alleles