Anatomy and Function of a Gene: Dissection Through Mutation III

Fine structure mapping
Monoploid

Cistron

Deletions are mutations that remove _______ nucleotide pairs along a DNA molecule. In crosses between bacteriophages carrying deletions of the corresponding region, no _____ ____ ________ progeny can arise, because neither ________ carries the proper info at the location of the ________

However, if the mutation lies outside the region deleted from the homologous chromosome, _____ _____ progeny can appear. This is true whether the mutation is a _____ mutation affecting one or a few nucleotides, or a large ______

Crosses between any uncharacterized mutation and known deletions thus immediately reveal?

Some sites within a gene spontaneously mutate more frequently than others and as a result are known as _____ ______

What does the existence of hotspots suggest?

Treatment with ________ also turns up hotspots but because they have specificities for particular nucleotides, the highly mutable sites that turn up with various _______ are often at _______ positions in a gene than the hotspots resulting from _______ mutation

Benzer's experiments imply, the molecular machinery responsible for mutation and recombination does not discriminate between those nucleotides that are _______ (within a gene) and those that are ______ (between genes)

The main distinction between DNA within and DNA outside a gene is that the array of nucleotides composing a gene has evolved a function that determines _________

In the 1940s, George Beadle and Edward Tatum carried out a series of experiments on the bread mold Neurospora crassa that demonstrated a direct relationship between genes and the enzymes that catalyze specific biochemical reaction. Their strategy was simple: (2-story)

auxotroph 
prototrop

Isolation of arginine auxotrophs (4-story)

They next asked whether any of the mutant Neurospora strains could grow in minimal medium supplemented with any of three known intermediates (orinthine, citrulline, and arginosuccinate) in the biochemical pathway leading to ______, instead of with _______ itself

This test would identify Neurospora mutants able to convert the ________ compound into _______. Beadle Tatum compiled a table describing which arginine auxotrophic mutants were able to grow on minimal medium supplemented with each of the ________

On the basis of the results, Beadle and Tum proposed a model fo how Neurospora cells synthesize arginine. In the linear progression of biochemical reactions by which a cell constructs arginine from the constituents of minimal medium, each intermediate is both the _____ of one step and the ______ for the next

Each reaction in the precisely ordered sequence is catalyzed by a specific ______, and the presence of each _______ depends on one of the four ______ genes.

A mutation in one gene blocks the pathway at a particular step because the cell lacks the corresponding enzyme and thus cannot make ______ on its own.

How does supplementing the medium with any intermediate that occurs beyond the blocked reaction restore growth?

Why doesn't supplementation with an intermediate that occurs before the missing enzyme work

Each mutation ______ the cell's ability to make an enzyme capable of catalyzing a certain reaction. By inference, then, each gene controls the synthesis or activity of an enzyme, or as stated by Beadle and Tatum:

All of the amino acids have certain basic features, encapsulated in what form?

The -COOH of amino acids aka the ______ ______ is, as the name implies, acidic; the -NH₂ component, aka the ______ group is ______. The R refers to _____ ______ that distinguish each of the amino acids

An R group can be as simple as a hydrogen atom (in the amino acid ______) or as complex as a benzene ring as in __________. Some side chains are relatively ________ and nonreactive, others are ______, and still others are ______

The chemical properties that enable structural proteins to give a cell its shape, or enzymes to catalyze specific reactions, are a direct consequence of the ______, ______, and _______ order of amino acids in the protein

Sickle cell anemia (5-story)

The glutamic acid-to-valine change affects the _______ of hemoglobin within the red blood cell. At low concentrations of oxygen, the ______ _______ sickle cell form of hemoglobin aggregates into _____ chains that deform the red blood cell

Despite the uniform nature of protein construction a string of amino acids joined by ______ bonds (each _______ folds into a unique three-dimensional shape)

Biochemists often distinguish between four levels of protein structure: ______, ______, _____ and _______. The first three of these apply to any one ________ ______, while the quaternary level describes _______ ______ within a protein complex

Primary structure

Each unique primary structure places constraints on how a chain can arrange itself in _____ ______ space. Because the R group distinguishing the 22 amino acids have dissimilar ______ _______, some amino acids form _______ bonds or ________ bonds when brought into proximity with other amino acids

Nonpolar amino acids, for example, may become associated with each other by interactions that ______ them from water in localized hydrophobic regions. As another example, two cysteine amino acids can form _______ ______ bridges (-S-S-) through the _______ of their -SH groups

The primary structure determines three dimensional shape by generating ________ ________

secondary structure

________ structure is responsible for other folds and twists that together with ________ structure produce the ultimate three-dimensional ______ ______ of the entire polypeptide

Tertiary structure
Native configuration

Types of interactions that help stabilize native configuration

It is worth repeating that primary structure (amino acid sequence) directly determines _______ and _______ structure. The info required for the chain to fold into its native config is inherent in its ____ ______ of amino acids

In one example of this principle, many proteins unfold, or become _______, when exposed to urea and mercaptoethanol or to increasing heat or pH. These treatments disrupt the interactions that normally stabilize the ________ and _______ structures

When conditions return to normal, many proteins spontaneously refold into their _______ _______ without help from other agents. No other info beyond the _______ ______ is needed to achieve the proper three-dimensional shape of such proteins

Certain proteins, such as ______ that promotes black-and-white vision, consist of a ________ polypeptide. Many other, however, such as the lens crystallin protein, which provides rigidity and transparency to the lenses of our eyes, or the hemoglobin molecule described earlier, are composed of ____ or ______ polypeptide chains that associate in a specific way

The individual polypeptides in an aggregate are known as _______, and the complex of subunits is often referred to as a ______. 
Define Quaternary structure

The same forces that stabilize the native form of a polypeptide also contribute to the maintenance of ________ structure

In some multimers, the two or more interacting subunits are ______ polypeptides and their chains are encoded by ______ gene. In other multimers, by contrast, more than one kind of polypeptide makes up protein. The ______ polypeptides in these multimers are encoded by ______ genes

Alterations in just one kind of ______, caused by a mutation in _____ gene, can affect the function of a ________

An example is an X-linked mutation in mice and humans that incapacitates several different proteins all known as ______ ______ (IL). Why does such a mutation cause the life-threatening condition known as X linked severe combined immune definciency (XSCID)

The polypeptides of complex proteins can assemble into extremely large structure capable of changing with the needs of the cell. State an example

The cell can organize these subunits into very long hollow tubes that _____ and ______ as needed at different stages of the cell cycle

People perceive light through neurons in the ______ at the back of the eye. These neurons are of two types: ______ and _____

The rods, which make up 95% of all light-receiving neurons, are stimulated by ______ light over a range of wavelengths.

At ________ light intensities, the rods become _______ and no longer send ______ info to the brain. This is when the ______ take over processing wavelengths of ______ light that enable us to see color

The cones come in three forms name them

For each phtoreceptor cell, the act of reception consists of ______ photons from light of a particular wavelength, ________ info about the number and energy of those photons to electrical signals, and ___________ the signals via the optic nerve to the brain. *This allows us to see over 1 million colors

The protein that receives photons and triggers the processing of info in rod cells is ______. It consists of a single ________ _______ containing 348 amino acids that snakes back and forth across the ______ _______

One lysine within the chain associates with retinal, a carotenoid pigment molecule that actually absorbs _______. The amino acids in the vicinity of the retinal connstitute rhodopsin's _____ ______; by positioning the retinal in a particular way, they determine its response to _____

Each rod cell contains approximately 100  million molecules of _______ in its specialized membrane

The protein that receives and initiates the processing of photons in the blue cones is a relative of rhodopsin, also consisting of a ______ _____ _____ containing 348 amino acids and also encompassing one molecule of retinal

Slightly less than ______ of the 348 amino acids in the blue-receiving protein are the same as those found in ________; the rest are different and account for the _______ light-receiving ability of the protein

Similarly related to rhodopsin are the red-and green- receiving proteins in the red and green cones. These are also polypeptides associated with retinal and embed in  the cell membrane, although they are both slightly _______ at 364 amino acids in length

Like the blue protein, the red and green proteins differ from rhodopsin in nearly _____ of their amino acids; they differ from each other in only ______ amino acids out of every hundred

The genes for the red and green proteins both reside on the _____ ______ in a tandem head-to-tail arrangement. Most individuals have one red gene and one to three green genes on their _____ ______

The similarities in structure and function among rhodopsin and the three rhodopsin related photoreceptor proteins suggests that the genes encoding these polypeptides arose by duplication of an ______ ______ gene and then divergence through accumulation of _______

Many of the mutations that promoted the ability to see color must have provided selective advantages to their bearers over the course of evolution

The red and green genes are the most ______, differing by less than _____ nucleotides out of every hundred. This fact suggests they diverged from each other in the relatively ______ evolutionary past

The less pronounced amino acid similarity of the red or green proteins with the blue protein, and the even lower relatedness between rhodopsin and any color photoreceptor, reflect ______ duplication and divergence

At least 29 different single nucleotide substitutions in the rhodopsin gene cause an autosomal dominant vision disorder known as ______  _______ that begins with an early loss of _____ function, followed by a ______ progressive degeneration of the _______ retina

Here we see the _______ of the amino acids affected by these mutations. These amino acid changes result in abnormal rhodopsin proteins that either do not _____ properly or, once ______ are unstable.

Although normal rhodopsin is an essential structural element of rod cell membranes, these nonfunctional _______ proteins are retained in the body of the cell, where they remain unavailable for ________ into the membrane. Rod cells that cannot incorporate enough _______ into their membranes eventually die

Depending on how many rod cells die, partial or complete _______ ensues

People with normal color vision have a single ____ gene; some of these normal individuals also have a single adjacent _____ gene, while others have _____ or even _____ green genes

Their proximity and high degree of homology (red and green) make these genes unusually prone to an error in meiotic recombination called _______ _______ ______

When homologous chromosomes associate during meiosis, two ______ _______ DNA sequences that are _______ to each other, like the red and green photoreceptor genes, can pair with each other _________

If recombination takes place between the mispaired sequences, photoreceptor genes may be _____, _______ or _______.

A variety of ____ _____ events produce DNA containing no red gene, no green gene, various combos of green genes, or hybrid red-green genes

These different DNA combos account for the large majority of known aberrations in red-green color perception, with the remaining abnormalities stemming from ____ mutations

Why do people with no red or no green gene perceive red and green as the same color?