Final exam additional reading guides

How can the human X and Y chromosomes pair during meiosis even though they are of different lengths and most of their genes are different?

The X and Y chromosomes can pair during meiosis through regions of homology located near the tips of the chromosomal arms

What is the biological basis for the 1:1 ratio of males and females at conception in mammals?

Meiosis in females results in X-bearing eggs only. In contrast, meiosis in males results in a 1 : 1 ratio of X-bearing and Y-bearing sperm. Random fertilization of the egg results in a 1 : 1 ratio of female : male offspring

For a recessive X-linked mutation, such as color blindness, what is the pattern of inheritance from an affected male through his daughters into her children

When an affected male mates with a homozygous nonmutant female, all of the sons are unaffected (because they receive their X chromosome from their mother), but all of the daughters are heterozygous (because they must receive their father’s X chromosome). When one of these heterozygous daughters mates with an unaffected male, half of the sons are affected (they inherit their grandfather’s X-linked allele) and half are unaffected (they inherit their grandmother’s X-linked allele). As for the daughters, although all of the daughters are phenotypically unaffected, half are heterozygous (they inherit their grandfather’s X-linked allele), whereas half are homozygous nonmutant (they inherit their grandmother’s X-linked allele).

Is it possible for an unaffected female to have female offspring with red–green color blindness?

Yes. A woman whose father is color blind must be heterozygous for the mutant allele. If she has children with a man who is color blind, then half of the female offspring are expected to be homozygous mutant and therefore color blind

What is the pattern of inheritance expected from a Y-linked gene in a human pedigree?

For a Y-linked gene, only males are affected with the trait and all sons of affected males are affected, which means males in every generation show the trait. Females never inherit or transmit the trait because females do not have a Y chromosome and males get their Y chromosome from their fathe

How can Y-chromosome data be used to trace paternal ancestry?

Y-linked genes show complete linkage, which means that sequences in the Y chromosome are not exchanged for others through crossing over and mutations can accumulate in a single line of inheritance. Because each hereditary lineage of Y chromosomes is separate from every other lineage, they can be used to trace an individual’s paternal ancestry

A man affected with a mitochondrial mutation mates with a woman who does not have the mutation. What is the probability that their offspring will be affected?

The offspring will likely not be affected by the mitochondrial mutation because mitochondria of the offspring come from the mother, not the fathe

How can mitochondrial DNA data be used to trace maternal ancestry?

Mitochondrial DNA does not undergo recombination, so mutations can accumulate in a single line of inheritance, inherited maternally. Because each hereditary lineage of mitochondria is separate from every other lineage, mitochondria can be used to trace an individual’s maternal ancestry

Why are some complex traits also called quantitative traits

Complex traits are often called quantitative traits because phenotype is measured on a scale with only small intervals between similar individuals. In many complex traits, the phenotype is determined by counting or by measuremen

What is an example of a complex trait?

Examples discussed in this chapter include height, weight, hair color, skin color, fingerprint ridge count, blood pressure, number of eggs laid by hens, quantity of milk produced by dairy cows, and yield of grain per acre

What are some factors that influence variation in complex traits?

Several factors that can influence variation in complex traits are environmental factors such as sunlight, moisture, or nutrition and genetic factors such as multiple genes affecting a single trait

Why does it not make sense to try to separate the effects of genes (“nature”) and the environment (“nurture”) in a single individual, whereas it does make sense to separate genetic and environmental effects among individuals?

It does not make sense to try and separate the effects of genes and the environment in a single individual because those effects are so intimately related. If you gain a pound of weight after eating a 14-inch pizza all by yourself, is it because of the calories in the pizza or because your genes make your digestion really efficient? Maybe a combination of both, but who can say? Similarly, how could you possibly tell to what extent it is breathing or the oxygen in the air that keeps you alive? On the other hand, although in each single individual, genetic and environmental effects are intertwined, in a population of individuals it is possible to separate genes and environment in regard to their effects on the differences, or variation, among individuals. For some traits, the variation seen among individuals is due largely if not exclusively to differences in the environment. For other traits, the variation is due mainly to genetic differences

Explain why the effect of a genotype on a phenotype cannot always be determined without knowing what the environment is, and why the effect of a particular environment on a phenotype cannot always be determined without knowing what the genotype is.

The effect of genotype on a phenotype cannot always be determined without knowing what the environment is and vice versa because genes and the environment can interact in unpredictable ways. Variation in the effects of the environment on different genotypes is called genotype-by- environment interaction. This type of interaction implies that the effect of a genotype cannot be specified without knowing the environment, and the effect of the environment cannot be specified without knowing the genotype.

What are three key structural features of DNA?

1) DNA is made up of subunits called bases. (2) DNA is a linear polymer of nucleotides with sugar subunits linked by phosphodiester bonds. (3) Cellular DNA is a double helix with two strands that are antiparallel to each other

The letter R is conventionally used to represent any purine base (A or G) and Y to represent any pyrimidine base (T or C). In double-stranded DNA, what is the relation between the number of molecules or R and the number of molecules of Y?

Because R = A or G, number of R = number of A + number of G. Also, because number of A = number of T and number of G = number of C, we can write number of R = number of A + number of G = number of T + number of C. But T or C = Y, so number of T + number of C = number of Y. It follows that number of R = number of Y

How does the sequence of a molecule of DNA, made up of many subunits of only four nucleotides, encode the enormous amount of genetic information present in living organisms?

Just four nucleotides can give rise to the vast diversity of genetic information because the nucleotides can occur in any order. Any base on a strand of DNA can be followed by any other base (A, T, G, or C), which gives rise to an enormous potential genetic diversity of any given gene

How are the parental strands in a DNA molecule used in DNA replication?

During DNA replication, the two strands of the double helix unwind and separate, disrupting the hydrogen bonds and base stacking that hold the strands together. Each parental strand serves as a template for a new complementary strand of DNA because of the specific pairing of the bases: an A on the template will always specify a T on the new strand, a G on the template will always specify a C on the new strand, and so on. The end result of DNA replication is two daughter DNA molecules that have identical sequences to the original parental molecule

What is the usual flow of genetic information in a cell?

The usual flow of genetic information in a cell is from DNA to RNA to protein

Suppose Meselson and Stahl had done their experiment (Fig.11.4) the other way around, starting with cells fully labeled with 14N light DNA and then transferring them to medium containing only 15N heavy DNA. What density of DNA molecule would you predict after one and two rounds of replication?

After one round of replication, you would predict only 14N/15N hybrid DNA, which has a density of 1.715 g/cm3. After two rounds of replication, you would predict half the molecules to be 14N/15N hybrid DNA (density 1.715 g/cm3) and half to be 15N/15N heavy DNA (density 1.722 g/cm3)

How does the structure of DNA itself suggest a mechanism of replication

The structure of DNA, featuring two complementary strands wound in a double helix, suggests replication occurs through strand separation, where each strand serves as a template for synthesizing a new complementary strand, ensuring accurate duplication.

How does the structure of DNA itself suggest a mechanism of replication

DNA consists of two antiparallel strands, meaning that the 3′-hydroxyl end of one strand is opposite the 5′-phosphate group of the other strand. In the antiparallel helical coil, a purine base (A or G) of one strand base pairs with a pyrimidine base (T or C, respectively) of the other strand. This mechanism allows for one strand to dictate the sequence of the other. When DNA replication occurs, the two strands separate (“unzip”) from each other, and both are used as a template for the replication of two new DNA strands

How does the chemical structure of deoxynucleotides determine the orientation of the DNA strands, and how does this affect the direction of DNA synthesis?

The orientation of the two DNA strands is antiparallel. This means that the 3′-hydroxyl end of one strand is opposite the 5′-phosphate group of the other strand. When the two strands separate and DNA replication begins, nucleotides are added to the 3′ end of both strands, so DNA replication occurs in the 5′-to-3′ direction in both strands

What are the similarities and differences in the way the two daughter strands of DNA are synthesized at a replication fork

The synthesis of the two daughter strands is similar in that they the chemistry of strand elongation is the same and, for both strands, replication occurs in the 5′-to-3′ direction. The two strands are different in the way that they are replicated: one is the leading strand, and the other the lagging strand. The leading strand has the 3′ end of its DNA pointed toward the replication fork and thus is synthesized as one long, continuous polymer. The replication of the other strand, or lagging strand, is a little more complex due to its 5′ end pointing toward the replication fork. Because DNA can only be replicated in the direction of 5′ to 3′, the lagging strand is synthesized in short, discontinuous pieces. Each new piece, or Okazaki fragment, is elongated at its 3′ end until it reaches the piece in front of it

Why is replicating the ends of linear chromosomes problematic?

Replicating the ends of linear chromosomes is problematic because during the synthesis of the lagging strand, about 100 base pairs at the 3′ end are not replicated. This is due to the fact that the RNA primer synthesized on this strand is about 100 nucleotides from the end

How does the cell overcome the challenge of replicating chromosome ends

The loss of sequence at the ends of replicated chromosomes is restored through an enzyme called telomerase, which is most active in germ and stem cells. The enzyme telomerase caps eukaryotic chromosomes with a repeating sequence called the telomere, which does not encode any genes. When 100 nucleotides of the telomere are lost, the telomerase replaces them. This shortening and lengthening of the chromosome are not detrimental to the cell because there are no coded genes in

What are four differences between the structures of DNA and RNA?

Structural differences between DNA and RNA include the following. (1) The sugar in RNA is ribose, whereas the sugar in DNA is deoxyribose. (2) The base thymine in DNA is replaced by uracil in RNA. (3) DNA molecules are usually double stranded, whereas RNA molecules are usually single stranded. (4) DNA molecules are typically very long, whereas RNA molecules are usually much shorter than DNA molecules

A segment of one strand of a double-stranded DNA molecule has the sequence 5′-ACTTTCAGCGAT-3′. What is the sequence of an RNA molecule synthesized from this DNA template?

The RNA transcript has the sequence 5′-AUCGCUGAAAGU-3

What is the consequence for a growing RNA transcript if an abnormal nucleotide has a 3′–H instead of a 3′–OH? What if the nucleotide has a 2′–H rather than a 2′–OH?

The incorporation of a nucleotide with a 3′–H group rather than a 3′–OH group will stop subsequent elongation because the 3′–OH group is necessary to attack the high-energy phosphate bond of the incoming nucleoside triphosphate. The incorporation of a nucleotide with a 2′–H group rather than a 2′–OH group will have no effect on elongation, as this group is not involved in the polymerization reaction

What are three mechanisms of RNA processing in eukaryotes?

Three mechanisms of RNA processing (chemical modification of the primary transcript to generate the finished mRNA) in eukaryotic cells are as follows:

a. Addition of the 5′ cap. This modified nucleotide (7‐methylguanosine) allows the mRNA to be

recognized by the translation initiation complex and helps stabilize the mRNA.

b. Addition of the poly(A) tail. This modification is important in the export of the mRNA into the

cytoplasm, and the poly(A) tail, like the 5′ cap, helps stabilize the mRNA.

c. RNA splicing. Splicing is the process by which introns are removed from a primary RNA transcript. A single transcript with multiple introns may be spliced in different ways to generate multiple mRNAs, each resulting in a different protein with somewhat different properties. Alternative splicing is therefore one more mechanism that increases the number of ways that the genetic information stored in DNA can contribute to the diversity of cellular proteins in eukaryotes

What are five types of noncoding RNA and their functions?

Five types of noncoding RNA are (1) ribosomal RNA (rRNA), which is found in all ribosomes and is essential in translation; (2) transfer RNA (tRNA), which carries individual amino acids to the ribosomes in translation; (3) small nuclear RNA (snRNA), which is involved in eukaryotic gene splicing, polyadenylation, and other processes in the nucleus; (4) microRNA (miRNA), which can destroy transcripts or inhibit translation; and (5) small interfering RNA (siRNA), which can also destroy transcripts or inhibit translation. snRNA, miRNA, and siRNA have other regulatory functions as well, and these are still not fully understood

When a region of DNA that contains the genetic information for a protein is isolated from a bacterial cell and inserted into a eukaryotic cell in a proper position between a promoter and a terminator, the resulting cell usually produces the correct protein. But when the experiment is done in the reverse direction (inserting eukaryotic DNA into a bacterial cell), the correct protein is often not produced. Why is this the case?

The eukaryotic DNA sequence contains introns, which the bacterial cell cannot splice out properly. Thus, the correct protein is not produced from the information in the bacterial RNA transcript.

What are the relationships among the template strand of DNA, codons in mRNA, anticodons in tRNA, and amino acids?

Codons in mRNA are groups of three nucleotides that each code for a specific amino acid. They are copied from the DNA template strand, but RNA uses U instead of T. The order of codons in mRNA determines the sequence of amino acids in a polypeptide chain. At the ribosome, tRNAs match their anticodons (three-nucleotide sequences) to the codons in mRNA. Each anticodon is complementary to its codon and similar to the DNA template strand, with U replacing T. Every tRNA carries a specific amino acid linked to its anticodon. As the ribosome reads the mRNA, amino acids are added in the correct order based on matching codons and anticodons.

Which polypeptide sequences would you expect to result from a synthetic mRNA with the repeating sequence 5′-UUUGGGUUUGGGUUUGGG-3′?

The three reading frames are as follows: UUU GGG UUU GGG..., which codes for repeating Phe–Gly–Phe–Gly... UUG GGU UUG GGU..., which codes for repeating Leu–Gly–Leu–Gly... UGG GUU UGG GUU..., which codes for repeating Trp–Val–Trp–Val...

What are the steps of translation? Name and describe each one

Translation involves three main steps: initiation, elongation, and termination. During initiation, the ribosome assembles around the mRNA and the first tRNA binds to the start codon. In elongation, tRNAs bring amino acids to the ribosome, which links them into a growing polypeptide chain according to the sequence of codons in the mRNA. Finally, termination occurs when the ribosome reaches a stop codon, prompting the release of the completed polypeptide.

What is initiation step of translation

Initiation: In eukaryotes, initiation factors bind to the 5′ cap of mRNA; in prokaryotes, they bind at the Shine–Dalgarno sequence. They help bring in the small ribosomal subunit and a tRNA carrying methionine. This complex moves along the mRNA until it finds the start codon (AUG). Then the large ribosomal subunit joins, releasing the initiation factors. The tRNAMet sits in the P site. The next tRNA enters the A site, matching the next codon. A peptide bond forms between methionine and the new amino acid. The ribosome shifts along the mRNA, moving the empty tRNAMet to the E site (where it leaves) and the peptide-carrying tRNA to the P site. The A site is ready for the next tRNA.

What is elongation step of translation

Elongation: The ribosome continues in this fashion, shifting down the mRNA one codon at a time, adding amino acids to the growing peptide chain. Elongation factors provide the energy needed for these reactions to happen

What is termination step of translation

Termination: When the ribosome complex comes across a stop codon (UAA, UAG, or UGA), a protein release factor binds in the A site of the ribosome and causes the bond between the polypeptide chain and the last tRNA to break. Once the polypeptide chain is released, the ribosomal subunits disassociate from the mRNA and each other, and translation is complete

Bacterial DNA containing an operon encoding three enzymes is introduced into chromosomal DNA in yeast (a eukaryote) in such a way that it is properly flanked by a promoter and a transcriptional terminator. The bacterial DNA is transcribed and the RNA correctly processed, but only the protein nearest the promoter is produced during translation. Why?

With proper eukaryotic processing, the RNA transcript from the bacterial DNA will be capped at the 5′ end. The initiation complex will form at the 5′ cap and move along the mRNA until the first AUG codon is encountered. At that point, translation begins. When one of the termination codons is encountered, the polypeptide is released. Translation of the downstream polypeptides cannot take place because the Shine–Dalgarno sequences preceding them are not recognized by the eukaryotic translational machinery

How does simultaneous regulation of protein synthesis at multiple levels offer advantages over regulation at only one level?

Simultaneous regulation of protein synthesis and activation at multiple, overlapping levels offers the advantage that, if regulation at any one level fails or is incomplete, regulation at later levels can compensate. Another advantage is that multiple levels of regulation allow for finer tuning of the amounts of active protein produced.

When might it be advantageous for a cell to have many copies of an inactive protein that can be activated by an enzymatic process, such as phosphorylation, rather than to synthesize the molecules when they are needed?

When many copies of an inactive protein are present, they can be activated almost instantaneously because activation is an enzymatic process. Transcribing and translating the proteins would require much more time and energy, which would not allow rapid cellular response to changing conditions.

How does a protein end up free in the cytosol, embedded in the cell membrane, or secreted from the cell?

Proteins made by free ribosomes in the cytosol are guided to their destinations by signal sequences—short amino acid sequences. Proteins with signals go to places like the nucleus, mitochondria, or chloroplasts; those without signals stay in the cytosol. Proteins made by ribosomes on the rough ER are sorted during translation. A signal sequence directs the ribosome to the ER, where the protein is threaded into a channel. These proteins are destined for the ER lumen, Golgi apparatus, lysosomes, or secretion outside the cell. If a protein has a signal-anchor sequence, it stays embedded in the ER membrane.

What are two ways that proteins can acquire new functions in the course of evolution? Explain each one

Two ways in which proteins can acquire new functions through the course of evolution are (1) mutation and natural selection and (2) combining different folding domains

How does mutation and natural selection allow for new functions through evolution

The amino acid sequence is crucial for a protein’s proper folding and function. A mutation that changes an amino acid can affect the protein’s function and its chances of being selected in a population. Harmful mutations usually lower survival and reproduction, so they are eliminated over time. Neutral mutations, which don’t affect function, can stay in the population. Rarely, a mutation can improve protein function, giving the organism a survival advantage.

How does combining different folding domains allow for new functions through evolution

Combining different folding domains: Form leads to function. If a gene gains a new folding domain by joining with a folding domain from another gene, for example, its product now has the additional function provided by that folding domain. If this function is beneficial or benign to the protein, and ultimately has a positive or neutral effect on the survival and reproductive ability of the organism, the new gene, and therefore the protein, will be maintained in the population

In the evolution of resistance in the malaria parasite to pyrimethamine, what do you think happened to the mutations that decreased survival or reproduction of the parasites?

A mutation that decreases survival or reproduction will likely decrease in number in each generation because mutant forms leave fewer offspring than nonmutant forms. Eventually, the harmful mutation may disappear from the population because its final carriers failed to survive or reproduce. In the extreme case when the harmful mutation causes death or sterility, it can disappear in just one generation.