Advanced bio questions genetics

Why is the "one gene, one polypeptide" description not accurate? You should include the roles of introns, alternative splicing, ribozymes, and small RNAs in your explanation. Give examples to support your explanation.

The statement "one gene, one polypeptide" is not accurate. After the production of a primary RNA transcript, large portions of the RNA molecule are removed in a process called RNA splicing that typically uses spliceosomes. Spliceosomes are large complexes of proteins and small RNA molecules that bind several short nucleotide sequences along the intron or non-coding sections of the RNA. The introns are then released (rapidly degraded), and the spliceosome joins together the two exons (coding region of RNA) that flanked the intron. The importance of these introns is that they may encode for more than one type of polypeptide. In fact, many genes have what is called alternative splicing in which genes can encode for multiple types of polypeptides depending on which segments of the RNA are treated as the exon during the RNA processing. For example, sex differences in fruit flies are largely due to differences in how males and females splice the RNA transcribed from certain genes. The Human Genome Project suggested that alternative splicing is one of the reasons that humans can get along with about the same number of genes as a nematode. Additionally, many genes code for RNA molecules that have important functions within cells even though they are never translated into proteins. The small RNA in the spliceosome assembly help to catalyze the splicing reaction. This catalytic role of the small RNA lead to the discovery of ribosomes, which are RNA molecules that act as enzymes. Three properties allow the RNA to function as an enzyme. First, RNA is single-stranded, a region of an RNA may base pair, in an antiparallel arrangement, with a complementary region elsewhere in the molecule, giving the molecule a three-dimensional structure. This allows the ribozymes to act just like protein enzymes. Second, some of the bases in RNA contain a functional group that can participate in the catalysis. Third, the ability of RNA to hydrogen-bond with other nucleic acids adds specificity to its catalytic activity

Discuss the characteristics of and important role of telomeres. Be sure to include the following terms in your essay (telomere, telomerase, heterochromatin, replication, cancer, and aging)

- Eukaryotic linear chromosomal DNA replication cannot complete the 5' end of the daughter DNA strands since a DNA polymerase can only add nucleotides to the 3' end of a preexisting polynucleotide. Even if an Okazaki fragment can be started with an RNA primer bound to the very end of the template strand, once that primer is removed it cannot be replaced with DNA since there is no 3' end available. Therefore, repeated rounds of replications should produce shorter DNA molecules with uneven ends, but that is not the case. - Eukaryotic chromosomal DNA contains telomeres which are special nucleotide sequences on their ends that do not contain genes but are made up of multiple repetitions of one short nucleotide sequence -Telomeres are heterochromatin which are tightly wound sections of DNA that cannot be transcripted but aid euchromatin in transcription. - The specific proteins associated with telomeric DNA prevent the staggered ends of daughter molecules from activating the cell's system for monitoring DNA damage (staggered ends can trigger signal transduction pathways leading to cell cycle arrest or cell death) and acts as a buffer zone that protects the organisms' genes from shortening - telomeres help protect gene erosion, they cannot completely prevent it, only postpone it. After each round of replication telomeres become shorter, therefore older individuals have shorter telomeres since their cells have divided many times. - shortening of telomeres has thought to be the cause of aging in organisms. An enzyme called telomerase helps compensate the shortening of the telomere by catalyzing the lengthening of telomeres in eukaryotic germ cells to help restore them to the original length. Telomerase activity in germ cells result in telomeres of maximum length in the zygote. - normal shortening of telomeres is thought to protect organisms from cancer by limiting the number of divisions that somatic cells can undergo. Tumor cells often have abnormally high telomerase activity, suggesting that its ability to stabilize the telomere length may allow these cancer cells to persist. Telomeres found in large tumor cells are often unusually short due to the many cell divisions

Explain how chromosomal sex is determined in humans and other mammals. Why is it that X-linked disorders are more common in males? Explain using a specific example.

- Humans and other mammals have two types of sex chromosomes, called X and Y. - Within the mammalian testes and ovaries, the two sex chromosomes segregate during meiosis. Each egg then receives one X chromosome whereas half of the sperm will receive an X chromosome and the other half receive the Y chromosome. - Therefore, if a sperm with an X chromosome fertilizes an egg, the offspring should be born chromosomally female (XX); if a sperm containing the Y chromosome fertilizes an egg, the offspring should be chromosomally male (XY). - Fathers can pass all X-linked alleles to their daughters but none to their sons - mothers can pass X-linked alleles to both their daughters and sons, since all eggs contain an X chromosome. - While the Y-linked genes determine sex, the X chromosome has genes for characteristics that are unrelated to sex. - homozygous and heterozygous lack meaning in the case of X-linked traits in males since they only have one locus; therefore, the term hemizygous is used in these cases. - X-linked trait is recessive, females must be homozygous to express the phenotype - Any male receiving a recessive allele from his mother will express the trait. Therefore, males are more likely to receive X-linked disorders than females who must receive the trait from both their father and mother - ex. red-green color blindness

What is self-incompatibility and what is the genetic basis of this mechanism?

- Self-incompatibility is the ability of a plant to reject its own pollen and the pollen of closely related individuals. This means if the pollen lands on the stigma of a flower of the same plant or of a closely related plant, a biochemical block prevents the pollen from fertilizing the egg. - The purpose of this ability is to ensure that the sperm and egg come from different plants and thus increase genetic diversity. The genetic basis of this mechanism is a set of genes called S-genes which allow the recognition of "self" pollen. - If a pollen grain has an S-gene allele that matches the S-gene allele of the stigma on which it lands, the pollen tube either fails to germinate or the tube fails to grow through the style into the ovary. - The self-incompatibility can be gametophytic (where the S-allele in the pollen genome governs the blocking of fertilization) or sporophytic (where fertilization is blocked by S-allele gene products in tissues of the parental plant). - gametophytic self-incompatibility an S1 pollen grain cannot fertilize an S1S2 flower but can fertilize an S2S3 flower whereas an S2 pollen grain would not be able to fertilize either. This type of self-incompatibility involves the enzymatic destruction of RNA within a pollen tube. The RNA-hydrolyzing enzymes are produced by the style and enter the pollen tube. - sporophytic self-incompatibility, neither an S1 or S2 pollen grain from a S1S2 parental sporophyte could fertilize eggs of an S1S2 or S2S3 flower due to the S1S2 parental tissue attached to the pollen wall. This type of incompatibility involves a signal transduction pathway in epidermal cells of the stigma that prevents the germination of the pollen grain.

The proportion of the eukaryotic genome that codes for genes (both protein-coding and noncoding RNA products) is very small. Describe the components of the genome that are known to comprise the remainder of the genome and explain how this might relate to the vast variation in genome size among eukaryotic organisms.

- The region of DNA in eukaryotes that codes for proteins and noncoding RNA products is very small while the bulk of the DNA is noncoding - Some of the noncoding area is comprised of introns and regulatory sequences. Between functional genes are unique (single-copy) noncoding DNA, such as gene fragments and pseudogenes (former genes that have accumulated mutations over a long time and no longer produce functional proteins). Both introns and pseudogenes can create some small noncoding RNA. - Most of the intergenic DNA is repetitive DNA that consists of sequences that are present in multiple copies of the genome. Of these repetitive DNA most are composed of transposable elements and sequences related to them. - During a process called transposition, transposable elements move from one site in the DNA to a different target site - the enzymes and proteins bend the DNA to bring these regions close to each other - by a type of recombination. Transposable elements can either be transposons or retrotransposons. - . Transposons use transposase (an enzyme that transposons encode) to move within a genome by means of a DNA intermediate either by a cut-and-paste method (removing the element from the original site) or a copy-and-paste method (leaves a copy behind). - Retrotransposons move by an RNA will always leave a copy at the original site during transposition. To insert at another site the RNA intermediate must reverse transcript into DNA using reverse transcriptase (which is encoded on the retrotransposon) and the insertion of the DNA is catalyzed by another cellular enzyme. - Species that have highly active transposable elements, especially those that use the copy-and-paste method, will have growing genomes which accounts for some of the variety of genomic size among eukaryotes - Other repetitive DNA, not related to transposable elements, are most likely the result of mistakes during replication that have moved segments from one chromosomal location to another site on the same or a different chromosome.

4 aspects of mendel's model explaining 3:1 F2 ratio

1. alternative versions of genes account for variations in inherited characters 2. for each character an organism inherits 2 copies of a gene, one from each parent 3. if 2 alleles differ at a locus then 1, the dominant allele, determines the organism's appearance, the other, recessive allele has no noticeable effect on phenotype 4. law of segregation

The term "alternation of generations" is used for one type of life cycle. What organisms have "alternation of generations"? Describe how it differs from the reproductive cycle of haplontic organisms (i.e. Chlamydomonas or Dictyostelium) and diplontic organisms (i.e. plasmodial slime mold).

Alteration of generations is a type of life cycle found in brown algae in which the organism alternates between multicellular haploid and diploid stages. The diploid individual is called a sporophyte since it creates spores called zoospores; these zoospores are haploid and are mobile via flagella. The zoospores than develop into haploid, multicellular male and female gametophytes which produce gametes. Fertilization between the two gametes results in a diploid zygote which will develop into a new sporophyte. Although haploid and diploid conditions alternate in all sexual life cycles - only the alteration of generations life cycle has multicellular forms for both the haploid and diploid form. The main difference between haplontic and diplontic life cycle is that the main form of the haplontic life cycle is haploid and its diploid zygote is formed for a short period of time whereas the main form of the diplontic life cycle is diploid, which produce gametes.

Compare and contrast the structures and functions of a seed with a fruit. In your discussion include the ploidy level of each component and its origin.

Angiosperms have a unique reproductive cycle known as double fertilization in which two haploid sperm enters the female gametophyte. One sperm will fertilize the haploid egg to form the diploid zygote and the other will combine with two polar nuclei to form a triploid nucleus in the center of the female gametophyte. Triploid nucleus will become the endo sperm, a food storing tissue of the seed the seed develops from the mature ovule and is comprised of the protective diploid seed coat, diploid embryo and triploid endo sperm fertilization triggers hormonal shift that causes ovary to develop into fruit ovary wall develops into pericarp - thickened cell wall of fruit. can dry out like in peas, remain fleshy like grape, or inner part can become stone-like (peach) once fully. matured. fruits can be simple - 1 carpel or fused carpels (pea) aggregate fruit - single flower with more than one separate carpel all forming one fruit (raspberry) multiple fruit - develops from inflorescence (pineapple) In accessory fruit, the ovary is embedded in the receptacle, and the fleshy part of this simple fruit is derived mainly from the enlarged receptacle. (apple)

Alterations of chromosome number or structure can cause genetic disorders. Explain why. Include in your answer the following terms - deletion, duplication, inversion, translocation, and define/describe/diagram each of these structural alterations of chromosomes.

Errors in meiosis or damaging agents such as radiation can cause the chromosome to break leading to four types of structural changes in the chromosome. this can lead to traits associated with abnormal dosages of genes - deletion - fragment of chromosome is lost causing the affected chromosome to lose certain genes - Embryos with a large deletion are usually missing essential DNA, a condition that is usually lethal; however, minor deletions can reduce the protein dosage that may be needed. - Ex. monosomy x - indiv are phenotypic fmale and are sterile due to sex organs not maturing. - "deleted" fragment may become attached as an extra segment to a sister chromatid creating a duplication. The detached fragment may also become attached to a nonsister chromatid of a homologous chromosome; however, the "duplicate" segments may not be identical since the homologs could carry different alleles of certain genes. Duplications can cause an excess of proteins to be created which leads to an exaggerated characteristic. - ex. trisomy 21 - most common type of dublication - indiv have characteristic facial features, short stature, correctable heart defects, and developmental delays -deletions and duplications common during crossing over - A chromosomal fragment can also reattach to the original chromosome but in reverse orientation causing an inversion. cause the balance of genes to be not abnormal (all genes are present in normal doses) - a chromosomal breakage can join a nonhomologous chromosome in translocation - translocation and inversion can alter the phenotype since a gene's expression can be influenced by its location among neighboring genes, this can lead to harmful effects.

What are types of asexual reproduction in plants? What are the advantages and disadvantages of asexual and sexual reproduction?

Fragmentation - separation of parent -plant into parts that develop into whole plants Some plants can have adventitious shoots produced from roots or leaves that eventually produce a whole offspring that is connected to the parent. apomixis - plants produce seeds without pollination or fertilization. The seed is a result of a diploid cell in the ovule that gives rise to an embryo and the ovules mature into seeds. This allows apomixis plants to have the benefits of seed-bearing fruit and dispersal that is usually only gained from sexually reproduction. does not need a pollinator for plants widely dispersed or unlikely to be visited. pass all of the parent genetic information on to offspring, favorable in stable environments asexual offspring tend to be stronger than sexually produced offspring lack of genetic variation created in sexual reproduction increasing risk of disturbances affecting organisms more severely no dormancy or seed dispursal

There are several key experiments that let to our understanding of DNA as the genetic material. Briefly describe the experimental method and the important conclusions of the following experiments: (a) Griffith in 1928, (b) Hershey and Chase in 1952, (c) Chargaff 1952

Griffith (1928) - In 1928, Griffith was trying to develop a vaccine for Streptococcus pneumoniae by using two strains of the bacteria (one pathogenic and one nonpathogenic). He tried to kill the pathogenic bacteria with heat, but when he mixed it with the nonpathogenic strain, some of the living cells became pathogenic. Additionally, he found that this new trait of pathogenicity was inherited by all the descendants of the transformed bacteria. Griffith thought some chemical component of the dead pathogenic cells caused this heritable change - although he didn't not know or identify the substance. Transformation, as coined by Griffith, would later become defined as the change in genotype and phenotype by assimilation of external DNA into a cell. Hershey and Chase (1952) - In 1952, Hershey and Chase created an experiment to determine whether protein or DNA was responsible for T2 (a type of phage that infects E. coli -a model organism) being able to infect E. coli cells and using the E. coli cells to create more T2 phage. In the experiment, they used radioactive sulfur to tag protein in one batch of T2 and radioactive phosphorus to tag DNA in a second batch. The decision was to use sulfur as a tag for proteins since proteins but not DNA contain sulfur and would incorporate the radioactive atoms into the proteins of the phage (T2). The decision to use phosphorus used a similar thought process. Separate samples of nonradioactive E. coli cells were infected with the protein-tag and the DNA-tag batches of T2. After the onset of infection, the mixture was agitated in a blender to free phage parts outside of the bacteria from the cell for both batches of T2. The mixture of each batch was then centrifuged so that bacteria formed a pellet at the bottom of the test tube and the free phages or phage parts would be suspended in the liquid. They then measured the radioactivity in the pellet and in the liquid since the DNA would be found in the pellet. They found that the phage DNA entered the host cell, but the phage protein had not. Additionally, when the bacteria were returned to a culture medium, E. coli released phages that contained radioactive phosphorus. This proved that DNA injected by the phage was the molecule that carried genetic information that makes the cell produce new viral DNA and proteins. Chargaff (1952) - Chargaff extracted DNA from multiple organisms (including: sea urchin, salmon, wheat, E. coli, human, and ox) and hydrolyzed to break apart the individual nucleotides. These nucleotides were then analyzed chemically through a series of experiments and provided an approximate value of each type of nucleotide. This showed that the percentages for Adenine and Thymine bases were roughly equal while the percentages for Cytosine and Guanine were roughly equal. This led Chargaff to create a series of rule: 1. Base composition of DNA varies between species and 2. For each species the percentages of A and T base are roughly equal, and the percentages of G and C bases are roughly equal.

DNA replication involves many enzymatically-controlled steps. List 5 of the enzymes required for DNA synthesis and clearly describe the detailed role of each. Make special note of the importance of 5' and 3' ends to the function of these enzymes (if applicable). During DNA replication, how can you identify the leading and the lagging strand?

Helicase - an enzyme that untwists the double helix at the replication fork (a Y-shaped region where the parental strands of DNA are unwound), making them available as template strands. A single-stranded binding protein then binds to and stabilizes the single-stranded DNA until the template is used. Topoisomerase - helps to relieve the strain caused by the untwisting of the double helix by breaking, swiveling, and rejoining the DNA strands. Primerase - synthesizes a short RNA primer at the 5' end of the leading strand (the new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory 5' - 3' direction) by adding RNA nucleotides together using the DNA template. The new DNA strand will start from the 3' end of the RNA primer. Additionally, Primerase synthesizes at the 5' of each Okazaki fragment (or a short segment of DNA synthesized away from the replication fork on a template strand during DNA replication and many of these strands join to making the lagging strand) of the lagging strands DNA polymerase III - using the parental DNA as a template synthesizes new DNA strand by adding nucleotides to the RNA primer or a pre-existing DNA strand in the 5' - 3' direction (for the leading strand, the DNA is synthesized continuous until it reaches the single-stranded binding protein. For the lagging strand DNA polymerase III must work along the other template strand in the direction away from replication fork and is synthesizing DNA discontinuously in a series of fragments (called Okazaki fragments). Therefore, the DNA polymerase III will start at the RNA primer closest to the leading strand and add DNA nucleotides in a 5' - 3' manner, but after reaching the next RNA primer to the right DNA polymerase III detaches and will move to the RNA primer to the left. DNA polymerase I - removes RNA nucleotides of the primer from the 5' end and replaces them with DNA nucleotides (moves in 5' to 3' manner). DNA ligase - joins the Okazaki fragments of the lagging strand together; on the leading strand, joins the 3' end of the DNA that replaces the primer to the rest of the leading strand.

Explain how regulating gene expression in bacteria and eukaryotic cells is similar and different with regards to gene organization, gene activation, gene repression, location of transcription, location of translation, polyribosomes, and timing of transcription and translation. You may use diagrams as long as they are clearly labeled and you refer to them in your written explanation.

In eukaryotes, almost all of the cells have the same genome. Different cell types have different functions with the differences in the cell types having to do with differential gene expression. Polyribosomes are strings of ribosomes that enable a cell to make many copies of a polypeptide quickly. In eukaryotes the polyribosomes are attached to the surface of the rough endoplasmic reticulum; in bacteria, they are found free in the cytoplasm. There are three main differences in gene expression between bacteria and eukaryotes. One is where transcription occurs, in bacteria, this takes place in the cytosol while eukaryotes have transcription in the nucleus. In both translation that occurs in the cytosol. Another is that mRNA in bacteria is translatable, while not all mRNA in eukaryotes is translatable. Lastly, bacteria have sets of genes under the control of one operon or regulatory control system while eukaryotes have one regulatory control system for each gene. Bacteria have a coding region in their genes while eukaryotes have both a coding and non-coding region. The operon model is a mechanism for the control of gene expression in bacteria. Bacteria groups genes of related functions into transcription units that form an "on-off switch" that can control the cluster of related genes. The on-off switch is a segment of DNA called an operator. The operator is positioned within the promotor or between the enzyme and the coding genes. The operator is a switch for transcription and controls access of RNA polymerase to the genes. The operator, the promoter, and the genes they control collectively make up the operon. When the operon is turned on, RNA polymerase can bind to the promoter and transcribe the genes of the operon. When the operon is turned off by a repressor, it binds to the operator and blocks the attachment of RNA polymerase to the promoter preventing transcription. Repressor proteins are operator-specific for a particular operon. Corepressors are small molecules that bind to a repressor to turn an operon off while Inducers inactivate repressors. An activator is a protein that binds to DNA and stimulates transcription of a gene. Regulatory genes continuously run; in contrast, inducible genes are usually off but can be switched on. Bacteria express only the genes whose products are needed by the cell.

Why are mutations important from an evolutionary perspective? Use the following DNA TEMPLATE strand sequence and the genetic code table (in Ch. 17) to give examples of the following types of mutation: silent, missense, nonsense, and frameshift. (The DNA sequence is from the middle of the coding region of a histone deacetylase gene.) 3' GAC CCC GAG TGC GAG 5'

Mutations are changes in genetic information of a cell and are ultimate source of new genes that natural selection can act on. While chromosomal rearrangements in structure or number be large-scale mutations, since they affect long segments of DNA, some mutations happen on a much smaller scale by only affecting one nucleotide pair, called point mutation. - If a point mutation happens in a gamete or in a cell that gives rise to a gamete, the mutation can be transmitted to offspring and future generations. Although a point mutation changes a single nucleotide pair, it may not cause a change in amino acid that is encoded by that segment of DNA. This type of mutation is called a silent mutation since there is no observable change in the phenotype. - The change in a single nucleotide pair may change what amino acid is encoded by the DNA and create a new phenotype in a process called missense mutation. Although these types of mutations do alter the protein slightly, they typically have little effect on the protein by the new amino acid may have properties similar to those of the amino acid it replaced or it may be in the region of the protein where the exact sequence of amino acids is not essential. - A nonsense mutation is when a change in a single nucleotide may change a codon from an amino acid to a stop codon and causes the translation to be terminated prematurely. This causes the resulting proteins to be much smaller and are typically nonfunctional. - Sometimes, pairs of nucleotides are not changed but are deleted or added into the DNA sequence altogether; when this occurs, it may alter the reading frame of the genetic message, or in other words the triplet grouping of nucleotides on the mRNA that is read during translation may be changed. This type of mutation is often called a frameshift mutation when the insertion/deletion is not a multiple of three and will alter the overall reading frame. All nucleotide downstream of the insertion/deletion will be improperly grouped into codons and result in an extensive missense and premature termination of the protein.

How is a retrovirus different from other viruses in structure? Compare and contrast the steps of the replicative cycle of a retrovirus with that of an RNA virus.

Retroviruses contain single stranded RNA along with an enzyme called reverse transcriptase that is used to transcribe the RNA into DNA inside of an envelope (sometimes with glycoprotein receptors). After retroviruses enter the host, reverse transcriptase catalyzes the synthesis of DNA complimentary to the viral RNA and catalyzes a second strand of DNA complimentary to the first strand. The double stranded DNA is incorporated into the cell's DNA as a provirus, and the proviral genes are transcribed into RNA molecules. - other enveloped RNA viruses which use the RNA as a template for mRNA synthesis or simply create mRNA which is translated directly into proteins. For most RNA viruses, the RNA inside the envelope is transcribed inside the host to make complementary RNA strands which are able to function as both mRNA and as a template for the synthesis of additional copies of genomic RNA. The mRNA is then translated to make the capsid proteins and the glycoproteins for the viral envelope. - Both RNA viruses and retroviruses, proteins and glycoproteins are then brought via vesicles to the plasma membrane where they are assembles into a new virus and released. These RNA molecules serve as genomes and mRNA for translation into protein of the viral progeny - similar to other RNA viruses

One advantage of sexual reproduction is the genetic diversity caused by new combinations of genes in offspring compared to the parents. Clearly describe two mechanisms that result in these new combinations of genes.

Sexually reproducing organisms can generate genetic variation through the mechanisms of independent assortment of chromosomes and crossing over during Meiosis I. Independent assortment is where two or more genes assort independently therefore each pair of alleles segregates independently of the other pair of alleles during gamete formation. 50/50 change for each gamete to receive a paternal or maternal chromosome. in humans this creates around 8.4 million different outcomes. offspring can have combinations of traits that do not match either of their parents. prior to independent assortment, crossing over of maternal and paternal homologs during prophase I creates recombinant chromosome - a chromosome with both parent's DNA The recombination of chromosomes resulting from the crossing over may bring alleles together in new combinations, and meiosis then distributes recombinant chromosomes in a multitude of combinations to the gametes.

1. More complex inheritance patterns arise when a particular gene has more than two alleles or when alleles are not completely dominant or recessive. Describe an example of each of these patterns and explain how the outcome differs from what would be expected of "simple" Mendelian inheritance.

alleles may have differing degrees of dominance in relation to each other snapdragon flowers exhibit incomplete dominance. homozygous flowers are either red (dominant) or white (recessive). when a True breeding red is crossed with a true breeding white the resulting F1 generation is pink. ABO blood types are determined by three alleles of a single gene IA, IB, and i. this results in four blood types A, B, AB, O. these letters refer to the type of carbohydrate on the surface of the red blood cell. A has carbohydrate A, B has carbohydrate B, AB has both, O has neither. AB blood type shows codominance - two alleles affect the phenotype in separate distinguishable ways. Both A and B show dominance over O. Mendelian genetics does not take differing degrees of dominance into account in its model. requires 2 alleles at a locus with one being dominant over the other.

1. Explain what two laws of inheritance Gregor Mendel discovered by breeding pea plants and 1) following a single character and 2) following two characters at the same time?

cross bread pure breeding plants over 2 generations opposed blending theory law of segregation - two alleles for a heritable characteristic separate from each other during gamete formation and end up in different gametes law of independent assortment - observed while following two traits - two or more genes assort independently therefore, each pair of alleles segregates independently of the other pair of alleles during gamete formation. Law of independent assortment only applies to genes r allele pairs on differing chromosomes or genes far apart on same chromosome