Biology 1207 Midterm 4 Review COMPLETE REVIEW

What 3 conditions or diseases are associated with faulty Nucleotide Excision Repair in humans?

*NER was discovered in humans from genetic diseases that affect DNA repair -Xeroderma pigmentosum (XP) -Cockayne's syndrome (CS) -PIBIDS (photosensitivity) *Photosensitivity is a common characteristic in all three syndromes because of an inability to repair UV-induced lesions

How do some activators affect DNA packing? What is an enzyme that would lead to more compact (denser) association of histones with DNA? Does this lead to DNA transcription? Which enzyme would have the opposite effect? Does this lead to DNA transcription? What effect do chromatin remodeling enzymes have on the position of nucleosomes?

*activtors can attrach chromatin remodling enzymes, which can control the density *Histone Metholaze, histone methyl transferase (add methyl groups to histons groups) *opposite: histone transactelyace becayse actely groups *

What can a dihybrid cross tell you about two genes (two traits)? How will the F2 generation look different if the two genes are linked versus if they are not linked?

- Follows inheritance of two different traits - Can determine linkage n Possible patterns: -Two genes are linked - found together in parents always inherited as a unit -Two genes are independent - variants are randomly distributed

What are X-linked traits? What term do we use to describe the genotype of human males who carry an X-linked gene? Make sure you can recognize X-linked inheritance in a cross scheme. Examining Morgan's experiments with the white gene would be a good way to study the inheritance of an X-linked trait. Be able to determine the outcome of a mating with an X-linked trait.

-In humans, X chromosome is larger and carries more genes than the Y chromosome -Genes found on the X (>1000 genes) but not the Y(<100 genes) are X-linked genes -Sex-linked genes are found on one sex chromosome but not the other -Males are hemizygous for X-linked genes -Hemophilia A is caused by recessive X -linked gene -Disease allele (Xh-A) encodes defective version ofa clotting protein

When is the product rule applied in predicting genetic outcome from a cross? When is the sum rule applied in predicting genetic outcome from a cross? Make sure you are able to apply these in the right cases to calculate the probability of a particular genotype or phenotype in a cross.

-Probability that two or more independent events will occur is equal to the product of their individual probabilities-If we toss a coin twice, what is the probability that we will get heads both times?-The product rule says that it is equal to the probability of getting heads on the first toss (1/2) times the probability of getting heads on the second toss (1/2), or one in four -Probability that one of two or more mutually exclusive outcomes will occur is the sum of the probabilities of the possible outcomes- In a cross between two heterozygous (Tt) pea plants, we may want to know the probability of a particular offspring being a homozygote (either TT or tt)

What is the normal function of Rb protein? What happens if both copies of Rb are defective?

-Rb protein inhibits the transcription factor of E2F, which activated genes for G1 to S phase cell cycle progression -prevents cell division -if both copies are defective, E2F protein is always active, resulting in uncontrolled cell division

How is sex determined in different organisms at a chromosomal level, such as in chickens?

-Sex chromosomes are found in many (but not all) species with two sexes -Several mechanisms for sex determination -Not all chromosomal mechanisms involve sex chromosomes -Bees are haplo-diploid - male is haploid (from an unfertilized egg) and female is diploid (includes both worker bees and queen bees). -Other mechanisms also exist -Sex is controlled by environment (temperature) in some reptiles and fish -Plants -Some have a single type of plant making male and female gametophytes -Others have sexually distinct plants making male or female gametophytes only

When you look at the genome of a malignant tumor cell, would you expect to see only one mutation or several?

-cancer requires multiple genetic changes to the same cell -begins w a benign genetic alteration that, over time leads to malignancy -malignancy can continue to accumulate genetic changes that make it even more difficult to treat

What are three ways a tumor-suppressor gene can lose function?

-mutation within a tumor-suppressor gene: to inactivate its function -chromosome loss: may contribute if the missing chromosome carries one or more tumor-suppressor genes -abnormal methylation of CpG islands: near promoter regions of the tumor-suppressor gene

What is the relationship between cell growth signaling proteins and oncogenes? How do oncogenes promote cancer?

-mutations of cell growth signaling proteins can create oncogenes(producing abnormally high level of activity ) -oncogenes promote cancer by keeping cell division signaling pathway in a permanent "on" position

How do tumor-suppressor genes act as negative regulators of cell division? What was the first tumor-suppressor gene identified in humans? What effect does this tumor-suppressor gene mutation have on the human?

-tumor suppressor genes that are necessary to halt cell division -retinoblastoma was the first tumor-suppressor gene identified, caused tumors that developed in the retina -inherited forms: occur earlier in life while other forms caused by environmental agent arise later in life

Will a p53 mutation affect normal healthy cells? Why not? What are such cells highly sensitive to, however?

-when checkpoint genes are mutated, the division of normal healthy cells may not be affected -cell division leading to normal growth is regulated properly -p53 not necessary for normal cell growth/division -sensitive to mutagens and easily develop cancer -loss of checkpoint protein will make it more likely that genetic changes will occu

What are the five components to the chromosomal theory of inheritance?

1. Chromosomes contain the genetic material (DNA). Genes are foundin the chromosomes. 2. Chromosomes are replicated and passed from parent to offspring. Also passed from cell to cell during the development of a multicellular organism. 3. The nucleus of a diploid cell contains two sets of chromosomes, found in homologous pairs.Maternal and paternal sets of homologous chromosomes are functionally equivalent;Each set carries a full complement of genes. 4. At meiosis, one member of each chromosome pair segregates into each daughter nucleus. During the formation of haploid cells, the members of different chromosome pairs segregate independently of each other. 5. Gametes are haploid cellsCombine to form a diploid cell during fertilizationEach gamete transmits one set of chromosomes to the offspring.

1. Which of the following choices will be affected by a cell containing two nonfunctional copies of p53? I. Apoptotic pathways II. DNA repair pathways III. Ability to arrest the cell cycle a. I and III b. I, II and III c. I and II d. II only

1. Which of the following choices will be affected by a cell containing two nonfunctional copies of p53? I. Apoptotic pathways II. DNA repair pathways III. Ability to arrest the cell cycle a. I and III b. I, II and III c. I and II d. II only

What are three levels gene regulation in prokaryotes can occur? Which is most prevalent and why?

1. transcription (efficient) 2.translation (less common) 3. protein or post-translation *Regulation at level of transcription is efficient - saves energy. *Remember, there is no nucleus in bacteria to act as a level of regulation

If two heterozygote individuals (Tt x Tt) mate, what is the probability that their first two children will both be affected with the recessive disorder (Child 1 and Child 2)? 1 1/2 1/4 1/16

1/16 Explanation In this question, the probability of one child being affected is 1/4, so the question asks what is the probablity that Child 1 AND Child 2 will be affected, so you apply the product rule: 1/4 x 1/4 = 1/16.

A woman has six sons. The chance that her next child will be a daughter is: 1/2 1 0 5/6 1/6

1/2

If two heterozygote individuals (Tt x Tt) mate, what is the probability that their first child will be an affected boy OR an affected girl? 1/2 1/4 1/8 1

1/2 Explanation Since this problem is asking you to calculate the probability of two mutually exclusive events (see "or" in question), you will apply the sum rule to the mutually exclusive events, but first you need to calculate the probablity of EACH event.The probability of being an affected male is: 1/2 (being a male) x 1/4 (being affected) = 1/8.The probability of being an unaffected girl is: 1/2 (being a girl) x 3/4 (being unaffected) = 3/8The SUM of 1/8 + 3/8 = 4/8 or 1/2.

How many replcation forks are there at an orgin of replication?

2

If non-disjunction occurred with Chromosome 1 during Meiosis I, in a diploid organism with three pairs of homologous chromosomes, how many chromosomes would each daughter cell have after Meiosis I is complete? 3 and 5 4 and 8 2 and 4 1 and 4

2 and 4

RNA polymerase reads sequence in which direction along the DNA

3' to 5' along the template strand

In bacteria, how does the small ribosomal subunit know where to associate with the mRNA? a. by recongnizing the ribsomal binding sequence at the 5' end of the mRNA. b. by binding to a release factor in the large ribosomal subunit c. by recognizing the ribsomal binding sequence at the 3' end of the mRNA d. by recognizing the guanosine cap at the end of the mRNA e. all of the above

A

What consistent observations did Mendel make in all of his monohybrid crosses?

All dominant in the F1 generation~3:1 in every case in the F2 generation!

What is the inducer of the Lac Operon? Lac A Allolactose Lac I ATP

Allolactose

What three things occur during anaphase I? What occurs during telophase I? What is the end result of meiosis I? What step is absent when the cell moves from Meiosis I to Meiosis II?

Anaphase 1 - action phase Segregation of homologues occurs Connections between bivalents break, but sister chromatids stay connected together Each pair of chromatids migrates to opposite poles

consider a diploid species where n=5. If an individual of this species was found to have 11 chromosomes, it would be categorized as: Polyploid Aneuploid Tetraploid Monosomic Triploid

Aneuploid

What happens to most aneuploidy embryos in humans? Why are some monosomic or trisomic individuals able to survive to birth? What is an example of trisomy in humans that can survive infancy? What is an example of monosomy in humans that can survive infancy? What are two examples of trisomies involving the sex chromosomes?

Aneuploidy in all eukaryotic species usually has detrimental consequences Polyploidy in mammals is generally a lethal condition Some exceptions: male bees (haploid) from unfertilized eggs, while female bees (diploid) from fertilized eggs Trisomic and monosomic individuals have an imbalance in the level of expression of genes on different chromosomes that interact in the cell This imbalance disrupts cell function

10. If this is a sex-linked recessive pedigree, what is the probability of individual 18 being neither affected nor a carrier? a. 0% b. 100% c. 25% d. 50%

Answer: Choice a, because as stated above half of their daughters will be affected and half of their daughters will be carriers.

7. If this is a sex-linked recessive pedigree, what is the probability of individual 22 being affected? a. 0% b. 100% c. 25% d. 50%

Answer: Choice b because #22 has an affected mother who must be homozygous for this X-linked trait. Therefore, she has only a mutant carrying X chromosome to pass on to all of her sons.

6. Consider the pedigree of a recessive trait. What is the mode of inheritance? a. It can only be autosomal b. It can only be sex-linked c. It can be either autosomal or sex-linked d. Mitochondrial inheritance

Answer: Choice b, #4 is an affected male from a carrier mother (#1) but his father (#2) is not a carrier, therefore, the only way #4 could be affected is if this were an X-linked trait. His mother, #1, was a carrier and passed her X-chromosome carrying the mutation to her son, #4 and he is affected. Let's test this hypothesis by looking at #16. His mother, #3, is also a carrier, but #16 has an affected daughter, #19. This could only happen if his mate (#10) was a carrier. So the evidence supports a sex-linked recessive trait. If it were autosomal recessive, then none of the offspring of #1 could be affected. If it were mitochondrial inheritance, then all of the offspring of females would be affected and none of the offspring of the males in the pedigree would be affected.

12. If this is a sex-linked recessive pedigree, if individual 20 is not affected, what is the probability individual 21 will be a carrier? a. 0% b. 100% c. 25% d. 50%

Answer: Choice b, because females get their X-chromosomes from their mother. If the father, #20, is not affected, the affected mother, #21, still can only give an X-chromosome with the mutation to her offspring because she is homozygous for this mutation (both of her X-chromosomes have this mutation). Therefore, it is with 100% probability that all of her daughters will be carriers because they can only receive an X-chromosome bearing the mutation from their mother.

Pedigree for Questions #5 through #12 These questions test your ability to recognize a particular pattern of inheritance from a pedigree and determine the probability of particular genotype from the pedigree. Note the pedigree here shows the carrier as well as the affected. This will NOT be the case on your exam. 5. Consider the pedigree. Is the trait dominant or recessive? a. The mode of inheritance cannot be determined. b. Dominant c. Recessive d. Codominant or incompletely dominant

Answer: Choice c, the fact that you find even one affected offspring (II-4) with unaffected parents, tells you that this trait is a recessive one.

9. If this is a sex-linked recessive pedigree, what is the probability of individual 18 being a carrier and not affected? a. 0% b. 100% c. 25% d. 50%

Answer: Choice d, because this individual has a hemizygous mutant father and a carrier mother. Choice d, because this individual has a hemizygous mutant father and a carrier mother. Half of their daughters will be affected and half of their daughters will be carriers. You know that individual 18 is a female because she is represented as a circle on the pedigree.You know that individual 18 is a female because she is represented as a circle on the pedigree.

8. If this is a sex-linked recessive pedigree, what is the probability of individual 18 being affected? a. 0% b. 100% c. 25% d. 50%

Answer: Choice d, because this individual has a hemizygous mutant father and a carrier mother. Half of their daughters will be affected and half of their daughters will be carriers. You know that individual 18 is a female because she is represented as a circle on the pedigree.

11. If this is a sex-linked recessive pedigree, if individuals 12 and 17 have a son, what is the probability of him being affected? a. 0% b. 100% c. 25% d. 50%

Answer: Choice d, since the mother (#12) is a carrier and the father (#17) is not, there is a 50% change that a son will inherit an X chromosome from his mother that carries the mutation.

How are homologues similar to one another? How can they be different?

Autosomes - each homologue is nearly identical in size and genetic composition Both may carry a gene for eye color but one may have brown and the other blue

What of the following is NOT one of the three discrete sites for tRNA binding and polypeptide synthesis in the ribsome? a. the aminoacyl site (A) b. the entrance site (E) c. the peptidyl site (P) d. the exit site (E)

B

3. Predict the phenotype of a promoter (lac P) mutant which has a mutation in the promoter for the lac operon. a. The lac genes would be expressed efficiently only in the absence of lactose. b. The lac genes would be expressed efficiently only in the presence of lactose. c. The lac genes would be expressed continuously. d. The lac genes would never be expressed efficiently.

Be sure to be able to predict whether AND explain why the lac operon is expressed or not under the following conditions: no lactose, no glucose; no lactose, glucose present; both lactose and glucose present; lactose present but no glucose. This question requires that you understand the function and position of each of the components of the lac operon, how they interact with one another and control gene expression. Do you know how an inducer (Allolactose) affects the lac operon? Answer: Choice (d). Since the Lac P region is the promoter that binds RNA polymerase, a mutation that would block the function of this region would prevent the structural genes (Lac A, B and Y) of the lac operon from ever being expressed, regardless of the lactose conditions.

What does cytokinesis begin with? How does this process differ between plants and animals?

Begins with building a contractile ring (actin) which builds the cleavage furrow Animals - cleavage furrow constricts like a drawstring to separate the cells Plants - cell plate forms a cell wall between the two daughter cells

How is a new DNA strand synthesized in nucleotide excision repair? By crossing-over between sister chromatids By DNA polymerase By DNA ligase By Uvr A

By DNA polymerase

What occurs during G1 phase? Under what conditions does the cell leave G1 and enter the next phase of the cell cycle?

Cell growth occurs Signaling molecules cause cells to accumulate molecular changes that promote progression through the cell cycleIf the cell passes the G1 checkpoint or restriction point, it becomes committed to enter S phase and replicate DNA

How is the mitotic spindle made? Do all eukaryotes have centrioles? What are three types of microtubules in the mitotic spindle and what is the function of each type?

Centrosomes - microtubule organizing center, duplicates during S phase Each defines a pole of the spindle apparatus Animal cells have centrioles, other eukaryotes don't Three types of microtubules: Astral microtubules - position spindle in cell Polar microtubules - separate two poles Kinetochore microtubules - attached to chromosome via kinetochore in the centromere

What two things occur during telophase?

Chromosomes have reached their respective poles and de-condense Nuclear membranes re-form to produce two separate nuclei

What three things occur during prophase?

Chromosomes have replicated, are joined as pairs of sister chromatids Nuclear membrane dissociates into small vesicles Chromatids condense into highly compacted structures that are readily visible by light microscopy

What occurs during S phase? What happens to the two copies of the chromosomes after replication and what are they called? Are sister chromatids exact copies of each other? When S phase is finished, how many chromatids does the cell have relative to the number of chromosome the cell had in G1 phase?

Chromosomes replicate After replication, two copies stay joined to each other and are called sister chromatids Human cell in G1 has 46 chromosomesSame cell in G2 has 46 pairs of sister chromatids or 92 chromatids total

What four things occur during anaphase?

Connections between sister chromatids are broken Each chromatid (now a chromosome) is linked to only one pole by kinetochore microtubules Kinetochore microtubules shorten, pulling chromosomes toward the pole to which they are attached The two poles move away from each other as overlapping polar microtubules lengthen and push against each other

The cell cycle is controlled by the changing concentrations of different ________: Cdks Cyclins Chromosomes Autosomes

Cyclins

How do chromosomes prepare for cell division? What are the centromere and kinetochore?

DNA replicated during S phase Sister chromatids - two identical copies with associated proteins Sister chromatids tightly associated at centromere Serves as attachment site for kinetochore used in sorting chromosomes

Because more than one codon can specify the same amino acid, the genetic code is said to be

Degnerate

What changes occur due to the following chromosomal "mutations": deletions, duplications, inversions, and translocations. Which of these involves two non-homologous chromosomes? Which of these will not alter the amount of genetic material on the chromosome?

Deletions - segment of chromosome missing Duplications - repeated segment of chromosome Inversions - a segment has a change in direction along a single chromosome (can break genes at ends or separate from regulatory regions) Translocations - one segment becomes attached to non-homologous chromosome, may be simple or reciprocal

What is the law of independent assortment? When does this occur during development of an organism?

Dihybrid offspring - hybrids with respect to both traits -Data for F2 hybrids is consistent with independent assortment Mendel's law of independent assortment states that the alleles of two (or more) different genes get sorted into gametes independently of one another. In other words, the allele a gamete receives for one gene does not influence the allele received for another gene.

What do diploid and haploid mean?

Diploid - 2n, humans have 23 pairs of chromosomes Haploid - n, gametes have 1 member of each pair of chromosomes 23 total for humans **know difference between these two

Which of the following is NOT required for the initiation of translation? a. small subunit of the ribsome b. mRNA c. initiator tRNA d. hydrolysis of GTP e. elongation factor

E

What is the function of the mitotic spindle? What is it composed of?

Ensures that each daughter cell obtains the correct number and types of chromosomes organizes and sorts the chromosomes during mitosis Composed of microtubules

Why did Mendel not recognize epigenetic inheritance or epistasis? What is epistasis? How was epistasis recognized in a typical dihybrid cross in sweet peas? What phenotypic ratio was observed in the F2?

Epistasis Alleles of one gene mask the expression of the alleles of another gene -Often arise because two or more different proteins are involved in a single cellular function -In sweet peas, a colorless precursor molecule must be acted on by two different enzymes to produce purple pigment Cross between true-breeding purple flowers and true-breeding white produced (as expected): -F1 - all purple-flowered plants -F2 - 3:1 purple to white-flowered Cross between two varieties of white-flowered peas crossed produced surprising results: -F1 - all purple-flowered plants -F2 - 9:7 purple to white-flowered Two genes are involved in flower color -C (color) dominant to c (no color - white) -P (purple) dominant to p (white) -If either cc or pp homozygous, flowers are white -Dihybrid cross does NOT give 9:3:3:1 A colorless precursor molecule must be acted on by two different enzymes to produce the purple pigment. Gene C encodes enzyme C, which converts the colorless precursor into a colorless intermediate. Gene P encodes enzyme P, which converts the colorless intermediate into the purple pigment

What are the following changes in chromosome number: euploidy, polyploidy, and aneuploidy? What is the difference between polyploidy and aneupoloidy? Be able to recognize examples of aneuploidy.

Euploidy - the normal number of chromosomes (in a diploid organism, two sets is normal) Polypoidy - 3 or more sets of chromosomes Triploid 3n Tetraploid 4n Aneuploidy - abnormal number of a particular chromosome

What external and internal factors influence whether a cell divides or not?

External factors: environmental conditions, signaling molecules (ex: growth factors) Internal factors: cell cycle control molecules, checkpoints

A gene that when mutant exhibits only a single trait or mutant phenotype is called Pleiotropic. True False

F

After Meiosis 1, cells are still diploid. True False

F

Controlled matings meant that a geneticist would allow plants or animals to mate at random. True False

F

Heterochromatin allows transcription of genes tightly packed into nucleosomes. True False

F

Mice that do not have a functional p53 gene will be born with many abnormalities. True False

F

Mutations can only occur in the coding sequence of a gene. True False

F

Polyploidy in plants is usually lethal, as in polyploid plants can never be bred or made. True False

F

Homologous chromosomes are completely identical to one another because they are direct copies of each other. True False

False Explanation No, sister chromatids are exact copies of each other.

What is cytogenetics? What information does a karyotype provide?

Field of genetics involving microscopic examination of chromosomes and cell division Karyotype reveals number, size, and form of chromosomes in an actively dividing cell

Who proposed the Central Dogma of Molecular Biology?

Francis Crick

What are the 5 phases of the cell cycle? What does each represent?

G1 - single chromosome pairs, cell growth, longest and most variable phase of cell cycle, 11 hrs (in 24 hr range) S - chromosome replication yields sister chromatids, occurs during interphase, 8 hrs G2 - cell prepares to divide, 4 hrs M - nucleus breaks apart, chromosomes condense, sister chromatids separate M - 2 cells are formed during cytokinesis

What are the three critical regulatory checkpoints in the cell cycle? What does each checkpoint evaluate in the cell cycle? How does checkpoint proteins act as sensors and what do they prevent from forming? How does the cell cycle respond? What can result from a loss of checkpoints?

G1 checkpoint (restriction point) - determines if conditions are favorable for cell division G2 checkpoint - checks for DNA damage and makes sure all the DNA has been replicated M checkpoint - senses integrity of spindle apparatus Checkpoint proteins act as sensors to determine if the cell is in proper condition to divide Prevent formation of active cyclin/cdk complex to form - stops cell cycle Cell cycle is delayed until problem is fixed Loss of checkpoints can lead to mutations and cancer

What happens during G2 and what happens during M phase (two events)?

G2: Cell synthesizes proteins needed for mitosis and cytokinesis M: two separate events Mitosis - division of one cell nucleus into two, with separation of sister chromatids into daughter cells Cytokinesis - follows mitosis to divide the cytoplasm into two daughter cells

Why did Mendel select the garden pea, Pisum sativum, to carry out his genetic crosses? What is a controlled crossing in this organism?

Garden Pea-many characteristics available to study in seeds, pods, flowers and stems-Each characteristic had two variants Normally self-fertilizing-Female gamete fertilized by male gamete from same plant-Easy to breed true-breeding lines (exhibit the same trait)-Large flowers make crosses easy when desired-Cross-fertilization or hybridization q Several advantageous traits many characteristics to study, self-fertilizing, large flowers make crosses easyremoved stamens from one flower and transfer the pollen to the stigma of another

What is gene interaction?

Gene interaction - a single trait is controlled by two or more genes, each of which has two or more alleles

Why is gene regulation important to multicellular eukaryotes? How does this affect the proteome versus the genome?

Gene regulation in eukaryotes because of cell differentiation Same genome, different proteomes due to gene regulation

What protein(s), together with RNA polymerase II, bind to the core promoter of a gene to form the pre-initiation complex?

General transcription factors

What is the definition of genotype and phenotype?

Genotype - The genetic composition of an individual TT - homozygous dominant Tt - heterozygous tt - homozygous recessive Phenotype - Physical or behavioral characteristics that are the result of gene expression TT and Tt are tall tt is dwarf

What is a bivalent or tetrad? What is the process called that forms this structure? What is a synaptonemal complex?

Homologous pairs of sister chromatids associate with each other, lying side by side to form a bivalent or tetrad Process called synapsis Synaptonemal complex - a protein structure that connects homologous chromosomes Not actually required for chromosome pairing or recombination Function is still uncertain

How many chromosomes and homologous pairs of chromosomes do humans have? How many autosomes and sex chromosomes?

Humans have 23 pairs of chromosomes (or 46 total chromosomes) Autosomes - 22 pairs in humans Sex chromosomes - 1 pair in humans

What is pleiotropy and what is its relevance to human medicine? How is cystic fibrosis an example of a pleiotropic gene?

In many human genetic diseases, a recessive allele fails to produce a specific functional protein Over 7,000 human disorders are caused by mutations in single genes Most single-gene diseases are recessive, but some are dominant Pleiotropy - mutation in a single gene has multiple effects on the organism Normal CF allele codes for transporter protein that regulates chloride ion balance Mutation diminishes function of transporter, causing multiple pleiotropic effects: -Thick mucus in lungs is due to water imbalance caused by ion balance -Sweat is very salty because salt cannot be recycled back into body without transporter -Some males are infertile because Cl- transporter is needed for proper development of vas deferens

Where is the TATA box located in a eukaryotic gene? In the upstream regulatory region In the core promoter In the coding region (part that contains exons and introns) At the termination site of the gene

In the core promoter

What part of the cell cycle includes interphase? What are the five stages of mitosis? What is cytokinesis?

Interphase - chromosomes are de-condensed and found in the nucleus (G1, S, G2) Mitosis - chromosomes are condensed, nuclei double Fivestages:Prophase,Prometaphase,Metaphase,Anaphase,Telophase,Cytokinesis - division into two daughter cells

2. In Drosophila flies, eye color is sex-linked. The allele for red eyes (XW) is dominant to the allele for white eyes (Xw) . A male fly with red eyes XWY and a carrier (heterozygote) female XWXw are mated. What is the probability that the female offspring will have white eyes? a. 0% b. 100% c. 25% d. 75% e. 50%

It is important for this problem to make a Punnet square. This is the only way to reliable find the answer to this problem. Predict the gametes each parent will make and complete the Punnet square to solve this sex-linked inheritance question. Answer: Choice a, because when you complete the Punnet square you will see that the females are 50% WW and 50% Ww (or carriers).

The structural genes in the Lac Operon are all dedicated to the breakdown of: Glucose Glycogen Lactose Sucrose

Lactose

What are three reasons for gene regulation? What are constitutive genes?

Majority of genes regulated to ensure that proteins are produced at the correct time, correct amount, and in the correct place. Gene regulation also saves energy. Constitutive genes are an unregulated gene that has a relatively constant level of expression in all conditions over time.

Do you know how to recognize the inheritance of an autosomal recessive trait versus an autosomal dominant trait in a human pedigree?

Many of the alleles causing human genetic disease are recessive, like Cystic Fibrosis But some are dominant, like Huntington's disease -Huntington disease has an autosomal dominant inheritance pattern (short arm of chromosome 4) -A dominant gene is on one of 22 pairs of autosomes Disease genes can also be found on the sex chromosomes

How does Meiosis I differ from Meiosis II?

Meiosis I separates homologous chromosomes Meiosis II separates sister chromatids

What are the three key differences between meiosis and mitosis?

Meiosis:Homologous pairs form bivalent or tetrad Crossing over occurs Two cellular divisions follow one DNA replication

With regard to chromosomes, how can Mendel's law of segregation be explained? What is a locus?

Mendel's Law of Segregation can be explained by the pairing and segregation of homologous chromosomes during meiosis locus: The physical location of a gene on a chromosome

A chromosome with its centromere in the middle of the chromosome is called: Acrocentric Metacentric Telocentric

Metacentric

The stage of Mitosis when the pairs of sister chromatids are aligned along the metaphase plate is: Prophase Prometaphase Metaphase Telophase

Metaphase

What different step takes place in Anaphase II versus Anaphase I? What separate during anaphase II? In terms of the products of mitosis and meiosis, what are the differences? Meiosis I produces how many haploid cells, while meiosis II produces how many haploid cells? A species that has three sets of homologous chromosomes can have up to how many different combinations of chromosomes in the gametes?

Mitosis produces two diploid daughter cells that are genetically identical Meiosis produces four haploid daughter cells

How are aneuploidy gametes made? What is this called? What would be the result if a cell had all its homologous chromosomes experience nondisjunction during meiosis I? during meiosis II?

Nondisjunction creates aneuploidies Chromosomes do not sort properly during cell division Meiosis can produce aneuploid gametes (too many or too few chromosomes) Tetrad chromosomes may not separate properly during meiosis I or sister chromatids may fail to separate during meiosis II

What five things occur during prometaphase?

Nuclear envelope completely fragments into small vesicles Mitotic spindle is fully formed Centrosomes move apart to two poles Spindle fibers interact with sister chromatids Two kinetochores on each pair of sister chromatids attach to kinetochore microtubules from opposite poles

What are the five levels of transcriptional regulation in eukaryotes?

One or more activators may stimulate the ability of RNA polymerase to initiate transcription. One or more repressors may inhibit the ability of RNA polymerase to initiate transcription. The function of activators and repressors may be modulated in several ways, which include the binding of small effector molecules, protein-protein interactions, and covalent modifications. Activators are necessary to alter chromatin structure in the region where a gene is located, thereby making it easier for the gene to be recognized and transcribed by RNA polymerase. DNA methylation usually inhibits transcription, either by preventing the binding of an activator or by recruiting proteins that inhibit transcription.

In humans, having dimples in the cheeks is a dominant trait. If a child has dimples but only one of her parents does, what are the genotypes of her parents? (D = dimples; d = no dimples) a. One parent must be DD, the other parent could be either dd or Dd b. One parent is dd, other parent must be DD c. One parent is Dd, other parent is DD d. One parent dd, other parent must be Dd e. One parent must be dd, the other parent could be either Dd or DD

One parent must be dd, the other parent could be either Dd or DD

What are the genotypes and phenotypes found in a monohybrid cross of pure breeding Tall x Dwarf plants?

P generation: TTxtt tall purple x dwarf purpleF1 generation: all Tt tall purpleF2 generation: TT, Tt, tt 3 tall purple: 1 dwarf purple

What occurs during metaphase? What role do centromeres play in this step?

Pairs of sister chromatids are aligned along the metaphase plate Centromeres aligned into a single row

In order to produce a single strand of DNA, the nucleotides combine to form what type of bond?

Phosphodiester

What happens during synapsis of homologous chromosomes? What effect does this have on the species? What is a chiasma and what does it represent?

Physical exchange between chromosome pieces of the crossing bivalent May increase the genetic variation of a species Chiasma - arms of the chromosomes tend to separate but remain adhered at a crossover site Number of crossovers carefully regulated (size of chromosome and species)

What are two types of point mutations?

Point mutation affects only a single base pair within the DNA. Base substitution: the base sequence within a gene can be changed, or Addition/deletion of one base (which will change the reading frame of the genetic code for the remainder of the sequence).

What is an example of prokaryotic gene regulation in E. coli using lactose? What advantage does this regulation give the cell?

Prokaryotic gene regulation *Responds to changes in the environment -ex: Escherichia coli and lactose *When lactose is available, two proteins are made: -lactose permease - transports lactose into the cell -β-galactosidase - breaks down lactose *When lactose levels drop, these proteins are no longer made *(ADVANTAGE)Regulation conserves energy to ensure that proteins needed for lactose utilization are made only when lactose is present in environment

What events occur during prophase I, prometaphase I and metaphase I? In prometaphase I, are pairs of sister chromatids attached to one or two poles?

Prophase 1 - chromosomes condense, bivalents form and the nuclear membrane breaks down Prometaphase 1 - spindle apparatus complete, chromatids attach to kinetochore microtubules Pairs of chromatids attached to SINGLE pole Metaphase 1 - bivalents organized along metaphase plate as DOUBLE row Mechanism to promote genetic diversity

What protien do transcription facotors directly affect?

RNA polymerase

What protein is involvd in synthesizing messenger RNA in eukaryotes?

RNA polymerase II

What happens when the cAMP-CAP complex binds the CAP site near the lac promoter?

RNA polymerase binds to the promoter and transcription rate increases.

In the Meselson and Stahl experiment, two rounds of DNA replication were observed. After the first round of replication, but before the second round had taken place, Meselson and Stahl could be confident of which of the following conclusions about replication?

Replication is not conservative

What are two ways a viral insertion can cause cancer?

Retroviral insertion -proto-oncogenes become overexpressed and can promote cancer -viruses carry an oncogene in the viral genome -mutagens mainly cause cancer

What effect do chromatin remodeling ezymes have on chromatin?

Shifts the position of the nucleosome on the DNA

In relation to the position of the centromere, what is meant by: p arm, q arm, metacentric, submetacentric, acrocentric, and telocentric? What is G banding?

Short arm is p, long arm is q Metacentric - middle Submetacentric - off center Acrocentric - near end Telocentric - at the end Giemsa stain gives G banding, unique for chromosome

What separate from each other in Anaphase II? Homologous chromosomes Sister chromatids

Sister chromatids

One result in Mendel's monohybrid cross was that the F1 offspring did not exhibit a blending of tall and short traits together. True False

T

Repressors and activators affect the level of transcription in the cell. True False

T

The amplification of the Myc gene will lead to the over replication of cells because Myc is a transcription factor that activates target genes in the EGF signaling pathway. True False

T

The progression from one phase in the cell cycle to the next (e.g. G1 to S) is dependent on the increase in concentration of a cyclin-cdk complex. True False

T

Tumor suppressor genes are activated at checkpoints when DNA damage is detected. True False

T

What observation made by Thomas H. Morgan, suggested that the inheritance of the white eyed mutation was not autosomal? a. More females than males were white eyed in the F2 generation. b. The F2 generation from the parental crossing of a white eyed male to a red eyed female resulted in an equal number of male and female white eyed progeny. c. The F2 generation from the parental crossing of a white eyed male to a red eyed female resulted in white eyed flies that were male and not female.

The F2 generation from the parental crossing of a white eyed male to a red eyed female resulted in white eyed flies that were male and not female.

Folowing its initial activation, how does a G protein become inactivated?

The G-protein alpha subunit GTP is hydrolyzed to GDP allowing reassociation of the G-protien alpha subunit and beta-gamma dimer.

With regard to chromosomes, how can Mendel's law of independent assortment be explained?

The Law of Independent Assortment can also be explained by the behavior of chromosomes during meiosis-Random alignment of chromosome pairs during meiosis I leads to the independent assortment of genes found on different chromosomes Law of independent assortment: Alleles of different genes assort independently of each other during gamete formation

If the cell's control of replication is like the brakes and accelerator of a car. An oncogene is similar to: The accelerator stuck in the "on" position The brakes of the car not working The accelerator not working The brakes of the car "on" all the time

The accelerator stuck in the "on" position

What part of the histone protein is modified to control nucleosome packing?

The amino end of the histone can be methylated, phosphorylated or acetylated.

What is the difference between complete dominance, incomplete dominance and codominance? Make sure you can recognize the inheritance associated with these patterns of inheritance.

The degree to which we judge an allele to exhibit incomplete dominance may depend on how closely we examine an individual's phenotype: sickle cell anemia due to abnormal hemoglobin protein. Heterozygotes appear normal unless they are at high altitude, under low Oxygen levels, then they are distinguishable from homozygous wild-type individuals. Heterozygote shows intermediate phenotype Neither allele is dominant Pink four-o'clocks -50% of normal protein not enough to give red color Codominance Multiple alleles - three or more variants in a population Phenotype depends on which two alleles are inherited example: ABO blood types in humans -Type AB is codominant - expresses both alleles equally

What role does environment play in the expression of a phenotype? How is PKU an example of this phenomenon? Make sure you know what enzyme is deficient in people who have PKU and what they must do to have a normal life.

The environment plays a vital role in phenotype Genotype provides the plan to create a phenotype; the environment provides nutrients and energy to carry out the plan Norm of reaction - effects of environmentalvariation on a phenotype Genetically identical plants grow to different heights in different temperatures Phenylketonuria (PKU) disease -Can develop normally if given a diet free of phenylalanine -If diet contains phenylalanine, symptoms includemental retardation, underdeveloped teeth and foul-smelling urine

Which of the following is most likely to occur when a tumor-suppressor gene is mutated? a. The tumor-suppressor gene may be overactive. b. The tumor-suppressor gene and resulting protein may lose its function and ability to suppress cell proliferation. c. The resulting tumor-suppressor protein would further suppress cell proliferation. d. The resulting tumor-suppressor protein would activate an oncogene. e. None of the choices are possible.

The tumor-suppressor gene and resulting protein may lose its function and ability to suppress cell proliferation.

How can complete dominance in a phenotype be explained at a molecular level for a gene that exhibits simple Mendelian inheritance?

This is an example of a typical monohybrid cross, but because the gene is on the X-chromosome, the distribution of the white trait in the F2 generation is different in males versus females. Notice when you ignore gender, you see the 3:1 ratio that Mendel predicted. Morgan recognized however, that when the gene is carried on the X-chromosome, the distribution of the phenotype will be 1:1 in males and absent in females.

9. Aneuploidy is the presence of an abnormal number of chromosomes in a cell. Monosomy is a "subtractive" form of aneuploidy due to the presence of only one chromosome from a pair while trisomy is an "additive" form where there are three instances of a particular chromosome, instead of the normal two. A strawberry plant is normally diploid, but a monosomic strawberry plant was observed with 9 chromosomes in its cells. Which of the following is NOT a correct possibility regarding the chromosomal material of a strawberry plant? a. A trisomic strawberry plant would have 11 chromosomes in its cells. b. A trisomic strawberry plant would have 15 chromosomes in its cells. c. Doubling the chromosomal number found in the normal haploid state would result in a strawberry plant with 10 chromosomes in its cells. d. During meiosis of the normal diploid, the chromosomal number is halved during the first meiotic division, yielding 5 chromosomes.

This question expects you to be able to use the information provided and first determine the normal diploid and then haploid number of chromosomes in this organism. With that information, you should be able to pick the correct answer. Answer: Choice b. To answer this question, first focus on the fact that the monosomic plant has 9 chromosomes. This tells you that the normal diploid number is 10, so the normal haploid number is 5. So, a trisomic plant would have one more chromosome in addition to the diploid number: 10 + 1 = 11 (choice a). Now choice c is what you expected, the diploid number is 10 and choice d is what you expected, that half of 10 = 5. So, the only choice that is NOT a correct possibility is choice b. Make sure that if the number of chromosomes in the monosomic plant is different, you could still answer the question. Also, be sure you know the difference between a trisomy (10 + 1) and a triploid (5 x 3).

4. In some chickens, feather color is controlled by codominance. When a black feathered chicken mates with a white feathered chicken, all of the offspring are covered in both black and white feathers. A farmer mates a black feathered chicken (BB) with a black-and-white feathered (BW) chicken. What are the predicted phenotypes of their offspring? a. All of the offspring will have black feathers. b. All of the offspring will have black-and-white feathers c. 75% of the offspring will be black feathered, and 25% of the offspring will be white feathered. d. 50% of the offspring will be black feathered and 50% of the offspring will be black-and-white feathered.

This question is testing your understanding of inheritance of codominant traits, where the phenotype associated with both alleles is expressed in the heterozygote. Answer: Choice d, because if you make a Punnet square for this mating (which I strongly suggest), you will find that 50% of the offspring are BB (black feathered) and 50% are BW which will be black and white feathered, due to the codominant inheritance pattern of these alleles.

8. A cell isolated from a tumor was studied and found to rapidly advance from G1 to S phase. This continued despite exposing the cell to UV irradiation. The irradiated cell continued to divide rapidly and passed through the G1 to S phase transition quickly. What aspect of cell cycle regulation could have been abnormal in this cell? a. Lack of production of cyclins b. Faulty G1 checkpoint c. Overexpression of p53 d. Lack of production of cyclin dependent kinases e. All of these choices could be responsible for the rapidly dividing tumor cell after UV irradiation.

This question is testing your understanding of the role of cyclins, checkpoints, p53 and cdk's in regulating the cell cycle. Answer: Choice (b), because the G1 checkpoint is where the cell can pause before advancing to S phase if DNA damage (such as UV irradiated induced damage) is detected. A lack of cyclins (choice a) and cdk's (choice d) would inhibit the cell advancing from G1 to S. In addition, the overexpression of p53 would immediately stop the cell from advancing in the cell cycle. So the only correct answer is (b).

Practice LEAPing - Chp 17 Here are examples of the types of questions you will see on your take home, open book exam. These are not identical to the test questions, nor do they include all the examples of the types of questions you will see on the exam. 1. In humans, hair texture exhibits incomplete dominance. The gene for curly hair (H) is incompletely dominant to the gene for straight hair (h). Individuals that are heterozygous (Hh) have wavy hair. Two heterozygous parents have a child. What is the chance that the child will have wavy hair? a. 0% b. 25% c. 50% d. 75% e. 100%

This question tests your ability to apply Mendelian genetics to human genetics. You should be able to interpret genetic questions that include incomplete dominance, complete dominance and sex-linked inheritance. Answer: Choice c, because a punnet square of the mating Hh x Hh will produce the following offspring: 25% HH, 50% Hh and 25% hh. Therefore, since the wavy hair trait is associated with the Hh genotype, 50% of their offspring can be expected to have wavy hair.

4. A cell has 12 pairs of homologous chromosomes. How many chromosomes does each daughter cell have after the completion of Meiosis I? a. 6 b. 12 c. 24 d. 48

This question tests your ability to follow the number of chromosomes versus chromatids versus chromosome pairs during Meiosis. Answer: Choice (b) because Meiosis I is called the reductive division when the homologous pairs of chromosomes separate into different daughter cells. This splits each homologous pair into a chromosome in each daughter cell.

5. A cell has 12 pairs of homologous chromosomes. How many chromosomes does each daughter cell have after the completion of Meiosis II? a. 6 b. 12 c. 24 d. 48

This question tests your ability to follow the number of chromosomes versus chromatids versus chromosome pairs during Meiosis. Answer: Choice (b) because the second Meiotic division just separates sister chromatids from one another (as in Mitosis). After the completion of Meiosis II, each chromatid represents a chromosome in the final daughter cells.

2. A cell has 12 pairs of homologous chromosomes. How many chromosomes does it have in Metaphase of Mitosis? a. 6 b. 12 c. 24 d. 48

This question tests your ability to follow the number of chromosomes versus chromatids versus chromosome pairs during Mitosis. Answer: Choice (c) because you are told that there are 12 pairs of homologous chromosomes which makes 24 total chromosomes. DNA synthesis prior to Mitosis does not increase the number of chromosomes, but does make sister chromatids that are attached at the centromere. Could you answer this question and the next three if the number of homologous chromosomes was different?

3. A cell has 12 pairs of homologous chromosomes. How many chromatids does it have in Metaphase of Mitosis? a. 6 b. 12 c. 24 d. 48

This question tests your ability to follow the number of chromosomes versus chromatids versus chromosome pairs during Mitosis. Answer: Choice (d) because as described above the number of chromatids doubles after DNA synthesis but the number of chromosomes does not.

6. Consider a diploid species where n = 6, where n is the number of chromosomes in a haploid gamete. If an individual of this species was found to have 18 chromosomes, it would be categorized as a. Aneuploid b. Tetraploid c. Polyploid d. Monosomic e. Trisomy:

This question tests your ability to interpret an abnormal chromosome number with regard to the different types of chromosomal abnormalities listed. Make sure you can determine which chromosome number would represent each of the five cases listed. Answer: Choice (c) because there are three copies of the haploid number of chromosomes (n = 6 x 3 = 18). This could also be expressed as triploid but that was not one of the answer choices. Choice a would have been either 11 or 13 (a change by one chromosome number from diploid = 12). Choice b would have been 24 which is 4 x 6. Choice d would have been 11 which is the diploid number (12) - 1. And Choice e would have been 13 which is the diploid number (12 + 1), when you would have 3 copies of one chromosome.

13. The pedigree shown tracks the presence of attached earlobes through a family's generation. Having attached earlobes is an autosomal recessive trait. What is the genotype of individual II-3? a. XeY b. XEY c. ee d. EE e. Ee

This question tests your ability to recognize a pattern of inheritance and to determine the chances of offspring having a particular genotype/phenotype in a given pedigree. Answer: Choice e, since you are told that this is an autosomally recessive trait, individual II-3 is not affected but has a homozygous, affected mother (I-2). So this makes clear that II-3 is a heterozygote since his mother can only pass a recessive allele to all of her offspring.

3. Hemophilia is an X-linked recessive condition in which blood does not clot properly. Queen Victoria of England had one allele for hemophilia. Most of her male descendants had the disorder, but few females had it. Why did hemophilia occur more frequently in Queen Victoria's male descendants? a. Only one copy of the X chromosome is found in cells of males, but two copies are found in cells of females. b. Replication of the X chromosome occurs often in males but rarely in females. c. Males have hormones that enhance the expression of X-linked traits. d. Males mature more slowly than females, allowing recessive traits more time to appear.

This question tests your understanding of sex-linked (or X-linked) recessive disorders and their inheritance. You should review the sex-linked pedigrees we will work out in class. Answer: Choice a, because this is the true issue in X-linked inheritance. Since males have only one X chromosome and one Y chromosome, there is not a homologous pair of like sex chromosomes. Any recessive mutation on the X in the male will be expressed. Not so with females who have 2 X chromosomes. The other choices make no sense. There is no difference in the replication of the X chromosome between male and female (choice b). Males cannot enhance the expression of the X-linked traits (choice c) and males do not mature slower than females (choice d).

7. A cell that is dividing lacks the ability to make kinetochore microtubules while it is still able to synthesize and use astral and polar microtubules and microfilaments. During which stage of Mitosis will this defect first be visibly evident under the microscope? a. Prophase b. Metaphase c. Anaphase d. Telophase e. Cytokinesis

This question tests your understanding of the function of the three types of microtubules (astral, polar and kinetochore) as well as the function of microfilaments during Mitosis. Answer: Choice (b) because it is during Metaphase that the effect of kinetochore microtubles attaching to and lining the chromosomes up on the Metaphase plate can be clearly visualized. During Prophase the astral, polar and kinetochore microtubules are all extending and making first contact with their targets but the chromosomes are still randomly distributed. Anaphase would not take place but that would not be the first visible sign of a problem. Telophase is after Anaphase and Cytokinesis is dependent on microfilaments constricting the cell membrane and the positioning of the spindle fiber by the polar microtubules.

1. Which is an example of aneuploidy in a human? a. A male somatic cell has one X chromosome and one Y chromosome. b. A female gamete contains two X chromosomes. c. A female somatic cell contains 46 chromosomes. d. A male gamete has only one Y-chromosome.

This question tests your understanding of what aneuploidy means, which is an abnormal number of chromosomes, but not a multiple of the entire genome (= polyploidy). Answer: Choice (b) because a female gamete would only have one X chromosome. The other choices describe normal genomes with the correct number of chromosomes. Be sure to know how to interpret the different sex chromosome aneuploidies shown in the textbook and discussed in class and that these sex chromosome aneuploidies do not result in the death of the individual.

10. If a cell with 4 pairs of chromosomes, skips Meiosis II while making a total of two gametes, how many total chromosomes and chromatids will each gamete have at the end of this abnormal Meiosis? a. 8 chromosomes and 8 chromatids b. 8 chromosomes and 4 chromatids c. 4 chromosomes and 4 chromatids d. 4 chromosomes and 8 chromatids

This question will require you to think carefully about what happens to the chromosomes and chromatids during Meiosis. Answer: Choice d. During Meiosis I, called the reductive division, the homologous pairs of chromosomes align on the Metaphase I plate and separate into separate daughter cells. Then in Meiosis II, the chromosomes align on the Metaphase II plate and the chromatids separate to opposite cells. So, if you begin with 4 pairs of chromosomes, each pair will align on the Metaphase I plate and the pairs will separate, resulting in each daughter cell after Meiosis I having 4 chromosomes and 8 chromatids (no pairs, but each chromosome has 2 chromatids). Now if Meiosis II did take place (which is doesn't in this question), at the end of Meiosis II, you would still have four chromosomes but four chromatids in each daughter cell, because the chromatids separate in Meiosis II.

What were the three important ideas Mendel developed from the results of his monohybrid crosses? Make sure you know the meaning of: dominant, recessive, genes, alleles, segregation of alleles.

Traits are dominant and recessive -Dominant variant is displayed in hybrids -Recessive variant is masked by dominantGenes and alleles -Particulate mechanism of inheritance - The recessives reappear! -His "unit factors" are genes -Every individual has two genes for a character -A gene may have variant forms, or allelesSegregation of alleles - F2 traits follow approximately 3:1 ratio - Two copies of a gene carried by an F1 plant segregate (separate) from each other - each sperm or egg carries only one allele - Alleles recombine randomly with one another at fertilization Dominant-Describes a trait that covers over, or dominates, another form of that trait. Recessive-An allele that is masked when a dominant allele is present Genes-DNA segments that serve as the key functional units in hereditary transmission. Alleles-Different forms of a gene Segregation of alleles-Alleles separate into different haploid cells that eventually give rise to gametes

When part of a chromosome becomes attached to a non-homologous chromosome, this type of chromosomal mutation is called a: Duplication Deletion Inversion Translocaton

Translocaton

Be able to state Mendel's law of segregation. When do alleles segregate?

Two copies of a gene segregate from each other during the transmission from parent to offspring.

Thymine Dimers are caused by: Chemical mutagens UV irradiation Smoking Spontaneous errors in DNA replication

UV irradiation

Chromosome identification is done on chromosomes at what stage in mitosis? What are the three criteria used to identify chromosomes from one another?

Variation in chromosome structure and/or number Important in several human diseases Important in evolution of new species Chromosome variation - changes in structure or number of chromosomes can occur Individual is different from other members of same species (abnormal) Between species, the structure and number of chromosomes normally varies

Which of the following statements about the cell cycle is correct? a. In actively dividing cells, the S and G2 phases are collectively known as interphase. b.T he phases of the cell cycle are G1, S, and M phases. c. When the S phase of the cell cycle is finished, a cell has twice as many chromatids as the number of chromosomes in the G1 phase. d. During G2 phase, the cell grows and copies its chromosomes in preparation for cell division.

When the S phase of the cell cycle is finished, a cell has twice as many chromatids as the number of chromosomes in the G1 phase.

Are the X and Y chromosomes homologs of one another? Why or why not?

X and y very different from each other in size and composition (NOT homologs) Inherited from different parents

1) How is a new DNA strand made in nucleotide excision repair? a) by DNA polymerase b) by crossing over between sister chromatids c) by DNA ligase d) by DNA exonuclease

a

10) Which of the following would occur from a mutation in the gene's promoter region? a) The rate of transcription may increase or decrease. b) The amino acid sequence of the translated protein would be altered. c) The sequence of the mature mRNA would change. d) The ability of mRNA to be translationally regulated would change. e) The ability of pre-mRNA to be properly spliced would change.

a

2) How does a mutation in p21 Ras result in an oncogene? a) p21 Ras normally encodes a G-protein that promotes cell division b) p21 Ras normally encodes a G-protein that represses cell division c) p21 Ras normally encodes the Philadelphia chromosome d) p21 Ras normally encodes a cyclin protein kinase that promotes cell division

a

21) During the cell cycle, how do checkpoint proteins function? a) they prevent the formation of an active cyclin/cdk complex to form b) they promote the formation of an active cyclin/cdk complex to form c) they synthesize cyclins d) they synthesize cdk's e) they add phosphate groups to cdk's

a

24) What is another way to describe Turner's Syndrome? a) Monosomy X b) Trisomy 13 c) XXX d) Polyploid

a

31) When does synapsis occur? a) Prophase I of Meiosis I b) Prophase II of Meiosis I c) Prophase II of Meiosis II d) Metaphase II of Meiosis I e) Metaphase II of Meiosis II

a

38) What is the genotype of Individual #6? a)XAXa b) XaXa c) XAXA d) XAY e) XaY

a

39) Which of the following terms best describes when the phenotype of the heterozygote differs from the phenotypes of both homozygotes? a) incomplete dominance b) recessive c) pleiotropy d) epistasis

a

4) What is the kinetochore? a) a protein complex that attaches to the centromere b) another name for the centromere c) the microtubule organizing center d) another name for the mitotic spindle

a

40) When a single-gene mutation can have phenotypic effects at multiple stages of development, it is a) pleiotropic. b) causing a disease. c) incompletely dominant. d) codominant. e) recessive.

a

6) In wolves, gray coat color (G) is dominant to black (g) and brown eyes (B) are dominant to blue (b). The genes that control these traits are located on different chromosomes. The alpha male of the pack has the dominant phenotype for both traits and is heterozygous for both traits. The alpha female has brown eyes and a black coat, she is heterozygous for eye color. Which option represents gametes that would be made by the alpha female? a) Bg and bg b) Bb and gg c) BG, Bg, bG, bg d) B, b, and g

a

What does DNA polymerase require to start replicating a bare template strand at the replication fork?

a RNA primer

What is the kinetochore? a protein complex that attaches to the centromere the microtubule organizing center another name for the centromere another name for the mitotic spindle

a protein complex that attaches to the centromere

Albinism in most animals is an epistatic trait characterized by a lack of melanin pigment in the eyes, skin, and hair. If the allele for albinism is a, the allele for brown coat color is B, and the allele for red coat color is b, which genotypes would result in an albino cow?

a. Albino- aaBB, aaBb, aabbb. Brown- A-BB, A-Bbc. Red- A-bb

How are discrete traits different from quantitative traits? What are polygenic traits?

a. Discrete- clearly defined phenotypic variantsi. Purple or white flowers, red or white eyesb. Quantitative- majority of traits, continuous variation over a range of phenotypesi. Height, skin color, number of fruits on a treec. Polygenic traits- multiple genes contribute to a phenotype, allele contributes to the phenotype in an additive way, environment plays a roll

How could these observations be explained from a biochemical perspective?

a. aa cannot deposit pigment - need A

Mendel's second law, Independent Assortment, has its basis in which of the following events of meiosis I? crossing over separation of homologs at anaphase separation of cells at telophase alignment of tetrads at the equator synapsis of homologous chromosomes

alignment of tetrads at the equator

What ensyme catalyzes the attachment of amino acids to tRNA molecules?

aminoacyl-tRNA synthhetase

The production of second messengers in signal transduction offers at least two advantages, speed and ______

amplification

Consider a diploid species where n=5. If an individual of this species was found to have 11 chromosomes, it would be categorized as triploid. tetraploid monosomic. aneuploid. polyploid.

aneuploid.

Microtubules that connect the centromeres to the inner edge (cortex) of the cell and keep the spindle fibers correctly positioned are called: polar microtubules astral microtubules kinetochore microtubules

astral microtubules

In a diploid cell, the major way that Meiosis II differs from Mitosis is that: a. during Meiosis II, a pair of sister chromatids move to one pole. b. during Meiosis II, sister chromatids align at the metaphase plate as a tetrad, while in Mitosis this doesn't occur. c. at the end of Meiosis II, the cells are haploid, while at the end of Mitosis the cells are diploid. d. during Meiosis II, a synaptonemal complex is formed, while this doesn't occur in Mitosis.

at the end of Meiosis II, the cells are haploid, while at the end of Mitosis the cells are diploid.

14) Which DNA repair system uses Uvr C to cleave the DNA on each side of the mutation? a) indirect repair b) nucleotide excision repair c) base excision repair d) direct repair

b

16) How does the Rb protein act as a product of a tumor suppressor gene? a) It activates the transcription factor, E2F. b) It binds to the transcription factor, E2F. c) It stimulates the cell to move from G1 to S phase in the cell cycle. d) All of these choices are correct.

b

17) A mutation causes a gene to become overactive, contributing to uncontrolled cell growth. Which term best describes this gene in its mutated state? a) tumor-suppressor gene b) oncogene c) alternatively spliced gene d) spliced gene e) malignant gene

b

19) What may happen when p53 is activated (or expressed)? a) Cyclins are made and the cell cycle proceeds from G1 to S phase. b) Genes that code for DNA repair are activated (expressed). c) Apoptosis is irreversibly repressed from occurring. d) Rb protein is phosphorylated.

b

20) Which protein directs apoptosis? a) chimeric gene b) caspase c) transposase d) growth factor e) oncogene

b

22) During which phase of the cell cycle is the chromosome replicated into sister chromatids? a) G0 phase b) S phase c) G1 phase d) G2 phase e) Metaphase

b

23) What is the purpose of the G2 checkpoint? a) To arrest the cell cycle if DNA replication is detected. b) To arrest the cell cycle if DNA synthesis is incomplete. c) To arrest the cell cycle if chromosome have not attached to the spindle fibers. d) None of these choices are correct.

b

25) Which of the following parts of the cell cycle are all included in interphase? a) G1 only b) G1, G2, S c) Only G1 and S d) Only S and G2 e) S only

b

27) During which stage of mitosis do spindle fibers interact with sister chromatids while the mitotic spindle begins to form? a) Prophase b) Prometaphase c) Metaphase d) Anaphase e) Telophase

b

3) Which of the following statements about the cell cycle is correct? a) During G2 phase, the cell grows and copies its chromosomes in preparation for cell division. b) When the S phase of the cell cycle is finished, a cell has twice as many chromatids as the number of chromosomes in the G1 phase. c) The phases of the cell cycle are G1, S, and M phases. d) In actively dividing cells, the S and G2 phases are collectively known as interphase.

b

35) In this pedigree, what is likely genotype of Female #5 (assume the trait in this pedigree is rare in the general population)? a) AA b) Aa c) aa d) Aa or AA, could be either one.

b

5) Consider a diploid species where n=5. If an individual of this species was found to have 11 chromosomes, it would be categorized as a) polyploid. b) aneuploid. c) tetraploid d) monosomic. e) triploid.

b

The likely outcome from a mutation in the lacO site (lac Operator) of the lac operon would be

binding of a repressor protein could be hindered

A cross between two pea plants results in 732 purple and 268 white plants. What is (are) the genotype(s) and phenotype(s) of the parents that produced these offspring? a. both parents are heterozygous purple b. one parent is homozygous purple, second parent is homozygous white c. one parent heterozygous purple, second parent homozygous white d. one parent is heterozygous purple, second parent is heterozygous white e. one parent is homozygous purple, second parent is heterozygous white

both parents are heterozygous purp

11) What would result from a single nucleotide deletion (point mutation) within the coding sequence of a structural gene? a) a silent point mutation that results in a change of one amino acid. b) a missense point mutation resulting in a change in the binding of RNA polymerase to its promoter. c) a frameshift mutation, producing a change in the amino acid sequence for some of the protein. d) A nonsense mutation with no effect on the resulting protein.

c

12) Which of the following is true concerning a single germ line mutation? a) It is passed on to only all of the somatic cells of the offspring. b) It is passed on to only a small fraction of somatic cells of the offspring. c) It is passed to both somatic and germ line cells of the offspring. d) It is not passed to any cells in the offspring.

c

13) What is one component of DNA repair? a) Crossing-over between sister chromatids b) replicating damaged DNA into new copies c) detecting DNA damage. d) making thymine dimers

c

15) Which is the most common type of DNA repair? a) methyl-directed mismatch repair b) indirect repair c) nucleotide excision repair d) base excision repair e) direct repair

c

26) Which of the following statements is FALSE concerning sister chromatids? a) The formation of sister chromatids doubles the amount of DNA in a cell. b) Sister chromatids are formed during the S phase of the cell cycle. c) Sister chromatids separate during telophase. d) Sister chromatids are held together at the centromere by kinetochore proteins. e) Sister chromatids consist of two identical copies of a single homolog.

c

30) What is one difference between meiosis and mitosis? a) Crossing over between sister chromatids occurs in mitosis and meiosis b) A tetrad is formed during mitosis but not during meiosis c) Two cellular divisions follow one DNA replication in meiosis but not in mitosis d) Both produce haploid cells.

c

32) How can you determine the genotype of a plant showing the dominant phenotype of red color. In other words, which cross below would be called a "test cross" ? a) Cross the red plant with another red plant, and then cross the F1 population with each other to see if any white plants appear. b) The phenotype reflects the genotype, so the plant must be homozygous for the trait. c) Cross the red plant with a white plant to see if any white plants appear. d) Cross the red plant with other red plants to see if any white plants appear.

c

33) A cross between homozygous purple-flowered and homozygous white-flowered pea plants results in offspring with purple flowers. This demonstrates a) the blending model of genetics. b) true bleeding c) dominance d) a dihybrid cross e) the mistakes make by Mendel

c

34) Mendel's second law of independent assortment has its basis in which of the following events of meiosis I? a) synapsis of homologous chromosomes b) crossing over c) alignment of tetrads at the equator d) separation of homologs at anaphase e) separation of cells at telophase

c

37) What is the most likely mode of inheritance of the trait in this pedigree? a. Autosomal recessive b. Autosomal dominant c. Sex-linked recessive d. Sex-linked dominant

c

42) A person who is homozygous for a mutation in the phenylalanine hydroxylase gene a) will require phenylalanine supplements throughout life. b) will always develop mental retardation in early infancy regardless of diet. c) can lead a normal life if diet does not include phenylalanine from birth. d) cannot give blood.

c

What immediate effect does activating GPCR have when binding epinephrine?

causes G-protein to bind to GTP

What proteins are responsible for advancing a cell through the cell cycle? The amount of which protein varies through the cell cycle? What enzymatic activity do Cdks have? What must Cdks do to be functional?

cdks responsible for advancing a cell through the cell cycle amount of cyclins varies through cycle cdks are kinases controlling the cell cycle cdks must bind to a cyclin to be functional

Liver cells, mammary cells and skin cells all contain the same genome; however, their respective proteomes vary drastically. This observation is best explained by what phenomenon?

cell differentiation

Liver cells, mammary cells, and skin cells all contain the same genome; however, their respective proteomes vary drastically. This observation is best explained by what phenomenon? a. evolution b. cell division c. cell differentiation d. crossing over

cell differentiation

What role do cyclins play in regulating the progression of the cell from one phase of the cell cycle to the next?

chp 16

36) What is the mode of inheritance in this pedigree? a)Sex-linked recessive b) Sex-linked dominant c) Autosomal dominant d) Autosomal recessive

d

41) In goats, the gene for coat color is on an autosome and pink color is dominant to blue. A pink male is mated to a blue female, producing a blue kid (baby goat). If they produce another kid, could it be pink? If so, what are the chances of it being pink? a) No, 0% (all offspring will be blue). b) Yes, 100% since the first kid was blue the next one must be pink c) Yes, 75% since the pink is dominant d) Yes, 50% since the father is heterozygous for pink color e) Yes, but it will depend on whether the kid is male or female

d

7) Mendel's observation of the segregation of alleles in gamete formation has its basis in which of the following phases of cell division? a) Prophase I of meiosis b) Prophase II of meiosis c) Metaphase I of meiosis d) Anaphase I of meiosis e) Anaphase of mitosis

d

8) In cats, black fur color is caused by an X-linked allele, the other allele at this locus (gene) causes orange color. The heterozygote is tortoiseshell. What kinds of offspring would you expect from the cross of a black female and an orange male? a) tortoiseshell females, tortoiseshell males b) black females, orange males c) orange females, orange males d) tortoiseshell females, black males e) orange females, black males

d

9) Which of the following types of physical mutagens produces thymine dimer mutations? a) ionizing radiation b) X-rays c) microwave d) ultraviolet light e) gamma rays

d

Which of the following statements best describes DNA polymerase? a. It is an enzyme required to glue pices of DNA fragments together. b.it is an enzyme required to produce a primer for DNA replication. c. it is an enzyme that catalyzes the addition of nucleotides to the 5' end of growing DNA strand. d. it is an enzyme that catalyzes the addition of nucleotides to the 3' end of growing DNA strand.

d

18) The "two hit" model of retinoblastoma says that one mutant copy of the Rb gene must always be inherited from a parent in order for retinoblastoma (the cancer) to arise in an individual. a. True b. False

f

28) After Meiosis I (but before Meiosis II), the two daughter cells are diploid because they have chromosomes with sister chromatids joined together at the centromere. a. True b. False

f

29) During Meiosis I, sister chromatids separate to opposite daughter cells. a. True b. False

f

The best description of the role of the mediator protein complex in eukaryotes is it a. is composed of a single protein. b. facilitates interactions between RNA polymerase II and regulatory transcription factors. c. controls the rate at which RNA polymerase translates mRNA. d. completely enfolds RNA polymerase and the general transcription factors.

facilitates interactions between RNA polymerase II and regulatory transcription factors.

An organized unit of DNA sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product is called a ______.

gene

When a neurotransmitter released from one neuron binds to a _______ on a second neuron, that neuron deploarizes and fires.

ligand-gated ion channel

When glucose is high, cAMP is _____________. high low doesn't change

low

What is a tumor-suppressor gene? What is its normal role? What are its two typical functions?

normal role to prevent cancerous growthfunctions: maintain genome integrity by monitoring or repairing DNA damage, checkpoint proteins check the integrity and prevent a cell from progressing past a certain pointinhibitors of cell division: halt cell division otherwise division becomes abnormally accelerated

Which of the following represents the order of increasingly higher levels of organization of chromatin?

nucleosome, 30-mn chromatin fiber, looped domain

Which is the most common type of DNA repair? base excision repair methyl-directed mismatch repair nucleotide excision repair direct repair indirect repair

nucleotide excision repair

Beginning with the simplest level of structure, whoch order of organization of gentic material is CORRECT?

nucleotide, DNA, gene, chromosome, genome

Bacteria grown in 15N (heavy) medium and then transferred to 14N (light) medium and are allowed to replicate for 2 generations. The DNA is subsequently isolated and centrifuged in a CsCL2 gradient to yield what type of gradient band(s)?

one light and one half-heavy band

How does a mutation in p21 Ras result in an oncogene? p21 Ras normally encodes a G-protein that represses cell division p21 Ras normally encodes a cyclin protein kinase that promotes cell division p21 Ras normally encodes a G-protein that promotes cell division p21 Ras normally encodes the Philadelphia chromosome

p21 Ras normally encodes a G-protein that promotes cell division

How does a mutation in p21 Ras result in an oncogene? p21 Ras normally encodes a G-protein that represses cell division. p21 Ras normally encodes a G-protein that promotes cell division.

p21 Ras normally encodes a G-protein that represses cell division.

When a cell secretes a growth factor that binds to receptors only on neighboring cells causing them to proliferate this is an example of ___.

paracrine signaling

The ensyme that is directly responsible for breaking down cAMP to inactive AMP is

phosphodiesterase

What hormone can induce apoptosis?

prednisolone

An activator is to an enhancer as a(n) _______ is to a silencer.

repressor

The ensyme that attaches DNA sequences at the ends of eukaryotic chromosomes in order to prevent chromosome shortening is called ________.

telomerase

What is a testcross? Make sure you know what a test cross tells you about an organism and why?

testing homo or heterozygous dominant A tall pea plant could be either TT or Tt, so genotype must be determined by a testcross-Cross the unknown individual (TT or Tt) to a homozygous recessive individual (tt) - If some offspring are dwarf, unknown individual must have been Tt -If all offspring are tall, unknown individual was TT

How does caffeine affect the epinephrine signaling pathway?

the conversion of cAMP to AMP is blocked

What happens to EGF receptors when they each bind one molecule to EGF?

they dimerize and autophosphorylate

In cats, black fur color is caused by an X-linked allele; the other allele at this locus (gene) causes orange color. The heterozygote is tortoiseshell. What kinds of offspring would you expect from the cross of a black female and an orange male? orange females; orange males tortoiseshell females; tortoiseshell males tortoiseshell females; black males black females; orange males orange females; black males

tortoiseshell females; black males

The event that occurs when alloclactose levels increase in E. coli (in the absence of glucose) is

transcription of genes within the lac operaon increases.

How is the Philadelphia chromosome an example of a chimeric gene or fusion protein? What type of cancer is it associated with?

translocation of the end of chromosome 9 to the end of chr. 22 created the new fusion protein-causes chronic myelogenous leukemia

To determine if a plant that displays the dominant tall trait is homozygous (TT) or heterozygous (Tt), the tall plant is crossed to a: TT Tt tt

tt

When does synapsis and crossing-over take place? What are the functions of crossing-over? What role does it play in the alignment of chromosomes in Meiosis I?

•Physical exchange between pieces of non-sister chromatids in the bivalent •May increase the genetic variation of a species Chiasma - arms of the chromosomes tend to separate but remain adhered at a crossover site Number of crossovers carefully regulated (size of chromosome and species) ~3 / chromosome in humans ONLY in Prophase I of Meiosis Generates genetic variation in gametes Very important in sexually reproducing species

How frequent is polyploidy found in plants? What are two examples?

•Plants commonly exhibit polyploidy -30-35% of fern and flowering plant species are polyploid -Important in agriculture - wheat *Every banana you have ever eaten has been triploid *Seedless watermelons are triploid

What is meiosis? Why is it required for sexual fertilization? In what important way does meiosis differ from mitosis?

•Sexual reproduction requires a fertilization event in which two haploid gametes unite to create a diploid cell called a zygote •Meiosis is the process by which haploid cells are produced from a cell that was originally diploid •For this to occur, the two cellular divisions follow one replication of DNA

Other than the coding region of a gene, where else can mutations occur that affect gene expression? (two places). What effect do these mutations have on gene expression?

* A mutation may alter the sequence within a promoter and affect the rate of transcription -May enhance or inhibit RNA transcription and therefore gene expression *Mutations may occur in other regulatory elements or operator sites -Mutation may alter DNA sequence so that repressor or activator proteins do not bind

When lactose is absent, what happens to the lac repressor and what effect does this have on RNA polymerase? Is the lac operon expressed? What is a lac operon inducer? How does it function to induce the expression of the lac operon?

*Lactose absent: Lac repressor protein binds to nucleotides of thelac operator site blocking RNA polymerase from transcribing lacZ, lacY and lacA *In the 1950s, French biologist François Jacob, French biochemist Jacques Monod, and their colleague, American biochemist Arthur Pardee, had identified a few rare mutant bacteria that expressed the genes of the lac operon constitutively, meaning that the lacZ, lacY, and lacA genes were expressed even in the absence of lactose in the environment. *When lactose is available, some molecules will be converted to allolactose inside the cell. Allolactose binds to the lac repressor and makes it change shape so it can no longer bind DNA. Allolactose is an example of an inducer, a small molecule that triggers expression of a gene or operon. *When allolactose binds to the repressor, a conformational change occurs that prevents the repressor from binding to the operator site so transcription can proceed *cannot repress?

Describe what happens when both glucose and lactose are high, and what are three reasons this occurs.

The presence of lactose cause lac repressor to be inactive, which prevents it from binding to the operator site. Even so, the presence of glucose decrease cAMP levels, and so cAMP is released from CAP, which prevents CAP from binding to the CAP site. The lack of CAP binding does not completely inhibit transcription. LOW RATE of transcription *Glucose uptake causes cAMP levels to drop *CAP does not activate transcription *Bacterium uses one sugar at a time, namely glucose

What is an operon and an operator? What is a polycistronic mRNA? What does this allow the bacteria to do?

* Operon-A set of two or more genes in bacteria that are under the transcriptional control of a single promoter. * Operator-A DNA sequence in bacteria that is recognized by activator or repressor proteins that regulate the level of gene transcription. (regulatory region of operon) *Polycistronic mRNA-An mRNA that contains the coding sequences for two or more protein-encoding genes. (operion transcribed into a single mRNA) *Allows coordinated regulation of a group of genes with a common function

What characterizes cancer? Do most cancers involve a heritable genetic change that is passed from parent to offspring?

*Disease of multicellular organisms *Characterized by uncontrolled cell division *~1.5 million Americans are diagnosed with cancer each year *0.5 - 0.6 million Americans / year will die from the disease *A higher predisposition to develop the disease is an inherited trait, called genetic predisposition.

What is the difference between spontaneous and induced mutations? How does each occur? Which has a higher rate of occurrence? What types of agents are responsible for induced mutations? How do spontaneous mutations arise?

*Spontaneous mutations -From abnormalities in biological processes (such as DNA replication, free radicals, or isomerization of nucleotides) -Rates vary species to species and gene to gene -Background mutation rate ~1 mutation/million genes/cell division *Induced mutations -Caused by environmental agents -Higher rate than spontaneous mutations -Mutagens - chemical or physical agents that alter DNA

A point mutation that results in an amino acid substitution is a __________ mutation. Nonsense Silent Missense

Missense

Which of the following is true concerning a somatic cell mutation? a. Half of the gametes carry the mutation. b. A small fraction of the gametes carry the mutation. c. Only a small group of cells within the organism is affected by the mutation. d. All cells within the organism are affected by the mutation. e. All of the gametes carry the mutation.

Only a small group of cells within the organism is affected by the mutation.

4. Which of the following will least likely affect the length of a protein product? a. Nonsense mutation b. Single-base deletion c. Missense mutation d. Frameshift mutation

This question requires that you understand the effect each of these types of mutations have on the resulting polypeptide. Answer: Choice (c) because a single amino acid is substituted for another in a missense mutation and this doesn't change the length of the protein. In choice a, the nonsense mutation will lead to a shortened protein (introduces an early stop codon, in choice b, a single-base deletion results in a frame-shift and that will often lead to an early stop codon, and choice d, as just mentioned, often leads to an early stop codon.

Describe what happens when lactose is high and glucose is low, and what are three reasons this occurs.

*When lactose is high and glucose is low, the lac operon is turned on -Allolactose levels rise and prevent lac repressor from binding to operator -CAP is bound to the CAP site -Bacterium uses lactose

How does p53 normally regulate the cell cycle? What does p53 do in the case of severe DNA damage (2 things)? Which protein directs apoptosis?

-G1 checkpoint protein -DNA damage induces p53 expression to prevent cell from progressing to S phaseif DNA damage is severe, p53 will activate programmed cell death (apoptosis) -caspases function as proteases that digest selected cellular proteins causing the cell to break down -prednisolone decreases number of adrenal cortex cells by inducing apoptosis

What are the checkpoint proteins that are associated with tumor-suppressor genes? What specific tumor-suppressor gene is associated with about 50% of all cancers?

-checkpoint proteins: cyclins and cyclin dependent protein kinases are responsible for advancing a cell through four phases of the cell cycle-formation of cyclin can be stopped by checkpoint proteins -p53- 50% of all human cancers are associated with defects in this gene

How does a mutation in p21 Ras result in an oncogene? How does this affect the control of cell growth?

-intracellular signaling protein hydrolyzes GTP when GTP is bound, Ras promotes cell division -oncogenic mutations decrease ability of Ras to hydrolyze GTP so both keep signaling pathway on

What are three ways to control RNA pol II?

1.Activators and repressors regulate RNA polymerase II by binding to GTFs (including TFIID) - influencing the formation of the preinitiation complex 2.Regulate RNA polymerase II via mediator *Activators stimulate mediator by allowing faster initiation *Repressors inhibit mediator so RNA polymerase II cannot progress to elongation 3.Recruit proteins that influence DNA packing

What three proteins mediate transcription? What does the mediator do?

1.An RNA polymerase II 2.5 different general transcription factors (GTFs) 3.Large protein complex called mediator Mediator = "mediates" interactions between the preinitiation complex and regulatory transcription factors such as activators or repressors that bind to enhancers or silencers

What are the three features of most eukaryotic promoters? You should know the relative positions of these three features of the promoter. How does a mutation in an exon versus a promoter affect the expression of a gene?

1.TATA box -5' - TATAAAA - 3' -25 base pairs upstream from transcriptional start site -Determines precise starting point for transcription 2.Transcriptional start site -Where transcription begins nWith TATA box forms core promoter -By itself results in low level basal transcription *Regulatory or response elements3.*Recognized by regulatory proteins that control initiation of transcription -Enhancers and silencers -Can be located 50-100bp upstream of transcriptional start site or quite distant from promoter. *

What are four levels gene regulation in eukaryotes can occur? What regulation occurs in the nucleus and what occurs in the cytosol?

1.Transcriptional (common) (nucleus) (RNA or not) 2. RNA processing (post transcription) (nucleus) (capping, splicing, tailing) 3.Translation (cytoplasm)(polypeptide) 4.Post-translation (cytoplasm)(posphate group or cleave polypeptide)

Which is one way a tumor suppressor gene could become mutated and lose function? Gene duplication Chromosome loss Insertion of active promoter infront of tumor suppressor gene

Chromosome loss

What advantages does early detection of cancer give you?

Early detection key to identifying cancer before malignancy and metastasis

The Mediator binds directly to the promoter in a eukaryotic gene. True False

F

With regard to the point mutation that results in sickle-cell disease, what effect does this mutation have on the amino acid sequence of globin, the association of Hb proteins and the shape and function of the red blood cell?

Missense mutation in Beta-globin gene (encodes polypeptides that make up hemoglobin. Sixth amino acid is changed from glutamic acid (hydrophilic) to valine (hydrophobic), altering the shape and function of the hemoglobin protein. Mutant hemoglobin stick together when oxygen is low.

Which type of repair is the most common and found in all eukaryotes and prokaryotes? What does it remove and how does it generate a normal complementary strand? Be sure to know the function of each component of this type of DNA repair, such as what functions as an endonuclease (cuts the damaged DNA strand), a helicase (unwinds the double stranded DNA), a polymerase (makes a new corrected strand), a ligase (joins together the old strand with the newly corrected segment to make a continuous DNA strand).

Nucleotide Excision Repair (NER) *Most common DNA repair system *Can fix many types of DNA damage: UV-induced, chemically modified bases, missing bases, crosslinks like thymine dimers. *Region encompassing several nucleotides in the damaged strand is removed from the DNA *Intact undamaged strand is used as a template for re-synthesis of a normal complementary strand *Found in all eukaryotes and prokaryotes

What part of the histone protein is modified to control nucleosome packing? a. The carboxyl end of the histone can be methylated, phosphorylated or acetylated b. The amino end of the histone can be methylated, phosphorylated or acetylated c. The entire length of the histone is covered with basic acetyl groups d. Segments of the histone are cleaved and removed so the DNA can be packed tighter around the nucleosome core.

The amino end of the histone can be methylated, phosphorylated or acetylated

What part of the histone protein is modified to control nucleosome packing? a. The carboxyl end of the histone can be methylated, phosphorylated or acetylated. b. The entire length of the histone is covered with basic acetyl groups. c. The amino end of the histone can be methylated, phosphorylated or acetylated. d. Segments of the histone are cleaved and removed so the DNA can be packed tighter around the nucleosome core.

The amino end of the histone can be methylated, phosphorylated or acetylated.

2. A non-conservative mutation is referred to as one that results in the exchange of a single, new amino acid that has different biochemical properties for the original one in the polypeptide. Which one of these could be a non-conservative mutation? a. Silent b. Missense c. Nonsense d. Frameshift

This question requires that you understand each of these four types of mutations, how they are different from one another, and what effect they have on the polypeptide product. Answer: Choice (b). The definition of a missense mutation is when one amino acid is switched for a different amino acid. A silent mutation results in no amino acid change, a nonsense mutation substitutes a stop codon for the codon calling for an amino acid, and a frameshift mutation inserts a base in the code, so that the reading frame for all the codons that follow has changed. This results in a complete change in many amino acids.

1. All the following mutations can result in a reduction of β-galactosidase synthesis (in the Lac Operon) except: a. A mutation in adenylate cyclase b. A mutation in catabolite activator protein (CAP). c. A mutation in the CAP site in the lac control region. d. A mutation in the repressor binding site in the operator.

This question requires that you understand the function and position of each of the components of the lac operon, how they interact with one another and control gene expression. Answer: Choice (d). A mutation in the Lac O region, binding site of the repressor, would not reduce the amount of B-gal because binding of the Lac repressor to Lac O normally blocks the synthesis of B-gal. All the other choices would prevent or reduce the synthesis of B-gal because the production and binding of the CAP protein (bound to cAMP made by adenyl cyclase) would be compromised by these mutations.

5. A point mutation within which functional part of a DNA sequence would be most likely to ultimately result in the production of proteins which differ from the non-mutated form by only a single amino acid? a. Exon b. Promoter c. Intron d. Telomere e. Any choice could be correct.

This question requires that you understand the function of each of these parts of the gene and which encodes amino acid sequence. What if the mutation didn't change the amino acid sequence but just affected the level of the protein in the cell? Answer: Choice (a), which is the only choice given that contains DNA sequence that codes for amino acid sequence. All the other choices are either not found in the mature/processed mRNA (choice b and choice c) or are a part of the chromosome that is never transcribed (choice d).

The likely outcome from a mutation in the lacO site (lac Operator) of the lac operon would be a. the order in which the genes of the lac operon are transcribed could be altered. b. binding of the activator protein could be hindered. duplication could be affected. c. binding of RNA polymerase could be hindered. d. binding of a repressor protein could be hindered.

binding of a repressor protein could be hindered.

How is a new DNA strand made in nucleotide excision repair? by crossing over between sister chromatids by DNA polymerase by DNA ligase by DNA exonuclease

by DNA polymerase

The chemical, EMS (ethyl methanesulfonate) can cause ____________ mutations. induced spontaneous

induced

Which statement is TRUE regarding the effect of alternative splicing of pre-mRNAs? a. it increases the size of both the genome and the proteome b. it has no effect on the genome, while increasing the size of the proteome c. it has no effect on the proteome, while increasing the size of the genome d. it decreases the size of both the genome and the proteome e. it increases the size of both the genome while decreasing the proteome

it has no effect on the genome, while increasing the size of the proteome

4. Predict the phenotype of an operator mutant (Oc) which prevents the binding of the repressor to lac O (the operator), where "c" means that the operator cannot bind to a repressor protein. a. The lac genes would be expressed efficiently only in the absence of lactose. b. The lac genes would be expressed efficiently only in the presence of lactose. c. The lac genes would be expressed continuously, sometimes at a basal level. d. The lac genes would never be expressed efficiently.

This question requires that you understand the function and position of each of the components of the lac operon, how they interact with one another and control gene expression. Mutations in the lac operon were critical in defining the role of each gene in the lac operon. It is important that you know which genes are regulatory (lac P = promoter, lac O = operator, binding site of lac repressor) and those that actually encode for proteins (lac Z = B-galactosidase that breaks lactose into glucose and galactose, lac Y = lactose permease that is a transporter that brings lactose into the bacterial cell, and lac A = B-galactoside transacetylase that modifies lactose. Answer: Choice (c). The whole purpose of the Lac repressor is to allow the lac operon to be repressed when it is not needed, when there is no lactose to be metabolized into glucose. Since a mutation in the operator (binding site of the Lac repressor) would prevent the shutting down of the lac operon in the absence of lactose, the lac genes would be expressed continuously. The lac operator is situated between the lac promoter and the structural genes of the lac operon to block the expression of the lac operon genes in the absence of lactose. If this repression doesn't take place, the lac structural genes are free to be expressed, even when there is no lactose to be metabolized into glucose.

What is a mutation? What is a polymorphism? What reverses DNA damage? What is a disease caused by gene mutations?

* mutation, which is defined as a heritable change in the genetic material. *Polymorphism, in biology, a discontinuous genetic variation resulting in the occurrence of several different forms or types of individuals among the members of a single species. A discontinuous genetic variation divides the individuals of a population into two or more sharply distinct forms. *DNA repair systems reverse DNA damage *Cancer is caused by mutation

Where are nucleosome free regions found relative to a gene?

*A nucleosome-free region of 150 bps (NFR) is found at the beginning and end of many genes *Core promoter in NFR, flanked by +1 and -1 nucleosomes *Less regular distribution elsewhere

How does chromatin packing affect gene expression? What type of chromatin allows GTFs and RNA pol II to be bound to DNA?

*DNA is associated with proteins to form compact chromatin *Chromatin packing affects gene expression *Transcription is difficult or impossible in the closed conformation of tightly packed chromatin (depending on the location of nucleosomes) *Access to the DNA is allowed in the loosely packed open conformation, accessible to GTFs and RNA polymerase *The accessibility of chromatin is in part due to the methylation of cytosines in the DNA, which affects chromatin conformation and gene expression.

Gene regulation involving CAP and cAMP is an example of what type of control? Where on the DNA does this complex bind? What does it do to the DNA and what effect does this have on RNA polymerase binding?

*Gene regulation involving CAP and cAMP an example of positive control *When cAMP binds to CAP, this complex binds to CAP site near lac promoter *Resulting bend in DNA enhances RNA polymerase binding which increases transcription *LOW/No Glucose conditions = High cAMP

What are about 80% of all human cancers related to? What are most carcinogens? Name two.

*About 80% of all human cancers are related to exposure to carcinogens - agents that increase the likelihood of developing cancer *Most carcinogens, such as UV light and cigarette smoke, are mutagensthat promote genetic changes in somatic cells *DNA alterations can lead to effects on gene expression that ultimately affect cell division and lead to cancer

What are the regions of DNA that bind activators and repressors called? Do they bind directly to RNA pol II?

*Activators - bind to DNA regions called enhancers *Repressors - bind to DNA regions called silencers *Regulate rate of transcription of a nearby gene *Most do not bind directly to RNA polymerase II *Mediator doesn't bind to the promoter of the gene.

Know the steps of cancer progression. Where does cancer originate and why? What pathways in a healthy cell are blocked in a cancer cell? What results in a cancer entering the malignant stage? What are three characteristics of the malignant stage of cancer? What is metastatic cancer?

*Cancers originate from a single cell *Cell and its offspring mutate so cells grow abnormally *Tumor - an overgrowth of cells with no useful purpose *Tumor may begin as benign or pre-cancerous -Do not invade or spread *Additional mutations lead to Malignant stage -Loss of normal growth regulation -Invasive - can invade healthy tissue -Metastatic - can migrate to other parts of the body thru bloodstream *are blocked in healthy cell The pathways to repair DNA damage and to stop cell division. *Metastatic cancer is a cancer that has spread from the part of the body where it started (the primary site) to other parts of the body

How does ionizing radiation alter DNA (what is created and what does this do to the DNA?) What effect does nonionizing radiation have on DNA? What type of radiation is UV? What type of radiation are X-rays?

*Radiation damage -Ionizing radiation has high energy (short wavelength) and penetrates deeply to create free radicals *X rays and gamma rays *Cause deletions or breaks in one or both DNA strands -Nonionizing radiation has less energy and can only penetrate the surface *UV rays can cause formation of thymine dimers, causing gaps or incorporation of incorrect bases (distorts backbone of DNA due to linkage of adjacent thymines)

What effect does DNA methylation have on transcription? What are particular sites in the DNA from methylation? What base is methylated?

*DNA methylase attaches methyl groups (-CH3) to cytosine base *Common in some eukaryotes (vertebrates and plants) but not all (yeast and Drosophila have little) *In mammals, 5% of DNA is methylated *Usually inhibits transcription *CpG islands near promoters in vertebrates and plants -Cytosine and guanine connected by phosphodiester bonds -Unmethylated CpG islands are correlated with active genes -Repressed genes contain methylated CpG islands Methylation can inhibit transcription two ways: 1.The Methylation of CpG islands may prevent an activator from binding to an enhancer element 2.Converting chromatin from an open to a closed conformation -Methyl-CpG-binding proteins bind to methylated sequences and recruit proteins that condense the chromatin

What are two mechanisms by with chemical mutagens can alter DNA?

*Disruption of base-pairing -Some modify nucleotide structure (results in single nucleotide change) *Nitrous acid deaminates bases, changing C to U, so that it pairs with the wrong nucleotide *Mustard gas or EMS alkylate bases, adding methyl or ethyl groups -Base analogues substitute into DNA (e.g. 5-bromouracil and 2-aminopurine) *Disruption of replication -Some insert between the bases and distort the helix *Benzopyrene, found in cigarettes and charbroiled food *Results in single nucleotide additions and deletions in newly synthesized strand

What are the two components of DNA repair? What are three types of DNA repair? What is the difference between direct repair and the other two types of repair? Which type of repair is used to correct thymine dimers induced by UV irradiation?

*Two components of DNA repair systems: *Detection of damage *Repair of damage *Direct repair A repair enzyme recognizes an incorrect structure in the DNA and directly converts it back (e.g. removal of alkyl group) *Nucleotide excision repair (thymine dimers) -Portion of DNA strand containing an abnormal nucleotide is removed and replaced with newly synthesized DNA *Methyl-directed mismatch repair (parent strand is methylated) -A base pair mismatch is detected, and a strand of surrounding DNA is removed and replaced with newly synthesized DNA

Describe what happens when lactose is low and glucose is high or low, and what are three reasons this occurs.

*When lactose is low and glucose is high or low, the lac operon is shut off -Under low lactose conditions, lac repressor prevents transcription of lac operon, evenwhen there is no glucose and high cAMP *There isn't enough allolactose to pull the Lac I off the Lac O site, plus cAMP is at a low level so CAP can't bind to CAP binding site. *There isn't enough allolactose to pull the Lac I off the Lac O site, which blocks RNA polymerase even if there is stimulation by CAP-cAMP.

What is the Lac I gene and what is it function? What are the two regulatory sites near the lac promoter called? What does each bind to?

*lacI gene - codes for lac repressor -Considered a regulatory gene since its sole function is to regulate other gene's expression (but technically a structural gene since it encodes a protein). -Has its own promoter (i) (not part of lac operon), but is constitutively expressed at low levels. *Near the lac promoter are two regulatory sequences designated the operator and the CAP site. The operator (lacO) is a regulatory sequence in the DNA. The sequence of bases at the operator provides a binding site for a repressor protein. The CAP site is a regulatory sequence recognized by an activator protein. *lacO - operator - provides binding site for repressor protein *CAP site - activator protein binding site

Describe the "two hit" model for retinoblastoma?

-people have two copies of the Rb gene (one from each parent )-individual with the inherited form of the disease have one mutant gene already from one parent -one additional mutation will cause disease -tends to occur early in life -people with the non inherited form of the disease must have two mutations in the same retinal cell to cause the disease

What is a proto-oncogene? What are four common genetic changes that cause a proto-oncogene to mutate into an oncogene? What is a chimeric gene and why would this result in an oncogene?

Proto-oncogene: normal gene that, if mutated, can become an oncogenei. *proto-oncogene= accelerator of carii. *oncogene= car speeds out of control -missense mutations: chemical mutagens cause missense mutations leading to cancer -gene amplifications: increase the copy number results in too much protein -chromosomal translocations: two non-homologous chromosomes break and switch ends can create chimeric genes: combination of two or more coding sequences to produce a new gene -retroviral insertions: viral DNA inserts into a chromosome, putting a viral promoter next to a proto-oncogene -Four common genetic changes 1.Missense mutations 2.Gene amplifications 3.Chromosomal translocations 4.Retroviral insertions

What are four types of mutations based on the effect the mutation has on the amino acid sequence? Make sure you understand and can recognize one type from another based on the effect each mutation has on the amino acid sequence. For example, which of these mutations can result in a shorter protein product? How does the degeneracy of the genetic code affect the frequency of point mutations that affect codons?

Silent mutations often occur in the third position of a codon, and due to the degeneracy of the genetic code, it will not result in an amino acid change. A missense mutation that substitutes an amino acid with a chemistry similar to the original amino acid is less likely to alter protein function: Glutamic acid for Aspartic acid (but this also depends on where in the protein the change takes place). A single aa change in the active site of an enzyme or in a structural domain could affect the function of the protein significantly. (e.g. sickle cell anemia). Nonsense mutation involves a change from a normal codon to a stop, or termination, codon. Resulting in a truncated polypeptide. Frameshift - addition or deletion of nucleotides that are not multiple of three. Changes the reading frame of all subsequent amino acids. Likely to inhibit protein function.

6. During which phase of the cell cycle are DNA repair mechanisms least active? a. G1 b. S c. G2 d. M

This question requires that you understand what is taking place in each of the phases of the cell cycle and when DNA repair mechanisms take place. [There is more than one way to repair DNA.] Answer: Choice d, because during Mitosis, the chromosomes are condensed, align during metaphase and move to opposite daughter cells during anaphase. There is no time for DNA repair during M phase, but DNA repair must take place during the checkpoints in G1, G2 and by DNA polymerase during the S phase (when the DNA is being synthesized).

What is an activator of the lac operon? What is a catabolite repressor of the lac operon? What is the small effector molecule that positively regulates the lac operon? How does it bind to, forming a complex? What does this complex bind to? How does glucose repress the lac operon? Why is this called catabolite repression?

the lac operon is also positively regulated by an activator called the catabolite activator protein (CAP). CAP is controlled by a small effector molecule, cyclic AMP (cAMP), which is produced from ATP via an enzyme known as adenylyl cyclase. Gene regulation involving CAP and cAMP is an example of positive control (Figure 14.10). When cAMP binds to CAP, the cAMP-CAP complex binds to the CAP site near the lac promoter. This causes a bend in the DNA that enhances the ability of RNA polymerase to bind to the promoter. In this way, the rate of transcription is increased. Glucose inhibits the production of cAMP, thereby preventing the binding of CAP to the DNA. In this way, glucose blocks the activation of the lac operon by inhibiting transcription. Though it may seem puzzling, the term catabolite repression was coined before the action of the cAMP-CAP complex was understood at the molecular level. Historically, the primary observation of researchers was that glucose (a catabolite) inhibited (repressed) lactose metabolism. Further experimentation revealed that CAP is actually an activator protein. *CAP (catabolite activator protein) is an activator *Catabolite repression - glucose, a catabolite, represses lac operon *Small effector molecule, cAMP, binds to activator protein called catabolite activator protein (CAP) and the cAMP-CAP complex binds to the CAP binding site near the lac promoter *Operon is turned off when CAP is not bound *Glucose inhibits production of cAMP and so prevents binding of CAP to DNA

Where do the GTFs and RNA pol II come together? What complex do they form? What does the mediator complex associate with? What does it actually mediate? How does this affect RNA polymerase?

*GTFs and RNA polymerase II must come together at the TATA box of the core promoter before transcription can be initiated *Preinitiation complex - assembled GTFs and RNA polymerase II at the TATA box -Form basal transcription apparatus *Mediator composed of several proteins -Partially wraps around GTFs and RNA polymerase II -Mediates interactions with activators or repressor that bind to enhancers or silencers -Controls rate at which RNA polymerase can begin transcription

What is the difference between a germ-line mutation and a somatic cell mutation? Which occurs late in development? Which gives rise to a mosaic of mutant cells?

*Germ-line cells give rise to gametes -Mutations can occur in sperm or egg cells, or in gamete progenitor cells *Somatic cells are all other body cells -Can occur early or late in development -Gives a genetic mosaic with patches of mutant tissue

What added benefit does RNA processing give eukaryotes over prokaryotes?

*Unlike bacteria, gene expression is commonly regulated at the level of RNA processing and translation in eukaryotes *Added benefits include... 1. Produce more than one mRNA transcript from a single gene (gene encodes 2 or more polypeptides) 2. Faster regulation achieved by controlling steps after RNA transcript made

Does alternative splicing correlate with biological complexity or the number of protein coding genes? Give an example to support your answer.

1. One general trend is that less complex organisms tend to have fewer genes. For example, unicellular organisms have only a few thousand genes, whereas multicellular species have tens of thousands. However, the trend is by no means a linear one. If we compare C. elegans and D. melanogaster, the fruit fly actually has fewer genes, even though it is more complex morphologically. 2.A second trend you can see in Table 14.1 concerns alternative splicing. This phenomenon does not occur in bacteria and is rare in S. cerevisiae. The frequency of alternative splicing increases from worms to flies to humans. For example, the level of alternative splicing is 10-fold higher in humans than in Drosophila. This trend can partially explain the increase in complexity among these species. Even though humans have only about 22,000 different protein-encoding genes, their cells make well over 100,000 different polypeptides because most genes are alternatively spliced in multiple ways. This increases the level of information contained within the human genome.

5. You have discovered a mutation in a gene that completely shuts down the initiation of transcription. You look at the sequence of the gene and find that the mutation in the: a. TATA box b. 5' splice site between the first exon and intron c. Termination of transcription sequence d. 5' cap site

This question tests your understanding of the different parts of the gene and the role certain parts of the gene play in regulating transcription. Answer: Choice (a). Initiation of transcription is focused in the promoter region of a gene. The only choices that are relevant to the initiation of transcription is the TATA box (choice a). The other choices relate to steps that occur after the initiation of transcription such as processing the mRNA (choice b), ending transcription (choice c) and processing the mRNA (choice d).

6. Histone Acetyltransferases are enzymes responsible for modifying histone structure. These enzymes add acetyl groups to amino acids on the histone protein that contain amine groups on their side chains (arginine and lysine). By adding acetyl groups to these amino acid side chains, the structure of the entire histone protein complex will change, thereby altering the expression of different genes associated with these histones. If histone X were to be acetylated, the expression of gene Y would be increased. If gene Y codes for protein Z, what would happen to the levels of protein Z if the concentration of histone acetylase were to decrease? a. The concentration of protein Z would increase, as the expression of gene Y is increasing. b. The concentration of protein Z would decrease, as the expression of gene Y is decreasing. c. The concentration of protein Z would increase, as the expression of gene Y is decreasing. d. The concentration of protein Z would decrease, as the expression of gene Y is increasing.

This question requires an understanding of the effect histone modifying enzymes have on gene expression. Most methylation of histone amino acids results in repressing transcription, while acetylation of certain histone amino acids result in the activation of transcription. Answer: Choice (b). The production of protein Z is dependent upon gene Y. Acetylation of the histones associated with gene Y will promote transcription of gene Y and thereby increase the production of protein Z. If acetylation of histones associated with gene Y would decrease, then the production of protein Z would also decrease.

When lactose is present, what small effector molecule is made and what effect does it have on the lac repressor? What effect does this have on RNA polymerase? Is the lac operon expressed? What is this phenomenon called? What is a lac operon inducer? How does it function to induce the expression of the lac operon?

*Allolactose is a small effector molecule - 4 molecules bind to lac repressor to prevent it from binding DNA *The regulation of the lac operon enables E. coli to conserve energy because lactose-utilizing proteins are made only when lactose is present in the environment. Allolactose is an inducer, a small effector molecule that increases the rate of transcription, and the lac operon is said to be an inducible operon. When the bacterium is not exposed to lactose, no allolactose is available to bind to the lac repressor. Therefore, the lac repressor binds to the operator site and inhibits transcription. In reality, the repressor does not completely inhibit transcription, so very small amounts of β-galactosidase, lactose permease, and galactoside transacetylase are made. However, the levels are far too low for the bacterium to readily use lactose. When the bacterium is exposed to lactose, a small amount can be transported into the cytoplasm via lactose permease, and β-galactosidase converts some of it to allolactose (see Figure 14.6b). The cytoplasmic level of allolactose gradually rises until allolactose binds to the lac repressor, which induces the lac operon and promotes a high rate of transcription of the lacZ, lacY, and lacA genes. Translation of the encoded polypeptides produces the proteins needed for lactose uptake and metabolism, as described previously in Figure 14.1

What is a histone code? What part of the histone protein is modified? What are three ways the histone is modified?

*a combination on amnio termial tail of histone. *Many different amino acids in the amino terminal tails of histone proteins subject to several types of covalent modification -Modified by acetyl, methyl, and phosphate groups *Pattern of modifications (histone code) is recognized by proteins which, in turn, affects degree of chromatin compaction Addition of acetyl group to amino terminal tails of histone proteins by histone acetyltransferase, causes histone proteins not to bind as tightly to the DNA, which aids in transcription. Over 50 different enzymes have been identified in mammals that selectively modify amino terminal tails. Histone code could attract proteins that inhibit transcription, while another histone code could attract ATP-dependent chromatin-remodeling complexes that promote gene transcription 1. Amino Terminal Tail of histones are modified to control tightness of histone association with DNA in the nucleosome 2.Amino Acids on the amino terminal tail of Histones are modified chemically 3. Histone tail modification status correlates with transcriptional activity

What are transcription factors (regulatory proteins) and in what way can they affect transcription? What is negative versus positive control? Where do they bind and what protein do they directly affect?

*general transcription factors (GTFs): Five different proteins that play a role in initiating transcription at the core promoter of protein-encoding genes in eukaryotes. *Repressors are regulatory transcription factors that bind to the DNA and decrease the rate of transcription. This is a form of regulation called negative control. *Activators bind to the DNA and increase the rate of transcription, a form of regulation termed positive control *Regulatory transcription factors are proteins that bind to regulatory sequences in the DNA in the vicinity of the promoter and affect the rate of transcription by RNA polymerase. Repressors bind to regulatory sequences and slow down the rate of transcription (negative control), while activators bind to regulatory sequences and speed up the rate of transcription (positive control).

In the lac operon, what are the following genes and their function? LacP, lacZ, lacY and lacA? What effect would mutations in each of these genes (one at a time, have on regulating or expressing the genes of the lac operon)?

*lacZ - β-galactosidase -Breaks down lactose *lacY - lactose permease -Membrane protein required for transport of lactose into the cytoplasm of the bacterium. *lacA - galactosidase transacetylase -Modified lactose by attaching an acetyl group (-COCH3). *lacP - lac promoter -involved in the transcription of three protein-encoding genes: lacZ, lacY, and lacA. Mutations: lacp-RNA polymerase will not be able to bind lacz-will affect β-galactosidase (responsible to breaking down lactose into allolactose) lacy-will afffect lactose permease (responisble for bring lactose into the cell) laca=makes accetylase which plays some role in breaking down lactose

What are small effector molecules and what is their relationship to a transcription factor? What are two functional domains in regulatory transcription factors (or regulatory proteins)? Be sure to know how they would function independently if in a synthesized protein.

*small effector molecule: A molecule that affects gene transcription by binding to a regulatory transcription factor, causing a conformational change in that protein. -cAMP+CAP protein in lac operon *Two functional domains in regulatory transcription factor that respond to small effector molecules 1.Site where protein binds to DNA 2.Site specifically for small effector molecule (activator/repressor domain) *function independently...for example let's say that this is a transcriptional activator And this is its DNA binding domain. I can make a synthetic protein in which I take this same DNA bonding domain. But now I hook it up to a Repressor. So now, wherever that normally would bind to the DNA where it normally would have activated the gene now it is going to repress the gene because we have hook and made a synthetic protein in which the activator domain has been replaced with repressor domain.

2. Which of the following is true about the DNA-binding and activation domains of transcription activators: a. The DNA-binding domain is always at the N-terminus, and the activation domain is at the C-terminus. b. The activation domain of one protein can be fused to the DNA-binding domain of another protein to generate a functional activator protein. c. The DNA-binding domain is always at the C-terminus, and the activation domain is at the N-terminus. d. The distance between a DNA-binding domain and activation domain cannot be altered.

This question requires that you understand the role of DNA-binding domains and activation or repression domains in regulatory protein. An activator is comprised of two separate domains within the same protein: a DNA-binding domain that directs this protein to bind to a certain DNA sequence and an activation domain that activates the transcription of the gene that the protein has bound to. One controls guiding the protein to its site in the genome, and the other domain executes the actual function, to activate the expression of the gene. The same is true for a repressor protein, only it has a domain that executes the repression of the target gene's expression when it binds. Both of these proteins have to have DNA-binding domains, or they cannot affect the transcription of their target genes. These domains (DNA-binding and activation/repression are interchangeable). For example, if a protein normally represses gene A, but has had its repressor domain replaced with an activator domain, now the same protein will activate gene A. Answer: Choice (b). The distance between a DNA-binding domain and an activation domain can be variable and these domains are not required to be near either end of the protein. Hybrid proteins are made routinely by fusing the coding region of the DNA-binding domain of one gene with the activation domain of another gene. This creates a protein that will bind to the DNA corresponding to the DNA-binding domain, while activating the expression of the target gene.

3. Which of the following represents a frameshift mutation of the given template strand (with the codons indicated) here: 5'-AGC-CTT-AGC-3' a. 5'-AGC-CTT-AGG-3' b. 5'-AGC-GCT-TAG-C-3' c. 5'-TTT-AGC-CTT-AGC-3' d. 5'-TGC-CTT-AGC-3' e. 5'-CTT-AGC-3'

This question requires that you understand what a frameshift mutation is and how to recognize it in a changed nucleotide sequence. Answer: Choice (b). This question requires that you understand that a frameshift mutation is the introduction of a base (or deletion of a base) that changes the reading frame or codons of the remaining sequence. In choice a, the last base in the sequence is changed from a C to a G, so this is not a frameshift mutation. In choice c, three T's are added to the 5' end of the template, so this would not change the reading frame because it is an insertion of three bases. In choice d, the first base is changed from A to T, so like choice a, this is not a frameshift mutation. Finally, choice e deletes the first three bases of the sequence and this itself doesn't change the reading frame of the sequence.