BIO315H5 Midterm: Test 2 Review - Lecture 8

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13 Feb 2017

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Begins in the nucleus when the gene that that encodes that protein is transcribed into a messenger rna. Transcription first generates a pre- messenger rna (hnrna heterogeneous nuclear rna). This needs to be processed before it reaches the mature mrna form that is exported out into the cytoplasm. Once have messenger rna, gets exported to the cytoplasm or it can undergo translation to generate the protein. Once synthesized needs to fold into final form to be active. Eventually that protein will also get turned over or degraded. Important for cell to ensure that whatever protein is generated, that it is correct. Ways to ensure translation only occurs on mrna that are not damaged. Usually export out of nucleus only happens on mrnas that are not damaged or correctly processed. Sometimes accidentally damaged mrnas may be exported out to cytoplasm. Sometimes mrnas may incur damage while in cytoplasm. Translation of damaged mrna can be detrimental to cell.

Related Questions

13. The arms of a human and the wing of a bat are _________________ structures, composed of the same bones that have been modified for different functions.

analogous

vestigial

c.	homologous

d.	convergent

14. Xeroderma pigmentosum is an autosomal recessive genetic disorder. People who are homozygous for the disease-causing allele have skin that is damaged by exposure to ultraviolet radiation; this can lead to skin cancer at an early age. The mutation that causes this disorder is in a gene that functions:

a.	to repair DNA by excising (removing) nucleotides damaged by UV light.

b.	in lysosomes, to break down lipids that otherwise accumulate in the nervous system.

c.	to produce the UV blocking pigment melanin in the skin cells

d.	in red blood cells to carry oxygen to the skin.

15. The Amish are a religious sect descended from a small group of colonists who came to the United States over 200 years ago. Their religious beliefs have kept them isolated from society. The Amish have a much higher than average incidence of both polydactyly (extra fingers and toes) and dwarfism in their communities. This is most likely explained by:

a.	inheritance of acquired characters.

b.	the founder effect.

c.	disruptive selection.

d.	natural selection.

16. In the structure of DNA that Watson and Crick proposed, the sides of the "ladder" of the DNA molecule are always the same distance apart, making the molecule a constant width. This occurs because when the bases hydrogen bond to form the rungs of the "ladder", a:

a.	purine always pairs with a pyrimidine.

b.	purine always pairs with a purine.

c.	pyrimidine always pairs with a pyrmidine.

d.	The structure of the double helix is not determined by how the bases pair.

17. The RNA transcript of DNA that travels to the cytoplasm, carrying the instructions to make a protein, is called:

rRNA.

tRNA.

mRNA.

d.	RNA polymerase.

18. When DNA is replicated, the error rate is approximately one error for every 10,000 nucleotides copied. However, that error rate is reduced to only 1 error for every 1 billion nucleotides. The DNA sequence is "corrected" by:

a.	repeating S phase to see if the error rate is lower the second time around.

b.	enzymes that proofread the DNA and repair errors.

c.	messenger RNA during the process of transcription.

d.	Any errors made during DNA replication cannot be corrected. If errors are detected after S phase, the cell is destroyed.

19. Mendel's principle of segregation says that:

a.	when gametes are formed, each gamete receives only one allele for a particular gene.

b.	some genes are dominant to others.

c.	a testcross must be used to determine the genotype of an organism with a dominant phenotype.

d.	all of the above

20. Tay-Sachs disease is lethal before reproductive age, but the allele persists in Louisiana French Canadians because:

a.	it is a dominant allele.

b.	new mutations causing this disease are common in that population.

c.	it is not expressed in the phenotype of heterozygous individuals.

d.	the disease is contagious and can be transmitted by nonheritable means.

21. Physical features that are similar in organisms which are not closely related to each other are most likely a result of ____________. A good example of this is the similarities seen between some marsupial and placental mammals.

a.	natural selection.

b.	adaptation to similar environments

c.	convergent evolution

d.	All of the above phrases can be used to correctly fill this blank.

22. In humans, which of the following sex chromosome compliments could be found in males?

23. The proteins that are associated with eukaryotic chromosomes:

a.	help to package the DNA within the nucleus.

b.	are involved in gene expression, through binding with the DNA.

c.	may be replicating or transcribing the DNA.

d.	All of these are true of proteins that are associated with eukaryotic chromosomes.

24. A sequence of DNA nucleotides that contains the information to produce a single protein is a(n):

codon.

gene.

c.	polypeptide.

d.	anticodon.

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QuestionGroup: #21 Gene expression 2

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The direct end result of gene expression is which of the following?

Amino acids

Translation

Proteins

Carbohydrates

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QuestionGroup: #22 Mutation

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Which of the following is the ways in which nucleotide mutations lead to altered proteins?

One nucleotide is substituted by another nucleotide, which can cause an early stop codon to be incorporated into the amino acid sequence resulting in a truncated protein.

One nucleotide is replaced by another nucleotide, which can change an amino acid in the protein sequence

Nucleotides are inserted into a nucleotide sequence causing a frameshift in the sequence.

All three choices may cause mutations.

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QuestionGroup: #23 Mutation 2

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Mutations are the result of which of the following?

Change in the normal nucleotide sequence in the DNA directly resulting in different carbohydrates

Change in the normal nucleotide sequence in the DNA directly resulting in different proteins

Change in the order of transfer RNA to messenger RNA so that the transfer RNA take over the role of Messenger RNA

Primarily an alteration in the sequence of nucleotides in the abnormal proteins

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QuestionGroup: #24 Cell division

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There are two major kinds of cell division. Which of the following plays a major role in promoting genetic diversity?

Meiosis since it causes the cells to make more daughter cells than mitosis

Mitosis since it causes the cells to duplicate and eventually have mutations

Meiosis since it causes the DNA sequences to be separated into new patterns in the daughter cells.

Mitosis since it essential for the ovaries in humans to separate and duplicate

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QuestionGroup: #25 Cancer

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Genes that slow down or stop the cell cycle are called...

Apoptotic genes

Oncogenes

Restriction genes

Tumor suppressor genes

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QuestionGroup: #26 Cancer2

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The common theme in the development of all cancers is...

Mutation

Evolution

Infection

Syncopation

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QuestionGroup: #27 Genetics

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Punnett's square is which of the following?

Example of all possible combinations of alleles

Example of all possible combinations of chromosomes

Example of only certain combination of alleles since some will not be expressed.

Example of all possible combinations of DNA

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QuestionGroup: #28 Embryo development

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Which of the following is the end of the cleavage phase?

A fetus

Formation of a blastocyst

Implantation to the lining of the uterus

Fewer number of cells

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QuestionGroup: #29 Development of organ system

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Homework

For organs to be differentiated, which of the following is the first step?

Stem cells trigger the development of differentiated cells

Tissues assemble into organ systems such as blood

Tissue specific genes in stem cells are triggered

Differentiated cells form tissues

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QuestionGroup: #30 Development and society

Assigned as

Homework

A pregnant mother ingests a chemical which her mother said would be great for the baby. When the baby was born, it had a large head and flippers for arms. What caused this phenotype?

The chemicals were teratogens which influenced oxidative phosphorylation causing the changes in the phenotype.

The chemicals influenced the expression of different stem cells.

There is no way to assume the chemicals caused the phenotype since we have no data on other mothers who took this medicine. It could have been purely by chance.

The chemicals were teratogens which caused the baby to show early signs of evolution.

a) You also wish to synthesize a degenerate oligonucleotide primer that could be used eventually to clone DNA that encodes your mutant protein. Design this degenerate oligo, keeping in mind the rules we talked about in class. More information about designing degenerate primers and primers in general are located on the following page.

Write out the sequence of this oligo here

b) If you synthesized the above oligonucleotide primer, how many different oligos would be present in the mixture?

RULES TO FOLLOW for creating primers (Modified from the Thermo Fisher web site):

Designing degenerate primers:

Write out your amino acid sequence, label amino and carboxy termini

For each amino acid, use the genetic code to predict the various nucleic acid codons that can encode this amino acid. For all but Met, you should have redundancy present.

Now you need think about 5â and 3â considerations, and keep in mind that DNA within genes is double-stranded. It is helpful to keep in mind that the 5â end of a gene corresponds to the amino terminus of a protein. Using 5â and 3â labels write out a single strand DNA sequence corresponding to the your amino seq of interest. You may choose to start with only possible codon for each amino acid, or you can do all possibilities using the notation I showed you in class to account for the wobble position of codons.

Now make your DNA double stranded by filling in the opposite DNA strand; label the 5â and 3â ends of this second strand and make sure you have an anti-parallel arrangement of DNA strands.

If you havenât already, now consider the redundancy present on both strands, and make sure you have indicated sequences that account for all possible redundancies.

Realize that when a researched synthesizes a degenerate oligo that the final synthesis contains oligos with every substitution possible. The amount of degeneracy is defined by the number of different primer combinations in the mix. You can determine the degree of degeneracy by multiplying the number of changes present at each position together. If a position has no degeneracy then you multiple by 1 for that position.

Keep in mind that the trade-off between primer specificity and efficiency can be modified by altering the degeneracy of the primer. For example, the more degenerate the primers, the less specific annealing will be; however, decreased degeneracy will allow more potential to identify unknown variants. Anything over 1024 fold degeneracy is at the upper limit of potential usefulness.

Designing Primers:

Good primer design is essential for a successful PCR reaction. There are many factors to take into account when designing the optimal primers for your gene of interest. This information is taken from the Fisher Scientific website and are used when actually designing an experiment. Here are some tips to consider when designing primers.

In general, a length of 18 nucleotides is the minimum necessary for efficient primer binding.

Try to make the melting temperature (Tmm) of the primers between 65Â°C and 75Â°C, and within 5Â°C of each other.

If the Tmm of your primer is very low, try to find a sequence with more GC content, or extend the length of the primer a little.

Aim for the GC content to be between 40 and 60%, with the 3' of a primer ending in C or G to promote binding. This is called a GC clamp.

Typically, 3 to 4 nucleotides are added 5â of the restriction enzyme site in the primer to allow for efficient cutting. Restriction enzymes are ENDO nucleases, so they cut better when their recognition site is not on the end of DNA.

Try to avoid regions of secondary structure, and have a balanced distribution of GC-rich and AT-rich domains.

Avoid intra-primer homology (more than 3 bases that complement within the primer) or inter-primer homology (forward and reverse primers having complementary sequences). These circumstances can lead to self-dimers or primer-dimers instead of annealing to the desired DNA sequences.

BIO315H5 Midterm: Test 2 Review - Lecture 8

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