Explain the following repair mechanisms:

-removal of thymine dimers

-base excision repair

-nucleotide excision repair.

1. (14 pts) Central Dogma – DNA to protein questions
   1. Think about the general flow of genetic information in living organisms. Summarize the three steps of the central dogm
   2. Imagine that a DNA section of the gene that codes for the enzyme phosphofructokinase read 3’ – TACTGGCGC-5’ What would be the resulting messenger RNA strand and why?

3. Use the codon chart above to answer this question. From left to right list, the exact amino acid chain that would be formed? (write the amino acids out in order).

4. Imagine that a mutation added an extra base was added at the start of the strand, so the strand now rea 3’-GTACTGGCGC-5’. How would this affect the outcome? Would a chain of amino acids still be created?

5. Imagine, a malfunction occurs in a cell.   The cell is no longer able to regulate the H₃O⁺ levels inside the cell, the amount of H₃O⁺ increases. Note you will have to call back on information from previous chapters (Ch 3, Ch 5) to answer this
   1. What would happen to the pH? Explain
   2. Which part of the central dogma steps would be most affected and why?
6. Why do genes code to make proteins, why don’t genes code to make carbohydrates, or fats, or nucleic acids? How do the proteins function in the body?
7. Imagine that a mutation occurred in the last codon in the DNA sequence from part B. Instead of 3’ – TACTGGCGC-5’ the DNA read 3’ – TACTGGTGC-5’.
   1. How would the amino acid sequence change? Explain how the mutation would or would not have an effect on the function of phosphofructokinase. You will need specific details relating to the chemistry of the molecules.
   2. How and why would a change in phosphofructokinase impact the health of the person with this mutation? Explain in details

1. (14 pts) Central Dogma – DNA to protein questions
   1. Think about the general flow of genetic information in living organisms. Summarize the three steps of the central dogm
   2. Imagine that a DNA section of the gene that codes for the enzyme phosphofructokinase read 3’ – TACTGGCGC-5’ What would be the resulting messenger RNA strand and why?

3. Use the codon chart above to answer this question. From left to right list, the exact amino acid chain that would be formed? (write the amino acids out in order).

4. Imagine that a mutation added an extra base was added at the start of the strand, so the strand now rea 3’-GTACTGGCGC-5’. How would this affect the outcome? Would a chain of amino acids still be created?

5. Imagine, a malfunction occurs in a cell.   The cell is no longer able to regulate the H₃O⁺ levels inside the cell, the amount of H₃O⁺ increases. Note you will have to call back on information from previous chapters (Ch 3, Ch 5) to answer this
   1. What would happen to the pH? Explain
   2. Which part of the central dogma steps would be most affected and why?
6. Why do genes code to make proteins, why don’t genes code to make carbohydrates, or fats, or nucleic acids? How do the proteins function in the body?
7. Imagine that a mutation occurred in the last codon in the DNA sequence from part B. Instead of 3’ – TACTGGCGC-5’ the DNA read 3’ – TACTGGTGC-5’.
   1. How would the amino acid sequence change? Explain how the mutation would or would not have an effect on the function of phosphofructokinase. You will need specific details relating to the chemistry of the molecules.
   2. How and why would a change in phosphofructokinase impact the health of the person with this mutation? Explain in details

1. (14 pts) Central Dogma – DNA to protein questions
   1. Think about the general flow of genetic information in living organisms. Summarize the three steps of the central dogm
   2. Imagine that a DNA section of the gene that codes for the enzyme phosphofructokinase read 3’ – TACTGGCGC-5’ What would be the resulting messenger RNA strand and why?

3. Use the codon chart above to answer this question. From left to right list, the exact amino acid chain that would be formed? (write the amino acids out in order).

4. Imagine that a mutation added an extra base was added at the start of the strand, so the strand now rea 3’-GTACTGGCGC-5’. How would this affect the outcome? Would a chain of amino acids still be created?

5. Imagine, a malfunction occurs in a cell.   The cell is no longer able to regulate the H₃O⁺ levels inside the cell, the amount of H₃O⁺ increases. Note you will have to call back on information from previous chapters (Ch 3, Ch 5) to answer this
   1. What would happen to the pH? Explain
   2. Which part of the central dogma steps would be most affected and why?
6. Why do genes code to make proteins, why don’t genes code to make carbohydrates, or fats, or nucleic acids? How do the proteins function in the body?
7. Imagine that a mutation occurred in the last codon in the DNA sequence from part B. Instead of 3’ – TACTGGCGC-5’ the DNA read 3’ – TACTGGTGC-5’.
   1. How would the amino acid sequence change? Explain how the mutation would or would not have an effect on the function of phosphofructokinase. You will need specific details relating to the chemistry of the molecules.
   2. How and why would a change in phosphofructokinase impact the health of the person with this mutation? Explain in details

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1. (14 pts) Central Dogma – DNA to protein questions
   1. Think about the general flow of genetic information in living organisms. Summarize the three steps of the central dogm
   2. Imagine that a DNA section of the gene that codes for the enzyme phosphofructokinase read 3’ – TACTGGCGC-5’ What would be the resulting messenger RNA strand and why?

3. Use the codon chart above to answer this question. From left to right list, the exact amino acid chain that would be formed? (write the amino acids out in order).

4. Imagine that a mutation added an extra base was added at the start of the strand, so the strand now rea 3’-GTACTGGCGC-5’. How would this affect the outcome? Would a chain of amino acids still be created?

5. Imagine, a malfunction occurs in a cell.   The cell is no longer able to regulate the H₃O⁺ levels inside the cell, the amount of H₃O⁺ increases. Note you will have to call back on information from previous chapters (Ch 3, Ch 5) to answer this
   1. What would happen to the pH? Explain
   2. Which part of the central dogma steps would be most affected and why?
6. Why do genes code to make proteins, why don’t genes code to make carbohydrates, or fats, or nucleic acids? How do the proteins function in the body?
7. Imagine that a mutation occurred in the last codon in the DNA sequence from part B. Instead of 3’ – TACTGGCGC-5’ the DNA read 3’ – TACTGGTGC-5’.
   1. How would the amino acid sequence change? Explain how the mutation would or would not have an effect on the function of phosphofructokinase. You will need specific details relating to the chemistry of the molecules.
   2. How and why would a change in phosphofructokinase impact the health of the person with this mutation? Explain in details

1. Given the following scenario, what would be the phenotypic outcome of this dihybrid cross for the F2 generation:

2. Given the following scenario, how many birds in the F2 generation would be homozygous recessive for the clear wing trait?

3. Given the following scenario, how many of the birds in the F2 generation would be heterozygous for both traits:

The energy from compounds like glucose can be harvested to generate ATP in aerobic respiration. This is a complex process that involves many chemical conversions.

Describe the main processes that occur. Include all critical concepts in your answer, and where in the cell they occur. You do not need to describe the individual chemical reactions, but do describe the most important elements of each part of aerobic respiration.

Make sure it is clear from your description that you understand how the different processes interconnect, and how ATP eventually is generated. Your answer should be approximately 200 words. In the answer terms like glucose, pyruvate, cyclical behavior of the citrate cycle, NAD+, OXPHOS complexes, proton motive force etc. should be included/ discussed.

Essay answers are limited to about 500 words

1. Discuss the composition and structure of enzymes and discuss the factors that modify enzyme structure and function

2. Describe the production and processing of a protein that will be exported from a eukaryotic cell. Begin with the separation of the mRNA from the DNA template and end with the release of the protein at the plasma membrane.

Describe the mechanisms by which B-cells and T-cells can recognize self from non-self antigens.

Propose a research study on the effects of warming climate and resulting advancing treeline. Assume that your hypothesis is that a bird's growth and reproduction will be negatively affected by the advancing treeline. The bird resides in one forest and flies at high elevations. What is an experiment that could take place? List the research design and methods. What are the materials, replicates for treatments, sampling and measurement procedures?

Genetics:

1) Gametogenesis in Neuropsora is different from gametogenesis in humans and fruit flies in that it includes:

a) Only Meiosis II (i.e., Meiosis I does not occur)

b) Mitosis

c) Unordered gametes

d) Only Meiosis I (i.e., Meiosis II does not occur)

2) Assume that a true-breeding female with the dominant phenotype is crossed to a true-breeding male with the recessive phenotype (Generation 0). Female offspring are then backcrossed to males with the recessive phenotype (Generation 1). This process is then repeated, with each new generation created by crossing the female offspring from the previous backcross generation to males with the recessive phenotype. If this trait is controlled by a maternal effect gene, in which backcross generation will some of the females used for the backcross have the recessive phenotype?

a) 4

b) None. The recessive phenotype will never reappear with this crossing scheme.

c) 1

d) 3

e) 2

3) Consider the following parental cross, involving genes A and B that are located 10 cM apart on the same chromosome:

AB/AB x ab/ab

If the F1 individuals are backcrossed to the ab/ab parent, what percentage of the offspring are expected to have the genotype ab/ab?

Express your answer as an integer between 0 and 100.

4) Consider a dihybrid cross in which one allele at each of the two genes contributes a value of 2 to a trait whereas the other allele contributes 0.

What proportion of offspring are expected to have a phenotype of 4?

Enter your answer as a decimal with two places (e.g., 0.10 or 0.01).

Sucrose is a disaccharide consisting of glucose and fructose. Following cleavage by sucrase glucose is readily metabolized through glycolysis. Explain how fructose serves as an alternative glycolytic intermediate?

Yeast Fermentation Results

1. Clearly stated hypothesis
2. Identify the independent and dependent variables
3. Your conclusion as to the sugar which produced the highest rate of fermentation by the yeast, citing evidence from the video to support your conclusion.
4. Was your hypothesis supported by the experimental data? Provide a biological explanation for the results that you observed.

Regulation of the lac operon is under both negative and positive control. Describe how these two transcriptional control mechanisms regulate expression of the lac operon in the presence of glucose and/or lactose.

If fungi were to disappear completely from earth what might happen? List at least 3 different consequences