Please answer only Question 12 and 13.

Question 12:

In reference to the original sequence (shown in Question 8), classify each type of mutation present from Questions 9 to 11. Choose the best option for each.

3 points   

QUESTION 13

Questions 9 to 13 are in reference to the DNA sequence shown in Question 8.

Question 13:

Most mutations have a neutral effect on the phenotype, function or survival of an organism because they do not elicit any noticeable change. Whereas other mutations can have a positive effect on an organism leading to new versions of proteins that help an organism adapt to changes in its environment; while other mutations can have a negative effect on the organism and result in a protein that does not function normally or at all.

Answer the following questions based on the responses you gave above in Questions 8 to 12.

(a) Based on the protein sequences that were produced as a result of mutation #1, mutation #2, or mutation #3, describe the effect, if any, these mutations would likely have on the function of the protein within the cell. Support your answer.

(b) If these mutations occurred within a germline cell and not a somatic cell, how would the effects of these mutations differ?

Here is Information you need to do Q 12 and 13.

The top strand of the following segment of DNA serves as the template strand:

3’ TACACCTTGGCGACGACT 5’

5’ ATGTGGAACCGCTGCTGA 3’

We will refer to this segment of DNA as the original (or unmutated) sequence.

Please answer the following questions:

(a) What is the mRNA sequence?

The mRNA sequence is  5'  3'.

**Please enter your sequence in the 5' to 3' direction. Deductions will be made if a sequence is inputted in the wrong direction.**

(b) Using the mRNA sequence you determined in part (a) of this question, give the sequence of the protein that would be translated.

The amino acid sequence for this protein is N-terminus  C-terminus.

**Please note**

The N-terminus refers to the beginning of the primary sequence for a protein, and the C-terminus refers to the end of the primary sequence for a protein.

i.e. input the amino acids in the order that they would be translated.

If a codon encodes for a stop codon, type STOP.

When inputting your sequence, separate each amino acid with a hyphen (e.g. Ser-Tyr-STOP).

You will need to consult the genetic code to answer this question.

4 points   

QUESTION 9

Questions 9 to 13 are in reference to the DNA sequence shown in Question 8.

Question 9:

The original (unmutated) DNA sequence (shown above in Question 8) has been mutated to the following (this represents the template strand):

3’ TACATCTTGGCGACGACT 5’.

We will refer to this sequence as mutation #1.

Please note that for simplicity only the template strand for this mutated segment of DNA is shown.

Answer the following questions:

(a) What is the complete mRNA sequence for the mutated segment mutation #1?

The mutated mRNA sequence is  5'  3'.

**Please enter your sequence in the 5' to 3' direction. Deductions will be made if a sequence is inputted in the wrong direction.**

(b) Using the mRNA sequence you determined in part (a) of this question, give the sequence of the protein that would be translated.

The amino acid sequence for this protein is N-terminus  C-terminus.

**Please note**

The N-terminus refers to the beginning of the primary sequence for a protein, and the C-terminus refers to the end of the primary sequence for a protein.

i.e. input the amino acids in the order that they would be translated.

If a codon encodes for a stop codon, type STOP.

When inputting your sequence, separate each amino acid with a hyphen (e.g. Ser-Tyr-STOP).

You will need to consult the genetic code to answer this question.

4 points   

QUESTION 10

Questions 9 to 13 are in reference to the DNA sequence shown in Question 8.

Question 10:

The original (unmutated) DNA sequence (shown above in Question 8) has been mutated to the following (this represents the template strand):

3’ TACGACCTTGGCGACGACT 5’

We will refer to this sequence as mutation #2.

Please note that for simplicity only the template strand for this mutated segment of DNA is shown.

Answer the following questions:

(a) What is the complete mRNA sequence for the mutated segment mutation #2?

The mutated mRNA sequence is  5'  3'.

**Please enter your sequence in the 5' to 3' direction. Deductions will be made if a sequence is inputted in the wrong direction.**

(b) Using the mRNA sequence you determined in part (a) of this question, give the sequence of the protein that would be translated.

The amino acid sequence for this protein is N-terminus  C-terminus.

**Please note**

The N-terminus refers to the beginning of the primary sequence for a protein, and the C-terminus refers to the end of the primary sequence for a protein.

i.e. input the amino acids in the order that they would be translated.

If a codon encodes for a stop codon, type STOP.

When inputting your sequence, separate each amino acid with a hyphen (e.g. Ser-Tyr-STOP).

You will need to consult the genetic code to answer this question.

4 points   

QUESTION 11

Questions 9 to 13 are in reference to the DNA sequence shown in Question 8.

Question 11:

The original (unmutated) DNA sequence (shown above in Question 8) has been mutated to the following (this represents the template strand):

3’ TACACCTTAGCGACGACT 5’.

We will refer to this sequence as mutation #3.

Please note that for simplicity only the template strand for this mutated segment of DNA is shown.

Answer the following questions:

(a) What is the complete mRNA sequence for the mutated segment mutation #3?

The mutated mRNA sequence is  5'  3'.

**Please enter your sequence in the 5' to 3' direction. Deductions will be made if a sequence is inputted in the wrong direction.**

(b) Using the mRNA sequence you determined in part (a) of this question, give the sequence of the protein that would be translated.

The amino acid sequence for this protein is N-terminus  C-terminus.

**Please note**

The N-terminus refers to the beginning of the primary sequence for a protein, and the C-terminus refers to the end of the primary sequence for a protein.

i.e. input the amino acids in the order that they would be translated.

If a codon encodes for a stop codon, type STOP.

When inputting your sequence, separate each amino acid with a hyphen (e.g. Ser-Tyr-STOP).

You will need to consult the genetic code to answer this question.

This data set was obtained by collecting information on a randomly selected sample of 93 employees working at a bank.

SALARY-  starting annual salary at the time of hire

EDUC  -  number of years of schooling at the time of the hire

EXPER -  number of months of previous work experience at the time of hire

TIME   -  number of months that the employee has been working at the bank until now

2. Use the least squares method to fit a simple linear model that relates the salary (dependent variable) toeducation (independent variable).

a)  What is your model? State the hypothesis that is to be tested, the decision rule, the test statistic, and your decision, usinga level of significance of 5%.

b)  What percentage of the variation in salary has been explained by the regression?

c) Provide a 95% confidence interval estimate for the true slope value.

d) Based on your model, what is the expected salary of a new hire with 12 years of education

e ) What is the 95% prediction interval for the salary of a new hire with 12 years of education? Use the fact that the distance value = 0.011286

1. In the complex reactions that make up cellular respiration, energy is transferred by

A. phosphorylation reactions

B. redox reactions  

C. neither 1 or 2

D. both 1 and 2

2. Respiration of carbohydrate substrates provides more energy than proteins substrates because

A. proteins have no C-H bonds

B. proteins cannot be processed by glycolysis

C. proteins compete with NADH reduction reactions

D. proteins release NH3

3. Which of the 4 stages of respiration is anaerobic, and can continue without oxygen?

A. citric acid cycle

B. glycolysis

C. electron transport and oxidative phosphorylation

D. pyruvate processing

4. ATP is a regulatory molecule for the allosteric enzyme phospho-fructose kinase. This regulatory mechanism of the activity of glycolysis is called:

A. interference inhibition

B. competitive inhibition

C. feedback inhibition

D. active site inhibition

5. The NET output of glycolysis of 1 glucose molecule is

A. 4 ATP, 2 NADH

B. 2ATP, 2 FADH2

C. 2 ATP, 2 NADH

D. 2 ATP, 2 FADH2

6. Which of the four stages of respiration does NOT take place in mitochondria

A. pyruvate processing

B. glycolysis

C. Citric acid cycle

D. electron transport and oxidative phosphorylation

7. The citric acid cycle is a set of sequential reactions where 2 carbon atoms from Acetyl CoA (that derives from a glucose molecule) are coupled to a 4 carbon molecule. The carbon atoms from Acetyl CoA are released as CO2. Redox reactions and phosphorylation reactions are used to harvest energy in the form of ATP, NADH and FADH2. The product of these reactions is again a 4 carbon molecule that can be coupled with 2 carbon atoms from another Acetyl CoA to repeat the whole process

A. true, this is a correct description of the citric acid cycle

B. false, the citric acid cycle starts with pyruvate as substrate

C. false, the citric acid cycle employs only redox reactions

D. false, the citric acid cycle does not yield NADH

8. The net total output of energy rich molecules from respiration of a molecule of glucose after the citric acid cycle is

A. 2 ATP, 50 NADH, 4 FADH2

B. 2 ATP, 10 NADH, 2 FADH2

C. 4 ATP, 10 NADH, 2 FADH2

D. 4 ATP, 2 NADH, 10 FADH2

9. In the absence of oxygen, cellular respiration switches to fermentation. Fermentation is a set of alternative reactions to complete glycolysis and produce 2 ATP for a glucose molecule, by making sure that the following reagent is available

A. NAD (oxidized electron carrier)

B. EtOH (alcohol)

C. NADH (reduced electron carrier)

D. Acetyl CoA (substrate for citric acid cycle)

The venom of the Eastern diamondback rattler and the Indian cobra contains phospholipase A2, which catalyzes the hydrolysis of fatty acids at the C-2 position of glycerophospholipids. The phospholipid breakdown product of this reaction is lysolecithin (lecithin is phosphatidylcholine). At high concentrations, this and other lysophospholipids act as detergents, dissolving the membranes of erythrocytes and lysing the cells. Extensive hemolysis may be life-threatening.

(a) All detergents are amphipathic. What are the hydrophilic and hydrophobic portions of lysolecithin?

(b) The pain and inflammation caused by a snake bite can be treated with certain steroids. What is the basis of this treatment?

(c) Though the high levels of phospholipase A2 in venom can be deadly, this enzyme is necessary for a variety of normal metabolic processes. What are these processes?

1. Which of the following criteria is not part of the ICTV classification system?
a. genome composition d. envelope
b. particle size e. spike proteins
c. Capsid symmetry f. host range

2. A viral Capsid is comprised of
a. nucleis acids c. carbohydrates
b. proteins d. lipopolysaccharides

3. fill in the blanks
In the Baltimore classification system, there are __________ classes of DNA viruses and __________ classes of RNA viruses (enter a number for each blank)

4. Plus strand RNA is
a. the mRNA c. the template strand
b. the coding strand d. the complement of the mRNA

5. fill in the blank
Reverse Transcriptase is an enzyme that catalyzes ____________ production from a ___________ template.

4) The importance of the translational molecular machinery to insert the correct amino acid into the primary structure of a polypeptide is of paramount importance to ensure the fidelity of the code. Part of the reason why this process is so accurate is due to the action of tRNA amino-acyl synthetase (ARSs) enzymes. Mutations within the genes for ARSs, are known to because of certain human maladies, such as the neurodegenerative disorder Charcot-Marie-Tooth (CMT) disease along with other central nervous system dysfunctions, and cancer. Interestingly, not all those who possess mutations within specific ARS genes do not display the disease phenotype. Provide at least one reason why a person might survive. Remember, do not just name a concept. Describe the concept and then explain WHY (on a molecular level) this explanation holds true.

The importance of the translational molecular machinery to insert the correct amino acid into the primary structure of a polypeptide is of paramount importance to ensure the fidelity of the code. Part of the reason why this process is so accurate is due to the action of tRNA amino-acyl synthetase (ARSs) enzymes. Mutations within the genes for ARSs, are known to cause certain human maladies, such as the neurodegenerative disorder Charcot-Marie-Tooth (CMT) disease along with other central nervous system dysfunctions, and cancer. Interestingly, not all those who possess mutations within specific ARS genes do not display the disease phenotype. Provide at least one reason why a person might survive. Remember, do not just name a concept. Describe the concept and then explain WHY (on a molecular level) this explanation holds true.

which pathway is more active when the energy status of a cell is low? (Explain briefly why)

                        Gluconeogenesis

                        Glycolysis

                        Both Gluconeogenesis and Glycolysis equally active

                        Neither Gluconeogenesis nor Glycolysis will be active

1.Which of the following statements regarding the reversible binding of ligands to proteins is not true?

A) Proteins generally bind only specific ligands.

B) Sometimes, ligand binding causes conformational change of the protein.

C) In proteins composed of multiple subunits, the conformational change in one subunit can

lead to conformational change in other subunits.

D) Protein–ligand interaction can be regulated by a third molecule.

E) Proteins which have a large number of alpha helices are easier to regulate than those

composed mainly of beta sheets.

2. Which of the following proteins is used for oxygen storage?

A) myoglobin

B) ferritin
C) hemoglobin

D) antibody

E) chymotrypsin

3.Which of the following proteins is an enzyme?

A) serotonin transporter

B) cytokine

C) actin

D) chymotrypsin

E) None of the above.

4.Which force does nature use to hold a protein and its ligand together?

A) hydrogen bond interaction

B) electrostatic interaction

C) hydrophobic interaction

D) van der Waals interaction

E) All of the above.

5. Which of the following descriptions of the induced fit model is false?

A) It was proposed by Emil Fisher in 1894.

B) Conformational changes may occur in the protein upon ligand binding.

C) Conformational changes may occur in the ligand upon ligand binding.

D) It allows for tighter protein–ligand interaction compared to the lock and key model.

E) It allows for binding of different ligands.

6. Which of the following is true about the “R” state of hemoglobin?

A) It contains fewer interactions compared to the “T” state.

B) It has a higher affinity for oxygen.

C) It is more flexible compared to the “T” state.

D) It adopts the “R” state conformation when oxygen binds to the “T” state.

E) All of the above.

7. Most enzymes are proteins, but a small number of enzymes are ___________.

A) carbohydrates

B) lipids

C) deoxyribonucleic acids

D) ribonucleic acids

E) saccharides

8. Why do cells use enzymes to carry out biochemical reactions?

A) In order to regulate the reactions taking place inside the cell.

B) In order to carry out reactions without the use of organic solvents.

C) In order to minimize the production of side products.

D) In order to accelerate the rate of reactions.

E) All of the above.

9. Enzyme–substrate complex is also called the ___________?

A) Menten complex
B) enzyme–product complex

C) Michaelis complex
D) transition state complex

E) intermediate complex

10. Which of the following statements about enzymes is false?

A) Enzymes are biological catalysts.

B) Enzymes accelerate reactions by lowering the activation barrier.

C) Enzymes push the reaction equilibrium toward product formation.

D) Enzymes can denature under a highly acidic condition.

E) Enzymes carry out multiple rounds of a given chemical reaction.

11. Which of the following statements regarding enzyme inhibitors is true?

A) A reversible inhibitor typically deactivates an enzyme permanently.

B) Irreversible inhibitors are often structural analogs of substrates or products.

C) Reversible inhibitors are often used as therapeutic drugs.

D) Reversible inhibitors cannot bind to the free enzyme.

E) Potent toxins are generally reversible inhibitors.

True of False:

Vitamins and minerals are very important to health, they are absorbed without any change during digestion. (     )

The human body needs fatty acids, and it can make all but two of them—linoleic acid (the 18-carbon omega-8 fatty acid) and linolenic acid (the 18-carbon omega-3 fatty acid). (     )

Sometimes a nonessential amino acid might become essential under special circumstances. (    )

the cells of the pancreas do not make the protein hemoglobin, which is needed only by the red blood cells.                                      (     )

When nutrients enter the body from the digestive tract, the stomach receives them first; then it metabolizes, packages, stores, or ships them out for use by other tissues. ( )

Acetyl CoA can readily make fat. And glucose.                   (     )

Choose the best answer to the following questions:

Which of the following sugar is NOT a monosaccharide:          (     )    

1. Glucose (B) Fructose (C) Galactose (D)Maltose

Which of the following statement about fatty acid is WRONG:     (      )

(A) All of the energy-yielding nutrients—protein, carbohydrates, and fat—can be broken down to acetyl CoA.

(B) Acetyl CoA can enter the TCA cycle or it can make fat.

(C) In the end of Energy Metabolism, oxygen is consumed, water and carbon dioxide are produced, and energy is captured in ATP

(D) Fatty acids can be used to make glucose.

In estimating energy requirements, the DRI Committee developed equations based on research measuring total daily energy expenditure. These equations consider how the following factors influence BMR and consequently energy expenditure, which of the following is not included:                         (      )

(A)Gender. (B) Race (C)Age. (D) Physical activity.

For building fitness and minimizing the risk of overuse injuries, which of the following tip should be considered: （）

(A) Be active all week, exceptt on the weekends.

(B) Use proper equipment and wear proper attire while doing dangerous exercises.

(C) Perform exercises using proper form.

(D) Include warm-up and cool-down activities in the beginning and at the end of exercise.