24. Put the following events in chronological order (oldest to most recent):

(1) Gorilla and Pan share a common ancestor.

(2) Homo and Pan share a common ancestor.

(3) hominins become bipedal.

(4) the onset of the Pleistocene epoch

a.   1,3,2,4

b.   1,2,3,4

c.    2,1,3,4

d.    2,1,4,3

e.   None of the above.

What are some of ways that allow coral reef and antarctic reef fishes to maintain a similar "pace of life"?

We talked about HLA genes in autoimmune diseases. However, HLA typing is also important in immunity with respect to organ and blood matching. Discuss the genetics of HLA typing. If genetic matches are best found among close relatives, how is it possible that matches for organs can be found in unrelated individuals?

Describe (i) how the process of molecular evolution generates protein

families, and (ii) how the amino acid sequence alignments based on sequence similarities for such

members of a protein family can be used to identify conserved regions of a protein and construct a

phylogenetic tree of such members of a protein family. (iii) Will amino acids at the active site of an

enzyme tend to be conserved in a protein family? Why?

A genetic defect in coagulation factor IX causes hemophilia b, a disease characterized by a tendency to bleed profusely after very minor trauma. However, a genetic defect in coagulation factor XI has only mild clinical symptoms. Explain this discrepancy in terms of the mechanism for activation of coagulation protease.

What is it about protein enzymes that confers upon them their specificity?

Farmers and foresters often inoculate seeds with fungal spores to promote plant growth and development. Based on what you have learned about fungi and plant nutrition, explain the rationales behind the seed treatment.

1. A ship carrying 2,000 passengers sets sail for an island with a population of 23,000. Both of these populations consist of an equal number of males and females.

21 male passengers on the ship have an X-linked recessive condition. 15 of the male island inhabitants have the same condition, and no females on the ship or the island show the phenotype.

1. The ship docks, and a woman from the island falls pregnant to an unaffected man from the ship. What are the chances their first son will be affected with the condition?

2. An affected man from the island and a woman from the ship have a girl. What is the daughter’s chance of being a carrier?

3. What is the daughter’s chance of being affected?

Please do not forget to write down all the names of your group members.

1. Please propose the mechanism for α−β C-C bond cleavage of G6P. Draw the mechanism clearly, give the structures of the product, and then explain why steps 2 and 3 of glycolysis are necessary.

2. If glucose is labeled at C1 carbon (the C1 carbon is tagged with radioactive 14C), where would this labeled C atom be (which carbon atom number, draw the structure and label this carbon atom) when glucose has been metabolized to:

A. DHAP

B. GAP (you should be able to figure which carbon atom is the original C1 if you draw the mechanism of step 5)

C. After the reaction with G6PD enzyme (first step in pentose phosphate pathway)

D. After the oxidative decarboxylation step in PPP

E. How many % of the total pyruvate produced via glycolysis will carry this label?

3. A. What would be the fate of glucose in cells that need ATP, but not NADPH and R5P?

B. How about cells that need a lot of NADPH, but not R5P?

C. Finally, what would be the fate of glucose if the cells need a lot of R5P, but not NADPH?

Here are some hints to help you answer Q3.

1) Remember that the reactions in PPP (with the exception of the 3 in oxidative phase) are FULLY reversible.

2) Remember that glycolysis and PPP are linked by the common metabolites: F6P and GAP.

3) Although the stoichiometry of the reactions shown in class is different: glycolysis starts from 1 glucose molecule and PPP needs 3 G6P. In reality, our cells will always have more than 1 glucose molecule. 180 g of glucose (4.5 cans of soft drink) is 6.022 x 1023 molecules of glucose. Bottom line: to answer Q3, please do not worry about stoichiometry and whether there is enough glucose in the cells or not. There is truly plenty of glucose to go to any pathways as needed.

UPDATE: Question 2 refers to question 1

Sliding clamps are loaded onto DNA by clamp loaders to serve the critical role of coordinating various enzymes on DNA. Clamp loaders must quickly and efficiently load clamps at primer/template (p/t) junctions containing a duplex region with a free 3′OH (3′DNA), but it is unclear how clamp loaders target these sites. To measure the Escherichia coli and Saccharomyces cerevisiae clamp loader specificity toward 3′DNA, fluorescent β and PCNA clamps were used to measure clamp closing triggered by DNA substrates of differing polarity, testing the role of both the 5′phosphate (5′P) and the presence of single-stranded binding proteins (SSBs). SSBs inhibit clamp loading by both clamp loaders on the incorrect polarity of DNA (5′DNA). The 5′P groups contribute selectivity to differing degrees for the two clamp loaders, suggesting variations in the mechanism by which clamp loaders target 3′DNA. Interestingly, the χ subunit of the E. coli clamp loader is not required for SSB to inhibit clamp loading on phosphorylated 5′DNA, showing that χ·SSB interactions are dispensable. These studies highlight a common role for SSBs in directing clamp loaders to 3′DNA, as well as uncover nuances in the mechanisms by which SSBs perform this vital role.”

https://academic.oup.com/nar/article/42/16/10655/2903350

(5 points) What is a sliding clamp and what is its function?

(5 points) What is a sliding clamp loader and how does it aid in the function of the sliding clamp?

(5 points) What is the significance of a recessed 3’-end DNA, during the p/t discrimination? What data and figure from the NAR paper, suggest this significance?

(5 points) What do you think would happen if the sliding clamp could not differentiate between 3’-OH and 5’-P ends of DNA? How would this effect DNA replication?

Describe the principles of diffusion and osmosis across cell membranes and how organisms maintain an optimal internal fluid environment. Can you please talk about:

a. the mechanisms by which freshwater paramecia rid their bodies of excess water

b. how invertebrates maintain osmotic balance and waste removal using four invertebrate types as examples: flatworms, annelid

worms, insects, and hemichordates

c. the general mechanisms of salt balance and metabolic waste removal in the kidney of a terrestrial vertebrate

d. a description of the special functions of the "multiplier effect" of mammalian kidneys and of the hormone ADH in regulating

salt and water balance

Linda is a half marathon runner. She read an article in a runner’s magazine promoting a new sports beverage that contains protein. She has always used a traditional carbohydrate-rich sports beverage, and has had great results. However, she wonders if this new product would work even better and help her run faster.
Would this new sports beverage containing protein work well for Linda?
        
How much protein should Linda be consuming before and during a half marathon?

Immunoassays can use polyclonal or monoclonal antibody preparations.

a) How do polyclonal antibodies differ from monoclonal antibodies?
(Marks: 2)
b) Describe one immunoassay that requires the use of polyclonal antibodies.
(Marks: 4)
c) Describe one immunoassay that requires the use of monoclonal antibodies.
(Marks: 4)

Kara is a 14-year-old, 125-pound, high school basketball player. She has been feeling fatigued and sore lately, and has been sick three separate times in the last 3–4 months. Kara typically eats the following on a daily basis:
7 AM: 10–12 oz orange juice (at home before school)
11:30 AM: 2 cups macaroni and cheese, and a small fruit cup (lunch in school cafeteria)
3 PM: granola bar (before basketball practice)
7 PM: 2–3 cups spaghetti with tomato sauce, 1 piece garlic bread, 10 oz skim milk (at home after practice)
10 PM: 2 cups ice cream (bedtime snack)
Why is Kara feeling fatigued, sore and sick? What dietary recommendations would you give to Kara? Please be specific with your recommendation, especially regarding protein intake