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

Question 1) Microscopy. Give realistic examples for (i) standard light microscopy, (ii)

immunofluorescence microscopy, and (iii) electron microscopy on how these three distinct forms of

microscopy can be used to examine biological questions in cell and molecular biology. Indicate

limitations for these techniques, including if living cells or tissue or fixed (dead) samples are involved,

what resolution is reasonably possible (smallest object that can be seen) and if special reagents such as

antibodies are needed.

Consider the ecosytem energy required for various foods in the human diet. Describe ways to conserve ecosystem energy by incorporating principles of energy flow between trophic levels.

During cellular respiration, what happens to the 6 carbons in glucose?

5. Explain how cell division is different in prokaryotic and eukaryotic cells. Also, compare the DNA of prokaryotic and eukaryotic cell.

4. Discuss mitosis: Name all the stages of mitosis. Describe the main events that happen during each phase.

Bioinformatics:

What could be some of the reasons why your query sequence did not exactly match the sequence in the database (think of sampling, sequencing, and biological reasons).

How to draw a regulatory graph of enzyme glycogen phosphorylase with high ATP and low glucose, with axes labeled, 3 plots on the graph and labeled with given regulators and no regulator present, and plots the correct shape

.What is the mechanism of the lipase? How do you think the enzyme specifies the cleavage of the C-1 and C-3 fatty acids from TAG? (hydrophobic, stearic, hydrophilic or ... )

What are viruses composed of? How do they differ from cellular life? What is their basic life cycle? Describe lytic and lysogenic cycles in bacteriophages. What are three hypotheses about how viruses originated?