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Foren Biochem Exam 2
| Question | Answer |
|---|---|
| origin of the term carbohydrate | Carbohydrates were originally regarded as hydrates of carbon because the empirical formula of many of them is CH2O |
| What are lipids | Lipids are water-insoluble molecules that are highly soluble in organic solvents. |
| Triacylglycerols are used for fuel storage in both plants and animals. The triacylglycerols from plants are often liquid at room temperature, whereas those from animals are solid. Suggest some chemical reasons for this difference. | Triacylglycerols from plants may have many cis double bonds or have shorter fatty acid chains than those from animals. |
| Distinguish between phosphoglycerides and triacylglycerols | Triacylglycerols = 3FA chains with a glycerol backbone & are storage form of fuel. Phosphoglycerides= 2 FA chains attached to a glycerol backbone. remaining alcohol of glycerol is bonded to a phosphate, & bonded to an alcohol & membrane components |
| Differentiate between a nucleoside and a nucleotide | A nucleoside is a base attached to a ribose sugar. A nucleotide is a nucleoside with one or more phosphoryl groups attached to the ribose. |
| What is a Watson–Crick base pair? | Hydrogen-bond pairing between the base A and the base T as well as hydrogen-bond pairing between the base G and the base C in DNA. |
| Why are GC and AT the only base pairs permissible in the double helix? | Two purines are too large to fit inside the double helix, and two pyrimidines are too small to form base pairs with each other |
| Write the complementary sequence (in the standard 5′ n 3′ notation) for GATCAA | TTGATC |
| Write the complementary sequence (in the standard 5′ n 3′ notation) for TCGAAC | GTTCGA |
| Write the complementary sequence (in the standard 5′ n 3′ notation) for ACGCGT | ACGCGT |
| Write the complementary sequence (in the standard 5′ n 3′ notation) for TACCAT | ATGGTA |
| Define template and primer as they relate to DNA synthesis | A template is the sequence of DNA or RNA that directs the synthesis of a complementary sequence. A primer is the initial segment of a polymer that is to be extended on which elongation depends |
| Explain why DNA synthesis depends on RNA synthesis | DNA polymerase cannot initiate primer synthesis. Consequently, an RNA polymerase, called primase, synthesizes a short sequence of RNA that is used as a primer by the DNA polymerase |
| What is an Okazaki fragment? | Okazaki fragments are short segments of DNA that are synthesized on the lagging stand of DNA. These fragments are subsequently joined by DNA ligase to form a continuous segment of DNA |
| Distinguish between the leading and the lagging strands in DNA synthesis | When DNA is being synthesized at the replication fork, the leading strand is synthesized continuously in the 5′-to-3′ direction as the template is read in the 3′-to-5′ direction. The lagging strand is synthesized as short Okazaki fragments. |
| Explain, on the basis of nucleotide structure, why DNA synthesis proceeds in the 5′-to-3 direction | The nucleotides used for DNA synthesis have the triphosphate attached to the 5′-hydroxyl group with free 3′-hydroxyl groups. Such nucleotides can be utilized only for 5′-to-3′ DNA synthesis |
| For long double-stranded DNA molecules, the rate of spontaneous strand separation is negligibly low under physiological conditions despite the fact that only weak reversible bonds hold the strands together. Explain. | rate of strand separation is low owing to the hydrogen bonds of helix and stacking forces between bases. Although individually weak, the thousands or millions of such bonds that hold a helix together make spontaneous separation of the strands unlikely. |
| Would there be advantages to direct sample testing without DNA extraction | Faster results, lower costs and reduced risk of contamination preserves more DNA from limited or degraded samples |
| Why are PCR inhibitors problematic | interfere with DNA amplification process, leading to inaccurate results like false negatives and PCR failure |
| What is the purpose of DTT in an extraction procedure | acts as a reducing agent that breaks disulfide bonds in proteins helps to denature proteins, release nucleic acids like DNA from their protective proteins and inactivate enzymes like RNase |
| Describe some situations where differential extraction will be able to help separate mixture components in a sexual assault case | vaginal swabs to get both victim's epithelial cells and perpetrator's sperm |
| How are hair and bone DNA extraction more challenging than blood or saliva | hair has very little nuclear DNA outside the root and contains degraded DNA bones are more dense and are time consuming to pulverize |
| What problems might exist with having quantitation assays that are less sensitive than downstream DNA testing methods | higher rate of failed downstream analysis, inaccurate results due to insufficient starting matier, and incorrect interpretations of sample quality |
| How can reliable DNA quantitation aid decisions in terms of what route to proceed with | prevents wasting effort and time on poor samples, and helps determine the next steps on if a full analysis can be preformed or if they should find more evidence. |
| What is the optimal quantity of DNA for most commercial STR kits? What is the effect of too much or too little DNA being amplified | 0.5 to 2 ng Too little DNA can lead to stochastic effects like allele drop-out and imbalance leading to incomplete profiles Too much DNA can inhibit PCR, false priming and biased results from DNA clumping |
| What challenges exist with designing multiplex PCR primers | Similar melting temperatures, avoiding primer interactions, specificity, competition for reagents |
| What are the advantages of a thermal stable, hot-start DNA polymerase | reduced non-specific amplification and primer-dimers and increased specificity, sensitivity and yield easier to complete reactions at room temperature with out affecting results |
| Why is it important to separate pre-PCR and post-PCR processes | to prevent contamination from amplified DNA could lead to false positive results |
| What is the purpose of a negative amplification control? positive amplification control? | negative amplification control detects contamination by omitting necessary components, like template DNA, to ensure no signal is generated from external sources positive amplification control confirms the process is working correctly |
| What are some effective means to prevent contamination | Hand and personal hygiene, proper cleaning procedures, physical controls, food safety |
| What are some effective means to clean up following a contamination event | contain spill, clean and decontaminate, dispose of waste properly, report incident |
| What are "stochastic effects" and why are they important to forensic DNA analysis | random, chance-based variations that occur during analysis can lead to unreliable results, such as the loss of an allele or appearance of an extra allele |
| Why are tetranucleotide repeat loci preferred over dinucleotide repeat loci in forensic testing | they produce less "stutter" during PCR, making clearer and more distinct allele peaks that are easier to interpret |
| What two innovations are used in the identifiler kit to enable 16 loci to be simultaneously amplified and detected in a single reaction | 5-dye fluorescent system and use of non-nucleotide linkers |
| Why is it valuable to include the sex-typing marker amelogenin in STR typing kits | provides a quick and cost-effective way to determine the sex of an individual |
| What is electro-osmotic flow and how does it impact DNA separations in a capillary | bulk movement of liquid through charged capillary when electric field is applied, caused by migration of counter-ions in electrical double layer helps move all charged DNA fragments toward detector |
| What component of a PCR reaction is labeled with a fluorescent dye to enable detection of amplified STR alleles | the primer |
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Kayla_K