Term
| Cis- vs. trans- fatty acids represent what class of isomerization? |
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Definition
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Term
| 2. (8) What is an INDEL? Under what circumstance would it NOT result in a frameshift? |
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Definition
| This is an insertion or deletion (when you compare two sequences you can’t tell whether one has had an insertion or the other a deletion). It would not create a frameshift were it not in a coding sequence, or if the insertion is of a full three-base codon, or some multiple of three bases. |
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Term
| 3. (8) What is the name of the bond that links each of the following monomers when forming polymers: |
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Definition
Nucleic acids: phosphodiester bond
Monosaccharides: glycosidic linkage |
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Term
| 4. (5) The amino acid cysteine contains a sulfhydryl. What is the physiological relevance of this functional group and how might this affect a protein containing cysteines? |
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Definition
| Sylfhydrils can form disulfide bonds, linking the two sulfurs with a covalent linkage. This can link distant parts of a polypeptide to help form tertiary structure, or link different polypeptides to form quaternary structure. |
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Term
| 5. (5) According to Chargaff’s rules, if the DNA of a thermophilic bacterium consists of 12% A, what proportion of the DNA will be cytosine? |
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Definition
| If 12% is A, then 12% would be T. Since total pyrimidines equal 50%, then C must be 38%. (alternatively, if A + T is 24%, G + C must be 76%, and C would be ½ that). |
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Term
| 6. (5) How, precisely, does an RNA nucleotide differ from a DNA nucleotide? |
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Definition
| An RNA nucleotide has a hydroxyl group at the 2’ position of the ribose sugar. A DNA nucleotide, based on deoxyribose sugar, is missing the 2’ hydroxyl. |
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Term
| 7. (13) Describe, in detail, the structure of DNA, including that of the individual monomers, their linkages, and the higher-order arrangement of the macromolecule. |
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Definition
| DNA is a polymer of deoxyribonucleotides, each of which monomers is made up of a nitrogenous base, a deoxyribose sugar, and a phosphate. Sequential bases are joined through a 5’ to 3’ phosphodiester bonds. The DNA molecule is a double right-handed helix, with the two strands running antiparallel (one 5’ to 3’, the other 3’ to 5’) with the sugar and phosphates pointing out and the bases pointed inward and interacting via hydrogen bonds to the bases of the other strand, with G interacting with C, and A with T. |
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Term
| 8. (5) An individual codon will move through each of the three sites of the ribosome. In which order will it occupy each of the three sites? |
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Definition
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Term
| 9. (10) What enzyme ‘cleans up’ the 5’ end of an Okazaki fragment in prokaryotes? What does this clean-up entail? |
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Definition
| DNA Pol I removes the RNA primer from the 5’ end of the Okazaki fragment, removing one base at a time and replacing them with deoxyribonucleotides. (Ligase will then seal the remaining gap.) |
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Term
| 10. (16) Name, describe and, where relevant, give examples of each level of protein structure. Indicate the types of intra- and/or inter-molecular bonds that contribute to these levels of structure. (Note: simply giving examples is an insufficient description.) |
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Definition
Primary structure is the linear order of amino acids in a polypeptide, joined through peptide bonds.
Secondary structure refers to the localized three-dimensional structures that form through the hydrogen bonding between carboxyl and amino groups on the backbone, forming alpha helices or beta sheets.
Tertiary structure represents the overall three-dimensional structure or a single polypeptide. This arises from the interactions among the side chains of the amino acids, via ionic bonds, hydrogen bonds, disulfide covalent bonds, and hydrophobic interactions.
Quaternary structure refers to the overall structure formed from interactions between two or more polypeptides. The types of bonds are the same as those in the tertiary structure. |
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Term
| 11. (12) Explain how the difference in chromosomal structure affects the process of DNA replication in eukaryotes, as compared to prokaryotes? |
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Definition
Prokaryotes have a relatively small circular chromosome. They start replicating at a single origin of replication and synthesize DNA bidirectionally until they meet up at the opposite side of the circle.
The much larger linear eukaryotic chromosomes have multiple origins of replication along each chromosome, and they replicate bidirectionally until they meet up with a replication fork coming from another origin. At the ends, they require a special structure, a telomere, to prevent the progressive loss that would result from removal of the RNA primer from the end after each round of replication. |
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Term
| 12. (10) DNA replication is said to be semi-conservative. What does this mean? How was this demonstrated? |
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Definition
| This means that the original DNA strands are separated, and each serves as template for a new strand, producing two daughter molecules, each of which has one old and one new strand. This was determined by labeling ‘old’ DNA with heavy nitrogen, transferring it to a normal nitrogen broth to make the new strands ‘light’, and using the relative densities of the strands to deduce their content of old versus new DNA. |
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Term
| 13. (3) Open chromatin, available for transcription, is called (euchromatin/heterochromatin). |
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Definition
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Term
14. (18) Describe the modification is made to the 3’ end of a pre-mRNA in eukaryotes?
What monomer is used for this modification?
What is the energy source for this modification?
Where in the cell does this occur? |
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Definition
This is polyadenylation, the addition of a stretch of As not encoded by the template.
ATP
ATP
Nucleus |
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Term
| 15. (5) What are enantiomers? |
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Definition
| These are isomers that represent a mirror image of each other. |
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Term
16. (8) In the presence of lactose and absence of glucose, which of the following is happening? (Yes/No)
Lac I is binding to the operator.
cAMP is bonding to CAP.
Allolactose is being produced.
High-level transcription is taking place. |
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Definition
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Term
Given the following template strand of DNA, answer the following questions, using the standard notation:
5’-GAATTCATGATACAGGCATGACC-3
(3) In which direction would RNA polymerase move along this template (left-to-right or right-to-left)? |
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Definition
| Right to left (the strands are antiparallel and DNA is made 5’ to 3’, so it must start on the 3’ side of the template) |
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Term
Given the following template strand of DNA, answer the following questions, using the standard notation:
5’-GAATTCATGATACAGGCATGACC-3
(6) What will be the sequence of the mRNA produced? |
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Definition
| 5’ – GGUCAUGCCUGUAUCAUGAAUUC – 3’ |
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Term
Given the following template strand of DNA, answer the following questions, using the standard notation:
5’-GAATTCATGATACAGGCATGACC-3
(6) What will be the sequence of the protein that can be made using the information from the mRNA? (label the ends to specify amino acid orientation) |
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Definition
N-Met Pro Val Ser-C
5’ – GGUC AUG CCU GUA UCA UGA AUUC – 3’
Start Stop |
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