BIO 315 - Exam 1

Mismatch repair

a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage

electron microscopy (EM)

a technique for obtaining high resolution images of biological and non-biological specimens; three types: transmission electron microscope (TEM), scanning electron microscope (SEM), and reflection electron microscope (REM.)

Immunoelectron microscopy

a technique to visualize the locations (localization) of specific proteins with a TEM (diagnosis of viral infections)

Ion exchange chromatography

separates ions and polar molecules based on their affinity to the ion exchanger

Nucleotide excision repair

the main pathway used by mammals to remove bulky DNA lesions such as those formed by UV light, environmental mutagens, and some cancer chemotherapeutic adducts from DNA

Proline

the only amino acid where the side chain is connected to the protein backbone twice, forming a five-membered nitrogen-containing ring

bright-field microscopy

the simplest optical microscopy- illumination light is transmitted through the sample and the contrast is generated by the absorption of light in dense areas of the specimen.

RFC

used in eukaryotic replication as a clamp loader, similar to the γ Complex in Escherichia coli; its role as clamp loader involves catalysing the loading of PCNA onto DNA

1. Glucose 1-phosphate ⟶⟶ Glucose 6-phosphate ΔG° = -1.7 kcal/mole 4. Glucose ⟶⟶ CO2 + H2O ΔG° = -686 kcal/mole

ΔG° indicates the change in the standard free energy as a reactant is converted to product. Given what you know about these values, which reaction below is energetically favorable, i.e. spontaneous? Choose all that apply. 1. Glucose 1-phosphate ⟶⟶ Glucose 6-phosphate ΔG° = -1.7 kcal/mole 2. Glucose + Fructose ⟶⟶ Sucrose ΔG° = +5.5 kcal/mole 3. ADP + Pi ⟶⟶ATP ΔG° = +7.3 kcal/mole 4. Glucose ⟶⟶ CO2 + H2O ΔG° = -686 kcal/mole

RPA

interacts with ssDNA and with protein partners to coordinate DNA replication, repair, and recombination.

γ-clamp loader

protein adds the ββ-clamp to newly primed DNA on the lagging strand so that DNA polymerase III can begin synthesis of the next Okazaki fragment

KM/Vmax

slope of Lineweaver-Burk plot

DNA fingerprinting

the analysis of DNA from samples of body tissues or fluids, especially when conducted in order to identify individuals

Coenzyme, Cofactor

Vitamins are an example of a ______. The iron atom of a heme group is an example of a ______.

SSB (single stranded DNA binding protein)

form the central nucleoprotein complex substrate for DNA replication, recombination, and repair processes.

PCR

(polymerase chain reaction)It's a test to detect genetic material from a specific organism, such as a virus

Topoisomerase

A class of enzymes that alter the supercoiling of double-stranded DNA

5. 5' to 3' exonuclease activity

Bacterial DNA polymerase I exhibits what type of activity that is lacking in DNA polymerase III? 1. 3' to 5' exonuclease activity 2. 5' to 3' polymerase activity, 5' to 3' exonuclease activity and 3' to 5' exonuclease activity 3. 5' to 3' polymerase activity and 5' to 3' exonuclease activity 4. 5' to 3' polymerase activity 5. 5' to 3' exonuclease activity

-1/x-intercept

Calculate the corresponding KM for the uninhibited enzyme.

1/y-intercept

Calculate the corresponding Vmax for the uninhibited enzyme.

1.The amino acid proline can readily be found in αα-helices and ββ -pleated sheets.

Concerning the chemistry of molecules, which of the following statements is false? 1.The amino acid proline can readily be found in αα-helices and ββ -pleated sheets. 2.DNA associating proteins, like histones, would be expected to contain a higher content of the amino acids lysine and arginine compared to cytoplasmic proteins. 3.The energy to break hydrogen bonds, in terms of kcal/mol, is greater than the energy needed to overcome Van der Waals forces. 4.Hydrogen bonds can be established between the side chain of asparagine (or glutamine) and water.

Shadow casting

Deposition of a film of carbon or certain metals such as palladium, platinum, or chromium on a contoured microscopic object in order to allow the object to be seen in relief with the electron microscope or sometimes with the light microscope

3. PCNA

During eukaryotic DNA replication, CAF-1 mediates the immediate histone packaging of DNA based on its interaction with which protein in the replication complex? 1. Topoisomerase 2. Fen-1 3. PCNA 4. RFC 5. RPA

1. α

During eukaryotic DNA replication, which DNA polymerase is found in the primase complex and helps synthesis primers needed for replication of the lagging strand? 1. α 2. δ 3. β 4. η 5. ϵ

1. Induced strain

Enzyme catalysis mechanism that utilizes a change in the conformation of the substrate to bring it closer to the conformation of the transition state. 1. Induced strain 2. Changing Substrate Reactivity 3. Substrate Orientation

4. 0.125

Given the Lineweaver-Burk plot, for the uninhibited enzyme you have the following values: X-intercept of -8 and Y-intercept of 0.2. Calculate the corresponding KM for the uninhibited enzyme. 1. -0.222 2. 0.222 3. -0.125 4. 0.125 5. 0.25

5. 5

Given the Lineweaver-Burk plot, for the uninhibited enzyme you have the following values: X-intercept of -8 and Y-intercept of 0.2. Calculate the corresponding Vmax for the uninhibited enzyme. 1. 2 2. 4 3. 1 4. 0.2 5. 5

Ion exchange chromatography; gel filtration chromatography

If you wanted to do a two-step protein purification, (sequentially using two columns) based first on charge and then on size, you would do __________ followed by __________.

5. Methylation of parental DNA strand

In bacteria, post-replicative mismatch repair of incorrectly added nucleotides after DNA replication is dependent on the detection of which of the following? 1. Acetylation of parental DNA strand 2. Acetylation of daughter DNA strand 3. Methylation of histones 4. Methylation of daughter DNA strand 5. Methylation of parental DNA strand

1. Lays down an RNA primer needed for replication

In bacterial replication, what is the function of primase? 1. Lays down an RNA primer needed for replication 2. Unwinds DNA double helix 3. Relieves tension in DNA through generation of positive supercoiling 4. Lays down a DNA primer needed for replication 5. Relieves tension in DNA through generation of negative supercoiling

Decreasing wavelength; increasing the numerical aperture

In bright-field microscopy, which of the following will increase the resolution (i.e. smaller value for d) of your compound microscope?

1. Homologous recombination

In mammalian cells, high energy sources can induce double stranded breaks in the DNA duplex to stimulate repair. Which of the following repair mechanisms would ensure the greatest chance of not introducing mutations at the repair site? 1. Homologous recombination 2. Mismatch repair 3. Base excision repair 4. Nucleotide excision repair 5. Non-homologous end joining

5. Non-homologous end joining

In mammalian cells, what double-stranded DNA break repair mechanism relies on the activity of Ku proteins, DNA-PKCS, and DNA ligase? 1. Nucleotide excision repair 2. Base excision repair 3. Homologous recombination 4. Mismatch repair 5. Non-homologous end joining

4. Nucleotides of a DNA strand are linked by 3',5'-phosphodiester bonds

In terms of DNA structure and composition, which of the following is true? 1. Pyrimidines are A and T 2. C and G pair with 2 hydrogen bonds 3. Bases are found on the outside of the DNA helix 4. Nucleotides of a DNA strand are linked by 3',5'-phosphodiester bonds 5. DNA strands of the double helix run parallel to each other

Fluorescent in situ hybridization

Methodology used to locate the position of a gene or sequence along a chromosome.

5. Fluorescent in situ hybridization

Methodology used to locate the position of a gene or sequence along a chromosome. 1. DNA fingerprinting 2. Southern blot 3. Electron microscopy 4. Pulse-chase 5. Fluorescent in situ hybridization

Fen-1

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair

Cysteine

The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile

2. γγ-clamp loader

What protein adds the ββ-clamp to newly primed DNA on the lagging strand so that DNA polymerase III can begin synthesis of the next Okazaki fragment? 1. Primase 2. γγ-clamp loader 3. Helicase 4. SSB 5. ββ-clamp loader

All 3' ends of lagging strands

Where would DNA polymerase III be able to add nucleotides in the growing DNA strands during DNA replication, as illustrated in the accompanying figure for bacterial DNA replication?

2.Proline

Which of the following amino acids would be expected to be found at the end of αα-helices and ββ-sheets, due to their kinked conformation that prevents them from participating in these types of secondary structures? 1.Cysteine 2.Proline 3.Phenylalanine 4.Alanine 5.Tryptophan

1. The melting temperature of DNA increases as its GC content increases

Which of the following statements concerning DNA is true? 1. The melting temperature of DNA increases as its GC content increases 2. Large structural changes in the human genome are more common than single nucleotide changes. 3. Type I topoisomerases make a nick in both strands of the DNA helix. 4. Most proteins interact with DNA along its minor groove. 5. Packaging of DNA into the nucleus is dependent upon positive supercoiling.

5.The resolution of the best light microscopes is better than that of electron microscopes

Which of the following statements concerning electron microscopy (EM) is NOT true? 1.Shadow casting can be used for viruses or bacteria to get a 3D image of their surfaces 2.Transmission electron microscopy relies on electromagnets to focus the electron beam 3.Immunoelectron microscopy uses gold-labelled antibodies to help localize a protein in a sample 4.Scanning electron microscopy forms images from electrons bouncing off the specimen surface 5.The resolution of the best light microscopes is better than that of electron microscopes

3.Genomic libraries can be used to examine differences in tissue/organ-specific gene expression.

Which of the following statements concerning molecular techniques is NOT correct? 1.Western blotting uses antibodies to characterize proteins. 2.PCR uses small amounts of starting template in order to amplify a specific DNA sequence. 3.Genomic libraries can be used to examine differences in tissue/organ-specific gene expression. 4.Southern blotting involves the analysis of DNA. 5.Northern blotting is associated with the analysis of RNA

3. Enzymes lower the free energy released by the reaction that they facilitate.

Which of the following statements is false? 1. Enzymes may require the presence of coenzymes or cofactors to function. 2. Enzymes lower the activation energy for a specific reaction. 3. Enzymes lower the free energy released by the reaction that they facilitate. 4. Enzymes have an optimum pH and temperature for maximum activity. 5. Enzyme specificity in substrate processing relies on complementary structures that form between enzyme and substrate at the active site.

2. N - serine - threonine - tyrosine - C

Which of the following tripeptides would be able to undergo post-translational modification? 1. N - glutamine - asparagine - proline - C 2. N - serine - threonine - tyrosine - C 3. N - tryptophan - phenylalanine - leucine - C 4. N - arginine - valine - histidine - C 5. N - glutamic acid - aspartic acid - glycine - C

5. Transposons have an RNA intermediate and require reverse transcriptase.

With respect to genome structure and stability, all of the following statements are true except: 1. Genome complexity in terms of size can be determined from DNA renaturation. 2. Gene families are represented in the non-repeated fraction of eukaryotic DNA. 3. The most common type of genetic variability in humans is from single nucleotide differences. 4. Movement of transposons require the enzyme transposase. 5. Transposons have an RNA intermediate and require reverse transcriptase.

4.Fibrous proteins tend to have a lot of αα-helical structure, whereas globular proteins tend to have predominantly ββ-pleated sheet structure.

With respect to protein structure, which of the following statements is false? 1.Protein folding in the cell is assisted by special proteins called chaperones whose function requires energy provided by ATP. 2.A protein can have more than one domain. 3.Formation of secondary structures is not dependent upon the amino acid side chains to generate hydrogen bonds. 4.Fibrous proteins tend to have a lot of αα-helical structure, whereas globular proteins tend to have predominantly ββ-pleated sheet structure. 5.The information needed to generate the secondary and tertiary of a protein is directed by the protein's primary structure.

3. Double-stranded genomes have equal amounts of A and T

You are a virologist interested in studying the evolution of viral genomes. You are studying two newly isolated viral strains and have sequenced their genomes. You find that the genome of strain 1 contains 25% A, 45% G, 20% C, and 10% T. You report that you have isolated a virus with a single-stranded DNA genome. Based on what evidence can you make this conclusion? 1. Using the formula: G - A = C + T 2. Single-stranded genomes have a higher rate of mutation 3. Double-stranded genomes have equal amounts of A and T 4. Single-stranded genomes always have a low percentage of Ts 5. Single-stranded genomes always have a large percentage of purines

Non-homologous end joining

a pathway that repairs double-strand breaks in DNA

Affinity chromatography

a separation method based on a specific binding interaction between an immobilized ligand and its binding partner

1.The specific location within the cell of the protein encoded by this gene

You create a recombinant DNA molecule that fuses the coding sequence of green fluorescent protein to the regulatory DNA sequences that control the expression of your favorite gene. Which of the following pieces of information can you NOT gain by examining the expression of this reporter gene? 1.The specific location within the cell of the protein encoded by this gene 2.The cell in which the protein encoded by this gene is expressed 3.When, during an organism's development, this gene is expressed 4.The tissue where the protein encoded by this gene is expressed

1. It will be more likely to generate mismatched base pairs.

You have discovered an "Exo-" mutant form of DNA polymerase in which the 3′-to-5′ exonuclease function has been destroyed but the ability to join nucleotides together is unchanged. Which of the following properties do you expect the mutant polymerase to have? 1. It will be more likely to generate mismatched base pairs. 2. It will fall off the template more frequently than the normal Exo+ polymerase. 3. It will polymerize in both the 5′-to-3′ direction and the 3′-to-5′ direction. 4. It will polymerize more slowly than the normal Exo+ polymerase. 5. It will polymerize in both the 5′-to-3′ direction and the 3′-to-5′ direction and will polymerize more slowly than the normal Exo+ polymerase.

Genomic libraries

a collection of the total genomic DNA from a single organism

Southern blotting

a laboratory method used to detect specific DNA molecules from among a many other DNA molecules

Northern blotting

a laboratory method used to detect specific RNA molecules among a mixture of RNA

Western blotting

a laboratory method used to detect specific protein molecules from among a mixture of proteins

Pulse-chase

a method for examining a cellular process occurring over time by successively exposing the cells to a labeled compound and then to the same compound in an unlabeled form

gel filtration chromatography

a method that separates molecules according to their size and shape

Cofactor

a non-protein chemical compound or metallic ion that is required for an enzyme's activity as a catalyst

Scanning electron microscopy

a type of electron microscope that produces images of a sample by scanning the surface with a focused beam of electrons that interact with atoms in the sample, producing various signals that contain information about the surface topography and composition of the sample

Homologous recombination

a type of genetic recombination that occurs during meiosis (the formation of egg and sperm cells) in whcih paired chromosomes from the male and female parent align so that similar DNA sequences from the paired chromosomes cross over each other

Primase

an enzyme that synthesizes short RNA sequences called primers; these primers serve as a starting point for DNA synthesis

Phenylalanine

an essential amino acid that is used to produce proteins and signaling molecules

Coenzymes

an organic molecule that binds to the active sites of certain enzymes to assist in the catalysis of a reaction

Alanine

an α-amino acid that is used in the biosynthesis of proteins

Base excision repair

corrects small base lesions that do not significantly distort the DNA helix structure

Helicase

enzymes that bind and may even remodel nucleic acid or nucleic acid protein complexes

β-clamp loader

loaded on the DNA, by clamp loader, a subunit of DNA Pol III. It interacts with several proteins other than DNA polymerase III subunits; it also freely slides along DNA and improves the processivity of other proteins

Transmission electron microscopy

microscopes that use a particle beam of electrons to visualize specimens and generate a highly-magnified image

Tryptophan

needed for normal growth in infants and for the production and maintenance of the body's proteins, muscles, enzymes, and neurotransmitters