BIOL 300 - Exam 1 Study Guide Questions

1. c 2. d 3. e 4. b 5. a

2. Match the enzymes used in DNA replication (1-5) with their functions or descriptions. a. binds to single-stranded DNA, preventing base pairs from re-forming before lagging strand is replicated b. opens the DNA double helix ahead of the replication fork c. catalyzes the addition of nucleotides to the 3′ end of DNA strand d. RNA polymerase that synthesizes RNA primers e. uses energy of ATP hydrolysis to join Okazaki fragments 1. DNA polymerase 2. primase 3. ligase 4. DNA helicase 5. single-stranded DNA-binding protein

True

A large number of noncovalent interactions is required to hold two regions of a polypeptide chain together in a stable conformation. True or false?

False

A single polypeptide tends to adopt three or four different conformations, which all have equivalent free-energy values (G). True or false?

False

After damaged DNA has been repaired, nicks in the phosphate backbone are maintained to identify the strand that was repaired. True or false?

False

All functional DNA sequences inside a cell code for protein products. True or false?

False

Antibodies are Y-shaped and are composed of six different polypeptide chains. True or false?

1. c 2. c 3. c 4. c 5. a 6. b 7. b 8. c 9. b

Because all DNA polymerases synthesize DNA in the 5′-to-3′ direction, and the parent strands are antiparallel, DNA replication is accomplished with the use of two mechanisms: continuous and discontinuous replication. Indicate whether the following items (1-9) relate to (A) continuous replication, (B) discontinuous replication, or (C) both modes of replication. a. continuous replication b. discontinuous replication c. both modes of replication 1. primase 2. single-strand binding protein 3. sliding clamp 4. RNA primers 5. leading strand 6. lagging strand 7. Okazaki fragments 8. DNA helicase 9. DNA ligase

True

Chromosomes exists at different levels of condensation, depending on the stages of the cell cycle. True or false?

False

Chromosomes of different length emit different wavelengths of light, making them appear colored under the microscope. True or false?

False

Comparing the relative number of chromosome pairs is a good way to determine whether two species are closely related. True or false?

As the helicase opens the double helix and moves forward, the replication fork gets wound more tightly. This can cause excess twisting in front of the replication fork and create tension in the DNA, which could cause the unwinding of the double helix to become increasingly difficult and negatively impact the forward movement of the replication machinery. Enzymes called DNA topoisomerases help relieve this tension by producing a single-strand break in the DNA backbone that releases the built-up tension. The enzyme will then reseal the nick before falling off the DNA.

DNA helicase has an essential role in DNA replication, but its unwinding activity also creates problems ahead of the replication fork, requiring the function of another class of enzymes. Describe the problem caused by DNA helicase, name the enzymes that resolve the problem, and explain the mechanism of resolution.

False

DNA in interphase chromosomes is as compact as DNA in mitotic chromosomes. True or false?

True

DNA ligase is required to seal the sugar-phosphate backbone between all the DNA fragments on the lagging strand. True or false?

True

DNA replication is a bidirectional process that is initiated at multiple locations along chromosomes in eukaryotic cells. True or false?

False

DNA replication origins are typically rich in G-C base pairs. True or false?

1. a 2. c 3. b 4. g 5. h 6. f 7. d 8. e

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Each word or phrase should be used only once. Any substance that will bind to a protein is known as its _____1_____. Enzymes bind their _____2_____ at the _____3_____. The enzyme hexokinase is so specific that it reacts with only one of the two _____4_____ of glucose. Enzymes catalyze a chemical reaction by lowering the _____5_____, because they provide conditions favorable for the formation of a _____6_____ intermediate called the _____7_____. Once the reaction is completed, the enzyme releases the _____8_____ of the reaction. a. ligand b. active site c. substrates d. transition state e. products f. high-energy g. isomers h. activation energy

1. a 2. e 3. f 4. b 5. d 6. c

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Each word or phrase should be used only once. The α helices and β sheets are examples of protein _____1_____ structure. A protein such as hemoglobin, which is composed of more than one protein _____2_____, has _____3_____ structure. A protein's amino acid sequence is known as its _____4_____ structure. A protein _____5_____ is a functional modular unit of a protein (e.g., may bind DNA or another protein) and is composed of a few protein folds. The three-dimensional conformation of a protein is its _____6_____ structure. a. secondary b. primary c. tertiary d. domain e. subunit f. quaternary

False

For most genes in the eukaryotic genome, the final product is an RNA molecule. True or false?

Heterochromatin is highly condensed and transcriptionally inactive. By moving Gene A closer to an area of heterochromatin, the effects essentially "rub off" on the gene as heterochromatin can spread, silencing its expression. Even though the DNA sequence of Gene A remains unchanged, its new position near heterochromatin prevents it from being turned on, and that's why none of the daughter cells express it.

Gene A, which is normally expressed, has been moved by DNA recombination near an area of heterochromatin. None of the daughter cells produced after this recombination event express gene A, even though its DNA sequence is unchanged. Explain this observation.

True

If an enzyme's allosteric binding site is occupied, the enzyme may adopt an alternative conformation that is not optimal for catalysis. True or false?

True

In many eukaryotic genomes, genes contain additional, interspersed, noncoding sequences. True or false?

Telomerase is more like DNA polymerase. This is because the function of these both include adding nucleotides to growing DNA strands, whereas primase creates RNA primers as a starting point for DNA polymerase rather than directly extending DNA.

In terms of its function, is telomerase more like DNA polymerase or primase? Explain your reasoning.

False

Interphase chromosomes represent a physical state of the chromatin with the highest order of packaging. True or false?

True

Ionizing radiation and oxidative damage can cause DNA double-strand breaks. True or false?

True

Linker histones help compact genomic DNA by influencing the path of the DNA after it has wrapped around the nucleosome core. True or false?

1. b 2. a 3. e 4. c 5. d

Match each phrase (a-e) to the number blanks (1-5) in Figure 2. a. constant domain of the light chain b. constant domain of the heavy chain c. antibinding site d. variable domain of the heavy chain e. variable domain of the light chain

1. d 2. c 3. a

Match each term related to chromosomes (1-3) with one of the correct descriptions provided (a-e). Note that not all descriptions may be used. a. contain nucleotide sequences required for full replication of ends of chromosome b. allows duplicated chromosome to be separated during interphase c. allows duplicated chromosome to be separated during mitosis d. location of DNA replication in interphase e. location of DNA replication in mitosis 1. replication origin 2. centromeres 3. telomeres

True

Meselson and Stahl ruled out the dispersive model for DNA replication. True or false?

False

There is a single enzyme that degrades the RNA primers and lays down the corresponding DNA sequence behind it. True or false?

1. c 2. e 3. b 4. a 5. d 6. f 7. e 8. b 9. a

Using terms from the list below, fill in the blanks in the following brief description of the experiment with Streptococcus pneumoniae that identified which biological molecule carries heritable genetic information. Some terms may be used more than once. Cell-free extracts from S-strain cells of S. pneumoniae were fractionated to _____1_____ DNA, RNA, protein, and other cell components. Each fraction was then mixed with _____2_____ cells of S. pneumoniae. Its ability to change these into cells with _____3_____ properties resembling the _____4_____ cells was tested by injecting the mixture into mice. Only the fraction containing _____5_____ was able to _____6_____ the _____7_____ cells into _____8_____ (or _____9_____) cells that could kill mice. a. S-strain b. pathogenic c. purify d. DNA e. R-strain f. transform

False

When DNA is being replicated inside a cell, local heating occurs, allowing the two strands to separate. True or false?

The following procedures might help obtain soluble, enzymatically active protein A: A, B, and D. High protein levels can overwhelm the bacteria's chaperone capacity. In procedure A, reducing protein A synthesis allows chaperones to fold the smaller amount of protein, resulting in soluble, active protein. In procedure B, exposing protein aggregates to urea breaks noncovalent bonds, denaturing the proteins. After diluting and removing urea, the proteins can refold properly, yielding soluble, active protein. In procedure D, overproducing chaperone proteins alongside protein A helps prevent aggregation and promotes solubility by assisting in proper folding.

You wish to produce a human enzyme, protein A, by introducing its gene into bacteria. The genetically engineered bacteria make large amounts of protein A, but it is in the form of an insoluble aggregate with no enzymatic activity. Which of the following procedures might help you to obtain soluble, enzymatically active protein? Select all options that may be useful. Explain your reasoning. A. Make the bacteria synthesize protein A in smaller amounts. B. Dissolve the protein aggregate in urea, then dilute the solution and gradually remove the urea. C. Treat the insoluble aggregate with a protease. D. Make the bacteria overproduce chaperone proteins in addition to protein A. E. Heat the protein aggregate to denature all proteins, then cool the mixture.

False

Protein phosphorylation is another way to alter the conformation of an enzyme and serves exclusively as a mechanism to increase enzyme activity. True or false?

True

Telomerase is a DNA polymerase that carries its own RNA molecule to use as a template at the end of the lagging strand. True or false?

False

Telomeres and telomerase are required for replication of bacterial chromosomes. True or false?

True

The amino acids in the interior of a protein most likely are hydrophobic and do not interact with the ligand and do not play a role in selective binding. True or false?

False

The histone proteins that constitute the core nucleosome include tetramers of histones H2A, H2B, H3, and H4. True or false?

True

The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior.

True

The repair polymerase does not require the aid of the sliding clamp, because it is only synthesizing DNA over very short stretches. True or false?

False

The repair polymerase is the enzyme that proofreads the newly synthesized strands to ensure the accuracy of DNA replication. True or false?

True

The sliding clamp is loaded once on each DNA strand, where it remains associated until replication is complete. True or false?

False

The telomere is a specialized DNA sequence where microtubules from the mitotic spindle attach to the chromosome so that duplicate copies move to opposite ends of the dividing cell. True of false?

1. a 2. e 3. g 4. b 5. d 6. c 7. f 8. h

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Each word or phrase should be used only once. Each chromosome is a single molecule of _____1_____ whose extraordinarily long length can be compacted by as much as _____2_____-fold during _____3_____ and tenfold more during _____4_____. This is accomplished by binding to _____5_____ that help package the DNA in an orderly manner so it can fit in the small space delimited by the _____6_____. The structure of the DNA-protein complex, called _____7_____, is highly _____8_____ over time. a. DNA b. mitosis c. nuclear envelope d. proteins e. 1000 f. chromatin g. interphase h. dynamic

1. b 2. d 3. c 4. e 5. a 6. f

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Each word or phrase should be used only once. In eukaryotic _____1_____, DNA is complexed with proteins to form _____2_____. The paternal and maternal copies of human Chromosome 1 are _____3_____, whereas the paternal copy of Chromosome 1 and the maternal copy of Chromosome 3 are _____4_____. Cytogeneticists can determine large-scale chromosomal abnormalities by looking at an individual's _____5_____. Fluorescent molecules can be used to paint a chromosome, by a technique that employs DNA _____6_____, and thereby to identify each chromosome by microscopy. a. karyotype b. chromosomes c. homologous d. chromatin e. nonhomologous f. hybridization

1. d 2. b 3. f 4. c 5. a 6. e

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Each word or phrase should be used only once. A newly synthesized protein generally folds up into a _____1_____ conformation. All the information required to determine a protein's conformation is contained in its amino acid _____2_____. On being heated, a protein molecule will become _____3_____ as a result of breakage of _____4_____ bonds. On removal of urea, an unfolded protein can become _____5_____. The final folded conformation adopted by a protein is that of _____6_____ energy. a. renatured b. sequence c. noncovalent d. stable e. lowest f. denatured

Statins and methotrexate are both reaction-specific drugs that inhibit different biochemical pathways crucial for maintaining healthy cells found in various tissues throughout the body, such as those involved in cholesterol synthesis and DNA replications, respectively. As a result, disease cells are not specifically targeted, and normal cellular functions are disrupted, leading to the development of side effects. In contrast, Gleevec is highly specific in targeting a protein produced only in certain types of leukemia cells, minimizing the impact on healthy cells and results in fewer, if any, side effects.

Enzymes generally make good drug targets because a specific reaction of interest can be targeted with a high degree of selectivity. Consider the following three drugs and explain why, although reaction-specific, the first two produce side effects, while the third does not. A. Statins inhibit HMG CoA reductase to block intracellular cholesterol synthesis. B. Methotrexate inhibits dihydrofolate reductase, which subsequently leads to blocked DNA replication. C. Gleevec® inhibits BCR, a kinase that is produced only in certain types of leukemia cells

True

Eukaryotic chromosomes contain many different sites where DNA replication can be initiated. True or false?

Heterochromatin is highly condensed and less accessible to the DNA replication machinery, and heterochromatin is also transcriptionally inactive as a result of the DNA packing nature. Therefore, more easily accessible DNA in euchromatin regions will be replicated first, leaving the most tightly packed structures last in line. Cells also need additional mechanisms to replicate DNA into heterochromatin (e.g., additional or removal of acetyl, phosphate, or methyl groups to histone tails to determine chromatin condensation and gene expression).

Evidence suggests that the replication of DNA packaged into heterochromatin occurs later than the replication of other chromosomal DNA. What is the simplest possible explanation for this phenomenon?

1. A 2. C 3. B

Examine the three protein monomers in Figure 1. Use the 2D depiction of complementary binding surfaces to match each monomer (A-C) to the likely higher-order protein complexes (1-3) they will form. 1. dimers and/or tetramers 2. filaments 3. sheets

A gene is a specific sequence of DNA that encodes the instructions for making proteins or functional RNA molecules, which also dictate the characteristics of phenotype of an organism. A genome consists of the total genetic information in an organism.

Explain the difference between a gene and a genome.

Telomerase is important for cancer cells because it helps them keep dividing without stopping. In normal cells, each time they divide, their telomeres (the protective caps at the ends of chromosomes) get shorter. Eventually, the telomeres become too short, and the cell either stops dividing or dies. However, telomerase can add back the missing pieces to the telomeres, keeping them long and allowing the cell to keep dividing. Most normal adult cells do not have active telomerase, so their telomeres shorten over time, limiting their ability to divide. In cancer cells, telomerase is turned back on, which prevents telomere shortening. This allows cancer cells to keep dividing without running into the normal limits, helping them grow uncontrollably and form tumors.

Most cells in the body of an adult human lack the telomerase enzyme because its gene is turned off and is therefore not expressed. An important step in the conversion of a normal cell into a cancer cell, which circumvents normal growth control, is the resumption of telomerase expression. Explain why telomerase might be necessary for the ability of cancer cells to divide over and over again.

A-T base pairs form 2 hydrogen bonds and G-C base pairs form 3 hydrogen bonds, signifying that bonds between A-T base pairs are weaker. This makes it easier for DNA helicase to break hydrogen bonds, unwind the sequence, and start replication. Thus, DNA replication can occur more efficiently.

Origins of replication typically have a relatively high number of A-T base pairs. How does this sequence feature relate to the function of these DNA regions?

True

Primase is needed to initiate DNA replication on both the leading strand and the lagging strand. True or false?

False

Primase requires a proofreading function that ensures there are no errors in the RNA primers used for DNA replication. True or false?