Cell Function (Ch. 1-7)

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Mitotic chromosomes are _______ times more compact than a DNA molecules in its extended form (a) 10,000 (b) 100,000 (c) 1000 (d) 100

(a) 10,000

The figure shows a ribose sugar. RNA bases are added to the part of the ribose sugar pointed by the arrow _________. (OH upper right corner). (a) 3 (b) 4 (c) 5 (d) 6

(a) 3

Below is the sequence from the 3' end of an mRNA.If you were told that this sequence contains the stop codon for the protein encoded by this mRNA, what is the anticodon on the tRNA in the P site of the ribosome when release factor binds to the A site?(a) 5'-CCA-3' (b) 5'-CCg-3' (c) 5'-UGG-3' (d) 5'-UUA-3'

(a) 5'-CCA-3'

Which of the following molecules of RNA would you predict to be the most likely to fold into a specific structure as a result of intramolecular base-pairing? (a) 5'-CCCUAAAAAAAAAAAAUUUUUUUUUUUUUUUUUUAGGG-3' (b) 5'-UGUGUGUUGUGUGUGUGUG-3' (c) 5'-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3' (d) 5'-GGAAAAGGAGAUGGGCAAGGGGGAUGGGCAAGG-3'

(a) 5'-CCCUAAAAAAAAAAAAUUUUUUUUUUUUUUUUUUAGGG-3'

Which of the following statements about allostery is true? (a) Allosteric regulators are often products of their chemical reactions in the same biochemical pathway. (b) Allosteric regulation is always used for negative regulation of enzyme activity (c) Enzymes are the only type of proteins that are subject to allosteric regulation (d) Binding of allosteric molecules usually locks an enzyme in its current conformation, such that enzyme cannot adopt a different conformation

(a) Allosteric regulators are often products of their chemical reactions in the same biochemical pathway

The repair of mismatched base pairs or damaged nucleotides in a DNA strand requires a multistep process. Which choice below describes the sequence of events in this process? (a) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment is removed by repair proteins, the gap is filled by DNA polymerase, and the strand is sealed by DNA ligase. (b) DNA repair polymerase simultaneously removes bases ahead of it and polymerizes the correct sequence behind it.

(a) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment is removed by repair proteins, the gap is filled by DNA polymerase, and the strand is sealed by DNA ligase.

A pregnant mouse is exposed to high levels of a chemical. Many of the mice in her liter are deformed, but when they are interbred with another, all of their offspring are normal. Which two of the following statements could explain these results? (a) In the deformed mice, somatic cells but not germ cells were mutated (b) The original mouse's germ cells were mutated (c) In the deformed mice, germ cells but not somatic cells were mutated (d) The toxic chemical affects development but is not mutagenic.

(a) In the deformed mice, somatic cells but not germ cells were mutated. and (d) The toxic chemical affects development but it not mutagenic

Genes in eukaryotic cells often have intronic sequences coded for within the DNA. These sequences are ultimately not translated into proteins. Why? (a) Intronic sequences are removed from RNA molecules by the spliceosome, which works in the nucleus. (b) Introns are not transcribed by RNA polymerase (c) Introns are removed by catalytic RNAs in the cytoplasm (d) The ribosome will skip over intron sequences when translating RNA into protein

(a) Intronic sequences are removed from RNA molecules by the spliceosome, which works in the nucleus.

Which of the following statements is true about the newly synthesized strand of a human chromosome? (a) It was synthesized from multiple origins by a mixture of continuous and discontinuous DNA synthesis. (b) It was synthesized from a single origin solely by continuous DNA synthesis. (c) It was synthesized from a single origin by a mixture of discontinuous and continuous synthesis.

(a) It was synthesized from multiple origins by a mixture of continuos and discontinuous DNA synthesis

Which of the following histone proteins does not form part of the octameric core? (a) H4 (B) H2A (C) H3 (D) H1

(D) H1

Which scientist or team of scientists first demonstrated that cells contain some component that can be transferred to a new population of cells and permanently causes changes in the new cells? (a) Griffith (b) Watson and Crick (c) Avery, MacLeod, and McCarty (d) Hershey and Chase

(a) Griffith

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? (a) It will be more likely to generate mismatched base pairs. (b) It will fall off the template more frequently than the normal. (c) It will polymerize more slowly (d) It will polymerize in both directions

(a) It will be more likely to generate mismatched base pairs.

Which amino acid would you expect tRNA with the anticodon 5'-CUU-3' to carry? (a) lysine (b) glutamic acid (c) leucine (d) phenylaline

(a) lysine

Because there are four different monomer building blocks that can be used to assemble RNA polymers, the number of possible sequence combinations that can be created for an RNA molecule made of 100 nucleotides is ____________. (a) 100^4 (b) 4^100 (c) 4x100 (d) 100/4

(b) 4^100

Which of the following is not neccessary for homologous recombination to occur? (a) 3' DNA strand overhangs (b) 5' DNA strand overhangs (c) a long stretch of sequence similarity (d) nucleases

(b) 5' strand overhangs

Which amino acid will be on the tRNA that is the first to bind to the A site of the ribosome? (a) methionine (b) arginine (c) cysteine (d) valine

(b) arginine

The chromatin structure in eukaryotic cells is much more complicated than that observed in prokaryotic cells. This is thought to be the reason that DNA replication occurs much faster in prokaryotes. How much faster is it? (a) 2x (b) 5x (c) 10x

If the isotope 32 S has 16 protons and 16 neutrons, how many protons, neutrons, and electrons will the isotope 35 have, respectively? (a) 16, 20, 15 (b) 16, 19, 15 (c) 16,19, 16 (d) 16, 19, 17

Which scientist or team of scientists obtained definitive results demonstrating that DNA is the genetic molecule? (a) Griffith (b) Watson and Crick (c) Avery, MacLeod, and McCarty (d) Hershey and Chase

(d) Hershey and Chase

How many moles and atoms are there in 120 grams of sulfur?

3.75 and 2.25x10^24

The mitochondrial proteins found in the inner membrane are involved in the conversion of ADP to ATP, a source of energy for the cell. This process consumes which of the following substances? (a) oxygen (b) nitrogen (c) sulfur (d) carbon dioxide

Purines

A+T

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A.) The terms "prokaryote" and "bacterium" are synonyms. B.) Prokaryotes can adopt several different basic shapes, including spherical, rod- shaped, and spiral. C.) Some prokaryotes have cell walls surrounding the plasma membrane.

A. False. Archaea that are significantly make up a class of prokaryotic organisms different from bacteria. B. True. C. True.

hydrolyzes ATP

ATPase

Pyrimidines

C+G

Complete the following reaction: CH3COOH+ H20 =

CH3COO-+H3O

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

False they are composed of four

True or false: There is no limit to the number of electrons that can occupy the fourth electron shell.

False- the fourth shell can hold up to 18 electrons

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

False.

True or false? Collagen is a protein that participates in both the cytoskeleton and the extracellular matrix.

False. Collagen is not used inside the cell

BEF CD A

The packing of DNA into chromatin also affects transcriptional initiation, and histone __________________ is an enzyme that can render the DNA less accessible to the general transcription factors.

deacetylase

Nucleosomes are present in [prokaryotic/eukaryotic] chromosomes, but not in [prokaryotic/eukaryotic] chromosomes.

eukaryotic, prokaryotic

joins two ends of DNA together

ligase

Transcription in bacteria differs from transcription in a eukaryotic cell because __________________. (a) RNA polymerase(along with it sigma unit) can initiate transcription on its own (b) RNA polymerase requires the general transcription factors to assemble the promoter before polymerase can begin transcription (c) the sigma subunit must associate with the appropriate type of RNA polymerase to produce mRNAs (d) RNA polymerase must be phosphorylated at its C-terminal tail for transcription to proceed.

(a) RNA polymerase(along with it sigma unit) can initiate transcription on its own

Which of the following statements is true with respect to this in virto replication system? (a) The leading and lagging strands compose one half of each newly synthesized DNA strand. (b) There will be only one leading strand and one lagging strand produced (c) The DNA replication machinery can assemble at multiple surfaces (d) One daughter DNA molecule will be slightly shorter than the other

(a) The leading and lagging strands compose one half of each newly synthesized DNA strand

The ribosome is important for catalyzing the formation of peptide bonds. Which of the following statements is true? (a) The number of rRNA molecules that make up a ribosome greatly exceed the number of protein molecules found in the ribosome.(b) The large subunit of the ribosome is important for the binding to the mRNA (c) The catalytic site for peptide bond formation is formed primarily from an rRNA. (d) Once the large and small units of the ribosome assemble, they will not separate from each other until degraded by the proteasome.

(a) The number of rRNA molecules that make up a ribosome greatly exceed the number of protein molecules found in the ribosome.

Protein folding can be studied using a solution of purified protein and a denatured (urea), a solvent that interferes with noncovelant interactions. Which of the following is observed after the denaturant is removed from the protein solution. (a) The polypeptide returns to its original form (b) The polypeptide remain denatured (c) The polypeptide forms solid aggregates and precipitates out of solution. (d) the polypeptide adopts a new, stable conformation.

(a) The polypeptide returns to its original form

Which of the following statement correctly explains what it means for DNA replication to be bidirectional? (a) The replication forks formed at the origin moved in opposite directions. (b) the DNA replication machinery can move in either direction on the template strand (c) The replication fork can either open or close depending on the condition (d) Replication form movement can switch directions when the fork converges on another replication fork.

(a) The replication forks formed at the origin move in opposite directions.

Which of the following does not occur before a eukaryotic mRNA is exported from the nucleus? (a) The ribosome binds to the mRNA (b) The mRNA is polyadenylated at its 3' end (c) 7-methyguanosine is added in a '5-to-5' linkage to the mRNA (d) RNA polymerase disocciates

(a) The ribosome binds to the mRNA

Which of the following best describes the mechanism by which chromatin remodeling complexes "loosen" the DNA wrapped around the core histones? (a) They use energy derived from ATP hydrolysis to change the relative position of the DNA and the core histone octamer. (b) They chemically modify the DNA, changing the affinity between histone octamer and the DNA (c) They remove histone H1 from the linker DNA adjacent to the core histone ocatmer (d) They chemically modify core histones to alter the affinity between the histone octamer and the DNA

(a) They use energy derived from ATP hydrolysis to change the relative position of the DNA and the core histone octamer.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A.) Oxygen is toxic to certain prokaryotic organisms. B.) Mitochondria are thought to have evolved from anaerobic bacteria. C.) Photosynthetic bacteria contain chloroplasts.

(a) True. (b) False. Mitochondria use oxygen to generate energy and are thought to have evolved from aerobic bacteria. (c) False. Photosynthetic bacteria have enzyme systems similar to those found in chloroplasts, which allow them to harvest light energy to fix carbon dioxide.

Polypeptides are synthesized from amino acid building blocks. The condensation reaction between the growing polypeptide chain and the next amino acid to be added involves the loss of ____________________. (a) a water molecule (b) an amino group (c) a carbon atom (d) a carboxyl acid group

(a) a water molecule

The process of generating monoclonal antibodies is labor-intensive and expensive. An alternative is to use polyclonal antibodies. A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated for chromatography. Which type is used for this purpose? (a) affintiy (b) ion-exchange (c) gel-filteration (d) any of the above

(a) affinity

Coiled coils are typically found in proteins that require an elongated structural framework. Which of the following proteins do you expect to have a coiled coil domain? (a) collagen (b) myoglobin (c) insulin

(a) collagen

Globular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form multisubunit complexes, which also have a rounded shape. Fibrous proteins, in contrast, span relatively large distances within the cell and in the extracellular space. Which of the proteins is not classified as a fibrous protein? (a) elastase (b) collagen (c) keratin (d) collagen

(a) elastase

Although covalent bonds are 10-1000 times stronger than noncovalent interactions, many biological processes depend upon the number and type of noncovalent interactions between molecules. Which of the noncovalent interactions below will contribute most to the strong and specific binding of two molecules, such as a pair of proteins? (a) electrostatic attractions (b) hydrogen bonds (c) hydrophobic interactions (d) Van dew Waals attractions

(a) electrostatic attractions

Which of the following methods would be the most suitable to assess whether your protein exists as a monomer or in a complex? (a) gel-filteration chromatography (b) gel electrophoresis (c) western blot (d) ion-exchange chromatography

(a) gel-filteration chromatography

Which of the following are examples of isomers? (a) glucose and galactose (b) alanine and glycine (c) adenine and guanine (d) glycogen and cellulose

(a) glucose and galactose

Cyclic AMP is a small molecule that associates with its binding site with a high degree of specificity. Which types of noncovalent interactions are the most important for providing the "hand in a glove" binding of cAMP? (a) hydrogen bonds (b) electrostatic interactions (c) van der Waals (d) hydrophobic interactions

(a) hydrogen bonds

DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strands. What prevents this enzyme from catalyzing the reverse reaction? (a) hydrolysis of pyrophosphate (PPi) to inorganic phosphate (Pi)+Pi (b) release of PPi from the nucleotide (c) hybridization of the new strand to the template (d) loss of ATP

(a) hydrolysis of pyrophosphate (PPi) to inorganic phosphate (Pi)+Pi

Each nucleotide in DNA and RNA has aromatic base. What is the principle force that keeps the bases in a polymer from interacting with water? (a) hydrophobic interactions (b) hydrogen bonds (c) covalent bonds (d) van der Waals interactions

(a) hydrophobic interactions

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking primase were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion

(a) initiation of DNA synthesis

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking helicase were used to make the cell extracts? (a) initiation of DNA synthesis (b)Okazaki fragment synthesis (c) leading strand elongation (d) lagging strand completion

(a) intiation of DNA synthesis

The amino acids glutamine and glutamic acid are shown in the figure. They differ only in the structure of their side chains (circled). At pH 7, glutamic acid can participate in molecular interactions that are not possible for glutamine. What types of interactions are these? (a) ionic bonds (b) hydrogen bonds (c) van der Waals interactions (d) covalent bonds

(a) ionic bonds

Which of the following is not a feature commonly observed in alpha helices? (a) left handedness (b) one helical turn every 3.6 amino acids (c) cylindrical shape (d) amino acid side chains that point outwards

(a) left handedness

The classic "beads-on-a-string" structure is the most decondensed chromatin structure possible and is produced experimentally. Which chromatin components are not retained when the structure is generated? (a) linker histones (b) linker DNA (c) nucleosome core particles (d) core histones

(a) linker histones

Methylation and acetylation are common changes to histone H3, and the specific combination of these changes is sometimes referred to as the "histone code" Which of the following patterns will probably lead to gene silencing? (a) lysine 9 methylation (b) lysine 4 methylation and lysine 9 acetylation (c) lysine 14 acetylation (d) lysine 9 acetylation and lysine 14 acetylation

(a) lysine 9 methylation

Which elements form stable but reactive diatomic gases? (a) nitrogen, oxygen (b) helium, neon (c) sodium, potassium (d) magnesium, calcium

(a) nitrogen, oxygen

The chromosomes we typically see in images are isolated from mitotic cells. These mitotic chromosomes are in the most highly condensed form. Interphase cells contain chromosomes that are less densely packed and ____________________. (a) occupy discrete territories in the nucleaus (b) share the same nuclear territory (c) are restricted to the nucleus (d) are completely tangled with other chromosomes

(a) occupy discrete territories in the nucleus

Which of the following expressions accurately describes the calculation of pH? (a) pH=-log10[H+] (b) pH=log10[H+] (c) pH=-log2[H+] (d) pH=-log10[OH-]

(a) pH=-log10[H+]

Instead of studying one or two proteins or protein complexes present in the cell at any given time, we can now look at a snapshot of all proteins being expressed in cells being grown in specific conditions. This large-scale, systematic approach to the study of proteins is called ___________________. (a) proteomics (b) structural biology (c) systems biology (d) genomics

(a) proteomics

Aromatic carbon compounds such as benzene are planar and very stable. Double bond character extends around the entire ring, which is why it is often drawn as a hexagon with a circle inside. This characteristic is caused by electron ____________. (a) resonance (b) pairing (c) partial charge (d) stacking

(a) resonance

For some proteins, small molecules are integral to their structure and function. Enzymes can synthesize some of these small molecules, whereas other, called vitamins, must be ingested in the food we eat. Which of the following molecules is not classified as a vitamin but does require the ingestion of a vitamin for its production? (a) retinal (b) biotin (c) zinc

(a) retinal

The three-dimensional coordinates of atoms within a folded protein are determined experimentally. After researchers obtain a protein's structural details, they can use different techniques to highlight particular aspects of the structure. What visual model best displays a protein's secondary structures? (a) ribbon (b) space-filling (c) backbone (d) wire

(a) ribbon

Match the labels given in the list below with the label lines in Figure Q7-56 of an mRNA molecule. (a) ribosome-binding site (b) initiator codon (c) stop codon (d) untranslated 3' region (e) untranslated 5' region (f) protein-coding region

(a) ribosome-binding site=3 (dark colored squares) (b) initiator codon= 2(AUG) (c) stop codon= 4 (UAG) (d) untranslated 3' region = 6 (right end)(e) untranslated 5' region= 1 (left end) (f) protein-coding region= 5(long white colored rectangle parts)

Oligosaccharides are short sugar polymers that can become covalently linked to proteins and lipids through condensation reactions. These modified proteins and lipids are called glycoproteins and glycolipids, respectively. Within a protein, which of the amino acids is the most probable target for this type of modification? (a) serine (b) glycine (c) phenylalnine (d) methionine

(a) serine

A covalent bond between two atoms is formed as a result of the ____________________________. (a) sharing of electrons (b) loss of electrons from both atoms (c) loss of a proton from one atom (d) transfer of electrons from one atom to the other

(a) sharing of electrons

Which of the following elements is least abundant in living organisms? (a) sulfer (b) carbon (c) oxygen (d) nitrogen

(a) sulfer

Specific regions of eukaryotic chromosomes contain sequence elements that are absolutely required for the proper transmission of genetic information from a mother cell to a daughter cell. Which of the following is not known to be one of these required elements in eurkaryotes? (a) terminators of replication (b) origins of replication (c) telomeres (d) centromeres

(a) terminators of replication

There are 20^100 different possible sequence combinations for a protein chain with 100 amino acids. In addition to the amino acid sequence of the protein, that other factors increase the potential for diversity in these macromolecules? (a) free rotation around single bonds during synthesis (b) noncovalent interactions sampled as protein folds (c) the directionality of amino acids being added (d) the planar nature of the peptide bond

(a) the free rotation around single bonds during synthesis

You have two purified samples of protein Y: the wild-type (nonmutated) protein and a mutant version with a single amino acid substitution. When washed through the same gel-filteration column, mutant protein Y runs through the column more slowly than the normal protein. Which of the following changes in the mutant protein is most likely to explain the result? (a) the loss of a binding site on the mutant-protein surface through which protein Y normally forms dimers (b) a change that results in the mutant protein acquiring an overall positive charge instead of a negative charge (c) a change that results in the mutant protein being larger than the wild-type protein (d) a change that results in the mutant protein having a slightly different shape from the wild-type protein

(a) the loss of a binding site on the mutant-protein surface through which protein Y normally forms dimers

The DNA from two different species can often be distinguised by a difference in the ______________________. (a) ratio of A+T to G+C (b) ratio of A+G to C+T (c) ratio of sugar to phosphate (d) presence of bases other than A,G ,C and T.

(a) the ratio of A+T to G+C

Nonhomologous end joining can result in all but which of the following? (a) the recovery of lost nucleotides on a damaged DNA strand (b) the interruption of gene expression (c) loss of nucleotides

(a) the recovery of lost nucleotides on a damaged DNA strand

Which of the following factors do not influence the length of a covalent bond? (a) the tendency of atoms to fill the outer electron shells (b) the attractive forces between negatively charged electrons and positively charged nuclei (c) the repulsive forces between the positively charged nuclei (d) the minimization of repulsive forces between the two nuclei by the cloud of shared electrons

(a) the tendency of atoms to fill the outer electron shells

When using a repeating trinucleotide sequence in a cell-free translation system you will obtain: (a) three different tyes of peptides, each made up of a single amino acid (b) peptides made up of three different amino acids in random order (c) peptides made up of three different amino acids each alternating each other in a repetitive function (d) polyasparagine as the codon for asparagine is AAC

(a) three different types of peptides, each made up of a single amino acid

Proteins can assemble to form large complexes that work coordinately, like moving parts inside a single machine. Which of the following steps in modulating the activity of a complex protein machine is least likely to be directly effected by ATP or GTP hydrolysis? (a) translation of protein components (b) conformational change of protein components (c) complex assembly (d) complex disassembly

(a) translation of protein components

Which of the following globular proteins is used to form filaments as an intermediate step to assembly into hollow tubes? (a) tubulin (b) actin (c) keratin (d) collagen

(a) tubulin

The process of sorting human chromosome pairs by size and morphology is called karyotyping. A modern method employed for karyotyping is called chromosome painting. How are individual chromosomes "painted"? (a) with a laser (b) using fluorescent antibodies (c) using fluorescent DNA molecules (d) using green fluorescent protein

(a) with a laser

Nucleosomes are formed with DNA wraps ______ times around the histone octamer in a ____________ coil. (a) 2, right handed (b) 1.7, left handed (c) 1. 3, right handed

(b) 1.7, left handed

In somatic cells, if a base is mismatched in one new daughter strand during DNA replication, and it is not repaired, what fraction of DNA duplexes will have a permanent change in the DNA sequence after the second round of replication? (a) 1/2 (b) 1/4 (c) 1/8 (d) 1/16

(b) 1/4

Interphase chromosomes are about ______ times less compact than mitotic chromosomes, but still are about _______ times more compact than a DNA molecule in its extended form. (a) 10, 1000 (b) 20, 500 (c) 5, 2000 (d) 50, 200

(b) 20, 500

The first task you are assigned in your summary lab job is to prepare a concentrated NaOH stock solution. The molecular weight of NaOH is 40. How many grams of solid NaOH will you need to weigh out to obtain a 500 mL solution that has a concentration of 10 M? (a) 800 g (b) 200 g (c) 400 g (d) 160 g

(b) 200 g

Which of the following RNA molecules could be transcribed from this piece of DNA? (a) 5'-UAUCCGUAAGCUAAGGCCUAUGCUA-3' (b) 5'-AUAGGCAUUCGAUCCGAUAGGCAU-3'

(b) 5'-AUAGGCAUUCGAUCCGAUAGGCAU-3'

Which of the following statements about RNA splicing is FALSE? (a) Conventional introns are not found in bacterial genes (b) For a gene to function properly, every extron must be removed from the primary transcript in the same fashion on every mRNA molecule produced from the same gene (c) Small RNA molecules in the nucleus perform the splicing reactions necessary for the removal of introns (d) Splicing occurs after the 5' cap has been added to the end of the primary transcript

(b) For a gene to function properly, every extron must be removed from the primary transcript in the same fashion on every mRNA molecule produced from the same gene

Most eukaryotic cells only express 20-30% of the genes the possess. The formation of heterochromatin maintains the other genes in a transcriptionally silent state. Which histone modification directs the formation of the most common type of heterochromatin? (a) H3 lysine and 4 methylation (b) H3 lysine and 9 methylation

(b) H3 lysine and 9 methylation

Which of the following is not a chemical modification commonly found on core histone N-terminal tails? (a) methylation (b) hydroxylation (c) phosphorylation (d) acetylation

(b) Hydroxylation

A postion added to an in vitro translation mixture containing mRNA molecules with the sequences " has the following effect: the only product made is a Met-Lys dipeptide that remains attached to the ribosome. What is the most likely way in which the position acts to inhibit protein synthesis? (a) It inhibits peptidyl transferase activity. (b) It inhibits movement of the small subunit relative to the large subunit (c) It inhibits release factor (d) It mimics release factor

(b) It inhibits movement of the small subunit relative to the large subunit

You wish to explore how mutations in specific genes affecting sugar metabolism might alter tooth development. Which organism is likely to provide the best model system for your studies, and why? (a) horses (b) mice (c) E. coli (d) Arabidopsis

(b) Mice are likely to provide the best model system. Mice have teeth and have long been used as a model organism. Mice reproduce relatively rapidly and the extensive scientific community that works with mice has developed techniques to facilitate genetic manipulations. E. coli (a bacterium) and Arabidopsis (a plant) do not have teeth. Horses like sugar and have big teeth, but they would not be a good model organism. There is not an extensive scientific community working on the molecular and biochemical mechanisms of cell behaviors in horses; they are expensive and have a long reproduction time, which makes genetic studies costly and slow; and tools for genetic manipulation (other than traditional breeding) have not been developed.

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking single-strand binding protein were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading strand elongation (d) lagging strand completion

(b) Okazaki fragment synthesis

There are several reasons why the primase used to make the RNA primer for DNA replication is not suitable for gene transcription. Which of the statements below is NOT one of those reasons? (a) Primase initiates RNA synthesis on a single-stranded DNA template (b) Primase can initiate RNA synthesis without the need for a base-paired primer (c) Primase synthesizes only RNAs of about 5-20 nucleotides in length. (d) The RNA synthesized by primase remains base-paired to the DNA template

(b) Primase can initiate RNA synthesis without the need for a base-paired primer

The information stored in the DNA sequences is used to direct as a template to make ____________. (a) lipids (b) RNA (c) polypeptides (d) expression

(b) RNA

You are studying a disease that is caused by a virus, but when you purify the virus particles and analyze them you find they contain no trace of DNA. Which of the following molecules are likely to contain the genetic information of the virus? (a) high-energy phosphate groups (b) RNA (c) lipids (d) carbohydrates q

(b) RNA

Which of the following statements about prokaryotic mRNA is false?(a) A single prokaryotic mRNA can be translated into several proteins (b) Ribosomes must bind to the 5' cap before initiating translation (c) mRNAs are not polyadenylated (d) Ribosomes can start translating an mRNA molecule before transcription is complete

(b) Ribosomes must bind to the 5' cap before initiating translation

Which of the following statements about sequence proofreading during DNA replication is false? (a) The exonuclease activity is in a different domain of the DNA polymerase. (b) The exonuclease activity cleaves DNA in the '5-to-3' direction. (c) The DNA proofreading activity occurs concomitantly with strand elongation. (d) If an incorrect base is added, it is unpaired before removal.

(b) The exonuclease activity cleaves DNA in the '5-to-3' direction.

Which of the following statement about the genetic code is correct? (a) All codons specify more than one amino acid (b) The genetic code is redundant (c) All amino acids are specified by more than one codon (d) All codons specify an amino acid

(b) The genetic code is redundant

You have discovered a protein that inhibits translation. When you add this inhibitor to a mixture capable of translating human mRNA and centrifuge the mixture to separate polyribosomes and single ribosomes, you obtain the results shown the figure of a bar graph. Which of the following interpretations is consistent with these observations? (a) The protein binds to the small ribosomal subunit and increases the rate of initiation of translation (b) The protein binds to sequences in the 5' region of the mRNA and inhibits the rate of initiation of translation (c) The protein binds to the large ribosomal subunit and slows down elongation of the polypeptide chain (d) The protein binds to sequences in the 3' region of the mRNA and prevents termination of translation

(b) The protein binds to sequences in the 5' region of the mRNA and inhibits the rate of initiation of translation

Which of the following statements is not an accurate statement about thymine dimers? (a) They can cause the DNA replication machinery to stall. (b) They are covalent links between thymidines on oppoiste DNA strands (c) Prolonged exposure to sunlight causes thymine dimers to form (d) Repair proteins recognize thymine dimers as a distortion in the DNA backbone

(b) They are covalent links between thymidines on opposite DNA strands

The DNA duplex consists of two long covalent polymers wrapped around each other many times over their entire length. The separation of DNA strands for replication causes the strands to be overwound in front of the replication fork. How does the cell relieve the torsional stress created along the DNA duplex during replication? (a) Nothing needs to be done because the two strands will be separated after replication is complete. (b) Topoisomerases break the covalent bonds of the backbone allowing the local unwinding of DNA ahead of the replication fork. (c) Helicase unwinds the DNA and rewinds it after replication is complete. (d) DNA repair enzymes remove stress as they replace incorrectly paired bases.

(b) Topoisomerases break the covalent bonds of the backbone allowing the local unwinding of DNA ahead of the replication fork.

Studies conducted with a lysozyme mutant contains an Asp?Asn change at position 52 and a Glu?Gln change at position 35 exhibited almost a complete loss in enzymatic activity. What is the most likely explanation for the decrease in enzyme activity in the mutant? (a) increased affinity for substrate (b) absence of negative charges in the active site (c) change in the active site scaffold (d) larger amino acids in the active site decreases the affinity for substrate

(b) absence of negative charges in the active site

Sickle-cell anemia is an inherited disease that causes a disorder where red blood cells are misshapen caused by a change in the sequence of the B-globin gene. What is the nature of this change? (a) chromosome loss (b) base-pair change (c) gene duplication (d) base-pair insertion

(b) base-pair change

Which of the following is not a feature commonly observed in beta sheets? (a) antiparallel regions (b) coiled-coil patterns (c) extended polypeptide backbone (d) parallel regions

(b) coiled-coil patterns

Mitotic chromosomes were first visualized with the use of very simple tools: a basic light microscope and some dyes. Which of the following characteristics of mitotic chromosomes reflects how they were named? (a) motion (b) color (c) shape (d) location

(b) color

Which of the following monomer building blocks is necessary to assemble selectively permeable boundaries around and inside cells? (a) sugars (b) fatty acids (c) amino acids (d) nucleotides

(b) fatty acids

Stepwise condensation of linear DNA happens in five different packing processes. Which of the following four processes has a direct requirement for histone H1? (a) formation of beads on a string (b) formation of 30nm fiber (c) looping of the 30 nm fiber (d) packing of loops to form interphase chromosomes

(b) formation of 30nm fiber

Which of the following methods would be most suitable to assess the relative purity of a protein in a sample you have prepared? (a) gel-filteration (b) gel electrophoresis (c) western blot analysis (d) ion-exchange chromatography

(b) gel electrophoresis

The N terminal tail of histone H3 can be extensively modified, and depending on the number, location, and combination of these modifications, these changes may promote the function of heterochromatin. What is the result of heterochromatin formation? (a) increasing in gene expression (b) gene silencing (c) recruitment of remodeling complexes (d) displacement of histone H1

(b) gene silencing

The manner in which a gene sequence is related to its respective protein sequence is referred to as the ________________ code. (a) protein (b) genetic (c) translational (d) expression

(b) genetic

Which elements are chemically inert? (a) carbon, sulfur (b) helium, neon (c) sodium, potassium (d) magnesium, calcium

(b) helium, neon

The figure clearly depicts the nucleolus, a nuclear structure that looks like a large, dark region when stained. The other dark, speckled regions in this image are the locations of particularly compact chromosomal segments called ________________. (a) euchromatin (b) heterochromatin (c) nuclear pores (d) nucleosomes

(b) heterochromatin

Both DNA and RNA are synthesized by covalently linking a nucleoside triphosphate to the previous nucleotide, constantly adding to a growing chain. In the case of DNA, the new strand becomes part of a stable helix. The two strands are complementary in sequence and antiparallel in directionality. What is the principal force that holds these two strands together? (a) ionic interactions (b) hydrogen bonds (c) covalent bonds (d) van der Waals interactions

(b) hydrogen bonds

Two or three alpha helices can sometimes wrap up around each other to form coiled coils. The stable wrapping of one helix around another is typically driven by ________________ interactions. (a) hydrophilic (b) hydrophobic (c) van der waals (d) ionic

(b) hydrophobic

Proteins bind selectively to small-molecule targets called ligands. The selection of one ligand out of a mixture of possible ligands depends on the number of weak, noncovalent interactions in the protein's ligand-binding site. Where is the binding-site typically located in the protein structure? (a) on the surface of the protein (b) inside a cavity on the protein surface (c) buried in the interior of protein (d) forms on the surface of the protein in the presence of ligand

(b) inside a cavity on the protein surface

When atoms are held together by ______________ _____________m they are typically referred to as __________. (a) hydrogen bonds, molecules (b) ionic interactions, salts (c) ionic interactions, molecules (d) double bonds, nonpolar

(b) ionic interactions, salts

DNA and RNA are different types of nuclei acid polymer. Which of the following is true of DNA but NOT true of RNA? (a) it contains uracil (b) it contains thymine (c) it is single-stranded (d) it has 5'-to-3' directionality

(b) it contains thymine

What do you predict to happen if you created a tRNA with an anticodon of 5'-CAA-3' that is charged with methionine and added this modification tRNA to a cell-free translation system that has all the normal components required for translating RNAs? (a) methionine would be incorporated into proteins at some positions where glutamine should be (b) methionine would be incorporated into proteins at some positions where leucine should be (c) it would be incorporated into proteins at some positions where valine should be (d) translation would no longer be able to continue

(b) methionine would be incorporated into proteins at some positions where leucine should be

Carbon 14 is an unstable isotope of carbon that decays very slowly. Compared to the common, stable carbon 12 isotope, carbon 14 has two additional _______________________. (a) electrons (b) neutrons (c) protons (d) ions

(b) neutrons

You have a bacterial strain with a mutation that removes the transcription termination signal from the Abd operon. Which of the following statements describes the most likely effect of this mutation on Abd transcription? (a) The Abd RNA will not be produced in the mutant strain (b) The Abd RNA from the mutant strain will be longer than normal (c) Sigma factor will not dissociate from RNA polymerase when the Abd operon is being transcribed in the mutant strain.

(b) or (c)

The variety and arrangement of chemical groups on monomer subunits contribute to the conformation, reactivity, and surface of the macromolecule into which they become incorporated. What type of chemical group is circled on the nucleotide shown? (a) pyrophosphate (b) phosphoryl (c) carbonyl (d) carboxyl

(b) phosphoryl

The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of a ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in _______________. (a) membrane association (b) protein degradation (c) protein secretion (d) nuclear translocation

(b) protein degradation

Which subatomic particles contribute to the atomic mass for any given element? (a) protons (b) protons and neutrons (c) protons and electrons (d) neutrons

(b) protons and neutrons

In eukaryotes, but not in prokaryotes, ribosomes find the start site of translation _____________________. (a) binding directly to a ribosome-binding site preceding the initation code (b) scanning along the mRNA from the 5' end (c) recognizing an AUG codon as the start of translation (d) binding an initiator tRNA

(b) scanning along the mRNA from the 5' end

The variations in the physical charactersitics between different proteins are influenced by the overall amino acid compositions, but even more important is the unique amino acid ___________________. (a) number (b) sequence (c) bond (d) orientation

(b) sequence

DNA polymerases are processive meaning that they remain tightly associated with the template strand while moving rapidly and adding nucleotides to the growing daughter strand. Which piece of replication machinery accounts for this characteristic? (a) helicase (b) sliding clamp (c) single-stranded binding protein (d) primase

(b) sliding clamp

Griffith studied two strains of S. pnemonia, one that causes a lethal infection when injected into mice, and a second that is harmless. He observed that pathogenic bacteria that have been killed by heating can no longer cause an infection. But when these heat-killed bacteria are mixed with live, harmless bacteria, this mixture is capable of infecting and killing a mouse. What did Griffith conclude from this experiment? (a) the infectious strain cannot be killed by heating (b) The heat-killed pathogenic bacteria "transformed" the harmless strain into a lethal one. (c) The harmless strain somehow revived the heat-killed pathogenic bacteria.

(b) the heat-killed pathogenic bacteria "transformed" the harmless strain into a lethal one.

Initiator proteins bind to replication origins and disrupt hydrogen bonds between the two DNA strands being copied. Which of the factors below does not contribute to the relative ease of strand separation by initiator proteins? (a) replication origins are rich in A-T base pairs (b) the reaction can occur at room temperature (c) they only separate a few base pairs at a time (d) once opened, other portions of the DNA replication machinery bind to the origin

(b) the reaction can occur at room temperature

To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denature the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in the denaturation process? (a) the solvents break all covalent interactions. (b) the solvents break all noncovalent interactions (c) the solvents break some of the noncovalent interactions, resulting in a misfolded protein. (d) the solvents create a new protein conformation.

(b) the solvents break all noncovalent interactions

Most types of molecules in the cell have asymmetric (chiral) carbons. Consequently there is the potential to have two different molecules that look much the same but are mirror images of each other and therefore not equivalent. These special types of isomers are called stereoisomers. Which of the four carbons circled in the figure is the asymmetric carbon that determines whether the amino acid (threonine in this case) is a D or an L stereoisomer? (a) 1 (b) 2 (c) 3 (d) 4

The figure shows a ribose sugar. The part of the ribose sugar where a new ribonucleotide will attach in an RNA molecule is pointed by arrow _______. (H-OH far left on the bottom) (a) 1 (b) 3 (c) 4 (d) 5

The figure shows a ribose sugar. The part of the ribose sugar that is different from the deoxyribose sugar used in DNA is pointed by arrow ________. (H-OH far right on the bottom) (a) 1 (b) 4 (c) 5 (d) 6

Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of the following would not occur to help accommodate an internal, polar side chain? (a) A hydrogen bond forms between two polar chains (b) A hydrogen bond forms between a polar side chain and the protein backbone. (c) A hydrogen bond forms between a polar side chain and an aromatic side chain. (d) Hydrogen bonds form between polar side chains and a buried water molecule.

The biosynthetic pathway for the two amino acids E and H is shown schematically. You are able to show that E inhibit enzyme V, and H inhibits enzyme X. Enzyme T is most likely to be subject to feedback inhibition by ____________ alone. (a) H (b) B (c) C (d) E

Which of the following pairs of codons might you expect to be read by the same tRNA as a result of wobble? (a) CUU and UUU (b) GAU and GAA (c) CAC and CAU

Which of the following statements is true? (a) disulfide bonds are formed by the cross linking of methiothine residues. (b) Disulfide bonds are formed mainly in proteins that are retained within the cytosol. (c) Disulfide bonds stabilize but do not change a protein's final conformation (d) Agents such as a mecraptoethanol can break disulfide bonds through oxidation.

You are a virologist studying the evolution of viral genomes. You are studying two newly isolated virus strains and have sequenced their genomes. You find that the genome of strain 1 contains 25% A, 55% 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? (a) single-stranded genomes always have a large percentage of purines (b) using the formula: G-A=C+T (c) Double-stranded genomes have equal amounts of A and T

You have discovered a gene that is alternatively spliced to produce several forms of mRNA in various cell types, three of which are shown in the figure. The lines connecting the exons that are included in the mRNA indicate the splicing. You known that protein translation begins in exon 1. For all forms of the mRNA, the encoded protein sequence is the same in the regions of the mRNA that correspond to exons 1 and 10. Exons 2 and 3 are alternative exons used in different mRNA, as are exons 7 and 8. Which of the following statements about exons 2 and 3 is the most accurate? (a) Exons 2 and 3 must have the same number of nucleotides (b) Exons 2 and 3 must contain an integral number of codons (c) Exons 2 and 3 must contain a number of nucleotides that when divided by 3, leaves the same remainder (that is, 0, 1, or 2). (d) Exons 2 and 3 must have different number of nucleotides

(c) Exons 2 and 3 must contain a number of nucleotides that when divided by 3, leaves the same remainder (that is, 0, 1, or 2).

Which DNA base pair is represent in the figure? (a) A-T (b) T-A (c) G-C (d) C-G

Consider two genes that are next to each other on a chromosome, labeled gene A and gene B. Which of the following statements is TRUE? (a) The two genes must be transcribed into RNA using the same strand of DNA. (b) If gene A is transcribed in a cell, gene B cannot be transcribed. (c) Gene A and gene B can be transcribed at different rates, producing different amounts of RNA within the same cell. (d) If gene A is transcribed in a cell, gene B must be transcribed.

The core histones are small, basic proteins that have a globular domain at the Cterminus and long, extended conformation at teh N terminus. Which of the following is not true of the N terminal tail of these histones? (a) it is subject to covalent modifications (b) it extends out of the nucleosome core (c) it binds to DNA in a sequence-specific manner (d) it helps DNA pack tightly

Which of the following statements about the proteasome is false? (a) Ubiquitin is a small protein that is covalently attached to proteins to mark them for delivery to the proteasome (b) Proteases reside in the central cylinder of a proteasome (c) Misfolded proteins are delivered to the proteasome, where they are sequestered from the cytoplasm and can attempt to refold (d) The protein stoppers that surround the central cylinder of the proteasome use the energy from ATP hydrolysis to move proteins into the proteasome inner chamber.

(c) Misfolded proteins are delivered to the proteasome, where they are sequestered from the cytoplasm and can attempt to refold

Which of the following molecules is thought to have arisen first during evolution? (a) protein (b) DNA (c) RNA (d) all came to be at the same time

Ribozymes catalyze which of the following reactions? (a) DNA synthesis (b) transcription (c) RNA splicing (d) protein hydrolysis

Which one of the following is the main reason that a typical eukaryotic gene is able to respond to a far greater variety of regulatory signals than a typical prokaryotic gene or operon? (a) Eukaryotes have three types of RNA polymerase (b) Eukaryotic RNA polymerases require general transcription factors (c) The transcription of a eukaryotic gene can be influenced by proteins that bind far from the promoter.

Which of the following is not true of molecular chaperones? (a) They assist polypeptide folding by helping the folding process follow the most energentically favorable pathway. (b) They can isolate proteins from other components of the cells until folding is complete. (c) They can interact with unfolded polypeptides in a way that changes the final fold of the protein. (d) They help streamline the protein folding process bu making it more efficient and reliable process inside the cell.

How do changes in histone modification lead to changes in chromatin structure? (a) They directly lead to changes in the position of the core histones. (b) They change the affinity between the histone octamer and DNA. (c) They help recruit other proteins to the chromatin (d) They cause the histone N-terminal tails to become hyperextended.

Scientists learned that cell death is a normal and even important part of life by studying the development of the nematode worm C. elegans. What was the most important feature of C. elegans for the study of programmed cell death? (a) The nematode is smaller and simpler than the fruit fly. (b) 70% of C. elegans genes have homologs in humans. (c) The developmental pathway of each cell in the adult worm was known. (d) Its genome was partially sequenced

(c) This is the best answer because it was the prior developmental studies tracing cell lineages from the egg to the adult that allowed scientists to identify the precise time and location of cells that were being targeted for cell death. It was observed that this cell death was a normal and necessary part of the developmental pathway in the worm. Programmed cell death has since become known to be an important process in all multicellular eukaryotic organisms.

A strain of yeast translates mRNA into protein inaccurately. Individual molecules of a particular protein isolated from this yeast have variations in the first 11 amino acids compared with the sequence of the same protein isolated from normal yeast cells. What is the most likely cause of this variation in protein sequence?(a) a mutation in the DNA coding for the protein (b) a mutation in the anticodon of the isoleucine-tRNA (tRNA^Ile) (c) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different amino acids (d) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different tRNA molecules

Beside the distortion in the DNA backbone caused by a mismatched base pair, what additional mark is there on eukaryotic DNA to indicate which strand needs to be repaired? (a) a nick in the template strand (b) a chemical modification of the new strand (c) a nick in the new strand (d) a sequence gap in the new strand

Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to power many of the cellular processes, increasing the pool of ADP. As the relative amount of ADP molecules increases, they can bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe this mechanism of regulation is ___________________. (a) feedback inhibition (b) oxidative phosphorylation (c) allosteric activation

Which of the following mechanisms best describes the manner in which lysozyme lowers the energy required for its substrate to reach its transition-state conformation? (a) by binding two molecules and orienting them in a way that favors a reaction between them (b) by altering the shape of the substrate to mimic the conformation of the transition state (c) by speeding up the rate at which water molecules collide with substrate (d) by binding irreversibly to the substrate so that it cannot dissociate

DNA replication is considered semiconservative because __________________________________. (a) after many rounds of DNA replication, the original DNA double helix is still intact. (b) each daughter DNA molecule consists of two new strands copied form the parent (c) each daughter DNA molecule consists of one strand from the parent DNA molecule and one new strand.

When there is a well established segment of heterochromatin on an interphase chromosome, there is usually a special barrier sequence that prevents the heterochromatin from expanding along the entire chromosome. 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. What is the best way to describe what has happened to the function of gene A in these cells? (a) barrier destruction (b) heterochromization (c) epigenetic inheritance (d) euchromatin depletion

Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which renders it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall? (a) isomerase (b) protease (c) hydrolase

Several members of the same family were diagnosed with the same kind of cancer when they were unusually young. Which one of the following is most likely explanation for this? It is possible that the individuals with cancer have ________________. (a) inherited a cancer causing gene that suffered mutation in somatic cells (b) inherited a mutation in a gene required for DNA synthesis (c) inherited a mutation in a gene required for mismatch repair

RNA in cells differs from DNA in that ________________________. (a) it contains the base uracil, which pairs with cytosine. (b) it is single-stranded and cannot form base pairs (c) it is single-stranded and can fold up into a variety of structures (d) the sugar ribose contains fewer oxygen atoms than deoxyribose does

Double covalent bonds are both shorter and stronger than single covalent bonds, but they also limit the geometry of the molecule because they ______________________. (a) create a new arrangement of electron shells (b) change the reactivity of the bonded atoms (c) limit the rotation of the bonded atoms (d) prevent additional bonds from being formed with the bonded atoms

The inactivation of one X chromosome is established by the direct spreading of heterochromatin. The silent state of this chromosome is _______________ in the subsequent cell divisions. (a) completed (b) switched (c) maintained (d) erased

In addition to the repair of DNA double strand breaks, homogolous recombination is a mechanism for generating genetic diversity by swapping segments of parental chromosomes. Which process does this swapping occur? (a) replication (b) DNA repair (c) meiosis (d) transportation

Which subatomic particles can vary between isotopes of the same element, without changing the observed chemical properties? (a) electrons (b) protons and neutrons (c) neutrons (d) neutrons and electrons

Which of the following statements is true? (a) Peptide bonds are the only covalent bonds that can link together two amino acids in proteins. (b) The polypeptide backbone is free to rotate about each peptide bond. (c) Nonpolar amino acids tends to be found in the interior of proteins (d) The sequence of the atoms in the polypeptide backbone varies between different proteins.

What method is used to study proteins limited to proteins with a molecular mass of 50 kD or less? (a) X-ray crystallography (b) fingerprinting (c) nuclear magnetic resonance (d) mass spectroscopy

What type of macromolecule helps package DNA in eukaryotic chromosomes? (a) lipids (b) carbohydrates (c) proteins (d) RNA

Which of the following statements is true? (a) Ribosomes are large RNA structures composed solely of rRNA. (b) Ribosomes are synthesized entirely in the cytoplasm (c) rRNA contains the catalytic activity that joins amino acids together (d) A ribosome binds one tRNA at a time

The sigma subunit of bacterial RNA polymerase __________________________. (a) contains the catalytic activity of the polymerase (b) remains part of the polymerase throughout transcription (c) recognizes promoter sites in the DNA (d) recognizes transcription termination of sites in the DNA

Which elements will form ions with a net charge of +1 in solution? (a) carbon, sulfur (b) helium, neon (c) sodium, potassium (d) magnesium, calcium

Antibody production is an indispensible part of our immune response, but it is not the only defense our bodies have. Which of the following is observed during an infection that is not a result of antibody-antigen interactions? (a) B cell proliferation (b) aggregation of viral particles (c) systemic temperature increase (d) antibody secretion

The process of DNA replication requires that each of the parental DNA strands be used as a ____________ to produce a duplicate of the opposing strand. (a) catalyst (b) competitor (c) template (d) copy

The concentration of a particular protein, X, in a normal human cell rises gradually from a low point, immediately after cell division, to a high point, just before cell division, and the drops sharply. Which of the following mutations in the gene for X could explain these results? (a) the introduction of a stop codon that truncates protein X at the fourth amino acid (b) a change of the first ATG codon to CCA (c) the deletion of a sequence that encodes sites at which ubiquitin can be attached to the protein (d) a change at a splice site that prevents splicing of the RNA

Nonhomologous end joining is a process by which a double-stranded DNA end is joined ____________________________. (a) to a similar stretch of sequence on the complementary chromosome (b) after repairing any mismatches (c) to the nearest available double stranded DNA end

Which of the following structural characteristics is not normally observed in a DNA duplex? (a) purine-pyrimidine pairs (b) external sugar-phosphate backbone (c) uniform left handed twist (d) antiparallel strands

Although the chromatin structure of interphase and mitotic chromosomes is very compact, DNA-binding protein complexes must be able to gain access to the DNA molecule. Chromatin-remodeling complexes provide this access by ____________________. (a) recruiting other enzymes (b) modifying the N terminal tails of core histones (c) using the energy of ATP hydrolysis to move nucleosomes

What method is used to assess levels of expressions of your target protein in different cell types? (a) gel filteration chromatography (b) gel electrophoresis (c) western blot analysis

To what degree does the mismatch repair system decrease the error rate arising from DNA replication? (a) 2 fold (b) 5 fold (c) 10 fold (d) 100 fold

(d) 100 fold

You have a concentrated stock solution of 10 M NaOh and want to use it to produce a 150mL solution of 3 NaOH. What volume of water and stock solutions will you measure out to make this new solution? (a) 135 mL of water, 15 mL of NaOH stock (b) 115 mL of water, 35 mL of NaOH stock (c) 100 mL of water, 50 mL of NaOh stock (d) 105 mL of water, 45 mL of NaOH stock

(d) 105 mL of water, 45 mL of NaOH stock

Hershey and Chase used radiolabeled macromolecules to identify the material that contains heritable information. What radioactive material was used to track DNA during this experiment? (a) 3 H (b) 14 C (c) 35 S (d) 32 P

(d) 32 P

The human genome is a diploid genome. However, when germ-line cells produces gametes, these specialized cells are haploid. What is the total number of chromosomes found in each of the gametes (egg or sperm) in your body? (a) 22 (b) 23 (c) 44 (d) 46

(d) 46

How many nucleotides does an ET codon contain? (a) 2 (b) 3 (c) 4 (d) 5 (e) 6

(d) 5

Which of the following DNA strands can form a DNA duplex by pairing itself at each position? (a) 5' AAGCCCAA-3' (b) 5' AAGCCCGTT-3' (c) 5' AAGCGCAA-3' (d) 5' AAGCGCTT-3'

(d) 5' AAGCGCTT-3'

Motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration, and move chromosomes during cell division. Which of the following mechanisms is sufficient to ensure the unindirectional movement of a motor protein along its substrate? (a) a conformational change is coupled to the release of a phosphate (b) The substrate on which the motor moves has a conformational polarity. (c) A conformational change is coupled to the binding of ADP (d) A conformational change is linked to ADP hydrolysis

(d) A conformational change is linked to ADP hydrolysis

Beta sheets can participate in the formation of amyloid fibers, which are insoluble protein aggregates. What drives the formation of amyloid fibers? (a) denaturation of proteins containing B sheets (b) extensions of B sheets into much longer B strands (c) formation of biofilms by infectious bacteria (d) B sheet stabilization of abnormally folded proteins

(d) B sheet stabilization of abnormally folded proteins

Which of the following peptides can be produced from poly UAUC? (a) Ile-Phe-Val-Tyr (b) Tyr-Ser-Phe-Ala (c) Ile-Lys-His-Tyr (d) Cys-Pro-Lys-Ala

(d) Cys-Pro_Lys-Ala

In the 1940s, proteins were thought to be the more likely molecules to house genetic information. What was the primary reason that DNA was not originally believed to be the genetic material? (a) DNA was a high density of negative charges (b) Nucleotides were known to be a source of chemical energy for the cell. (c) Both protein and nucleic acids were found to be components of chromosomes. (d) DNA was found to contain only four different chemical building blocks.

(d) DNA was found to contain only four different chemical building blocks

Which of the following questions would not be answered by using karyotyping? (a) Is the individual genetically female or male (b) Do any of the chromosomes contain pieces that belong to the other chromosome? (c) Does the individual have an extra chromosome (d) Do any chromosomes contain point mutations?

(d) Do any chromosomes contain point mutations?

If the genome of the bacterium E. coli requires about 20 minutes to replicate itself, how can the genome of a fruit fly be replicated in only 3 minutes? (a) The fruit fly genome is smaller than E coli (b) Eukaryotic DNA polymerase synthesizes DNA at a much faster rate than prokaryotic (c) The nuclear membrane keeps the fruit fly DNA concentrated in one place in the cell, which increases the rate of polymerization (d) Fruit fly DNA contains more origins of replication than E coli DNA.

(d) Fruit fly DNA contains more origins of replication than E coli DNA

You are examining the DNA sequences that code for the enzyme phosphofructokinase in skinks and komodo dragons. You notice that the coding that actually directs the sequence of amino acids in the enzyme is very similar in the two organisms but that the surrounding sequences vary quite a bit. What is the most likely explanation? (a) coding sequences are repaired more efficiently (b) coding sequences are replicated more accurately. (c) Coding sequences are packaged more tightly in the chromosomes to protect them from DNA damage. (d) Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences.

(d) Mutations in coding sequence are more likely to be deleterious to the organism than mutations in noncoding sequences.

Which of the following methods is not used by cells to regulate the amount of a protein in the cell? (a) Genes can be transcribed into mRNA with different efficiencies (b) Many ribosomes can bind to a single mRNA molecule (c) Proteins can be tagged with ubiquitin, marking them for degradation (d) Nuclear pore complexes can regulate the speed at which newly synthesized proteins are exported from the nucleus into the cytoplasm

(d) Nuclear pore complexes can regulate the speed at which newly synthesized proteins are exported from the nucleus into the cytoplasm

Unlike DNA, which typically forms a helical structure, different molecules of RNA can fold into a variety of three-dimensional shapes. This is largely because _________________________. (a) RNA contains uracil and uses ribose as the sugar (b) RNA bases cannot form hydrogen with each other (c) RNA nucleotides use a different chemical linkage between nucleotides compared to DNA. (d) RNA is single-stranded

(d) RNA is single-stranded

Molecular chaperones can work by creating an "isolation chamber" What is the purpose of this chamber? (a) The chamber acts as a garbage disposal, degrading improperly folded proteins so that they do not interact with properly folded proteins. (b) This chamber is used to increase the local protein concentration, which will help speed up the folding processes. (c) This chamber serces to transport unfolded proteins out of the cell (d) This chamber serves to protect unfolded proteins from interacting with other proteins in cytosol, until protein folding is completed.

(d) This chamber serves to protect unfolded proteins from interacting with other proteins in cytosol, until protein folding is complete.

Which of the following statements is false? (a) A new RNA molecule can begin to be synthesized from a gene before the previous RNA molecule's synthesis is completed (b) If two genes are to be expressed in a cell, these two genes can be transcribed with different efficiencies (c) RNA polymerase is responsible for both unwinding the DNA helix and catalyzing the formation of the phosphodiester bonds between nucleotides. (d) Unlike DNA, RNA uses a uracil base and a deoxyribose sugar.

(d) Unlike DNA, RNA uses a uracil base and a deoxyribose sugar.

The Ras protein is a GTPase that functions in many growth-factor signaling pathways. In its active form, with GTP bound, it transmits a downstream signal that leads to cell proliferation; in its inactive form, with GDP bound, the signal is not transmitted. Mutations in the gene for Ras are found in many cancers. Of the choices below, which alteration of Raas activity is most likely to contribute to the uncontrolled growth of cancer cells? (a) a change that prevents Ras from being made (b) a change that increases the affinity of Ras for GDP (c) a change that decreases the affinity of Ras for GTP (d) a change that decreases the rate of hydrolysis of GTP by Ras

(d) a change that decreases the rate of hydrolysis of GTP by Ras

Which of the following might decrease the transcription of only one specific gene in a bacterial cell? (a) a decrease in the amount of sigma factor (b) a decrease in the amount of RNA polymerase (c) a mutation that introduced a stop codon into the DNA that precedes the gene's coding sequence (d) a mutation that introduced extensive sequence changes into the DNA that precedes the gene's transcription start site

(d) a mutation that introduced extensive sequence changes into the DNA that precedes the gene's transcription start site

Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term "protein domain" (a) A small cluster of alpha helices and beta sheets (b) the tertiary structure of a substrate-binding pocket (c) a complex of more than one polypeptide chain (d) a protein segment that folds independently

(d) a protein segment that folds independently

Cholesterol is an essential component of biological membranes. Although it is much smaller than the typical phospholipids and glycolipids in the membrane, it is a(n) ________________ molecule, having both hydrophilic and hydrophobic regions. (a) polar (b) oxygen-containing (c) hydrophobic (d) amphipathic

(d) amphipathic

Chemical reactions in living systems occur in an ____________________ environment, within a narrow range of temperatures. (a) optimal (b) organic (c) extracellular (d) aqueous

(d) aqueous

snRNAs ___________________________. (a) are translated into snRNPs (b) are important for producing mature mRNA transcripts in bacteria (c) are removed by the spliceosome during RNA splicing (d) can bind to specific sequences at intron-extron boundaries through complementary base-pairing.

(d) can bind to specific sequences at intron-extron boundaries through complementary base-pairing.

The complete set of information found in a given organism's DNA is called its ____________. (a) genetic code (b) coding sequence (c) gene (d) genome

(d) genome

The pH of an aqueous solution is an indication of the concentration of available protons. However, you should not expect to find lone protons in solution: rather, the proton is added to a water molecule to form a(n) _______________ ion. (a) hydroxide (b) ammonium (c) chloride (d) hydronium

(d) hydronium

A molecule of bacterial DNA introduced into a yeast cell is imported into the nucleus but fails to replicate with the yeast of DNA. Choose the protein or protein complex below that is most likely responsible for the failure to replicate bacterial DNA. (a) primase (b) helicase (c) DNA polymerase (d) initiator proteins

(d) initiator proteins

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking DNA ligase were used? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading strand elongation (d) lagging strand completion

(d) lagging strand completion

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking the exonuclease activity of DNA polymerase were used to make the cell extracts? (a) initiation of DNA synthesis (b) Okazaki fragment synthesis (c) leading-strand elongation (d) lagging-strand completion

(d) lagging strand completion

Total nucleic acids are extracted from a culture of yeast cells and are then mixed within resin beads to which the polynucleotide 5'-TTTTTTTTTTTTTTTTT-3' has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you anaylze the cellular nucleic acids that have stuck to beads, which of the following is most abundant? (a) DNA (b) tRNA (c) rRNA (d) mRNA

(d) mRNA

According to current thinking, the minimum requirement for life to have originated on Earth was the formation of a _____________. (a) molecule that could provide a template for the production of a complementary molecule (b) double-stranded DNA helix (c) molecule that could direct protein synthesis (d) molecule that could catalyze its own replication

(d) molecule that could catalyze its own replication

Transcription is similar to DNA replication in that __________________________. (a) an RNA transcript is synthesized discontinously and the pieces are then joined together. (b) it uses the same enzyme as that used to synthesize RNA primers during DNA replication (c) the newly synthesized RNA remains paired to the template DNA (d) nucleotide polymerization occurs only in the '5-to-3' direction

(d) nucleotide polymerization occurs only in the '5-to 3' direction

Cells require one particular monosaccharide as a starting material to synthesize nucleotide building blocks. Which of the monosaccharides below fills this important role? (a) glucose (b) fructose (c) ribulose (d) ribose

(d) ribose

Which of the following chemical groups is not used to construct a DNA molecule? (a) five-carbon sugar (b) phosphate (c) nitrogen-containing base (d) six-carbon sugar

(d) six-carbon sugar

Macromolecules in the cell can often interact transiently as a result of noncovalent interactions. These weak interactiosn also produce stable, highly specific interactions between molecules. Which of the factors below is the most significant in determining whether the interaction will be transient or stable? (a) the size of each molecule (b) the concentration of each molecule (c) the rate of synthesis (d) surface complementarity between molecules

(d) surface complementarity between molecules

Telomeres serve as caps at the ends of linear chromosomes. Which of the following is not true regarding the replication of telomeric sequences? (a) The lagging strand telomeres are not completely replicated by DNA polymerase. (b) Telomeres are made of repeating sequences (c) Additional repeated sequences are added to the template strand (d) the leading strand doubles back on itself to form a primer for the lagging strand

(d) the leading strand doubles back on itself to form a primer for the lagging strand

In a DNA double helix, ___________________________. (a) the two DNA strands are identical (b) purines pair with purines (c) thymine pairs with cystosine (d) the two DNA strands run antiparallel

(d) the two DNA strands run antiparallel

What is the ultimate fate of disease-causing, unfolded proteins. (a) They are degraded (b) They bind a different target protein (c) They form structured filaments. (d) They form protein aggregates

(d) they form protein aggregates

An ionic bond between two atoms is formed as a result of the __________________. (a) sharing of electrons (b) loss of electrons from both atoms (c) loss of a proton from one atom (d) transfer of electrons from one atom to the other

(d) transfer of electrons from one atom to the other

Many types of cells have stores of lipids in their cytoplasm, usually seen as fat droplets. What is the lipid most commonly found in these droplets? (a) cholesterol (b) palmitic acid (c) isoprene (d) triacylglycerol

(d) triacylglycerol

Human beings with the inherited disease xeroderma pigmentosum have serious problems with lesions on their skin and often develop skin cancer with repeated exposure to sunlight. What type of DNA damage is not being recognized in the cells of these individuals? (a) chemical damage (b) X ray irradiation damage (c) mismatched bases (d)ultraviolet irradiation damage

(d) ultraviolet irradiation damage

Polar covalent bonds are formed when the electrons in the bond are not shared equally between the two nuclei. Which one of these molecules contains polar bonds? (a) molecular oxygen (b) methane (c) propane (d) water

(d) water

If 0.5 kilocalories of energy are required to break 6x10^23 bonds of a particular type, what is the strength of this bond?

0.5kcal/mol

How does the total number of replication origins in bacterial cells compare with the number of origins in human cells?

1 versus 10,000

Name three covalent modifications that can be made to an RNA molecules in eukaryotic cells before the RNA molecule becomes a mature mRNA.

1. A poly-A tail is added 2. A 5' cap is added 3. Introns can be spliced out

List three ways in which the process of eukaryotic transcription differs form the process of bacterial transcription.

1. Bacterial cells contain a single RNA polymerase where as eukaryotic cells have three. 2. Bacterial RNA polymerase can initiate transcription without the help of additional proteins, but eukaryotic RNA polymerases need general transcription factors. 3. Eukaryotic transcription is affected by chromatin structure and nucleosomes, whereas bacteria lack nucleosomes.

The following segment of DNA is from a transcribed region of a chromosome. You know that RNA polymerase moves from left to right along this piece of DNA, that the promoter for this gene is to the left of the DNA shown, and that this entire region of DNA is made into RNA: 5′-GGCATGGCAATATTGTAGTA-3′ 3′-CCGTACCGTTATAACATCAT-5′ Given this information, a student claims that the RNA produced from this DNA is: 3′-GGCATGGCAATATTGTAGTA-5′ Give 2 reasons why this answer is incorrect.

1. The RNA should have uracil instead of thymine 2. The polarity of the molecule is incorrectly labeled.

What concentration of hydronium ions does a solution of pH 8 contain?

10^-8 M

If 0.5 mole of glucose weighs 90 g, what is the molecular mass of glucose?

180 daltons. A mole of a substance has a mass equivalent to its molecular weight expressed in grams.

In what decade did scientists first identify chromosomes?

1880s

How many replication forks are formed when an origin of replication is opened?

How many different peptides could potentially be made from this sequence of RNA, assuming that translation initiates upstream of this sequence? What are these peptides?

2, VAYP, SLPIG

How many carbon atoms does the molecule represented in the figure have? How many hydrogens? What type of molecule is it?

20 carbon atoms, 31 hydrogen atoms, fatty acid

The instructions specified by the DNA will ultimately specify the sequence of proteins. This process involves DNA, made up of _____ different nucleotides, which gets ______________ into RNA, which is then _______________ into proteins, made up of _____ different amino acids.

4, transcribed, translated, 20

What is the concentration, in grams per liter (g/L), of a 0.25 M solution of glucose?

45g/L

How many hydrogen bonds can urea form if dissolved in water?

What is the correct atomic number and atomic weight respectively for an atom of carbon?

6, 12

How many molecules are there in 1 mole of glucose?

6X10^23

By definition, prokaryotic cells do not possess __________. (a) a nucleus. (b) replication machinery. (c) ribosomes. (d) membrane bilayers.

Drosophila melanogaster is a/an __________. This type of animal is the most abundant of all animal species, making it an appropriate choice as an experimental model. (a) insect (b) bird (c) amphibian (d) mammal

Eukaryotic cells are able to trigger the release of material from secretory vesicles to the extracellular space using a process called exocytosis. An example of materials commonly released this way is _____________. (a) hormones. (b) nucleic acids. (c) sugars. (d) cytosolic proteins

Many of the mechanisms that cells use for maintenance and reproduction were first studied at the molecular level in bacteria. Which bacterial species had a central role in advancing the field of molecular biology? (a) E. coli (b) D. melanogaster (c) S. pombe (d) C. elegans

Select the option that best finishes the following statement: "Evolution is a process __________." (a) that can be understood based on the principles of mutation and selection. (b) that results from repeated cycles of adaptation over billions of years. (c) by which all present-day cells arose from 4-5 different ancestral cells. (d) that requires hundreds of thousands of years.

The flow of genetic information is controlled by a series of biochemical reactions that result in the production of proteins, each with its own specific order of amino acids. Choose the correct series of biochemical reactions from the options presented here. A) replication, transcription, translation B) replication, translation, transcription C) translation, transcription, replication D) translation, replication, transcription

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. The paramecium is a multicellular microorganism covered with hairlike cilia. B. Cells of different types can have different chemical requirements. C. The branchlike extensions that sprout from a single nerve cell in a mammalian brain can extend over several hundred micrometers.

A) False. The paramecium is a single-celled organism. B) True. C) True.

Although there are many distinct prokaryotic species, most have a small range of shapes, sizes, and growth rates. Which of the following characteristics are not observed in prokaryotes? (a) a highly structured cytoplasm (b) endoplasmic reticulum (c) the ability to divide rapidly (d) a cell wall

A,B

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. Plants do not require a cytoskeleton because they have a cell wall that lends structure and support to the cell. B. The cytoskeleton is used as a transportation grid for the efficient, directional movement of cytosolic components. C. Thermal energy promotes random movement of proteins, vesicles, and small molecules in the cytosol.

A. False. Although plant cells do have a cell wall that lends structure and support, they still need a cytoskeleton, which also helps with connections between cells and the transport of vesicles inside the cell. B. True. C. True.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. With respect to cellular respiration, the only organelles used by animal cells are mitochondria, while plant cells use both mitochondria and chloroplasts. B. The number of mitochondria inside a cell remains constant over the life of the cell.

A. False. In plants, only mitochondria perform cellular respiration (using oxygen to break down organic molecules to produce carbon dioxide) just as in animal cells. Chloroplasts perform photosynthesis in which water molecules are split to generate oxygen and fix carbon dioxide molecules. B. False. Mitochondria have their own division cycle and their numbers change based on the rate of division.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. Primitive plant, animal, and fungal cells probably acquired mitochondria after they diverged from a common ancestor. B. Protozoans are single-celled eukaryotes with cell morphologies and behaviors that can be as complex as those of some multicellular organisms. C. The first eukaryotic cells on Earth must have been aerobic; otherwise, they would not have been able to survive when the planet's atmosphere became oxygen-rich.

A. False. The mitochondria in modern plant, animal, and fungal cells are very similar, implying that these lines diverged after the mitochondrion was acquired by the ancestral eukaryote. B. True. C. False. The first eukaryotic cells likely contained a nucleus but no mitochondria. These ancestral eukaryotes subsequently adapted to survive in a world filled with oxygen by engulfing primitive aerobic prokaryotic cells.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A) The nucleus of an animal cell is round, small, and difficult to distinguish using light microscopy. B) The presence of the plasma membrane can be inferred by the well-defined boundary of the cell. C) The cytosol is fairly empty, containing a limited number of organelles, which allows room for rapid movement via diffusion.

A. False. The nucleus is one of the largest organelles and is the easiest organelle to discern within a typical cell. B. True. C. False. The cytosol is actually brimming with individual proteins, protein fibers, extended membrane systems, transport vesicles, and small molecules. And although cellular components do move by diffusion, the rate of movement is limited by the space available and the size of the component in question.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. The human genome is roughly 30 times larger than the Arabidopsis genome, but contains approximately the same number of protein-coding genes. B. The variation in genome size among protozoans is larger than that observed across all species of mammals, birds, and reptiles. C. The vast majority of our genome encodes functional RNA molecules or proteins and most of the intervening DNA is nonfunctional.

A. True. B. True. C. False. It is a relatively small proportion of our DNA that encodes RNA and protein molecules. The majority of nonencoding sequences is probably involved in critical regulatory processes.

Indicate whether the following statements are true or false. If the statement is false, explain why it is false. A. Membrane components in the cell are made in the endoplasmic reticulum. B. The Golgi apparatus is made up of a series of membrane-enclosed compartments through which materials destined for secretion must pass. C. Lysosomes are small organelles where fatty acid synthesis occurs.

A. True. B. True. C. False. Lysosomes house enzymes that break down nutrients for use by the cell and help recycle materials that cannot be used, which will later be excreted from the cell.

Given what you know about the differences between prokaryotic cells and eukaryotic cells, rate the following things as "good" or "bad" processes to study in the model organism E. coli. A. formation of the endoplasmic reticulum B. DNA replication C. how the actin cytoskeleton contributes to cell shape D. how cells decode their genetic instructions to make proteins E. how mitochondria get distributed to cells during cell division

A. bad B. good C. bad D. good E. bad

A. thaliana, or Arabidopsis, is a common weed. Biologists have selected it over hundreds of thousands of other flowering plant species to serve as an experimental model organism because __________________. (a) it can withstand extremely cold climates. (b) it can reproduce in 8-10 weeks. (c) it produces thousands of offspring per plant. (d) Both (b) and (c) are true

Brewer's yeast, apart from being an irreplaceable asset in the brewery and in the bakery, is an experimental organism used to study eukaryotic cells. However, it does have some limitations. Which of the processes below cannot be studied in yeast? (a) DNA replication (b) cell motility (c) exocytosis (d) cell division

Caenorhabditis elegans is a nematode. During its development, it produces more than 1000 cells. However, the adult worm has only 959 somatic cells. The process by which 131 cells are specifically targeted for destruction is called ______________. (a) directed cell pruning. (b) programmed cell death. (c) autophagy. (d) necrosis.

Changes in DNA sequence from one generation to the next may result in offspring that are altered in fitness compared with their parents. The process of change and selection over the course of many generations is the basis of __________. (a) mutation. (b) evolution. (c) heredity. (d) reproduction.

Living systems are incredibly diverse in size, shape, environment, and behavior. It is estimated that there are between 10 million and 100 million different species. Despite this wide variety of organisms, it remains difficult to define what it means to say something is alive. Which of the following can be described as the smallest living organism? A) DNA B) cell C) organelle D) protein

Photosynthesis enables plants to capture the energy from sunlight. In this essential process, plants incorporate the carbon from CO2 into high-energy __________ molecules, which the plant cell mitochondria use to produce ATP. (a) fat (b) sugar (c) protein (d) fiber

Select the option that correctly finishes the following statement: "A cell's genome _________________." (a) is defined as all the genes being used to make protein. (b) contains all of a cell's DNA. (c) constantly changes, depending upon the cell's environment. (d) is altered during embryonic development.

The cytoskeleton provides support, structure, motility, and organization, and it forms tracks to direct organelle and vesicle transport. Which of the cytoskeletal elements listed below is the thickest? (a) actin filaments (b) microtubules (c) intermediate filaments (d) none of the above (all the same thickness)

The nucleus, an organelle found in eukaryotic cells, confines the __________, keeping them separated from other components of the cell. (a) lysosomes (b) chromosomes (c) peroxisomes (d) ribosomes

What is the smallest distance two points can be separated and still resolved using light microscopy? (a) 20 nm (b) 0.2 µm (c) 2 µm (d) 200 µm

Which of the following choices best describes the role of the lysosome? (a) transport of material to the Golgi (b) clean-up, recycling, and disposal of macromolecules (c) sorting of transport vesicles (d) the storage of excess macromolecules

Which of the following organelles has both an outer and an inner membrane? (a) endoplasmic reticulum (b) mitochondrion (c) lysosome (d) peroxisome

Which statement is NOT true about the events/conclusions from studies during the mid- 1800s surrounding the discovery of cells? (a) Cells came to be known as the smallest universal building block of living organisms. (b) Scientists came to the conclusion that new cells can form spontaneously from the remnants of ruptured cells. (c) Light microscopy was essential in demonstrating the commonalities between plant and animal tissues. (d) New cells arise from the growth and division of previously existing cells.

Match each biological process with the model organism that is best suited or most specifically useful for its study, based on information provided in your textbook. You may list individual processes more than once. A. cell division B. development (multicellular) C. programmed cell death D. photosynthesis E. immunology _____ A. thaliana (Arabidopsis) _____ M. musculus (mouse) _____ S. pombe _____ C. elegans _____ S. cerevisiae _____ D. rerio (zebrafish) _____ D. melanogaster

B, D A. thaliana (Arabidopsis) B, E M. musculus (mouse) A S. pombe C C. elegans A S. cerevisiae B D. rerio (zebrafish) B D. melanogaster

Choose the phrase that best completes this sentence: Microtubules ____________ and are required to pull duplicated chromosomes to opposite poles of dividing cells (a) generate contractile forces (b) are intermediate in thickness (c) can rapidly reorganize (d) are found in especially large numbers in muscle cells

Mitochondria contain their own genome, are able to duplicate, and actually divide on a different time line from the rest of the cell. Nevertheless, mitochondria cannot function for long when isolated from the cell because they are __________________. (a) viruses. (b) parasites. (c) endosymbionts. (d) anaerobes.

Mitochondria perform cellular respiration, a process that uses oxygen, generates carbon dioxide, and produces chemical energy for the cell. Which answer below indicates a correct pairing of material "burned" and the form of energy produced during cellular respiration? (a) fat, ADP (b) sugar, fat (c) sugar, ATP (d) fat, protein

Proteins are important architectural and catalytic components within the cell, helping to determine its chemistry, its shape, and its ability to respond to changes in the environment. Remarkably, all of the different proteins in a cell are made from the same 20 __________. By linking them in different sequences, the cell can make protein molecules with different conformations and surface chemistries, and therefore different functions. (a) nucleotides. (b) sugars. (c) amino acids. (d) fatty acids.

Some prokaryotes can live by utilizing entirely inorganic materials. Which of the following inorganic molecules would you predict to be the predominant building block for fats, sugars, and proteins? (a) O2 (b) N2 (c) CO2 (d) H2

Which statement is NOT true about mutations? (a) A mutation is a change in the DNA that can generate offspring less fit for survival than their parents. (b) A mutation can be a result of imperfect DNA duplication. (c) A mutation is a result of sexual reproduction. (d) A mutation is a change in the DNA that can generate offspring that are as fit for survival as their parents are.

Zebrafish (Danio rerio) are especially useful in the study of early development because their embryos ______________. (a) are exceptionally large. (b) develop slowly. (c) are transparent. (d) are pigmented.

_________ are fairly small organelles that provide a safe place within the cell to carry out certain biochemical reactions that generate harmful, highly reactive oxygen species. These chemicals are both generated and broken down in the same location. (a) Nucleosomes (b) Lysosomes (c) Peroxisomes (d) Endosomes

Biologists cannot possibly study all living species. Instead, they try to understand cell behavior by studying a select subset of them. Which of the following characteristics are useful in an organism chosen for use as a model in laboratory studies? (a) amenability to genetic manipulation (b) ability to grow under controlled conditions (c) rapid rate of reproduction (d) all of the above

Cell biologists employ targeted fluorescent dyes or modified fluorescent proteins in both standard fluorescence microscopy and confocal microscopy to observe specific details in the cell. Even though fluorescence permits better visualization, the resolving power is essentially the same as that of a standard light microscope because the resolving power of a microscope is limited by the __________ of light. (a) absorption (b) intensity (c) filtering (d) wavelength

Chloroplasts are found only in eukaryotic cells that carry out photosynthesis: plants and algae. Plants and algae appear green as a result of the presence of chlorophyll. Where is chlorophyll located in the chloroplast? (a) in the first, outer membrane (b) in the space between the first and second membranes (c) in the second, inner membrane (d) in the third, innermost membrane

Despite the differences between eukaryotic and prokaryotic cells, prokaryotes have proteins that are distantly related to eukaryotic actin filaments and microtubules. What is likely to be the most ancient function of the cytoskeleton? (a) cell motility (b) vesicle transport (c) membrane support (d) cell division

Prokaryotic cells are able to evolve very fast, which helps them to rapidly adapt to new food sources and develop resistance to antibiotics. Which of the options below lists the three main characteristics that support the rapid evolution of prokaryotic populations? (a) microscopic, motile, anaerobic (b) aerobic, motile, rapid growth (c) no organelles, cell wall, can exchange DNA (d) large population, rapid growth, can exchange DNA

The __________ __________ is made up of two concentric membranes and is continuous with the membrane of the endoplasmic reticulum. (a) plasma membrane (b) Golgi network (c) mitochondrial membrane (d) nuclear envelope

The cell constantly exchanges materials by bringing nutrients in from the external environment and shuttling unwanted by-products back out. Which term describes the process by which external materials are captured inside vesicles and brought into the cell? (a) degradation (b) exocytosis (c) phagocytosis (d) endocytosis

What unit of length would you generally use to measure atypical plant or animal cell? (a) centimeters (b) nanometers (c) millimeters (d) micrometers `

Which of the following characteristics would not support the idea that the ancestral eukaryote was a predator cell that captured and consumed other cells? (a) dynamic cytoskeleton (b) large cell size (c) ability to move (d) rigid membrane

Which pair of values best fills in the blanks in this statement: On average, eukaryotic cells are __________ times longer and have _________ times more volume than prokaryotic cells. (a) 5, 100 (b) 10, 200 (c) 10, 100 (d) 10, 1000

Match the type of microscopy on the left with the corresponding description provided below. There is one best match for each. A. confocal B. transmission electron C. fluorescence D. phase-contrast E. scanning electron F. bright-field ___ uses a light microscope with an optical component to take advantage of the different refractive indices of light passing through different regions of the cell. ___ employs a light microscope and requires that samples be fixed and stained in order to reveal cellular details. ___ requires the use of two sets of filters. The first filter narrows the wavelength range that reaches the specimen and the second blocks out all wavelengths that pass back up to the eyepiece except for those emitted by the dye in the sample. ___ scans the specimen with a focused laser beam to obtain a series of two-dimensional optical sections, which can be used to reconstruct an image of the specimen in three dimensions. The laser excites a fluorescent dye molecule, and the emitted light from each illuminated point is captured through a pinhole and recorded by a detector. ___ has the ability to resolve cellular components as small as 2 nm. ___ requires coating the sample with a thin layer of a heavy metal to produce three- dimensional images of the surface of a sample.

D F C A B E

Give one reason why DNA makes a better material than RNA for the storage of genetic information, and explain.

DNA is double stranded and therefore the complementary strand provides a template from which damage can be repaired accurately.

Each chromosome is single molecule of ________ whose extraordinarily long length can be compacted by as much as ___________-fold during ___________________ and tenfold more during _______________. This is accomplished by binding to ________________ that help package the DNA in an orderly manner so it can fit in the small space delimited by the _____________________. The structure of the DNA-protein complex, called _________________, is highly _______________ over time.

DNA, 1000, interphase, mitosis, proteins, nuclear envelope, chromatin, dynamic

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

False

True or false? Depurination of DNA is rare event that is caused by ultraviolet irradiation.

False

True or false? Nonhomologous end joining is a mechanism that ensures that DNA double strand breaks are repaired with a high degree of fidelity to the original DNA sequence.

False

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

False.

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

False. Some sequences encode only RNA molecules, some bind to specific regulatory proteins, and others are sites where specific chromosomal protein structures are built.

True or false: A disaccharide consists of a sugar covalently linked to another molecule such as an amino acid or a nucleotide.

False. A disaccharide consists of two sugar molecules that undergo a condensation reaction to form a covalent bond.

True or false? ATPases generate ATP for the cell.

False. ATPases hydrolize chains. They do not produce it.

The DNA template used to repair the broken strand is the homologous chromosome inherited from the other parent.

False. Although it is called homologous recombination, this is not a process that depends on the proximity of parental homologs. When used as a mechanism for DNA repair, homologous recombination uses the sister chromatids in an undamaged, newly replicated (homologous) DNA helix as a template.

True or False? Explain your answer. "Since introns do not contain protein-coding information, they do not have to be removed precisely (meaning, a nucleotide here and there should not matter) from the primary transcript during RNA splicing."

False. Although it is true that the sequences within the introns are mostly dispensable, the introns must still be removed precisely because an error of one or two nucleotides would shift the reading frame, of the resulting mRNA molecule and change the protein it encodes.

True or false: The chemistry of life is carried out and coordinated primarily by the action of small molecules.

False. Although small molecules are important in many processes, the chemical reactions in living systems are regulated by the coordinated action of large polymeric molecules.

True or false: Atoms with unfilled outer electron shells are especially stable and are therefore less reactive.

False. Atoms that have their outer shells filled are the most stable and least reactive. Atoms with unfilled outer shells are more reactive because they tend to transfer electrons to fill and stabilize the outer shell.

True or false? DNA molecules, like proteins, consist of a single, long polymeric chain that is assembled from small monomeric subunits.

False. DNA is double stranded and made of two polymers that are complementary in sequence

True or false? Feedback inhibition is defined as a mechanisms of down-regulating enzyme activity by the accumulation of a product earlier in the pathway.

False. Feedback inhibition is what occurs when an enzyme activity occurs early in a metabolic pathway and is inhibited by the accumulation of a product late in the pathway. The inhibitory product binds to a site on the enzyme that lowers catalytic activity.

True or false? Gene sequences correspond exactly to the respective protein sequences produced from them.

False. Genes often contain intron sequences and genes always contain nucleotides flanking the protein coding sequences that are required for the regulation of transcription and translation.

Homologous recombination cannot occur in prokaryotic cells, because they are haploid, and therefore have no extra copy of the chromosome to use as a template for repair.

False. Homologous recombination also occurs in prokaryotic cells, and typically occurs very shortly after DNA replication, when the newly replicated duplexes are in close proximity.

True or false: Any covalently bonded H atom can participate in a hydrogen bond if it comes in close proximity with an oxygen atom that forms part of a water molecule.

False. Hydrogen atoms that are covalently bonded to carbon atoms do not participate in hydrogen bonds because these hydrogens have almost no net positive charge.

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

False. It does not need one becayse the RNA primers are not permanent

True or false: Approximately 0.9% of the atoms in the human body come from seven essential elements-Na, Mg, K, Ca, P, S, and Cl-all of which form stable ions in aqueous solution.

False. Na, Mg, K, Ca, and Cl form ions in aqueous solution, but P and S form covalent bonds in order to fill their outer electron shells.

True or false? Hydrogen bonds between each nucleotide hold individual DNA strands together.

False. Nucleotides are linked covalently through phosphodiester bonds. Hydrogen bonding between nucleotides from opposite strands holds the DNA together.

True or False: The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds.

False. Peptide bonds are planar amide bonds that are central to the polypeptide backbone formation. The atoms in the amino acid side chains are not considered to be part of the backbone.

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

False. Phosphorylation of a protein can change its conformation, but this modification may be a positive or a negative regulator of enzyme activity dependent on what protein it is.

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

False. The chromosomes still undergo at least one more level of packaging when they undergo mitosis

True or false: Generally, the total number of nonpolar amino acids has a greater affect on protein structure than the exact order of amino acids in a polypeptide chain.

False. The order in which amino acids are linked is unique for each protein and is the most important factor in determining the overall protein factor.

True or false: The presence of double bonds in the hydrocarbon tail of a fatty acid does not greatly influence its structure.

False. The presence of a double bond in the hydrocarbon chain of a fatty acid causes a kink in the chain, decreasing its flexibilty and packing with neighboring hydrocarbon chains.

True or 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.

False. The telomere is a specialized DNA sequence, but not for the attachment of spindle microtubules. They form special caps that stabilize the ends of linear chromosomes.

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

False. There are H2A and H2B tetramers and H3 and H4 tetramers in the solution. Each of the tetramers are two subunits of the respective proteins.

True or false? There are five different nucleotides that become incorporated into a DNA strand.

False. There are four different nucleotides that are used to make a DNA polymer.

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

False. There are several examples where related species have different numbers of chromosome pairs.

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

False. There are two enzymes needed because it is a two step process

True or False? A single polypeptide bond tends to adopt 3-4 different conformations, which all have equilvalent free-energy values (g).

False. There is a single final fold for every polypeptide. The fold adopted is the best conformation for which the free energy (G) of the molecule is at a minimum.

True or false? Collagen fibers and elastin fibers serve similar functions, which is expected because the structure of these two types of fibers is quite similar.

False. These two fibers are very different in structure and function. Collagen fibers are highly organized, triple strand coils that provide strength to hold tissue together. Elastin fibers are linked together in a loose network with disulfide bonds allowing it to stretch and be very flexible.

True or false: Copper, zinc, and manganese are among 11 nonessential trace elements that contribute less than 0.1% of all atoms in the human body.

False. They are essential trace elements in the human body.

True or false: H, C, O, and N are the most common elements in biological molecules because they are the most stable.

False. They are the most common elements in biological molecules because their outer shells are unfilled, making them highly reactive.

True or false? Histone proteins have a lower than average number of lysines and arginines in their polypeptide chains.

False. They have a higher than average number present that are positively charged and help to increase the nonspecific affinity between the histones and the negatively charged phosphates in the DNA backbones.

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

False. This is accomplished by initiated proteins binding at the origin of replication.

True or false? Van der Waals interactions and hydrophobic interactions are two ways to describe the same type of weak forces that help proteins fold.

False. Van der Waals attractions are weakly attractive forces that occur between all atoms. Hydrophobic interactions are only observed between nonpolar molecules in the context of an aqueous solution.

True or False: Nonpolar interaction is simply another way of saying van der Waals attractions.

False. Van der Waals attractions describe the general attractive forces between all atoms. The contact distance between any two non-bonded atoms is the sum of the van der waals radii. Nonpolar interactions are based on the exclusion of hydrophobic molecules from a hydrophilic environment.

The more __________ content, the higher the Tm (melting temperature).

G+C

True or false? Gene expression is the process of duplicating genes during DNA replication.

Gene expression is the process of going from sequences to RNA sequence to protein sequence

A nucleosome contains two molecules each of histones [H1 and H2A/H2A and H2B] as well as of histones H3 and H4.

H2A and H2B

How many hydrogen bonds can a hydrogen atom in a water molecule form? How many hydrogen bonds can the oxygen atom in a water molecule form?

Hydrogen can form one, oxygen can form two

How does cellular specialization serve multicellular organisms and how might a high degree of specialization detrimental?

In a multicellular organism, the specialization of cells creates a division of labor and each type of cell relies on the activities of other cell types for survival. This cooperation between specialized cells is essential for the organism as a whole. If one of these overly specialized cells were removed from the context of the organism, it would not have the capabilities needed to generate offspring and would probably not even live very long.

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.

In the absence of telomerase, the life-span of a cell and its progeny cells is limited. With each round of DNA replication, the length of telomeric DNA will shrink, until finally all the telomeric DNA has disappeared. Without telomeres capping the chromosome ends, the ends might be treated like breaks arising from DNA damage, or crucial genetic information might be lost. Cells whose DNA lacks telomeres will stop dividing or die. However, if telomerase is provided to cells, they may be able to divide indefinitely because their telomeres will remain a constant length despite repeated rounds of DNA replication.

What does the repair polymerase do?

It is used to fill in the spaces left vacant after RNA primers are degraded.

In which scientific unit is the strength of a chemical bond usually expressed?

Kilocalories per mole

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. Cells can be very diverse: superficially, they come in various sizes, ranging from bacterial cells such as Lactobacillus, which is a few ___ in length, to larger cells such as a frog's egg, which has a diameter of about one ___. Despite the diversity, cells resemble each other to an astonishing degree in their chemistry. For example, the same 20 ___ are used to make proteins. Similarly, the genetic information of all cells is stored in their ___. Although ___ contain the same types of molecules as cells, their inability to reproduce themselves by their own efforts means that means that they are not considered the living matter. amino acids, micrometer(s), viruses, DNA, millimeter(s), yeast, fatty acids, plants, meter, plasma membranes.

Micrometers Millimeters Amin acids DNA viruses

Write the same sequence with the single-letter code for amino acids. (pro-val-thr-gly-lys-cys-glu)

PVTGKCE

Types of RNAs: A. most rRNA genes B. tRNA genes C. 55 rRNA genes D. protein-coding genes E. miRNA genes Polymerases: 1. RNA polymerase I 2. Polymerase II 3. Polymerase III

Polymerase I= most rRNA genes Polymerase II=tRNA genes and 55 rRNA genes Polymerase III=protein-coding genes, miRNA genes

Write out the sequence of amino acids in the following peptide, using the full names of the amino acids. Pro-Val-Thr-Gly-Lys-Cys-Glu.

Proline-valine-threonine-glycine-lysine-cysteine-glutamic acid

Below is a segment of RNA from the middle of an mRNA: 5'-UAGUCUAGGCACUGA-3' If you were told that this segment of RNA was part of the coding region of an mRNA for a large protein, give the amino acid sequence for the protein that is encoded by this segment of mRNA. Write your answer using the one-letter amino acid code.

SLGT

This factor binds at the DNA sequence called the ___________ box, which is typically located 25 nucleotides upstream from the transcription start site.

TATA

Sometimes, chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before it is duplicated. This gives rise to mutation. If the adenosine in the sequence TCAT is depurinated and not repaired, what is the point mutation you would observe after this segment has undergone two rounds of replication?

TCT

In eukaryotic cells, general transcription factors are required for the activity of all promoters transcribed by RNA polymerase II. The assembly of the genral transcription factors being with binding of the factor _________________ to DNA, causing a marked local distortion in the DNA.

TFIID

Once RNA polymerase II has been brought to the promoter DNA, it must be released to begin making transcripts. This release process is facilitated by the addition of phosphate groups to the tail of RNA polymerase by the factor ______________.

TFIIH

Sometimes, chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated. This gives rise to mutation. If the cytosine in the sequence TCAT is deaminated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication?

TTAT

On a DNA strand that is being synthesized, which end is growing—the 3′ end, the 5′ end, or both ends? Explain your answer.

The 3′ end. DNA polymerase can add nucleotides only to the 3′-OH end of a nucleic acid chain.

According to the conventional way of writing the sequence of a peptide or a protein, which is the C-terminal amino acid and which is the N-terminal amino acid?

The C-terminal is the glutamic acid and the N-terminal is the proline

A mismatched base pair causes a distortion in the DNA backbone. If this were the only indication of an error in replication, the overall rate of mutation would be much higher. Explain why.

The distortion in the DNA backbone is insufficient information for the mismatch repair system to identify which base is incorrect and which was originally part of the chromosome when replication began. Without additional marks that identify the difference between the newly synthesized strand and the template strand, the repair would be corrected only 50% of the time by random chance. The error rate (and therefore the mutation rate) would still be less than in a system that lacked the mismatch repair enzymes (1 mistake per 107 base pairs), but greater than the error rate in a system that accurately identifies the newly synthesized strand (1 mistake per 109 base pairs).

The length of a particular gene in human DNA, measured from the start site for transcription to the end of the protein-coding region, is 10,000 nucleotides whereas the length of the mRNA produced from this gene is 4000 nucleotides. What is the most likely reason for this difference?

The gene contains one or more introns.

Why is the old dogma "one gene-one protein" not always true for eukaryotic genes?

The transcripts from some genes can be spliced in more than one way to give mRNAs containing different sequences, thus encoding different proteins. A single eukaryotic gene may therefore encode more than one protein.

Use your knowledge of how a new strand of DNA is synthesized to explain why DNA replication must occur in the 5′-to-3′ direction. In other words, what would be the consequences of 3′-to-5′ strand elongation?

There would be several detrimental consequences to 3′-to-5′ strand elongation. One of those most directly linked to the processes of DNA replication involves synthesis of the lagging strand. After the RNA primers are degraded, the DNA segments remaining will have 5′ ends with a single phosphate group. The incoming nucleotide will have a 3′-OH group. Without the energy provided by the release of PPi from the 5′ end, the process of elongation would no longer be energetically favorable.

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

They are rich in A-T base pairs which makes it easier for them to separate the strands because they are only held together by two hydrogen bonds

True or False: The chemical properties of amino acid side chains include charged, uncharged polar and nonpolar.

True

True or False: Condensation reactions occur in synthesis of all the macromolecules found in cells.

True

True or False: 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

True or False? Chromosomes exist at different levels of condensation, depending on the stage of the cell cycle.

True

True or false: All proteins and RNAs pass through many unstable conformations as they are folded, finally settling on one single, preferred conformation.

True

True or false: Carbon-based compounds make up the vast majority of molecules found in cells.

True

True or false: Some atoms are more stable when they lose lose one or two electrons, even though this means they will have a net positive charge.

True

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

True

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

True

True or false? Each strand of DNA contains all the information needed to create a new double-stranded DNA molecule with the same sequence information.

True

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

True

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

True

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

True

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

True

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

True

True or false? The assembly of both collagen and elastin fibers requires the formation of disulfide bonds.

True

The 3′ overhang "invades" the homologous DNA duplex, which can be used as a primer for the repair DNA polymerase.

True.

The first step in repair requires a nuclease to remove a stretch of base pairs from the 5′ end of each strand at the site of the break.

True.

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

True.

The deamination of cytosine generates a uracil base. This is a naturally occurring nucleic acid base, and so does not represent a DNA lesion caused by damage due to chemicals or irradiation. Why is this base recognized as "foreign" and why is it important for cells to have a mechanism to recognize and remove uracil when it is found in the DNA duplex?

Uracil is an RNA base and it is recognized as a mutational lesion because, as it is formed from the deamination of cytosine, it will be paired with a guanine in the context of the DNA duplex. Uracil pairs by forming two hydrogen bonds, similar to thymine, and is thus a poor partner for guanine, which forms three hydrogen bonds with cytosine. The mismatch causes a distortion of the DNA backbone, allowing the repair machinery to recognize the uracil as a lesion. Because uracil pairs preferably with adenine (its partner in double-stranded RNA), the deamination of cytosine to uracil is highly mutagenic. If unrepaired, it can result in the transition of a C-G base pair to a T-A base pair.

Assuming that all mutations are caused by the mutagen are due to single nucleotide changes, deduce the codons that are used for valine, alanine, methionine, and threonine at the affect site.

Valine=GUG Alanine=GCG Methionine=AUG Threonine= ACG

Will the reaction in (C) occur more readily if the pH of the solution is high?

Yes, if the pH is high then the concentration of hydronium ions will be low. Therefore the rightward reaction which produces hydronium ions will be favored.

Can RNA in cells form base pairs?

Yes, it can form base pairs with complementary RNA and DNA sequences.

The RNA base uracil pairs with ______________.

adenine

Although all protein structures are unique, there are common structual building blocks that are referred to as regular secondary structures. Some proteins have alpha helices, some have beta sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements? (a) specific amino acid structures (b) side-chain interactions (c) the hydrophobic-core interactions (d) hydrogen bonds along the protein backbone

all of the above

the nitrogen-containing aromatic ring

base

A protein chain folds into its stable and unique three-dimensional structure, or conformation, by making many noncovalent bonds between different parts of the chain. Such noncovalent bonds are also critical for interactions with other proteins and cellular molecules. From the list provided, choose the class(es) of amino acids that are most important for the interactions detailed below. (acidic, basic, nonpolar, uncharged polar) A. Forming ionic bonds with negatively charged DNA

basic

Nucleosomes are aided in their formation by the high proportion of [acidic/basic/polar] amino acids in histone proteins.

basic

The human immune system produces ________________ of different immunoglobins, also called ________________, which enable the immune system to recognize and fight germs by specifically binding one or a few related _________________. The hypervariable structural element that forms ligand-binding site is comprised of several ____________. Purified antibodies are useful for a variety of experimental purposes, including protein purification using ___________ chromotography.

billions, antibodies, antigens, loops, affinity

Imagine that an RNA polymerase is transcribing a segment of DNA that contains the following sequence: 5'-AGTCTAGGCACTGA-3'3'-TCAGATCCGTGACT-5' If the polymerase is transcribing from this segment of DNA from left to right, which strand (top or bottom) is the template?What will be the sequence of that RNA?

bottom strand, 5-AGUCUAGGCACUGA-3

In eukaryotic ______________________, DNA is complexed with proteins to form ______________. The paternal and maternal copies of human Chromosome 1 are _________________, whereas the paternal copy of Chromosome 3 are _______________________. Cytogeneticists can determine large-scale chromosomal abnormalities by looking at a patient's __________________. Fluorescent molecules can be used to paint a chromosome, by a technique that employs DNA __________________, and thereby to identify each chromosome by microscopy.

chromosomes, chromatin, homologous, nonhomologous, karyotype, hybridization

In eukaryotic cells, where does transcription take place?

cytoplasm

Which of the following statements is FALSE? a. RNA polymerase can start making a new RNA molecule without a primer; DNA polymerase cannot. b. RNA polymerase does not proofread its work; DNA polymerase does. c. RNA polymerase catalyzes the linkage of ribonucleotides while DNA polymerase catalyzes the linkage of deoxyribonucleotides. d. RNA polymerase adds bases in a 3′-to-5′ direction; DNA polymerase adds bases in a 5′-to-3′ direction.

d. Both polymerases will add bases in the same direction (5' to 3' direction)

five-carbon sugar found in DNA

deoxyribose

homeo domain proteins

gene regulator

The segment of DNA called a _________ is the portion that is copied into RNA; this process is catalyzed by RNA _________________.

gene, polymerase

For each of the following decide whether the individual folded polypeptide chain forms a globular or fibrous protein molecule. (a) keratin (b) lysozyme (c) elastin (d) collagen (e) hemoglobin (f) actin

globular: lysozyme, hemoglobin, actin fibrous: keratin, elastin, collagen

linkage between the sugar and the base

glycosidic bond

Interphase chromosomes contain both darkly staining ___________________ and more lightly staining __________________. Genes that are being transcribed are thought to be packaged in a ___________ condensed type of euchromatin. Nucleosomes core particles are seperated from each other by stretches of ____________ DNA. A string of nucleosomes coils up with the help of _________________ to form the more compact structure of ________________. A _____________ model describes the structure of the 30 nm fiber. The 30nm chromatin fiber is further compacted by the formation of _________ that emanate from a central ________.

heterochromatin, euchromatin, less, linker, histone 1, 30 nm fiber, zigzag, loops, axis

The bottom strand can ___________ with the RNA molecule and thus is the template strand. The polymerase moves from 3' to 5' because the RNA ___________ are joined in a 5' to 3' polarity.

hyberdize, nucleotides

organic or inorganic? calcium

inorganic

organic or inorganic? iron

inorganic

organic or inorganic? oxygen

inorganic

organic or inorganic? sodium chloride

inorganic

organic or inorganic? water

inorganic

rearranges bonds within a single molecule

isomerase

adds phosphate groups to molecules

kinase

Once an mRNA is produced, its message can be decoded on ribosomes. The ribosome is composed of two subunits: the __________ subunit, which catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain, and the __________ subunit, which matcher the tRNAs to the codons of the mRNA. During the chain elongation process of translating an mRNA into a protein, the growing polypeptide chain attached to a tRNA is bound to the _______ site of the ribosome. An incoming aminoacyl-tRNA carrying the next amino acid in the chain will bind to the ________ site forming base pairs with the exposed codon in the mRNA. The _____________________ enzyme catalyzes the formation of a new peptide bond between the growing polypeptide chain and the newly arriving amino acid. The end of a protein-coding message is signaled by the presence of a stop codon, which binds the ______________ called release factor. Eventually, most proteins will be degraded by a large complex of proteolytic enzymes called the ________________.

large, small, P, A, peptidyl transferase, protein, proteasome

Any substance that will bind to a protein is known as its ___________. Enzymes bind their _________________ (or inhibitors) at the __________________. The enzyme hexokinase is so specific that it reacts with only one of the two ______________ of glucose. Enzymes catalyze a chemical reaction by lowering the ______________________ because they provide conditions favorable for the formation of a _________________ intermediate called the _________________. Once the reaction is completed, the enzyme releases the _______________ of the reaction.

ligands, substrates, active site, isomers, activation energy, high-energy, transition, products

Various kinds of RNA are produced, each with different functions. ___________ molecules code for proteins.

mRNA

It must be remembered that the general transcription factors and RNA polymerase are not sufficient to initiate transcription in the cell and are affected by proteins bound thousands of nucleotides away from the promoter. Proteins that link distantly bound transcription regulators to RNA polymerase and the general transcription factors include the large complex of proteins called the ___________________.

mediator

myosin

motor

nonpolar

hydrolyzes bonds between nucleotides

nuclease

sugar unit linked to a base

nucleoside

sugar linked to a base and a phosphate

nucleotide

In eukaryotic cells, DNA gets made into RNA in the _________________.

nucleus

RNA splicing, RNA capping, and polyadenylation all take place in the ___________ of eukaryotic cells.

nucleus

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. Eukaryotic cells are bigger and more elaborate than prokaryotic cells. By definition, all eukaryotic cells have a __________________, usually the most prominent organelle. Another organelle found in essentially all eukaryotic cells is the for the cell. In __________________, which generates the chemical energy contrast, the __________________ is a type of organelle found only in the cells of plants and algae, and performs photosynthesis. If we were to strip away the plasma membrane from a eukaryotic cell and remove all of its membrane- enclosed organelles, we would be left with the __________________, which contains many long, fine filaments of protein that are responsible for cell shape and structure and thereby form the cell's __________________. chloroplast cytosol nucleus chromosome endoplasmic reticulum ribosomes cytoskeleton mitochondrion

nucleus mitochondrion chloroplast cytosol cytoskeleton

The sugar ribose in RNA contains _______ more oxygen atom than deoxyribose.

one

Nucleosome formation compacts the DNA into approximately [onethird/one-hundredth/one-thousandth] of its original length.

one-third

organic or inorganic? adenosine

organic

organic or inorganic? cholesterol

organic

organic or inorganic? ethanol

organic

organic or inorganic? glucose

organic

organic or inorganic? glycine

organic

organic or inorganic? phospholipid

organic

catalyzes reactions in which one molecule is oxidized and another is reduced

oxido-reductase

What is the pH of pure water?

pH 7

removes a phosphate group from a molecule

phosphatase

linkages between phosphate groups

phosphoanhydride bond

the linkage between two nucleotides

phosphodiester bond

the linkage between the 5' sugar hydroxyl and a phosphate group

phosphoester bond

catalyzes and synthesis of polymers such as RNA and DNA

polymerase

Proteins are ______________ built from amino acids, which each have an amino group and a ______________ group attached to the central ___________________. There are twenty possible ________________ that differ in structure and are generally referred to as "R." In solutions of neutral pH, amino acids are _________________, carrying both a positive and negative charge. When a protein is made, amino acids are linked together _________________ which are formed by condensation reactions between the carboxyl end of the last amino acid and the __________ end of the next amino acid to be added to the growing chain. amino carbon carboxyl side chains peptide bonds ionized amino a(alpha) carbon

polypeptides, carboxyl, a-carbon, side chains, ionized, peptide bonds, amino

What enzyme is used to synthesize RNA primers during DNA replication?

primase

hydrolyzes peptide bonds

protease

Cell-free extracts from S-strain cells of S. pneumoniae were fractioned to ______________ DNA, RNA, protein, and other cell components. Each fractions was then mixed with ______________ cells of S. pneumoniae. Its ability to change these into cells with _________________ properties resembling the ___________ cells was tested by injecting the mixture into mice. Only the fraction containing ________ was able to ______________ the ______________ cells to _____________(or __________) cells that could kill mice.

purify, R-strain, pathogenic, S-Strain, DNA, transform, R-strain, pathogenic, s-strain

_________ molecules are integral components of the ribosome.

rRNA

five-carbon sugar found in RNA

ribose

The nucleolus is where _____________ _________ are synthesized and combined with proteins to form ribosomes, which are then exported to the cytoplasm.

ribosomal RNAs

In eukaryotic cells, where does translation take place?

ribosomes

Fill in the blank from the following word bank: charge, covalent, double bond, ionic, length, molecule, noncovalent, nonpolar, polar, salt, single bond, weight. Whereas ionic bonds form a(n) _______________, covalent bonds between atoms form a(n) ____________________. These covalent bonds have a characteristic bond __________________ and become stronger and more rigid when two electrons are shared in a(n) ___________________. Equal sharing of electrons yields a ______________________ covalent bond. If one atom participating in the bond has a stronger affinity for the electron, this produces a partial negative charge on one atom and a partial positive charge on the other. These ______________ covalent bonds should not be confused with the weaker ___________________ bonds that are critical for the three-dimensional structure of biological molecules and for interactions between these molecules.

salt, molecule, length, double bond, nonpolar, polar, noncovalent

The alpha helices and beta sheets are examples of protein _____________ structure. A protein such as hemoglobin, which is composed of more than one protein ____________, has ___________________ structure. A protein's amino acid sequence is known as its _______________ structure. A protein _____________ is the modular unit from which many larger single-chain proteins are constructed. The three-dimensional conformation of a protein is its _______________ structure.

secondary, subunit, quaternary, primary, domain, tertiary

The classic experiment conducted by Meselson and Stahl demonstrated that DNA replication is accomplished by employing a ______________ mechanism.

semiconservative

___________ molecules are important in the splicing of RNA transcripts.

snRNA

green fluorescent protein

special purpose

A newly synthesized protein generally folds up into a ______________ conformation. All the information required to determine a protein's conformation is contained in its amino acid ______________________. On being heated, a protein molecules will become __________________ as a result of breakage of _________________ bonds. On removal of urea, an unfolded protein can become _____________. The final folded conformation adopted by a protein is that of ___________ energy.

stable, sequence, denatured, noncovalent, renatured, lowest

ferritin

storage

tubulin

structural

__________ RNA molecules act as adaptors for protein synthesis.

tRNA

RNA __________ is synthesized by a single polymerase molecule from the start site to the termination site without falling off.

transcript

For a cell's genetic material to be used, the information is first copied from the DNA into the nucleotide sequence of RNA in a process called _________________.

transcription

hemoglobin

transport

True or False? The polarity of a DNA strand results from the polarity of the nucleotide subunits.

true

True or false: A strong base is defined as a molecule that can readily remove protons from water.

true

True or false: Electron shells fill discrete regions around the nucleus of the atom and limit the number of electrons that can occupy a specific orbit.

true

True or false: Electrons are constantly moving around the nucleus of the atom, but they can move only in discrete regions.

true

True or false: Protons are constantly moving between water molecules, which means there is an overall equilibrium between hydroxyl ions and hydronium ions in aqueous solutions.

true

True or false: The chemical reactions in living systems are loosely regulated allowing for a wide range of products and more rapid evolution.

true

True or false: The hydroxyl groups on monosaccharides are reaction hot spots and can be replaced by other functional groups to produce derivatives of the original sugar.

true

True or false: There are four elements that constitute 99% of all the atoms found in the human body.

true

True or false? GTP-binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation.

true

True or false? Hexokinase recognizes and phosphorylates only one of the glucose stereoisomers.

true

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

true

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

true

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

true

A nucleosome core particle contains a core of histone with DNA wrapped around it approximately [twice, three times, four times].

twice

uncharged polar

uncharged polar, basic and acidic

A fifth nucleotide, _______, is found in RNA replacing thymine nucleotides in the DNA sequence.

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