BIOL 3260 FINAL EXAM

chloroplasts use the energy of (1) to produce (2) in a process called (3)

1. sunlight 2. sugar 3. photosynthesis

Which of the following statements about RNA splicing is FALSE?

For a gene to function properly, every intron must be removed from the pre-mRNA transcript in the same fashion on every mRNA molecule produced from the same gene.

Using your knowledge about purines, pyrimidines, and the number of hydrogen bonds between complementary bases, which DNA base pair is represented in this figure?

G-C

mitochondria oxidize (1) to produce (2)

1. sugar 2. ATP

calcium

inorganic

amino acids

proteins

β sheets can participate in the formation of amyloid fibers, which are insoluble protein aggregates. What drives the formation of amyloid fibers?

β-sheet stabilization of abnormally folded proteins.

Electrostatic interactions are an important type of noncovalent bond that helps proteins adopt their most stable, lowest energy conformation. It is possible for electrostatic bonds to form between atoms found in which of the following parts of a polypeptide? (choose ALL correct answers)

- The free amino and carboxyl termini of a protein. - Charged amino acid side chains.

hydrolysis rxn (1) a molecule of water and commonly occur during the (2) of large organic molecules

1. consume 2.breakdown

In a DNA double helix, the (1) has/have the same biochemical properties along the whole length of the DNA molecule, but the (2) contain(s) specific information determined by the nucleotide sequence.

1. sugar phosphate backbone 2. major and minor grooves

In addition to its usefulness in brewing and baking, Brewer's yeast is an experimental organism used to study eukaryotic cells. However, it does have some limitations. Select all the processes below that CANNOT be studied in yeast (choose ALL correct answers).

- cell differentiation - cell motility - photosynthesis

Which method or methods of controlling eukaryotic gene expression is NOT employed in prokaryotic cells? Select all that apply.

- controlling which mRNAs are exported from the nucleus to the cytosol - controlling how an RNA transcript is spliced - combinatorial control of gene expression to generate multiple cell types during development

Biologists cannot possibly study all living species. Instead, they try to understand cell behavior by studying a select subset of species. Which of the following characteristics are useful in an organism chosen for use as a model in laboratory studies? (choose ALL correct answers)

- ethical considerations - amenability to genetic manipulation - rapid rate of reproduction - ability to grow under controlled conditions

Although covalent bonds are 10-100 times stronger than noncovalent interactions, many dynamic biological processes depend upon the number and type of noncovalent interactions between molecules. Which two noncovalent interactions below will contribute most to the strong and specific binding of two molecules, such as a pair of proteins?

- hydrogen bonds - electrostatic attractions

The CAP activator protein and the Lac repressor both control the Lac operon (see figure below). You create cells that are mutant in the gene coding for the Lac repressor so that these cells lack the Lac repressor protein under all conditions. For these mutant cells, choose all conditions from the list in which the Lac operon will be switched ON.

- in the absence of glucose and the presence of lactose - in the absence of glucose and the absence of lactose

A covalent bond between two atoms is formed as a result of the (1) An ionic bond between two atoms is formed as a result of the (2)

1. sharing of electrons 2. transfer of electrons from one atom to the other

During transcription in (1) cells, transcription regulators that bind to DNA thousands of nucleotides away from a gene's promoter can affect a gene's transcription. The (2) is a complex of proteins that links distantly bound transcription regulators with the proteins bound closer to the transcription start site. Transcription activators can also interact with histone (3) which alter chromatin by modifying lysines in the tail of histone proteins to allow greater accessibility to the underlying DNA. Gene repressor proteins can reduce the efficiency of transcription initiation by attracting histone (4) Sometimes, many contiguous genes can become transcriptionally inactive as a result of chromatin remodeling, like the (5) found in interphase chromosomes

1, eukaryotic 2. Mediator 3. acetyltransferases 4. deacetylases 5.heterochromatin

Humans cells each contain almost (1) of DNA that is packaged up into a nucleus ~ 10 µm in diameter. Packing this much DNA into the nucleus is analogous to stuffing (2) of spaghetti into a (3)

1. 2 meters 2. 10,000 miles 3. basketball

This process involves DNA, made up of (1) different nucleotides, which gets (2) into RNA which is then (3) into proteins, made up of (4) different amino acids. In eukaryotic cells, RNA is synthesized and processed in the (5) while proteins are produced from RNA in the (6) The segment of DNA called a (7) is the portion that is copied into RNA; this process is catalyzed by RNA (8)

1. 4 2. transcribed 3. translated 4. 20 5. nucleus 6. cytoplasm 7. gene 8. polymerase

The figure below shows a polycistronic mRNA molecule from a prokaryote. Match the labels given in the list below with the label lines in the figure. 1. 2. 3. 4. 5. 6.

1. 5' untranslated region 2. initiator codon 3. ribosome binding site 4. stop codon 5. protein coding sequences 6. 3' untranslated region

In eukaryotic cells, the genome is divided into linear segments of (1) and packaged into structures called (2)

1. DNA 2. chromosomes

Match each term related to the structure of nucleic acids with one of the descriptions provided. 1.ribose 2.deoxyribose 3. glycosidic bond 4. nucleotide 5. base 6. nucleoside 7. phosphoester bond 8. phosphodiester bond 9. phosphoanhydride bond

1. Five-carbon sugar found in RNA 2. Five-carbon sugar found in DNA 3. Linkage between the sugar and the base. 4. Sugar linked to a base and one or more phosphates. 5. Nitrogen-containing aromatic ring. 6. Sugar linked to a base. 7. The linkage between the 5′ sugar hydroxyl and a phosphate group. 8. The linkage between two nucleotides. 9. Linkages between phosphate groups.

Match the general type of biochemical reaction catalyzed with the class of enzyme. 1. protease 2. polymerase 3. nuclease 4. ATPase 5. ligase 6. protein kinase 7. phosphatase 8. isomerase

1. Hydrolyzes peptide bonds. 2. Catalyzes the synthesis of polymers such as RNA and DNA. 3. Hydrolyzes bonds between nucleotides. 4. Hydrolyzes ATP. 5. Joins two ends of DNA together. 6. Adds phosphate groups to proteins. 7. Removes a phosphate group from a protein. 8. Rearranges bonds within a single molecule.

Consider this polypeptide that is five amino acids long: Phe-Ala-Arg-Met-Ile (1) is the N terminal amino acid and (2) is the c terminus

1. PHE 2. LLE

In eukaryotic cells, general transcription factors are required for the activity of all promoters transcribed by (1) The assembly of the general transcription factors begins with the binding of the factor (2) to DNA, causing a marked local distortion in the DNA. This factor binds at the DNA sequence called the (3) which is typically located approximately 30 nucleotides upstream from the (4). once (5) 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 (6) 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 to (7) thousands of nucleotides away from promoter

1. RNA polymerase II 2. TFIID 3. TATA box 4. transcription start site 5. RNA Polymerase II 6. TFIIH 7. enhancers

two or three (1) can sometimes wrap around each other to form coiled-coils. The stable wrapping of one helix around another is typically driven by (2) interactions. Coiled-coils are typically found in proteins that form an elongated structural framework, such as (3)

1. alpha helices 2. hydrophobic 3. collagen

proteins with similar sequences of (1) are (2) to perform similar functions even if they are from distantly related organisms

1. amino acids 2. more likely

Cell-free extracts from the S-strain cells of S. pneumoniae were fractionated to purify lipids, DNA, RNA, protein, and (1) Each purified fraction was then mixed with the (2) of S. pneumoniae. The researchers injected the mixtures into mice to test the ability of each purified macromolecule to give this (3) strain the same (4) prop as the original (5) cells. only the fraction containing (6) was able to (7) the (8)

1. carbohydrate 2. r strain 3. nonpathogenic 4. pathogenic 5. s strain 6. DNA 7. transform 8. R-strain, nonpathogenic

Even though a squid giant axon cell and a Mycoplasma bacterium are very different in size and shape, they are similar in that they share a basic fundamental (1). for example, they both use the genetic information stored in (2) to (3) RNA, which is often (4) into protein

1. chemistry 2. DNA 3. transcribe 4. translated

(1) is an essential component of biological membranes. Although it is much smaller than the typical phospholipids and glycolipids in the membrane, it is a/an (2) molecule, having both hydrophilic and hydrophobic regions.

1. cholesterol 2. amphipathic

(1) are long molecules of DNA held within the (2) of eukaryotic cells

1. chromosomes 2. nucleus

Polypeptides are synthesized from amino acid building blocks through a (1) rxn b/w the (2) of growing polypeptide chain and the (3) of the next amino acid to be added

1. condensation 2. c terminal carboxyl group 3. amino group

In a multicellular organism, cells with very different appearance and function can share the exact same genetic information. Consider the example of a neuron and a liver cell as discussed in lecture. is what makes these cells different from one another. In the liver cell, you may expect that genes required for neuron function would have a (1) chromatin structure. Furthermore, you would predict that (2) modifications would be less prevalent than (3) modifications within the chromatin of neuron genes in liver cells.

1. condensed 2. H3K27Ac 3. H3K27Me

The primary structure of a polypeptide is held together by (1) bonds. The α helices and β sheets form because of (2) bonds and are examples of a protein's (3) structure. The three-dimensional conformation of a properly folded protein is its (4) structure. A protein such as hemoglobin, which is composed of more than one (5) provides good example of proteins (6) structure

1. covalent 2. noncovalent 3. secondary 4. tertiary 5. subunit 6. quaternary

programmed cell death (1) chloroplast function (2) immunology (3) neuron development (4) cell movements during early vertebrate development (5)

1. cultured human fibroblasts 2. arabidopsis 3. mouse 4. drosophila 5. zebrafish

Unsaturated fatty acids contain carbon-carbon (1) and their presence in phospholipids (2) fluidity of cell membranes

1. double bonds 2. increases

Most eukaryotic cells only express 20-30% of the genes they possess. The formation of (1) maintains genes in a transcriptionally active state. There are specific histone tail modifications, such as (2) that are typically associated with the actively transcribed genes.

1. euchromatin 2. H3 lysine 9 methylation

Several experiments were required to demonstrate that DNA was the genetic material. (1) first demonstrated that cells contain some component that can be transferred to a new population of cells and permanently cause changes in the new cells. Later, (2) provided strong evidence that DNA was the genetic molecule. However, those results were met with skepticism, some scientists feeling that protein contamination or a mutagen in the macromolecular fractions could account for the results. Finally, the bacteriophage experiments of (3) provided definitive proof that DNA, and not protein, was the genetic material.

1. griffith 2. avery macleod and mccarty 3. hershey and chase

Interphase chromosomes contain both darkly staining (1) and more lightly staining (2) Genes that are being transcribed are thought to be packaged in a (3) condensed type of euchromatin. Nucleosome core particles are separated from each other by stretches of (4) DNA. A string of nucleosomes coils up with the help of (5) to form the more compact structure of the (6) Highly condensed chromatin is called (7) Regions of the genome called (8) feature specific nucleotide sequences that can be recognized by chromatin modifying enzymes like (9) that prevent spread of (10)

1. heterochromatin 2. euchromatin 3. less 4.linker 5. histone H1 6. 30 nm fiber 7. heterochromatin 8. barriers. 9. acetyltransferases 10. heterochromatin

Which combination of answers best completes the following statement: When atoms are held together by (1) they are typically referred to as (2)

1. ionic interactions 2. salts

Interphase cells are characterized by (1) chromosomes that are (2) w/in nucleus

1. less condensed 2. organized in discrete regions

Any substance that will bind to a protein is known as a/an (1) enzymes bind their (2) at the (3). The enzyme hexokinase is so specific that it reacts with only one of the two (4) of glucose. Enzymes catalyze a chemical reaction by lowering the (5) because they provide conditions favorable for the formation of a/an (6) intermediate called the (7) Once the reaction is completed, the enzyme releases the (8) of the reaction

1. ligand 2. substrates 3. active site 4. isomers 5. activation energy 6. high energy 7. transition site 8. products

The chromosomes we typically see in images are isolated from (1) cells. These chromosomes are in the most highly condensed form. But most of the time, cells are in the (2) part of the cell cycle. During this phase, the chromosomes are (3) and less densely packed

1. mitotic 2. interphase 3. still organized w/in nucleus

Macromolecules in the cell can often interact transiently as a result of (1) these (2) interactions also produce stable highly specific interactions b/w molecules

1. noncovalent 2. weak

Biochemical subcompartments form because of a large number of (1) between macromolecules. These intracellular condensates (2) important biochemical reactions by concentrating macromolecules within a specific region of the cell.

1. noncovalent interactions 2 facilitate

the (1) interaction between DNA and nucleosome core octamer is primarily mediated by (2). This occurs because the surface of the octamer contains a lot of (3) amino acid side chains and the (4) of DNA have (5)

1. noncovalnet 2. electrostatic attractions 3. basic 4. sugar phosphate backbones 5. negative charge

The genes of a bacterial (1) are transcribed into a single mRNA. Many bacterial promoters contain a region known as a/an (2) to which a specific transcription regulator binds. Genes in which transcription is prevented are said to be (3) The interaction of small molecules, such as tryptophan, with (4) DNA-binding proteins, such as the tryptophan repressor, regulates bacterial genes. Genes that are being (5) expressed are being transcribed all the time.

1. operon 2. operator 3. repressed 4. allosteric 5. constitutively

Deoxyribonucleic acid is classified as an (1) molecule bc it contains (2)

1. organic 2. carbon

On the phospholipid molecule in the figure below, match each numbered structure with the correct term. 1. 2. 3. 4. 5. 6. 7.

1. polar head group 2. phosphate 3. glycerol 4. unsat fatty acid 5. hydrophilic region 6. hydrophobic region 7. sat fatty acid

proteins are (1) built from amino acids, which each have an amino group and a (2) group attached to the central (3) There are 20 possible (4) that differ in structure and are generally referred to as "R." In solutions of neutral pH, amino acids are (5) carrying both a positive and a negative charge. When a protein is made, amino acids are linked together through (6)which are formed by condensation reactions between the carboxyl end of the last amino acid and the (7) end of the next amino acid to be added to the growing chain

1. polypeptides 2. carboxyl 3. alpha carbon 4. side chains 5. ionized 6. peptide bonds 7. amino

nurse and hartwell first treated (1) cells with a chemical mutagen. The mutated population of cells was then grown and observed. Cells that demonstrated defects in cell-cycle regulation (2) were isolated, including mutants for a gene they called cdc2. The scientists were able to "rescue" the mutant by supplying a normal copy of the cdc2 gene from (3) a distantly-related yeast species. After this big result, the scientists went on to show that the homologous gene from humans could also rescue the mutant phenotype. These results demonstrated that there are common principles underlying cell-cycle regulation across a large range of (4) organisms

1. s pombe 2. larger 3. s cerevisiae 4. eukaryotic

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 (1) Various kinds of RNA are produced, each with different functions (2) molecules code for proteins, (3) molecules act as adaptors for protein synthesis, (4) molecules are integral components of the ribosome, and (5) molecules are important in the splicing of RNA transcripts.

1. transcription 2. mRNa 3. tRNA 4. rRNA 5.snRNA

This figure shows a eukaryotic transcription initiation complex. Match the following structures (1-7) in the figure with an item in the list. Not all items will be used. 1. 2. 3. 4. 5. 6. 7.

1. transcriptional activator 2. mediator 3. general transcription 4. RNA polymerase 5. enhancer element 6. promoter 7. transcribed region

In principle, a eukaryotic cell can regulate gene expression at any step in the pathway from DNA to the active protein. match the types of control listed below at the appropriate places on the diagram in the figure. 1. 2. 3 4 5 6 7

1. transcriptional control 2. RNA processing control 3. mRNA transport and localization control 4. mRNA degradation control 5. translation control 6. protein degradation control 7. protein activity control

Carbon, hydrogen, oxygen, and nitrogen are the most abundant elements in living things. These elements all have (1) outer electron shells, making them (2) likely to react with one another to form molecules.

1. unfilled 2. more

The ribosome is composed of two subunits: the (1) subunit, which catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain, and the (2) subunit, which contains the binding site for the mRNA. During the chain elongation process of translating an mRNA into protein, the growing polypeptide chain attached to a tRNA is bound to the (3) site of the ribosome. An incoming aminoacyl-tRNA carrying the next amino acid in the chain will bind to the (4) site by forming base pairs with the exposed codon in the mRNA. The (5) 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 (6) called release factor. Eventually, most proteins will be degraded by a large complex of proteolytic enzymes called the (7)

1.large 2. small 3. P 4. A 5. peptidyl transferase 6. protein 7. proteasome

There are 90 naturally occurring elements on the earth, __________ of which compose 96% of the mass of living organisms.

4

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 Ras activity is most likely to result in Ras being "turned on" and contribute to the uncontrolled growth of cancer cells?

A change that decreases the rate of hydrolysis of GTP by Ras.

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 unidirectional movement of a motor protein along its substrate?

A conformational change is coupled to ATP hydrolysis.

Consider the definitions below and select the one that best fits the term "protein domain."

A segment of a polypeptide that folds independently into a stable structure.

Which of the following statements is TRUE?

Acidic and basic amino acids tend to be found on the exterior of properly folded proteins.

Which of the following statements about allostery is TRUE?

Allosteric regulators are often products of other chemical reactions in the same biochemical pathway.

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. Which of the follow is NOT a reason that Arabidopsis was chosen as a model plant?

Arabidopsis is a valuable cash crop species.

Sutton and Boveri correctly identified that chromosomes contain the genetic material. Why was their discovery not sufficient to conclude that DNA was the genetic material?

Because chromosomes are contain both DNA and protein.

Enhancers can act over long stretches of DNA, but are specific about which genes they affect. How do eukaryotic cells prevent these transcription regulators from looping in the wrong direction and inappropriately turning on the transcription of a neighboring gene?

Chromosome loop-forming proteins arrange the DNA into topological associated domains such that individual genes and their associated enhancer binding regions are in proximity.

Sugars form part of many organic molecules in the cell. In which of the following macromolecules contain one or more sugar molecules as part of their structure? (choose ALL correct answers)

DNA glycolipids

DNA is an information storage molecule, whose sequences directly serve as a template to make (1) and (2)

DNA RNA

Which of the following statements about disulfide bonds is TRUE?

Disulfide bonds stabilize but do not change a protein's final conformation.

proteins destined for secretion from an animal cell must first go through two membrane bound compartments called the

ER and golgi apparatus

Which of the following statements about mRNA stability is FALSE?

Eukaryotic mRNA molecules do not have lifetimes longer than 30 minutes.

Consider two genes that are next to each other on a chromosome, as arranged in the figure below. Which of the following statements is TRUE?

Gene A and gene B can be transcribed at different rates, producing different amounts of RNA within the same cell.

The octameric histone core is composed of four different histone proteins, assembled in a stepwise manner. Once the core octamer has been formed, DNA wraps around it to form a nucleosome core particle. Which of the following histone proteins does NOT form part of the octameric core?

H1

The classic "beads-on-a-string" structure is the most decondensed chromatin structure possible. Which component of chromatin is important for bundling up the beads-on-a-string into the more compact 30 nm fiber?

H1 linker histones

Most eukaryotic cells only express 20-30% of the genes they possess. The formation of heterochromatin maintains the other genes in a transcriptionally silent (unexpressed) state. Which histone modification is associated with the formation of the most common type of heterochromatin?

H3 lysine 9 methylation

Which of the following statements about nucleosomes is TRUE?

Histone acetyltransferases affect transcription by both altering chromatin structure to allow accessibility to the DNA and by adding acetyl groups to histones that can bind proteins that promote transcription.

Some proteins have α helices, some have β sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements?

Hydrogen bonds along the protein backbone.

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?

Inside a cavity on the protein surface.

Genes in eukaryotic cells often have intronic sequences coded for within the DNA. These sequences are ultimately not translated into proteins. Why?

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

Lysozyme lowers the activation energy for the hydrolysis of a glycosidic bond in its polysaccharide substrate. Which of the following statements about the lysozyme-catalyzed reaction is FALSE?

Lysozyme binds irreversibly to the substrate so that it cannot dissociate.

Which of the following statements about the proteasome is FALSE?

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

Noncovalent interactions mediate specific binding of a ligand to a protein. Which of the following noncovalent interactions are NOT involved in binding between a protein and its ligand?

None of the above. All of these are examples of noncovalent interactions that mediate protein-ligand interactions.

Which of the following methods is not used by cells to regulate the amount of a protein in the cell?

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

When talking about coding information for genes, which of the following statements is FALSE?

Protein sequences correspond to the nucleotide sequence of the complementary strand.

Which of the following statements comparing DNA and RNA is FALSE?

RNA polymerase adds bases in a 3′-to-5′ direction; DNA polymerase adds bases in a 5′-to-3′ direction.

Which of the following statements about RNA transcription is FALSE?

Ribonucleotides are added to the 5' end of a growing RNA strand.

Which of the following statements about prokaryotic mRNA molecules is FALSE?

Ribosomes must bind to the 5′ cap before initiating translation.

Which of the following statements about differentiated cells is TRUE?

Some of the proteins found in differentiated cells are found in all cells of a multicellular organism.

Suppose that you used cryo-EM to determine the structure of your favorite protein. What visual model would best display the surface features of your protein's tertiary structure?

Space-filling

methyl group

hydrophobic

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?

The Abd RNA from the mutant strain will be longer than normal.

What do you predict would happen if you replace the Lac operator DNA from the Lac operon with the DNA from the operator region from the tryptophan operon?

The Lac operon will not be transcribed when tryptophan levels are high.

Which of the following statements about the Lac operon is FALSE?

The Lac repressor binds to the operator when lactose is present in the cell.

You have a segment of DNA that contains the following sequence: 5′-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3′ 3′-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5′ You know that the RNA transcribed from this segment contains the following sequence: 5′-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA-3′ Which of the following choices best describes how transcription occurs on this segment of DNA?

The bottom strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′.

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?

The developmental pathway of each cell in the adult worm was known.

Bacterial cells can take up the amino acid tryptophan from their surroundings, or, if the external supply is insufficient, they can synthesize tryptophan by using enzymes in the cell. In some bacteria, the control of glutamine synthesis is similar to that of tryptophan synthesis, such that the glutamine repressor inhibits the transcription of the glutamine operon, which contains the genes that code for the enzymes required for glutamine synthesis. On binding to cellular glutamine, the glutamine repressor binds to a site in the promoter of the operon. What would you expect to happen to the regulation of the enzymes that synthesize glutamine in cells expressing a mutant form of the glutamine repressor that cannot bind to DNA?

The glutamine synthesis enzymes would be permanently switched on, regardless of the level of glutamine in the cells.

Fred Griffith studied two strains of Streptococcus pneumonia, 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?

The heat-killed pathogenic bacteria "transformed" the harmless strain into a lethal one.

Studies conducted with a lysozyme mutant that 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? (Hint: Use the amino acid structures on pg. 76-77 of your text. How is aspartic acid different from asparagine? How is glutamic acid different from glutamine?)

The mutant protein lacks negative charges in the active site that are required for catalysis.

Which of the following statements about ribosomes is TRUE?

The ribosome is a ribozyme, meaning that rRNA contains the catalytic activity that joins amino acids together.

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?

The transcription of a eukaryotic gene can be influenced by proteins that bind far from the promoter.

How do changes in histone modifications lead to changes in chromatin structure?

They act as binding sites to help recruit other chromatin-regulating proteins to the chromatin.

Which of the following statements about molecular chaperones is FALSE?

They can interact with unfolded polypeptides in a way that changes the final fold of the protein.

Which of the following best describes the mechanism by which chromatin-remodeling complexes "loosen" the DNA wrapped around the core histones?

They use an irreversible ATP hydrolysis step to change the relative position of the DNA and the core histone octamer.

Which of the following statements about transcriptional regulators is FALSE?

Transcription regulators interact only with the sugar-phosphate backbone on the outside of the double helix to determine where to bind on the DNA helix.

Enzymes generally make good drug targets because a specific reaction of interest can be targeted with a high degree of selectivity. Consider the following three drugs and choose the correct answer from the dropdowns to make each sentence true. 1. Statins inhibit (a) to block intracellular cholesterol synthesis. 2. Methotrexate inhibits (b) which subsequently leads to blocked DNA replication. Because they proliferate at a high rate, cancer cells are (c) sensitive to inhibition of chromosome replication. 3. Gleevec inhibits the BCR-ABL oncoprotein, a kinase that is only produced in certain types of leukemia cells. It blocks the activity of this protein by binding tightly in the (d) site of the enzyme

a. HMG CoA reductase b. dihydrofolate reductase c. more d. substrate-binding

Which of the following tripeptides are most likely to be in the inner core of a cytosolic protein?

alanine-glycine-leucine

Squid and sea slugs (Aplysia) may seem like odd choices as animal models for neuroscience. However, these creatures have provided important insights into the fundamental mechanisms of neuronal function. Why are these marine invertebrates good models for neuroscientists?

all answers are correct - large identifiable neurons - creatures have simple behaviors - neurons from both vertebrates and invertebrates operate using similar principles

The fact that all cells share a similar basic chemistry and store genetic information in the form of DNA supports which of the three tenets of cell theory?

all cells come from pre existing cells

Energy required by the cell is generated in the form of ATP. The hydrolysis of ATP is used to power many cellular processes. A byproduct of ATP hydrolysis is ADP. As ATP is used up, the relative amount of ADP molecules also increases. When present at high levels, ADP can bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe this mechanism of regulation is

allosteric activation.

Complete the sentence with the best option provided below. The primary structure of a protein is the...

amino acid sequence

Select the answer that BEST completes the following statement: Chemical reactions in living systems occur in an __________ environment, within a narrow range of temperatures.

aqueous

You are a virologist interested in studying the evolution of viral genomes. You are studying two newly isolated viral strains and have sequenced their genomes. You find that the genome of strain 1 contains 25% A, 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?

because double-stranded genomes have equal amounts of A and T

The human genome encodes about 21,000 protein-coding genes. Approximately how many such genes does the typical differentiated human cell express at any one time?

between 5000 and 15,000.

The core histones are small, basic proteins that have a globular domain at the C-terminus and a long, extended conformation at the N-terminus. Which of the following is NOT true of the N-terminal "tail" of these histones?

bind to DNA in a sequence specific manner

Mice and zebrafish are both very popular vertebrate model organisms. However, mice have some advantages over zebrafish for modeling human health and disease. For which of the following studies would zebrafish be a poor choice? (choose ALL correct answers)

breast cancer asthma

How are most eukaryotic transcription regulators able to affect transcription when their binding sites are far from the promoter?

by looping out the intervening DNA between their binding site and the promoter

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 unit?

cell

The macromolecular complex of DNA, histones, and nonhistone chromosomal proteins is called

chromatin

operons

contain a cluster of genes transcribed as a single mRNA.

Which species was the key model organism for the advancement of molecular biology (understanding DNA replication, decoding the DNA to make proteins, etc.)?

e coli

Multicellular organisms are composed of cells that all share the same genome, but can look and function very differently from one another. This is possible because genetically identical cells can

express different genes

5' and 3' UTRs are transcribed into RNA, but not translated into protein. Therefore, they are considered to be nonfunctional parts of a gene.

false

All functional DNA sequences inside a cell code for protein products.

false

Gene sequences correspond exactly to the respective protein sequences produced from them.

false

Introns are spliced out of DNA before a gene is transcribed to RNA and therefore do not contribute to the final protein sequence.

false

Prokaryotes and eukaryotes use the same mechanisms to package up their DNA.

false

The elemental composition of the human body is similar to that of the earth's crust.

false

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

false

the cytosol contains very few proteins and has water like consistency

false

Which of the following monomer building blocks is necessary to assemble selectively permeable boundaries around and inside cells?

fatty acids

The correct folding of proteins is necessary to maintain healthy cells and tissues. The presence of unfolded proteins are associated with some neurodegenerative disorders as Alzheimer's disease, Huntington's disease, and Creutzfeldt-Jakob disease (the specific faulty protein is different for each disease). What happens to these disease-causing, unfolded proteins?

form protein aggregates

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 formation of heterochromatin. What is the result of heterochromatin formation?

gene silencing

The Table below indicates the number and arrangement of electrons in the first four atomic electron shells for selected elements. Based on the information in the chart and what you know about atomic structure and biology, which elements are least likely to be involved in biological chemistry?

helium and neon

Which of the following is not a good example of a housekeeping protein (i.e. a protein that is required for basic cellular functions in all cells)?

hemoglobin

Which of the following atoms comprise 60% of the atoms in the human body?

hydrogen

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?

hydrogen bonds

Cyclic AMP (cAMP) is a small molecule (derived from ATP) 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?

hydrogen bonds

Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which renders it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall?

hydrolase

amino group

hydrophilic

carboxyl group

hydrophilic

hydroxyl group

hydrophilic

phosphate group

hydrophilic

GTP-binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the (1) conformation

inactive

oxygen

inorganic

phosphate

inorganic

sodium chloride

inorganic

water

inorganic

The amino acids glutamine and glutamic acid are shown in the figure below. They differ only in the structure of part of their side chains (circled). At pH7, what type of interactions are possible for glutamic acid but not for glutamine?

ionic bonds

The tryptophan operator...

is a regulatory DNA sequence that binds to the tryptophan repressor when the repressor is bound to tryptophan.

Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product (1) in the pathway.

late

Methylation and acetylation are common changes made to histone H3, and the specific combination of these changes is sometimes referred to as the "epigenetic histone code." Which of the following patterns will most likely lead to gene silencing?

lysine 9 methylation and lysine 27 methylation

Caenorhabditis elegans is a nematode worm that produces more than 1000 cells during its development. However, the adult worm has only 959 somatic cells. The process by which 131 cells are specifically targeted for destruction is called

programmed cell death

You want to measure the size of a typical cell in the leaf of a peanut plant. What unit of length should you use to report this cell's dimensions?

micrometers

The cytoskeleton in animal cells is comprised of three major types of protein filaments: actin filaments, intermediate filaments, and ________________.

microtubules

Out of the researchers mentioned in the lecture, which one(s) can best be credited with discovering DNA?

miescher

A neuron and a white blood cell have very different functions. For example, a neuron can receive and respond to electrical signals, while a white blood cell defends the body against infection. This is because...

neurons and white blood cells express different genes.

nucleotides

nucleic acids

adenosine triphosphate

organic

cholesterol

organic

ethanol

organic

glucose

organic

glycine

organic

phospholipid

organic

triacylglycerol

organic

fatty acids

phospholipids

sugars

polysaccharides

The biosynthetic pathway for the two amino acids E and H is shown schematically in Figure 4-33. You are able to show that E inhibits enzyme V, and H inhibits enzyme X. Which biosynthetic product is most likely the inhibitor of enzyme T?

product c

The phosphorylation of a protein is typically associated with a change in its activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in

protein degradation.

What type of macromolecule helps package DNA in eukaryotic chromosomes?

proteins

The sigma subunit of bacterial RNA polymerase...

recognizes promoter sites in the DNA.

Complete the sentence with the best option provided below. The secondary structures of a protein are the

regular, repeated folds present in a lowest energy conformation.

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 (α helices and β sheets)?

ribbon

Which of the following occurs after a eukaryotic mRNA is exported from the nucleus?

ribosome binds to the mRNA

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 (shown in the figure below) is the most probable target for this type of modification? Hint: find the side chain of each amino acid and determine which is most likely to participate in a condensation reaction.

serine

Unlike DNA, which typically forms a helical structure containing two strands of DNA, different molecules of RNA can fold into a variety of three-dimensional shapes. This is largely because RNA...

single stranded

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?

solvents disrupt all noncovalent interaction

Which of the following is NOT a chemical group commonly found on core histone N-terminal tails for chromatin regulation?

sulfhydryl (-SH)

The distinct characteristics of different cell types in a multicellular organism result mainly from the differential regulation of the...

transcription of genes transcribed by RNA polymerase II.

Each eukaryotic chromosome must contain the following DNA sequence elements: multiple origins of replication, two telomeres, and one centrosome. These are examples of functional DNA sequences that do not code for RNAs or proteins

true

True/false: Binding of an allosteric regulator to an enzyme's regulatory site can cause a conformational change in the protein that may either increase or decrease its catalytic activity, depending on the specific enzyme.

true

True/false: Condensation reactions occur in the synthesis of all the macromolecules found in cells.

true

True/false: Hydrophobic forces play an important role in the formation of both lipid droplets and phospholipid bilayers.

true

True/false: Researchers learned a lot about human cancers by studying cell cycle genes in yeast.

true

True/false: Van der Waals attractions are weakly attractive forces that influence how polypeptides fold into their stable, lowest energy conformation. Van der Waals attractions occur between all atoms (polar or nonpolar) that are in close proximity to one another.

true

in a DNA double helix

two DNA strands run antiparallel

Applying the same logic as the scheme below, how many cells types could be produced if regulatory protein 4 was produced in only one daughter cell after cell types A through H underwent a round of cell division? Try drawing it out.

up to 16

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?

water

In some cases, small molecules are integral to the function of enzymes, and are dubbed "coenzymes." Which of the following is a coenzyme for the enzyme carboxypeptidase?

zinc