BIO 209 Exam 1 Review

1. continuous synthesis 2. lagging strand A. when a new strand needs to be initiated only once B. strand where discontinuous synthesis occurs C. strand where continuous synthesis occurs D. when a new strand needs to be initiated multiple times E. name of short strands of DNA important in replication

1. A 2. B Continuous synthesis is when a new strand needs to be initiated only once. This is true because of how continuous synthesis happens on the leading strand, and thus only one primer is needed to carry out the synthesis. Lagging strand is where discontinuous synthesis occurs. This is true because of how the lagging strand is composed of fragments, and therefore is not a continuous process. D is incorrect for both questions because of how the definition that when a new strand needs to be initiated multiple times is actually defining discontinuous synthesis. E is incorrect for both questions because the name of short strands of DNA important in replication describes Okazaki fragments.

A point mutation is BEST defined by which of the following? a) mutation that alters a single nucleotide b) Replacement of a purine with another purine c) Replacement of a pyrimidine with another pyrimidine d) Replacement of a purine with a pyrimidine

A A point mutation is a mutation either deleting, adding, or replacing a single nucleotide in a DNA chain. B, C, and D are all possible answers but are not all encompassing for point mutations.

An Enzyme with an active site that recognize a substrate's native conformation rather than the transition state tends to be poor catalysts of biochemical reactions because A. The ES complex is highly stable which requires a greater amount of activation energy to catalyze the reaction. B. Such an enzyme lowers the activation energy which slows the forward and reverse rates of the reaction. C. Such an enzyme is more prone to degradation. D. Such an enzyme will alter the reaction equilibrium E. None of the above

A Enzymes work by "recognizing" the transition state of a substrate as opposed to its native state, thus placing stress on the bonds within the substrate in order to reduce the required energy to reach the transition state. This means that a stable E.S. complex would have less free energy than an unstable one, thus requiring more energy to reach the transition state.

Which ONE of the following statements about telomerase is true? A. It prevents telomeres from becoming shorter B. It uses a built-in DNA to act as a template for synthesis of the telomeric repeat. C. Telomerase activity tends to increase as cell age. D. The absence of telomerase is thought to be a requirement for cancer development. E. All of the above statements are true.

A Telomerase prevents telomeres from becoming shorter by using an inbuilt RNA template to add the repeat telomeric sequence to cells post DNA synthesis. Telomerase activity decreases with cell age, and is increased in cancerous cells in order to maintain high rate of replication and thus DNA synthesis.

In proofreading newly synthesized DNA, some DNA polymerases utilize a 3' to 5' exonuclease activity to remove nucleotides A. True B. False

A This statement is true because exonuclease activity occurs when there is an incorrect nucleotide added to the growing chain. This activity removes incorrectly matched base pairs. The DNA polymerase essentially corrects itself as nucleotide errors occur along the DNA.

The prokaryotic equivalent (or homologue; performs the same function) to the eukaryotic protein PCNA is A. β subunit of DNA pol III B. The entire DNA pol I holoenzyme C. SSB D. DNA helicase E. None of the above

A. PCNA and Replication factor C both bind to polymerase delta to allow for completion of okazaki fragment synthesis. SSB proteins keep the chain uncoiled prior to replication fork. DNA helicase separates the two DNA strands, and DNA pol I is involved in RNA primer synthesis in initiation phase.

One strand of a DNA molecule has the following sequence 5'-AGCTGCATA-3'. The complementary strand must be: a. 3'-ATAGCACGA-5' b. 5'-TATGCAGCT-3' c. 5'-ATACGTCGA-3' d. 3'- AGCTGCATA-5' e. 5'-ATAGCACGA-3'

B Based on the base pairing rules, and having the other strand run in the 3' to 5' direction, we can follow the 5' to 3' strand from left to right then reverse the sequence to make it correct. A bonds with T, and C bonds with G. 3' TCGACGTAT 5' then reverse it. The other options have the wrong sequence or direction.

8. Intrachain hydrogen bonding involving the peptide backbone would describe which of the following structures? A. Triple-stranded helix B. Alpha-helix C. Beta-pleated sheet D. Disulfide bonds E. All of the above

B The alpha helix is the only type of secondary structure that has intra-chain bonding between carbonyl and amine functional groups. Alpha helices have intrachain hydrogen bonding. With triple-stranded helices, the hydrogen bonding is present between chains. With beta-pleated sheets, hydrogen bonding is present in an interchain manner. With disulfide bonding, there is no hydrogen bonding present because a disulfide bond entails a bond between two sulphur atoms. Moreover, the n+4 rule facilitates intrachain hydrogen bonding specifically with a-helices.

10. A biochemical reaction, X → Y, has an equilibrium constant of 2500 in the presence of an enzyme that catalyzes the formation of the product, Y, from the substrate, X. Which of the following statements would best describe what happens in the absence of the enzyme? A. The equilibrium constant would decrease, but the forward and reverse rates of the reaction would remain the same B. The equilibrium constant would remain the same, but the forward and reverse rates of the reaction would be decreased C. The equilibrium constant and the forward and reverse rates of the reaction would all decrease D. The equilibrium constant would remain the same, but the forward and reverse rates of the reaction would be increased

B The equilibrium constant remains the same whether or not an enzyme is present. This is because of how the forward and reverse rates of reaction are impacted by the same amount. Enzymes increase the speed of a reaction, but do not get consumed in the process of the reaction. Thus, when an enzyme is not present, the rates of reaction would be slower.

Initiation of DNA replication involves: A. the requirement for a free 3' PO4. B. the requirement for one primer on the leading strand C. the requirement for multiple primers on the leading strand D. DNA primase that produces DNA primers E. a single origin of replication in prokaryotes and eukaryotes.

B The initiation of DNA replication at the replication fork requires the attachment of a short RNA primer attached by DNA Primase which is then removed by 5' to 3' exonuclease activity. DNA synthesis requires deoxynucleoside triphosphates, which is 2 additional phosphates as opposed to 1. Replication only requires 1 short primer to begin, no more. DNA primase produces RNA, not DNA primers. Eukaryotes use multiple replication forks, while prokaryotes use one.

The replication of telomeres A. Presents a problem for the leading strand B. Presents a problem for the lagging strand C. Presents no problem for replication D. Requires a primer to provide the 5' PO4 E. None of the above

B There is no available primer to add the necessary free 3' OH on the lagging strand to continue synthesis, so there is an overhang on the leading strand but not the lagging strand. Telomerase uses its own RNA template to synthesize, does not require a primer as it is included in the enzyme. Loss of overhang sequences can eventually result in loss of coding DNA.

Which ONE of the following causes formation of thymine dimers in DNA? a) Alkylating agents b) Ultra violet light c) Acridine dyes d) Hydroxylating agents e) None of the above

B UV light, specifically UV-C (254nm) results in thymine dimers in adjacent nucleotides, resulting in loss of cross-linking in DNA chain (strand to strand). Acridine dyes intercalate into strands, increasing rigidity and mutation rate. Alkylating agents attach alkyl groups, which alter base pairing potential but don't induce thymine dimers. Hydroxylating agents add hydroxyl groups to amino groups in cytosine which results in a transition mutation.

Which of the following is NOT a required co-factor for DNA polymerases to function? A. Mg2+ B. Template DNA C. ATP D. Primers E. dNTPs

C ATP is not a required co-factor for DNA polymerases to function because ATP actually provides energy that is garnered from pyrophosphate cleavage to provide the needed energy the addition of nucleotides. DNA polymerases need Mg2+ to balance the phosphate groups' negative charges when phosphodiester bonds are formed. DNA polymerases need template DNA as a reference to match base pairs. DNA polymerases need primers to initiate replication as it provides 3' OH groups. DNA polymerases need dNTPs to provide a source for the pyrophosphate cleavage and it also the 3'OH group for the chain as it grows.

Which of the following type(s) of interactions are NOT likely to contribute to enzyme-substrate (ES) complex formation? A. Hydrogen bonding B. Electrostatic interactions C. Disulfide bonds D. Hydrophobic interactions E. Van der Waals interactions

C Disulfide bonds are a bond between two sulfur atoms - which is a covalent bond as there is a sharing of electrons. Enzyme-substrate complexes are usually formed via non-covalent interactions. Hydrogen bonding, electrostatic interactions, hydrophobic interaction, and Van der Waals interactions are examples of covalent interaction that could contribute to enzyme-substrate complex formation.

Which ONE of the following DNA repair mechanisms represents a "last ditch" effort to repair badly damaged DNA? a) Base excision repair b) Nucleotide excision repair c) Error-prone repair system (SOS) d) Post-replication repair e) Mismatch repair (MMR) f) None of the above

C Error-prone repair involves procession of replication even though accurate replication may not be possible. The rest of these methods have very high success rates and typically deal with point mutations, as opposed to error-prone repair dealing with multiple thymine dimers.

1. Who was credited with the discovery of "nuclein"? a. Watson & Crick b. Rosalind Franklin c. Johann Miescher d. Linus Pauling

C Johann Miescher discovered nuclein in 1868. In 1953, Watson and Crick were the first to put all the pieces together as they contributed to the discovery of the DNA double helix. Although Rosalind Franklin helped to contribute to the discovery of the DNA double helix, she was not given the credit for a long time. Linus Pauling was responsible for proposing the idea/model of the triple helix.

Which of the following is NOT found in DNA or does NOT contribute to the stability of DNA structure? a. Hydrogen bonding b. Base-stacking hydrophobic effects c. Peptide bond d. Phosphodiester bond

C Peptide bonds do not contribute to the stability of DNA structure because peptide bonds are bonds that are present between the amino group of an amino acid and the carboxylic group on another amino acid so that a protein chain can be created. Hydrogen bonding is present in DNA and contribute to the structure of DNA because of how the hydrogen bonding occurs between the adjacent chains of the DNA. Base-stacking hydrophobic effects does contribute to the stability of the DNA structure because of how the bases are hydrophobic and the backbone is hydrophilic. Phosphodiester bonds contribute to the structure of DNA because the bonds link two nucleotides together.

In eukaryotes, synthesis of the lagging strand of DNA is primarily carried out by ____________. A. Pol I B. Pol α C. Pol δ D. Pol III E. Pol β

C Polymerase delta copies the lagging strand of DNA while polymerase III handles the leading strand. Polymerase I is involved in 5' to 3' and 3' to 5' exonuclease activity (removing RNA primers and correcting mistakes in replication) similar to polymerase beta's base excision repair.

The peptide sequence, YRVHLWN, is part of an α-helix. With which amino acid would arginine form a hydrogen bond? A. Lysine B. Asparagine C. Tryptophan D. Histidine E. None of the above

C The N+4 rule applies here, W is the 4th amino acid from R meaning arginine's carbonyl would hydrogen bond with tryptophan's amine group.

The technique used to determine whether DNA replication occurs in a unidirectional or bidirectional manner is called A. Cesium chloride density ultracentrifugation B. Agarose gel electrophoresis C. Denaturation mapping of phage DNA D. Polyacrylamide gel electrophoresis E. Fluorescence in-situ hybridization (FISH)

C The technique used is called denaturation mapping of phage DNA. This is because of how phages have regions where AT is abundant and therefore by manipulating different melting temperatures of such regions, bubbles are formed because of how AT regions have a lower melting point than GC regions. These bubbles can be used to see the direction of replication. Cesium chloride density ultracentrifugation is used to separate DNA based on density. Agarose gel electrophoresis is used in mixing DNA and proteins. Polyacrylamide gel electrophoresis involves using electrophoretic properties to separate macromolecules.

Which ONE of the following statements about centromeres is NOT CORRECT? a. Mitotic spindle fibers attach to the centromere b. Centromeres are not found in prokaryotes c. Centromeres of multicellular eukaryotes contain alpha satellite sequences d. Centromeres are located at the ends of a chromosome

Centromeres are not located at the ends of a chromosome. In eukaryotic chromosomes, the ends of them have telomeres as a means of protection. Centromeres are actually located at the center of a chromosome. Mitotic spindle fibers do attach to the centromere during metaphase and anaphase. Centromeres are not found in prokaryotes, they are found in eukaryotes. Prokaryotes do however, contain a plasmid centromere. Centromeres of multicellular eukaryotes do contain alpha satellite sequences.

7. Which of the following is NOT an example of a non-covalent interaction/bond? A. H-bonding B. Electrostatic interaction C. Van der Waals interaction D. Disulfide bond E. Hydrophobic effect

D A disulfide bond is actually a covalent bond because within the bond there is a sharing of electrons. A disulfide bond is a bond between two sulfurs. A covalent bond consists of a bond between two nonmetal atoms. H-bonding, electrostatic interactions, Van der Waals interaction, and the hydrophobic effect, are examples of intermolecular forces where a noncovalent interaction is present.

Which of the following is consistent with Chargaff's results? a. [Adenine] = [Guanine] b. [Adenine] + [Thymine] = [Guanine] + [Cytosine] c. [Thymine] = [Cytosine] d. [Guanine] = [Cytosine] e. [Adenine] = [Cytosine]

D Chargaff's rules helped to indicate the relationship that [Thymine] = [Adenine] and that [Cytosine] = [Guanine], thus [Thymine] + [Cytosine] = [Adenine] + [Guanine]. Each base has the same concentrations as its complementary base pair.

Nitrous acid does all of the following to DNA EXCEPT? a) It removes (deaminates) amino groups b) Causes transition mutations c) Converts cytosine to uracil d) Converts adenine to guanine e) Converts guanine to xanthine

D Deamination of adenine results in the conversion to hypoxanthine, causing A:T to C:G changes as hypoxanthine bonds to cytosine (transition mutation). Removal of the amine groups through oxidation from guanine and cytosine result in conversion to xanthine and uracil respectively.

Eukaryotic chromosomal replication: A. occurs from a single origin. B. is bi-directional. C. has sequence-specific origins (termed autonomously replicating sequences). D. b and c E. all of the above.

D Eukaryotic chromosomal replication is both bi-directional and has sequence-specific origins (termed autonomously replicating sequences). Eukaryotic chromosomal replication is bidirectional 5' to 3' with the leading and lagging strands. Eukaryotic chromosomal replication has sequence-specific replication as high AT content is targeted in efforts of easier separation. In eukaryotes there are multiple origins of replication, but in prokaryotes there is a single origin.

Mendel's wrinkled pea allele is caused by a a) single base deletion b) single base insertion c) recombination d) Transposon

D Mendel's wrinkled pea is caused by a transposon. Transposons are DNA fragments that have the ability to move from one site to another in a genome. With Mendel's wrinkled pea allele, the insertion of a transposon within an expressed gene often causes for the gene to be non-functional. Both single base deletions and insertions are frameshift mutations that change the reading frame. Recombination refers to the crossing over of homologous chromosomes in prophase, and this causes genetic variation.

Which ONE of the following DNA repair systems relies, in part, upon the activities of rec A? a) Mismatch repair (MMR) b) Nucleotide excision repair c) Error-prone repair system (SOS) d) Post-replication repair e) None of the above

D Rec A, or recombinase A is related to post-replication repair and carries out homologous recombination by restarting replication downstream of thymine dimers. This leaves the template strand with a thymine dimer. Error-prone repair utilizes polymerase III and a beta clamp along with polymerase IV or V. Mismatch repair uses the Mut family of endo and exonucleases. Nucleotide excision repair involve polymerase delta and epsilon.

. RNA differs from DNA in that a. RNA uses thymine instead of uracil b. In DNA the 2'OH is involved in phosphodiester bond formation c. In RNA the 2'OH is involved in phosphodiester bond formation d. DNA does not have a 2' OH e. RNA does not have a 3'OH

D The pentose sugar in DNA is deoxyribose, meaning that an oxygen is removed from the 2' carbon's OH group in ribose, thus the name deoxyribose. In both DNA and RNA, only the 3' and 5' carbons are involved in phosphodiester bond formation. RNA uses uracil, and not thymine.

Which ONE of the following prokaryotic replication events is correct? A. Interaction of the ARS sequence with prepriming proteins, such as DnaA, DnaB, and DnaC. B. Initiation of Okazaki fragments on the lagging strand carried out by the primosome, a protein complex of DNA polymerase alpha and DNA helicase. C. RNA primers are covalently extended with deoxynucleotides by Pol I D. Topoisomerase II prevents overwinding

D Topoisomerase II is an example of a gyrase that reduces positive supercoiling by cleaving both DNA strands before the replication fork to reduce torsional strain on the DNA double helix created by straightening and unzipping at the replication fork. ARS sequences are found in eukaryotes and act as origins of replication. The primosome is specific to eukaryotes and consists of different enzymes in prokaryotes. DNA polymerase III covalently extends from primers.

Transposons are a. Mutations that arise from over-transcription of a gene b. RNA elements that alter mRNA processing and produce mutations c. Proteins that control mismatch repair d. DNA fragments that can insert into a gene causing mutation e. Alkylating agents that mutate DNA

D Transposons are DNA fragments that can insert into a gene causing mutation. Transposons have the ability to change its position within a genome as they reverse or create mutations. Transposons are not mutations that arise from over-transcription. Transposons are not apart of RNA. Transposons are not proteins. Transposons are not alkylating agents that mutate DNA.

8. Complementary bases in DNA bond to each other via a. Hydrophobic interactions b. Covalent bonds c. Strong ionic interactions d. Weak H-bonds between partial (+) charge of H and partial (-) charge from the unpaired electron of N or O e. Weak H-bonds between partial (-) charge of H and partial (+) charge from the unpaired electron of N or O

D Unlike the covalent (phosphodiester) bond backbone (sides of the ladder) of DNA, the two strands are stabilized in the double helix by hydrogen bonding between nitrogenous bases. Cytosine and guanine contain 3 H bonds between each other, and adenine + thymine (or uracil) produce 2 H bonds, which is what created the pairing rules (purine to pyrimidine) (AG= purine <- 2 rings TCU=pyrimidine <-single ring). Hydrogens are partially positively charged when involved in H-bonding, and DNA's hydrophobic interactions only have to do with the base-stacking effect WITHIN a single strand. Covalent and ionic interactions are too strong, and would never allow for DNA replication/separation of strands.

An individual (one) nucleotide contains all of the following EXCEPT: a. One, two, or three Phosphate group(s) b. Deoxyribose or ribose c. Nitrogen-containing base d. 3' OH group e. Phosphodiester bond

E An individual nucleotide does not contain a phosphodiester bond because a phosphodiester bond is responsible for linking two nucleotides together in a double-helix. A nucleotide contains phosphate groups. DNA nucleotides contain deoxyribose and RNA nucleotides contain ribose. Nucleotides contains nitrogenous bases (in DNA the nitrogenous bases consist of adenine, guanine, thymine, and cytosine; and in RNA the nitrogenous bases consists of adenine, guanine, uracil, and cytosine). Nucleotides have 3' OH groups.

6. Which of the following is NOT true about enzymes A. they accelerate the reverse rate of a reaction B. they accelerate the forward rate of a reaction C. they do not alter reaction equilibria D. they stabilize transition states E. they increase EA of a reaction

E Enzymes reduce activation energy of the reaction. They have no effect on equilibrium constants, and increase both forward and reverse rates of the reaction (although not in the same manner). Enzymes only change the total number of reactants with sufficient activation energy for a reaction.

Before direct proof of DNA being the genetic material, several lines of indirect evidence had suggested DNA as the appropriate macromolecule. Which ONE of the following statements supports the hypothesis that DNA is the genetic material? a. RNA is more stable than DNA or protein. b. Molecular composition of DNA is variable in different cells of an organism, whereas the molecular composition of RNA and protein does not change in different cells of an organism. c. DNA consists of only four bases while proteins are comprised of twenty different amino acids. d. protein content is most abundant in cells just prior to division. e. Gametes have 1/2 the amount of DNA as somatic cells.

E Gametes have ½ the amount of DNA as somatic cells supports the hypothesis that DNA is the genetic material. This is true because each parent would donate half of their respective genetic material to help provide the full genetic makeup of an offspring's somatic cell. Within diploid organisms, somatic cells have two times the amount of DNA as germ cells. DNA is more stable than RNA or proteins because of the double helix structure. The molecular composition of DNA is actually unchanged throughout the cells of an organism, but the composition of RNA and proteins are varied in different cell types. DNA does consist of four nitrogenous bases and there are twenty different amino acids, but this does not provide a source of evidence that DNA is the genetic material. Although protein content is most abundant in cells before division, this does not help to support why DNA is the genetic material.

Which ONE of the following DNA repair systems contains an enzyme called photolyase? a) Mismatch repair (MMR) b) Nucleotide excision repair c) Error-prone repair system (SOS) d) Post-replication repair e) None of the above

E Photolyase is involved in light-dependent repair in prokaryotes only, the rest of these options are common to prokaryotes and eukaryotes and do not involve photolyase.

Mutations are ALWAYS bad for the organism! T/F

FALSE Mutations are not always bad for the organism. There are instances where mutations can be beneficial, like with sickle cell anemia. Sickle cell anemia has a heterozygote advantage by with malaria is protected against. Moreover, mutations in general help create genetic variation. Plus, certain mutations may allow for certain organisms to better fit to live in the environment they are in.

Protein phosphorylation is an example of "covalent modification" of proteins. However, it is NOT understood what enzymes catalyze phosphorylation nor is the importance of phosphorylation well understood. T/F

FALSE The first part of the statement is correct. Protein phosphorylation is covalent modification. However, it is understood that kinases are the primary group of proteins responsible for protein modification. Phosphorylation is known to be important in cell signaling, as phosphorylation of proteins causes conformational changes. For example, eNOS (endothelial nitric oxide synthase) phosphorylation causes a beneficial dimerization which releases nitric oxide instead of promoting formation of superoxides. Phosphorylation can also deactivate proteins.

The hydrophobic effect maximizes the area of contact between water and nonpolar groups. T/F

FALSE The hydrophobic effect does exactly the opposite. Amino acids with non-polar R-groups tend to face towards the center of the protein while hydrophilic R-groups face towards the outside.

In β-pleated sheets the structure is stabilized by hydrogen bonding between amino acid R groups on the adjacent polypeptide strands that make up the β-pleated sheet. T/F

FALSE The structure is stabilized by hydrogen bonds but between amine groups and carbonyl groups WITHIN the polypeptide chain

Proline is distinctive from the other amino acids discussed in class in that it is a cyclic amino acid with a secondary amino group bonded to the carboxyl group carbon (Assume the statement refers to proline as a free amino acid, not part of a polypeptide). T/F

FALSE This is false because the secondary amino group is actually bonded to the R group, and is not bonded to the carboxyl group carbon. In the structure diagram below, it is evident that the secondary amine group is bonded to the carbon in the carboxyl group

Glycosylases and AP endonucleases are NOT part of the same DNA repair pathway. T/F

FALSE Glycosylases and AP endonucleases are part of the same DNA repair pathway. This is evident because of how glyclosases detect specific base alterations, and then AP endonucleases work to remove the backbone so that the polymerase can insert new bases.

The best way to differentiate between a back mutation and a suppressor mutation is to perform a genetic cross between two individuals of the same species that both are heterozygous for the original mutation. T/F

FALSE The best way to differentiate between a back mutation and a suppressor mutation is to perform a backcross. This means that a genetic cross between two individuals that have the same wild-type phenotype for the original mutation.

There are no known examples of deleterious ("bad") mutations that are thought to have occurred as a form of "adaptation" to an endemic infectious disease. T/F

FALSE There is an example of deleterious mutations that have occurred as a form of "adaptation" to an endemic infectious disease. Examples are inclusive of sickle cell anemia and malaria. Sickle cell anemia has a heterozygote advantage by with malaria is protected against.

Xeroderma pigmentosum (XP) involves defects in genes encoding proteins involved in base excision repair. T/F

FALSE Xeroderma pigmentosum (XP) does not involve defects in genes encoding proteins involved in base excision repair. XP results from defects in nine different genes that are involved in nucleotide excision repair. XP is specifically scene in exinuclease activity, not base repair.

The peptide "backbone" consists of repetitive "units" of amino group nitrogen-alpha carbon-carbonyl carbon, moving from the N-terminus to the C-terminus. T/f

TRUE The polypeptide backbone (primary structure) is built on peptide bonds between amino and carbonyl groups with R-groups being rotated around the backbone based on phi and psi bonds. This is true for all proteins.

Mutations in nature that affect phenotypes are usually deleterious and recessive. T/F

TRUE Mutations in nature that affect phenotypes are usually deleterious and recessive. This is true because such mutations often result in changes within amino acids which are in-turn deleterious to the proper functioning of the protein.