BIO EXAM 4

deletion

(1) A deficiency in a chromosome resulting from the loss of a fragment through breakage. (2) A mutational loss of one or more nucleotide pairs from a gene.

domain

(1) A taxonomic category above the kingdom level. The three domains are Archaea, Bacteria, and Eukarya. (2) A discrete structural and functional region of a protein.

DNA was the genetic material evidence

(1) Griffith's transformation phenomenon (2) viruses that infect bacteria, aka bacteriophages or phages (3) Hershey & Chase Experiment with protein vs DNA in phage T2 (4)Chargaff's Experiment with analyzation of base composition of DNA from multiple organisms

transformation

(1) The process by which a cell in culture acquires the ability to divide indefinitely, similar to the division of cancer cells. (2) A change in genotype and phenotype due to the assimilation of external DNA by a cell. When the external DNA is from a member of a different species, transformation results in horizontal gene transfer.

do not code for amino acids that allow a releasing factor to bind to the A site of the ribosome

*Stop codons are unique because they __________.* do not code for amino acids that allow a releasing factor to bind to the A site of the ribosome do not code for amino acids that allow a releasing factor to bind to the P site of the ribosome code for releasing factors do not code for amino acids that allow a releasing factor to bind to the E site of the ribosome code for a specific amino acid that binds to a releasing factor

wild-type5'-AUGCAUACAUUGGAGUGA-3' & mutant5'-AUGCAUACAUCUGGAGUGA-3'

*Which of the following sequences shows a frameshift mutation compared to the wild-type mRNA sequence?* wild-type5'-AUGCAUACAUUGGAGUGA-3' & mutant5'-AUGCAUACGUUGGAGUGA-3' wild-type5'-AUGCAUACAUUGGAGUGA-3' & mutant5'-AUGCAUACAUCUGGAGUGA-3' wild-type5'-AUGCAUACAUUGGAGUGA-3' & mutant5'-AUGCAUACAGAGUGA-3' wild-type5'-AUGCAUACAUUGGAGUGA-3' & mutant5'-AUGCAUGUGACAUUGGAGUGA-3'

It unwinds the double helix and adds nucleotides to a growing strand of RNA.

*Which of the following statements about the function of RNA polymerase is correct?* It proceeds slowly along the DNA strand, requiring about a minute to add two nucleotides to the growing mRNA molecule. It relies on other enzymes to unwind the double helix. It adds nucleotides to the 5′ end of the growing mRNA molecule. It unwinds the double helix and adds nucleotides to a growing strand of RNA. All of the listed choices are correct.

terminator gene promoter

*Which of the following terms associated with transcription describe regions of nucleic acid?* RNA polymerase terminator gene promoter

None of the listed answers are correct.

*Which one of the following statements is true of tRNAs?* There are four types of tRNA. Each tRNA binds a particular codon. tRNAs are double-stranded. tRNAs carry special sequences known as codons. None of the listed answers are correct.

Introns are cut out of the primary transcript, and the resulting exons are spliced together.

*Which statement correctly describes mRNA processing?* Introns are cut out of the primary transcript, and the resulting exons are spliced together. Introns are cut out of the primary transcript and spliced together at the end of the transcript. Exons are cut out of the primary transcript and transported to the endoplasmic reticulum. Exons are cut out of the primary transcript, and the introns are spliced together.

In bacteria, proteins called transcription factors enhance the affinity of RNA polymerase to the promoter sites of genes.

*Which statement is false?* In bacteria, transcription of a gene is initiated when the RNA polymerase by itself recognizes and binds to the promoter of the gene. All of the listed responses are correct. In bacteria, proteins called transcription factors enhance the affinity of RNA polymerase to the promoter sites of genes. The initiation of gene transcription in eukaryotes requires the binding of proteins called transcription factors to the TATA box in the promoter region of a gene.

Each amino acid in a protein is coded for by three bases in the DNA.

*Which statement is true?* Each DNA base codes for three amino acids. It takes three genes to code for one protein. Each amino acid in a protein is coded for by three bases in the DNA. Each gene codes for three proteins.

Although each tRNA consists of a relatively short, single RNA strand, this single strand can achieve a three-dimensional structure by folding back upon itself and forming covalent bonds between complementary bases.

*Which statement regarding the structure and function of tRNA is false?* Although each tRNA consists of a relatively short, single RNA strand, this single strand can achieve a three-dimensional structure by folding back upon itself and forming covalent bonds between complementary bases. Although there are 61 codons that code for amino acids, there are only 45 different tRNA molecules. The nucleotide sequence at both the amino acid attachment and the anticodon ends of each tRNA is instrumental in specifying which amino acid is attached to the tRNA by aminoacyl-tRNA synthetase. Each type of tRNA molecule translates a particular mRNA codon into a particular amino acid.

DNA ligase

-A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3′ end of one DNA fragment (such as an Okazaki fragment) to the 5′ end of another DNA fragment (such as a growing DNA chain) -Joining the sugar-phosphate backbones of all the Okazaki fragments into a continuous DNA strand

single-strand binding protein

-A protein that binds to the unpaired DNA strands during DNA replication -Stabilizing them and holding them apart while they serve as templates for the synthesis of complementary strands of DNA after the parental strands separate

topoisomerase

-A protein that breaks, swivels, and rejoins DNA strands. -During DNA replication, topoisomerase helps to relieve strain in the double helix ahead of the replication fork

Okazaki fragment

-A short segment of DNA synthesized away from the replication fork on a template strand during DNA replication -Many such segments are joined together to make up the lagging strand of newly synthesized DNA -Reiji Okazaki, the Japanese scientist discovered them

primer

-AKA a short stretch of RNA -A short polynucleotide with a free 3′ end, bound by complementary base pairing to the template strand and elongated with DNA nucleotides during DNA replication -Once completed, it is generally five to ten nucleotides long, thus base-paired to the template strand. The new DNA strand will start from the 3′ end of this

nucleic acids

-Ability to dictate their own replication from monomers

Dispersive Model of DNA replication

-All four strands of DNA following replication have a mixture of old and new DNA -Each strand of both daughter molecules contains a mixture of old and newly synthesized DNA. -Start: Parental DNA molecule; follow for two replications. -Result: is four DNA molecules that contain both parental and new DNA. -Parental DNA undergoes first replication; result is two DNA molecules that contain both parental and new DNA. -These molecules then undergo a second replication; result is (for each) 2 DNA molecules that contain both parental and new DNA.

DNA polymerase

-An enzyme that catalyzes the elongation of new DNA (for example, at a replication fork) by the addition of nucleotides to the 3' end of an existing chain. -There are several different DNA polymerases; DNA polymerase III and DNA polymerase I play major roles in DNA replication in E. coli. -Most require a primer and a DNA template strand, along which complementary DNA nucleotides are lined up, one by one

primase

-An enzyme that joins RNA nucleotides to make a primer during DNA replication, using the parental DNA strand as a template. -starts a complementary RNA chain with a single RNA nucleotide and adds RNA nucleotides one at a time

helicase

-An enzyme that untwists the double helix of DNA at replication forks -Separating the two strands of DNA and making them available as template strands

Virus

-An infectious particle incapable of replicating outside of a cell -Consisting of an RNA or DNA genome surrounded by a protein coat (capsid) and, for some viruses, a membranous envelope -Much simpler than cells -To produce more, it must infect a cell and take over the cell's metabolic machinery

replication fork

-At each end of a replication bubble -A Y-shaped region where the parental strands of DNA are being unwound

Nucleotide carbon sugar

-Beginning with carbon bonded to nitrogenous base-> around ring -> carbon bonded to phosphate -3rd carbon is bonded to next nucleotide -assembled from 5' to 3' direction, covalent bond

T2

-DNA is the genetic material of a phage known as this -Alfred Hershey and Martha Chase (1952) -Was composed almost entirely of DNA and protein -Could quickly turn an E. coli cell into a factory that released many copies of new phages when the cell ruptured -Could reprogram its host cell to produce viruses

chromatin

-DNA of eukaryotic cells is packaged with proteins in an elaborate complex -basic unit of which is the n​ucleosome -helps regulate gene expression in several ways

phage infects a bacterial cell with CRISPR-Cas system

-DNA of the invading phage is stored, integrated into the genome between two repeat sequences -if the cell survives the infection, any further attempt by the same type of phage to infect this cell (or its offspring) triggers transcription of the CRISPR region into RNA molecules -these RNAs are cut into pieces and then bound by Cas protein​s, such as the Cas9 protein -the Cas protei​n uses a portion of the phage-related RNA as a homing device to identify the invading phage DNA and cut it, leading to its destruction

Erwin Chargaff (1950)

-DNA was known to be a polymer of nucleotides, each having three components: a nitrogenous (adenine, thymine, guanine, or cytosine) base, a pentose sugar called deoxyribose, and a phosphate group -Base composition of DNA varies from one species to another -Evidence of molecular diversity among species, which most scientists had presumed to be absent from DNA -Made DNA a more credible candidate for the genetic material -Noticed a peculiar regularity in the ratios of nucleotide bases

central dogma

-DNA-transcription-RNA-translation-protein -flow of information went only one way -idea from Francis Crick -although, some enzymes that use RNA molecules as templates for DNA synthesis -th​ese exceptions do not discredit the idea that, in general, genetic information flows from DNA to RNA to protein

DNA repair enzymes

-Each cell continuously monitors and repairs its genetic material -Most cellular systems for repairing incorrectly paired nucleotides, whether they are due to DNA damage or to replication errors, use a mechanism that takes advantage of the base-paired structure of DNA -In many cases, a segment of the strand containing the damage is cut out (excised) by a DNA-cutting enzyme—a nuclease—and the resulting gap is then filled in with nucleotides, using the undamaged strand as a template -The enzymes involved in filling the gap are a DNA polymerase and DNA ligase

heterochromatin

-Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed -More dense appearing and condensed -10-nm fiber is folded and bent back on itself to a much greater degree than in euchromatin, accounting for its denser appearance -Because so compacted, it is largely inaccessible to the proteins responsible for transcribing the genetic information, a crucial early step in gene expression

Nucleotide

-Monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base -DNA sugar=deoxyribose -RNA sugar=ribose (one more oxygen atom than deoxyribose) -DNA bases-adenine, guanine, cytosine, thymine -RNA bases- adenine, guanine, cytosine, uracil

DNA polymerases

-Proofread each nucleotide against its template as soon as it is covalently bonded to the growing strand -Upon finding an incorrectly paired nucleotide, the polymerase removes the nucleotide and then resumes synthesis

uniform diameter for the double helix

-Purine with a pyrimidine is consistent with X-ray -Purine with a purine is too wide -Pyrimidine with a pyrimidine is too narrow

retroviruses (class VI)

-RNA animal viruses with the most complicated replicative cycles -viruses have a reverse transcriptase that transcribes an RNA template into a DNA copy, an RNA →DNA information flow that is the opposite of the usual direction -are enveloped viruses that contain two identical molecules of single-stranded RNA and two molecules of reverse transcriptase

Some RNA molecules function as enzymes

-RNA is single-stranded, a region of an RNA molecule may base-pair, in an antiparallel arrangement, with a complementary region elsewhere in the same molecule; this gives the molecule a particular three-dimensional structure -like certain amino acids in an enzymatic protein, some of the bases in RNA contain functional groups that can participate in catalysis -the ability of RNA to hydrogen-bond with other nucleic acid molecules (either RNA or DNA) adds specificity to its catalytic activity

ribosomal RNA (rRNA)

-RNA molecules that, together with proteins, make up ribosomes; the most abundant type of RNA. -in eu​karyotes, the subunits are made in the nucleolus -_________ genes are transcribed, and the RNA is processed and assembled with proteins imported from the cytoplasm -completed subunits are then exported via nuclear pores to the cytoplasm -in both bacteria and eukaryotes, a large and a small subunit join to form a functional ribosome only when attached to an mRNA molecule -because most cells contain thousands of ribosomes, _____ is the most abundant type of cellular RNA -primarily responsible for both the structure and the function of the ribosome -main constituent of the A and P sites and of the interface between the two subunits -acts as the catalyst of peptide bond formation

gene

-a DNA sequence that codes for a specific polypeptide chain or a functional RNA molecule, such as a tRNA -a discrete unit of inheritance that affects a phenotypic charac​ter -specific loci on chromosomes -a region of specific nucleotide sequence along the length of the DNA molecule of a chromo​some -a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule -some code for polypeptides

transfer RNA (tRNA)

-a RNA molecule that functions as a translator between nucleic acid and protein languages by picking up a specific amino acid and carrying it to the ribosome, where the _______ recognizes the appropriate codon in the mRNA -transfer an amino acid from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome -each ____ enables translation of a given mRNA codon into a certain amino acid, can do this bc ______ bears a specific amino acid at one end of its three-dimensional structure, while at the other end is a nucleotide triplet that can base-pair with the complementary codon on mRNA -consists of a single RNA strand that is only about 80 nucleotides long -twists and folds into a compact 3-D struct​ure that is roughly L-shaped, with the 5′ and 3′ ends ​of the linear _____ both located near one end of the structure, the protruding 3′ end acts as the attachment site for an amino acid, the loop extending from the other end of the L includes the anticodon, the particular nucleotide triplet that base-pairs to a specific mRNA codon -it can read a nucleic acid word (the mRNA codon) and interpret it as a protein word (the amino acid) -transcribed from DNA templates -made in the nucleus and then travels to the cytoplasm, where it will participate in the process of translation -in both bacterial and eukaryotic cells, each ________ is used repeatedly, picking up its designated amino acid in the cytosol, depositing this cargo onto a polypeptide chain at the ribosome, and then leaving the ribosome, ready to pick up another of the same amino acid

point mutation

-a change in a single nucleotide pair of a gene -If it occurs in a gamete or in a cell that gives rise to gametes, it may be transmitted to offspring and to future generations; if the mutation has an adverse effect on the phenotype of a person, the mutant condition is referred to as a genetic disorder or hereditary disease -leads to an altere​​d mRNA and the production of an abnormal protein -ex. sickle cell disease & familial cardiomyopathy

mutation

-a change in the nucleotide sequence of an organism's DNA or in the DNA or RNA of a virus -ultimate source of new genes -responsible for the huge diversity of genes fo​und among organisms -many occur in regions outside of protein-codi​ng​ genes -if an incorrect nucleotide is added to a growing chain during replication, for example, the base on that nucleotide will then be mismatched with the nucleotide base on the other strand; in many cases, the error will be corrected by DNA proofreading and repair systems; otherwise, the incorrect base will be used as a template in the next round of replication

Mutagens

-a chemical or physical agent that interacts with DNA and can cause a mutation -Muller recognized: X-rays and other forms of high-energy radiation pose hazards to the genetic material of people as well as laboratory organisms -Mutagenic radiation, a physical agent, includes ultraviolet (UV) light, which can cause disruptive thymine dimers in DNA -Chemical agents fall into several categories; nucleotide analogs are chemicals similar to normal DNA nucleotides but that pair incorrectly during DNA replication; other chemical mutagens interfere with correct DNA replication by inserting themselves into the DNA and distorting the double helix or cause chemical changes in bases that change their pairing properties -Test the mutagenic activity of chemicals: preliminary screening of chemicals to identify those that may cause cancer

immune system

-a critical part of the body's natural defens​es -the basis for vaccines used to prevent viral infections

domain

-a discrete structural and functional region of a protein

oncogene

-a gene found in viral or cellular genomes that is involved in triggering molecular events that can lead to cancer -arises from a genetic change that leads to an increase either in the amount of the proto-oncogene's protein product or in the intrinsic activity of each protein molecule -genetic changes that convert proto-oncogenes to oncogenes fall into four main categories: epigenetic changes, translocations, gene amplification, and point mutations

regulatory gene

-a gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes

maternal effect gene

-a gene that, when mutant in the mother, results in a mutant phenotype in the offspring, regardless of the offspring's genotype -AKA egg-polarity genes -were first identified in Drosophila melanogaster -control the orientation (polarity) of the egg and consequently that of the fly -two groups of these genes set up the anterior-posterior and dorsal-ventral axes of the embryo -like mutations in segmentation genes, mutations in maternal effect genes are generally embryonic lethals

tumor-suppressor gene

-a gene whose protein product inhibits cell division, there by preventing the uncontrolled cell growth that contributes to cancer -any mutation that decreases the normal activity of a tumor-suppressor protein may contribute to the onset of cancer, in effect stimulating growth through the absence of suppression

polyribosome (polysome)

-a group of several ribosomes attached to, and translating, the same messenger RNA molecule -can be either free or bound -enable a cell to rapidly make many copies of a polypeptide

vaccine

-a harmless variant or derivative of a pathogen that stimulates a host's immune system to mount defenses against the pathogen

spliceosome

-a large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons -binds to several short nucleotide sequences along an intron, including key sequenc​es at each end -small RNAs in the _______ not only participate in ____________ assembly and splice site recognition, but also catalyze the splicing reaction; like proteins, RNAs can act as catalysts

cytoplasmic determinant

-a maternal substance, such as a protein or RNA, that when placed into an egg influences the course of early development by regulating the expression of genes that affect the developmental fate of cells -combination of these in a cell helps determine its developmental fate by regulating expression of the cell's genes during the course of cell differentiation

RNA interference (RNAi)

-a mechanism for silencing the expression of specific genes -double-stranded RNA molecules that match the sequence of a particular gene are processed into siRNAs that either block translation or trigger the degradation of the gene's messenger RNA -happens naturally in some cells and can be carried out in laboratory experiments as well -can process double-stranded RNAs into homing devices that lead to the destruction of related RNAs, some scientists think that this pathway may have evolved as a natural defense against infection by such viruses -can also affect the expression of nonviral cellular genes may reflect a different evolutionary origin for the RNAi pathway

viral envelope

-a membrane, derived from membranes of the host cell, that cloaks the capsid, which in turn encloses a viral genome -contain proteins and glycoproteins of viral origin

Viral Envelopes

-a membranous outer layer -animal virus equipped with this uses it to enter the host cell -protruding from the outer surface are viral glycoproteins that bind to specific receptor molecules on the surface of a host cell -ribosomes bound to the endoplasmic reticulum (ER) of the host cell make the protein parts of the envelope glycoproteins; cellular enzymes in the ER and Golgi apparatus then add the sugars -the resulting viral glycoproteins, embedded in membrane derived from the host cell, are transported to the cell surface -n​ew viral capsids are wrapped in membrane as they bud from the cell, the viral envelope is usually derived from the host cell's plasma membrane, although all or most of the molecules of this membrane are specified by viral genes -the enveloped viruses are now free to infect other cells, this replicative cycle does not necessarily kill the host cell, in contrast to the lytic cycles of phages -some viruses have these that are not derived from plasma membrane

5′ cap

-a modified form of guanine nucleotide added onto the 5′ end of a pre-mRNA molecule

Insertion

-a mutation involving the addition of one or more nucleotide pairs to a gene

frameshift mutation

-a mutation occurring when nucleotides are inserted in or deleted from a gene and the number inserted or deleted is not a multiple of three, resulting in the improper grouping of the subsequent nucleotides into codons -all nucleotides downstream of the deletion or insertion will be improperly grouped into codons; the result will be extensive missense mutations, usually ending sooner or later in a nonsense mutation that leads to premature termination -unless the frameshift is very near the end of the gene, the protein is almost certain to be nonfunctional

nonsense mutation

-a mutation that changes an amino acid codon to one of the three stop codons -resulting in a shorter and usually nonfunctional protein -causes translation to be terminated prematurely

embryonic lethal

-a mutation with a phenotype leading to death of an embryo or larva

intron

-a noncoding, intervening sequence within a primary transcript that is removed from the transcript during RNA processing; also refers to the region of DNA from which this sequence was transcribed -the sequence of DNA nucleotides that codes for a eukaryotic polypeptide is usually not continuous; it is split into segments, the noncoding segments of nucleic acid that lie between coding regions -AKA intervening sequences -cut out from the molecule -may facilitate the evolution of new and potentially beneficial proteins (exon shuffling) -increase the probability of crossing over between the exons of alleles of a gene—simply by providing more terrain for crossovers without interrupting coding sequences

proto-oncogene

-a normal cellular gene that has the potential to become an oncogene

anticodon

-a nucleotide triplet at one end of a tRNA molecule that base-pairs with a particular complementary codon on an mRNA molecule -conventionally written 3'→5' to align properly with codons written 5'→3'

silent mutation

-a nucleotide-pair substitution that has no observable effect on the phenotype -ex. within a gene, a mutation that results in a codon that codes for the same amino acid -can occur outside genes as well -some may indirectly affect where or at what level the gene gets expressed, even though the actual protein is the same

missense mutation

-a nucleotide-pair substitution that results in a codon that codes for a different amino acid -may have little effect on the protein: The new amino acid may have properties similar to those of the amino acid it replaces, or it may be in a region of the protein where the exact sequence of amino acids is not essential to the protein's function -ex. alteration of a single amino acid in a crucial area of a protein can significantly alter protein activity -occasionally, such a mutation leads to an improved protein or one with novel capabilities, but much more often such mutations are neutral or detrimental, leading to a useless or less active protein that impairs cellular function

binding domain

-a part of the protein's three-dimensional structure that binds to DNA

prophage

-a phage genome that has been inserted into a specific site on a bacterial chromosome

temperate phage

-a phage that is capable of replicating by either a lytic or lysogenic cycle -ex. lambda, phage λ resembles T4, but its tail has only one short tail fiber

virulent phage

-a phage that replicates only by a lytic cycle

vertical transmission

-a plant inherits a viral infection from a parent -can occur in asexual propagation (for example, through cuttings) or in sexual reproduction via infected seeds

induction

-a process in which a group of cells or tissues influences the development of another group through close-range interactions

activator

-a protein that binds to DNA and stimulates gene transcription -in prokaryotes, activators bind in or near the promoter -in eukaryotes, activators generally bind to control elements in enhancers -indirectly affect chromatin structure -some recruit proteins that acetylate histones near the promoters of specific genes, thus promoting transcription

repressor

-a protein that inhibits gene transcription -in prokaryotes, repressors bind to the DNA in or near the promoter -in eukaryotes, repressors may bind to control elements within enhancers, to activators, or to other proteins in a way that blocks activators from binding to DNA -binds to the operator, preventing RNA polymerase from transcribing the genes, often by preventing RNA polymerase from binding -turns off operon -specific for the operator of a particular operon -encoded by a regulatory gene -some repressors bind directly to control element DNA (in enhancers or elsewhere), blocking activator binding; other repressors interfere with the activator itself so it can't bind the DNA -indirectly affect chromatin structure -some recruit proteins that remove acetyl groups from histones, leading to reduced transcription, meaning the genes are silenced

signal-recognition particle (SRP)

-a protein-RNA complex that recognizes a signal peptide as it emerges from a ribosome and helps direct the ribosome to the endoplasmic reticulum (ER) by binding to a receptor protein on the ER

transcription unit

-a region of DNA that is transcribed into an RNA molecule -stretch of DNA downstream from the promoter that is transcribed into an RNA molecule

transcription factor

-a regulatory protein that binds to DNA and affects transcription of specific gene -help guide the binding of RN​A polymerase and the initiation of transcription

Termination of Translation

-a release factor, a protein shaped like an aminoacyl tRNA, binds directly to the stop codon in the A site -the release factor causes the addition of a water molecule instead of an amino acid to the polypeptide chain (Water molecules are abundant in the cytosol.) -this reaction hydrolyzes (breaks) the bond between the completed polypeptide and the tRNA in the P site, releasing the polypeptide through the exit tunnel of the ribosome's large subunit -the remainder of the translation assembly then comes apart in a multistep process, aided by other protein factors; breakdown of the translation assembly requires the hydrolysis of two more GTP molecules.

p53 protein

-activates expression of a group of miRNAs that inhibit the cell cycle -activates several other genes -can also turn on genes directly involved in DNA repair. If DNA damage is irreparable, ____ activates "suicide" genes, whose protein products bring about programmed cell death, aka ap​optosis

Insertions and deletions

-additions or losses of nucleotide pairs in a gene -have a disastrous effect on the resulting protein more often than substitutions do -may alter the reading frame of the genetic message, the triplet grouping of nucleotides on the mRNA that is read during translation -frameshift mutation -occur outside of coding regions(not frameshift mutations) but can have effects on the phenotype—for instance, they can affect how a gene is expressed

RNA splicing

-after synthesis of a eukaryotic primary RNA transcript, the removal of portions of the transcript (introns) that will not be included in the mRNA and the joining together of the remaining portions (exons)

chromosome conformation capture techniques

-allow researchers to cross-link and identify regions of chromosomes associating with each other during interphase -the territory of each chromosome is divided into regions of chromatin loops (topologically associated domains, or TADs), within which chromatin sites associate mainly with each other -loops of chromatin, each likely a TAD, extend from individual chromosomal territories into specific sites in the nucleus -different loops from the same chromosome and loops from other chromosomes may congregate in such sites, some of which are rich in RNA polymerases and other transcription-associated protein (*transcription factories*), thought to be areas specialized for a common function

gene editing

-altering genes in a specific, predictable way -try to correct genes that cause disease -ex. CRISPR-Cas9 system

Elongation of the Polypeptide Chain

-amino acids are added one by one to the previous amino acid at the C-terminus of the growing chain -each addition involves several proteins called elongation factors and occurs in a three-step cycle -energy expenditure occurs in the first and third steps -codon recognition requires hydrolysis of one molecule of GTP, which increases the accuracy and efficiency of this step -one more GTP is hydrolyzed (broken up) to provide energy for the translocation step -the mRNA is moved through the ribosome in one direction only, 5′ end first; this is equivalent to the ribosome moving 5′→3′ on the mRNA -the ribosome and the mRNA move relative to each other, unidirectionally, codon by codon -this cycle takes less than a tenth of a second in bacteria and is repeated as each amino acid is added until the polypeptide is completed -the empty tRNAs that are released from the E site return to the cytoplasm, where they will be reloaded with the appropriate amino acid -continues until a stop codon, UAG, UAA, and UGA (all written 5′→3′) reaches the A site, stops translation of mRNA

long noncoding RNA (lncRNA)

-an RNA between 200 and hundreds of thousands of nucleotides in length that does not code for protein but is expressed at significant levels -almost 28,000 known; 20,000 were functional and that some were associated with specific diseases -responsible for X chromosome inactivation, which prevents expression of genes located on one of the X chromosomes in most female mammals -transcripts of the XIST g​ene located on the chromosome to be inactivated -bind back to and coat that chromosome, leads to condensation of the en​tire chromosome into heterochromatin -involve chromatin remodeling in large regions of the chromosome -act as a scaffold, bringing DNA, proteins, and other RNAs together into complexes; these associations may act either to condense chromatin or, in some cases, to help bring the enhancer of a gene together with mediator proteins and the gene's promoter, activating gene expression in a more direct fashion

ribozyme

-an RNA molecule that functions as an enzyme, such as an intron that catalyzes its own removal during RNA splicing

restriction enzyme

-an endonuclease (type of enzyme) that recognizes and cuts DNA molecules foreign to a bacterium (such as phage genomes) -the enzyme cuts at specific nucleotide sequences (restriction sites)

aminoacyl-tRNA synthetases

-an enzyme that joins each amino acid to the appropriate tRNA -active site of each type of __________ fits only a specific combination of amino acid and tRNA -20 different ________, one for each amino acid joins a given amino acid to an appropriate tRNA -one _____ is able to bind to all the different tRNAs for its particular amino acid -catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the hydrolysis of ATP -results of ______, AKA charged tRNA, is released from the enzyme and is then available to deliver its amino acid to a growing polypeptide chain on a ribosome

RNA polymerase

-an enzyme that links ribonucleotides into a growing RNA chain during transcription, based on complementary binding to nucleotides on a DNA template strand -pries the two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand, thus elongating the RNA polynucleotide -can assemble a polynucleotide only in its 5′→3′ direction, adding onto its 3′ end -are able to start a chain from scratch; they don't need to add the first nucleotide onto a pre-existing primer

horizontal transmission

-an external source infects the plant -invading virus must get past the plant's outer protective layer of cells (the epidermis), a plant becomes more susceptible to viral infections if it has been damaged by wind, injury, or herbivores -herbivores, especially insects, pose a double threat because they can also carry viruses, transmitting disease from plant to plant -gardeners may transmit plant viruses inadvertently on pruning shears and other tools.

Regulatory proteins

-commonly activated or inactivated by the reversible ad​dition of phosphate groups, and protei​ns destined for the surface of animal cells acquire su​gars -cell​-surface proteins and many others must also be transported to target destinations in the cell in order to fun​ction -regul​ation might occur at any of the steps involved in modifying or transporting a protein

egg's cytoplasm

-contains both RNA and proteins encoded by the mother's DNA -unfertilized: not homogeneous -mRNAs, proteins, other substances, and organelles are distributed unevenly in the unfertilized egg, and this unevenness has a profound impact on the development of the future embryo in many species

genes

-control development and have led to an understanding of the key roles that specific molecules play in defining position and directing differentiation -few code for RNA molecules that have important functions in cells even though they are never translated into protein -others code for proteins, or more specifically polypeptides -provide the instructions for making specific proteins, but a gene does not build a protein directly -typically hundreds or thousands of nucleotides long, each gene having a specific sequence of nucleotides

proximal control elements

-control elements located close to the promoter

distal control elements

-control elements located far from the promoter -may be thousands of nucleotides upstream or downstream of a gene or even within an intron

point mutation either in the promoter or an enhancer

-could cause an increase in proto-oncogene expression -this in the coding sequence of the proto-oncogene could change the gene's product to a protein that is more active or more resistant to degradation than the normal prote​in

azidothymidine (AZT)

-curbs HIV replication by interfering with the synthesis of DNA by reverse transcriptase

model of a nucleus

-defined architecture and regulated movements of chromatin -unexpressed genes are located in the outer edges of the nucleus -expressed genes are found in its interior region -relocation of particular genes from their chromosomal territories to transcription factories in the interior may be part of the process of readying genes for transcription

viral damage

-depends partly on the ability of the infected tissue to regenerate by cell division -people usually recover completely from colds because the epithelium of the respiratory tract, which the viruses infect, can efficiently repair itself -damage inflicted by poliovirus to mature nerve cells is permanent because these cells do not divide and usually cannot be replaced -many of the temporary symptoms associated with viral infections, such as fever and body aches, actually result from the body's own efforts to defend itself against infection rather than from cell death caused by the virus

tissue-specific proteins

-determination in terms of molecular changes that result in observable cell differentiation that is marked by the expression of genes for this -give the cell its characteristic structure and function

alternative RNA splicing

-different mRNA molecules are produced from the same primary transcript -depending on which RNA segments are treated as exons and which as introns (regulatory proteins specific to a cell type control intron/exon choices by binding to regulatory sequences within the primary transcript) -can significantly expand the repertoire of a eukaryotic genome -was proposed as one explanation for the surprisingly low number of human genes counted when the human genome was sequenced -more than 90% of human protein-coding genes likely undergo alternative splicing -the extent of this greatly multiplies the number of possible human proteins, which may be better correlated with complexity of form than the number of genes -a type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns -presence of introns in genes allows a single gene to be able to encode more than one kind of polypeptide -the number of different protein products an organism produces can be much greater than its number of genes

downstream

-direction of transcription -used to describe the positions of nucleotide sequences within the DNA or RNA

CRISPR-Cas system

-discovered during a study of repetitive DNA sequences present in the genomes of many prokaryotes -DNA sequences were called clustered regularly interspaced short palindromic repeats (CRISPRs) because each sequence reads the same forward and backward (a palindrome), with different stretches of "spacer DNA" in between the repeats -each spacer sequence corresponded to DNA from a particular phage that had infected the cell -particular nuclease proteins, specifically Cas (CRISPR-associated) proteins, interact with the CRISPR region and can identify and cut phage DNA, thereby defending the bacterium against phage infection

swine flu

-disease caused by H1N1 -parts of the viral genome were very similar to strains of influenza in pigs -studies revealed that the virus was not transmitted from pigs to humans -H1N1 was a unique combination of swine, avian, and human influenza genes that allowed it to spread among humans

chromatin modifications

-do not change the DNA sequence -may be passed along to future generations of cells -mutations in the DNA are permanent changes -modifications to the chromatin can be reversed -respond more rapidly to environmental conditions

Protein folding

-during its synthesis, a polypeptide chain begins to coil and fold spontaneously as a consequence of its amino acid sequence (primary structure), forming a protein with a specific shape: a three-dimensional molecule with secondary and tertiary structu​re -a gene determines prim​ary structure, which determines shape

polypeptide chain

-during translation, the sequence of codons along an mRNA molecule is decoded, or translated, into a sequence of amino acids making up this

combination of control elements

-each can activate transcription only when the appropriate transcription activators are present, which may occur at a precise time during development or in a particular cell type -just a few can allow differential regulation of transcription, this can occur because each cell type contains a different group of transcription activators

cell specialization

-each cell type must maintain a specific program of gene expression in which certain genes are expressed and others are not​

viral replicative cycle

-ends with the exit of hundreds or thousands of viruses from the infected host cell, a process that often damages or destroys the cell

RNA processing

-enzymatic addition of a 5′cap and a poly-A tail -splicing out of introns -to yield a mature mRNA -modification of RNA primary transcripts, including splicing out of introns, joining together of exons, and alteration of the 5' and 3′ ends -both ends of the primary transcript are altered -in most cases, certain interior sections of the RNA molecule are cut out and the remaining parts spliced together -these modifications produce an mRNA molecule ready for translation

general transcription factors

-essential for the transcription of all protein-coding genes -few bind to a DNA sequence, such as the TATA box in most promoters, but many bind to proteins, including other transcription factors as well as RNA polymerase II

a) some substance from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic.

In his work with pneumonia-causing bacteria and mice, Griffith found that a) some substance from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic. b) the polysaccharide coat of bacteria caused pneumonia. c) the protein coat from pathogenic cells was able to transform nonpathogenic cells. d) bacteriophages injected DNA into bacteria. e) heat-killed pathogenic cells caused pneumonia.

c) much faster than

In prokaryotes, the rate of elongation during DNA replication is __________ the rate in eukaryotes. a) The rates are not comparable because elongation only occurs in prokaryotes. b) much slower than c) much faster than d) sometimes faster and sometimes slower than e) about the same as

a) nucleosomes

In the "beads on a string" structure of unfolded chromatin, the "beads" are __________. a) nucleosomes b) genes c) nucleoids d) looped domains e) heterochromatin

B

In the accompanying image, a nucleotide is indicated by the letter _____.

post-translational modifications

-may be required before the protein can begin doing its particular job in the cell -certain amino acids may be chemically modified by the attachment of sugars, lipids, phosphate groups, or other additions -enzymes may remove one or more amino acids from the leading (amino) end of the polypeptide chain -in some cases, a polypeptide chain may be enzymatically cleaved into two or more pieces -in other cases, two or more polypeptides that are synthesized separately may come together, if the protein has quaternary structure

expression of a protein-coding gene

-measured by the amount of functional protein a cell makes, and much happens between the synthesis of the RNA transcript and the activity of the protein in the cell

ribosomes

-molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains -adds each amino acid brought to it by a tRNA to the growing end of a polypeptide chain -facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis -consists of a large subunit and a small subunit, each made up of proteins and one or more ribosomal RNAs -bout one-third of the mass of a ribosome is made up of proteins; the rest consists of three rRNA molecules (in bacteria) or four (in eukaryotes) -has a binding site for mRNA, as well as three binding sites for tRNA -holds the tRNA and mRNA in close proximity and positions the new amino acid so that it can be added to the carboxyl end of the growing polypeptide -it then catalyzes the formation of the peptide bond -as the polypeptide becomes longer, it passes through an exit tunnel in the ribosome's large subunit -when the polypeptide is complete, it is released through the exit tunnel

positional information

-molecular cues that control pattern formation in an animal or plant embryonic structure by indicating a cell's location relative to the organism's body axes -these cues elicit a response by genes that regulate development -cues tell a cell its location relative to the body axes and to neighboring cells, and determine how the cell and its descendants will respond to future molecular signals

interactions between embryonic cells

-molecules that transmit these signals within the target cell are cell-surface receptors and other signaling pathway proteins -in general, the signal sends a cell down a specific developmental path by causing changes in its gene expression that lead to observable cellular changes -helps induce differentiation into the many specialized cell types making up a new organism

antiviral drugs

-most resemble nucleosides and thus interfere with viral nucleic acid synthesis -ex. acyclovir, azidothymidine (AZT) -multidrug treatments, sometimes called "cocktails," are considered to be most effective, commonly include a combination of two nucleoside mimics and a protease inhibitor, which interferes with an enzyme required for assembly of the viruses -multidrug treatments originally involved taking up to 20 pills multiple times per day but now usually consist of a single daily tablet -effective treatment is maraviroc, which blocks a protein on the surface of human immune cells that helps bind the HIV ​virus, been used ​successfully to prevent infection in individuals who either have been exposed to, or are at risk of exposure to, HIV

myoblasts

-muscle cells that develop from embryonic precursor cells and have the potential to develop into a number of cell types, including cartilage cells and fat cells -particular conditions then commit them to becoming muscle cells -eventually start to churn out large amounts of muscle-specific proteins and fuse to form mature, elongated, multinucleate skeletal muscle cells

eukaryotic polypeptides

-must be processed to yield functional protein molecules -ex. cleavage of the initial insulin polypeptide forms the active hormone or chemical modifications can make protein functional

Ras protein

-mutuations of this occur in about 30% of human cancers -encoded by the ras gene -is a G protein that relays a signal from a growth factor receptor on the plasma membrane to a cascade of protein kinases -the cellular response at the end of the pathway is the synthesis of a protein that stimulates the cell cycle -normally, such a pathway will not operate unless triggered by the appropriate growth factor, but certain mutations in this was gene can lead to production of a hyperactive ________ that triggers the kinase cascade even in the absence of growth factor, resulting in increased cell division; hyperactive versions or excess amounts of any of the pathway's components can have the same outcome: excessive cell division

coding strand

-nontemplate strand of DNA, which has the same sequence as the mRNA except it has thymine (T) instead of uracil (U) -the sequence of the coding strand is used when a gene's sequence is reported

small-scale mutations

-of one or a few nucleotide pairs, including point mutations, changes in a single nucleotide pair of a gene -Two types: (1) single nucleotide-pair substitutions and (2) nucleotide-pair insertions or deletions(can involve one or more nucleotide pairs)

coordinately controlled genes

-often clustered into an operon

Coordinate control of dispersed genes in a eukaryotic cell

-often occurs in response to chemical signals from outside the cell -genes with the same sets of control elements are activated by the same chemical signals

reading frame

-on an mRNA, the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis -important in the molecular language of cells

P site(peptidyl-tRNA binding site)

-one of a ribosome's three binding sites for tRNA during translation -holds the tRNA carrying the growing polypeptide chain

A site(aminoacyl-tRNA binding site)

-one of a ribosome's three binding sites for tRNA during translation -holds the tRNA carrying the next amino acid to be added to the polypeptide chain

E site(exit site)

-one of a ribosome's three binding sites for tRNA during translation -the place where discharged tRNAs leave the ribosome

small interfering RNA (siRNA)

-one of multiple small, single-stranded RNA molecules generated by cellular machinery from a long, linear, double-stranded RNA molecule -associates with one or more proteins in a complex that can degrade or prevent translation of an mRNA with a complementary sequence -blocking of gene expression by this is called *RNA interference (RNAi)*, is used in the laboratory as a means of disabling specific genes to investigate their function

regulatory mechanisms

-operate at the various stages after transcriptio​n -these mechanisms allow a cell to rapidly fine-tune gene expression in response to environmental changes without altering its transcription patterns

untranslated regions (UTRs)

-parts of the mRNA that will not be translated into protein, but they have other functions, such as ribosome binding

Mutations

-permanent changes in DNA -change the phenotype of an organism -original source of the variation on which natural selection operates during evolution and are ultimately responsible for the appearance of new species -over long periods of time, this process leads to new species and thus to the rich diversity of life on Earth today

histone chemical modifications

-play a direct role in the regulation of gene transcription -

Viruses

-play a role in about 15% of the cases of human cancer -can interfere with gene regulation in several ways if they integrate their genetic material into the DNA of a cell -may donate an oncogene to the cell, disrupt a tumor-suppressor gene, or convert a proto-oncogene to an oncogene -some produce proteins that inactivate p53 and other tumor-suppressor proteins, making the cell more prone to becoming cancerous

RNA polymerase II

-proceeds to transcribe the gene, synthesizing a primary RNA transcript ​(pre-mRNA) -transcribes both introns and exons from the DNA

molecular recognition in translation

-tRNA that binds to an mRNA codon specifying a particular amino acid must carry that amino acid, and no other, to the ribosome, the correct matching up of tRNA and amino acid is carried out by a family of related enzymes that are aptly named aminoacyl-tRNA synthetases -pairing of the tRNA anticodon with the appropriate mRNA codon

template strand

-the DNA strand that provides the pattern, or template, for ordering, by complementary base pairing, the sequence of nucleotides in an RNA transcript -for any given gene, the same strand is used as the template every time that gene is transcribed -farther along on the same chromosomal DNA molecule, the opposite strand may function as the template for a different gene

genome of class V viruses

-the RNA genome serves instead as a template for mRNA synthesis -the RNA genome is transcribed into complementary RNA strands, which function both as mRNA and as templates for the synthesis of additional copies of genomic RNA -all viruses that use an RNA genome as a template for mRNA transcription require RNA → RNA synthesis -use a viral enzyme capable of carrying out this process; there are no such enzymes in most cells -the enzyme used in this process is encoded by the viral genome -after the protein is synthesized, it is packaged during viral self-assembly with the genome inside the viral capsid

histone acetylation

-the attachment of acetyl groups to certain amino acids of histone proteins -appears to promote transcription by opening up chromatin structure

oper​on not switched off ​permanently

-the binding of repressors to operators is reversible(alternates between two states: one with the repressor bound and one without the repressor bound. The relative duration of the repressor-bound state is higher when more active repressor molecules are present) -repressor is an allosteric protein, with two alternative shapes: active and inactive, synthesized in the inactive form, which has little affinity for the operator (Only when a tryptophan molecule binds to the trp repressor at an allosteric site does the repressor protein change to the active form that can attach to the operator, turning the operon off)

transcription initiation complex

-the completed assembly of transcription factors and RNA polymerase II bound to a promoter -cluster of proteins​​​ -assembles​​ on the promoter sequence at the "upstream" end of the gene

pattern formation

-the development of a multicellular organism's spatial organization, the arrangement of organs and tissues in their characteristic places in three-dimensional space -begins in the early embryo, when the major axes of an animal are established -in a bilaterally symmetrical animal, the relative positions of head and tail, right and left sides, and back and front—the three major body axes—are set up before the organs appear

morphogenesis

-the development of the form of an organism and its structures -each has a particular mix of specific transcription factor activators that turn on the collection of genes whose products are required in the cell

differential gene expression

-the expression of different sets of genes by cells with the same genome

prophage genes

-the gene for the viral protein that prevents transcription and others may be expressed during lysogeny -expression of these genes may alter the host's phenotype, a phenomenon that can have important medical significance

HIV (human immunodeficiency virus)

-the infectious agent that causes AIDS -a retrovirus

host range

-the limited number of species whose cells can be infected by a particular virus -host specificity results from the evolution of recognition systems by the virus

co-expressed eukaryotic genes

-typically scattered over different chromosomes -coordinate gene expression depends on every gene of a dispersed group having a specific combination of control elements, transcription activators in the nucleus that recognize the control elements bind to them, promoting simultaneous transcription of the genes, no matter where they are in the genome

RNA viruses

-use virally encoded RNA polymerases that can use RNA as a template -some phages and most plant viruses

Adrian Srb and Norman Horowitz

-used a collection of arginine-requiring mutants to investigate the biochemical pathway for arginine synthesis in Neurospora -pinned down each mutant's defect more specifically, using additional tests to distinguish among three classes of arginine-requiring mutants -Mutants in each class required a different set of compounds along the arginine-synthesizing pathway, which has three steps -results suggested that each class was blocked at a different step in this pathway because mutants in that class lacked the enzyme that catalyzes the blocked step

inducible operon

-usually off but can be stimulated (induced) to be on when a specific small molecule interacts with a different regulatory protein -ex. lac operon

viral genome

-usually organized as a single linear or circular molecule of nucleic acid, although some consist of multiple molecules of nucleic acid -may consist of double-stranded DNA, single-stranded DNA, double-stranded RNA, or single-stranded RNA, depending on the type -three to 2,000 genes

Frederick Griffith (1928)

-vaccine against pneumonia, chemical component change of living nonpathogenic bacteria when mixed with dead pathogenic cell remains -Called this phenomenon transformation -Now defined as a change in genotype and phenotype due to the assimilation of external DNA by a cell -Transforming substance later identified DNA

Pithovirus sibericum

-with a diameter of 1.5µm and 500 genes -was discovered in permanently frozen soil in Siberia

bacterial genome

200 to a few thousand genes

Human's somatic cells

23 pairs of chromosomes 46 DNA molecules in its nucleus 6 billion nucleotide pairs

rate of elongation

500 nucleotides per second in bacteria 50 per second in human cells

TATA box

A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex.

replication fork

A Y-shaped region on a replicating DNA molecule where the parental strands are being unwound and new strands are being synthesized.

T4 protein and T4 DNA.

A bacterium is infected with an experimentally constructed bacteriophage composed of the T2 phage protein coat and T4 phage DNA. The new phages produced would have T4 protein and T2 DNA. T2 protein and T2 DNA. a mixture of the DNA and proteins of both phages. T4 protein and T4 DNA. T2 protein and T4 DNA.

d) DNA ligase

A biochemist isolates, purifies, and combines in a test tube a variety of molecules needed for DNA replication. When she adds some DNA to the mixture, replication occurs, but each DNA molecule consists of a normal strand paired with numerous segments of DNA a few hundred nucleotides long. What has she probably left out of the mixture? a) primase b) Okazaki fragments c) DNA polymerase d) DNA ligase e) nucleotides

point mutation

A change in a single nucleotide pair of a gene.

Mutation

A change in the nucleotide sequence of an organism's DNA or in the DNA or RNA of a virus.

mutagen

A chemical or physical agent that interacts with DNA and causes a mutation.

ribosome

A complex of rRNA and protein molecules that functions as a site of protein synthesis in the cytoplasm; consists of a large and a small subunit. In eukaryotic cells, each subunit is assembled in the nucleolus.

lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.

lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5′ → 3′ direction away from the replication fork

triplet code

A genetic information system in which a series of three-nucleotide-long words specifies a sequence of amino acids for a polypeptide chain.

polyribosome (polysome)

A group of several ribosomes attached to, and translating, the same messenger RNA molecule.

vaccine

A harmless variant or derivative of a pathogen that stimulates a host's immune system to mount defenses against the pathogen.

c) a phosphate group

A hydroxyl is present at the 3' end of the growing DNA strand. What is at the 5' end? a) a deoxyribose b) a ribose c) a phosphate group d) a nitrogenous base

spliceosome

A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

DNA ligase

A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain.

viral envelope

A membrane, derived from membranes of the host cell, that cloaks the capsid, which in turn encloses a viral genome.

The viral envelope forms as the virus leaves the host cell.

A microbiologist analyzes chemicals obtained from an enveloped RNA virus that infects monkeys. He finds that the viral envelope contains a protein characteristic of monkey cells. Which of the following is the most likely explanation? The virus forced the monkey cell to make proteins for its envelope. The viral envelope forms as the virus leaves the host cell. The virus fools its host by mimicking its proteins. Its presence is a result of the monkey's immunological response. The virus is a prophage.

5′ cap

A modified form of guanine nucleotide added onto the 5′ end of a pre-mRNA molecule.

insertion

A mutation involving the addition of one or more nucleotide pairs to a gene.

frameshift mutation

A mutation occurring when nucleotides are inserted in or deleted from a gene and the number inserted or deleted is not a multiple of three, resulting in the improper grouping of the subsequent nucleotides into codons.

nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

All of the listed responses are correct.

A new pathogenic form of influenza A can emerge when __________. there is a concurrent infection of a pig or bird by two or more different strains of influenza A a mutation occurs in a virus as it passes from one host to another a virus with a novel genetic makeup recombines with viruses that circulate widely among humans the genomes of two or more influenza A strains mix and match during viral assembly within a host All of the listed responses are correct.

b) C

A nitrogenous base is indicated by the letter _____. a) D b) C c) B d) A

intron

A noncoding, intervening sequence within a primary transcript that is removed from the transcript during RNA processing; also refers to the region of DNA from which this sequence was transcribed.

anticodon

A nucleotide triplet at one end of a tRNA molecule that base-pairs with a particular complementary codon on an mRNA molecule.

silent mutation

A nucleotide-pair substitution that has no observable effect on the phenotype; for example, within a gene, a mutation that results in a codon that codes for the same amino acid.

prophage

A phage genome that has been inserted into a specific site on a bacterial chromosome.

lysogenic

A phage that inserts itself into the host DNA is called __________. semipermeable a bacteriophage a bud lysogenic a capsomere

temperate phage

A phage that is capable of replicating by either a lytic or lysogenic cycle.

virulent phage

A phage that reproduces only by a lytic cycle.

The viral infection was acquired by vertical transmission.

A plant that has been raised in a sterile environment shows symptoms of a viral infection. How would you explain this? The viral infection was acquired by vertical transmission. A plant raised in a sterile environment cannot show symptoms of viral infection. The viral infection was acquired from the environment. The viral infection was acquired by horizontal transmission. A group of plant genes mutated to become a viral genome.

viral genome that has been incorporated into a bacterial cell's chromosome

A prophage is a(n) __________. type of retrovirus emerging virus viral genome that has been incorporated into a bacterial cell's chromosome virus that infects other viruses prion that has been integrated into a bacterial cell's chromosome

single strand binding proteins

A protein that binds to the unpaired DNA strands during DNA replication, stabilizing them and holding them apart while they serve as templates for the synthesis of complementary strands of DNA.

Topoisomerase

A protein that breaks, swivels, and rejoins DNA strands. During DNA replication, topoisomerase helps to relieve strain in the double helix ahead of the replication fork.

signal-recognition particle (SRP)

A protein-RNA complex that recognizes a signal peptide as it emerges from a ribosome and helps direct the ribosome to the endoplasmic reticulum (ER) by binding to a receptor protein on the ER.

transcription unit

A region of DNA that is transcribed into an RNA molecule.

transcription factor

A regulatory protein that binds to DNA and affects transcription of specific genes.

nucleotide excision repair

A repair system that removes and then correctly replaces a damaged segment of DNA using the undamaged strand as a guide.

b) the protein and DNA of T4

A scientist assembles a bacteriophage with the protein coat of phage T2 and the DNA of phage T4. If this composite phage were allowed to infect a bacterium, the phages produced in the host cell would have __________. a) the protein of T2 and the DNA of T4 b) the protein and DNA of T4 c) the protein of T4 and the DNA of T2 d) a mixture of the DNA and proteins of both phages e) the protein and DNA of T2

poly-A tail

A sequence of 50-250 adenine nucleotides added onto the 3′ end of a pre-mRNA molecule.

signal peptide

A sequence of about 20 amino acids at or near the leading (amino) end of a polypeptide that targets it to the endoplasmic reticulum or other organelles in a eukaryotic cell.

exon

A sequence within a primary transcript that remains in the RNA after RNA processing; also refers to the region of DNA from which this sequence was transcribed.

primer

A short polynucleotide with a free 3' end, bound by complementary base pairing to the template strand and elongated with DNA nucleotides during DNA replication

Okazaki fragment

A short segment of DNA synthesized away from the replication fork on a template strand during DNA replication. Many such segments are joined together to make up the lagging strand of newly synthesized DNA.

histone

A small protein with a high proportion of positively charged amino acids that binds to the negatively charged DNA and plays a key role in chromatin structure.

promoter

A specific nucleotide sequence in the DNA of a gene that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place.

CRISPER-Cas9

A technique for editing genes in living cells, involving a bacterial protein called Cas9 associated with a guide RNA complementary to a gene sequence of interest.

codon

A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.

Messenger RNA (mRNA)

A type of RNA, synthesized using a DNA template, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.

alternative RNA splicing

A type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.

lysogenic cycle

A type of phage replicative cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage, is replicated along with the chromosome, and does not kill the host

lytic cycle

A type of phage replicative cycle resulting in the release of new phages by lysis (and death) of the host cell

nucleotide-pair substitution

A type of point mutation in which one nucleotide in a DNA strand and its partner in the complementary strand are replaced by another pair of nucleotides.

provirus

A viral genome that is permanently inserted into a host genome.

b) bacteriophage; DNA; protein

A virus that infects bacteria is called a __________, which is made up of the macromolecules __________ and __________. a) Streptococcus; DNA; protein b) bacteriophage; DNA; protein c) Streptococcus; DNA; RNA d) bacteriophage; RNA; protein e) bacteriophage; DNA; RNA

phage

A virus that infects bacteria; also called a bacteriophage

Bacteriophage

A virus that infects bacteria; also called a phage.

bacteriophage

A virus that infects bacteria; also called a phage.

epidemic

A widespread outbreak of a disease.

restriction enzyme

An endonuclease (type of enzyme) that recognizes and cuts DNA molecules foreign to a bacterium (such as phage genomes). The enzyme cuts at specific nucleotide sequences (restriction sites).

reverse transcriptase

An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis.

DNA polymerase

An enzyme that catalyzes the elongation of new DNA at a replication fork by the addition of nucleotides to the existing chain.

Nuclease

An enzyme that cuts DNA or RNA, either removing one or a few bases or hydrolyzing the DNA or RNA completely into its component nucleotides.

nuclease

An enzyme that cuts DNA or RNA, either removing one or a few bases or hydrolyzing the DNA or RNA completely into its component nucleotides.

primase

An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.

aminoacyl-tRNA synthetase

An enzyme that joins each amino acid to the appropriate tRNA.

RNA polymerase

An enzyme that links ribonucleotides into a growing RNA chain during transcription, based on complementary binding to nucleotides on a DNA template strand.

helicase

An enzyme that untwists the double helix at the replication forks, separating the two parental strands and making them available as template strands.

prion

An infectious agent that is a misfolded version of a normal cellular protein. Prions appear to increase in number by converting correctly folded versions of the protein to more prions.

virus

An infectious particle incapable of replicating outside of a cell, consisting of an RNA or DNA genome surrounded by a protein coat (capsid) and, for some viruses, a membranous envelope.

primary transcript

An initial RNA transcript; also called pre-mRNA when transcribed from a protein-coding gene.

natural reservoir

Animals that harbor and can transmit a particular virus but are generally unaffected by it are said to act as a __________ for that virus. natural reservoir nontransmitter viroid retrovirus vaccine

a) 3′ end; 3′ end

DNA polymerase adds nucleotides to the __________ of the leading strands and to the __________ of the lagging strands (Okazaki fragments). a) 3′ end; 3′ end b) 5′ end; 3′ end c) 3′ end; 5′ end d) 5′ end; 5′ end e) sugar group; phosphate group

a) 3' end; 3' end

DNA polymerase adds nucleotides to the __________ of the leading strands, and to the __________ of the lagging strands (Okazaki fragments). a) 3' end; 3' end b) 5' end; 5' end c) 3' end; 5' end d) 5' end; 3' end e) sugar group; phosphate group

a) replication fork; helicases

DNA replication begins at a site called the origin of replication, forming a bubble, which is followed by a __________, where parental strands are unwound by __________. a) replication fork; helicases b) replication Y; topoisomerases c) replication fork; topoisomerases d) replication Y; helicases e) replication fork; RNA primers

DNA vs RNA strand

DNA: -bases together are called genes -base-pairing rules dictate the combinations of nitrogenous bases that form the "rungs" of the double helix -Do not restrict the sequence of nucleotides along each DNA strand. The linear sequence of the four bases can be varied in countless ways, and each gene has a unique base sequence

provirus

Double-stranded viral DNA is incorporated into a host cell as a _____. promoter provirus transposon lac homeoboxes

c) Complementary DNA strands are separated or "unzipped" for the replication process. Weak hydrogen bonds between complementary strands are easily disrupted during DNA replication because they are not high-energy chemical bonds.

Duplication of chromosomes occurs during S phase of the cell cycle. Duplication requires the separation of complementary DNA strands to allow for DNA replication. Which of the following statements best explains how weak hydrogen bonds function better in this situation than stronger bonds would? a) Complementary DNA strands are easily mutated by environmental factors. These changes lead to evolution. Therefore, weak hydrogen bonds support continued evolution by allowing mutations during DNA replication. b) Duplicated DNA molecules must be extremely flexible in order to fit sister chromatid pairs into the nucleus of a eukaryotic cell. Weak hydrogen bonds between complementary strands are easily bent and modified, allowing for this type of flexibility. c) Complementary DNA strands are separated or "unzipped" for the replication process. Weak hydrogen bonds between complementary strands are easily disrupted during DNA replication because they are not high-energy chemical bonds. d) Hydrogen is used in many metabolic functions; therefore its function connecting complementary DNA strands stores hydrogen atoms for use in the G2 phase of the cell cycle.

c) heat-killed pathogenic; living nonpathogenic

During Griffith's experiments with Streptococcus pneumoniae in mice, material from __________ bacteria transformed __________ bacteria. a) living pathogenic; heat-killed nonpathogenic b) living nonpathogenic; heat-killed pathogenic c) heat-killed pathogenic; living nonpathogenic d) living nonpathogenic; living pathogenic e) heat-killed nonpathogenic; living pathogenic

e) both strands of a molecule act as templates

During the replication of DNA, __________. a) only one strand of the molecule acts as a template b) the reaction is catalyzed by RNA polymerase c) the cell undergoes mitosis d) errors never occur e) both strands of a molecule act as templates

c) one low-density and one intermediate-density band

E. coli cells grown on 15N medium are transferred to 14N medium and allowed to grow for two more generations (two rounds of DNA replication). DNA extracted from these cells is centrifuged. What density distribution of DNA would you expect in this experiment? a) one high-density and one intermediate-density band b) one low-density band c) one low-density and one intermediate-density band d) one intermediate-density band e) one high-density and one low-density band

all of the above

Emerging viruses arise by none of the above all of the above the spread of existing viruses to new host species. the spread of existing viruses more widely within their host species. mutation of existing viruses.

All of the listed responses are correct.

Emerging viruses can originate from which of the following sources? Animal viruses The mutation of existing human viruses Viruses previously confined to small, isolated populations that can now spread due to technological or social changes such as the development of affordable international travel All of the listed responses are correct. None of the listed responses is correct.

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.

a) that the sugar-phosphate backbones are to the inside of the molecule

Evidence to support that DNA strands run antiparallel to each other includes all of the following except __________. a) that the sugar-phosphate backbones are to the inside of the molecule b) X-ray measurement data c) hydrogen bonding interactions d) that the nitrogenous bases are on the inside e) Chargaff's rules

wobble

Flexibility in the base-pairing rules in which the nucleotide at the 5' end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position of a codon.

d) 5'-TACGAACC-3'

Given a template strand of 3'-ATGCTTGGACA-5' and a partially-made complementary strand containing only 5'-TAC-3', what would be the sequence of the new strand of DNA (including the 5'-TAC-3') if the only additional nucleotides available to DNA polymerase were those containing the bases G, A, and C? a) 5'-TAC-3'; All four nucleotides are required for DNA polymerase to function. b) 3'-TACGAACCTGT-5' c) 5'-GAACC-3' d) 5'-TACGAACC-3'

c) pathogenic; transform; nonpathogenic; pathogenic

Griffith showed that dead __________ cells __________ living __________ cells into living __________ cells. a) pathogenic; transform; pathogenic; nonpathogenic b) nonpathogenic; transform; nonpathogenic; pathogenic c) pathogenic; transform; nonpathogenic; pathogenic d) nonpathogenic; transform; pathogenic; nonpathogenic

reverse transcription

HIV uses which of the following processes to synthesize a DNA strand using its RNA genome as a template? transcription reverse transcription conjugation translation reverse translation

the virus binds to specific receptors that are only present on certain immune cells

HIV, the virus that causes AIDS, only infects certain cells within the immune system. This is because __________. infection requires the presence of a specific DNA sequence that is only present in the genome of certain immune system cells other cells produce toxins that destroy the virus before infection can take place the virus is not very mobile within the body and only comes into contact with a limited number of immune cells the virus binds to specific receptors that are only present on certain immune cells the virus gets into all cells, but the viral RNA is immediately destroyed in all but a small number of immune system cells

Retroviruses use the enzyme reverse transcriptase to transcribe a copy of DNA from their own RNA.

How are retroviruses different from other types of viruses? Retrovirus RNA is incorporated into the host cell's DNA in order to be translated. Retrovirus DNA is incorporated into the host cell's DNA in order to be translated. Retrovirus DNA is used directly by the infected cell to transcribe and translate viral proteins. Retroviruses use the enzyme reverse transcriptase to transcribe a copy of DNA from their own RNA. Retrovirus RNA is used directly by the infected cell to produce viral proteins.

Unlike viruses, prions are infectious proteins. Unlike viruses, prions do not include any nucleic acids. Unlike a virus, a prion is a single molecule.

How do prions differ from viruses? Select all that apply. Unlike viruses, prions are infectious proteins. Unlike viruses, prions do not include any nucleic acids. Unlike a virus, a prion is a single molecule.

Prions enter brain cells and cause normal forms of the protein to refold into the prion form.

How do prions, which are misfolded proteins, infect organisms? Prions enter brain cells through the lymphatic system and make copies of themselves. Prions recruit ribosomes to make more copies of the wrong form of the protein. Prions only arise through spontaneous mutation. They are not transmissible. Prions enter brain cells and cause normal forms of the protein to refold into the prion form. None of the above.

They can transcribe a DNA copy from a RNA template.

How do retroviruses, such as HIV, differ from other viruses? They contain DNA that is used as a template to make RNA. They have much simpler reproductive cycles than other RNA viruses. They can reproduce only inside living cells. They can transcribe a DNA copy from a RNA template. They contain nucleic acids that code for proteins.

Glycoproteins on the viral envelope bind to receptors on the host cell. The viral envelope fuses with the host cell's plasma membrane, facilitating uptake of the virus by the host cell.

How does a retrovirus like HIV enter a host cell? HIV passes through the lipid bilayer of the plasma membrane. Glycoproteins on the viral envelope bind to receptors on the host cell. The viral envelope fuses with the host cell's plasma membrane, facilitating uptake of the virus by the host cell. HIV binds to the host cell and injects its DNA. HIV passes through a channel protein in the lipid bilayer of the plasma membrane. HIV binds to the host cell and injects its RNA.

Viruses, unlike bacteria, lack metabolic enzymes.

How does a virus differ from a bacterium? Select all that apply. Viruses, unlike bacteria, lack metabolic enzymes. A virus, unlike a bacterium, lacks a genome. Viruses are two-dimensional, whereas bacteria are three-dimensional.

e) 3ꞌ (hydroxyl) end; DNA polymerase

In DNA replication, the next nucleotide is incorporated into the growing polymer at the __________ of the molecule by an enzyme called __________. a) 5ꞌ (phosphate) end; DNA polymerase b) 3ꞌ (phosphate) end; RNA polymerase c) 5ꞌ (hydroxyl) end; RNA polymerase d) 3ꞌ (hydroxyl) end; topoisomerase e) 3ꞌ (hydroxyl) end; DNA polymerase

d) adenine and guanine; cytosine and thymine

In DNA, the two purines are __________, and the two pyrimidines are __________. a) adenine and thymine; cytosine and guanine b) adenine and cytosine; guanine and thymine c) cytosine and guanine; adenine and thymine d) adenine and guanine; cytosine and thymine e) cytosine and thymine; adenine and guanine

a) thymine ... cytosine

In a DNA double helix an adenine of one strand always pairs with a(n) _____ of the complementary strand, and a guanine of one strand always pairs with a(n) _____ of the complementary strand. a) thymine ... cytosine b) uracil ... cytosine c) cytosine ... thymine d) guanine ... adenine e) cytosine ... uracil

c) Because they are asexual and single-celled, all uncorrected errors of replication in bacteria are transmitted to subsequent generations. Multicellular eukaryotes typically reproduce sexually, so uncorrected errors are transmitted only if they occur in germ cells that meiotically divide to produce gametes.

In a comparison between asexually reproducing bacteria and sexually reproducing multicellular eukaryotes, uncorrected errors in replication are more likely to be transmitted to subsequent generations in bacteria than in multicellular eukaryotes. Which of the following provides the best evidence-based explanation for this difference? a) Although the genome for each is represented as pairs of homologous chromosomes, errors in bacteria affect both homologs, but only one is affected in eukaryotes. b) Unlike multicellular eukaryotes, bacteria lack DNA repair enzymes, so there are just more uncorrected errors at play. c) Because they are asexual and single-celled, all uncorrected errors of replication in bacteria are transmitted to subsequent generations. Multicellular eukaryotes typically reproduce sexually, so uncorrected errors are transmitted only if they occur in germ cells that meiotically divide to produce gametes. d) Only errors that lead to faster-growing strains are left uncorrected in bacteria, whereas all errors are detected and repaired in multicellular eukaryotes. e) The third and fourth listed responses can explain this phenomenon.

e) histones.

In a nucleosome, the DNA is wrapped around a) a thymine dimer. b) satellite DNA. c) polymerase molecules. d) ribosomes. e) histones.

d) 1' ... 5'

In a nucleotide, the nitrogenous base is attached to the sugar's _____ carbon and the phosphate group is attached to the sugar's _____ carbon. a) 2' ... 1' b) 1' ... 3' c) 2' ... 3' d) 1' ... 5' e) 1' ... 2'

c) the genetic material of the phage is DNA

In an important experiment, a radioactively labeled bacteriophage was allowed to infect bacteria. In a first trial, the phage contained radioactive DNA, and radioactivity was detected inside the bacteria. Next, phage-containing radioactive protein was used, and the radioactivity was not detected inside the bacteria. These experiments led to the conclusion that __________. a) the genetic material of the phage is protein b) DNA is made of nucleotides c) the genetic material of the phage is DNA d) bacteriophages can infect bacteria e) genes are on chromosomes

b) A + G = C + T

In analyzing the number of different bases in a DNA sample, which result would be consistent with the base-pairing rules? a) A + T = G + T b) A + G = C + T c) G = T d) A = C e) A = G

terminator

In bacteria, a sequence of nucleotides in DNA that marks the end of a gene and signals RNA polymerase to release the newly made RNA molecule and detach from the DNA.

d) DNA polymerase III; DNA polymerase I

In bacterial DNA replication of the lagging strand, __________ is required for the synthesis of a new DNA strand whereas __________ is required for removing the RNA primer and replacing it with DNA nucleotides. a) DNA polymerase I; DNA polymerase III b) DNA ligase; DNA polymerase I c) DNA polymerase III; DNA ligase d) DNA polymerase III; DNA polymerase I e) DNA polymerase I; DNA ligase

RNA processing

Modification of RNA primary transcripts, including splicing out of introns, joining together of exons, and alteration of the 5' and 3' ends.

d) nucleotides

Monomers for the synthesis of DNA are called __________. a) amino acids b) fatty acids c) disaccharides d) nucleotides e) monosaccharides

d) conservative, semiconservative, and dispersive; semiconservative

Of the three alternative models of DNA replication, which are the __________ models, the one that explains how DNA replicates is the __________ model. a) conservative, nonconservative, and dispersive; nonconservative b) conservative, nonconservative, and dispersive; dispersive c) conservative, semiconservative, and dispersive; conservative d) conservative, semiconservative, and dispersive; semiconservative e) conservative, semiconservative, and dispersive; dispersive

reading frame

On an mRNA, the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis.

c) Single-strand binding proteins bind the unwound DNA and prevent the double helix from re-forming.

Once the DNA at the replication fork is unwound by helicases, what prevents the two strands from coming back together to re-form a double helix? a) One of the strands is rapidly degraded, preventing the double helix from re-forming. b) The helicase modifies the DNA in such a way as to eliminate the affinity between the two strands. c) Single-strand binding proteins bind the unwound DNA and prevent the double helix from re-forming. d) DNA polymerase follows the helicase so closely that there is no chance for the strands to come back together. e) The helicase pushes the two strands so far apart that they have no chance of finding each other.

E site

One of a ribosome's three binding sites for tRNA during translation. The E site is the place where discharged tRNAs leave the ribosome. (E stands for exit.)

b) TATCCA

One strand of a DNA molecule has the base sequence 5'-ATAGGT-3'. The complementary base sequence on the other strand of DNA will be 3'-__________-5'. a) UAUCCA b) TATCCA c) TGGATA d) ATAGGT e) TGGAUA

e) TATCCA

One strand of a DNA molecule has the base sequence 5′-ATAGGT-3′. The complementary base sequence on the other strand of DNA will be 3′- __________-5′. a) TGGATA b) ATAGGT c) TGGAUA d) UAUCCA e) TATCCA

e) nuclease, DNA polymerase, DNA ligase

The spontaneous loss of amino groups from adenine in DNA results in hypoxanthine, an uncommon base, opposite thymine. What combination of proteins could repair such damage? a) telomerase, helicase, single-strand binding protein b) telomerase, primase, DNA polymerase c) DNA ligase, replication fork proteins, adenylyl cyclase d) nuclease, telomerase, primase e) nuclease, DNA polymerase, DNA ligase

AIDS (acquired immunodeficiency syndrome)

The symptoms and signs present during the late stages of HIV infection, defined by a specified reduction in the number of T cells and the appearance of characteristic secondary infections.

All of the listed responses are correct.

The symptoms of a viral infection in a person can be caused by __________. the death of infected cells the production of toxins by infected cells toxic viral components, such as envelope proteins the reaction of the individual's immune system to the infection All of the listed responses are correct.

translation

The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of language from nucleotides to amino acids.

Telomere

The tandemly repetitive DNA at the end of a eukaryotic chromosome's DNA molecule. Telomeres protect the organism's genes from being eroded during successive rounds of replication. See also repetitive DNA.

d) hydrogen bonds between nucleotide bases

The two antiparallel strands of nucleotides that form the DNA double helix are held together by __________. a) 5' deoxyribose and phosphate bonds b) ionic bonds between guanine and cytosine c) covalent bonds between carbon atoms in deoxyribose molecules d) hydrogen bonds between nucleotide bases e) covalent bonds between nitrogen atoms in adenine and in thymine

c) one strand runs in the 5' to 3' direction and the other runs in the 3' to 5' direction

The two strands of a DNA double helix are antiparallel. This means that __________. a) the two strands are mirror images b) they both run in the 3' to 5' direction c) one strand runs in the 5' to 3' direction and the other runs in the 3' to 5' direction d) only one of the two strands can be used as a template for replication because DNA polymerase only works in one direction e) one strand is actually composed of RNA

c) hydrogen bonds between nucleotide bases

The two sugar-phosphate strands that form the rungs of a DNA double helix are joined to each other through __________. a) ionic bonds between guanine and cytosine b) covalent bonds between nitrogen atoms in adenine and in thymine c) hydrogen bonds between nucleotide bases d) covalent bonds between carbon atoms in deoxyribose molecules e) 5' deoxyribose and phosphate bonds

b) topoisomerase

The unwinding of DNA at the replication fork causes twisting and strain in the DNA ahead of the fork, which is relieved by an enzyme called __________. a) relievase b) topoisomerase c) helicase d) ligase e) primase

telomerase

This enzyme catalyzes the lengthening of telomeres in eukaryotic germ cells, thus restoring their original length and compensating for the shortening that occurs during DNA replication -This enzyme contains its own RNA molecule that it uses as a template to artificially "extend" the leading strand, allowing the lagging strand to maintain a given length

d) nucleotide

This is an image of a(n) _____. a) nucleic acid b) thiol c) amino acid d) nucleotide e) none of the above

become capable of human-to-human transmission.

To cause a human pandemic, the H5N1 avian flu virus would have to arise independently in chickens in North and South America. spread to primates such as chimpanzees. become much more pathogenic. become capable of human-to-human transmission. develop into a virus with a different host range.

semiconservative model

Type of DNA replication in which the replicated double helix consists of one old strand, derived from the old molecule, and one newly made strand.

b) cannot be completed by DNA polymerase

Unlike prokaryotic DNA replication, replication of eukaryotic chromosomes __________. a) has a single origin b) cannot be completed by DNA polymerase c) is error-free d) is semiconservative e) involves two leading strands and no lagging strands

e) Watson and Crick

Who is credited with explaining the structure of the DNA double helix? a) Griffith b) Jacob and Monod c) Avery, McCarty, and MacLeod d) Hershey and Chase e) Watson and Crick

d) Watson and Crick

Who is credited with explaining the structure of the DNA double helix? a) Hershey and Chase b) Avery, McCarty, and MacLeod c) Griffith d) Watson and Crick e) Rosalind Franklin

Viruses do not carry out metabolic processes, a primary characteristic of living organisms.

Why are viruses often considered to be nonliving? Viruses carry genetic information. Viruses do not carry out metabolic processes, a primary characteristic of living organisms. Viruses can replicate outside of a host cell. Viruses can reproduce. Viruses have plasma membranes similar to those of other types of cells.

Herpes virus can leave its DNA behind as minichromosomes in nerve cell nuclei. Stress can trigger another round of virus production, producing characteristic blisters and sores.

Why can flare-ups of herpes virus infection recur throughout a person's life? Herpes virus is very common in the environment, so it is easy for a person to become re-infected. Herpes virus can leave its DNA behind as minichromosomes in nerve cell nuclei. Stress can trigger another round of virus production, producing characteristic blisters and sores. The herpes virus becomes a prophage during the lysogenic cycle of the infection, so the viral genome is recombined with the host DNA. The herpes virus always kills its host cell when it leaves. Cycles of cell death cause the recurring flare-ups. Herpes virus may cloak itself in a cell's nuclear envelope, making it very difficult for the immune system to recognize it.

Mimivirus

a double-stranded DNA (dsDNA) virus with an icosahedral capsid that is 400 nm in diameter, the size of a small bacterium. Its genome contains 1.2 million bases (Mb)—about 100 times as many as the influenza virus genome—and an estimated 1,000 genes. Perhaps the most surprising aspect of mimivirus, however, was that its genome included genes previously found only in cellular genomes. Some of these genes code for proteins involved in translation, DNA repair, protein folding, and polysaccharide synthesis. Whether mimivirus evolved before the first cells and then developed an exploitative relationship with them or evolved more recently and simply scavenged genes from its hosts is not yet settled

chromosome

a dynamic structure that is condensed, loosened, modified, and remodeled as necessary for various cell processes, including DNA replication, mitosis, meiosis, and gene expression

missense mutation

a nucleotide-pair substitution that results in a codon that codes for a different amino acid

secondary transcription factors

activate the genes for proteins such as myosin and actin that confer the unique properties of skeletal muscle cells

thymine (T)

adenine (A) 2 hydrogen bonds

reverse transcriptase

an enzyme encoded by certain viruses (retroviruses) that uses RNA as a template for DNA synthesis

some tRNAs must be able to bind to more than one codon

bc of -rules for base pairing between the third nucleotide base of a codon -the corresponding base of a tRNA anticodon are relaxed compared to those at other codon positions

Enzymes

can only add DNA nucleotides to the end of an already existing chain that is base-paired with the template strand

missense mutation

causes a wild-type amino acid to be replaced by a different amino acid

nonsense mutation

causes an early Stop codon to occur

Cytoplasmic determinants and inductive signals

contribute to spatially organizing the tissues and organs of an organism in their characteristic places, or pattern formation

Pyrimidines

cytosine, thymine, and uracil

silent mutation

does not change the wild-type amino acid sequence

hemorrhagic fever

fatal illness characterized by fever, vomiting, massive bleeding, and circulatory system collapse -ex. ebola

C-terminus

final amino acid at the carboxyl end

pandemic

global epidemic

genes are coordinately controlled

grouping genes of related function into one transcription unit allows a single "on-off switch" can control the whole cluster of functionally related genes

cytosine (C)

guanine (G) 3 hydrogen bonds

Purines

guanine and adenine

p21 protein

halts the cell cycle by binding to cyclin-dependent kinases, allowing time for the cell to repair the DNA

viral proteins

host provides the nucleotides for making viral nucleic acids, as well as enzymes, ribosomes, tRNAs, amino acids, ATP, and other components to make this

plasmodesmata

Plant viruses spread throughout the plant by way of __________. vertical transmission central vacuoles plasmodesmata chloroplasts the lymphatic system

abnormally shaped proteins; inducing similar but normally shaped proteins in the brain to adopt the abnormal form

Prions are __________ that are thought to cause disease by __________. an abnormal type of capsid; dramatically enhancing the rate of viral infection mutant DNA molecules; encoding toxic proteins abnormally shaped proteins; inducing similar but normally shaped proteins in the brain to adopt the abnormal form RNA molecules; encoding toxic proteins DNA molecules; jumping around the genome and mutating genes

e) nucleosomes; histones

Proteins that are involved in packaging the eukaryotic chromosome into "beads" called __________ are __________. a) a helix; nucleosomes b) nucleosomes; looped domains c) chromatids; histones d) histones; nucleosomes e) nucleosomes; histones

ribosomal RNA (rRNA)

RNA molecules that, together with proteins, make up ribosomes; the most abundant type of RNA.

host cells lack enzymes that can replicate the viral genome.

RNA viruses require their own supply of certain enzymes because these enzymes translate viral mRNA into proteins. these enzymes cannot be made in host cells. host cells rapidly destroy the viruses. these enzymes penetrate host cell membranes. host cells lack enzymes that can replicate the viral genome.

d) short RNA primers; Okazaki fragments

Replication of the lagging strand of DNA is accomplished by repeatedly making __________ followed by 1,000-2,000 nucleotide segments called __________. a) DNA ligase; Watson fragments b) long RNA primers; Okazaki segments c) short primers; Okazaki segments d) short RNA primers; Okazaki fragments e) short DNA primers; Watson segments

cutting viral DNA once it has entered the cell

Restriction enzymes help defend bacteria against viral infections by __________. preventing the binding of the virus to the cell surface preventing the synthesis of viral capsomeres in the cell preventing entry of the viral DNA into the cell preventing integration of the viral genome into the host chromosome cutting viral DNA once it has entered the cell

RNA information is copied into DNA

Reverse transcription, carried out by retroviruses, is the process by which __________. DNA is duplicated RNA information is copied into DNA DNA information is copied into RNA RNA information is "read" to form a protein molecule information is copied from a protein molecule into RNA

origin of replication

Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.

Membranes from the host cell

Some viruses have membranous envelopes. Where do viral envelopes typically originate from? They come from other viruses. Membranes from the host cell The virus produces the envelope itself. They develop from the capsid. They come from the cell walls of bacteria. Capsomeres produce them.

d) is an enzyme that lengthens telomeres

Telomerase __________. a) prevents the loss of centromeric DNA b) speeds cell aging c) slows the rate of cancer cell growth d) is an enzyme that lengthens telomeres e) splits telomeres

e) get shorter with each round of DNA replication

Telomeres __________. a) are shorter for younger individuals b) get longer with each round of DNA replication c) are found in both prokaryotic and eukaryotic cells d) remain the same regardless of the frequency of DNA replication e) get shorter with each round of DNA replication

a) repeating noncoding sequences at the ends of linear eukaryotic chromosomes

Telomeres are __________. a) repeating noncoding sequences at the ends of linear eukaryotic chromosomes b) repeating noncoding sequences at the ends of circular bacterial chromosomes c) None of the listed responses is correct. d) nonrepeating noncoding sequences at the ends of linear eukaryotic chromosomes e) nonrepeating noncoding sequences at the ends of circular bacterial chromosomes

a) phosphate; hydroxyl

The 5ꞌ end of a DNA strand always has a free __________ group while the 3ꞌ end always has a free __________ group. a) phosphate; hydroxyl b) amine; phosphate c) phosphate; amine d) hydroxyl; phosphate e) phosphate; acidic

template strand

The DNA strand that provides the pattern, or template, for ordering, by complementary base pairing, the sequence of nucleotides in an RNA transcript.

a pandemic

The H1N1 2009 outbreak is considered to have been which of the following? an influenza of type C a virus that is found in the human species only an emerging virus a retrovirus a pandemic

it has a significantly higher mortality rate

The avian flu virus H5N1 is considered a greater long-term threat than the swine flu virus H1N1 because __________. H5N1 is a DNA virus and the similarity of genome chemistry can promote greater virulence and therefore the likelihood of death in humans it is more readily transmitted between human hosts more people eat chicken meat than pork H5N1 has a greater tendency to become a prophage it has a significantly higher mortality rate

Nucleosome

The basic, bead-like unit of DNA packing in eukaryotes, consisting of a segment of DNA wound around a protein core composed of two copies of each of four types of histone.

van der Waals interactions

The bonds or interactions between stacked nucleotide units that help hold the DNA molecule together are

covalent bonds

The bonds or interactions that hold together adjacent nucleotides in the sugar-phosphate backbone of DNA are

hydrogen bonds

The bonds or interactions that hold together complementary bases from opposite strands of DNA are

mismatch repair

The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides

mismatch repair

The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides.

transcription initiation complex

The completed assembly of transcription factors and RNA polymerase bound to a promoter.

chromatin

The complex of DNA and proteins that makes up eukaryotic chromosomes. When the cell is not dividing, chromatin exists in its dispersed form, as a mass of very long, thin fibers that are not visible with a light microscope

b) depends on the action of DNA polymerase.

The elongation of the leading strand during DNA synthesis a) produces Okazaki fragments. b) depends on the action of DNA polymerase. c) does not require a template strand. d) progresses away from the replication fork. e) occurs in the 39 S59 direction.

e) replicates in a semiconservative fashion

The experiments of Meselson and Stahl showed that DNA __________. a) contains complementary base pairing b) is composed of nucleotides c) codes for the amino acid sequences of proteins d) is the genetic material e) replicates in a semiconservative fashion

double helix

The form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape.

single-stranded RNA

The genetic material of HIV consists of _____. single-stranded DNA single-stranded RNA double-stranded DNA double-stranded RNA none of the above

d) can be repaired by the mismatch repair system

The incorporation of an incorrect base into the DNA during replication __________. a) is virtually im, as the accuracy of DNA polymerase is such that errors almost never occur b) will almost certainly lead to the death of the cell c) will trigger the cell to destroy the new strand, and replication will begin again d) can be repaired by the mismatch repair system e) cannot be repaired, and a new mutation will invariably result

HIV (human immunodeficiency virus)

The infectious agent that causes AIDS. HIV is a retrovirus.

a) the sequence of nucleotides along the length of the two strands of the DNA molecule

The information in DNA is contained in __________. a) the sequence of nucleotides along the length of the two strands of the DNA molecule b) the types of sugars used in making the DNA molecule c) the variation in the structure of nucleotides that make up the DNA molecule d) the sequence of amino acids that makes up the DNA molecule e) All of the listed responses are correct.

b) the sequence of nucleotides along the length of the two strands of the DNA molecule

The information in DNA is contained in __________. a) the types of sugars used in making the DNA molecule b) the sequence of nucleotides along the length of the two strands of the DNA molecule c) All of the listed responses are correct d) the sequence of amino acids that makes up the DNA molecule e) the variation in the structure of nucleotides that make up the DNA molecule

Euchromatin

The less condensed form of eukaryotic chromatin that is available for transcription.

b) phosphate group

The letter A indicates a _____. a) nucleotide b) phosphate group c) nitrogenous base d) sugar e) none of the above

host range

The limited number of species whose cells can be infected by a particular virus.

rupture of the bacterium

The lytic cycle of bacteriophage infection ends with the _____. replication of viral DNA entry of the phage protein coat into the host cell assembly of viral particles into phages the injection of phage DNA into a bacterium rupture of the bacterium

leading strand

The new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory 5′ → 3′ direction.

capsid

The nucleic acid of a virus particle is enclosed in a protein coat. What is it called? genome nuclear envelope nucleoid envelope capsid

P site

one of a ribosome's three binding sites for tRNA during translation. It holds the tRNA carrying the growing polypeptide chain.

helical viruses

rod-shaped viruses

transcription

synthesis of an RNA molecule from a DNA template

DNA viruses

the DNA polymerases of the host cell to synthesize new genomes along the templates provided by the viral DNA

Kuru

identified in the early 1900s among the South Fore indigenous people of New Guinea->peaked in the 1960s, scientists at first thought the disease had a genetic basis because family members also often contracted the disease, but after a death, family members practiced ritual cannibalism, eating organs of the deceased, and this was transmitted primarily in brain tissue: women got kuru more often than men because men ate the more "prestigious" organs, like the heart, while women and children ate the brains

start point

in transcription, the nucleotide position on the promoter where RNA polymerase begins synthesis of RNA

chromatin structure and gene expression

influenced by chemical modifications of both the histone proteins of the nucleosomes around which DNA is wrapped and the nucleotides that make up that DNA

N-terminus (amino terminus)

initial methionine at the amino end

t​hree stages of transcription

initiation, elongation, and termination

addition of methyl groups to histones

lead to the condensation of chromatin and reduced transcription

Genes within heterochromatin

usually not expressed

Genes within euchromatin

whether or not a gene is transcribed is affected by the location of nucleosomes along a gene's promoter and also the sites where the DNA attaches to the protein scaffolding of the chromosome

Making Multiple Polypeptides

*1ST WAY* -a single mRNA is used to make many copies of a polypeptide simultaneously by multiple ribosomes translating an mRNA at the same time -once a ribosome is far enough past the start codon, a second ribosome can attach to the mRNA, eventually resulting in a number of ribosomes trailing along the mRNA; creating a polyribosome *2ND WAY* -transcribing multiple mRNAs from the same gene -transcription and translation differ in the bacteria & eukaryotes bc of the lack of compartmental organization in bacteria ---bacterial cell ensures a streamlined operation by coupling the two processes; ith no nuclear envelope, it can simultaneously transcribe and translate the same gene, and the newly made protein can quickly diffuse to its site of function ---eukaryotic cell's nuclear envelope segregates transcription from translation and provides a compartment for extensive RNA processing; this processing stage includes additional steps, the regulation of which can help coordinate the eukaryotic cell's elaborate activities

three, amino acid

*A codon consists of __________ bases and specifies which __________ will be inserted into the polypeptide chain.* three, amino acid four, fatty acid four, amino acid three, nucleotide two, nucleotide

a silent or neutral mutation

*A particular mutation had no effect on the polypeptide encoded by a gene. This mutation probably involves __________.* the insertion of one nucleotide a silent or neutral mutation a missense mutation the deletion of one nucleotide

frameshift mutation

*A point mutation in which a single base pair is inserted or deleted from DNA is called a(n) __________.* nonsense mutation frameshift mutation silent mutation inversion mutation

manufactured proteins to be short and defective

*A virus infects a cell and randomly inserts many short segments of DNA containing a stop codon throughout an organism's chromosomes. This will probably cause __________.* the DNA to break up into thousands of short segments manufactured proteins to be short and defective no bad effects, as long as the stop codons are not also inserted into tRNA incorrect pairing between mRNA codons and amino acids

introns, exons

*After an RNA molecule is transcribed from a eukaryotic gene, what are removed, and what are spliced together, to produce an mRNA molecule with a continuous coding sequence?* introns, exons promoters, operators operators, promoters exons, introns silencers, enhancers

Noncoding sequences called introns are spliced out by molecular complexes called spliceosomes. A cap consisting of a modified guanine nucleotide is added to the 5' end of the pre-mRNA. A poly-A tail (50-250 adenine nucleotides) is added to the 3' end of the pre-mRNA.

*After transcription begins, several steps must be completed before the fully processed mRNA is ready to be used as a template for protein synthesis on the ribosomes. Which three statements correctly describe the processing that takes place before a mature mRNA exits the nucleus?* Noncoding sequences called introns are spliced out by molecular complexes called spliceosomes. A translation stop codon is added at the 3' end of the pre-mRNA. A cap consisting of a modified guanine nucleotide is added to the 5' end of the pre-mRNA. Coding sequences called exons are spliced out by ribosomes. A poly-A tail (50-250 adenine nucleotides) is added to the 3' end of the pre-mRNA.

that not all genes code for enzymes; some genes code for structural proteins such as keratin

*An exception to the one gene-one enzyme hypothesis is __________.* that not all amino acids code for enzymes; some amino acids code for structural proteins such as keratin None of the listed responses is correct. that not all genes code for enzymes; some genes code for structural proteins such as keratin that all genes code for enzymes that produce structural proteins such as keratin that the genetic code is for enzymes, while the structural code is for structural proteins such as keratin

during transcription

*At one point, as a cell carried out its day-to-day activities, the nucleotides GAT were paired with the nucleotides CUA. This pairing occurred __________. * during translation during transcription when an mRNA codon paired with a tRNA anticodon in a double-stranded DNA molecule

the genetic code is nearly universal

*Bacteria can transcribe and translate human genes to produce functional human proteins because __________. * bacterial and eukaryotic RNA polymerases are identical the genetic code is nearly universal bacterial ribosomes and eukaryotic ribosomes are identical eukaryotes do not really need a nucleus

coupled transcription and translation

*Because the bacterial cell's DNA is not surrounded by a nuclear envelope, __________ occur(s).* segregated splicing and tailing of the message alternative splicing coupled splicing and tailing of the message coupled transcription and translation segregated transcription and translation

nutritional mutants; biochemical pathway

*By bombarding the fungus Neurospora crassa with X-rays, Beadle and Tatum were able to study __________ and characterize enzymes in a __________.* nutritional mutants; biochemical pathway wild-type mutants; biochemical pathway phenotypic mutants; biochemical pathway phenotypic mutants; glycolysis nutritional mutants; glycolysis

some proteins, as they begin to be synthesized, contain a signal region that causes the ribosome with its growing polypeptide to attach to the ER and translocate the polypeptide into the lumen (space) of the ER

*Cells are able to distinguish proteins destined for secretion or for segregation to specific intracellular compartments from those that will remain in the cytoplasm because __________.* each compartment in the cell (the nucleus, lysosome, and so forth) has its own set of ribosomes that synthesize proteins unique to that compartment there are two types of ribosomes: one group that synthesizes cytoplasmic proteins only and another type that synthesizes secreted or compartment-specific proteins only some proteins, as they begin to be synthesized, contain a signal region that causes the ribosome with its growing polypeptide to attach to the ER and translocate the polypeptide into the lumen (space) of the ER proteins destined for secretion or for a specific compartment are all synthesized in the nucleus, whereas cytoplasmic proteins are all synthesized in the cytoplasm

promoter

*One strand of a DNA molecule has the following sequence: 3′-AGTACAAACTATCCACCGTC-5′. In order for that strand to be transcribed, there would have to be a specific recognition sequence, called a(n) __________, to the left of the DNA sequence indicated.* intron promoter centromere AUG codon

the base sequence of the gene's promoter

*During transcription in eukaryotes, a type of RNA polymerase called RNA polymerase II moves along the template strand of the DNA in the 3'→5' direction. However, for any given gene, either strand of the double-stranded DNA may function as the template strand.For any given gene, what ultimately determines which DNA strand serves as the template strand?* which of the two strands of DNA carries the RNA primer the base sequence of the gene's promoter the location along the chromosome where the double-stranded DNA unwinds the location of specific proteins (transcription factors) that bind to the DNA

polypeptides are synthesized at ribosomes, according to instructions carried by mRNA

*During translation in a eukaryotic cell, __________.* mRNA is synthesized by the bonding of free nucleotides to the bases on the template strand of DNA ribosomes move into the nucleus tRNA carries amino acid molecules to the nucleus, where they are added to a growing polypeptide chain polypeptides are synthesized at ribosomes, according to instructions carried by mRNA

the ribosome encounters a "stop" codon

*During translation, amino acid chain elongation occurs until __________.* no further amino acids are needed by the cell the ribosome encounters a "stop" codon the polypeptide is long enough all tRNAs are empty

the addition of a 5ꞌ cap, a 3ꞌ poly-A tail, and the splicing out of introns

*Eukaryotic processing of the primary transcript includes __________.* the addition of a 5ꞌ cap, a 3ꞌ poly-A tail, the splicing out of introns, and a polyadenylation signal the addition of a 5ꞌ cap, a 3ꞌ poly-A tail, and the splicing out of exons the addition of a 5ꞌ poly-A tail, a 3ꞌ cap, and the splicing out of introns the addition of a 5ꞌ poly-A tail, a 3ꞌ cap, and the splicing out of exons the addition of a 5ꞌ cap, a 3ꞌ poly-A tail, and the splicing out of introns

the process by which DNA directs the synthesis of proteins

*Gene expression is __________.* the way that an individual appears the process by which DNA directs the synthesis of proteins the genetic makeup of an individual None of the listed responses is correct. the way that some genes express themselves at different times of the day, giving an individual a new appearance

One

*Generally speaking, how many genetic codes are there?* 20 Four One for each organism One

RNA

*Genetic information of eukaryotic cells is transferred from the nucleus to the cytoplasm in the form of __________.* DNA carbohydrates proteins RNA

All of the listed answers are correct.

*How is translation initiated?* the small ribosomal subunit binds to the mRNA the tRNA bearing methionine binds to the start codon the start codon signals the start of translation the large ribosomal subunit binds to the small one All of the listed answers are correct.

At least 1,350

*How many nucleotides are needed to code for a protein with 450 amino acids?* At least 1,800 At least 900 At least 1,350 At least 150

in the nucleus

*In a eukaryotic cell, transcription takes place __________.* in the rough endoplasmic reticulum in the cytoplasm in the nucleus on the cell membrane

RNA splicing

*In eukaryotes, which mechanism operates after transcription, but before translation of mRNA into protein?* Construction of a transcription initiation complex DNA packaging into nucleosomes Action of repressors and activators RNA splicing

signal peptide; signal-recognition particle

*In eukaryotic cells, a __________ by a __________ targets a growing peptide to the endoplasmic reticulum.* signal-recognition particle; signal peptide signal-recognition particle; ribosome signal peptide; signal-recognition particle ribosome; signal-recognition particle signal peptide; polyribosome

a) formation of ribosomal subunits b) attachment of an amino acid to tRNA c)translation of cytoplasmic proteins d) transcription and RNA processing e)translation of secreted proteins

*In eukaryotic cells, the processes of protein synthesis occur in different cellular locations.* transcription and RNA processing formation of ribosomal subunits attachment of an amino acid to tRNA translation of cytoplasmic proteins translation of secreted proteins

several transcription factors have bound to the promoter.

*In eukaryotic cells, transcription cannot begin until* DNA nucleases have isolated the transcription unit. several transcription factors have bound to the promoter. the DNA introns are removed from the template. the two DNA strands have completely separated and exposed the promoter. the 59 caps are removed from the mRNA.

redundant

*In many cases, more than one codon codes for the same amino acid. Because of this, we say that the code is __________.* not specific incomplete redundant inaccurate

All of the answer choices are correct.

*In transcription, __________.* only one of the DNA strands is used as the template the promoter region acts as an initial binding site for RNA polymerase the RNA nucleotides used are produced by the cell All of the answer choices are correct.

frameshift

*Insertions and deletions are called __________ mutations.* missense nucleotide-pair substitution nonsense frameshift silent

5 bases

*Life as we know it depends on the genetic code: a set of codons, each made up of three bases in a DNA sequence and corresponding mRNA sequence, that specifies which of the 20 amino acids will be added to the protein during translation. Imagine that a prokaryote-like organism has been discovered in the polar ice on Mars. Interestingly, these Martian organisms use the same DNA → RNA → protein system as life on Earth, except that there are only 2 bases (A and T) in the Martian DNA, and there are only 17 amino acids found in Martian proteins. Based on this information, what is the minimum size of a codon for these hypothetical Martian life-forms?* 2 bases 3 bases 4 bases 5 bases 6 bases

promoter

*One strand of a DNA molecule has the following sequence: 3-AGTACAAACTATCCACCGTC-5.* *In order for transcription to occur in that strand, there would have to be a specific recognition sequence, called a(n) __________, to the left of the DNA sequence indicated.* AUG codon promoter intron exon centromere

groups of ribosomes translating the same mRNA

*Polysomes may be defined as __________.* groups of ribosomes translating the same mRNA groups of lysosomes degrading the same protein groups of chromosomes microfilaments and microtubules

The two flanking codons would be altered, but the rest of the amino acid sequence would be the same because there would be no frameshift.

*Suppose that the triplet of nucleotides indicated in bold (AGC) spans two codons, that is, CTA and GCC. If the triplet AGC were deleted from this DNA coding sequence, what effect would it have on the resulting protein? 5'-ATGCTAGCCTATCGTAAC-3'* The two flanking codons would be altered, but the rest of the amino acid sequence would be the same because there would be no frameshift. All of the amino acids up to the deletion would be altered due to the frameshift. All of the amino acids after the deletion would be altered due to the frameshift. The entire amino acid sequence would be altered due to the frameshift.

three nucleotides code for a single amino acid

*The "triplet code" refers to the fact that _________.* the three-letter code for each amino acid is a triplet three sets of nucleotides are required for each amino acid three amino acids code for a single nucleotide three nucleotides code for a single amino acid None of the listed responses is correct.

It holds the tRNA carrying the growing polypeptide chain.

*The P site of a ribosome does which of the following?* It holds the tRNA carrying the growing polypeptide chain. It holds the tRNA that is carrying the next amino acid to be added to the growing polypeptide chain. It catalyzes the addition of amino acids to the tRNAs. It helps "unzip" DNA during transcription.

eukaryotic promoter; transcription factors; RNA polymerase II

*The TATA box is a __________ that allows for the binding of __________ and __________.* eukaryotic promoter; transcription factors; ribozymes prokaryotic promoter; translation factors; ribosome eukaryotic promoter; transcription factors; RNA polymerase II eukaryotic promoter; translation factors; ribosome prokaryotic promoter; transcription factors; RNA polymerase II

complementary to the corresponding mRNA codon.

*The anticodon of a particular tRNA molecule is* catalytic, making the tRNA a ribozyme. the part of tRNA that bonds to a specific amino acid. complementary to the corresponding mRNA codon. changeable, depending on the amino acid that attaches to the tRNA. complementary to the corresponding triplet in rRNA.

hydrogen bonds

*The bonds that hold tRNA molecules in the correct three-dimensional shape are __________.* hydrophobic interactions covalent bonds peptide linkages hydrogen bonds

pro-lys-phe-gly

*The codons AAA, CCC, GGG, and UUU specify the amino acids lysine, proline, glycine, and phenylalanine, respectively. If the base sequence 5′-CCCAAATTTGGG-3′ is present in the coding strand of a stretch of DNA, what polypeptide sequence would be encoded by the corresponding template strand?* gly-phe-lys-pro lys-pro-gly-phe pro-lys-phe-gly phe-gly-pro-lys

a nonsense mutation resulting in early termination of translation

*The diagram below shows an mRNA molecule that encodes a protein with 202 amino acids. The start and stop codons are highlighted, and a portion of the nucleotide sequence in the early part of the molecule is shown in detail. At position 35, a single base-pair substitution in the DNA has changed what would have been a uracil (U) in the mRNA to an adenine (A). Based on the genetic code chart, which of the following would be the result of this single base-pair substitution?* a silent mutation (no change in the amino acid sequence of the protein) a nonsense mutation resulting in early termination of translation a missense mutation causing a single amino acid change in the protein a frameshift mutation causing extensive change in the amino acid sequence of the protein a frameshift mutation causing a single amino acid change in the protein

methionine

*The first amino acid inserted into a new polypeptide chain in eukaryotic cells is usually __________.* methionine alanine glycine serine

from DNA to RNA to protein

*The flow of information in a cell proceeds in what sequence?* from protein to RNA to DNA from RNA to DNA to protein from RNA to protein to DNA from DNA to RNA to protein from DNA to protein to RNA

deliver amino acids to their proper site during protein synthesis

*The function of tRNA during protein synthesis is to __________.* deliver amino acids to their proper site during protein synthesis attach mRNA to the small subunit of the ribosome guide ribosomal subunits out of the nucleus through nuclear pores process mRNA

the same tRNA with the anticodon 3′-GUU-5′

*The mRNA codons 5′-CAA-3′ or 5′-CAG-3′ are translated as the amino acid glutamine by __________.* the same tRNA with the anticodon 3′-GUU-5′ tRNA molecules that have been charged with glutamine by two different aminoacyl-tRNA synthetases separate tRNA molecules with anticodons 3′-GUU-5′ and 3′-GUC-5′, respectively the tRNA with an anticodon 5′-GUU-3′ and glutamine at its other end

three; codon

*The number of nucleotide bases "read" together on the mRNA to designate each amino acid is __________; this unit is called a(n) __________.* three; codon two; anticodon two; dipeptide three; triose

missense mutation

*The sickle-cell β-globin mutation is an example of a __________.* nonsense mutation silent mutation base deletion missense mutation pointless mutation

part of a spliceosome

*The structures called snRNPs are __________.* involved in the removal of exons from DNA All of the listed responses are correct. a critical component of the initiation complex part of a spliceosome a type of specialized carbohydrate

nonsense

*The type of point mutation that results in a premature stop codon is called a _________ mutation.* inversion nonsense missense silent deletion

It could cause a silent, missense, or nonsense mutation because those are the types that can be caused by a nucleotide-pair substitution like this one.

*Think about the DNA coding sequence of a gene. If an A were swapped for a T, what kind of mutation could it cause and why?* It could cause a silent, missense, or nonsense mutation because those are the types that can be caused by a nucleotide-pair substitution like this one. It could cause a nonsense mutation because the sequence would no longer be the same, so the protein would be shorter and non-functional. It could cause a frameshift nonsense or frameshift missense mutation because it would change the reading frame of the codon triplet. It could cause a silent mutation because A and T are complementary to each other so it is not really a substitution mutation.

polypeptide

-_______ of a protein also has monomers arranged in a particular linear order, but its mo​nomers are amino acids

Exons from the same gene could be spliced in different ways to make different mRNAs.

*Two different proteins with mostly different structures are translated from two different mRNAs. These mRNAs, however, were transcribed from the same gene. Which mechanism could best account for this?* Different transcription factors were involved in the transcription of the two mRNAs. A point mutation might have altered the gene. Exons from the same gene could be spliced in different ways to make different mRNAs. Different systems of DNA unpacking could result in two different mRNAs.

causes mutations in the DNA

*Ultraviolet (UV) radiation is damaging to cells because it __________.* pokes holes in the nuclear envelope deactivates the enzymes needed for DNA replication blocks all translation causes mutations in the DNA

5'-CTTCGGGAA-3'

*Using Figure 17.5, identify a 59 S39 sequence of nucleotides in the DNA template strand for an mRNA coding for the polypeptide sequence Phe-Pro-Lys.* 5'-CTTCGGGAA-3' 5'-GAACCCCTT-3' 5'-AAAACCTTT-3' 5'-UUUGGGAAA-3' 5'-AAACCCUUU-3'

RNA polymerase

*What catalyzes the linkage between ribonucleotides to form RNA during gene expression?* A ribozyme Tyrosinase Aminoacyl-tRNA synthetase RNA polymerase

In prokaryotic cells, the RNA transcript is immediately available as mRNA without processing.

*What is a key difference between eukaryotic and prokaryotic gene expression?* In prokaryotes, proteins are assembled directly from DNA. In prokaryotic cells, the RNA transcript is immediately available as mRNA without processing. In eukaryotic cells, transcribed RNA sequences function as termination signals. RNA polymerases are involved only in initiation of transcription in eukaryotes.

In prokaryotic cells, the mRNA transcript is immediately available as mRNA without processing.

*What is a key difference in gene expression between eukaryotic and prokaryotic cells?* In prokaryotic cells, the mRNA transcript is immediately available as mRNA without processing. Prokaryotes do not contain ribosomes. RNA polymerases are involved only in initiation in eukaryotes. In eukaryotic cells, transcribed RNA sequences function as termination signals. In prokaryotes, proteins are assembled directly from DNA.

a biological catalyst made of RNA

*What is a ribozyme?* a DNA sequence near the promoter that assists in the binding of RNA polymerase a mutated ribosome a biological catalyst made of RNA a biological catalyst consisting of DNA an enzyme that holds open the DNA double helix while RNA polymerase adds nucleotides

3, 2, 1, 4

*What is their proper sequence for these steps?* *1. translation* *2. RNA processing* *3. transcription* *4. modification of protein* 2, 3, 4, 1 4, 2, 3, 1 3, 2, 1, 4 1, 2, 3, 4

U; A

*When RNA is being made, the RNA base __________ always pairs with the base __________ in DNA.* U; A A; U U; T T; G

it starts after a certain nucleotide sequence called a promoter

*Where does RNA polymerase begin transcribing a gene into mRNA?* it starts at one end of the chromosome the ribosome directs it to the correct portion of the DNA molecule it starts after a certain nucleotide sequence called a promoter transfer RNA acts to translate the message to RNA polymerase it looks for the AUG start codon

Both introns and exons are transcribed, but the RNA transcribed from introns does not leave the nucleus.

*Which accurately describes the usual process of eukaryotic transcription?* Both introns and exons are transcribed, but the RNA transcribed from introns does not leave the nucleus. Introns are not transcribed. Exons are not transcribed. Both introns and exons are transcribed, but neither type of transcribed region leaves the nucleus.

DNA

*Which component is not directly involved in translation?* ribosomes Mrna tRNA DNA GTP

Cleavage of a polypeptide into two or more chains

*Which is a post-translational modification of a polypeptide?* Formation of a polysome that allows simultaneous formation of many polypeptides from one mRNA transcript Removal of introns and splicing of exons Cleavage of a polypeptide into two or more chains The growing polypeptide signals the ribosome to attach to the ER.

The three-nucleotide words of a gene are arranged in a nonoverlapping series on the DNA template strand.

*Which of the following best describes the arrangement of genetic information in a DNA molecule?* By analyzing the linear order of amino acids in a polypeptide, the exact order of the three-nucleotide words of a gene arranged on the template strand of DNA can be determined. A gene is composed of overlapping, three-nucleotide words on a template strand of DNA. The three-nucleotide words of a gene are arranged in a nonoverlapping series on the DNA template strand. By overlapping the three-nucleotide words of a gene, the amount of information a DNA molecule can hold is maximized. The three-nucleotide words of a gene are serially arranged on both strands of DNA at a specific locus.

RNA polymerase

*Which of the following catalyzes the linkage between ribonucleotides to form RNA during gene expression?* tRNA Reverse transcriptase RNA polymerase A ribozyme RNA ligase

Exons are cut out before mRNA leaves the nucleus.

*Which of the following is not true of RNA processing?* Exons are cut out before mRNA leaves the nucleus. A primary transcript is often much longer than the final RNA molecule that leaves the nucleus. Ribozymes may function in RNA splicing. RNA splicing can be catalyzed by spliceosomes. Nucleotides may be added at both ends of the RNA.

It extends from one end of a tRNA molecule.

*Which of the following is not true of a codon?* It may code for the same amino acid as another codon. It is the basic unit of the genetic code. It consists of three nucleotides. It extends from one end of a tRNA molecule. It never codes for more than one amino acid.

a single nucleotide insertion downstream of, and close to, the start of the coding sequence

*Which of the following mutations would be most likely to have a harmful effect on an organism?* a nucleotide-pair substitution a single nucleotide insertion downstream of, and close to, the start of the coding sequence a single nucleotide deletion in the middle of an intron a deletion of three nucleotides near the middle of a gene a single nucleotide deletion near the end of the coding sequence

TATA box

-a DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex

Messenger RNA is made on a DNA template, and then amino-acid-bearing transfer RNAs bind to the mRNA through codon-anticodon pairing.

*Which summary of protein synthesis is correct?* Transfer RNAs line up on a ribosome, and amino acids bind to them with hydrogen bonds. Messenger RNA is made on a DNA template, and then amino-acid-bearing transfer RNAs bind to the mRNA through codon-anticodon pairing. DNA exchanges its thymine units with uracil in polymerase. This activates polymerase, and it starts joining amino acids together. Replicated DNA leaves the nucleus, is transported to a ribosome, and catalyzes the polymerization of amino acids in a protein.

Base-pair substitution

*Which type of mutation is least likely to affect protein function?* Insertion of three bases Base-pair substitution Deletion of single bases Addition of single bases

Beadle and Tatum

*Who formulated the one gene-one enzyme hypothesis?* Hershey and Chase Franklin Beadle and Tatum Watson and Crick

A substitution missense affects only one codon, but a frameshift missense affects all codons downstream of the frameshift.

*Why is a frameshift missense mutation more likely to have a severe effect on phenotype than a nucleotide-pair substitution missense mutation in the same protein?* A substitution missense mutation causes the protein to be shorter and thus non-functional. A frameshift missense mutation will cause an early Stop codon, but a substitution missense might be silent. A frameshift missense will cause the codons to be out of order, but a substitution missense does not change the order of the codons. A substitution missense affects only one codon, but a frameshift missense affects all codons downstream of the frameshift.

Transcription

*__________ is the synthesis of RNA using information in the DNA.* Translation Alternative splicing Transcription Splicing The polypeptide hypothesis

new strains of virus come from

*mutation of existing viruses into new viruses that can spread more easily* -RNA viruses have a high rate of mutation because viral RNA polymerases do not proofread and correct errors in replicating their RNA genomes -some mutations change existing viruses into new viral strains that can cause disease, even in people immune to the original virus *the emergence of viral diseases is the spread of a viral disease from a small, isolated human population* -HIV, the virus that causes AIDS, went unnamed and virtually unnoticed for decades before spreading around the world -technological and social factors, including affordable international travel, blood transfusions, unprotected sexual intercourse, and reuse of needles to inject intravenous drugs, allowed a previously rare human disease to become a global scourge *the spread of existing viruses from other animals* -scientists estimate that about three-quarters of new human diseases originate in this way -animals infected with a virus that can be transmitted to humans are said to be a natural reservoir for that virus -HIV is an example, as scientists believe that it originated from a version of the virus found in chimpanzees in central Africa, after people ate chimpanzee meat for food and were infected by exposure to chimpanzee blood

emerging viruses

- Viruses that suddenly become apparent. - Ex: HIV -are usually existing viruses that mutate, spread more widely in the current host species, or spread to new host species -changes in host behavior or environmental changes can increase the viral traffic responsible for emerging diseases -genetic mutations and changes in host ranges can allow viruses to jump between species, many viruses are transmitted by mosquitoes -possible effects of climate change on worldwide viral transmission

bicoid

-"two-tailed" -embryo or larva whose mother has two mutant bicoid alleles lacks the front half of its body and has posterior structures at both ends -it led to the identification of a specific protein required for some of the earliest steps in pattern formation -it helped us understand how different regions of the egg can give rise to cells that go down different developmental pathways -it increased our understanding of the mother's critical role in the initial phases of embryonic development -the principle that a gradient of morphogens can determine polarity and position has proved to be a key developmental concept for a number of species, just as early embryologists had hypothesized

Eukaryote Transcription Termination

-RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence, which specifies a polyadenylation signal (AAUAAA) in the pre-mRNA, called a "signal" because once this stretch of six RNA nucleotides appears, it is immediately bound by certain proteins in the nucleus -then, at a point about 10-35 nucleotides downstream from the AAUAAA, these proteins cut the RNA transcript free from the polymerase, releasing the pre-mRNA -the pre-mRNA then undergoes processing, the topic of the next section -although that cleavage marks the end of the mRNA, the RNA polymerase II continues to transcribe. Enzymes begin to degrade the RNA made after cleavage, starting at its newly exposed 5′ end -the polymerase continues transcribing, pursued by the enzymes, until they catch up to the polymerase and it dissociates from the DNA.

Eukaryotic regulation of gene expression

-RNA processing in the nucleus & the export of mature RNA to the cytoplasm provide opportunities -ex. @ RNA-processing​ level: alternative RNA splicing -ex. @ export of mature RNA to the cytoplasm: initiation of translation or after translation

origins of replication

-Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides -Proteins that initiate DNA replication recognize this sequence and attach to the DNA, separating the two strands and opening up a replication "bubble"

trombone model

-Some experimental evidence supports a model in which two DNA polymerase molecules, one on each template strand, "reel in" the parental DNA and extrude newly made daughter DNA molecules -The lagging strand is also looped back through the complex

Telomeric DNA

-Tends to be shorter in dividing somatic cells of older individuals and in cultured cells that have divided many times -It has been proposed that shortening of telomeres is somehow connected to the aging process of certain tissues and even to aging of the organism as a whole

dATP

-The adenine nucleotide used to make DNA -Each nucleotide to be added to a growing DNA strand consists of a sugar attached to a base and to three phosphate groups -Difference from ATP of energy metabolism is the sugar component, which is deoxyribose in the building block of DNA but ribose in ATP -Like ATP, the nucleotides used for DNA synthesis are chemically reactive, partly because their triphosphate tails have an unstable cluster of negative charge -DNA polymerase catalyzes the addition of each monomer to the growing end of a DNA strand by a condensation reaction in which two phosphate groups are lost as a molecule of pyrophosphate (Ⓟ-Ⓟi)(Ⓟ - Ⓟi) -Subsequent hydrolysis of the pyrophosphate to two molecules of inorganic phosphate (Ⓟi)(Ⓟi) is a coupled exergonic reaction that helps drive the polymerization reaction

euchromatin

-The less condensed form of eukaryotic chromatin that is available for transcription -AKA "true chromatin" -looser packing makes its DNA accessible to those proteins, and the genes present in euchromatin are available for transcription -the basic organizing unit is the 10-nm fiber—nucleosomes joined by linker DNA

DNA replication

-The process by which a DNA molecule is copied -AKA DNA synthesis

telomere

-The tandemly repetitive DNA at the end of a eukaryotic chromosome's DNA molecule. -Protects the organism's genes from being eroded during successive rounds of replication -Eukaryotic chromosomal DNA molecules have special nucleotide sequences -Do not contain genes; instead, the DNA typically consists of multiple repetitions of one short nucleotide sequence -specific proteins associated with telomeric DNA prevent the staggered ends of the daughter molecule from activating the cell's systems for monitoring DNA damage -telomeric DNA acts as a kind of buffer zone that provides some protection against the organism's genes shortening, somewhat like how the plastic-wrapped ends of a shoelace slow down its unraveling -Do not prevent the erosion of genes near the ends of chromosomes; they merely postpone it

Conservative Model of DNA replication

-The two parental strands reassociate after acting as templates for new strands, thus restoring the parental double helix. -Start: Parental DNA molecule (shown as a ribbon double helix); follow for two replications. -Result: is one parental DNA molecule and 3 new molecules. -Parental DNA molecule undergoes first replication; the result is a parental DNA molecule and a new DNA molecule. -Each molecule then goes through a second replication, resulting in two new DNA molecules from the new DNA molecule, and a new molecule, and a parental molecule from the parental molecule.

"DNA replication machine"

-The various proteins that participate in DNA replication actually form a single large complex -Many protein-protein interactions facilitate the efficiency of this complex -DNA replication complex may not move along the DNA -DNA may move through the complex during the replication process. In eukaryotic cells, multiple copies of the complex, perhaps grouped into "factories," may be anchored to the nuclear matrix, a framework of fibers extending through the interior of the nucleus

Semiconservative Model of DNA replication

-Type of DNA replication in which the replicated double helix consists of one old strand -Derived from the parental molecule -One newly made strand. -Distinguished in which the two parental strands somehow come back together after the process (that is, the parental molecule is conserved) -The two strands of the parental molecule separate, and each functions as a template for synthesis of a new, complementary strand. -Start: parental DNA molecule; follow for two replications. -Result: two DNA molecules that are half parental strand DNA and half new strand, and two DNA molecules that are new. -Parental DNA molecule undergoes first replication; result is two DNA molecules that are half parental strand DNA and half new strand DNA. -Each of these molecules then undergoes a second replication; result is, for each, one DNA molecule that is half parental strand and half new strand DNA and one DNA molecule that is new.

Alfred Hershey and Martha Chase (1952)

-Used radioactive markers in experiments to show that DNA was the genetic material of phage T2 -DNA entered the cells and could reprogram them to make more phages -DNA injected by the phage must be the molecule carrying the genetic information that makes the cells produce new viral DNA and proteins -Landmark study because it provided powerful evidence that nucleic acids, rather than proteins, are the hereditary material, at least for certain viruses

enhancer

-a segment of eukaryotic DNA containing multiple distal control elements -given gene may have multiple, each active at a different time, cell type, or location in the organism -each is generally associated with only that gene and no other -rate of gene expression can be strongly increased or decreased by the binding of specific transcription factors, either activators or repressors, to the control elements of _________ -composed of about ten control elements, each binding only one or two specific transcription factors -the particular combination of control elements in an ______ is associated with a gene, rather than a single unique control element, that is important in regulating transcription of the gene

control element

-a segment of noncoding DNA that helps regulate transcription of a gene by serving as a binding site for a transcription factor -multiple control elements are present in a eukaryotic gene's enhancer

poly-A tail

-a sequence of 50-250 adenine nucleotides added onto the 3′ end of a pre-mRNA molecule

signal peptide

-a sequence of about 20 amino acids at or near the N-terminus of the polypeptide

corepressor

-a small molecule that binds to a bacterial repressor protein and changes the protein's shape, allowing it to bind to the operator and switch an operon off -more molecules, bind to operator, shut down production -one example of how gene expression can respond to changes in the cell's internal and external environment

microRNA (miRNA)

-a small, single-stranded RNA molecule, generated from a double-stranded RNA precursor -associates with one or more proteins in a complex that can degrade or prevent translation of an mRNA with a complementary sequence -a single-stranded RNA of about 22 nucleotides that forms a complex with one or more proteins -allows the miRNA-protein complex to bind to any mRNA molecule with at least seven or eight nucleotides of complementary sequence, the complex then degrades the target mRNA or, less often, simply blocks its translation -approximately 1,500 genes for this in the human genome -expression of at least one-half of all human genes may be regulated by this

inducer

-a specific small molecule that binds to a bacterial repressor protein and changes the repressor's shape so that it cannot bind to an operator, thus switching an operon on

morphogen

-a substance, such as Bicoid protein in Drosophila, that provides positional information in the form of a concentration gradient along an embryonic axis

codon

-a three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal -the basic unit of the genetic code -customarily written in the 5′→3′ direction -also used for the DNA nucleotide triplets along the nontemplate strand -mRNA nucleotide triplets -complementary to the template strand and thus identical in sequence to the mRNA -are read by the translation machinery in the 5′→3′ direction along the mRNA -specifies which one of the 20 amino acids will be incorporated at the corresponding position along a polypeptide -the number of nucleotides making up a genetic message must be three times the number of amino acids in the protein product

p53 gene

-a tumor-suppressor gene that codes for a specific transcription factor that promotes the synthesis of proteins that inhibit the cell cycle -protein it encodes is a specific transcription factor that promotes the synthesis of cell cycle-inhibiting proteins -why a mutation that knocks out the _______ or in a gene required to activate the p53 protein can lead to excessive cell growth and cancer ​ -"guardian angel of the genome"

messenger RNA (mRNA)

-a type of RNA -synthesized using a DNA template -attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein -in eukaryotes, the primary RNA transcript must undergo RNA processing to become mRNA -complementary rather than identical to its DNA template because RNA nucleotides are assembled on the template according to base-pairing rules -contains U instead of T -ribose sugar -synthesized in an antiparallel direction to the template strand of DNA -transcribed from the template strand of a gene

lysogenic cycle

-a type of phage replicative cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage, is replicated along with the chromosome, and does not kill the host -prophages are capable of generating active phages that lyse their host cells, occurs when the λ genome (or that of another temperate phage) is induced to exit the bacterial chromosome and initiate a lytic cycle, an environmental signal, such as a certain chemical or high-energy radiation, usually triggers the switchover from the lysogenic to the lytic mode

lytic cycle

-a type of phage replicative cycle resulting in the release of new phages by lysis (and death) of the host cell -last stage of infection, during which the bacterium lyses (breaks open) and releases the phages that were produced within the cell -each can then infect a healthy cell, and a few successive lytic cycles can destroy an entire bacterial population in just a few hours -phage that replicates only by this cycle is a virulent phage -ex. T4

nucleotide-pair substitution

-a type of point mutation in which one nucleotide in a DNA strand and its partner in the complementary strand are replaced by another pair of nucleotides -silent mutation -missense mutation -usually missense mutations; that is, the altered codon still codes for amino acid and thus makes sense, although not necessarily the right sense. -nonsense mutation

operon

-a unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway -regulated by a single promoter and transcribed into a single mRNA molecule

Smallpox

-a viral disease that was once a devastating scourge in many parts of the world -was eradicated by 1980 due to a vaccination program carried out by the World Health Organization (WHO) -very narrow host range of the smallpox virus—it infects only humans—was a critical factor in the success of this program

provirus

-a viral genome that is permanently inserted into a host genome

epidemic

-a widespread outbreak of a disease -occur when genetic changes allow a new viral strain to be easily transmitted between humans

histone tails

-accessible to various modifying enzymes that catalyze the addition or removal of specific chemical groups

prion

-an infectious agent that is a misfolded version of a normal cellular protein -appear to increase in number by converting correctly folded versions of the protein to more of this -appear to cause degenerative brain diseases in various animal species -ex. 1: mad cow disease->plagued the European beef industry about 20 years ago->Creutzfeldt-Jakob disease in humans -can be transmitted in food, as may occur when people eat beef from cattle with mad cow disease -ex. 2: Kuru -act very slowly, with an incubation period of at least ten years before symptoms develop, the lengthy incubation period prevents sources of infection from being identified until long after the first cases appear, allowing many more infections to occur -are not destroyed or deactivated by heating to normal cooking temperatures, there is no known cure for these diseases, and the only hope for developing effective treatments lies in understanding the process of infection -a misfolded form of a protein normally present in brain cells -when enters a cell with normal proteins, somehow converts normal protein molecules to the misfolded prion versions -then aggregate into a complex that can convert other normal proteins to prions, which join the chain -this aggregation interferes with normal cellular functions and causes disease symptoms -proposed by Stanley Prusiner in the early 1980s -are involved in neurodegenerative diseases such as Alzheimer's and Parkinson's disease

virus

-an infectious particle consisting of little more than genes packaged in a protein coat -lacking the structures and metabolic machinery found in a cell -cannot reproduce or carry out metabolic activities outside of a host cell -most cannot be cultivated on nutrient media in test tubes or petri dishes -an infectious particle consisting of one or more molecules of a nucleic acid enclosed in a protein coat and, for some, surrounded by a membranous envelope -DNA ________ -RNA ________ -some have accessory structures that help them infect their hosts -some carry a few viral enzymes, such as viral polymerase, within their capsids -lack metabolic enzymes and equipment for making proteins, such as ribosomes -obligate intracellular parasites or can replicate only within a host cell -usually identify host cells by a "handshake" fit between viral surface proteins and specific receptor molecules on the outside of cells -biologically inert, unable to replicate its genes or regenerate its own ATP -use of the genetic code makes it hard to deny their evolutionary connection to the living world -have been found that infect every form of life—not only bacteria, animals, and plants, but also archaea, fungi, and algae and other protists

primary transcript

-an initial RNA transcript from any gene; also called pre-mRNA when transcribed from a protein-coding gene

Translation

-another stage where gene expression is regulated, most commonly at the initiation stage -initiation of this in mRNA can be blocked by regulatory proteins that bind to specific sequences or structures within the untranslated region (UTR) at the 5‵or 3‵ end, preventing the attachment of ribosomes -all the mRNAs in a cell may be regulated simultaneously -in eukaryotic cell, such "global" control usually involves the activation or inactivation of one or more protein factors required to initiate translation -plays a role in starting this in mRNAs that are stored in eggs -just after fertilization, this is triggered by the sudden activation of translation initiation factors, the response is a burst of synthesis of the proteins encoded by the stored mRNAs -some plants and algae store mRNAs during periods of darkness; light then triggers the reactivation of the translational apparatus

homeotic gene

-any of the master regulatory genes that control placement and spatial organization of body parts in animals, plants, and fungi by controlling the developmental fate of groups of cells

Transposons

-are DNA segments that can move from one location to another within a cell's genome

Normal seasonal flu viruses (influenza types A and B)

-are not considered emerging viruses because variations of seasonal flu viruses have been circulating among humans for long enough that most components are recognized by the immune system -these viruses still undergo mutation and reassortment of genome segments, and variations of the HA protein are used each year to generate vaccines against the strains predicted most likely to occur the following year

Herpesviruses

-are temporarily cloaked in membrane derived from the nuclear envelope of the host; they then shed this membrane in the cytoplasm and acquire a new envelope made from membrane of the Golgi apparatus -these viruses have a double-stranded DNA genome and replicate within the host cell nucleus, using a combination of viral and cellular enzymes to replicate and transcribe their DNA -copies of the viral DNA can remain behind as mini-chromosomes in the nuclei of certain nerve cells -there they remain latent until some sort of physical or emotional stress triggers a new round of active virus production -the infection of other cells by these new viruses causes the blisters characteristic of herpes, such as cold sores or genital sores

bound ribosomes

-attached to the cytosolic side of the endoplasmic reticulum (ER) or to the nuclear envelope -make proteins of the endomembrane system as well as proteins secreted from the cell, such as insulin

Prokaryotic genetic information flow

-bacteria do not have nuclei -nuclear membranes do not separate bacterial DNA and mRNA from ribosomes and the other protein-synthesizing equipment -This lack of compartmentalization allows translation of an mRNA to begin while its transcription is still in progress

Cas9

-bacterial protein that helps defend bacteria against the viruses that infect them (bacteriophages) -in bacterial cells, ____ acts together with "guide RNA" made from the CRISPR region of the bacterial genome -a nuclease that cuts double-stranded DNA molecules -_____ protein will cut any sequence to which it is directed -directed to its target by a guide RNA molecule that it binds and uses as a homing device, cutting both strands of any DNA sequence that is complementary to the guide RNA -the guide RNA in the complex is engineered to be complementary to the "target" gene -the resulting broken ends of DNA trigger a DNA repair system -when there is no undamaged DNA for the enzymes of the repair system to use as a template, the repair enzymes introduce or remove random nucleotides while rejoining the ends -this process alters the DNA sequence so that the gene no longer works properly -this technique is a highly successful way for researchers to "knock out" (disable) a given gene to study what that gene does in an organism

triplet code

-genetic information system in which a series of three-nucleotide-long words specifies a sequence of amino acids for a polypeptide chain

pandemic

-global epidemic of a disease

viral infection

-begins when a virus binds to a host cell and the viral genome makes its way inside -mechanism of genome entry depends on the type of virus and the type of host cell -injection, taken up by endocytosis or, in the case of enveloped viruses, by fusion of the viral envelope with the host's plasma membrane -can produce symptoms by a number of different mechanisms -may damage or kill cells by causing the release of hydrolytic enzymes from lysosomes -some cause infected cells to produce toxins that lead to disease symptoms, and some have molecular components that are toxic, such as envelope proteins

Infection of an E. coli cell by phage λ

-begins when the phage binds to the surface of the cell and injects its linear DNA ge​nome -within the host,​ the λ DNA molecule forms a circle, next step depends on the replicative mode: lytic cycle or lysogenic cycle LYTIC CYCLE -the viral genes immediately turn the host cell into a λ-producing factory -the cell soon lyses and releases its virus progeny LYSOGENIC CYCLE -λ DNA molecule is incorporated into a specific site on the E. Coli chromosome by viral proteins that break both circular DNA molecules and join them to each other -when integrated into the bacterial chromosome in this way, the viral DNA is known as a prophage -one prophage gene codes for a protein that prevents transcription of most of the other prophage genes -phage genome is mostly silent within the bacterium -every ti​me the E. coli cell prepares to divide, it​ replicates the phage DNA along with its own chromosome such that each daughter cell inherits a prophage -a single infected cell can quickly give rise to a large population of bacteria carrying the virus in prophage form -enables viruses to propagate without killing the host cells on which they depend.

activation domains

-bind other regulatory proteins or components of the transcription machinery -facilitating a series of protein-protein interactions that result in enhanced transcription of a given gene

signaling molecules

-bind to receptors on a cell's surface and never actually enter the cell -can control gene expression indirectly by triggering signal transduction pathways that activate particular transcription fa​ctors -

structural domains of transcription activators groupings

-binding domain -activation domains

Initiation of Translation

-brings together an mRNA, a tRNA bearing the first amino acid of the polypeptide, and the two subunits of a ribosome -First, a small ribosomal subunit binds to both the mRNA and a specific initiator tRNA, which carries the amino acid methionine (*in bacteria*, the small subunit can bind the two in either order; it binds the mRNA at a specific RNA sequence, just upstream of the AUG start codon & *in eukaryotes*, the small subunit, with the initiator tRNA already bound, binds to the 5′ cap of the mRNA and then moves, or scans, downstream along the mRNA until it reaches the AUG start codon, where the initiator tRNA ​then hydrogen-bonds) -in either bacteria or eukaryotes, the AUG signals the start o​f translation; establishes the codon reading frame for the mRNA -the union of mRNA, initiator tRNA, and the small ribosomal subunit by initiation factor proteins -> attachment of a large ribosomal subunit, completing the translation initiation complex -the cell also expends energy obtained by hydrolysis of a GTP molecule to form the initiation complex -at the completion of the initiation process, the initiator tRNA sits in the P site of the ribosome, and the vacant A site is ready for the next aminoacyl tRNA -polypeptide is always synthesized in one direction, N-terminus to C-terminus

miRNAs and siRNAs

-can associate with the same proteins, producing similar results -are RNA molecules that are mostly double-stranded

genome of class IV viruses

-can directly serve as mRNA and thus can be translated into viral protein immediately after infection

alterations in epigenetic modifications

-can lead to abnormal chromatin condensation in a cell are often found in tumor cells -if a mutation in a gene for a chromatin-modifying enzyme leads to loosening of chromatin in a region that is normally not being expressed, a proto-oncogene in that region could be expressed at abnormally h​igh levels

viruses that cause illness

-can replicate only inside host cells -many variations on the basic scheme of viral infection and replication are represented among the animal viruses -key variables are the nature of the viral genome (double- or single-stranded DNA or RNA) and the presence or absence of an envelope: only a few bacteriophages have an envelope or RNA genome, many animal viruses have both, nearly all animal viruses with RNA genomes have an envelope, as do some with DNA genomes

Papillomaviruses

-cause cancer of the cervix, and a virus called HTLV-1 -causes a type of adult leukemia

Epstein-Barr virus

-causes infectious mononucleosis -has been linked to several types of cancer in humans -notably Burkitt's lymphoma

metabolic pathway regulation

-cells can adjust the activity of enzymes already present, a fairly rapid physiological response, which relies on the sensitivity of many enzymes to chemical cues that increase or decrease their catalytic activity -cells can adjust the production level of certain enzymes via a genetic mechanism; that is, they can regulate the expression of the genes encoding the enzymes; the control of enzyme production occurs at the level of transcription, the synthesis of messenger RNA from the genes that code for these enzymes -feedback inhibition, typical of anabolic (biosynthetic) pathways, allows a cell to adapt to short-term fluctuations in the supply of a substance it needs

RNA

-chemically similar to DNA except that it contains ribose instead of deoxyribose as its sugar and has the nitrogenous base uracil rather​ than thymine -bridge between DNA and protein synthesis -A, G, C, or U as its base -this molecule usually consists of a single strand

codon AUG

-codes for the amino acid methionine (Met, or M) -functions as a "start" signal, or initiation codon

viral diseases of plants

-common signs include bleached or brown spots on leaves and fruits, stunted growth, and damaged flowers or roots -have the same basic structure and mode of replication as animal viruses -most have RNA genome(ex. tobacco mosaic virus (TMV)) -many have a helical capsid, like TMV, while others have an icosahedral ​capsid

Targeting Polypeptides to Specific Locations

-eukaryotic cells active in protein synthesis, two populations of ribosomes are evident: free and bound -the ribosomes themselves are identical and can alternate between being free ribosomes one time they are used and being bound ribosomes the next -Polypeptide synthesis always begins in the cytosol as a free ribosome starts to translate an mRNA molecule and the process continues to completion—unless the growing polypeptide itself cues the ribosome to attach to the ER -the polypeptides of proteins destined for the endomembrane system or for secretion are marked by a signal peptide, which targets the protein to the ER -signal-recognition particle (SRP) recognizes the signal peptide; this particle escorts the ribosome to a receptor protein(part of a multiprotein translocation complex) built into the ER membrane -polypeptide synthesis continues there, and the growing polypeptide snakes across the membrane into the ER lumen via a protein pore -the signal peptide is removed by an enzyme; the rest of the completed polypeptide, if it is to be secreted from the cell, is released into solution within the ER lumen or if the polypeptide is to be a membrane protein, amino acid sequences further in the chain cause that part to remain embedded in the ER membrane -in either case, it travels in a transport vesicle to its destination -other kinds of signal peptides are used to target polypeptides to mitochondria, chloroplasts, the interior of the nucleus, and other organelles that are not part of the endomembrane system; only differences are translation is completed in the cytosol before the polypeptide is imported into the organelle & translocation mechanisms vary, but the "postal zip codes" that address proteins for secretion or to cellular locations are signal peptides of some sort -bacteria also employ signal peptides to target proteins to the plasma membrane or for secretion

Eukaryotic genetic information flow

-eukaryotic cells have nuclei -the presence of a nuclear envelope separates transcription from translation in space and time -transcription occurs in the nucleus, but the mRNA must be transported to the cytoplasm for translation -before RNA transcripts from protein-coding genes can leave the nucleus, they are modified in various ways to produce the final, functional mRNA -transcription of a protein-coding gene results in pre-mRNA, and further RNA processing yields the finished mRNA -the initial RNA transcript from any gene, including those specifying RNA that is not translated into protein is more generally called a primary transcript

exon

-eventually expressed, usually by being translated into amino acid sequences -exceptions include the UTRs at the ends of the RNA, which make up part of the mRNA but are not translated into protein-prefer to think of this as sequences of RNA that exit the nucleus -a sequence within a primary transcript that remains in the RNA after RNA processing; also refers to the region of DNA from which this sequence was transcribe -forming an mRNA molecule with a continuous coding sequence

la​rge-scale mutations

-ex. chromosomal rearrangements that affect long segments of DNA

spontaneous mutations

-ex. incorrect base will be used as a template in the next round of replication, resulting in a mutation -difficult to calculate the rate at which such mutations occur -rough estimates have been made of the rate of mutation during DNA replication for both E. coli and eukaryotes, and the numbers are similar: About one nucleotide in every 10^10 is altered, and the change is passed on to the next generation of cells

natural selection

-favors bacteria that have receptors altered by mutation or that have enzymes that cut phage DNA -favors phage mutants that can bind to altered receptors or that are resistant to enzymes -the bacterium-phage relationship is in constant evolutionary flux

Robert Waterland and Randy Jirtle

-feeding methyl groups to the mothers at a key time during gestation led to a change in gene expression in the offspring's phenotype -extent of the color shift correlated with the level of DNA methylation

Marshall Nirenberg

-first codon was deciphered

Zika virus

-first observed in Uganda in 1947, but for decades only a few cases occurred per year -in the spring of 2015, however, it became an emerging virus when it caused a large outbreak in Brazil -symptoms are often mild, the infection of pregnant women was correlated with a striking increase in the number of babies born with abnormally small brains, a condition called microcephaly -is a mosquito-borne flavivirus (like West Nile virus) that infects neural cells, posing a particular danger to fetal brain development.

Archibald Garrod

-first to suggest that genes dictate phenotypes through enzymes -postulated that the symptoms of an inherited disease reflect an inability to make a particular enzyme, aka "inborn errors of metabolism." -the inability to make a particular enzyme that breaks down a certain substance, so that substance is expelled in urine -a gene dictates the production of a specific enzyme, later named the one gene-one enzyme hypothesis

wobble

-flexibility in the base-pairing rules in which the nucleotide at the 5′ end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position (3′ end) of a codon -explains why the synonymous codons for a given amino acid most often differ in their third nucleotide base

specific transcription factors

-for genes not expressed all the time, meaning they are regulated -the interaction of general transcription factors and RNA polymerase II with a promoter usually leads to a low rate of initiation and production of few RNA transcripts from genes that are not expressed at significant levels all the time or in all cells -in eukaryotes, high levels of transcription of these particular genes at the appropriate time and place depend on the interaction of control elements with another set of proteins

adenomatous polyposis coli (APC)

-gene has multiple functions in the cell, including regulation of cell migration and adhesion -even in patients with no family history of the disease, the APC gene is mutated in 60% of colorectal cancers -new mutations must have occurred in both alleles before the gene's function is lost -currently, only 15% of colorectal cancers are associated with known inherited mutations, so researchers continue to try to identify "markers" that could predict the risk of developing this type of cancer

Repressible enzymes

-generally function in anabolic pathways, which synthesize essential end products from raw materials (precursors) -by suspending production of an end product when it is already present in sufficient quantity, the cell can allocate its organic precursors and energy for other uses

bread mold (Neurospora crassa)

-haploid -genome contains only one copy of each gene, that single copy determines the individual's expressed phenotype -to discover the function of any gene, only needed to mutate and disable that one allele -can chose to study the protein-coding genes required for a specific nutritional activity -caused mutations in genes by bombarding Neurospora with X-rays and looked among the survivors for mutants that differed in their nutritional needs from the wild-type bread mold -wild-type mold cells use their metabolic pathways to produce all the other nutrient molecules (like amino acids) they need for growth, dividing repeatedly and forming visible colonies of genetically identical cells -generated different "nutritional mutants" of Neurospora cells, each of which had a mutation in one gene and was unable to synthesize a particular essential nutrient (such cells could not grow on minimal medium but could grow on complete medium, which contains all nutrients needed for growth) -For Neurospora, the complete medium consists of the minimal medium supplemented with all 20 amino acids and a few other nutrients -hypothesized that in each nutritional mutant, the gene for the enzyme that synthesizes a particular nutrient had been disabled by the mutation -able to determine experimentally which nutrient each mutant strain (original cell and its descendants) was unable to synthesize.

mosquito-borne chikungunya virus

-has long been considered a tropical virus, but it has now appeared in Italy, France, and Spain -causes an acute illness with fever, rashes, and persistent joint pain

Influenza viruses

-have a high rate of mutation

antibiotics

-help us recover from bacterial infections are powerless against viruses -kill bacteria by inhibiting enzymes specific to bacteria but have little or no effect on eukaryotic or virally encoded enzymes -the few enzymes that are encoded only by viruses have provided targets for other drugs

Viral spread of diseases-plants

-horizontal transmission -vertical transmission -viral genomes and associated proteins can spread throughout the plant through pl​asmodesmata, the cytoplasmic connections that penetrate the walls between adjacent plant cells -the ​passage of viral macromolecules from cell to cell is facilitated by virally encoded proteins that cause enlargement of plasmodesmata

acyclovir

-impedes herpesvirus replication by inhibiting the viral polymerase that synthesizes viral DNA but not the eukaryotic one

terminator

-in bacteria, a sequence of nucleotides in DNA that marks the end of a gene and signals RNA polymerase to release the newly made RNA molecule and detach from the DNA

operator

-in bacterial and phage DNA, a sequence of nucleotides near the start of an operon to which an active repressor can attach -the binding of the repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon -on-off switch is a segment of DNA -positioned within the promoter or, in some cases, between the promoter and the enzyme-coding genes, the operator controls the access of RNA polymerase to the genes

alternative splicing

-in many cases, a eukaryotic gene can code for a set of closely related polypeptides via a process

start point

-in transcription, the nucleotide position on the promoter where RNA polymerase begins synthesis of RNA

hereditary nonpolyposis colon cancer (HNPCC)

-increases an individual's lifetime risk of colon cancer to 50-70% -AKA Lynch syndrome -caused by an autosomal dominant allele of any one of a group of DNA repair genes, underscoring the importance of DNA repair systems -this syndrome is responsible for 2-5% of colon cancers

amplification

-increases the number of copies of the proto-oncogene in the cell through repeated gene duplication

piwi-interacting RNAs (piRNAs)

-induces formation of heterochromatin, blocking expression of some parasitic DNA elements in the genome known as transposons -usually 24-31 nucleotides in length -are processed from a longer, single-stranded RNA precursor -play an indispensable role in the germ cells of many animal species, where they appear to help reestablish appropriate methylation patterns in the genome during gamete formation

epigenetic inheritance

-inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence

Chromatin-modifying enzymes

-initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery

synthesis of a polypeptide

-initiation, elongation, and termination -all three require protein "factors" that aid in the translation process -some steps of initiation and elongation also require energy, provided by the hydrolysis of guanosine triphosphate (GTP)

pandoraviruses

-is 1µm (1,000 nm) in diameter, with a dsDNA genome of around 2-2.5 Mb, larger than that of some small eukaryotes -over 90% of its 2,000 or so genes are unrelated to cellular genes -the number of genes varies from 1,500 to 2,500 genes

repressible operon

-its transcription is usually on but can be inhibited (repressed) when a specific small molecule binds allosterically to a regulatory protein -ex. trp operon

ribosomal proteins

-largely on the exterior of ribosomes -support the shape changes of the rRNA molecules as they carry out catalysis during translation

Protein

-link between genotype and phenotype -bring about an organism's observable phenotype

Bacterial Defenses Against Phages

-lysogeny- one major reason why bacteria have been spared from extinction caused by phages -bacteria have their own defenses against phages -natural selection favors bacterial mutants with surface proteins that are no longer recognized as receptors by a particular type of phage -when phage DNA does enter a bacterium, the DNA often is identified as foreign and cut up by cellular enzymes called restriction enzymes, which are so named because they restrict a phage's ability to replicate within the bacterium; the bacterium's own DNA is methylated in a way that prevents attack by its own restriction enzymes -a system present in both bacteria and archaea called the CRISPR-Cas system

some double-stranded DNA viruses can replicate

-lytic cycle -lysogenic cycle

mRNA molecules

-produced during transcription -lifespan in the cytoplasm is important in determining the pattern of protein synthesis in a cell -bacterial: typically are degraded by enzymes within a few minutes(why bacteria can change their patterns of protein synthesis so quickly in response to environmental changes) -multicellular eukaryotes: typically survive for hours, days, or even weeks -nucleotide sequences can affect how long this remains intact are often found in the untranslated region at the 3‵ end of the molecule -most important RNAs because they code for proteins needs revision

Genome sequencing

-protein-coding DNA accounts for only 1.5% of the human genome and a similarly small percentage of the genomes of many other multicellular eukaryotes

protein-protein interactions

-protein-mediated bending of the DNA brings the bound activators into contact with a group of mediator proteins, which in turn interact with general transcription factors at the promoter -help assemble and position the initiation complex on the promoter -allow these two DNA regions to come together in a very specific fashion, in spite of the many nucleotide pairs between them

mediator proteins

-proteins that mediate the interaction between regulatory proteins and the transcription factors

repression

-recruitment of chromatin-modifying proteins, most common mechanism in eukaryotic cells

selective degradation

-regulates length of time each protein functions in the cell -to mark ​a protein for destruction, the cell commonly attaches molecules of a small protein called ubiquitin to the protein -giant protein complexes called proteasomes then recognize the ubiquitin tagged proteins and degrade them

small noncoding RNAs

-regulating mRNAs -can cause remodeling of chromatin structure -ex. The siRNA system in yeast interacts with other, larger noncoding RNAs and with chromatin-modifying enzymes to condense the centromere chromatin into heterochromatin(not yet known for mammalian cells)

CRP

-regulating the lac operon -helps regulate other operons that encode enzymes used in catabolic pathways

non-protein-coding RNAs (noncoding RNAs, or ncRNAs)

-regulation from this occurs at several points in the pathway of gene expression, including mRNA translation and chromatin modification -microRNA (miRNA) -small interfering RNA (siRNA)

transcription factors

-segments of noncoding DNA that serve as binding sites for the proteins -bind to the control elements and regulate transcription -control elements on the DNA and the ___________ that bind to them are critical to the precise regulation of gene expression seen in different cell types 2 TYPES -General ________- act at the promoter of all genes -Specific ________- that bind to control elements that may be close to or farther away from the promoter

promoter

-site where RNA polymerase can bind to DNA and begin transcription -a specific nucleotide sequence in the DNA of a gene that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place

eukaryotic ribosomes

-slightly larger and differ somewhat in molecular composition -certain antibiotic drugs can inactivate bacterial ribosomes without affecting the ability of eukaryotic ribosomes to make proteins

CRISPR-Cas9 system

-small ncRNAs used by bacteria as a defense system -a technique for editing genes in living cells, involving Cas9 associated with a guide RNA complementary to a gene sequence of interest -direct manipulation of genes for​ practical purposes -can be used to repair a gene that has a harmful mutation: introduce a segment from the normal (functional) gene along with the CRISPR-Cas9 system, after Cas9 cuts the target DNA, repair enzymes can use the normal DNA as a template to repair the target DNA at the break point; the CRISPR-Cas9 system edits the defective gene so that it is corrected

Plasmids

-small, circular DNA molecules found in bacteria and in the unicellular fungi called yeasts -exist apart from the genome, can replicate independently of the genome, and are occasionally transferred between cells

protein products of tumor-suppressor genes

-some repair damaged DNA, which prevents the cell from accumulating cancer-causing mutations -others control adhesion of cells to each other or to the extracellular matrix; proper cell anchorage is crucial in normal tissues and is often absent in cancers -others are components of cell-signaling pathways that inhibit the cell cycle

Differentiated cells

-specialists at making tissue-specific proteins -each is a long fiber containing many nuclei within a single plasma membrane

monomers

-specific sequences convey information in polymers like nucleic acids and proteins -in DNA or RNA, the _________ are the four types of nucleotides listed previously, which differ in their nitrogenous bases

George Beadle and Boris Ephrussi

-speculated that in Drosophila, each mutation affecting eye color blocks pigment synthesis at a specific step by preventing production of the enzyme that catalyzes that step. But neither the chemical reactions nor the enzymes that catalyze them were known at the time. -bread mold, Neurospora crassa(haploid)

Free ribosomes

-suspended in the cytosol and mostly synthesize proteins that stay in the cytosol and function there

inducible enzymes

-synthesis is induced by a chemical signal -usually function in catabolic pathways, which break down a nutrient to simpler molecules -by producing the appropriate enzymes only when the nutrient is available, the cell avoids wasting energy and precursors making proteins that are not needed

pre-mRNA molecule 3' end modification

-synthesized first -receives a 5′ cap, added onto the 5′ end after transcription of the first 20-40 nucleotides have been transcribed -modified before the mRNA exits the nucleus (Recall that the pre-mRNA is cut and released soon after the polyadenylation signal, AAUAAA, is transcribed) -an enzyme then adds 50-250 more adenine (A) nucleotides, forming a poly-A tail

DNA methylation

-the presence of methyl groups on the DNA bases (usually cytosine) of plants, animals, and fungi (The term also refers to the process of adding methyl groups to DNA bases.) -occurs in most plants, animals, and fungi -long stretches of inactive DNA, such as that of inactivated mammalian X chrom​osomes, are generally m​o​re methylated than regions of actively transcribed DNA -DNA of individual genes is usually more heavily methylated in cells in which those genes are not expressed -removal of the extra methyl groups can turn on some of these genes -permanently regulates expression of either the maternal or paternal allele of particular genes at the start of development

Gene expression

-the process by which DNA directs the synthesis of proteins (or, in some cases, just RNAs) aka code for proteins -includes two stages: transcription and translation.

Differentiation

-the process by which a cell attains its determined fate -1st sign: appearance of mRNAs for tissue-specific proteins -later, observable with a microscope as changes in cellular structure: different sets of genes are sequentially expressed in a regulated manner as new cells arise when their precursors divide

differentiation

-the process by which a cell or group of cells becomes specialized in structure and function -not randomly distributed but are organized into tissues and organs in a particular three-dimensional arrangement

determination

-the progressive restriction of developmental potential in which the possible fate of each cell becomes more limited as an embryo develops -at the end, a cell is committed to its fate -an embryonic cell can be experimentally placed in another location in the embryo and it will still differentiate into the cell type that is its normal fate

upstream

-the promoter sequence in DNA is said to be _________ from the terminator

capsid

-the protein shell that encloses a viral genome -it may be rod-shaped, polyhedral, or more complex in shape -are built from a large number of protein subunits called capsomeres, but the number of different kinds of proteins is usually small

epigenetics

-the study of the inheritance of traits transmitted by mechanisms that do not involve the nucleotide sequence

AIDS (acquired immunodeficiency syndrome)

-the symptoms and signs present during the late stages of HIV infection -defined by a specified reduction in the number of T cells and the appearance of characteristic secondary infections

transcription

-the synthesis of RNA using a DNA template -the two nucleic acids are written in different forms of the same language, and the information is simply transcribed, or "rewritten," from DNA to RNA -DNA strand provides a template for making a new complementary strand during DNA replication and it also ​can serve as a template for assembling a complementary sequence of RNA nucleotides -for a protein-coding gene, the resulting RNA molecule is a faithful transcript of the gene's protein-building instructions -gene determines the sequence of nucleotide bases along the length of the RNA molecule that is being synthesized -particular DNA sequences associated with a gene determine how the enzyme that ________ genes is oriented when it binds, and this establishes which strand will be used as the template -gives rise to one long mRNA molecule that codes for the five polypeptides making up the enzymes in the tryptophan pathway (cell can translate this one mRNA into five separate polypeptides because the mRNA is punctuated with start and stop codons that signal where the coding sequence for each polypeptide begins and ends) -protein-protein interactions are crucial to the initiation of eukaryotic __________

translation

-the synthesis of a polypeptide using the genetic information encoded in an mRNA molecule -there is a change of "language" from nucleotides to amino acids, the cell must translate the nucleotide sequence of an mRNA molecule into the amino acid sequence of a polypeptide -sites of __________ are ribosomes

RNA genomes

-there are three types of single-stranded found in animal viruses -classes IV-VI

5′ cap and poly-A tail

-they seem to facilitate the export of the mature mRNA from the nucleus -they help protect the mRNA from degradation by hydrolytic enzymes -they help ribosomes attach to the 5′5′ end of the mRNA once it reaches the cytoplasm

chromosomes that have broken and rejoined incorrectly

-this translocates fragments from one chromosome to another -if a translocated proto-oncogene ends up near an especially active promoter (or other control element), its transcription may increase, making it an ​oncogene

Bacterial Transcription Termination

-transcription proceeds through a terminator sequence in the DNA -the transcribed terminator (an RNA sequence) functions as the termination signal, causing the polymerase to detach from the DNA and release the transcript, which requires no further modification before translation.

gene expression

-typical human cell might express about a third to a half of its protein-coding genes at any given time -highly differentiated cells, such as muscle or nerve cells, express a smaller fraction of their genes -commonly controlled at transcription; regulation at this stage often occurs in response to signals coming from outside the cell, such as hormones or other signaling molecules -often equated with transcription for both bacteria and eukaryotes, not necessarily the case for eukaryotes -RNA-based regulation of chromatin structure plays in an important role of this

HIV replicative cycle

-typical of a retrovirus -after HIV enters a host cell, its reverse transcriptase molecules are released into the cytoplasm, where they catalyze synthesis of viral DNA -the newly made viral DNA then enters the cell's nucleus and integrates into the DNA of a chromosome -the integrated viral DNA, called a provirus, never leaves the host's genome, remaining a permanent resident of the cell (Recall that a prophage, in contrast, leaves the host's genome at the start of a lytic cycle) -the RNA polymerase of the host transcribes the proviral DNA into RNA molecules, which can function both as mRNA for the synthesis of viral proteins and as genomes for the new viruses that will be assembled and released from the ​cell

b) Release of pyrophosphate from the incoming nucleotide, and then hydrolysis of the pyrophosphate to inorganic phosphate

Addition of a nucleotide onto a DNA strand is an endergonic reaction. What provides the energy to drive the reaction? a) Binding of the pre-existing new strand, the template strand, and the incoming nucleotide to the active site of the DNA polymerase b) Release of pyrophosphate from the incoming nucleotide, and then hydrolysis of the pyrophosphate to inorganic phosphate c) The dehydration reaction between the 5'-phosphate of the incoming nucleotide and the 3'-OH of the growing strand of DNA d) Complementary bases on the template and the incoming nucleotide are attracted to each other, releasing free energy.

RNA splicing

After synthesis of a eukaryotic primary RNA transcript, the removal of portions of the transcript (introns) that will not be included in the mRNA and the joining together of the remaining portions (exons).

b) Helicase, primase, DNA polymerase, ligase

After the formation of a replication bubble, which of the following is the correct sequence of enzymes used for the synthesis of the lagging DNA strand? a) Primase, helicase, DNA polymerase, ligase b) Helicase, primase, DNA polymerase, ligase c) Helicase, DNA polymerase, primase, ligase d) Helicase, primase, ligase, DNA polymerase e) Ligase, primase, DNA polymerase, helicase

picornovirus

All of the following types of viruses have envelopes except __________. picornovirus herpesvirus poxvirus flavivirus retrovirus rhabdovirus

repair enzymes defect

Allows cancer-causing errors to accumulate in the DNA faster than normal

gene editing

Altering genes in a specific, predictable way.

Transfer RNA (tRNA)

An RNA molecule that functions as a translator between nucleic acid and protein languages by picking up a specific amino acid and carrying it to the ribosome, where the tRNA recognizes the appropriate codon in the mRNA.

ribozyme

An RNA molecule that functions as an enzyme, such as an intron that catalyzes its own removal during RNA splicing.

retrovirus

An RNA virus that replicates by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses.

binds at the replication fork breaks H-bonds between bases

As DNA replication continues and the replication bubble expands, the parental double helix is unwound and separated into its two component strands. This unwinding and separating of the DNA requires three different types of proteins: *helicase*, topoisomerase, and single-strand binding proteins. binds ahead of the replication fork binds at the replication fork binds after the replication fork prevents H-bonds between bases breaks covalent bonds in DNA backbone single-strand binding protein breaks H-bonds between bases

breaks covalent bonds in DNA backbone binds ahead of the replication fork

As DNA replication continues and the replication bubble expands, the parental double helix is unwound and separated into its two component strands. This unwinding and separating of the DNA requires three different types of proteins: helicase, *topoisomerase*, and single-strand binding proteins. binds ahead of the replication fork binds at the replication fork binds after the replication fork prevents H-bonds between bases breaks covalent bonds in DNA backbone single-strand binding protein breaks H-bonds between bases

prevents H-bonds between bases binds after the replication fork

As DNA replication continues and the replication bubble expands, the parental double helix is unwound and separated into its two component strands. This unwinding and separating of the DNA requires three different types of proteins: helicase, topoisomerase, and *single-strand binding proteins*. binds ahead of the replication fork binds at the replication fork binds after the replication fork prevents H-bonds between bases breaks covalent bonds in DNA backbone single-strand binding protein breaks H-bonds between bases

a) 1 error per 10,000,000,000 nucleotides

As a result of proofreading by DNA polymerases, the overall error rate in the completed DNA molecule is approximately __________. a) 1 error per 10,000,000,000 nucleotides b) 1 error per 1,000 nucleotides c) 1 error per 100 nucleotides d) 1 error per 1,000,000,000 nucleotides e) 1 error per 1,000,000 nucleotides

the host cell's DNA is destroyed

As a result of the lytic cycle, _____. the host cell is not destroyed the host cell's DNA is destroyed viral ribosomes are produced viral DNA is incorporated into host cell DNA a prophage is created

made continuously only one primer needed daughter strand elongates toward replication fork

As the two parental (template) DNA strands separate at a replication fork, each of the strands is separately copied by a DNA polymerase III (orange), producing two new daughter strands (light blue), each complementary to its respective parental strand. Because the two parental strands are antiparallel, the two new strands (the leading and lagging strands) cannot be synthesized in the same way. Determine whether it describes the synthesis of the *leading strand*, the synthesis of the lagging strand, or the synthesis of both strands. daughter strand elongates away from replication fork only one primer needed synthesized 5' to 3' made in segments daughter strand elongates toward replication fork multiple primers needed made continuously

daughter strand elongates away from replication fork made in segments multiple primers needed

As the two parental (template) DNA strands separate at a replication fork, each of the strands is separately copied by a DNA polymerase III (orange), producing two new daughter strands (light blue), each complementary to its respective parental strand. Because the two parental strands are antiparallel, the two new strands (the leading and lagging strands) cannot be synthesized in the same way. Determine whether it describes the synthesis of the leading strand, *the synthesis of the lagging strand*, or the synthesis of both strands. daughter strand elongates away from replication fork only one primer needed synthesized 5' to 3' made in segments daughter strand elongates toward replication fork multiple primers needed made continuously

synthesized 5' to 3'

As the two parental (template) DNA strands separate at a replication fork, each of the strands is separately copied by a DNA polymerase III (orange), producing two new daughter strands (light blue), each complementary to its respective parental strand. Because the two parental strands are antiparallel, the two new strands (the leading and lagging strands) cannot be synthesized in the same way. Determine whether it describes the synthesis of the leading strand, the synthesis of the lagging strand, or *the synthesis of both strands*. daughter strand elongates away from replication fork only one primer needed synthesized 5' to 3' made in segments daughter strand elongates toward replication fork multiple primers needed made continuously

d) a replication fork

At each end of a DNA replication bubble is __________. a) a ribosome b) a gene c) a telomere d) a replication fork e) an origin of replication

d) was the substance that transformed the bacteria in Griffith's experiment

Avery and his colleagues' 1944 experiment showed that DNA __________. a) uses three bases to code for one amino acid b) contains adenine, guanine, thymine, and cytosine c) has two strands held together with hydrogen bonds d) was the substance that transformed the bacteria in Griffith's experiment e) consists of sugars, phosphate groups, and bases

reservoir; A

Birds act as a natural __________ for the influenza __________ virus. pandemic; B defense; A reservoir; A buffer; B reservoir; C

origin of viruses

Candidates for the original sources of viral genomes include plasmids and transposons -are not the descendants of precellular forms of life but evolved—possibly multiple times—after the first cells appeared. Most molecular biologists favor the hypothesis that viruses originated from naked bits of cellular nucleic acids that moved from one cell to another, perhaps via injured cell surfaces. The evolution of genes coding for capsid proteins may have allowed viruses to bind cell membranes, thus facilitating the infection of uninjured cells

a) thymine; guanine; cytosine

Chargaff analyzed DNA and found that the numbers of adenine molecules is approximately equal to the numbers of __________ molecules and that the numbers of __________ molecules is approximately equal to the numbers of __________ molecules. a) thymine; guanine; cytosine b) guanine; thymine; cytosine c) adenine; guanine; guanine d) cytosine; thymine; adenine e) cytosine; guanine; thymine

b) the ratio of A to T is close to 1:1 and the ratio of G to C is close to 1:1

Chargaff found that for DNA __________. a) the ratio of A to G is close to 1:1 and the ratio of T to C is close to 1:1 b) the ratio of A to T is close to 1:1 and the ratio of G to C is close to 1:1 c) A + T = G + C d) A + T = 50% of the total bases e) the ratio of A to C is close to 1:1 and the ratio of G to T is close to 1:1

viroids

Circular RNA molecules that function like a virus in plants are termed __________. rhabdovirus None of the listed responses is correct. prion retrovirus viroids

single-stranded RNA that serves as mRNA

Class IV viruses are characterized by which of the following types of genomes? single-stranded RNA that serves as mRNA single-stranded RNA that serves as a template for DNA synthesis single-stranded DNA single-stranded RNA that serves as a template for mRNA synthesis double-stranded RNA double-stranded DNA

e) protein; DNA; DNA

In the famous Hershey and Chase "blender experiment," radioactive sulfur was used to label __________, and radioactive phosphorus was used to label __________, demonstrating that the genetic material of a bacteriophage is __________. a) DNA; RNA; protein b) protein; DNA; RNA c) RNA; protein; DNA d) DNA; protein; DNA e) protein; DNA; DNA

viral DNA is replicated along with host DNA

In the lysogenic cycle _____. host DNA is destroyed and viral DNA is replicated a bacterium replicates without passing viral DNA to its daughter cells viral DNA is destroyed and host DNA is replicated a bacterium divides once before the lytic cycle is initiated viral DNA is replicated along with host DNA

All of the listed responses are correct.

In the lysogenic cycle of phages, __________. the nucleic acid core of the phage is all that enters the host cell only a small number of the viral genes are expressed the viral nucleic acid is replicated along with the host DNA the viral nucleic acid inserts itself into the host chromosome All of the listed responses are correct.

the cell typically dies, releasing many copies of the virus

In the lytic life cycle of phages, __________. phage DNA is incorporated into the host cell's genome DNA replication is not part of the life cycle the entire phage is taken into the bacterium the cell typically dies, releasing many copies of the virus the viral capsid is assembled according to the genetic information of the bacterium

coding strand

Nontemplate strand of DNA, which has the same sequence as the mRNA except it has thymine (T) instead of uracil (U).

b) 5' to 3'

Nucleic acids are assembled in the _____ direction. a) 4' to 5' b) 5' to 3' c) 1' to 5' d) 5' to 1' e) 2' to 3'

lytic; virulent

The phage reproductive cycle that kills the bacterial host cell is a __________ cycle, and a phage that always reproduces this way is a __________ phage. virulent; lytic lysogenic; temperate lytic; virulent lysogenic; virulent lytic; lysogenic

viral protein coat

The pointer is indicating the _____. viral envelope viral nucleic acid genome bacterium's nucleic acid genome viral protein coat bacterium's plasma membrane

gene expression

The process by which information encoded in DNA directs the synthesis of proteins or, in some cases, RNAs that are not translated into proteins and instead function as RNAs.

DNA replication

The process in which DNA makes a duplicate copy of itself; also called DNA synthesis

capsid

The protein shell that encloses a viral genome. It may be rod-shaped, polyhedral, or more complex in shape.

c) DNA polymerase I

The removal of the RNA primer and addition of DNA nucleotides to the 3' end of Okazaki fragments in its place is carried out by __________. a) primase b) ligase c) DNA polymerase I d) nuclease e) DNA polymerase III

a) attach free nucleotides to the new DNA strand

The role of DNA polymerases in DNA replication is to __________. a) attach free nucleotides to the new DNA strand b) synthesize an RNA primer to initiate DNA strand synthesis c) separate the two strands of DNA d) link together short strands of DNA e) All of the listed responses are correct.

c) attach free nucleotides to the new DNA strand

The role of DNA polymerases in DNA replication is to __________. a) link together short strands of DNA b) synthesize an RNA primer to initiate DNA strand synthesis c) attach free nucleotides to the new DNA strand d) All of the listed responses are correct. e) separate the two strands of DNA

c) Proteins because they were thought to be the only molecule with both the variety and specificity of function to account for the array of heritable traits observed

Until Hershey and Chase showed that DNA was the genetic molecule of the phages they studied, what class of molecules was considered the best candidate for carrying genetic information and why? a) Carbohydrates because they are found in abundance in all organisms b) Amino acids because of all the ways they can join together c) Proteins because they were thought to be the only molecule with both the variety and specificity of function to account for the array of heritable traits observed d) Nucleoside triphosphates because of the ability to add and remove phosphate groups e) Sterols because of the different variations on their ring structure

harmless derivatives of pathogenic viruses; stimulating the immune system to mount a defense against the actual pathogen

Vaccines for viral diseases are __________ and help prevent infection by __________. nucleoside inhibitors; inhibiting the replication of the viral genome antibiotic formulations; killing bacteria that assist viruses in infecting animal cells harmless derivatives of pathogenic viruses; stimulating the immune system to mount a defense against the actual pathogen protease inhibitors; preventing synthesis of envelope proteins antibiotic formulations; specifically killing infected cells

prophage

Viral DNA incorporated into a bacterial chromosome is known as a(n) __________. virulent phage bacteriophage retrovirus prophage adenovirus capsid

the presence or absence of metabolic machinery

Viruses can vary with respect to all of the following characteristics except __________. the type of host cell it can infect the presence or absence of a membranous envelope the presence or absence of metabolic machinery DNA or RNA as the genetic material single- or double-stranded nucleic acids

bacteriophages

Viruses that infect bacteria are called __________. bacteriophages proviruses bacterioviruses retroviruses capsomeres

a) DNA ligase

What enzyme joins Okazaki fragments? a) DNA ligase b) Topoisomerase c) Primase d) DNA polymerase e) Helicase

a) DNA polymerase can join new nucleotides only to the 3' end of a growing strand.

What is the basis for the difference in how the leading and lagging strands of DNA molecules are synthesized? a) DNA polymerase can join new nucleotides only to the 3' end of a growing strand. b) Helicases and single-strand binding proteins work at the 5' end. c) DNA ligase works only in the 3' to 5' direction. d) Polymerase can work on only one strand at a time. e) The origins of replication occur only at the 5' end.

Hemagglutinin is the protein that helps the influenza virus attach to host cells.

What is the function of hemagglutinin in the influenza virus? Hemagglutinin is involved in assembling the membrane envelope that the virus uses as a cloak when it leaves an infected cell. Hemagglutinin is the name of the reverse transcriptase enzyme in the influenza virus. Hemagglutinin is the protein that helps the influenza virus attach to host cells. Hemagglutinin is part of the protein capsid of the influenza virus. Hemagglutinin helps release new viruses from infected cells.

It catalyzes the formation of DNA from an RNA template.

What is the function of reverse transcriptase? It catalyzes the formation of a polypeptide from an RNA template. It catalyzes the formation of DNA from a polypeptide template. It catalyzes the formation of RNA from a polypeptide template. It catalyzes the formation of RNA from a DNA template. It catalyzes the formation of DNA from an RNA template.

a) Bacteria usually have a single circular chromosome whereas eukaryotes have several linear chromosomes.

What is the major difference between bacterial chromosomes and eukaryotic chromosomes? a) Bacteria usually have a single circular chromosome whereas eukaryotes have several linear chromosomes. b) Bacterial chromosomes have much more protein associated with the DNA than eukaryotes. c) Eukaryotes have a single circular chromosome, whereas bacteria have several linear chromosomes. d) The DNA molecules of bacterial chromosomes have a slightly different structure than those of eukaryotic chromosomes. e) There is no difference between bacterial and eukaryotic chromosomes.

c) Bacteria have a single circular chromosome whereas eukaryotes have several linear chromosomes.

What is the major difference between bacterial chromosomes and eukaryotic chromosomes? a) Bacterial chromosomes have much more protein associated with the DNA than eukaryotes. b) The DNA of bacterial chromosomes has a slightly different structure. c) Bacteria have a single circular chromosome whereas eukaryotes have several linear chromosomes. d) There is no difference between bacterial and eukaryotic chromosomes. e) Eukaryotes have a single circular chromosome whereas bacteria have several linear chromosomes.

vaccines

What is the most effective way to stop viral infections? drug cocktails wear a hat when you go outside in the winter antibiotics vaccines antiviral drugs

It is "stolen" from the host cell, but it contains some proteins encoded by the viral genome.

What is the origin of the phospholipid membrane that envelops many animal viruses? It is "stolen" from the host cell and contains only host cell proteins and phospholipids. It is produced by viral enzymes and contains only viral proteins and phospholipids. It is assembled in the ER based on signals sent out by the viral genome. It is assembled from free phospholipids floating in the cell's cytoplasm. It is "stolen" from the host cell, but it contains some proteins encoded by the viral genome.

d) DNA polymerase is the enzyme that catalyzes the addition of a nucleotide onto the 3' end of a growing DNA strand.

What is the role of DNA polymerase during DNA synthesis? a) DNA polymerase catalyzes the synthesis of the template strand of DNA. b) DNA polymerase removes inorganic phosphate from the template strand of DNA to catalyze the polymerization reaction. c) DNA polymerase provides the free energy to catalyze the endergonic addition of a nucleotide onto the 3' end of a growing DNA strand. d) DNA polymerase is the enzyme that catalyzes the addition of a nucleotide onto the 3' end of a growing DNA strand.

host cell membrane

What is the source of a viral envelope? host cell DNA prophages provirus host cell membrane viral glycoproteins

All four deoxyribonucleotides triphosphates (containing A, C, T, or G) 3'-OH end of the new DNA strand Single-stranded DNA template

What materials does DNA polymerase require in order to synthesize a complete strand of DNA? Select all that apply. Inorganic phosphate All four deoxyribonucleotides triphosphates (containing A, C, T, or G) 3'-OH end of the new DNA strand ATP Single-stranded DNA template

d) thymidine dimers; nucleotide excision repair enzyme

When __________ form after an exposure to ultraviolet (UV) light, a __________ can remove the damaged nucleotides and replace them with normal nucleotides. a) thymidine dimers; nucleotide incision repair enzyme b) cytosine dimers; nucleotide excision repair enzyme c) guanosine dimers; nucleotide excision repair enzyme d) thymidine dimers; nucleotide excision repair enzyme e) guanosine dimers; nucleotide incision repair enzyme

Only the nucleic acid

When a virus infects an E. coli cell, what part of the virus enters the bacterial cytoplasm? The entire virus The tail fibers Only the nucleic acid The protein capsid only The protein capsid and enclosed nucleic acid

RNA viruses because no proofreading is done on RNA molecules

When comparing DNA and RNA viruses, which mutate more quickly, and why? DNA viruses because the host cell's proofreading enzymes do not work on viral DNA DNA viruses because they usually have larger genomes and thus more loci for mutations to occur They all mutate at the same rate. RNA viruses because no proofreading is done on RNA molecules RNA viruses because RNA is single-stranded and thus more prone to mutations

RNA viruses, because no proofreading is done on RNA molecules

When comparing DNA and RNA viruses, which mutate more quickly, and why? RNA viruses, because RNA is single-stranded and thus more prone to mutations DNA viruses, because the host cell's proofreading enzymes do not work on viral DNA They all mutate at the same rate RNA viruses, because no proofreading is done on RNA molecules DNA viruses, because they usually have larger genomes and thus more loci for mutations to occur

Both produce protein coats via translation of mRNA.

Which statement below is a correct comparison of a "regular" RNA virus and an RNA retrovirus? Both produce protein coats via translation of mRNA. Only RNA retroviruses produce DNA using DNA replicase. Only the RNA retrovirus performs translation. Only the regular RNA virus produces DNA from an RNA template. Only the regular RNA virus performs transcription.

a) Helicases separate the two strands of the double helix, and DNA polymerases then construct two new strands using each of the original strands as templates.

Which description of DNA replication is correct? a) Helicases separate the two strands of the double helix, and DNA polymerases then construct two new strands using each of the original strands as templates. b) Ligase separates the two strands of the DNA double helix. Then, DNA polymerase synthesizes the leading strand and primase synthesizes the lagging strand. c) The two strands of DNA separate, and restriction enzymes cut up one strand. Then, the DNA polymerase synthesizes two new strands out of the old ones. d) The two strands separate, and each one receives a complementary strand of RNA. Then this RNA serves as a template for the assembly of many new strands of DNA. e) Ligase assembles single-stranded codons, then polymerase knits these codons together into a DNA strand.

b) Its specific base pairing through hydrogen bonds

Which of the following attributes of DNA is most crucial to its accurate duplication? a) Its helical nature and hydrogen bonding b) Its specific base pairing through hydrogen bonds c) Its specific sequence of bases d) Its phosphodiester linkages and complementary strands e) Its deoxyribose sugar and phosphate groups

None of the listed responses is correct.

Which of the following can a virus do without a host cell? Produce nucleotides for use in replication and transcription Synthesize proteins Produce ATP for energy Transcribe DNA None of the listed responses is correct.

genetic material composed of nucleic acid

Which of the following characteristics, structures, or processes is common to both bacteria and viruses? metabolism cell division ribosomes genetic material composed of nucleic acid independent existence

c) RNA primer

Which of the following components is required for DNA replication? a) Messenger RNA b) Ligase c) RNA primer d) Ribosomes e) Proteases

a) RNA primer

Which of the following components is required for DNA replication? a) RNA primer b) Sucrases c) Transfer RNA d) Proteases e) Ribosomes

e) All of the listed responses are correct.

Which of the following considerations was/were important in the choice of viruses and bacteria for early experiments on DNA? a) They typically have relatively small genomes. b) Their chromosomes have a simpler structure. c) They have short generation times. d) They can interact with each other. e) All of the listed responses are correct.

The host cell usually dies, releasing many new copies of the virus.

Which of the following events occurs during the lytic life cycle of phages? The phage capsid fuses with the host cell membrane, thus allowing the viral genome to be inserted into the host cell. The host cell usually lives and secretes the copies of the virus. The host cell lives, with the viral genome becoming incorporated into the host cell's own genome. The phage enters the host cell intact during infection. The host cell usually dies, releasing many new copies of the virus.

An infected plant produces seeds that contain the virus, giving rise to infected progeny.

Which of the following is an example of vertical transmission of a virus in plants? An infected plant produces seeds that contain the virus, giving rise to infected progeny. Two neighboring plants touch each other, allowing viruses present in one plant to infect the other plant. Viral particles are carried by the wind from one plant to another. Viral particles are carried from one plant to another by a pair of pruning shears. All of the listed responses are correct.

parvovirus

Which of the following is not a class I virus? polyomavirus parvovirus adenovirus poxvirus herpesvirus papillomavirus

e) All of the listed responses are correct.

Which of the following statements about replication origins is/are correct? a) The DNA sequence at the origin of replication is recognized by specific proteins that bind to the origin. b) The two strands of DNA at the origin of replication are separated, creating a replication bubble. c) Replication proceeds in both directions from each origin. d) Bacterial chromosomes have a single origin of replication, but eukaryotic chromosomes have many origins. e) All of the listed responses are correct.

Virulent phages replicate through the lytic cycle only, and temperate phages replicate using both the lytic and the lysogenic cycles.

Which of the following statements correctly describes one difference between virulent phages and temperate phages? Temperate phage DNA is methylated to prevent digestion by bacterial restriction enzymes, but virulent phage DNA is not. None of the listed responses is correct. Temperate phages replicate through the lytic cycle only, and virulent phages replicate using both the lytic and the lysogenic cycles. Virulent phages replicate through the lytic cycle only, and temperate phages replicate using both the lytic and the lysogenic cycles. Virulent phages infect only animal cells, and temperate phages infect only bacterial cells. Virulent phage DNA can be integrated into the bacterial chromosome and become a prophage, but temperate phages cannot do this.

e) All of the listed responses are correct.

Which of the following statements is/are correct with regard to individuals with the disorder xeroderma pigmentosum? a) These individuals have high rates of skin cancer. b) These individuals usually have inherited defects in the nucleotide excision repair system. c) Cells in these individuals have difficulty repairing thymine dimers. d) These individuals are extremely sensitive to sunlight. e) All of the listed responses are correct.

b) X-ray crystallography

Which of the following techniques was most helpful to Watson and Crick in developing their model for the structure of DNA? a) Radioactive labeling b) X-ray crystallography c) Cloned DNA d) Transgenic animals e) Electrophoresis

All of the listed responses are correct.

Which of the following, if any, may be a component of a virus? Phospholipid bilayer Protein Single-stranded (ss) RNA Double-stranded (ds) DNA All of the listed responses are correct.

A

Which of these binds to receptor molecules on the host cell membrane? A B C D E

d) DNA is usually double-stranded, whereas RNA is usually single-stranded.

Which of these is a difference between a DNA and an RNA molecule? a) DNA contains nitrogenous bases, whereas RNA contains phosphate groups. b) DNA contains uracil, whereas RNA contains thymine. c) DNA is a polymer composed of nucleotides, whereas RNA is a polymer composed of nucleic acids. d) DNA is usually double-stranded, whereas RNA is usually single-stranded. e) DNA contains five-carbon sugars, whereas RNA contains six-carbon sugars.

C

Which of these is reverse transcriptase? A B C D E

E

Which of these is the viral genome? A B C D E

b) C, D, and E

Which of these is(are) pyrimidines? a) A and B b) C, D, and E c) B and C d) B, C, and D e) A, B, and C

a) thymine

Which of these nitrogenous bases is found in DNA but not in RNA? a) thymine b) guanine c) cytosine d) adenine e) uracil

b) Adenine forms two hydrogen bonds with thymine; guanine forms three hydrogen bonds with cytosine.

Which one of the following statements is correct? a) Adenine forms two hydrogen bonds with guanine; thymine forms three hydrogen bonds with cytosine. b) Adenine forms two hydrogen bonds with thymine; guanine forms three hydrogen bonds with cytosine. c) Adenine forms two covalent bonds with thymine; guanine forms three covalent bonds with cytosine. d) Adenine forms three hydrogen bonds with thymine; guanine forms two hydrogen bonds with cytosine. e) Adenine forms three covalent bonds with thymine; guanine forms two covalent bonds with cytosine.

e) Helicases separate the two strands of the double helix, and DNA polymerases then construct two new strands using each of the original strands as templates.

Which one of the following statements regarding DNA replication is correct? a) Ligase assembles nucleotides into Okazaki fragments. Then polymerase joins these fragments together into a DNA strand. b) The two strands separate, and each one receives a complementary strand of RNA. Then this RNA serves as a template for the assembly of many new strands of DNA. c) The two strands of DNA separate, and nuclease enzymes digest one strand. Then DNA polymerase synthesizes two new strands out of the old ones. d) Ligase separates the two strands of the DNA double helix. Then DNA polymerase synthesizes the leading strand and primase synthesizes the lagging strand. e) Helicases separate the two strands of the double helix, and DNA polymerases then construct two new strands using each of the original strands as templates.

c) nuclease, DNA polymerase, and ligase

Which set of enzymes is involved in nucleotide excision repair? a) Nuclease, DNA polymerase, primase b) DNA polymerase, helicase, primase c) nuclease, DNA polymerase, and ligase d) Hydrolase, nuclease, and ligase e) Ligase, nuclease, and primase

Herpesvirus can leave its DNA behind as minichromosomes in nerve cell nuclei. Stress can trigger another round of virus production, producing characteristic blisters and sores.

Why can flare-ups of herpesvirus infection recur throughout a person's life? The herpesvirus becomes a prophage during the lysogenic cycle of the infection, so the viral genome is recombined with the host DNA. Herpesvirus is very common in the environment, so it is easy for a person to become re-infected. The herpesvirus always kills its host cell when it leaves. Cycles of cell death cause the recurring flare-ups. Herpesvirus can leave its DNA behind as minichromosomes in nerve cell nuclei. Stress can trigger another round of virus production, producing characteristic blisters and sores. Herpesvirus may cloak itself in a cell's nuclear envelope, making it very difficult for the immune system to recognize it.

Antibiotics inhibit enzymes specific to bacteria and have no effect on virally encoded enzymes.

Why is it ineffective to treat viral disease with antibiotics? Pathogenic RNA viruses have a high rate of mutation, producing new genetic varieties that are insensitive to antibiotic treatment. Antibiotics inhibit enzymes specific to bacteria and have no effect on virally encoded enzymes. Due to excessive antibiotic use, most viruses have evolved to be resistant to antibiotics.

c) Franklin; double helix

X-ray diffraction images produced by __________ showed that DNA is a __________. a) Wilkins; triple helix b) Crick; double helix c) Franklin; double helix d) Watson; double helix e) Pauling; triple helix

a) sugar with two, and not three, oxygen atoms

You can tell that this is an image of a DNA nucleotide and not an RNA nucleotide because you see a _____. a) sugar with two, and not three, oxygen atoms b) phosphate group, not a uracil c) uracil nitrogenous base, not a thymine nitrogenous base d) double-stranded molecule, not a single-stranded molecule e) thymine nitrogenous base, not a uracil nitrogenous base

plasmids, transposons, and viruses

mobile genetic elements

master regulatory genes

protein products commit the cells to becoming skeletal muscle cells

enzyme

proteins that catalyze specific chemical reactions in the cell

Antiparallel

referring to the arrangement of the sugar-phosphate backbones in a DNA double helix (they run in opposite 5' -3' directions).

E. coli cell can sense the glucose concentration and relay this information to the lac operon

the mechanism depends on the interaction of an allosteric regulatory protein with a small organic molecule, cyclic AMP (cAMP) in this case, which accumulates when glucose is scarce -the regulatory protein, called cAMP receptor protein (CRP), is an activator, a protein that binds to DNA and stimulates transcription of a gene(CRP is also called catabolite activator protein, or CAP.) -when cAMP binds to this regulatory protein, CRP assumes its active shape and can attach to a specific site at the upstream end of the lac promoter -this attachment increases the affinity of RNA polymerase for the lac promoter, which is actually rather low even when no lac repressor is bound to the operator -by facilitating the binding of RNA polymerase to the promoter and thereby increasing the rate of transcription of the lac operon, the attachment of CRP to the promoter directly stimulates gene expression -this mechanism qualifies as positive regulation.

leading strand

the new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory 5' to 3' direction