Final Exam Flashcards

Question

what is a locus

Answer 1

a specific place on a chromosome occupied by an allele

Answer 2

a set of alleles possessed by an individual organism

Answer 3

an individual organism possessing 2 of the same alleles at a locus

Answer 4

an individual organism possessing two different alleles at a locus

Answer 5

am attribute or feature possessed by an organism

Answer 6

the appearance or manifestation of a characteristic

Answer 7

when two different alleles are present in a genotype, only the trait encoded by one of them --- the "dominant" allele is observed in the phenotype

Answer 8

(Mendel's first law) each individual diploid organism possesses two alleles for any particular characteristic, one inherited from mom and one from dad. These two alleles segregate (separate) when gametes are formed and one allele goes into each gamete

Answer 9

the multiplication rule states that the probability of two or more independent events taking place together is calculated by multiplying their independent probabilities. The key indicator for applying this rule is the word and; additionally, the two events must be independent meaning the outcome of one will not influence the outcome of the other

Answer 10

the addition rule states that the probability of any two or more mutually exclusive events is calculated by adding the probabilities of the events. the key indicator of this rule are the words either and or. For this rule to be valid the events of must be mutually exclusive meaning that one event excludes the outcome of the other

Answer 11

a testcross is used to analyze genetic crosses. One individual of an unknown genotype is crossed with an individual who is homozygous recessive for the trait in question. The testcross reveals the genotype of the unknown individual.

Answer 12

(Mendel's second law) states that the alleles at different loci separate independently from one another. This is an extension of the principle of segregation. The separation is independent of the separation of alleles other loci

Answer 13

it is used to evaluate the role of chance in producing deviations between observed and expected values. It indicates that the probability that the difference between the observed and expected value is due to chance. It must always be applied to numbers of progeny not proportions or percentages.

Answer 14

P= probability that the deviation between expected and observed values are due to chance. high p= chance alone produced the differences in observed and expected numbers low p= some other factor produced the differences in observed and expected numbers

Answer 15

sex chromosomes differ between males and females autosomes are non sex chromosomes and they are the same between males and females

Answer 16

Even though they are different in size and content they are homologous at their pseudoautosomal regions which allows them to find each other and pair up during Prophase I

Answer 17

it is determined by the SRY gene on Y chromosome (not by the whole Y chromosome). Without the SRY gene the gonads will develop into ovaries

Answer 18

Klinefelter syndrome: xxy; phenotype: male Turner syndrome: xo; phenotype: female Triple-X: xxx; phenotype: female XYY male: xyy; phenotype: male

Answer 19

women with androgen insensitivity syndrome have x and y chromosomes. Testosterone must bind to an androgen receptor in order to stimulate the development of male characteristics, but with the absence of testosterone female characteristics develop. In androgen insensitivity there is nothing for the testosterone to bind to so the body develops as a female.

Answer 20

x linked traits: genes on the x chromosome that determine specific characteristics y linked traits: genes on the y chromosome that determine specific characteristics. will only ever be present in males and always inherited from the father

Answer 21

a reciprocal cross crosses a male and female with different phenotypes and then does it again with the phenotypes corresponding to the opposite sex. This will help indicate if a trait is sex linked or not.

Answer 22

failure of chromosomes to separate properly during anaphase

Answer 23

only 1 x chromosome is expressed in each cell of female mammals. Which X is inactivated is random and set early in development. In cells with more than 2 X chromosomes, all but one X will become inactivated

Answer 24

Inactivated X chromosome that appears as a condensed, darkly staining body in the nuclei of most cells of female placental mammals.

Answer 25

Xa or XA depending on which X gets inactivated, some cells express a, others A

Answer 26

complete dominance: phenotype of the heterozygote is the same as the phenotype of one of the homozygotes incomplete dominance: phenotype of the heterozygote is intermediate (falls within the range) between the phenotypes of the two homozygotes Codominance: phenotype of the heterozygote includes the phenotype of both the homozygotes

Answer 27

percent of individuals having a particular genotype that express the expected phenotype

Answer 28

degree to which the phenotype is expressed

Answer 29

alleles that cause death at an early stage of development

Answer 30

more than two alleles are present within a group of organisms

Answer 31

ABO blood group is a multi allele system. AA or Ai= blood type A (anti-B) BB or Bi= blood type B (anti-A) AB= blood type AB (universal receiver) ii= blood type O (anti-A anti-B)

Answer 32

the effects of genes at one locus depend on the presence of genes at other loci.

Answer 33

one gene masks or hides the effect of another gene at a different locus

Answer 34

recessive epistasis needs both epistatic genes present in order to mask dominant epistasis needs one epistatic gene present in order to mask

Answer 35

sex influenced characteristics are determined by autosomal genes and are inherited according to Mendel's principles, but they are expressed differently in males and females (the trait has higher penetrance in one of the sexes)

Answer 36

sex limited characterisitics are encoded by autosomal genes that are expressed in only one sex; the trait has zero penetrance in the other sex.

Answer 37

characteristics encoded by genes located in the cytoplasm exhibit cytoplasmic inheritance. cytoplasmic genes come from only one gamete and it is usually the egg. most cytoplasmically inherited traits are present in both males and females and are passed from mother to offspring, never from father to offspring. There is no mechanism to ensure cytoplasmic genes are evenly distributed during cell division so different cells and different individual offspring will contain various proportions of cytoplasmic genes

Answer 38

the phenotype of the offspring is determined by the genotype of the mother. The offpsrings phenotype is determined not by its genotype but by the genotype of the mother

Answer 39

differential expression of genetic material depending on whether it is inherited from the male or female parent

Answer 40

- sex linked characteristic: genes located on the sex chromosomes - sex influenced traits: autosomal genes that are more readily expressed on one sex - sex limited characteristic: autosomal genes whose expression is limited to one sex - genetic maternal effect: nuclear genotype of the maternal parent - cytoplasmic inheritance: cytoplasmic genes, which are usually inherited from only one parent - genomic imprinting: genes whose expression is affected by the sex of the transmitting parent

Answer 41

a genetic trait becomes more strongly expressed, or is expressed at an earlier age, as it is passed from generation to generation

Answer 42

a phenotype that is produced by environmental factors alone but it is the same phenotype produced by a genotype

Answer 43

characteristics encoded by genes at many loci are polygenic characteristics pleiotropy is when one gene affects multiple characteristics (inverse of polygenic)

Answer 44

- usually appears in both sexes with equal frequency - tends to skip generations - affected offspring are usually born to unaffected parents - when both parents are heterozygous approximately 1/4 of the offspring will be affected - appears more frequently in children of consanguineous marriages

Answer 45

- usually appears in both sexes with equal frequency - both sexes transmit the trait to their offspring - does not skip generations - affected offspring must have an affected parent unless they possess a new mutation - when one parent is affected (heterozygous) and the other parent is unaffected, approximately half the offspring will be affected - unaffected parents do not transmit the trait

Answer 46

- usually more males than females are affected - affected sons are usually born to unaffected mothers; thus, the trait skips generations - approximately half of carrier (heterozygous) mothers sons are unaffected - never passed from father to son - all daughters of affected fathers are carries

Answer 47

- both males and females are usually affected: often, more females than males - does not skip generations. Affected sons must have an affected mother; affected daughters must have either an affected mother or an affected father - affected fathers pass the trait to all their daughters - affected mothers (if heterozygous) pass the trait to half of their sons and half of their daughters

Answer 48

- only males are affected - passed from father to all sons - does not skip generations

Answer 49

the genetic analysis of complex characteristics

Answer 50

continuous traits: also called qualitative traits, vary continuously on a scale of measurement exhibiting many overlapping phenotypes discontinuous traits: possess only a few distinct phenotypes

Answer 51

1. many are polygenic (influenced from genes at many loci.) 2. often arise when environmental factors affect the phenotype because environmental variation results in a single genotype producing a range of phenotypes. most continuous traits are both polygenic and influence by environmental factors

Answer 52

meristic characteristics are measured in whole numbers (like litter size) but they are considered quantitative because they are determined by multiple genetic and environmental factors

Answer 53

threshold characteristics are either present or absent. they are considered quantitative because they are determined by multiple genetic and environmental factors. the expression of the characteristic depends on an underlying susceptibility that varies continuously

Answer 54

the complete set of chromosomes possessed by an organism

Answer 55

they alter the structure of chromosomes: a piece of chromosome may be added duplicated, deleted or inverted

Answer 56

the number of chromosomes is altered: one or more individual chromosomes are added or deleted

Answer 57

one or more complete sets of chromosomes are added. a polyploid is an organism that has more than two sets of chromosomes

Answer 58

unbalanced gene dosage

Answer 59

inversions often have pronounced phenotypic effects. it may break a gene into two parts with one part moving to a new location and destroying the function of that gene

Answer 60

the short arm of one acrocentric chromosome is exchanged with the longer arm of another creating a large metacentric chromosome and a fragment that often fails to segregate is lost this results in an overall reduction in chromosome number - they are the cause of some cases of downsyndrome

Answer 61

the loss of a single chromosome. it is represented as 2n-1

Answer 62

the gain of a single chromosome represented as 2n +1. The gain of a chromosome means that there are three homologous copies of one chromosome. Most cases of downsyndrome are a result of trisomy of chromosome 21

Answer 63

the loss of both members of a homologous pair of chromosomes. It is represented as 2n-2 where n refers to the haploid number of chromosomes

Answer 64

the gain of two homologous chromosomes represented as 2n + 2. It is not the gain of any 2 homologous chromosomes but the gain of two homologous chromosomes, so that there are four homologous copies of a particular chromosome

Answer 65

familial downsyndrome arises in offspring whose parents are carriers of a chromosome that has undergone a robertsonian translocation usually between chromosome 14 and 21. the long arm of 21 and the short arm of 14 exchange places. The exchange results in one chromosome that includes the long arms of 14 and 21 and another very small chromosome that contains the short arms, which generally is lost after several cell divisions

Answer 66

nondisjunction is the failure of homologous chromosomes or sister chromatids to separate in meiosis or mitosis. nondisjunction leads to some gametes or cells that contain an extra chromosome and other gametes or cells that are missing a chromosome

Answer 67

There is familial Down syndrome and primary Down syndrome. Familial Down syndrome has a tendency to run in families and it is a result of a Robertsonian translocation, it has the same phenotypic characteristics as primary downsyndrome Primary down syndrome is also known as trisomy 21 and it is a result of a spontaneous nondisjunction during egg formation. about 75% of nondisjunction events that cause downsyndrome are of maternal origin mostly arising during meiosis 1

Answer 68

there is no mechanism of dosage compensation for autosomes most embryos with autosomal aneuploidies are spontaneously aborted most commonly seen autosomal aneuploidy is downsydrome which is likely because chromosome 21 is relatively small and carries relativity few genes, so the presence of extra copies is less detrimental

Answer 69

Genetic mosaicism is nondisjunction in mitotic division that generates patches of cells in which every cell has a chromosome abnormality and other patches in which every cell has a normal karyotype. This type of nondisjunction leads to regions of tissue with different chromosome constitutions.

Answer 70

polyploids are organisms that possess two or more sets of chromosomes autopolyploidy: all chromosome sets are from a single species allopolyploidy: chromosome sets are from two or more species (hybridization between two species)

Answer 71

DNA from different organisms vary significantly in base compositions, but between each organism, there is regularity in the ratios of the bases: A=T and G=C

Answer 72

Griffith discovered the phenomenon of transformation. (discovered that transformation existed BUT NOT WHAT the transformation factor is) Experiment: virulent bacteria injected into a mouse --> mouse died nonvirulent bacteria injected into a mouse --> mouse lived heat killed virulent bacteria injected into a mouse --> mouse lived mixture of virulent and heat killed viruletn injected into a mouse --> mouse died conclusion: a substance in the heat-killed virulent bacteria genetically transformed the nonvirulent bacteria into live virulent bacteria.

Answer 73

They identified WHAT the transforming substance was (DNA is) Experiment: they took virulent material and used heat to to kill it. They then separated it into three samples one with RNase (destroys RNA), one with protease (destroys proteins), and one with DNase (destroys DNA) They added all the treated samples to cultures of nonvirulent DNA. Cultures treated with protease or RNase contained transformed bacteria but the culture with DNase did not Conclusion: because only DNase destroyed the transforming substance, the transforming substance is DNA

Answer 74

worked with T2 bacteriophage to determine what part of the phage served as genetic material Phage genome is DNA. All other parts of the bacteriophage are protein. Phage attaches to E. coli and injects its chromosome. Bacterial chromosome breaks down, and the phage chromosome replicates. Expression of phage genes produces phage structural components. Progeny phage particles assemble. Bacterial wall lyses, releasing progeny phages. Experiment: ingect E.coli grown in medium containing sulfur marker and one grown in medium with a phosphorus marker. sulfur marker is taken up in phage protein which contains S but not P. Phosophurs marker is takin up in phage DNA, whihc contains p but not s. phages with s and p marker infect unlabled E.coli shear off protein coats and separate protein from cells by centrifuging. Results: S is recovered in fluid containing virus coats and infected bacter form a pellet containing P at the bottom of the tube. Progengy phages are radioactive indicating that DNA has been transmitted to the progeny phages Conclusion: DNA (not protein) is the genetic material in bacteriophages

Answer 75

question: what substance- RNA or protein - carries the genetic material in tobacco mosaic virus (TMV) Experiment Have 2 types of TMV (type A and type B) degrade both types to yield RNA and coat proteins. Mix RNA of one type with protein of the other to create hybrid viruses. Infect tobacco with the hybrids Results: the type of RNA in the hybrid parent TMV determines the RNA and protein of the progeny viruses Conclusion: RNA is the genetic material of TMV

Answer 76

a nucleotide contains a sugar, a phosphate, and a nitrogen containing base DNA consists of a large number of linked repeating units (nucleotides)

Answer 77

DNA runs in opposite directions; antiparallel DNA has deoxyribes sugar (missing an oxygen compared to RNA). composed of polynucleotide strands CG pairs have three hydrogen bonds and TA pairs have two hydrogen bonds A phosphodiester linkage connects the 5'- phosphate group and the the 3' OH group of adjoining nucleotides

Answer 78

also composed of polynucleotide strands Uracil (U) replaces thymine (T) RNA has a ribose sugar (an OH group where DNA just has an H)

Answer 79

Eukaryotic DNA in the cells is closely associated with proteins. The complex of DNA and proteins is called chromatin

Answer 80

euchromatin undergoes the normal process of condensation and decondensation in the cell cycle

Answer 81

heterochromatin remains in a highly condensed state throughout the cell cycle, even during interphase.

Answer 82

euchromatin constitutes the majority of the chromosomal material and is where most transcription takes place all chromosomes have permanent heterochromatin at the centromeres and telomeres; the y chromosome consists largely of constitutive heterochromatin heterochromatin may also occur during certain developmental stages heterochromatin is also characterized by a general lack of transcription, the absence of crossing over, and replication late in the S phase

Answer 83

must abundant proteins in chromatin are the histones, which are small, positively charged proteins of five major types: H1, H2A, H2B, H3, and H4 all histones have a % of bargaining and lysine which gives them their net positive charge. These positive charges attack the negative charges on the phosphates of DNA; this attraction holds the DNA in contact with the histones.

Answer 84

the positive charges attract the negative charges on the phosphates of DNA, which holds the DNA in contact with the histones

Answer 85

The core of protein and DNA produced by digestion with nuclease enzymes is the simplest level of chromatin structure (the nucleosome) The nucleosome is a core particle consisting of DNA wrapped about two times around an octamer of eight histone proteins (2 copies each of H2A, H2B, H3, and H4) each of the histone proteins that make up the nucleosome particle has a flexible "tail" positively charged amino acids in the tails of the histones interact with negative charges of the phosphates on the DNA, keeping the DNA and histones tightly associated

Answer 86

mitochondrial and chloroplast DNA is inherited through replicative segregation

Answer 87

around 1 billion years ago an anaerbic cell engulfed an aerobic bacterium through endocytosis. The aerobic endosymbiont evolved into mitochondria. Endocytosis of a photosynthesizing bacterium led to the evolution of modern eukaryotic cells with mitochondria and chloroplasts The endosymbiotic theory proposes that mitochondria and chloroplasts in eukaryotic cells arose from bacteria

Answer 88

a heteroplasmic cell has two distinct varieties of DNA contained in its organelles the organelles segregate randomly in cell division, replicate, and again segregate random in cell division and organelles replicate again this happens a total of three times. cell division --> replication of mitochondria --> cell division --> replication of mitochondria most of the resulting cells are heteroplasmic, but, just by chance, some cells may receive only one type of organelle

Answer 89

the goal was determine what model of replication of DNA was accurate filled a centrifuge tube with a heavy salt solution and DNA fragments then spun the centrifuge for several days a density gradient developed and heavy DNA (15n marker) moved toward the bottom and light DNA (14n marker) moved toward the top After one round of replication, DNA appeared as a single band at intermediate weight after a second round of replication, DNA appeared as two bands 1 light and the other intermediate conclusion: DNA replication in E.coli is semiconservative

Answer 90

DNA: composed of nucleotides deoxyribose sugar no 2' OH group nucleotides are joined by phosphodiester bonds usually double stranded secondary structure is a double helix stable RNA: composed of nucleotides ribose sugar has a 2' OH group nucleotides are joined by phosphodiester bonds usually single stranded many types of secondary structures easily degradable

Answer 91

Cell type: prokaryotic and eukaryotic Location of function in eukaryotic cells: cytoplasm Function: structural and functional components of the ribosome

Answer 92

Cell type: prokaryotic and eukaryotic Location of function in eukaryotic cells: nucleus and cytoplasm Function: carries genetic code for proteins

Answer 93

Cell type: prokaryotic and eukaryoitc Location and Function in Eukaryotic cells: cytoplasm Function: helps incorporate amino acids into polypeptide chain

Answer 94

Transcription: synthesis of an RNA molecule from a DNA template RNA synthesis is complementary and antiparallel to template strand Only certain regions of the DNA are transcribed (mostly gene regions) rather than the entire chromosome Only 1 of the 2 DNA strands is transcribed for each gene Nucleotides are added to the 3’ end of the RNA molecule so the direction of synthesis is 5’-3’ * refer to Fig 13.8

Answer 95

Bacterial cells only possess one type of RNA polymerase, which catalyzes the synthesis of all classes of bacterial RNA. 5 sub units make up the core enzyme: 2 copies of alpha, 1 beta, 1 beta prime, 1 omega The core enzyme catalyzes the elongation of RNA molecules by the addition of RNA nucleotides. The sigma factor controls the binding of RNA polymerase to the promoter forming a holoenzyme. It is said to move downstream during transcription: it binds to the promoter and moves toward the terminator.

Answer 96

bacteria only have one RNA polymerse that transcribes all RNA, eukaryotes have many RNA polymerases (named with roman numerals) that transcribe different RNAs know that in eukaryotes there are different RNA polymerases that transcribe different types of RNA RNA pol II transcribes pre-mRNA

Answer 97

the promoter is a DNA sequence that the transcription factor recognizes and binds. It indicates which of the 2 DNA strands is to be read as the template and the direction of transcription. In most cases, the promoter is located next to the transcription start site but is not itself transcribed

Answer 98

A consensus sequence is the set of most commonly encountered nucleotides among sequences that possess considerable similarity, or consensus. The presence of a consensus within a set of nucleotides usually implies that the sequence is associated with an important function. The holoenzyme initially binds weakly to the promoter but then undergoes a change in structure that allows it to bing more tightly and unwind the double stranded DNA

Answer 99

Initiation (fig 13.12): - sigma and core RNA polymerase bind to promoter - unwinds DNA - nucleotides incorporated -- no primer required - 2 phosphates cleaved for each new nucleotide added - sigma released Elongation: - RNA polymerase continues adding nucleotides - unwinding at front of bubble and rewinding behind bubble - proofreading Termination- different genes can use different termination mechanism 1. RNA polymerase transcribes a terminator sequence, which consists pf a sequence that forms a hairpin structure in the RNA followed by several uracils in the RNA 2. the hairpin structure causes the RNA polymerase to pause 3. at this point, only A-U bonds (weak bonds) are holding DNA and RNA together -- DNA and RNA separate (13.14)

Answer 100

general transcription factors combine with RNA polymerase to form basal transcription factors. It is needed to initiate minimal levels of transcription other transcription factors bind to other DNA sequences and bring about higher levels of transcription by stimulating the assembly of the basal transcription apparatus at the start site

Answer 101

Core Promoter: - immediately upstream of a gene - basal transcription apparatus binds here, which is required for transcription - there are several consensus sequences within the core promoter that are recognized by many different proteins, but the important one to remember is the TATA box at -25 Regulatory Promoter: - immediately upstream of core promoter - affects rate of transcription - not required for transcription

Answer 102

Initiation (fig 13.6): - TFIID contains a TATA-binding protein (TBP) which binds to the TATA box within the core promoter - General TFs + RNA pol + mediator bind to the core promoter via TFIID - TBP of TFIID positions active site of RNA polymerase over the start site - other transcription factors: may bind to regulatory promoter, may bind to enhancers, affect transcription rate by interacting with the basal transcription apparatus via the mediator Elongation (fog 13.80: - similar to bacterial elongation Termination: - there are proteins that assist to remove the RNA polymerase and the RNA transcript from the DNA

Answer 103

exons are RNA coding regions, and the noncoding regions are called introns. All the introns and exons are initially transcribed into RNA but during or after transcription the introns are removed and the exons are joined to yield mature RNA.

Answer 104

common in eukaryotic genes but rare in bacterial genes introns have been observed in archaea, bacteriophages, and some bacteria present in mitochondrial and chloroplast genes as well as in the nuclear genes of eukaryotes.

Answer 105

1. Addition of the 5-cap 2. Addition of the poly(A) tail 3. RNA splicing

Answer 106

it occurs in eukaryotic cells within the nucleus

Answer 107

It is a guanine nucleotide added backwards (5’ to 5’ bond) to the 5’ end of the mRNA. then methyl groups are added to the mRNA Function: 1. assist with binding of ribosome to mRNA for translation 2. stabilizes mRNA

Answer 108

How: cleavage 11-30 nucleotides downstream of AAUAA consensus near 3’ end Polyadenylation: many adenines are added Function: increases stability of mRNA required for ribosome binding to 5’ cap

Answer 109

RNA splicing is the removal of introns. This takes place in the nucleus before the RNA moves to the cytoplasm. Splicing requires the presence of of 3 seuqneces in the intron ( 5’ splice site, 3’ splice site, and branch point)

Answer 110

splicesome is a large complex where splicing occurs consists of several snRNPs ( ‘snurps’ ) snRNP= 1 snRNA + proteins each snRNP plays a different role in the splicing process

Answer 111

alternative splicing is when the same pre-mRNA can be spliced in more than one way to yield different mRNAs that are translated into different amino acid sequences thus different proteins. Alternative splicing uses different combinations of exons

Answer 112

Two or more potential sites for cleavage and polyadenylation are present in pre-mRNA. mRNA products of different lengths are produced after splicing *the calcitonin gene is a good example but it doesn’t need to be memorized

Answer 113

defense mechanism against viruses regulation of gene expression *RNAi is only found in eukaryotes

Answer 114

Double-stranded RNA gets chopped up by the enzyme dicer The resulting RNA pieces are called microRNAs (miRNAs) or small interfering RNAs (siRNAs) miRNAs/siRNAs form a complex with proteins- this complex is called RISC RISC pairs with the target mRNA (because the miRNA/siRNA is complementary to the target mRNA) The target mRNA can no longer be translated Thus the mRNA has been ‘interefered’ with so that the gene that the mRNA came from will no longer be expressed (no protein produced)

Answer 115

it is like the immune system of prokaryotes they defend prokaryotic cells against invasion of foreign DNA (DNA from bacteriophages and plasmids)

Answer 116

- Foreign DNA (ie phage DNA) gets incorporated into the bacterial DNA – specifically it is inserted into a CRISPR array region of the bacterial genome - The CRISPR array gets expressed (transcribed into crRNA) - the crRNA and CAS protein form a complex - now when the foreign DNA enters the cell again, the crRNA-CAS complex will bind to it (because the crRNA is complementary to it) and CAS cuts the foreign DNA rendering it non functional

Answer 117

a set of nucleotides that encodes a single amino acid. They are the basic unit of genetic code.

Answer 118

genetic code is redundant: amino acids may be specified by more than one codon. Because there are 64 codons but only 20 amino acids; 1 amino acid may be specified by more than one codon

Answer 119

there are 61 different sense codons, but there are less than 61 different tRNAs. Wobble is a non standard base pairing at the third position of the codon (3’) and it allows 1 anti codon to pair with more than one codon

Answer 120

translation is how amino acids are assembled into proteins. Only mRNAs are translated into proteins

Answer 121

Translation takes place on the ribosomes. Ribosomes can be thought of as moving protein-synthesis machines.

Answer 122

- IF-3 bind to small ribosomal subunit - IF-3/small subunit bind to mRNA - the rRNA in the small subunit is complementary to Shine-Dalgarno sequence - tRNA carrying n-formyl methionine + IF-2 + GTP all come in together and and anticodon binds to start codon - IF-1 joins this complex - GTP is hydrolyzed to GDP and all IF's leave the complex - Large subunits join

Answer 123

- after initiation, the fMet-tRNA is in the P site of the ribosome - EF-Tu + GTP + charged tRNA enter A site - GTP hydrolyzed to GDP and EF-Tu/GDP leaves - peptide bind forms between amino acids in P and A sites (peptidyl transferase is the enzyme that does this) - tRNA in P site releases its amino acid so now the peptide chain is entirely on the tRNA at the A site - ribosome shifts down by one codon (translocation) with the help of EF-G and GTP - tRNA that was at the P site is now in the E site and then immediately leaves - A site in now available to receive the next charged tRNA and the cycle continues

Answer 124

- when a stop codon is in the A site, a release factor comes to the A site - another release factor joins the ribosome and all components are released

Answer 125

in prokaryotic cells transcription and translation are simultaneous; multiple ribosomes may be attached to the 5’ end of the mRNA while transcription is still taking place at the 3’ end. (mRNA molecules are translated simultaneously in both prokaryotes and eukaryotes but that is different)

Answer 126

an mRNA with several ribosomes attached is a polyribosome this occurs in both prokaryotes and eukaryotes

Answer 127

transcription can not take place when DNA is wrapped tightly around histone proteins because there is no room for the transcription machinery to fit and get by. Before transcription, chromatin structure changes so that DNA becomes more accessible to transcription machinery

Answer 128

1. Methylation of histones: - the addition of methyl groups to the tails of histone proteins. This results in activation or repression depending on which histone is modified. - Enzymes called histone methyltransferases add methyl groups to specific amino acids of histones. - enzymes called histone demethylases, remove methyl groups from histones. 2. Acetylation of histones: - the addition of acetyl groups to histones. This usually stimulates transcription - in general, acetyl groups destabilize chromatin structure allowing transcription to take place. - acetyl groups are added to the histones through acetyltransferase enzymes. - deacetylases strip acetyl groups from histones and restore chromatin structure, which represses transcription

Answer 129

DNA methylation is most common on cytosine bases adjacent to guanine nucleotides. -heavily methylated DNA is associated with the repression of transcription - when genes are not being transcribed CpG islands are often methylated, but the methyl groups are removed before the initiation of transcription. CpG methylation is also associated with long-term gene repression

Answer 130

DNA regions with many CpG sequences and they are commonly found near transcription start sites.

Answer 131

General transcription factors: bind to the core promoter and are part of the basal transcription apparatus. These are required for transcription

Answer 132

bind to regulatory promoter which is located upstream of the core promoter. They bring about higher levels of transcription by stimulating the assembly of the basal transcription apparatus at the start site

Answer 133

a group of proteins that assembles near the transcription start site and is sufficient to initiate minimal levels of transcription

Answer 134

Core promoter: located immediately upstream of a gene and is capable of minimal levels of transcription

Answer 135

Regulatory promoter: others transcription factors bind here and it is located upstream of the core promoter.

Answer 136

Enhancers are regulatory elements that affect the transcription of distant genes. In many eukaryotes, enhances are highly abundant. Enhancers usually regulate genes in a cell type specific manner- they turn on different sets of genes in different cell types and help establish the traits that characterize cells of different tissues. Silencers have an inhibitory effect on the transcription of distant genes.

Answer 137

- Regulatory promoters typically contain several different consensus sequences to which different transcription factors . Each promoter is regulated by a unique combo of transcription factors - The binding of transcription factors to the consensus sequences in the regulatory promoter affects the assembly or stability of the basal transcription apparatus at the core promoter - The mediator is a component of the basal transcription apparatus; it is a complex of proteins that interacts with RNA polymerase. Transcription factors that bind to sequences in the regulatory promoter (or enhancer) make contact with the mediator and affect the rate at which transcription is initiated

Answer 138

insulators are DNA sequences that block the effect of enhancers in a position-dependent manner. If an insulator lies between an enhancer and a promoter, it blocks the action of the enhancer, but if it lies outside that region it has no effect. Insulators are important because most enhancers are capable of stimulating any promoter in their vacinity

Answer 139

an inherited change in the DNA sequence of genetic information

Answer 140

an alteration of a single nucleotide in the DNA. It can be a transition or a transversion

Answer 141

transitions are when a purine is replaced by a different purine or a pyrimidine is replaced by a different pyrimidine. transversions are when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine. Transitions are more likely to happen than transversions

Answer 142

insertions and deletions are collectively called indels insertions and deletions are the addition or removal of one or more nucleotide pairs. these can cause frameshift mutations: changes in the reading frame of the gene. Frameshift mutations usually alter all amino acids encoded by the nucleotides following the mutation.

Answer 143

insertions or deletions consisting of any multiple of 3 nucleotides leaves the reading frame intact.

Answer 144

mutations in which the number of copies of a set of nucleotides increases

Answer 145

strand slippage is the misalignment of the sequences or stalling of replication. If a DNA molecule has 8 copies of a CAG repeat, the two strands separate and replicate. In the course of replication, a hairpin forms on the newly synthesized strand, causing part of the template to be replicated twice and increasing the number of repeats on the newly synthesized strand, causing part of the template to be replicated twice and increasing the number of repeats on the newly synthesized strand. The 2 new strands of the new DNA molecule separate. The strand with the extra CAG copies serves as a template for replication. The resulting DNA molecule contains five additional copies of the CAG repeats.

Answer 146

Number of copies of the repeat also correlates with its instability: when more repeats are present, the probability of expansion is more to even more repeats increases. diseases caused by expanding nucleotide repeats gets more severe with each generation (attenuation)

Answer 147

Missense mutation: the new codon encodes a different amino acid; there is a change in amino acid sequence Nonsense mutation: The new codon is a stop codon; there is a premature termination of translation Silent mutation: The new codon encodes the same amino acid; there is no change in amino acid sequence

Answer 148

a forward mutation alters the wild-type phenotype to a mutant a reverse mutation changes a mutant phenotype back into the wild type.

Answer 149

a missense mutation that alters the amino acid sequence of a protein but does not significantly alter its function.

Answer 150

these are mutations that cause partial or complete loss of normal protein function. This mutation alters the structure of the protein that the protein no longer works anymore.

Answer 151

this mutation causes the cell to produce a protein or gene product whose function is not normally present. Gain of function mutations are frequently dominant in their expression because a single copy of the mutation leads to the presence of a new gene product.

Answer 152

conditional mutations are expressed only under certain conditions

Answer 153

mutations that cause premature death.

Answer 154

It is a genetic change that hides or suppresses the effect of another mutation. A suppressor mutation occurs at a site distinct from the site of the original mutation; thus an individual with a suppressor mutation is a double mutant, possessing both the original mutation and the suppressor mutation this mutation can either be intragenic or intergenic

Answer 155

An intragenic mutation takes place in the same gene that contains the mutation being suppressed. This may work by the suppressor changing a second nucleotide in the same codon altered by the original mutation, producing a codon that specifies the same amino acid that was specified by the original, nonmutated codon. They can also work by suppressing frameshift mutation. Lastly, it may work by making compensatory changes in the protein. An intergenic mutation occurs in a gene other than the one bearing the original mutation that it suppresses. They sometimes work by changing the way the mRNA is translated. They can also work through gene interactions.

Answer 156

spontaneous mutations result under normal conditions induced mutations results from changes caused by environmental chemicals

Answer 157

Strand slippage occurs when one nucleotide strand forms a small loop. If the looped-out nucleotides are on the newly synthesized strand, it will cause an insertion. If the looped-out nucleotides are on the template strand, it will cause a deletion. Nucleotide repeat expansion occurs when repeats of nucleotides cause a hairpin structure to form on the newly synthesized strand (strand slippage). The more strand slippage happens, the more likely it is to occur again, causing expanding nucleotide repeats.

Answer 158

Misaligned pairing can cause unequal crossing over that results in one DNA molecule with an insertion and the other with a deletion.

Answer 159

depurination is the loss of a purine base form a nucleotide. This creates an apurinic site. In the absence of a base an incorrect nucleotide is incorporated into the newly synthesized DNA (usually adenine)

Answer 160

base analogs are a class of chemical mutagens with chemical structures similar to those of any of the 4 standard bases of DNA. If base analogs are present during replication, they may be incorporated into newly synthesized DNA molecules. If incorporated, it will pair with the wrong base, and then in the next replication, it will lead to a permanent mutation.

Answer 161

Ionizing radiation (X-rays, gamma rays, and cosmic rays): dislodge electrons from the atoms they encounter, changing stable molecules into free radicals and reactive ions, which alter the structures of bases and break phosphodiester bonds in DNA. It also frequently results in double-stranded breaks in DNA UV light: pyrimidine bases readily absorb UV light causing chemical bonds to form between adjacent pyrimidines on the same strand of DNA, creating pyrimidine dimers. These are bulky lesions that distort the configuration of DNA and often block replication.

Answer 162

intercalating agents produce mutations by sandwiching (intercalating) themselves between adjacent bases in DNA. This distorts the 3D structure of the DNA helix causing single nucleotide insertions and deletions in replication. These often produce frame shift mutations (since only one base is added or deleted) Ethidium bromide is an intercalating agent

Answer 163

DNA sequences that can move about the genome and they are often causes of mutations. Because they can move around they are also called jumping genes. Cause gene mutations and chromosome rearrangements

Answer 164

There are several mechanisms that repair errors and there is overlap between the mechanisms with respect to the types of mutations they repair.

Answer 165

DNA molecules cut with the same restriction enzyme have complementary sticky ends that pair if fragments are mixed together Nicks in the sugar-phosphate backbone of the two fragments can be sealed by DNA ligase

Answer 166

- Scientists have engineered crRNA from bacteria with a sequence that is specific to the target sequence of interest - The other part of the crRNA contains a sequence that pairs with CAS9 protein which creates a crRNA/Cas9 complex - This complex finds and binds to to the target DNA sequence - Cas9 makes double-stranded cuts within the target DNA sequence The cells DNA repair mechanisms kick in to try and repair the cut– 2 things can happen 1. Nonhomologous end joining is a repair pathway that repairs chromosome breaks but often causes insertions/deletions within the process – this would inactivate the gene 2. Donor DNA can be inserted into the cell with ends complementary to the break sequence– homologous recombination would insert this sequence to repair the gene

Answer 167

Gel electrophoresis separates molecules on a basis of size and electrical charge. DNA fragments are placed in the wells of the gel and an electrical current is passed through the gel (negative next to DNA positive at the bottom) DNA fragments move toward the positive end of the gel (because DNA is negatively charged). The smaller the DNA fragment the faster it moves.

Answer 168

- Taq polymerase (DNA polymerase) - dNTPs - Template DNA - Primers - Magnesium ions (to mimic cellular conditions)

Answer 169

1. DNA is heated to 90-100 C to separate the two strands 2. The DNA is quickly cooled to 30-65 C to allow short single-stranded primers to anneal to their complementary sequences 3. The solution is heated to 72 C; DNA polymerase synthesizes new strands, creating two new double-stranded DNA molecules 4. The entire cycle is repeated. Each time the cycle is repeated the amount of target DNA doubles

Answer 170

Produces identical copies of genes. Process: plasmid --> digest with restriction enzyme ---> join with DNA ligase ---> recombinant plasmid

Answer 171

1. the plasmid and foreign DNA are cute by the same restriction enzyme 2. when mixed, the sticky ends anneal, joining the foreign DNA and plasmid 3. nicks in the sugar-phosphate bonds are sealed by DNA ligase

Answer 172

the mechanism where bacterial cells take up DNA from the external environment. Inside the cell, the plasmids replicate and multiply as the cells themselves multiply

Answer 173

bacteria with an original (nonrecombinant) plasmid produce B-gal, which cleaves X-gal and makes the colonies blue Bacteria with a recombinant plasmid do not synthesize B-gal. Their colonies remain white Bacteria without a plasmid will not grow

Answer 174

Most next-generation sequencing technologies do sequencing in parallel, meaning millions of DNA fragments can be sequenced simultaneously. Illumina sequencing is the most widely used sequencing technology today. 1. Primers, DNA polymerase, and dNTPs are added to the flow cell. The primer attaches to the template 2. The first nucleotide is incorporated into the new strand. The tag is excited with a laser and fluoresces 3. The fluorescence is recorded by a computer. Thousands of fragments are sequenced and imaged simultaneously. 4. The tag and the terminator are removed 5. New dNTPs and polymerase are added 6. The next nucleotide is incorporated and excited with a laser

Answer 175

It is a technique used to identify individuals by examining their DNA sequences.

Answer 176

Most DNA fingerprinting uses microsatellites or short tandem repeats (STRs)

Answer 177

DNA samples are collected and subjected to PCR. The fragments are separated by gel electrophoresis. Different-sized fragments appear as different bands. 13 core STRs are used for DNA fingerprinting

Answer 178

RNAi can be used to silence genes by 1. designing siRNAs that will be recognized and cleaved by Dicer. The complementary sequence must be unique to the target mRNA and must not be found on other mRNAs. Next, the double-stranded siRNA is delivered to the target cells. The RNAi sequence has the potential to become a permanent part of the cell’s genome and be passed on to progeny

Answer 179

genetic maps provide a rough approximation of the locations of genes relative to the locations of other known genes. they are based on the process of recombination. They are measured in centimorgans genetic maps are low in details and they do not always correspond to physical distances between genes (there are sometimes discrepancies. Physical maps are based on the direct analysis of DNA and they place genes in relation to distances measured in number of base pairs. They generally have higher resolution and are more accurate than genetic maps.

Answer 180

only small fragments (500-700 bp) can be sequenced at a time. must fragment the genome into millions of small overlapping fragments for sequencing. difficulty ordering the sequenced genome

Answer 181

single nucleotide polymorphism is a site in the genome where individual members of a species differ in a single base pair (SNP) The specific set of SNPs and other genetic variants observed on a single chromosome or part of a chromosome is called a haplotype

Answer 182

genome-wide association studies use numerous SNPs scattered across the genome to find genes of interest. SNPs have been used in genome-wide association studies to successfully locate genes that influence many additional traits, such as height, body mass index, the age of puberty, etc. The genes identified often explain only a modest proportion of the genetic influence on the trait.

Answer 183

ab initio approach scans the sequence, looking for features that are usually found within a gene. Specific sequences mark the splice sites at the beginnings and ends of introns; other specific sequences are present in promoters immediately upstream of start codons. It looks for similarities between a new sequence and a sequence of all known genes.

Answer 184

annotation means linking its sequence information to other information about its function and expression, the protein it encodes, and similar genes in other species.

Answer 185

metagenomics is an emerging field in which the genome sequences of an entire group of organisms that inhabit a common environment are sampled and determined. it mostly applies to microbial communities. It provides the ability 1) the identification and study of microbes that cannot be cultured in the laboratory and 2) the study of the community structure of microorganisms.

Answer 186

homology search is used to determine gene function. It relies on comparisons of DNA and protein sequences from the same species and from different species. Homologous genes are genetically related genes

Answer 187

orthologs are homologous genes found in different species that evolved from the same gene in a common ancestor paralogs are homologous genes in the same species

Answer 188

Microarrays: rely on nucleic acid hybridization RNA sequencing: provides detailed information about gene expression, including the types and number of RNA molecules produced by transcription, the presence of alternatively processed RNA molecules, differential expression of the two alleles in a diploid individual, and different RNA molecules generated by bidirectional or overlapping transcription of DNA sequences.

Answer 189

used with cDNA, microarrays can provide information about the expression of thousands of genes, enabling scientists to determine which genes are active in particular tissues. A microarray consists of DNA probes fixed to a solid support, such as nylon. Each spot consists of a different DNA probe. Cancer and noncancer cells are removed from 78 women with breast cancer cells. mRNA from the cells is converted into cDNA and labeled with red or green nucleotides. The cDNAs are mixed and hybridized to DNA probes on a chip. The chip is scanned by spot. Yellow indicates equal expression of the gene in both types of cells. The microarray scan is converted to a heat map. Each spot represents the expression of one gene in one patient's tumor compared with the expression of that gene in noncancer cells.

Answer 190

- collect total RNA from cells - isolate mRNA -reverse transcribed into cDNA - fragment cDNA - sequence with next-gen sequencing - assemble sequences into RNA transcripts

Answer 191

biological evolution refers only to a specific type of change: genetic change happening taking place in a group of organisms. This includes only genetic change and it takes place in groups never just an individual step one: genetic variation arises second step: change in the frequencies of genetic variants

Answer 192

molecular variation: we can investigate evolutionary change directly by analyzing protein and nucleic acid sequences. Variation in protein and nucleic acid sequence is has a clear genetic basis and is easy to interpret.All organisms have certain molecular traits in common. These molecules offer a valid basis for comparisons among all organisms. Molecular data is quantifiable, which facilitates the objective assessment of evolutionary relationships. It can also reveal clues about the process of evolution

Answer 193

it is a widely used definition of a species. It defines species as a group of organisms whose members are capable of interbreeding with one another but are reproductively isolated from the members of other species. TLDR; members of the same species have the biological potential to exchange genes, and members of other different species cannot exchange genes. Because different species do not exchange genes, each species evolves independently

Answer 194

any biological factor mechanism that prevents gene exchange

Answer 195

Prezygotic: prevent gametes from two different species from fusing and forming a hybrid zygote. Includes 5 different types Postzygotic: gametes of two species may fuse and form a zygote, but there is no gene flow between the two species, either because resulting hybrids are inviable/sterile or because reproduction breaks down in subsequent generations. 3 different types

Answer 196

1. Ecological isolation: members of 2 species do not encounter each other so they do not reproduce with each other (dif ecological niches) 2. Behavioral isolation: differences in behavior prevent interbreeding (ex: dif mating calls) 3. Temporal isolation: reproduction in different species takes place at different times of year 4. Mechanical isolation: results from anatomical differences that prevent successful exchange of gametes 5. Gametic isolation: mating between individuals of different species may take place, but the gametes do not form zygotes

Answer 197

1. Hybrid inviability: incompatibility between the genomes of the two species prevents the hybrid zygote from developing. (ex: gamete forms but resulting embryos never complete development) 2. Hybrid sterility: hybrid embryos complete development but are sterile, so that genes are not passed between the two parental species. (ex: donkeys and horses make mules but mules are sterile) 3. Hybrid breakdown: species are able to mate and produce viable and fertile F1 progeny but further crossing of the hybrids produces enviable or sterile offspring

Answer 198

the process by which new species arise. It comes through the evolution of reproductive isolating mechanisms

Answer 199

Allopatric speciation: occurs when a geographic barrier splits the population into two groups and blocks the exchange of genes between them Sympatric speciation: speciation that arises in the absence of any external barrier to gene flow, reproductive isolating mechanisms evolve within a single population

Answer 200

Phylogeny: evolutionary relationships among a group of organisms Phylogenetic tree: a graphical representation of phylogeny Branches: evolutionary connections between organisms Nodes: points where the branches split, representing a common ancestor that existed before divergence took place Rooted: A tree is rooted when one node represents a common ancestor to all other nodes on the tree Gene tree: shows evolutionary relationship among prolactin and somatropin genes in vertebrates (evolutionary relationship among a group of genes)

Answer 201

They do not respond to normal cell cycle controls They rob healthy tissues of nutrients

Answer 202

distinct mass of abnormal cells.

Answer 203

When the tumor cells remain localized

Answer 204

When the tumor cells invade other tissues

Answer 205

When the tumor cells have traveled to other sites in the body and established secondary tumors.

Answer 206

- Genetic disease: cancer cells arise from defects of DNA - Not genetic disease: if cancer is inherited, every cell in body should have the cancer-causing gene and every cell should become cancerous; however, tumors typically appear only in certain tissues - Not a genetic disease: many cancers do not run in families - Not a genetic disease: huge environmental influence

Answer 207

Suggests that cancer is the result of a multi-step process that requires several mutations. If one or more of the required mutations are inherited, fewer additional mutations are required to produce cancer and the cancer tends to run in families. In retinoblastoma, only two mutations are necessary to cause the tumor. In the case of retinoblastoma, the two required mutations occur at the same locus, but mutations at different loci are required for the development of many other cancers.

Answer 208

- as cells acquire more mutations, they become the dominant cell type within the tumor - examples of these mutations: - DNA repair pathway - chromosome segregation (many cancer cells are aneuploids) - structural change that allows cell to invade other tissues

Answer 209

- Chemical mutagens and radiation can mutate genes that predispose a cell to cancer (we talked about how these environmental factors cause mutations in Ch 18) - Environmental factors can interact with genetic predispositions to cancer; ie some people carry a genetic variant of a gene that predisposes them to lung cancer, so smoking would further increase the chance for these people to develop lung cancer

Answer 210

- Oncogenes and tumor-suppressor genes - Genes that control the cell cycle - DNA repair genes - Telomerase - Genes that promote vascularization and tumor spread - miRNAs

Answer 211

Normal cellular genes are called proto-oncogenes. They are responsible for basic cellular function or normal cells, but when mutated, they become oncogenes that contribute to the development of cancer.

Answer 212

proto-oncogenes that have been mutated that contribute to the development of cancer

Answer 213

Genes that inhibit cancer and are recessive. Both alleles must be mutated before the inhibition of cell division is removed. Because the failure of their function promotes cell proliferation, tumor suppressor genes cannot be identified by adding them to cells and looking for cancer. Defects in both copies of a tumor suppressor gene are usually required to cause cancer.

Answer 214

the cell cycle needs stimulatory (proto-oncogenes) and inhibitory (tumor-suppressor genes) signals to function properly

Answer 215

Car has accelerator (proto-oncogene) and brake (tumor-suppressor gene). The car will be uncontrollable if the accelerator becomes hyperactive or if the brake does not work. A bad mechanic (defective DNA repair pathway) would not be able to fix the accelerator/brake

Answer 216

- cyclins and CDKs are proteins that regulate checkpoints of the cell cycle; mutations in the genes that encode these proteins can cause the disruptions in normal cell cycle control, leading to cancer - external signals (hormones and growth factors) trigger a cascade of intracellular reactions that ultimately stimulate/inhibit cell cycle (signal transduction pathway); a mutation in genes that play a role in any of these reactions can lead to cancer

Answer 217

Activation of the enzyme telomerase can contribute to the progression of cancer. Telomerase becomes shorter with each cell division. The shortening eventually leads to the destruction of the chromosomes and cell death. In many tumor cells, sequences that regulate the expression of the telomerase gene are mutated, allowing the enzyme to be expressed and the cell is capable of unlimited cell division. This allows cancer cells to divide indefinitely.

Answer 218

Oxygen and nutrients are essential to the survival and growth of tumors are supplied by blood vessels, and the growth of new blood vessels (angiogenesis) is important to tumor progression. In tumor cells, genes encoding these proteins are often overexpressed compared with normal cells and inhibitors of angiogenesis-promoting factors may be inactive or under-expressed.

Answer 219

miRNAs are important in controlling gene expression and development. Many tumor cells exhibit widespread reduction in the expression of many miRNAs Lowered levels of miRNAs may contribute to cancer by allowing oncogenes that are normally controlled by the miRNAs to be expressed at high levels. Overexpression of miRNAs can also be associated with cancer. Several miRNAs have been implicated in the process of metastasis

Answer 220

- hypomethylation may activate oncogenes - hypermethylation may silence tumor-suppressor genes

Answer 221

many cancers arise through the sequential mutation of a number of genes. An example of this is seen with colon cancer (Fig 23.10—don’t memorize this figure)

Answer 222

Many cancer cells have chromosomal mutations. - Cause: some cancers are associated with specific chromosome mutations - Effect: most cancer cells have chromosomal mutations that result from the cancer

Answer 223

- Deletion of tumor-suppressor gene - Inversions - Translocations

Answer 224

- Both of these require breaks within the chromosome. Cancer may result if the breakpoints lie within a tumor-suppressor gene, which would mutate the tumor-suppressor gene - Both of these can rearrange the chromosome and may bring together sequences that stimulate cancer - For example, the rearrangement may place a cancer-causing gene under a different regulatory sequence that would upregulate its expression (Fig 23.11 and 23.12 give examples but don’t memorize these)

Answer 225

- Most cancer-causing viruses are retroviruses but some are also DNA viruses

Answer 226

Two different ways: mutating or rearranging proto-oncogenes or by inserting strong promoters near proto-oncogenes Mutating or rearranging proto-oncogenes: 1. A retrovirus inserts its RNA into the cell. The viral RNA undergoes reverse transcription and inserts into the host chromosome next to a proto-oncogene. 2. When the virus reproduces, the proto-oncogene is incorporated into the virus. 3. After repeated rounds of viral infection and reproduction, the proto-oncogene becomes rearranged or mutated or both, producing an oncogene that is inserted back into the host chromosome. Inserting strong promoters near proto-oncogenes Retrovirus infects the cell and the provirus inserts near a proto-oncogene. The strong viral promoter stimulates overexpression of the proto oncogene.

Answer 227

1. Theta model: common in bacteria (fig 12.4) 2. Rolling circle model: some viruses and bacteria (12.5) 3. Linear model: eukaryotic chromosomes (fig 12.6)

Answer 228

New DNA is synthesized from deoxyribonucleicoside triphosphates (dNTPs)

Answer 229

dATP dTTP dGTP dCTP

Answer 230

- In replication, the 3'-OH group of the last nucleotide on the strand attacks the 5'-phosphate group of the incoming dNTP. - Two phosphates are cleaved off. - Phosphodiester bond forms between the two nucleotides.

Answer 231

Nucleotides added to 3'-OH of growing chain; so chain grows in a 5' to 3' direction. Template strand is read in a 3' to 5' direction because it is antiparallel to the new strand.

Answer 232

- Because two template strands are antiparallel, and DNA synthesis is always 5' to 3'. DNA synthesis proceeds from right to left on one strand and from the left to right on the other strand. - On the lower template strand, DNA synthesis proceeds continuously in the 5' to 3' direction (the same way it is unwinding) - On the upper template strand, DNA synthesis begins at the fork and proceeds in the direction opposite of unwinding, so it soon runs out of template. DNA synthesis starts again at the fork on the upper strand, each time proceeding away from the fork. DNA synthesis on this strand is discontinuous

Answer 233

1) initiation (Fig 12.11) 2) unwinding (Fig 12.12) – Helicase – SSBs – Gyrase (topoisomerase) 3) elongation (Fig 12.13, 12.14) - DNA polymerase: requires 3’ OH in order to add a nucleotide - DNA polymerases in bacteria: - *DNA Polymerase III - synthesizes DNA from primers: *- 5’→ 3’ polymerase activity (DNA synthesis), *- 3’→ 5’ exonuclease activity (proofreading), *- High processivity: can add many nucleotides,* - DNA Polymerase I - removes and replaces primers: *- 5’ → 3’ polymerase activity, *- 3’ → 5’ exonuclease activity, *- 5’ → 3’ exonuclease activity (remove primers), *- DNA Polymerase II, IV, V - DNA repair - Primase: creates primer (RNA) to initiate DNA synthesis - Primase = RNA polymerase; does not require 3’ OH - Ligase 4) termination - Usually occurs when replication forks run into each other

Answer 234

telomerase is present in single-celled eukaryotes, germ cells, early ebryonic cells, and certain proliferative somatice cells, all of which must undergo continuous cell division Most somatic cells have little or no telomerase activity; these cells are capable of only a limited number of cell divisions Telomerase appears to play a role in cancer. cancer cells have the capactiy to divide indefiniely and telomerase is expressed in 90% of all cancers

Answer 235

- The telomere has a protruding end with a G-rich repeated sequence - The RNA part of telomerase is complementary to the G-rich strand aand it pairs with it, providing a template for the synthesis of copies of teh repeats - nucleotides are aded to the 3' end of teh G-rich strand - After several nucleotides have been added, the RNA template moves along the DNA - more nucloeitdes are added - the telomerase is removed - synthesis takes place on the complementary strand, filling the gap due to the removal of the RNA primer at the end