Exam 1 Flashcards

Question

DNA polymerase

Answer 1

an enzyme that synthesizes DNA from a DNA template

Answer 2

an enzyme that synthesizes RNA using a DNA template

Answer 3

an enzyme that synthesizes DNA using an RNA template - used by some viruses

Answer 4

* complementary base pairing between two different strands of nucleic acids * DNA to DNA * DNA to RNA * RNA to RNA

Answer 5

complementary base pairing between different sections of the **same** nucleic acid * RNAs * tRNA

Answer 6

* heating causes the two strands of a DNA duplex to separate or denature * melting temperature (Tm) - the midpoint of the temperature range for denaturation * reduce temperature - complementary single strands can renature or anneal (hybridize)

Answer 7

* denature a known DNA and attach to a solid filter * denature unknown DNA in solution * mix - if DNAs have similar sequences, they will anneal * the ability of two single stranded nucleic acids to hybridize is a measure of their **complementarity**

Answer 8

* DNA-DNA * DNA-RNA * RNA-RNA it can be intermolecular or intramolecular

Answer 9

changes in the sequence of DNA may occur - spontaneously - or induced by mutagens

Answer 10

* chemicals that can cause mutations * radiation (UV, gamma)

Answer 11

**changes a single base pair** _may be due to_ * chemical conversion of one base into another * or errors that occur during replication

Answer 12

a type of point mutation * replaces a G-C base pair with an A-T base pair or vice versa

Answer 13

type of point mutation * replaces a purine with a pyrimidine, such as changing A-T to T-A

Answer 14

the movement of **transposable elements** (DNA segments that can be inserted in chromosomes

Answer 15

alter the function of a gene

Answer 16

reverse their effects

Answer 17

deletion of the inserted material

Answer 18

* suggested by Beadle and Tatum in 1940s * a gene is a stretch of DNA encoding one or more isoforms of a _single_ polypeptide chain

Answer 19

a molecular complex (such as a protein) composed of **different** subunits

Answer 20

a molecular complex (such as a protein) composed of **identical** subunits

Answer 21

**a modified version** * a gene is responsible for the production of a single polypeptide * then polypeptides are put together to form the enzyme but: most genes do not encode polypeptides, but encode **structural or regulatory RNAs**

Answer 22

* multiple alleles - wild type = w+ (red eye) - various mutants: W^h (honey eye) * since have 2 homologous chromosomes * allows for heterozygotes with any pairs of combination of alleles

Answer 23

* a locus may be **polymorphic** in alleles * no individual allele is considered to be the only wild type

Answer 24

* it's the code on mRNA (DNA>mRNA>protein) * the **genetic code** is read in _triplet nucleotides called codons_ * the triplets are _non-overlapping_ and are read from a fixed starting point each codon triplet codes for: - a specific amino acid - or a stop codon

Answer 25

**yes** ex: UUU and UUC code for Phenylalanine

Answer 26

* insertion or deletion of bases * cause a _shift_ in the triplet sets after the site of mutation

Answer 27

* insertion or deletion of three bases (or multiples of three) * inserts or deletes amino acids * but reading (or AA sequence) remains the same _after_ the third insertion/deletion * **they happen after the deletion of 4 bases**

Answer 28

* a sequence of DNA consisting of triplet codons that can be translated into a string of amino acids * starts with an **initiation codon** and end with a **termination (stop) codon**

Answer 29

**three** * usually only one of the three possible reading frames is translated * the other two are closed by frequent termination signals (stop codons)

Answer 30

* functional mRNA * ribosome - a large complex of ribosomal RNA and proteins that synthesize polypeptides using an mRNA template * tRNAs

Answer 31

* a tRNA has an **anticodon** sequence that is complementary to the **codon** representing an amino acid * each tRNA molecule is linked to that amino acid

Answer 32

* protein coding genes * regulatory sequences * epigenetics

Answer 33

gene regulation

Answer 34

* proteins that regulate gene transcription bind to control sites next to the coding regions

Answer 35

sites located on the same DNA strand

Answer 36

sites located on different DNA strands

Answer 37

* all gene products (RNA or polypeptides) are **trans-acting** * they can act on any copy of a gene in the cell * regulatory proteins are trans-acting - they act on _any_ gene regulatory region - copies of the same protein can act on _both_ homologous alleles * a cis-acting DNA site controls expression of the adjacent DNA - but does not influence the homologous allele on the other chromosome * a mutation in the control site of a gene is cis-acting - affects the adjacent gene - does not affect the homologous allele * a trans-acting mutation in a gene for a regulatory protein affects both alleles of a gene that it controls

Answer 38

* cloning genes by placing a gene DNA from one organism into another DNA or organism to allow it to be replicated -ex: placing a mouse enzyme gene into a bacterial plasmid * creates recombinant DNA - a DNA molecule composed of sequences from two (or more) different sources

Answer 39

* direct manipulation of an organism's genome through the use of biotechnology to insert or delete genes * often involves the production and use of recombinant DNA to transfer genes between organisms

Answer 40

* enzyme that recognizes short specific sequences of DNA and cleaves the duplex * it cleaves sometimes at the target site, sometimes elsewhere, depending on type of enzyme

Answer 41

* hydrolyze phosphodiester bonds * separates the nucleotides

Answer 42

* nuclease that cleaves phosphoester bonds **within** a nucleic acid chain * breaks the chain * it may be specific for RNA or for single-stranded or double-stranded DNA * cleave within the strand

Answer 43

* nuclease that cleaves phosphoester bonds one at a time **from the end** of a polynucleotide chain * chews off nucleotides from the end * it may be specific for either the 5' or 3' end of DNA or RNA * cleave at the terminal nucleotide

Answer 44

* broad specificity e.g. exonuclease that cleaves any nucleotide from the end of DNA e.g. pancreatic RNase = cleaves RNA after any pyrimidine * sequence specific - restriction endonucleases -Type I, II, and III

Answer 45

* most common * many derived from bacteria - EcoRI from E.coli * recognition sites are 4-8 bp * sites are typically **inversely palindromic** - reads the same forward and backward

Answer 46

cut DNA in **two** different ways: * **staggered cut** -leaves "sticky ends" of complementary bases * **blunt ds cut** -no sticky ends

Answer 47

* a map can be generated by using the overlaps between the fragments generated by different restriction enzymes * used to find sites of restriction enzymes in your DNA

Answer 48

**cloning** - to make an identical copy of something - DNA, Dolly the sheep etc. - cloning DNA uses **recombinant DNA** **what you need to clone DNA** - an _insert_ : the gene or DNA fragment you want to clone - a _cloning vector_

Answer 49

* bacteria have two different types of DNA 1) **circular chromosome**: genes for the bacteria to function 2) **plasmids** - small circular dsDNA - often contain survival genes - antibiotic resistance - ARGs - self replicating

Answer 50

* a genetically engineered modified plasmid * DNA that can be used to propagate an incorporated DNA sequence in a host cell * often derived from a **plasmid** or a **bacteriophage** (virus that attacks a bacteria)

Answer 51

* replication origins * selectable markers * known restriction enzyme sites

Answer 52

* **ORI** (origin of replication initiation) * where DNA replication can start * allows replication of the plasmid

Answer 53

* allows you to identify cells that contain the plasmid * Ampicillin Antibiotic resistance gene * lacZ gene

Answer 54

* **multiple cloning site (MCS)** e.g EcoRI

Answer 55

* a plasmid section containing a _series of tandem restriction endonuclease sites_ used in cloning vectors for creating recombinant molecules

Answer 56

* fragments of genomic DNA that has been treated with restriction enzymes - size selected from an agarose gel * a PCR fragment - specific DNA selected and amplified by PCR * DNA fragments synthesized in the lab

Answer 57

1. cut the insert DNA and the plasmid DNA with the **SAME** restriction enzyme - easiest if use an enzyme that makes sticky ends 2. mix the insert and plasmid - allows sticky ends to hybridize - insert sticky ends anneals to the sticky ends of the plasmid 3. add **DNA ligase** enzyme - seals the phosphodiester bonds 4. the plasmid circle is now - sealed - may contain the insert - may be larger than before *Note*: the insert has disrupted the lacZ gene

Answer 58

* use the bacteria to replicate the plasmid **transformation** - the process of introducing the DNA into a cell

Answer 59

method for transformation **competent cell** = capable of taking in DNA 1. **high salt wash of calcium chloride** (CaCl2) - creates small holes or pores in the bacteria cell wall - allows the DNA to bind to the bacteria to be taken into the cell 2. **electroporation** - add the bacteria and the plasmid to a small chamber - add an electrical current to the liquid - creates small holes or pores in the cell wall - allows the DNA to be taken into the cell *note*: both methods will transform only a fraction of the cells grow the bacteria on agar with Ampicillin (only bacteria with plasmid will grow)

Answer 60

* plasmid has **lacZ gene** -codes for bacterial gene for beta-galactosidase enzyme -cleaves lactose sugar -also will cleave X-gal * **multiple cloning site** is in the **middle** of the lacZ gene -cloning a DNA insert into the MCS will disrupt the lacZ gene

Answer 61

* bacteria without the plasmid will not grow why? - agar has ampicillin and only bacteria with plasmid will survive * bacteria with the empty plasmid -colonies will be **blue** * bacteria with the insert, has disrupted lacZ -colonies will be **white** * so white colonies are the ones we want!

Answer 62

1. plasmid inserted into the plasmid - disrupts the lacZ = white colonies - but no insert 2. insertion of random, non-target DNA - disrupts the lacZ = white colonies solution: * collect the plasmids * restriction enzymes to remove the insert * agarose gel to confirm size of the insert * sequence the insert

Answer 63

if need to clone larger DNA segments * **bacteriophage vector** -infects the bacteria and inserts the DNA into the bacterial chromosome -package larger DNA segment -can get the bacteria to express or produce the gene product * **cosmid** -plasmid with insertion sequences of a bacteriophage -combines best of both * **YAC** (yeast artificial chromosome) -use yeast as the host

Answer 64

* control regions of genes contain **promoters** -the region of DNA where the RNA polymerase binds to start transcription * for genes in plasmids/vectors to be: -to be replicated = need ORI -to be expressed (the protein produced) = need a promoter * **expression vectors** contain promoters that allow _transcription_ of any cloned gene

Answer 65

1. continuously active (constitutive) promoters 2. inducible promoters

Answer 66

* if it is in the vector, the inserted DNA will be transcribed and the protein produced **ALL THE TIME** * use to have the bacteria/yeast/eukaryotic cell produce your protein - recombinant protein: protein produced from recombinant DNA - e.g. recombinant insulin produced by biotech company

Answer 67

* the inserted DNA will only be transcribed when the promoter is turned on * so, transform the bacteria/yeast/eukaryotic cell * then you determine when to turn on the gene expression - provide a chemical/hormone/etc. that turns on the promoter

Answer 68

* a gene attached to a promoter and/or your gene * its product is an easily identified protein * can show **when** and **where** the gene or promoter is activated - used to measure **promoter activity** or **tissue-specific expression**

Answer 69

* insert your gene between the plasmid expression promoter and the lacZ gene -when your protein is produced, it will be linked to beta-galactosidase enzyme * transform your bacteria/yeast/mammalian cell * add X-gal * wherever your protein is found, blue stain will be seen *your protein attached to B-galactosidase*

Answer 70

* insert your **promoter and gene** in front of the lacZ gene -your gene and the lacZ gene are under control of your _promoter_ -when your promoter is activated, your protein will be linked to beta-galactosidase enzyme * transform - add X-gal * wherever your protein is **produced**, blue stain will be seen

Answer 71

* green fluorescent protein (GFP) -protein from the *Aequorea victoria* jellyfish -is a green fluorescing protein * genetically mutated variations -YFP - yellow -CFP - cyan

Answer 72

* fluorescent molecules absorb light at excitation wavelength * give off light at emission wavelength -lower energy -longer wavelength

Answer 73

* DAPI - stains DNA * CFP * GFP * FITC - replaced by Cy2/Alexa488

Answer 74

fluorescent DNA and RNA stains - ethidium bromide - DAPI - propidium iodide * bind to the nucleic acid and fluoresce * stain ALL nucleic acid * cannot distinguish your gene from all other DNA

Answer 75

* based on the specific DNA sequence * use **nucleic acids hybridization and complementary base pairing** * **probe** -short DNA or RNA segment of known sequence of the gene you are looking for -radioactively label the short DNA used to identify a complementary binding DNA or RNA

Answer 76

* synthesizes a short DNA sequence that matches your gene * label the probe

Answer 77

1. radioactive phosphorous - can use radioactive tritium * end labeling -use phosphorous and a kinase to add the phosphate to the end * labeling by incorporating a 32P labeled nucleotide -DNA synthesis using DNA polymerase -polymerase chain reaction (PCR) 2. fluorescent labeled nucleotides

Answer 78

separating the DNA duplex strands * must overcome the stable hydrogen bonds of base pairing * more G-C content = more stable * high temperature "melts" the DNA * low salt concentrations -high salt = Na+ stabilizes the phosphate backbone -low salt = negative charged phosphates in backbone repel each other

Answer 79

**autoradiography** a method of capturing an image of radioactive materials on a photographic film * ethidium bromide stains **all** DNA * autoradiograph shows **only** the radioactive probe labeled DNA binding to the complementary DNA

Answer 80

**agarose gel electrophoresis** * uses agarose as a matrix gel -can use polyacrylamide * uses an **electric current** to cause the DNA to migrate toward a positive charge * remember - DNA has a negative charge due to phosphate backbone * separates DNA fragments by **size** (smaller travel faster = end up further) * compare to migration of known DNA size standards

Answer 81

* transfer the separated DNAs to: -a stronger matrix -an easier to manipulate matrix * nitrocellulose membrane -good but easily cracks * nylon membrane -strong

Answer 82

* invented by Dr. Edwin Southern * transfer of **DNA** from a gel to a membrane (in alkaline solution to denature the DNA) * followed by detection of specific sequences by hybridization with a labeled probe

Answer 83

* involves the transfer of separated **RNA** from a gel to a membrane

Answer 84

* separation of **proteins** on a sodium dodecyl sulfate (SDS) gel * transfer to a nitrocellulose membrane * detection of proteins of interest using antibodies * proteins are separated by size

Answer 85

* many types of RNA 1. primary RNA transcripts 2. mRNA 3. tRNA 4. rRNA 5. small heterogeneous RNAs * mRNA always have a poly-adenylated tail - string of deoxyAdenines added to the 3' end * can isolate mRNA from everything else by using Oligo (dT) bound to beads - short strands of **deoxy Thymidine**

Answer 86

* oligo (dT) bound to Sepharose beads * packed into a small column * add RNA mixture to the column - mRNA binds to the Oligo(dT) * wash out the other RNAs to pass through * then pass through denaturing solution to wash out mRNA

Answer 87

* developed by Kary Mullis - Nobel prize in 1993 * continuous cycling of - denature DNA - hybridize primers - allow polymerase to copy the DNA - repeat 20-40 times * _exponential_ amplification of a desired sequence

Answer 88

* DNA primers that flank the gene you want - single stranded primers complementary to 3'-->5' end of gene on each strand of DNA - primers run 5'-->3' - 18 to 25 bases long - easily synthesized (purchased)

Answer 89

* a DNA or RNA template * a free 3' end to add nucleotides to -satisfy this using primers * must know sequence to make the primers * target DNA -genomic DNA containing a gene you want -pieces of DN of a gene you want * Taq polymerase -from *Thermus aquaticus* bacterium -lives in very hot springs -very temp resistant -works best at 72 degrees * excess of the four deoxynucleotides (dNTPs) to make DNA

Answer 90

A. mix template, primers, Taq, and dNTPs B. heat to 95-100 degrees * melts (denatures) the DNA template * 15 seconds C. rapidly cool to temperature optimal for primers to anneal to template * too low = primers anneal anywhere * too high - primers won't anneal * is different for each set of primers * 30 seconds D. heat to optimal temperature for Taq polymerase to function * 72 degrees * 30 seconds _Result_: - one new copies of the target gene - plus the original copy repeat 20-40 cycles * 2nd cycle - 4 copies of the gene * 3rd cycle - 8 copies of the gene, now see copies that are only the gene plus the primers * by 20 cycles - almost all are the gene+primers only, up to a million copies

Answer 91

* must be long enough to be specific for your DNA only * usually ~20 nucleotide sequence is specific * for any 20 nucleotide sequence -occurs ONCE in 4^20 nucleotides -human genome is 3.2x10^9 base pairs -so will occur only once in the genome -many use 23 to 25 nucleotides for primers

Answer 92

* MUST know nucleotide sequences at the ends of the DNA to be amplified * amplify short DNAs without having to use plasmids and cloning -works great for single genes or gene sequences -does not work for large DNAs or genomic DNA -generally best with 100 to 500 bp of DNA * isolate DNA segments from mutants * excellent for producing DNAs for cloning in E.coli * use to label DNA for probes -add fluorescent dNTP * identify bacteria/virus/infection

Answer 93

* transcribes single-strand RNA into single-strand complementary DNA **(cDNA)** * from retroviruses * transcribe viral RNA into cDNA * integrate viral DNA into the host genome * requires a DNA primer -short strand of DNA complementary to the RNA to be copied

Answer 94

1. oligo(dT) primer for mRNA 2. random primers for any RNA - mixture of short random sequences (usually hexomers) 3. gene-specific primers for specific RNAs - determined from the gene sequence

Answer 95

* isolate RNA * reverse transcribe to cDNA -use oligo(dT) for mRNA -makes cDNA from _ALL mRNA_ only * add specific PCR primers, dNTPs, and Taq polymerase -first round copies ONLY the specific cDNA to be dsDNA -subsequent rounds amplify the specific cDNA

Answer 96

* detects the PCR _products_ during PCR amplification - fluorescent dye to label dsDNA * allows monitoring the increase in fluorescent labeled PCR products * is more sensitive and quantitative than conventional PCR * can now make copies for jsut about any gene by cloning and expanding E.coli or PCR

Answer 97

Yes! DNA microarrays * backwards of the southern/northern blots * immobilize the known DNAs (different genes) on a membrane * then add the labeled unknown nucleic acid sample * see where the labeled nucleic acids bind (hybridize)

Answer 98

* initially, 30-100 different DNAs "spotted" on membranes and dried * 1000 DNAs spotted onto glass slides * thousands to millions of DNAs spotted onto silicon chips * use fluorescent labels instead of autoradiography -allows better resolution -automated optical microscopy for detection * allows comparisons -experimental to control -disease versus normal

Answer 99

* label control mRNA/cDNA with green during reverse transcription * label experimental mRNA/cDNA with red * mix together and add to the microarray * ssDNAs bind to specific gene DNAs on the DNA chip * wash and scan

Answer 100

* usually continuous sequences of nucleotides * encodes the amino acids to create a polypeptide **NOT TRUE FOR EUKARYOTES**

Answer 101

* the coding sequences are _not_ continuous * coding regions of eukaryotic genes are interrupted by segments of _non coding_ regions *note*: not necessarily true for yeasts

Answer 102

the DNA sequences of the gene that code for the gene product (polypeptide or RNA)i

Answer 103

* a segment of DNA that does **not** code for the product * lie between exons

Answer 104

* the original _unmodified_ RNA product that is transcribed - contains the exons and the introns - is only a _precursor RNA_ * it is NOT the final mRNA

Answer 105

* a mature mRNA is made by **RNA splicing** of the primary RNA transcript * the process of -excising introns from RNA -then connecting the exons into a continuous mRNA

Answer 106

primary RNA transcript is equal to the **entire gene** minus the **control DNA sequences**

Answer 107

**cis** * affects only _within_ the same RNA * does not affect other RNAs * exons remain in the same order in mRNAs as in DNA, but _distances along the gene_ are not the same as those of mRNA or polypeptide products

Answer 108

* mutations in exons can affect polypeptide sequence * mutations in introns do not directly affect the polypeptide sequence - but may affect RNA processing - mutations at the exon-intron junctions may affect the splicing event - point mutations may yield stop codons affecting the final protein

Answer 109

* compare the gene to the mRNA - usually compare DNA gene to cDNA of the mRNA **restriction mapping** - treat gene DNA and cDNA with the same restriction enzyme(s) - restriction sites in the gene and mRNA/cDNA are the same in exons - restriction sites in introns are missing in the mRNA/cDNA * introns can also be detected by **sequencing the gene and the cDNA**, then matching the two together

Answer 110

**no** an intact open reading frame is created in the mRNA sequence by removing the introns

Answer 111

* genes coding for polypeptides, rRNA, and tRNA can all have introns * introns have been found in every class of eukaryote * introns are rare in prokaryotic genes * animal mitochondria do not have introns - but some plants, fungi, and protists do

Answer 112

e.g. mammalian genes for dihydrofolate reductase * the **number** of exons and introns is maintained * the **relative position** of the introns to the exons is maintained * but the **length** of the exons and especially the introns **can vary**

Answer 113

* normally, **exon** sequences do not vary much from species to species for the same gene * sequences of **introns** show differences from species to species for the same genes **why?** * introns lack of selective pressure to produce a polypeptide with a useful sequence * while exons must produce a useful product (not always true for exons producing beneficial mutations)

Answer 114

**1. alternative start codons in the same reading frame** * alternative initiation or termination codons allows multiple variants of a polypeptide chain * produces a _short form_ and _full-length_ form of the polypeptide **2. overlapping gene** - a gene in which part of the sequence is found _within_ part of the sequence of another gene * different polypeptides can be produced from the same sequence of DNA * the mRNA is read in **different reading frames** (as two overlapping genes) so _sequence is different_ * found in some viral and mitochondrial genes **3. alternative splicing of the primary transcript** * one gene may be alternative spliced to exclude exons or choose between alternative exons * yields otherwise identical polypeptides, differing by the presence or absence of certain regions

Answer 115

* a discrete part of an amino acid sequence that has a particular function (e.g. the immunoglobulin domain) * exons may be **functional building blocks** of genes * genes that share related exons may code for proteins with similar functions * possibly suggests a common exon ancestry * low-density lipoprotein (LDL) - gene has 18 exons * gene has similar exons as - complement 9 - EGF

Answer 116

* a set of genes within a genome that encodes _identical or related_ proteins of RNAs * the members were derived by duplication of an ancestral gene * followed by accumulation of changes in sequence between the copies - most often the members are _related_ but _not identical_

Answer 117

* a set of genes all related by presumed descent from a common ancestor, but now showing _considerable_ variation * myoglobin = oxygen binding protein in animals * similar amino acid sequence to alpha globin and beta globin * leghemoglobins = oxygen binding protein in legume plants together make up the **Globin Superfamily**

Answer 118

* similar exons * Leghemoglobin gene has an extra intron * suggests they are descended from a single ancestral gene

Answer 119

* related genes in different species * should share common features that preceded their evolutionary separation * rat has two different genes for insulin * one similar to chicken insulin gene * one missing an intron * suggests the 1-intron gene evolved from the other

Answer 120

* the complete set of DNA sequences in the genetic material of an organism * it includes the sequence of each chromosome plus any DNA in organelles

Answer 121

* the complete set of RNAs present in a cell, tissue, or organism * its complexity is due mostly to mRNAs, but it also includes noncoding RNAs * mRNAs, tRNAS, rRNAS, microRNAs, etc

Answer 122

* the complete set of proteins expressed by the entire genome * also could be the proteins expressed by a cell at any one time

Answer 123

* the complete set of protein complexes and protein-protein interactions present in a cell, tissue, or organism * multiproteins or complexes * DNA and RNA polymerase haloenzymes * enzymes clustered into metabolic pathways

Answer 124

* based on the _frequency of recombination_ between genetic markers * monitoring genetic cross-over occurrence and the resulting phenotype

Answer 125

* based on the _physical distances_ between markers * using restriction enzymes

Answer 126

DNA is sequenced to identify the position of functional genes, introns, exons, etc.

Answer 127

variation in sequence between individuals can be seen: * at the **phenotypic level** when a sequence affects gene function or a characteristic (variations in eye color) * at the **restriction fragment** level when it affects a restriction enzyme target site * at the **sequence level** by direct analysis of DNA - however, a different in gene sequence may not result in a difference in phenotype

Answer 128

**may change the DNA sequence but:** * NOT change the polypeptide sequence -redundant codons -changes in introns * change the polypeptide sequence but NOT change the polypeptide function -amino acids with similar characteristics * may change the polypeptide function * result in altered polypeptides that are not functional

Answer 129

* a polymorphism caused by a change in a **single nucleotide** * responsible for most of the genetic variation between individuals

Answer 130

the particular combination of alleles in a defined region of some chromosome; in effect, the genotype is miniature

Answer 131

generally encodes for polypeptides

Answer 132

* sequences present at more than one copy in the haploid genome * larger genomes within a taxonomic group do not contain more genes but have large amounts of repetitive DNA * most bacteria have all **nonrepetitive DNA** * larger animals and plants have large amounts of repetitive DNA

Answer 133

* sequences without any apparent function * may have functions we do not understand?? -gene control regions (promoters) -code for microRNA * a large part of moderately repetitive DNA can be made up of **transposons** -short sequences of DNA (up to ~5000 bp) -have the ability to move to new locations in the genome -can make more copies of themselves

Answer 134

mitochondria and chloroplasts

Answer 135

* genes that reside outside the nucleus, in organelles such as mitochondria and chloroplasts * organelle genomes are usually (but not always) _circular molecules of DNA_ - mitochondrial DNA - chloroplast DNA (cpDNA or ctDNA)

Answer 136

* typically encodes 13 proteins, 2 rRNAs, and 22 tRNAs * proteins are ones involved in respiration/electron transport Complexes I to IV

Answer 137

* both mitochondria and chloroplasts are descended from bacteria ancestors * most of the mitochondrial and chloroplast genes have been transferred to the nucleus during the organelles evolution * mitochondria originated by an endosymbiotic event when a bacterium was captured by a eukaryotic cell

Answer 138

* not found in bacterial genomes * hypothesis = the earliest genes did not contain introns -introns were subsequently added to some genes * how? possibly they have always been an important part of the gene -splice sites, providing the correct reading frame, etc.

Answer 139

* originally estimated that the human genome contained 30-40,000 genes * sequencing revealed the actual number is ~20,000 * only 1% of the human genome is exons * 24% are introns * so genes are only about 25% of the genome * most is repetitive DNA

Answer 140

* the hypothesis that genes have evolved by the recombination of various exons encoding functional protein domains -creating proteins with greater function and value * most successful shufflings were once where the exons was flanked by intron sequences -containing 5' and 3' splicing sites on either side of the exon * exons were inserted into large introns * however, only 1 in 3 chance of a correct reading frame

Answer 141

**50%** * the majority of repeated sequences are copies of **nonfunctional transposons** * Pseudogenes * tandem repeats at the centromere and telomeres

Answer 142

* 12% (~3000) code for RNAs -rRNAs, tRNAs, regulatory RNAs, etc. * 4.8% (1200) are **pseudogenes**

Answer 143

* stable but inactive genes derived by mutation of an ancestral active gene * often inactive due to mutations that stop transcription or translation (or both)

Answer 144

21% housekeeping genes

Answer 145

* transcription and translation * metabolism * transport * DNA replication and modification * protein folding and degradation

Answer 146

* as morphological complexity increases, additional genes are needed with increased complexity * most of the genes that are unique to vertebrates/animals are concerned with the immune or nervous systems

Answer 147

* there are many more unique proteins compared to other eukaryotes * but relatively few unique protein domains * most protein domains are common to animals * the greatest proportion of unique proteins are the _transmembrane_ and _extracellular_ proteins - cell-cell communication secreted proteins and receptors

Answer 148

* exons can be modules for building new genes * exon could be copies and used in another gene - provides new function - enzyme function - structural function * entire gene (exons + introns) is duplicated * duplicated genes can then allow mutations to collect and evolve - becomes a new gene/function - or becomes a pseudogene * as long as the original gene stays functional

Answer 149

* copies of functional genes with altered or missing regions * produce polypeptides that are _nonfunctional_ or have _altered_ functions

Answer 150

* a group of adjacent genes that are identical or related * may be simply two adjacent identical genes to hundreds of identical genes in a tandem array * e.g. Immunoglobulin genes have: - ~300 variable region gene segments - 20 D region segments - 6 J region segments - 9 heavy chain region segments

Answer 151

* tandem repeats due to a need for large amount of the product - rRNA for protein synthesis - histone proteins for replicated DNA

Answer 152

* regions of chromosomes that are permanently tightly coiled * DNA is not active

Answer 153

* parts of chromosomes that are less tightly coiled * contain most of the active or potentially active genes

Answer 154

the region in the nucleus where: * the rRNAs are produced * the rRNA and proteins are put together to form ribosomes

Answer 155

**Fibrillar core** - where the rRNA is transcribed from the DNA template (rDNA) **Granular cortex** - area around the fibrillar core - where the rRNAs and proteins are actually put together to form the ribosome

Answer 156

a region where chromosomes "stick" their DNA to pre-make ribosomes each nucleus can have many nucleoli, but usually only have one or two

Answer 157

* composed of **rRNA(( and **protein** (ribonucleoprotein) * two subunits: 1. large subunit (60S) - 5S rRNA - 28S rRNA 2. small subunit (40S) - 18S rRNA

Answer 158

**tandem repeats** * rRNA is encoded by a large number of _identical genes_ that are tandemly repeated to form one or more _clusters_

Answer 159

* DNA where the ribosomal genes are located - the genes in an rDNA cluster all have an identical sequence * each rDNA cluster organization - transcription units for a precursor containing both the major rRNAs alternating with **nontranscribed spacers**

Answer 160

* shorter repeating units whose number varies so that the lengths of individual spacers are different * allow several RNA polymerases to attach and transcribe rRNAs at the same time

Answer 161

very short sequences of DN repeated many times in tandem and in large clusters * also called **satellite DNA** * no coding function * usually less than 10% of the genome

Answer 162

* DNA that consists of many _tandem repeats_ (identical or related) of a short basic repeating unit - repeating unit is ~100bp or more * usually located in _heterochromatin_ * commonly found at the _centromeres_ of chromosomes - suggests it has a structural role in chromosome segregation in mitosis and meiosis

Answer 163

* DNAs of tandemly repeated copies of a short repeating sequence * **minisatellite DNA** - length of repeating unit is ~10 to 100 bp * **microsatellite DNA** - length of repeating unit is usually less than 10 bp * the number of repeats varies between individual genomes

Answer 164

* varies quite a bit between individuals * very consistent for a single individual * therefore mini- and microsatellites lengths are _unique_ for an individual - one set of sizes inherited from the mother - a different set of sizes inherited from father * we can use these unique mini- and microsatellites to identify individuals

Answer 165

* PCR of a person's DNA with a mixture of primers for unique sequences flanking the microsatellite DNAs * PCR amplify these microsatellite DNAs * creates a **DNA fingerprint** of the microsatellites for that person * these DNA fingerprints are unique for that person

Answer 166

* collect DNA from crime scene * collect DNA from suspects * analyze microsatellite DNA fingerprints * compare for matches

Answer 167

* collect DNA from mother, child, and potential fathers * child's DNA fingerprint is _inherited from mother and father_ * child's DNA fingerprint will match with _both_

Exam 1 Flashcards

(193 cards)