Flashcards
Book 1 Chapter 5 Genes and Genomes
Cards in this deck (126)
- 1Is DNA a right handed or left handed helix?Right handed.
- 2What type does most DNA come in? what other type might it have?Most DNA is BDNA
It can also occur as ZDNA which is a left handed helix. - 3What does each nucleotide consist of?A ring shaped deoxyribose sugar
A base attached to the 1' carbon on the sugar ring.
A phosphate group attached to the 5' carbon on the sugar ring.(1 phosphorous atom and 4 oxygen atoms which are negatively charged attached to phosphorous by 3 single bonds and a double bond) - 4Describe the bonds that form the sugar backbone.They are covalent bonds between the sugar of one nucleotide and the phophate group of the previous nucleotide.
- 5Is DNA negatively charged, positively charged or neutral? Why?It is negatively charged due to the phosphate group on the deoxyribose sugar backbone. The four oxygen molecules are negatively charged.
- 6What kind of bond holds the base pairs together? How many are there between A-T and how many between C-G?Hydrogen bonds.
There are two between A-T and 3 between C-G. - 7What properties of these hydrogen bonds allows DNA to maintain structure and function as a replicating molecule?Hydrogen bonds are weaker than covalent bonds and so can be more easily unzipped to allow the template strand to be exposed for replication however they also confer enough strength when added together to give the DNA structural stability.
- 8What does the 3' carbon with the OH group bond to in the sugar backbone?To the phosphate group of the next nucleotide.
- 9The DNA strands are said to run anti-parallel. What does this mean?Due to the bonds on the sugar backbone the DNA strand has a 3' end and a 5' end. In the double helix they run in opposite directions so that on one strand it runs 3' to 5' and in the other it runs 5' to 3'.
- 10Thymine and cytosine have a single sugar ring. What are they collectively referred to as?Pyrimidines.
- 11Adenine and guanine have double sugar rings. What are they collectively referred to as?Purines.
- 12The two DNA strands are said to be complementary. What does this mean?Because of complementary base pairing rules where A can only pair with T and C with G the sequence of one strand can be inferred from the other.
- 13With nucleotides of different sizes how do the sugar backbones maintain a constant distance from one another?When added together the length and A-T and C-G is the same.
- 14What important function does the specificity of base pairing allow?It allows one strand to act as a template for the other during replication and as a template for an mRNA during transcription.
- 15What are the single nucleotide precursors that nucleotides are synthesised from?They are called dNTPs (deoxyribonucleotide triphosphates)
Specifically dATP, dCTP, dGTP and dTTP. They have three linked phosphate groups - the last two bonds store a lot of energy and they are similar to ATP. - 16When the bond holding 2 terminal phosphates onto the 1st phosphate group is broken it releases a lot of energy. What is this energy used for?It is used to create a new covalent bond between the 5' phosphate of the nucleotide and the free3' hydroxyl group of the existing DNA chain.
- 17Nucleotides are added to the DNA chain - in a certain direction because the phosphate group of the new nucleotide is added to the 3' OH group forming a phosphodiester bond. What direction is this?In the 5' to 3' direction.
- 18Which enzyme synthesizes strands of DNA by adding nucleotides to the DNA strand? What else does it do?DNA polymerase which also acts as a nuclease which breaks nucleotides apart if they are found to be incorrect after checks.
- 19Which enzyme nicks the overwound strand and then reseals it after it has unwound at the replciation fork of the DNA strand? What problem does it solve?Topoisomerase. It solves the topological problem.
- 20What do helicases do?Break the bonds between the base pairs allowing the two strands to unwind for replication.
- 21Which enzyme generates an RNA primer to initiate the beginning of a new Okazaki fragment on the lagging strand?Primase
- 22What does DNA ligase do?Follows along removing the RNA primers, fills the gaps with DNA nucleotides and ligates the fragments together to form the single DNA strand.
- 23Which enzyme can break the bonds between nucleotides?Nucleases do this. DNA polymerase can also act as a nuclease.
- 24What protein binds to the exposed DNA strand to prevent the nucleotides from reannealing?The single strand binding protein. (SSB protein)
- 25What is PCR? What are the three phases and the four ingredients needed for the procedure?polymerase chain reaction. 3 phases
1.denaturation
2. primer annealing
3. elongation.
Ingredients: DNA template, oligonucleotide primers, dNTPs and DNA polymerase - 26Describe the PCR procedure.4 ingredients heated at 94 degrees C to denature template DNA into two single strands. (hydrogen bonds disrupted).
55-58 degrees to allow the primer to anneal to the templates.
Incubated at 78 degrees C to allow elongation. Repeat x 30-40 times for amplification. - 27What proteins does the replication complex contain?DNA helicase - unwinds and separates the DNA strands.
Primase - provides RNA primers to initiate new strand synthesis.
DNA polymerase - links nucleotides to the new DNA strands. - 28What other function does DNA polymerase have?proof-reading functionwhich monitors the DNA for misincorporation of nucleotides.
- 29What mechanisms exist to repair DNA?MMR - mismatch repair of errors in replication.
Base excision repair.
Nucleotide excision repair. - 30How does MMR work in prokaryotes and eukaryotes?In prokaryotes enzymes seem to recognise lack of methylation in newly synthesised DNA. In eukaryotes it is less clear but a mismatch will be of a different length to a correctly matched pair and so enzymes may spot this.
- 31How does base excision repair (BER) work? Give an example of what it might be used to fix.Often used to repair a deanimated cytosine base that has had an NH3 replaced by a OH group turning it to uracil. DNA glycosylase ecognises the uracil and excises it leaving an abasic site. Nucleases remove the sugar-phosphate backbone. DNA polymerase synthsises a new base and ligase ligates the backbone.
- 32How does nucleotide excision repair (NER) work? Give an example of what it might repair.It might be used to repair a thymine dimer where thymine and cytosine undergo photochemical reaction from UV-B and form a covalent bond. The dimer is cleaved at either side by nucleases. DNA helicase unwinds and separates the strand. New DNA is synthesised and ligated.
- 33What is XP?(xeroderma pigmentosum)People who are highly sensitive to UV DNA damage due to defects in nucleotide excision repair mechanisms. There are 7 different types.
- 34What causes double strand breaks and why is a double strand break more serious?Replication errors or highly energetic ionising radiation.
They can lead to fragmentation of the chromosomes. - 35What are the two repair mechanisms for double strand breaks?Non-homologous end-joining and homologous end-joining.
- 36How is non homologous end-joining carried out? Why is it very error prone?A protein complex simply trims the ends and ligates them back together again. It is very error prone because bases are lost before the break is repaired. If many DSB happen at the same time they might be joined up onto different strands or even strands from different chromosomes.
- 37How is homologous end joining carried out and why is it more accurate?A homolous DNA molecule can act as a template for the repair. The broken strands pair with their homologue so that both strands can be repaired accurately. It uses the same molecular mechanism as with crossing over or recombination during meiosis.
- 38IN which direction is the template strand read during transcription?IN the 3' to 5' direction.
- 39In which direction is the mRNA synthesised?In the 5' to 3' direction.
- 40What is the central dogma?DNA makes RNA makes protein.
- 41What are the four RNA bases?A U C G
- 42How does translation occur?The mRNA bases are recognised in groups of three, each called a codon. An anti codon on a tRNA. At the other end of the tRNA is a specific amino acid. As the mRNA passes through the ribosome the tRNA anticodons are added to the codons and a peptide bond is formed between the amino acids. The tRNAs fall off leaving the emerging polypeptide chain.
- 43What is the relationship between the triple base codons and the amino acids they specify called?The genetic code.
- 44What is the redundancy in the genetic code?There are 64 combinations that the four bases can be arranged in, but only 20 naturally occuring amino acids so some amino acids have multiple codons.
- 45What do codons code for apart from amino acids?START (AUG)
STOP (UAA, UAG and UGA) - 46What is an open reading frame (ORF)?A section of sequence that encodes a polypeptide sequence (or part of one). It is uninterupted by a stop codon.
- 47How can the rate of mutation be estimated?By observing the rate at which spontaneous changes arise in specific genes. Either in populations, individual organisms or in laboratory cells. I the mouse genome these methods have resulted in an estimated base pair change in every 10 to the 9 bp for every cell generation.
- 48The number of mutations can vary - to what extent?It can be as low as one in every 10 to the 10 bp per genome per cell division or be as high as one in every 100 bp per genome per cell division.
- 49In eukaryotes mutations in some cells have consequences for future generations. Which ones?In germ cells.
- 50What different kinds of simple base exchange mutations can occur?Spontaneous chemical modification:
Cytosine for uracil /Depurination - loss of G or A
Transitions
Transversions
mis-sence
nonsense
silent - 51What is a frame shift mutation and why is it more serious?The insertion or deletion of one or more nucleotides. The ORF will be shifted along by one for all subsequent codons resulting in the subsequent amino acids all being different. The protein structure would be different, affecting function.
- 52What spontaneous chemical modifications can occur to cause a simple base substitution?Cytosine for uracil when a NH3 is replaced by a C=0 (Carboxyl) group.
Depurination - loss of G or A. - 53The other single base mutations occur during replication. What is a transition mutation?A transition involves the substitution of one pyrimidine for another (C or T) or of one purine for another (A or G)
- 54What is a transversion?The substitution of a pyrimidine for a purine or vice versa.
- 55What is a miss-sense mutation?The substitution of one amino acid for another.
- 56What is a nonsense mutation?The premature introduction of a STOP codon resulting in the premature end of the polypeptide. The protein is said to be trunicated.
- 57What is a silent mutation?A mutation that causes no change in the resulting protein sequence.
- 58Why might a single base substitution have no effect on the encoded protein?Some amino acids are encoded by more than one codon which only differ in the third base and so don't alter the amino acid incorporated into the protein.
- 59What would be the consequence of the insertion of three nucleotides side by side?The ORF reading frame would not shift unless the three nucleotides were inserted midway between one of the codons triplets.
- 60What is the biochemical explanation for recessive alleles?Recessive genes generally represent a loss or reduction of function of the gene, either because the biochemical activity of the protein is reduced or because the expression of the protein is reduced.
e.g. Drosphilia W+ encodes a protein for import of pigment from blood. w1 is a loss of function allele. - 61What are the 2 loss of function mutations called?null mutations (amorphs) - complete loss of function.
partial loss of function mutations (hypomorphs) - 62What DNA changes might result in loss of function?(null mutations)Deletion of whole gene or part, expression of a trunicated protein.
Single nucleotide change could remove a start codon or introduce a stop codon. Insertion or deletion may introduce a frameshift in the ORF.
A single nucleotide may alter the catalytic function of the protein.
A change in a regulatory region may alter gene expression. - 63What would happen if a whole gene rearrangement resulted in the gene being moved to a silent region i.e. in a heterochromatin region?The transcription factors, enzymes and protein complexes would have difficulty accessing the gene which would lead to a loss of expression.
- 64What could insertion of a large DNA fragment lead to?It would disrupt transcription of a gene and probably lead to a null mutation.
- 65What is the biochemical explanation for dominant alleles?They generally represent a change in function or an increase in the activity of the gene product.. They are called gain of function mutations.
- 66What may hypermorphs be due to?increased activity of the gene product
increased levels of transcription
inappropriate patterns of gene expression (temporal or spatial - when or where a gene is transcribed.)
large chromosomal rearrangements that move the gene to an area close to transcriptional control sequences that normally activate another gene. - 67What is a neomorph?A mutation that causes the gene to have a completely different function. Usually though, mutation leads to a subtle gradation of phenotypes.
- 68Why do most mutations have no effect in eukaryotes?Because they occur in regions of of the genome that do not encode a product or regulate transcription.
- 69The protein coding region of a prokaryotic gene is an uninterupted series of codons. It starts with one particular codon and finsishes with one of the STOP codons. What are they? Are they different or the same as in Humans?ATG -Start is methionine.
TAA, TAG, TGA - stop
Different. - 70What is the ORF of a protein encoding region proceeded by in the prokaryotic genome?By a regulatory region that contains genes that regulate the level of gene expression. It includes the binding site for RNA polymerase which synthesises mRNA. It also includes sequences to which regulatory proteins can bind.
- 71Regulatory proteins interact with RNA polymerase to increase/decrease efficiency of transcription. thay are often sensitive to the cells physiology. What factors may influence this efficiency?Availability of nutrients in the environment or availability of molecules required in metabolic pathways in the cell.
- 72What are genes in prokaryotes often arranged in units called what?Operons - a group of genes with related functions under the control of a single regualtory DNA region.
- 73The genes in the operon are often transcribed together as a single mRNA called a -?Polycistronic transcript.
- 74Name one operon in e.coli that has been well studied.The lac operon, has three genes lacZ (encodes beta-galactosidase which converts disaccharide lactose into monosaccharide glucose and galactose) lac Y encodes a protein required for the import of lactose into the cell and lacA, an enzyme that is not essential for lactose metabolism. The single regulatory region ensures that they are expressed only when lactose is available.
- 75What is involved in the DNA super-coiling of the circular prokaryotic DNA?The DNA is compacted by twisting the of the DNA duplex like coiling up a cable. Topoisomerases act to add or remove these twists in response to tortional stresses of the supercoiling. (Same enzymes as in the replication fork in eukaryotes.)
- 76Most chromosomes have extrachromosomal elements - What are they called? What properties do they have?plasmids or episomes
They can replicate independently from the genomic chromosome and function as small independant geneomes with a single origin of replication. replication may be linked to the cells division cycle. - 77What genes may plasmids carry?They often carry a small number of genes associated to a specific set of functions. for example, they encode proteins that facilitate their own movement from cell to cell. F plasmids (F for fertility factor) encode genes for the bacterium to form sex pili. Some encode gene to produce toxins damaging to human health.
- 78What genes encoded by plasmids can be damaging to human health?virilence factors in E.coli can cause diarrhoea.
Other virilence factors can increace infectivity, or harmful effects like adherance to cells or ability to penetrate cells. Plasmids have also increased antibiotic resistence, peventing some from binding to their target bacteria. - 79What is gene cloning?A set of techniques by which individual genes can be isolated manipulated and transferred between species.
(genetic engineering in common parlance) - 80What property of DNA does it depend on?The universality of DNA across species. DNA derived from one species has the capacity to be replicated, transcribed, and translated in a second species.
- 81What three technical advances were necessary before genes could be cloned?1. A reproducible means of cleaving DNA in to defined sections.
2. - 82What enabled the cleaving of DNA into defined sections?The discovery of restriction endonucleases, enzymes that catalyse the the cleavage of isolated molecules at specific sequences in vitro.
- 83What enzyme enables the joining of DNA fragments in vitro?DNA ligase - ligates the fragments together.
- 84How are multiple copies of DNA fragments propagated in vitro?Cloning vectors.
The DNA fragment must be inserted into a DNA molecule that can replicate independently within an appropriate host cell. The DNA molecules is engineered in vitro to possess such features that facilitate this function. The DNA molecule is called a cloning vector. - 85What are cloning vectors developed from?Naturally ocurring plasmids, bacteriophage and virus genomes.
- 86How is gene cloning performed using a bacterial plasmid vector?With restriction endonucleases ( or restriction enzymes), isolated from prokaryotes.their natural function is to cleave any foreign DNA. Some target specific sequences and cleave DNA in a staggered fashion. Leaving sticky ends of complementary bases because the DNA target is palindromic. In plasmid vectors the circle is opened Incubating with DNA ligase can permanently rejoin them.
- 87How is gene cloning performed using a bacterial plasmid vector?The circular DNA molecule (plasmid vector) is opened (cleaved), mixed with a DNA fragment of interest. Incubating this mixture with DNA ligase can permanently join them together, reforming the circle.
Recombinant DNA where the circular DNA has the DNA DNA of interest inserted can be obtained. - 88What happens after the recombinant DNA has been obtained?The final stage is to propagate the DNA fragment of interest. Typically this is done inside a bacterium as the plasmid is able to replicate within a bacterial cell. This is acheived by transformation, where certain treatments induce the cell to take the recombinant plasmid. Once the plasmid replicates it provides a source of large quantities of the DNA fragment of interest.
- 89Plasmids are engineered to have a useful features. What are they?1. An origin of replication.
2. an antibiotic (e.g. ampicillan) resistance gene so only recombinant plasmids will grow in an antibiotic plate.
3. several rescriction enzyme sites at which DNA may be inserted.
4. another means of distinguishing recombinant plasmids e.g. has a restriction enzyme cloning site in the lacZ gene the enzyme beta-galactosidase can then be visualised. - 90How is beta-galactosidase visualised?The cells are spead on an agar plate which includes a substrate that the enzyme converts from colourless to blue. The substrate is called chromogenic substrate. The recombinant plasmids have had the lacZ gene disrupted so they will not appear blue.
- 91How does replication differ in plasmids from gram negative bacteria and gram positive bacteria?In plasmids from gram negative bacteria replication tends to be bidirectional.
In plasmids from gram positive bacteria it tend to be rolling circle. - 92How does rolling circle replication proceed?Replication begins at the origin where one strand is nicked, providing a starting point for replication. Many copies of the template strand are made as one long strand. They are cut into separate lengths and then they recircularise and provide a template for the second strand, becoming double stranded.
- 93How do organelle genomes ressemble prokaryotic genomes? What are the differences?They are small and circular and the DNA is not packaged in proteins in the same way as a eukaryotic genome. However Mitochondrial and chloroplast genomes are substantially smaller than bacterial ones as many of the proteins for them are encoded by the nucleus of the cell.
- 94The genetic code is universal for all taxonomic groups however there are differences for mitochondria. What are they?UGA usually codes Stop but codes for tryptophan in mitochondria.
AGA and AGG usually code for arginine but code for STOp in mitochondria.
AUA usually codes for isoluecine but codes for methionine in mitochondria. - 95What other proerties do mitchondrial geneomes have?They are very compact with virtually no non coding DNA (except near origin)
ORFs sometimes overlap.
it encodes tRNAs, rRNAs and proteins for the electron transport chain for ATP synthesis. - 96How do prokaryotes pass on their genes to their daughter cells?By asexual binary fission, producing clones fo the original parent.
Or by three methods of horizontal gene transfer. - Conjugation, transformation or transduction. - 97What is conjugation in prokaryotes?One bacteria extends a sex pili to another and transfers genes to the recipient cell.
In E.coli F plasmids are needed and the F plasmid is transmited (often from a F+ to an F- cell) to the recipient. Some F plasmids are intergrated into the bacterial chromosome which can lead to transfer of the whole bacterial chromosome during conjugation as the oriT is retained which initiates conjugation. - 98What is the amount of chromosomal DNA transfered dependent on?On how long contact can be maintained - it is usually broken due to the fragile sex pili physically breaking.
- 99How can gene maps be created using plasmids incorporated into the bacteria genome?F+ bacteria (Hfr) are mixed with F- bacteria to conjugate. Conjugation is interrupted at several points and when genes have been transfered in relation to the OriT starting point can be mapped. Which genes have been transferred can be tested by studying the appearance of new genotypes.
- 100What is transformation in terms of horizontal gene transfer?Bacteria can take up naked DNA from their surroundings and incorporate it into their genome. Some do it naturally and some need treatment with metal ions like calcium,electroporation(pulsed electrical fields) to increase membrane permeability.
- 101How can transformation be used to create a genetic map?Whilst artificial transformation is less efficient high concentrations of DNA fragments make it useful experimentally. Genes close together on the fragment are more likely to be cotransformed than those far apart. repaeated experiments allow scientists to build up a genetic map.
- 102What other technique is transformation used for?Gene cloning. As a way of introducing recombinant plasmid DNA into host E.coli cells.
- 103What is transduction? (in relation to conjugation)The transfer of DNA from one cell to another mediated by a virus. IN lysogeny viral DNA is incoprorated into the bacterial chromosome and stays dormant. When it becomes active it excises from the chromosome, often taking bacterial DNA with it,. When it is repackaged it infects other bacteria.
- 104How is the eukaryotic genome more complex than the prokaryotic genome?They are not organised into operons and so each gene has its own regulatory sequence. The protein coding sequences (exons) are interuppted by non coding sequences (introns)
- 105How are the introns removed post transcription?By mRNA splicing to yield the mature mRNA in which exons are contiguous and form the ORF required for translation.
- 106What form of regulation, (extra to the regulatory sequences up or downstream of the gene,) can be exercised due to mRNA splicing?Different versions of proteins can be translated by splicing different combinations of exons.
- 107What region might you expect to find in the regulatory sequences?A promoter region. Which lies just upstream of the gene sequence where transcription factors assemble to promote the binding of RNA polymerase.
- 108Why are some genes present in multiple copies?They may be needed on large amounts. e.g. histone proteins.
They may be part of gene families with related but distinct functions. - 109What might the repeated sections of DNA contain?Transposable elements or transposons.
- sequences that under certain circumstances are able to excise and and reintegrate elsewhere in the genome. - 110Name the proportions of the genome sequences24% introns and regulatory seq.
44% repetitive DNA incl. transposons and related seq.
15% unique non coding DNA of unknown function.
15.5% of non trasposable elements.
1.5% codes for proteins,rRNA or tRNA - 111What are transposable elements?Like molecular parasites that can relocate throughout the genome as they often have no obvious function except to maintain themselves. They move by transposition (cut and paste).
- 112What consequence might a transposon have if moved to another part of the genome?It might insert into the middle of an ORF and disrupt the expression of the gene causing a mutation. (However they are highly conserved so they must have some advantage?)
- 113What are simple sequence repeats?They are often clustered around structural features such as centromeres. They are also referred to as satelite DNA as they are more easily separated during centrfugation. The term satelite DNA is often used interchanably with heterochromatin.
- 114What are telomeres?Telomeres are short sequence repeats that are on the ends of chromosomes. In humans this is TTAGG repaeated many thousands of times.
- 115What problem do telomeres overcome?During replication the leading strand can be copied to the end. THe lagging strand has a final section where the last RNA primer is degraded. It cannot be filled in as there is no 3' OH group for DNA polymerase to initiate DNA synthesis. Telomeres on the end of chromosomes shorten after every replication ensuring the gene does not become trunicated.
- 116Telomeres shorten over time but after 30 or 50 divisions they enter senescence which means they stop proliferating. What can prevent this from happening and in what cells is it found?Telomerase, an enzyme that adds additional nucleotide repeats to the ends of chromosomes. They tend to be found in stem cells and germ cells.
We may not have telomerase in somatic cells because whilst they protect from aging they also appaer in tumours and may be responsible for some cancers. - 117Viral DNA is very varied in composition and structure. Describe some of these variations.They may be single or double stranded.
They may use DNA or RNA in several structural forms.
Most encode proteins to produce a protective capsid for escape or produce proteins for biochemical functions for propagation.
Retroviruses make a DNA copy of their RNA to infect a cell where it is later copied to produce new viral RNA. (reverse transcription.) - 118What principle is DNA sequencing based upon.DNA fragments of different lengths can be separated from one another by gel electrophoresis.
- 119How does gel electrophoresis work?A gel is formed between two plates Ionic salts make it conductive. Electric current applied makes the neg charged DNA fragments move through the gel. Smaller ones move more easily and so different sizes are separated out.
- 120What is Chain termination sequencing?Carry out DNA replication in vitro but spike the mix with defective a dNTP which act as chain terminators as they lack an 3' OH group. (ddATP, ddCTP, ddTTP or ddGTP). Fragments are made that terminate in a specific letter. Then gel electrophoresis separates them out and the position of the fragment terminating in A,G,C or T is visualised.
- 121What are homologous genes in terms of phylogenetic relationships?They are genes that share a degree of similarity due to their common evolutionary origins.
- 122What are single nucleotide polymorphisms? (SNPs)The sites in the genome where there are single nucleotide differences between individuals.
- 123What are copy number variations? (CNVs)Multiple copies of a gene may be present in variable numbers resulting in differences in gene expression in individuals of the same species. It is the result of gene duplication.
- 124What can gene duplication lead to as well as CNVs?It can lead to the evolution of gene families -structurally related genes that may have similar or different functions.
- 125By what mechanisms may genes be duplicated?Errors during replication.
Unequal crossing over during meiosis.
The action of transposons taking genes with them when they relocate. - 126What does a GWAS genome-wide association study make use of?Single nucleotide polymorphisms (SNPs) to look for a association between genetic variation and certain traits.
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- Flashcards on Book 1 Chapter 5 Genes and Genomes, created by vicstevens on 05/09/2014.
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