Genomics. Flashcards
Define an allele?
A different version of a gene.
E.g. the gene that codes for hair colour is made up of different alleles that code for different hair colours.
Define the banding pattern on a chromosome?
How the individual genes are arranged on a chromosome.
Define cytogenetics?
The study of different karyotypes from different organisms.
Define DNA sequencing?
The process of determining the exact order of nucleotides within a DNA molecule.
Define the exome?
The part of the genome that is composed of exons.
Define a gene?
A discrete hereditary unit that codes for a trait or a specific protein.
Define the genome?
All the genes that an organism possesses.
Define genomics?
The study of all of the genes within an organism.
Define a genotype?
The genotype consists of the specific genes that an organism possesses e.g. genes for and eye colour.
Define a haplotype?
A combination of alleles that are located next to each other on a chromosome.
Are haplotypes usually inherited together?
Yes.
Define a karyotype?
The arrangement of all of an organisms chromosomes into an order of size.
Define a microdeletion?
A deletion of between a few hundred and a few million base pairs on a chromosome.
These deletions are too small to be picked up via light microscopy.
Define Northern blot?
A molecular technique that evaluates different RNA’s.
What does the suffix omics represent?
It is used to indicate a genome wide approach or study.
E.g. genomics is the study of all the genes in the genome.
Define a phenotype?
The physical expression of an organisms genotype e.g. genes that code for blue eyes or blond hair.
Define a single nucleotide polymorphism?
Polymorphisms where the variance between alleles is caused by the difference of a single nucleotide within a genetic sequence.
Define Southern blot?
A molecular technique that evaluates different forms of DNA.
Define Western blot?
A molecular technique that evaluates different proteins.
What does the study of genomics look at?
All of the genes that are found within a particular organism.
Does the number of genes within an organism vary over time?
No.
What can lead to an increase or decrease of genes in an organism?
Mutations such as insertions and deletions.
Is genomics context dependent?
No, as the amount of genes in an organism does not change over time.
Is transcriptomics context dependent?
Yes, as the amount of mRNA in a cell will change over time.
What contributes to the overall phenotype of an organism?
The genome, the transcriptome, the proteome and the metabolome.
What will an mRNA dictate?
The protein that is produced.
What is the proteome directed by?
The transcriptome.
What is the transcriptome directed by?
The genome.
Is the production of mRNA context dependent?
Yes, as humans will produce different mRNAs at different stages throughout their life.
Will the environment influence the phenotype?
Yes, as the transcriptome and the proteome are dictated by the environment.
What are the 3 disciplines that are involved in the study of genomics?
Molecular biology.
Bioinformatics.
Computing.
Why are robots and computers often used in genomics?
To save time.
What are 6 things that an organisms genome can tell us about its life?
Developmental pattern.
Disease resistance or susceptibility.
Metabolism.
How the organism will react to specific drugs or toxins.
The history of the organism.
The environment that the organism lives in.
What are the 2 types of genomes that exist in nature?
Eukaryotic and prokaryotic genomes.
What kind of genomes tend to be more complex?
Eukaryotic genomes.
What material do most genomes tend to be made up of?
Deoxyribonucleic acid.
The exception to this is a few viruses that have RNA genomes.
What is the specific region of the cytoplasm of prokaryotic cells is the genome found in?
The nucleoid region.
Do prokaryotes contain extrachromosomal DNA?
Yes, in the form of plasmids.
What are plasmids?
Circular regions of DNA that can be acquired from the environment.
Is plasmid DNA part of the prokaryotic genome?
Yes.
Why is the eukaryotic genome more complex than the prokaryotic genome?
As it contains many more genes.
What are the 2 genomes that make up the eukaryotic genome?
The nuclear genome.
The mitochondrial genome.
Where is the nuclear genome found in eukaryotic cells?
In the nucleus.
What genes make up the mitochondrial genome?
All of the genes located within the mitochondria of eukaryotic cells.
What are mitochondria in plant cells known as?
Chloroplasts.
What is cytogenetics?
A branch of genomics where scientists look at the different karyotypes of different organisms.
What does the study of karyotypes allow scientists to do?
To identify different chromosomal abnormalities e.g. Downs syndrome.
What does euploidy refer to?
To the normal complement of 46 chromosomes that are found in humans.
What is aneuploidy?
When the number of chromosomes found in an organism differs from what is normally found.
What happens to most organisms that suffer from aneuploidy, before they are born?
They will be aborted before they are born as most forms of aneuploidy are not compatible with life.
What are 4 common types of aneuploidy that appear in humans?
Downs syndrome.
Edwards syndrome.
Patau syndrome.
Klinefelters syndrome.
What is downs syndrome charactersied by?
An extra chromosome 21 resulting in 47 chromosomes.
How will a males genome read if he is infected with Downs syndrome?
XY-47+21.
What is Edwards syndrome charactersied by?
An extra chromosome 18 resulting in 47 chromosomes in total.
How will a males genome read if he is infected with Edwards syndrome?
XY-47+18.
What is Patau syndrome charactersied by?
An extra chromosome 13 resulting in 47 chromosomes in total.
How will a females genome read if she is infected with Patau syndrome?
XX-47+13.
What is Klinefelters syndrome charactersied by?
When an organism contains an extra X or Y chromosome resulting in a genome of XXY or XYY.
What is Turner syndrom charactersied by?
When an organism only receives a single X chromosome.
What are strucutural chromosmal abnormalities caused by?
By damage to the chromosome or when a segment of the chromsome falls off from the original chromosome.
What results from strucutural chromosmal abnormalities?
A deletion of part of the genome.
What kind of scientists will create cytogenetic maps?
Cytogeneticist.
What will cytogenentic mapes be used to highlight?
How densely DNA is packaged into various areas of the chromosome.
What are bands on a cytogenetic map?
The areas where DNA is tightly packed into a chromosome.
How do cytogeneticists get bands to show up on a chromosome?
By staining the chromosomes with with a particular dye known as Geisma.
Will each chromosome within an organism display the same banding pattern?
No.
Each chromosome will display a different banding pattern.
What can the positioning of a band on a chromosome tell us?
Where a particular gene is located on a chromosome.
What does FISH allow scientists to do?
To view large DNA fragments on metaphase chromosomes or on interphase chromatin strands.
What is probe DNA labelled before it undergoes FISH?
Radioactive probes.
What will the lablled DNA be hybridised to when FISH is being performed?
Metaphase chromosomes.
What happens to chromosomes after they have undergone FISH?
They can be compared.
What are 3 common methods of comparing chromosomes after FISH has occurred?
Standard karyotype analysis.
Aneuploid screen test.
Detecting micro-deletions via FISH.
What is the standard karyotype analysis used to test for?
For major chromosomal abnormalities.
How is a standard karyotype analysis carried out?
By arranging the fluorescent chromosomes into order of size.
The chromosomes are then examined for abnormalities such as major size differences or extra chromosomes.
What is the major drawback of a standard karyotype analysis?
It cannot be used to detect microdeletions.
How is an aneuploid screen test carried out?
It involves using specific probes to show if a developing foetus suffers from aneuploidy.
What will the specific probes used in an aneuploid screen test bind to?
To specific chromosomes within the genome of the developing foetus.
What does the binding of specific propes to specific chromosmes in an aneuploid screen test tell us?
How many chromosomes are present.
How are the probes labelled in an aneuploid screen test?
Each probe is labelled with a different colour.
How many chromosomes are assigned to each probe in an aneuploid screen test?
For each probe there should be 2 chromosomes.
If 3 chromosomes align to a single probe in an aneuploid screen test what will that individual be suffering from?
The individual will be suffering from trisomy.
How can an aneuploid screen test tell physicians what kind of trisoomy an individual is suffering from?
The colour of the probe indicates what kind of trisomy the individual is suffering from.
E.g. If there are 3 red dots then the individual has 3 versions of chromosome 21.
What microdeletions can be detected by FISH?
A steroid sulphatase deficiency.
What causes a steroid sulphatase deficiency?
A micro-deletion on the X chromosome.
What kind of probe is used in FISH to detect a steroid sulphatase deficiency?
A specific probe called an X cen probe
Where does a X-cen probe bind to on the X chromosome?
To the centromere on the X chromosome.
How can the X-cen probe determine the sex of a baby?
If 2 probes bind to different X chromosomes then the foetus will be born female.
If only a single X chromosome shows up then the baby will be born male.
How many probes are involved in detecting a steroid sulphatase deficiency?
2 probes.
The X-cen probe.
Another probe that binds to the micro-deletion that causes the steroid sulphatase deficiency.
What does the identification of specific DNA sequences within a genome allow scientists to do?
To search for specific coding regions or regions of DNA that are markers for a disease.
What is restriction fragment length polymorphism (RFLP) and Southern blot use for?
To detect specific DNA sequences on a chromosome.
What is the first step of RFLP?
To extract genomic DNA from the organism of interest.
What happens in RFLP after the genomic DNA has been extracted?
The genomic DNA is digested into smaller fragments by a restriction enzyme.
What happens in RFLP after the genomic DNA has been digested by restriction enzymes?
They are separated by electrophoresis and transferred to a nitrocellulose membrane to undergo Southern blot.
What happens to the DNA fragments when they undergo Southern blot analysis in RFLP?
The electrophoresis gel and the DNA samples are copied.
What happens after Southern blot analysis in RFLP?
The DNA bands are de-natured to form single stranded DNA.
What happens in RFLP after the DNA bands have been denatured into single strands?
A DNA probe is inserted into the single stranded DNA strands.
What will is the DNA probe looking for in RFLP?
For a complimentary strand.
What is significant if the RFLP probe matches to a single stranded region of SSDNA in an RFLP experiment?
It means that the chromosome or DNA strand contained the same sequence of DNA that was on the probe.
What mutation will RFLP and Southern blot often be use to find?
The mutation that leads to sickle cell anaemia.
What is the result of the mutation that causes sickle cell anaemia?
It changes a single nucleotide and this causes the codon to code for valine instead of for glutamic acid.
Will the mutation that causes sickle cell destroy an restriction sites?
1 restriction site is destroyed.
What happens to the restrcition enzymes in RFLP and Southern blot if a person has sickle cell anaemia?
They enzymes cannot cleave the deleted restriction site, so the move down to cleave at the next restriction site.
How does the cleaved DNA of a person who has sickle cell differ from the cleaved DNA of a person who does not have sickle cell?
If the person has sickle cell then the cleaved DNA always contains 1350 base pairs.
If the person does not have sickle cell then the cleaved DNA always contains 1150 base pairs.
Why does a person who has sickle cell contain more base pairs in their DNA segment after RFLP?
Because the restriction enzyme cleaves at a restriction site that is further down the DNA strand.
What probes are used in allele specific oligonucleotide probes and SNPs (ASO)?
Short oligonucleotide probes that are complimentary to a certain allele.
What will the probes used in ASO bind to?
A specific allele
E.g. different versions of the beta globin gene.
How can an ASO probe detect the mutation that causes sickle cell?
Becuase, the mutation creates a new allele which matches up to the probe.
Why is ASO an easier method of detecting sickle cell than RFLP and Southern blot?
Because ASO can be used to test directly for the sickle cell allele without having count the number of base pairs.
What kind of polymorphisms can ASO be used to detect?
Single nucleotide polymorphisms.
What is DNA sequencing?
The process of determining the exact order of nucleotides within a DNA or RNA strand.
Who developed di-deoxy sequencing in the 1970s?
Fredrick Sanger.
What is a di-deoxyribose?
A deoxyribose that has lost its hydroxyl group from carbon 3.
What happens during DNA synthesis if DNA polymerase adds a di-deoxyribose
If a di-deoxyribose is present there is no hydroxyl group, so DNA polymerase cannot add the new nucleotide.
Where does DNA polymerase add new nucleotides on a DNA strand?
To the hydroxyl group on carbon 3.
What is the first step of Sanger sequencing?
To denature the DNA strand into single stranded DNA.
How is the single stranded DNA that is used in Sanger sequencing prepared?
A primer is added to the 5 prime end.
What happens to the primed single-stranded DNA after it has been prepared?
The DNA strand is amplified to produce 4 copies which are then placed into 4 different test tubes.
What 4 things are present in each test-tube during Sanger sequencing?
The single-stranded DNA.
A DNA polymerase.
A number of DNTPs.
A single class of DDNTP.
What classes of DDNTP are addedd to each of the 4 test-tubes in Sanger sequencing?
A single type of DDNTP is added e.g.
Di-deoxyadenine to tube 1.
Di-deoxythymine to tube 2.
Di-deoxycytosine to tube 3.
Di-deoxyguanine to tube 4.
What happens during Sanger sequencing after the 4 ingredients have been added to each test-tube?
DNA polymerase adds DNTPS to the SSDNA eventually it adds a DDNTP which prevents the addition of any more DNTPs.
What is produced in each test-tube during Sanger sequencing?
Many double stranded DNA fragments that are of different lengths.
What happens to the DNA sequences in the test-tubes after the double stranded sequences have been formed?
The contents of each tube are separated into order of size by electrophoresis.
Why are the DNA strands from the test-tubes separated during Sanger sequencing?
Each lane on the gel represents a single test tube therefore, the final nucleotide on each individual strand represents the DDNTP that was in that tube.
How is the order of nucleotides worked out during Sanger sequencing?
By following the order of DDNTPs in the gel.
E.g. If the fragment that migrated the furthest is a T then the first nucleotide will be thymine.
If the next fragment represents a G then the second nucleotide is guanine and so on.
How can we make Sanger sequencing even faster?
Each DDNTP is labelled with a fluorescent probe and will show up as a different colour.
All of the fragments are placed in a single line and their individual colours tell us what the final nucleotide was.
E.g. Green probes could represent thymine and red probes could represent adenine.
What will usually read the results of Sanger sequencing?
A computer which will read the results and describe the sequence of nucleotides.
Where is genetic information usually stored?
In gene libraries.
What are 2 forms of storage for genetic information?
Physical gene maps.
Hierarchical shotgun sequencing.
How do scientists store individual genes on a gene map?
As contigs which are overlapping sequences of a genome.
How is a genome divided into contigs?
The genome is cleaved at different restriction sites.
How will scientists remove individual genes from a contig?
By cleaving at the restriction sites on the contigs.
What does the collection of individual contigs contribute to on a gene map?
A physical map of the genome.
What information is known about each contig?
The specific genes and restriction sites.
How do maps of the genome help scientists?
They help scientists to understand the genome and to learn where mutations arise within the genome.
What is hierarchical shotgun sequencing?
A form of genetic sequencing that places specific regions of DNA inside a cloning vector such as a BAC or a YAC.
How are the genes prepared for hierarchical shotgun sequencing?
The genes are removed and cut into contiguous fragments via restriction enzymes.
What happens to the contiguous DNA fragments in hierarchical shotgun sequencing after they have been cut into contigs?
These fragments of DNA are cloned and placed into a cloning vector where they can be later removed for study.
How can a map of the genome be created after hierarchical shotgun sequencing?
The fragments from different cloning vectors can be spliced together allowing for an organised map of the genome to be created.
What occurs when individual fragmnets undergo shotgun sequencing in hierarchical shotgun sequencing?
The fragment is cloned multiple times and restriction enzymes will break the clones into smaller fragments.
The small fragments are sequenced and to reveal the order of nucleotides within the genome.
This is applied to other fragments allowing scientists to determine the genetic sequence throughout the entire DNA strand.
When did the human genome project manage to sequence the human genome?
In 2002.
What method of gene sequencing was used at the beginning of the human genome project?
Sanger sequencing.
What was the 2 original goals of the human genome project?
To identify all of the genes within the human genome.
To determine the exact sequence of nucleotides within the human genome.
Where is the information obtained by the human genome project stored?
In a database that is accessible to all members of the public.
Why is the information in the human genome project stored in a public database?
To allow all researchers the ability to obtain the information and advance the project.
Why did scientists sequence the genomes of multiple organisms?
To compare the human genome to the genomes of other organisms.
What is the aim of the HAP-map project?
To catalogue and map all of the common genetic variants that occur in human beings.
Why did scientists want to map common genetic variants in the HAP-map project?
So they could note what the variants are.
Where they occur within the genome.
How they are distributed amongst different populations.
How was the HAP-map project carried out?
By closely scrutinising genomes for an SNPs associated with characteristics such as diseases or special traits.
What has the HAP-map project allowed genetic researchers to do?
To access important information that helps them link diseases to certain SNPs e.g. sickle cell.
How was the 1000 genome project carried out?
By sequencing the genomes from 1000 individuals from around the world.
What was the aim of the 1000 genome project?
To find the most common genetic variants.
What percentage was required for a genetic variant to be cosidered common after the 1000 genome project was carried out?
Any genetic variants that had a frequency of over 1% were deemed to be common.
How does the genome browser help geneticisits?
It allows them to compare different genomes to determine the prevalence of genetic diseases.
What is the genome browser?
A website that displays information obtained by various genome projects.
What is a microarray?
A laboratory tool that is used to detect the expression of thousands of genes at the same time.
What do microarrays allow scientists to do?
To compare gene expression between different people or different populations.
What is comparative genome hybridisation (CGH)?
This microarray that compares a patients DNA to a control DNA.
What does CGH allow scientists to detect?
Missing regions or duplicated regions within the patients DNA.
How can insertions and deletions be detected within a patients DNA?
CGH can detect the amount of copies of each gene.
Usually each person has 2 copies of a gene.
However, people that have suffered from insertions or deletions will have more or less copies of each gene.
How does CGH allow scientists detect for insertions or deletions within a patients DNA?
By comparing the patient’s genome with a control genome to determine if insertions or deletions have occurred.
What kind of DNA from patients is often compared to a standard DNA via CGH?
DNA that is found in cancer cells.
How is the patient and control DNA prepared for CGH?
It is extracted and labelled with a fluorescent dye.
The control DNA is labeled with a fluorescent dye of a different colour.
The 2 DNA fragments are hybridised and then added to the array
What happens in CGH when the 2 sets of DNA are added to the array?
They will compete with each other to attach to the array.
How is the hybridisation of DNA to the array detected in CGH?
Patient DNA is given a green dye and the control DNA is given a red dye.
Areas where patient DNA has been deleted is represented by control DNA and these areas turn red.
Areas where patient DNA has suffered from insertions have 3 copies of a gene and these areas turn green.
Areas where both sets of DNA have hybridised to the array will show up as yellow areas.
How many copies of a gene will a patient have if they have suffered from a deletion?
1 copy.
How many copies of a gene will a patient have if they have suffered from an insertion?
3 copies.
What are SNP chip arrays used to detect?
This microarray looks for all of the unique single base pair changes that are known.
What does the SNP chip technique use to detect single base pair change?
A DNA marker that arises from a single base pair difference at one particular site in the genome.
What are the DNA markers that are used for SNP chips made up of?
Of oligonucleotides that contain known DNA sequences that can hybridise to the same sequences within the DNA strand.
How do SNP chips detect a SNP within a DNA strand?
If the DNA sequence contains an SNP then the oligonucleotide will not hybridise to the DNA strand.
What will represent the hybridisation of the oligonucleotide to the DNA
By a fluorescent marker.
What conditions must the oligonucleotides that are used for SNP chips be synthesised under?
Under high stringency conditions which are high temperature and low salt.
What kind of sequencing can be carried out by next generation sequencing (NGS)?
Massively parallel sequencing which is a very quick way of sequencing the genome.
How is NGS carried out?
By sequencing millions of DNA fragments at the same time.
This allows for an entire genome to be sequenced in one day.
Why is NGS better than Sanger sequencing?
Because it is quicker and cheaper.
What are expression and tiling arrays used to detect?
Theycan both detect the expression of mRNA within different tissues.
Knowledge of the human genome allows physicians to develop what?
Drugs that are tailored to a persons immune system.
Knowledge of persons genetic sequence allows physicians to determine what?
Whether a person is susceptible to a certain disease or whether they are resilient to other diseases.
The likelihood of a person acquiring a disease before they display symptoms.
What is a major problem that is associated with personalised medicine?
The privacy of the information that is obtained.
What is the genetic information non discrimination act (GINA)?
It prevents discrimination against an individual that is likely to develop a disease.
It prevents high insurance premiums that are associated with the likelihood of developing a disease.
