Midterm 1 Flashcards
What is genetic mapping?
Figuring out the order and distance between genes and a chromosome based on recombination frequency
Genetic mapping helps in understanding gene linkage and inheritance patterns.
Define recombination frequency.
The likelihood that two genes will be inherited together during recombination.
Closer distance between genes results in lower recombination frequency.
What are the units used in genetic mapping?
Centimorgan (cM) or Relative map units (m.u.)
1 cM = 1 Mbp.
What are markers in genetic mapping?
Landmarks used to help map the genes.
Markers can be phenotypic or genetic.
What are phenotypic markers?
Observed traits used to indicate the presence/absence of certain genes/alleles.
Example: Red eyes in flies indicating a close association with white skin.
What are genetic markers?
Using polymorphisms - unique DNA sequences - as a landmark.
Genetic markers help in locating genes on chromosomes.
Define Restriction fragment length polymorphism (RFLP).
Using changes in restriction site activity to predict the relative location of a given gene.
RFLP analysis helps identify disease-related genes.
What are Single Nucleotide Polymorphisms (SNPs)?
Using the minor allele frequency (MAF) and/or a haplotype as a landmark to predict the relative location of a gene.
SNPs are critical for genetic variation studies.
What is a Simple sequence length polymorphism (SSLP)?
Using the variation in tandem repeated sequences as a landmark for relative gene position.
SSLPs can be microsatellites or minisatellites.
What are microsatellites?
Uses the variation of repeated sequences as a landmark.
Microsatellites are more stable and predictable due to shorter repeats.
What are minisatellites?
Less stable due to long repeated sequences and more complex.
Minisatellites are typically located at telomeres and centromeres.
Define biochemical markers.
Uses changes in physiological changes to manipulate the environment to see if the culture grows or not when a given gene is present.
Biochemical markers help understand gene functions in specific conditions.
What is physical mapping?
The actual positions of the gene on the chromosome, independent of recombination and polymorphisms.
Physical mapping provides high and low resolution data.
What units are used in physical mapping?
Base pairs (bp) or million base pairs (Mbp).
1 Mbp = 1 cM.
What are physical markers?
Physical landmarks that show the actual location of a given gene.
Typically, there is 1 marker for every 100 kb.
Define restriction site mapping.
Identifying non-polymorphic restriction sites by mixing DNA with specific restriction enzymes to determine the exact location of the restriction sites.
This method uses variation in fragment length.
What is Fluorescence in Situ Hybridization (FISH)?
Uses fluorescent probes that are complementary to a known non-polymorphic unique sequence to visualize their location in the chromosome.
Visualization occurs only if the probe is 100% complementary.
What are Sequence Tag Sites (STS)?
Using primers that are complementary to the flank regions of a known unique non-polymorphic sequence to properly identify its location.
STS serves as a landmarker in physical mapping.
What are clones in genomic research?
Fragments of DNA that match certain regions of a given genome.
Clones allow for further analysis into physical marker identification.
What is genomic sequencing?
Figuring out the order and location of an unknown sequence of DNA.
Genomic sequencing is crucial for understanding genetic information.
What is the Shot-Gun Method?
Sequences small fragments of DNA that are completely unknown.
This method includes organizing fragments by size and inserting them into vectors.
What are paired-end reads?
Both the 3’ to 5’ and the 5’ to 3’ ends are sequenced.
This method enhances the accuracy of sequencing.
What is the Contig Method?
Assembles reads into contiguous sequences and anchors those contigs to a physical map using physical markers.
This method helps in assembling large genomic regions.
Define annotating in genomic studies.
Identifying the significant elements of a DNA sequence.
Annotation is crucial for understanding gene functions.
What is an Open Reading Frame (ORF)?
A sequence within a genome that contains a start and stop codon and is used to produce a functional protein.
ORFs are critical for identifying genes.
What is a closed reading frame?
A sequence within a genome that does not produce a functional protein.
Closed reading frames typically represent introns.
What is codon bias?
Using the frequency of certain triplet codons to predict the correct reading frame based on the AAs produced.
Codon bias is important for accurate gene prediction.
What are exon-intron boundaries?
Unique consensus sequences derived from splice sites that help identify the boundaries between exons and introns.
These boundaries are crucial for correct gene expression.
What are CpG islands?
Unique regulatory sequences that are rich in CGs and tend to be protected from methylation.
CpG islands are often associated with gene regulatory regions.
Define homology search.
Comparing a given sequence to known related genomes in search of similar sequences with similar functions.
This method helps in predicting gene functions.
What is synteny?
The tendency of exons to be conserved within the same location of a chromosome through evolutionary processes.
Synteny can indicate evolutionary relationships.
What is exon trapping?
Using splicing vectors to help identify coding regions by inserting DNA fragments into an intron of a known splicing vector.
This method allows observation of gene expression.
What is the human genome’s gene-related sequence percentage?
38%.
This includes exons, pseudogenes, and introns.
What are retrotransposons?
RNA elements inserted back into DNA in a different location using RNA intermediates.
Retrotransposons contain both coding and non-coding regions.
What are LINEs?
Long interspersed nuclear elements, autonomous transposable elements containing non-coding and coding regions of DNA.
LINE-1 is an example of an active LINE.
What are SINEs?
Short interspersed nuclear elements, short non-coding DNA sequences that rely on LINE for transposition.
Alu is a common example of a SINE.
Define transposons.
Transposable elements of DNA that move from one position of the genome to another.
Transposons can be conservative or replicative.
What are terminal inverted repeats (TIR)?
The sequence on one end is reversed and complementary to the sequence on the other end.
TIRs are often mutated or missing in transposons.
What is comparative genomics?
A comparison of two or more genomes to discover similarities and differences between them.
Comparative genomics helps in understanding evolutionary relationships.
Define homolog.
A gene related to a second gene by descent from a common ancestral DNA sequence.
Homologs can be orthologs or paralogs.
What are orthologs?
Genes in different species that evolved from a common ancestral gene by speciation.
Orthologs typically retain the same function through evolution.
What are paralogs?
Genes related by duplication within a genome.
Paralogs can evolve new functions over time.
What does GC-rich areas indicate?
Likely maintained to aid in the initiation of transcription, thus making them gene-rich regions.
GC content can provide insights into genomic structure.
What is codon bias used for?
Observing the frequencies of certain codons for certain amino acids to provide information about evolutionary relationships.
Codon bias can indicate potential gene function.
What is the significance of conserved domains?
Specific structures conserved in one species may indicate a similar function in other species.
Conserved domains can reveal evolutionary relatedness.
What does the diversity in protein production and function between species indicate?
It indicates the identification of important genes through conservation over evolutionary processes.
Conservation of genes suggests that these genes have significant roles in the biology of the species.
What explains the differences in traits between species?
The differences in how certain genes are expressed and the presence of conserved regulatory regions.
Regulatory elements can significantly influence gene expression, affecting phenotypic traits.
What are conserved domains?
Specific structures that are conserved across species, indicating similar functions and relatedness.
Conserved domains can suggest evolutionary relationships between species.
What is the significance of conserved proteins?
They may indicate significance in cellular function and aid in predicting the function of unknown proteins.
Similar protein structures across species can provide insights into evolutionary adaptations.
What are orthologues?
Genes in different species that evolved from a common ancestor and retain the same function.
Studying orthologues can help in reconstructing ancestral genomes.
What does GWR stand for in genomic studies?
Genomic Wide Repeats.
GWR analysis can reveal how genomes have expanded or contracted over time.
What does transposon selectivity indicate?
It indicates evolutionary constraints and can predict future transposition preferences.
Transposons can play a significant role in genome evolution.
How can drug discovery benefit from genomic comparisons?
By identifying the effectiveness of drugs that target specific genes in pathogenic organisms.
Understanding viral factors can lead to the development of species-specific antibiotics.
What is Sanger Sequencing?
A method using chain termination via ddNTPs to generate DNA fragments of varying lengths for sequencing.
Sanger sequencing involves gel electrophoresis to read DNA sequences.
What is a di-deoxy nucleotide (ddNTP)?
An NTP missing a 3’OH that results in chain termination during DNA synthesis.
ddNTPs are critical for the chain termination process in Sanger sequencing.
What are the steps involved in classic Sanger Sequencing?
- Divide DNA templates into 4 tubes. 2. Add primers, polymerase, NTPs, and one ddNTP per tube. 3. Perform chain termination. 4. Analyze fragments via gel electrophoresis.
Each tube corresponds to a different ddNTP, creating varied lengths of DNA fragments.
What is modern Sanger Sequencing?
A method that uses one tube with all 4 ddNTPs tagged with fluorescent dyes for sequencing.
Capillary electrophoresis is used to detect the fluorescent signals.
What are the advantages of Sanger Sequencing?
Produces high-quality and accurate reads.
However, it has low throughput and is expensive.
What is 2nd Generation Sequencing?
A method using in vitro amplification to produce millions of copies of DNA fragments for sequencing.
It allows for massive parallel sequencing, significantly increasing throughput.
What are adaptors in 2nd Generation Sequencing?
Synthetic DNA sequences ligated to the ends of target fragments that serve as PCR primer binding sites.
Adaptors enable the hybridization of fragments to solid surfaces.
What is emulsion PCR?
A method that amplifies DNA fragments in microreactors by encapsulating them into oil droplets.
This technique allows for massive parallel amplification of DNA.
What is bridge PCR?
A method that amplifies DNA fragments on a flow cell by forming a bridge between adaptors.
Bridge amplification allows for high-density sequencing on a solid surface.
What does pyrosequencing detect?
It detects a light signal when pyrophosphates (PPi) are released during DNA synthesis.
The intensity of the light indicates the number of incorporated NTPs.
What is a major disadvantage of pyrosequencing?
High error rate due to difficulties in detecting homopolymers.
Homopolymers are sequences of the same nucleotide repeated multiple times.
