Chapter 15: Genomics and Proteomics Flashcards
What are omics?
- Field of biology aims at the collective characterization and qualification of pools of biological molecules that translate into the structure, function, and dynamics of an organism
- Large-scale
What are genomics?
Attempts to understand the content, organization, function, and evolution of the genetic information contained in whole genomes
What are genetic maps?
- Rough approximation of the locations of genes relative to the locations of other known genes
- Based on the genetic process of recombination
What are physical maps?
Based on the direct analysis of DNA (physical distance measured in base pairs)
How are distances on a genetic map measured?
CentiMorgans
What was the first free-living organism to be sequenced?
The bacteria Haemophilas
How do physical maps compare to genetic maps?
Physical maps generally have a higher resolution and are more accurate than genetic maps
What are collinear relationships?
- Comparing a genome with little known information to other genomes helps determine their origins, and their genomic characteristics
- Concerns species that are linked in evolution
- Many genes are present in the same order in related genomes
Provide an example of a collinear relationship.
- Rice was compared to Brachypodium, which was then used to uncover characteristics about Sorghum
- Sorghum was difficult to characterize
What are homologous sequences?
Sequences that are evolutionarily related
What are orthologs?
Homologous sequences found in different species
What are paralogs?
Homologous genes in the same species that arise from gene duplication
What were the overall steps to determining the human genome?
1) Map-based sequencing
2) Flow cytometry
3) Partial digestion of each chromosome
4) DNA fragments are cloned
5) Large-insert clones are put together in the correct order based on their overlapping features
What is map-based sequencing?
- Short sequenced fragments are assembled into a whole-genome sequence
- By first creating detailed genetic and physical maps of the genome, which provide known locations of genetic markers at regularly spaced intervals
- These markers are later used to help align the short sequenced fragments in the correct order
What is flow cytometry?
Used to separate individual chromosomes from a single unique cell
What is partial digestion?
- Restriction enzymes are allowed to act for only a limited time
- Produces a set of large overlapping DNA fragments
What is a contig?
A set of two or more overlapping DNA fragments that form a contiguous stretch of DNA
A contig is
A) A set of molecular markers used in genetic mapping
B) A set of overlapping fragments that form a continuous stretch of DNA
C) A set of fragments generated by a restriction enzyme
D) A small DNA fragment used in sequencing
B) A set of overlapping fragments that form a continuous stretch of DNA
What is whole-genome shotgun sequencing?
The entire genome is assembled based on sequence overlap
What is a single-nucleotide polymorphism?
A site in the genome at which individual members of a species differ in a single base pair
What is a haplotype?
- The specific set of SNPs and other genetic variants observed on a single chromosome or part of a chromosome
- Each haplotype is made up of a particular set of alleles at each SNP
Why are SNPs used as a marker for linkage studies in diseased states?
- When a SNP is physically close to a disease-causing locus, it will tend to be inherited along with the disease-causing allele
- People with a diseased tend to have different SNPs than healthy people
How do SNPs compare to RFLPs?
There are many more SNPs, providing a dense set of variable markers covering the entire genome
What is the transcriptome?
All the RNA molecules transcribed from a genome
What are microarrays?
Rely on nucleic acid hybridization, in which a known DNA fragment is used as a probe to find complementary sequences
What information can microarrays provide?
- Information about gene expression (which RNA molecules are synthesized)
- How gene expression changes in the course of biological processes (development, or disease)
What do red and green fluorescence indicate in microarrays?
- Red: overexpression of a gene in a cancer cell
- Green: overexpression of a gene in a non-cancer cell
What is mass spectrometry used for?
Method to determine the precise molecular mass of a molecule
Mass spectrometry separates molecules on the basis of their _________ ratio
mass-to-charge
What are the dimensions of two-dimensional acrylamide gel electrophoresis?
- One dimension separates based on charge
- Another dimension separates based on mass
What method may be utilized to analyze protein-protein interactions?
Protein microarrays
What are some of the limitations of genetic maps?
Accuracy and resolution
What is the difference between orthologs and paralogs?
A) Orthologs are homologous sequences; paralogs are analogous sequences.
B) Orthologs are more similar than paralogs.
C) Orthologs are in the same organism; paralogs are in different organisms.
D) Orthologs are in different organisms; paralogs are in the same organism.
D) Orthologs are in different organisms; paralogs are in the same organism.
