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Genomics is closely related to --------- which uses computers, computational tools, and databases to organize and analyze DNA and protein information
T OR F ?
One goal of genomics is compilation and organization of both expressed gene sequences and other
INSULIN RESISTANT DIABETES AND HYPER CHOLESTREOLMIA (LDLR) GENES CAN BE FOUND ON WHAT CHROMOSOME?
CHROMOSOME 19 HAS ------- BASES.
CHROMOSOMAL BANDING PATTERENS ARE CAUSED BY WHAT?
differences in the ratio of the bases adenine and thymine to guanine and cytosine
Karyotype is generated....HOW?
by grouping all chromosomes of an individual together
-------------- ------------- can be used to examine metaphase chromosomes (condensed version)
HUMAN CHROMOSOME. HOW MANY?
- 22 AUTOSOMES &
- X AND Y SEX CHROMOSOMES.
- (X IS BIGGER)
CONTINUOUS SEQUENCE OF BP FROM ONE MARKER TO THE NEXT
CONSTRUCT A CONTIG
- 1. RFLP MARKER TO RESTRICTION SITE OF DISEASE.
- 2. PROBE ON 5'
- 3. ID SEQUENCE AND MAKE PROBE FOR 3'
- 4. RUN AGAIN
- 5. YOU NOW HAW A CONTINUOUS SEQUENCE OF BP FROM ONE MARKER TO THE NEXT.
Genetic Linkage Maps
NAME 3 POINTS
- -Genes on the same chromosome
- -Genes can be followed from generation to generation within famlies, 5000 disorders have been studied this way
IN A GENETIC LINKAGE MAP, genes A and B are separated by recombination 1% of the time (1:100) then they------ APART
1 cM apart (1 million bp)
Homologous recombination can occur during meiosis via ------- ------ events. HOW MANY PER PAIR?
- crossing over
- 1.5 cross overs per pair of chromosomes
T OR F?
IF GENES ARE LINKED CROSSOVER IS UNLIKLY, WHY?
Frequency of cross over is a measure of the linear distance between ---- ----- ----- -----.
genes on linkage map
CROSSOVER UNITS (MEASUREMENTS)
Distances are measured in centrimorgans (cM)
WHEN DOES CROSSOVER OCCUR?
DISEASE GENE FOR BREST AND PROSTATE CANCER ARE ON WHAT CHROMOSOME?
Specific physical regions of the DNA with
variations in DNA sequence within a specific region for different individuals...KNOWN AS WHAT?
IF A DNA POLYMORPHISM IS LOCATED ON AN INTRON, WILL CHANGE BE PRECEIVABLE?
- HAS TO BE ON CODEING GENE.
T OR F?
polymorphisms are detectable at the DNA level and can serve as markers
Restriction fragment length polymorphisms (RFLPs) ARE DETECTED HOW?
YACs cloning vectors are used to
fit the large fragments of about ------- TO --------- BP
roughly 7,500 clones for the entire human genome
------- --------- ------ can be used to clone pieces of DNA of up to 200,000 base pairs in length
- Bacterial artificial chromosomes
THE ENTIRE GENOME IS STUDIED YSING A GENOMIC LIBARARY AND WHAT?
Yeast Artificial Chromosomes (YACs)
THIS PROCESS SHOWS THE ORIENTATION OF GENES ON INDIVIDUAL CHROMOSOMES
- Fluorescence in situ hybridization
- Fluorescence in situ hybridization.
- PROBES FOR METAPHASE CHROMOSOMES IN 2 LOCATIONS.
Localizes coding regions to specific chromosome regions or bands (exons) AND Combine
linkage maps with this method to locate disease causing genes....MAP TYPE?
cDNA (PHYSICAL MAP)
-Also called bottom-up mapping
-Chromosome cut into overlapping fragments
-Clone fragments and determine order
-Fragments will form continuous DNA blocks
WHAT MAP TYPE ?
HIGH RES PHYSCIAL MAP
HOW TO YOU MAP A PART OF A CHROMOSOME?
piece is cut out and restricted, fragments cloned in YACs, mapped and sequenced using standard methods
map types range from course
to fine resolution of genetic locations:
NAME THEM FROM LOWEST TO HIGHEST
- Lowest: genetic map
- -Measures frequency of recombination between linked markers, genes or noncoding (GENES)
- MID LOW: Restriction
- - DNArestriction fragments:1-2 Mb fragments are separated and mapped.( BIG FRAGMENTS)
- MID HIGH YAC
- -0.4 cM to 1 cM fragments.
- -subclones is 20,000 to 40,000 bp (SML FRAGS)
- Highest: DNA base sequence map
- -Separate each chromosome to make 24 libraries (22 autosomal + 1each for X andY)
Human genome project REFERENCE SYSTEM, HOW MANY BP?
- 200-500 of partially sequenced DNA are used to
- identify clones, contigs, long stretches
Standard markers used for physical mapping of DNA.
Can use cDNA region as STS that is called an
---------- --- -------
- expressed-sequence tag (EST).
- -ESTs are landmarks along the map
T OR F ?
HGP Goal to generate STSs every 100,000 bp for each human chromosome (30,000 STSs)
Powerful method for finding location of genes that cause inherited diseases, and track chromosome walking.
- polymorphic DNA markers
- -Need flanking DNA markers as starting points, Hybridization to clones with contigs in the disease region...get 2 maps...compare and find region.
All genes in the entire----- chromosome genome
Human genome contains
-------- TO ------- genes on --- pairs of chromosomes
Smallest chromosome is ---- AT -------- BASE PAIRS
Y at 50 million
#1 WITH 250BP
-------- bp in a haploid genome
HGP HAS A GOAL TO MAKE TWO MAPS NAME THEM
- Genetic linkage maps:
- -Determine the relative arrangement and distances between genes and markers on chromosomes
- Physical maps specify two things:
- -The physical location, in base pairs
- -Distance between genes or DNA fragments with unknown functions
Distance between genes or DNA fragments with unknown functions
WHAT MAP WOULD YOU LOOK AT?
Genome Project Timeline
----- First physical map published.
-----The public human genome sequence draft was published
--------Close to 99.9%
Potential Uses for Genome-Related Information
- treatments and diagnostic methods
- identification of all the genes and other
- technologies to analyze genome-related information
- understanding of human evolution, gene regulation.
- genetic counseling
T OR F?
HGP.....DNA samples were from males, although female donors were used to refine DNA
sequences in later stages of the project
The human genome contains a little more than ----- BP
- 3 billion base pairs
- (3164.7 million nucleotides)
The number of genes found was close to one-third1/3 of the expected number of genes in the genome ------------------- ---------------- --------------- PREDICTED-------------- + more random than other genomes
(23,000–30,000 protein-encoding genes rather than the predicted 80,000–100,000)
approximately ----% of the human genome encodes for the production of -------- with similar protein families to other organisms
Repeated sequences that do not encode proteins make up at least ----% of the genome
—they are thought to affect ------ ----------and dynamics and is a much higher %
than all other organisms, but have stopped accumulating repeats (not so in mice)
The average length of a gene is
------- nucleotides, although sizes vary greatly
T OR F ?
Genes are not evenly distributed
across a chromosome;Genes concentrate in random regions, with large amounts of noncoding DNA between them
Gene-dense areas are composed primarily of --- & --- nucleotides.
Gene-poor regions have more --- & ---- nucleotides
- Gene-dense:G- and C
- Gene-poor: A- and T
Chromosome: FEWEST AND MOST GENES
- Y 231 GENES
- #1 2968 GENES
Approximately ----- genes originated directly from --------.
T OR F ?
Human proteins are more complex than proteins with similar functions in lower
The germline mutation rate in ----- is two times higher than in -----
MALES HIGHT THEN FEMALES
The nucleotide sequence in all humans is ------% identical
More than ------% of newly discovered genes have unknown functions
How chromosomes are organized AND The roles of DNA that doesn’t code for proteins ARE NOT COMPLETELY UNDERSTOOD.
Proteomics involve the following aspects:
- -expression and id of proteins in a given cell
- -structure of proteins (for example, tertiary folding)
- - interactions with each other in the cell
Proteomics is difficult...2 POINTS
- each cell type has the same DNA complement, but a
- different proteome
proteome can change depending on the physiological state of the cell or the organism
Full complement of genes called “transcripts” that are made in a specific cell type under a specific set of conditions, revealing changes in transcription for every gene in the genome
- Entire metabolic state of a cell, including the array of substrates, metabolites, and other small molecules that are made in different cells and tissues
- EX:four varieties of Arabidopsis
Pharmaceutical companies mostly use ------------------- in drug development
An example of a DNA database is ------, which is hosted at the National Center for Biotechnology
OTHERS 2 ARE----- AND ------
- European Molecular Biology Laboratory (EMBL)
- DNA DataBank of Japan (DDBJ)
Tools of Bioinformatics
- DNA and protein sequences COMPARISON
- Prediction of RNA secondary structure—RNA folding
- Protein classification
- Gene prediction using DNA sequences
- Genome analysis
MYTONIC DYSTROPHY...WHAT CHROMOSOME?
WHAT DOES ELSI MEAN?
- The HGPs ethical, legal, and social implications (ELSI) working group established by the DOE and NIH
- (HGP action plan co-sponsors)