Human Genome Organization - Sikela Flashcards
Of the _________ base pairs in the human genome, only ___% code for proteins and ___% are regulatory.
3 billion
1.5%
5%
Inheritance pattern of mitochondrial DNA?
How many genes does mitoch. DNA code for?
Maternal inheritance
codes for 37 genes
What is single-copy DNA?
DNA whose nucleotide sequence appears once (or only a few times) in the genome.
What is repetitive DNA?
DNA whose nucleotide sequence is repeated (exactly or very nearly so) hundreds to millions of times in the genome.
Normal human chromosomes:
_____ autosomal pairs
_____ pair of sex chromosomes ____
22
1, XX or XY
Typical vs. Retroposed gene?
typical = intron-containing retroposed = intronless
Give two types of repetitive DNA.
- Tandem repeats (head-to-tail)
2. Interspersed throughout the genome
What / Where is the alpha-satellite family of DNA?
Composed of tandem arrays of a 171-bp repeat located at the centromere of each chromosome.
Critical for attachment of centromeres to the microtubules of the spindle apparatus during cell division.
LINE and Alu sequences?
dispersed repeats making up a significant portion of the genome (Alu 10%, LINE 20%).
implicated in some hereditary diseases
About _____ new mutations occur in each individual.
Genotype + ______ = phenotype.
30
environment
Why might it be the case that trisomy of chromosomes 13, 18 and 21 are the ones where the fetus survives to live birth?
These genes are the three most “gene poor” of all the autosomal chromosomes. Only the Y chromosome has fewer genes.
Does the human genome has more A-T rich regions or more C-G rich regions?
A-T
54% A-T rich
38% C-G rich
Euchromatic regions of the genome are more __________ while Heterochromatic regions are more _______ and _______.
relaxed
condensed and repeat-rich
Medically important genes: beta-globin, BRCA1 and MYH7 (beta-myosin heavy chain).
How many exons in each and what diseases are each linked to?
beta-globin: 3 exons, hemoglobin disorders
BRCA1: 24 exons, breast and ovarian cancer
MYH7: 40 exons, inherited hypertrophic cardiomyopathy
Beta-like globin genes on chromosome 11. What are they and in what order are they turned on?
Beta-like globin genes code for hemoglobin subunits and are positioned along the chromosome and turned on in the following order (5’ to 3’)
- Epsilon; embryonic yolk sac
- G_gamma, A_gamma; fetal liver, spleen and bone marrow
- Delta, Beta; birth –> adulthood
In general, two individuals’ genomes will be ______% identical and differ by ________ base pairs.
99.9%
3,000,000
What is special about the repeats found on the long arms of chromosomes 1, 9, 16 and Y
These contain a pentaneucleotide repeat and are hotspots for human-specific evolutionary changes
What is a retrotransposition product?
when RNA –> cDNA and this cDNA gets inserted into the genome.
may inactivate genes
What is NAHR?
non-allelic homologous recombination
as a result of repeats, non-allelic repeats line up (incorrectly) and undergo recombination at the wrong spot.
–> microdeletions / microduplications
What are copy number variations? (CNV’s)
What percentage of the genome do they cover?
a form of structural variation:
variation in segments of the genome (200bp - 2Mb) that can range from one add’l copy to many or in a deletion of a segment.
may cover 12% of the loci in the genome
Gene families arise through _____________ and are a major mechanism behind _____________.
gene duplication
evolutionary change
Between any to human genomes there is roughly one SNP every _________ base pairs.
1000
Give two examples of intronless genes.
Histones
Interferon
What is a gene family?
A set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions.
Describe the Alu gene family
a family of dispersed repetitive elements
about 300 bp in length (similar but not identical to each other)
about a million of them in the total genome (10% of the DNA)
Describe the LINE gene family
LINE = Long Interspersed Nuclear Element
up to 6 kb in length
about 850,000 copies per genome (20% of the genome)
The OR family of genes is really a part of what “super-family” of genes?
The G protein gene superfamily.
G protein-coupled receptors, characterized by a conserved membrane-spanning protein motif, are critical for the function of a diverse repertoire of receptors. (see ch. 12)
What is a pseudogene?
What are the two main types of pseudogenes?
DNA sequences that closely resemble known genes (e.g. globin family or OR family) but are non-functional.
- Non-processed pseudogenes are thought to be byproducts of evolution & are perhaps “dead” genes (vestigial)
- Processed pseudogenes are formed by retrotransposition (incorporation of cDNA into the genome)
What is unique about processed pseudogenes?
Since processed pseudogenes are retrotransposed (RNA –> cDNA –> incorporated back into the genome) they lack introns and may not be on the same chromosome as their progenitor gene.
What is an important class of non-coding RNA genes.
Non-coding RNA genes for microRNA (miRNA).
miRNA’s are short (22-bp) that (often) control expression or repression of other genes throughout development.
What are micro and mini satellite genes?
Two different types of multi-allelic insertion / deletion (indels) polymorphisms
What is a microsatellite?
di-, tri-, or tetra-nucleotide repeats. Repeated one to a few dozen times.
5 x 10^4 per genome
a.k.a. Short Tandem Repeat Polymorphisms (STRP’s)
What is a minisatellite?
10-100 bp, tandem repeat blocks of DNA
a.k.a. Variable Number Tandem Repeats (VNTR’s)
Used in Southern Blot DNA fingerprinting. Only identical twins will have identical versions of their VNTR’s
What is the missing heritability problem?
Many regions of the genome remain unexamined.
The currently implicated loci for genetic contribution (to complex diseases) do not seem “sufficient” to account for the observed variability and number of diseases.
