Genetics/Genomics/Human Variation Flashcards
1
Q
how much DNA is in the human cell?
A
- About 3 billion bp (haploid), over 23 chromosomes
2
Q
describe single copy genes
A
- Unique sequences in the genome that code for a protein:
- receptors, enzymes, hormones, structural cellular elements, etc.
3
Q
describe multigene families
A
- Can be clustered together or dispersed in different genomic locations
- Genes with similar functions that have arisen by gene duplication
-
Classic gene families
- multicopy genes that show a high degree of homology
-
Gene superfamilies
- multicopy genes with similar function but limited gene homology
4
Q
describe tandem repeated DNA sequences
A
- Tandem repeated DNA sequences consist of blocks of tandem repeats of non-coding DNA
- length of repeat sequences determines how it is named
- The shorter the repeat length, the more polymorphic that sequence is
- Tandem repeats inherited in a co-dominant fashion; one from each parent
- Used as basis of DNA fingerprinting
5
Q
explain SNP
A
- Single nucleotide polymorphism
- Formally defined as a variant that is found at least in 1% of the population
- Single base pair change between individuals
6
Q
explain SSR
A
- Simple Sequence Repeat
- these are the most simply type of repetitive sequence and most polymorphic
- These are tandem repeats of 2, 3, or 4 bp repeated many times
7
Q
explain VNTR
A
- Variable number tandem repeat
- These repeats are a bit longer than the SSR, maybe 5 bp or 10 bp, or 100 bp; repeating many times
8
Q
explain LCR
A
- LCR: Low copy repeat
- may be very large
9
Q
explain low copy repeat
A
- These may be thousands (kb) to many hundreds of thousands of bp long
- May be repeated just twice in the genome or many times
- May cause mispairing during meiosis or mitosis
10
Q
explain long interspersed nuclear elements (LINEs)
A
- Highly repeated interspersed repetitive sequences
- ~6000 bps
- Found in large numbers in eukaryotic genomes
- Able to make an RNA
- LINEs include a gene that encodes reverse transcriptase
- LINEs are capable of copying themselves and may enlarge the genome
- Human genome contains 100,000s LINEs
- LINE and SINE sequence repeats may contribute to mutation by leading to unequal crossover during meiosis
- Same idea as for Low Copy Repeat Sequences
11
Q
explain short interspersed nuclear elements (SINEs)
A
- Also a highly repeated interspersed repetitive sequence
- Short sequence of <500 bp that are found up to 1.5 million times in the genome–approxiamtely 10% of the human genome
- Appear to be “normal” RNAs that were coverted to DNA by reverse transcriptase and were reinserted into genome
- Reverse transcriptase hijacked from a LINE
- Most common SINE in humans is the Alu sequence. Called Alu because SINEs contain a sequence that is recognized by the Alu restriction enzyme
12
Q
SNPs vs Rare variants
A
- SNPs
- commonly found in many individuals (at least 1% of pop)
- In total, there are only about 3 million or so of them
- So there are not many of them, but they are common
- Thought to have arisen early in human evo.
- Rare variants
- Rare in the pop…but may be found in any of the 3 billion base pairs of the haploid genome
- So rare variants are “rare” in that they are not freq. found in the pop. but there may be billions of them
- Rare variants are thought to contribute to human disease more than SNP
13
Q
describe pseudogenes
A
- Sequences that look like real genes but are not functional (no protein product)
- Arose during evol. by:
- gene duplication and subsequent mutation
- copying of RNA back to DNA (by viral reverse transcriptases) and reinsertion into genome
- The gene is turned off for some reason
14
Q
describe mitochondrial DNA
A
- Single circular DNA of 16.6 kb
- Codes for some mitochondrial tRNA and other factors needed for mito gene expression
- Most mitochondrial proteins are encoded by nuclear genes
- Maternally inherited (all mitochondria come from the cytoplasm of the oocyte)
- More prone for mutation
15
Q
describe the chromosome at metaphase
A
- Appearace of a chromosome during metaphase when they are maximally condensed and most visible
- The MTs attach to the centromere kinetochores during cell division
- The ends of a chromosome are “telomeres”
