1. The Human Genome and Normal Variation (2) Flashcards
WHAT IS A GENE? (3)
- Genes are made up of DNA
- Basic physical unit of inheritance
- Contain information needed to specify trait
How many genes do we have?
- Size of the genome
- DNA consists of two chains of two polynucleotide
chains in an antiparallel configuration - Upstream vs downstream
- 5’ = _______
- 3’ = ________
upstream
downstream
COMPONENTS OF THE GENE: (8)
- Exons
- Introns
- Regulatory regions
- Enhancers
- Promoter
- Transcription start site
- Transcription end site
- Translation start and stop sites
- Untranslated regions
What are exons? (3)
What are introns? (4)
- Non-coding regions between exons
- Larger than exons ~3000bp long (length varies)
- Interrupted genes consist of introns and exons
- Intron position usually conserved
REGULATORY SEQUENCES/ REGIONS: (3)
Upstream of the gene
Enhancers and Promoters
Regulate transcription of gene to mRNA
What are ENHANCERS? (4)
- Increase efficiency and rate of transcription
- Found on same strand of DNA
- Upstream
- downstream
- Proximal or thousands of nucleotides away
- Act as silencers
- Control region of a gene
What are PROMOTERS? (4)
- Special sequence that signals the start of the gene (TATAA Box)
- Located upstream of a gene (5’ end)
- Binds transcription factors
- Facilitates recruitment and binding of RNA polymerase II and initiation of transcription
What is the transcription start site? (4)
- Promoter = signal for transcription factors and RNA polymerase
- Terminator sequence signals for the end of transcription
- Transcription starts at the beginning of exon 1 and ends at the end of the last exon
- RNA sequence = pre-mRNA
RNA PROCESSING
* Gene is ________ (pre-mRNA)
* Modifications
* _____ are removed (Spliced out)
* Mature mRNA
* Ready for _______ process
transcribed
Introns
translation
What is SPLICING? (4)
- Pre-mRNA = mRNA prior removal of introns
- Removal of the intron sequences from the pre-mRNA
- Occurs specifically at the intron/exon boundaries
- The intron sequences immediately flanking the exon/intron boundarie
Which regions are conserved during splicing?
- Regions are largely conserved,
- splice sites or splice junctions
- 5’ splice site
- 3’ splice site
What are the SPLICE SITES?
What is the difference between splicing and transcription?
What is TRANSLATION? (3)
What are the start and stop codons?
What are UNTRANSLATED REGIONS (UTR’S)? (2)
- 5’ UTR: upstream of the initiation codon –region at the 5’ end of a mature mRNA transcript that is not translated into a protein
- the region of the first exon that IS transcribed, but NOT translated
- 3’ UTR: downstream of the stop codon - region at the 3’ end of a mature mRNA transcript that is not translated into a protein
- the region of the last exon that IS transcribed, but NOT translate
What does translation lead to?
Polymorphisms
* A DNA polymorphism is a change in a sequence, when
compared to a reference standard, that is present in at
least ___ of a population.
* Found throughout the genome
* If the location of a polymorphic sequence is known, it can serve as a _____ or marker for locating other genes or genetic regions
* Each polymorphic marker has different versions or alleles. The more possible alleles a _____ has, the more useful it will be.
1%
landmark
locus
What are the types of polymorphisms? (3)
What are short tandem repeats? (6)
- Also called microsatellites
- Tandemly repeated nucleotide units of 2 – 6 base pairs (bp)
- STR loci account for ± 3% of the human genome
- Most STRs are found in non-coding regions of genes (± 8% are located in coding regions)
- In humans, chromosome 19 has the highest density of STRs
- The most common STRs in humans are A-rich.
Types of STRS are classified according to: (2)
Naming of STRs
Example: D3S1266
D
3
S
1266
D represents DNA
3 means chromosome 3
S stands for STR
1266 is the unique identifier.
Example D7S280
* Tetrameric repeat sequence “______”
* Different alleles of this locus have from 6 to
15 repeats of the “gata” sequence
gata
Typing STRs - PCR: (2)
- Primers are designed to flank the repeated region
- PCR amplification generates products that differ in
length depending on the number of repeats
Visualisation of PCR products: (2)
What is Quantitative fluorescence PCR (QF-PCR)? (2)
What is an Electropherogram?
How do interpret an electropherogram? (4)
- If two peaks of the same colour appear directly next to each other, it indicates a _________ locus
- 1:1 ratio
- Generally, when peaks stand-alone, it indicates a ________ genotype at that locus
- Note that the height of the peak is approximately
double that of the stand-alone peaks
heterozygous
homozygous
What is Amelogenin? (4)
- The AMEL marker amplifies non-polymorphic sequences on the X (104bp) and Y (110bp)
chromosomes - Determine the presence or absence of a Y chromosome
- Represents the relative amount of X to Y sequence
- Since females are XX, only a single peak is observed whereas males, which possess both X and Y
chromosomes, exhibit two peaks.
What is TAF9L and SRY? (3)
- TAF9L is an invariant marker with sequences on chromosomes X and 3
- The chromosome 3 specific peak (116bp, representing two copies of chromosome 3) can be used as a reference peak to assist in the determination of
the number of X chromosomes present (121bp) - The Y specific marker, SRY, will give a single peak in normal males and will not amplify in normal females
What does the electropherogram for a male XY look like?
What does the electropherogram for a female XX look like?
What are the applications of STRs? (2)
What is percentage testing?
By comparing the DNA profile of a mother and her child it is possible to identify DNA fragments in the child that are absent from the mother and must therefore have been inherited from the biological father.
Parentage testing - why is it done?
Parentage testing
* Two main outcomes:
- Alleged parent excluded
- Alleged parent NOT excluded
- NOT 100%
Who is excluded?
Alledged father is excluded.
Who is excluded?
Alledged father is NOT excluded.
Where are samples taken?
