L1: Human Genome Organization (farook) Flashcards
how many copies of DNA are found in the nucleus and how many in the mitochondria?
- Nuclear genome is comprised of 2 copies of 23 chromosomes
- Each mitochondria has several copies (2-10 copies) of mitochondrial DNA
What is the structure of nuclear and mitochondrial genomes?
Nuclear: Linear structure
Mitochondrial: Circular structure
compare gene and genome
What is the mode of inheritance for mitochondrial and nuclear genomes?
Nuclear: both mother and father (diploid)
Mitochondrial: only mother (haploid)
Which genome size is bigger?
Nuclear genome (3.2 x 10^9)
Which genome has more genes?
Nuclear genome
What is the coding region for mitochondrial and nuclear genomes?
Nuclear:
2% coding (for proteins & survival/adaptation)
98% non-coding (indirectly involved in cell regulation/gene expression)
Mitochondrial:
97% coding
3% non coding
Who stated that the dna is double stranded and helical?
Franklin
What did chargaff discover?
The 2 strands of dna are attached to each other by 4 bases A, T, C, G
What is a nucleotide made up of?
How are 2 nucleotides linked together?
By phosphodiester bond (covalent bond) between the sugar of one nucleotide and phosphate group of another nucleotide
What links the 2 STRANDS together? (Not 2 nucleotides)
Hydrogen bonds between complementary base pairings
How are such large DNA fibers (2 meter long, 3 billion base pairs distributed over 46 chromosomes) compactly packaged in a small nucleus?
In which stage of mitosis does the Linear DNA pack with histones and supercoil?
In the Metaphase stage
What is the significance of metaphase chromosome?
Metaphase chromosomes are used in karyotyping to identify the chromosome number and structure anomalies. For e.g. if a chromosome is lost, translocation
What is DNA denaturation?
When heating breaks the hydrogen bonds between the 2 strands
Denaturation of a DNA at a particular temperature depends on what?
The G-C and A-T contents of a DNA DNA containing A-T base pairs need about 70°C to melt bc of weaker 2H bonds DNA containing G-C base pairs need about 95°C to melt bc of stronger 3H bonds
What is the melting temperature?
The temperature at which the DNA strands are 50% denatured
How are denaturation and renaturation used?
1) Hybridization 2) PCR
Why is hybridization used?
What is the use of PCR?
It is used to amplify (increase) the amount of DNA so it can be used or analyzed a certain way
What are the main differences between a prokaryotic and a eukaryotic structure?
1) Prokaryotes do not have introns, therefore they do not have non coding regions 2) eukaryotes are monocistronic = one mRNA is translated into one protein Prokaryotes are polycistronic= one mRNA is translated into 3 proteins
What is the typical structure of a gene in a eukaryote?
Humans 2% of coding genes are homologous to who?
98% of our 2% of coding genes are similar to those of chimpanzees
Non Coding (98%) is divided into what?
Repetitive (47%) DNA is divided into what?
What are satellites and where are they located?
Satellite DNA is a type of non coding tandem repeat, they are repeated many times on a chromosome but adjacent to each other on HETEROCHROMATIN regions (telomeres and centromeres)
How are tandem repeats/satellite DNA’s classified?
They are classified based on the number of base pairs
Which type of repetitive DNA is more common; Interspersed or tandem?
Interspersed (44%) > Tandem (3%)
Transposons are also known as? What are they?
Jumping genes, they can randomly move from one genomic location to another
When can transposons become an issue?
If they jumped into a non coding region they are safe, but if they jumped into a coding region they can alter the protein and cancer may be formed
What are the types of transposons?
DNA transposons (3%) RNA transposons (41%)
Why’s it called RNA transposon?
Because it needs to be converted to RNA form first before being pasted in another location first
What are the types of RNA transposons?
LTR 8%
Non-LTR 33% :
- LINES 20%
- SINES 13%
How do transposons move from one genomic location to another?
DNA transposons do that by simple cut and paste mechanisms
Retrotransposons:
- They first copy themselves into RNA using host RNA polymerase
- RNA will then be reverse transcribed into DNA using transposon encoded RNA transcriptase
- Finally DNA will be encoded into another location using transposon encoded integrase
What triggers the transposons moving from one genomic location to another ?
Factors triggering transpositions are not well known. • However, environmental (Radiation and cold temperatures) & genomic stresses seem to activate transpositions.
Transposition occurring in promoter region of a gene alters its
Gene expression
Transposition occurring in coding region of a gene disrupts its
protein sequences
Transposition occurring in intron/exon boundaries of a gene disrupts its
mRNA splicing
What transpositions have been associated with various forms of cancer?
Alu transpositions
What is one of the best studied transposons affecting coding region? And what do they belong to? How long are they w shkthr fee?
- Alu elements (sequences) & they belong to SINEs retrotransposons.
- They are about 300 base pairs in long.
- Over one million copies are interspersed throughout the human genome.
What might have played a role in Human/Chimp evolution/differentiation?
retrotransposons (About 4.0% of sequence differences were primarily identified in the 41% of the RNA transposons sequences. )
What retro transposition was similar between humans and chimpanzees and which one was different?
Similar: SINE
Different: LINE1
What are considered as important drivers of Human evolution?
Moving from one location to another and inducing mutations are considered as important drivers of Human evolution.
What 3 species is this slide talking about?
Humans Chimpanzees Bonobos
What is a nucleosome?
Octamer histones with dna wrapped around them twice
Nucleosomes are separated by what?
30 bp linker dna between H1
What prevents the nucleosomes from becoming a mess/tangled?
H1 histone binding on the 30 bp linker site
What structure is formed by the binding of histone proteins with DNA? 2018
Nucleosome
To which human genome do Alu element belongs? 2017
Short interspersed sequence
Where can we find Satellite DNA?
Heterochromatin
What differentiates a prokaryotic gene from a eukaryotic in terms of gene structure? 2014
Absence of introns
What is the most common sequence on human genome? 2013-2012-2011
Alu family
Which Histone is NOT present in the nucleosome core? 2012
H1
What is the characteristic of metaphasic chromosome? 2012-2011-2010
4 strands of DNA with histones
Which DNA sequence is used for DNA fingerprinting? 2012-2010
Hypervariable minisatellite
