Nuclear Genome Flashcards
Approximately what percentage of human genes code for more than one protein?
60%
What allows one gene to code for more than one protein?
Differences due to alternative splicing: different exons are used in different kinds of cell
Different products of a gene have related but not identical functions; can be specific to a particular tissue or developmental stage. Give an example of this
The gene for alpha-tropomyosin, which:
.Helps to regulate muscle contraction
. Stabilises actin filaments in the cytoskeleton
Different types of muscle and non-muscle cells have different forms of tropomyosin. There are at least 8 different tropomyosin mRNAs. How are they different?
Different by mixing up exons, can mean they are terminated in a different place/ substitute one exon for another
Introns can contribute to variation in gene size. Give an example of this:
The Huntington gene in humans and Pufferfish. Gene codes for a very large protein (3143 amino acids in humans, 3148 amino acids in pufferfish) found in the brain. In humans mutations cause Huntington’s.
In both species they have 67 exons, so 66 introns but the introns are larger in humans
What is repetitive DNA?
DNA that occurs in many copies (generally similar, not identical, to one another) in the genome
Give an example of a very simple tandem repeat
AAGAG/AAGAG/AAGAG… in Drosophila melanogaster; this repeat makes up about 6% of the genome
What do tandem repeats/ simple sequence repeats contribute to?
Contribute to the organisation of chromosome structure, including centromeres, telomeres
Give an example of a tandem repeat that contributes to organisation of chromosome structure, including centromeres, telomeres
Alpha satellite (density of the DNA is different characteristic base composition) DNA: 171bp sequence repeated thousands of times (imperfectly) at centromeres of all human chromosomes. Make up at least 5%of human genome
Much of repetitive DNA consists of mobile DNA elements (transposons). What are these?
. Essentially ‘molecular parasites’
. Can be duplicated and transpose/ move into new regions of the genome into new sits in the genome- very slowly (because it may cause mutation) 1 copy, then 2, then 3
What are the major classes of transposons in the human genome?
. LINES: long interspersed element = 6kbp
. SINES: short interspersed elements = 100-400
What is the mechanism of transposition?
LINES, SINES and retro viral-like elements all transpose via an RNA intermediate (DNA -> RNA -> DNA). The RNA is copies to DNA by reverse transcription (RNA binding protein, reverse transcriptase) then the DNA will insert itself into the genome
What do LINES code for?
Code for enzymes requires for transposition. (RNA binding protein, reverse transcriptase). However, <100 out of >500,000 in the genome are active. Estimated current transposition rate in humans: 1 insertion for every 20 to 200 births
Why are SINE elements controlled by LINE elements?
Because they are non-autonomous (they can’t transpose themselves): transposition depends on LINE elements (can transpose them), so SINE elements are controlled by the LINE elements.
Describe Alu elements
Make up about 10% of human DNA. They are about 300 bp long- members of the SINE class. There are >1 million Alu elements in the human genome; any region of 5kbp is likely to have one
Where did the alpha and beta subunits in haemoglobin diverge from?
From the original 1 about 500 million years ago (the genes for the whole and beta subunits are at different loci. Each locus has several genes)
Describe the human beta-globin cluster
5 gene splus 1 non-functional pseudogene, spread over about 50 kbp
How did the beta-globin cluster form?
Revolves by gene duplication, followed by change or loss of function
What is the LINEs and SINEs arrangement in the beta-globin cluster in human and mice?
. Similar arrangement of genes
. Different arrangment of SINEs and LINEs
Describe the yeast genome
Is compact:
. Approx 4% repetitive DNA
. Average of 2kbp per gene
. Almost 70% of genome consists of open reading frames
. Little spears between genes
. 96% of genes have no introns
. Remaining genes usually have only one intron
Describe he human genome
. Less than 2% of the human genome codes for proteins
. >50% repetitive DNA
. Average of one gene per about every 90kb
. Genes commonly have multiple introns, which in many genes are longer than the exons
. The average primary transcript is about 30kb but the average coding sequence is about 1.4kb. Most of the human genome is transcribed; functions of many transcripts are unknown
What is synteny?
Comparison of genomes of different organisms shows that the order of genes in chromosomes is partly conserved through evolution.
Comparison of whole chromosomes can show extensive conserved blocks, especially in relatively closely related organisms (e.g. humans and mice). Conservation can even be detected even between pufferfish and humans (corresponding large fragments of chromosome 2 of both species)
Give the essential concepts of eukaryotic genomes
. Eukaryotic genomes are large and variable in size
. Number of genes varies less than genome size
. Variability comes from: introns and intervenor (including repetitive DNA)
. Alternative splicing can give >1 gene product per gene
. Order of genes is partly conserved among related organisms
How many chromosomes do humans have?
46
Describe a chromosome
Contains a single DNA molecule complexes with proteins to form chromatin
Proximately how long is DNA in a human cell?
2m
Give the essential sequences in chromosomes
- Multiple replication origins, typically 30,000 to 250,000 bases apart
- Because DNA is linear, ends must be protected: ends are telomeres, defined by specific repetitive DNA sequences to which specific proteins attach
- Specific repetitive DNA sequences with specific proteins attached also define the centromeres, where sister chromatids are held together and then pulled apart during mitosis
Describe nucleosomes
The nucleosome is the basic building block of chromatin:
. 8polypeptides: 2 copies each of his tones H2A, H2B, H3, H4 (positively charged)
. DNA forms 2 loops around the histones
What is the standard for further levels of packaging DNA?
View has been that nucleosomes are packed by Huston’s H1 into 30nm fibres. However, recent evidence indicates that “chromatin is a flexible and disordered 5-to -24nm diameter granular chain that is packed together at different concentration densities in interphase nuclei and mitotic chromosomes”
Describe further packaging of DNA
Most popular model suggests that chromosome is folded up into loops attached to central scaffold (which is protein in nature). DNA is probably attached to the scaffold via specific DNA sequences
During mitosis and meiosis how are chromosomes densely packed together?
By further coiling of the chromosome scaffold
