Genome Structure Flashcards
What is the genome
The entire genetic contents of an organisms
The genome of an organims can be
- Single Stranded DNA/RNA (bacterial viruses)
- Double Stranded DNA/RNA (most organisms will have this)
- Linear or Circular (most bacteria have circular DNA)
- Contained in single or multiple units
The bacteria E.coil has a Haploid size of 4.1Mbp
The simple single celled eukaryote (like Saccaromyces cervisiae - yeast) is how many times bigger
only 3 times bigger
There is not a big difference in the number of genes between some eukaryotes
The difference in sophisticated organisms (liked humans) and a little nematode worm is …
the control of the gene
Not the number or type of genes
What is the Chromosome
The physical location of the genes
Unlike prokaryotes (nucleoid) the genomes of eukaryotic cells can be found in several compartments
What are they
Nucleus
Mitocondria
Chloroplast
This is a picture of e.coil
What is the white arrow pointing to
The nucleoid
E.coil have one chromosome
Yeast has 32
What does this show
Genomes of organisms vary widely in chromosome number
Why are genes arranged in chromosomes?
Grouping together genes into chromosomes provides a convenient parcel of DNA that can be duplicated during DNA replication and partitioned into the daughter cells at cell division
(Down to natural selection)
What to chromosomes contain which allows them to be replicated
Chromosomes contain at least one origin of replication (ori), per chromosome
For some really long chromosomes you can have multiple points of origins or replication
Why do we have multiple chromosomes, rather than just one long one
If you had only one very long chromosome, the level of condensation found in normal chromosomes would not be sufficient in order to segregate into the two halfs of the cell (as shown in a normal cell below)
How can chromosome structures differ
The structures may be incredibly complex and ranges from pure nucleic acids (like in virsuses)
How many bases are there usually in a gene
1000 Bp to a gene
How many bases are there usually in a gene
1000 Bp to a gene
The DNA in bacteria chromosomes is folded
How
DNA is negatively charged
There is a set of proteins similar to hisotones, which are positively charged
The positively charged protein bind and wrap the DNA - sort of a loose arragment which is constantly associating and dissociating (fluid)
The DNA is also supercoiled - this supercoiling does not affect these loops which are formed however
What is the molecular material of a chromosome
- Ranges from pure nucleic acids as in Viruses
- Through a DNA/protein complex as in bacteria
- DNA in the chromosomes of eukaryotic cells is even more highly compacted being complexed with many different types of proteins at several levels to form ‘chromatin’
How do histones work in eukaryotic DNA?
147 base pairs of DNA wound around auto matic nucleosome core, with a short linker region, which is formed from chromatin
Apart from when DNA is being replicated, DNA is sequestered within these structures
How are the nucleosome structures affected when DNA is replicating
When the gene is being expressed you still have nucleosomes on the DNA, which are displaced the reassociated after the passage of RNA polymerase
But some DNA is so condensed that transcription is inhibited all together
What are 3 key features of gene organisation in bacteria (E.coil)
- Gene density around the circular chromosome
- Operons
- Overlapping genes
Where is the promoter found on bacterial DNA and what is its function
The promoter sequence is where DNA polymerase binds (this is the little arrow next to RNA polymerase)
They are very short non-coding regions between bacterial genes
The promoter has a start codon and the terminator site a stop codon to start and end translation
These regions are very short
Genes are often crowed together into these constructs called operons
What is it?
Something that controls the expression of genes
In bacteria, genes with link functions are strung together into these operons
Example: two genes both controlled by the same promoter. Immediately after the translation of gene one you will have another start codon, to translate gene two
There can also be translation coupling: where there is overlap between the start and stop codon, so it reduced time for ribosome to move from gene 1 to gene 2
We have seen translational coupling
To what extent can this occur in viruses
In viruses you can actually find one gene nested entirely within another
And these genes can be red almost in opposite directions
This is benefical for small organisms
In the case of lactose, given an example of why operon organisation is important
permits the coordinated expression of genes encoding functionally-related products needed in the metabolism of lactose
One promoter controls three genes - simply regulate 3 genes with a single repressor (turns gene off) rather than having 3 different repressors
It is a form of gene control
Say in humans vs bacteria
How muc of the genome encodes proteins
High proportion of sequences in bacteria code for proteins (98%)
In contrast this is only about (2%) in humans
This non-coding sequences are able to exist in humans due to their large size, not such a need for compact DNA compared to bacteria
What is the ‘C value paradox’
Genome size does not scale with the complexity of an organism
What is the ‘C value’
Is the weight in grams of the DNA in a haploid genome
(convient measure before DNA sequencing)
If one purified the DNA from a million cells and weighed it, one could get the C value by…
If this genome was for a diploid, you would then…
- Divide by a million
- Diploid: divide by 2
How can DNA-specific stains be used to work out the amount of DNA
By working out the wavelength of light being emitted from a nucleus, this can be compared against a standard of a known volume of DNA
What is the explanation for the ‘C-value paradox’
is that non-coding DNA can be present in variable amounts that are not directly related to genetic/organismal complexity
How does gene density vary along the chromosome
Very few genes at the ends telomere) or near the centromere
What is the difference between an α-gene and a pseudogene
An α-gene codes for the usual function
A pseudogene is a section of DNA which read alomst like the α-gene but there are lots of mistakes within it (e.g. many stop codons within) - hence doesn’t produce a functional protein
Define ‘introns’
Interruptions in coding DNA
= non coding DNA
What part of protein synthesis are the introns removed
Removed from mRNA by splicing before translation
What it the Untranslated region (UTR)
The region before the promoter and after the termination codon
It does not code for anything
What does CDS stand for
Coding sequence
How long is an exon before it is usually interupted by an intron
30 amino acids long
(50-200 bp)
What does the typical trend of intron length look like
Across many species there are generally two typical sizes of introns (a smaller length and and a larger length)
A suggested advantage of the intron/exon organisation of genes is ‘optional exons’
What does this suggest
Allows for alternative splicing
More than one protein form per gene
Where is it, that introns were thought to have come from
Paracites
What are exon/intron junctions
There is usually a GU at the start of an intro and a AG at the end of an intron
What type of repeat will occur between genes
How can it arise
Tandem repeat
‘AGGCT’
Arise from replication slippage
Why are tandem repeat unstable
Because they form hairpin structures that are attacked by nucleases
What are transposons
What are the two classes of transposons
Repeated sequences - it is how the majority of the human genome has come to exist
Transposons (DNA intermediate) and Retro Transposons (RNA intermediate)
