Download MCB Lecture 4 – Genes and Chromosomes

Lecture 4 – Genes and Chromosomes
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How many genes are in E. Coli? 4300 genes
How many Mbp in E. Coli? 4.6 Mbp
How many genes in the human genome? 25000 genes
How many Mbp in the human genome? 2900 Mbp
Do bacteria have polycistronic or monocistronic mRNA? Polycistronic
Do bacteria have polycistronic or monocistronic mRNA? Monocistronic
What is Polycistronic/Monocistronic DNA? Polycistronic DNA is where
genes that participate in the same pathway are located next to each other and
transcribed together. Monocistronic is where each section of DNA codes for
a separate polypeptide.
Plasmids – segments (a few thousand base pairs) of DNA in bacteria that
code for antibiotic resistance genes.
Mitochondrial DNA – 16.6 kbp long, in mitochondrion, circular.
How is the circular in a bacterial DNA formed? What holds it together?
Bacterial DNA is about 100,000 basepairs. It forms about 40 loops around
histone like proteins (HU). RNase can completely unfold it.
What genes are repeated in the human genome? Histone proteins and
Ribosomal RNA genes.
Highly Repeated Sequences – repeating unit is always always the same,
typically short sequences, and are present in clusters without interruption
o Satellite DNA – in centromeres, 171 bp repeat.
o Microsatellite DNA – less than 100 bp in length, spread over the
genome
o Minisatellite DNA – 6-64 bp in length, telomeres (TTAGGG) (for
telomerase)
Moderately Repeated Sequences – repeated sequence may diverge, but it can
be traced back to the original sequence, repeats are longer. Represent 42%
of the genome.
o SINE’s (Short Interspersed Elements) – Alu fragments, 300 bp long,
13% of genome. Non-functional retrotransposon
o LINE’s (Long Interspersed Elements) – 900 bp long, 21% of genome.
Non-functional retrotransposon
Retrotransposon – pieces of DNA that copy and paste into other areas. They
use RNA Polymerase and Reverse Transcription, Endonuclease
Relaxed, Watson and Crick DNA – lowest energy state, 10.5 bp per turn
Positive Supercoiled DNA – overwound DNA, less than 10.5 bp per turn, more
turns
Negative Supercoiled DNA – underwound DNA, more than 10.5 bp per turn,
less turns, energetically favored.
What enzyme causes supercoiling? Topoisomerases.
Linking Number Lk – The length of the DNA molecule/the number of bases
per turn (10.5)
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Topoisomerases – enzymes that change the supercoiling of DNA by using
tyrosine (Y) residues
o Type I – do not require energy, nick DNA, involved in removing
positive and negative supercoiling. Change the Lk by 1. Can be used
for anti-tumor drugs.
o Type II – require ATP, make double stranded cuts in DNA, can induce
supercoils. Change the Lk by 2. Have G segment (Gate) and T
Segment. ATP is used to cut, the removal of ATD+P resets the enzyme.
 Gyrase – Type II Topoisomerase in Bacteria that induces
negative supercoils. Inhibited by Quinolones. Can function as
antibiotics. No ortholog for eukaryotes.
Nucleosome – includes 200 nucleotides. 146 are bound to protein core of 8
histone proteins (wrapped 1.8 times), and the other 54 are considered linker
DNA.
o Nuclease – can digest the linker proteins but cannot digest the
nucleotides wrapped around the histone
Histone Proteins – H2A, H2B, H3, H4. Extremely well conserved. They have
large amount of Arginine and Lysine (+Amino Acids) so that they can bind to
negative DNA.
o Histone Proteins bind in MINOR GROOVE.
What domain of the histone protein is in the hydrophobic core? Carboxyterminal.
What domain of the histone protein forms the long, flexible tail? N-terminal
What do acetyl groups do to Lysine and Arginine? Remove the positive
charge on them to release bond between histone and DNA.
What do methyl groups do to Lysine and Arginine? They affect the
interaction with transcription factors.