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Biochemistry 2280A Lecture Notes - P53, Start Codon, Dna Microarray

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Topic 18:
Purine = 2 ring structure, A and G, attach to c1 via N9 position
Pyrimidine = 1 ring structure, C and T, attach via the N1 position
CG has 3 hydrogen bonds, AT has only 2
The anomeric carbon of ribose is in the B-configuration when attached to the nitrogenous base,
and are joined in an N-glycosidic bond
Phosphates attach to the C5 by a phosphoester linkage, make the DNA negative
5’ 3’
The double helix is stabilized by base stacking and base pairing
DNA is 2nm wide and can be very long. The distance between bases is 0.34nm
Topic 19:
Chromatin is a complex of DNA and its organizing proteins
Histones have fewer than 200 amino acids, and have many lysine and arginine (which are
positively charged), and so interacts well with the negative DNA
DNA wraps around a cluster of 8 histones to make the nucleosome core particle. The DNA
makes 1.7 circuits around the histone core (147 base pairs)
o Nucleosomes compact the DNA by a factor of 3
The nucleosomes can pack into a 30nm-chromatin fibre, and is stabilized in a ‘zig-zag’ by histone
H1. The DNA has been compacted by a factor of 100
The 30nm chromatin fibres form large loops of 30000-200000 base pairs
Topic 22-24:
DNA RNA protein, gene expression
To express the genetic information stored in DNA, the nucleotide sequence of a gene is
transcribed into RNA
o Transcription is catalyzed by RNA polymerase
RNA differs from DNA, as it contains ribose, and uracil, single-stranded, and can fold into 3D
Cells can make mRNA, rRNA (ribosomes), and tRNA
Transcription begins at DNA sites called promoters. To initiate, RNA polymerases require
transcription factors at the promoter in eucaryotes, only needs a sigma factor in bacteria
Most genes are composed of exons with Introns, and during transcription, both introns and
exons are transcribed
Introns are removed via RNA splicing, catalyzed by snRNPs, and exons are joined
mRNAs go through processing before they leave the nucleus, capping and addition of a poly-A-
tail, this occurs as splicing and transcription are happening, and then complete mRNAs are
transported to the cytoplasm
translation takes place in the cytoplasm on a ribosome
the nucleotide sequence in mRNA is read out in sets of codons, each codon representing one
amino acid
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