6 - Nucleic Acids
6 - Nucleic Acids
6 - Nucleic Acids
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NUCLEIC ACIDS DNA structure and replication
Nucleosomes are the units into which chromatin is organized in the eukaryotic nucleus.
One nucleosome consists a globular structure, with a core of 8 histone proteins with
DNA wrapped around them. Histone H1 links DNA to the protein core, and each
“bundle” of DNA is linked to the next by linker histones. The N-terminal tails of the
histones extend outwards from the core of the nucleosome and can attach to
neighbouring nucleosomes, pulling them closer together and enabling these to supercoil
during the condensation of chromosomes in mitosis. Additional protein modification to
the histones (e.g., methylation and acetylation) affects their level of condensation. This
serves to influence processes like trancsription, by making the DNA available for
enzymatic action, or supercoiling to prevent enzyme access. Molecular visualization
software can be used to analyse the association of protein and DNA in nucleosomes.
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NUCLEIC ACIDS DNA structure and replication 7
DNA consists of two antiparallel strands, both of which are in turn made of a
sugar-phosphate backbone and one of 4 nitrogenous bases that attach the antiparallel
strands through complementary hydrogen bonding:
The binding specificity reduces the risk of mutations, as each nigtrogenous base has a
high binding affinity for its complementary base, and a lower one for the two remaining
bases.
Next, an explanation of the replication process in prokaryotes at the two parent strands,
also known as leading strand (where replication occurs continuously from the end of
chromosome towards replication fork) and the lagging strand (where replication is not
continuous and occurs from the replication fork towards the end of the chromosome):
1. Helicase unwinds and separates the DNA double-helix into the two parent strands,
and DNA gyrase binds at the replication fork to stabilize the DNA during this
process
2. Single strand binding proteins bind to the resulting parent strands to stabilize them
and prevent them from reattaching and coiling once more
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NUCLEIC ACIDS Transcription and gene expression
It is important to realize that not all of the DNA present in the cell nucleus is later
transcribed and translated to form proteins. Regions of DNA that code for proteins are
called “exons” and regions that do not are called “introns.” Some special cases of
non-coding DNA have very important functions in and outside the nucleus:
• Regulating gene expression: sites where proteins can bind to promote or repress
transcription of specific genes
• Genes for tRNAs and rRnas: while these genes do not code for proteins, they do
code for essential machinery needed during translation
7.2.1 Transcription
Initiation: RNA polymerase binds to the promoter region of the gene (this region
contains a specific base sequence and signals the enzyme to initiate transcription)
Elongation: RNA polymerase simultaneously uncoils and transcribes the coding region
in a 50 –30 direction
Termination: RNA polymerase detaches from the mRNA strand after reaching the
terminating sequence, the mRNA then “peels” away from the DNA template away
from the DNA template and moves to be modified and later translated outside the
nucleus
The DNA strand that is translated is called the “antisense” strand (the mRNA of interest
will contain the sequence that is identical to the “sense” strand, which codes for genes of
interest, with uracil instead of thymine).
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NUCLEIC ACIDS Transcription and gene expression 7
• microRNAs: can bind to mRNA, leading to the degradation of the entire complex
→ gene cannot be translated
As mentioned earlier, the coiling and uncoiling of DNA by nucleosome interactions can
regulate the process of translation. DNA regions of highly condensed chromatin will
usually not be transcribed, as enzymes cannot easily access the DNA (regions that
remain highly condensed at all times are known as heterochromatin, and are normally
not transcribed). On the other hand, decondensed chromatin is easily accessible for
transcription enzymes and transcription factors, and is readily transcribed.
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NUCLEIC ACIDS Translation
7.3 Translation
7.3.1 Translation
Ribosome tRNA
P
exit site
E A
peptide chain site
amino acid site
mRNA binding site
AA binding site
small subunit
AA
amino acid
Figure 7.2: Ribosome structure and tRNA.
The process of translation is divided into three main stages and termination:
Initiation
The tRNA molecule with the start anticodon UAC binds to the small subunit of the
ribosome (peptide chain site on diagram).
The small subunit then binds the 50 end of the mRNA strand and slides along it in a 50 to
30 direction until it finds the start codon on the mRNA (AUG).
The large and small subunit of the ribosome then bind together.
A tRNA molecule with the anticodon complementary to the next mRNA codon on the
chain binds to the amino acid site of the ribosome.
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NUCLEIC ACIDS Translation 7
Elongation
The incoming tRNA pairs with its complementary mRNA codon at the amino acid site
of the ribosome.
The amino acids in the tRNAs at the peptide and amino acid sites form a peptide bond,
and the growing polypeptide chain remains attached to the tRNA at the amino acid site.
Translocation
The large subunit od the ribosome moves forward and the small unit slides after it,
moving the entire ribosome 3 nucleotides down the mRNA strand.
The tRNA in the peptide site moves to the exit site (where the tRNA is released and can
attach a new amino acid).
The tRNA carrying the growing polypeptide chain now moves to the peptide site.
The next codon to be translated is at the amino acid site, where its complementary
tRNA codon can bind.
Termination
When one of three stop codons (UAG, UAA, UGA) reaches the amino acid site of the
ribosome, the large subunit advances over the small subunit, detaching from it and
causing the polypeptide chain to be released from the last tRNA.
The polypeptide can then fold and be further modified to create a functional protein.
It is important to realize that translation of a single mRNA sstrand can occur in multiple
ribosomes (many can attach), creating a polysome. Polysomes can be visualized using
molecular visualization software.
It is important to realize that each tRNA molecule can only bind a specific amino acid,
depending on its anticodon (triplet of bases located on the middle loop of the tRNA).
The amino acid binds at the 30 end of the single stranded molecule
20 different amino acids, some of which can bind to several tRNAs (same amino acid,
different anticodons)
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NUCLEIC ACIDS Translation
Free ribosomes release the protein into the cytoplasm, and the proteins formed by these
organelles are mostly for use inside the cell (e.g., transcription factors, intracellular
enzymes, etc.)
Bound ribosomes release the polypeptide chain into the rough endoplasmic reticulum,
where the protein is modified, folded and packaged into vesicles that can then be secreted
out of the cell or taken up by lysosomes.
To review the 4 levels of protein organization, refer to the section “Amino acids: the
building blocks of proteins” in Chapter 2.
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