cundliffe

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Lecture 6: The 'central dogma' of molecular biology
Information stored as the base pair sequence of DNA encodes the amino acid sequences of the
thousands of proteins present in any given cell. The coded information in a gene sequence is first
TRANSCRIBED into an RNA nucleotide sequence and then TRANSLATED into a protein amino acid
sequence. Therefore, the process of RNA biosynthesis is referred to as TRANSCRIPTION and protein
synthesis is known as TRANSLATION.
Note: some genes encode RNA molecules (e.g. ribosomal RNAs or transfer
RNAs) rather than proteins, so the information they encode is transcribed but
not translated
RNA is a polymer of ribonucleotides linked via 3' 5' phosphodiester bonds
that differs from DNA in several respects:
RNA contains ribose, not dribose. How do these sugars
differ?
Deoxyribose has an oxygen atom on the 2' carbon atom
RNA contains Uracil not Thymine. How does the U base differ from T?
Uracil only differs from thymine in that it has a methyl on the 5 carbon
RNA is usually single stranded and does not contain equal amounts of A versus U or G versus C.
RNA molecules typically fold back on themselves to give stem-loop structures (secondary
structures) with base-pairing in the helical stems.
Non-standard base-pairs are common in RNA secondary structures even though the
vast majority of the pairings are the familiar A**U and G***C. Give an example of a
non-standard base-pair.
G-U is a non standed base pair with one hydrogen bond between them
RNA (particularly tRNA) contains 'odd' nucleosides although the standard ones
predominate by far. Give an example of an 'odd' nucleoside.
Types of RNA

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RNA' as if it were a homogeneous substance but there are different functional types of RNA.
Some are enzymes (!) others have unknown functions.
Messenger RNA (mRNA).
This acts as genetic intermediate, carrying information from the gene (i.e. DNA) to the protein
synthesis machinery (i.e.ribosomes).
In eukaryotes, this means that mRNA passes from the nucleus to the cytosol: bacteria do not
have nuclei but they still use mRNA in a similar manner.
programmes ribosomes
length depends on gene size
Ribosomal RNA (rRNA).…read more

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In this context, what is meant by the term COGNATE?
a tRNA and its corresponding amino acid
Transcription (RNA synthesis) in E. coli
RNA polymerase is a highly processive enzyme that catalysis the reaction:
(RNA)n + NTP (RNA)n+1 + PPi
RNA polymerase requires NTPs plus Mg 2+ and a double-stranded (ds) DNA template.
Synthesis precedes 5' - 3' via the formation of 3' - 5' phosphodiester bonds and is driven by
hydrolysis of inorganic pyrophosphate (PPi).…read more

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In bacteria, a single type of RNA polymerase makes all of the different kinds of RNA. In
eukaryotes, there are multiple RNA polymerases each making a different type of RNA.
Both strands of DNA are used as templates for transcription but not over their whole length, so that,
at any position along a DNA molecule, one strand or the other may be transcribed.…read more

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If the heat-denatured DNA is then cooled rapidly, the strands will stay apart because they will
not have time to line up correctly and ANNEAL together again.
Annealing (a process also referred to as RENATURATION or HYBRIDISATION) will occur, however,
if the DNA is cooled slowly.…read more

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Following the action of E. coli RNA polymerase on phage DNA, the resultant
TRANSCRIPT (i.e. the RNA product) was found to hybridise with only one
Strand of the DNA.
Thus, RNA polymerase makes a complimentary copy
Of only one DNA strand during transcription.
In summary, each RNA molecule (messenger, ribosomal or transfer) is made
as a complementary copy of one of the DNA strands (the 'TRANSCRIBED
STRAND' or 'TEMPLATE STRAND') so that the RNA product has the same
sequence as the 'NON-TRANSCRIBE.…read more

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DNA where transcription begins ( promoter site)
at these sites participate in the initiation of RNA synthesis and then dissociates to from
the rest of the enzyme
random starts on foreign DNA
Both forms can transcribe 'foreign' DNA, but they do so with random starts, as does the core enzyme
acting on E. coli DNA. Holoenzyme from E. coli recognises specific sequences in E. coli DNA.…read more

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Post-transcriptional modification
RNA synthesis involves TRANSCRIPTION plus POST-TRANSCRIPTIONAL MODIFICATION. Understand the
meaning of: PRIMARY TRANSCRIPT; RNA PROCESSING; MATURE RNA. Here, we consider processing of
tRNA andrRNA. Processing of eukaryotic mRNA will be discussed in the next lecture.
Bacterial mRNA is not processed at all.
The primary transcript ('precursor tRNA') from each tRNA gene gets shortened at both ends
and then, if necessary, -CCA is added at the 3'-end of the product.…read more

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Mature tRNAs and the long rRNAs from both prokaryotes and eukaryotes are chemically
modified post-transcriptionally.
This occurs mainly on the primary transcripts although some modifications take place after
length-shortening.
The principal forms of chemical modification are: pseudouridine formation (Greek letter psi,
) via isomerisation of specific (not all) uridine
nucleosides in the primary transcript
ribose-methylation at the 2'-OH group
base-modification (most commonly,
N-methylation).…read more

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Rifamycin (semi-synthetic derivative = rifampicin) and Actinomycin D are specific inhibitors of
prokaryotic transcription although they act in fundamentally different ways.…read more

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