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The Central Dogma

Image Credits: Biology (Campbell) 9th edition, copyright Pearson 2011, & The Internet. Provided under the terms of a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Adapted from work by David Knuffke.
by

Alan Allmen

on 25 March 2016

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Transcript of The Central Dogma

Universal across all domains of life.
The Central Dogma
DNA
RNA
Protein
Replication
Transcription
Translation
Once the structure of DNA was determined, it was time to figure out how it worked

"
Central Dogma
": Term coined by Francis Crick to explain how information flows in cells.

Allows for Gene Expression
It is easy to see how DNA is copied by looking at it's structure
"It has not escaped our attention that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material,"
-End of Watson & Crick's 1953 paper
But it still needed to be proven...
"
Semi-Conservative
" Replication
Meselson & Stahl
3 Possible Hypotheses
Conducted an experiment in 1958 that supported the
semi-conservative model of replication
How Replication Happens:
1. Initiation
Replication can only begin at specific locations ("
origins
") on a chromosome
DNA Polymerase I and III
: Enzymes Responsible for DNA synthesis.

Helicase
: Opens the helix (which causes strand separation)

Single Strand Binding Proteins
(SSBPs): Keep the strand open

Primase
: Puts down a small RNA
primer
which is necessary for DNA polymerase to bind to at the origin.

DNA gyrase
: Rotates the DNA to decrease torque (which would shred the helix.



Nucleotides are automatically added to the 3' end of the DNA strand, due to complementary base pairing.

DNA is "
anti-parallel
": Both strands have opposite 5' to 3' orientations
2. Elongation
Nucleotides are added by polymerase in the 5' to 3' direction.

PROBLEM: DNA is anti-parallel

As the replication machinery moves along the chromosome, only one strand of DNA (the "
leading strand
") can be made in a continuous, 5' to 3' piece.
The other strand (the "
lagging strand
") has to be made in smaller, discontinuous 5' to 3' segments ("
Okazaki fragments
") which are then stitched together by the enzyme ligase.
Leading Strand
Lagging Strand
The "
Replication Fork
":
Once it begins, replication proceeds in two directions from the origin
The "
Replication Bubble
"
3. Termination
Elongation continues.

Challenge: the ends of chromosomes

Each round of replication shortens the 5' end of the lagging strand (by about 100-200 bp).

If this continued indefinitely, chromosomes would get shorter and shorter after each replication. Information would start to be lost.
"Proof-Reading"
Telomeres:
The ends of eukaryotic chromosomes.
Consist of a short, repeating DNA sequence

Vertebrate Telomere: TTAGGG
Telomerase:
The enzyme responsible for replicating the ends of eukaryotic chromosomes.

Uses an RNA template to add more bases during replication.

Not active in
senescent
cells.

The initial error rate during elongation is 1 in 10,000 mismatched bases.

(This would create 300,000 mutations every time a human cell divided.)

Many molecules help to "
proof-read
" DNA.

Proof-reading reduces the error rate to 1 in 10 billion nucleotides during replication (less than 1 per 3 human cell divisions).

Proof-reading is a continual process.
Allows for
Heritability
DNA
RNA
How transcription happens:
1. Initiation
RNA polymerase attaches to a "
promoter
" region slightly in front of the gene
eukaryotes: RNA polymerase requires "
Transcription factor
" proteins to be able to bind to the promoter.

Promoters have characteristic DNA sequences (ex "
TATA Box
" in eukaryotes)
2. Elongation
RNA production occurs in a 5' to 3' direction.

The "
template strand
" of DNA is the one that is used to produce the RNA

RNA Polymerase is the enzyme that builds an RNA strand that is complementary to the DNA strand
Adenine --> Uracil
Guanine --> Cytosine
Cytosine --> Guanine
Thymine --> Adenine

3. Termination
Transcript production continues until the end of the gene is reached

Then the RNA will fully detach from the DNA and leave the nucleus
What Happens Next?
Many Kinds of RNA
Unlike DNA, RNA plays many roles in the cell
There are ~10 described types of RNA, each with different functions, but there are three major types:

Messenger RNA (
mRNA
): Carries DNA sequence information to the ribosome
Transfer RNA (
tRNA
): Carries specific amino acids to the ribosome
Ribosomal RNA (
rRNA
): Major structural building block of ribosomes



In eukaryotes, the mRNA transcript is extensively processed in the nucleus before it leaves to be translated.
Post-Transcriptional mRNA Processing
(Eukaryotes ONLY!)
5'Cap and poly-A tail
Exon Splicing
A modified nucleotide is added to the 5' end of the transcript.

A tail of several hundred adenine residues is put on the 3' end of the transcript.

These modifications function in nuclear export and maintenance of the mRNA
Eukaryotic genes contain large stretches of non-coding DNA ("
introns
") interspersed between coding DNA ("
exons
")
To produce a functional protein, the introns must be removed and the exons must be spliced together prior to the movement of the mRNA transcript to the nucleus.

This process is accomplished by a
spliceosome
(a type of enzymatic RNA molecule)
Why Introns?
It's a great question. Not really answered.

Evolutionary baggage? Selfish genes?

We do know that having multiple exons in a gene allows eukaryotes to make multiple functional proteins from one gene ("
alternative splicing
")
RNA
polypeptide
The Genetic Code:
The Ribosome
tRNA
The site of protein synthesis.

All cells have ribosomes.

Composed of two subunits.

Has three "sites":
A site
: "Aminoacyl"- where amino acids enter the ribosome
P site
: "peptidyl"- where the growing polypeptide is kept.
E site
: "exit"- where empty tRNA molecules leave.
Transfer RNA molecules.

Responsible for bringing amino acids to the ribosome
Triplet code: mRNA is read in units of three bases ("
codons
")

There are 64 possible codons (for 20 possible amino acids).

The code is redundant and unambiguous.

The code has "
start
" and "
stop
" punctuation.
pig with GFP from a jellyfish
tobacco plant with luciferase from a firefly
How translation happens:
1. Initiation
The mRNA attaches to the small ribosomal subunit.

When the start codon (AUG) is read by the ribosome, the first tRNA molecule, carrying the amino acid Methionine is brought in to the ribosome.
2. Elongation
The next codon determines the next amino acid to be brought to the ribosome.
The incoming charged tRNA enters at the A-site.
The growing polypeptide is transferred to the new tRNA molecule. A
peptide bond
is formed.
The ribosome shifts ("
Translocates
"). The tRNA with the polypeptide is now in the P-site.

The uncharged amino acid is now in the E-site.
The next codon is now available in the A-site for the next incoming charged tRNA
3. Termination
When a stop codon (
UAG
,
UAA
, or
UGA
) is encountered, a release factor binds to the A-site.

The polypeptide chain is released.

The ribosome disassembles.
tRNA binding at the ribosome is mediated by an "
anti-codon
" loop in the tRNA molecule
tRNA "anti-codon"
Protein Synthesis in Total
Prokaryote & Eukaryote
Translation Specifics
Prokaryotes
Since prokaryotes do not have a nucleus, transcription and translation can be coupled.
Eukaryotes
Eukaryotes can not couple transcription and translation.

Eukaryotes also need to target different polypeptides to different areas of the cell.
Genetic Information
Early 20th century: What contains the genetic information - DNA or proteins?
1952: Alfred Hershey and Martha Chase

What we know now
Central Dogma of "one gene-one polypeptide" is too simplistic.

Not all genes are for enzymes.
Not all genes are for protein.
Not all genes are for polypeptides.

Still, it's a good place to start.
Mutation Revisited
It becomes clear how changes in DNA can affect changes in protein structure, and in physiology. There are 2 major types of DNA-level mutations:
Point mutations
: One DNA base is replaced by another DNA base.
Frame-shift mutations
: DNA bases are inserted or deleted, shifting the DNA triplets for the remainder of the gene.
Point Mutations
Silent
The base change does not alter the resulting amino acid sequence.
Substitution
The substitution results in a different amino acid.
Frameshift Mutations
Missense
The reading frame of the ribosome is altered so that all amino acids downstream are altered
Nonsense
The reading frame of the ribosome is altered so that a stop codon is introduced prematurely
Limited Effect
One or more amino acids are altered, but the reading frame is restored when the mutation occurs in multiples of three.
Make Sure You Can
An RNA "
hairpin
" loop, similar to what happens in Rho-independent termination
Sickle Cell Anemia is due to a point mutation.
Outline DNA transcription.

Outline the process of translation.

Explain the conservation of information encoded in DNA.
DNA Replication
Transcription
Translation
Mutation
Blame it on the DNA
Sickle Cell Again!
The Genetic Code
Splicing
Need more help?
T2 Phage:
scourge of bacteria everywhere
DNA moves from virus to bacteria, not the proteins
segment of DNA that encodes for a protein
Gene
Full transcript