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Gene Expression
6.1: The Transfer of Information from DNA
Establishing a Link between Genes and Protein
In 1902, English chemist and physician Archibald Garrod
conducted study on alcaptonuria patients, a disease that causes
urine to turn black when exposed to air.
Proposed that build-up of homogentistic acid in urine was due to
a defective enzyme, discovered that patients had blood relations
which led to the conclusion that the black urine phenotype was
due to a recessive inheritance factor.
Defective factor = defective Enzyme
Beadle and Tatum and the One-Gene/One-Enzyme Hypothesis
Wanted to determine whether all enzymes were controlled by
one gene, or if one gene controlled one enzyme
Used bread mold, created mutant strains by exposing them to Xrays
Minimal medium: medium that contains only the nutritional
substances to synthesize other biochemical compounds
Some mutants could only grow when medium was supplemented
with the amino acid arginine
Hypothesized that the appearance of a defective enzyme in one
of the steps would mean that the intermediate compound wont
be synthesized, ergo, there would be no growth without the
missing intermediate.
Supplemented growth media with intermediates of arginine
synthesis
Growth would only occur on media provided with intermediate
produced after the step that involves the defective enzyme
B and T were able to isolate mutant strains that were defective
at one specific step in the arginine synthesis pathway
Concluded that one gene specifies one enzyme one-gene/onepolypeptide hypothesis
Finding a Messenger between DNA and Proteins

Eukaryotic cells only have genes in nucleus chromosomes

Protein synthesis only occurs in cytoplasm
Therefore, proteins couldnt be directly synthesized from DNA
Evidence that RNA could be the link:

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o RNA exists in both nucleus and cytoplasm

o Concentration of RNA correlated with level of protein
production
o RNA is synthesized in the nucleus and transported to the
cytoplasm
1961 Jacob and Monod proposed the messenger RNA
(mRNA)
o RNA that contains the genetic information of a gene and
carries it to the protein synthesis machinery; it provides
the information that determines the amino acid sequence
of a protein
o When bacteria were infected by virus, a specific RNA was
synthesized and associated with pre-existing bacterial
ribosomes. Ribosomes are the site of protein assembly.
o New RNA molecule has complimentary base sequence to
DNA
o Viral RNA was newly synthesized and not a permanent part
of the bacterial ribosomes

The Genetic Code

Genetic Code: a set of rules for determining how genetic information
in the form of a nucleotide sequence is converted to an amino acid
sequence of a protein; a code specifying the relationship between a
nucleotide codon and an amino acid
4 nucleotides, 20 amino acids
Therefore the least number of nucleotides for each amino acid
would be 3
Triplet hypothesis: a proposal that the genetic code is read three
nucleotide bases at a time called a codon
Proven by Crick and Brenner in 1961
When one or two nucleotides were removed, protein was not
produced
When three consecutive nucleotides were removed, protein
production occurred
Determining the Genetic Code
Genetic code is always interpreted in terms of the mRNA codon
rather than the nucleotide sequence of the DNA
Three characteristics of the genetic code:
1. Code is redundant more than one codon can code for the same
amino acid. Only three codons do not code for an amino acid
(stop codons)
2. Code is continuous a series of three-letter codons without
spaces, punctuation, or overlap.
3. Code is nearly universal almost all organisms build proteins with
the same genetic code. A codon in a fruit fly codes for the same

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amino acid as in a human. A gene taken from one organism and
inserted into another kind will produce the same protein (cloning
implications)
Gene Expression
Gene Expression: The transfer of genetic information from DNA to
RNA to protein
The theory that genetic information flows from DNA to RNA to
protein is called the central dogma of genetics
DNA transcription RNA translation Protein
Transcription and Translation
Transcription: The synthesis of RNA from a DNA template
Translation: The synthesis of protein from an mRNA template

6.2 Transcription: Synthesizing RNA from DNA

RNA production is required in order to read the genetic

information stored in DNA
RNA is single stranded, and it can fold back on itself
Complementary base pairing within the same molecule stabilizes
the looped structure
All RNA are produced from a DNA template and synthesized in the
nucleus
o mRNA is an intermediary between DNA and protein, used as
a template that determines the amino acid sequence of the
protein it codes for
o many RNAs do not code for proteins and are involved in
translation

The Molecular Events of Transcription

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Main objective of transcription is to produce a copy of a small

section of genomic DNA
Three stages: initiation, elongation, and termination
Similar in eukaryotes and prokaryotes, differ in proteins involved
More proteins are required in eukaryotes

Initiation
Starting position is selected
Transcription machinery, a large protein-DNA complex, is
assembled
Only one strand of the double-stranded DNA molecule is
transcribed for each gene
o Transcribed strand is called antisense strand or template
strand
o Non-transcribed strand is called the sense strand or coding
strand
o Same sequence as the product mRNA
o Either strand can serve as sense strand for different genes
RNA Polymerase: the main enzyme that catalyzes the
formation of RNA from a DNA template
o Eukaryotes: each RNA polymerase has specific function
o When the RNA polymerase binds to DNA, it unwinds and
opens a section of the double helix
Transcription begins with RNA polymerase binds to a promoter
region
Promoter region: a sequence of nucleotides in DNA that
indicates where the RNA polymerase complex should bind to
initiate transcription
o Two sets of sequences are required and need to be
correctly positioned in order for RNA polymerase to bind to
correct strand in correct orientation to ensure correct copy
Elongation
RNA polymerase travels along DNA molecule to synthesize a
strand of mRNA that is complementary to the template strand of
DNA
o T is replaced with U in mRNA
o RNA polymerases work from 5 to 3 by adding new
nucleotides to the 3-OH group of the previous nucleotide
o RNA polymerases only transcribe one strand therefore no
Okazaki fragments
As soon as the RNA polymerase complex starts moving along the
DNA, a second RNA polymerase complex can bind to the
promoter region to synthesize another mRNA molecule

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Hundreds of mRNA molecules can be made from on gene at one

time
mRNA is synthesized faster than DNA
o RNA polymerase complex doesnt proofread
o Transcription error only results in error in one protein
molecule, not the entire organism
o mRNA synthesis: quantity over quality

Termination
Specific nucleotide sequences in the template DNA signal end of
transcription
When RNA polymerase reach this signal, they detach from DNA
strand
New mRNA strand is released from transcription assembly
DNA double helix reforms
mRNA Modifications in Eukaryotes
Prokaryotes: mRNA molecule can be used in protein synthesis
immediately after its made
o Transcription and translation occur simultaneously
Eukaryotes: newly made mRNA go through modifications before
its transported across nuclear membrane into cytoplasm
o Convert precursor mRNA (pre-mRNA) to mature
mRNA
o Precursor mRNA (pre-mRNA): mRNA that has not
undergone processing
o Mature mRNA: mRNA that has undergone processing
Modifications include:
o Addition of a 5 cap: covalent linkage of a modified G
nucleotide to the 5 end of the pre-mRNA, recognized by
the protein synthesis machinery
o Addition of a 3 poly-A-tail: covalent linkage of a series of A
nucleotides to the 3 end of the pre-mRNA makes mRNA

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more stable and lengthens its life span in the cy

o Removal of introns.
Introns are non-coding regions on eukaryotic genes,
there are interspersed among coding regions called
exons
Introns are removed from pre-mRNA, and exons are
joined together to form mature mRNA splicing
Splicing: in mRNA, a process of excising out the
introns and combining in the exons
snRNPs (particles composed of snRNA and proteins),
recognize regions where exons and introns meet and
bind to those areas
snRNPs interact with other proteins, forming a larger
spliceosome complex that remove introns
For most gene expressions, all exons are spliced
together
In some cases, only certain exons are used to form a
mature RNA transcript alternative splicing:
allows for one gene to code for more than one
protein
Certain cell types are able to produce forms of a
protein that are specific for that cell

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6.3 Transcription: Synthesizing Proteins from mRNA

Second stage of gene expression

Translates the nucleic acid code of mRNA into the amino acid
code of a protein
Requires assembly of a complex translation machinery composed
of different nucleic acid and protein components

Transfer RNA
Transfer RNA (tRNA): an RNA molecule that links the codons on
mRNA to the corresponding amino acid for protein synthesis
Single strand that folds into a 2D cloverleaf shape
Consists of three stem-loops and a single-stranded region
Folds into a 3D boot-shaped structure
Stem-loops are double-stranded areas that form through
intramolecular base pairing
tRNA contains two functional regions
Anticodon loop: a triplet of bases positioned at one end of a
tRNA that recognizes and base-pairs with a codon on mRNA
during protein synthesis
o Written from 3 to 5
Acceptor stem: the 3 end of a tRNA molecule that is the site of
attachment for a particular amino acid, based on the anticodon
o Aminoacyl-tRNA synthetase: an enzyme responsible for
attaching an amino acid to a tRNA
o 20 enzymes, one for each amino acid
o Correct amino acid must be linked to the appropriate
mRNA codon
Ribosomes
Ribosomes: a cell structure composed of proteins and rRNA that
provides the site where protein synthesis occurs
Ribosomal RNAs: the RNA that is associated with proteins in the
ribosome

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Cytoplasmic structures that provide a place for mRNA, tRNAs w/

amino acids, and protein synthesizing enzymes can assemble
and interact.
Each ribosome is comprised of two sub-units
Each sub-unit is composed of different proteins and rRNA
molecules
Ribosome has one binding site for mRNA and three for tRNA
o Permit complementary base-pairing between tRNA
anticodons and mRNA codons