Genes Expression or Genes and

How They Work: Transcription,

Translation.

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c, g, i, b, d, k, f, j, a, e, h

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Transcription of the following sequence of the tryptophan
operon occurs in the direction indicated by the arrow. What
would be the base sequence of the mRNA produced?
3’ CGTCAGC 5’
Transcription → Which product?
5′…GCAGTCG…3′

A. 5′…GCAGUCG…3′
B. 5′…CGUGAGC…3′
C. 5′…GCUGACG…3′
D. 5′…CGUCAGC…3′
E. 5′…CGUGAGC…3′
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 Overview: Central Dogma
• Central Dogma
– DNA  RNA Protein

• During polypeptide synthesis, ribosomal

RNA (rRNA) is the site of polypeptide
assembly.
– Transfer RNA (tRNA) transports and

positions amino acids.

– Messenger RNA (mRNA) directs which

amino acids are assembled into

polypeptides.
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The Central Dogma
Central Dogma

DNA
Proposed by Francis Crick in 1958 to describe the flow
of information in a cell.

Information stored in DNA is transferred

residue-by-residue to RNA which in turn transfers the
information residue-by-residue to protein.

The Central Dogma was proposed by Crick to help

RNA scientists think about molecular biology. It has
undergone numerous revisions in the past 45 years.

Protein
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Central Dogma of Gene Expression

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 Transcription Overview

Def: DNA sequence is transcribed into RNA

sequence
– initiated when RNA polymerase binds to

promoter binding site


moves along DNA strand and adds
corresponding complementary RNA
nucleotide

disengages at stop signal

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 Eukaryotic RNA Polymerases

 Nuclear DNA is transcribed by three different RNA

polymerases
 RNA pol I

Transcribes all rRNA genes (except for the 5S rRNA)
 RNA pol II

Transcribes all structural genes
 Thus, synthesizes all mRNAs

Transcribes some snRNA genes
 RNA pol III

Transcribes all tRNA genes

And the 5S rRNA gene

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 Translation Overview
• Def: nucleotide sequence of mRNA transcript
is translated into amino acid sequence in the
polypeptide

rRNA recognizes and binds to start
sequence

moves three nucleotides at a time

disengages at stop signal
• Gene expression - collective of transcription
and translation
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 Genetic Code
• How does the order of nucleotides in a DNA
molecule encode the information that
specifies the order of amino acids in a
polypeptide?
• The answer came in 1961 through an
experiment lead by Crick.

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 Genetic Code
• Crick and colleagues reasoned that there must be
codons or block of info that coded for an amino
acid
• They hypothesized that it was most likely 3
nucleotides
– Why 3?

– 2 nucleotides did not have enough combinations

(42 is only 16 possible amino acids)

– 3 nucleotides (43 is 64 which is enough to cover

the roughly 20 known amino acids)

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 Genetic Code
• Now known
• Genetic code consists of a series of
information blocks called codons.
– reading frame (triplet)


each codes for one amino acid

highly redundant

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Genetic Code

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carboxyl group

amino group

20 amino acids

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 Genetic Code
• Could be punctuated or not
– Punctuated code would have a something

in the code that separates codons

– Non-punctuated code would not

• In the following example, O is not a base

pair but the “punctuation.”

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 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Delete 1 base
15_06.jpg
WHYDIDTHEREDBATEATTHEFATRAT?
Hypothesis A : Delete T
unpunctuated WHY DID HER EDB ATE ATT HEF ATR AT?
(Nonsense)

WHYODIDOTHEOREDOBATOEATOTHEOFATORAT?
Hypothesis B : Delete T
punctuated O O R B E T F R
WHY DID HEO EDO ATO ATO HEO ATO AT?
(Nonsense)
Delete 3 bases
Hypothesis A : WHYDIDTHEREDBATEATTHEFATRAT?
unpunctuated Delete T,R,and A
WHY DID HEE DBT EAT THE FAT RAT?
(Sense)
(Nonsense)

WHYODIDOTHEOREDOBATOEATOTHEOFATORAT?
Hypothesis B : Delete T,R,and A
punctuated O O E T T E T T
WHY DID HEO DOB OEA OTH OFA ORA?
(Nonsense)
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 Genetic Code
• Could be punctuated or not
– Punctuated code would have a something

in the code that separates codons

– Non-punctuated code would not

• In the following example, O is not a base

pair but the “punctuation.”
• Crick concluded that it is not punctuated as
mutations lead to a different sequence of
amino acids, not nonsense.
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 Genetic Code
• Code is practically universal
– ex: AGA codes for arginine in bacteria,

humans and all other organisms studied

– great evidence that all life has a common

ancestor
– Genes coded in one organism can be

transcribed in another

SWEET biotechnology

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 Genetic Code
• Code is practically universal…but not quite
• In 1979 mammalian mitochondria found to
have different “universal code”
– In mitochondrial DNA, UGA is not a stop

codon as it is in “universal code”

– Other codons are different

– Chloroplasts and ciliates (protists) have

minor differences as well

• It is thought that the changes to
mitochondria and chloroplasts happen after
their endosymbiotic existence 23
 More on RNA
• Central Dogma shows
how information is
passed from DNA
RNA Protein
• RNA’s structure is
different from DNA
– single stranded not

Double Stranded
– uracil not Thymine

– ribose not

deoxyribose
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RNA Structure

• RNA like DNA, is a nucleic acid. RNA

structure differs from DNA structure.
• First, RNA is single stranded—it looks like
one-half of a zipper—whereas DNA is
double stranded.
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RNA Structure
• The sugar in RNA is ribose; Ribose
DNA’s sugar is
deoxyribose.

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RNA Structure
• Both DNA and RNA contain four nitrogenous
bases, but rather than thymine, RNA contains a
similar base called uracil (U).
• Uracil forms a
base pair with
adenine in
RNA, just as
thymine does in
DNA.
Uracil

Hydrogen bonds Adenine

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 Transcription
• RNA polymerase
– only one of two DNA strands (template or

antisense strand) is transcribed

– non-transcribed strand is termed coding

strand or sense strand

– In both bacteria and eukaryotes, the

polymerase adds ribonucleotides to the

growing 3’ end of an RNA chain.

synthesis proceeds in 5’3’ direction
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Transcription Bubble

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 Transcription
• Promoter
– Transcription starts at RNA polymerase

binding sites called promoters on DNA

template strand.
• Initiation
– Other eukaryotic factors bind, assembling

a transcription complex.

RNA polymerase begins to unwind DNA
helix.
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 Transcription
• Elongation
– Transcription bubble moves down DNA at

constant rate leaving growing RNA

strands protruding from the bubble.
• Termination
– Stop sequences at the end of the gene

cause phosphodiester bond formation to

cease, transcription bubble to dissociate,
and RNA polymerase to release DNA.

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tion Complex (Transcription Comp

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 Eukaryotic Transcription
• Eukaryotic transcription differs from
prokaryotic transcription:
– three RNA polymerase enzymes

– initiation complex forms at promoter

– RNAs are modified after transcription

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Translation: From mRNA to Protein

• The process of converting the information in a

sequence of nitrogenous bases in mRNA into a
sequence of amino acids in protein is known as
translation.
• Translation takes place at the ribosomes in the
cytoplasm.

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 Translation: From mRNA to Protein
• The role of transfer RNA Amino
acid
• For proteins to be built, the 20
different amino acids dissolved in
the cytoplasm must be brought to
the ribosomes.
Chain of RNA
• This is the role of transfer RNA nucleotides

(tRNA)
• Each tRNA molecule attaches to Transfer RNA
molecule
only one type of amino acid.

Anticondon

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Translation: From mRNA to Protein

Ribosome

mRNA codon

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 Translation: From mRNA to Protein
• The first codon on mRNA is AUG, which codes for the
amino acid methionine
• AUG signals the start of protein synthesis.
• When this signal is given, the ribosome slides along the
mRNA to the next codon.

Methionine

tRNA
anticodon

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Translation: From mRNA to Protein

• A new tRNA molecule carrying an amino

acid pairs with the second mRNA codon.

Alanine

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Translation: From mRNA to Protein
• The amino acids are joined when a peptide
bond is formed between them.
Methionine Alanine

Peptide
bond

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Translation: From mRNA to Protein
• A chain of amino acids is formed until the stop codon is
reached on the mRNA strand.

Stop codon

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 Translation (in more detail)
• Begins when initial portion of mRNA
molecule binds to rRNA in a ribosome
– tRNA molecule with complimentary

anticodon binds to exposed codon on

mRNA

some tRNA molecules recognize more
than one codon

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 Translation (in more detail)
• Activating enzymes
– tRNA molecules attach to specific amino

acids through the action of activating

enzymes (aminoacyl-tRNA syntheases).

must correspond to specific anticodon
sequences on a tRNA molecule as well
as particular amino acids

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 Translation (in more detail)
• Start and stop signals
– start signal coded by AUG codon

– stop signal coded by one of three

nonsense codons: UAA - UAG – UGA

– What do you think “nonsense codons”

means here?
• Initiation
– Polypeptide synthesis begins with the

formation of an initiation complex.


initiation factors
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Formation of Initiation Factor

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 Translation (in more detail)
• Elongation
– After initiation complex forms, large

ribosome subunit binds, exposing mRNA

codon adjacent to the initiating codon,
positioning it for interaction with another
amino acid-bearing tRNA molecule.

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 Translation (in more detail)
• Translocation
– ribosome moves nucleotides along mRNA

molecule

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 A bit about the peptide bond formation
• A peptide bond (or amide bond) is a covalent chemical
bond formed between two molecules when the carboxyl
group of one molecule reacts with the amine group of the
other molecule, thereby releasing a molecule of water.
• This is a dehydration synthesis reaction (also known as a
condensation reaction), and usually occurs between amino
acids.
• The resulting C(O)NH bond is called a peptide bond, and
the resulting molecule is an amide.
• The four-atom functional group -C(=O)NH- is called a
peptide link

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 Translation (in more detail)
• Termination
– Nonsense codons are recognized by

release factors that release the newly

made polypeptide from the ribosome.
– There is no tRNA with complimentary

antidcodon to (UAA, UAG, UGA)

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 Spliced Gene Transcripts
• DNA sequence specifying a protein is broken
into segments (exons) scattered among longer
noncoding segments (introns).
• Initially, primary RNA transcript is produced for
the entire gene.
– Small nuclear ribonuclearproteins (snRNPs)

associate with proteins to form

spliceosomes.

Lariat forms, excising introns and splicing
exons to form mature mRNA.

alternative splicing
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Spliceosome (Spliceosome.EXE)

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 RNA Splicing
• During RNA processing, intron sequences
are cut out of primary transcript before it is
used in polypeptide synthesis.
– remaining sequences are not translated


remaining exon sequences are spliced
together to form final processed mRNA

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Eukaryotic Genes are Fragmented

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Compartmentalization
of processes (thus, replication
transport is
important)

DNA Replication
nucleus

Transcription 
Nucleus

mRNA transferred to
cytoplasm

Translation 
Ribosome (in
cytoplasm)

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From a sequence to a protein

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 Copyright © The McGraw - Hill Companies, Inc. Permission required for reproduction or dis play.

An overview of gene expression in eukaryotes

1 Nuclear
membrane

3‘
DNA

RNA polymerase
5‘

Primary RNA 3‘
Nucleus transcript
5‘
In the cell nucleus, RNA polymerase transcribes RNA from DNA.
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An overview of gene expression in eukaryotes

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An overview of gene expression in eukaryotes

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An overview of gene expression in eukaryotes

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An overview of gene expression in eukaryotes

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An overview of gene expression in eukaryotes

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 Differences Between Prokaryotic and
Eukaryotic Gene Expression
• Most eukaryotic genes possess introns
(prokaryotic genes do not.)
• Individual bacterial mRNA molecules often
contain transcripts of several genes.
• Eukaryotic mRNA molecules must be
completely formed and must pass across the
nuclear membrane before translation.
• In prokaryotes, translation begins at the AUG
codon preceded by a special nucleotide
sequence.
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 Differences Between Prokaryotic and
Eukaryotic Gene Expression
• Eukaryotic mRNA molecules have introns cut
out and exons joined together before
translation.
• Eukaryotic ribosomes are larger than
prokaryotic ribosomes.

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Exceptions to the Central Dogma
Nobel Prizes Epigenetic marks, such as patterns of
DNA methylation, can be inherited and
provide information other than the DNA
sequence
DNA

retroviruses use reverse transcriptase

mRNA introns (splicing) to replicate their genome
(Philip Sharp and Richard Roberts) (David Baltimore and Howard Temin)

RNA editing (deamination of cytosine

to yield uracil in mRNA) RNA RNA viruses

RNA interference (RNAi) a mechanism

of post-transcriptional gene silencing
utilizing double-stranded RNA Prions are heritable proteins responsible
for neurological infectious diseases
RNAs (ribozymes) can catalyze an (e.g. scrapie and mad cow)
enzymatic reaction (Stanley Pruisner)
(Thomas Cech and Sidney Altman) Protein

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How do mutation effect proteins
• Any change in DNA sequence is called a mutation.
• Mutations can be caused by errors in replication,
transcription, cell division, or by external agents

The effects of point mutations

• A point mutation is a change in a single base pair
in DNA
• A change in a single nitrogenous base can change
the entire structure of a protein because a change
in a single amino acid can affect the shape of the
protein
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Mutations – the effects of point
mutations

mRNA
Normal
Protein
Stop

Replace G with A

Point mRNA
mutation Protein
Stop

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Frameshift mutations
• A mutation in which a single base is added or
deleted from DNA is called a frameshift mutation
because it shifts the reading of codons by one
base.
• Structural changes in chromosomes are
called chromosomal mutations.

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Causes of Mutations
• Any agent that can cause a change in DNA is
called a mutagen.
• Mutagens include radiation, chemicals, and even
high temperatures.
• Forms of radiation, such as X rays, cosmic
rays, ultraviolet light, and nuclear radiation,
are dangerous mutagens because the energy
they contain can damage or break apart DNA.

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Chromosomal Alterations
• When a part of a chromosome is left out, a deletion
occurs.

A B C D E F G A B C E F G
H H

Deletion

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Chromosomal Alterations
• When part of a chromatid breaks off and
attaches to its sister chromatid, an insertion
occurs.

• The result is a duplication of genes on the same

chromosome.

A B C D E F G H A B C B C D E F G H

Insertion

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Chromosomal Alterations
• When part of a chromosome breaks off and
reattaches backwards, an inversion occurs.

A B C D E F G H A D C B E FGH

Inversion

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Chromosomal Alterations

• When part of one chromosome breaks off and

is added to a different chromosome, a
translocation occurs.

AB C D E F GH W X AB C DE F GH

WX Y Z Y Z
Translocation

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