DNA & Proteins

)'
 Objectives
• Describe the structure of DNA and RNA structure
• Describe how eukaryotic and prokaryotic DNA is arranged in the cell
• Explain the process of DNA replication, and the importance of telomerase to DNA
replication
• Describe mechanisms of DNA repair
• State the central dogma, and explain the main steps of transcription
• Describe how eukaryotic mRNA is processed
• Describe the different steps in protein synthesis or translation
• Discuss the role of ribosomes in protein synthesis
• Describe the genetic code and how the nucleotide sequence determines the amino acid
and the protein sequence
• Discuss why every cell does not express all of its genes
• Describe how prokaryotic gene expression occurs at the transcriptional level
• Understand that eukaryotic gene expression occurs at the epigenetic, transcriptional,
post-transcriptional, translational, and post-translational levels
Bad Guess…
DNA Application
• The three letters “DNA” have become associated with
• crime solving
• paternity testing
• human identification
• genetic testing & diagnostics
• Genealogy
• identifying pathogens
• vaccine development
• cancer therapy
• DNA stands for Deoxyribonucleic Acid
How DNA is Used?
• DNA is the genetic material passed from parent to offspring for all
life on Earth
• DNA sequencing is a laboratory technique used to determine the
exact sequence of the nucleotides in a DNA molecule
• The nucleotide sequence of hundreds of species of organisms
including humans have been determined
• Sequences allow us to understand human disease and the
relationship of humans to the rest of the tree of life
Watson and Crick and Franklin!
DNA Structure -1/6
• Watson and Crick predicted the structure of DNA using Franklin's data
and other information such as Chargaff’s rules
• Chargaff’s rule states that in DNA there is always equality in quantity
between the bases A and T and between the bases G and C (A is adenine, T
is thymine, G is guanine, and C is cytosine).
• The building blocks of DNA are nucleotides, which are made up of
three parts: a deoxyribose (5-carbon sugar), a phosphate group, and
a nitrogenous base
DNA Structure – 2/6
• Macromolecule composed of IStructure of Nucleotide! H N/H
repeating monomers of
nucleotides PhOSt)hateester t ond H
• Each nucleotide has three
components: 0
• a 5-carbon sugar (deoxyribose) PhoSJlhate _ II 5 H
O-P-0-CH
• a phosphate group
• and a nitrogenous base
gr llJ
I
o- 1%
4C Sugar
• Adenine IH
• Cytosine t':11111-~2
• Guanine I
HO+-RNA
• Thymine (H)+-DNA
DNA Structure – Polymerization 3/6
Nucleotides bond together by Result of polymerization is a
dehydration reactions single strand of DNA with two
different ends

5' end of strand Nitrogen

containing bases
Sugar-phosphate project from
backbone of r---+ backbone
DNA strand I
()

Phosphodiester ~ t
' p (
I

bond links I
deoxyribonucleotides
/
I I OI I
OH OH
3' end of strand
DNA in the cell consists of 2 nucleotide strands
coiled around each other to form a double helix
 DNA Structure - the 4 bases of DNA 4/6
• Two types of bases • \
bonds
Adenine
Nitrogenous bases:
5' ThyKmme O ••• H2~N N~ i~
• Purines 3' 5' -Adenine
c:::::::::::r
Thymine O~p~- NH··· -N ' ~
e
• Adenine A
-Guanine
Cytosine
_CfO
N
-{ '=N O
0,,0 Adenx:·neNH 2 Thymi~e
H3 C
f
~ o _.H2N Vc\o.P·-o ( I ~N I NH
NH )

• Guanine G
N NH~O
o:P:o (N o---·· __
.Nf \ e
eO ~N~NH··· nJ- 0 9
O'p:::::O
-~ H······°
N
Cytosine d 5, Guan~nx:e f CytosinecNH2
Sugar o Guanine 2 e !.( I NH I ~N
phosphate II II NH ~NH2

• Pyrimidines
NH~O
backbone I I
Sugar-phosphate Bases Sugar-phosphate
3' 5' backbone backbone

• Cytosine C (a) (b)

Figure 9.4 DNA (a) forms a double stranded helix, and (b) adenine pairs with
• Thymine T thymine and cytosine pairs with guanine. (credit a: modification of work by Jerome
Walker, Dennis Myts)

A – T and G – C
DNA: Structure 5/6
• Because of this base pairing the pa.irs
HO

sequence of one strand

determines the sequence of the
other strand of DNA
• The two strands of DNA are
complementary
• Complementarity allows for the
precise duplication of DNA
during cell division ®
011

phosphate m-, ~ nitrog~~­

Q sugar
containing
S::: --IIIEJ bases

© 200 7 Encyclopaedia Britannica, Inc.

DNA: Structure 6/6
3'end
• The two strands of DNA in the
helix are Antiparallel
• The head of one strand is laid
against the tail of the other strand
• Its important in replication– The
two strands replicate differently!

3'end 5'end
DNA: Complementarity

TACGGCAAACTTACT

2. TACGCCATT

3. TACAAAAAGTGGATC
The Structure of RNA 1/2

OH 0 OH

o:
Ribose
1
Deoxyribose
1

Figure 9.15The diifference between the rib ose found 1n RNA and
1

the deoxyriibose found in DNA i,sthat rib ose has a hydroxyl group
1

at the 2 1 carbon.
The Structure of RNA 2/2
• Bases
• Cytosine
• Guanine
• Adenine
• Uracil (takes Thymine’s place) ble- strended*
Generally d d*
Sing\e-stran e

• Sugar
• Ribose
• Phosphate group(s)
Three Types of RNA + Function
• All necessary to do protein synthesis
• rRNA: Ribosomal RNA, RNA that is part of the structure of
ribosome

• tRNA: Transfer RNA functions as helper and brings correct amino

acids to ribosome to build new protein

• mRNA: Messenger RNA carries the code from DNA to ribosomes

where proteins are made
Comparing DNA & RNA
Nucleic Acid DNA RNA
Where it is In the nucleus In the nucleus and
located: in the cytoplasm
Sugar Deoxyribose Ribose
molecule:
Number of Double Single
Strands:
Nitrogenous A-T, C-G A-U, C-G
bases:
DIFFERENCES BETWEEN DNA AND RNA IN EUKARYOTIC CELLS
 Why Do Cells Need Both DNA & RNA?

tRNA b1ings me.ach

amino acid to add to
the ro:·o,tVingchain

Because DNA codes for the instructions

to make a protein, do not leave the llt--------->t-
mRNA :ilstranslated
b y the 1ibosornes
nucleus of eukaryotic cells, and ribosomes (made up of rRNA}
do not attach to DNA. The ribosomes, into a chain of
located in the cytoplasm, attach to the ammo ac:ilds

RNA to assemble the protein.

DNA - codes for the mRNA-:ils

amino acid transcribed to lea\,e
sequence the nucleus
How DNA is Stored in Cells

Nucleus _ ___..,_;~~......,!H!;,Mo-"J'II'

Nucleolus-- ......---~...,...,.." ucleoid

Chromatin----~~-.~~
----
Eukaryote Prokaryote

A eukaryote contains a well-defined nucleus, whereas in prokaryotes,

the chromosome lies in the cytoplasm in an area called the nucleoid.
How DNA is Stored in Prokaryotic Cells
• In cytoplasm (no nucleus) - Nucleoid
• Chromosome is circular
– Single copy
• E. coli chromosome is 4.6 million Supercoiling

bases long
• 1mm long – 1000X longer than the
length of the organism!
• The entire genome does not have
genes – there are noncoding regions
• DNA is supercoiled – DNA is tightly
wound up and twisted
 How DNA is Stored in Eukaryotic Cells
• Linear Chromosomes in eukaryotic cells of Eukaryotic Chromosomes

are packaged differently in the nucleus DNA double

helix

• DNA is wrapped tightly around proteins

known as histones to form structures
called nucleosomes DNA wrapped
around histone

• This nucleosome is linked to the next

one by a short strand of DNA that is
Nucleosomes
coiled into a
chromatin

free of histones
fiber

• This is also known as the “beads on a Further

condensation

string” structure; the nucleosomes are of chromatin

the “beads” and the DNA between

them are the “string” Duplicated
chromosome

Figure 9.7 These figures illustrate the compaction of

the eukaryotic chromosome.
DNA REPLICATION 1/3
• DNA of cells are doubled before cell division in order for each
daughter cell to have an identical copy of DNA
• This is accomplished by the process of DNA replication
• The replication of DNA occurs during the synthesis phase, or S phase,
of the cell cycle, before the cell enters mitosis or meiosis
• RECALL:
• DNA is double helix
• The two DNA strands are complementary to each other
• For example: a strand of DNA with a nucleotide sequence of: AGTCATGA
will have a complementary strand with the sequence of: TCAGTACT
 DNA REPLICATION – 2/3 3'

• Because of the complementarity of

the two strands, having one strand
means that it is possible to recreate
the other strand

• This model for replication suggests

that the two strands of the double
helix separate during replication,
and each strand serves as a
template from which the new 3'

complementary strand is copied Figure 9.8: The two strands of DNA are complementary,
meaning the sequence of bases in one strand can be used to
create the correct sequence of bases in the other strand.
 DNA REPLICATION 3/3
• During DNA replication, each of the Semi-conservative model of DNA Replication

two strands that make up the - -

double helix serves as a template
from which new strands are copied
• The new strand will be
complementary to the parental or - -
“old” strand
- -
I\ - -
• Each new double strand consists of
one parental strand and one new
daughter strand
• This is known as semiconservative - - --
replication
Figure 9.9: The semiconservative model of DNA
replication is shown. Gray indicates the original
DNA strands, and blue indicates newly synthesized DNA.
 DNA Replication in Eukaryotes – 1/2
• Because eukaryotic genomes are very complex, DNA replication is a
very complicated process that involves several enzymes and other
proteins
• It occurs in three main stages:
• Initiation
• Elongation
• Termination
• During initiation, the DNA is made accessible to the proteins and
enzymes involved in the replication process
DNA Replication in Eukaryotes 2/2
• There are specific nucleotide sequences called origins of replication at
which replication begins
• Certain proteins bind to the origin of replication while an enzyme called
helicase unwinds and opens up the DNA helix
• As the DNA opens up, Y-shaped structures called replication forks are
formed
• Two replication forks are formed at the origin of replication, and these
get extended in both directions as replication proceeds
• There are multiple origins of replication on the eukaryotic chromosome,
such that replication can occur simultaneously from several places in the
genome
DNA Replication in Eukaryotes 1/5
4------------0rigin-----------.,..

5' 3'

3'
◄
3' 5' 5' 5'

Lagging
strand

RNA Okazaki Leading Newly made DNA

primer fragment strand DNA strands polymerase

Figure 9.10: A replication fork is formed by the opening of the origin of replication, and helicase
separates the DNA strands. An RNA primer is synthesized, and is elongated by the DNA
polymerase. On the leading strand, DNA is synthesized continuously, whereas on the lagging
strand, DNA is synthesized in short stretches. The DNA fragments are joined by DNA ligase (not
shown).
DNA Replication in Eukaryotes – ELONGATION 2/5
• An enzyme called DNA
polymerase adds DNA
nucleotides to the 3' end of the
template ------------Origin------------

• DNA polymerase can only add 5' 3' 5' 3' 5' 3'

new nucleotides at the end of a .......

3'

backbone 3' 5' 3' 5' 3' 5'

• a primer sequence, which

Lagging Helicase
strand

provides this starting point, is RNA

primer
Okazaki
fragment
Leading
strand
Newly made
DNA strands
DNA
polymerase

added with complementary RNA

nucleotides
• this primer is removed later,
replaced with DNA nucleotides
DNA Replication in Eukaryotes – ELONGATION 3/5
• One strand, which is
complementary to the parental
DNA strand, is synthesized
continuously toward the ------------Origin------------

replication fork 5' 3' 5' 3' 5'

• Polymerase can add .......

3'

nucleotides in this direction 5’ 3' 5' 3' 5' 3' 5'

to 3’ Lagging
strand

• This continuously synthesized

RNA Okazaki Leading Newly made DNA
primer fragment strand DNA strands polymerase

strand is known as the leading

strand
DNA Replication in Eukaryotes – ELONGATION 4/5
• DNA polymerase can only
synthesize DNA in a 5' to 3'
direction, the other new strand is
put together in short pieces
called Okazaki fragments •------------Origin------------•

• The Okazaki fragments each 5' 3' 5' 3' 5' 3'

require a primer made of RNA to ◄

3'

start the synthesis 3' 5' 3' 5' 3' 5'

• The strand with the Okazaki fragments Lagging

strand
Helicase

is known as the lagging strand RNA

primer
Okazaki
fragment
Leading
strand
Newly made
DNA strands
DNA
polymerase

• An enzyme removes the RNA

primer, which is then replaced with
DNA nucleotides, and the gaps
between fragments are sealed by
an enzyme called DNA ligase
DNA Replication in Eukaryotes – ELONGATION 5/5
The process of DNA replication can
be summarized as follows:
1. DNA unwinds at the origin of
replication -------------Origin------------•

2. New bases are added to the

complementary parental strands 5' 3'

(one new strand is made

3'
◄
continuously, while the other 3' 5' 3' 5' 3' 5'

strand is made in pieces) Lagging

strand

3. Primers are removed, new DNA RNA Okazaki Leading Newly made DNA

nucleotides are put in place of

primer fragment strand DNA strands polymerase

the primers and the backbone is

sealed by DNA ligase
Telomere Replication 1/3
• Because eukaryotic
chromosomes are linear, DNA GGTAC
3' I I I I I 5'
C AUCCC
telomerase
UC

replication comes to the end of a Telomerase has an associated RNA that complements
the 3' overhang at the end of the chromosome.

t
line in eukaryotic chromosomes
• In the leading strand, synthesis
GGTAC CAAUCCCAMUC
3' I I I I I 5' telomerase

continues until the end of the

The RNA template is used to synthesize the complementary
strand.

chromosome is reached 51 I I I ' I I I

CCATGCATTGGTTAGGGTTAG
GGTAC C
I I I I I I I I I I I I I .. 3'

UCCCAAUC

• However, on the lagging strand

3' I I I I 1 5' telomerase
Telomerase shifts, and the process is repeated.

t
there is no place for a primer to 5' 1 1 1 1 1 1 1 1 ; 1 • , , 1 1 1 I I I I .. I I ; I ; - 3'
CCATGCATTGGTTAGGGTTAGGGTTAG

be made for the DNA fragment GGTAC

3' I I I I I 5'
AATCCCAAT
- I I I I I I I I

to be copied at the end of the

Primase and DNA polymerase synthesize the complementary
strand.

chromosome Figure 9.11: The ends of linear chromosomes are

maintained by the action of the telomerase
enzyme.
Telomere Replication 2/3
• This presents a problem for the
cell because the ends remain GGTAC
3' I I I I I 5'
C AUCCC UC

unpaired, and over time these

telomerase
Telomerase has an associated RNA that complements

ends get progressively shorter as the 3' overhang at the end of the chromosome.

t
cells continue to divide
GGTAC CAAUCCCAMUC
• The ends of the linear 3' I I I I I 5' telomerase

chromosomes are known as The RNA template is used to synthesize the complementary
strand.

telomeres, which have repetitive 51 I I I ' I I I I I I I I I I I I I I I I .. 3'

sequences that do not code for a

CCATGCATTGGTTAGGGTTAG
GGTAC C UCCCAAUC

particular gene
3' I I I I 1 5' telomerase
Telomerase shifts, and the process is repeated.

t
• As a consequence, it is telomeres 5' 1 1 1 1 1 1 1 1 ; 1 • , , 1 1 1 I I I I .. I I ; I ; - 3'
CCATGCATTGGTTAGGGTTAGGGTTAG
that are shortened with each GGTAC
3' I I I I I 5'
AATCCCAAT
- I I I I I I I I

round of DNA replication instead Primase and DNA polymerase synthesize the complementary
strand.

of genes (which is believed to Figure 9.11: The ends of linear chromosomes are
play a role in the aging process) maintained by the action of the telomerase
enzyme.
Telomere Replication 3/3
The telomerase attaches to the
GGTAC
• 3' I I I I I 5'
C U CCC UC
telomerase

end of the chromosome, and Telomerase has an associated RNA that complements

complementary bases to the RNA

the 3' overhang at the end of the chromosome.

J
template are added on the end of
the DNA strand GGTAC
3' I I I I I 5'
C uccc'"'
telomerase
uc

• Once the lagging strand template The RNA template is used to synthesize the complementary

is sufficiently elongated, DNA

strand.

polymerase can now add 51

' ' I I I I
CCATGCATTGGTTAGGGTTAG
I ' I ' ' I I I I I I I I I .. 3'

nucleotides that are GGTAC C UCCCA UC

complementary to the ends of

3' I I • I I 5' telomerase

Telomerase shifts, and the process is repeated.

the chromosomes J
• Thus, the ends of the
5' I I I I I I I I I I , , , I I I I I I I .. I I I I I - 3'
CCATGCATTGGTTAGGGTTAGGGTTAG

chromosomes are replicated

GGTAC AATCCCAAT
3' I I I I I 5' - I I I I I I I I

Telomerase is typically found to

Primase and DNA polymerase synthesize the complementary
strand.

be active in germ cells, adult Figure 9.11: The ends of linear chromosomes are
stem cells, and some cancer cells maintained by the action of the telomerase
enzyme.
DNA Replications in Prokaryotes
• Recall that the prokaryotic chromosome is a circular molecule with a
less extensive coiling structure than eukaryotic chromosomes
• Escherichia coli has 4.6 million base pairs in a single circular
chromosome, and all of it gets replicated in approximately 42 minutes
• starts from a single origin of replication and proceeds around the
chromosome in both directions
• This means that approximately 1000 nucleotides are added per
second; the process is much more rapid than in eukaryotes
DNA Replication - Comparison
between Prokaryotic and Eukaryotic Replications

Property Prokaryotes Eukaryotes

Origin of replication Single Multiple

Rate of replication 1000 nucleotides/s 50 to 100 nucleotides/s

Chromosome structure circular linear

Telom erase Not present Present

Table 9.1
DNA Repair 1/3
• DNA polymerase checks every 5'

nucleotide added to be make

sure the correct base paring A-T, ®--® Extension
(error)

C-G and fixes any mistakes!

5'

• DNA by proofreading. Proofreading

~
• Mismatch repair - repair
enzymes recognize the wrongly 5'

incorporated base and excise it

Extension
5'

from the DNA, replacing it with 5'

the correct base Proofreading by DNA polymerase

DNA Repair 2/3 I I I
GGTTA
I I I
cc
I , , I
ATTC
I
~3•

Nucleotide excision repair

CCAATC• CTAA TAAC TCAT
3' I I I I I I I I I I I I I I I I I I I 5'
DNA polymerase

(a) Proofreading

• DNA double strand is unwound

and separated, the incorrect I I I I I I
CCGATCACGAA
I I I I I
Daughter

bases are removed along with a

strands
GGCTAGTAGAC
I I I I I I I I I I I
AGc

few bases on the 5' and 3' end

AG

• These are replaced by copying I , , , I I I

l
I I I I

the template with the help of

CCGATCACGAA

GGCTAGTAGAC
I I I I I I I I I I I

DNA polymerase
(b) Mismatch Repair

• Important in correcting thymine I ~ I

' - ..,.' I I ~ I

dimers, which are primarily

C A "'{ C T G

G T A A G A C

caused by ultraviolet light l

C A T T C T G
G T A A G A C

(c) Nucleotide Excision

DNA Repair 3/3
Nucleotide excision repair
• Individuals with flaws in their nucleotide excision repair genes show
extreme sensitivity to sunlight and develop skin cancers early in life
Most mistakes are corrected; if they are not, they may result in a
mutation—defined as a permanent change in the DNA sequence
Mutations in repair genes may lead to serious consequences like cancer
TRANSCRIPTION
• In both prokaryotes and eukaryotes, the second function of DNA
(the first was replication) is to provide the information needed to
construct the proteins necessary for cell functions
• Through the processes of transcription and translation, a protein is
built with a specific sequence of amino acids that was originally
encoded in the DNA
 The Central Dogma: DNA Encodes RNA; RNA
Encodes Protein
• The flow of genetic information
in cells from DNA to mRNA to
protein is described by the
central dogma
• Central Dogma - states that
genes specify the sequences of
mRNAs, which in turn specify
the sequences of proteins
• The copying of DNA to mRNA is
relatively straightforward, the
translation to protein is more Figure 9.14: The central dogma states that
complex DNA encodes RNA, which in turn encodes
protein.
Transcription: from DNA to mRNA
• Transcription is the process of “transcribing” the code from the DNA
to make the mRNA
• Both prokaryotes and eukaryotes perform fundamentally the same
process of transcription having three main stages:
• initiation
• elongation
• termination
• Eukaryotic transcription occurs in the nucleus of the cell and the
mRNA transcript must be transported to the cytoplasm
• Prokaryotic transcription occurs in the cytoplasm of the cell
Initiation
• Transcription requires the DNA
double helix to partially unwind
in the region of mRNA synthesis, DNA RNA
this region is called a nontemplate
transcription bubble strand

• Promoter – the DNA sequences

to which the involved proteins
and enzymes bind to initiate the DNA
RNA polymerase

process of transcription template

strand Promoter
• Promoters are very important
because they determine whether
the corresponding gene is Figure 9.15: The initiation of transcription begins when DNA is
unwound, forming a transcription bubble. Enzymes and other
transcribed all of the time, some proteins involved in transcription bind at the promoter.
of the time, or hardly at all
Elongation
• Transcription always proceeds from
one of the two DNA strands, which
is called the template strand 5'
RNA
Nontemplate strand
• The mRNA product is 4'c t t+t'f~ I
~
complementary to the template 5' .,..,
AT
..,,-,,..,.,..,,_, ..,., (' ~---"•
CC CA-</-</ T
' 1 7 I I I',
TACCAC
I I I I
TA
3'

strand and is almost identical to v C'

v I..J
Dire .
ct,on of synthesis__..--~
.A 3'

the other DNA strand, called the TAC C TTA C /Jc \) \) TG T CAT

nontemplate strand,
3' I I I I I

DNA
I
, , 1 1 , -1 C

"··••J,r,T,~,1.Y
C CUC

RNA polymerase
e, t t t '( • • • • 5'
\
Template strand
• with the exception that RNA contains
a uracil (U) in place of the thymine (T)
found in DNA During elongation, RNA polymerase tracks along the
DNA template, synthesizes mRNA in the 5' to 3’
• During elongation, an enzyme direction, and unwinds then rewinds the DNA as it is
read.
called RNA polymerase proceeds
along the DNA template adding
nucleotides by base pairing
Termination
• There are two kinds of termination
signals present
• Both involve repeated nucleotide
sequences in the DNA template (Prokaryotic):
• result in RNA polymerase stalling, Directionof 0.25 µm

leaving the DNA template, and freeing

transcription-----1►
RNA
Simultaneous polymerase
DNA

the mRNA transcript Transcription/

Translation
• On termination, the process of
Polyribosome
{

Polypeptide

transcription is complete
(aminoend)

• Transcription and protein synthesis

(translation) occurs concurrently
using polyribosomes.
Eukaryotic RNA Processing 1/3
• Once elongation is complete, an enzyme then adds a string of
approximately 200 adenine residues to the 3' end, called the poly-A tail
• This modification further protects the pre-mRNA from degradation and
signals to cellular factors that the transcript needs to be exported to the
cytoplasm
• Eukaryotic genes are composed of protein-coding sequences called exons
(ex-on signifies that they are expressed) and intervening sequences called
introns (int-ron denotes their intervening role)
• Introns are removed from the pre-mRNA during processing. Intron
sequences in mRNA do not encode functional proteins
• The process of removing introns and reconnecting exons is called splicing
Eukaryotic RNA Processing 2/3
Pnmary RNAtranscript
------ -----~-

Exon 1 lntron Exon 2 lntron Exon 3

RNAprocessing

Spl1icedRNA
-- ----
Exon 1 2 Exon 3
S'cap / Poly-A tail
5' u. translated 3' untrans
. ated
reg1:on region

Figure 9.18: Eukaryotic mRNA contains introns that must be spliced out. A 5' cap and 3' tail are also added.
Eukaryotic RNA Processing 3/3
• Alternative splicing - different
protein product are produced Exon skipping

from one gene when different

combinations of introns (and Mutually exclusive exons

sometimes exons) are removed

from the transcript Alternative 5' donor sites

• May lead to genetic diseases

• May also an important
Alternative 3' acceptor sites

mechanisms of gene control that

has let to the evolution of new
lntron retention

Figure 9.23 There are five basic modes of alternative

functions splicing. Segments of pre-mRNA with exons shown in blue,
red, orange, and pink can be spliced to produce a variety
of new mature mRNA segments.
TRANSLATION
• The general structures and
functions of the protein synthesis
machinery are comparable from
Growing ------1
protein chain Ribosome

bacteria to human cells tRNA

• Translation requires the input of

an mRNA template, ribosomes,
tRNAs, and various enzymatic
factors
• Translation is the process that
“translates” the nucleic acid
language of the mRNA into the Figure 9.19: The protein synthesis machinery includes
amino acid language of the the large and small subunits of the ribosome, mRNA,
protein and tRNA. (credit: modification of work by NIGMS, NIH)
The Protein Synthesis Machinery
• Ribosome - a complex macromolecule composed of structural and
catalytic rRNAs, and many distinct polypeptides
• Ribosomes are located in the cytoplasm in prokaryotes and in the
cytoplasm and endoplasmic reticulum of eukaryotes
• Ribosomes are made up of a large and a small subunit that come
together for translation
• The small subunit is responsible for binding the mRNA template,
whereas the large subunit sequentially binds tRNAs
• tRNA is an RNA molecule that brings amino acids to the growing chain of the
polypeptide
The Genetic Code 1/2
• Protein sequences consist of 20 Second letter
commonly occurring amino u C A G

acids; therefore, it can be said uuu}

UUC Phe ucu} UAU}Tyr
UAC
UGU}cys
UGC
u
C
that the protein alphabet u UCC Ser
UUA }Leu UCA UAA Stop UGA Stop A
UUG UCG UAG Stop UGG Trp G
consists of 20 letters CAU}H· u
cuu}
CUC CCU} CAC 15 CGU} C
• Each amino acid is defined by a
CCC Pro CGC Arg
...
Q)
C CUA Leu
CCA CAA} CGA A
~ CUG CCG CAG Gin CGG G
three- nucleotide sequence ~
...
...
Cl)
AGU }ser u
called the triplet codon
AUU} ACU} AAU}Asn
LL AUC lie ACC AAC AGC C
A AUA ACA Thr A
~}Lys AGA}Arg
AUG Met ACG AGG G
• The relationship between a u
nucleotide codon and its GUU} GCU} GAU}Asp GGU}
GAC GGC GIi C
G GUC Val GCC Ala
GCA GGA y A
GUA GAA}
corresponding amino acid is GUG GCG GAG Glu GGG G

called the genetic code This figure shows the genetic code for translating each
nucleotide triplet, or codon, in mRNA into an amino acid or a
• There are 64 possible codons termination signal in a nascent protein. (credit: modification of
work by NIH)
The Genetic Code 2/2
• Stop codons – The three triplets of the 64 codons that terminate
protein synthesis and release the polypeptide from the translation
machinery
• Start codon – AUG codon serves as the start signal to initiate
translation. Also codes for the amino acid methionine
• The genetic code is universal; with a few exceptions, virtually all
species use the same genetic code for protein synthesis
• A powerful evidence that all life on Earth shares a common origin
CC CAAUCU UUCAC CACUCAU U U
RNA

Translation

Protein Met Pro Gin Ser Val His Ala Leu Met Cys
 Codon - Anticodon
3'
- AminoAcid
attachment site
5'
tRNA

• tRNA contains a sequence called the

anticodon, complementary to the mRNA
codon Dloop
Tloop

- recognizes and bind the codon

• Each tRNA has its corresponding amino acid
attached to its end Anticodon loop

Anticodon
cue
GUC CAG GAG CCA UAG
111111 Ill
1 I
111111
mRNA
Codon
TRANSLATION - The Mechanism of Protein
Synthesis 1/4
• Just as with mRNA synthesis, protein synthesis can be divided into
three phases:
• initiation
• elongation
• termination
• Protein synthesis begins with the formation of an initiation complex
which involves the small ribosome subunit, the mRNA template,
three initiation factors, and a special initiator tRNA
 The Mechanism of Protein Synthesis 2/4
• The large ribosomal subunit consists
of three compartments:
• The A site binds incoming charged
tRNAs with their attached specific Ribosome

amino acids
• The P site binds charged tRNAs
carrying amino acids that have
formed bonds with the growing
polypeptide chain but have not
yet dissociated from their Components needed to begin
translation come together.
G On the assembled ribosome, a tRNA carrying the first
amino acid is paired with the start codon on the mRNA.

corresponding tRNA
The place where this first tRNA sits is called the P site.
A tRNA carrying the second amino acid approaches.

• The E site releases dissociated

tRNAs so they can be recharged
with free amino acids
Translation – the process of protein synthesis 3/4
bond forms

Ribosome moves
along mRNA

E) The second codon of the mRNA pairs with a tRNA 0 The ribosome moves along the mRNA until the second
carrying the second amino acid at the A site. The first tRNA is in the P site. The next codon to be translated is
amino acid joins to the second by a peptide bond. This brought into the A site. The first tRNA now occupies the E
attaches the polypeptide to the tRNA in the P site. site.

Growing
olypeptide

~ C e,
-+
u u
\) <">
~

C) The second amino acid joins to the third by another C) The ribosome continues to move along the mRNA,
peptide bond, and the first tRNA is released from the E and new amino acids are added to the polypeptide.
site.
Translation – the process of protein synthesis 4/4
Initiation Elongation Termination

-~-<.,,__
~ -Q,.,
Polypeptide
released
Gly
/
= Larg
ubunit
.,'-\ ~
__,,,,..Ribosome
\ G1y,~
,.I'll

New protein
---+ mall
subunit
mRNA

0 When the ribosome reaches a stop 0 Finally, the last tRNA is released, and the ribosome
codon, the polypeptide is released. comes apart. The released polypeptide forms a new
protein.

After many ribosomes have completed translation, 3'

the mRNA is degraded so the nucleotides can be

reused in another transcription reaction
Transcription and translation occurs concurrently
in prokaryotes.
HOW GENES ARE REGULATED
• The process of turning on a gene to produce RNA and protein is called
gene expression
• For a cell to function properly, necessary proteins must be
synthesized at the proper time
• All organisms and cells control or regulate the transcription and
translation of their DNA into protein
• Cells in multicellular organisms are specialized; liver cells are different
from muscle cells
• These differences are a consequence of the expression of different
sets of genes in each of these cells
• Cells will turn on or off certain genes at different times in response to
changes in the environment or at different times during the
development of the organism
Prokaryotic vs Eukaryotic Gene Expression 1/4
• RECALL: prokaryotic organisms lack a cell nucleus, the processes of
transcription and translation occur almost simultaneously
• The control of gene expression in prokaryotic cells is almost entirely
at the transcriptional level.
• Lactose is a food source for E. coli
• When lactose is not present in the bacterium’s environment, the lac
genes are transcribed in small amounts
• When lactose is present, the genes are transcribed and the bacterium
is able to use the lactose as a food source
 Prokaryotic Gene Expression – Lac Operon 2/4

1he ,-oparan:,
Prom:allr

Genes are expressed when lactose is present

but genes are repressed when lactose is
absent.
prcnol8I ANA T
PD"""8NIJlndng + -T
bladCIRNA
polymenlle
Prokaryotic versus Eukaryotic Gene Expression 3/4
• The regulation of gene expression in eukaryotic cells can occur at all
stages of the process
• Regulation may occur:
• when the DNA is uncoiled and loosened from nucleosomes to bind
transcription factors (epigenetic level)
• when the RNA is transcribed (transcriptional level)
• when RNA is processed and exported to the cytoplasm after it is transcribed
(post-transcriptional level)
• when the RNA is translated into protein (translational level)
• after the protein has been made (post-translational level)
 Eukaryotic Gene Expression 4/4 Transcription
5' Nontemplate strand
'1(.i

s·,''' o ~f' ~-<;cAC CACTCAr .,. ,_ .......-~3•

AT CC CA-1,q D· \S TA TA
Uc,: "ecrion of syntnes 3•
V - ..

Eukaryotic gene expression is regulated during transcription RNA processing

D
and RNA processing, which take place in the nucleus, as well as primary RNA transcript
Exon 1 lnlan Elal 2 lnlan Exon 3
during protein translation, which takes place in the cytoplasm. spliced RNA
Further regulation may occur through post-translational - Exon 1 Elal 2 Exon 3

modifications of proteins.
Translation
Met-
D polypeptide chain

p
A

Ribosome