2B: 3 Nucleic acids
Introduction
Proteins are the actors of cells
Each amino acid in the protein: 20 choices
Protein of 100 aa = 20100 different possibilities
Huge variety of proteins
Information for primary structure of proteins is contained in genes
Genes made of DNA
Transcription
mRNA
Translation
Protein
Introduction
Nucleic acids = DNA and RNA
DNA and RNA are Polynucleotides
One Nucleotide
Monomer
Up to 5 million
condensation reactions
Polynucleotides
Strand of nucleotides
Polymer
Only in DNA
Basic structure of mononucleotides
Only in RNA
Found both in DNA and RNA
There are similitudes between
DNA structure
and RNA structure
There are differences between
DNA structure
and RNA structure
Only in DNA
Only inRNA
Only in DNA
Basic structure of mononucleotides
Only in RNA
Nucleotides
Pentose sugar + Nitrogen base + Phosphate Group
Nucleic Acids
Polymers of Nucleotides = Polynucleotides
Deoxyribonucleic acid
Ribonucleic acid
DNA
RNA
Deoxyribose
Phosphate Group
Nitrogen base
(A, C, G, or T)
Ribose
Phosphate Group
Nitrogen base
(A, C, G, or U)
Basic structure of mononucleotides
Only in DNA
Only in RNA
Nucleotides
Pentose sugar + Nitrogen base + Phosphate Group
DNA and RNA were first found in nucleus
Eukaryotes:
DNA never leaves the nucleus (eukaryotes)
RNA is produced in nucleus,
then leaves nucleus for cytoplasm
Nucleic Acids
Polymers of Nucleotides = Polynucleotides
Prokaryotes:
Both DNA and RNA in cytoplasm
Deoxyribonucleic acid
Ribonucleic acid
DNA
RNA
Deoxyribose
Phosphate Group
Nitrogen base
(A, C, G, or T)
Ribose
Phosphate Group
Nitrogen base
(A, C, G, or U)
Only in DNA
Basic structure of mononucleotides
Only in RNA
Nucleotides
Pentose sugar + Nitrogen base + Phosphate Group
Both DNA and RNA contain phosphate groups
Related to phosphoric acids
Acidify solution
Nucleic Acids
Polymers of Nucleotides = Polynucleotides
Deoxyribonucleic acid
Ribonucleic acid
DNA
RNA
Deoxyribose
Phosphate Group
Nitrogen base
(A, C, G, or T)
Ribose
Phosphate Group
Nitrogen base
(A, C, G, or U)
Basic structure of mononucleotides
Only in DNA
Only in RNA
DNA
Nitrogen bases
RNA
6
7
1
5
8
00
4
2
9
3
Two rings
4
5
3
00
1
2
6
One ring
00
00
Basic structure of mononucleotides
Only in DNA
Only in RNA
Pentose sugar
DNA
RNA
Ribose
Deoxyribose
5’
5’
4’
1’
3’
2’
4’
1’
3’
2’
OH
Only in DNA
Basic structure of mononucleotides
Only in RNA
Phosphoric acid / Phosphate group
DNA
RNA
Basic structure of mononucleotides
Only in DNA
Only in RNA
Formation of nucleotide: Two condensation reactions
Phosphate linked to 5’ Carbon of pentose
By ester bond
Base linked to 1’Carbon of pentose
By glycosidic bond
deoxyribose
One out of the 5 nucleotides
3’ Carbon of pentose free for bond with another nucleotide
DNA and RNA are polynucleotides
Nucleic acids = DNA and RNA
DNA and RNA are Polynucleotides
One Nucleotide
Pentose sugar + Nitrogen base + Phosphate
Monomer
Up to 5 million
condensation reactions
Polynucleotides
Strand of nucleotides
Polymer
DNA and RNA are polynucleotides
A Polynucleotide = Single STRAND
One Nucleotide
Sugar + Nitrogen base + Phosphate
DNA and RNA are polynucleotides
A Polynucleotide = Single STRAND
One Nucleotide
Sugar + Nitrogen base + Phosphate
Sugar-phosphate backbone
Never changes
Sequence of bases varies
DNA and RNA are polynucleotides
Bonds between nucleotides= Phosphodiester bonds
A Polynucleotide = Single STRAND
Nucleotide
Sugar + Nitrogen base + Phosphate
DNA and RNA are polynucleotides
A Polynucleotide = Single STRAND
Nucleotide
Sugar + Nitrogen base + Phosphate
Two nucleotides are
bound together:
3’C from nucleotide n
with
5’C from nucleotide
n+1
DNA and RNA are polynucleotides
5’
A Polynucleotide = Single
FirstSTRAND
nucleotide
5’C Phosphate free
“5’ end” = “5’ Phosphate”
Nucleotide
Sugar + Nitrogen base + Phosphate
A polynucleotide strand has an overall direction
5’ to 3’ or
3’
3’ to 5’
Last nucleotide
3’C OH free
“3’ end” = “3’ OH”
Only in DNA
Complementary base pairing and the DNA double helix
Sugar-phosphate backbone
One DNA strand
“single-stranded DNA”
5’ end
Thymine (T)
Adenine (A)
Cytosine (C)
Guanine (G)
3’ end
Phosphate Deoxyribose
Nitrogen bases
Only in DNA
Complementary base pairing and the DNA double helix
Sugar-phosphate backbone
One DNA strand
“single-stranded DNA” ssDNA
5’ end
Thymine (T)
Adenine (A)
Cytosine (C)
Guanine (G)
3’ end
Phosphate Deoxyribose
Nitrogen bases
“Double helix” two strands of DNA
“double-stranded DNA” dsDNA
Only in DNA
Complementary base pairing and the DNA double helix
Base pairs hold the two DNA strands together
A /T
G/C
A and T are complementary
G and C are complementary
BASE PAIRS
Hydrogen bonds
Only in DNA
Complementary base pairing and the DNA double helix
Sequence second strand deduced from
sequence first strand
Two strands are complementary
Only in DNA
Complementary base pairing and the DNA double helix
The two strands of DNA are antiparallel (opposite directions)
5’ end
3’ end
Hydrogen bond
1 nm
3.4 nm
0.34 nm3’ end
5’ end
Structure of RNA
Only in RNA
Sugar-phosphate backbone
One RNA strand
“single-stranded RNA”
5’ end
Uracil (U)
OH
RNA is always single-stranded
Adenine (A)
OH
Cytosine (C)
OH
Guanine (G)
OH
3’ end
Phosphate
ribose
Nitrogen bases
Structure of RNA
Only in RNA
Sugar-phosphate backbone
One RNA strand
“single-stranded RNA”
5’ end
Uracil (U)
OH
mRNA = Messenger RNA
Used as a template for protein synthesis
Adenine (A)
tRNA = Transfer RNA
Used for protein synthesis
Brings amino acids
Cytosine (C)
rRNA = Ribosomal RNA
Part of Ribosomes
OH
OH
Guanine (G)
3’ end
OH
Phosphate Deoxyribose
Nitrogen bases
Only in DNA
Structure of DNA and RNA
Only in RNA
One strand
ACG
U
Two strands
ACGT
Complementarity
Shorter
100-2000 bases
Long
Millions of base pairs
Question:
• If there is 30% Adenine, how much Cytosine is
present?
•There would be 20% Cytosine
•Adenine (30%) = Thymine (30%)
•Guanine (20%) = Cytosine (20%)
•Therefore, 60% A-T and 40% C-G
4: How DNA works
The need for DNA replication
Cell division requires replication of genetic material
Before (almost) each cell division, DNA is replicated
DNA replication occurs during the S phase
of the cell cycle
S = Synthesis of DNA
Each strand of the double-stranded DNA is used as a template
One double helix….. Two double helices
After the cell division, each daughter cell
owns the same genetic material
The same genetic material as their parent cell
No DNA replication between
Meiosis I and Meiosis II
Process of DNA replication
Parent molecule
ssDNA
New strand
ssDNA
New strand
ssDNA
Parent molecule
ssDNA
Addition of
Denaturation
Parent molecule
dsDNA
Parent molecule
ssDNA
Parent molecule
ssDNA
New nucleotides
Parent molecule
ssDNA
Parent molecule
ssDNA
Process of DNA replication
Template strand
New strand
Already added ACG
Parental strand
New strand = “Template”
5‘ end
 DNA Polymerase
Adds nucleotides
One by one
 The parental strand is
used as a template
Nitrogenous base
Sugar
Phosphate
 To know which nucleotide
is to be added next
By complementarity
A
T
C
G
T
A
G
C
3‘
end
3‘ end
dTTP)
Will be added
5‘ end
Process of DNA replication
Template strand
New strand
Already added ACG
Parental strand
New strand = “Template”
3‘
end
5‘ end
Nitrogenous base
DNA Polymerase NEEDS the
3’OH from the last added
nucleotide to add another
nucleotide
Via making a phosphodiester
bond
Sugar
Phosphate
3‘ end
A
T
C
G
T
A
G
C
dTTP)
Will be added
5‘ end
New strand and
template strand
are antiparallel
Process of DNA replication
Template strand
New strand
Already added ACG
Parental strand
New strand = “Template”
5‘ end
DNA replication has
an overall direction
From 5’ to 3’ of the
3‘
end
Nitrogenous base
Sugar
Phosphate
new strand
3‘ end
A
T
C
G
T
A
G
C
dTTP)
Will be added
5‘ end
Multiple sites
The DNA double helix has to be “opened/unwound”
To access the information of both strands
To know which nucleotides have to be added, and in the right order
The replication starts at a Replication
5’ end
fork opened by DNA Helicase
3’ end
Strands from template
Base pairs still
held by hydrogen bonds
Nucleotide to be added
at the 3’end of the new strand
3’ end
New strands
5’ end
3’ end
5’ end
5’ end
3’ end
Multiple sites
Two replication forks make a replication eye/bubble
Multiple sites
The speed of DNA replication in humans is about 50 nucleotides
per second per replication fork
The whole human Genome can be copied only in a few hours
because there are many replication eyes at the same time
The speed of DNA replication in bacteria is much higher (1000 nucleotides per second)
The whole bacterial Genome can be copied only in a few minutes.
Multiple sites
Many sites for DNA replication (replication forks)
in Eukaryotes
DNA replication only happens during the S phase of the cell cycle
Eukaryotes have LONG chromosomes
Replication speed: 50 nucleotides per second
3000 nucleotides per minute
Longest chromosome of Drosophila (fly)
6.5 x 107 (650 000 000) nucleotides.
If only one replication fork, time needed is 150 DAYS
This chromosome is replicated in 4 minutes !!
The replication of this chromosome uses 54 000 replication forks
Three models for DNA replication?
 Watson and Crick’s model = semiconservative replication
 Two other models: the conservative model and the dispersive model.
Old DNA
NewDNA
Three models for DNA replication?
Which of the three models is right ?
Experiments in the late 1950s
Matthew Meselson and Franklin Stahl
Three models for DNA replication?
Centrifugation
Centrifugation of DNA
DNA
DNA
Three models for DNA replication?
Bacteria:
Fast growing
One generation = 20 minutes
Fast DNA replication
All DNA contains…
15N ONLY
centrifugation
Three models for DNA replication?
Old DNA 15N
NewDNA 14N
New DNA is lighter than old DNA
Three models for DNA replication?
Old DNA 15N
NewDNA 14N
New DNA is lighter than old DNA
Three models for DNA replication?
Old DNA 15N
NewDNA
14N
New DNA is lighter than old DNA
Three models for DNA replication?
Old DNA 15N
NewDNA 14N
New DNA is lighter than old DNA
Three models for DNA replication?
Old DNA 15N
NewDNA 14N
New DNA is lighter than old DNA
Three models for DNA replication?
Old DNA 15N
NewDNA 14N
New DNA is lighter than old DNA
Three models for DNA replication?
Old DNA 15N
NewDNA 14N
New DNA is lighter than old DNA
Three models for DNA replication?
Old DNA 15N
NewDNA 14N
New DNA is lighter than old DNA
Three models for DNA replication?
Old DNA 15N
NewDNA 14N
New DNA is lighter than old DNA
Three models for DNA replication?
Old DNA 15N
NewDNA 14N
New DNA is lighter than old DNA
Three models for DNA replication?
“Semi-conservative”: KEEP 50%
After each DNA Replication,
Each double helix contains
One strand from the parent molecule
One newly made strand
Original double helix
New strands
Review of DNA Replication
Important things to remember
To ‘copy’ each strand of the double-stranded DNA
To “copy” = to complement
DNA Helicase breaks
hydrogen bonds
between paired bases
DNA Polymerase
adds nucleotides
One by one
DNA Ligase joins
short new strands
together into one
DNA replication is semi-conservative
Bases are added at the 3’OH end of the NEW strand
From the 5’P end to the 3’ OH end of the NEW strand
From the 3’ OH end to the 5’P end of the TEMPLATE strand
5:Genetic Code
The need for a genetic code
• Proteins are the actors of cells
• Each protein: 20 choices
Protein of 100 aa = 20100 different possibilities
• Huge variety of proteins
• Information for primary structure of proteins is contained in genes
Genes made of DNA
Transcription
mRNA
Translation
Protein
The need for a genetic code
There are many types of RNAs
tRNAs = transfer RNA
rRNAs = Ribosomal RNA
mRNAs = Messenger RNA
etc…
ONLY mRNA are used in translation
rRNAs = ribosomal RNAs are parts of ribosomes
tRNA = transfer RNAs bring amino acid to the ribosome to elongate a protein being made
.
The need for a genetic code
Why the word “Translation” ?
From one language to another
From “mRNA language” to “protein language”
Goal of translation ?
Use the information in mRNA to make protein
=
Translate the sequence in mRNA to know the sequence of protein
that has to be made
The need for a genetic code
How to know which amino acid is needed?
Out of 20 possibilities
When we can only use nucleotides
Out of only 4 nucleotides ???
We need a CODE
The Genetic code
The genetic code
Four different bases are used to be translated into a combination of 20 different amino acids
One base
Combinations of
two bases
Combinations of
three bases
A C G U
41 = Four combinations
Not enough
AA AC AG AU
CA CC CG CU
GA GC GG GU
UA UC UG UU
42 = 16 combinations
Not enough
AAA AAC AAG AAU
ACA ACC ACG ACU
.......
UUA UUC UUG UUU
43 = 64 combinations
Enough
+ EXTRA
The genetic code
Triplet = codon
The genetic code
The need for a genetic code
An overview of gene expression
Characteristics of the genetic code
The genetic code
1. Is degenerate
2. Contains “punctuation codons”
3. Is non-overlapping
4. Is more-or-less universal
The genetic code is degenerate
•There are four bases, so there are 64 different codons
(triplets) possible (43 = 64), yet there are only 20 amino
acids that commonly occur in biological proteins
• This is why the code is said to be degenerate:
multiple codons can code for the same amino
acids
• The degenerate nature of the genetic code
can limit the effect of mutations
Characteristics of the genetic code
1. The genetic code is degenerate
The genetic code requires at least 20 codons minimum
 It contains 64 codons
Contains more information than required
 While Methionine and Tryptophane are encoded by single codons
All other amino acids are encoded by more than one codon
 “Degeneracy” = the third base of the codon looks less important than
the first and second bases
e.g. Phenylalanine encoded by UUU and UUC
e.g. Proline encoded by CCU, CCC, CCA and CCG
Characteristics of the genetic code
1. The genetic code is degenerate
Transfer RNAs = tRNAs
tRNAs bring/transfer the amino acids
One given tRNA always brings the SAME amino acid
When making the protein, the mRNA sequence is used as a template
First codon – First amino acid is brought
Second codon – Second amino acid is brought
etc…
The tRNAs recognise the codons
How ?
Using the complementarity of bases between mRNA and tRNAs
Characteristics of the genetic code
1. The genetic code is degenerate
An anticodon is complementary to a
codon
Genetic code is
degenerate
One amino acid will be attached to
One tRNA - one anticodon (TRP and Met)
Or
More than one tRNA – more than one anticodon
(LEU – 6 tRNAs – 6 anticodons)
Characteristics of the genetic code
2. The genetic code contains “punctuation codons”
2.1 The three stop codons
 Three codons do not encode any amino acids
UAA UAG UGA
 If they are “read” by the ribosome, translation will end
 They do not attract any tRNA+amino acid
 They attract a release factor = a protein that can fit
in the ribosome where
new tRNA+amino acid
enter the ribosome
 Presence of release factor in ribosome ends translation
 The last amino acid is encoded by the codon
just before the stop codon
Characteristics of the genetic code
2. The genetic code contains “punctuation codons”
2.2 The Start/Methionine codon
 The codon AUG encodes the amino acid Methionine
AND
The codon AUG marks the position where translation starts
CONFUSION ?
What if a mRNA contains several AUG codons ?
Start translation at each AUG?
Multiple proteins out of
one single mRNA?
 Only the first AUG is THE start codon
Any other AUG is used for Methionine
 All proteins have Methionine as their
first amino acid
Characteristics of the genetic code
3. The genetic code is non-overlapping
 In a mRNA molecule, codons are consecutive.
 The non-overlapping nature of the genetic code means that each base is only
read once.
 The adjacent codons do not overlap
 A non-overlapping code means that the same letter is not used for two different
codons; in other words, no single base can take part in the formation of more than
one codon
Characteristics of the genetic code
3. The genetic code is non-overlapping
An anticodon is complementary to a
codon
Genetic code is
non-overlapping
A tRNA matches one codon, then the next
tRNA matches the next codon
Characteristics of the genetic code
4. The genetic code is more-or-less universal
 All organisms use the same genetic code
 The same triplet codes code for the same
amino acids
in all living things (meaning that genetic
information is transferable between species)
 exception = mitochondria in humans
 A few exceptions (reality)
 Consequence: Transgenic organisms are possible
The universal nature of the genetic code is why
genetic engineering , the transfer of genes from
one species to another is possible
6: Protein Synthesis
Key Players
• mRNA carries the
information from a
gene in DNA.
• Ribosomes, made of
rRNA, consist of
subunits and carry out
an enzyme-like role.
• tRNA carries specific
amino acids to the
ribosome.
Transcription
• RNA polymerase is the enzyme responsible for
making mRNA copies of genes. DNA unzips at the site
of the gene that is needed.
Transcription
• RNA polymerase matches bases in the sense strand
with RNA bases, building a strand of mRNA that
carries the information encoded in the DNA.
Transcription
• Encoded in DNA is a signal telling RNA polymerase
where to stop. Transcription ends at that point.
Transcription
• The completed mRNA primary transcript then
undergo mRNA processing and moves from the
nucleus to the ribosomes for translation.
Translation
• Initiation begins with
a tRNA bearing
methionine (met)
attaching to one of
the ribosomal units.
The codon for
methionine is a
universal “start”
codon for “reading”
the mRNA strand.
Translation
• The ribosomal
unit binds to
mRNA where the
code for met is
located (AUG).
The anticodon
(UAC) of the tRNA
matches the
“start” codon on
mRNA (AUG).
Translation
• The larger ribosomal
subunit now binds to
the smaller unit,
forming a ribosomal
complex. The tRNA
binds to the first
active site on the
ribosome. Translation
may now begin.
Translation
• The second codon
in mRNA (GUU)
matches the
anticodon of a tRNA
carrying the amino
acid valine (CAA).
The second tRNA
binds to the second
active site on the
large subunit.
Translation
• A catalytic site on
the larger subunit
binds the two
amino acids
together using
dehydration
synthesis, forming
a peptide bond
between them.
Translation
• The first tRNA now
detaches and goes
of to find another
met in the
cytoplasm. The
mRNA chain shifts
over one codon,
placing the second
codon (CAU) over
the second active
site.
Translation
• A tRNA with an
anticodon (GUA)
matching the
exposed codon
(CAU) moves onto
the ribosome. This
tRNA carries
histidine (his).
Translation
• A new peptide bond
forms between val and
his on the catalytic site.
The tRNA that carried
val will detach and find
another val in the
cytoplasm. The mRNA
strand will then shift
over one more codon.
Translation
• The process continues
until the ribosome
finds a “stop” codon.
The subunits detach
from one another, the
mRNA is released, and
the polypeptide chain
moves down the ER for
further processing. The
initial met is removed
and the chain is folded
into its final shape.
Summary