Download Chapter 22

Chemistry 203
Chapter 22
Nucleic acids and Protein Synthesis
Introduction
– Each cell of our bodies contains thousands of different proteins.
– How do cells know which proteins to synthesize out of the extremely
large number of possible amino acid sequences?
– the transmission of hereditary information took place in the nucleus,
more specifically in structures called chromosomes.
– The hereditary information was thought to reside in genes within the
chromosomes.
– Chemical analysis of nuclei showed chromosomes are made up
largely of proteins called histones and nucleic acids.
Nucleic acids
Backbones of chromosomes
Ribonucleic acids (RNA)
Nucleic acids
Deoxyribonucleic acids (DNA)
Nucleic acids
DNA stores the genetic information of an organism and transmits
that information from one generation to another.
RNA translates the genetic information contained in DNA into proteins
needed for all cellular function.
RNA and DNA are unbranched polymers (monomers: nucleotides).
Nucleotide
A nucleotide is composed of:
• Nitrogen-containing bases (amines)
• Sugars (monosaccharides)
• Phosphate
Phosphate
Bases
N H2
O
4
N
3
2
N
5
6
N
O
1
2
5
N
8
N
3
N9
4
H
Puri ne
N
H
Thymine (T)
(DNA onl y)
N
Uraci l (U)
(in RNA only)
O
N
N
N
O
N H2
N
HN
H
Cytosine (C)
(DNA and
some RNA)
7
6
1
O
H
Pyri mi dine
CH3
HN
N
O
N
H
Adenine (A)
(DNA and RNA)
N
HN
H 2N
N
N
H
Guani ne (G)
(DNA and RNA)
Sugars (monosaccharide)
RNA contains:
• D-Ribose sugar
DNA contains:
• 2-Deoxy-D-Ribose sugar (without O on carbon 2)
Nucleoside
When a N atom of the base forms a glycosidic bond to C1’ (anomeric C) of
a sugar.
Base + Sugar
O
Nucleoside
O
CH3
HN
N
O
H
hymine (T)
NA onl y)
uracil
N
-D -ribos ide
H
5'
Uraci l (U)
(in RNA only)
H
N
3'
H
2'
HO
OH
Urid ine
O
HN
1
O
H
4'
HN
O
HOCH 2
N
O
1'
H
a -N -glycosid ic
bond
bonß-N-glycosidic
d
anomeric
carb on
Nucleoside
To name a nucleoside derived from a pyrimidine base, use the suffix “-idine”.
To name a nucleoside derived from a purine base, use the suffix “-osine”.
For deoxyribonucleosides, add the prefix “deoxy-”.
Nucleotide
A nucleotide forms with the −OH on C5’ of a sugar bonds to
phosphoric acid.
NH2
NH2
Phosphate ester bond
N
N
O
O- P OH
O-
5’
+
O
HO CH2
N
1’
deoxycytidine and phosphate
5’
O
O- P O CH2
O
OH
O
-
N
O
O
OH
deoxycytidine
monophosphate (dCMP)
A nucleotide
The name cytidine 5′-monophosphate is abbreviated as CMP.
Nucleotide
The name deoxyadenosine 5’-monophosphate is abbreviated as dAMP.
Primary structure of DNA and RNA
Polynucleotide
Carry all information
for protein synthesis.
Phosphodiester
bond
Sequence of nucleotides.
Each phosphate is linked to C3’ and C5’ of two sugars.
Primary structure of DNA and RNA
A nucleoside = Base + Sugar
A nucleotide = Base + Sugar + Phosphate
A nucleic acid = A chain of nucleotides
Like amino acids
(C-terminal and N-terminal):
Base sequence is read from the C5’ (free phosphate) end to the C3’ (free hydroxyl) end.
-ACGU-
Secondary structure of DNA
• The DNA model is proposed by
Watson and Crick in 1953.
5’
3’
• Two strands of polynucleotide form a
double helix structure like a spiral.
Sugar phosphate
backbone
3D structure
• Hydrogen bonds link paired bases:
Adenine-Thymine (A–T)
Guanine-Cytosine (G-C)
• Sugar-Phosphate backbone is
hydrophilic and stays on the outside
(bases are hydrophobic).
3’
5’
Secondary structure of DNA
A Purine base always hydrogen bonds with a pyrimidine.
Complementary base pairs
A-T base pair
2 H bonds
G-C base pair
3 H bonds
Higher structure of DNA
• DNA is coiled around proteins called histones.
• Histones are rich in the basic amino acids
• Acidic DNA basic histones attract each other and form a
chain of nucleosomes.
Core of eight histones
Higher structure of DNA
Chromatin:
Condensed nucleosomes
Higher structure of DNA
Chromatin fibers are organized into loops, and the loops into the bands
that provide the superstructure of chromosomes.
Chromosome & Gene
- DNA molecules contain several million nucleotides, while RNA
molecules have only a few thousand.
- DNA is contained in the chromosomes of the nucleus, each
chromosome having a different type of DNA.
- Humans have 46 chromosomes (23 pairs), each made up of many
genes.
- A gene is the portion of the DNA molecule responsible for the synthesis
of a single protein (1000 to 2000 nucleotides).
Difference between DNA & RNA
1. DNA has four bases: A, G, C, and T.
RNA has four bases: A, G, C, and U.
2. In DNA: Sugar is 2-deoxy-D-ribose.
In RNA: Sugar is D-ribose.
3. DNA is almost always double-stranded (helical structure).
RNA is single strand.
4. RNA is much smaller than DNA.
RNA molecules
Transmits the genetic information needed to operate the cell.
1. Ribosomal RNA (rRNA)
Most abundant RNA – is found in ribosomes: sites for protein synthesis.
2. Messenger RNA (mRNA)
Carries genetic information from DNA (in nucleus) to ribosomes (in cytoplasm)
for protein synthesis. They are produced in “Transcription” from DNA.
3. Transfer RNA (tRNA)
The smallest RNA. Translates the genetic information in mRNA and brings specific
Amino acids to the ribosome for protein synthesis.
Functions of DNA
1. It reproduces itself when a cell divides (Replication).
2. It supplied the information to make up RNA, proteins, and enzymes.
Replication
Separation of the two original strands and synthesis
of two new daughter strands using the original strands as templates.
By breaking H-bonds
Replication
Replication is bidirectional: takes place at the same speed in both directions.
Replication is semiconservative: each daughter molecule has one parental strand
and one newly synthesized one.
Origin of replication: specific point of DNA where replication begins.
Replication fork: specific point of DNA where replication is proceeding.
Replication occurs at many places simultaneously along the helix.
Replication
Leading strand: is synthesized continuously in the 5’  3’ direction
toward the replication fork.
Lagging strand: is synthesized discontinuously in the 5’  3’ direction
away from the replication fork.
Replication
Replisomes: assemblies of “enzyme factories”.
Component
Function
Helicas e
Primas e
Clamp protein
DNA polymerase
Ligase
Unwinds the DNA double helix
Synthesizes primers
Threads leading s trand
Joins as sembled nucleotides
Joins Okazaki fragments in
lagging strand
Helicases
Unwinds the DNA double helix.
- Replication of DNA starts with unwinding of the double helix.
- Unwinding can occur at either end or in the middle.
- Attach themselves to one DNA strand and cause separation of the
double helix.
Primases
Catalyze the synthesis of primers.
Primers: are short nucleotides (4 to 15).
- They are required to start the synthesis of both daughter strands.
- Primases are placed at about every 50 nucleotides in the lagging
strand synthesis.
DNA Polymerase
It catalyzes the formation of the new strands.
- It joins the nucleoside triphosphates found in the nucleus.
- A new phosphodiester bond is formed between the 5’-phosphate of the
nucleoside triphosphate and the 3’-OH group of the new DNA strand.
Ligase
In formation of lagging strand, small fragments (Okazaki) are
join together by ligase enzyme.
Protein Synthesis
Gene expression: activation of a gene to produce a specific protein.
Only a small fraction (1-2%) of the DNA in a chromosome contains genes.
Base sequence of the gene carries the information
to produce one protein molecule.
Change of sequence
New protein
Gene expression
Transcription: synthesis of mRNA (messenger RNA)
Translation
DNA
replication
RNA
replication
DNA Transcription mRNA
Reverse
transcription
Revers
e transcriptase
Translation
protein
Transcription
Genetic information is copied from a gene in DNA to make a mRNA.
Begins when the section of a DNA that contains the gene to be copied unwinds.
Polymerase enzyme identifies a starting point to begin mRNA synthesis.
Transcription
The DNA splits into two strands:
Template strand: it is used to synthesize RNA.
Coding Strand (Informational strand): it is not used to synthesize RNA.
- Transcription proceeds from the 3’ end to the 5’ end of the template.
(informational strand, non-template strand)
Direction of transcription
- When mRNA is released, the double helix of the DNA re-forms.
Transcription
C is paired with G, T pairs with A
But A pairs with U (not T).
Polymerase enzyme moves along the unwound DNA,
forming bonds between the bases.
RNA Polymerase
Section of bases on DNA (template strand):
-G–A–A–C–T-
Complementary base sequence in mRNA:
-C–U–U–G–A-
Transcription
Sample Problem 22.6
From the template strand of DNA below, write out the mRNA and
informational strand of DNA sequences:
Template strand:
3’—C T A G G A T A C—5’
mRNA:
5’—G A U C C U A U G—3’
Informational
strand:
5’—G A T C C T A T G—3’
Translation
mRNA (as a carrier molecule) moves out of the nucleus and goes to ribosomes.
tRNA converts the information into amino acids.
Amino acids are placed in the proper sequence.
Proteins are synthesized.
Gene expression
Overall function of RAN’s in the cell: facilitate the task of synthesizing protein.
Genetic code
Genetic code: language that relates the series of nucletides in mRNA
to the amino acids specified.
• The sequence of nucleotides in the mRNA determines the amino
acid order for the protein.
• Every three bases (triplet) along the mRNA makes up a codon.
• Each codon specifies a particular amino acid.
• Codons are present for all 20 amino acids.
Genetic code
5'
U
C
U
UUU
UUC
UUA
UUG
CUU
CUC
CUA
CUG
AU U
AU C
A
AU A
AU G
GU U
G GU C
GU A
GU G
Phe
Phe
Leu
Leu
Leu
Leu
Leu
Leu
Ile
Ile
Ile
Met*
Val
Val
Val
Val
C
UCU
UCC
UCA
UCG
Ser
Ser
Ser
Ser
A
U AU
U AC
U AA
U AG
CAU
CAC
CAA
CAG
Tyr
Tyr
Stop
Stop
His
His
Gln
Gln
G
U GU
U GC
U GA
U GG
CGU
CGC
CGA
CGG
Cys
Cys
S top
Trp
Arg
Arg
Arg
Arg
CCU
CCC
CCA
CCG
Pro
Pro
Pro
Pro
ACU
ACC
ACA
ACG
GCU
GCC
GCA
GCG
Thr
Thr
Thr
Thr
Ala
Ala
Ala
Ala
AAU
AAC
AAA
AAG
GAU
GAC
GAA
GAG
As n
As n
Lys
Lys
A sp
A sp
Glu
Glu
A GU
A GC
A GA
A GG
GGU
GGC
GGA
GGG
Ser
Ser
Arg
Arg
Gly
Gly
Gly
Gly
3'
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G
*AUG s ign als tran slation initiation as w ell as codin g for Met
Genetic code
• 64 condons are possible from the triplet combination of A, G, C, and U.
•Codons are written from the 5’ end to the 3’ end of the mRNA molecule
• UGA, UAA, and UAG, are stop signals.
(code for termination of protein synthesis).
• AUG has two roles:
1. Signals the start of the proteins synthesis (at the beginning of an mRNA).
2. Specifies the amino acid methionine (Met) (in the middle of an mRNA).
tRNA (transfer RNA)
tRNA translates the codons into specific amino acids.
Serine
- It contains 70-90 nucleotides.
- The 3’ end, called the acceptor stem and
always has the nucleotide ACC and a free
OH group that binds a specific amino acid.
- Anticodon: a sequence of three
nucleotides at the bottom of tRNA, which
is complementary to three bases in an mRNA
and it can identify the needed amino acid.
Anticodon loop
A G U
Codon on mRNA
U C A
Transcription
Translation
Protein synthesis
• mRNA attaches to smaller subunit of a ribosome.
• tRNA molecules bring specific amino acids to the mRNA.
• Peptide bonds form between an amino acid and the end of the
growing peptide chain.
• The ribosome moves along mRNA until the end of the codon
(translocation).
• The polypeptide chain is released from the ribosome and
becomes an active protein.
Sometimes several ribosomes (polysome) translate the same strand of mRNA
at the same time to produce several peptide chains.
Termination
5'
U
C
A
G
3'
C
A
G
3'
UCU
Ser
U GU Cys
UUU
Phe
U AU Tyr
U
Ribosome
encounters
a
stop
condon.
UCU Ser
Phe
U AU
UCCCys
Ser U U AC Tyr
U GC Cys
UUCTyr
Phe U GU
C
UCC
Ser
U
GC
Phe
UCACys
Ser C U AA Stop
UUATyr
Leu
U U AC
U GA S top A
UCA Ser
U AA
Stop
Leu
Ser A U AG Stop
UCGS top
UUG
Leu U GA
U GG Trp
G
UCG Ser
U AG Stop
Leu
U GG Trp
G
CUU Leu
CCU Pro
CAU His
CGU Arg
U
His
Leu
CCU Pro
CAU
CUC Leu CGU
CCCArg
Pro U CAC His
CGC Arg
C
No
tRNA
to
complement
the
termination
codon.
HisLeu CGC
Leu
CCC Pro C CAC
CUA
CCAArg
Pro C CAA Gln
CGA Arg
A
GlnLeu CGA
Leu
CCA Pro
CAA
CUG
CCGArg
Pro A CAG Gln
CGG Arg
G
Leu
CCG Pro
CAG Gln
CGG Arg
G
AU U Ile
AAU As n
U
ACU Thr
A GU Ser
An
enzyme
releases
the
complete
polypeptide
chain
from
the
ribosome.
AsIle
n
Ile
AAU
Ser
U AAC As n
ACU Thr
A GU
C
AU
C
ACC
Thr
A GC Ser
A
AsIle
n
Ile
ACC Thr
AAC
A GC
A
AU A
ACASer
Thr C AAA Lys
A GA Arg
Ile
ACA Thr
AAA
LysMet*A GA
Arg
G
AU G
ACG
Thr A AAG Lys
A GG Arg
G
Met* ACG Thr
AAG Lys
A GG Arg
GU U Val
GCU Ala
GAU A sp
GGU Gly
U
Val
GCU Ala
GAU
A sp
GGU
Gly
Val
Ala Ustructure
sp
Gly
GU
C
GCC
GAC A(active
GGC
C
Amino acids
form
the
three-dimensional
protein).
G
Val
Ala
A
sp
Gly
GCC
GAC
GU A Val GGC
GCA Ala C GAA Glu
GGA Gly
A
Val
GCA Ala
GluVal GGA
Gly
GAA
GU G
GCG
Ala A GAG Glu
GGG Gly
G
Val
GCG Ala
GGG Gly
G
GAG Glu
*AUG s ign als tran slation initiation as w ell as codin g for Met
ign als tran slation initiation as w ell as codin g for Met
Translation
There are 3 stages in translation:
1. Initiation begins with mRNA
binding to the ribosome.
2. Elongation proceeds as the next
tRNA molecule delivers the next
amino acid, and a peptide bond
forms between the two amino acids.
Translation
3. Termination: Translation continues until a stop codon
(UAA, UAG, or UGA) is reached and the completed
protein is released.
Often the first amino acid (methionine) is not needed
and it is removed after protein synthesis is complete.
Mutation
A heritable change in DNA nucleotide sequence.
It changes the sequence of amino acids (structure and function of proteins).
Enzyme cannot catalyze.
X rays, Overexpose to sun (UV light), Chemicals (mutagens), or Viruses
However, some mutations are random events.
Effect of Mutation
Somatic cell (nonreproductive cell):
Altered DNA will be limited to that cell and its daughter cells.
Cancer
Germ cell (reproductive cell like an egg or sperm):
All new DNA will contain the same default
and it is passed on to the next generation.
Genetic diseases
Type of Mutations
Point (substitution) Mutation
The most common
Replacement of one base in the coding strand of DNA with another.
Different amino acid
Frameshift Mutation
One or more bases is/are added to or deleted from
the normal order of bases in DNA.
All the triplets shift over by one base.
Different sequence of amino acids
Point Mutation
In hemoglobin, substitution of just one amino acid can result in the fatal
disease sickle cell anemia.
No more amino acids are added. A need protein is not synthesized. The
organism may die.
Frameshift Mutation
1. A deletion mutation occurs when one or more nucleotides is/are
lost from a DNA molecule.
2. An insertion mutation occurs when one or more nucleotides is/are
added to a DNA molecule.
Silent Mutation
A silent mutation has a negligible effect to the organism, because the
resulting amino acid is identical.
The mutation has no effect.
Recombinant DNA
Recombinant DNA is synthetic DNA that contains segments from more
than one source.
Three key elements are needed to form recombinant DNA:
1. A DNA molecule into which a new DNA segment will be inserted.
2. An enzyme that cleaves DNA at specific locations.
3. A gene from a second organism that will be inserted into the
original DNA molecule.
Recombinant DNA
First, bacterial plasmid DNA
is cut by the restriction
endonuclease EcoRI, which
cuts in a specific place.
This gives a double strand
of linear plasmid DNA with
two ends ready to bond,
called sticky ends.
Recombinant DNA
Then, a second sample
of human DNA is cut
with the same EcoRI.
This forms human DNA
segments with sticky
ends that are
complimentary to the
plasmid DNA.
Recombinant DNA
Combining the two pieces of DNA (with DNA ligase enzyme) forms DNA
containing the new segment.
This DNA chain is slightly larger because of its additional segment.
This new DNA is re-inserted into a bacterial cell. Large amounts of
needed proteins can be synthesized by bacteria.
Polymerase Chain Reaction (PCR)
Polymerase chain reaction (PCR) amplifies a specific portion of a
DNA molecule, producing millions of exact copies.
Four elements are needed to amplify DNA by PCR:
1. The segment of DNA that must be copied.
2. Two primers—short polynucleotides that are complementary to
the two ends of the segment to be amplified.
3. A DNA polymerase enzyme to catalyze the synthesis of a
complementary strand.
4. Nucleoside triphosphates—the source of the A, T, C, and G needed
to make the new DNA.
HOW TO Use the Polymerase Chain Reaction to
Amplify a Sample of DNA
Step [1]
Heat the DNA segment to unwind the
double helix to form single strands.
HOW TO Use the Polymerase Chain Reaction to
Amplify a Sample of DNA
Step [2]
Add primers that are complementary to
the DNA sequence at either end of the
DNA segment.
HOW TO Use the Polymerase Chain Reaction to
Amplify a Sample of DNA
Step [3]
Use a DNA polymerase and added
nucleotides to lengthen the DNA segment.
After each cycle the amount of DNA is doubled, so after 20 cycles,
1,000,000 copies have been made.
DNA Fingerprinting
The DNA of each individual person is unique, so DNA can be used as
a method of identification.
•Any type of cell (skin, saliva, semen, blood, etc.) can be used to
obtain a DNA fingerprint.
•The DNA is first amplified by PCR, and then cut into fragments
by restriction enzymes.
•The DNA fragments are then separated by size by
gel electrophoresis.
DNA Fingerprinting
DNA fragments can be visualized on X-ray film after they have been
separated:
Viruses
A virus is an infectious agent consisting of a DNA or RNA molecule
that is contained within a protein coating.
- It is incapable of replicating alone (no enzyme, no free nucleotide),
so it invades a host organism and makes the host replicate the virus.
- Many prevalent diseases like the common cold, influenza, and
herpes are viral in origin.
- A vaccine is an inactive form of a virus that causes a person’s immune
system to produce antibodies to the virus to ward off infection.
Viruses
A virus with an RNA core is called a retrovirus.
Retroviruses invade a host and then synthesize viral DNA by reverse
transcription.
DNA
replication
RNA
replication
DNA Transcription mRNA
Revers e transcriptase
Translation
protein
Viruses
The viral DNA can then transcribe RNA, which then directs
protein synthesis (new retroviral particles to infect other cells).
AIDS (Acquired Immune Deficiency Syndrome) is caused by the
retrovirus HIV (Human Immunodeficiency Virus) .