Nucleic acids and Protein Synthesis

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Chemistry 203
Chapter 22 Nucleic acids and Protein Synthesis
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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.

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Nucleic acids
Backbones of chromosomes
Ribonucleic acids (RNA) Deoxyribonucleic acids
(DNA)
Nucleic acids
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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).
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Nucleotide

• A nucleotide is composed of
• Nitrogen-containing bases (amines)
• Sugars (monosaccharides)
• Phosphate

Phosphate
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Bases
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Sugars (monosaccharide)

• RNA contains
• D-Ribose sugar
• DNA contains
• 2-Deoxy-D-Ribose sugar (without O on carbon 2)

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Nucleoside
When a N atom of the base forms a glycosidic
bond to C1 (anomeric C) of a sugar.
Base Sugar
Nucleoside
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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-.
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Nucleotide
A nucleotide forms with the -OH on C5 of a sugar
bonds to phosphoric acid.
Phosphate ester bond
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5
1
A nucleotide
The name cytidine 5'-monophosphate is abbreviated
as CMP.
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Nucleotide
The name deoxyadenosine 5-monophosphate is
abbreviated as dAMP.
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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.
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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-
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Secondary structure of DNA

• The DNA model is proposed by Watson and Crick in
  1953.
• Two strands of polynucleotide form a double helix
  structure like a spiral.
• Hydrogen bonds link paired bases
• Adenine-Thymine (AT)
• Guanine-Cytosine (G-C)
• Sugar-Phosphate backbone is hydrophilic and stays
  on the outside (bases are hydrophobic).

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3
Sugar phosphate backbone
3D structure
5
3
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Secondary structure of DNA
A Purine base always hydrogen bonds with a
pyrimidine.
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Complementary base pairs
A-T base pair
2 H bonds
G-C base pair
3 H bonds
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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
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Higher structure of DNA
Chromatin Condensed nucleosomes
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Higher structure of DNA
Chromatin fibers are organized into loops, and
the loops into the bands that provide the
superstructure of chromosomes.
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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).
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Difference between DNA RNA

• 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.
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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.
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Functions of DNA
1. It reproduces itself when a cell divides
(Replication).
2. It supplied the information to make up RNA,
proteins, and enzymes.
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Replication
Separation of the two original strands and
synthesis of two new daughter strands using the
original strands as templates.
By breaking H-bonds
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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.
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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.
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Replication
Replisomes assemblies of enzyme factories.
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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.

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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.

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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.
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Ligase
In formation of lagging strand, small fragments
(Okazaki) are join together by ligase enzyme.
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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
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Gene expression
Transcription synthesis of mRNA (messenger RNA)
Translation
Reverse transcription
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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.
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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.
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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
- G A A C T -
Section of bases on DNA (template strand)
- C U U G A -
Complementary base sequence in mRNA
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Transcription
Sample Problem 22.6
From the template strand of DNA below, write out
the mRNA and informational strand of DNA
sequences
Template strand 3C T A G G A T A C5
mRNA 5G A U C C U A U G3
Informational 5G A T C C T A T G3 strand
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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.
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Gene expression
Overall function of RANs in the cell facilitate
the task of synthesizing protein.
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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.

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Genetic code
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Genetic code

• 64 condons are possible from the triplet
  combination of A, G, C, and U.
• UGA, UAA, and UAG, are stop signals.
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  (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).

• Codons are written from the 5 end to the 3 end
  of the mRNA molecule

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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
U
G
U C A
Codon on mRNA
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Transcription
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Translation
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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.
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Termination
Ribosome encounters a stop condon.
No tRNA to complement the termination codon.
An enzyme releases the complete polypeptide chain
from the ribosome.
Amino acids form the three-dimensional structure
(active protein).
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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.
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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.
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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.
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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
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Type of Mutations
Point (substitution) Mutation
The most common
Replacement of one base in the coding strand of
DNA with another.
Different amino acid
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Point Mutation
In hemoglobin, substitution of just one amino
acid can result in the fatal disease sickle cell
anemia.
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Frameshift Mutation
1. A deletion mutation occurs when one or more
nucleotides is/are lost from a DNA molecule.
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Silent Mutation
A silent mutation has a negligible effect to the
organism, because the resulting amino acid is
identical.
The mutation has no effect.
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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.

1. An enzyme that cleaves DNA at specific locations.

• A gene from a second organism that will be
  inserted into the
• original DNA molecule.

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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.
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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.
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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.
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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.

1. Two primersshort polynucleotides that are
   complementary to the two ends of the segment to
   be amplified.

1. A DNA polymerase enzyme to catalyze the synthesis
   of a complementary strand.

1. Nucleoside triphosphatesthe source of the A, T,
   C, and G needed to make the new DNA.

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HOW TO Use the Polymerase Chain Reaction to
Amplify a Sample of DNA
Heat the DNA segment to unwind the double helix
to form single strands.
Step 1
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HOW TO Use the Polymerase Chain Reaction to
Amplify a Sample of DNA
Add primers that are complementary to the DNA
sequence at either end of the DNA segment.
Step 2
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HOW TO Use the Polymerase Chain Reaction to
Amplify a Sample of DNA
Use a DNA polymerase and added nucleotides to
lengthen the DNA segment.
Step 3
After each cycle the amount of DNA is doubled, so
after 20 cycles, 1,000,000 copies have been made.
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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.

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DNA Fingerprinting
DNA fragments can be visualized on X-ray film
after they have been separated
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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 persons immune system to produce
antibodies to the virus to ward off infection.
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Viruses
A virus with an RNA core is called a retrovirus.
Retroviruses invade a host and then synthesize
viral DNA by reverse transcription.
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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) .