CHAPTER 21
NUCLEIC ACIDS AND PROTEIN
SYNTHESIS
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What Role Do Nucleic Acids Play?
• DNA
 Contained in cell nucleus
 All information needed for the development of a complete living
system
 Every time a cell divides, cell’s DNA is copied and passed to the
new cells.
• RNA
 Part of the process of making proteins from genetic information
encoded in DNA
 RNA transcribes the information contained in the genes and
carries the code out to the protein-making machinery
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A. Components of Nucleic Acids
• DNA and RNA are both nucleic acids
 Both: unbranched polymers of repeating nucleotide monomers
 Each nucleotide has three components: a nitrogenous base, a
five-carbon sugar, and a phosphate group.
• Nitrogen-containing bases:
 Derivatives of pyrimidine or purine.
 Adenine (A) and guanine (G) are purines, and cytosine C and
thymine (T) are pyrimidines. RNA uses the same bases, except
that T is replaced by uracil (U).
Nitrogenous Base Structures
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The Four DNA Bases, and Uracil
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Ribose/Deoxyribose
• Both RNA and DNA contain 5-carbon sugars.
 RNA: ribose
 DNA: deoxyribose
• The carbons in the sugars are numbered with primes.
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Nucleosides/Nucleotides
• Nucleoside: base + sugar
• Nucleotide: base + sugar + phosphate group
“Tide contains phosphates!”

Naming: Adenine + ribose = adenosine
Adenine + deoxyribose = deoxyadenosine
Naming nucleosides of the other bases follows the same
pattern.
Naming nucleotides: nucleoside name followed by
5’-monophosphate
ex. Adenosine 5’-monophosphate (AMP) or deoxyadenosine 5’monophosphate (dAMP)
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Nucleosides/Nucleotides
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Nucleoside Di- and Triphosphates
• Any nucleoside 5’-monophosphate can bind additional
phosphate groups, forming a diphosphate or
triphosphate
• For example, you can form the famous ADP (adenosine
5’-diphosphate) and ATP (adenosine 5’-triphosphate)
through the addition of phosphate groups.
• The same can be done for nucleosides of other bases
(ex. GTP, CDP, etc)
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Nucleoside Di- and Triphosphates
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Let’s practice…
• Identify each of the following as a nucleoside or
a nucleotide:
 Guanosine
Nucleoside -- “phosphate” not part of the name
 Deoxythymidine
Nucleoside
 Cytidine 5’-monophosphate
Nucleotide -- “phosphate” is part of the name
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B. Primary Structure of Nucleic Acids
• The nucleotides are linked together from the 3’ -OH of
the sugar in one nucleotide to the phosphate on the 5’
carbon of the next nucleotide.
• This phosphate link is called a phosphodiester bond.
The chain formed from multiple phosphodiester bonds
forms the backbone of a strand of DNA.
Phosphodiester bond formation
• Sequence of bases in the nucleic acid = primary
structure. The sequence is written with 5’ and 3’ ends
labeled, for instance -- 5’-ACGT-3’
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A Single
Strand of
RNA (ACGU)
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C. DNA Double Helix
• In the 1940’s, it was discovered that the percent of A in
an organism = % T. Likewise, %C = %G.
What might this suggest?
• Base pairing rules: in two complementary strands of
DNA, A always base pairs with T, and C always base
pairs with G.
• 1953: DNA discovered to be a double helix (winds like a
spiral staircase)
DNA Double Helix
• The strands are antiparallel.
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A DNA Molecule (at least according to the
computer)
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D. DNA Replication
• Whenever cells divide, the DNA in the cells needs to
replicate -- an exact copy of the DNA needs to be
passed to the new cells.
• Replication begins when the enzyme helicase unwinds
a portion of the helix by breaking hydrogen bonds
between the strands.
• A nucleoside triphosphate bonds to the sugar at the end
of the growing new strand. Two phosphate groups are
cleaved (this provides the energy for the reaction)
• And DNA polymerase catalyzes the formation of the
new phosphodiester bond.
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DNA Replication
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DNA Replication cont.
• When the entire DNA double helix has been replicated,
one strand will be from the original DNA and one will be
a newly synthesized strand.
 This is why the process is called semi-conservative replication
 Ensures an exact copy of the original DNA through base pairing
rules
• The process of replication has directionality. New
nucleotides are only added onto the 3’ end of a growing
chain.
 The chain that grows in the 5’ --> 3’ direction: leading strand.
Continuously synthesized.
 The chain that grows in the 3’ --> 5’ direction: lagging strand.
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How is the lagging strand synthesized?
• As replication forks (bubbles along the double helix)
open up, short fragments of the lagging strand are
synthesized in the 5’ --> 3’ direction as space allows.
These fragments are called Okasaki fragments.
• These fragments are eventually joined by DNA ligase to
create a continuous strand of DNA.
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Synthesis of Lagging Strand
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E. RNA and Transcription
•
RNA is similar to DNA, except…
1. Different sugar (ribose instead of deoxyribose)
2. The nitrogen base uracil replaces thymine
3. RNA molecules are single stranded (not double
stranded)
4. RNA molecules are much smaller than DNA
molecules
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Three Types of RNA
1.
Ribosomal RNA (rRNA) -- contained in ribosomes, the
site of protein synthesis
Messenger RNA (mRNA)
2.


3.
Carries genetic info from DNA in nucleus to ribosomes in
cytoplasm for protein synthesis
Is a copy of the gene
Transfer RNA (tRNA) -- brings the appropriate amino
acid to the ribosome during the process of protein
synthesis. Each tRNA contains an anticodon (three
bases complementing a three-base segment on the
mRNA) which allows for match-up with exact amino
acid.
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Transcription: Synthesis of mRNA
• Begins with unwinding of a section of the DNA containing
the gene needing to be copied
• Initiation point (signal) for transcription: TATAAA
• RNA polymerase moves along the template strand in the
3’ to 5’ direction, allowing it to synthesize RNA adding
new nucleotides to the 3’ end of the new strand.
• When a termination signal is reached, the mRNA is
released, and DNA recoils back into its double helix
structure.
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Transcription
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Processing of mRNA
• Happens in eukaryotic cells, but not in prokaryotes
• Eukaryotic genes contain introns -- sections that do not
code for protein -- interspersed with coding sections
called exons
• Prokaryotic genes do not contain exons and introns
• Prior to leaving the nucleus, the eukaryotic mRNA
undergoes processing -- introns get snipped out, or
spliced.
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mRNA Processing
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Regulation of Transcription
• The cell goes not make mRNA randomly. There are
certain proteins which are constantly needed, but not
very many.
• Most mRNA is synthesized in response to cellular needs
for a particular protein. Regulation is at the level of
transcription.
• Prokaryotic cells regulate transcription by means of the
operon -- more than one gene under the control of the
same regulatory center.
 Control site: promoter (place where RNA polymerase binds) and
operator (place where repressor may or may not bind)
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The lac operon (prokaryotes)
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F. The Genetic Code: Codons
• A sequence of three bases is called a codon.
• Each codon specifies an amino acid in the protein.
• All 20 amino acids have their own codon -- some amino
acids have more than one.
• Three codons specify the stop of protein synthesis -they are UAG, UGA, and UAA.
• AUG signals the start of protein synthesis and also
encondes the amino acid methionine.
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The Genetic Code
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G. Protein Synthesis: Translation
• Occurs at ribosomes, outside of nucleus
• tRNA are used to translate each codon into an amino
acid
• Anticodon in the bottom loop is a three-base
complement to the codon in the mRNA
• Amino acid is attached to the stem on the opposite end
of the tRNA via an aminoacyl-tRNA synthetase..
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A Single tRNA
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Initiation of Protein Synthesis
• Both ribosomal subunits and an mRNA combine,
recognizing the start codon on the mRNA
• The appropriate tRNA binds to the codon
• Next, the appropriate tRNA binds to the second codon
on the mRNA; a peptide bond is formed between the
two neighboring amino acids.
 The first tRNA dissociates
 The ribosome shifts down the mRNA chain, allowing space for
the next tRNA down the line to float in and bind
• This process continues until a stop codon is reached.
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Termination of Protein Synthesis
• When the ribosome reaches a stop codon, protein
synthesis ends.
• The entire complex dissociates, and the peptide is
released. The peptide can fold.
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Translation
Overview
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H. Genetic Mutations
• Mutation = change in DNA sequence, altering the amino
acid sequence as well
• Causes of mutation: radiation (X rays/UV light),
chemicals called mutagens, perhaps viruses
• Mutation in somatic cell: body cells resulting from
division contain the mutation
 Could lead to tumor/cancer
• Mutation in germ cell (egg or sperm): offspring will
contain mutation
• Mutations can affect function of important enzymes
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Types of Mutations
• Replacement of one base with another: substitution
mutation
 May or may not change the individual amino acid, but no
downstream effect
• Frameshift mutation: base is added to, or deleted from,
the sequence. Changes reading frame.
 The amino acid in question is affected, as well as all downstream
amino acids (out of frame)
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Types
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Effect of Mutations
• If an enzyme, may completely lose activity
 Does the mutation change the active site directly?
 If not, does it alter the 3D shape of the protein enough so that
the substrate can no longer bind?
• A defective protein (due to mutation) may result in
genetic disease.
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Practice…
For the following mRNA sequence:
5’-ACA-UCA-CGG-GUA-3’
If a mutation changes UCA to ACA, what happens to the
protein?
What happens if the first U is removed from the sequence?
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Genetic Diseases
• Result of a defective enzyme, resulting from a mutation
• Example -- albinism
 An enzyme normally converts tyrosine to melanin (pigment
causing hair/skin color)
 If this enzyme is defective, no melanin produced = albinism
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J. Recombinant DNA
• “Cutting and pasting” DNA from the same organism, or
from different organisms
• The resulting DNA is called recombinant
• Has allowed for the production of human insulin,
interferon, human growth hormone…
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Preparing Recombinant DNA
•
1.
2.
3.
4.
Using E. coli (prokaryotic) as an example… some
bacteria contain circular DNA called plasmids.
Plasma membranes are dissolved and plasmid DNA
isolated
A restriction enzyme (recognizes a certain DNA
sequence and cuts) cuts through the plasmid
Another piece of DNA can be placed into the cut
plasmid, and ends sealed
The recombinant plasmids can be placed into cells
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Recombinant DNA Prep
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The Point of Recombinant DNA…
• If you have a cell containing your recombinant plasmid…
when the cell multiplies, each new cell will contain this
plasmid
• If your recombinant plasmid contains a gene (protein) of
interest following a promoter, you can stimulate the cells
to make large amounts of your protein of interest
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Polymerase Chain Reaction
•
•
If you only have one copy (or a few copies) of one
gene, this is a method to amplify (make a lot of copies)
the gene quickly.
Three steps:
1.
2.
3.
Heat your DNA of interest -- the double strands will separate
Primers (short sequence complementary to each end) are
added -- they anneal to the end of your single strands
The addition of DNA polymerase and free nucleotides extends
along the single strand, filling in until each double strand is
complete.
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PCR
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K. Viruses
• Cannot replicate without a host cell
• Invades the host cell, taking over materials
necessary for protein synthesis and growth
• Viral infection:
 Virus inserts its genetic material (DNA or RNA) into
host cell
 Material is replicated into DNA form
 The viral DNA is used to make viral proteins via
transcription and translation
 In some cases, the host cell will lyse, releasing new
viral particles
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Life Cycle of a (Lytic) Virus
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Reverse Transcription
• Viruses that use RNA as their genetic material must
make viral DNA once inside the host cell
• It does so via the enzyme reverse transcriptase.
• A virus which contains RNA and uses this process is
called a retrovirus.
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AIDS/HIV: A Retrovirus
• HIV destroys helper T cells (important in the
immune response)
• Thus, AIDS is defined by opportunistic infections
• Treatments for AIDS?
 Nucleoside analogs: transcription enzymes put false
nucleotides into strands, proteins can’t be made
 Protease inhibitors: HIV protease “chops” the final
viral peptide into useable form. If protease blocked,
viral proteins are nonfunctional
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