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

Nucleic acids are complex organic molecule consisting of

nucleotides.

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).

Chromosomes
- contain DNA and histone proteins
- found primarily in the nucleus

Chromatin
- tightly packed DNA and histones
- condensed to become chromosomes
 Nucleotide

A nucleotide is composed of:

• Nitrogen-containing bases (amines)

• Sugars (monosaccharides)
• Phosphate

Phosphate
 Bases

NH2 O O
4
CH3
3 N 5 N HN HN
2 6
N O N O N O N
1
H H H
Pyrimidine Cytosine (C) Thymine (T) Uracil (U)
(DNA and (DNA only) (in RNA only)
some RNA)

6 7 NH2 O
1
N
5 N N N
8
N HN
2
N 4 N9 N N N N
3
H2N
H H H
Purine Adenine (A) Guanine (G)
(DNA and RNA) (DNA and RNA)
 Sugars (monosaccharide)

RNA contains:
• D-Ribose sugar

DNA contains:
• 2-Deoxy-D-Ribose sugar (without O on carbon 2)
 Purine Bases

NH2 O

N N
N HN

N H2N N N
N H
H
 Pyrimidine Bases

NH2
O O
CH3
HN HN HN

O N O N O N
H H
 Sugar

Ribose 2’-Deoxyribose

HOH2C OH OH
HOH2C
O O

OH OH OH
 Nucleoside

When a N atom of the base forms a glycosidic bond to C 1’ (anomeric C) of

a sugar.

Base + Sugar Nucleoside

O O
uracil O
CH3
N HN
HN
N O N -D-riboside 1
H H 5' O N a -N-glycosidic
HOCH2 O bond
ß-N-glycosidic bond
hymine (T) Uracil (U) 1'
DNA only) (in RNA only) 4' H H
H 3' 2' H anomeric
HO OH carbon

O
Uridine

HN N
 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-”.
 Nucleoside
NH2

N
N

N N
HO
O
H H
H H
OH H
 Nucleosides
• Nucleoside: a compound that consists of D-
ribose or 2-deoxy-D-ribose bonded to a purine
or pyrimidine base by a -N-glycosidic bond

uracil O

HN
-D-riboside 1
5' O N a -N-glycosidic
HOCH2 O bond
1'
4' H H
H 3' 2' H anomeric
HO OH carbon
Uridine
 Nucleotide

A nucleotide forms with the −OH on C5’ of a sugar bonds to

phosphoric acid.

NH2 Phosphate ester bond

O O N 5’
5’
O- P OH + HO CH2
O
O- 1’

OH

deoxycytidine and phosphate A nucleotide

The name cytidine 5′-monophosphate is abbreviated as CMP.

 Nucleotide

The name deoxyadenosine 5’-monophosphate is abbreviated as dAMP.

 Nucleotide
• Nitrogenous base
• Ribose sugar
• Phosphoric acid
residue
 Nucleotide
NH2

N
N

O N N
-O P O O
O- H H
H H
OH H
 Nucleotides
• Nucleotide: a nucleoside in which a
molecule of phosphoric acid is esterified
with an -OH of the monosaccharide, most
commonly either the 3’ or NH
the2 5’-OH
N
N
O 5'
- N
O-P-O-CH2 O N
-
O H H 1'
H 3' H
HO OH
Adenosine 5'-monophosphate
(5'-AMP)
 Nucleotides
– adenosine 5’-triphosphate (ATP) serves as a
common currency into which energy gained
from food is converted and stored NH2
N N
O O O
-
O-P-O-P-O-P-O-CH2 O N N
- - -
O O O H H
H H
HO OH
Adenosine 5'-triphosphate
(ATP)
 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 5’ 3’

and Crick in 1953.

• 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).

5’
3’
 Secondary structure of DNA

A Purine base always hydrogen bonds with a pyrimidine.

 DNA -
• Secondary structure:
2° Structure
Secondary structure: the ordered arrangement of
nucleic acid strands
– Double helix model of DNA 2° structure was proposed
by James Watson and Francis Crick in 1953
– Based on two primary sources of information
• Irwin Chargaff: A = T and C = G
• X-ray diffraction picture of DNA taken by Rosalind Franklin
 Nucleic Acid Structure
• DNA has a double helix structure
– Phosphates on outside
• Complementary Base Pairs on inside

• RNA is single stranded

– Messenger RNA (m-RNA)

• Transfer RNA (t-RNA) has some double

stranded loops
• Double helix:
– a type of 2° structure of DNA molecules in
which two anti-parallel polynucleotide strands
are coiled in a right-handed manner about the
same axis
 DNA – Double Helix
Double helix:
• Two DNA strands
• Anti-parallel strands
– One is 3’ to 5’ Other is 5’ to 3’
• Strands are coiled in a right-handed helix about the
same axis
• Backbone has alternating sugar and phosphate
groups
• Complementary Base Pairs on inside of helix
Rosalind
Franklin
p. 640
James
Watson
&
Francis
Crick

p. 640
 Complementary Base Pairs
DNA Base Pairs Double-Stranded
A-T %A = %T
C-G %C = %G

RNA Base Pairs Single-Stranded

A-U
C-G
 Complementary Base Pairs
• Must be one purine and one pyrimidine to fit
properly

• Two purines too big

• Two pyrimidines too small

• Not every purine-pyrimidine pair forms

naturally
Complementary base pairs

A-T base pair

2 H bonds

G-C base pair

3 H bonds
Non-Complementary Base Pairs
Chains are anti-parallel
Fig. 24.5
Fig. 24.4
 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.
 DNA and RNA
• The three differences in structure between
DNA and RNA are
– DNA bases are A, G, C, and T; the RNA bases
are A, G, C, and U
– the sugar in DNA is 2-deoxy-D-ribose;
2-deoxy-D-ribose in RNA
it is D-ribose
– DNA is always double stranded;
stranded there are several
kinds of RNA, all of which are single-stranded
 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
Helicase Unwinds the DNA double helix
Primase Synthesizes primers
Clamp protein Threads leading strand
DNA polymerase Joins assembled nucleotides
Ligase 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 RNA
replication replication

DNA Transcription
mRNA Translation protein

Reverse transcriptase
Reverse transcription
 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 5’—G A T C C T A T G—3’

strand:
 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 A G 3'
UUU Phe UCU Ser UAU Tyr UGU Cys U
UUC Phe UCC Ser UAC Tyr UGC Cys C
U UUA Leu UCA Ser UAA Stop UGA Stop A
UUG Leu UCG Ser UAG Stop UGG Trp G
CUU Leu CCU Pro CAU His CGU Arg U
CUC Leu CCC Pro CAC His CGC Arg C
C CUA Leu CCA Pro CAA Gln CGA Arg A
CUG Leu CCG Pro CAG Gln CGG Arg G
AUU Ile ACU Thr AAU Asn AGU Ser U
Asn C
A AUC Ile ACC Thr AAC AGC Ser
AUA Ile ACA Thr AAA Lys AGA Arg A
AUG Met* ACG Thr AAG Lys AGG Arg G
GUU Val GCU Ala GAU Asp GGU Gly U
GUC Val GCC Ala GAC Asp GGC Gly C
G
GUA Val GCA Ala GAA Glu GGA Gly A
GUG Val GCG Ala GAG Glu GGG Gly G
*AUG signals translation initiation as well as coding 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'
Ribosome UUU
encounters aPhe
stop UCU
condon. Ser UAU Tyr UGU Cys U
Phe UCU Ser UAU UUC Phe UGU
Tyr UCCCysSer U UAC Tyr UGC Cys C
Phe UCC Ser UUAC UUATyrLeu UGC UCACysSer C UAA Stop UGA Stop A
Leu UCA Ser UAA UUG Stop
Leu UGA Ser A UAG Stop UGG Trp G
UCGStop
Leu UCG Ser UAG Stop UGG Trp G
CUU Leu CCU Pro CAU His CGU Arg U
Leu CCU Pro CAU His
CUC Leu CGU CCCArgPro U CAC His CGC Arg C
Leu No tRNA to complement
CCC Pro C CAC CUAHis the
Leu CGCtermination
CCAArg codon.
Pro C CAA Gln CGA Arg A
Leu CCA Pro CAACUGGlnLeu CGA CCGArgPro A CAG Gln CGG Arg G
Leu CCG Pro CAG Gln CGG Arg G
AUU Ile ACU Thr AAU Asn AGU Ser U
Ile An enzyme
ACU Thr releases
AAUAUCthe
Asn complete
Ile AGUACCpolypeptide
Ser
Thr chain
U AAC Asn from the ribosome.
AGC Ser C
A Asn
Ile ACC Thr AACAUA Ile AGC ACA Thr C AAA Lys
Ser AGA Arg A
Ile ACA Thr AAAAUG LysMet*AGA ACG Thr A AAG Lys
Arg AGG Arg G
Met* ACG Thr AAG Lys AGG Arg G
GUU Val GCU Ala GAU Asp GGU Gly U
Val GCU
Amino Ala
acids GAUGUC
form Asp
the Val GGUGCC Gly
Ala U
three-dimensional GAC Asp
structure (activeGGC Gly
protein). C
Val GCC Ala G Asp
GACGUA Val GGC GCAGlyAla C GAA Glu GGA Gly A
Val GCA Ala GAAGUGGlu Val GGA GCG Gly
Ala A GAG Glu GGG Gly G
Val GCG Ala GAG Glu GGG Gly G
*AUG signals translation initiation as well as coding for Met
ignals translation initiation as well as coding 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

Heat the DNA segment to unwind the

Step [1]
double helix to form single strands.
HOW TO Use the Polymerase Chain Reaction to
Amplify a Sample of DNA

Add primers that are complementary to

Step [2]
the DNA sequence at either end of the
DNA segment.
 HOW TO Use the Polymerase Chain Reaction to
Amplify a Sample of DNA

Use a DNA polymerase and added

Step [3]
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 RNA
replication replication

DNA Transcription
mRNA Translation protein

Reverse transcriptase
 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) .