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Molecular Biology of the Gene
DNA Structure and Function
History of DNA
• 1869 Johann Friedrich Miescher
• 1924 Microscope studies using stains for DNA and
protein show that both substances are present in
chromosomes.
• 1952 Alfred Hershey and
Martha Chase
SCIENTIFIC DISCOVERY:
DNA is a double-stranded helix
 Erwin Chargaff
 Rosalind Franklin / Maurice Wilkins
 James Watson and Francis Crick
 In 1962, the Nobel Prize
SCIENTIFIC DISCOVERY: Experiments
showed that DNA is the genetic material
 Until the 1940s, the case for proteins serving as
the genetic material was stronger than the case
for DNA.
– Proteins are made from ____different amino acids.
– DNA was known to be made from just ____ kinds of
nucleotides.
 Studies of bacteria and viruses
– ushered in the field of molecular biology, the study of
heredity at the molecular level, and
– revealed the role of DNA in heredity.
DNA and RNA are polymers of nucleotides
 DNA and RNA are nucleic acids.
 The building blocks or monomers of nucleic acids
are ____________________
 A nucleotide is composed of a
– _________________
– _________________
– __________________
 The nucleotides are joined to one another by a
bond creating the sugar-phosphate backbone.
T
A
C
T
G
Sugar-phosphate
backbone
A
C
G
T
A
C
G
A
G
T
Covalent
bond
joining
nucleotides
T
C
A
C
A
C
A
A
G
T
Phosphate
group
Nitrogenous
base
Nitrogenous base
(can be A, G, C, or T)
Sugar
C
G
T
A
A DNA
double helix
DNA
nucleotide
T
Thymine (T)
T
Phosphate
group
G
G
G
G
Sugar
(deoxyribose)
DNA nucleotide
Two representations
of a DNA polynucleotide
4 Different
Types of
Nucleotides
Found in DNA
Hydrogen bond
Base pair
Ribbon
model
Partial chemical
structure
Computer
model
3’ and 5’ ends of nucleotide strand
Purine or
pyrimidine ?
Hydrogen bonds hold
the 2 strands
together
2 General Functions for DNA
1.
2.
DNA replication depends on specific base pairing
 In their description of the structure of DNA,
Watson and Crick noted that the structure of DNA
suggests a possible copying mechanism.
 DNA replication follows a semiconservative
model.
DNA Replication
SEMICONSERVATIVE
1. Helix unwinds
2. 2 strands separate
3. Free nucleotides bind to open bases
according to pairing rules
(parent strand acts as template)
4. 2 identical strands consist of one parent
strand and one newly formed strand.
DNA replication proceeds in two directions at
many sites simultaneously
 DNA replication begins at the origins of replication
where
– DNA unwinds at the origin to produce a “bubble,”
– replication proceeds in both directions from the origin,
and
– replication ends when products from the bubbles
merge with each other.
 DNA replication occurs in the 5 to 3 direction.
– Replication is continuous on the 3 to 5 template.
– Replication is discontinuous on the 5 to 3 template,
forming short segments.
Leading and Lagging strands
Why?
DNA polymerases can only
assemble new strands in
the 5’-> 3’ direction, need a
3’ end
(-OH) provided by RNA
primer.
DNA polymerase
molecule
5
3
Parental DNA
Replication fork
5
3
DNA ligase
Overall direction of replication
3
5
This daughter
strand is
synthesized
continuously
This daughter
strand is
3 synthesized
5 in pieces
DNA replication proceeds in two directions at
many sites simultaneously
 Key proteins are involved in DNA replication.
– Helicase
– DNA Polymerases– Primase
– Proofreader
– DNA ligase
Parental
DNA
molecule
Origin of
replication
“Bubble”
Two
daughter
DNA
molecules
Parental strand
Daughter strand
ANIMATION…Replication
http://highered.mcgraw-hill.com/olc/dl/120076/bio23.swf
http://207.207.4.198/pub/flash/24/menu.swf
http://www.phschool.com/science/biology_place/biocoach/dnarep/intro.html
DNA Repair
DNA processes
• Replication
• Protein Synthesis
–Transcription
–Translation
Protein Functions….
•
•
•
•
•
Metabolism (enzymes are proteins)
Structural (build form)
Transport (ex- hemoglobin)
Protection (antibodies are proteins)
Cell communication (hormones)
Review of Protein Structure…
Only 20
different
common amino
acids
Hundreds of
thousands of
different
proteins !
Structure
determines
function !
The DNA genotype is expressed as proteins,
which provide the molecular basis for
phenotypic traits
 DNA specifies traits by dictating protein synthesis.
 The molecular chain of command is from
– DNA in the nucleus to RNA and
– RNA in the cytoplasm to protein.
 __________________ is the synthesis of RNA
under the direction of DNA.
 __________________ is the synthesis of proteins
under the direction of RNA.
Nucleotides: 2 types DNA & RNA
3 parts of RNA (the other nucleic acid) nucleotide
sugar = _________
phosphate group
nitrogenous base (A,U,C,G)
U=Uracil
3 Types of RNA Required for
Protein Synthesis
• mRNA= messenger RNA
• tRNA= transfer RNA
• rRNA= ribosomal RNA
DNA
Transcription
RNA
NUCLEUS
Translation
Protein
CYTOPLASM
Strand to be transcribed
T A C T
T
C A A A A T
C
DNA
A T G A A G T
T T
T A G
Transcription
RNA
A U G A A G U U U U A G
Translation
Start
codon
Polypeptide
Met
Stop
codon
Lys
Phe
The DNA genotype is expressed as proteins,
which provide the molecular basis for
phenotypic traits
The connections between genes and proteins
– The initial one gene–one enzyme hypothesis was
based on studies of inherited metabolic diseases.
– The one gene–one enzyme hypothesis was expanded
to include all proteins.
– Most recently, the one gene–one polypeptide
hypothesis recognizes that some proteins are
composed of multiple polypeptides.
Transcription- overview
 Transcribing (writing) information from DNA
 Takes place in the nucleus
 Promoter region is recognized by RNA polymerase
as a start location
 Assembles mRNA strand
mRNA
TRANSCRIPTION
Free RNA
nucleotides
RNA
polymerase
C C A A
A U C C A
T A G G T
Direction of
transcription
Newly made RNA
T
Template
strand of DNA
RNA polymerase
DNA of gene
Terminator
DNA
Promoter
DNA
1
Initiation
2
Elongation
Area shown
in Figure 10.9A
3
Termination
Growing
RNA
Completed
RNA
RNA
polymerase
Genetic information written in codons is
translated into amino acid sequences
 The sequence of nucleotides in DNA provides a
code for constructing a protein.
Transcription produces
genetic messages in the form of RNA
 Overview of transcription
– An RNA molecule is transcribed from a DNA template
by a process that resembles the synthesis of a DNA
strand during DNA replication.
– RNA nucleotides are linked by the transcription
enzyme RNA polymerase.
– Specific sequences of nucleotides along the DNA mark
where transcription begins and ends.
– The “start transcribing” signal is a nucleotide sequence
called a promoter.
Transcription produces
genetic messages in the form of RNA
– Transcription begins with initiation, as the RNA
polymerase attaches to the promoter.
– During the second phase, elongation, the RNA grows
longer.
– As the RNA peels away, the DNA strands rejoin.
– Finally, in the third phase, termination, the RNA
polymerase reaches a sequence of bases in the DNA
template called a terminator, which signals the end of
the gene.
– The polymerase molecule now detaches from the RNA
molecule and the gene.
POST-TRANSCRIPTIONAL
Exon Intron
MODIFICATION
Exon
Intron
Exon
DNA
Cap
RNA
transcript
with cap
and tail
Transcription
Addition of cap and tail
Introns removed
Tail
Exons spliced together
mRNA
Coding sequence
NUCLEUS
CYTOPLASM
Post-Transcriptional Modification:
Eukaryotic RNA is processed
before leaving the nucleus as mRNA
 Eukaryotic mRNA
– RNA splicing
– Additions- cap and tail
Post-Transcriptional Modification:
Eukaryotic RNA is processed
before leaving the nucleus as mRNA
 Messenger RNA (mRNA)
– encodes amino acid sequences and
– conveys genetic messages from DNA to the translation
machinery of the cell, which in
– prokaryotes, occurs in the same place that mRNA is made,
but in
– eukaryotes, mRNA must exit the nucleus via nuclear pores to
enter the cytoplasm.
– Eukaryotic mRNA has
– introns, interrupting sequences that separate
– exons, the coding regions.
Genetic information written in codons is
translated into amino acid sequences
The flow of information from gene to protein is based on a
triplet code: the genetic instructions for the amino acid
sequence of a polypeptide chain are written in DNA and
RNA as a series of nonoverlapping three-base “words”
called codons.
Each amino acid is specified by a codon.
– 64 codons are possible.
– Some amino acids have more than one possible codon.
Transfer RNA molecules
serve as interpreters during translation
 Transfer RNA (tRNA)
Ribosomes build polypeptides
 rRNA and proteins make up the ribosome.
 Translation occurs on the surface of the ribosome
The genetic code dictates how codons are
translated into amino acids
 Characteristics of the genetic code
– _______ nucleotides specify one amino acid.
– 61 codons correspond to amino acids.
– AUG is the start codon; codes for methionine and signals the
start of transcription.
– 3 “stop” codons signal the end of translation; _____, ____, ____
– __________- with more than one codon for some amino
acids
– _______________- the genetic code is shared by
organisms from the simplest bacteria to the most
complex plants and animals
GENETIC CODE
Practice
•
•
•
•
DNA is
TACAGGCGATGGATT
mRNA is ____________________
Divide into codons (reading frames)
Amino acids coded for are:
An initiation codon marks
the start of an mRNA message (Initiation)
 Translation can be divided into the same three
phases as transcription:
1. initiation,
2. elongation, and
3. termination.
 Initiation brings together…
An initiation codon marks
the start of an mRNA message (Initiation)
 Initiation establishes where translation will begin.
 Initiation occurs in two steps.
1. An mRNA molecule binds to a small ribosomal subunit and
the first tRNA binds to mRNA at the start codon.
– The start codon reads AUG and codes for methionine.
– The first tRNA has the anticodon UAC.
2. A large ribosomal subunit joins the small subunit, allowing
the ribosome to function.
– The first tRNA occupies the P site, which will hold the growing
peptide chain.
– The A site is available to receive the next tRNA.
Elongation adds amino acids to
the polypeptide chain
 Once initiation is complete, amino acids are
added one by one to the first amino acid.
 Elongation is the addition of amino acids to the
polypeptide chain.
Elongation adds amino acids
to the polypeptide chain
 Each cycle of elongation has three steps.
1. Codon recognition: The anticodon of an incoming
tRNA molecule, carrying its amino acid, pairs with the
mRNA codon in the A site of the ribosome.
2. Peptide bond formation: The new amino acid is
joined to the chain.
3. Translocation: tRNA is released from the P site and
the ribosome moves tRNA from the A site into the P
site.
Polypeptide
Elongation
P
site
mRNA
Amino
acid
A
site
Anticodon
Codons
1
Codon recognition
mRNA
movement
Stop
codon
2
New
peptide
bond
3
Translocation
Peptide bond
formation
Elongation adds amino acids
to the polypeptide chain
until a stop codon; Termination
 Termination stage of translation, when
– the ribosome reaches a stop codon,
– the completed polypeptide is freed from the last tRNA,
and
– the ribosome splits back into its separate subunits.
Other Helpful Animations….
 http://highered.mcgraw-hill.com/sites (there are
selections at this site that will help with replication,
transcription and translation)
Review:
The flow of
Genetic
information in
the cell is
DNA
RNA
Transcription
DNA
1
mRNA
Transcription
RNA
polymerase
CYTOPLASM
Translation
Amino acid
Amino acid
attachment
2
Enzyme
tRNA
ATP
Anticodon
Initiator
tRNA
Large
ribosomal
subunit
Start Codon
mRNA
Protein
Initiation of
polypeptide synthesis
3
Small
ribosomal
subunit
New peptide
bond forming
Growing
polypeptide
4
Elongation
Codons
mRNA
Polypeptide
5
Stop codon
Termination
Mutations can change the meaning of genes
 A mutation is any change in the nucleotide
sequence of DNA.
 Mutations can involve
– large chromosomal regions or
– just a single nucleotide pair.
 Mutations can be spontaneous (mistakes during
replication) or caused by mutagens.
Examples- UV light, chemicals
Mutations can change the meaning of genes
. A mutation can be:
– Harmful, giving rise to cancers.
– Cause genetic disorders (if in sperm or egg)
– Create new traits/variation
in the species
Normal hemoglobin DNA
C T
Mutant hemoglobin DNA
C A T
T
mRNA
mRNA
G A A
G U A
Normal hemoglobin
Sickle-cell hemoglobin
Val
Glu
Normal
gene
mRNA
Protein
Nucleotide
substitution
A
U G A A G U
Met
A U G A
Met
Lys
U
U G G C G
C
Phe
Gly
Ala
U A G C
A G U U
Lys
Phe
Ser
G C
A
A
Ala
U Deleted
Nucleotide
deletion
A U G A A G
Met
U
U G G C G
Ala
Leu
Lys
C A
U
His
Inserted
Nucleotide
insertion
A U G A A G
Met
Lys
U
U G
Leu
U G G
C G C
Ala
His
You should now be able to
1. Compare the structures of DNA and RNA.
2. State the contributions of Chargaff, Franklin,
Wilkins, Watson and Crick to our understanding
of DNA.
3. Describe the process of DNA replication. State
the role of helicase, DNA polymerases, primase,
and DNA ligase
4. Describe the general purpose of protein
synthesis; relate DNA sequence to the specific
protein produced.
You should now be able to
5. State the general flow of genetic information as
genes are expressed.
6. Explain transcription and how mRNA is
produced using DNA.
7. Explain how eukaryotic RNA is processed
before leaving the nucleus.
8. Discuss the role of mRNA, tRNA and rRNA in
translation.
9. Explain translation; initiation, elongation,
translocation and termination.
You should now be able to
10. Describe the structure and function of ribosomes
11. .Define mutation, causes of mutations, and
potential consequences.
12. State the amino acid sequence in a polypeptide
given the mRNA.
© 2012 Pearson Education, Inc.
DNA
is a polymer
made from
monomers called
is performed
by an
enzyme called
(b)
(a)
(c)
(d)
RNA
comes
in three
kinds called
(e)
(f)
(g)
is performed
by structures
called
Protein
molecules are
components of
use amino-acid-bearing
molecules called
(h)
one or more polymers
made from
monomers called
(i)