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DNA: STRUCTURE AND REPLICATION

– DNA
• was known to be a chemical in cells by the end of the
nineteenth century,
• has the capacity to store genetic information, and
• can be copied and passed from generation to
generation.
– The discovery of DNA as the hereditary material
ushered in the new field of molecular biology,
the study of heredity at the molecular level.
DNA and RNA Structure

DNA and RNA are nucleic


acids.
•They consist of chemical
units called nucleotides.
•A nucleotide polymer is a
polynucleotide.
•Nucleotides are joined by
covalent bonds between
the sugar of one nucleotide
and the phosphate of the
next, forming a sugar-
phosphate backbone.
DNA and RNA Structure

• The four nucleotides found in


DNA differ in their nitrogenous
bases. These bases are
– thymine (T),
– cytosine (C),
– adenine (A), and
– guanine (G).
• RNA has uracil (U) in place of
thymine.
Watson and Crick’s Discovery of the
Double Helix
– James Watson and Francis Crick determined that DNA is a
double helix.
– Watson and Crick used X-ray crystallography data to reveal the
basic shape of DNA.
– Rosalind Franklin produced the X-ray diffraction image of DNA.
James Watson (left) and Francis Crick
Watson and Crick’s Discovery of the Double Helix
Watson and Crick’s Discovery of the Double Helix

– DNA bases pair in a complementary fashion:


• adenine (A) pairs with thymine (T) and
• cytosine (C) pairs with guanine (G).
DNA Base Pairing
Chargaff’s Rule of
Base Pairing
Chargaff's rules state that:
– DNA base composition varies
between species

– for each species, the percentages


of A and T bases are roughly
equal, as are those of G and C
bases; DNA from any cell of any
organisms should have a 1:1 ratio
(base Pair Rule) of pyrimidine and
purine bases and, more
specifically, that the amount of
guanine should be equal to
cytosine and the amount of
adenine should be equal to
thymine.
DNA Replication
– When a cell reproduces, a complete copy of the
DNA must pass from one generation to the next.
– Watson and Crick’s model for DNA suggested
that DNA replicates by a template mechanism.
The Basic Principle: Base Pairing to a Template
Strand
• Since the two strands of DNA are complementary, each
strand acts as a template for building a new strand in
replication
• In DNA replication, the parent molecule unwinds, and
two new daughter strands are built based on base-
pairing rules
Figure 16.9-1

A T
C G
T A
A T
G C

(a) Parent molecule


Figure 16.9-2

A T A T
C G C G
T A T A
A T A T
G C G C

(a) Parent molecule (b) Separation of


strands
Figure 16.9-3

A T A T A T A T
C G C G C G C G
T A T A T A T A
A T A T A T A T
G C G C G C G C

(a) Parent molecule (b) Separation of (c) “Daughter” DNA molecules,


strands each consisting of one
parental strand and one
new strand
Figure 10.6

Parental (old)
DNA molecule

Daughter
(new) strand
Parental
(old) strand

Daughter DNA
molecules
(double helices)
Figure 16.12
(a) Origin of replication in an E. coli cell (b) Origins of replication in a eukaryotic cell
Origin of Double-stranded
Parental (template) strand Origin of replication DNA molecule
replication
Daughter (new)
strand Parental (template) Daughter (new)
Replication strand strand
Double- fork
stranded
DNA molecule Replication
bubble Replication fork
Bubble

Two daughter
DNA molecules
Two daughter DNA molecules

0.25 m
0.5 m
Antiparallel Elongation
Figure 16.16b-1
3
5 3
Template
strand 5
Figure 16.16b-2
3
5 3
Template
strand 5
3 RNA primer
5 for fragment 1
1 3
5
Figure 16.16b-3
3
5 3
Template
strand 5
3 RNA primer
5 for fragment 1
1 3
5

3 Okazaki
fragment 1
5
1 3
5
Figure 16.16b-4
3
5 3
Template
strand 5
3 RNA primer
5 for fragment 1
1 3
5

3 Okazaki
fragment 1
5
1 3
RNA primer
for fragment 2 5 5
3
2
Okazaki
1 3
fragment 2 5
Figure 16.16b-5
3
5 3
Template
strand 5
3 RNA primer
5 for fragment 1
1 3
5

3 Okazaki
fragment 1
5
1 3
RNA primer
for fragment 2 5 5
3
2
Okazaki
1 3
fragment 2 5
5
3
2
1 3
5 5
3
Figure 16.16b-6
3
5 3
Template
strand 5
3 RNA primer
5 for fragment 1
1 3
5

3 Okazaki
fragment 1
5
1 3
RNA primer
for fragment 2 5 5
3
2
Okazaki
1 3
fragment 2 5
5
3
2
1 3
5 5
3
2
1 3
5
Overall direction of replication
What is the importance of DNA Replication

1. DNA replication ensures that all the body cells


in multicellular organisms carry the same
genetic information.

2. It is the means by which genetic information is


passed along to offspring.

© 2013 Pearson Education, Inc.


Proofreading and Repairing of DNA
DNA Repair System
End-Replication
Problem
What protects the genes of linear eukaryotic chromosomes
from being eroded away during successive rounds of DNA
replication?
• Some cells have the ability to reverse telomere
shortening. An example is the germ cells.

• What is responsible for preventing/reversing telomere


shortening in germ cells?
Telomerase
Gene Expression:
From Gene to Protein
• Genotype
– The genetic makeup.
– The heritable information contained in the sequence
of nucleotide bases in the DNA of an individual.
– The information content of DNA is in the form of
specific sequences of nucleotides
• Phenotype
– The organism’s physical traits that arises from the
actions of a wide variety of proteins.
• What is the
connection
between the
genotype and
the phenotype?

• What links
genotype to the
phenotype?
Central Dogma
Transcription
Transcription: A Closer Look
Figure 17.7-1
Promoter Transcription unit

5 3
3 DNA 5
Start point
RNA polymerase
Figure 17.7-2
Promoter Transcription unit

5 3
3 DNA 5
Start point
RNA polymerase 1 Initiation

Nontemplate strand of DNA


5 3
3 5
RNA Template strand of DNA
Unwound
DNA transcript
Promoter Transcription unit

5 3
3 DNA 5
Start point
RNA polymerase 1 Initiation

Nontemplate strand of DNA


5 3
3 5
RNA Template strand of DNA
Unwound
DNA transcript
2 Elongation
Rewound
DNA
5 3
3 3 5
5
RNA
transcript
Figure 17.7-4
Promoter Transcription unit

5 3
3 DNA 5
Start point
RNA polymerase 1 Initiation

Nontemplate strand of DNA


5 3
3 5
RNA Template strand of DNA
Unwound
DNA transcript
2 Elongation
Rewound
DNA
5 3
3 3 5
5
RNA
transcript 3 Termination

5 3
3 5
5 3
Completed RNA transcript
Direction of transcription (“downstream”)
After transcription is
RNA processing

• The pre-mRNA will undergo processing or


modifications before it can be exported to the
cytoplasm for translation.
What is the purpose of adding the 5’ cap and
the poly-A tail?

1. They facilitate the export of mRNA to the cytoplasm.

2. They protect mRNA from degradation by hydrolytic


enzymes.

3. They help ribosomes attach to the mRNA once the


mRNA reaches the cytoplasm.
RNA Processing (continued)
RNA Splicing
How is RNA splicing done?

Figure 17.12-2
RNA transcript (pre-mRNA)
5
Exon 1 Intron Exon 2
Protein
Other
snRNA proteins
snRNPs

Spliceosome

5
Figure 17.12-3
RNA transcript (pre-mRNA)
5
Exon 1 Intron Exon 2
Protein
Other
snRNA proteins
snRNPs

Spliceosome

5

Spliceosome
components
Cut-out
mRNA intron
5
Exon 1 Exon 2
Translation
• the synthesis of protein (polypeptide) as directed by
the mRNA.
Genetic Code
• The set of rules that convert a nucleotide sequence
in RNA to amino acid sequence.

– “the flow of information from gene to protein is


based on a triplet code called codon, a triplet of
mRNA nucleotide that codes for a particular
amino acid.”
Genetic Code
Reading Frame:
How is the nucleotide sequence in the mRNA
converted into a series of amino acids?
• The red dog ate the bug.
• T her edd oga tet heb ug.

• 5’-AGAGCAAUGGGAGCCGAUGCGGAG-3’
• AGA GCA AUG GGA GCC GAU GCG GAG UAA
Met----Gly----Ala----Asp----Ala----Glu
(start)---------------------------------------(stop)
Reading Frame
• The cell’s protein-synthesizing machinery reads the
message as a series of non-overlapping three-letter
words.

• Example:
UGG UUU GGC UCA = Trp---Phe---Gly---Ser
UGGUUUGGCUCA = Trp---Gly---Val---Phen---Leu
• transfer RNA (tRNA)
Other Components for Translation

• Ribosomes
Translation: Initiation
Translation: Elongation
Figure 17.19-1
Amino end of
polypeptide

E
mRNA 3
P A
site site
5
Figure 17.19-2
Amino end of
polypeptide

E
mRNA 3
P A
site site GTP
5
GDP  P i

P A
Figure 17.19-3
Amino end of
polypeptide

E
mRNA 3
P A
site site GTP
5
GDP  P i

P A

P A
Figure 17.19-4
Amino end of
polypeptide

E
mRNA 3
Ribosome ready for P A
site site GTP
next aminoacyl tRNA 5
GDP  P i

E E

P A P A

GDP  P i

GTP

P A
Termination of Translation
Figure 17.20-1

Release
factor

3
5
Stop codon
(UAG, UAA, or UGA)
Figure 17.20-2

Release
factor Free
polypeptide

3 3
5 2 GTP
5
2 GDP  2 P i
Stop codon
(UAG, UAA, or UGA)
Figure 17.20-3

Release
factor Free
polypeptide

5
3 3
5 2 GTP 3
5
2 GDP  2 P i
Stop codon
(UAG, UAA, or UGA)
Gene Expression: Central Dogma
Mutations
– A mutation is any change in the nucleotide
sequence of DNA.
– Mutations can change the amino acids in a
protein.
– Mutations can involve
• large regions of a chromosome or
• just a single nucleotide pair, as occurs in sickle-cell
disease.
Figure 10.21

Normal hemoglobin DNA Mutant hemoglobin DNA

mRNA mRNA

Normal hemoglobin Sickle-cell hemoglobin


Glu Val
Types of Mutations

– Mutations within a gene can be divided into two


general categories:
1. nucleotide substitutions (the replacement of one base
by another) and
2. nucleotide deletions or insertions (the loss or addition
of a nucleotide).
– Insertions and deletions can
• change the reading frame of the genetic message and
• lead to disastrous effects.
Figure 10.22

Met Lys Phe Gly Ala


mRNA and protein from a normal gene

Met Lys Phe Ser Ala


(a) Base substitution

Deleted

Met Lys Leu Ala


(b) Nucleotide deletion
Inserted

Met Lys Leu Trp Arg


(c) Nucleotide insertion
Figure 10.22a

Met Lys Phe Gly Ala


mRNA and protein from a normal gene

Met Lys Phe Ser Ala


(a) Base substitution
Figure 10.22b

Met Lys Phe Gly Ala


mRNA and protein from a normal gene
Deleted

Met Lys Leu Ala


(b) Nucleotide deletion
Figure 10.22c

Met Lys Phe Gly Ala


mRNA and protein from a normal gene
Inserted

Met Lys Leu Trp Arg


(c) Nucleotide insertion
Mutagens

– Mutations may result from


• errors in DNA replication or recombination or
• physical or chemical agents called mutagens.
– Mutations
• are often harmful but
• are useful in nature and the laboratory as a source of
genetic diversity, which makes evolution by natural
selection possible.

© 2013 Pearson Education, Inc.


Reference:

Reece, J. B., Urry, L. A., Cain, M. L. 1.,


Wasserman, S. A., Minorsky, P. V., Jackson, R., &
Campbell, N. A. (2014). Campbell biology (Tenth
edition.). Boston: Pearson.