Chapter 22-1Chemistry 121 Winter 2010 LA Tech Introduction to
Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane
(Ph.D. Ohio State) E-mail: [email protected] Office: 311 Carson
Taylor Hall ; Phone: 318-257-4941; Office Hours: MWF 8:00 am -
10:00 am; TT 9:00 10:00 am & 1:00-2:00 pm. December 18, 2009
Test 1 (Chapters 12-13) January 20, 2010 Test 2 (Chapters 14,15
& 16) February 8, 2010 Test 3(Chapters 17, 18 & 19) March
1, 2010 Test 4 (Chapters 20, 21 & 22) March 2, 2010
Comprehensive Make Up Exam: Chemistry 121(01) Winter 2009-10
Slide 2
Chapter 22-2Chemistry 121 Winter 2010 LA Tech Sections Chapter
22. Nucleic Acids Human egg and sperm.
Slide 3
Chapter 22-3Chemistry 121 Winter 2010 LA Tech Chapter 22.
Nucleic Acids-Sections 22.1 Types of Nucleic Acids 22.2
Nucleotides: Building Blocks of Nucleic Acids 22.3 Primary Nucleic
Acid Structure 22.4 The DNA Double Helix 22.5 Replication of DNA
Molecules 22.6 Overview of Protein Synthesis 22.7 Ribonucleic Acids
Chemistry at a Glance: DNA Replication 22.8 Transcription: RNA
Synthesis 22.9 The Genetic Code 22.10 Anticodons and tRNA Molecules
22.11 Translation: Protein Synthesis 22.12 Mutations Chemistry at a
Glance: Protein Synthesis 22.13 Nucleic Acids and Viruses 22.14
Recombinant DNA and Genetic Engineering 22.15 The Polymerase Chain
Reaction 22.16 DNA Sequencing
Slide 4
Chapter 22-4Chemistry 121 Winter 2010 LA Tech 4 Cells in an
organism are exact replicas Cells in an organism are exact replicas
Cells have information on how to make new cells Cells have
information on how to make new cells Molecules responsible for such
information are nucleic acids Molecules responsible for such
information are nucleic acids Found in nucleus and are acidic in
nature A nucleic acid is a polymer in which the monomer units are
nucleotides. A nucleic acid is a polymer in which the monomer units
are nucleotides. Two Types of Nucleic Acids: Two Types of Nucleic
Acids: DNA: Deoxyribonucleic Acid: Found within cell nucleus DNA:
Deoxyribonucleic Acid: Found within cell nucleus Storage and
transfer of genetic information Passed from one cell to other
during cell division RNA: Ribonucleic Acid: Occurs in all parts of
cell RNA: Ribonucleic Acid: Occurs in all parts of cell Primary
function is to synthesize the proteins Why Nucleic Acid is
Important to life?
Slide 5
Chapter 22-5Chemistry 121 Winter 2010 LA Tech Nucleic Acids:
Polymers in which repeating unit is nucleotide Nucleic Acids:
Polymers in which repeating unit is nucleotide A Nucleotide has
three components: A Nucleotide has three components: Pentose Sugar:
Monosaccharide Phosphate Group (PO 4 3- ) Heterocyclic Base Nucleic
AcidsNucleic Acids
Slide 6
Chapter 22-6Chemistry 121 Winter 2010 LA Tech Pentose Sugar
Ribose is present in RNA and 2-deoxyribose is present in DNA Ribose
is present in RNA and 2-deoxyribose is present in DNA Structural
difference: Structural difference: a OH group present on carbon 2
in ribose a H atom in 2-deoxyribose RNA and DNA differ in the
identity of the sugar unit in their nucleotides. RNA and DNA differ
in the identity of the sugar unit in their nucleotides.
Slide 7
Chapter 22-7Chemistry 121 Winter 2010 LA Tech
Nitrogen-Containing Heterocyclic Bases There are a total five bases
(four of them in most of DNA and RNAs) There are a total five bases
(four of them in most of DNA and RNAs) Three pyrimidine derivatives
- thymine (T), cytosine (C), and uracil (U) Three pyrimidine
derivatives - thymine (T), cytosine (C), and uracil (U) Two purine
derivatives - adenine (A) and guanine (G) Two purine derivatives -
adenine (A) and guanine (G) Adenine (A), guanine (G), and cytosine
(C) are found in both DNA and RNA. Uracil (U): found only in RNA
Thymine (T) found only in DNA.
Slide 8
Chapter 22-8Chemistry 121 Winter 2010 LA Tech Phospate
Phosphate - third component of a nucleotide, is derived from
phosphoric acid (H 3 PO 4 ) Phosphate - third component of a
nucleotide, is derived from phosphoric acid (H 3 PO 4 ) Under
cellular pH conditions, the phosphoric acid is fully dissociated to
give a hydrogen phosphate ion (HPO 4 2- ) Under cellular pH
conditions, the phosphoric acid is fully dissociated to give a
hydrogen phosphate ion (HPO 4 2- )
Slide 9
Chapter 22-9Chemistry 121 Winter 2010 LA Tech Nucelotide
Formation The formation of a nucleotide from sugar, base, and
phosphate is visualized below. The formation of a nucleotide from
sugar, base, and phosphate is visualized below. Phosphate attached
to C-5 and base is attached to C-1 position of pentose
Slide 10
Chapter 22-10Chemistry 121 Winter 2010 LA Tech Nucleotide
Nomenclature
Slide 11
Chapter 22-11Chemistry 121 Winter 2010 LA Tech (a) The
generalized structure of a nucleic acid. (b) The specific backbone
structure for a deoxyribonucleic acid (DNA). (c) The specific
backbone structure for a ribonucleic acid (RNA). Backbone structure
for nucleic acid
Slide 12
Chapter 22-12Chemistry 121 Winter 2010 LA Tech Molecule of
Adenine, a nitrogen-containing heterocyclic base present in both
RNA and DNA. Adenine, a nucleic acid base
Slide 13
Chapter 22-13Chemistry 121 Winter 2010 LA Tech Two purine bases
and three pyrimidine bases are found in the nucleotides present in
nucleic acids. Nucleic acid bases
Slide 14
Chapter 22-14Chemistry 121 Winter 2010 LA Tech Nucleic acid
bases
Slide 15
Chapter 22-15Chemistry 121 Winter 2010 LA Tech Table 22.1
Nucleotides
Slide 16
Chapter 22-16Chemistry 121 Winter 2010 LA Tech Fig. 22.3 The
general structure of a nucleic acid in terms of nucleotide
subunits. Lipids contd
Slide 17
Chapter 22-17Chemistry 121 Winter 2010 LA Tech A
four-nucleotide- long segment of DNA. DNA Fragment
Slide 18
Chapter 22-18Chemistry 121 Winter 2010 LA Tech Chromosomes Upon
DNA replication the large DNA molecules interacts with histone
proteins to fold long DNA molecules. Upon DNA replication the large
DNA molecules interacts with histone proteins to fold long DNA
molecules. The histoneDNA complexes are called chromosomes: The
histoneDNA complexes are called chromosomes: A chromosome is about
15% by mass DNA and 85% by mass protein. Cells of different kinds
of organisms have different numbers of chromosomes. Example: Number
of chromosomes in a human cell 46, a mosquito 6, a frog 26, a dog
78, and a turkey 82 Chromosomes occur in matched (homologous)
pairs. Chromosomes occur in matched (homologous) pairs. Example:
The 46 chromosomes of a human cell constitute 23 homologous
pairs
Slide 19
Chapter 22-19Chemistry 121 Winter 2010 LA Tech A comparison of
the primary structures of nucleic acids and proteins. Protiens and
DNA Comparison
Slide 20
Chapter 22-20Chemistry 121 Winter 2010 LA Tech A schematic
drawing of the DNA double helix that emphasizes the hydrogen
bonding between bases on the two chains. DNA double helix
Slide 21
Chapter 22-21Chemistry 121 Winter 2010 LA Tech Hydrogen bonding
possibilities Hydrogen bonding in Base Pairs
Slide 22
Chapter 22-22Chemistry 121 Winter 2010 LA Tech DNA
replication
Slide 23
Chapter 22-23Chemistry 121 Winter 2010 LA Tech One strand of
DNA grows continuously in the direction of the unwinding, and the
other grows in the opposite direction. DNA Replication
Slide 24
Chapter 22-24Chemistry 121 Winter 2010 LA Tech DNA replication
usually occurs at multiple sites within a molecule, and the
replication is bidirectional from these sites. DNA replication at
multiple sites
Slide 25
Chapter 22-25Chemistry 121 Winter 2010 LA Tech Identical twins
share identical physical characteristics because they received
identical DNA from their parents. What in Common Twins Have? Erica
Stone / Peter Arnold, Inc.
Slide 26
Chapter 22-26Chemistry 121 Winter 2010 LA Tech DNA replication
contd
Slide 27
Chapter 22-27Chemistry 121 Winter 2010 LA Tech Protein
synthesis is directly under the direction of DNA Protein synthesis
is directly under the direction of DNA Proteins are responsible for
the formation of skin, hair, enzymes, hormones, and so on Proteins
are responsible for the formation of skin, hair, enzymes, hormones,
and so on Protein synthesis can be divided into two phases. Protein
synthesis can be divided into two phases. Transcription A process
by which DNA directs the synthesis of mRNA molecules Translation a
process in which mRNA isdeciphered to synthesize a protein molecule
DNARNAProtein Transcription Translation
Slide 28
Chapter 22-28Chemistry 121 Winter 2010 LA Tech Differences
Between RNA and DNA Molecules The sugar unit in the backbone of RNA
is ribose; it is deoxyribose in DNA. The sugar unit in the backbone
of RNA is ribose; it is deoxyribose in DNA. The base thymine found
in DNA is replaced by uracil in RNA The base thymine found in DNA
is replaced by uracil in RNA RNA is a single-stranded molecule; DNA
is double-stranded (double helix) RNA is a single-stranded
molecule; DNA is double-stranded (double helix) RNA molecules are
much smaller than DNA molecules, ranging from 75 nucleotides to a
few thousand nucleotides RNA molecules are much smaller than DNA
molecules, ranging from 75 nucleotides to a few thousand
nucleotides
Slide 29
Chapter 22-29Chemistry 121 Winter 2010 LA Tech Types of RNA
Molecules Heterogeneous nuclear RNA (hnRNA): Formed directly by DNA
transcription. Heterogeneous nuclear RNA (hnRNA): Formed directly
by DNA transcription. Post-transcription processing converts the
hnRNA to mRNA Post-transcription processing converts the hnRNA to
mRNA Messenger RNA: Carries instructions for protein synthesis
(genetic information) from DNA Messenger RNA: Carries instructions
for protein synthesis (genetic information) from DNA The molecular
mass of mRNA varies with the length of the protein Small nuclear
RNA: Facilitates the conversion of hnRNA to mRNA. Small nuclear
RNA: Facilitates the conversion of hnRNA to mRNA. Contains from 100
to 200 nucleotides Ribosomal RNA (rRNA): Combines with specific
proteins to form ribosomes - the physical site for protein
synthesis Ribosomal RNA (rRNA): Combines with specific proteins to
form ribosomes - the physical site for protein synthesis Ribosomes
have molecular masses on the order of 3 million
Slide 30
Chapter 22-30Chemistry 121 Winter 2010 LA Tech Types of RNA
Molecules Transfer RNA (tRNA): Delivers amino acids to the sites
for protein synthesis Transfer RNA (tRNA): Delivers amino acids to
the sites for protein synthesis tRNAs are the smallest (7590
nucleotide units)
Slide 31
Chapter 22-31Chemistry 121 Winter 2010 LA Tech Transcription
Transcription: A process by which DNA directs the synthesis of mRNA
molecules Transcription: A process by which DNA directs the
synthesis of mRNA molecules Two-step process - (1) synthesis of
hnRNA and (2) editing to yield mRNA molecule Gene: A segment of a
DNA base sequence responsible for the production of a specific
hnRNA/mRNA molecule Gene: A segment of a DNA base sequence
responsible for the production of a specific hnRNA/mRNA molecule
Most human genes are ~10003500 nucleotide units long Genome: All of
the genetic material (the total DNA) contained in the chromosomes
of an organism Human genome is about 20,00025,000 genes
Slide 32
Chapter 22-32Chemistry 121 Winter 2010 LA Tech Steps in the
Transcription Process Unwinding of DNA double helix to expose some
bases (a gene): Unwinding of DNA double helix to expose some bases
(a gene): The unwinding process is governed by RNA polymerase
Alignment of free ribonucleotides along the exposed DNA strand
(template) forming new base pairs Alignment of free ribonucleotides
along the exposed DNA strand (template) forming new base pairs RNA
polymerase catalyzes the linkage of ribonucleotides one by one to
form mRNA molecule RNA polymerase catalyzes the linkage of
ribonucleotides one by one to form mRNA molecule Transcription ends
when the RNA polymerase enzyme encounters a stop signal on the DNA
template: Transcription ends when the RNA polymerase enzyme
encounters a stop signal on the DNA template: The newly formed RNA
molecule and the RNA polymerase enzyme are released
Slide 33
Chapter 22-33Chemistry 121 Winter 2010 LA Tech
Post-Transcription Processing: Formation of mRNA Involves
conversion of hnRNA to mRNA Involves conversion of hnRNA to mRNA
Splicing: Excision of introns and joining of exons Splicing:
Excision of introns and joining of exons Exon - a gene segment that
codes for genetic information Intron a DNA segments that interrupt
a genetic message The splicing process is driven by snRNAThe
splicing process is driven by snRNA Alternative splicing - A
process by which several different protein variants are produced
from a single gene Alternative splicing - A process by which
several different protein variants are produced from a single gene
The process involves excision of one or more exons
Slide 34
Chapter 22-34Chemistry 121 Winter 2010 LA Tech Heterogenous
nuclear RNA contains both exons and introns. Exons and Introns of
RNA
Slide 35
Chapter 22-35Chemistry 121 Winter 2010 LA Tech Transcriptome
Transcriptome: All of the mRNA molecules that can be generated from
the genetic material in a genome. Transcriptome: All of the mRNA
molecules that can be generated from the genetic material in a
genome. Transcriptome is different from a genome Responsible for
the biochemical complexity created by splice variants obtained by
hnRNA.
Slide 36
Chapter 22-36Chemistry 121 Winter 2010 LA Tech A hairpin loop
is produced when a single-stranded RNA doubles back on itself and
complementary base pairing occurs. RNA hairpin loop
Slide 37
Chapter 22-37Chemistry 121 Winter 2010 LA Tech Classification
of RNA According to the function of RNA, it can be classified as:
Messenger RNA: (m-RNA) synthesized on chromosome and carries
genetic information to the ribosomes for protein synthesis. It has
short half-life. Transfer RNA (t-RNA) is a relatively small and
stable molecule that carries a specific amino acid from the
cytoplasm to the site of protein synthesis on ribosomes. Ribosomal
RNA (r-RNA) is the major component of ribosomes, constituting
nearly 65%. r-RNA is responsible for protein synthesis. Ribozymes
are RNA molecules that have catalytic properties.
Slide 38
Chapter 22-38Chemistry 121 Winter 2010 LA Tech Types of
RNA
Slide 39
Chapter 22-39Chemistry 121 Winter 2010 LA Tech The
transcription of DNA to form RNA involves an unwinding of a portion
of the DNA double helix. Transcription of DNA to form RNA
Slide 40
Chapter 22-40Chemistry 121 Winter 2010 LA Tech An hnRNA
molecule containing four exons. Exons and Introns of RNA contd
Slide 41
Chapter 22-41Chemistry 121 Winter 2010 LA Tech Codes for Amino
Acids
Slide 42
Chapter 22-42Chemistry 121 Winter 2010 LA Tech A tRNA molecule
tRNA molecule
Slide 43
Chapter 22-43Chemistry 121 Winter 2010 LA Tech An
aminoacyl-tRNA synthetase has an active site for tRNA and a binding
site for the particular amino acid that is to be attached to that
tRNA. Aminoacyl-tRNA synthetase
Slide 44
Chapter 22-44Chemistry 121 Winter 2010 LA Tech The interaction
between anticodon an codon. Anticodon and Codon
Slide 45
Chapter 22-45Chemistry 121 Winter 2010 LA Tech Ribosomes have
structures that contain two subunits. Ribosome Structure
Slide 46
Chapter 22-46Chemistry 121 Winter 2010 LA Tech Initiation of
protein synthesis begins with the formation of an initiation
complex. Protein Synthesis: Initiation
Slide 47
Chapter 22-47Chemistry 121 Winter 2010 LA Tech The process of
translation that occurs during protein synthesis. Protein
Synthesis: Translation
Slide 48
Chapter 22-48Chemistry 121 Winter 2010 LA Tech Effects of
Antobiotics
Slide 49
Chapter 22-49Chemistry 121 Winter 2010 LA Tech Several
ribosomes can simultaneously proceed along a single strand of mRNA.
Such a complex of mRNA and ribosomes is called a polysome.
Polysome
Slide 50
Chapter 22-50Chemistry 121 Winter 2010 LA Tech Protein
Synthesis Summary
Slide 51
Chapter 22-51Chemistry 121 Winter 2010 LA Tech Image of an
influenza virus. Influenza virus. NIBSC / SPL / Photo
Researchers
Slide 52
Chapter 22-52Chemistry 121 Winter 2010 LA Tech Recombinant DNA
is made by inserting a gene obtained from DNA of one organism into
the DNA from another kind of organism. Recombinant DNA
Slide 53
Chapter 22-53Chemistry 121 Winter 2010 LA Tech Cleavage
patterns resulting from the use of a restriction enzyme that
cleaves DNA between G and A bases. Cleaving DNA patterns using
restriction enzymes
Slide 54
Chapter 22-54Chemistry 121 Winter 2010 LA Tech The sticky ends
of the cut plasmid and the gene are complementary and combine to
form recombinant DNA. sticky ends of recombnants
Slide 55
Chapter 22-55Chemistry 121 Winter 2010 LA Tech Polymerase chain
reaction process
Slide 56
Chapter 22-56Chemistry 121 Winter 2010 LA Tech Polymerase chain
reaction process
Slide 57
Chapter 22-57Chemistry 121 Winter 2010 LA Tech Selected steps
in the DNA sequencing procedure for the 10-base DNA segment 5
AGCAGCTGGT 3. DNA sequencing
Slide 58
Chapter 22-58Chemistry 121 Winter 2010 LA Tech Summary of
Nucleic Acids Nucleotides are basic units of nucleic acids DNA and
RNA. Nucleotides include pentose, base and phosphoric acid. Bases
include purine or pyrimidine. Two major purines present in
nucleotides are adenine (A) and guanine (G), and three major
pyrimidines are thymine (T), cytosine (C) and uracil (U).
Ribonucleotides - adenosine triphosphate (ATP) stores energy. - NAD
and NADP are important carriers of reducing power.
Slide 59
Chapter 22-59Chemistry 121 Winter 2010 LA Tech DNA DNA contains
genetic information. DNA contains adenine (A) and guanine (G), and
thymine (T), and cytosine (C). A-T G-C DNA has a double helical
structure. The bases in DNA carry the genetic information. Summary
of Nucleic Acids
Slide 60
Chapter 22-60Chemistry 121 Winter 2010 LA Tech RNA RNA
functions as genetic information-carrying intermediates in protein
synthesis. It contains adenine (A) and guanine (G), and cytosine
(C) and uracil (U). m-RNA carries genetic information from DNA to
the ribosomes for protein synthesis. t-RNA transfers amino acid to
the site of protein synthesis r-RNA is for protein synthesis.
Summary of Nucleic Acids
Slide 61
Chapter 22-61Chemistry 121 Winter 2010 LA Tech Summary of Cell
Construction BiopolymersproteinCarbohydrates (polysaccharides)
DNARNAlipids subunit bonds for subunit linkage functions
Characteristic three-D structure
Slide 62
Chapter 22-62Chemistry 121 Winter 2010 LA Tech Primary
Structure A ribonucleic acid (RNA) is a nucleotide polymer in which
each of the monomers contains ribose, a phosphate group, and one of
the heterocyclic bases adenine, cytosine, guanine, or uracil A
ribonucleic acid (RNA) is a nucleotide polymer in which each of the
monomers contains ribose, a phosphate group, and one of the
heterocyclic bases adenine, cytosine, guanine, or uracil A
deoxyribonucleic acid (DNA) is a nucleotide polymer in which each
of the monomers contains deoxyribose, a phosphate group, and one of
the heterocyclic bases adenine, cytosine, guanine, or thymine. A
deoxyribonucleic acid (DNA) is a nucleotide polymer in which each
of the monomers contains deoxyribose, a phosphate group, and one of
the heterocyclic bases adenine, cytosine, guanine, or thymine.
Slide 63
Chapter 22-63Chemistry 121 Winter 2010 LA Tech Primary
Structure Structure: Sequence of nucleotides in DNA or RNA
Structure: Sequence of nucleotides in DNA or RNA Primary structure
is due to changes in the bases Primary structure is due to changes
in the bases Phosphodiester bond at 3 and 5 position Phosphodiester
bond at 3 and 5 position 5 end has free phosphate and 3 end has a
free OH group 5 end has free phosphate and 3 end has a free OH
group Sequence of bases read from 5 to 3 Sequence of bases read
from 5 to 3
Slide 64
Chapter 22-64Chemistry 121 Winter 2010 LA Tech Comparison of
the General Primary Structures of Nucleic Acids and Proteins
Backbone: -Phosphate-Sugar- Nucleic acids Backbone:
-Phosphate-Sugar- Nucleic acids Backbone: -Peptide bonds - Proteins
Backbone: -Peptide bonds - Proteins
Slide 65
Chapter 22-65Chemistry 121 Winter 2010 LA Tech Nucleic acids
have secondary and tertiary structure Nucleic acids have secondary
and tertiary structure The secondary structure involves two
polynucleotide chains coiled around each other in a helical fashion
The secondary structure involves two polynucleotide chains coiled
around each other in a helical fashion The poly nucleotides run
anti-parallel (opposite directions) to each other, i.e., 5 - 3 and
3 - 5 The poly nucleotides run anti-parallel (opposite directions)
to each other, i.e., 5 - 3 and 3 - 5 The bases are located at the
center and hydrogen bonded (A=T and GC) The bases are located at
the center and hydrogen bonded (A=T and GC) Base composition: %A =
%T and %C = %G) Base composition: %A = %T and %C = %G) Example:
Human DNA contains 30% adenine, 30% thymine, 20% guanine and 20%
cytocine
Slide 66
Chapter 22-66Chemistry 121 Winter 2010 LA Tech DNA Sequence:
the sequence of bases on one polynucleotide is complementary to the
other polynucleotide DNA Sequence: the sequence of bases on one
polynucleotide is complementary to the other polynucleotide
Complementary bases are pairs of bases in a nucleic acid structure
that can hydrogen-bond to each other. Complementary bases are pairs
of bases in a nucleic acid structure that can hydrogen-bond to each
other. Complementary DNA strands are strands of DNA in a double
helix with base pairing such that each base is located opposite its
complementary base. Complementary DNA strands are strands of DNA in
a double helix with base pairing such that each base is located
opposite its complementary base. Example : Example : List of bases
in sequential order in the direction from the 5 end to 3 end of the
segment: List of bases in sequential order in the direction from
the 5 end to 3 end of the segment: 5-A-A-G-C-T-A-G-C-T-T-A-C-T-3
5-A-A-G-C-T-A-G-C-T-T-A-C-T-3 Complementary strand of this sequence
will be: 3-T-T-C-G-A-T-C-G-A-A-T-G-A-5 Complementary strand of this
sequence will be: 3-T-T-C-G-A-T-C-G-A-A-T-G-A-5
Slide 67
Chapter 22-67Chemistry 121 Winter 2010 LA Tech Base Pairing One
small and one large base can fit inside the DNA strands: One small
and one large base can fit inside the DNA strands: Hydrogen bonding
is stronger with A-T and G-C A-T and G-C are called complementary
bases
Slide 68
Chapter 22-68Chemistry 121 Winter 2010 LA Tech Practice
Exercise Predict the sequence of bases in the DNA strand
complementary to the single DNA strand shown below: Predict the
sequence of bases in the DNA strand complementary to the single DNA
strand shown below: 5 AATGCAGCT 3 Answer: 3 TTACGTCGA 5
Slide 69
Chapter 22-69Chemistry 121 Winter 2010 LA Tech Replication:
Process by which DNA molecules produce exact duplicates of
themselves Replication: Process by which DNA molecules produce
exact duplicates of themselves Old strands act as templates for the
synthesis of new strands Old strands act as templates for the
synthesis of new strands DNA polymerase checks the correct base
pairing and catalyzes the formation of phosphodiester linkages DNA
polymerase checks the correct base pairing and catalyzes the
formation of phosphodiester linkages The newly synthesized DNA has
one new DNA strand and old DNA strand The newly synthesized DNA has
one new DNA strand and old DNA strand
Slide 70
Chapter 22-70Chemistry 121 Winter 2010 LA Tech DNA polymerase
enzyme can only function in the 5-to-3 direction DNA polymerase
enzyme can only function in the 5-to-3 direction Therefore one
strand (top; leading strand ) grows continuously in the direction
of unwinding Therefore one strand (top; leading strand ) grows
continuously in the direction of unwinding The lagging strand grows
in segments (Okazaki fragments) in the opposite direction The
lagging strand grows in segments (Okazaki fragments) in the
opposite direction The segments are latter connected by DNA ligase
The segments are latter connected by DNA ligase DNA replication
usually occurs at multiple sites within a molecule (origin of
replication) DNA replication usually occurs at multiple sites
within a molecule (origin of replication) DNA replication is
bidirectional from these sites (replication forks) DNA replication
is bidirectional from these sites (replication forks) Multiple-site
replication enables rapid DNA synthesis Multiple-site replication
enables rapid DNA synthesis
Slide 71
Chapter 22-71Chemistry 121 Winter 2010 LA Tech Characteristics
of Genetic Code The genetic code is highly degenerate: The genetic
code is highly degenerate: Many amino acids are designated by more
than one codon. Arg, Leu, and Ser - represented by six codons. Most
other amino acids - represented by two codons Met and Trp - have
only a single codon. Codons that specify the same amino acid are
called synonyms There is a pattern to the arrangement of synonyms
in the genetic code table. There is a pattern to the arrangement of
synonyms in the genetic code table. All synonyms for an amino acid
fall within a single box in unless there are more than four
synonyms The significance of the single box pattern - the first two
bases are the same For example, the four synonyms for Proline -
CCU, CCC, CCA, and CCG.
Slide 72
Chapter 22-72Chemistry 121 Winter 2010 LA Tech Characteristics
of Genetic Code The genetic code is almost universal: The genetic
code is almost universal: With minor exceptions the code is the
same in all organisms The same codon specifies the same amino acid
whether the cell is a bacterial cell, a corn plant cell, or a human
cell. An initiation codon exists: An initiation codon exists: The
existence of stop codons (UAG, UAA, and UGA) suggests the existence
of start codons. The codon - coding for the amino acid methionine
(AUG) functions as initiation codon.
Slide 73
Chapter 22-73Chemistry 121 Winter 2010 LA Tech Practice
Exercise Answers: a. 3 GCGGCAUCAACCGGG CCUCCU 5 b. 3 GCGACCCCUCCU
5
Slide 74
Chapter 22-74Chemistry 121 Winter 2010 LA Tech During protein
synthesis amino acids do not directly interact with the codons of
an mRNA molecule. During protein synthesis amino acids do not
directly interact with the codons of an mRNA molecule. tRNA
molecules as intermediaries deliver amino acids to mRNA. tRNA
molecules as intermediaries deliver amino acids to mRNA. Two
important features of the tRNA structure Two important features of
the tRNA structure The 3 end of tRNA is where an amino acid is
covalently bonded to the tRNA. The 3 end of tRNA is where an amino
acid is covalently bonded to the tRNA. The loop opposite to the
open end of tRNA is the site for a sequence of three bases called
an anticodon. The loop opposite to the open end of tRNA is the site
for a sequence of three bases called an anticodon. Anticodon - a
three-nucleotide sequence on a tRNA molecule that is complementary
to a codon on an mRNA molecule. Anticodon - a three-nucleotide
sequence on a tRNA molecule that is complementary to a codon on an
mRNA molecule.
Slide 75
Chapter 22-75Chemistry 121 Winter 2010 LA Tech Translation a
process in which mRNA codons are deciphered to synthesize a protein
molecule Translation a process in which mRNA codons are deciphered
to synthesize a protein molecule Ribosome an rRNAprotein complex -
serves as the site of protein synthesis: Ribosome an rRNAprotein
complex - serves as the site of protein synthesis: Contains 4 rRNA
molecules and ~80 proteins - packed into two rRNA-protein subunits
(one small and one large) ~65% rRNA and 35% protein by mass A
ribosomes active site Large subunit Ribosome is a RNA catalyst The
mRNA binds to the small subunit of the ribosome.
Slide 76
Chapter 22-76Chemistry 121 Winter 2010 LA Tech Five Steps of
Translation Process Activation of tRNA: addition of specific amino
acids to the 3-OH group of tRNA. Activation of tRNA: addition of
specific amino acids to the 3-OH group of tRNA. Initiation of
protein synthesis: Begins with binding of mRNA to small ribosomal
subunit such that its first codon (initiating codon AUG) occupies a
site called the P site (peptidyl site) Initiation of protein
synthesis: Begins with binding of mRNA to small ribosomal subunit
such that its first codon (initiating codon AUG) occupies a site
called the P site (peptidyl site) Elongation: Adjacent to the P
site in an mRNA ribosome complex is A site (aminoacyl site) and the
next tRNA with the appropriate anticodon binds to it. Elongation:
Adjacent to the P site in an mRNA ribosome complex is A site
(aminoacyl site) and the next tRNA with the appropriate anticodon
binds to it. Termination: The polypeptide continues to grow via
translocation until all necessary amino acids are in place and
bonded to each other. Termination: The polypeptide continues to
grow via translocation until all necessary amino acids are in place
and bonded to each other. Post-translational processing gives the
protein the final form it needs to be fully functional
Post-translational processing gives the protein the final form it
needs to be fully functional
Slide 77
Chapter 22-77Chemistry 121 Winter 2010 LA Tech Efficiency of
mRNA Utilization Polysome (polyribosome): complex of mRNA and
several ribosomes Polysome (polyribosome): complex of mRNA and
several ribosomes Many ribosomes can move simultaneously along a
single mRNA molecule Many ribosomes can move simultaneously along a
single mRNA molecule The multiple use of mRNA molecules reduces the
amount of resources and energy that the cell expends to synthesize
needed protein. The multiple use of mRNA molecules reduces the
amount of resources and energy that the cell expends to synthesize
needed protein. In the process several ribosomes bind to a single
mRNA - polysomes. In the process several ribosomes bind to a single
mRNA - polysomes.
Slide 78
Chapter 22-78Chemistry 121 Winter 2010 LA Tech Mutation An
error in base sequence reproduced during DNA replication An error
in base sequence reproduced during DNA replication Errors in
genetic information is passed on during transcription. Errors in
genetic information is passed on during transcription. The altered
information can cause changes in amino acid sequence during protein
synthesis and thereby alter protein function The altered
information can cause changes in amino acid sequence during protein
synthesis and thereby alter protein function Such changes have a
profound effect on an organism. Such changes have a profound effect
on an organism.
Slide 79
Chapter 22-79Chemistry 121 Winter 2010 LA Tech Mutagens
Mutations are caused by mutagens Mutations are caused by mutagens A
mutagen is a substance or agent that causes a change in the
structure of a gene: A mutagen is a substance or agent that causes
a change in the structure of a gene: Radiation and chemical agents
are two important types of mutagens Ultraviolet, X-ray,
radioactivity and cosmic radiation are mutagenic cause cancers
Chemical agents can also have mutagenic effects E.g., HNO 2 can
convert cytosine to uracilE.g., HNO 2 can convert cytosine to
uracil Nitrites, nitrates, and nitrosamines can form nitrous acid
in cellsNitrites, nitrates, and nitrosamines can form nitrous acid
in cells Under normal conditions mutations are repaired by repair
enzymes Under normal conditions mutations are repaired by repair
enzymes
Slide 80
Chapter 22-80Chemistry 121 Winter 2010 LA Tech Viruses Viruses:
Tiny disease causing agents with outer protein envelope and inner
nucleic acid core Viruses: Tiny disease causing agents with outer
protein envelope and inner nucleic acid core They can not reproduce
outside their host cells (living organisms) They can not reproduce
outside their host cells (living organisms) Invade their host cells
to reproduce and in the process disrupt the normal cells operation
Invade their host cells to reproduce and in the process disrupt the
normal cells operation Virus invade bacteria, plants animals, and
humans: Virus invade bacteria, plants animals, and humans: Many
human diseases are of viral origin, e. g. Common cold, smallpox,
rabies, influenza, hepatitis, and AIDS
Slide 81
Chapter 22-81Chemistry 121 Winter 2010 LA Tech Vaccines
Inactive virus or bacterial envelope Inactive virus or bacterial
envelope Antibodies produced against inactive viral or bacterial
envelopes will kill the active bacteria and viruses Antibodies
produced against inactive viral or bacterial envelopes will kill
the active bacteria and viruses
Slide 82
Chapter 22-82Chemistry 121 Winter 2010 LA Tech Viruses Viruses
attach to the host cell on the outside cell surface and proteins of
virus envelope catalyze the breakdown of the cell membrane and
forms a hole Viruses attach to the host cell on the outside cell
surface and proteins of virus envelope catalyze the breakdown of
the cell membrane and forms a hole Viruses then inject their DNA or
RNA into the host cell Viruses then inject their DNA or RNA into
the host cell The viral genome is replicated, proteins coding for
the viral envelope are produced in hundreds of copies. The viral
genome is replicated, proteins coding for the viral envelope are
produced in hundreds of copies. Hundreds of new viruses are
produced using the host cell replicated genome and proteins in
short time Hundreds of new viruses are produced using the host cell
replicated genome and proteins in short time
Slide 83
Chapter 22-83Chemistry 121 Winter 2010 LA Tech DNA molecules
that have been synthesized by splicing a sequence of segment DNA
(usually a gene) from one organism to the DNA of another organism
DNA molecules that have been synthesized by splicing a sequence of
segment DNA (usually a gene) from one organism to the DNA of
another organism Genetic Engineering (Biotechnology): Genetic
Engineering (Biotechnology): The study of biochemical techniques
that allow the transfer of a foreign gene to a host organism and
produce the protein associated with the added gene Bacterial
strains such as E. coli inserted with circular plasmids, and/or
yeast cells carrying vectors containing foreign genes are used for
this purpose Plasmids (double stranded DNA) replicate independently
in bacteria or yeast
Slide 84
Chapter 22-84Chemistry 121 Winter 2010 LA Tech Recombinant DNA
Production using a Bacterial Plasmid Dissolution of cells:
Dissolution of cells: E. coli cells of a specific strain containing
the plasmid of interest are treated with chemicals to dissolve
their membranes and release the cellular contents Isolation of
plasmid fraction: Isolation of plasmid fraction: The cellular
contents are fractionated to obtain plasmids Cleavage of plasmid
DNA: Cleavage of plasmid DNA: Restriction enzymes are used to
cleave the double-stranded DNA Gene removal from another organism:
Gene removal from another organism: Using the same restriction
enzyme the gene of interest is removed from a chromosome of another
organism Geneplasmid splicing: Geneplasmid splicing: The gene (from
Step 4) and the opened plasmid (from Step 3) are mixed in the
presence of the enzyme DNA ligase to splice them together. Uptake
of recombinant DNA: Uptake of recombinant DNA: The recombinant DNA
prepared in stept 5 are transferred to a live E. coli culture where
they can be replicated, trasncribed and translated.
Slide 85
Chapter 22-85Chemistry 121 Winter 2010 LA Tech Transformed cell
can reproduce a large number of identical cells clones: Transformed
cell can reproduce a large number of identical cells clones: Clones
are the cells that have descended from a single cell and have
identical DNA Given bacteria grow very fast, within few hours 1000s
of clones will be produced Given bacteria grow very fast, within
few hours 1000s of clones will be produced Each clone can
synthesize the protein directed by foreign gene it carries Each
clone can synthesize the protein directed by foreign gene it
carries Clones
Slide 86
Chapter 22-86Chemistry 121 Winter 2010 LA Tech The polymerase
chain reaction (PCR) is a method for rapidly producing multiple
copies of a DNA nucleotide sequence (gene). The polymerase chain
reaction (PCR) is a method for rapidly producing multiple copies of
a DNA nucleotide sequence (gene). This method allows to produce
billions of copies of a specific gene in a few hours. This method
allows to produce billions of copies of a specific gene in a few
hours. PCR is very easy to carryout and the requirements are: PCR
is very easy to carryout and the requirements are: Source of gene
to be copied Thermostabel DNA polymerase Deoxynucleotide
triphosphates (dATP, dGTP, dCTP and dTTP) A set of two
oligonucleotides with complementary sequence to the gene (primers)
Thermostable plastic container and Source of heat The polymerase
chain reaction (PCR)The polymerase chain reaction (PCR)
Slide 87
Chapter 22-87Chemistry 121 Winter 2010 LA Tech DNA sequencing
is a method by which the base sequence in a DNA molecule (or a
portion of it) is determined. DNA sequencing is a method by which
the base sequence in a DNA molecule (or a portion of it) is
determined. Discovered in 1977 by Fredrick Sanger Discovered in
1977 by Fredrick Sanger Concept in DNA sequencing: Concept in DNA
sequencing: Selective interruption of polynucleotide synthesis
using 2,3-dideoxyribonucleotide triphosphates (ddNTPs). Selective
interruption of polynucleotide synthesis using
2,3-dideoxyribonucleotide triphosphates (ddNTPs). DNA sequencingDNA
sequencing
Slide 88
Chapter 22-88Chemistry 121 Winter 2010 LA Tech This
interruption of synthesis leads to the formation of every possible
nucleotide site mixture. This interruption of synthesis leads to
the formation of every possible nucleotide site mixture. These
nucleotides are labeled using radioactive dNTP during their
synthesis. These nucleotides are labeled using radioactive dNTP
during their synthesis. The radiolablled nucleotides are then
separated on a gel by electrophoresis The radiolablled nucleotides
are then separated on a gel by electrophoresis ddNTPs
FragmentsddNTPs Fragments
Slide 89
Chapter 22-89Chemistry 121 Winter 2010 LA Tech Basic steps
involved in DNA sequencing Step 1: Cleavage of DNA using
restriction enzymes: Restriction enzymes are used to cleave the
large DNA molecule into smaller fragments (100200 base pairs). Step
1: Cleavage of DNA using restriction enzymes: Restriction enzymes
are used to cleave the large DNA molecule into smaller fragments
(100200 base pairs). Step 2: Separation into individual components:
The mixture of small DNA fragments generated by the restriction
enzymes is separated into individual components via gel
electrophoresis techniques. Step 2: Separation into individual
components: The mixture of small DNA fragments generated by the
restriction enzymes is separated into individual components via gel
electrophoresis techniques. Step 3: Separation into single strands:
A given DNA fragment is separated into its two strands by chemical
methods to use it as a template in step 4. Step 3: Separation into
single strands: A given DNA fragment is separated into its two
strands by chemical methods to use it as a template in step 4.
Slide 90
Chapter 22-90Chemistry 121 Winter 2010 LA Tech Basic steps
involved in DNA sequencing
