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Week 10-Nucleic Acids
biochem
Course
BIOCHEMISTRY (CHM3)
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Lecture by: Mr. Joseph Deuel Casinsinan | Transes made by: Nicole Maranan
Week 10: Nucleic Acids
Nucleic Acid
- a polymer in which the monomer units
are nucleotides.
Types of NA:
Deoxyribonucleic acid (DNA) – nearly
all DNA is found within cell nucleus;
primary function is storage and
transfer of genetic information
Ribonucleic acid (RNA)- for synthesis
of proteins
Nucleotide
- Building blocks of
NA
- Three-subunit
molecule in which
a pentose sugar is bonded to both a
phosphate group and a nitrogen-
containing heterocyclic base
Pentose Sugars
- The sugar unit of a nucleotide is
either the pentose ribose or the
pentose 2’-deoxyribose
- RNA and DNA differ in the identity of
the sugar unit in their nucleotides. In
RNA the sugar unit is ribose-hence the
R in RNA. In DNA the sugar unit is 2’-
deoxyribose-hence the D in DNA
Nitrogen-Containing Heterocyclic Base
- Five nitrogen-containing heterocyclic
bases are nucleotide components.
- Three of them are derivatives of
pyrimidine (six membered ring) and
two are derivatives of purine (bicyclic
base with fused five- and six-
membered rings).
- Both of these heterocyclic compounds
are bases* because they contain
amine functional groups, and amine
functional groups exhibit basic
behavior
*Bases- because they contain amine
functional groups
To avoid confusion:
The systems for numbering the atoms in the
pentose and nitrogen-containing base
subunits of a nucleotide are important and
will be used extensively in this lesson. The
convention is that
1. Pentose ring atoms are designated
with primed numbers.
2. Nitrogen-containing base ring
atoms are designated with unprimed
numbers.
Pyrimidine Derivatives
- Thymine (T)
- Cytosine ©
- Uracil (U)
Purine Derivatives
- Adenine (A)
- Guanine (G)
Adenine, guanine, and cytosine are found in
both DNA and RNA.
Uracil is found only in RNA, and thymine
usually occurs only in DNA
Lecture by: Mr. Joseph Deuel Casinsinan | Transes made by: Nicole Maranan
Phosphate
- the third component of a nucleotide,
is derived from phosphoric acid
(H3PO4).
- Under cellular pH conditions, the
phosphoric acid loses two of its
hydrogen atoms to give a hydrogen
phosphate ion (HPO4 2- ).
Nucleotide Formation
1. Condensation: removal and
formation of water molecule. Occurs
between sugar and base, sugar and
phosphate [yung nakabox is where
condensation occurs]
Added notes:
Base is always attached at C1 sugar
Purine: C1 sugar attached on N
Pyrimidine: C1 attached on N
C1 is always on beta configuration; beta-N-
glycosidic linkage
Phoshphate group attached to C5;
phosphate-ester linkage
Nucleotide Nomenclature
1. All the names end in 5-
monophosphate, which signifies the
presence of a phosphate group
attached to the 5-carbon atom of
ribose or deoxyribose.
2. Preceding the monophosphate ending
is the name of the base present in a
modified form. The suffix -osine is
used with purine bases, the suffix -
idine with pyrimidine bases.
3. The prefix deoxy- at the start of the
name signifies that the sugar present
is deoxyribose. When no prefix is
present, the sugar is ribose.
4. The abbreviations for the nucleotides
come from the one-letter symbols for
the bases (A, C, G, T, and U), the use
of MP for monophosphate, and a
lower-case d at the start of the
abbreviation whenever deoxyribose is
the sugar.
Primary Nucleic Acid Structure
The nucleotide units within a nucleic acid
molecule are linked to each other through
sugar–phosphate bonds (backbone).
Lecture by: Mr. Joseph Deuel Casinsinan | Transes made by: Nicole Maranan
Base composition data for DNA molecules
from many different organisms revealed a
definite pattern of base occurrence.
The amounts of A and T were always equal,
and the amounts of C and G were always
equal, as were the amounts of total purines
and total pyrimidines.
For example, human DNA contains
30% adenine, 30% thymine, 20% guanine,
and 20% cytosine.
Additionally, the two strands of the double
helix are antiparallel—that is, they run in
opposite directions. One strand runs in the
5’-to-3’ direction, and the other is oriented
in the 3’-to-5’ direction
It also has unequal spaces in between.
Base Pairing
- Only pairs involving one small base (a
pyrimidine) and one large base (a
purine) correctly “fit” within the helix
interior.
- hydrogen-bonding possibilities are
most favorable for the A–T and G–C
pairings, and these two combinations
are the only two that normally occur
in DNA
- The pairing of A with T and that of G
with C are said to be complementary.
- 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.
Wherever G occurs in one strand,
there is a C in the other strand; wherever T
occurs in one strand, there is an A in the
other strand.
Example: Predict the sequence of bases in
the DNA strand that is
Base-Stacking Interactions
The bases in a DNA double helix are
positioned with the planes of their rings
parallel (like a stack of coins).
Stacking interactions involving a given base
and the parallel bases directly above it and
below it also contribute to the stabilization of
the DNA double helix.
DNA Replication
DNA molecules are the carriers of genetic
information within a cell; that is, they are the
molecules of heredity. Each time a cell
divides, an exact copy of the DNA of the
parent cell is needed for the new daughter
cell.
DNA replication is the biochemical process
by which DNA molecules produce exact
duplicates of themselves.
Lecture by: Mr. Joseph Deuel Casinsinan | Transes made by: Nicole Maranan
The key concept in understanding DNA
replication is the base pairing associated
with the DNA double helix.
DNA Replication is said to be conservative.
Step 1:
Hydrogen bonds b/w base pairs are broken
by the enzyme helicase and DNA molecule
unzips. DNA molecule separates into
complementary halves
Step 2:
Nucleotides match up with complementary
bases. Free nucleotides abundant in nucleus.
After a free nucleotide formed hydrogen
bonds with the base of an old
strand/template...
DNA polymerase verifies that the base
pairing is correct and then catalyzes the
formation of a new phosphodiester linkage
between the nucleotide and the growing
strand
The enzyme DNA polymerase can operate on
a forming DNA daughter strand only in the
5’-to-3’ direction
- Only one strand can grow
continuously in the 5’to- 3’direction.
- The other strand must be formed in
short segments, called Okazaki
fragments (after their discoverer,
Reiji Okazaki), as the DNA unwinds
- The breaks or gaps in this daughter
strand are called nicks.
- To complete the formation of this
strand, the Okazaki fragments are
connected by action of the enzyme
DNA ligase.
It shows DNA replication doesn’t occur in one
location only. DNA replication is bidirectional,
5’ to 3’ and 3’ to 5’
When a DNA is replicated, it interacts
with proteins called histones. Together,
they form structural units that provides the
most stable arrangements for long chain
DNA.
These DNA-histone complexes are
called chromosomes. Normal human being
has 46 chromosomes, with 23 homologous
pairs.
DNA Replication
Topoisomerase - makes temporary nicks in
the helix to release the tension, then sealing
the nicks to avoid permanent damage.
Helicase – enzyme that breaks H-bonds
DNA
Lecture by: Mr. Joseph Deuel Casinsinan | Transes made by: Nicole Maranan
Steps in Transcription
Post-Transcription Processing:
Formation of mRNA
This is a splicing method.
Translation
The Genetic Code
The base sequence in a given mRNA
determines the amino acid sequence for the
protein synthesized under that mRNA’s
direction.
Research has verified that sequences of
three nucleotides in mRNA molecules specify
the amino acids that go into synthesis of a
protein.
A codon is a three-nucleotide sequence in
an mRNA molecule that codes for a specific
amino acid.
It was found that 61 of the 64 codons formed
by various combinations of the bases A, C,
G, and U were related to specific amino
acids; the other 3 combinations were
termination codons (“stop” signals) for
protein synthesis.
The genetic code is the assignment of the 64
mRNA codons to specific amino acids (or
stop signals).
Translation: Protein Synthesis
the process by which mRNA codons are
deciphered and a particular protein molecule
is synthesized.
Five General Steps to the Translation
Process:
1. activation of tRNA
2. initiation
3. elongation
4. termination
5. post-translational processing
Anticodons and tRNA molecules
The amino acids used in protein synthesis do
not directly interact with the codons of an
mRNA molecule.
Instead, tRNA molecules function as
intermediaries that deliver amino acids to
the mRNA.
Lecture by: Mr. Joseph Deuel Casinsinan | Transes made by: Nicole Maranan
At least one type of tRNA molecule
exists for each of the 20 amino acids found
in proteins.
The general two-dimensional
“cloverleaf” shape of a tRNA molecule is
a shape produced by the molecule’s folding
and twisting into regions of parallel strands
and regions of hairpin loops
The 3’ end of the open part of the
cloverleaf structure is where an amino acid
becomes covalently bonded to the tRNA
molecule through an ester bond.
Each of the different tRNA molecules is
specifically recognized by an aminoacyl tRNA
synthetase enzyme.
These enzymes also recognize the one kind
of amino acid that “belongs” with the
particular tRNA and facilitates its bonding to
the tRNA
The loop opposite the open end of the
cloverleaf is the site for a sequence of three
bases called an anticodon.
An anticodon is a three-nucleotide sequence
on a tRNA molecule that is complementary
to a codon on an mRNA molecule
Ribosomes are like typewriters.
Mutations
A mutation is an error in base sequence in a
gene that is reproduced during DNA
replication
Such errors alter the genetic information
that is passed on during transcription. The
altered information can cause changes in
amino acid sequence during protein
synthesis.
A mutagen is a substance or agent that
causes a change in the structure of a gene.
Examples of mutagen:
- physical agents :heat and radiation
- chemical agents
- biological agents: viruses, bacteria
Side notes:
Physical agents:
Radiation: UV, X rays, cosmic light. UV
can cause skin cancer.
Chemical agents:
Chemical agents can cause mutagenic
effect.
Nitrous acid (HNO2) is a mutagen that
causes deamination of heterocyclic nitrogen
bases. For example, HNO2 can convert
cytosine to uracil.
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Week 10-Nucleic Acids
Course: BIOCHEMISTRY (CHM3)
365 Documents
Students shared 365 documents in this course
University: Our Lady of Fatima University
Was this document helpful?
BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE (CHEM113lec)
Lecture by: Mr. Joseph Deuel Casinsinan | Transes made by: Nicole Maranan
Please do not distribute the transes, especially w/o permission of the owner.
Week 10: Nucleic Acids
Nucleic Acid
- a polymer in which the monomer units
are nucleotides.
Types of NA:
Deoxyribonucleic acid (DNA) – nearly
all DNA is found within cell nucleus;
primary function is storage and
transfer of genetic information
Ribonucleic acid (RNA)- for synthesis
of proteins
Nucleotide
- Building blocks of
NA
- Three-subunit
molecule in which
a pentose sugar is bonded to both a
phosphate group and a nitrogen-
containing heterocyclic base
Pentose Sugars
- The sugar unit of a nucleotide is
either the pentose ribose or the
pentose 2’-deoxyribose
- RNA and DNA differ in the identity of
the sugar unit in their nucleotides. In
RNA the sugar unit is ribose-hence the
R in RNA. In DNA the sugar unit is 2’-
deoxyribose-hence the D in DNA
Nitrogen-Containing Heterocyclic Base
- Five nitrogen-containing heterocyclic
bases are nucleotide components.
- Three of them are derivatives of
pyrimidine (six membered ring) and
two are derivatives of purine (bicyclic
base with fused five- and six-
membered rings).
- Both of these heterocyclic compounds
are bases* because they contain
amine functional groups, and amine
functional groups exhibit basic
behavior
*Bases- because they contain amine
functional groups
To avoid confusion:
The systems for numbering the atoms in the
pentose and nitrogen-containing base
subunits of a nucleotide are important and
will be used extensively in this lesson. The
convention is that
1. Pentose ring atoms are designated
with primed numbers.
2. Nitrogen-containing base ring
atoms are designated with unprimed
numbers.
Pyrimidine Derivatives
- Thymine (T)
- Cytosine ©
- Uracil (U)
Purine Derivatives
- Adenine (A)
- Guanine (G)
Adenine, guanine, and cytosine are found in
both DNA and RNA.
Uracil is found only in RNA, and thymine
usually occurs only in DNA
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