CHEM113 – BIOCHEMISTRY

1ST SEMESTER – MIDTERM – A.Y. 2023-2024

LESSON: NUCLEIC ACIDS

Nucleic Acids
→ discovered in 1869 by Swiss Physiologist Friedrich
Miescher.
→ unbranched polymer containing monomers called
nucleotides; repeating unit is nucleotides.
→ two types: DNA and RNA.
→ end products are protein or amino acids.
→ adenine (A), guanine (G), and cytosine (C) are found
in both RNA and DNA.
→ pyrimidines and purines both contain amine
functional groups.
→ uracil (U) – found only in RNA.
→ thymine (T) – found only in DNA.

Nucleotide
→ three-subunit molecule; building block of nucleic
acids.
→ contains a pentose sugar (monosaccharide),
phosphate group, and nitrogen base (heterocyclic Purine Pyrimidine
base).
Pyrimidine Derivatives
→ thymine (T), cytosine (C), and uracil (U).

C5
C1
C4

C3 C2

Purine Derivatives
Pentose Sugar → adenine (A) and guanine (G).
→ 5 carbons
→ RNA and DNA differ in the identity of the sugar unit
in their nucleotides; ribose for RNA – hence the R in
its name, deoxyribose for DNA – hence the D in its
name (deoxy means “without oxygen).
→ base is attached at Carbon 1 (C1), while phosphate
group is attached at Carbon 5 (C5).
→ in terms of structure, RNA and DNA only differs at
Carbon 2 (C2). −OH for ribose; −H for deoxyribose. Phosphate
→ third component of nucleotide; derived from
phosphoric acid.
→ H3PO4 (phosphoric acid) → HPO42- (hydrogen
phosphate ion)

Nucleotide Formation
Nucleoside
→ two-subunit molecule composed of pentose sugar
bonded with a nitrogen base.

Nucleic Acid Backbone Nucleoside Formation

→ phosphate – sugar; found in all nucleic acids. → eight molecules associated with nucleic acid
chemistry (sugar-nitrogen base – ribose-adenine).
Nitrogen Base → -idine for pyrimidine bases; -osine for purine bases
→ 5 bases; 3 are derived from pyrimidine – thymine (T), → prefix -deoxy means deoxyribose sugar is present.
cytosine (C), and uracil (U); 2 are from purines –
adenine (A), and guanine (G). Nucleoside (RNA) Nucleoside (DNA)
→ pyrimidine – monocyclic (single ring) base with a adenosine deoxyadenosine
six-membered ring; purines – bicyclic (double ring) guanosine deoxyguanosine
base with fused five and six-membered rigs. cytidine deoxycytidine
uridine deoxythymidine
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TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: NUCLEIC ACIDS

Nucleotide Formation Deoxyribonucleic Acid

→ formation of a nucleotide from sugar, base, and
phosphate is visualized below.
→ phosphate attached to C5 and base is attached to
C1 position of pentose.
→ molecule of water is produced in nucleotide
formation. Two molecules of water are produced in
combining a sugar, base, and phosphate
→ nucleotide polymer in which each of the monomers
contains deoxyribose, a phosphate group, and one
of the nitrogen bases adenine, guanine, cytosine, or
thymine.
→ backbone – alternating phosphate and deoxyribose.
Primary Nucleic Acid Structure
→ sequence in which nucleotides are linked together in
a nucleic acid.

Nucleotide Nomenclature

DNA Nomenclature
Base Nucleoside Nucleotide Name
deoxyadenosine 5’-
Adenine deoxyadenosine
monophosphate
deoxyguanosine 5’-
Guanine deoxyguanosine
monophosphate
deoxycytidine 5’-
Cytosine deoxycytidine
monophosphate
deoxythymidine 5’-
Thymine deoxythymidine
monophosphate

RNA Nomenclature
Base Nucleoside Nucleotide Name
adenosine 5’-
Adenine adenosine
monophosphate
guanosine 5’-
Guanine guanosine
monophosphate
cytidine 5’-
Cytosine cytidine
monophosphate
uridine 5’-
Uracil uridine
monophosphate
.
→ sequence is: phosphate-sugar-phosphate-sugar
→ nucleoside – sugar and nitrogen base
→ backbone – sugar and phosphate
→ nucleotide – all tree (sugar, phosphate, base).

Primary Nucleic Acid Structure

Ribonucleic Acid
→ nucleotide polymer in which each of the monomers
contains a ribose, a phosphate group, and one of the
nitrogen bases adenine, cytosine, guanine, or uracil.
→ backbone – alternating phosphate and ribose.
→ each nonterminal phosphate group of the sugar-
phosphate backbone is bonded to two sugars
molecules through a 3’, 5’ phosphodiester lingkage.

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TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: NUCLEIC ACIDS
→ nucleotide chain has directionality; one end of the
nucleotide chain, the 5’ end, normally carries a free
phosphate group attacheed to the 5’ carbon atom.
The other end of the nucleotide chain, the 3’ end,
normally has a free hydroxyl group attached to the 3’
carbon atom.
→ always start at 5’ and ends at 3’
DNA
→ deoxyribonucleic acid
→ double helix / double stranded
→ location: inside the nucleus
→ replication / duplication
→ genetic information
→ amounts of complementary bases are always equal
(A% = T% and C% = G%)
→ two strands are anti-pallarel; run in opposite
directions; one runs in the 5’-to-3’ direction and vice
versa.
Base Pairing
→ one small base (pyrimidine) and one large base
(purine) can fit within the helix interior.
→ hydrogen bonding is stronger with A-T and G-C
Complementary Bases
→ are pairs of bases in a nucleic acid structure that is
hydrogen-bonded to each other.
→ complementary bases: A ↔ T and G ↔ C.
Complementary DNA Strands
→ strands of DNA in a double helix with base pairing
such that each base is located opposite to its
complementary base (e.g., G occurs in one strand,
there is a C on the other strand – opposite).
Replication of DNA Molecules
→ DNA replication – biochemical process by which
DNA molecules produce exact duplicates of
themselves.
→ two strands of DNA double helix are regarded as pair
of templates or patterns.
→ DNA ligase – connects the segments latter.
→ DNA helicase – enzyme that breaks the hydrogen
bond between complementary bases.
→ replication fork – point at which the DNA double
helix is unwinding, which is constantly changing
(moving).
→ antimetabolites – drugs in which they inhibit DNA-
replication process.
Chromosomes
→ histones – proteins; form structural units that
provide the most stable arrangement for the long
DNA molecules.
TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
→ chromosomes – histone-DNA complexes;
individual DNA molecule bounded to a group of
proteins.
→ 15% by mass DNA and 85% by mass protein.
→ different organism have different numbers of
chromosomes; human – 46; mosquito – 6; frog – 26;
dog – 78; turkey – 82.
→ occurs in matched (homologous) pairs.
Protein Synthesis
→ under the direction of DNA molecules.
→ proteins are responsible for the formation of skin,
hair, enzymes, hormones, and so on.
→ transcription – first phase; process by which DNA
directs the synthesis of mRNA (RNA) molecules.
→ translation – second phase; process in which
mRNA is deciphered to synthesize a protein
molecule
.
RNA
→ ribonucleic acid
→ location: outside nucleus
→ single stranded
→ protein synthesis
→ sugar unit is ribose
→ uracil instead of thymine
→ does not contain equal amount of specific bases.
→ much smaller than DNA molecules.
→ three major types: transfer, messenger, and
ribosomal.
→ G ↔ C, A → U, and T → A
Types of RNA Molecules
1. Heterogenous Nuclear RNA (hnRNA)
→ formed directly by DNA transcription.
→ post-transcription converts hnRNA to mRNA.
2. Messenger RNA (mRNA)
→ carries instructions for protein synthesis (genetic
information) to the sites for protein sysnthesis.
3. Small Nuclear RNA (snRNA)
→ facilitates the conversion of hnRNA to mRNA.
4. Ribosomal RNA (rRNA)
→ combines with specific proteins to form ribosomes,
the physical site for protein synthesis.
5. Transfer RNA (tRNA)
→ delivers amino acids to the sites for protein
synthesis; serves as a link (or adaptor) between the
messenger RNA (mRNA) molecule and the growing
chain of amino acids that make up a protein.
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: NUCLEIC ACIDS

together to form an mRNA molecule; involves

Transcription: RNA Synthesis
→ process by which DNA directs the synthesis of
hnRNA / mRNA molecule that carry the coded
information needer for protein synthesis (DNA to
hnRNA / mRNA).
→ mRNA production – two step process; hnRNA
molecule is initially produced and then is “edited” to
yield the desired mRNA molecule.
→ gene – segment of DNA strand that contains the
base sequence for the production of a specific
hnRNA / mRNA molecule.
→ genome – all of the genetic material (total DNA)
contained in the chromosome of an organism.
snRNA molecules.
→ small nuclear ribonucleoprotein particle (snRNP)
– complex formed from an snRNA molecule and
several proteins; always further collect together into
a larger complexes called spliceosomes.
→ spliceosome – large assembly of snRNA molecules
and proteins involved in the conversion of hnRNA
molecules to mRNA molecules.
Alternative Splicing
→ birdges the gap between the larger estimated
number of proteins and the now-smaller estimated
number of genes.
→ process by which several different proteins that are
variations of a basic structural motif can be produced
from a single gene.

Transcription Process
1. Unwinding of DNA double helix to expose some bases
(gene)
→ governed by RNA polymerase; RNA polymerase – Transcriptome
transcription enzyme; DNA helicase – replication
→ all of the mRNA molecules that can be generated
enzyme.
from the genetic material in a genome.
→ different from genome
2. Alignment of free ribonucleotides along the exposed DNA
strand (template) forming new base pair. → responsible for biochemical complexity created by
splice variants obtained by hnRNA.
→ template strand – strand of DNA used for hnRNA /
mRNA synthesis
Genetic Code
→ information strand – non-template strand of DNA.
→ codon – three-nucleotide sequence in an mRNA
molecule that code for a specific amino acid.
3. RNA polymerase is involved in the linkage of
ribonucleotides, one by one, to the growing hnRNA → base sequence in a mRNA determines the amino
molecule. acid sequence for the protein synthesized.
→ involves only four different bases: A, C, G, and U.
4. Transcription ends when the RNA polymerase enzyme → genetic code – assignment of the 64 mRNA codons
encounters a stop signal on the DNA template. to specific amino acids (or stop signals); 3 out of the
→ newly formed RNA molecule and the RNA 64 codons are termination codons (“stop” signals).
polymerase enzyme are released.

Post-Transcription Process
→ conversion of hnRNA to mRNA.
→ exon – is a gene segment that conveys (codes
for)genetic information; DNA segment that help
express a genetic message.
→ introns – is a gene segment that does not convey
(code for) genetic information; DNA segment that
interrupt a genetic message.
→ splicing – process of removing introns from an
hnRNA molecule and joining the remaining exons

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TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: NUCLEIC ACIDS
Chracteristics of Genetic Code
1. 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 to codons.
→ Met and Trp – have only a single codon.
→ codons that specify the same amino acid are called
“synonyms”.
2. 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 unless there are more than four synonyms.
→ the significance of the single box pattern – the first
two bases are the same.
3. 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
whtether the cell is a bacterial cell, a corn plant cell,
or a human cell.
4. An initiation codon exists.
→ existence of “stop” codons suggest the existence of
“start” codons.
→ AUG functions as an initiator of protein synthesis.
Anticodons and tRNA Molecules
→ anticodon – three-nucleotide sequence on an tRNA
molecule that is complementary to a codon on an
mRNA molecule.
→ 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 sit
for a sequence of three bases called anticodons.
Translation: Protein Synthesis
→ translation – process by which mRNA codons are
deciphered and a particular protein molecule is
synthesized (mRNA to protein / amino acid
molecule).
→ translocation – part of translation in which a
ribosome moves down an mRNA molecule three
base positions (one codon) so that a new codon can
occupy the ribosomal A site.
→ subtances needed are mRNA molecules, tRNA
molecules, amino acids, ribosomes, and different
enzymes (ribozyme).
→ ribosome – rRNA-protein complex that serves as
the site for the translation phase of protein synthesis.
→ involves 5 general steps: activation of tRNA,
initiation, elongation, termination, and post-
translation processing.
TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
5 Steps to the Translation Process
1. Activation of tRNA
→ addition of specific amino acids to the 3’ –OH group
of tRNA.
2. Initiation
→ initiation of protein synthesis; begins with binding of
mRNA to small ribosomal subunit such that its first
codon (initiatin codon AUG) occupies a site call the
P site (peptidyl site).
3. Elongation
→ adjacent to the P side in an mRNA – ribosome
comples is A site (aminoacyl site) and the next tRNA
with the appropriate anticodon binds to it (peptidyl
transferase).
4. Termination
→ the polypeptide continues to grow via translocation
until all necessary amino acids are in place and
bonded to each other.
5. Post-Translation Processing
→ gives the protein the final form it need to be fully
functional.
DNA Sequencing
→ method by which the base sequence in a DNA
molecule (or portion of it) is determined.
→ discovered in 1977 by Fredrick Sanger.
Concepts in DNA Sequencing
→ selective interruption of polynucleotide synthesis
using 2’, 3’ -dideoxyribonucleotide triphosphates
(ddNTPs).
→ this interruption of synthesis leads to the formation of
every possible nulceotide site mixture.
→ the radiolablled nucleotides are then separated on a
gel electrophoresis.
Basic Steps Involved in DNA Sequencing
1. Cleavage of DNA using Restrcition Enzymes
→ restriction enzymes are used to cleave the large
DNA molecule into smaller fragments (100 – 200
base pair).
2. Separation into Individual Components
→ mixture of small DNA fragments generated by the
restriction enzymes is separated into individual
components via gel electrophoresis techniques.
3. Separation into Single Stand
→ given DNA fragment is separated into its two strands
by chemical methods to use it as a template in step
4.
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: NUCLEIC ACIDS
Efficiency of mRNA Utilization
→ many ribosomes can move simultaneously along a
single mRNA molecule.
→ multiple use of mRNA molecules reduced the
amount of resources and energy that the cell
expends to synthesize needed protein.
→ polyribosome – is a complex of mRNA and several
ribosomes.
→ polysome – several ribosomes that are attached to
a single mRNA.
Mutations
→ mutation – error in a base sequence in a gene that
is reproduced during DNA replication.
→ two common types: point and frameshift.
→ point mutation – mutation in which one base in a
DNA base sequence is replaced with another base.
→ frameshift mutation – mutation that inserts or
delete a base in a DNA molecule base sequence.
→ mutagen – substance or agent that causes a
damage in the structure of a gene; e.g., radaitaion,
UV rays, chemicals.
Nucleic Acids and Viruses
→ virus – small particle that contains DNA or RNA (but
not both) surrounded by a coat of protein and that
cannot reproduce without a host cell; tiny disease
causing agents.
→ virus does not contain molecules necessary to
replicate their nucleic acid or to synthesize proteins.
→ retrovirus – RNA-containing virus.
→ vaccine – preparation containing an inactive or
weakened form of a virus or bacterium; inactive virus
or bacterial envelope.
→ antibodies – produced against inactive or viral or
bacterial envelopes will kill the active pathogens.
Recombinant DNA and Genetic Engineering
→ genetic engineering – process whereby an
organism is intentionally changed at the molecular
(DNA) level so that it exhibits different traits; the
sutyd of biochemical techniques that allow the
transes of a foreign gene to a host organism and
produce the protein associated with the added gene
→ transformation – proccess of incorporating
recombinant DNA into a host cell.
→ 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.
→ recombinant DNA – contains genetic material from
two different organisms; create genes with new
functions.
→ clones – cells with identical DNA that have
descended from a single cell.
TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
Procedures of Genetic Engineering
1. Cell Membrane Dissolution
→ E. coli cells of a specific strain are placed in a
solution that dissolves cell membranes, thus
releasing the contents of the cell.
2. Isolation of Plasmid Fraction
→ the cellular contents are fractionated to obtain
plasmids.
3. Cleavage of Plasmid DNA
→ restriction enzymes are used to cleave the double-
stranded DNA.
→ restriction enzymes – enzyme that recognizes
specific base sequences in DNA and cleaves the
DNA in a predictable manner at these sequences.
4. Gene Removal from Another Organism
→ using the same restriction enzyme, the gene of
interest is removed from a chromosome of another
organism.
5. Gene-Plasmid Splicing
→ the gene (from step 4) and the opened plasmid (from
step 3) are mized in the presence of the enzyme
DNA ligase to splice them together.
6. Uptake of Recombinant Dna
→ the recombinant DNA prepared in step 5 are
transferred to a live E. coli culture where they can be
replicatedm transcribed and translated.
Polymerase Chain Reaction
→ method for rapidly producing multiple copies of a
DNA nucleotide sequence.
→ allows production of billion of copies of a specific
gene within a few hours.
→ DNA polymerase – enzyme present in all living
organisms; key substance in the PCR process.
→ PCR is very easy to carryout and the requirements
are:
1. source of gene to be copied
2. thermostabel DNA polymerase
3. deoxynucleotide triphosphates (dATP, dGTP,
dCTP and dTTP)
4. set of two oligonucleotides with complementary
sequence to the gene (primers)
5. thermostable plastic container and
6. source of heat
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