Nucleic Acid Biochemistry

DNA & RNA: DNA REPLICATION AND RNA TRANSCRIPTION

- In RNA, thymine is replaced with Uracil (U)
NUCLEIC ACIDS ▪ PURINES: Nine-member double rings adenine
○ Large biomolecules that play essential roles in all and guanine
cells and viruses.
1. major function of nucleic acids involves the
storage and expression of genomic
information.
2. Deoxyribonucleic acid, or DNA, encodes
the information cells need to make proteins.
3. A related type of nucleic acid, called
ribonucleic acid (RNA), comes in different
molecular forms that play multiple cellular ▪ PYRIMIDINES: six-member single ring thymine,
roles, including protein synthesis. uracil and cytosine

DNA

✓ phosphate group,
- when attaches to a nucleoside through
phosphoester bond, entire complex
becomes nucleotide.
✓ pentose sugar (a 5-carbon sugar)

○ Nucleotides
○ Deoxyribonucleic acid
○ The molecule inside cells that contains the genetic
information responsible for the development and
function of an organism. DNA molecules allow this
information to be passed from one generation to the
next.
○ Nucleic acid
▪ are macromolecules that exist as polymers called
polynucleotides. A polynucleotide consists of
many monomers called nucleotides, and is
considered the building block of all nucleic acid
molecules. These structural units of nucleic acids
consist of three essential components:
✓ a nitrogenous base,
- 4 nitrogenous bases found in DNA:
➢ Adenine (A)
➢ Thymine (T)
➢ Cytosine (C)
➢ Guanine (G)
▪ Single units within nucleotides are also called
nucleoside monophosphates (addition of 1 or 2
phosphate group result in nucleoside
diphosphates and triphosphates, respectively)
▪ Triphosphate form is significant because it
serves as precursor molecule during nucleic acid
synthesis within the cell.
▪ DNA is made up of four building blocks called
nucleotides: adenine (A), thymine (T), guanine
(G), and cytosine (C). The nucleotides attach to
each other (A with T, and G with C) to form
chemical bonds called base pairs, which connect
the two DNA strands.

NAME: ALAN LOUISE Y. BUALAT 1

 TRANS: Module 1

DNA REPLICATION
○ a process to ensure that the DNA is duplicated before
cell division so that each offspring cell receives
chromosome(s) identical to the parent’s
○ SEMI-CONSERVATIVE MODEL
▪ the two parental strands separate, allowing each
separated strand to serve as a template for the
synthesis of a complementary strand
➢ STEPS:
✓ INITIATION PHASE
• the DNA double helix is opened at
origins of replication, moves away from
ALTERNATIVE FORMS OF DNA origin, creating structure known as
replication bubble. DNA double helix is
opened and unwound both sides of the
origin to form two structure called
replication forks which unwind double
helix in opposite directions. Replication
forks are the site at which single-
stranded DNA is exposed, and at which
DNA synthesis occurs. Once double helix
is opened, replication enzymes and
proteins are loaded to the single strand,
forming templates for daughter strand to
be synthesized.
✓ ELONGATION PHASE
• the replication machinery moves along
the parent DNA strands and forms the
daughter strands as it proceeds.
✓ TERMINATION PHASE
• occurs when the two replication forks
moving in opposite directions meet, and
RNA the replication complexes are
○ Ribonucleic acid disassembled
○ Genetic material for viruses
○ Ribonucleic acid (abbreviated RNA) is a nucleic acid
present in all living cells that has structural similarities
to DNA. Unlike DNA, however, RNA is most often
single- stranded. An RNA molecule has a backbone
made of alternating phosphate groups and the sugar
ribose, rather than the deoxyribose found in DNA
▪ Classes of RNA
- rRNA
✓ structural components of ribosome
- tRNA
✓ carries amino acids to the ribosome during
translation
- mRNA
✓ carry genetic information from the DNA of the
gene

NAME: ALAN LOUISE Y. BUALAT 2

 TRANS: Module 1

RNA TRANSCRIPTION can signal termination of

○ Template strand transcription.
- Used as template - Hairloop formation
- Directs the synthesis of RNA ▪ Rho (p) dependent termination
- Also called antisense strand, because its code is
the complement of the RNA produced
- Sometimes called (-) strand by convention

○ Coding strand
- Other strand, sequence is the same as the RNA
sequence that is produced, with exception of U
replacing T
- Also called sense strand, RNA sequence is the
sequence that we use to determine what amino
acids are produced through mRNA.
- Also called (+) strand, or nontemplate strand

○ Promoters
- Three components:
✓ TSS (core promoter)
✓ -10 box (Pribnow box)
✓ -35 box (core promoter)
- DNA sequences that provide signal for RNA
polymerase; where RNA polymerase binds
- STRUCTURES:
✓ Consensus sequences
o -10 box and -35 box (bear greater or
lesser resemblance to two
consensus sequences: TATAAT
and TTGACA, respectively)
o Represents probabilities of specific
base being found in given position
✓ UP element
o Enhances binding of RNA
polymerase
○ the process by which the information is transferred
from one strand of the DNA to RNA by the enzyme
RNA Polymerase.
➢ STEPS:
✓ INITIATION
o Four steps in transcription initiation:
▪ Formation of closed promoter complex
▪ Conversion of closed promoter complex
to open promoter complex
▪ Polymerizing first few nucleotides (up to
10) while polymerase remains at
promoter
▪ Promoter clearance, the transcript
becomes long enough to form stable
hybrid with template strand
➢ Helps to stabilize transcription complex, and
polymerase moves away from promoter and
transcription starts elongation stage.
✓ ELONGATION
o RNA polymerase directs sequential
binding of ribonucleotides to growing
RNA chain in 5’ to 3’ direction, while RNA
polymerase and transcription bubble
move along template DNA in 3’ to 5’
direction.
✓ TERMINATION
o Two types of termination mechanism:
▪ Intrinsic termination
- Regions at end of genes called
terminator/termination sites

NAME: ALAN LOUISE Y. BUALAT 3

 TRANS: Module 1

Protein and Protein Synthesis TRANSLATION

AMINO ACIDS POLYMERIZATION

○ Amino acids are polymerized into proteins, using

RNA as a guide (translation).

STEPS

1. DNA is transcribed into mRNA, which is then translated into

an amino acid sequence of a protein.

RIBONUCLEOTIDE SEQUENCE
○ Derived from the complementary nucleotide bases in
the DNA template strand

NUCLEOTIDE SEQUENCE
○ Same as the DNA coding strand

GENETIC CODE
○ Consists of three ribonucleotide letters, thus referred to
as triplet code
○ Degenerate; more than one triplet can encode the
same amino acid.
○ Universal; the code can be used by all viruses,
prokaryotes, archaea, and eukaryotes.

o Each amino acid can have more than one codon, but
no codon can encode more than one amino acid

TRANSLATION: LOCATION
o Within all cells, the translation machinery resides within
a specialized organelle called the ribosome. In
eukaryotes, mature mRNA molecules must leave the
nucleus and travel to the cytoplasm, where the
ribosomes are located. On the other hand, in
prokaryotic organisms, ribosomes can attach to mRNA
while it is still being transcribed.

CODON

○ Each group of three ribonucleotides, called codon,

specifies one amino acid.
○ Unambiguous, as each triplet specifies only a single
amino acid.

NAME: ALAN LOUISE Y. BUALAT 4

 TRANS: Module 1

DNA DAMAGE, REPAIR, AND MUTATION

OVERVIEW

o DNA, like any other molecule, can undergo a variety of

chemical reactions. Because DNA uniquely serves as
a permanent copy of the cell genome, however,
changes in its structure are of much greater
consequence than are alterations in other cell
components, such as RNAs or proteins.

MUTATION

- can result from the incorporation of incorrect o ALKYLATING AGENTS

bases during DNA replication. In addition, various
chemical changes occur in DNA either
spontaneously or as a result of exposure to
chemicals or radiation.
DNA REPAIR
▪ Are reactive compounds that can transfer methyl
or ethyl groups to a DNA base, thereby chemically
modifying the base.

- These mechanisms of DNA repair can be divided

into two general classes:
• direct reversal of the chemical reaction
responsible for DNA damage
• removal of the damaged bases followed
by their replacement with newly
synthesized DNA.
- Where DNA repair fails, additional mechanisms
have evolved to enable cells to cope with the
damage.

DIRECT REVERSAL OF DNA DAMAGE

○ UV LIGHT
▪ formation of pyrimidine dimers, in which adjacent
pyrimidines on the same strand of DNA are joined
by the formation of a cyclobutane ring resulting
from saturation of the double bonds between
carbons 5 and 6. The formation of such dimers
distorts the structure of the DNA chain and blocks DNA REPAIR
transcription or replication past the site of damage,
so their repair is closely correlated with the ability EXCISION REPAIR
of cells to survive UV irradiation. • most important DNA repair mechanisms in both
prokaryotic and eukaryotic cells.
• the damaged DNA is recognized and removed,
either as free bases or as nucleotides.
• The resulting gap is then filled in by synthesis of a
new DNA strand, using the undamaged
complementary strand as a template.

➢ TYPES OF EXCISION REPAIR:

NAME: ALAN LOUISE Y. BUALAT 5

 TRANS: Module 1

BASE-EXCISION REPAIR MISMATCH REPAIR

▪ Enable cells to cope with a variety of different

kinds of DNA damage

NUCLEOTIDE-EXCISION REPAIR

POST-REPLICATION REPAIR

o Recombinational repair depends on the fact that one

strand of the parental DNA was undamaged and
therefore was copied during replication to yield a
normal daughter molecule.
○ Error-prone repair, a gap opposite a site of DNA
damage is filled by newly synthesized DNA.

NAME: ALAN LOUISE Y. BUALAT 6

 TRANS: Module 1

CHROMOSOMAL ALTERATIONS

- Mutations that change chromosome structure

- Occur when a section of a chromosome breaks off
and rejoins incorrectly or does not rejoin at all

DNA MUTATION
○ A change in the sequence of bases in DNA or RNA
➢ TYPES OF MUTATIONS:
- There are variety of types of mutations. Two major
categories of mutations are germline mutations
and somatic mutations.

GERMLINE MUTATIONS

- Occur in gametes
POINT MUTATION
- Especially significant because they can be
transmitted to offspring and every cell in the - Is a change in a single nucleotide in DNA
offspring will have the mutation - Usually less serious than chromosomal alteration

SOMATIC MUTATIONS

- Occurs in other cells of the body

- May have little effect on the organism because
they are confined to just one cell and its daughter
cells.
- Somatic mutations cannot be passed on to
offspring

FRAMESHIFT MUTATION

- Is a deletion or insertion of one or more

nucleotides that changes the reading frame of the
base sequence
➢ DELETION- removes nucleotides
➢ INSERTION- add nucleotides

NAME: ALAN LOUISE Y. BUALAT 7

 TRANS: Module 1

NAME: ALAN LOUISE Y. BUALAT 8