BIOCHEM (LEC) o Separation of the DNA strands due to heat

or alkali exposure without breaking the

DNA and RNA phosphodiester bond
DNA STRUCTURE RENATURATION
o Contains nucleosides that is made up of a o Upon heating, DNA strands separate the
nitrogenous base, deoxyribose, and base pairs reform once the temperature is
phosphate. slowly decreased.
o The nitrogenous bases are classified into
Purine and Pyrimidines HYBRIDIZATION
o The primary structure of DNA and RNA is
linear polynucleotide chain made up of o A single strand of DNA or RNA pairs with
mononucleotides which are linked by a a complementary base sequence on
3’,5’ phosphodiester bond (3’ C of one another strand of DNA or RNA.
sugar to the 5’C of the next sugar)
HISTONES
PURINES - PURGA
o These are small of DNA small, basic
proteins rich in Arg and Lys; not
presenting prokaryotes.
o Eukaryotic chromatins consist of a DNA
complexed with histones.

RNA VS. DNA

o RNA contains ribose as sugar instead of

deoxyribose.

PYRIMIDINES - PYRCUT

o Uracil replaces Thymine.

o Single stranded with extensive base
pairing.
o RNA can sometimes act as catalysts and
enzymes (ribonucleases, Peptidyl
transferase).

TYPES OF RNA

1. Messenger (mRNA)
DNA DOUBLE HELIX
o Contains a cap consisting of a methylated
o Proposed by Watson and Crick in 1953 guanine triphosphate attached to the
o The secondary structure of DNA is formed hydroxyl group on the ribose at the 5’ end.
by the pairing two polynucleotide chains o The poly(A) tail contains up to 200
that are antiparallel. Adenine nucleotides.
o One chain rubs 5’–3 ’and the other 3’–5’
o The base sequences of the two strands 2. Ribosomal (rRNA)
are complementary. o Aids in the formation of ribosomes
 Adenine and Thymine via 2 o Prokaryotic: 70s (Large subunit = 50s;
hydrogen bonds (major groove) Small subunit = 30s)
 Guanine and Cytosine via 3 o Eukaryotic: 80s (Large subunit = 60s;
hydrogen bonds (minor groove)
Small subunit = 40s)
o One full turn of DNA helix contains
3. Transfer (tRNA)
nucleotides.
o Has 3 different conformations: o Has a characteristic clover leaf structure.
 B form: Right-handed
 Z form: Left-handed DNA REPLICATION
 A form: dehydrated and compact;
Right-handed o Known as the transfer of genetic formation
within single class of nucleic acids, i.e.,
from DNA to DNA or, as in certain viruses
DENURATION from RNA to RNA.
o DNA Replication is:
 o Is the major control point in gene
Bidirectional expression and protein production.
o Replication begins at a specific origin and o Catalyzed by DNA – dependent DNA
simultaneously moves out in both polymerase.
directions. o No primer is needed.
o Prokaryotes have one site of origin while o Uses one strand of DNA as template.
eukaryotes can have multiple sites of
origin. RNA POLYMERASE
Semiconservative
o The resulting daughter DNA contains one o Can initiate synthesis of new chains
intact parenteral strand and newly without primer.
synthesized complementary strand. o Copies the DNA template in a 3’ – 5’
direction and resulting RNA elongates in a
STEPS IN REPLICATION 5’ – 3’ direction.
o Precursors: Ribonucleoside Triphosphate
1. Initiation (ATP, UTP, GTP, and CTP)
a. The parenteral DNA is separated and
uncoiled by helicases where the uncoiled STEPS IN PROKARYOTIC TRANSCRIPTION
DNA strand serves as the template.
b. As the strands separate. An active site for 1. Initiation and Elongation
synthesis known as replication fork is a. Rifampin inhibits the beta subunit of
formed where each separated strand is bacterial dependent RNA Polymerase
stabilized by a single – stranded protein. Actinomycin D binds to DNA and inhibits the
c. As the strands separate, supercoiling elongation or RNA Transcription by RNA
happens which is removed by DNA Polymerase:
Topoisomerase.
• Etoposide inhibits topoisomerase. o RNA polymerase is directed by the sigma
d. The primase aids in the production of the factor to bind to the promoter Promoters
RNA primer in a 5’ – 3’ direction. contain a sequence TATAAT known as
the Pribbenow box or TATA BOX
2. Elongation & Termination
a. From the initiation site, DNA Polymerase o In eukaryotes, Hogness box (TATA Box)
III adds deoxyribonucleotides at the 3’ OH has a sequence of TATATAA.
end of the primer.
o DNA polymerase can only copy as 3’ b. An RNA Polymerase – closed promoter
– 5’ direction and produce the complex is formed.
daughter strand in a 5’ – 3’ direction. c. The DNA unwinds at promoter and forms
o DNA polymerase always requires the open promoter complex.
primers and cannot initiate the d. RNA Polymerase initiates the mRNA
formation of new strands. synthesis with a purine ribonucleoside
b. DNA Polymerase III forms continuous triphosphate.
strands in a 3’ – 5’ direction forming the e. RNA Polymerase holoenzyme catalyzes
leading strand. the elongation of mRNA by about 4 more
c. In the 5’ – 3’ strand, a discontinuous units.
formation of DNA happens forming smaller f. Upon reaching about 10 nucleosides, the
fragments known as Okazaki fragments. sigma – subunit dissociates and will bind
These fragments are joined together by to another RNA Polymerase.
DNA ligase.
d. Once complete, RNA primer is removed 2. Termination
by the exonuclease activity of DNA a. Intrinsic (Rho – independent
Polymerase I Transcription Termination)
e. Gaps are filled with the complementary o Controlled by specific sequences called
bases. termination sites wherein the sequences
f. Replication is terminated, forming 2 form a hairpin loop structure that allows
daughter DNA molecules. the RNA Polymerase to detach from the
DNA template strand.

b. Rho – dependent Transcription

RNA TRANSCRIPTION Termination
o Involves the Rho – Protein
o The process of making an RNA form a o The rho –protein binds to the RNA and
DNA template is known as transcription. chases the polymerase until it reaches the
 termination site to facilitate the o
Characteristics:
dissociation of the RNA Polymerase from •
It is degenerate (Redundant;
the DNA Template Strand. Many amino acids have
numerous codons)
EUKARYOTIC TRANSCRIPTION •
It is non – overlapping.
•
Begins with the start codon AUG
1. RNA Polymerase (Promoters) (Methionine) near the 5’ end of
the mRNA which determines the
a. RNA Polymerase I reading frame.
o Found in the nucleolus and synthesizes • Ends with a stop codon (UGA,
the precursors of ribosomal RNA. UAA, UAG) near the 3’ end.
o The code is comma less (no markers
b. RNA Polymerase II to differentiate one codon from one
o Found in the nucleoplasm and synthesizes another)
mRNA precursors. o The code is nearly universal.
o α-Amanitin (a toxin from the mushroom C0DONS
Amanita phalloides) binds and inhibits o A sequence of 3 bases in mRNA that
RNA Polymerase II which halts mRNA specifies a particular Amino acid.
synthesizes resulting to severe GIT
symptoms, liver toxicity, and death. MUTATIONS

c. RNA Polymerase III o Mutations in DNA are carried over

o Found in the nucleoplasm and synthesizes into the mRNA that causes changes
the tRNA precursors. in the encoded protein.

2. Steps in Eukaryotic Transcription 1. Point mutations

o A base in the DNA is replaced by
a. mRNA Synthesis another which alters the codon in the
1. RNA Polymerase II produces a MRNA.
heterogenous nuclear RNA (hnRNA)
containing exons and introns. a. Silent
 Exons are sequences appearing o
The codon containing the changed
in the mature mRNA. base codes for the same amino acid.
 Introns are the non-coding region b. Missense
and are removed during splicing. o The codon containing the changed
2. The primary transcript (hnRNA) is base codes for a different amino acid.
capped at the 5’ end.
3. A poly(A) tail with a nucleotide length Nonsense
c.
range of 20 – 200 is added at the 3’ o
The codon containing the changed
end of the transcript. base codes for a stop codon.
4. The introns are removed, and the 2. Insertions
exons are connected to form the o Occur when a base or several bases
mature mRNA through splicing are added to the DNA.

3. Reverse Transcription 3. Deletions

• The process of transcribing the single o Occur when a base or a number of
stranded RNA into a double – stranded bases are deleted to the DNA
DNA
• Enzyme: Reverse Transcriptase (RNA – 4. Frameshift
dependent DNA Polymerase) o Occurs when the number of bases
• Retrovirus contain RNA as genetic
added or deleted is not a multiple of 3
material
which shifts the reading frame to a
completely different set of codons.

STEPS IN EUKARYOTIC TRANSLATION

RNA TRANSLATION AND PROTEIN SYNTHESIS
1. Initiation

GENETIC CODE
a. The 40s ribosomal subunit binds close to the
5’ cap until it recognizes the start codon
o A collection of codons that specify all the
(AUG).
amino acids found in proteins.
 • The ribosomes recognize the AUG in o Epimers: Stereoisomers that differ in the
the correct context known as the position of the hydroxyl group at only one
Kozak Sequence (ACCAUGG) asymmetric carbon.
• In prokaryotes, Streptomycin binds to
the 30s subunit which hinders MONOSACCHARIDES
initiation.
b. A special initiator tRNA recognizes the start o These are simple carbohydrates that are
codon carriers a non formylated Methionine. named depending on the number of
c. The 60s ribosomal subunit is recruited from Carbon atoms and the specific carbonyl
the 80s initiation complex. group present.
o They can either be Dextrorotatory or
2. Elongation Levorotatory
o Examples: D – Galactose, L - Fructose
a. The ribosome moves from 5’ to 3’ direction.
b. The amino acid containing tRNA (aminoacyl- OLIGIOSACCHARIDES
tRNA’s) forms a complex with elongation
factor and enters the empty A-site.
o Composed of 2 to 12 monosaccharide
c. The anticodon of the aminoacyl-tRNA is
units linked by glycosidic bond.
matched against the mRNA codon in the A-
o Sucrose
site.
o Table Sugar
d. When the correct aminoacyl-tRNA enters the
o Glucose + Fructose
A-site, the polypeptide chain in the P-site is
linked to the new amino acid in the A-site via o Lactose
a peptide bond. o Milk Sugar
• The reaction is catalyzed by peptidyl o Galactose – linked β-1,4 to glucose
transferase.
• Chloramphenicol inhibits POLYSACCHARIDES
prokaryotic peptidyl transferase.
• The new peptidyl-tRNA is left in the A o These are high – molecular carbohydrates
site. with more than ten monosaccharide units
e. The peptidyl-tRNA is translocated from the linked by glycosidic bonds.
A-site to the P- site facilitated by an o Neutral Polysaccharides such as Starch
elongation factor. (Plants) and Glycogen (human and
• Erythromycin binds to a site on the animals) are found inside the cells as
50s subunit which inhibits reserve material.
translocation. o Acidic polysaccharides such as
f. A new aminoacyl-tRNA in the A-Site is made Chondroitin sulfate and Hyaluronic acid
available for the next codon in the mRNA. are found extracellularly.
g. The steps are repeated until the ribosome
encounters a stop codon. DIGESTION OF CARBOHYDRATES

3. Termination o Salivary α-amylase, which is present in

the saliva, cleaves starch by breaking the
a. The stop codon is recognized by a release α-1,4 linkage between glucose residues.
factor. o Sucrase converts sucrose to glucose and
b. The newly synthesized protein is released, fructose.
and the synthesizing complex dissociates. o Lactase coverts lactose to glucose and
galactose
CARBOHYDRATES o α-glucosidase inhibitors work in the
intestine to slow down the digestion of
o The most widespread compounds carbohydrates to facilitate better post
involved in the buildup functions of the digestive blood glucose control
cell.
o Presence of a carbonyl (Aldo or Keto
group) and at least two hydroxyl groups
o Stereoisomers: Same chemical formula QUALITATIVE TESTS FOR CARBOHYDRATES
but differs in the position of hydroxyl
groups 1. Molisch Test
o Enantiomers: Stereoisomers that are o General test for Carbohydrates
mirror images o Monosaccharides give the most rapid
result
o Uses α-naphthol and sulfuric acid
 o (+) result: purple ring

2. Benedict’s test
o Tests for the presence of reducing sugars
o All monosaccharides give a positive result
o Uses Copper (III) sulfate, Sodium citrate
and Sodium carbonate in a mildly basic
solution
o (+) result: red to orange precipitate

3. Barfoed’s Test
o Uses Copper (III) in a slightly acidic
medium
o Used to differentiate a reducing
monosaccharide from a reducing
disaccharide
o (+) result: red ppt (within 3 minutes =
Monosaccharide, longer than 3 minutes =
disaccharide)

4. Bial’s Test
o Test for differentiating pentose and
hexose monosaccharides
o Used concentration HCl and orcinol +
ferric chloride
o (+) result: Pentoses = bluish to green,
Hexoses + brownish to gray

5. Seliwanoff’s Test
o Test for differentiating aldoses from
ketoses
o Uses 6M HCl and resorcinol
o (+) result: Ketoses = Cherry red, Aldoses
= bluish-green to peach