Polytechnic University of the Philippines  Phosphate attached to carbon #5 of

BIOCHEMISTRY REVIEWER the sugar.

MARIA CARMELA R. LIPO

NUCLEIC ACIDS

2 types of Nucleic Acids

1. Ribonucleic Acid (RNA)
 Single stranded
 Less stable than DNA NITROGENOUS BASES
2. Deoxyribonucleic Acid
 Double stranded
 Stable
 Can be separated
 Can be either singles stranded or
double stranded
 MELTING is the process of
separating the double stranded
DNA to single stranded DNA
 Can store better genetic
information than RNA
 Melting point of DNA is 100o and
above. Adenosine

Use of Nucleic Acid

 Storage of genes
 Medium of information

Components of Nucleic Acid

1. Phosphates
2. Sugar
 ** ribose
3. Nitrogenous Base
 ** called NUCLEOSIDE if no
phosphate group is attached
SUGAR
 ** nucleotide//adenine
 C5H10o5
 The compound will be called
 Exclusive to RNA
deoxyadenosine if it lacks 1 oxygen
molecule.
 TO NAME IT--- identify the
nucleotide added and change the
end name of the nucleotide from
nine to sine

Adenosine Monophosphate
PHOSPHATE
 PO43-
 Anion
 The conjugate base of an acid is the
PHOSPHORIC ACID
 Because of the production of
phosphate, the nucleus is acidic,
hence the name Nucleic Acid.
  To name it—identify the nucleotide
added and the number of
phosphates.
SIDE NOTES:
 When ATP is reduced it becomes
ADP + Pi
 Pi= is an inorganic phosphate
dNTP – deoxy nucleotide triphosphate
 Used when producing new DNA
NTP - nucleotide triphosphate
 Used when producing RNA
N-glycosidic bond – the bond that connects
NITROGEN AND BASE.
Phosphoesther bond- bond that
PHOSPHATE TO SUGAR
H-bonding- bond between water and ice
 Physical separation through
Melting.
Hydrophobic bonding- interaction between
carbons.
SIDE NOTES:
 Bonding;
- Pyramidine = 1N:1C
- Purine = 9N:1C
NUCLEOTIDES= BUILDING BLOCKS
o NTPs : RNA
o dNTPs : DNA
 Micromolecules (simple) : Macromolecule
(complex)
 Monomers : Polymers
 Mononucleotide (single) : Polynucleotide
(Chain)
Phosphodiesther bond- bond that connects
nucleotides.
What is the direction of the synthesis of
nucleotides?
 All synthesis of nucleotide chains occurs
in the 5’ to 3’ direction.
 The direction is due to the nature of the
reaction of DNA synthesis.
 The last nucleotide added to a growing
chain has a 3’-hydroxyl on the sugar.
 The incoming nucleotide has a 5’-
triphosphate on its sugar.
 The 3’- hydroxyl group at the end of the
growing chain is a nucleophile. It attacks
the phosphorus adjacent to the sugar in
the nucleotide to be added to the
growing chain, leading to the
elimination of the pyrophosphate and
the formation of the new
phosphodiesther bond.
 SA FREE PHOSPHATE PWEDE KUMAPIT
KAYA SA 5’ KUMABIT
 MAY FREE OH SA 3’ KAYA DUN KUMAPIT
Direction in Reading RNA
 5’ to 3’ = sense
 From left to right
binds Direction in Reading DNA
 3’ to 5’ = antisense
Writing the Sequence
 5’ AUG 3’
 If wala number, yung left side ay
automatic na 5’
 Lahat naka sulat sa 5’ to 3’ order
 Do not write anti-sense without
sense. Dapat may contradiction.
 5’ A T G 3’
 5’ dA dT dG 3’ ; D=deoxyribose
DNA
5’ 3’ sense
3’ 5’ anti-sense
Rules in Writing Chargaff’s Rule
 A with T:
 the purine adenine (A) always pairs
with the pyrimidine thymine (T)
 C with G:
 the pyrimidine cytosine (C) always
pairs with the purine guanine (G)
  %GC – is a determinant of the melting
temperature to be used to denature the
bond of the DNA
 It is also the determinant of the
stability of GC
 Mas mabilis mag dikit si GC bond dahil triple
bond ito. Mas madaming pagkakapitan, to bind
kasi dapat may isang mag kabit na.
 Mas sticky din si GC kesa ki AT dahil triple bond
ito.
CENTRAL DOGMA
1. Replication- DNA to DNA
 Also called DNA synthesis
2. Transcription- DNA to RNA
 RNA synthesis
3. Translation - RNA to Protein
 Protein synthesis
4. Reverse transcription- RNA to DNA
 Made by the reverse transcriptase
enzyme
 They are retroviruses
 Not all viruses are retroviruses but
all retroviruses have a reverse
transcriptase.
REPLICATION
 An enzyme (HELICASE) enters the DNA
and unwinds the double stranded DNA.
 Super coiling occurs when the DNA is
unwind---- SUPER COILED DNA.
 DNA feels tension that might lead to
breakage.
 The TOPOISOMERASE relieves the
tension in the supercoiled DNA by
cutting a strand.
 DNA ligase- the enzyme that links the
separate stretches of DNA.
 Replication bubble- the space between
the separated strand cause by helicase.
 Replisome- complex cells related to
replication.
 A complex of DNA polymerase, the
RNA primer, primase, and helicase
at a replication fork.
 Replication fork- in DNA replication, the
point at which the new DNA strands are
formed.
 SSB proteins- prevents the unwounded
SSDNA
 Replication: Initiation
 Priming means “annealing of
primers”
 Replication: Elongation
 Addition of dNTP from 5’ to 3’
Two types of Strand
1. Sense/Leading strand- the primes only
once and elongation is continuous.
2. Anti-sense/ Lagging strand- primes
multiple times and elongates many
times.
 Replication: Termination
 DNA polymerase I and II- fixes the
fragments in the Okazaki
fragments
 DNA Polymerase III- connects the
dNTP
 Okazaki fragments- DNA anti-
sense na walang primers
 “polymerase” an enzyme that creates a
polymer
2 types of DNA Polymerase
1. DNA polymerase III- mabilis maglagay
pero may infidelity
2. DNA Polymerase I or II- adheres the
Chargaff’s rule.
 DNA replication is error free because DNA
I and II repairs the error in replication.
 DNA replication is nonconservative if all of
the daughter strands are new (no parent
strand)
 DNA replication is semi-conservative may
parent strand
 Messelson-Stahl- proved na semi-
conservative using P32 and N15.
(Replication from YT)
 DNA is a double helix strand
 Each strand is made up of four chemical
bases, A,C,G,T.
  The two strands are complimentary- A:T, Proofreading- the process of removing incorrect
C:G. nucleotides when DNA replication is in progress.
 Each strand has a 5’ and 3’ end.
 Strands run in opposite directions. Primer- a short stretch of RNA hydrogen-bonded
 1. The strands are separated into two using to the template DNA to which the growing DNA
HELICASE. Results in the formation of the strand is bonded at the start of synthesis.
Replication Fork.
 Each strand has a template for correcting new DNA Ligase- the enzyme that links separate
strand of DNA. stretches of DNA.
 2. PRIMASE makes a small pieces of RNA called
Primer. DNA polymerase- the enzyme that form DNA
 Primer marks the starting point for the from deoxyribonucleotides on a DNA template.
construction of new strand of DNA.
 3. DNA polymerase binds the primer and makes Mutations- changes in DNA, causing subsequent
a new strand of DNA. changes in an organism that can be transmitted
 DNA polymerase can add only in one direction, genetically.
5’ to 3’.
TRANSCRIPTION
 3. The leading strand is made continuously – the
DNA polymerase adding bases one by one in the
INITIATION
5’ to 3’ direction.
 RNA polymerase binds to the
 3. The lagging strand cannot be made in
promoter and forms cloud
continuous way but runs in opposite direction.
complex.
Therefore, the DNA polymerase make this
strand in a series of small chunks called OKAZAKI  Promoter site yung Pribnow box
FRAGMENTS. or TATA Box.
 Each fragment is started with an RNA primer.  Core enzymes binding the O
subunit binds to areas of DNA
 Then DNA polymerase adds a short row of DNA
that lack promoters.
bases in the 5’ to 3’ direction.
 No promoter is required.
 Exonuclease removes all the RNA primers from
ELONGATION
both strands of DNA.
 The anti-sense DNA strand is used
 DNA polymerase fills in the gaps that are left
as the template so that the RNA
with DNA.
made has the same base
 DNA ligase seals up the fragment of DNA in both
sequence as the sense (coding)
strand that form a continuous double strand.
strand, except that U replaces T.
 DNA replication is describe as semi-conservative
 The O subunit dissociates from
because each DNA molecule is made up of one
RNA polymerase to the leave the
old, conserved strand of DNA and one new one.
core enzyme that continues RNA
synthesis in a 5’ to 3’ direction
Primase- the enzyme that makes a short section
using the four ribonucleptides 5’-
of RNA to act as a primer for DNA synthesis.
triphospahte as a precursor.
TERMINATION
Single strand binding protein- a protein that
 A common termination signal is a
protects exposed single-strand of DNA from
hairpin structure followed by a
nucleases.
palindromic GC-rich region,
followed by an AT-rich sequence.
DNA gyrase- an enzyme that introduces
supercoiling into closed circular DNA.
2 termination of Transcription
1. P-dependent- may nabangga na
Repair- the enzymatic removal of incorrect
termination site kaya nag sstop ang apg
nucleotides from DNA and their replacement
transcribe/elongate.
correct ones.
 2. P-independent- nag sstop ang pag
transcribe/elongate kasi paulit uli na
hanggan sa wala ng sense.
Termination Site- kinakabitan
TRANSLATION
- Occurs in the ribosome
- Requires ribosomes, mRNA, tRNA, and protein
factors
- mRNA and tRNA are responsible for the correct
order of amino acids in the growing protein chain.
- Before an amino acid is incorporated into a
protein chain, it is activated by the process
involving both tRNA and specific enzyme
AMINOACYL-tRNA synthases.
- In this process, the amino acid is covalently
bonded to the tRNA forming aminoacyl-tRNA.
INITIATION
- The first aminoacyl-Trna is bound to the mRNA at
the site that encodes the start of polypeptide
synthesis.
- In this, the Mrna and the ribosome are bound to
each other.
- The next aminoacyl-trna forms a complex with the
ribosome and with the Mrna.
- The binding site is close to that of first aminoacyl-
Trna.
 The synthesis of polypeptide chains starts at
rhe N-terminal end. (the chain grows from N-
terminal end.
 The start of polypeptide chain synthesis
requires the formation of an initiation
complex.
 At least 8 components enter into the
formation of the initiation complex,including
mRNA, the 30s ribosomal subunits, fmet
tRNA, GTP, and 3 protein initiation factors
called IF-1, IF-2,IF-3. It also prevents
premature binding of the 50s subunit/
 The IF-3 facilitates the binding of the mRNA to
the 30s ribosomal subunit. Also prevent
premature binding of the 50s subunit.
 IF-1 binds to IF-3 AND IF-2 and facilitates the
action of both. It also catalyzes the separation
of the 30s and the 50s ribosomal subunits
being recycled for other round of translation.
 The resulting combination of mRNA, the 30s
ribosomal subunit and fmet-tRNA is the 30s
initiation complex.
 A 50s ribosomal subunit binds to the 30s
initiation complex to produce the 70s
initiation complex.
ELONGATION
- Peptide bond is formed between the amino acids
- The process repeat itself until the polypeptide
chain is complete.
The 3 binding sites
1. P(peptidyl)site- binds a tRNA that
carries a peptide chain
2. A (aminoacyl) site- binds an incoming
aminoacyl-tRNA
3. E (exit) site- carries an uncharged tRNA
that is about to be released from the
ribosome.
 (1) Chain elongation begins with the
addition of the second amino acid specified
by the mRNA to the 70s initiation complex.
 The P site on the ribosome is the one
initially occupied by the fmet-tRNA in the
70s initiation complex.
 The second aminoacyl-tRNA binds at the A
site.
 (2) GTP and three protein elongation
factors, EF-P, EF-Tu, and EF-Ts
(temperature-untable and temperature
stabele) are require.
 EF-Tu guides the aminoacyl-tRNA into part
of thee A site and align the anti-codpn with
the mRNA codon.
 EF-P is bound to the P site and E site and
help catalyze the first peptide bond
formed.
 EF-Ts is involved in regeneration of EF-Tu
GTP.
 (3) A peptide bond is then formed in a
reaction catalyzed by peptidyl transferase,
which is a part of the 50s subunit.
 The alpha-amino group of the amino acid in
the A site performs a nucleophilic attack on
the carbonyl group of the amino acid linked
to the tRNA in the P site.
 (4) Translocation takes places before
another amino acid can be added to the
growing chain. In the process, the
uncharged tRNA moves from the P site to
the E site. The Peptidyl-tRNA moves from
the A site to the vacated P site.
 In eukaryotes, there is no elongation sites.
 In eukaryotes, there are 2 eukaryotic
elongation factors, eEF1 and eEF2(=EF-G).
  The eEF1 consist of two subunits, Eef1a(=EF
Tu)) and EEF1B (=EF-Ts)
 eEF2 causes translocation.
TERMINATION
- The release of a newly formed protein from the
ribosome.
 A stop signal is required for the termination.
 The codons UAG,UGA,UAA
 These codonos are not recognized by any
tRNAs but they are recognized by proteins
called RELEASE FACTORS.
 The release factor not only blocks the binding
of a new aminoacyl-tRNA but also affects the
activity of the peptidyl transferase so that the
bond between the carboxyl end of the
peptide and the tRNA is hydrolyzed.
 In prokaryotes, the RF-1 binds to the UAA and
UAG; RF-2 binds to UAA ang UGA, RF-3 does
not bind to any codon,
 In enukaryotes, one release factor binds to all
three stop codons.
THE GENETIC CODE FEATURES
1. Triplet code/Codon
- Means a sequence of three bases
- With 3 bases, there are 64 possible codons
2. Nonoverlapping
- No bases are shared between connective codons.
- The ribosome moves along the mRNA three bases
at a time.
3. Commaless
- No intervening bases exist between codons.
4. Degenerate
- More than one triplet can encode the same amino
acid.
- Each amino acid may have more than one codo,
- No codon can encode more than one amino acid.
*there are 61 codons for amino acids and 3 for
termination signals.
 The bases that are common to several codons
are the 1st and 2nd bases with more room for
variation in the third base which is called
WOBBLE BASE.
 Variation in the 3rd base would not change the
amino acid in that location
 A mutation in the DNA that does not lead to a
change in the amino acid translated is called
SILENT MUTATION.
 The second base is important for determining
the type of amino acid.
 * Second Base=U ; means that the amino acid
is hydrophobic.
 Codons sharing the same first letter often
code for amino acids that are product of one
another or precursors of one another.
 Anti-codon- a base pairs complementing to
the codons.
- - the sequence of 3 bases in tRNA that hydrogen-
bonds with the mRNA that specifies a given amino
acid.
Nucleases – enzyme that digest nucleic acid
through hydrolysis.
2 something of Nucleases
1. RNAses- targets the RNA
2. DNAses- targets the DNA
Apoptosis- cell death/ programmed cell death.
2 TYPES OF NUCLEASES
1. Exonucleases are enzymes that work
by cleaving nucleotides one at a time
from the end (exo) of a polynucleotide
chain. A hydrolyzing reaction that
breaks phosphodiester bonds at either
the 3' or the 5' end occurs.
three types of exonucleases
i. 5' to 3' exonuclease (Xrn1),
which is a
dependent decapping protein;
ii. 3' to 5' exonuclease, an
independent protein; and
iii. poly(A)-specific 3' to 5'
exonuclease.[1][2]
2. Endonuclease, which
cleaves phosphodiester bonds in the
middle (endo) of a polynucleotide
chain.
mRNA – brings the gene into the ribosome
-protected through capping/mGRNA
- nadadamaged yung message kapag
yung gitna ng sequence ang nasisira hindi yung
dulo.
 Loops are formed when there is inverted
repeats. The inverted repeat s are called-
PALINDSOME
tRNA- may dalang amino acid
- tRNA + amino acid = aminoacyl tRNA
- aminoacyl tRNA synthase connects tRNA to the
amino acid
TRNA + AMINO ACID + ATP TRNA-AA+ AMP+PPi
(inactive) (active)