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 What is the direction of the synthesis of
added and the number of nucleotides?
phosphates.  All synthesis of nucleotide chains occurs
in the 5’ to 3’ direction.
SIDE NOTES:
 The direction is due to the nature of the
 When ATP is reduced it becomes
ADP + Pi
reaction of DNA synthesis.
 Pi= is an inorganic phosphate  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
dNTP – deoxy nucleotide triphosphate the formation of the new
 Used when producing new DNA phosphodiesther bond.
 SA FREE PHOSPHATE PWEDE KUMAPIT
NTP - nucleotide triphosphate KAYA SA 5’ KUMABIT
 Used when producing RNA  MAY FREE OH SA 3’ KAYA DUN KUMAPIT

N-glycosidic bond – the bond that connects Direction in Reading RNA

NITROGEN AND BASE.  5’ to 3’ = sense
 From left to right
Phosphoesther bond- bond that binds Direction in Reading DNA
PHOSPHATE TO SUGAR  3’ to 5’ = antisense

H-bonding- bond between water and ice Writing the Sequence

 Physical separation through  5’ AUG 3’
Melting.  If wala number, yung left side ay
automatic na 5’
Hydrophobic bonding- interaction between  Lahat naka sulat sa 5’ to 3’ order
carbons.  Do not write anti-sense without
sense. Dapat may contradiction.
SIDE NOTES:
 5’ A T G 3’
 Bonding;
- Pyramidine = 1N:1C  5’ dA dT dG 3’ ; D=deoxyribose
- Purine = 9N:1C
DNA
5’ 3’ sense
NUCLEOTIDES= BUILDING BLOCKS 3’ 5’ anti-sense
o NTPs : RNA
o dNTPs : DNA Rules in Writing Chargaff’s Rule

 Micromolecules (simple) : Macromolecule  A with T:

(complex)  the purine adenine (A) always pairs
 Monomers : Polymers with the pyrimidine thymine (T)
 Mononucleotide (single) : Polynucleotide  C with G:
(Chain)  the pyrimidine cytosine (C) always
pairs with the purine guanine (G)
Phosphodiesther bond- bond that connects
nucleotides.
  %GC – is a determinant of the melting  A complex of DNA polymerase, the
temperature to be used to denature the RNA primer, primase, and helicase
bond of the DNA at a replication fork.
 It is also the determinant of the  Replication fork- in DNA replication, the
stability of GC point at which the new DNA strands are
 Mas mabilis mag dikit si GC bond dahil triple formed.
bond ito. Mas madaming pagkakapitan, to bind
 SSB proteins- prevents the unwounded
kasi dapat may isang mag kabit na.
SSDNA
 Mas sticky din si GC kesa ki AT dahil triple bond
ito.  Replication: Initiation
 Priming means “annealing of
CENTRAL DOGMA 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.
1. Replication- DNA to DNA
 Replication: Termination
 Also called DNA synthesis
 DNA polymerase I and II- fixes the
2. Transcription- DNA to RNA
 RNA synthesis fragments in the Okazaki
3. Translation - RNA to Protein fragments
 Protein synthesis  DNA Polymerase III- connects the
4. Reverse transcription- RNA to DNA dNTP
 Made by the reverse transcriptase  Okazaki fragments- DNA anti-
enzyme sense na walang primers
 They are retroviruses  “polymerase” an enzyme that creates a
 Not all viruses are retroviruses but polymer
all retroviruses have a reverse
transcriptase. 2 types of DNA Polymerase

REPLICATION 1. DNA polymerase III- mabilis maglagay

pero may infidelity
 An enzyme (HELICASE) enters the DNA 2. DNA Polymerase I or II- adheres the
Chargaff’s rule.
and unwinds the double stranded DNA.
 DNA replication is error free because DNA
 Super coiling occurs when the DNA is
I and II repairs the error in replication.
unwind---- SUPER COILED DNA.  DNA replication is nonconservative if all of
 DNA feels tension that might lead to the daughter strands are new (no parent
breakage. strand)
 The TOPOISOMERASE relieves the  DNA replication is semi-conservative may
tension in the supercoiled DNA by parent strand
cutting a strand.  Messelson-Stahl- proved na semi-
 DNA ligase- the enzyme that links the conservative using P32 and N15.
separate stretches of DNA.
 Replication bubble- the space between (Replication from YT)
the separated strand cause by helicase.  DNA is a double helix strand
 Replisome- complex cells related to  Each strand is made up of four chemical
replication. 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  A 50s ribosomal subunit binds to the 30s
transcribe/elongate kasi paulit uli na initiation complex to produce the 70s
hanggan sa wala ng sense. initiation complex.

Termination Site- kinakabitan

ELONGATION
TRANSLATION - Peptide bond is formed between the amino acids
- The process repeat itself until the polypeptide
- Occurs in the ribosome chain is complete.
- Requires ribosomes, mRNA, tRNA, and protein The 3 binding sites
factors 1. P(peptidyl)site- binds a tRNA that
- mRNA and tRNA are responsible for the correct carries a peptide chain
order of amino acids in the growing protein chain. 2. A (aminoacyl) site- binds an incoming
- Before an amino acid is incorporated into a aminoacyl-tRNA
protein chain, it is activated by the process 3. E (exit) site- carries an uncharged tRNA
involving both tRNA and specific enzyme that is about to be released from the
AMINOACYL-tRNA synthases. ribosome.
- In this process, the amino acid is covalently  (1) Chain elongation begins with the
bonded to the tRNA forming aminoacyl-tRNA. addition of the second amino acid specified
by the mRNA to the 70s initiation complex.
INITIATION  The P site on the ribosome is the one
- The first aminoacyl-Trna is bound to the mRNA at initially occupied by the fmet-tRNA in the
the site that encodes the start of polypeptide 70s initiation complex.
synthesis.  The second aminoacyl-tRNA binds at the A
- In this, the Mrna and the ribosome are bound to site.
each other.  (2) GTP and three protein elongation
- The next aminoacyl-trna forms a complex with the factors, EF-P, EF-Tu, and EF-Ts
ribosome and with the Mrna. (temperature-untable and temperature
- The binding site is close to that of first aminoacyl- stabele) are require.
Trna.  EF-Tu guides the aminoacyl-tRNA into part
 The synthesis of polypeptide chains starts at of thee A site and align the anti-codpn with
rhe N-terminal end. (the chain grows from N- the mRNA codon.
terminal end.  EF-P is bound to the P site and E site and
 The start of polypeptide chain synthesis help catalyze the first peptide bond
requires the formation of an initiation formed.
complex.  EF-Ts is involved in regeneration of EF-Tu
 At least 8 components enter into the GTP.
formation of the initiation complex,including  (3) A peptide bond is then formed in a
mRNA, the 30s ribosomal subunits, fmet reaction catalyzed by peptidyl transferase,
tRNA, GTP, and 3 protein initiation factors which is a part of the 50s subunit.
called IF-1, IF-2,IF-3. It also prevents  The alpha-amino group of the amino acid in
premature binding of the 50s subunit/ the A site performs a nucleophilic attack on
 The IF-3 facilitates the binding of the mRNA to the carbonyl group of the amino acid linked
the 30s ribosomal subunit. Also prevent to the tRNA in the P site.
premature binding of the 50s subunit.  (4) Translocation takes places before
 IF-1 binds to IF-3 AND IF-2 and facilitates the another amino acid can be added to the
action of both. It also catalyzes the separation growing chain. In the process, the
of the 30s and the 50s ribosomal subunits uncharged tRNA moves from the P site to
being recycled for other round of translation. the E site. The Peptidyl-tRNA moves from
 The resulting combination of mRNA, the 30s the A site to the vacated P site.
ribosomal subunit and fmet-tRNA is the 30s  In eukaryotes, there is no elongation sites.
initiation complex.  In eukaryotes, there are 2 eukaryotic
elongation factors, eEF1 and eEF2(=EF-G).
  The eEF1 consist of two subunits, Eef1a(=EF  Codons sharing the same first letter often
Tu)) and EEF1B (=EF-Ts) code for amino acids that are product of one
 eEF2 causes translocation. another or precursors of one another.
 Anti-codon- a base pairs complementing to
TERMINATION the codons.
- The release of a newly formed protein from the - - the sequence of 3 bases in tRNA that hydrogen-
ribosome. bonds with the mRNA that specifies a given amino
 A stop signal is required for the termination. acid.
 The codons UAG,UGA,UAA
 These codonos are not recognized by any Nucleases – enzyme that digest nucleic acid
tRNAs but they are recognized by proteins through hydrolysis.
called RELEASE FACTORS. 2 something of Nucleases
 The release factor not only blocks the binding 1. RNAses- targets the RNA
of a new aminoacyl-tRNA but also affects the 2. DNAses- targets the DNA
activity of the peptidyl transferase so that the Apoptosis- cell death/ programmed cell death.
bond between the carboxyl end of the
peptide and the tRNA is hydrolyzed. 2 TYPES OF NUCLEASES
 In prokaryotes, the RF-1 binds to the UAA and 1. Exonucleases are enzymes that work
UAG; RF-2 binds to UAA ang UGA, RF-3 does by cleaving nucleotides one at a time
not bind to any codon, from the end (exo) of a polynucleotide
 In enukaryotes, one release factor binds to all chain. A hydrolyzing reaction that
three stop codons. breaks phosphodiester bonds at either
THE GENETIC CODE FEATURES the 3' or the 5' end occurs.
1. Triplet code/Codon three types of exonucleases
- Means a sequence of three bases i. 5' to 3' exonuclease (Xrn1),
- With 3 bases, there are 64 possible codons which is a
2. Nonoverlapping dependent decapping protein;
- No bases are shared between connective codons. ii. 3' to 5' exonuclease, an
independent protein; and
- The ribosome moves along the mRNA three bases
iii. poly(A)-specific 3' to 5'
at a time. exonuclease.[1][2]
3. Commaless 2. Endonuclease, which
- No intervening bases exist between codons. cleaves phosphodiester bonds in the
4. Degenerate middle (endo) of a polynucleotide
- More than one triplet can encode the same amino chain.
acid.
- Each amino acid may have more than one codo, mRNA – brings the gene into the ribosome
- No codon can encode more than one amino acid. -protected through capping/mGRNA
- nadadamaged yung message kapag
*there are 61 codons for amino acids and 3 for yung gitna ng sequence ang nasisira hindi yung
termination signals. dulo.
 Loops are formed when there is inverted
 The bases that are common to several codons repeats. The inverted repeat s are called-
are the 1st and 2nd bases with more room for PALINDSOME
variation in the third base which is called
WOBBLE BASE. tRNA- may dalang amino acid
 Variation in the 3rd base would not change the - tRNA + amino acid = aminoacyl tRNA
amino acid in that location - aminoacyl tRNA synthase connects tRNA to the
 A mutation in the DNA that does not lead to a amino acid
change in the amino acid translated is called
SILENT MUTATION. TRNA + AMINO ACID + ATP TRNA-AA+ AMP+PPi
 The second base is important for determining (inactive) (active)
the type of amino acid.
 * Second Base=U ; means that the amino acid
is hydrophobic.