Republic of the Philippines

EULOGIO “AMANG” RODRIGUEZ

INSTITUTE OF SCIENCE AND TECHNOLOGY
Nagtahan, Sampaloc, Manila

COLLEGE OF EDUCATION

PHYSICAL SCIENCE DEPARTMENT

BIOCHEMISTRY MIDTERM REPORT

NUCLEIC ACIDS:
STRUCTURE AND FUNCTIONS

Submitted by:
Pepito, Rahny S.
Guillermo, Roselyn M.
Epiz, Kristine Mae G.
Clavillas, Julie Ann F.
Carle, Cristhine Anne A.
Famodulan, Evangeline V.
BSE – Physical Science III

Submitted to:
Prof. Trinidad D. Macasil
Amino Acids – Structure and Peptide
Formation

The formula of an amino acid comprises, bound to a carbon (alpha carbon):

o a carboxyl group -COOH
o an amine group -NH2
o an atom of hydrogen –H
o A variable radical -R, which is the functional group (in red in the table) of the
amino acid.
Chemically speaking, an amino acid is a carboxylic acid which has an amine group
attached to it. The general linear formula of an amino acid is R-CH (NH2)-COOH.
The 20 common amino acids are grouped in classes according to their side chains.

Structural Formula
Amino acids with uncharged side chains
POLAR SIDE CHAINS NON POLAR SIDE CHAINS
Serine Glycine

Threonine Alanine

Tyrosine Cysteine [1]

Asparagine Valine
Glutamine Leucine

Isoleucine

Proline

Methionine

Phenylalanine

Tryptophan

Amino acids with charged side chains.

Charged side chains are POLAR.
ACIDIC SIDE CHAINS BASIC SIDE CHAINS
Aspartic Lysine
acid

Glutamic Arginine
acid

Histidine
(1)
Paired cysteines allow disulfide bonds to form in proteins: -CH2-S-S-CH2-

Nucleoside, Nucleotide, and Nucleic Acid

Formation

Pyrimidines and Purines

 These are the "nitrogen bases" that are a key structural unit within nucleic
acids.
 If you manipulate the 3D-JMOL images, you'll see that they are planar structures
(this is important for later).
 These are weak bases, similar to pyridine and are not very reactive
to electrophilic aromatic substitution.
 Note that it is derivatives of pyrimidine and purine that are important in the
nucleic acids.

Pyrimidine Uracil (U) Thymine (T) Cytosine (C)

Purine
Adenine (A) Guanine (G)

 The bases with the carbonyl groups (uracil, thymine, cytosine and guanine)
are not aromatic as drawn.
  However, if we consider the important resonance contributor from the amide
systems, then we can see their aromatic character as shown for cytosine below:

Nucleosides
 Nucleosides are N-glycosides in which
A schematic diagram of a
the pyrimidine or purine N is bonded to
generic nucleoside: two
the anomeric carbonin the
structural subunits: a nitrogen
carbohydrate by a β-N-glycosidic
base and a carbohydrate.
bond.
 In RNA, the carbohydrate is ribose (D-ribofuranose) while in DNA the
carbohydrate is deoxyribose (2-deoxy-D-ribofuranose) which lacks the hydroxyl
group at C2.

Ribose Deoxyribose
 In RNA the bases are adenine, cytosine guanine and uracil (i.e. A, C, G, U)
 In DNA the bases are adenine, cytosine, guanine and thymine (i.e. A, C, G, T)
 The base portion is cis to the -CH2OH group hence they are β-glycosides.
 The base is normally anti with respect carbohydrate so that the hydrogen
bonding C=O and N-H groups in the base are away from the furanose (as shown
below):
 pyrimidine base = adenine

carbohydrate = D-ribofuranose or ribose

9-β-D-ribofuranosyladenine
or
adenosine

Nucleotides
 Nucleotides are the 5'-phosphate
esters nucleosides.
 Phosphate esters are esters of
phosphoric acid, H3PO4
 Remember an ester has an alkyl
group, -OR, whereas an acid has
a hydroxyl group, -OH.
 Nucleotides contain three
structural subunits, a nitrogen
base, a carbohydrate and a
phosphate ester.
 DNA and RNA nucleotides are
different because of :
o different carbohydrate unit
o different bases

pyrimidine base = adenine

carbohydrate = ribose
phosphate esters = 1 unit
 Adenosine 5'-monophosphate (AMP)

Nucleic Acids
 Nucleic acids are polymers built of nucleotide monomers : hence they
are polynucleotides

 Note that the backbone consists of alternating carbohydrate and phosphate units,
coupled at the 3'- and 5'- positions.
 In ribonucleic acids, RNA, the carbohydrate is ribose with cytosine, uracil,
adenine and guanine bases.
 In deoxyribonucleic acids, DNA, the carbohydrate is deoxyribose with cytosine,
thymine, adenine and guanine bases.

Deoxyribose Nucleic Acid: DNA

 There 2 important biological processes involving DNA:
 o replication to produce a "copy" of the DNA
o protein biosynthesis via RNA
 DNA is based on the carbohydrate deoxyribose and the pyrimidine bases
cytosine and thymine and the purine bases adenine and guanine.
 The structure is the famous double helix discovered by Watson and Crick
(shared Nobel Prize1962).
 There are 3 forms of DNA : A-DNA (compact), B-DNA (common) and Z-
DNA (left hand double helix)
 B-DNA involves two strands of nucleic acids twisted around each other with a
right hand twist in an antiparallel fashion.
 Antiparallel means the sense of the individual strands is in opposite directions.
 The double helix is stabilized by H-bonding between the nitrogen bases in the
interior of the helix.
 Note how the bases in the helix are π-stacked parallel to each other 3.4
Angstroms apart.
 Careful inspection of the DNA helix shows a wide gap = the major groove, and a
narrow gap = the minor groove between the strands.