Download chp-5 nucleic acid

NUCLEIC
ACIDS
OBJECTIVES
Identify/ recognize nucleic acid
 Components in nucleic acid – monosaccharide,
nucleobases, phosphoric acid
 Differentiate - between 2 types of nucleic acids,
DNA and RNA
- between nucleotide and nucleoside
 Definition – nucleotide, nucleoside, DNA and
RNA

Nucleic Acids


Nucleic acid: a biopolymer containing three types of
monomer units
– a nitrogenous base (nucleobases), either purine or
pyrimidine
– a monosaccharide (aldopentose), either D-ribose or 2deoxy-D-ribose
– phosphoric acid/phospharyl group
Two types - RNA (Ribonucleic Acid)
- DNA (Deoxyribonucleic Acid)
Nucleobases
Nonpolar

Heterocylic compounds containing C, H, N, and O

Purine and pyrimidine
methyl
(C)
(T)
(A)
(U)
(G)
Monosaccharide/sugar
Polar
Only  anomer
present in nucleic
acid
2 type of aldopentoses found
- Ribose (RNA)
- 2-deoxyribose (DNA)
 Deoxyribose, derivative of ribose – lacks an oxygen
atom at C2

Nucleosides

Nucleoside:

Covalent linkage forms between
Lack phosphate group
Pyrimidine
Purine
Nucleotides


Nucleotide: a nucleoside in
which a molecule of phosphoric
acid/phosphoryl group is
esterified with an -OH of the
monosaccharide, at the 5’-OH
As constituents of cofactors,
Coenzyme A (CoA), flavin
adenine dinucleotide (FAD) &
nicotinamide adenine
dinucleotides (NAD)
Nucleobase, aldopentose
sugar and phosphoryl group
Phosphoric acid - polar
5’ = attach to
C5 of pentose
SUGAR?
NOMENCLATURE of
Nucleotide
Based on the nucleoside,
plus the phosphate group
Nucleotide Sequence
 Gene:
 Gene:
 The
nucleotide sequence is depending on
the bases (nucleobases) present
Nucleic Acid:
DNA
Nucleoside
1. Bases =
2. Aldopentose =
3. Phosphoryl group
Naming of nucleotide: if
Base adenine  Deoxyadenosine 5’
monophosphate
Biopolymer,
nucleotide
as monomer
RNA
1. Bases =
2. Aldopentose =
3. Phosphoryl group
Naming of nucleotide: if
Base adenine Adenosine
5’monophosphate
Nucleic Acid - DNA and RNA
 DNA
stands for deoxyribonucleic
acid. It is the genetic code molecule
for most organisms.
 RNA
stands for ribonucleic acid. RNA
molecules are involved in converting
the genetic information in DNA into
proteins. In retroviruses, RNA is the
genetic material.
NUCLEIC ACIDS ARE POLYMERS OF NUCLEOTIDES
DNA


DNA and RNA are polymers
whose monomer units are
nucleotides =
polynucleotides
Polynucleotide = DNA
and RNA
Hydrolysis – break bond
Condensation – form bond
Deoxyribonucleic acids,
DNA: a biopolymer that
consists of a backbone of
alternating units of 2deoxy-D-ribose and
phosphoryl group
–
the 3’-OH of one
nucleotide is joined to
the 5’ P of the next
nucleotide by a
phosphodiester bond
3’ 5’ -phosphodiester bond
DNA structure

Levels of structure
– 1° structure:
– 2° structure:
= double helix structure
– 3° structure:
– 4° structure:
DNA - 1° Structure

Primary Structure: the
sequence of bases along
the pentosephosphodiester backbone
of a DNA molecule
– base sequence is read
from the 5’ end to the
3’ end
– System of notation
single letter (A,G,C
and T) Pg 237, Campbell
and Farrel. READ!
5’ – G G C A T T G C G C - 3’
On the right
3’ 5’ -phosphodiester bond
Segment of DNA Chain
5’-end
N
O
C
C N
C N
C
H2N
N
-2
O3PO CH2
O
H
H
H
H
H
O
CH
N
C
guanine
O
C
O
N
O P O CH2
O
O
H
H
H
H
H
O
3’-5’
link
CH3
C
CH
thymine
NH2
C
N
CH
C
CH
O
N
O P O CH2
O
O
H
H
H
H
OH H
3’-end
• 5’ end –
phosphate group
is free
• 3’end – 3’ OH
in deoxyribose is
free
cytosine
DNA - 2° Structure

Secondary structure: the ordered
arrangement of nucleic acid
strands
 Double helix: a type of 2°
structure of DNA molecules in
which two antiparallel
polynucleotide strands are coiled
in a right-handed manner about
the same axis
• The chains run antiparallel and are
held together by hydrogen
bonding between complementary
base pairs: A=T, G=C.
DNA double helix
DNA structural elements
2 right-handed, helical, polynucleotide chains,
coiled around a common axis to form a double helix
 2 characteristic: Major groove and minor groove –
binding site for drug or polypeptide
 2 strands run in opposite direction
(antiparallel)-3’,5’-phosphodiester bridges run in
opposite direction
 1 base (purine) from single strand link to
1 base (pyrimidine) from other stand
(complimentary)
 Bases are perpendicular to helix axis
 Polarity and non-polarity regions
 Aqueous environment – polar, charged, covalent
backbone deoxyribose and phosphate groups
outside of the helix
 Hydrophobic purine and pyrimidine bases avoid
water by turning towards the inside of the structure

OH
P
T-A Base Pairing



Base pairing is complementary: A=T, GC
A major factor stabilizing the double helix is base
pairing by hydrogen bonding between T-A and
between C-G
T-A base pair comprised of 2 hydrogen bonds
Complementary base pairing
G-C Base Pair

G-C base pair comprised of 3 hydrogen bonds

G-C base pair comprised of 3 hydrogen bonds
Forms of DNA



B-DNA
– considered the
– a right-handed helix, inside diameter 11Å
– 10 base pairs per turn (34Å) of the helix
A-DNA
– a right-handed helix, but thicker than B-DNA
– 11 base pairs per turn of the helix
Z-DNA
• a left-handed double helix
• may play a role in gene expression
• Z-DNA occurs in nature, usually consists of
alternating purine-pyrimidine bases
• Methylated cytosine found also in Z-DNA
Structural features of A-, B-, and Z- DNA
Type
Helical senses
Diameter (Å)
Base pairs/turn
Major groove
Minor groove
Pg 294, Concepts
in Biochemistry.
3/e 2006 John
Wiley & Sons
A-DNA
right handed
~26
11
narrow/deep
wide/shallow
B-DNA
right handed
~20
10
wide/deep
narrow/deep
20 Å
Z-DNA
left handed
~18
12
Flat
narrow/deep
DNA - 3° Structure
Tertiary structure: the
three-dimensional
arrangement of all atoms
of a nucleic acid;
commonly referred to as
supercoiling
 Supercoiling- Further
coiling and twisting of
DNA helix.

DNA
DNA can forms tertiary structure by twist
into complex arrangement – supercoil
 Circular DNA:


Can be found in
Circular twisted into supercoiled
DNA - 3° Structure
 Supercoil - results of extra
twisting in the linear duplex form

DNA

Circular DNA: In microorganisms
(bacteriophages, bacteria)

Circular twisted into supercoiled
DNA - 3° Structure

In eukaryotes, the 3° structure
involves histone (protein)Chromatin: DNA molecules
wound around particles of
histones in a beadlike structure
PROPERTIES OF
SUPERCOIL
 Supercoiled
is
 Compact
 Play
a regulatory role in DNA replication
Bacteriophage :
DNA – threadlike
structure
Super DNA Coiled Topology
Double helix can be considered to a 2-stranded,
right handed coiled rope
 Can undergo positive/negative supercoiling

Counterclockwise
clockwise
DNA - 4° Structure
Four stranded form of DNA (quadruplex DNA)
 Role in regulating and stabilizing telomeres and in
regulation of gene expression
 Small molecules such as porphyrins and
anthraquinones present, to stabilize the structure

G-quadruplex
NUCLEIC
ACIDS
(2)
OBJECTIVES
 Denaturation
of DNA
 Identify/ recognize RNA
 Differentiate between DNA and RNA
 Differentiate between mRNA, tRNA, rRNA
DNA
Can be disrupted by
heat, acids, bases or
organic solvents
(double helix
denatured = unwinding
of the DNA double
helix)

In nature, the
unwinding of the DNA
double helix is the
important step in DNA
replication

Involves the nitrogenous bases

Denaturation
of
DNA
Denaturation: disruption of 2°
structure
– most commonly by heat
denaturation (melting- the heat
denaturation of DNA)
– as strands separate, absorbance
at 260 nm increases
– increase is called hyperchromicitythe wavelength of absorption does not change but
the amount of light absorbed increases
– midpoint of transition (melting)
curve = Tm
– the higher the % G-C, the higher
the Tm
– Renaturation/annealing is possible
on slow cooling
 Principal use in PCR
At the nitrogenous bases
Denaturation of DNA


Double helix unwinds when DNA is denatured
Can be re-formed with slow cooling and
annealing
RNA
 consist of long, unbranched chains of nucleotides
joined by phosphodiester bonds between the 3’-OH
of one pentose and the 5’-P of the next nucleotide
 the pentose unit is -D-ribose (it is 2-deoxy-Dribose in DNA)- the extra OH present in RNA makes
this nucleotide more susceptible to hydrolysis than
DNA.
 the pyrimidine bases are uracil and cytosine (they
are thymine and cytosine in DNA)
 RNA is single stranded (DNA is double stranded)
The bases sequences of all types of RNA are
determined by that of DNA
RNA

RNA molecules are classified according to
their structure and function
RNA structure
 Levels
of structure
– 1° structure: the order of bases on
the polynucleotide sequence;
complementary to the DNA template
– 2° structure: no specific 2°
arrangements, but RNA is not
completely lacking of regular
structure
– 3° structure:interaction between
DNA and proteins
RNA- 1° Structure
 Polymer
of nucleotide
 Involves single polynucleotide strand
RNA- 2° Structure
 Loop
back onto themselves to
fold into conformation containing
several different structural
elements:
1-hairpin turns
2-right-handed double helixes
3-internal loops
All classes of RNA synthesized as singlestranded molecules
3’OH
5’P

-
Hairpin turn
Loops in the single chain
Right-handed double helixes
- result of intrastrand folding
- Trigger by hairpin turn
- Antiparallel & stabilized in the same
direction as in DNA
- Hold by H bond & stacking interaction


-
Internal loops
Common in RNA
Structural features that disrupt the
formation of continuous double helix
regions
tRNA
 Transfer
tRNA:
RNA,
– the smallest kind of
the three RNAs
– a single-stranded
polynucleotide chain
between 73-94
nucleotide residues
– carries an amino
acid at its 3’ end
– intramolecular
hydrogen bonding
occurs in tRNA
Function: Involves in
synthesis of polypeptide,
to carry amino acid to
site of protein synthesis
Cloverleaf
structure
tRNA structure
Smallest types of RNA
 Highly structured
 All tRNAs contain between 74 and 93 nucleotides in
a single chain
 Structural features: hairpin turns, regions of double
helix and loops (non-hydrogen bonded portions)
 Carriers of specific amino acids used for protein
synthesis
 Reads the codon message on mRNA and
incorporates amino acid into the protein being
synthesized
 20 amino acid – 20 tRNA

tRNA –

o
3
structure
To produce tertiary structure, tRNA folds into an Lshaped conformation
The 3D structure of yeast tRNA
for phenylalanine
rRNA
Ribosomal RNA, rRNA: a ribonucleic acid
found in ribosomes, the site of protein
synthesis
– only a few types of rRNA exist in cells
– ribosomes (protein-synthesizing organelles) consist of
60 to 65% rRNA and 35 to 40% protein
– in both prokaryotes and eukaryotes, ribosomes
consist of two subunits, one larger than the
other
– analyzed by analytical ultracentrifugation
– particles characterized by sedimentation
coefficients, expressed in Svedberg units (S)
– Sequencing of 16S RNA (small subunit of
bacteria rRNA) - identification of bacteria
rRNA structure
 Secondary
& tertiary structures of rRNA
display same elements as tRNAs
Secondary structure for
E. coli 16S rRNA.
mRNA
 Messenger
Structure: Linear
polynucleotide
strand
RNA, mRNA:
a ribonucleic acid that carries coded
genetic information from DNA to
ribosomes for the synthesis of proteins
present in cells in relatively small amounts and
very short-lived (less abundant form of RNA)
– single stranded
– biosynthesis is directed by information
encoded on DNA
– Synthesize from DNA, the nucleotide sequence
in mRNA is similar with the 5’-3’ strand of
DNA, with the exception of U replacing T
–
5’-3’ DNA sequence is the same with RNA sequence (complementary to
3’-5’DNA) sequence
mRNA structure
Serves as a template for protein synthesis (Carries
the transient message for protein synthesis from
nuclear DNA to the ribosomes)
 Move the information contained in DNA to the
translation machinery
 Each molecule carries the instruction for each gene
(codes for one type of polypeptide product)

5’ – G G C A U U G C G C - 3’
 Initiation
-
-
codon
codes for the 1st amino acid in all polypeptide
sequences
N-formyl methionine in prokaryotes and
methionine in eukaryotes
 Termination
-
-
codon
do not code for an amino acid & thus signal
the end of protein synthesis
Also called stop codon or nonsense codon