Download BIOCHEMISTRY Nucleic Acids

BIOCHEMISTRY
Nucleic Acids
BIOB111
CHEMISTRY & BIOCHEMISTRY
Session 17
Session Plan
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Types of Nucleic Acids
Nucleosides
Nucleotides
Primary Structure of
Nucleic Acids
• DNA Double Helix
• DNA Replication
• Types of RNA
Stoker 2014, Figure 23-2 p843
Nucleic Acids (NAs)
• Cells in a living organism are able to produce exact replicas of
themselves.
• Cells contain all the information needed to produce the complete
organism, they are part of.
• Nucleic acids store this information.
• Nucleic acids are found in the nucleus & are acidic.
• Nucleic acids are polymers of Nucleotides (the monomers).
2 Types of Nucleic Acids
• DNA – Deoxyribonucleic acid
• Found in the nucleus, stores & transfers genetic info.
• Passed from one cell to another during cell division.
• RNA – Ribonucleic acid
• Found in the nucleus & cytoplasm.
• Its primary function is to synthesize proteins.
• The hereditary information, required for protein synthesis, is
stored in the molecules of DNA in the nucleus & mitochondria
(mitochondrial DNA).
Chromosomes
• The DNA in the nucleus wraps
around proteins Histones, joining
them together into a fibre, forming
Chromosomes.
• Chromosome mass is about 15%
DNA & 85% proteins.
• Cells of different organisms have
different numbers of
chromosomes in cell nuclei.
• The nucleus of human somatic
cells contains 23 pairs of
chromosomes.
Tortora & Grabowski 2003, Figure 3.26, p.85
Nucleotides
• Nucleic acids (DNA & RNA) are polymers of Nucleotides.
• Nucleotides are the monomer building blocks of NAs, just like
monosaccharides are building blocks of polysaccharides &
AAs are building blocks of proteins.
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A Nucleotide has 3 components:
Nitrogen-Containing Base
Pentose Monosaccharide
Phosphate Group
N-containing Bases
• Heterocyclic amines
• Basic / alkaline (pH > 7)
• Derived from:
• Pyrimidine
• A mono-cyclic base with a ring of 6 atoms
(4C + 2N)
• Purine
• A bi-cyclic base with 2 fused rings
(a 5-membered & a 6-membered ring)
Pyrimidine & Purine Bases
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3 derivatives of Pyrimidine:
Cytosine ( C ) – DNA & RNA
Thymine ( T ) – DNA only
Uracil ( U ) – RNA only
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2 derivatives of Purine:
Adenine ( A )
Guanine (G )
Both are present in DNA & RNA
Stoker 2014, Figure 22-2 p790
Pentose Sugars
• Pentose monosaccharides
• Ribose – in RNA.
• Deoxyribose – in DNA. Deoxyribose is lacking O atom on C2’.
Phosphate Group
• Derived from from phosphoric acid (H3PO4).
• The cellular pH leads to full dissociation of the phosphoric acid,
producing a hydrogen phosphate ion (HPO42-).
• Instead of writing the full ionic version, Biochemistry commonly
uses an abbreviation to express the phosphate ion.
• Pi = Inorganic Phosphate or
Nucleoside
• Base + Sugar = NUCLEOSIDE
Nucleotide
• Nucleoside + Pi attached to C5’ position of pentose sugar via
phosphate-ester bond.
• Base + Sugar + Phosphate group = NUCLEOTIDE
Stoker 2014, Table 22-1 p792
Nucleic Acids
• Nucleic acids = polymers of Nucleotides
Stoker 2014, Figure 22-3 p793
Structure of Nucleic Acids
• Nucleic acids have primary & secondary structure (like proteins).
• Primary structure of both DNA & RNA = the sequence of
nucleotides.
• The primary structure has 2 parts:
• 1) Backbone composed of sugars & phosphate groups –
constant through entire molecule.
• 2) Nitrogen Bases as side chains – sequence of bases is
variable & distinguishes 1 molecule of NA from another one.
Stoker 2014, Figure 22-4 p794
Structure of Nucleic Acids
• Backbone = Phosphate + Sugar (different in DNA & RNA)
Primary Structure of Nucleic Acids
• The Sequence of Bases attached to the sugar units of the backbone
changes & determines the Primary Structure of NAs (like in proteins).
• Each non-terminal Pi of the backbone is bonded to 2 sugar molecules
via a 3’,5’-phosphodiester bond – one phosphoester bond to C5’ of one
sugar & another phosphoester bond to C3’ of the next sugar – both of
these bonds originate from one & the same Pi.
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The nucleotide chain has a direction.
One end – 5’ end – carries a free Pi attached to C5’ of the sugar.
The other end – 3’ end – has a free –OH on C3’ of the sugar.
By convention, the sequence of bases on a NA strand (DNA or RNA)
is read from the 5’ end to the 3’ end.
Stoker 2014, Figure 22-5 p795
Segment
of
DNA
Secondary Structure of DNA
• The DNA of very animal & plant has a unique base composition
but the relationships between the bases are always the same.
• %A=%T
• %C=%G
• Human DNA contains 30% each of A & T & 20% each of C & G.
• In 1953, Watson & Crick received the Nobel Price for ‘explaining’
the secondary structure of DNA as a Double Helix, which has
now been validated.
DNA Double Helix
• Double Helix = 2 strands of DNA in their primary structure,
wound up around each other like a spiral staircase.
• The sugar + Pi backbones of the 2 strands are like banisters of
the staircase.
• The bases of both strands extend inwards towards the bases of
the other strand & are bonded together via Hydrogen bonds.
• The 2 strands are anti-parallel = run in opposite directions –
one strand runs 5’→3’ & the other 3’→5’ direction.
Base Pairing
• Always 1 purine base (large) & 1 pyrimidine base (small) are
linked together via Hydrogen bonds between each other,
forming a pair of bases.
• The interior of the Double helix is small & 2 large purine bases
would not fit, whereas 2 small pyrimidine bases would be too far
apart to form Hydrogen bonds.
• When linking together via Hydrogen bonds, the bases form the
Secondary structure of DNA & are known as Complementary
bases.
Complementary Base Pairs
• In DNA
• A=T
• G≡C
• In RNA
• A=U
• G≡C
Stoker 2014, Figure 22-7 p798
Stoker 2014, Figure 22-8 p799
Hydrogen
Bonding
is more
favourable
between
A=T
G≡C
DNA Double Helix
• The Double Helix of DNA = 2 complementary DNA strands.
• If the sequence of bases in 1 strand is known, the
sequence of bases in the complementary strand can be
predicted.
• 5’ A – A – T – G – C – A – G – C – T 3’
• 3’ T – T – A – C – G – T – C – G – A 5’
DNA Replication
• The process by which a DNA molecule produces an exact
duplicate of itself.
• This process takes place in the nucleus when the parent DNA
divides into 2 daughter DNA molecules, identical to the parent
DNA molecule.
• Replication uses the same principle of base pairing as
encountered in the Secondary structure of DNA double helix.
DNA Replication
• Both of the 2 strands of DNA forming the double helix serve as
Templates for copying.
• The enzyme DNA-helicase unwinds the double helix & breaks
the hydrogen bonds between the bases (like undoing a zipper).
• Replication fork = the point at which the double helix is
unwinding & constantly moving.
• The 2 strands separate & each of them serves as a template for
the synthesis of a new complementary strand.
DNA Replication
• The bases of the separated strands are not connected by hydrogen
bonds anymore – they can now pair with free individual nucleotides
present in the nucleus (C≡G & A=T) one at a time & form new
hydrogen bonds with the old strand (= the template).
• The enzyme DNA-polymerase checks if the pairing of bases is correct
& joints the new bases to a new backbone (catalyzes formation of new
phosphodiester bonds between nucleotides).
• Each of the 2 daughter molecules of double-stranded DNA, formed
during replication, contains 1 strand from the original parent molecule
& 1 newly formed strand.
DNA Replication
Stoker 2014, Figure 22-9 p801
DNA Replication
• The 2 daughter DNA molecules are synthesized in different ways.
• DNA-polymerase can function only in 5’→3’ direction.
• However the 2 strands of parent DNA run in opposite directions,
therefore only one new strand can continuously grow in 5’→3’
direction = Leading strand.
• The other strand – Lagging strand – is synthesized in short
segments = Okazaki Fragments (= sequences of about 200
nucleotides with gaps between them), which are eventually
joined together by the enzyme DNA-ligase.
Stoker 2014, Figure 22-11 p803
DNA Replication
• Replication usually occurs at multiple sites within the DNA molecule &
proceeds in both directions.
• This multiple-site replication enables rapid DNA synthesis.
• Note:
• Anti-metabolites
• Anti-cancer drugs that interfere with DNA-replication in cancer cells,
causing them to die.
• Examples: 5-fluorouracil (5-FU), 6-mercaptopurine (6-MP), Floxuridine
Stoker 2014, Figure 22-12 p803
Summary of DNA
Replication
Stoker 2104, p804
Differences between DNA & RNA
DNA
RNA
Pentose Sugar
in backbone
Deoxyribose
Ribose
Complementary
Base Pairs
Strand
A=T
C≡G
Double helix
A=U
C≡G
Single strand
Size
Very large
Much smaller
(1-100 million nucleotides)
(75-few 1,000 nucleotides)
Stoker 2014, Figure 22-14 p807
RNA Molecule
• Even though the RNA molecule is a single strand it often folds
upon itself in certain parts and forms double-helical regions.
Secondary Structure of RNA
• RNA forms only a single strand,
which is the Primary structure.
• Secondary structure – portions of
the strand fold onto itself, forming
loops of double helical regions.
• Contains Uracil instead of Thymine.
Stoker 2014, Figure 22-19 p819
Types of RNA Molecules
• There are 5 types of RNA but only 3 types will be discussed:
• Messenger RNA
• Ribosomal RNA
• Transfer RNA
Messenger RNA – mRNA
• Carries the genetic information from the DNA in the
nucleus to the site of protein synthesis in the cytoplasm.
• Its nucleotide sequence is exactly complementary to that of
one of the DNA strands.
• It is not very stable, it is synthesized when needed & then
degraded.
• Size varies according to the length of the protein to be
synthesized.
• The average size is about 750 nucleotides.
• Constitutes about 5-10% of overall RNA mass.
Ribosomal RNA – rRNA
• Combines with specific proteins & forms ribosomes = the site of
protein synthesis.
• The composition of ribosomes:
• Proteins – 35%
• rRNA – 65%
• rRNA molecules are large.
• The most abundant RNA-type, constitutes about 75-80% of
overall RNA mass.
Stoker 2014, Figure 22-19 p819
Transfer RNA – tRNA
• Transport amino acids to the
site of protein synthesis
(= ribosomes).
• Contain 75-90 nucleotides.
• Are the smallest of the RNAs.
• There is at least one different
tRNA molecule for each of the
20 standard amino acids.
• The 3D-structure of tRNA is
an L-shape but by convention
it is represented in 2-D as a
clover leaf structure.
Readings & Resources
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Stoker, HS 2014, General, Organic and Biological Chemistry, 7th edn,
Brooks/Cole, Cengage Learning, Belmont, CA.
Stoker, HS 2004, General, Organic and Biological Chemistry, 3rd edn,
Houghton Mifflin, Boston, MA.
Timberlake, KC 2014, General, organic, and biological chemistry:
structures of life, 4th edn, Pearson, Boston, MA.
Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K & Walter P 2008,
Molecular biology of the cell, 5th edn, Garland Science, New York.
Berg, JM, Tymoczko, JL & Stryer, L 2012, Biochemistry, 7th edn, W.H.
Freeman, New York.
Dominiczak, MH 2007, Flesh and bones of metabolism, Elsevier Mosby,
Edinburgh.
Tortora, GJ & Derrickson, B 2014, Principles of Anatomy and Physiology,
14th edn, John Wiley & Sons, Hoboken, NJ.
Tortora, GJ & Grabowski, SR 2003, Principles of Anatomy and Physiology,
10th edn, John Wiley & Sons, New York, NY.