MSE 693N Materials Science Technologies For Applications in Life Sciences

MSE 693N
Materials Science Technologies for

Applications in Life Sciences
Introduction to Life Sciences
MSE 693: Materials Science Technologies for Applications in Life Sciences Instructor: Vivek Verma
Families of Small Organic Molecules in Cells
B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
MSE 693N: Materials Science Technologies for Applications in Life Sciences Instructor: Vivek Verma
DNA
DNA
Introduction
• Structure and function of DNA
• DNA replication
• DNA repair
Introduction
• Gene
– The information containing element that determine
the characteristics of a species as a whole and of the
individual within it
– Genes are made of DNA
• DNA molecule consists of two complementary
chains of nucleotides
• The structure of DNA provides a mechanism for
heredity
Structure and Function of DNA
• Genes are made of DNA
– Adding purified DNA to a bacterium changed its
properties
– Change was faithfully passed on to subsequent
generations of bacteria
• DNA molecule consists of two complimentary
chains of nucleotides
– Four type of nucleotides
– Each chain is called DNA chain, or a DNA strand
– Two chains are held together by hydrogen bonds
Basic Monomeric Building Blocks
• Nucleotides ( DNA and RNA)
– Made up of a nitrogen-containing ring compound
linked to a five-carbon sugar and carry one or more
phosphate groups
Nucleotides
Nucleotides
• Sugar group in nucleotides
– Ribose: Ribonucleotides
– Deoxyribose: Deoxyribonucleotides
Nucleic Acids
• Deoxyribonycleic acids
– Adenine (A)
– Guanine (G)
– Cytosine (C)
– Thymine (T)
• Linear sequence of nucleotides in a DNA or an
RNA encodes the genetic information of the cell
• Only the base differs
Nucleotides
Nucleotides
Nucleosides
Nucleotides
• Short term carrier of chemical energy
– Adenosine triphosphate (ATP)
• Formed through oxidative breakdown of foodstuff
Nucleotides
• Serve as building blocks for the construction of
nucleic acids
– Nucleotide subunits are covalently linked by the
formation of phosphodiester bond between the
phosphate group attached to the sugar of one
nucleotide and a hydroxyl group of the sugar of the
next nucleotide
Nucleotides
http://amazingbeauty.org/nature/nucleotides-500x.jpg
Nucleic Acids
• Deoxyribonycleic acids
– Adenine (A)
– Guanine (G)
– Cytosine (C)
– Thymine (T)
• Linear sequence of nucleotides in a DNA or an
RNA encodes the genetic information of the cell
• Only the base differs
Nucleotide Vs Nucleic Acid
• A nucleotide (with a t) consists of a nitrogenous
base, a sugar, and a phosphate group. So, a
nucleotide is a "nucleoside mono-phosphate“
• Nucleoside: Base + Sugar
• Nucleotide: Base + Sugar + Phosphate
• A nucleic acid contains a chain of nucleotides
covalently linked together to form a sugar-
phosphate backbone with protruding
nitrogenous bases
• DNA strand has chemical polarity
– Hole and knob mechanism
– 3’ and 5’ ends
– Depends on the details of chemical linkages
• Double helix
– Two polynucleotide chains are held together by hydrogen-
bonding between bases on the different strands
– Bases inside helix and sugar phosphate backbone on the
outside
– A pairs with T
– G pairs with C
– Bulky two ring base (purine) pairs with single-ring base
(pyrimidine)
• Double helix
– Two polynucleotide chains are held together by hydrogen-
bonding between bases on the different strands
– Bases inside helix and sugar phosphate backbone on the
outside
– A pairs with T
– G pairs with C
• Double helix
– Complimentary base pairing
enables the base pairs to be
packed in the energetically
most favourable
arrangement
– Two strands of the helix are
antiparallel
– Each strand of a DNA
molecule contains a
sequence of nucleotides
that is exactly
complimentary to the
nucleotide sequence of its
partner strand
Structure Provides Mechanism for Heredity
• Genes carry biological information that must be
copied accurately and transmitted during cell
division
• A, T, G, C spell out biological messages in the
chemical structure of DNA
• Complete set of information in and organism’s DNA

is called its genome
DNA Replication
• Each strand serve as a template / mold for the
synthesis of a new complimentary strand
DNA Replication
DNA Replication
• Produces two complete double
helices from the original DNA
molecule
– Each new DNA helix is identical in
nucleotide sequence to the
parental DNA double helix
Replication Origins
• The position at which the DNA is first opened
are called replication origins
– Replication origin span ~100 base pairs
• Although the two strands are held strongly by
hydrogen bonds, however, breaking few
hydrogen bonds does not require lot of energy
• A-T base pair is held together by fewer hydrogen
bonds than is G-C base pair
Replication Origins
New DNA Synthesis and Replication Forks
New DNA Synthesis and Replication Forks
• Y-shaped junctions in DNA are called replication forks
• Replication machine move along these forks opening up the two
strands of double helix and using each strand as a template to
make a new daughter strand
– DNA replication is bidirectional
• DNA polymerase
– Enzyme that synthesizes new DNA using one of the old strands as a
template
– This enzyme catalyzes the addition of nucleotides to the 3’ end of a
growing DNA strand by the formation of a phosphodiester bond between
this end and the 5’ phosphate group of the incoming nucleotide
– Nucleotide enter the reaction as energy-rich nucleoside triphosphate
• Provides energy for the reaction
New DNA Synthesis
Replication Fork is Asymmetrical
• At the replication fork
– 3’ – to – 5’ in one strand and 5’ – to – 3’ in other
• Replication fork is therefore asymmetrical

• Appears one strand polymerized in 3’ – to – 5’ and
other 5’ – to – 3’
• DNA polymerase can catalyze the growth of DNA chain
in only one direction
– Can add new subunit only to 3’ end of the chain
• Backstitching manoeuvre
– The DNA strand whose 5’ must grow is made discontinuously,
in successive separate small pieces, with the DNA polymerase
working backward from the replication fork in the 5’- to- 3’
direction for each piece
– Lagging strand
• Leading strand
– Strand that is synthesized continuously
DNA Polymerase is Self-correcting
• DNA polymerase make one error per 107 nucleotide
replication
• A-T, G-C (most stable)
• G-T and C-A (less stable)
– 1 error per 107 is lethal to cell due to accumulation of
mistakes
• Proofreading
– Before DNA polymerase adds a nucleotide to a growing DNA
chain, it checks whether the previous nucleotide added is
correctly base-paired to the template strand
– Incorrect base-paired nucleotides are removed by cutting the
phosphodiester bond
• DNA polymerase posses both a 5’- to- 3’
polymerization activity and a 3’- to- 5’ nuclease
(nucleic-acid-degrading) activity
• Proofreading mechanism explains why DNA
polymerase synthasize DNA only in 5’- to- 3’
direction
Short Lengths of RNA act as Primers for DNA Synthesis
• Polymerase join a nucleotide only to a base-
paired nucleotide in a DNA double helix
– It cannot start a new DNA strand
• Primase (Enzyme)
– Synthesizes short length (~10 nucleotide long)
ribonucleic acid (RNA) using DNA strand as template
• Ribonucleic acid (RNA)
– Serve as primer for DNA synthesis
– RNA is base paired to the template strand and
provides a base-paired 3’ end as a starting point for
DNA polymerase
DNA Vs RNA
• RNA is made of ribonucleotide subunits
– Sugar is ribose, not deoxyribose
• RNA contains base uracil (U) instead of thymine
(T)
• U can pair with A so the RNA primer is
synthesized on the DNA strand by
complimentary base-pairing in exactly the same
way as DNA
• Primers in lagging Vs leading strand?
• Three enzymes are needed to make continuous strand
from separate pieces of DNA made on lagging strand
(Okazaki fragments)
• These enzymes remove RNA primer, replace with DNA
and join the DNA fragments together
• Nuclease
– Breaks apart RNA primer
• Repair polymerase (a DNA polymerase)
– Replaces RNA with DNA
• DNA ligase
– Joins the 5’-phospate end of one new DNA fragment to the 3’-
hydroxyl end of the next
Proteins at Replication Fork
Proteins at Replication Fork
• Helicase
– Protein that uses energy of ATP hydrolysis to speed along DNA, opening
the double helix as it moves
• Single-strand binding protein
– Clings to the single-stranded DNA exposed by the helicase and transiently
prevents it from re-forming base pairs
• Sliding clamp
– Keeps the DNA polymerase firmly attached to the DNA template
– On lagging strand the sliding clamp releases the polymerase from DNA
each time an Okazaki fragment is completed
– Forms a ring around the DNA helix and binds polymerase
– Allows polymerase to slide along a template strand as it synthesizes new
DNA
DNA Repair
http://images.fanpop.com/images/image_uploads/X-Men-x-men-58082_1024_768.jpg
DNA Repair
• Genetic changes over million of years
– Adapt to changing conditions
• Genetic changes detrimental in the short term
are detrimental to the organism
• DNA repair
– Mechanism for correcting the rare copying mistakes
made by the replication machinery and for repairing
the accidental damage that is continually occuring to
the DNA
DNA Repair
• Mutation
– Permanent changes in DNA
– Change in even single nucleotide pair can destroy an
organism if the change is in a vital position in the
DNA sequence
DNA Repair
• The mutation
responsible for the
disease sickle-cell
anaemia
DNA Repair
• Nucleotide changes in
somatic (non-germ) cells
can give rise to variant
cells
– Some grow in an
uncontrolled fashion at
the expense of other cells
– Extreme case: Cancer
• Cancer
– 30% death in North
America and Europe
– Due to gradual
accumulation of changes
in DNA sequence

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MSE 693N

Materials Science Technologies for

Introduction to Life Sciences

• Complete set of information in and organism’s DNA

• Replication fork is therefore asymmetrical

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