Download Lecture 4

Lecture 4
Cell Biology ٢٢٢
١
NUCLEIC ACIDS
1- They are the most important macromolecules in the cells of all
microorganisms
2- They are carriers of genetic information
3-There have Two forms (RNA and DNA)
Composition and structure of nucleic acids
Nucleic acid molecule is a polymers of monomeric unit called
nucleotides. These nucleotide monomer unit
are joined by the formation of phosphodiester bond
Cell Biology ٢٢٢
٢
NUCLEIC ACIDS
Phosphodiester Bond
Phosphate linkage that connects two sugars by ester linkage
Diester bond is one which involves two ester bond
Phosphodiester bond will be formed between any two adjacent nucleotides
(bet. The 5’ phosphate of one nucleotide and the 3’ hydroxyl of another)
Cell Biology ٢٢٢
٣
Nucleotide
Nucleotides composed of:
- Pentose (C5) sugar, either ribose (RNA) or deoxyribose (DNA)
-Nitrogen bases which belong to two chemical classes
- Purine bases (adenine and guanine): contain two fused heterocyclic rings
Pyrimidine bases (thymine, cytosine, and uracil): contain a single six-membered
heterocyclic ring
-Phosphate group
Cell Biology ٢٢٢
٤
Nucleotide
„
„
Nucleoside: nitrogen base bonded to its C5 sugar
Nucleotide: nitrogen base attached to C5 sugar by glycosidic
linkage and bonded to a phosphate
‰ Major components of nucleic acids
‰ Key forms of chemical energy (e.g., ATP)
‰ Carriers of sugars in biosynthesis of polysaccharides
‰ Regulatory molecules for certain enzymes or metabolic events
Cell Biology ٢٢٢
٥
-
O
-
O
P
O
-
O
PO4
Deoxyribose
DNA
Nucleotid
e
Pentose
Sugar
RNA
Ribose
Nucleoside
Nitrogen base
(T)
Pyrimidines
(U)
Purines
(G)
(A)
(C)
Cell Biology ٢٢٢
٦
Primary Structure of nucleic acid
„
Is a Sequence of nucleotides in a DNA or RNA molecule
- oligonucleotide: small polymer contains only a few nucleotides
- polynucleotide: very large polymer contains thousand or
millions of nucleotides
- the polynucleotide chain (strand) has a sense of direction with
one end of the chain terminating in a 5’ phosphate group and
the other in a 3’ hydroxyl group of growing Chain
- the sequence of bases in RNA and DNA is written in the 5’ to 3’
direction
- Two polynucleotide strands wrap around each other to form a
DNA double helix
- The two strands are associated because particular bases always
hydrogen bond to one another A pairs with T, and C pairs with
G, producing base pairs
- RNA is usually a single polynucleotide strand
Cell Biology ٢٢٢
٧
Base –pairing of nitrogen bases
Cell Biology ٢٢٢
٨
Types of nucleic acid
„
„
Base
pair
DNA
Double-stranded
molecules
consisting of two
complementary
polynucleotide
chains running in
opposite direction
‰
Cell Biology ٢٢٢
Strands held
together by
hydrogen bonds
٩
Types of nucleic acid
„
Cell Biology ٢٢٢
RNA
‰ Typically single-stranded
‰ Demonstrates secondary
structure (folding back
upon itself)
‰ Four classes: mRNAs,
tRNAs, rRNAs, and small
RNAs
١٠
Gene
„
A particular nucleotide
sequence that can instruct the
formation of a polypeptide is
called a gene
- Most DNA molecules consist
of millions of base pairs and,
consequently, many genes
- These genes, many of which
are unique to the species,
determine the structure of
proteins and, thus, life’s
structures and functions
Cell Biology ٢٢٢
١١
Enzymes
„
„
„
„
„
„
„
Enzymes are specialized macromolecules that speed up
chemical reactions in cells
They are characterized by the following fundamental properties:
1- They are Catalytic proteins( biological catalysts) that
accelerate the rate of biological reactions by reducing the
activation energy (energy required to reach the substrate to the
transition state (high energy state)
2- enzymes can be denatured and precipitated with salts,
solvents and other reagents.
3- Many enzymes require the presence of other compounds cofactors - before their catalytic activity can be exerted.
This entire active complex is referred to as the holoenzyme; i.e.,
apoenzyme (protein portion) plus the cofactor (coenzyme,
prosthetic group or metal-ion-activator) is called the
holoenzyme.
Cell Biology ٢٢٢
١٢
Apoenzyme + Cofactor = Holoenzyme
Cell Biology ٢٢٢
١٣
Enzymes
4- increase the rate of chemical reaction without themselves being
consuming or permanently altered by the reaction
5- increase reaction rates without altering the chemical equilibrium
between reactants and products Therefore : the enzyme must
accelerate both forward and reverse reaction equally
6- Enzymes are usually very specific as to which reactions they
catalyze and the substrates that are involved in these
reactions.
Cofactors and coenzymes
„
some enzymes do not need any additional components to
show full activity.
„
others require non-protein molecules called cofactors to be
bound for activity
Cell Biology ٢٢٢
١٤
Cofactors
„
„
Cofactors can be either:
- inorganic (e.g., metal ions and iron-sulfur clusters)
- organic compounds (e.g., flavin and heme). which can be
either:
- prosthetic groups, which are tightly bound to an enzyme
and play critical function roles (e.g : heme, Zinc)
- coenzymes, which are released from the enzyme's active
site during the reaction, they called coenzymes because they
work together with enzymes to enhance reaction rate.
Coenzymes include NADH, NADPH and adenosine triphosphate.
These molecules transfer chemical groups between enzymes.
Cell Biology ٢٢٢
١٥
Coenzymes
„
„
„
Coenzymes are small organic molecules that transport
chemical groups from one enzyme to another.
The chemical groups carried include the hydride ion (H-)
carried by NAD or NADP+, the acetyl group carried by
coenzyme A
Coenzymes are usually regenerated and their
concentrations maintained at a steady level inside the
cell
Cell Biology ٢٢٢
١٦
Enzyme classification
„
„
„
„
„
„
EC 1 Oxidoreductases: catalyze oxidation/reduction
reactions
EC 2 Transferases: transfer a functional group (e.g. a
methyl or phosphate group)
EC 3 Hydrolases: catalyze the hydrolysis of various
bonds
EC 4 Lyases: cleave various bonds by means other
than hydrolysis and oxidation
EC 5 Isomerases: catalyze isomerization changes
within a single molecule
EC 6 Ligases: join two molecules with covalent bonds
Cell Biology ٢٢٢
١٧
many factors influence enzyme
function
„
pH Enzymes in your stomach may prefer an acidic environment
with a low pH while enzymes elsewhere may not.
„
higher temperatures speed reactions -- to a point. Above 104
degrees fahreinheit, enzymes become denatured and can no
longer catalyze reactions.
„
Higher concentrations of substrate also speed reactions until
the solution reaches a saturation point .Past that point, the
addition of substrate will not affect the velocity of the reaction.
„
Irreversible inhibition occurs when the inhibitor added
denatures or destroys the enzyme.
Cell Biology ٢٢٢
١٨
Remember
„
„
„
Monomers
‰ Small molecules that are the building blocks of larger
molecules
‰ Chemical elements bond in different combinations to
form monomers
Polymers
‰ Larger molecules composed of bonded monomers
Macromolecules
‰ Larger molecules composed of covalently bonded
polymers
Cell Biology ٢٢٢
١٩
References
„
Gupta, K, (2008) Cell and Molecular biology (Third edition.
Rastogi publication, Meerut, New Delhi. ISBN: 61-7133-617-8.
„
Lodish, H., Berk, A., Zipursky, S. L., Matsudaire, P., Baltimore,
D. and Darnell, J. (1999) Molecular cell biology (Fourth edition).
Freeman company. ISBN: 0-7167-3136-3.
„
Cooper, G.M.and Hausman, R.E. (2004) The cell a molecular
approach (Third edition). Sinauer publication
„
Campbell, Reece, Taylor , Simon, Dickey . BIOLOGY – Concepts
& Connections, Sixth Edition. 2009
Cell Biology ٢٢٢
٢٠