i want 20  multiple choice questions with their model answer below each question that covers various aspects of all the following information :
Lecture objectives
1. Recognize linear structure of DNA with respect to polarity, sugar phosphate backbone and purine and pyrimidine base.
2. 3. 4.
Describe base complementarity.
Describe the DNA double helix (Watson and Crick model). Describe factors affecting the stability of the DNA double helix.
5. Explain denaturation/renaturation and how CG content affect that. 6. Compare between A,B,Z forms of DNA. 7.
Describe the organization & 3ry structure of DNA. 8. Describe the nucleosome structure. 9. Compare gene, genome and chromosome.NUCLEIC ACIDS
Nucleic acids are required for the storage and expression
of genetic information.
Includes
DNA: Deoxyribonucleic acid
RNA: Ribonucleic acidDNA (Deoxyribonucleic acid):
 Site : 1- Mostly found in the nucleus in
chromosomes and small amount is found in the
mitochondria in Eukaryotic cells.
2- Prokaryotic cells, which lack nuclei, have a single
chromosome but may also contain non-
chromosomal DNA in the form of plasmids.
3- The chloroplasts of plants.
 DNA carries all the genetic information of the
individual
- Nuclear DNA: carries the genetic information
in the chromosomes that encode functional
proteins or functional RNA.Mitochondrial DNA:
• closed, circular, dsDNA molecules
• contains:
1- genes encode proteins of the electron transport chain (13 protein).
2- genes encoding 22 transfer RNA (tRNA) and 2 ribosomal RNA (rRNA).• Functions of DNA:
1- Store genetic information and transmit it to next
cell generations. (DNA must be to replicated
precisely each time the cell divides, in such a way
that each daughter cell acquires the same amount
of genetic material).
2- Control selective protein synthesis inside each
cells to be able to perform its physiologic functions.
“Differential gene expression”Central Dogma of Biology Structure:
• DNA is formed of two chains (strands).
• The 2 strands wind around each other
forming a double helix (Watson and crick
model).Nucleotides structure
The nucleotide has three characteristic components
Nitrogenous base
Pentose sugar
PhosphateNitrogenous Bases
Nitrogenous base: derivatives of Purines and pyrimidines
DNA and RNA contain the same purine bases and the pyrimidine base
Cytosine But Thymine found only in DNA and Uracil found only in RNA
(A)
(G)
(C)
(U)
(T)Pentoses of Nucleotides
• D-ribose (in RNA)
• 2-deoxy-D-ribose (in
DNA)
• The difference - 2'-OH
vs 2‘-H
• This difference affects
secondary structure and
stability• Linking of the base to the sugar (at the 1’
carbon of the sugar) is called nucleoside
Figure: β-Glycosidiclinkage in a deoxyribonucleoside.Linking of nucleoside to phosphate group ( at
the 5’ carbon of the sugar) is called nucleotideDNA PRIMARY STRUCTURE
• Nucleotides are linked in each DNA strand
through Phosphodiester bond between the sugars
and phosphatesFigure: Formation of a phosphodiester bond between 2 successive nucleotides
Ester bonds are strong covalent bonds formed by the reaction of an acid and alcohol(- OH).
Phosphodiester bond is a group of strong covalent bonds between a phosphate group and two
5-carbon ring carbohydrates (pentoses) over two ester bonds.Fig.: A polynucleotide chain of DNA
Each DNA strand (chain) has 2 ends:
1. The 5’ end has a free phosphate group.
2. The 3’ end has a free hydroxyl group.
Note the direction of DNA replication is in a 5’ -3’ direction.DNA SECONDARY STRUCTURE
• The hydrophilic (polar) deoxyribose phosphate backbone
of each chain is on the outside of the DNA molecule,
whereas the hydrophobic (nonpolar bases) are stacked
inside perpendicular to the axis of the helix.
• The 2 DNA strands wind around each other in antiparallel
manner, one strand is oriented in the 5′ 3′ direction and
the other in the 3′ 5′ direction.
• The double helix made by winding of the 2 DNA strands
around each other, is stabilized by hydrogen bonding
between the bases of the 2 strands and by the
hydrophobic interactions between the stacked bases.• Base pairing rule: Thymine always pair with
adenine and cytosine always pair with guanine.
So one polynucleotide chain is of the double
helix is always complementary to the other.
• Thymine and adenine bases are connected by 2
hydrogen bonds , while cytosine and guanine
are connected by 3 hydrogen bonds. This makes
G-C base pairs more stable than A-T base pairs• The spatial relationship between the two strands
in the helix creates a major (wide) groove and a
minor (narrow) groove. These grooves provide
access for the binding of regulatory proteins to
their specific recognition sequences along the
DNA chain.Structural forms
• Polymorphism of DNAParameters A -DNA Direction of helical rotation Residues per turn of helix Right 11 Rotation of helix per residue (in degrees) 33 Base tilt relative to helix axis (in degrees) 20 B-DNA Right 10 36 6 Major groove Minor groove
Orientation of N-glycosidic Bond
Comments narrow and deep wide and deep Z-DNA Left 12 base pairs -30 7 Flat wide and shallow narrow and deep narrow and deep Anti Anti
most prevalent within cells
Anti for Pyrimidine, Syn for Purine
occurs in stretches of alternating purinepyrimidine base pairs for example, poly GCDNA TERTIARY STRUCTURE
• Double stranded linear: Eukaryotic nuclear
chromosome).
• Double stranded circular: Mitochondrial,
plasmid, viral and chloroplast).
• Single stranded circular DNA: (small viruses).DNA DENATURATION (MELTING)
Def.: Separation of the 2 DNA strands by disruption of
H- bonds between the 2 DNA strands.
Denaturation factors: 1- Change in pH: Change the pH
ionization of base disruption of H-bonds.
2- Heating (thermal denaturation): - Heating will
disrupt hydrogen bonds.
The base composition of DNA varies widely from
molecule to molecule, and even within different
regions of the same molecule. So regions that have
predominantly A-T base-pair will be less stable than
those rich in G-C base-pairs.Melting temperature (TM):
Temperature at which 50% of the DNA molecule exist
as single strands. N.B.: The TM differ according to base
composition of the DNA molecule, with high TM value
in DNA molecule rich in C-G base pair.
DNA denaturation can be monitored by measuring its
absorbance at 260 nm. Single stranded DNA has a
higher relative absorbance at this wave length.
Complementary DNA strands
separated
by
denaturation can reform double helix if treated well
(cooling). This is called renaturationDNA organization• A typical (diploid) human somatic cell contains
46 chromosomes, whose total DNA is ~2 m
long! It is difficult to imagine how such a large
amount of genetic material can be effectively
packaged into a volume the size of a cell
nucleus so that it can be efficiently replicated
and its genetic information expressed.
• To do so requires the interaction of DNA with a
large number of proteins, each of which
performs a specific function in the ordered
packaging of these long molecules of DNA.The chromatin in eukaryotic cells consists of:
Nuclear DNA
bound to
Histones proteins
&
smaller amounts of non histone proteins
(Enzymes involved in DNA replication and
transcription)
&
Small amount of RNA
(snRNA)HISTONES
-Are basic proteins (having positive charges as a result of
their high content of lysine and arginine.), so they form ionic
bonds with the negatively charged DNA so their
binding is facilitated.
- 5 types: H1, H2A, H2B, H3, H4.
- Functions:
• They help condensation of the DNA into more
compact chromosomes.
• Protect the DNA from digestion by exonucleases.
• Modified histones: Has an important role in changing
the structure of chromatin and chromatin function
e.g. acetylation of H3 and H4 is associated with
activation or inactivation of gene expression
(epigenetics).Nucleosome structureNucleosome consists of
1- DNA core:
Formed of supercoiled DNA surrounding
histone octamer (2 molecules of each of H2A,
H2B, H3, H4).
2- Linking region:
It joins one nucleosome core to the next
Formed of ~50 bp of DNA and 1 molecule of
histone (H1) which protects the linker DNA
from digestion by exonucleasesChromatin is built from
repeating nucleosomes
units
If the chromatin is placed in low salt buffer
and viewed with E/M (i.e If the chromatin
is pulled into a linear strucrure)→→→→ It
resembles a string of beads( with the
beads representing nucleosome cores and
the string representing the DNA linker)Compaction of chromatin
 Condensation of the nucleosomes with histone H1 in the
centre form the 10 nm fibril which represents 7 fold
shortening of the linear ß- form DNA.
 Supercoiling of the 10 nm fibril with 6-7 nucleosomes per
turn form the 30 nm fiber which represents 50 fold
shortening of the length of DNA.
 Supercoiling of the 30 nm fiber into superloops (700 nm in
diameter).
 Each 6 superloops attached to a protein scaffold form a
rosette.
 Each 30 rosette form one coil.
 Each 10 coils form one chromatid.Chromosomes 2 identical sister chromatids attached at the centromere →→ one chromosome (in the metaphase)
The centromere - is rich in A=T and is about 130 bp long. - is connected to specific proteins to form a complex known as kinetochore which is connected to mitotic spindle. This complex is essential
structure for segregation during mitosis. • chromosomal