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BSci 121M.


DNA Structure, Replication and Manipulation:

Eukaryote- cell with a true nucleus (DNA enclosed in a membranous envelope) in
which cell division takes place by mitosis or meiosis.
Prokaryote- An organism that lacks a nucleus; prokaryotic cells divide by fission.
Genome- commonly used to refer to one complete haploid set of chromosomes such as
that found in a sperm or egg.
The units of length of nucleic acids in which genome sizes are typically expressed are as
Kilobase (Kb)- 103 nucleotide subunits
Megabase (Mb)- 106 nucleotide subunits
Gigabase (Gb)- 109 nucleotide subunits
Viral genomes- typically range between 100 -1000 Kb; Bacterial genomes- range
between 1- 10 Mb
Eukaryotic genomes- typically range between 100 to 1000 Mb (The smallest
eukaryotic genomes are about 10 Mb.)
DNA is a polymer- a large molecule that contains repeating units.
- Composed of 2 deoxyribose, Phosphoric acid and the four nitrogencontaining bases.
- Purines: Adenine(A) & Guanine (G) with a Double- ring structure; and
Pyrimidines: Thymine(T) & Cytosine (C) with a Single- ring structure.
- Each base is chemically linked to one molecule of the sugar
Deoxyribose forming a compound called Nucleoside. When a
phosphate group is also attached to the sugar, the Nucleoside
becomes a Nucleotide.
- In nucleic acids, the nucleotides are joined to form a Polynucleotide
chain in which the phosphate attached to the 5 carbon of one sugar is
linked to the hydroxyl group attached to the 3 carbon of the next
sugar in line.
Phosphodiester bonds- Chemical bonds by which the sugar
components of adjacent nucleotides are linked through the phosphate
groups. The 5 3 5 3 orientation of these linkages continues
throughout the chain, which typically consists of millions of
nucleotides. The terminal groups of each polynucleotide chain are a 5phosphate (5-P) group at one end (tail of the broad arrow) and a 3hydroxyl (3-OH) group at the other ( head of the arrow)
For encoding genetic information, the central feature of DNA structure is the A-T and the
G-C pairing between the bases. The principles of base pairing explain 2 generalizations
about the relative amounts of the bases found in all double stranded DNA:
1.) Number of adenine bases (A) equals number of thymine bases (T), so (A) = (T)
2.) Number of guanine bases (G) equals number of cytosine (C ) bases, so (G) = (C )

Replication - Each strand of the double helix serves as a template for the synthesis
of a new
strand (semiconservative replication). As each new strand is formed, it is
hydrogen- bonded
to its parental template. As replication proceeds, the parental double helix
unwinds and then rewinds again into two new double helices, each of which
contains one originally parental strand and one newly formed daughter strand.
-Requires only that the hydrogen bonds joining the bases break to allow
separation of the chains and that appropriate free nucleotides of the four types
pair with the newly accessible bases in each strand. In practice, it includes
complex geometric processes that require a variety of enzymes: (page 202)
1. Topoisomerase Enzymes capable of catalyzing breakage and rejoining of
DNA strands.
2. Gyrase (Topoisomerase II) -a type of Topoisomerase that cleaves and rejoins
both strands of a DNA duplex to relieve torsional stress/ mechanical stress of
3. Helicase- Enzyme that hydrolyzes ATP thus unwinding the double helix to
separate the
parental strands.
4. Single- stranded DNA binding protein (SSB)- binds single- stranded DNA
tightly and
cooperatively thus offers stability of single strands after coming together
spontaneously, and
providing a good template for replication.
5. RNA primase- Initiates new- strand synthesis.
Primer RNA- very short, usually 2-5 nucleotides; a short stretch of RNA which
provides Free 3OH unto which the DNA polymerase can add deoxynucleotides.
6.DNA polymerase- catalyzes the synthesis of DNA from deoxynucleoside 5triphosphates, using a template strand. Forms the sugar- phosphate bond
(phosphodiester bond) between adjacent nucleotides in a new DNA acid chain.
Synthesis proceeds by the elongation of primer chains, always in the 5 to 3
7. DNA ligase- joins Okazaki fragments (short DNA strands produced during
discontinuous replication) on the lagging strand.
8. RNA polymerase- catalyzes RNA synthesis. A DNA strand is used as a
template to form a complementary strand in which the bases in the DNA are
paired with those in the RNA. Does not need a primer for RNA synthesis.
9. Leading strand- The DNA strand whose complement is synthesized as a
continuous unit.

10.Lagging strand- The DNA strand whose complement is synthesized in short

(Okazaki) fragments that are ultimately joined together by DNA ligase.

Molecular Mechanisms of Mutation:

Mutations- any heritable change in the genetic material.
Major types of Mutations:
1. Spontaneous- Occurs in absence of any known mutagens.
2. Induced- Formed under the influence of a chemical mutagen or radiation.
3. Somatic- Occurs in nonreproductive cells (somatic cells).
4. Germ- line- Occurs in reproductive cells.
5. Conditional - Expressed in mutant phenotypes only under certain
restrictive environmental conditions ( ex, high temperature), but results in a
wildtype phenotype under other (permissive) conditions.
6. Unconditional- Expressed in mutant phenotypes both under permissive
conditions as well as restrictive conditions.
7. Loss of function (Null mutation)- Mutation that eliminates gene function .
8. Hypomorphic- Results when the wildtype gene function is underexpressed
or only partially active.
9. Hypermorphic- Results when the wildtype gene function is overactive or
10. Gain of function- Results from a gene which is overexpressed or
inappropriately expressed.
11. Base substitution- Incorporation of an incorrect base into a DNA duplex.
12. Transition- Results from the substitution of one Purine for another Purine,
or a Pyrimidine for another Pyrimidine.
13. Transversion- Results from the substitution of a Pyrimidine for a Purine, or
a Purine for a Pyrimidine
14. Insertion- One or more extra nucleotides present in a DNA sequence.
15. Deletion- Loss of a segment of the genetic material from a chromosome.
16. Synonymous (silent)- a change in the coding region that alters the
sequence of a codon without changing the amino acid that is specified.
17. Missense (nonsynonymous)- An alteration in a coding sequence of DNA
that results
in an amino acid replacement in the polypeptide.
18. Nonsense (termination)- characterized by changes in the codon specifying
an amino
acid into a stop codon ( UAA, UAG or UGA), resulting in premature
polypeptide chain

termination. Also called a chain termination mutation.

19. Frameshift- caused by the insertion or deletion of one or more nucleotide
pairs in a
gene, resulting in a shift in the reading frame of all codons following the
mutational site.

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