Lecture 3 (recording3)
Not dynamic types of likages:
* phospho-diestro bonds
-Linkages b/w individual nucleic acids in DNA chain.
-covalent linkages, very hard to break apart. Provide stability.
* Peptide bonds
-linkages of individual amino acids
Interactions b/c Macromolecule (DNA, RNA, Proteins)
-It is dynamic (there are more than one forces)
- Electrostatic attractions (useful interior a protein)
- Hydrogen bonds ( very important)
- van der Waals attractions ( results of dipole b/w closely located macromolecules)
- Hydrophobic force (combination of hydrophilic, the aqueous environment of a cell,
coming close to hydrophobic component in the cell
(ex) *amino acids are hydrophobic-so it hides away from water, becoming the interior
part of folding protein
*Nitrogenous bases are very hydrophobic-so they interiorize inside the double helix
structure. And also interact vertically, so pull themselves more
tightly in double helix structure.
DNA and RNA are the linear chain with polarities (the 5’ end and 3’ end structure (specific
*5’ end: represents the free-phosphate group (compose of Phosphate group (-PO4)).
Found on the first nucleotide of a chain that is being formed.
*3’ end: refers to the free-hydroxyl group (composed of Hydroxyl group (OH)). Found on
the last (end) of a chain that is being formed.
5’, 3’ polarities structure occurs in DNA, RNA and
also in Protein( 5’ end: amine group& 3’ end: carboxyl group)
-DNA is synthesized from deoxyribonucleoside triphosphates, otherwise known as: dNTP’s
-RNA is synthesized from ribonucleoside triphosphates, or: NTP’s
-Nucleotides are linked by: phosphodiester bonds Ppt8
*The strands in a double delix are antiparallel sturucture (one strand is 5’→ 3’ while it’s partner is
*the base parings
1. Holds the DNA double helix together
A – T (2 H-bonds)
G – C (3 H-bonds)
3 forces that keeps DNA together
1. Hydrogen bonds
(A-T, G-C, in linear direction)
2. Van der Waals Attractions
(Allows helix to get tighter)
3. Hydrophobic interactions
(Nitrogenous bases also hold DNA to be
tighter spiral by the vertical interaction)
-Helix is energetically favorable configuration
-Sugar-phosphate backbones are hydrophyllic.
-Minor/major grooves: distance b/w phosphate backbone at each case
-Major groove: has functional significant, provides an access to proteins (enzymes)since it is wide
enough compare to minor groove. So proteins can interact with specific bases sequences inside
the helix and this is how enzyme recognizes the DNA’s.
Lec3 (recording 4)
-Phosphate is highly charged, polar.
-Bases are planer, perpendicular to backbones.
-Complementary of Bases A-T, C-G, are important not only for transition and translation but also
important for fidelity(정확도) from one generation to another. Though there’s a deletion or
mutation in one strand, it can be fixed by checking partner strand. -DNA can be denatured (pulled apart) to single strands and renatured( resorted to double helix)
Denaturation occurs when h bonds get disrupted by heating to Tm (melting temperature) (or
increase pH), and denautration is reversible (renaturation) by cooling (or lower pH).
In other words, the stands can be unzipped. It is important for DNA replication and RNA
-If DNA sequence is simple/ highly repeated (ex) AAAAA) then it takes shorter times to renature.
But it does not have much information
The extremely high temperature tolerant bacteria found around deep sea
volcanic vents all seem to have genomic DNA with an elevated GC:AT ratio
when compared with other bacteria. This is because...
A. GC-rich codons encode more thermo-stable amino acids
B. The enzymatic synthesis of guanine and cytosine is favoured at higher
C. GC-rich DNA is more stable at high temperatures