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Chapter 2

BIO130H1 Chapter Notes - Chapter 2: Nitrogenous Base, Alpha And Beta Carbon, Alpha Helix

Course Code
Melody Neumann

of 7
Textbook Quiz 1
Readings - 77-79 (from last week); 393-397; 33-42 (chemistry review); 50-63; 70-72
Readings: 411-414; 400-406 (skip human perspectives and focus on complexity of eukaryotic
genomes section)
10.3 the chemical nature of the gene
The structure of DNA
Base composition
nucleotide: the basic building blocks of DNA
consists of the five-carbon sugar deoxyribose
phosphate attached to 5’ and nitrogen base attached to 1’
To types of Nitrogen base
pyrimidine: contain a single ring
thymine, cytosine,
purine:two rings
guanine, adenine
the nucleotides are covalently linked to one another
a nucleotide has a polarized structure: 5’ to 3’
Chargaff: determine the relative amounts of each base in various samples of DNA --
base composition
the ratio of the bases varies from sample to sample
[A] = [T], [G]=[C]
The Watson-Crick Proposal
1. two chains of nucleotides
2. the two chains spiral around each other to form a pair of right-handed helices.
3. the two chains run in opposite direction -- antiparallel
4. sugar- phosphate backbone on the outside, nitrogen base on the inside
a. the phosphate groups give the molecule a negative charge
5. the base occupy planes so they stack on top of each other like a pile of plates
a. Hydrophobic interactions and van der Waals forces provides stability
6. the two strands are held together by hydrogen bonds
a. they can be separated
b. still stable
7. 1nm from phosphorus to the center
a. thus the width is 2 nm
8. the N linked to carbon 4 of cytosine and carbon 6 of adenine ar predominantly the
amino configuration; the O linked to C6 of guanine and C4 of thymine are
predominantly keto C=O
a. gives them the A-T and G-C pairs
9. the spaces have different width
a. major groove: wider
b. minor groove: narrower
c. protein forms domains to fit in these grooves
10. one complete turn every 10 residues (3.4nm)
11. the two chains of the double helix are complementary to one another
The Importance of Watson- Crick Proposal
1. Storage of genetic information
must contain the information for the specific order of amino acids in all
2. Replication and inheritance
info for synthesis
3. Expression of the genetic message
the information in DNA must be used to direct the order
DNA breaks as a zipper, serve as a template directing the order
generates two DNA that are identical to one another and the original DNA
Covalent Bonds
Definition: electrons are shared between paired atoms
polar: have an asymmetrical distribution of charge (dipole)
nonpolar: molecules that lack electronegative atoms
Noncovalent Bonds
Ionic: attractions between fully charged components
weak ionic bonds between oppositely charged groups are important
Hydrogen Bonds
the shared electron is displaced toward the nucleus of the electronegative
atom (e.g. O or N)-- partial + on H ---- it can approach another electronegative
atom to form H bond
e.g. between 2 strands of DNA -- many H bonds stabilize DNA
Hydrophobic interaction
e.g. fat on water
they do not result from an attraction between hydrophobic molecules
van der Waals force
if two molecules with transitory shocks are very close to one another and
oriented in the appropriate manner, they experience a weak attractive force
that bond them together .
asymmetric distribution in electron resulting in momentary separation
of charges (dipole) -- two dipoles can have a weak attractive force
the formation of separation can induced similar separation in adjacent
molecules weak
Classification of Biological Molecules
building blocks of Macros
3. Metabolic intermediates (metabolites)
complex chemical structure, synthesized in a step-by-step sequence
molecules of miscellaneous function
act as enzymes
accelerate of metabolic reactions
structural cables
provide mechanical support within cells and outside
hormone, growth factors
The building blocks of Proteins
The structures of Amino Acids
carboxyl, alpha carbon, amino
asymmetric Carbon atoms
forms peptide bonds: linkage of carboxyl of
one and amino of the other, with the
elimination of a water
polypeptide chain
once in the chain, the AAs are termed
N term
C term
The Properties of the Side Chains
side chain=R group
bonded to the a-carbon
gives protein their diverse
structures and activities
4 categories of Amino Acids: ( refer to p52)