BIOL 2P02 Chapter Notes - Chapter 3: Phosphodiester Bond, Nitrogenous Base, Chemical Bond
24 May 2018
School
Department
Course
Professor
Spring BIOL 2P93 Textbook Notes Chapter 3
Chapter 3: Chemical Basis of Information Molecules
• Molecular bio involves the study of molecules which store & process genetic info
o Storage & the use of genetically encoded info involves nucleic acids & proteins, macromolecules
which are major constituents of cells
• Functionality of nucleic acids & proteins depends on their chemical properties
o Shape, electrical charge, weak/strong bonds, hydrophobic/hydrophilic interactions
• Proteins enable cells to communicate and respond to their environment
• Biologist say that:
o Poteis eogize a faget of DNA
o ‘NA ids to a potei
o Seeal poteis assele ito a ulti-subunit
3.1: Chemical Bonds Block of Nucleic Acids & Proteins
• Nucleic Acids are Long Chains of Nucleotides
o DNA (Deoxyribonucleic Acid) & RNA (Ribonucleic Acid)
▪ Store & transmit genetic info by coding for proteins
▪ Some RNA molecules function catalytically/structurally w/n larger, multimolecular complexes
▪ Composed of building blocks (monomers) nucleotides
• Linked together by phosphodiester bonds
o Forming long unbranched chains
• Nucleotides are made up of 3 components
o Nitrogenous base, 5-Carbon Sugar (pentose), Phosphate group
o A base & a sugar w/o a phosphate group is called a nucleoside
o Sugars & phosphates of adjacent, individual nucleotides are chemically linked to form a sugar-
phosphate backbone
▪ Has characteristic directionally
• Defined by the chemical convention for numbering carbon atoms in nucleotide sugar
ring
o 5 ed & ed
• Nucleotides making up DNA polymers are Deoxyribonucleotides
o Pentose sugar -> deoxyribose
o 4 nitrogenous based
▪ Thymine (T), Adenine (A), Guanine (G), Cytosine (C)
• RNA is similar to DNA
o 2 differences
▪ The sugar: ribose
• Called ribonucleotides
• Has 1 more -OH than Deoxyribose
▪ Nitrogenous Base
• Instead of thymine (T), it has Uracil (U)
• Proteins Are Long Polymers of Amino Acids
o Unbranched polymers
o When joined together by a peptide bond b/n amino group of one amino acid & the carboxyl group
of another a peptide is formed
o Longer chains of amino acids are called polypeptides
find more resources at oneclass.com
find more resources at oneclass.com
Spring BIOL 2P93 Textbook Notes Chapter 3
▪ Have directionality defined by free amino group of the amino acid at 1 end of the polymer
(the N-terminus) and the free carboxyl group at the other (C- terminus)
o Once incorporated into a polypeptide chain
▪ Referred to as amino acid residues
o Most proteins found in cells & viruses are composed of 20 amino acids
o All 20 amino acids have a central carbon atom -> α-Carbon
▪ Bonded to four different chemical groups -> α-amino acids
• These aminos have a carboxyl group, an amino group, a H atom, and an R group
(unique side chain) which varies in structure, size, hydrophobicity, electrical charge.
• Chemical Composition Helps Determine Nucleic Acid & Protein Structure
o Huge variety of nucleic acids & proteins can be produced by altering the sequence of nucleotides or
amino acid monomers
o DNA molecules are millions of nucleotides long, but they form relatively uniform structures and the
two strands pair up to form a double helix.
o RNA molecules, except those that store genetic info of viruses, are shorter and more structurally
diverse than DNA
▪ One strand can fold back on itself forming short helices creating a 3D shape
o These differences b/n DNA & RNA ste fo the ole of ‘NAs -hydroxyl groups
• Chemical Composition Can be Altered by Postsynthetic Changes
o Modifications of nucleotides/amino acids often occur once DNA/RNA/protein has been synthesized.
o Primary modification of DNA nucleotides is the addition of methyl groups to the C, A & G bases.
▪ DNA based methylation is critical for accurate DNA replication
• In bacteria -> protection of DNA from degradative enzymes
• Humans/eukaryotic cells -> activating/silencing gene expression
o ‘NA odified addig ethl goups to uleotide ases, -hydroxyl groups of ribose & the
substitution of less-common bases for the usual A, C, G, U
▪ Affects the folding ability
o Example: addition of a phosphate group to hydroxyl groups in the side chains of serine, tyrosine &
threonine change the proteins shape and function
o Proteins can be modified by the phosphorylation, dephosphorylation, the addition of sugars
(glycosylation) or methyl groups
3.2 Chemical Bonds
• Electrons are Shared in Covalent Bonds & Transferred in Ionic Bonds
o Covalent bond -> formed when 2 atoms share a pair of electrons (e-) b/n their positively charged
nuclei
▪ allows outer shell to be filled.
o ionic bond -> complete transfer of one or more e- from one atom to another
▪ when e- tasfe, atos eoe ios, oe thats positie, the othe egatie
o electronegativity -> the propensity of an atom w/n a molecule to attract electrons to itself
▪ unequal e- sharing results in different affinities of the bonded atoms
• atoms that gain e- are electropositive
• atoms that lose e- are electronegative
▪ trend: as the atomic radius decreases, electronegativity increases
• greater likelihood of an ionic bond forming than a covalent one
• bond b/n metal & non-metal
find more resources at oneclass.com
find more resources at oneclass.com
Spring BIOL 2P93 Textbook Notes Chapter 3
o metal atom donates e- to non-metal -> NaCl
o Pauling scale -> 0.7-3.98
▪ <1.67, bond is polar covalent
• e- ae shaed ut iased to oe pole of the oded atos
• If the difference b/n the two values is zero or very small, it is covalent
▪ >1.67, bond is ionic
o ionic bonds are weaker than covalent bonds
▪ ioi ods dot estit the oietatio of oded atos
▪ ionic bond strength varies w/ the salt concentration & hydrophobicity
• NaCl is an example of a molecule having a strong ionic bond
o Na loses an e- producing a positive ion which is attracted to a negative Cl ion
• Chemical Bonds are Explainable in Quantum Mechanical Terms
o Valence bond model -> chemical bond forms when there is suitable overlap b/n the e- clouds
(atomic orbitals)
▪ Atomic orbitals have specific interrelationships meaning that the model can predict bond
angles
o Molecular orbital model -> atomic orbitals of bonded atoms interact forming hybrid molecular
orbitals
o Octet rule -> the valence shell can have 8 e-
o Max number of bonds an atom can form is called its valence -> Dictates shape, chemical properties
o Single bond b/n 2 atoms involve 2 e-
o Double bond b/n 2 atoms involve 4 e-
o Bond angle -> angle b/n two bonded atoms
▪ Covalent bond angles are always the same
• 4 covalent bonds of carbon create a tetrahedron w/ 109.5º angle
▪ single bonds allow free rotation of the bound atoms, but double bonds are more rigid
o molecules w/ adjacent single & double bonds they can exist as an average of multiple structures->
resonance
▪ resonance hybrid is a molecule which exists in an average of 2 forms
▪ resonance affects behaviour of nucleic acids
• phosphodiester bond that link nucleotides have a tetrahedral shape with two bonds
to oxygen atoms
o negative charge shifts / the to oge atos that aet oded to the
sugar backbone
• Forming & Breaking Chemical Bonds Involves Energy Transfer
o A chemical bond forms when the total energy of the system (molecule & its environment) must be
lower in the bonded state than in the nonbonded state.
▪ Bonding is exothermic
o Strength of a covalent bond increases w/ decreasing bond length
o Stronger bonds release more energy on formation than weaker bonds
o Rate of bond formation is proportional to the rate at which two atoms collide
▪ More likely to bond if they bump into each other more often
o Calorie -> amount of energy required to raise the temperature of water by 1 gram by 1ºC from 14.5
ºC to 15.5 ºC
o Joule -> 0.239 calories, defined as the energy required to apply a force of 1 newton through a
distance of 1m
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Chapter 3: metal atom donates e- to non-metal -> nacl, pauling scale -> 0. 7-3. 98, <1. 67, bond is polar covalent, e- a(cid:396)e sha(cid:396)ed (cid:271)ut (cid:271)iased to o(cid:374)e (cid:858)pole(cid:859) of the (cid:1006) (cid:271)o(cid:374)ded ato(cid:373)s. Joule -> 0. 239 calories, defined as the energy required to apply a force of 1 newton through a distance of 1m. Chapter 3: stronger vdw contact arises when a macromolecule contains a surface that precisely fits the shape of the molecule that it binds, antibodies, the proteins that recognize antigens- specific molecules of viruses, bacteria that enter the body. Since the digestive enzymes are chiral, they do not recognize or digest l-glucose (opposite chirality) 3. 5 the role of ph & ionization: most biological processes occur w/n a narrow ph range -> cells must regulate ph to suit their needs, the hydrogen ion concentration of a solution is measured by ph.
