BIO 101 - Module 2

• Nucleic Acids

  • Chemical repositories of genetic information

  • Located inside the nucleus (for eukaryotes) or in the nucleoid region (for prokaryotes)

  • Biopolymers of nucleotides linked together by phosphodiester bond
• • Two forms of nucleic acid:

  • DNA (2’-deoxyribonucleic acid)

  • RNA (ribonucleic acid)
• Pentoses in nucleotides

  A) B-D-2'-deoxyribose

  B) B-D-ribose

  
• Nitrogenous Bases

  • Flat aromatic rings

  • Basic

  • Have conjugated double bonds

  • Have multiple sites for hydrogen bonding
• Purine

  A) 6-aminopurine

  B) 2-amino-6-oxypurine

  
• Pyrimidine

  A) 2-oxy-4-aminopyrimidine

  B) 2,4-dioxy-5-methylpyrimidine

  C) 5-methyluracil

  D) 2,4-dioxypyrimidine

  
• Tautomerization

  • Rapid interconversion of isomeric forms

  • amino-imino forms of cytosine and adenine

  • keto-enol forms of guanine and thymine
• Tautomeric Shift in Bases

  A) imino

  B) keto

  C) enol

  D) amino

  
• Anomalous base pairing of tautonomic forms:

  A) Thymine

  B) Guanine

  C) Cytosine

  D) Adenine

  
• Formation of Nucleotides

  • 2 moles of water are liberated upon formation of a nucleotide (dehydration)
• nucleotide bonds

  A) phosphoester

  B) B-N-glycosidic

  
• nucleosides

  A) sugar + base

  B) Uridine

  C) 2'-deoxythymidine

  D) cytidine

  E) 2'-deoxyadenosine

  F) guanosine

  
• naming nucleotide

  A) nucleoside + phosphate

  B) 2'-deoxyribose

  C) adenine

  D) 2'-deoxyadenosine-5'-monophosphate

  
• naming nucleotide

  A) ribose

  B) cytosine

  C) cytidine-5'-diphosphate

  
• Phosphate Groups

  • Form the backbone of the polynucleotide together with the pentose

  • Imparts negative charge to the DNA

  • Enables DNA to associate with the positively charged histones
• Primary Structure of DNA

  • Linear sequence of deoxyribonucleotides

  • Two complementary strands held together by hydrogen bonds

  • Backbone: Alternating sugar and phosphate groups linked together by phosphodiester bonds
• The 5’-end contains the free 5’-phosphate group while the 3’-end contains the free 3’-OH group
• The sequence of nucleic acids are, by convention, stated as sequence of bases from the 5’- to the 3’-end.
• Secondary Structure of DNA

  • The DNA molecule has the form of a double helix:

  • Two intertwined antiparallel strands of nucleotide
• • Has major and minor grooves

  • Essential in binding with proteins

  • Major grooves are being accessed by polymerases
• Secondary Structure of DNA

  • Most DNAs are right-handed helices (rotates clockwise); only a few are left-handed (counterclockwise)
• Secondary Structure of DNA

  • Base pairs stacking

  • Maximizes hydrophobic interactions for greater stability

  • Distance between two base pairs: 3.4 Angstrom or 0.34 nm

  • Helix constant diameter: 20 Angstrom or 2 nm

  • Maintained by the right pairing of bases
• DNA Supercoiling

  • All organisms store their DNA as negatively supercoiled

  • decreases storage space; more conducive for replication, transcription, etc
• Mirror Repeats • Symmetrical sequence within each strand
• Palindromes or Inverted Repeats • two copies of an identical sequence present in the reverse orientation
• Hairpins • formed from intra-strand base pairing when only a single palindromic DNA (or RNA) strand is involved
• Cruciform • formed from intra-strand base pairing involving both strands of a duplex palindromic DNA
• Ribonucleic Acids (RNA)

  • Exist mostly as single-stranded polynucleotides

  • Sugar: ribose

  bases: A, C, G, U

  • Genetic material of some viruses
• Segments of RNA molecules may:

  • form RNA-DNA hybrid

  • pair temporarily in double-helical form

  • fold back on themselves to set up extensive double-helical regions
• stem-loop structure

  -similar with a hairpin

  -loop at the end would have many unpaired bases

  -plays an important role in attenuation
• cloverleaf structure

  • characteristic conformation of the tRNA molecule

  • made up of three stem-loops

  • has four arms
• RNA structure in teriary/quaternary: inverted L-shaped
• Significance of 2°/3° Structures

  • Means of stabilizing genome structure

  • Serve as recognition site for initiation of DNA replication in ssDNA viruses

  • Serve as signals for the initiation & termination of transcription

  • Important in the function of the NA made from it

  • Form the core of catalytic RNA molecules (ribozymes)
• Chromosomes

  • Composed of chromatin (DNA + associated proteins)
• Types of chromatin proteins:

  • Histones - small, well-defined proteins

  • Non-histone chromosomal proteins - include diverse structural, enzymatic and regulatory functions
• Arg and Lys make histones good DNA packaging proteins
• The Nucleosome

  • Repeating units of chromatin composed DNA and histones

  • About 147 bp supercoiled DNA wrapped twice around the histone octamer

  • Classes of histones:

  • H2A, H2B, H3, H4
  • H1
• Histone H1

  • the linker histone that associates with the linker DNA

  • Runs down through the center of the coil acting as a stabilizer

  • Condenses the “beads on a string”
• 30-nm Chromatin Fiber

  • Approximately 30-nm thick

  Two models:

  • Solenoid

  • Zigzag
• Non-histone Protein Scaffold

  -holds the looped domains