Outline • Cellular Overview • Anatomy of the Nucleic Acids • Building blocks • Structure (DNA, RNA) • Looking at the Central Dogma • DNA Replication • RNA Transcription • Protein Synthesis
DNA and RNA in the Cell Cellular Overview
Classes of Nucleic Acids: DNA • DNA is usually found in the nucleus • Small amounts are also found in: • mitochondria of eukaryotes • chloroplasts of plants • Packing of DNA: • 2-3 meters long • histones • genome = complete collection of hereditary information of an organism
Classes of Nucleic Acids: RNA FOUR TYPES OF RNA • mRNA - Messenger RNA• tRNA - Transfer RNA• rRNA - Ribosomal RNA• snRNA - Small nuclear RNA
THE BUILDING BLOCKS Anatomy of Nucleic Acids
Nucleic acids are linear polymers. Each monomer nucleotide consists of: 1. a sugar 2. a phosphate 3. a nitrogenous base
Nitrogenous Bases DNA (deoxyribonucleic acid): adenine (A) guanine (G) cytosine (C) thymine (T) Why ? RNA (ribonucleic acid): adenine (A) guanine (G) cytosine (C) uracil (U)
Properties of purines and pyrimidines: • keto – enoltautomerism • strong UV absorbance
Pentose Sugars of Nucleic Acids This difference in structure affects secondary structure and stability. Which is more stable?
Nucleosides linkage of a base and a sugar.
Nucleotides - nucleoside + phosphate - monomers of nucleic acids - NA are formed by 3’-to-5’ phosphodiester linkages
Shorthand notation: • sequence is read from 5’ to 3’ • corresponds to the N to C terminal of proteins
DNA Nucleic Acids: Structure
Primary Structure • nucleotide sequences
Secondary Structure DNA Double Helix • Maurice Wilkins and Rosalind Franklin • James Watson and Francis Crick • Features: • two helical polynucleotides coiled around an axis • chains run in opposite directions • sugar-phosphate backbone on the outside, bases on the inside • bases nearly perpendicular to the axis • repeats every 34 Å • 10 bases per turn of the helix • diameter of the helix is 20 Å
Double helix stabilized by hydrogen bonds. Which is more stable?
A and B forms are both right-handed double helix. A-DNA has different characteristics from the more common B-DNA.
Z-DNA • left-handed • backbone phosphates zigzag
Comparison Between A, B, and Z DNA: • A-DNA: right-handed, short and broad, 11 bp per turn • B-DNA: right-handed, longer, thinner, 10 bp per turn • Z-DNA: left-handed, longest, thinnest, 12 bp per turn
Tertiary Structure Supercoiling supercoiledDNA relaxed DNA
Consequences of double helical structure: • 1. Facilitates accurate hereditary information transmission • Reversible melting • melting: dissociation of the double helix • melting temperature (Tm) • hypochromism • annealing
Structure of Single-stranded DNA Stem Loop
RNA Nucleic Acids: Structure
Secondary Structure transfer RNA (tRNA) : Brings amino acids to ribosomes during translation
Transfer RNA • Extensive H-bonding creates four double helical domains, three capped by loops, one by a stem • Only one tRNA structure (alone) is known • Many non-canonical base pairs found in tRNA
ribosomal RNA (rRNA) : Makes up the ribosomes, together with ribosomal proteins. • Ribosomes synthesize proteins • All ribosomes contain large and small subunits • rRNA molecules make up about 2/3 of ribosome • Secondary structure features seem to be conserved, whereas sequence is not • There must be common designs and functions that must be conserved
small nuclear RNA (snRNA) :With proteins, forms complexes that are used in RNA processing in eukaryotes. (Not found in prokaryotes.)
DNA Replication, Recombination, and Repair Central Dogma
DNA Replication – process of producing identical copies of original DNA • strand separation followed by copying of each strand • fixed by base-pairing rules
DNA replication is bidirectional. • involves two replication forks that move in opposite direction
DNA replication requires unwinding of the DNA helix. • expose single-stranded templates • DNA gyrase– acts to overcome torsional stress imposed upon unwinding • helicases– catalyze unwinding of double helix • disrupts H-bonding of the two strands • SSB (single-stranded DNA-binding proteins)– binds to the unwound strands, preventing re-annealing
Primer RNA primes the synthesis of DNA. Primase synthesizes short RNA.
DNA replication is semidiscontinuous • DNA polymerase synthesizes the new DNA strand only in a 5’3’ direction. Dilemma: how is 5’ 3’ copied? • The leading strand copies continuously • The lagging strand copies in segments called Okazaki fragments (about 1000 nucleotides at a time) which will then be joined by DNA ligase