1/17/2012 1 NUCLEIC ACIDS Nucleic Acids • DNA (Deoxyribonucle ic Acid) • RNA (Ribonucleic Acid) Nucleic Acids • Nucleic acid:a biopolymer containing three types of monomer units • a sugar (a pentose) , either D-ribose or 2-deoxy-D-ribose • a base derived from purine or pyrimidine (nucleobases) • phosphate Pyrimidine/Purine Bases • The structures of pyrimidine and purine:
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• RNA is synthesized on a DNA template, catalyzed byDNA-dependent RNA polymerase
• ATP, GTP, CTP, and UTP are required, as is Mg2+
• no RNA primer is required • the RNA chain is synthesized in the 5’ -> 3’ direction;
the nucleotide at the 5’ end of the chain retains itstriphosphate (ppp) group
• RNA polymerase unwinds the helix • the DNA base sequence contains signals for initiation
and termination of RNA synthesis; the enzyme bindsto and moves along the DNA template in the 3’ -> 5’direction
• the DNA template is unchanged
Transcription in Prokaryotes
• E. coli RNA Polymerase:• four different types of subunits: , , ’, and s • the core enzyme is 2’
• the holoenzyme is 2’s • the role of the s subunit is recognition of the
promoter locus; the s subunit is released aftertranscription begins
• of the two DNA strands, the one that serves as thetemplate for RNA synthesis is called the template strand or antisense strand; the other is called thecoding (or nontemplate) strand or sense strand
• the holoenzyme binds to and transcribes only thetemplate strand
• The sequence of aminoacids, derived from thesequence of DNA bases,is specified by the genetic
code, using 4 RNA basesA, U, G, and C taken threeat a time (triplet code).
• There 64 possible “code
words”, called codons
• 1 start codon - AUG• 3 are stop signals:
UAG, UGA, UAA
• 61 specify the 20amino acids withconsiderableredundancy.
The Genetic Code
• Salient features of the geneticcode• triplet: a sequence of three
bases (a codon) is needed tospecify one amino acid
• nonoverlapping: no basesare shared betweenconsecutive codons
• commaless: no interveningbases between codons
• degenerate: more than onetriplet can code for the sameamino acid; Leu, Ser, and Arg,for example, are each codedfor by six triplets
• universal: the same inviruses, prokaryotes, andeukaryotes; the onlyexceptions are some codons inmitochondria
The Genetic Code (Cont’d)
• All 64 codons haveassigned meanings•only Trp and Met have onecodon each
•the third base is irrelevantfor Leu, Val, Ser, Pro, Thr,Ala, Gly, and Arg
•the second base isimportant for the type ofamino acid; for example, ifthe second base is U, theamino acids coded for arehydrophobic
•for the 15 amino acidscoded for by 2, 3, or 4triplets, it is only the thirdletter of the codon thatvaries. Gly, for example, iscoded for by GGA, GGG,GGC, and GGU
Translating the Genetic Message
• Protein biosynthesis isa complex processrequiring ribosomes,mRNA, tRNA, andprotein factors
• Several steps areinvolved
• Before beingincorporated intogrowing protein chain,a.a. must be activatedby tRNA andaminoacyl-tRNAsynthetases
which binds to UAA andUAG or RF-2 (Releasefactor-2) which binds toUAA and UGA
• RF-3 which does notbind to any terminationcodon, but facilitates thebinding of RF-1 and RF-2
• GTP which is bound toRF-3
• The entire complexdissociates setting free thecompleted polypeptide, therelease factors, tRNA,mRNA, and the 30S and50S ribosomal subunits
UAG Simultaneous Protein Synthesis onPolysomes
Post-translational Modification
• Newly synthesized polypeptides are frequently modifiedbefore they reach their final form where they exhibitbiological activity• N-formylmethionine in prokaryotes is cleaved
• specific bonds in precursors are cleaved , as for example,
preproinsulin to proinsulin to insulin• leader sequences are removed by specific proteases ofthe endoplasmic reticulum; the Golgi apparatus then directsthe finished protein to its final destination
• factors such as heme groups may be attached
• disulfide bonds may be formed• amino acids may be modified, as for example, conversion
of proline to hydroxyproline• other covalent modifications; e.g., addition of
1° structure: the sequence of amino acids in apolypeptide chain, read from the N-terminal end tothe C-terminal end
• 2°
structure: the ordered 3-dimensionalarrangements (conformations) in localized regions ofa polypeptide chain; refers only to interactions of thepeptide backbone• e. g., -helix and -pleated sheet
• 3˚ structure: 3-D arrangement of all atoms
• 4˚ structure: arrangement of monomer subunitswith respect to each other
2o Structure: the ordered 3-dimensionalarrangements (conformations) in localized regions of apolypeptide chain; refers only to interactions of thepeptide backbone
α-Helix β-pleated sheet
3o Structure: 3-D arrangement of all atoms
Forces That Stabilize Protein Structure
4o Structure: arrangement of monomer subunits withrespect to each other