CHEM  30 B  Dr. R. Rinehart

 Ch. 21 Nucleic Acids & Protein Synthesis 

I. Nucleic Acids and their components

A. DNA:  polymer of deoxynucleotides; primarily in cell nucleus
            B. RNA:  polymer of nucleotides; primarily in cytoplasm, but made in nucleus
            C. Nucleotide composition = base + 5C sugar + phosphate
                                    (a nucleoside is just base + 5C sugar)

1. Base: heterocyclic group, attached to 1’ position of sugar
                        a. Purines:  Adenine [A] and Guanine [G]
                        b. Pyrimidines: Cytosine [C]  Uracil [U]  Thymine [T]
            2. Sugar: 5C in 1-b-furanose form
                                    a. DNA:  D-2’-deoxyribose
                                    b. RNA:  D-ribose
            3. Phosphate: attached  at  5’ position  of  sugar  by  phosphoester  linkage  

See my table of bases, base pairs, nucleosides, nucleotides, and coenzymes

II. DNA :  the  “hard drive” of  genetic  information  (with “auto-backup” features!) 
   
         A. Backbone:  alternating sugar and phosphate groups
            B. Phosphodiester linkages connecting 3’ of one sugar to 5’ of next sugar
                  note 5’ ŕ 3’ direction of chain:  the termini are defined by the free –OH groups

            C. Secondary structure:  double helix held by specific H-bonds and nonspecific
                               hydrophobic interactions (pi-stacking of bases)
            D. Antiparallel, complementary strands with base-pairing
                        A=T  has 2 H-bonds   and GC has 3 H-bonds
            E. Chromosomes    tertiary structure; each has many genes

            F.  Replication
                       
uses DNA polymerase, unwinding proteins, gyrases, swivelases, etc. etc.
                               and deoxynucleoside triphosphates 

See a Chime structure of  a short piece of DNA
You can see some JPEG images of nucleic acids and links to Chime structures at
http://www.bio.cmu.edu/courses/03231/LecF04/Lec17/lec17img.html
Notes on DNA and RNA structure by Gordon Rule at CMU
 http://stingray.bio.cmu.edu/~web/bc/Lec/Lec34/lec34.html
 
DNA tutorial by Frieda Reichsman at U Mass
 http://www.umass.edu/molvis/freichsman/StryerDnaTut/index.html 
Chime + Netscape = success!
Nucleic Acids page by Duane W. Sears at UC Santa Barbara
 http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/ > Nucleic Acids
You need Chime; use Netscape
DNA replication video posted by megh2748
http://www.youtube.com/watch?v=L9RjNNfgaEQ
DNA and Molecular Genetics
 in the Online Biology Text by Michael J. Farabee at Estrella Mountain CC, Maricopa County, AZ  
is quite good and does NOT require Chime
http://www.estrellamountain.edu/faculty/farabee/biobk/BioBookDNAMOLGEN.html
http://gened.emc.maricopa.edu/bio/bio181/BIOBK/BioBookDNAMOLGEN.html

III. RNA:   Three classes with different specialized functions. 
      Each class is transcribed by a different RNA polymerase using nucleoside triphosphates.   
            A. Messenger RNA (mRNA):   gene copy;  directs amino acid sequence of protein
            B. Ribosomal RNA (rRNA):   structural framework of ribosome and possible catalysis
                        1. Ribosomes contain small and large rRNAs  and  >30 proteins/enzymes
                        2. Bacterial ribosomes different from eukaryotic ones; antibiotics like
                                    chloramphenicol and erythromycin inhibit theirs, but not ours
            C. Transfer RNA (tRNA): brings in amino acids
                        1. specific “ligases” attach specific proper amino acids to tRNAs using ATP energy
                        2. “anticodon loop  reads codons in mRNA

Lecture notes on tRNA structure by Gordon Rule at CMU
http://www.bio.cmu.edu/Courses/BiochemMols/tRNA_Tour/tRNA_Tour.html
 http://stingray.bio.cmu.edu/~web/bc1_S01/LecS01/Lec39/lec39.html 

D. Flow of genetic information: 
   
                         DNA ŕ RNA ŕ protein   this is called the “central dogma” of  molecular biology
   
                          what about reverse transcriptase???       

E. Transcription:  RNA synthesis
                       
in eukaryotes, there are separate RNA polymerases for mRNA, tRNA, and rRNA

F. “Processing” of mRNA
                       
Get those damn introns out of here!  dice and splice!   

Chime tutorials on DNA and tRNA structure by Steve Minchin at U. Birmingham
 http://www.biosciences.bham.ac.uk/labs/minchin/tutorials/default.html

IV. Translation and Protein Synthesis           

A. The GENETIC CODE [see table below]
                       
1.  Each amino acid has at least one specific “codon
                       
2.  Codons are “triplets  4x4x4 = 64 possible
                       
3.  some are “degenerate”, but at least 40 different tRNA’s needed to read them
                        4.      there is one INITIATION codon (AUG)
                                and three TERMINATION codons (UAA, UAG, UGA

B. TRANSLATION (of mRNA): protein synthesis by ribosomes
                        1. Initiation
                        2. Elongation: energy from GTP
                        3. Termination
                        4. Post-translational modifications
    

Protein Synthesis in the Online Biology Text by Michael J. Farabee at Estrella Mountain CC, Maricopa County, AZ  
is quite good and does NOT require Chime
http://www.estrellamountain.edu/faculty/farabee/biobk/BioBookPROTSYn.html
 http://gened.emc.maricopa.edu/bio/bio181/BIOBK/BioBookPROTSYn.html   
Protein Synthesis lecture notes by Gordon Rule at CMU --
the notes are more detailed than what you need but there are links to pages on ribosome structure and an animation
http://stingray.bio.cmu.edu/~web/bc1_S01/LecS01/Lec40/lec40.html   
Protein Synthesis lecture notes by Dr. Grotzinger at CMU
http://www.bio.cmu.edu/courses/03231/LecF04/Lec21/lec21.html
 and
http://www.bio.cmu.edu/courses/03231/LecF04/Lec22/lec22.html
the latter page has links to Chime tutorials on ribosome structure and function
A QuickTime animation of translation by Robert J. Huskey of U Virginia
 http://wsrv.clas.virginia.edu/~rjh9u/gif/protein.mov 
Virtual Cell animations from North Dakota State University
transcription  http://vcell.ndsu.nodak.edu/animations/transcription/movie.htm
mRNA processing  http://vcell.ndsu.nodak.edu/animations/mrnaprocessing/movie.htm
mRNA splicing  http://vcell.ndsu.nodak.edu/animations/mrnasplicing/movie.htm
translation  http://vcell.ndsu.nodak.edu/animations/translation/movie.htm
protein transport  http://vcell.ndsu.nodak.edu/animations/mito-pt/movie.htm
the lac operon  http://vcell.ndsu.nodak.edu/animations/lacOperon/movie.htm
Protein synthesis: an epic on the cellular level
Directed in 1971 by Robert Alan Weiss for the Department of Chemistry of Stanford University
Narrated by Paul Berg, 1980 Nobel prize for Chemistry.

http://www.youtube.com/watch?v=u9dhO0iCLww
sooooooooo 1970's...
"The Inner Life of the Cell"
by Alain Viel and Robert Lue, Harvard University, animation by John Liebler, XVIVO LLC
http://www.youtube.com/watch?v=jjexZ88wIno&mode=related&search=
perhaps the most worthwhile way a biology student could possibly spend eight minutes...
and a short unnarrated version at
http://www.xvivo.net/press/harvard_university.htm
Tons of cell bio vids posted by megh2748
http://www.youtube.com/profile_videos?user=megh2748

            C. Mutations and their consequences
                        1. Point mutations
                        2. Insertions and deletions
           

D. Recombinant DNA: genetic engineering

V. Applications: scholarly, medical, forensic, agricultural, ...

           

 

 2nd base -->

 U

C

A

G

1st base

       

3rd  base

 U

UUU      Phe

UUC      Phe

UUA      Leu

UUG     Leu

UCU      Ser

UCC        Ser

UCA        Ser

UCG        Ser

UAU        Tyr

UAC        Tyr

UAA    STOP

UAG    STOP

UGU     Cys

UGC       Cys

UGA    STOP

UGG       Trp

U

C

A

G

 C

CUU      Leu

CUC      Leu

CUA      Leu

CUG      Leu

CCU        Pro

CCC        Pro

CCA         Pro

CCG        Pro

CAU        His

CAC        His

CAA        Gln

CAG        Gln

CGU       Arg

CGC       Arg

CGA        Arg

CGG       Arg

U

C

A

G

A

AUU       Ile

AUC       Ile

AUA       Ile

AUG      Met

ACU        Thr

ACC        Thr

ACA        Thr

ACG        Thr

AAU     Asn

AAC        Asn

AAA        Lys

AAG        Lys

AGU        Ser

AGC        Ser

AGA        Arg

AGG        Arg

U

C

A

G

 G

GUU       Val

GUC       Val

GUA       Val

GUG       Val

GCU       Ala

GCC        Ala

GCA        Ala

GCG        Ala

GAU       Asp

GAC       Asp

GAA        Glu

GAG        Glu

GGU        Gly

GGC        Gly

GGA        Gly

GGG        Gly

U

C

A

G

 © Ronald W. Rinehart, 2002-2007