Fall 2019HFH1104
Armen ZakarianOffice: Chemistry Bldn 2217
Chem 109 CBioorganic Compounds
http://labs.chem.ucsb.edu/~zakariangroup/courses.html
CLAS Instructor: Dhillon [email protected]
DNA, RNA, etc.
DNA is stable, RNA is not
Obase
OHO
OP
Obase
OHO
O
PO O-
O O-
2'5'
RNA
Obase
OO
OP
Obase
OHO
O
P-O O-
O O-
:B
B H
Obase
OO
OP
PO-
O O-
O
Obase
OHO
OH
2',3'-phosphodiester
+
DNA, RNA, etc.
spontaneous deamination
NH
N
O
NH2
NH
NH
O
OH2O
+ NH3
cytosine
PRACTICE PROBLEM 16 Adenine can be deaminated to hypoxanthine, and guanine can be deaminated to xanthine. Draw structures for the deamination products.
Overview
OVERVIEW o structures of DNA vs. RNA - riboseo structures of bases: Adenine, Uracil/Thymine, Guanine, Cytosine. “Enol forms”o hydrogen bonding between A-T(U) and G-C. H-donors/acceptorso Base complementarityo RNA strand cleavage assisted by the 2’-OH group in the ribose unit (cyclic PDE)o Deamination: RNA genetic instabilityo DNA replicationo RNA synthesis: transcription. Template strand (read 3’ to 5’). Sense strand and
the RNA primary structure (T −> U).o Protein synthesis: translation. mRNA determines the amino acid sequence.
tRNAs are amino acid carriers. rRNA - part of ribosomes
o no section 26.12, 26.13
DNA, RNA, etc.
DNA (bio)synthesis
is called replication
done by DNA polymerase
! strand separation, replication fork
! again, always in 5’ → 3’ direction
using nucleoside triphosphates
RNA biosynthesis.
DNA RNA proteins
DNA: ~2% genes (exons), ~98% introns
transcription translation
DNA, RNA, etc.
RNA biosynthesis
initial transcript
RNA splicing
final RNA
DNA, RNA, etc.
RNA biosynthesis
initial transcript
RNA splicing
final RNA
DNA, RNA, etc.
RNA biosynthesis
mRNA, messenger RNA: protein synthesis template rRNA, ribosomal RNA: a part of ribosomes
tRNA, transfer RNA: amino acid carrier
DNA, RNA, etc.
RNA biosynthesis mRNA, messenger RNA: protein synthesis template
DNA, RNA, etc.
RNA biosynthesis mRNA, messenger RNA: protein synthesis template
codons: three nucleotides code for one amino acid
DNA, RNA, etc.
Protein biosynthesis rRNA, ribosomal RNA: a part of ribosome
blue - proteinorange - rRNAred - active site
atomic structure of 50S larger subunit of a prokaryotic ribosome
DNA, RNA, etc.
RNA biosynthesis tRNA, transfer RNA: amino acid carrier
DNA, RNA, etc.
RNA biosynthesis
each amino acid has a specific aminoacyl-tRNA synthetase
tRNAHistRNA, transfer RNA: amino acid carrier
DNA, RNA, etc.
RNA biosynthesis
R
NH3+O-
OO
Ad
O
HO
POO-
OPO
OO-
PO
-OO-
+
amino acid
at the active site of aminoacyl-tRNA syntetase
tRNA, transfer RNA: amino acid carrier
DNA, RNA, etc.
RNA biosynthesis
R
NH3+O-
OO
Ad
O
HO
POO-
OPO
OO-
PO
-OO-
+
amino acid
at the active site of aminoacyl-tRNA syntetase
tRNA, transfer RNA: amino acid carrier
DNA, RNA, etc.
RNA biosynthesis
R
NH3+O-
OO
Ad
O
HO
POO-
OPO
OO-
PO
-OO-
+
amino acid
OAd
O
HO
POO-
OOR
NH3+O-P
O
OO-
PO
-OO-
+
amino-acyl adenylate
at the active site of aminoacyl-tRNA syntetase
tRNA, transfer RNA: amino acid carrier
DNA, RNA, etc.
RNA biosynthesis
R
NH3+O-
OO
Ad
O
HO
POO-
OPO
OO-
PO
-OO-
+
amino acid
OAd
O
HO
POO-
OOR
NH3+O-P
O
OO-
PO
-OO-
+
amino-acyl adenylate
2 HPO42-
H2O
at the active site of aminoacyl-tRNA syntetase
tRNA, transfer RNA: amino acid carrier
DNA, RNA, etc.
RNA biosynthesis
R
NH3+O-
OO
Ad
O
HO
POO-
OPO
OO-
PO
-OO-
+
amino acid
OAd
O
HO
POO-
OOR
NH3+O-P
O
OO-
PO
-OO-
+
amino-acyl adenylate
2 HPO42-
H2O
H O ACC5'
tRNA
O ACC5'
tRNA
C
O-
O+H3N
R P OO-
OO
HO
Ad
at the active site of aminoacyl-tRNA syntetase
tRNA, transfer RNA: amino acid carrier
DNA, RNA, etc.
RNA biosynthesis
R
NH3+O-
OO
Ad
O
HO
POO-
OPO
OO-
PO
-OO-
+
amino acid
OAd
O
HO
POO-
OOR
NH3+O-P
O
OO-
PO
-OO-
+
amino-acyl adenylate
2 HPO42-
H2O
H O ACC5'
tRNA
O ACC5'
tRNA
C
O-
O+H3N
R P OO-
OO
HO
Ad
O ACC5'
tRNA
RO
NH3+AMP +
an amino acyl tRNA
at the active site of aminoacyl-tRNA syntetase
tRNA, transfer RNA: amino acid carrier
DNA, RNA, etc.
DNA, RNA, etc.
Midterm 1 [same sections]
Midterm 2 [same sections]
Midterm 3 [same sections]
Chapter 25, sections 25.1 – 25.7, 25.10
Chapter 26, sections 26.1 – 26.11
Evenly distributed, ~40 m.c. + 20 regular
Same material provided, + genetic code Table
Final Exam