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Fall 2019HFH1104
Armen ZakarianOffice: Chemistry Bldn 2217
Chem 109 CBioorganic Compounds
http://labs.chem.ucsb.edu/~zakariangroup/courses.html
CLAS Instructor: Dhillon [email protected]
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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
+
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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.
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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
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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
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RNA biosynthesis.
DNA RNA proteins
DNA: ~2% genes (exons), ~98% introns
transcription translation
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DNA, RNA, etc.
RNA biosynthesis
initial transcript
RNA splicing
final RNA
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DNA, RNA, etc.
RNA biosynthesis
initial transcript
RNA splicing
final RNA
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DNA, RNA, etc.
RNA biosynthesis
mRNA, messenger RNA: protein synthesis template rRNA, ribosomal
RNA: a part of ribosomes
tRNA, transfer RNA: amino acid carrier
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DNA, RNA, etc.
RNA biosynthesis mRNA, messenger RNA: protein synthesis
template
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DNA, RNA, etc.
RNA biosynthesis mRNA, messenger RNA: protein synthesis
template
codons: three nucleotides code for one amino acid
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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
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DNA, RNA, etc.
RNA biosynthesis tRNA, transfer RNA: amino acid carrier
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DNA, RNA, etc.
RNA biosynthesis
each amino acid has a specific aminoacyl-tRNA synthetase
tRNAHistRNA, transfer RNA: amino acid carrier
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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
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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
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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
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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
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DNA, RNA, etc.
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DNA, RNA, etc.
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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
