Chem 109 C Bioorganic CompoundsDNA, RNA, etc. spontaneous deamination N H N O NH2 N H NH O O H2O + NH3 cytosine PRACTICE PROBLEM 16 Adenine can be deaminated to hypoxanthine, and guanine

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

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


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



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-

+


2 HPO42-

H2O



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-

+


2 HPO42-

H2O

H O ACC5'

tRNA

O ACC5'

tRNA

C

O-

O+H3N

R P OO-

OO

HO

Ad



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-

+


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



DNA, RNA, etc.

Midterm 1 [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

Chem 109 C Bioorganic CompoundsDNA, RNA, etc. spontaneous deamination N H N O NH2 N H NH O O H2O + NH3 cytosine PRACTICE PROBLEM 16 Adenine can be deaminated to hypoxanthine, and guanine

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