Fall 2019HFH1104

Armen ZakarianOffice: Chemistry Bldn 2217

Chem 109 CBioorganic Compounds

http://labs.chem.ucsb.edu/~zakariangroup/courses.html

CLAS Instructor: Dhillon Bhavanbdhillon@ucsb.edu

Average 49.1St Dev 14.1

Max 87.5

Min 15

Midterm 3 stats

test are available outside room 2135 (Chemistry, 2nd floor)in a box, sorted in alphabetical order, by color

Each test will be curved individually to 75% average

Lowest midterm will be dropped

Scores from 2 best M and the Final will be added

Grades will be assigned according to the syllabus

Final Course Grading

22. 11 ptDraw all reactions required to convert hexanoic acid to 3 molecules of acetyl CoA through the β-oxidation cycles. Name all necessary coenzymes and enzymes. How many molecules of ATP and CO2 will be produced from hexanoic acid after its entire metabolism through all 4 stages ?

O

O

hexanoic acid (hexanoate)

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. Structure and Classification •  DNA: Deoxyribonucleic acid

encodes hereditary information controls cell division and growth

•  RNA: Ribonucleic acid

transcription and translation stores genetic information in viruses

DNA, RNA, etc. Structure and Classification

Obase

O

O

Obase

O

O

PO O-

PO O-

Obase

O

O

2'

5'

PO O-

DNA

Obase

OHO

OP

Obase

OHO

O

PO O-

PO O-

Obase

OHO

O

O O-

2'5'

RNA

DNA, RNA, etc. Structure and Classification

DNA and RNA RNA only

DNA only

DNA, RNA, etc. Structure and Classification

DNA and RNA RNA only

DNA only

DNA, RNA, etc.

DNA and RNA RNA only

DNA only

Structure and Classification

DNA, RNA, etc.

DNA and RNA RNA only

DNA only

Structure and Classification

DNA, RNA, etc.

DNA and RNA RNA only

DNA only

Structure and Classification

DNA, RNA, etc.

DNA and RNA RNA only

DNA only

Structure and Classification

DNA, RNA, etc. Structure and Classification

nucleosides = base + sugar

ON

NN

N

NH2

HO

HO

2'-deoxyadenosine

ON

NN

N

NH2

HO

OHHO

adenosine

PRACTICE PROBLEM Draw the structures and provide names for all other nucleosides

DNA, RNA, etc. Structure and Classification

nucleotides = base + sugar + phosphate

2'-deoxyguanosine5'-monophsphate

guanosine3'-monophosphate

O

N

NHN

N

O

O

HO

P-OO-

OH2N

O

N

NHN

N

O

HO

O

H2N

OH

O

N

NHN

N

O

O

O

P-OO-

OH2N

OH

PO-

O O- POO-

O-

a deoxynucleotise

a ribonucleotide

DNA, RNA, etc. Structure and Classificationnucleotides = nucleoside phosphates

cytidine5'-triphosphate

ON

O

OHHO

POO-

OPO

OO-

PO

-OO-

N

NH2

OON

O

OHHO

POO-

O

N

NH2

O

cytidine5'-monophosphate

CMP CTP

dAMP2’-deoxy Adenosine Mono Phosphate

PRACTICE PROBLEM 2 Draw the structures for: dCMP, UDP, dTTP

2'-deoxycytidine5'-monophosphate

dCMP

ON

O

HO

POO-

O

N

NH2

O

dCDP

ON

O

HO

POO-

OPO

-OO-

N

NH2

O

2'-deoxycytidine5'-diphosphate

DNA, RNA, etc. Structure and Classification

dinucleotides 2 nucleotides oligonucleotides 3-10 nucleotides polynucleotides many (human DNA - 3,100,000,000 bp)

dCTP

ON

O

HO

POO-

OPO

OO-

N

NH2

O

ON

NN

N

NH2

O

HO

POO-

OPO

OO-

PO

-OO-

P-O

O

O-+

dATP

DNA, RNA, etc.

ON

O

O

POO-

OPO

OO-

N

NH2

OP-O

O

O-

POO

O-

O N

HO

N

N

N

NH2O-P

O

OO-

PO

-OO-

+

CAGTAACCTGAGAACCAATCGGAA…

Synthesis: nucleotide triphosphates, 5’ 3’

DNA or RNA polymerase

primary structure

DNA, RNA, etc.

Facts about DNA

!  double helix

!  two anti-parallel strands

A pairs with T, G pairs with C

pairing through hydrogen bonds

stacking interactions

3’

5’

5’

3’

DNA, RNA, etc.

Facts about DNA

double helix

two anti-parallel strands

!  A pairs with T, G pairs with C

pairing through hydrogen bonds

stacking interactions

DNA, RNA, etc.

Facts about DNA

double helix

two anti-parallel strands

A pairs with T, G pairs with C

!  pairing through hydrogen bonds

stacking interactions

NN

O

O

R

ribose

HN

N N

NN

ribose

HH

R-CH3, thymine adenine

2 hydrogen bonds

NN

N

ribose O

HH

NN N

NO

NH

H

Hribose

cytosine guanine

3 hydrogen bonds

DNA, RNA, etc.

Facts about DNA

double helix

two anti-parallel strands

A pairs with T, G pairs with C

pairing through hydrogen bonds

!  stacking interactions

DNA, RNA, etc.

PRACTICE PROBLEM 4 and 5 Indicate which functional group of the five heterocyclic bases can function as a hydrogen bond donor (D), a hydrogen bond acceptor (A), or both (D/A) How would the base pairing be affected if the bases existed in the “enol” form?

DNA, RNA, etc.

PRACTICE PROBLEM 4 and 5 Indicate which functional group of the five heterocyclic bases can function as a hydrogen bond donor (D), a hydrogen bond acceptor (A), or both (D/A) How would the base pairing be affected if the bases existed in the “enol” form?

NN

O

O

R

ribose

HN

N N

NN

ribose

HH

R-CH3, thymine adenine

A A

AA

D

D

A

NN

N

ribose O

HH

NN N

NO

NH

H

Hribose

cytosine guanine

A A

A

A

A

D

D

D

DNA, RNA, etc.

PRACTICE PROBLEM 4 and 5 Indicate which functional group of the five heterocyclic bases can function as a hydrogen bond donor (D), a hydrogen bond acceptor (A), or both (D/A) How would the base pairing be affected if the bases existed in the “enol” form?

NN

O

O

R

ribose

HN

N N

NN

ribose

HH

R-CH3, thymine adenine

A A

AA

D

D

A

NN

O

O

R

riboseN

N N

NN

ribose

HH

R-CH3, thymine adenine

D A

AA

D

A

H

A

“enol” form of T

DNA, RNA, etc.

PRACTICE PROBLEM 4 and 5 Indicate which functional group of the five heterocyclic bases can function as a hydrogen bond donor (D), a hydrogen bond acceptor (A), or both (D/A) How would the base pairing be affected if the bases existed in the “enol” form?

NN

N

ribose O

HH

NN N

NO

NH

H

Hribose

cytosine guanine

A A

A

A

A

D

D

D

DNA, RNA, etc.

PRACTICE PROBLEM 7 If one of the strands of DNA has the following sequence of bases running in the 5’ → 3’ direction,

GGACAATCTGC a. what is the sequence of bases in the complementary strand? b. what base is closest to the 5’-end in the complementary strand?

DNA, RNA, etc.

DNA is stable, RNA is not: chemical stability

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.

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 is stable, RNA is not: chemical stability

DNA, RNA, etc.

DNA is stable, RNA is not: genetic stability

DNA has thymine, RNA has uracil

N

N

NH2

O

RNAcytosine

H2O N

N

OH

OR

tautomerizationHN

N

O

O

RNAuracil

MUTATION !

spontaneous deamination

DNA, RNA, etc.

DNA is stable, RNA is not: genetic stability

DNA has thymine, RNA has uracil

N

N

NH2

O

RNAcytosine

H2O N

N

OH

OR

tautomerizationHN

N

O

O

RNAuracil

MUTATION !

N

N

NH2

O

DNAcytosine

H2O N

N

OH

OR

tautomerizationHN

N

O

O

DNAuracil, NOT found

in DNA

HN

N

O

O

DNA

NOT recognized asdefect and repaired

spontaneous deamination

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.

DNA, RNA, etc. DNA (bio)synthesis

!  is called replication

!  done by DNA polymerase

strand separation, replication fork

again, always in 5’ → 3’ direction

using the nucleotide triphosphates

X-ray structure of rb69 gp43 + thymine glycol

DNA, RNA, etc. DNA (bio)synthesis

!  is called replication

!  done by DNA polymerase

strand separation, replication fork

again, always in 5’ → 3’ direction

using the nucleotide triphosphates