UCSC, Binder Name______________________________________ Student ID # _____________________ Section Day/Time ____________

CHEM 109 - Organic Chemistry with Biological Applications EXAM 1A (200 points)

DO NOT BEGIN THE EXAM OR TURN THE PAGE UNTIL INSTRUCTED TO DO SO.

In the meantime, please read the instructions below.

In each of the following problems, use your knowledge of organic chemistry conventions to answer the questions in the proper manner. Be sure to read each question carefully. You have 1.5 hours to complete this exam. Point distributions are given throughout the exam so you can use your time wisely. Keep your eyes on your own paper. “Cheat sheets” and electronic devices of any kind are not allowed, including cell phones, smart watches, and calculators. Any student found using any of said devices, or found examining another student’s exam, will be promptly removed from the exam room and at minimum will receive a zero on this exam. Such an incident may also be considered a form of academic dishonesty and reported to the UCSC Judiciary Affairs Committee.

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Page 6 (35)

Total

Key

CHEM 109, EXAM 1A, Sp ‘19 Last Name, First Initial _________________________

The correct start & end points of arrows are crucial for full credit! 1________

1. Fundamentals (a) (10 points) Provide the name of the circled functional group in each compound below.

(b) (5 points) Indicate whether each term below is an example of an intermolecular or intramolecular force by checking the appropriate box. INTERmolecular Force INTRAmolecular force

Ion-Dipole Ionic Bond

Dipole-Dipole Covalent Bond

Hydrogen Bonding

(c) (5 points) Which are being broken when pure water boils? Circle one. Covalent Bonds Ion-Dipole Hydrogen-Bonds Ionic Bonds (d) (5 points) Provide the approximate pKa of each compound on the lines provided.

OHCl H2S NH3 NH4

+

Lptseach

aldehyde alkene thioester

esters IptO

#nNHz

ketone amide

Ipteach

✓

✓✓

✓✓

lpteaen

Ipt each

tzpkawits -7 20 7 35 10OK

25

CHEM 109, EXAM 1A, Sp ‘19 Last Name, First Initial _________________________

The correct start & end points of arrows are crucial for full credit! 2________

2. Amino Acids (a) Draw the dominant ionic species of the amino acids at the indicated pH ranges based on the given pKa’s. Indicate all charged atoms. Circle any formal charges.

(i) (15 points) Titration of Histidine - pKa1 1.8; pKa2 9.2; pKaR 6.1

(ii) (15 points) Titration of Glutamic Acid – pKa1 2.2; pKa2 9.7; pKaR 4.3

(b) (10 points) Amino Acids – fill in the table. The full name or abbreviation is given for an amino acid. Fill in the blank cells with the corresponding missing name or abbreviation. Given the pKa’s, determine the charge of the dominant ionic species at pH 3 and pH 11. Full Name Single-Letter

Abbreviation Three-Letter Abbreviation

pKa1 pKa2 pKaR Charge pH 3 pH 11

His 1.8 9.2 6.0

Glutamic Acid 2.2 9.7 4.3

R 2.2 9.0 12.5

2.2 < pH < 4.3 4.3 < pH < 9.7

Charge:

pH > 9.7pH < 2.2

3.pt/ure ① ③struc

¥¥÷÷:*

:*.¥÷÷i :*:÷÷:c .÷i÷

:Npotsere'- I O - I

① ③ -0 -0

COZHCOZH coz Coz

I I

① H ①③ H A A ③HOzc~NFtz-OOC~NHz-oozc~NHz-oozc~NHz.tl

O - I -2

pthotentialz

Ipt each -52 potential extra

Histidine H t t - I

E Glu O -2

Arginine Arg H O

4042 max

CHEM 109, EXAM 1A, Sp ‘19 Last Name, First Initial _________________________

The correct start & end points of arrows are crucial for full credit! 3________

3. Arrow-Pushing Warm-up (a) (10 points) Resonance – add formal charges where appropriate and arrow(s) to complete each transformation from left to right.

(b) (10 points) Resonance – Follow the arrows and draw the resulting resonance structure. Include formal charges where appropriate.

(c) (5 points) Provide a list of all bonds broken and formed in the reaction below. Make sure to account for type and quantity of bonds.

(d) (5 points) Arrow story – indicate which bonds are broken & formed as a product of the indicated arrow.

H2N NH2

NH2

H2N NH2

NH2

H2N NH2

NH2

OO

O

O

H+

O

B:

OH

(i)

(ii)

(iii)

(i) ________________________

(ii) ________________________

(iii) ________________________

'plunked

②①to

%.

↳

to

⑤d②① ①

②② O_O①12⑧potential

8.cn#o-o1extraC=Nt-⇐OILH -O_O,

N - It-QB - H formed

'O

C- H broken '0C - C formed -0GOT broken ①O - H formed -0

3032 potential

CHEM 109, EXAM 1A, Sp ‘19 Last Name, First Initial _________________________

The correct start & end points of arrows are crucial for full credit! 4________

4. Mechanism Warm-Up

(a) (5 points) This is not a mechanism question, but didn’t fit anywhere else on the exam… List the approximate pKa of each molecule in the box provided.

(b) (10 points) Add arrows to complete the mechanism. Do not add more intermediates. You will need a base (:B) and/or acid (H+).

(c) (10 points) Follow the arrows and draw all of the products.

(d) (10 points) Follow the arrows in this active site. The numbers are not important for this problem but indicate the position on the peptide chain, in case you’re interested. Draw the released product and the resultant amino acid side chains.

O

OH

OH

OH

OH

HO

H A

0 ① 20 ① 10 ② 5 ①

②②

B :↳ If ↳ ②⑤

Hoy ①① charge

TOH2O Ao

OH It

HTO ⑦

2ftthereOH

HisAsp ② f ②

0*00 ANSer I ④

② bit HER

35

CHEM 109, EXAM 1A, Sp ‘19 Last Name, First Initial _________________________

The correct start & end points of arrows are crucial for full credit! 5________

5. Fill in the Box (7 points each) Each reaction below is missing a component (reactant or product). There is ample information/clues given to reasonably complete the reaction scheme. Be sure to balance reaction if needed. No arrows necessary! Draw full structures – no defining R groups on this page. (a)

(b)

(c)

(d)

(e)

CHOOHHHHOOHHOHH

CH2O

Glucose

+

ATP

hexokinase

H

O PO

OO ADP

CHOOHHHHOOHHOHH

CH2O

NucleophilicAcyl

Substitution

ADP

(3S)-Hydroxyacyl CoA

Hydroxyacyl CoADehydrogenase

NAD+ NADH

SCoA

O

β-Ketoacyl CoA

O

O

CO2-

Pyruvate

HN

PO

NH2

OH

Pyridoxaminephosphate

An Imine

+ H2O

⑦EI

"

999¥II'onO'P' - oo

⑦i - ④Oo

O ⑦

3pts-ooekha.iowrong stereochromynot shown -*5ptsOH O ⑦

CoA

%×n¥copr"

"Indio

.io#oHHoKwHN+oyHoH5pts

35

CHEM 109, EXAM 1A, Sp ‘19 Last Name, First Initial _________________________

The correct start & end points of arrows are crucial for full credit! 6________

6. More Mechanisms! (a) (15 points) Unsaturated carbonyls can be hydrated through a conjugate addition mechanism. Show the full arrow-pushing mechanism, bringing in acid(s) (H+) and/or base(s) (:B) as needed. It is possible to complete this mechanism in one step, but it is also acceptable to have more steps with one or more intermediates.

(b) (20 points) The first step in the melavonate pathway for lipid biosynthesis is shown below. This is a carbonyl condensation (Claisen) reaction between two acetyl CoA units. Since this is a type of nucleophilic acyl substitution (NAS), this mechanism has at least one intermediate. Show the full arrow-pushing mechanism, bringing in acid(s) (H+) and/or base(s) (:B) as needed. It is possible to complete this mechanism in two steps, but it is also acceptable to have more steps with two or more intermediates.

SCoA

O

α,β-UnsaturatedAcyl CoA

H2O

SCoA

O

(3S)-Hydroxyacyl CoA

OH

Enoyl CoAHydratase

SCoA

O

SCoA

O+

Claisen Product

+ HSCoASCoA

O O

⑦③ B:¥i9H③③

" EEE. s.*÷÷¥¥ .! + .③③ ③ r

"

"

soon.→

÷±⇒sI"hairs

③ ③met

②②B. .hr

520Hy ←②↳ is:÷÷÷÷:p②② ② intend

galternateiscore. scores con ② mechanism

① µ Slot

zg