Document:

Amendment No. 1 to the Subordinated Convertible Note Purchase Agreement

 Exhibit 10.41 
 AMENDMENT NO. 1 TO 
 SUBORDINATED CONVERTIBLE NOTE PURCHASE AGREEMENT

 This Amendment No. 1 to the Subordinated Convertible Note Purchase Agreement (this
“Amendment”) is made and entered into as of June 1, 2010, by and among Mascoma Corporation, a Delaware corporation (the “Company”), and the Purchasers parties hereto. Capitalized terms used
herein, but not otherwise defined herein, shall have the meanings ascribed to such terms in the Note Purchase Agreement (as defined below). 
 WHEREAS, the Company and certain Purchasers are parties to that certain Subordinated Convertible Note Purchase Agreement, dated as of April 7, 2010 (the “Note Purchase
Agreement”); 
 WHEREAS, the Company and the Purchasers whose signatures are affixed below desire to
amend the Note Purchase Agreement to modify the process for selling certain of the Notes; 
 WHEREAS, pursuant to
Section 5.02 of the Note Purchase Agreement, any provision of the Note Purchase Agreement can be amended if the Company shall obtain consent thereto in writing from the Purchasers holding at least 66 2/3% of the principal outstanding under the
then outstanding Notes (the “Requisite Purchasers”); and 
 WHEREAS, the undersigned
Purchasers represent the Requisite Purchasers. 
 NOW THEREFORE, the parties hereby agree as follows: 

 

	 	1.	Section 1.02(b) of the Note Purchase Agreement shall be amended and restated in its entirety as set forth below: 

“(b) The Follow-On Closing. Following the Initial Closing, the Company will offer up to $1,419,000 total
principal amount of Notes, on a pro rata basis (based on shares of the Company’s Common Stock, par value $0.001 per share (the “Common Stock”) issuable upon conversion of the Preferred Stock (as defined below) held by
such holders), to the holders of the Company’s Preferred Stock who are not Initial Purchasers (the “Other Investors”). Any Other Investor who commits to purchase Notes shall execute an Additional Purchaser signature page
to this Agreement, in substantially the form attached hereto as Schedule A, and shall thereafter be bound to this Agreement as an Additional Purchaser, and Exhibit B attached hereto shall be updated to include the principal amount of
Notes that each Additional Purchaser has committed to purchasing. Forty percent (40%) of each Additional Purchaser’s commitment shall be funded at the Follow- On Closing (as defined below) and the remaining sixty percent (60%) shall
be funded at the Second Closing (as defined below). The initial purchase and sale of the Notes to the Additional Purchasers shall take place at a closing (the “Follow-On Closing”) to be held no later than sixty (60) days
after the Initial Closing.” 

 Any Notes offered to the Other Investors that are not purchased by the Other Investors at
the Follow-On Closing (the “Additional Follow-On Notes”) may be offered and sold by the Company in accordance with Section 1.02(c) below.” 

 

	 	2.	Section 1.02(c) of the Note Purchase Agreement shall be amended and restated in its entirety as set forth below: 

“(c) The Second Closing. After the Initial Closing and the Follow-On Closing, the Company shall sell, and the Purchasers shall
purchase, Notes in the principal amounts set forth opposite each Purchaser’s name on Exhibit A (for Initial Purchasers) or Exhibit B (for Additional Purchasers) under the heading “Principal Amount of Notes to Be Purchased at
the Second Closing.” Such purchase and sale shall take place at a closing (the “Second Closing,” and together with the Initial Closing, the Follow-On Closing and the Final Closing (as defined below), the
“Closings” and each individually a “Closing”) to be held no sooner than two (2) days and no later than ten (10) days following the approval by (A) the Board of Directors of the Company
and (B) the Purchasers holding at least sixty-six and two-thirds percent (66 2/3%) of the principal amount of the outstanding Notes then held by all Purchasers of (i) a business plan and strategy for monetization of the Company’s corn
CBP business and (ii) a plan for near- term acquisition opportunities for the Company (the “Second Closing Approval”); provided that if the Second Closing Approval does not occur on or before June 15, 2010,
the Purchasers shall be relieved of their obligation to purchase any additional Notes hereunder. Notwithstanding the foregoing, if a Purchaser (an “Opting Out Purchaser”) obligated to purchase a Note at the Second Closing
chooses not to purchase such Note at the Second Closing, such Opting Out Purchaser shall be relieved of its obligation to purchase such Note, but such Opting Out Purchaser shall be subject to the Mandatory Conversion described in
Section 1.02(e). Each Purchaser shall give the Company notice, at least two (2) days prior to the Second Closing, if such Purchaser shall be an Opting Out Purchaser. 
 The Additional Follow-On Notes and any Notes not purchased at the Second Closing by Opting Out Purchasers (the “Additional Opt Out Notes,” and together with the Additional
Follow-On Notes, the “Additional Notes”) may be offered by the Company to Purchasers who have funded or committed to fund their entire pro rata portion of Notes (collectively, the “Participating
Purchasers”) on a pro rata basis to the Notes purchased by all Participating Purchasers. If and to the extent that the Participating Purchasers do not agree to purchase all Additional Notes, the Company may, in its sole discretion,
apportion and offer the Additional Notes as to which one or more Participating Purchasers has declined the Company’s offer to purchase to one or more of the Participating Purchasers. Upon the acceptance by any Participating Purchaser of the
Company’s offer to purchase Additional Notes, the principal amount of Notes set forth opposite such Purchaser’s name under the column “Principal Amount of Notes Purchased at the Second Closing” or “Principal Amount of
Additional Notes Purchased at the Final Closing” on Exhibit A or Exhibit B, as the case may be, shall be increased by the 

  
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Company in an amount equal to the principal amount of the Additional Notes agreed to be purchased by such Participating Purchaser. The purchase and sale of the Additional Notes shall take place
either at the Second Closing or at a final closing to be held within ten (10) business days following the Second Closing (the “Final Closing”), as determined by the Company.” 

 

	 	3.	Except as amended hereby, the remainder of the Note Purchase Agreement shall remain in full force and effect. 

 

	 	4.	This Amendment shall be governed by, and construed and enforced in accordance with, the substantive laws of the State of Delaware without regard to its principles of
conflicts of laws. 

  

	 	5.	This Amendment may be executed in any number of counterparts, each of which shall be deemed an original, but all of which taken together shall constitute one and the
same instrument, and any of the parties hereto may execute this Agreement by signing any such counterpart. This Amendment may be executed and delivered by facsimile, or by e-mail in portable document format (.pdf) and delivery of the signature page
by such method will be deemed to have the same effect as if the original signature had been delivered to the other parties. This Amendment shall take effect when executed by the Company and the Requisite Purchasers. 

[REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK] 

  
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 IN WITNESS WHEREOF, the parties hereto have executed this Amendment No. 1 to
Subordinated Convertible Note Purchase Agreement on the day, month and year first above written. 
  

			
	MASCOMA CORPORATION
		
	By:	 	  

		 	Name:
		 	Title:

 
	
	 /s/ R. Jeremy Grantham

	R. Jeremy Grantham

 Mascoma Corp. Amendment No 1 to Subordinated Convertible Note Purchase Agreement dated June 1, 2010

 
			
	 PINNACLE VENTURES II-A, L.P
 PINNACLE VENTURES II-B, L.P.
 PINNACLE VENTURES II-C, L.P.

PINNACLE VENTURES II-R, L.P.
 PINNACLE
VENTURES EQUITY FUND I, L.P.

	PINNACLE VENTURES EQUITY FUND I-O, L.P.
	PINNACLE VENTURES EQUITY FUND I AFFILIATES, L.P.
	
	 By Pinnacle Ventures Equity Management I, L.L.C.,
 its general partner

		
	By:	 	 /s/ Robert N. Savoie

	Name:	 	Robert N. Savoie
	Title:	 	Chief Financial Officer

 
			
	ATLAS VENTURE FUND VII, L.P.
	By:	 	 Atlas Venture Associates VII, L.P.,
Its General Partner

	By:	 	 Atlas Venture Associates VII, Inc.,
Its General Partner

		
	By:	 	 /s/ Kristen Laguerre

	Name:	 	Kristen Laguerre
	Title:	 	VP

 
					
	GENERAL MOTORS HOLDINGS LLC
		
	By:	 	 /s/ Rajesh Yadava

		 	Name:	 	 Rajesh Yadava 

		 	Title:	 	Director of Business Development, Treasurer’s Office

 
			
	FLAGSHIP VENTURES FUND 2004, L.P.
	
	 By: its General Partner
 Flagship Ventures General Partner LLC

		
	By:	 	 /s/ Noubar B. Afeyan

		 	Name:
		 	Title:

 
					
	 GENERAL CATALYST GROUP IV, L.P.
 By: General Catalyst Partners IV, L.P., its General Partner

	
	By: General Catalyst GP IV, LLC, General Partner
	By:	 	 /s/ William J. Fitzgerald

		 	Name:	 	William J. Fitzgerald
		 	Title:	 	Member and Chief Financial Officer
	
	 GC ENTREPRENEURS FUND IV, L.P.
 By: General Catalyst Partners IV, L.P., its General Partner

	
	By: General Catalyst GP IV, LLC, its General Partner
		
	By:	 	 /s/ William J. Fitzgerald

		 	Name:	 	William J. Fitzgerald
		 	Title:	 	Member and Chief Financial Officer

 
					
	KHOSLA VENTURES I, LP
	
	By: Khosla Ventures Associates I, LLC, a Delaware limited liability company and general partner of Khosla Ventures I, LP
		
	By:	 	 /s/ SAMIR KAUL

		 	Name:	 	SAMIR KAUL
		 	Title:	 	PARTNER

 
					
	KPCB HOLDINGS, INC., as nominee
		
	By:	 	 /s/ ERIC KELLER

		 	Name:	 	ERIC KELLER
		 	Title:	 	PRESIDENT

 
					
	BLUESTEM GROWTH & INCOME FUND III, LLC
	
	By: Bluestem Capital Company, LLC
		
	By:	 	 /s/ Steve Kirby

		 	Name:	 	Steve Kirby
		 	Title:	 	President

 
					
	BLUESTEM SELECT OPPORTUNITIES FUND, LLC
	
	By: Bluestem Capital Company, LLC
		
	By:	 	 /s/ Steve Kirby

		 	Name:	 	Steve Kirby
		 	Title:	 	President

 
					
	MPC INVESTMENT LLC
		
	By:	 	 /s/ Clifford C. Cook

		 	Name:	 	 Clifford C. Cook 

		 	Title:	 	Manager
			
		 		 	

 
					
	MALAYSIAN LIFE SCIENCES CAPITAL FUND
		
	By:	 	 /s/ ROGER WYSE

		 	Name:	 	ROGER WYSE
		 	Title:	 	CO-CHAIRMAN

 
					
	PIPER JAFFRAY & CO.
		
	By:	 	 /s/ Robert P. Rinek

		 	Name:	 	Robert P. Rinek
		 	Title:	 	Managing Director

 
	
	 /s/ David Mann

	David Mann

 
					
	CRM HOLDINGS, LLC
		
	By:	 	 /s/ Michael Ladiseh

		 	Name:	 	Michael Ladiseh
		 	Title:	 	Partner
		 		 	6/7/2010

 
			
	ATLAS VENTURE FUND VII, L.P.
	 By:
	 	 Atlas Venture Associates VII, L.P.,
Its General Partner

	By:	 	 Atlas Venture Associates VII, Inc.,
Its General Partner

		
	By:	 	 /s/ Kristen Laguerre

	Name:	 	Kristen Laguerre
	Title:	 	VP

 
	
	 /s/ Bruce A. Jamerson 6/9/10

	Bruce A. Jamerson

 
			
	VPVP CLEANTECH HOLDINGS 2006, L.L.C.
		
	By:	 	 VantagePoint Venture Partners 2006 (Q), L.P.,
 Its Sole Member

	By:	 	 VantagePoint Venture Associates 2006, L.L.C.,
 Its Managing Member

		
	By:	 	 /s/ Alan E. Salzman

	Name:	 	Alan E. Salzman
	Title:	 	Managing Member
	
	VANTAGEPOINT CLEANTECH PARTNERS, L.P.
		
	By:	 	 VantagePoint CleanTech Associates, L.L.C.,
 Its General Partner

		
	By:	 	 /s/ Alan E. Salzman

	Name:	 	Alan E. Salzman
	Title:	 	Managing Member

 
					
	FAGEN, INC.
		
	By:	 	 /s/ Ron Fagen

		 	Name:	 	Ron Fagen
		 	Title:	 	CEO & President

 
					
	STACK, LLC
		
	By:	 	 /s/ Fred M. Fehsenfeld, Jr.

		 	Name:	 	Fred M. Fehsenfeld, Jr.
		 	Title:	 	Chief Operating OfficerSubordinated Convertible Promissory Note and Warrant Purchase Agreement

 Exhibit 10.42 
 Execution Version 
 SUBORDINATED CONVERTIBLE PROMISSORY NOTE AND WARRANT
PURCHASE AGREEMENT 
 This SUBORDINATED CONVERTIBLE NOTE AND
WARRANT PURCHASE AGREEMENT (the “Agreement”) is made and entered into as of August 5, 2011, by and among Mascoma Corporation, a Delaware corporation (the
“Company”), the initial purchasers listed on Exhibit A attached hereto (each an “Initial Purchaser” and collectively the “Initial Purchasers”) and the additional
purchasers listed on Exhibit B attached hereto (each an “Additional Purchaser” and collectively the “Additional Purchasers”). The Initial Purchasers and the Additional Purchasers are referred to
herein as the “Purchasers,” and each individually a “Purchaser.” Capitalized terms used herein but not defined herein shall have the meanings ascribed to them in the Notes (as defined below).

 A. The Company currently requires funds to help finance its continued operations. 

B. The Purchasers are willing to advance funds to the Company in exchange for the issuance to them of certain subordinated convertible
promissory notes evidencing the Company’s obligation to repay the Purchasers’ loans of the advanced funds, all as provided in this Agreement. 
 NOW THEREFORE, the parties hereby agree as follows: 
 ARTICLE 1 

PURCHASE, SALE AND TERMS OF NOTES; ISSUANCE OF WARRANTS 
 1.01 The Notes. The Company has authorized the issuance and sale to the Purchasers of the Company’s Subordinated Convertible Promissory Notes in the original aggregate principal amount of up
to $50,000,000. The Subordinated Convertible Promissory Notes shall be substantially in the form set forth as Exhibit C hereto and are herein referred to individually as a “Note” and collectively as the
“Notes,” which terms shall also include any notes delivered in exchange or replacement therefor. 
 1.02
Purchase and Sale of Notes. 
 (a) The Initial Closing. The Company agrees to issue and sell to the Initial
Purchasers, and, subject to and in reliance upon the representations, warranties, covenants, terms and conditions of this Agreement, the Initial Purchasers agree to purchase the Notes in the principal amounts set forth opposite each Initial
Purchaser’s name on Exhibit A hereto under the heading “Principal Amount of Notes To Be Purchased at the Initial Closing”. Such purchase and sale shall take place at a closing (the “Initial Closing”) to
be held remotely via the exchange of documents on the date hereof at 12:00 p.m., Boston time, or at such other time or place as may be mutually 

 
agreed upon by the Company and the Initial Purchasers purchasing at least a majority of the principal amount of the Notes actually purchased at the Initial Closing. 

(b) Follow-On Closings. Following the Initial Closing and no later than August 15, 2011, Company will offer up to $40,000,000
in the total principal amount of Notes to (i) the Additional Purchasers on a pro rata basis (based on shares of the Company’s Common Stock, par value $0.001 per share (the “Common Stock”), issuable upon conversion
of the Preferred Stock (as defined below) held by such holders), and (ii) the Initial Purchasers who wish to purchase in excess of the amounts purchased at the Initial Closing. Any Additional Purchaser who commits to purchase Notes shall
execute an Additional Purchaser signature page to this Agreement, in substantially the form attached hereto as Schedule A, and shall thereafter be bound by this Agreement as an Additional Purchaser. Exhibit A and Exhibit B
attached hereto shall be updated to include the principal amount of Notes that each Initial Purchaser or Additional Purchaser, as applicable, has committed to purchasing at the Follow-On Closings (as defined below). The purchase and sale of the
Notes to the Additional Purchasers and the Initial Purchasers who have elected to participate in one or more closing or a series of closings subsequent to the Initial Closing will be held no later than August 15, 2011 (the “Follow-On
Closings” and, together with the Initial Closing, the “Closings”). Any Notes offered to the Additional Purchasers that are not purchased by the Additional Purchasers may be purchased by the Initial Purchasers or
the Additional Purchasers on a pro rata basis to the Notes purchased by such other Purchasers or on such other basis as may be agreed upon by the Company and the Purchasers holding at least a majority of the principal outstanding under the then
outstanding Notes. 
 (c) The Closings. At each Closing, each Purchaser participating in such Closing will deliver to the
Company as payment in full for the Note to be purchased by such Purchaser at such Closing, by (i) a check payable to the Company’s order, (ii) wire transfer of funds to the Company, or (iii) any combination of the foregoing. At
each Closing, the Company will issue and deliver to each Purchaser participating in such Closing a duly executed Note in the principal amount funded by such Purchaser at such Closing. The Company shall send the Notes to the Purchasers at the
addresses furnished to the Company for that purpose. 
 1.03 Issuance of Warrants. The Company shall issue a warrant in
substantially the form attached hereto as Exhibit D (each, a “Warrant” and collectively the “Warrants”) to each Purchaser upon the first to occur of a (i) Qualified Financing or
(ii) IPO , in accordance with the following terms: 
 (a) Issuance upon a Qualified Financing: Provided a Purchaser
has purchased at least its Pro Rata Portion of Notes (as defined below), the following shall apply: (i) if the Notes are converted into New Equity Securities upon a Qualified Financing Closing, in connection with such conversion, the Company
shall issue to each such Purchaser a Warrant, for that number of shares of New Equity Securities as is equal to twenty-five percent (25%) of the New Equity Securities acquired by such Purchaser upon conversion of that portion of the Notes that
such Purchaser purchased up to and including such Purchaser’s Pro Rata Portion of Notes (as defined below); (ii) provided 

  
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that if such Purchaser has purchased greater than such Purchaser’s Pro Rata Portion of Notes, such Purchaser additionally shall be entitled to receive that number of shares of New Equity
Securities as is equal to fifty percent (50%) of the New Equity Securities acquired by such Purchaser upon conversion of that portion of the Notes that such Purchaser purchased in excess of such Purchaser’s Pro Rata Portion of Notes; and

 (b) Issuance upon an IPO: Provided a Purchaser has purchased at least its Pro Rata Portion of Notes, the following
shall apply: (i) if the Notes are converted into Common Stock upon an IPO, in connection with such conversion, the Company shall issue to each such Purchaser a Warrant for that number of shares of Common Stock as is equal to twenty-five percent
(25%) of the Common Stock acquired by such Purchaser upon conversion of that portion of the Notes that such Purchaser purchased up to and including such Purchaser’s Pro Rata Portion of Notes (as defined below); (ii) provided
that if such Purchaser has purchased greater than such Purchaser’s Pro Rata Portion of Notes, such Purchaser additionally shall be entitled to receive that number of shares of Common Stock as is equal to fifty percent (50%) of the Common
Stock acquired by such Purchaser upon conversion of that portion of the Notes that such Purchaser purchased in excess of such Purchaser’s Pro Rata Portion of Notes. 
 For purposes of this Agreement, “Pro Rata Portion of Notes” means the aggregate principal amount of Notes for such Purchaser set forth opposite such Purchaser’s name on
Schedule 1.03 attached hereto, which shall be updated in connection with the Follow-On Closings to add in the Additional Purchasers. 
 1.04 No Usury. This Agreement and each Note issued pursuant to the terms of this Agreement are hereby expressly limited so that in no event whatsoever, whether by reason of deferment or advancement
of loan proceeds, acceleration of maturity of the loan evidenced hereby, or otherwise, shall the amount paid or agreed to be paid to the Purchasers hereunder for the loan, use, forbearance or detention of money exceed the maximum interest rate
permitted by the laws of the Commonwealth of Massachusetts and the State of New Hampshire. If at any time the performance of any provision hereof or any Note involves a payment exceeding the limit of the price that may be validly charged for the
loan, use, forbearance or detention of money under applicable law, then automatically and retroactively, ipso facto, the agreed upon interest rate as set forth in the Notes shall be reduced to such limit, it being the specific intent of the Company
and the Purchasers hereof that all payments under this Agreement or any Note are to be credited first to interest as permitted by law, but not in excess of (i) the agreed rate of interest set forth in the Note, or (ii) that permitted by
law, whichever is the lesser, and the balance toward the reduction of principal. The provisions of this paragraph shall never be superseded or waived and shall control every other provision of this Agreement and any Note. 

  
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 ARTICLE 2 
 CONDITIONS TO THE PARTIES’ OBLIGATIONS 
 2.01 Conditions to the
Purchasers’ Obligations. The respective and several obligations of each Purchaser to purchase and pay for the Notes to be purchased by it at each Closing are subject to the fulfillment or waiver, on or before each Closing, of each of the
following conditions: 
 (a) Representations and Warranties. Each of the representations and warranties of the Company
set forth in Article III hereof shall be true in all material respects on the date of each Closing. 
 (b) Performance by the
Company. The Company shall have performed and complied with all agreements, obligations and conditions contained in this Agreement that are required to be performed or complied with by it on or before each Closing and shall have obtained all
approvals, consents and qualifications necessary to complete the purchase and sale described herein. 
 (c) Delivery of
Notes. The Company shall have executed and delivered to each Purchaser a Note, in the form attached hereto as Exhibit C, evidencing the Company’s indebtedness to such Purchaser in the amount set forth opposite such Initial
Purchaser’s name on Exhibit A under the heading “Principal Amount of Notes To Be Purchased at the Initial Closing” (in the case of the Initial Closing) or the amount set forth such Purchaser’s name on Exhibit A or
Exhibit B, as applicable, under the heading “Principal Amount of Additional Notes to be Purchased at the Follow-On Closings” (in the case of Additional Notes issued at the Follow-On Closings). 

(d) Anti-Dilution Waiver. The holders of the Company’s Preferred Stock shall have waived the application of the anti-dilution
rights of the Preferred Stock contained in the Company’s Eighth Amended and Restated Charter, as amended from time to time (the “Restated Charter”), with respect to the sale and issuance of the Notes and Warrants in
addition to any equity securities, including the New Equity Securities or Common Stock, as the case may be, issued upon conversion of the Notes or exercise of the Warrants (the “Conversion Securities”), and shares of Common Stock issuable
upon conversion of the Conversion Securities, if applicable. 
 2.02 Condition to the Company’s Obligations. The
respective and several obligations of the Company to issue and sell the Notes to the Purchasers at each Closing are subject to the fulfillment or waiver, on or before each Closing of the following condition: 

(a) Subordination Agreement. On or prior to the Initial Closing, in the case of the Initial Purchasers, and the applicable
Follow-On Closing with respect to the Additional Purchasers, the Company and each of Purchasers shall have entered into a subordination agreement with Pinnacle Ventures L.L.C. (“Pinnacle”) to acknowledge that the Notes issued
pursuant to this Agreement are subordinated to the amounts owed 

  
 4 

 
by the Company pursuant to that certain Loan and Security Agreement, dated as of June 1, 2011, by and between the Company and Pinnacle, as amended from time to time. 

ARTICLE 3 

REPRESENTATIONS AND WARRANTIES OF THE COMPANY 
 The Company represents and warrants to each of the Purchasers as follows, each of which representation and warranty is true and correct as of the date hereof: 

3.01 Organization. The Company is a corporation duly organized, validly existing and in good standing under the laws of the State
of Delaware and has all requisite corporate power and authority to own and lease its properties, to carry on its business as currently conducted and as proposed to be conducted and to carry out the transactions contemplated hereby. Except as set
forth in Section 3.01 of the Disclosure Schedule attached hereto as Exhibit E, the Company is duly qualified as a foreign corporation and is in good standing in all such other jurisdictions (which jurisdictions are listed in
Section 3.01 of the Disclosure Schedule) in which the conduct of its business or its ownership or leasing of property requires such qualification and in which the failure so to qualify or so to be in good standing would have a materially
adverse effect on the Company’s operations or financial condition. 
 3.02 Authorization. The execution, delivery
and performance by the Company of this Agreement has been duly authorized by all requisite corporate action. This Agreement has been duly executed and delivered on behalf of the Company and constitute the valid and binding obligations of the
Company, enforceable in accordance with their respective terms. The execution, delivery and performance of this Agreement, the issuance, sale and delivery of the Notes and compliance with the provisions hereof and thereof by the Company, do not and
will not, with or without the passage of time or the giving of notice or both, (a) violate any provision of current law, statute, rule, regulation, ordinance or any ruling, writ, injunction, order, judgment or decree of any court,
administrative agency or other governmental body binding upon the Company or (b) conflict with or result in any breach of any of the terms, conditions or provisions of, or constitute a default (or give rise to any right of termination,
cancellation or acceleration) under, or result in the creation of any lien, security interest, charge or encumbrance upon any of the properties or assets of the Company under the Restated Charter or the Company’s By-laws or any note, indenture,
mortgage, lease, contract, purchase order or other instrument, document or agreement to which the Company is a party or by which it or any of its property is bound or affected. 

3.03 Capitalization. The entire authorized capital stock of the Company, immediately prior to the Initial Closing, consists of:

 (a) 75,000,000 shares of Common Stock, par value $0.001 per share, of which (i) 7,724,742 shares have
been duly and validly issued and are outstanding, fully paid and nonassessable, with no person liability attaching to the ownership thereof; (ii) 5,000,000 shares have been 

  
 5 

 
reserved for issuance upon conversion of the Company’s Series A Preferred Stock, par value $0.001 per share (the “Series A Preferred Stock”); (iii) 5,162,500
shares have been reserved for issuance upon conversion of the Company’s Series Al Preferred Stock, par value $0.001 per share (the “Series A-1 Preferred Stock”); (iv) 11,498,128 shares have been reserved for
issuance upon conversion of the Company’s Series B Preferred Stock, par value $0.001 per share (the “Series B Preferred Stock”); (v) 9,957,105 shares have been reserved for issuance upon conversion of the
Company’s Series C Preferred Stock, par value $0.001 per share (the “Series C Preferred Stock”); (vi) 17,996,223 shares have been reserved for issuance upon conversion of the Company’s Series D Preferred Stock,
par value $0.001 per share (the “Series D Preferred Stock” and, together with the Series A Preferred Stock, the Series A-1 Preferred Stock, the Series B Preferred Stock and the Series C Preferred Stock, the
“Preferred Stock”); (vii) 14,250,000 shares are reserved for issuance pursuant to the exercise of options that have or may be granted from time to time under any Plan (as defined in the Stockholders Agreement); and
(viii) 1,000,000 shares have been reserved for issuance upon the exercise of certain warrants issued in connection with a financing and a strategic acquisition; and 

(b) 49,613,956 shares of Preferred Stock, par value $0.001 per share, of which: (i) 5,000,000 shares have been
designated shares of Series A Preferred Stock and have been duly and validly issued and are outstanding, fully paid and nonassessable, with no personal liability attaching to the ownership thereof, (ii) 5,162,500 shares have been designated
shares of Series Al Preferred Stock, of which, (A) 5,000,000 shares have been duly and validly issued and are outstanding, fully paid and nonassessable, with no personal liability attaching to the ownership thereof, and (B) 162,500 shares
have been reserved for issuance upon conversion of a certain warrant issued in connection with a debt financing, (iii) 11,498,128 shares have been designated shares of Series B Preferred Stock of which, (A) 11,235,955 shares have been duly
and validly issued and are outstanding, fully paid and nonassessable, with no personal liability attaching to the ownership thereof, and (B) 262,173 shares have been reserved for issuance upon conversion of a certain warrant issued in
connection with a debt financing; (v) 9,957,105 shares have been designated shares of Series C Preferred Stock, of which, (A) 9,777,418 shares have been duly and validly issued and are outstanding, fully paid and non-assessable, with no
personal liability attaching to the ownership thereof, and (B) 179,687 shares have been reserved for issuance upon conversion of a certain warrant issued in connection with a debt financing; and (vi) 17,996,223 shares have been designated
shares of Series D Preferred Stock, of which, (A) 15,305,084 shares have been issued and are outstanding, and (B) 2,691,139 shares have been reserved for issuance upon conversion of certain warrants issued in connection with a financing.

 Section 3.03 of the Disclosure Schedule contains a list of all holders of Common Stock and options, warrants or rights
to purchase Common Stock, in each case including the number of shares of Common Stock held by, or subject to purchase pursuant to the 

  
 6 

 
exercise of any option, warrant or right held by, each such holder. Except as set forth in Section 3.03 of the Disclosure Schedule or as being issued pursuant to this Agreement, there are no
outstanding shares of capital stock of the Company or warrants, options, agreements, convertible securities or other commitments pursuant to which the Company is or may become obligated to issue any shares of its capital stock or other securities of
the Company. Except as set forth in Section 3.03 of the Disclosure Schedule, the number of shares of capital stock, if any, reserved for issuance is not subject to adjustment by reason of the issuance of the Notes and Warrants. Except as set
forth in Section 3.03 of the Disclosure Schedule and except as set forth in the Stockholders Agreement, or that certain Third Amended and Restated Voting Agreement, dated as of August 31, 2010, as amended, by and among the Company and the
other parties thereto, as amended, there are no preemptive or similar rights to purchase or otherwise acquire shares of capital stock of the Company pursuant to any provision of law, the Restated Charter or the By-laws or any agreement to which the
Company is a party, or otherwise, and there is no agreement, restriction or encumbrance with respect to the sale or voting of any shares of the Company’s capital stock (whether outstanding or issuable upon conversion or exercise of outstanding
securities). The Company has not violated the Securities Act of 1933, as amended (the “Securities Act”), or any state blue sky or securities law in connection with the issuance of any shares of Common Stock or other
securities prior to the date hereof. 
 (c) Except as set forth in Section 3.03 of the Disclosure Schedule,
all Common Stock issued vests in equal monthly installments over four years following the vesting commencement date and no stock plan, stock purchase, stock option or other agreement or understanding between the Company and any holder of any equity
securities or rights to purchase equity securities provides for acceleration or other changes in the vesting provisions or other terms of such agreement or understanding as the result of (i) termination of employment or consulting services
(whether actual or constructive); (ii) any merger, consolidated sale of stock or assets, change in control or any other transaction(s) by the Company; or (iii) the occurrence of any other event or combination of events. 

(d) All outstanding shares of Common Stock and Preferred Stock, and all shares of Common Stock and Preferred Stock
issuable upon the exercise or conversion of outstanding options, warrants or other exercisable or convertible securities are subject to a market standoff or “lockup” agreement of not less than 180 days following the Company’s initial
public offering. 
 3.04 Litigation. There is no action, suit, claim, proceeding or investigation pending or, to the
Company’s knowledge, threatened against the Company or any of its properties, at law or in equity, or before or by any Federal, state, municipal or other governmental department, commission, board, bureau, agency or instrumentality, domestic or
foreign that challenges the validity or enforceability of, or seeks the enjoin the performance of this Agreement or the transactions contemplated hereby. 

  
 7 

 3.05 Complete Disclosure. To the Company’s knowledge, neither the Agreement, as
qualified by the Disclosure Schedule, nor any other documents or certificates furnished or to be furnished in connection herewith, when taken as a whole, contains any untrue statement of a material fact or omits to state a material fact necessary in
order to make the statements contained herein or therein not misleading in light of the circumstances under which they were made. 
 3.06 Financial Statements. The Company has delivered to the Purchasers its unaudited balance sheet and statement of operations for the fiscal year ended December 31, 2010 and the period
ended June 30, 2011 (the “Financial Statements”). As of the Initial Closing, the Financial Statements are correct in all material respects and present fairly the financial condition and operating results of the Company
as of the date(s) and during the period(s) indicated therein. The unaudited Financial Statements have been prepared in accordance with generally accepted accounting principles (“GAAP”) applied on a consistent basis throughout
the period indicated, except as disclosed therein. The unaudited Financial Statements do not contain additional financial statements and footnotes required under GAAP, and are subject to normal year-end adjustments. 

ARTICLE 4 

REPRESENTATIONS AND WARRANTIES OF THE PURCHASERS 
 Each Purchaser represents and warrants to the Company that: (a) it has full power and authority to enter into and perform this Agreement in accordance with its terms, and it was not organized for the
specific purpose of acquiring the Notes, the Warrants, or shares of Common Stock or New Equity Securities issuable upon conversion of the Notes (collectively, the “Securities”); (b) it has sufficient knowledge and
experience in investing in companies similar to the Company in terms of the Company’s stage of development so as to be able to evaluate the risks and merits of its investment in the Company and it is able financially to bear the risks thereof;
(c) it has made an investigation of the Company and its business as it deemed necessary and has had an opportunity to discuss and review the Company’s business, management and financial affairs with the Company’s management as it
deemed necessary; (d) the Securities being purchased by it are being acquired for its own account for the purpose of investment and not with a view to the public resale or distribution thereof within the meaning of the Securities Act;
(e) it understands that (i) the Securities have not been registered under the Securities Act by reason of their issuance in a transaction exempt from the registration requirements of the Securities Act pursuant to Section 4(2) thereof
or Rule 504, 505 or 506 promulgated under the Securities Act, (ii) under the Securities Act and applicable regulations thereunder the Securities may be resold without registration under the Securities Act only in certain limited circumstances,
(iii) the certificates evidencing the Securities will bear a legend substantially similar to that set forth below: 

THE SECURITIES REPRESENTED HEREBY HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE
“ACT”), OR UNDER THE SECURITIES LAWS OF APPLICABLE STATES. THESE SECURITIES ARE SUBJECT TO RESTRICTIONS ON 

  
 8 

 
TRANSFERABILITY AND RESALE AND MAY NOT BE TRANSFERRED OR RESOLD EXCEPT AS PERMITTED UNDER THE ACT AND APPLICABLE STATE SECURITIES LAWS, PURSUANT TO REGISTRATION UNDER SUCH LAWS OR AN EXEMPTION
FROM SUCH REGISTRATION REQUIREMENT. INVESTORS SHOULD BE AWARE THAT THEY MAY BE REQUIRED TO BEAR THE FINANCIAL RISKS OF THIS INVESTMENT FOR AN INDEFINITE PERIOD OF TIME. THE ISSUER OF THESE SECURITIES MAY REQUIRE AN OPINION OF COUNSEL IN FORM AND
SUBSTANCE SATISFACTORY TO THE ISSUER TO THE EFFECT THAT ANY PROPOSED TRANSFER OR RESALE IS IN COMPLIANCE WITH THE ACT AND ALL APPLICABLE STATE SECURITIES LAWS. 
 and (iv) the Company will make a notation on its transfer books to such effect; (f) this Agreement has been duly executed and delivered by it and constitutes the legal, valid and binding
obligation of it, enforceable in accordance with the terms of the Agreement; and (g) it is an “accredited investor” as that term is defined in Rule 501 promulgated under the Securities Act. 

ARTICLE 5 

MISCELLANEOUS 

5.01 No Waiver; Cumulative Remedies. No failure or delay on the part of any party to this Agreement in exercising any right, power
or remedy hereunder shall operate as a waiver thereof; nor shall any single or partial exercise of any such right, power or remedy preclude any other or further exercise thereof or the exercise of any other right, power or remedy hereunder. The
remedies herein provided are cumulative and not exclusive of any remedies provided by law. 
 5.02 Amendments, Waivers and
Consents. Any provision in this Agreement to the contrary notwithstanding, changes in or additions to this Agreement, the Notes or the Warrants may be made, and compliance with any covenant or provision herein or therein set forth may be omitted
or waived, if the Company shall obtain consent thereto in writing from the Purchasers holding at least a majority of the principal outstanding under the then outstanding Notes (the “Requisite Purchasers”), provided that the
Company shall be permitted to update Schedule 1.03, and Exhibits A and B without the consent of the Requisite Purchasers. Any amendment or waiver effected in accordance with this Section 5.02 shall be binding upon each holder of
Notes then outstanding, each future holder of such securities and the Company; provided, however, that no amendment shall be effective against a Purchaser which materially and adversely affects such Purchaser’s rights under this Agreement or
under any Notes in a manner that is adverse to and materially different from the effect on other Purchasers in Notes, without such Purchaser’s written consent. 
 5.03 Addresses for Notices, etc. Any notice required or permitted hereunder shall be given in writing and shall be conclusively deemed effectively given upon

  
 9 

 
personal delivery or delivery by courier, or on the first business day after transmission if sent by confirmed facsimile transmission, or four (4) business days after deposit in the United
States mail, by registered or certified mail, postage prepaid, addressed (i) if to the Company, as set forth below the Company’s name on the signature page of this Agreement, and (ii) if to a Purchaser, at such Purchaser’s
address as set forth on Exhibit A or Exhibit B, or at such other address as the Company or such Purchaser may designate by advance written notice to the other parties hereto. For purposes of this Section 5.03, a
“business day” means a weekday on which banks are open for general banking business in New York City, New York. 
 5.04 Binding Effect; Assignment. The terms and conditions of this Agreement shall be binding upon and inure to the benefit of the Company and the Purchasers and their respective heirs, successors
and assigns. 
 5.05 Headings; Interpretation. In this Agreement, (i) the meaning of defined terms shall be equally
applicable to both the singular and plural forms of the terms defined; (ii) the captions and headings are used only for convenience and are not to be considered in construing or interpreting this Agreement and (iii) the words
“including,” “includes” and “include” shall be deemed to be followed by the words “without limitation”. All references in this Agreement to sections, paragraphs, exhibits and schedules shall, unless otherwise
provided, refer to sections and paragraphs hereof and exhibits and schedules attached hereto, all of which exhibits and schedules are incorporated herein by this reference. 
 5.06 No Finder’s Fees. Each party represents that it neither is nor will be obligated for any finder’s or broker’s fee or commission in connection with the transactions contemplated
by this Agreement. Each Purchaser agrees to indemnify and to hold harmless the Company from any liability for any commission or compensation in the nature of a finder’s or broker’s fee (and any asserted liability) for which the Purchaser
or any of its directors, officers, partners, members, employees or representatives is responsible. The Company agrees to indemnify and hold harmless each Purchaser from any liability for any commission or compensation in the nature of a
finder’s or broker’s fee (and any asserted liability) for which the Company or any of its officers, employees or representatives is responsible. 
 5.07 Survival of Representations and Warranties. The representations and warranties of the Company and the Purchasers contained herein shall survive each Closing. Each of the Purchasers and the
Company may rely on such representations and warranties irrespective of any investigation made, or notice or knowledge held by, it or any other person. 
 5.08 Prior Agreements. This Agreement constitutes the entire agreement between the parties and supersedes any other prior understandings or agreements concerning the subject matter hereof.

 5.09 Severability. The invalidity or unenforceability of any provision hereof shall in no way affect the validity or
enforceability of any other provision. 

  
 10 

 5.10 Governing Law. This Agreement shall be governed by, and construed and enforced
in accordance with, the substantive laws of the State of Delaware without regard to its principles of conflicts of laws. 
 5.11
Payment of Fees. Each of the Company and the Purchasers shall pay its own legal and financial advisory fees. 
 5.12
Counterpart; Facsimile Signatures. This Agreement may be executed in any number of counterparts, each of which shall be deemed an original, but all of which taken together shall constitute one and the same instrument, and any of the parties
hereto may execute this Agreement by signing any such counterpart. This Agreement may be executed and delivered by facsimile, or by e-mail in portable document format (.pdf) and delivery of the signature page by such method will be deemed to have
the same effect as if the original signature had been delivered to the other parties. 
 5.13 Entire Agreement. This
Agreement, together with all exhibits hereto and the Notes, constitute the entire agreement and understanding of the parties with respect to the subject matter hereof and supersede any and all prior negotiations, correspondence, agreements,
understandings duties or obligations between the parties with respect to the subject matter hereof. 
 5.14 Further
Assurances. From and after the date of this Agreement, upon the request of any Purchaser or the Company, the Company and the Purchasers shall execute and deliver such instruments, documents or other writings as may be reasonably necessary or
desirable to confirm and carry out and to effectuate fully the intent and purposes of this Agreement. 
 5.15 Amendment to
the Restated Charter. The Company and the Purchasers shall use their best efforts, immediately prior to an IPO or a Qualified Financing, as the case may be, to amend the Restated Charter to authorize sufficient additional capital stock of the
Company to allow for the issuance of the applicable Conversion Securities and shares of Common Stock issuable upon conversion of the Conversion Securities, if applicable. 
 5.16 Amendment to the Registration Rights Agreement. The Company and the Purchasers shall use their best efforts, immediately prior to an IPO or a Qualified Financing, as the case may be, to amend
the Third Amended and Restated Registration Rights Agreement, dated as of August 31, 2010, by and among the Company and the other parties thereto, as amended (the “Registration Rights Agreement”) to include the
applicable Conversion Securities and shares of Common Stock issuable upon conversion of the Conversion Securities, if applicable, as part of the term, “Registrable Securities,” defined therein. 

[REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK] 

  
 11 

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	MASCOMA CORPORATION
		
	By:	 	 /s/ William J. Brady

		 	Name: William J. Brady
		 	Title: Chief Executive Officer

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	KHOSLA VENTURES I, L.P.
		
	By:	 	Khosla Ventures Associates I, LLC, a Delaware limited liability company and general partner of Khosla Ventures I, LP
		
	By:	 	 /s/ David Weiden

	Name:	 	David Weiden
	Title:	 	Member

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	SUNOPTA INC.
		
	By:	 	 /s/ Chris Snowden

		 	Name: Chris Snowden
		 	Title: VP & Treasurer

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	FLAGSHIP VENTURES FUND 2004, L.P.
		
	By:	 	its General Partner
		 	Flagship Ventures General Partner LLC
		
	By:	 	 /s/ Noubar B. Afeyan

		 	Manager

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	GC ENTREPRENEURS FUND IV, L.P.
	By	 	General Catalyst Partners IV, L.P.,
		 	 its General Partner

	By	 	General Catalyst GP IV, LLC,
		 	 its General Partner

		
	By:	 	 /s/ William J. Fitzgerald

	Name:	 	William J. Fitzgerald
	Title:	 	Member and Chief Financial Officer

  

			
	GENERAL CATALYST GROUP IV, L.P.
	By	 	General Catalyst Partners IV, L.P.,
		 	 its General Partner

	By	 	General Catalyst GP IV, LLC,
		 	 its General Partner

		
	By:	 	 /s/ William J. Fitzgerald

	Name:	 	William J. Fitzgerald
	Title:	 	Member and Chief Financial Officer

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	KPCB HOLDINGS, INC.
		
	By:	 	 /s/ Eric Keller

	Name:	 	Eric Keller
	Title:	 	President

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

									
		 		 		 	BLACKROCK INVESTMENT MANAGEMENT (UK) LIMITED ACTING AS DISCRETIONARY INVESTMENT MANAGER FOR BGF NEW ENERGY FUND
					
		 	 /s/ J. Freedman
	 		 	By:	 	 /s/ Peppy Allonby

		 	J. Freedman	 		 		 	Name: P. Allonby
		 	Fund Manager	 		 		 	Title: Fund Manager
				
		 		 		 	BLACKROCK INVESTMENT MANAGEMENT (UK) LIMITED ACTING AS DISCRETIONARY INVESTMENT MANAGER FOR BLACKROCK NEW ENERGY INVESTMENT TRUST PLC
					
		 	 /s/ J. Freedman
	 		 	By:	 	 /s/ Peppy Allonby

		 	J. Freedman	 		 		 	Name: P. Allonby
		 	Fund Manager	 		 		 	Title: Fund Manager

 [Signature page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement] 

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	VANTAGEPOINT CLEANTECH PARTNERS, L.P.
	By:	 	VantagePoint Clean Tech Associates, L.L.C.
		
	By:	 	 /s/ Alan E. Salzman

	Name:	 	Alan E. Salzman
	Title:	 	Managing Member
	
	VANTAGEPOINT VENTURE PARTNERS 2006 (Q), L.P.
	By:	 	VantagePoint Venture Associates 2006, L.L.C.
		
	By:	 	 /s/ Alan E. Salzman

	Name:	 	Alan E. Salzman
	Title:	 	Managing Member

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	MPC INVESTMENT LLC
		
	By:	 	 /s/ David L. Whikehart

		 	Name: David L. Whikehart
		 	Title: Director, Product Supply
		 	

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	DIAMOND ALTERNATIVE ENERGY, LLC
		
	By:	 	 /s/ George Stutzmann

		 	Name: George Stutzmann
		 	Title: Vice President

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	PINNACLE VENTURES II-A, L.P.
	PINNACLE VENTURES II-B, L.P.
	PINNACLE VENTURES II-C, L.P.
	PINNACLE VENTURES II-R, L.P.
		
	By:	 	Pinnacle Ventures Management II, L.L.C.,
		 	Their general partner
		
	By:	 	 /s/ Robert N. Savoie

	Name:	 	Robert N. Savoie
	Title:	 	Chief Financial Officer
	
	PINNACLE VENTURES EQUITY FUND I AFFILIATES, L.P.
	PINNACLE VENTURES EQUITY FUND I, L.P.
	PINNACLE VENTURES EQUITY FUND I-O, L.P.
		
	By:	 	Pinnacle Ventures Equity Management I, L.L.C.,
		 	Their general partner
		
	By:	 	 /s/ Robert N. Savoie

	Name:	 	Robert N. Savoie
	Title:	 	Chief Financial Officer

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	GENERAL MOTORS VENTURES LLC
		
	By:	 	 /s/ Jon Lauckner

	Name:	 	 Jon Lauckner

	Title:	 	President

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	ATLAS VENTURE FUND VII, L.P.
	By:	 	Atlas Venture Associates VII, L.P.,
		 	Its General Partner
	By:	 	Atlas Venture Associates VII, Inc.,
		 	Its General Partner
		
	By:	 	 /s/ Kristen Laguere

	Name:	 	Kristen Laguere
	Title:	 	Vice President

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	BLUESTEM GROWTH & INCOME FUND III, LLC
	By:	 	Bluestem Capital Company, LLC
		
	By:	 	 /s/ Tyler Stowater

	Name:	 	Tyler Stowater
	Title:	 	Vice President
	
	BLUESTEM SELECT OPPORTUNITIES FUND, LLC
	By:	 	Bluestem Capital Company, LLC
		
	By:	 	 /s/ Tyler Stowater

	Name:	 	Tyler Stowater
	Title:	 	Vice President

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	MALAYSIAN LIFE SCIENCES CAPITAL FUND
		
	By:	 	 /s/ Roger Wyse

	Name:	 	Roger Wyse
	Title:	 	Co-Chairman

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	CRM HOLDINGS, LLC
		
	By:	 	 /s/ Michael Ladisch

	Name:	 	Michael Ladisch
	Title:	 	Partner
		 	 1014 Kingswood Rd W.
 W.
Lafayette, IN 47906

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

	
	 /s/ Bruce A. Jamerson

	Bruce A. Jamerson

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

	
	DAVID NODA AND KAY M. NISHIYAMA
	(as joint tenants with right of survivorship)
	
	 /s/ David Noda

	David Noda
	
	 /s/ Kay M. Nishiyama

	Kay M. Nishiyama

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	CANACCORD GENUITY CORP.
		
	By:	 	 /s/ Donald D. MacFayden

	Name:	 	Donald D. MacFayden
	Title:	 	SVP

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	ROCH ENTERPRISES, L.P.
		
	By:	 	 /s/ Lewis M. Roch

	Name:	 	Lewis M. Roch
	Title:	 	CFO

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 IN WITNESS WHEREOF, the parties hereto have executed this Subordinated Convertible
Promissory Note and Warrant Purchase Agreement on the day, month and year first above written. 
  

			
	STACK, LLC
		
	By:	 	 /s/ Fred Fehsenfeld, Jr.

	Name:	 	 Fred Fehsenfeld, Jr.

	Title:	 	

 [Signature Page to Subordinated Convertible Promissory Note and Warrant Purchase Agreement]

 SCHEDULE A 
 Additional Purchaser Signature Page 
 By executing this page in the space
provided, the undersigned hereby agrees that [he/she/it] is becoming an “Additional Purchaser” as defined in that certain Subordinated Convertible Promissory Note and Warrant Purchase Agreement dated as of August
[    ], 2011, by and among Mascoma Corporation, a Delaware corporation (the “Company”) and the other parties thereto, as the same may be amended, restated or otherwise modified from time to time
(the “Purchase Agreement”) and as such shall be a party to, and bound by all terms and conditions of, the Purchase Agreement. The undersigned further confirms that the representations and warranties contained in Article IV of the
Purchase Agreement are true and correct with respect to the undersigned, as of the date hereof. 
 EXECUTED this
                 day of 2011. 
  

			
	  

	
	(print name)
		
	By:	 	  

		
	Title:	 	  

		
	Address:	 	
		
	Fax:	 	

  

			
	Accepted:
	
	MASCOMA CORPORATION
		
	By:	 	  

	Name:	 	
	Title:	 	

 SCHEDULE 1.03 
 PRO RATA PORTION OF NOTES 
  

					
	 Purchaser
	  	Pro Rata Portion of Notes ($)	 
	 Khosla Ventures I, L.P.
	  	 	1,977,315.00	  
	 SunOpta, Inc.
	  	 	1,420,786.97	  
	 Flagship Ventures Fund 2004, L.P.
	  	 	977,397.20	  
	 General Catalyst Group IV, L.P.
	  	 	912,252.32	  
	 GC Entrepreneurs Fund IV, L.P.
	  	 	24,204.39	  
	 KPCB Holdings, Inc.
	  	 	808,424.17	  
	 Blackrock Investment Management (UK) Limited acting as Discretionary Investment Manager for BGF New Energy Fund
	  	 	708,486.47	  
	 Blackrock Investment Management (UK) Limited acting as Discretionary Investment Manager for BlackRock New Energy Investment Trust
Plc
	  	 	67,474.83	  
	 VantagePoint Cleantech Partners, L.P.
	  	 	158,216.90	  

					
	 Purchaser
	  	Pro Rata Portion of Notes ($)	 
	 VantagePoint Venture Partners 2006 (Q), L.P.
	  	 	474,650.68	  
	 MPC Investment LLC
	  	 	371,886.96	  
	 Diamond Alternative Energy, LLC
	  	 	287,862.14	  
	 Pinnacle Ventures II-A, L.P.
	  	 	1,492.93	  
	 Pinnacle Ventures II-B, L.P.
	  	 	62,698.55	  
	 Pinnacle Ventures II-C, L.P.
	  	 	5,224.91	  
	 Pinnacle Ventures II-R, L.P.
	  	 	5,224.70	  
	 Pinnacle Ventures Equity Fund I Affiliates, L.P.
	  	 	8,056.62	  
	 Pinnacle Ventures Equity Fund I, L.P.
	  	 	88,622.77	  
	 Pinnacle Ventures Equity Fund I-O, L.P.
	  	 	64,452.92	  

					
	 Purchaser
	  	Pro Rata Portion of Notes ($)	 
	 General Motors Ventures LLC
	  	 	183,104.98	  
	 Atlas Venture Fund VII, L.P.
	  	 	106,088.38	  
	 Bluestem Growth & Income Fund III, LLC
	  	 	38,498.04	  
	 Bluestem Select Opportunities Fund, LLC
	  	 	38,498.04	  
	 Malaysian Life Sciences Capital Fund
	  	 	73,242.08	  
	 CRM Holdings, LLC
	  	 	54,300.82	  
	 Bruce Jamerson
	  	 	40,649.45	  
		  	  
	  
	 
	 SUBTOTAL INITIAL CLOSING INVESTORS
	  	 	8,959,113.22	  
		  	  
	  
	 
	 Bershaw & Co. c/o Citibank Canada, Securities Cage
	  	 	57,373.89	  
	 Eric Lemelson
	  	 	54,931.45	  

					
	 Purchaser
	  	Pro Rata Portion of Notes ($)	 
	 Fagen, Inc.
	  	 	36,621.04	  
	 Stack, LLC
	  	 	36,621.04	  
	 Wildstoic LLC
	  	 	33,737.52	  
	 Jayvee & Co. on behalf of MacKenzie Financial Corp.
	  	 	33,737.52	  
	 Wilsey Invest Ltd.
	  	 	33,737.52	  
	 Dean W. Rybeck
	  	 	29,269.33	  
	 Roytor & Co/ c/o RT. Acct #790973
	  	 	23,616.29	  
	 Brant Investments Limited A/C 99480027
	  	 	4,331.32	  
	 Brant Investments Limited A/C 99480072
	  	 	17,017.84	  
	 Jayvee & Co. INVF0004002
	  	 	13,055.05	  

					
	 Purchaser
	  	Pro Rata Portion of Notes ($)	 
	 Barbara D. Rybeck
	  	 	12,440.18	  
	 David Noda and Kay M. Nishiyama (as joint tenants with right of survivorship)
	  	 	7,684.84	  
	 Todd Nofke
	  	 	5,398.06	  
	 Canaccord Genuity Corporation ITF Peter J Chandler AC# 139-264S-4
	  	 	3,373.82	  
	 Canaccord Genuity Corporation ITF Peter J Chandler AC# 139-264M-2
	  	 	1,686.80	  
	 Roch Enterprises, L.P.
	  	 	4,368.67	  
	 Rod Fuller
	  	 	3,373.82	  
	 Canaccord Genuity Corp.
	  	 	3,036.37	  
	 Wendy Strub
	  	 	1,686.80	  
	 Jayvee & Co. INVF0013002
	  	 	1,000.03	  

					
	 Purchaser
	  	Pro Rata Portion of Notes ($)	 
	 David Mann
	  	 	245.69	  
	 SUBTOTAL SUBSEQUENT CLOSING INVESTORS
	  	 	418,344.89	  
		  	  
	  
	 
	 TOTAL
	  	$	9,377,458.11	  
		  	  
	  
	 

 EXHIBIT A 
 Initial Purchasers 
  

							
	 Name and Address
	  	Principal Amount of
Notes Purchased at the
Initial Closing
($)	 	  	Principal Amount of
Additional Notes
Purchased at the Follow-
On Closings
($)
	Khosla Ventures I, L.P.	  	 	500,000	  	  	
	 Khosla Ventures
	  				  	
	 3000 Sand Hill Road
	  				  	
	 Bldg. 3, Suite 190
	  				  	
	 Menlo Park, CA 94025
	  				  	
	 Attn: Kim Totah
	  				  	
	SunOpta, Inc.	  	 	500,000	  	  	
	 2838 Bovaird Drive West
	  				  	
	 Brampton, Ontario
	  				  	
	 Canada, L7A 0H2
	  				  	
	Flagship Ventures Fund 2004, L.P.	  	 	977,397.20	  	  	
	 Flagship Ventures
	  				  	
	 One Memorial Drive, 7th Floor
	  				  	
	 Cambridge, MA 02142
	  				  	
	 Attn: Jim Matheson
	  				  	
	General Catalyst Group IV, L.P.	  	 	912,252.32	  	  	
	 General Catalyst Partners
	  				  	
	 200 University Road, Suite 450
	  				  	
	 Cambridge, MA 02138
	  				  	
	 Attention: Hemant Taneja
	  				  	
	GC Entrepreneurs Fund IV, L.P.	  	 	24,204.39	  	  	
	 General Catalyst Partners
	  				  	
	 200 University Road, Suite 450
	  				  	
	 Cambridge, MA 02138
	  				  	
	 Attention: Hemant Taneja
	  				  	

							
	 Name and Address
	  	Principal Amount of
Notes Purchased at the
Initial Closing 
($)	 	  	Principal Amount of
Additional Notes
Purchased at the Follow-
On Closings
($)
	KPCB Holdings, Inc.	  	 	808,424.17	  	  	
	 KPCB Holdings, Inc.
	  				  	
	 2750 Sand Hill Road
	  				  	
	 Menlo Park, CA 94025
	  				  	
	 Attention: John Denniston
	  				  	
	  
 with a copy
to
	  				  	
	  
 Sayre E. Stevick,
Esq.
	  				  	
	 Fenwick & West LLP
	  				  	
	 801 California Street
	  				  	
	 Mountain View, CA 94041
	  				  	
	 Blackrock Investment Management (UK) Limited
 acting as Discretionary Investment Manager for
 BGF New Energy Fund
	  	 	708,486.47	  	  	
	 33 King William Street, London,
	  				  	
	 England EC4R 9AS
	  				  	
	 Blackrock Investment Management (UK) Limited
 acting as Discretionary Investment Manager for
 BlackRock New Energy Investment Trust
Plc
	  	 	67,474.83	  	  	
	 33 King William Street, London,
	  				  	
	 England EC4R 9AS
	  				  	
	VantagePoint Cleantech Partners, L.P.	  	 	158,216.90	  	  	
	 1001 Bayhill Drive, Suite 300
	  				  	
	 San Bruno, CA 94066
	  				  	
	VantagePoint Venture Partners 2006 (Q), L.P.	  	 	474,650.68	  	  	
	 1001 Bayhill Drive, Suite 300
	  				  	
	 San Bruno, CA 94066
	  				  	
	MPC Investment LLC	  	 	371,886.96	  	  	
	 5555 Felipe Rd.
	  				  	
	 Houston, TX 77050
	  				  	

							
	 Name and Address
	  	Principal Amount of
Notes Purchased at the
Initial Closing
($)	 	  	Principal Amount of
Additional Notes
Purchased at the Follow-
On Closings
($)
	Diamond Alternative Energy, LLC	  	 	287,862.14	  	  	
	 One Valero Way
	  				  	
	 San Antonio, Texas 78249
	  				  	
	Pinnacle Ventures II-A, L.P.	  	 	1,492.93	  	  	
	 Attn: Chief Financial Officer
	  				  	
	 Pinnacle Ventures, L.L.C.
	  				  	
	 130 Lytton Avenue, Suite 220
	  				  	
	 Palo Alto, CA 94301
	  				  	
	Pinnacle Ventures II-B, L.P.	  	 	62,698.55	  	  	
	 Attn: Chief Financial Officer
	  				  	
	 Pinnacle Ventures, L.L.C.
	  				  	
	 130 Lytton Avenue, Suite 220
	  				  	
	 Palo Alto, CA 94301
	  				  	
	Pinnacle Ventures II-C, L.P.	  	 	5,224.91	  	  	
	 Attn: Chief Financial Officer
	  				  	
	 Pinnacle Ventures, L.L.C.
	  				  	
	 130 Lytton Avenue, Suite 220
	  				  	
	 Palo Alto, CA 94301
	  				  	
	Pinnacle Ventures II-R, L.P.	  	 	5,224.70	  	  	
	 Attn: Chief Financial Officer
	  				  	
	 Pinnacle Ventures, L.L.C.
	  				  	
	 130 Lytton Avenue, Suite 220
	  				  	
	 Palo Alto, CA 94301
	  				  	
	Pinnacle Ventures Equity Fund I Affiliates, L.P.	  	 	8,056.62	  	  	
	 Attn: Chief Financial Officer
	  				  	
	 Pinnacle Ventures, L.L.C.
	  				  	
	 130 Lytton Avenue, Suite 220
	  				  	
	 Palo Alto, CA 94301
	  				  	
	Pinnacle Ventures Equity Fund I, L.P.	  	 	88,622.77	  	  	
	 Attn: Chief Financial Officer
	  				  	
	 Pinnacle Ventures, L.L.C.
	  				  	
	 130 Lytton Avenue, Suite 220
	  				  	
	 Palo Alto, CA 94301
	  				  	

									
	 Name and Address
	  	Principal Amount of
Notes Purchased at the
Initial Closing
($)	 	  	Principal Amount of
Additional Notes
Purchased at the Follow-
On
Closings ($)	 
	Pinnacle Ventures Equity Fund I-O, L.P.	  	 	64,452.92	  	  			
	 Attn: Chief Financial Officer
	  				  			
	 Pinnacle Ventures, L.L.C.
	  				  			
	 130 Lytton Avenue, Suite 220
	  				  			
	 Palo Alto, CA 94301
	  				  			
	General Motors Ventures LLC	  	 	183,104.98	  	  			
	 Attn: A. Mistry
	  				  			
	 300 Renaissance Center
	  				  			
	 Detroit, MI 48265
	  				  			
	Atlas Venture Fund VII, L.P.	  	 	106,088.38	  	  			
	 Atlas Venture
	  				  			
	 890 Winter Street, Suite 320
	  				  			
	 Waltham, MA 02476
	  				  			
	Bluestem Growth & Income Fund III, LLC	  	 	38,498.04	  	  			
	 Attn: Tyler Stowater
	  				  			
	 122 S. Phillips Avenue
	  				  			
	 Suite 300
	  				  			
	 Sioux Falls, SD 57104
	  				  			
	Bluestem Select Opportunities Fund, LLC	  	 	38,498.04	  	  			
	 Attn: Tyler Stowater
	  				  			
	 122 S. Phillips Avenue
	  				  			
	 Suite 300
	  				  			
	 Sioux Falls, SD 57104
	  				  			
	Malaysian Life Sciences Capital Fund	  	 	73,242.08	  	  	 	176,757.92	  
	 Attn: Roger Wyse
	  				  			
	 No. 36-01, Level 36 Mendra
	  				  			
	 Dion
	  				  			
	 27, Jalan Sultan Ismail
	  				  			
	 50250 Kuala Lumpur
	  				  			
	CRM Holdings, LLC	  	 	54,300.82	  	  	 	145,699.18	  
	 Attn: Dr. Ladisch
	  				  			
	 1014 Kingswood Road
	  				  			
	 West Lafayette, IN 47906
	  				  			

									
	 Name and Address
	  	Principal Amount of
Notes Purchased at the
Initial Closing
($)	 	  	Principal Amount of
Additional Notes
Purchased at the Follow-
On
Closings ($)	 
	Bruce Jamerson	  	 	40,649.45	  	  			
	 c/o Mascoma Corporation
	  				  			
	 67 Etna Road, Suite 300
	  				  			
	 Lebanon, NH 03766
	  				  			
		  	  
	  
	 	  	  
	  
	 
	 Total
	  	 	6,561,011.25	  	  	 	322,457.10	  
		  	  
	  
	 	  	  
	  
	 

 EXHIBIT B 
 Additional Purchasers 
  

					
	 Name and Address
	  	Principal Amount 
of
Notes Purchased at
the
Follow-On
Closings ($)	 
	 David Noda and Kay M. Nishiyama
 (as joint tenants with right of survivorship)
	  	 	10,000	  
	 175 East 96th Street
	  			
	 Apartment 10N
	  			
	 New York, NY 10128
	  			
	Canaccord Genuity Corp.	  	 	3,036.37	  
	 99 High Street
	  			
	 Boston, MA 02110
	  			
	Roch Enterprises, L.P.	  	 	4,368.67	  
	 2006 N. Robinwood Drive
	  			
	 Muncie, IN 47304
	  			
	Stack, LLC	  	 	36,621.04	  
	 4415 West 116th Street
	  			
	 Zionsville, IN 46077
	  			
		  	  
	  
	 
	 Total
	  	$	54,026.08	  
		  	  
	  
	 

 EXHIBIT C 
 Form of Subordinated Convertible Promissory Note 

 THIS PROMISSORY NOTE AND THE SECURITIES ISSUABLE UPON CONVERSION HEREOF HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR UNDER THE SECURITIES LAWS OF APPLICABLE STATES. THESE SECURITIES ARE SUBJECT TO RESTRICTIONS ON TRANSFERABILITY AND RESALE AND MAY NOT BE TRANSFERRED OR RESOLD EXCEPT AS PERMITTED
UNDER THE ACT AND APPLICABLE STATE SECURITIES LAWS, PURSUANT TO REGISTRATION UNDER SUCH LAWS OR AN EXEMPTION FROM SUCH REGISTRATION REQUIREMENT. INVESTORS SHOULD BE AWARE THAT THEY MAY BE REQUIRED TO BEAR THE FINANCIAL RISKS OF THIS INVESTMENT FOR
AN INDEFINITE PERIOD OF TIME. THE ISSUER OF THESE SECURITIES MAY REQUIRE AN OPINION OF COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER TO THE EFFECT THAT ANY PROPOSED TRANSFER OR RESALE IS IN COMPLIANCE WITH THE ACT AND ALL APPLICABLE STATE
SECURITIES LAWS. 
 THIS PROMISSORY NOTE IS SUBJECT TO THAT CERTAIN SUBORDINATION AGREEMENT AMONG THE LENDER (AS DEFINED BELOW) AND PINNACLE
VENTURES L.L.C. 
 SUBORDINATED CONVERTIBLE PROMISSORY NOTE 

 

			
	$ [            ]	  	August 5, 2011

 Subject to the terms and conditions of this Note, for value received, Mascoma Corporation, a Delaware
corporation (the “Borrower”), hereby promises to pay to [                    ] (the “Lender”), the
principal sum of [                    ] ($[            ]) (the
“Principal Amount”), together with interest thereon accruing on and from the date hereof until the entire Balance is paid (or converted, as provided in Section 6 hereof), at an annual rate
equal to eight percent (8%). Interest shall be calculated based on a 365-day year, compounded annually, but in no event shall the rate of interest exceed the maximum rate, if any, allowable under applicable law.
“Balance” means, at the applicable time, the sum of all then outstanding principal of this Note, all then accrued but unpaid interest and all other amounts then accrued but unpaid under this Note. 

This subordinated convertible promissory note (the “Note”) is issued by the Borrower
pursuant to that certain Subordinated Convertible Promissory Note and Warrant Purchase Agreement dated as of the date hereof (the “Purchase Agreement”), entered into among the Borrower and the
other parties thereto (the “Purchasers”), and is subject to, and Borrower and Lender shall be bound by, all the terms, conditions and provisions of the Purchase Agreement. This Note, and the other notes issued pursuant to the
Purchase Agreement, are sometimes hereinafter referred to as the “Notes”. This Note is subordinated to indebtedness of the Borrower owed to Pinnacle Ventures L.L.C.
(“Pinnacle”) pursuant to that certain Loan and Security Agreement, dated as of June 1, 2011, as amended from time to time (the “Pinnacle Agreement”), and any subsequent debt that the Borrower
obtains from Pinnacle, or another 

 
senior lender in lieu of Pinnacle, whether through an amendment to the Pinnacle Agreement or entry into a new agreement, in addition to any amounts owed by Borrower to Citibank under that standby
letter of credit (the “Senior Debt”). Capitalized terms used herein but not defined herein shall have the meanings ascribed to them in the Purchase Agreement. 

The following is a statement of the rights of Lender and the terms and conditions to which this Note is subject and to which the Lender,
by acceptance of this Note, agrees: 
 1. Payment. If this Note has not been previously converted (as provided in
Section 6 hereof), then at any time on or after August 1, 2016, provided that all Senior Debt has been repaid as of such date, the Requisite Purchasers shall have the right to require the Borrower to repay the Balance of all of the Notes
then outstanding. The date on which the Balance of all of the Notes is repaid is referred to herein as the “Repayment Date.” Unless the indebtedness outstanding under this Note is converted in accordance with Section 6
hereof, all payments on account of principal and interest shall be made in lawful money of the United States of America at the principal office of the Lender, or such other place as the holder hereof may from time to time designate in writing to the
Borrower. 
 2. No Prepayment. Except with regard to conversion of this Note under Section 6, Borrower may not
prepay this Note without the written consent of the Requisite Purchasers. 
 3. Notes Pari Passu; Application of
Payments. Each of the Notes shall rank equally without preference or priority of any kind over one another, and all payments and recoveries payable on account of principal and interest on the Notes shall be paid and applied ratably and
proportionately on the Balances of all outstanding Notes on the basis of their original principal amount. Subject to the foregoing provisions, all payments will be applied first to the repayment of accrued fees and expenses under this Note,
then to accrued interest until all then outstanding accrued interest has been paid in full, and then to the repayment of principal until all principal has been paid in full. If after all applications of such payments have been made as
provided in this paragraph, then the remaining amount of such payments that are in either case in excess of the aggregate Balance of all outstanding Notes shall be returned to Borrower. 

4. Transfer and Exchange. The holder of this Note may, prior to the Repayment Date or the conversion in full of such Note in
accordance with Section 6, surrender such Note at the principal office of the Borrower for transfer or exchange. Within a reasonable time after notice to the Borrower from such holder of its intention to make such exchange and without expense
to such holder, except for any transfer or similar tax which may be imposed on the transfer or exchange, the Borrower shall issue in exchange therefor another note or notes for the same aggregate principal amount as the unpaid principal amount of
the Note so surrendered, having the same maturity and rate of interest, containing the same provisions and subject to the same terms and conditions as the Note so surrendered. Each new Note shall be made payable to such person or persons, or
transferees, as the holder of such surrendered Note may designate, and such transfer or exchange shall be made in such a manner that no gain or loss of principal or interest shall result therefrom. The Borrower may elect not to permit a transfer of
the Note if it has not obtained satisfactory assurance that such transfer: (a) is exempt from the registration requirements of, or covered by an effective registration statement under, the Securities Act of 1933, as amended, and the rules and
regulations thereunder and (b) is in compliance with all 

  
 2 

 
applicable state securities laws, including without limitation receipt of an opinion of counsel, which opinion shall be satisfactory to the Borrower. 

5. New Note. Upon receipt of evidence reasonably satisfactory to the Borrower of the loss, theft, destruction or mutilation of the
Note, the Borrower will issue a new Note, of like tenor and amount and dated the date to which interest has been paid, in lieu of such lost, stolen, destroyed or mutilated Note, and in such event the Lender agrees to indemnify and hold harmless the
Borrower in respect of any such lost, stolen, destroyed or mutilated Note. 
 6. Conversion or Acceleration of Note. If
the Borrower has not paid the entire Balance prior to the occurrence of such event, then the Balance then outstanding under this Note shall be automatically converted into equity securities of the Company upon the first to occur of (i) a
Qualified Financing Closing (as defined below) and (ii) an IPO. 
 (a) Conversion of Note upon a
Qualified Financing. If a Qualified Financing Closing occurs prior to an IPO or a Change of Control Event (as defined below) and the Borrower has not paid the entire Balance at the time of the Qualified Financing Closing, then at the Qualified
Financing Closing, the entire Balance then outstanding under this Note shall be automatically converted into that number of shares of the security sold by the Borrower in the Qualified Financing (as defined below) as is equal to the Conversion
Amount (as defined below) divided by the Qualified Financing Purchase Price (as defined below). 
 (i)
Notice. Borrower shall deliver to Lender notice of the Qualified Financing as soon as practicable, but in any event no fewer than five (5) days prior to the scheduled closing date of the Qualified Financing, notifying the Lender of the
conversion to be effected, including specifying (i) the Conversion Amount (calculated as of the Conversion Date), (ii) the Qualified Financing Purchase Price and (iii) the Conversion Date (as defined below). 

(ii) Qualified Financing Defined. For purposes of this Note, the term “Qualified Financing”
shall mean the Borrower’s sale of its equity securities (the “New Equity Securities”) in a single transaction or in a series of related transactions in each case occurring after the date hereof and approved by the
Borrower’s Board of Directors and the applicable stockholders of the Borrower, in which Borrower receives aggregate gross proceeds of at least $15,000,000 (excluding all amounts payable under the Notes). For purposes of this Note,
“Qualified Financing Closing” means the closing of the Qualified Financing. 
 (iii)
Qualified Financing Purchase Price Defined. For purposes of this Note, the term “Qualified Financing Purchase Price” shall mean an amount equal to the lowest per share purchase price at which shares of the New Equity
Securities are or have been sold in the Qualified Financing as of the date of the conversion of this Note into such New Equity Securities. 
 (iv) Conversion Amount Defined. For purposes of this Note, the term “Conversion Amount” shall mean the sum of all unpaid principal and accrued

  
 3 

 
interest outstanding under this Note as of the Qualified Financing Closing or an IPO, as applicable. 
 (v) Conversion Date Defined. For purposes of this Note, the term “Conversion Date” shall mean the Qualified Financing Closing. 

(b) Conversion of Note upon an IPO. 

(i) If an IPO occurs before a Qualified Financing Closing or a Change of Control Event, and the Borrower has not paid the
entire Balance at the time of the IPO, then the entire Balance outstanding under this Note immediately prior to the IPO shall be automatically converted into Common Stock of the Borrower, par value $0.001, (the “Common
Stock”) at the IPO. The number of shares of Common Stock into which this Note will convert pursuant to this Section 6(b) shall be determined by dividing (a) the Conversion Amount by (b) the price per share paid by the
public for shares of the Borrower’s Common Stock in the IPO discounted by thirty percent (30%). 
 (ii) An
“IPO” means the closing of the Company’s first sale of its Common Stock to the public in an offering underwritten by an investment banking firm, pursuant to an effective registration statement under the Securities Act of
1933, as amended. 
 (c) Termination of Rights. Except for the rights to obtain certificates representing
Equity Securities set forth in Section 6(d) below, all rights with respect to this Note shall terminate upon the effective conversion or repayment of the entire Balance of the Note, whether or not this Note has been surrendered to Borrower for
cancellation. 
 (d) Delivery of Stock Certificates; No Fractional Shares. Subject to Section 6(c)
above, as promptly as practicable after any conversion of this Note, Borrower at its expense will issue and deliver to Lender a certificate or certificates evidencing the number of full Equity Securities as are issuable to Lender in connection with
a conversion under this Section 6. No fractional shares of any Equity Securities will be issued in connection with any conversion hereunder. In lieu of fractional shares which would otherwise be issuable, Borrower shall pay cash equal to the
product of such fraction multiplied the price per share of the Equity Securities issuable to Lender upon such conversion. 
 (e) Acceleration on Change of Control Event. 
 (i) Upon a
Change of Control Event (as defined below), the Lender will be entitled to receive an amount equal to (i) one and a half times (1.5x) the principal amount of the Note then outstanding, plus (ii) any accrued and unpaid interest
thereon, without any action of the Lender of any kind. Immediately upon receipt by the Lender of payment pursuant to this Section 6(e), this Note shall no longer be deemed to be outstanding and all rights with respect to this Note shall
immediately cease and terminate. 

  
 4 

 (ii) A “Change of Control Event” shall mean a Merger
or Asset Transfer as defined in Article Fourth, Section B 2(c) of the Company’s Eighth Amended and Restated Certificate of Incorporation, as amended from time to time (the “Restated Certificate”). 

7. Covenants. For so long as the Borrower shall have any amounts outstanding under any of the Notes, unless otherwise consented to
in advance by the Requisite Purchasers: 
 (a) Limitations on Certain Indebtedness. While any amounts owned under
this Note are outstanding, the Borrower will not itself, and will not permit any subsidiary to, create, assume, incur or in any manner become liable in respect of any Indebtedness (as defined below) other than Senior Debt. For purposes of this
Agreement, “Indebtedness” shall mean and include the aggregate amount of, without duplication (i) all obligations for borrowed money, (ii) all obligations evidenced by bonds, debentures, notes or other similar
instruments, (iii) all obligations to pay the deferred purchase price of property or services (other than accounts payable incurred in the ordinary course of business determined in accordance with generally accepted accounting principles),
(iv) all obligations under capital leases, (v) all obligations or liabilities of others secured by a lien on any assets, whether or not such obligation or liability is assumed, (vi) all guaranties of the obligations of another
individual or entity, (vii) all obligations created or arising under any conditional sale or other title retention agreement with respect to property acquired (even if the rights and remedies of the seller or lender under such agreement upon an
event of default are limited to repossession or sale of such property), (viii) net exposure under any interest rate swap, currency swap, forward, cap, floor or other similar contract that is not entered to in connection with a bona fide hedging
operation that provides offsetting benefits, which agreements shall be marked to market on a current basis, and (ix) all reimbursement and other payment obligations, contingent or otherwise, in respect of letters of credit. 

(b) Limitations on Liens. The Borrower will not itself, and will not permit any subsidiary to, create, assume or suffer to
exist any Lien (as defined below) upon all or any part of its property of any character, whether owned at the date hereof or thereafter acquired, except for any Liens created with respect to the Senior Debt. For purposes of this Agreement,
“Lien” shall mean with respect to any property, any security interest, mortgage, pledge, lien, claim, charge or other encumbrance in, of, or on such property or the income therefrom, including, without limitation, the
interest of a vendor or lessor under a conditional sale agreement, capital lease or other title retention agreement, or any agreement to provide any of the foregoing, and the filing of any financing statement or similar instrument. 

8. Events of Default. Each of the following shall constitute an “Event of Default” hereunder: 

(a) The Borrower shall fail to pay any principal, interest or other amount payable hereunder on the applicable due date
and such failure continues for five (5) days; 
 (b) The Borrower shall (1) voluntarily terminate
operations or apply for or consent to the appointment of, or the taking of possession by, a receiver, custodian, trustee or liquidator of the Borrower or of all or a substantial part of the assets of the

  
 5 

 
Borrower, (2) admit in writing its inability, to pay debts as the debts become due, (3) make a general assignment for the benefit of its creditors, (4) commence a voluntary case
under the Federal Bankruptcy Code (as now or hereafter in effect), (5) file a petition seeking to take advantage of any other law relating to bankruptcy, insolvency, reorganization, winding-up, or composition or adjustment of debts,
(6) fail to controvert in a timely and appropriate manner, or acquiesce in writing to, any petition filed against it in an involuntary case under the Federal Bankruptcy Code or applicable state bankruptcy laws or (7) take any corporate
action for the purpose of effecting any of the foregoing; 
 (c) Without the Borrower’s application,
approval or consent, a proceeding shall be commenced, in any court of competent jurisdiction, seeking in respect of the Borrower: the liquidation, reorganization, dissolution, winding-up, or composition or readjustment of debt, the appointment of a
trustee, receiver, liquidator or the like relief in respect of the Borrower or all or any substantial part of the assets of the Borrower, or other like relief in respect of the Borrower under any law relating to bankruptcy, insolvency,
reorganization, winding-up, or composition or adjustment of debts; and, if the proceeding is being contested in good faith by the Borrower, the same shall continue undismissed, or unstayed and in effect for any period of 90 consecutive days, or an
order for relief against the Borrower shall be entered in any case under the Federal Bankruptcy Code or applicable bankruptcy laws; 
 (d) The Borrower shall violate any of the covenants contained in Section 7 of this Note, or be in default under, any material agreement, instrument or other document relating to any indebtedness for
money borrowed, including without limitation, any of the other Notes and such default persists beyond any applicable cure period; or 
 (e) The Borrower’s representations and warranties contained in the Purchase Agreement shall prove to have not been true in any material respect when made. 

If an Event of Default shall occur pursuant to Sections 8(a), 8(d) and 8(e), then, at any time thereafter while such Event of Default is
continuing, the Requisite Purchasers may by sending written notice to the Borrower (the “Default Notice”) declare the entire unpaid principal amount of this Note, together with all accrued and unpaid interest thereon, to be
due and payable immediately. If an Event of Default shall occur pursuant to Sections 8(b) and 8(c), then the entire unpaid principal amount of this Note, together with all accrued and unpaid interest thereon shall be due and payable immediately.

 9. Senior Debt. Notwithstanding anything herein to the contrary, Lender hereby agrees that Borrower’s failure to
pay any amounts or otherwise comply with any terms or provisions of this Note as a result of its obligations under the Senior Debt shall not constitute a default or an Event of Default under this Note. 

10. Governing Law. This Note shall be governed by, and construed and enforced in accordance with, the substantive laws of the
State of Delaware without regard to its principles of conflicts of laws. 

  
 6 

 11. Collection Expenses. The Borrower further agrees, subject only to any limitation
imposed by applicable law, to pay all expenses, including reasonable attorneys’ fees, incurred by the holder of this Note in endeavoring to collect any amounts payable hereunder which are not paid when due. 

12. Amendment. Any provision of this Note, except for the principal amount of this Note and the interest rate in connection
therewith, may be amended or waived in accordance with Section 5.02 of the Purchase Agreement. 
 13. Waiver.
Borrower hereby waives presentment, protest, demand for payment, notice of dishonor, and any and all other notices or demands in connection with the deliver, acceptance, performance, default, or enforcement of this Note. 

14. Severability. The invalidity or unenforceability of any provision hereof shall in no way affect the validity or enforceability
of any other provision. 
 15. Addresses for Notices, etc. Any notice required or permitted hereunder shall be given in
writing and shall be conclusively deemed effectively given upon personal delivery or delivery by courier, or on the first business day after transmission if sent by confirmed facsimile transmission, or four (4) business days after deposit in
the United States mail, by registered or certified mail, postage prepaid, addressed (i) if to Borrower, as set forth below the Borrower’s name on the signature page of this Note, and (ii) if to Lender, at Lender’s address as set
forth below Lender’s name on the signature page of this Note, or at such other address as the Borrower or Lender may designate by advance written notice to the other parties hereto. For purposes of this Section 15, a “business
day” means a weekday on which banks are open for general banking business in New York City, New York. 
 16.
Headings; Interpretation. In this Note, (i) the meaning of defined terms shall be equally applicable to both the singular and plural forms of the terms defined; (ii) the captions and headings are used only for convenience and are
not to be considered in construing or interpreting this Note and (iii) the words “including,” “includes” and “include” shall be deemed to be followed by the words “without limitation”. All references in
this Note to sections, paragraphs, exhibits and schedules shall, unless otherwise provided, refer to sections and paragraphs hereof and exhibits and schedules attached hereto, all of which exhibits and schedules are incorporated herein by this
reference. 
 [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK] 

  
 7 

 IN WITNESS WHEREOF, the undersigned has caused this instrument to be executed by its duly
authorized officers as of the date first above written. 
 BORROWER: 

 

			
	MASCOMA CORPORATION
		
	By:	 	  

	Name:	 	
	Title:	 	

  

			
	Acknowledged and agreed by Lender:
		
	[	 	]
		
	 By:
	 	  

	 Name:
	 	
	 Title:
	 	
	
	 Address:

 EXHIBIT D 
 Form of Warrant 

 THIS WARRANT AND THE UNDERLYING SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
AMENDED (THE “ACT”), OR UNDER THE SECURITIES LAWS OF APPLICABLE STATES. THESE SECURITIES ARE SUBJECT TO RESTRICTIONS ON TRANSFERABILITY AND RESALE AND MAY NOT BE TRANSFERRED OR RESOLD EXCEPT AS PERMITTED UNDER THE ACT AND APPLICABLE STATE
SECURITIES LAWS, PURSUANT TO REGISTRATION UNDER SUCH LAWS OR AN EXEMPTION FROM SUCH REGISTRATION REQUIREMENT. INVESTORS SHOULD BE AWARE THAT THEY MAY BE REQUIRED TO BEAR THE FINANCIAL RISKS OF THIS INVESTMENT FOR AN INDEFINITE PERIOD OF TIME. THE
ISSUER OF THESE SECURITIES MAY REQUIRE AN OPINION OF COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER TO THE EFFECT THAT ANY PROPOSED TRANSFER OR RESALE IS IN COMPLIANCE WITH THE ACT AND ALL APPLICABLE STATE SECURITIES LAWS. 

WARRANT TO PURCHASE STOCK 
  

			
	No. W-        	 	  

 THIS CERTIFIES THAT, for value
received,                                        
, with its principal office
at                                        , or
its assigns (the “Holder”), is entitled to subscribe for and purchase from MASCOMA CORPORATION, a Delaware corporation (the “Company”), with its principal office at 67
Etna Road, Suite 300, Lebanon, NH 03766, [            ] shares of the Company’s [            ] [INSERT NUMBER (AS
CALCULATED BELOW) AND TYPE OF SHARES] at the Exercise Price (each as defined below). 
 This Warrant is being issued
as one of a series of warrants pursuant to the terms of the Subordinated Convertible Promissory Note and Warrant Purchase Agreement, dated August 1, 2011, by and among the Company and the purchasers therein (the “Purchase
Agreement”). Capitalized terms not otherwise defined herein shall have the meaning given to such terms in the Notes (as defined below). Pursuant to the Purchase Agreement, the Company issued and sold certain Subordinated Convertible
Promissory Notes to the purchasers (individually, the “Note” and collectively, the “Notes.”). Unless indicated otherwise, the Holder may purchase up to
[            ] shares of the Company’s [            ] (the “Shares”) upon exercise of this Warrant.

 [INSERT NUMBER AND TYPE OF SHARES IN THE BLANKS ABOVE, WITH THE NUMBER OF SHARES BASED ON THE BELOW FORMULAS IN THE EVENT
OF A QUALIFIED FINANCING OR AN IPO, WHICHEVER OF THE TWO EVENTS IS THE FIRST TO OCCUR: 
 Provided a Holder has purchased
at least its Pro Rata Portion of Notes (as defined in the Purchase Agreement), and in connection with a Qualified Financing, where the Notes convert into the equity securities of the Company sold in such Qualified

 
Financing, that number of shares equal to twenty-five percent (25%) of the equity securities acquired by the Holder upon conversion of that portion of the Notes that such Holder purchased up
to and including such Purchaser’s Pro Rata Portion of Notes ; provided that with respect to a Holder that purchases greater than such Holder’s Pro Rata Portion of Notes, such Holder shall receive, for that portion of the Notes that
such Holder purchased in excess of such Holder’s Pro Rata Portion of Notes, that number of shares equal to fifty percent (50%) of the equity securities acquired by the Holder upon conversion of such portion in excess of such Holders’
Pro Rata Portion of Notes. 
 In connection with an IPO, where the Notes convert into Common Stock of the Company, par
value $0.001 (the “Common Stock”), that number of shares equal to twenty-five percent (25%) of the Common Stock acquired by the Holder upon conversion of that portion of the Notes that such Holder purchased up to and including such
Purchaser’s Pro Rata Portion of Notes; provided that with respect to a Holder that purchases greater than such Holder’s Pro Rata Portion of Notes, such Holder shall receive, for that portion of the Notes that such Holder purchased
in excess of such Holder’s Pro Rata Portion of Notes, that number of shares equal to fifty percent (50%) of the equity securities acquired by the Holder upon conversion of such portion in excess of such Holders’ Pro Rata Portion of
Notes.] 
 1. DEFINITIONS. As used herein, the following terms shall have the following respective
meanings: 
 (a) “Exercise Period” shall mean the period commencing on the date hereof and ending
the earlier of (i) the fifth anniversary of the date hereof, and (ii) the occurrence of a Change of Control Event. 

(b) “Exercise Price” shall mean [            ]
[INSERT PRICE PER SHARE], which shall equal the price (i) at which the securities are sold in the Qualified Financing or (ii) at which the Common Stock is offered to the public in an IPO, less a 30% discount per share, as
applicable], subject to adjustment pursuant to Section 5 below. 
 2. EXERCISE OF
WARRANT. The rights represented by this Warrant may be exercised in whole or in part at any time during the Exercise Period, by delivery of the following to the Company at its address set forth above (or at such other address as
it may designate by notice in writing to the Holder):  
 (a) An executed Notice of Exercise in the form attached
hereto; 
 (b) Payment of the Exercise Price either (i) in cash or by check, or (ii) by cancellation of
indebtedness; and 
 (c) This Warrant. 
 Upon the exercise of the rights represented by this Warrant, a certificate or certificates for the Shares so purchased, registered in the name of the Holder or persons affiliated with the

  
 2 

 
Holder, if the Holder so designates, shall be issued and delivered to the Holder within a reasonable time after the rights represented by this Warrant shall have been so exercised. 

The person in whose name any certificate or certificates for Shares are to be issued upon exercise of this Warrant shall be deemed to
have become the holder of record of such shares on the date on which this Warrant was surrendered and payment of the Exercise Price was made, irrespective of the date of delivery of such certificate or certificates, except that, if the date of such
surrender and payment is a date when the stock transfer books of the Company are closed, such person shall be deemed to have become the holder of such shares at the close of business on the next succeeding date on which the stock transfer books are
open. 
 2.1 Net Exercise. Notwithstanding any provisions herein to the contrary, immediately following an IPO, if
the fair market value of one share of the Company’s Common Stock issuable hereunder is greater than the Exercise Price (at the date of calculation as set forth below), in lieu of exercising this Warrant by payment of cash, the Holder may elect
to receive shares equal to the value (as determined below) of this Warrant (or the portion thereof being canceled) by surrender of this Warrant at the principal office of the Company together with the properly endorsed Notice of Exercise in which
event the Company shall issue to the Holder a number of shares of Common Stock computed using the following formula: 
  

					
		 		  	X = Y (A-B)
		 		  	   A

			
	 Where
	 	 X =
	  	the number of Shares to be issued to the Holder
			
		 	Y =	  	the number of shares of Common Stock purchasable under the Warrant or, if only a portion of the Warrant is being exercised, the portion of the Warrant being canceled (at the date
of such calculation)
			
		 	A =	  	the fair market value of one share of the Company’s Common Stock purchasable under the Warrant (at the date of such calculation)
			
		 	B =	  	Exercise Price (as adjusted to the date of such calculation)

 For purposes of the above calculation, the fair market value per share of Common Stock shall be the average of the
closing prices of the Common Stock, on the securities exchange on which such Common Stock is traded following the Initial Public Offering, for five trading days immediately prior to the exercise date. If the Common Stock is traded on other than a
securities exchange, then the fair market value per share of Common Stock shall be determined in good faith by the Company’s Board of Directors. 
 3. COVENANTS OF THE COMPANY. 
 3.1 Covenants as to Shares. The Company covenants and agrees that all Shares that may be issued upon the exercise of the rights represented by this Warrant will, upon issuance, be validly issued
and outstanding, fully paid and nonassessable, and free from all taxes, liens and charges with respect to the issuance thereof. The Company further covenants and 

  
 3 

 
agrees that the Company will at all times during the Exercise Period, have authorized and reserved, free from preemptive rights, a sufficient number of shares of its shares of
[            ] [NTD: INSERT TYPE OF STOCK] to provide for the exercise of the rights represented by this Warrant. If at any time during the Exercise Period the number of authorized
but unissued shares of [            ] [NTD: INSERT TYPE OF STOCK] shall not be sufficient to permit exercise of this Warrant, the Company will take such corporate action as may, in
the opinion of its counsel, be necessary to increase its authorized but unissued shares of [            ] [NTD: INSERT TYPE OF STOCK] to such number of shares as shall be sufficient
for such purposes. 
 3.2 No Impairment. Except and to the extent as waived or consented to by the Holder, the
Company will not, by amendment of its certificate of incorporation or through any reorganization, transfer of assets, consolidation, merger, dissolution, issue or sale of securities or any other voluntary action, avoid or seek to avoid the
observance or performance of any of the terms to be observed or performed hereunder by the Company, but will at all times in good faith assist in the carrying out of all the provisions of this Warrant and in the taking of all such action as may be
necessary or appropriate in order to protect the exercise rights of the Holder against impairment. 
 3.3 Notices of Record
Date. In the event of any taking by the Company of a record of the holders of any class of securities for the purpose of determining the holders thereof who are entitled to receive any dividend (other than a cash dividend which is the same as
cash dividends paid in previous quarters) or other distribution, the Company shall mail to the Holder, at least ten (10) days prior to the date specified herein, a notice specifying the date on which any such record is to be taken for the
purpose of such dividend or distribution. 
 4. REPRESENTATIONS OF HOLDER.

 4.1 Acquisition of Warrant for Personal Account. The Holder represents and warrants that it is acquiring the
Warrant and the Shares solely for its account for investment and not with a view to or for sale or distribution of said Warrant or Shares or any part thereof. The Holder also represents that the entire legal and beneficial interests of the Warrant
and Shares the Holder is acquiring is being acquired for, and will be held for, its account only. 
 4.2 Securities Are Not
Registered. 
 (a) The Holder understands that the Warrant and the Shares have not been registered under the Act on
the basis that no distribution or public offering of the stock of the Company is to be effected. The Holder realizes that the basis for the exemption may not be present if, notwithstanding its representations, the Holder has a present intention of
acquiring the securities for a fixed or determinable period in the future, selling (in connection with a distribution or otherwise), granting any participation in, or otherwise distributing the securities. The Holder has no such present intention.

 (b) The Holder recognizes that the Warrant and the Shares must be held indefinitely unless they are subsequently
registered under the Act or an exemption from such registration is available. The Holder recognizes that the Company has no obligation to 

  
 4 

 
register the Warrant or the Shares of the Company, or to comply with any exemption from such registration. 
 (c) The Holder is aware that neither the Warrant nor the Shares may be sold pursuant to Rule 144 adopted under the Act unless certain conditions are met, including, among other things, the
existence of a public market for the shares, the availability of certain current public information about the Company, the resale following the required holding period under Rule 144 and the number of shares being sold during any three month period
not exceeding specified limitations. Holder is aware that the conditions for resale set forth in Rule 144 have not been satisfied and that the Company presently has no plans to satisfy these conditions in the foreseeable future. 

4.3 Disposition of Warrant and Shares. 
 (a) The Holder further agrees not to make any disposition of all or any part of the Warrant or Shares in any event unless and until: 

(i) The Company shall have received a letter secured by the Holder from the Securities and Exchange Commission stating that no
action will be recommended to the Commission with respect to the proposed disposition; 
 (ii) There is then in effect a
registration statement under the Act covering such proposed disposition and such disposition is made in accordance with said registration statement; or 
 (iii) The Holder shall have notified the Company of the proposed disposition and shall have furnished the Company with a detailed statement of the circumstances surrounding the proposed
disposition, and if reasonably requested by the Company, the Holder shall have furnished the Company with an opinion of counsel, reasonably satisfactory to the Company, for the Holder to the effect that such disposition will not require registration
of such Warrant or Shares under the Act or any applicable state securities laws. 
 (iv) Notwithstanding the provisions
of paragraphs (i), (ii) and (iii) above, no such registration statement or opinion of counsel shall be necessary for a transfer by a Holder that is (A) a partnership transferring to its partners or former partners in accordance with
partnership interests or to an affiliate of such partnership, (B) a corporation transferring to a wholly-owned subsidiary or a parent corporation that owns all of the capital stock of the Holder, (C) a limited liability company
transferring to its members or former members in accordance with their interest in the limited liability company or to an affiliate of such limited liability company, or (D) an individual transferring to the Holder’s family member or trust
for the benefit of an individual Holder; provided that in each case the transferee will be subject to the terms of this Warrant to the same extent as if it were an original Holder hereunder. 

(b) The Holder understands and agrees that all certificates evidencing the shares to be issued to the Holder may bear the
following legend: 
 “THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE
“ACT”), OR UNDER THE 

  
 5 

 
SECURITIES LAWS OF APPLICABLE STATES. THESE SECURITIES ARE SUBJECT TO RESTRICTIONS ON TRANSFERABILITY AND RESALE AND MAY NOT BE TRANSFERRED OR RESOLD EXCEPT AS PERMITTED UNDER THE ACT AND
APPLICABLE STATE SECURITIES LAWS, PURSUANT TO REGISTRATION UNDER SUCH LAWS OR AN EXEMPTION FROM SUCH REGISTRATION REQUIREMENT. INVESTORS SHOULD BE AWARE THAT THEY MAY BE REQUIRED TO BEAR THE FINANCIAL RISKS OF THIS INVESTMENT FOR AN INDEFINITE
PERIOD OF TIME. THE ISSUER OF THESE SECURITIES MAY REQUIRE AN OPINION OF COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER TO THE EFFECT THAT ANY PROPOSED TRANSFER OR RESALE IS IN COMPLIANCE WITH THE ACT AND ALL APPLICABLE STATE SECURITIES
LAWS.” 
 5. Adjustments. Subject to the expiration of this Warrant pursuant to Section 1, the number and kind
of shares purchasable hereunder and the Exercise Price therefor are subject to adjustment from time to time, as follows: 

(a) Merger or Reorganization. If at any time there shall be any reorganization,
recapitalization, merger or consolidation (other than a merger solely to effect a reincorporation of the Company into another state) (a “Reorganization”) involving the Company (other than as otherwise provided for herein or
as would cause the expiration or termination of this Warrant under Section 1(a)) in which shares of the Company’s stock are converted into or exchanged for securities, cash or other property, then, as a part of such Reorganization, lawful
provision shall be made so that the Holder shall thereafter be entitled to receive upon exercise of this Warrant, the kind and amount of securities, cash or other property of the successor corporation resulting from such Reorganization, equivalent
in value to that which a holder of the Shares deliverable upon exercise of this Warrant would have been entitled in such Reorganization if the right to purchase the Shares hereunder had been exercised immediately prior to such Reorganization. In any
such case, appropriate adjustment (as determined in good faith by the board of directors of the successor corporation) shall be made in the application of the provisions of this Warrant with respect to the rights and interests of the Holder after
such Reorganization to the end that the provisions of this Warrant shall be applicable after the event, as near as reasonably may be, in relation to any shares or other securities deliverable after that event upon the exercise of this Warrant.

 (b) Reclassification of Shares. If the securities issuable upon exercise of this Warrant are
changed into the same or a different number of securities of any other class or classes by reclassification, capital reorganization, conversion of all outstanding shares of the relevant class or series (other than as would cause the expiration of
this Warrant pursuant to Section 1) or otherwise (other than as otherwise provided for herein) (a “Reclassification”), then, in any such event, in lieu of the number of Shares which the Holder would otherwise have been
entitled to receive, the Holder shall have the right thereafter to exercise this Warrant for a number of shares of such other class or classes of stock that a holder of the number of securities deliverable upon exercise of this Warrant immediately
before that change would have been entitled to receive in such Reclassification, all subject to further adjustment as provided herein with respect to such other shares. 

  
 6 

 (c) Subdivisions and Combinations. In the event that the
outstanding shares of preferred stock are subdivided (by stock split, by payment of a stock dividend or otherwise) into a greater number of shares of such securities, the number of Shares issuable upon exercise of the rights under this Warrant
immediately prior to such subdivision shall, concurrently with the effectiveness of such subdivision, be proportionately increased, and the Exercise Price shall be proportionately decreased, and in the event that the outstanding shares of preferred
stock are combined (by reclassification or otherwise) into a lesser number of shares of such securities, the number of Shares issuable upon exercise of the rights under this Warrant immediately prior to such combination shall, concurrently with the
effectiveness of such combination, be proportionately decreased, and the Exercise Price shall be proportionately increased. 

(d) Redemption. In the event that all of the outstanding shares of the securities issuable
upon exercise of this Warrant are redeemed in accordance with the Company’s certificate of incorporation, this Warrant shall thereafter be exercisable for a number of shares of the Company’s Common Stock equal to the number of shares of
common stock that would have been received if this Warrant had been exercised in full immediately prior to such redemption and the preferred stock received thereupon had been simultaneously converted into common stock. 

(e) Notice of Adjustments. Upon any adjustment in accordance with this Section 5, the
Company shall give notice thereof to the Holder, which notice shall state the event giving rise to the adjustment, the Exercise Price as adjusted and the number of securities or other property purchasable upon the exercise of the rights under this
Warrant, setting forth in reasonable detail the method of calculation of each. The Company shall, upon the written request of any Holder, furnish or cause to be furnished to such Holder a certificate setting forth (i) such adjustments,
(ii) the Exercise Price at the time in effect and (iii) the number of securities and the amount, if any, of other property that at the time would be received upon exercise of this Warrant. 

6. FRACTIONAL SHARES. No fractional shares shall be issued upon the exercise of this Warrant as a
consequence of any adjustment pursuant hereto. All Shares (including fractions) issuable upon exercise of this Warrant may be aggregated for purposes of determining whether the exercise would result in the issuance of any fractional share. If, after
aggregation, the exercise would result in the issuance of a fractional share, the Company shall, in lieu of issuance of any fractional share, pay the Holder otherwise entitled to such fraction a sum in cash equal to the product resulting from
multiplying the then current fair market value of a Share by such fraction. 
 7. AUTOMATIC
EXERCISE. If subsequent to an IPO, the Holder of this Warrant has not elected to exercise this Warrant prior to the expiration or termination of this Warrant pursuant to Section 1(a), then this
Warrant shall automatically (without any act on the part of the Holder) be exercised pursuant to Section 2.1 effective immediately prior to the expiration of the Warrant to the extent such net issue exercise would result in the issuance of
Shares. If this Warrant is automatically exercised, the Company shall notify the Holder of the automatic exercise as soon as reasonably practicable, and the Holder shall surrender the Warrant to the Company in accordance with the terms hereof.

  
 7 

 8. NO STOCKHOLDER RIGHTS. This Warrant
in and of itself shall not entitle the Holder to any voting rights or other rights as a stockholder of the Company. 
 9.
TRANSFER OF WARRANT. Subject to applicable laws and the restriction on transfer set forth on the first page of this Warrant, this Warrant and all rights hereunder are transferable, by the Holder in
person or by duly authorized attorney, upon delivery of this Warrant and the form of assignment attached hereto to any transferee designated by Holder. The transferee shall sign an investment letter in form and substance satisfactory to the Company.

 10. LOST, STOLEN, MUTILATED OR DESTROYED
WARRANT. If this Warrant is lost, stolen, mutilated or destroyed, the Company may, on such terms as to indemnity or otherwise as it may reasonably impose (which shall, in the case of a mutilated Warrant, include the surrender
thereof), issue a new Warrant of like denomination and tenor as the Warrant so lost, stolen, mutilated or destroyed. Any such new Warrant shall constitute an original contractual obligation of the Company, whether or not the allegedly lost, stolen,
mutilated or destroyed Warrant shall be at any time enforceable by anyone. 
 11. NOTICES, ETC.
All notices required or permitted hereunder shall be in writing and shall be deemed effectively given: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed telex, facsimile or electronic mail if sent
during normal business hours of the recipient, if not, then on the next business day, (c) five (5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after
deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All communications shall be sent to the Company at the address listed on the signature page and to Holder at its address
listed on the first page of this Warrant or at such other address as the Company or Holder may designate by ten (10) days advance written notice to the other parties hereto. 

12. ACCEPTANCE. Receipt of this Warrant by the Holder shall constitute acceptance of and agreement to all of the
terms and conditions contained herein. 
 13. AMENDMENT AND WAIVER. Any term
of this Warrant may be amended or waived with the written consent of the Company and the Requisite Purchasers as provided in Section 5.02 of the Purchase Agreement; provided, however, that any amendment or waivers must apply to all
Holders in the same manner. Holder acknowledges that because this Warrant may be amended with the consent of the Requisite Purchasers, Holder’s rights hereunder may be amended or waived without Holder’s consent. Upon the effectuation of
such waiver or amendment in conformance with this Section 13, the Company shall promptly give written notice thereof to the record Holders of the Warrants who have not previously consented thereto in writing. 

14. GOVERNING LAW. This Warrant and all rights, obligations and
liabilities hereunder shall be governed by, and construed and enforced in accordance with, the substantive laws of the State of Delaware without regard to its principles of conflicts of laws. 

  
 8 

 IN WITNESS WHEREOF, the
Company has caused this Warrant to be executed by its duly authorized officer as of                     ,
        . 
  

			
	MASCOMA CORPORATION
		
	By:	 	  

		
	Name:	 	  

		
	Title:	 	  

	
	HOLDER:
		
	By:	 	  

		
	Name:	 	  

		
	Title:	 	  

 SIGNATURE PAGE TO 

WARRANT 

 NOTICE OF EXERCISE 

(1)  ̈ The undersigned hereby elects to purchase
             shares of [            ] (the “Shares”) of Mascoma Corporation (the
“Company”) pursuant to the terms of the attached Warrant, and tenders herewith payment of the exercise price in full, together with all applicable transfer taxes, if any. 

 ̈ The undersigned hereby elects to purchase
             shares of [            ] (the “Shares”) of Mascoma Corporation (the
“Company”) pursuant to the terms of the net exercise provisions set forth in Section 2.1 of the attached Warrant, and shall tender payment of all applicable transfer taxes, if any. 

(2) Please issue a certificate or certificates representing said shares of the Shares in the name of the undersigned or in such
other name as is specified below: 
  
  

(Name) 
  

 
  

 
 (Address)

 (3) The undersigned represents that (i) the aforesaid Shares are being acquired for the account of the
undersigned for investment and not with a view to, or for resale in connection with, the distribution thereof and that the undersigned has no present intention of distributing or reselling such shares; (ii) the undersigned is aware of the
Company’s business affairs and financial condition and has acquired sufficient information about the Company to reach an informed and knowledgeable decision regarding its investment in the Company; (iii) the undersigned is experienced in
making investments of this type and has such knowledge and background in financial and business matters that the undersigned is capable of evaluating the merits and risks of this investment and protecting the undersigned’s own interests;
(iv) the undersigned understands that the Shares issuable upon exercise of this Warrant have not been registered under the Securities Act of 1933, as amended (the “Securities Act”), by reason of a specific exemption from
the registration provisions of the Securities Act, which exemption depends upon, among other things, the bona fide nature of the investment intent as expressed herein, and, because such securities have not been registered under the Securities Act,
they must be held indefinitely unless subsequently registered under the Securities Act or an exemption from such registration is available; (v) the undersigned is aware that the aforesaid Shares may not be sold pursuant to Rule 144 adopted
under the Securities Act unless certain conditions are met and until the undersigned has held the shares for the number of years prescribed by Rule 144, that among the conditions for use of the Rule is the availability of current information to the
public about the Company and the Company has not made such information available and has no present plans to do so; and (vi) the undersigned agrees not to make any disposition of all or any part of the aforesaid Shares unless and until there is
then in effect a registration statement under the Securities Act covering such proposed disposition and such disposition is made in accordance with said registration statement, or the undersigned has provided the Company with an opinion of counsel
satisfactory to the Company, stating that such registration is not required. 

					
	  
	 		  	  

	(Date)	 		  	(Signature)
			
		 		  	  

		 		  	(Print name)

 ASSIGNMENT FORM 

(To assign the foregoing Warrant, execute this form and supply required information. Do not use this form to purchase shares.)

 FOR VALUE RECEIVED, the foregoing Warrant and all rights
evidenced thereby are hereby assigned to 
  

					
	 Name:
	 	  

		 	(Please Print)
		
	 Address:
	 	  

		 	(Please Print)
	 Dated:                 ,
20    
	  	
			
	 Holder’s
	 		  	
	 Signature:
	 	  
	  	
			
	 Holder’s
	 		  	
	 Address:
	 	  
	  	

 NOTE: The signature to this Assignment Form must correspond with the name as it appears on the face of the
Warrant, without alteration or enlargement or any change whatever. Officers of corporations and those acting in a fiduciary or other representative capacity should file proper evidence of authority to assign the foregoing Warrant. 

 EXHIBIT E 
 Disclosure Schedule 

 EXHIBIT E 
 DISCLOSURE SCHEDULE 
 This Disclosure Schedule is delivered in connection
with the Subordinated Convertible Note and Warrant Purchase Agreement (the “Agreement”) by and among Mascoma Corporation, a Delaware corporation (the “Corporation”), and the Purchasers party thereto. Capitalized
terms used, but not defined, herein shall have the meaning set forth in the Agreement. This Disclosure Schedule is arranged in Sections corresponding to the numbered and lettered paragraphs contained in Section 3 of the Agreement. 

Except as otherwise limited herein, all information and disclosures contained in this Disclosure Schedule are made as of the date of the
Agreement, and their accuracy is confirmed only as of that date and not at a time thereafter. Any matter disclosed in any section of the Disclosure Schedule shall qualify the corresponding paragraph of the Agreement. Any information disclosed in a
specific section shall be deemed to be disclosed and incorporated into any other section where such disclosure is reasonably apparent from the context of the disclosure. 
 No implication shall be drawn that any information provided herein is necessarily material or otherwise required to be disclosed, or that the inclusion of such information establishes or implies a
standard of materiality or any other standard for disclosure under the Agreement. The information provided herein is provided for the purpose of disclosure under the Agreement and shall not be deemed to constitute an acknowledgement by the
Corporation of any liability or obligation set forth herein. 
 This Disclosure Schedule is qualified in its entirety by
reference to specific provisions of the Agreement, and is not intended to broaden the scope of any representation or warranty of the Corporation contained in the Agreement. Headings have been inserted for each section of this Disclosure Schedule for
convenience and reference only and shall not have the effect of amending or changing the express description of such sections as set forth in the Agreement or altering the disclosures contained therein 

The following Sections are attached hereto: 
  

			
	 Section 3.01
	    	Organization
	 Section 3.03
	    	Capitalization

 Section 3.01 

Organization 
  

	1.	The Corporation is qualified to do business in the Commonwealth of Massachusetts. 

 

	2.	The Corporation is qualified to do business in the State of New York. 

  

	3.	The Corporation is qualified to do business in the State of New Hampshire, under the name Mascoma Bioethanol. 

 Section 3.03 

Capitalization 
  

	1.	The following table lists all holders of Common Stock: 

  

					
	 Name
	  	Shares	 
	 Lee R. Lynd
	  	 	500,000	  
	 Charles E. Wyman
	  	 	400,000	  
	 Colin R. South
	  	 	400,000	  
	 Dartmouth College
	  	 	400,000	  
	 Robert J. Johnsen
	  	 	212,498	  
	 Bruce A. Jamerson
	  	 	417,840	  
	 Blair R. Collins
	  	 	79,008	  
	 Ginja R. Collins
	  	 	79,007	  
	 Peter H. Rothstein
	  	 	24,000	  
	 John C. Niles
	  	 	22,988	  
	 The Thomas A Daschle Revocable Trust dated 6/15/2006 and the Linda H. Daschle Revocable Trust dated 6/5/2006, as tenants in
common
	  	 	20,000	  
	 John P. Ellersick
	  	 	20,000	  
	 Karyn Anderson
	  	 	5,000	  
	 Jesse McCool
	  	 	4,375	  
	 Richard Martin
	  	 	2,865	  
	 David Hogsett
	  	 	100,000	  
	 Jonathan Mielenz
	  	 	100,000	  
	 Lee Lynd 2007 Grantor Retained Annuity Trust
	  	 	300,000	  
	 Stellenbosch University Investment Trust
	  	 	200,000	  
	 Susan Nedell
	  	 	10,000	  
	 Sivasubramanian, M.S.
	  	 	35,937	  
	 Herve Garant
	  	 	29,687	  
	 Vineet Rajgarhia
	  	 	15,185	  
	 Daniel Olson
	  	 	6,406	  
	 Ana Echaniz
	  	 	1,000	  
	 Bethany Miller
	  	 	925	  
	 Shitai Tripathi
	  	 	874	  
	 Patrick Williams
	  	 	600	  
	 Jeff Villari
	  	 	500	  

					
	 Name
	  	Shares	 
	 SunOpta Inc.
	  	 	3,756,290	  

  

	2.	The following table lists all holders of holders of Series A Preferred Stock: 

 

					
	 Name
	  	Shares	 
	 Flagship Ventures Fund 2004, L.P.
	  	 	1,250,000	  
	 Khosla Ventures I, LP
	  	 	3,750,000	  

  

	3.	The following table lists all holders of Series A-1 Preferred Stock: 

  

					
	 Name
	  	Shares	 
	 Khosla Ventures I, LP
	  	 	3,750,000	  
	 Flagship Ventures Fund 2004, L.P.
	  	 	1,250,000	  

  

	4.	The following table lists all holders of Series B Preferred Stock: 

  

					
	 Name
	  	Shares	 
	 General Catalyst Group IV, L.P.
	  	 	3,374,875	  
	 GC Entrepreneurs Fund IV, L.P.
	  	 	89,544	  
	 KPCB Holdings, Inc., as Nominee
	  	 	2,996,255	  
	 Khosla Ventures I, LP
	  	 	561,798	  
	 Flagship Ventures Fund 2004, L.P.
	  	 	1,217,228	  
	 VantagePoint Venture Partners 2006 (Q), L.P.
	  	 	1,123,596	  
	 VantagePoint CleanTech Partners, L.P.
	  	 	1,123,595	  
	 Pinnacle Ventures II-A, L.P.
	  	 	4,495	  
	 Pinnacle Ventures II-B, L.P.
	  	 	188,764	  
	 Pinnacle Ventures II-C, L.P.
	  	 	15,730	  
	 Pinnacle Ventures II-R, L.P.
	  	 	15,730	  
	 Atlas Venture Fund VII, L.P.
	  	 	374,532	  
	 Dean W. Rybeck
	  	 	93,633	  
	 Barbara D. Rybeck
	  	 	37,453	  
	 Susan Williams*
	  	 	5,618	  
	 David Noda and Kay M. Nishiyama
(as joint tenants with right of survivorship)
	  	 	18,727	  

  

	5.	The following table lists all holders of Series C Preferred Stock: 

					
	 Name
	  	Shares	 
	 MPC Investment LLC
	  	 	1,562,500	  
	 General Catalyst Group IV, L.P.
	  	 	517,519	  
	 GC Entrepreneurs Fund IV, L.P.
	  	 	13,731	  
	 KPCB Holdings, Inc., as nominee
	  	 	453,125	  
	 Khosla Ventures I, LP
	  	 	375,000	  
	 Flagship Ventures Fund 2004 L.P.
	  	 	453,125	  
	 VantagePoint Venture Partners 2006 (Q), L.P.
	  	 	226,563	  
	 VantagePoint CleanTech Partners, L.P.
	  	 	226,562	  
	 Pinnacle Ventures II-A, L.P.
	  	 	1,875	  
	 Pinnacle Ventures II-B, L.P.
	  	 	78,750	  
	 Pinnacle Ventures II-C, L.P.
	  	 	6,563	  
	 Pinnacle Ventures II-R, L.P.
	  	 	6,562	  
	 Pinnacle Ventures Equity Fund I, L.P.
	  	 	378,125	  
	 Pinnacle Ventures Equity Fund I-O, L.P.
	  	 	275,000	  
	 Pinnacle Ventures Equity Fund I Affiliates, L.P.
	  	 	34,375	  
	 Atlas Venture Fund VII, L.P.
	  	 	78,125	  
	 Purdue Research Foundation*
	  	 	76,425	  
	 David Mann
	  	 	1,048	  
	 Larry Hannah*
	  	 	420	  
	 Bowen Engineering Corporation*
	  	 	48,283	  
	 Terry L. Bowen*
	  	 	22,119	  
	 Lowe’s Ltd., L.P.*
	  	 	22,109	  
	 Robert L. Bowen*
	  	 	22,077	  
	 Roch Enterprises, L.P.
	  	 	18,640	  
	 Bradley D. Spindler*
	  	 	5,242	  
	 Bowen Bio-Energy, LLC*
	  	 	335,525	  
	 CRM Holdings, LLC
	  	 	226,480	  
	 Brian J. Stater*
	  	 	41,939	  
	 R. Jeremy Grantham
	  	 	2,343,750	  
	 Bluestem Growth & Income Fund III, LLC
	  	 	156,250	  
	 Bluestem Select Opportunities Fund, LLC
	  	 	156,250	  
	 Eric Lemelson
	  	 	234,375	  
	 David Noda & Kay M. Nishiyama
	  	 	14,062	  
	 Barbara D. Rybeck
	  	 	15,625	  

					
	 Name
	  	Shares	 
	 Dean W. Rybeck
	  	 	31,250	  
	 Malaysian Life Sciences Capital Fund
	  	 	312,500	  
	 Piper Jaffray & Co.
	  	 	312,500	  
	 General Motors Ventures LLC
	  	 	781,250	  
	 Fagen, Inc.
	  	 	156,250	  
	 Stack, LLC
	  	 	156,250	  
	 Bruce A. Jamerson
	  	 	173,438	  

  

	6.	The following table lists all holders of Series D Preferred Stock: 

  

					
	 Name
	  	Shares	 
	 MPC Investment LLC
	  	 	160,023	  
	 General Catalyst Group IV, L.P.
	  	 	333,018	  
	 GC Entrepreneurs Fund IV, L.P.
	  	 	8,836	  
	 KPCB Holdings, Inc., as nominee
	  	 	295,116	  
	 Khosla Ventures I, LP
	  	 	721,820	  
	 Flagship Ventures Fund 2004 L.P.
	  	 	356,800	  
	 VantagePoint Venture Partners 2006 (Q), L.P.
	  	 	184,823	  
	 VantagePoint CleanTech Partners, L.P.
	  	 	46,206	  
	 Pinnacle Ventures II-A, L.P.
	  	 	545	  
	 Pinnacle Ventures II-B, L.P.
	  	 	22,896	  
	 Pinnacle Ventures II-C, L.P.
	  	 	1,908	  
	 Pinnacle Ventures II-R, L.P.
	  	 	1,908	  
	 Pinnacle Ventures Equity Fund I, L.P.
	  	 	32,362	  
	 Pinnacle Ventures Equity Fund I-O, L.P.
	  	 	23,536	  
	 Pinnacle Ventures Equity Fund I Affiliates, L.P.
	  	 	2,942	  
	 Atlas Venture Fund VII, L.P.
	  	 	38,728	  
	 David Mann
	  	 	90	  
	 Roch Enterprises, L.P.
	  	 	1,595	  
	 CRM Holdings, LLC
	  	 	25,033	  
	 R. Jeremy Grantham
	  	 	200,522	  
	 Bluestem Growth & Income Fund III, LLC
	  	 	22,067	  
	 Bluestem Select Opportunities Fund, LLC
	  	 	22,067	  
	 Eric Lemelson
	  	 	20,059	  
	 David Noda & Kay M. Nishiyama
(as joint tenants with right of survivorship)
	  	 	2,806	  

					
	 Name
	  	Shares	 
	 Barbara D. Rybeck
	  	 	4,543	  
	 Dean W. Rybeck
	  	 	10,688	  
	 Malaysian Life Sciences Capital Fund
	  	 	26,746	  
	 Piper Jaffray & Co.
	  	 	26,746	  
	 General Motors Ventures LLC
	  	 	66,864	  
	 Fagen, Inc.
	  	 	13,373	  
	 Stack, LLC
	  	 	13,373	  
	 Bruce A. Jamerson
	  	 	14,844	  
	 SunOpta Inc.
	  	 	6,580,866	  
	 Roytor & Co/ c/o RT. Acct #790973
	  	 	109,387	  
	 Wildstoic LLC
	  	 	156,267	  
	 Rod Fuller
	  	 	15,627	  
	 Wendy Strub
	  	 	7,813	  
	 Canaccord Genuity Corporation ITF Peter J. Chandler
ac# 139-264S-4 (RRSP)
	  	 	15,627	  
	 Canaccord Genuity Corporation ITF Peter J. Chandler
ac# 139-264M-2
	  	 	7,813	  
	 Todd Nofke
	  	 	25,003	  
	 Brant Investments Limited A/C 99480027
	  	 	20,062	  
	 Brant Investments Limited A/C 99480072
	  	 	78,824	  
	 Jayvee & Co. INVF0004002
	  	 	60,469	  
	 Jayvee & Co. INVF0013002
	  	 	4,632	  
	 Jayvee & Co.
	  	 	156,267	  
	 Bershaw & Co.
	  	 	265,747	  
	 Canaccord Genuity Corp.
	  	 	14,064	  
	 Wilsey Invest Ltd.
	  	 	156,267	  
	 Hare & Co.
	  	 	3,594,133	  
	 Diamond Alternative Energy, LLC
	  	 	1,333,333	  

  

	*	The Corporation is currently in the process of converting the holdings of these holders to Common Stock. 

 

	7.	Attached hereto as Exhibit A is a listing of all of the Corporation’s outstanding options to purchase shares of its Common Stock as of July 27, 2011.
On July 22, 2011, the Board of Directors of the Corporation approved resolutions to issue an aggregate of 2,054,325 options to purchase Common Stock, as disclosed in further detail on Exhibit A, but these options have not yet been granted to
the respective individuals indicated therein. 

	8.	In connection with the execution of the Loan and Security Agreement between the Corporation and Pinnacle Ventures, L.L.C. (“Pinnacle”), as agent for
the lenders identified on Schedule 1 thereto (the “Pinnacle Lenders”), dated October 6, 2006, and as amended by an Amendment to Loan Agreement dated October 30, 2006 (as amended, the “Pinnacle Loan
Agreement”), the Corporation granted to an affiliate of Pinnacle, Pinnacle Ventures II Equity Holdings, L.P. (the “Pinnacle Warrant Holder”), a warrant (the “Pinnacle Warrant”) exercisable for 162,500
shares (the “Pinnacle Shares”) of either: (i) the Corporation’s Series Al Preferred Stock, par value $.001 per share (“Series A-l Preferred Stock”); or, under certain circumstances as defined therein,
(ii) Common Stock or (iii) any security into which the Series A-l Preferred Stock or Common Stock may be converted, exchanged, reclassified or otherwise changed. The exercise price of the Pinnacle Warrant is $1.00 per share.

  

	9.	In connection with the execution of the Loan and Security Agreement between the Corporation and Pinnacle, as agent for the lenders identified on Schedule 1B thereto,
dated February 5, 2008 (the “Pinnacle 2008 Loan Agreement”), the Corporation granted to an affiliate of Pinnacle, Pinnacle Ventures II Equity Holdings, L.L.C. (the “Pinnacle Warrant Holder”), a warrant (the
“Pinnacle Series B Warrant”) exercisable for a certain number of shares by a calculation provided therein (the “Pinnacle Series B Shares”) of either: (i) the Corporation’s Series B Preferred Stock, par
value $.001 per share (“Series B Preferred Stock”); or, under certain circumstances as defined therein, (ii) Common Stock or (iii) any security into which the Series B Preferred Stock or Common Stock may be converted,
exchanged, reclassified or otherwise changed. The exercise price of the Pinnacle Series B Warrant is $2.67 per share. 

  

	10.	In connection with the execution of the Pinnacle 2008 Loan Agreement between the Corporation and Pinnacle, as agent for the lenders identified on Schedule 1B thereto,
the Corporation granted to the Pinnacle Warrant Holder a warrant (the “Pinnacle Series C Warrant”) exercisable for a certain number of shares by a calculation provided therein (the “Pinnacle Preferred Shares”) of
either: (i) the Corporation’s Series B Preferred Stock or the Company’s Series C Preferred Stock, par value $.001 per share (“Series C Preferred Stock”); or, under certain circumstances as defined therein,
(ii) Common Stock or (iii) any security into which the Series B Preferred Stock, Series C Preferred Stock, or Common Stock may be converted, exchanged, reclassified or otherwise changed. The exercise price of the Pinnacle Series C Warrant
is an amount to be determined by a calculation provided in the Pinnacle 2008 Loan Agreement. 

  

	11.	In connection with the execution of the Note Conversion Agreement, dated as of August 31, 2010, by and among the Corporation and the purchasers identified therein
(the “Note Conversion Agreement”), the Corporation granted to the purchasers listed on Schedule I to the Note Conversion Agreement certain warrants (the “SunOpta Series D Warrants”) exercisable for an aggregate of
1,357,806 shares (the “SunOpta Preferred Shares”) of the Corporation’s Series D Preferred Stock, par value $.001 per share (“Series D Preferred Stock”). The exercise price of each of the SunOpta Series D
Warrants is $3.75 per share. 

  

	12.	 In connection with the execution of the Share Purchase Agreement, dated as of August 31, 2010, by and between the Corporation, Mascoma Canada
Inc., SunOpta Inc., SunOpta BioProcess Inc., and the parties identified on Schedule A thereto (the “Share 

	 	
Purchase Agreement”), the Corporation granted to SunOpta Inc. a warrant to purchase 1,000,000 shares of Common Stock with an exercise price of $3.75 per share.

  

	13.	In connection with the execution of the Series D Preferred Stock and Warrant Purchase Agreement, dated as of January 7, 2011, by and between the Corporation and
Diamond Alternative Energy, LLC (the “Valero Agreement”), the Corporation granted Diamond Alternative Energy, LLC a warrant (the “Valero Warrant”) exercisable for an aggregate of 1,333,333 shares of the Series D
Preferred Stock (the “Valero Shares”). The exercise price of the Valero Warrant is $3.75 per share. 

  

	14.	In connection with the execution of the Amended and Restated Loan and Security Agreement between the Corporation, the subsidiaries of the Corporation listed on Schedule
1A thereto and Pinnacle, as agent for the lenders identified on Schedule 1B thereto, dated as of June 1, 2011 (the “Pinnacle 2011 Loan Agreement”), the Corporation granted to each of Pinnacle Ventures II Equity Holdings, L.L.C.
and Pinnacle Ventures III Equity Holdings, L.L.C. (the “Pinnacle Warrant Holders”), a warrant (the “Pinnacle 2011 Warrant”) exercisable for a certain number of shares by a calculation provided therein of Common
Stock. The exercise price of each of the Pinnacle 2011 Warrants is determined by a calculation provided therein, not to exceed $1.97 per share. 

  

	15.	The Stock Purchase Agreement between Dartmouth College (“Dartmouth”) and the Corporation, dated July 10, 2006 (the “Dartmouth
SPA”), provides that Dartmouth shall have the right (the “Dartmouth Put”) for a period of three months after the fifth anniversary of the Dartmouth SPA, subject to certain limitations described therein, to put the shares of
Common Stock issued and sold to Dartmouth pursuant to the Dartmouth SPA (the “Dartmouth Shares”) to the Corporation at the fair market value of such Shares at the time that the Dartmouth Put is exercised. 

 

	16.	Pursuant to the Letter of Understanding to Conduct an Executive Search between Schweichler Price & Partners, Inc. (“Schweichler”) and the
Corporation, dated January 1, 2007 (the “Schweichler Agreement”), Schweichler has a right to purchase up to 7,634 shares of Common Stock (the “Schweichler Shares”), at an aggregate purchase price of $10,000.54.
On July 11, 2007, the Corporation notified Schweichler of its right purchase the Schweichler Shares and, on November 12, 2007, the Corporation received notice from Schweichler that Schweichler would not purchase the Schweichler Shares.

  

	17.	In connection with the Corporation’s issuance of stock options to its employees in the State of New York pursuant to the option plan, the Corporation failed to
timely file the paperwork qualifying the Corporation, pursuant to N.Y. GEN. BUS. LAW § 359-f-2-e, for an exemption from registration in the State of New York as required by N.Y. GEN. BUS. LAW § 359-e. The Corporation filed documents with
the State of New York to obtain an exemption from registration. 

  

	18.	The Dartmouth Shares, the Stellenbosch Shares and the shares of Common Stock held by David Hogsett and Jonathan Mielenz, transferred from Advanced Bioconversion
Technologies, Inc. (the “ABT Shares”) are not subject to vesting in favor of the Corporation. 

  

	19.	 The shares of Common Stock held by Robert J. Johnsen are not subject to vesting in favor of the Corporation. Such shares vested in accordance with the
stock restriction and 

	 	
repurchase agreement between the Corporation and Mr. Johnsen (the “Johnsen Stock Agreement”) when his employment was terminated by the Corporation without Cause (as defined
therein), effective July 7, 2006, pursuant to a separation agreement between Mr. Johnsen and the Corporation, dated September 19, 2006 (the “Johnsen Separation Agreement”). The Corporation elected to repurchase at
cost the shares held by Mr. Johnsen that were subject to the Johnsen Stock Agreement and which had not become vested thereunder. 

  

	20.	As noted above and in Exhibit A, certain options for the purchase of the Corporation’s Common Stock do not vest over four years in monthly installments.
Certain of the options granted to William J. Brady are subject to accelerated vesting in connection with a Change of Control (as defined in the terms of the applicable options grants). Certain of the options to be granted to David Arkowitz pursuant
to his Offer Letter dated as of May 3, 2011 are subject to accelerated vesting in connection with an initial public offering or a Change of Control (as defined in the terms of the applicable options grants).

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