Amended and Restated Warrant Purchase Agreement dated July 1, 2009



 Exhibit 10.49 
 AMENDED AND RESTATED WARRANT PURCHASE AGREEMENT 
 This Amended and
Restated Warrant Purchase Agreement (this “Agreement”) is made and entered into as of July 1, 2009 by and between Mascoma Corporation, a Delaware corporation (the “Company”), and
Pinnacle Ventures II Equity Holdings, L.L.C., a Delaware limited liability company (“Purchaser”). 
 WHEREAS, on December 30, 2008 the Company and the Purchaser entered into that certain Warrant Purchase Agreement (the “Prior Agreement”); 

WHEREAS, the Company and the Purchaser desire to amend and restate the Prior Agreement in its entirety 

WHEREAS, the Company desires to sell and the Purchaser desires to purchase an amended and restated warrant substantially in the form
attached hereto as Exhibit A (the “Warrant”), to purchase shares of the Company’s preferred stock (the “Warrant Shares”), on the terms and conditions set forth herein; and 

WHEREAS, the Prior Agreement may be amended in writing signed by the Company and the Purchaser. 

NOW THEREFORE, the Company and the Purchaser hereby agree that the Prior Agreement shall be amended and superseded in its entirety, and,
in consideration of the foregoing and the mutual promises contained herein and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, accepted and agreed to, the Company and the Purchaser hereby
agree as follows: 
 1. Purchase of Warrant. Subject to the terms and conditions of this Agreement, the Purchaser agrees
to purchase the Warrant from the Company and the Company agrees to sell and issue the Warrant to the Purchaser. 
 2.
Representations of Purchaser. In connection with the purchase of the Warrant and the Warrant Shares, the Purchaser specifically represents to the Company as follows: 
 (a) The Purchaser is aware of the Company’s business affairs and financial condition, and has acquired information about the Company sufficient to reach an informed and knowledgeable decision to
acquire the Warrant and the Warrant Shares. The Purchaser is acquiring the Warrant and the Warrant Shares for its own account for investment purposes only and not with a view to, or for the resale in connection with, any “distribution”
thereof in violation of the Securities Act of 1933, as amended (the “Act”). 
 (b) The Purchaser
understands that neither the Warrant nor the Warrant Shares have been registered under the Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of the Purchaser’s investment
intent as expressed herein. 
 (c) The Purchaser further understands that the Warrant and the Warrant Shares must be held
indefinitely unless subsequently registered under the Act and qualified under any applicable state securities laws, or unless exemptions from registration and qualification are otherwise available. The Purchaser is aware of the provisions of Rule
144, promulgated under the Act. 
 (d) The Purchaser is an “accredited investor” as such term is defined in Rule 501
of Regulation D promulgated under the Act. 

  
 -1-









 3. Legends. The Purchaser acknowledges and understands that the instruments
evidencing the Warrant and any certificates evidencing the Warrant Shares shall bear the legends as specified in the Warrant (and any other legends required under state or federal securities laws in the opinion of legal counsel for the Company).

 4. General Provisions. 
 (a) This Agreement represents the entire agreement between the Company and Purchaser regarding the subject matter hereof, supersedes all prior agreements and understandings (other than, for the avoidance
of doubt, the Warrant Purchase Agreement by and among the Company and the Purchasers dated as of February 5, 2008), and may only be amended in writing signed by the Company and the Purchaser. 

(b) This Agreement shall bind and benefit the successors, assigns, heirs, executors and administrators of the parties. 

(c) This Agreement shall be governed in all respects by the laws of the State of California. 

(d) The Agreement may be executed in counterparts, each of which shall be an original, but all of which together shall constitute an
instrument. 
 [Remainder of page intentionally left blank.] 

  
 -2-









 IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the day and year
first set forth above. 
  

									
	COMPANY	 		 	PURCHASER
			
	 MASCOMA CORPORATION
 a Delaware corporation
	 		 	PINNACLE VENTURES II EQUITY HOLDINGS, L.L.C., a Delaware limited liability company
					
	By:	 	 /s/ Bruce A. Jamerson
	 		 	By:	 	 /s/ Robert N. Savoie

					
	Name:	 	Bruce A. Jamerson	 		 	Name:	 	Robert N. Savoie
					
	Title:	 	Chief Executive Officer	 		 	Title:	 	Chief Financial Officer


  
 -3-









 EXHIBIT A 
 FORM OF WARRANT 







 THIS AMENDED AND RESTATED WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED OR
ANY STATE SECURITIES LAWS. NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT (i) EFFECTIVE REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION OF COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATIONS
ARE NOT REQUIRED, (iii) RECEIPT OF NO-ACTION LETTERS FROM THE APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE PROVISIONS OF SECTION 8 OF THIS AMENDED AND RESTATED WARRANT. 

MASCOMA CORPORATION 
 AMENDED AND RESTATED WARRANT TO PURCHASE PREFERRED STOCK 
 WHEREAS, on
December 30, 2008 MASCOMA CORPORATION, a Delaware corporation (the “Company”) issued a warrant (the “Initial Warrant”) to PINNACLE VENTURES II EQUITY HOLDINGS, L.L.C. (the
“Purchaser”) to purchase shares of the Company’s preferred stock on the terms and conditions set forth therein; 
 WHEREAS, the Company and the Purchaser desire to amend and restate the Initial Warrant in its entirety pursuant to this amended and restated warrant (the “Warrant”); and

 WHEREAS, the Initial Warrant may be changed, waived, discharged or terminated by an instrument in writing signed by the party
against which enforcement of the same is sought. 
 NOW THEREFORE, the Company and the Purchaser hereby agree that the Initial
Warrant shall be amended and superseded in its entirety, and for value received and subject to the provisions set forth in this Warrant, the Purchaser and its assigns are entitled to purchase from the Company: 

 

			
	Shares of Preferred Stock:	  	The number of Shares for which this Warrant is exercisable shall equal $650,000 divided by the Exercise Price (as adjusted pursuant to Section 7 hereof)
		
	Exercise Price:	  	See Section 1 (c)
		
	Term of Warrant:	  	See Section 2 below.
		
	Warrant Date:	  	                    , 2009

 The number of Shares for which this Warrant is exercisable and the Exercise Price may be adjusted as specified in
Section 5. 
 1. Definitions. As used herein, capitalized terms not otherwise defined herein shall have the
meanings set forth in the introductory paragraph of this Warrant or the following meanings: 
 (a) “Applicable
Stock” means (i) the series of convertible preferred stock sold in the Company’s next Qualified Financing, or, if such Qualified Financing has not occurred within 1 year from the Warrant Date, the Company’s presently
authorized Series C Preferred Stock, (ii) after the conversion of all of the outstanding shares of such series of preferred stock into Common Stock, either automatically or by vote of








 
the requisite holders thereof, the Company’s Common Stock, and (iii) upon any conversion, exchange, reclassification or change, any security into which the securities described in
clauses (i) or (ii) of this definition may be converted, exchanged, reclassified or otherwise changed. 
 (b)
“Common Stock” means the common stock of the Company. 
 (c) “Exercise Price”
means the exercise price per share of Applicable Stock and shall equal the Next Round Price of a Qualified Financing occurring after the Warrant Date, or, in the event the Applicable Stock is Series C Preferred Stock, $6.40. 

(d) “Holder” means the initial holder of this Warrant set forth in the first paragraph of this Warrant and any
other person or entity which becomes a holder of this Warrant pursuant to the terms of this Warrant. 
 (e) “Loan
Agreement” means that certain Loan and Security Agreement, dated as of the date hereof, by and among the Company, Pinnacle Ventures, L.L.C., as Agent, and the Lenders party thereto. 

(f) “Next Round Price” means the price per share of the equity securities sold in the Company’s next
Qualified Financing occurring after the Warrant Date. 
 (g) “Qualified Financing” means the sale after
the date hereof and prior to the Company’s initial public offering, of a series of convertible preferred stock of the Company to purchasers resulting in gross proceeds to the Company of not less than $10,000,000 (excluding any bridge debt
financing except to the extent actually converted to equity in the Company). 
 (h) “Shares” means the
shares of Applicable Stock of Company issuable upon exercise of this Warrant. 
 (i) “Warrant Date”
means the date of this Warrant specified in the introductory paragraph of this Warrant. 
 2. Term. The right to
purchase Applicable Stock upon exercise hereof is exercisable at any time and from time to time from the Warrant Date until the earliest to occur of: (a) the tenth anniversary of the Warrant Date, or (b) the completion of (i) a
consolidation or merger of the Company into or with any other entity or entities that results in the exchange of outstanding shares of the Company for securities or other consideration issued or paid or caused to be issued or paid by any such entity
or affiliate thereof (except a consolidation or merger into a wholly owned subsidiary or merger in which the Company is the surviving corporation and, in either case, the holders of the Company’s voting stock outstanding immediately prior to
the transaction constitute a majority of the holders of voting stock outstanding immediately following the transaction) or (ii) the sale or transfer by the Company of all or substantially all its assets. 

3. Payment and Exercise. 
 (a) Methods of Exercise. The purchase right represented by this Warrant may be exercised by the Holder, in whole or in part and from time to time, at the election of the Holder, by (i) the
surrender of this Warrant (with the notice of exercise substantially in the form attached hereto as Exhibit A duly completed and executed) at the principal office of the Company and by the payment to the Company, by check, or by wire transfer to an
account designated by the Company of an amount equal to the then applicable Exercise Price multiplied by the number of Shares then being purchased (the “Aggregate Purchase Price”); (ii) if in connection with a registered
public offering of the Company’s securities, the surrender of this Warrant (with the notice of exercise form attached hereto as Exhibit B duly completed and executed) at the principal office of the Company together with notice of arrangements
reasonably satisfactory to the Company for payment to the Company from the proceeds of the sale of shares to be sold by the Holder in such public offering of the Aggregate Purchase Price; or (iii) exercise of the “net issuance” right
provided 

  
 -2-









 
for in Section 3(b) hereof. The person or persons in whose name(s) any certificate(s) representing shares of Applicable Stock issuable upon exercise of this Warrant shall be deemed to have
become the holder(s) of record of, and shall be treated for all purposes as the record holder(s) of, the Shares represented thereby (and such Shares shall be deemed to have been issued) immediately prior to the close of business on the date or dates
upon which this Warrant is exercised. In the event of any exercise of the rights represented by this Warrant, certificates for the Shares so purchased shall be delivered to the Holder as soon as possible and in any event within thirty (30) days
after such exercise and, unless this Warrant has been fully exercised or expired, a new Warrant representing the portion of the Shares, if any, with respect to which this Warrant shall not then have been exercised shall also be issued to the Holder
as soon as possible and in any event within such thirty-day period; provided, however, that at such time as the Company is subject to the reporting requirements of the Securities Exchange Act of 1934, as amended, if requested by the Holder, the
Company shall cause its transfer agent to deliver the certificate representing Shares issued upon exercise of this Warrant to a broker or other person (as directed by the Holder exercising this Warrant) within the time period required to settle any
trade made by the Holder after exercise of this Warrant. 
 (b) Right to Convert Warrant into Stock: Net Issuance.

 (i) Net Issuance Right. In addition to and without limiting the rights of the Holder under the terms of this Warrant,
the Holder shall have the right to convert this Warrant or any portion thereof (the “Net Issuance Right”) into shares of Applicable Stock as provided in this Section 3(b) at any time or from time to time during the term
of this Warrant. Upon exercise of the Net Issuance Right with respect to a particular number of shares subject to this Warrant (the “Converted Warrant Shares”), the Company shall deliver to the Holder (without payment by the
Holder of any exercise price or any cash or other consideration) that number of shares of fully paid and nonassessable Applicable Stock as is determined according to the following formula: 

 

					
	 X =
	 	A - B	  	
		 	Y	  	

  

					
	Where: X	  	=	  	the number of shares of Applicable Stock that shall be issued to Holder
			
	 Y
	  	=	  	the fair market value of one share of Applicable Stock
			
	 A
	  	=	  	the aggregate fair market value of the specified number of Converted Warrant Shares (i.e., the number of Converted Warrant Shares multiplied by the fair market value
of one Converted Warrant Share)
			
	 B
	  	=	  	the aggregate Exercise Price of the specified number of Converted Warrant Shares immediately prior to the exercise of the Net Issuance Right (i.e., the number of Converted
Warrant Shares multiplied by the Exercise Price)

 No fractional shares shall be issuable upon exercise of the Net Issuance Right, and, if the number of shares to be issued
determined in accordance with the foregoing formula is other than a whole number, the Company shall pay to the Holder an amount in cash equal to the fair market value of the resulting fractional share on the Conversion Date (as hereinafter defined).
For purposes of Section 10 of this Warrant, shares issued pursuant to the Net Issuance Right shall be treated as if they were issued upon the exercise of this Warrant. 
 (ii) Exercise of Net Issuance Right. The Net Issuance Right may be exercised by the Holder by the surrender of this Warrant at the principal office of the Company together with a written statement
(which may be in the form of Exhibit A or Exhibit B hereto) specifying that the Holder thereby intends to exercise the Net Issuance Right and indicating the number of shares subject to this Warrant which are being surrendered (referred to in
Section 3(b)(i) hereof as the Converted Warrant Shares) in exercise of the Net Issuance Right. Such conversion shall be effective upon receipt by the Company of this Warrant 

  
 -3-









 
together with the aforesaid written statement, or on such later date as is specified therein (the “Conversion Date”), and, at the election of the Holder, may be made
contingent upon the closing of the sale of the Company’s Common Stock to the public in a public offering (a “Public Offering”) pursuant to a Registration Statement under the Securities Act of 1933, as amended (the
“Act”). Certificates for the shares issuable upon exercise of the Net Issuance Right and, if applicable, a new warrant evidencing the balance of the shares remaining subject to this Warrant, shall be issued as of the
Conversion Date and shall be delivered to the Holder within thirty (30) days following the Conversion Date. 
 (iii)
Determination of Fair Market Value. For purposes of this Section 3(b), “fair market value” of a share of Applicable Stock (which shall be Common Stock if the Applicable Stock has been converted into Common Stock) as of a
particular date (the “Determination Date”) shall mean: 
 (1) If the Net Issuance Right is exercised in
connection with and contingent upon a Public Offering, and if the Company’s Registration Statement relating to such Public Offering (“Registration Statement”) has been declared effective by the Securities and Exchange
Commission, then the initial “price to the public” specified in the final prospectus with respect to such offering. 

(2) If the Net Issuance Right is not exercised in connection with and contingent upon a Public Offering, then as follows: 

(A) If traded on a securities exchange, then the fair market value shall be the average of the closing prices of the
Common Stock on such exchange over the five trading days immediately prior to the Determination Date; 
 (B) If
traded on an over-the-counter system, then the fair market value shall be the average of the closing bid prices of the Common Stock over the five trading days immediately prior to the Determination Date; and 

(C) If there is no public market, then fair market value shall be determined in good faith by the Company’s Board of
Directors. 
 In making a determination under clauses (A) or (B) above, if on the Determination Date, five trading days have not
passed since the Company’s initial Public Offering then the fair market value of the Common Stock shall be the average closing prices or closing bid prices, as applicable, for the shorter period beginning on and including the date of the
initial Public Offering and ending on the trading day prior to the Determination Date (or if such period includes only one trading day the closing price or closing bid price, as applicable, for such trading day). If closing prices or closing bid
prices are no longer reported by a securities exchange or other trading system, the closing price or closing bid price shall be that which is reported by such securities exchange or other trading system at 4:00 p.m. New York City time on the
applicable trading day. 
 (c) Exercise Prior to Expiration. To the extent this Warrant is not previously exercised as to
all of the Shares subject hereto, and if the fair market value of one share of the Applicable Stock is greater than the Exercise Price then in effect, this Warrant shall be deemed automatically exercised pursuant to Section 3(b) (even if not
surrendered) immediately before its expiration, including but not limited to expiration pursuant to Section 2. For purposes of such automatic exercise, the fair market value of one share of the Applicable Stock upon such expiration shall be
determined pursuant to Section 3(b)(iii). To the extent this Warrant or any portion thereof is deemed automatically exercised pursuant to this Section 3(c), the Company agrees to promptly notify the Holder of the number of Shares, if any,
the Holder is to receive by reason of such automatic exercise. 
 4. Stock Fully Paid; Reservation of Shares. All Shares
that may be issued upon the exercise of the rights represented by this Warrant will, upon issuance pursuant to the terms and conditions herein, be fully paid and nonassessable, and free from all preemptive rights and taxes, liens and charges with
respect to the issuance thereof. During the period within which the rights represented by this Warrant may be exercised, the 

  
 -4-









 
Company will at all times have authorized, and reserved for the purpose of the issue upon exercise of the purchase rights evidenced by this Warrant, a sufficient number of shares of its
Applicable Stock to provide for the exercise of the rights represented by this Warrant and, while the Applicable Stock is convertible preferred stock, a sufficient number of shares of its Common Stock to provide for the conversion of the Applicable
Stock into Common Stock. 
 5. Adjustment of Exercise Price and Number of Shares. The number and kind of securities
purchasable upon the exercise of this Warrant and the Exercise Price shall be subject to adjustment from time to time upon the occurrence of certain events, as follows: 
 (a) Reclassification or Merger. In case of any reclassification or change of securities of the class issuable upon exercise of this Warrant (other than a change in par value, or from par value to
no par value, or from no par value to par value, or as a result of a subdivision or combination), the Company shall duly execute and deliver to the Holder a new Warrant (in form and substance satisfactory to the Holder), or the Company shall make
appropriate provision without the issuance of a new Warrant, so that the Holder shall have the right to receive upon exercise of this Warrant, at a total purchase price not to exceed that payable upon the exercise of the unexercised portion of this
Warrant, and in lieu of the shares of Applicable Stock theretofore issuable upon exercise of this Warrant, the kind and amount of shares of stock, other securities, money and property receivable upon such reclassification or change by a holder of
the number of shares of Applicable Stock then purchasable under this Warrant. The provisions of this Section 5(a) shall similarly apply to successive reclassifications and changes. 

(b) Subdivision or Combination of Shares. If the Company at any time while this Warrant remains outstanding and unexpired shall
subdivide or combine its outstanding shares of Applicable Stock, the Exercise Price shall be proportionately decreased and the number of Shares issuable hereunder shall be proportionately increased in the case of a subdivision and the Exercise Price
shall be proportionately increased and the number of Shares issuable hereunder shall be proportionately decreased in the case of a combination. 
 (c) Stock Dividends and Other Distributions. If the Company at any time while this Warrant is outstanding and unexpired shall (i) pay a dividend with respect to Applicable Stock payable in
Applicable Stock, then the Exercise Price shall be adjusted, from and after the date of determination of shareholders entitled to receive such dividend or distribution, to that price determined by multiplying the Exercise Price in effect immediately
prior to such date of determination by a fraction (A) the numerator of which shall be the total number of shares of Applicable Stock outstanding immediately prior to such dividend or distribution, and (B) the denominator of which shall be
the total number of shares of Applicable Stock outstanding immediately after such dividend or distribution; or (ii) make any other distribution with respect to Applicable Stock (except any distribution specifically provided for in Sections 5(a)
and 5(b)), then, in each such case, provision shall be made by the Company such that the Holder shall receive upon exercise of this Warrant a proportionate share of any such dividend or distribution as though it were the holder of the Applicable
Stock as of the record date fixed for the determination of the shareholders of the Company entitled to receive such dividend or distribution. 
 (d) Adjustment of Number of Shares. Upon each adjustment in the Exercise Price, the number of Shares of Applicable Stock purchasable hereunder shall be adjusted, to the nearest whole share, to the
product obtained by multiplying the number of Shares purchasable immediately prior to such adjustment in the Exercise Price by a fraction, the numerator of which shall be the Exercise Price immediately prior to such adjustment and the denominator of
which shall be the Exercise Price immediately thereafter. 
 (e) Antidilution Rights. The other antidilution rights
applicable to the Shares of Applicable Stock purchasable hereunder are set forth in the Company’s Certificate of Incorporation, as amended through the Warrant Date, a true and complete copy of which is attached hereto as Exhibit C (the
“Charter”). The Company shall promptly provide the Holder with any restatement, amendment, modification or waiver of the Charter promptly after the same has been made. 

  
 -5-









 6. Notice of Adjustments. Whenever the Exercise Price or the number of Shares
purchasable hereunder shall be adjusted pursuant to Section 5 hereof, the Company shall make a certificate signed by its chief financial officer setting forth, in reasonable detail, the event requiring the adjustment, the amount of the
adjustment, the method by which such adjustment was calculated, and the Exercise Price and the number of Shares purchasable hereunder after giving effect to such adjustment, and shall cause copies of such certificate to be delivered to the Holder.
In addition, whenever the conversion price or conversion ratio of the Applicable Stock shall be adjusted, the Company shall make a certificate signed by its chief financial officer setting forth, in reasonable detail, the event requiring the
adjustment, the amount of the adjustment, the method by which such adjustment was calculated, and the conversion price or ratio of the Applicable Stock after giving effect to such adjustment, and shall cause copies of such certificate to be
delivered to the Holder. 
 7. Fractional Shares. No fractional shares of Applicable Stock will be issued in connection
with any exercise hereunder, but in lieu of such fractional shares the Company shall make a cash payment therefor based on the fair market value of the Applicable Stock on the date of exercise as reasonably determined in good faith by the
Company’s Board of Directors. 
 8. Compliance with Act: Disposition of Warrant or Shares of Applicable Stock.

 (a) Compliance with Act. The Holder, by acceptance hereof, agrees that this Warrant, and the shares of Applicable
Stock to be issued upon exercise hereof and any Common Stock issued upon conversion thereof are being acquired for investment and that the Holder will not offer, sell or otherwise dispose of this Warrant, or any shares of Applicable Stock to be
issued upon exercise hereof or any Common Stock issued upon conversion thereof except under circumstances which will not result in a violation of the Act or any applicable state securities laws. Upon exercise of this Warrant, unless the Shares being
acquired are registered under the Act and any applicable state securities laws or an exemption from such registration is available, the Holder shall confirm in writing that the shares of Applicable Stock so purchased (and any shares of Common Stock
issued upon conversion thereof) are being acquired for investment and not with a view toward distribution or resale in violation of the Act and shall confirm such other matters related thereto as may be reasonably requested by the Company. This
Warrant and all shares of Applicable Stock issued upon exercise of this Warrant (unless registered under the Act and any applicable state securities laws) shall be stamped or imprinted with a legend in substantially the following form: 

“THE SECURITIES EVIDENCED HEREBY HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS. NO SALE OR
DISPOSITION MAY BE EFFECTED WITHOUT (i) EFFECTIVE REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION OF COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT
OF NO-ACTION LETTERS FROM THE APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE PROVISIONS OF SECTION 8 OF THE WARRANT UNDER WHICH THESE SECURITIES WERE ISSUED, DIRECTLY OR INDIRECTLY.” 

Said legend shall be removed by the Company, upon the request of the Holder, at such time as the restrictions on the transfer of the applicable security
shall have terminated. 
 (b) Disposition of Warrant or Shares. With respect to any offer, sale or other disposition of
this Warrant or any shares of Applicable Stock acquired pursuant to the exercise of this Warrant prior to registration of such Warrant or shares, the Holder agrees to give written notice to the Company prior thereto, describing briefly the manner
thereof, together with a written opinion of counsel, if requested by the Company, or other evidence, if reasonably satisfactory to the Company, to the effect that such offer, sale or other disposition may be effected without registration or
qualification (under the Act as then in effect or any federal or state securities law then in effect) of this Warrant or such shares of Applicable Stock and indicating whether or not under the Act certificates for this Warrant or such shares of
Applicable Stock to be sold or otherwise disposed of require any restrictive legend as to applicable restrictions on transferability in order to ensure compliance with such law. Upon receiving such written notice and reasonably satisfactory opinion
or 

  
 -6-









 
other evidence, the Company shall have the right to consent to such transfer, which shall not be unreasonably withheld (except with respect to any transfer to any affiliate of the Holder, in
which case no consent shall be required) (any such transfer as to which no consent is required or consent has been granted, a “Permitted Transfer”), and shall, as promptly as practicable but no later than fifteen
(15) days after receipt of the written notice, shall notify the Holder whether the Holder may sell or otherwise dispose of this Warrant or such shares of Applicable Stock, all in accordance with the terms of the notice delivered to the Company.
If a determination has been made pursuant to this Section 8(b) that the opinion of counsel or other evidence is not reasonably satisfactory to the Company, the Company shall so notify the Holder promptly with details thereof after such
determination has been made. Notwithstanding the foregoing, but subject to the right of the Company to consent, if applicable, this Warrant or such shares of Applicable Stock may, as to such federal laws, be offered, sold or otherwise disposed of in
accordance with Rule 144 or 144A under the Act, provided that the Company shall have been furnished with such information as the Company may reasonably request to provide a reasonable assurance that the provisions of Rule 144 or 144A have been
satisfied. Each certificate representing this Warrant or the shares of Applicable Stock thus transferred (except a transfer pursuant to Rule 144 or 144A) shall bear a legend as to the applicable restrictions on transferability in order to ensure
compliance with such laws, unless in the aforesaid opinion of counsel for the Holder, such legend is not required in order to ensure compliance with such laws. The Company may issue stop transfer instructions to its transfer agent in connection with
such restrictions. 
 (c) Applicability of Restrictions. Neither any restrictions of any legend described in this Warrant
nor the requirements of Section 8(b) above shall apply to any transfer of, or grant of a security interest in, this Warrant (or the Applicable Stock or Common Stock obtainable upon exercise thereof) or any part hereof (i) to a partner of
the Holder if the Holder is a partnership or to a member of or other holder of an interest in the Holder if the Holder is a limited liability company, (ii) to a partnership of which the Holder is a partner or to a limited liability company of
which the Holder is a member or other holder of an interest, or (iii) to any affiliate of the Holder if the Holder is a corporation; provided, however, in any such transfer, if applicable, the transferee shall on the
Company’s request agree in writing to be bound by the terms of this Warrant as if an original holder hereof. 
 9.
Rights as Shareholders; Information. No Holder, as a holder of this Warrant, shall be entitled to vote or receive dividends or be deemed the holder of Applicable Stock or any other securities of the Company which may at any time be issuable
upon the exercise hereof for any purpose, nor shall anything contained herein be construed to confer upon the Holder, as such, any of the rights of a shareholder of the Company or any right to vote for the election of directors or upon any matter
submitted to shareholders at any meeting thereof, or to receive dividends or subscription rights or otherwise until this Warrant shall have been exercised and the Shares purchasable upon the exercise hereof shall have become deliverable, as provided
herein. Notwithstanding the foregoing, the Company will transmit to the Holder such information, documents and reports as are generally distributed to the holders of any class or series of the securities of the Company concurrently with the
distribution thereof to the shareholders. 
 10. Registration Rights. In connection with the closing of its next round of
equity financing, the Company shall amend that certain Second Amended and Restated Registration Rights Agreement by and among the Company, the Investors (as defined therein), Pinnacle Ventures, L.L.C. and Key Stockholders (as defined therein) dated
as of February 5, 2008 (the “Investor Rights Agreement”) to grant registration rights to the Holder for any Applicable Stock of the Company (after its conversion to Common Stock) obtained upon exercise of this Warrant,
comparable to the registration rights granted to the investors in the Investor Rights Agreement, with the following exceptions and clarifications: 
 (1) The Holder will have not have the right to demand registration (other than a registration on Form S-3 or any successor form), but can otherwise participate in any registration demanded by others.

 (2) The Holder will be subject to the same provisions regarding indemnification as contained in the Investor Rights
Agreement. 

  
 -7-









 (3) The registration rights are freely assignable by the Holder in connection with a
Permitted Transfer of this Warrant or the Shares. 
 (4) Any underwriter’s “cut back” shall first apply to the
rights of the Holder with respect to shares issued upon the exercise of this Warrant and then to the rights of other holders of the Company’s preferred stock (including the Holder with respect to any shares of preferred stock held other than as
a result of the exercise of this Warrant). 
 11. Notice Rights. 

(a) Acquisition Transactions. The Company shall provide the Holder with at least ten (10) days’ written notice prior to
closing thereof of the terms and conditions of any of the following transactions (to the extent the Company has notice thereof): (i) the sale, lease, exchange, conveyance or other disposition of all or substantially all of the Company’s
property or business, or (ii) its merger into or consolidation with any other corporation (other than a wholly-owned subsidiary of the Company), or any transaction (including a merger or other reorganization) or series of related transactions,
in which more than 50% of the voting power of the Company is disposed of. 
 (b) Dividends and Repurchases. The Company
shall provide the Holder with at least ten (10) days notice prior to the record date of any cash dividend with respect to or offer to repurchase the Applicable Stock. 
 (c) Liquidation. The Company shall provide the Holder with at least ten (10) days notice prior to any voluntary or involuntary dissolutions, liquidation or winding-up of the Company.

 12. Representations and Warranties. The Company represents and warrants to the Holder as follows: 

(a) This Warrant has been duly authorized and executed by the Company and is a valid and binding obligation of the Company enforceable in
accordance with its terms, subject to laws of general application relating to bankruptcy, insolvency and the relief of debtors and the rules of law or principles at equity governing specific performance, injunctive relief and other equitable
remedies. 
 (b) The Shares have been duly authorized and reserved for issuance by the Company and, when issued in accordance
with the terms hereof, will be validly issued, fully paid and nonassessable and free from preemptive rights. 
 (c) The rights,
preferences, privileges and restrictions granted to or imposed upon the Applicable Stock and the holders thereof are as set forth in the Charter, and on the Warrant Date, each share of the Applicable Stock represented by this Warrant is convertible
into one share of Common Stock. 
 (d) The shares of Common Stock issuable upon conversion of the Shares have been duly
authorized and reserved for issuance by the Company and, when issued in accordance with the terms of the Charter will be validly issued, fully paid and nonassessable. 
 (e) The execution and delivery of this Warrant are not, and the issuance of the Shares upon exercise of this Warrant in accordance with the terms hereof will not be, inconsistent with the Company’s
Charter or by-laws, do not and will not contravene any law, governmental rule or regulation, judgment or order applicable to the Company, and do not and will not conflict with or contravene any provision of, or constitute a default under, any
indenture, mortgage, contract or other instrument of which the Company is a party or by which it is bound or require the consent or approval of, the giving of notice to, the registration or filing with or the taking of any action in respect of or
by, any Federal, state or local government authority or agency or other person, except for the filing of notices pursuant to federal and state securities laws, which filings will be effected by the time required thereby. 

  
 -8-









 (f) There are no actions, suits, audits, investigations or proceedings pending or, to the
knowledge of the Company, threatened against the Company in any court or before any governmental commission, board or authority which, if adversely determined, could have a material adverse effect on the ability of the Company to perform its
obligations under this Warrant. 
 (g) The number of shares of Common Stock of the Company outstanding on the date
hereof, on a fully diluted basis (assuming the conversion of all outstanding convertible securities and the exercise of all outstanding options and warrants), does not exceed [44,390,967] shares. [Note: Mascoma to provide] 

13. Modification and Waiver. This Warrant and any provision hereof may be changed, waived, discharged or terminated only by an
instrument in writing signed by the party against which enforcement of the same is sought. 
 14. Notices. Any notice,
request, communication or other document required or permitted to be given or delivered to the Holder or the Company shall be delivered, or shall be sent by certified or registered mail, postage prepaid, or overnight courier or delivered personally
to the Holder at its address as shown on the books of the Company or to the Company at the address indicated therefor on the signature page of this Warrant. 
 15. Binding Effect on Successors. This Warrant shall be binding upon any corporation succeeding the Company by merger, consolidation or acquisition of all or substantially all of the Company’s
assets, and all of the obligations of the Company relating to the Applicable Stock issuable upon the exercise or conversion of this Warrant shall survive the exercise, conversion and termination of this Warrant and all of the covenants and
agreements of the Company shall inure to the benefit of the successors and assigns of the Holder. 
 16. Lost Warrants or
Stock Certificates. The Company covenants to the Holder that, upon receipt of evidence reasonably satisfactory to the Company of the loss, theft, destruction or mutilation of this Warrant or any stock certificate and, in the case of any such
loss, theft or destruction, upon receipt of an indemnity reasonably satisfactory to the Company, or in the case of any such mutilation upon surrender and cancellation of such Warrant or stock certificate, the Company will make and deliver a new
Warrant or stock certificate, of like tenor, in lieu of the lost, stolen, destroyed or mutilated Warrant or stock certificate. 

17. Descriptive Headings. The descriptive headings of the various Sections of this Warrant are inserted for convenience only and
do not constitute a part of this Warrant. The language in this Warrant shall be construed as to its fair meaning without regard to which party drafted this Warrant. 
 18. Governing Law. This Warrant shall be construed and enforced in accordance with, and the rights of the parties shall be governed by, the laws of the State of California. 

19. Survival of Representations, Warranties and Agreements. All representations and warranties of the Company and the Holder
contained herein shall survive the Warrant Date, the exercise or conversion of this Warrant (or any part hereof) or the termination or expiration of rights hereunder. All agreements of the Company and the Holder contained herein shall survive
indefinitely until, by their respective terms, they are no longer operative. 
 20. Remedies. In case any one or more of
the covenants and agreements contained in this Warrant shall have been breached, the Holder (in the case of a breach by the Company), or the Company (in the case of a breach by the Holder), may proceed to protect and enforce their or its rights
either by suit in equity and/or by action at law, including, but not limited to, an action for damages as a result of any such breach and/or an action for specific performance of any such covenant or agreement contained in this Warrant. 

21. No Impairment of Rights. The Company will not, by amendment of its Charter or through any other means, avoid or seek to avoid
the observance or performance of any of the terms of this Warrant, but 

  
 -9-









 
will at all times in good faith assist in the carrying out of all such terms and in the taking of all such action as may be necessary or appropriate in order to protect the rights of the Holder
against impairment. 
 22. Severability. The invalidity or unenforceability of any provision of this Warrant in any
jurisdiction shall not affect the validity or enforceability of such provision in any other jurisdiction, or affect any other provision of this Warrant, which shall remain in full force and effect. 

23. Recovery of Litigation Costs. If any legal action or other proceeding is brought for the enforcement of this Warrant, or
because of an alleged dispute, breach, default, or misrepresentation in connection with any of the provisions of this Warrant, the successful or prevailing party or parties shall be entitled to recover reasonable attorneys’ fees and other costs
incurred in that action or proceeding, in addition to any other relief to which it or they may be entitled. 
 24. Entire
Agreement; Modification. This Warrant constitutes the entire agreement between the parties pertaining to the subject matter contained in it and supersedes all prior and contemporaneous agreements, representations, and undertakings of the
parties, whether oral or written, with respect to such subject matter (other than, for the avoidance of doubt, the Warrant to purchase Series B Preferred Stock of the Company and the Warrant to purchase Series C Preferred Stock of the Company, each
dated as of February 5, 2008). 

  
 -10-









 The Company has caused this Warrant to be duly executed and delivered as of the Warrant Date
specified above. 
  

			
	MASCOMA CORPORATION
		
	By	 	  

		
	Name:	 	Bruce A. Jamerson
	Title:	 	Chief Executive Officer


 
			
		
	Address:	 	Mascoma Corporation
		 	1380 Soldiers Field Road, Second Floor
		 	Boston, MA 02135



  
 -11-









 EXHIBIT A 
 NOTICE OF EXERCISE 
  

	To:	MASCOMA CORPORATION (the “Company”) 

 1. The undersigned hereby: 
  

	 	 ̈	elects to purchase                shares of [Applicable Stock] [Common Stock] of the
Company pursuant to the terms of the attached Warrant, and tenders herewith payment of the purchase price of such shares in full, or 

  

	 	 ̈	elects to exercise its net issuance rights pursuant to Section 3(b) of the attached Warrant with respect
to                Shares of [Applicable Stock] [Common Stock]. 

 2. Please issue a certificate or certificates representing                shares in the name of the undersigned or in such
other name or names as are specified below: 
  

					
		  	  
	  	
		  	(Name)	  	
			
		  	  
	  	
			
		  	  
	  	
		  	(Address)	  	

 3. The undersigned represents that 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, all except as in compliance with applicable
securities laws. 
  

	
	  

	(Signature)


  

							
	
                  
   
	 		 		 	
	(Date)	 		 		 	








 EXHIBIT B 
 NOTICE OF EXERCISE 
  

	To:	MASCOMA CORPORATION (the “Company”) 

 1. Contingent upon and effective immediately prior to the closing (the “Closing”) of the Company’s public offering contemplated by the Registration Statement on Form
S        , filed                    , 200  , the undersigned hereby: 

 ̈ elects to
purchase                    shares of [Applicable Stock] [Common Stock] of the Company (or such lesser number of shares as may be sold on behalf of
the undersigned at the Closing) pursuant to the terms of the attached Warrant, or 

 ̈ elects to exercise its net issuance rights pursuant to Section 3(b) of the attached
Warrant with respect to                      Shares of [Applicable Stock] [Common Stock]. 

2. Please deliver to the custodian for the selling shareholders a stock certificate representing
such                    shares. 
 3. The undersigned has instructed the custodian for the selling shareholders to deliver to the Company $        or, if less, the net proceeds due the undersigned
from the sale of shares in the aforesaid public offering. If such net proceeds are less than the purchase price for such shares, the undersigned agrees to deliver the difference to the Company prior to the Closing. 

 

	
	  

	(Signature)


  

							
	
                  
   
	 		 		 	
	(Date)	 		 		 	








 EXHIBIT C 
 CHARTER