Document:

exv4w9

Exhibit 4.9

AMENDMENT NO. 1

Dated February 28, 2011

          THIS AMENDMENT NO 1 (“Amendment 1”) to that certain Loan and Security Agreement No. 1451 dated
as of December 30, 2008 (“Agreement”), by and between Lighthouse Capital Partners VI,
L.P., (“Lender”) and Kior, Inc. (“Borrower”).

RECITALS

          WHEREAS, Borrower and Lender have previously entered into that certain Loan and Security
Agreement No. 1451 dated December 30, 2008 (the “Agreement”) (all capitalized terms not otherwise
defined herein are defined in the Agreement);

          WHEREAS, Borrower has requested that Lender modify certain terms of its existing equipment
loan financing; and

          WHEREAS, Lender has agreed to do so under the Agreement, subject to all of the terms and
conditions hereof and of the Agreement.

          NOW, THEREFORE, in consideration of the foregoing and the mutual covenants herein contained,
the parties
hereby agree to modify the Agreement and to perform such other covenants and conditions as follows:

     I. Section 1.1, the following definitions shall be added to the Agreement:

“Amendment 1” means this Amendment No. 1 to Loan and Security Agreement by and Borrower and Lender.

“Columbus” means Kior Columbus LLC, a limited liability company organized under the laws of
Delaware and a wholly-owned subsidiary of Borrower.

“Interest Only Period” means the period commencing on February 1, 2011 and continuing through the
day immediately preceding the Loan Commencement Date.

“New Warrant” means the warrant agreement in the form attached to this Amendment 1 as Exhibit C-2.

“Subsidiary” means any entity of which a majority of the outstanding capital interest entitled to
vote for the election of directors (otherwise than as the result of a default) is owned by Borrower
directly or indirectly through Subsidiaries.

     II. Section 1.1, the following definitions of the Agreement shall be deleted in its entirety
and replaced with the following:

“Basic Rate” a per annum rate of interest equal to (i) 10% during the Interest Only Period and (ii)
7.5% on and after the Loan Commencement Date.

“Disclosure Schedule” means the updated schedule attached as Schedule 1-1 hereto.

“Loan Documents” means, collectively, the Agreement, Amendment 1, the Warrant, the Notes, and all
other documents, instruments and agreements entered into between Borrower or any Subsidiary or
affiliate of Borrower and Lender in connection with the Loan, all as amended or extended from time
to time.

“Incumbency Certificate” means the document in the form of Exhibit E attached to the Agreement for
Borrower and in the form of Exhibit E-1 attached to this Amendment 1.

 

 

“Loan Commencement Date” means March 1, 2012.

“Note” means collectively the Amended and Restated Secured Promissory Note (the “LCP Amended Note”)
in the form of Exhibit B-1 attached to Amendment 1, which shall amend and restate the Notes issued
by Borrower to Lender on (i) February 26, 2009 in the principal amount of $576,190.81; (ii) March
12, 2009 in the principal amount of $100,092.54; (iii) April 3, 2009 in the principal amount of
$1,864,400.86; (iv) May 1, 2009 in the principal amount of $377,698.02; (v) June 1, 2009 in the
principal amount of $300,333.71; (vi) July 1, 2009 in the principal amount of $169,844.64; (vii)
July 31, 2009 in the principal amount of $6200,939.00; (viii) September 1, 2009 in the principal
amount of $362,258.63; and (ix) September 30, 2009 in the principal amount of $628,241.79.

“Warrant” or “Warrants” means the Warrant in favor of each of the Lender and its affiliates to
purchase securities of Borrower substantially in the form of Exhibit C attached to the Agreement
and the New Warrants in the form of Exhibit C-2 attached to this Amendment 1.

	 	III.	 	Section 5 of the Agreement. Section 5.3 of the Agreement shall be deleted and replaced
with the following:

5.3 Disclosure Schedule. All information on the Disclosure Schedule is true, correct and complete
as of the date of this Amendment 1.

     IV. Section 6 of the Agreement. Section 6.1 of the Agreement shall be deleted and replaced
with the following:

6.1 Good Standing and Compliance. Borrower and its Subsidiaries shall maintain all governmental
licenses, rights and agreements necessary for its operations or business and comply in all material
respects with all statutes, laws, ordinances and government rules and regulations to which it is
subject, except where the failure to do so would not reasonably be expected to result in a Material
Adverse Effect.

     V. Section 6 of the Agreement. Section 6.10 of the Agreement shall be deleted and replaced
with the following:

6.10 Taxes. Borrower and its Subsidiaries shall file all required tax returns, and shall pay all
taxes they owe other than where the failure to comply would not reasonably be expected to have a
Material Adverse Effect.

     VI. Section 6 of the Agreement. A new Section 6.11 shall be added:

     6.11 Issuance of New Warrants. On or before March 31, 2011, Borrower shall issue to Lender a
New Warrant for the purchase of the $50,000 of Borrower’s Series C Preferred Stock, which series of
preferred stock is to be authorized, designated, issued and sold for purposes of an equity
financing of Borrower after the date hereof in the amount of at least $60,000,000 (the “Series C
Offering”). In the event that the Series C Offering is not completed by such date, then in such
event, Borrower shall issue to Lender a New Warrant for the purchase of 5,081 shares of Borrower’s
existing Series B Preferred Stock, with an exercise price of $9.84, and Borrower shall take all
steps necessary to authorize additional shares of Series B Preferred Stock (with identical terms,
rights and privileges as the authorized and issued Series B Preferred Stock) for issuance under the
New Warrant, including the amendment of Borrower’s Amended and Restated Certificate of
Incorporation of Kior, Inc. Borrower’s failure to issue and deliver the New Warrants to Lender by
March 31, 2011 shall be an Event of Default.

     VII. Section 7. Section 7.10 shall be deleted in its entirety.

     VIII. Section 8. Section 8.5 shall be deleted and replaced with the following:

8.5 Other Agreements. There is a default in any agreement to which Borrower is a party,
including any loan agreement with Lender, resulting in a right by a third party, whether or not
exercised, to accelerate the maturity of any Indebtedness, in an amount greater than $200,000.

 

 

     IX. Conditions Precedent to the effectiveness of Amendment 1:

          The obligation of Lender to enter into this Amendment 1 is subject to the performance and
fulfillment of each and every of the following conditions precedent in form and substance
satisfactory to Lender in its sole discretion:

          (a) This Amendment 1 shall have been duly executed and delivered by Borrower.

          (b) The LCP Amended Note shall have been duly executed and issued by Borrower to Lender.

          (c) Without limiting the foregoing or Lender’s rights or Borrower’s Obligations under the
Agreement, such consents, including the approvals of Borrower’s board of directors, amendments,
filings, recordations, or other documents from any persons or entities necessary to maintain the
perfection and priority of Lender’s security interest in the Collateral as amended hereby and as
originally configured, in form and substance satisfactory to Lender in its sole discretion, shall
have been delivered by Borrower to Lender.

          (d) A good standing certificate from Borrower’s state of incorporation or formation and the
state in which Borrower’s principal place of business is located, together with certificates of the
applicable governmental authorities stating that Borrower is in compliance with the franchise tax
laws of each such state, each dated as of a recent date shall have been delivered to Lender.

          (e) All necessary consents of shareholders, members, and other third parties with respect to
the execution, delivery and performance of this Amendment 1, and the other Loan Documents shall
have been delivered to Lender.

          X. Additional Terms and Conditions

          (a) Further Conditions. The following are conditions precedent to Lenders’
obligations hereunder, without delivery and performance of which to Lenders’ satisfaction, the
original payment terms of the Loan Documents and the Notes shall remain in full force and effect,
unamended hereby:

               (i) Borrower shall deliver an Incumbency Certificate, in the form attached hereto as Exhibit
E-1, certified by responsible officers of Borrower, and attachments thereto including the
resolutions adopted by Borrower’s board of directors authorizing the execution and delivery of this
Amendment 1 and the other documents referred to in this Amendment 1 and the performance by Borrower
of its obligations under such documents.

               (ii) Borrower shall execute and deliver all other documents, as Lenders shall have reasonably
requested prior to the execution by Borrower and Lender of this Amendment 1.

               (iii) Borrower shall agree to pay all reasonable Lender’s Expenses up to a maximum of $5,000
for the preparation and negotiation of this Amendment 1 when requested.

          (b) Representations and Warranties of Borrower. Giving effect to this Amendment 1 and
the Disclosure Schedules attached hereto and made a part hereof, Borrower reaffirms the
representations and warranties made to Lender in the Agreement as of the date hereof as though
fully set forth herein. Borrower further warrants and represents, as a significant material
inducement to Lender to enter hereinto, that: (i) no Events of Default have occurred that have not
been disclosed to Lender by Borrower in writing; and (ii) it is not and has no reason to believe it
may be named as a party to any judicial or administrative proceeding, litigation or arbitration,
and has not received any communication from any person or entity (whether private or governmental)
threatening or indicating the same, except as previously disclosed to Lender in writing.

          (c) No Control. Borrower warrants and represents, as a significant material
inducement to Lender to enter hereinto, that none of Lender nor, to the Borrower’s knowledge, any
affiliate, officer, director, employee, agent, or attorney of Lender, have at any time, from
Borrower’s date of formation through to the date hereof, (i) exercised

 

 

management or other control
over the Borrower, (ii) exercised undue influence over Borrower or any of its officers, employees
or directors, (iii) made any representation or warranty, express or implied, to any party on behalf
of Borrower, (iv) entered into any joint venture, agency relationship, employment relationship, or
partnership with Borrower, (v) directed or instructed Borrower on the manner, method, amount, or
identity of payee of any payment made to any creditor of Borrower, and further, Borrower warrants
and represents that by entering hereinto with Lender has not, are not and will not have engaged in
any of the foregoing.

          XI. Integration Clause. This Amendment 1, together with all Loan Documents required to be
entered into in connection with this Amendment 1, represents and documents the entirety of the
agreement and understanding of the parties hereto with respect to its subject matter. All prior
understandings, whether oral or written, other than the Loan Documents, are hereby merged hereinto.
NONE OF THE AGREEMENT OR THIS AMENDMENT 1 MAY BE MODIFIED EXCEPT BY A WRITING SIGNED BY LENDERS
AND BORROWER. Each provision hereof shall be severable from every other provision when determining
its legal enforceability such that Lenders’ rights and remedies under this Amendment 1 and the
Agreement may be enforced to the maximum extent permitted under applicable law. This Amendment 1
shall be binding upon, and inure to the benefit of, each party’s respective permitted successors
and assigns. This Amendment 1 may be executed in counterpart originals, all of which, when taken
together, shall constitute one and the same original document. No provision of any other document
between Lenders and Borrower shall limit the effectiveness hereof or the rights and remedies of
Lenders against Borrower.

Except as amended hereby, the Agreement remains unmodified and unchanged.

	 	 	 	 	 	 	 	 	 	 	 

	BORROWER:	 	 	 	LENDER:	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	Kior, Inc.	 	 	 	Lighthouse Capital Partners VI, L.P.	 	 
	 

	 	 	 	 	 	By: Lighthouse Management Partners VI,

L.L.C., its general partner
	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By: 

Name:

	 	/s/ Fred Cannon
 

Fred Cannon
	 	 
	 	By:

Name:
	 	/s/ Ryan Turner
 

Ryan Turner
	 	 
	Title:

	 	President & CEO
	 	 	 	Title:
	 	Managing Director	 	 

	 	 	 

	Attachments
	 	 
	 
	 	 
	Exhibit B-1

	 	Amended and Restated Promissory Note
	Exhibit C-1

	 	From of New Warrant
	Exhibit E-1

	 	Form of Incumbency Certificate
	 
	 	 
	Schedule 1-1

	 	Disclosure Schedule

 

 

Exhibit B-1

	 	 	$2,416,338.04

Amended and Restated Secured Promissory Note 

This Amended and Restated Secured Promissory Note (this “Note”) is made effective
February 1, 2011, by Kior, Inc. (“Borrower”) in favor of Lighthouse Capital Partners
VI, L.P. (collectively with its assigns, “Lender”) and amends, restates and replaces in its
entirety those certain Secured Promissory Notes dated (i) February 26, 2009 in the principal amount
of $576,190.81; (ii) March 12, 2009 in the principal amount of $100,092.54; (iii) April 3, 2009 in
the principal amount of $1,864,400.86; (iv) May 1, 2009 in the principal amount of $377,698.02; (v)
June 1, 2009 in the principal amount of $300,333.71; (vi) July 1, 2009 in the principal amount of
$169,844.64; (vii) July 31, 2009 in the principal amount of $6200,939.00; (viii) September 1, 2009
in the principal amount of $362,258.63; and (ix) September 30, 2009 in the principal amount of
$628,241.79, made by Borrower in favor of Lender pursuant to that certain Loan and Security
Agreement No. 1451 between Borrower and Lighthouse Capital Partners VI, L.P. (“Lender”) dated
December 30, 2008 (the “Loan Agreement”). Initially capitalized terms used and not otherwise
defined herein shall have the meaning defined in the Loan Agreement.

For Value Received, Borrower promises to pay in lawful money of the United States, to the
order of Lender, at 3555 Alameda de las Pulgas, Suite 200, Menlo Park, CA 94025, or such other
place as Lender may from time to time designate (“Lender’s Office”), the principal sum of
$2,416,338.04 (the “Advance”), including interest on the unpaid balance and all other amounts due
or to become due hereunder according to the terms hereof and of the Loan Agreement.

“Amendment Fee” means $50,000; $10,000 of which has been paid as of the date hereof; the remaining
$40,000 of which shall be due and payable on the Maturity Date.

“Basic Rate” a per annum rate of interest equal to (i) 10% during the Interest Only Period and (ii)
7.5% on and after the Loan Commencement Date.

“Final Payment” means $375,000.

“Interest Only Period” means the period commencing on February 1, 2011 and continuing through the
day immediately preceding the Loan Commencement Date.

“Loan Commencement Date” means March 1, 2012.

“Maturity Date” means the last day of the Repayment Period, or if earlier, the date of prepayment
under the Note.

“Payment Date” means the first day of each calendar month.

“Prepayment Fee” means (i) 3% of the outstanding principal amount being prepaid for any prepayment
made on or before December 31, 2011; (ii) 2% of the outstanding principal amount being prepaid for
any prepayment made during calendar year 2012; and (iii) 1% of the outstanding principal amount
being prepaid for any prepayment made during calendar year 2013 or thereafter.

“Repayment Period” means the period beginning on the Loan Commencement Date and continuing for 24
calendar months.

1. Repayment. Borrower shall pay principal and interest due hereunder from the Funding Date, until
this Note is paid in full, on each Payment Date pursuant to the terms of the Loan Agreement and
this Note. Prior to the Loan Commencement Date, Borrower shall pay to Lender, monthly in advance
on each Payment Date, interest calculated using the Basic Rate. Beginning on the Loan Commencement
Date and on each Payment Date thereafter during the Repayment Period, Borrower shall make equal
installments of principal and interest in advance,

 

 

calculated at the Basic Rate. On the Maturity
Date, Borrower shall pay, in addition to all unpaid principal and interest outstanding hereunder,
the Final Payment and the Amendment Fee.

2. Interest. Interest not paid when due will, to the maximum extent permitted under applicable
law, become part of principal, at Lender’s option, and thereafter bear like interest as principal.
All interest computation shall be based on a 360-day year and actual days elapsed prior to the Loan
Commencement Date and on a 360-day year and 30 day month on and after the Loan Commencement Date.
All Obligations not paid when due shall bear interest at the Default Rate unless waived in writing
by Lender. All amounts paid hereunder will be applied to the Obligations in Lender’s discretion and
as provided in the Loan Agreement.

3. Voluntary Prepayment. Borrower may prepay the Note if and only if Borrower pays to Lender (i)
the outstanding principal amount of this Note and any unpaid accrued interest; (ii) the Final
Payment; (iii) the Prepayment Fee, if applicable; (iv) the Amendment Fee; and (v) all other sums,
if any, that shall have become due and payable hereunder with respect to this Note.

4. Collateral. This Note is secured by the Collateral.

5. Waivers. Borrower, and all guarantors and endorsers of this Note, regardless of the time, order
or place of signing, hereby waive notice, demand, presentment, protest, and notices of every kind,
presentment for the purpose of accelerating maturity, diligence in collection, and, to the fullest
extent permitted by law, all rights to plead any statute of limitations as a defense to any action
on this Note.

6. Choice of Law; Venue. This Note shall be governed by, and construed in accordance with the
internal laws of the State of California, without regard to principles of conflicts of law. Each
of Borrower and Lender hereby submits to the exclusive jurisdiction and venue of the State and
Federal courts located in the City and County of San Francisco, State of California. Borrower and
Lender each hereby waive their respective rights to a jury trial of any claim or cause of action
based upon or arising out of this Note. Each party further waives any right to consolidate any
action in which a jury trial has been waived with any other action in which a jury trial cannot be
or has not been waived.

7. Miscellaneous. This Note may be modified only by a writing signed by Borrower and
Lender. Each provision hereof is severable from every other provision hereof and of the Loan
Agreement when determining its legal enforceability. Sections and subsections are titled for
convenience, and not for construction. “Hereof,” “herein,” “hereunder,” and similar words refer to
this Note in its entirety. “Or” is not necessarily exclusive. “Including” is not limiting. The
terms and conditions hereof inure to the benefit of and are binding upon the parties’ respective
permitted successors and assigns. This Note is subject to all the terms and conditions of the Loan
Agreement.

In Witness Whereof, Borrower has caused this Note to be executed by a duly authorized
officer as of the day and year first above written.

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	 	 	 
	 

	 	 	 	 	 	 
	 

	 	Name:
	 	
Fred Cannon
	 	 
	 

	 	Title:
	 	President & CEO	 	 

 

 

Exhibit C-1

New Warrant

 

 

Exhibit E-1

Incumbency Certificate

     The undersigned, Andre Ditsch, hereby certifies that:

1. He/She is the duly elected and acting Secretary of Kior, Inc., a Delaware corporation
(the “Company”).

2. That on the date hereof, each person listed below holds the office in the Company indicated
opposite his or her name and that the signature appearing thereon is the genuine signature of each
such person:

	 	 	 	 	 	 	 
	NAME	 	OFFICE	 	SIGNATURE	 	 
	 
	 	 	 	 	 	 
	Fred Cannon

	 	President & Chief Operating Officer
	 	 

	 	 
	 
	 	 	 	 	 	 
	Andre Ditsch

	 	Secretary
	 	 

	 	 
	 
	 	 	 	 	 	 
	John H. Karnes

	 	Chief Financial Officer
	 	 

	 	 

3. Attached hereto as Exhibit A is a true and correct copy of the Certificate of Incorporation of
the Company, as amended, as in effect as of the date hereof.

4. Attached hereto as Exhibit B is a true and correct copy of the Bylaws of the Company, as
amended, as in effect as of the date hereof.

5. Attached hereto as Exhibit C is a copy of the resolutions of the Board of Directors of the
Company authorizing and approving the Company’s execution, delivery and performance of an amendment
to the loan facility with Lighthouse Capital Partners VI, L.P.

     IN WITNESS WHEREOF, the undersigned has executed this Incumbency Certificate on February 28,
2011.

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	Name:
	 	 

Andre Ditsch
	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	Secretary	 	 

     I, the President and Chief Operating Officer of the Company, do hereby certify that Andre
Ditsch is the duly qualified, elected and acting Secretary of the Company and that the above
signature is his or her genuine signature.

     IN WITNESS WHEREOF, the undersigned has executed and delivered this Incumbency Certificate on
February 28, 2011.

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	Name:
	 	 

Fred Cannon
	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:
	 	President and Chief Operating Officer	 	 

 

 

Schedule 1-1

Disclosure Schedule

Subsidiaries

Kior BV in liquidation, a wholly owned subsidiary of Borrower organized under the laws of The
Netherlands.

Kior Columbus LLC, a limited liability company organized under the laws of Delaware and a
wholly-owned subsidiary of Parent.

Prior Names

Bio Catalytic Cracking, Inc.

5.6 Litigation and Administrative Proceedings

Parent has initiated a lawsuit against George Huber (“Huber”), a prior member of the Borrower’s
scientific advisory board, based in part on a belief that Huber may have breached the terms of his
consulting agreement with Borrower.

A former employee has instituted summary proceedings against Kior BV in Dutch courts claiming
continuation of employment even though his employment contract ended April 30, 2010.

Business Premises

[TO BE PROVIDED BY BORROWER — indicate street address and landlord contact information]

	 	 	 	 	 	 	 	 	 
	 	 	Each Location Address where Lighthouse	 	Landlord/Property Management
	 	 	Capital Partners has financed assets:	 	Information:
	Current

	 	Contact Name:
	 	Gene Staggs
	 	Contact Name:
	 	Milton Sundbeck, President
	Headquarters

	 	Address:
	 	13001 Bay Park Road
	 	Company Name:
	 	Southern Ionic Incorporated
	(Location 1)

	 	City, State, Zip:
	 	Pasadena, TX 77507
	 	Address:
	 	Drawer 1217
	 

	 	Phone:
	 	(281) 694-8710
	 	City, State, Zip:
	 	West Point, MS 39701
	 

	 	Fax:
	 	(281) 694-8799
	 	Phone:
	 	(662) 494-3055 x 201
	 

	 	 	 	 	 	Fax:
	 	(662) 495-2590
	 

	 	 	 	 	 	Local Contact:
	 	Craig Cantrell, Plant Manager
	 

	 	 	 	 	 	Local Address:
	 	12901 Baypark Rd.
	 

	 	 	 	 	 	City, State, Zip:
	 	Pasadena, TX 77507
	 

	 	 	 	 	 	Phone:
	 	(281) 474-4826 x 131
	 

	 	 	 	 	 	Cell:
	 	(281) 703-3439
	 

	 	 	 	 	 	Fax:
	 	(281) 474-4973exv4w11

Exhibit 4.11

Loan and Security Agreement

This Loan and Security Agreement No. 1452 (this “Agreement”) is entered into as of January
27, 2010, by and between Kior, Inc., a Delaware corporation (“Borrower”) and
Lighthouse Capital Partners VI, L.P as “Agent” for the lenders identified on Schedule
A hereto (such lenders, together with their respective successors and assigns are referred to
herein each individually as a “Lender” and collectively as “Lenders”), and the Lenders. This
Agreement sets forth the terms and conditions upon which Lenders will lend and Borrower will repay
money. In consideration of the mutual covenants herein contained, the parties agree as follows:

1. Definitions and Construction

1.1 Definitions. Initially capitalized terms used and not otherwise defined herein are defined in
the California Uniform Commercial Code (“UCC”).

“ACH” means the Automated Clearing House electronic funds transfer system.

“Advance” means a Loan advanced by Lender to Borrower hereunder.

“Agent” means Lighthouse Capital Partners VI, L.P. or any successor Agent appointed by the Lenders.

“Basic Rate” a per annum rate of interest equal to (i) for Advances funded under Tranche 1, 12% and
(ii) for Advances funded under Tranche 2, 14% during the Interest Only Period and 12% on and after
the Loan Commencement Date.

“Borrower’s Books” means all of Borrower’s books and records, including records concerning
Collateral, Borrower’s assets, liabilities, business operations or financial condition, on any
media, and the equipment containing such information.

“Collateral” means: (i) all property in which Agent on behalf of Lenders now has or hereafter
obtains a security interest under this Agreement or which is listed on any UCC-1 naming Borrower as
Debtor in any capacity and Agent, Lenders or an affiliate of Lenders as Secured Party including
Exhibit A attached hereto; and (ii) all products and proceeds of the foregoing, including proceeds
of insurance and proceeds of proceeds. Notwithstanding the foregoing, Collateral shall not include
(i) any Eligible Equipment financed under (and as defined under) the Lighthouse Equipment Loan, but
only for so long as the Obligations under the Lighthouse Equipment Loan are outstanding or (ii)
property secured pursuant to clause (v) of the definition of Permitted Liens.

“Commitment” means $10,000,000, available in 2 tranches. Tranche 1, in the amount of $7,000,000
(“Tranche 1”) shall be available immediately upon the closing of this Agreement; Tranche 2, in the
amount of $3,000,000 (“Tranche 2”) shall be available upon Borrower reaching any of the following
milestones: (i) formal approval of a United Stated Department of Energy or United States Department
of Agriculture (or a combination of both) commercialization grant totaling at least $20,000,000;
(ii) proof reasonably acceptable to Agent of Demonstration Facility’s full operational capability
of at least 10 barrels per day of bio-oil within a 24 hour operation period; (iii) close of a
preferred stock equity financing led by a new outside investor of at least $30,000,000 (which
amount may include conversion of a $15,000,000 bridge facility provide by Khosla Ventures); or (iv)
finalization of a strategic partnership agreement with a large, multinational oil company deemed
acceptable to Agent in its reasonable discretion. Each Lender shall be responsible for no more
than the percentage amount of each Advance, as reflected on Schedule A hereto and shall
have no liability for the Commitment to make Advances of any other Lender.

“Commitment Fee” means $15,000.

“Commitment Termination Date” means the earliest to occur of (i) (a) for Tranche 1, January 31,
2010; and (b) for Tranche 2, July 31, 2010; (ii) any Event of Default or, during the pendency of a
Default unless and until such time as such Default is cured to Agent’s sole reasonable
satisfaction; (iii) the date on which Mr. Fred Cannon, Borrower’s President or at least one
representative of Khosla Ventures II, LP or its affiliated funds ceases to serve as a member of
Borrower’s Board of Directors; or (iv) the date on which Borrower ceases to be in the business of
developing and manufacturing biofuels.

“Control Agreement” means an agreement substantially in the form of Exhibit I or otherwise
acceptable to Agent.

“Default” means any event that with the passing of time or the giving of notice or both would
become an Event of Default.

“Default Rate” means the lesser of 18% per annum or the highest rate permitted by applicable law.

“Demonstration Facility” means Borrower’s facility located at 13001 Bay Park Road, Pasadena, TX
77507.

“Disclosure Schedule” means the schedule attached as Schedule 1 hereto.

1

 

“Event of Default” is defined in Section 8.

“Funding Date” means any date on which an Advance is made to or on account of Borrower hereunder.

“Incumbency Certificate” means the document in the form of Exhibit E.

“Indebtedness” means (i) all indebtedness for borrowed money or the deferred purchase of property
or services (other than trade payables), (ii) all obligations evidenced by notes, bonds, debentures
or similar instruments, (iii) all capital lease obligations, and (iv) all contingent obligations,
including guaranties and obligations of reimbursement or respecting letters of credit.

“Interest Only Period” means, for Advances funded under Tranche 2, the period commencing on the
Funding Date of such Advance and continuing through the day immediately preceding the Loan
Commencement Date.

“Investment” means any beneficial ownership of (including stock, partnership or limited liability
company interest or other securities) any entity, or any loan, advance or capital contribution of
any entity or person.

“Kior BV” means Kior BV, a wholly-owned subsidiary of Borrower organized under the laws of The
Netherlands.

“Lenders’ Expenses” means all reasonable costs or expenses (including reasonable attorneys’ fees
and expenses) incurred in connection with the preparation, negotiation, modification,
administration, or enforcement of the Loan or Loan Documents, or the exercise or preservation of
any rights or remedies by Agent or Lenders, whether or not suit is brought. Agent and Lenders
will apply deposits received before the date hereof, if any, towards Lender’s Expenses.

“Lien” means any lien, security interest, pledge, bailment, lease, mortgage, hypothecation,
conditional sales and title retention agreement, charge, claim, or other encumbrance.

“Lighthouse Equipment Loan” means that certain Loan and Security Agreement No. 1451 dated December
30, 2008 by and between Lighthouse Capital Partners VI, L.P. and Borrower.

“Loan” means all of the Advances, however evidenced, and all other amounts due or to become due
hereunder.

“Loan Commencement Date” means August 1, 2010.

“Loan Documents” means, collectively, this Agreement, the Warrant, the Notes, and all other
documents, instruments and agreements entered into between Borrower and Lenders in connection with
the Loan, all as amended or extended from time to time.

“Material Adverse Effect” means a material adverse effect on (i) the financial condition of
Borrower and its Subsidiaries taken as a whole or (ii) the validity or enforceability of the Loan
Documents or the rights and remedies of the Lenders thereunder or with respect to the Collateral.

“Negative Pledge Agreement” means an agreement in the form of Exhibit H.

“Note” means a Secured Promissory Note in the form of Exhibit B.

“Notice of Borrowing” means the form attached as Exhibit D.

“Obligations” means all Loans, debt, principal, interest, fees, charges, Lender’s Expenses and
other amounts, obligations, covenants, and duties owing by Borrower to Agent or Lenders of any kind
or description (pursuant to the Loan Documents (with the exception of the Warrant), and whether or
not for the payment of money), whether direct or indirect, absolute or contingent, due or to become
due, now existing or hereafter arising, and including any of the same obtained by Agent or Lenders
by assignment or otherwise, and all amounts Borrower is required to pay or reimburse by the Loan
Documents, by law, or otherwise.

“Permitted Indebtedness” means: (i) the Loan; (ii) unsecured trade debt incurred in the ordinary
course of Borrower’s or any Subsidiary’s business; (iii) Indebtedness secured by clauses (ii), (v),
and (vi) of Permitted Liens; (iv) Indebtedness of the Borrower or any Subsidiary to the Borrower or
any Subsidiary in the ordinary course of business; (v) Indebtedness set forth on the Disclosure
Schedule as of the date of this Agreement; (vii) Subordinated Indebtedness; and (vii) extensions,
refinancing, modifications, amendments and restatements of any items of Permitted Indebtedness
above, provided that the principal amount thereof is not increased or the terms thereof are not
modified to impose more burdensome terms upon Borrower or a Subsidiary, as the case may be.

“Permitted Investments” means (i) Investments existing as of the date hereof and disclosed on the
Disclosure Schedule; (ii) (a) marketable direct obligations issued or unconditionally guaranteed by
the United States of America or any agency or any State thereof

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maturing within 1 year from the
date of acquisition thereof, (b) commercial paper maturing no more than one year from the date of
creation thereof and currently having a rating of at least A-2 or P-2 from either Standard & Poor’s
Corporation or Moody’s Investors
Service, (c) certificates of deposit maturing no more than 1 year from the date of investment
therein, and (d) money market accounts; (iii) Investments made pursuant to an investment policy
approved by the Board of Directors that is designed to maintain liquidity and preserve capital with
respect to Borrower’s excess cash; (iv) Investments not to exceed $100,000 in the aggregate in any
fiscal year consisting of (a) travel advances and employee relocation loans and other employee
loans and advances in the ordinary course of business and (b) loans to employees, officers and
directors relating to the purchase of equity securities of Borrower pursuant to employee stock
purchase plan agreements approved by Borrower’s Board of Directors; (v) Investments (including debt
obligations) received in connection with the bankruptcy or reorganization of customers or suppliers
and in settlement of delinquent obligations of, and other disputes with, customers or suppliers
arising in the ordinary course of Borrower’s business; (vi) Investments consisting of notes
receivable of, or prepaid royalties and other credit extensions, to customers and suppliers who are
not affiliates, in the ordinary course of business; and (vii) deposit accounts maintained by
Borrower in the ordinary course of business; and (viii) Investments by Borrower into Subsidiary or
by a Subsidiary into another Subsidiary to fund such Subsidiary’s ordinary course operations.

“Permitted Liens” means: (i) Liens in favor of Lender; (ii) Liens disclosed in the Disclosure
Schedule; (iii) Liens for taxes, fees, assessments or other governmental charges or levies not
delinquent or being contested in good faith by appropriate proceedings, that do not jeopardize
Lender’s interest in any Collateral; (iv) Liens to secure payment of worker’s compensation,
employment insurance, old age pensions or other social security obligations of Borrower or any
Subsidiary on which Borrower or any Subsidiary is current and are in the ordinary course of its
business; provided none of the same diminish or impair Lender’s rights and remedies respecting the
Collateral; (v) Liens on any property held or acquired by Borrower or any Subsidiary in the
ordinary course of business securing Indebtedness incurred or assumed for the purpose of financing
all or any part of the cost of acquiring such property, provided such Lien attaches solely to the
property acquired with such Indebtedness and that the principal amount of such Indebtedness does
not exceed 100% of the cost of such property, in an aggregate amount not to exceed $1,000,000 and
provided further such Indebtedness is on commercially reasonable terms; (vi) licenses or
sublicenses of intellectual property granted in the ordinary course of business; (vii) banker’s
Liens, rights of setoff and similar Liens incurred on deposit and securities accounts of such
entities for fees due on such accounts incurred in the ordinary course of business; (viii)
carriers’, warehousemen’s, mechanics’, materialmen’s, repairmen’s or other like Liens arising in
the ordinary course of business which are not delinquent or remain payable without penalty or which
are being contested in good faith and by appropriate proceedings for which adequate reserves are
kept; (ix) Liens in favor of customs and revenue authorities which secure payment of customs duties
in connection with the importation of goods; and (x) Liens incurred in the extension, renewal or
refinancing of the Indebtedness secured by Liens described above but any extension, renewal or
replacement Lien must be limited to the property originally encumbered by the existing Lien and the
principal amount of any Indebtedness associated therewith may not increase.

“Regulated Substance” means any substance, material or waste the use, generation, handling,
storage, treatment or disposal of which is regulated by any local or state government authority,
including any of the same designated by any authority as hazardous, genetic, cloning, fetal, or
embryonic.

“Responsible Officer” means the President, Chief Financial Officer/Treasurer and Secretary of
Borrower and each person as authorized by the board of directors of Borrower as set forth on the
Incumbency Certificate.

“Subordinated Indebtedness” means Indebtedness in an amount not to exceed $5,000,000 that is
subordinated in both security and right of payment to the Obligations on terms and conditions
satisfactory to Lenders as evidenced by a subordination agreement between Lenders and the
provider(s) of such Subordinated Indebtedness.

“Subsidiary” means any corporation of which a majority of the outstanding capital stock
entitled to vote for the election of directors (otherwise than as the result of a default) is owned
by Borrower directly or indirectly through Subsidiaries.

“Term” means the period from and after the date hereof until the full, final and indefeasible
payment and performance of all Obligations.

“Tranche 2 Warrants” means the Warrant in favor of each of the Lenders and its affiliates to
purchase securities of Borrower substantially in the form of Exhibit C-1 issued in conjunction with
the availability of Tranche 2 of the Commitment.

“Warrant” or “Warrants” means the Warrant in favor of each of the Lenders and its affiliates to
purchase securities of Borrower substantially in the form of Exhibit C and the Tranche 2 Warrants.

1.2 Interpretation. References to “Articles,” “Sections,” “Exhibits,” and “Schedules” are to
articles, sections, exhibits and schedules herein and hereto unless otherwise indicated. “Hereof,”
“herein” and “hereunder” refer to this Agreement as a whole. “Including” is not limiting. All
accounting and financial computations shall be computed in accordance with generally accepted
accounting principles consistently applied (“GAAP”). “Or” is not necessarily exclusive. All
interest computation shall be based on a 360-day year and actual days elapsed prior to the Loan
Commencement Date and on a 360-day year and 30 day month on and after the Loan Commencement Date.

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2. The Loans

2.1 Commitment. Subject to the terms hereof, Lenders will make Advances to Borrower up to the
principal amount of their respective shares of the Commitment, on or before the Commitment
Termination Date. Notwithstanding anything in the Loan Documents to the contrary, Lenders’
obligation to make any Advances or to lend the undisbursed portion of the Commitment shall
terminate on the Commitment Termination Date. Repaid principal of the Advances may not be
re-borrowed.

2.2 The Advances. A Note setting forth the specific terms of repayment will evidence each Advance.
No Advance will be made for less than $500,000, unless less than $500,000 remains available under
the Commitment for borrowing. Absence of a Note evidencing any portion of the Loan shall not
impair Borrower’s obligation to repay it to Lenders under the terms outlined in Exhibit B for the
applicable Note for the amount of each Advance. Each Lender will receive a Note from Borrower
evidencing the Advances funded by such Lender at the time of each such Advance (if any).

2.3 Terms of Payment, Repayment.

     (a) Repayment. Borrower shall repay the principal and pay interest on each Advance on the
terms set forth in the applicable Note. Amounts not paid when due hereunder or under the Note
shall bear interest at the Default Rate. If a court of competent jurisdiction determines that a
Lender has received payments that, if interest, would exceed the maximum lawfully permitted, such
Lender will instead apply such money to fees and expenses and then to early prepayment of principal
(without any Prepayment Fee (as defined in the Note).

     (b) ACH. All payments due to Lenders must be, at each Lender’s option, paid to Lender in cash
or through ACH. Borrower shall execute and deliver the ACH Authorization Form for each Lender
substantially in the form of Exhibit G. If the ACH payment arrangement is terminated for any
reason with respect to any Lender, Borrower shall make all payments due to such Lender at such
Lender’s address specified in Section 11.

     (c) Default Rate. While an Event of Default has occurred and is continuing, interest on the
Loan shall be increased to the Default Rate. Any Lender’s failure to charge or accrue interest at
the Default Rate during the existence of a Default shall not be deemed a waiver by any Lender of
any right or claim thereto.

     (d) Date. Whenever any payment due under the Loan Documents is due on a day other than a
business day, such payment shall be made on the next succeeding business day, and such extension of
time shall be included in the computation of interest or fees, as the case may be.

2.4 Fees. Borrower shall pay to Lenders the following:

     (a) Commitment Fee. The Commitment Fee, which has been previously paid by Borrower to Agent,
and shall be applied by Agent to Lenders’ Expenses and other Obligations.

     (b) Late Fee. On demand, a late charge on any sums due hereunder that are not paid when due,
in an amount equal to 2% of the past due amount, payable on demand.

     (c) Lender’s Expenses. When requested, all Lenders’ Expenses. Lenders’ Expenses not paid
when due shall bear interest as principal at the Default Rate.

3. Conditions of Advances; Procedure for requesting Advances

3.1 Conditions Precedent to any and all Advances. The obligation of Lenders to make any Advances
is subject to each and every of the following conditions precedent in form and substance
satisfactory to Agent in its sole discretion: (i) this Agreement, a Note evidencing the Advance,
the Warrants (with respect to Tranche 2, the Tranche 2 Warrants), and all other UCC financing
statements, and other documents required or as specified herein have been duly authorized, executed
and delivered to the Agent and/or the Lenders; (ii) no Default or Event of Default has occurred and
is continuing; (iii) delivery of a Notice of Borrowing to Agent with respect to the proposed
Advance; (iv) Lenders’ security interests in the Collateral are valid and first priority, except
for Permitted Liens; and (v) all such other items as Agent may reasonably deem necessary or
appropriate have been delivered or satisfied. The extension of an Advance prior to the receipt by
Lenders of any of the foregoing shall not constitute a waiver by any of the Lenders of Borrower’s
obligation to deliver such item. In addition to the foregoing, it shall be a condition to the
funding of any Advances under Tranche 2, that Borrower shall issue Lenders the Tranche 2 Warrants.

3.2 Procedure for Making Advances. For any Advance, Borrower shall provide Agent an irrevocable
Notice of Borrowing at least 10 business days prior to the desired Funding Date and Lenders shall
only be required to make Advances hereunder based upon

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written requests which comply with the terms
and exhibits of this Loan Agreement (as the same may be amended from time to time), and which are
submitted and signed by a Responsible Officer. Borrower shall execute and deliver to Lenders a Note
and such other documents and instruments as Lenders may reasonably require for each Advance made.

4. Creation of Security Interest

4.1 Grant of Security Interest. Borrower grants to Agent on behalf of all Lenders a valid, first
priority (subject to Permitted Liens), continuing security interest in all present and future
Collateral in order to secure prompt, full, faithful and timely payment and performance of all
Obligations.

4.2 Inspections. Agent shall have the right upon reasonable prior notice to inspect Borrower’s
Books, including computer files, and to make copies, and to test, inspect and appraise the
Collateral, in order to verify any matter relating to Borrower or the Collateral. Lenders may
accompany Agent on such inspections.

4.3 Authorization to File Financing Statements. Borrower irrevocably authorizes Agent on behalf of
all Lenders at any time and from time to time to file in any jurisdiction any financing statements
and amendments that: (i) name Collateral as collateral thereunder, regardless of whether any
particular Collateral falls within the scope of the UCC; (ii) contain any other information
required by the UCC for sufficiency or filing office acceptance, including organization
identification numbers; and (iii) contain such language as Lender determines helpful in protecting
or preserving rights against third parties. Borrower ratifies any such filings made prior to the
date hereof.

5. Representations and Warranties

Borrower represents and warrants as follows:

5.1 Due Organization and Qualification. Borrower is a corporation duly formed, existing and in
good standing under the laws of its state of incorporation and qualified and licensed to do
business in, and is in good standing in, any state in which the conduct of its business or its
ownership of property requires that it be so qualified or in which the Collateral is located,
except states other than Texas and Delaware where non-compliance would not reasonably be expected
to have a Material Adverse Effect on Borrower or any of the Collateral.

5.2 Authority. Borrower has all corporate power and authority, and has taken all actions, and has
obtained all third party consents necessary to execute, deliver, and perform the Loan Documents.

5.3 Disclosure Schedule. All information on the Disclosure Schedule is true, correct and complete.

5.4 Authorization; Enforceability. The execution and delivery hereof, the granting of the security
interest in the Collateral, the incurring of the Obligations, the execution and delivery of all
Loan Documents and the consummation of the transactions herein and therein contemplated have been
duly authorized by all necessary action by Borrower. The Loan Documents constitute legal, valid
and binding obligations of Borrower, enforceable in accordance with their terms, except as
enforceability may be limited by bankruptcy or similar laws relating to enforcement of creditors’
rights generally.

5.5 Name and Location. Borrower has not done business under any name other than that specified on
the signature page hereof or as set forth on the Disclosure Schedule. Except as provided in any
written notice from Borrower to Lender, (i) the chief executive office, principal place of
business, and the place where Borrower maintains its records concerning the Collateral is set forth
in Section 11 and (ii) the Collateral is presently located at the address(es) set forth in Section
11 and on the Disclosure Schedule. Borrower has no subsidiaries except as set forth on the
Disclosure Schedule.

5.6 Litigation. All actions or proceedings pending or, to Borrower’s knowledge, threatened by or
against Borrower before any court or administrative agency are set forth on the Disclosure
Schedule.

5.7 Financial Statements. All financial statements of the Borrower and its consolidated
Subsidiaries delivered by Borrower to Lender fairly present in all material respects the financial
condition of the Borrower and its consolidated Subsidiaries, taken as a whole. All schedules
respecting Collateral that have been or may hereafter be delivered by Borrower to Lender are true,
complete and correct in all material respects for the periods indicated.

5.8 Solvency. Borrower is solvent and able to pay its debts (including trade debts) as they come
due.

5.9 Taxes. Borrower has filed all required tax returns, and has paid all taxes it owes other than
where the failure to comply would not reasonably be expected to have a Material Adverse Effect.

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5.10 Rights; Title to Assets. Borrower possesses and owns all necessary assets, rights,
trademarks, trade names, copyrights, patents, patent rights, franchises and licenses which it needs
to conduct its business as now operated or proposed to be operated. Borrower has good title to its
assets, free and clear of any Liens, except for Permitted Liens.

5.11 Full Disclosure. No written representation, warranty or other statement made by Borrower in
any Loan Document, certificate or statement furnished to Lender contains any untrue statement of a
material fact or omits to state a material fact necessary in order to make the statements contained
in such certificates or statements not misleading.

5.12 Regulated Substances. Borrower complies with all laws respecting Regulated Substances in all
material respects.

5.13 Reaffirmation. Each Notice of Borrowing will constitute (i) a warranty and representation in
favor of Agent and Lenders that there does not exist any Default and (ii) a reaffirmation as of the
date thereof of all of the representations and warranties contained in this Agreement and the Loan
Documents.

5.14 Auction Rate Securities. The Borrower (i) owns no auction rate securities or similar
financial instruments directly or indirectly in any brokerage, securities account or other account
created by or for the benefit of the Borrower; and (ii) has not created any standing or
discretionary purchase order or directive with any brokerage account or broker service to purchase
auction rate securities or similar financial instruments on behalf of the Borrower.

5.15 Kior BV. Borrower represents and warrants that Kior BV (i) has no property, assets,
operating contracts or business operations, except for any assets that are immaterial to the
business of Borrower, and is not bound by and is not a party to, any contacts that are material to
the Borrower (ii) has no employees (iii) has not issued any stock certificates and (iv) has no
material liabilities on its balance sheet for which it or Borrower is responsible. Neither
Borrower nor Kior BV has granted a security interest in any of the shares of capital stock of Kior
BV. Kior BV is a wholly subsidiary of Borrower.

6. Affirmative Covenants

Borrower covenants and agrees that it shall do all of the following:

6.1 Good Standing and Compliance. Borrower shall maintain all governmental licenses, rights and
agreements necessary for its operations or business and comply with all statutes, laws, ordinances
and government rules and regulations to which it is subject, except where the failure to do so
would not reasonably be expected to result in a Material Adverse Effect.

6.2 Financial Statements, Reports, Certificates. Borrower shall deliver to Agent: (i) as soon as
prepared, and no later than 30 days after the end of each calendar month, a balance sheet, income
statement and cash flow statement covering Borrower’s operations during such period; (ii) as soon
as prepared, but no later than 120 days after the end of the fiscal year or such other time period
as approved by Borrower’s Board of Directors, (x) audited financial statements prepared in
accordance with GAAP, together with an opinion that such financial statements fairly present
Borrower’s financial condition by an independent public accounting firm reasonably acceptable to
Agent, or (y) in the absence of an initial audit, financial statements for such fiscal year
prepared in accordance with GAAP and certified by a Responsible Officer or approved by the Board of
Directors of Borrower; (iii) immediately upon notice thereof, a report of any legal or
administrative action pending or threatened against Borrower which is likely to result in liability
to Borrower in excess of $200,000; and (iv) such other financial information that is periodically
delivered to Borrower’s preferred stockholders or as Lender may reasonably request from time to
time. Financial statements delivered pursuant to subsections (i) and (ii) above shall be
accompanied by a certificate signed by a Responsible Officer (each an “Officer’s Certificate”) in
the form of Exhibit F.

6.3 Notice of Defaults. Promptly following any Default or Event of Default, deliver an Officer’s
Certificate to Agent setting forth the facts relating to or giving rise thereto, and the Borrower’s
proposed action with respect thereto.

6.4 Use; Maintenance. Borrower, at its expense, shall (i) maintain the Collateral in good
condition, reasonable wear and tear excepted, and will comply in all material respects with all
laws, rules and regulations regarding use and operation of the Collateral and (ii) repair or
replace any lost or damaged Collateral.

6.5 Insurance. Borrower, at its own expense, shall maintain insurance in amounts and coverages
reasonably satisfactory to Lender. Each insurance policy shall: (i) name Agent on behalf of all
Lenders as loss payee or additional insured, as appropriate, (ii) provide for insurer’s waiver of
its right of subrogation against Lenders and Borrower, (iii) provide that such insurance shall not
be invalidated by any action of, or breach of warranty by, Borrower and waive set-off, counterclaim
or offset against Lenders, (iv) be primary without a right of contribution of Lenders’ insurance,
if any, or any obligation on the part of Lenders to pay premiums of Borrower, and (v) require the
insurer to give Agent at least 30 days prior written notice of cancellation, unless such
cancellation is on account of non-payment in which case 10 days prior written notice shall be
sufficient. Borrower shall furnish all certificates of insurance required by Agent.

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6.6 Loss Proceeds. So long as no Event of Default has occurred and is continuing, any proceeds of
insurance on or condemnation of Collateral shall, at Borrower’s election and so long as Lenders’
security interest in such proceeds remains first priority, be used either to repair or replace such
Collateral or otherwise applied to the purchase or acquisition of property useful to Borrower’s
business.

6.7 Taxes. Borrower will file all required tax returns, and will pay all taxes it owes other than
where the failure to comply would not reasonably be expected to have a Material Adverse Effect.

6.8 Regulated Substances. Borrower will comply with all laws respecting Regulated Substances and
shall not incur any penalties with regards to such Regulated Substances in an amount not to exceed
$200,000 of remedial cost, which penalty has not been dismissed or paid within 30 days.

6.9 Further Assurances. At any time and from time to time, Borrower shall execute and deliver such
further instruments and take such further action as Agent may reasonably request to effect the
intent and purposes hereof, to perfect and continue perfected and of first priority Lenders’
security interests in the Collateral, and to effect and maintain ACH payment arrangements with each
of the Lenders.

6.10 Dissolution of Kior BV. Borrower shall not permit a Lien on the capital stock of Kior
BV, or pledge the stock certificates of Kior BV, in favor of any other party other than Lender and
Borrower shall take all steps necessary to dissolve the existence of Kior BV within 150 days from
the date of this Agreement.

7. Negative Covenants

Borrower will not do any of the following:

7.1 Location of Collateral. Change its chief executive office or principal place of business or
remove, except in the ordinary course of Borrower’s business, the Collateral or Borrower’s Books
from the premises listed in Section 11 without giving 30 days prior written notice to Agent.

7.2 Extraordinary Transactions. Sell, lease, license or otherwise dispose of its assets, other
than (i) sales of inventory in the ordinary course of Borrower’s business; (ii) licenses of
Borrower’s intellectual property assets entered into in the ordinary course of business; and (iii)
any other sale, lease, license or disposition (excluding Collateral hereunder) the net proceeds of
which, does not, taken together with each other sale, lease, license or disposition made in such
fiscal year, exceed $200,000.

7.3 Restructure. Make any material change in Borrower’s financial structure or business operations
(other than through the sale of preferred stock to equity investors which does not result in a
change of control of Borrower); or suspend operation of Borrower’s business.

7.4 Liens. (i) Create, incur, assume or suffer to exist any Lien of any kind with respect to any
of its property, whether now owned or hereafter acquired, except for Permitted Liens, or (ii) enter
into or permit to exist any agreement that restricts the ability of Borrower to grant a Lien to
Agent or Lenders in any of Borrower’s Intellectual Property (as defined in Exhibit A) (other than
restrictions that world be unenforceable or ineffective pursuant to Section 9-408 of the UCC or the
Uniform Commercial Code as adopted in any other applicable jurisdiction).

7.5 Indebtedness. Create, incur, assume or suffer to exist any Indebtedness, other than Permitted
Indebtedness.

7.6 Distributions. Pay any dividends or distributions, or redeem or purchase, any capital stock,
except for (i) repurchases of capital stock from departing employees or directors, under repurchase
agreements approved by the Borrower’s Board of Directors and (ii) dividends or distributions
payable solely in capital stock of Borrower.

7.7 Investments. Acquire or own, or make any Investment in or to any entity, other than Permitted
Investments.

7.8 Transactions with Affiliates. Directly or indirectly enter into any transaction with any
affiliate which is on terms less favorable to Borrower than would be obtained in an arm’s length
transaction with a non-affiliated entity; provided, any such transaction shall not be a breach of
this Section 7.7 if approved by a disinterested majority of the Borrower’s Board of Directors.

7.9 Compliance. (i) Become an “investment company” under the Investment Company Act of 1940 or
extend credit to purchase or carry margin stock; (ii) fail to meet the minimum funding requirements
of ERISA; (iii) permit a Reportable Event or Prohibited Transaction, as defined in ERISA, to occur;
(iv) fail to comply with the Federal Fair Labor Standards Act; or (v) violate any other material
law or material regulation.

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7.10 UCC Effectiveness. Change its name, jurisdiction of organization, or take any other action
that could render Lender’s financing statements misleading under the UCC, without giving Lender 30
days advance written notice.

7.11 Deposit and Securities Accounts. Maintain any deposit accounts or accounts holding
securities owned by Borrower except accounts in which Agent on behalf of all Lenders has obtained a
perfected first priority security interest. Notwithstanding the
foregoing, Lender shall not have a perfected security interest in (i) Borrower’s certificate of
deposit account no. 0910-00121407355 with Bank of America which secures Borrower’s commercial
credit card facility, provided the amount of such account shall not exceed 5125,000; (ii)
Borrower’s checking account no. 488019490275 with Bank of America, provided the amount of such
account shall not exceed $$2,000,000 and Borrower shall close such account no later than February
28, 2010 and provide Lender with notice thereof; or (iii) Borrower’s account no. 3300709750 with
Silicon Valley Bank which secures Borrower’s obligations under a commercial credit card facility,
provided the amount of such account shall not exceed $100,000. For so long as the Obligations are
outstanding, Borrower shall not hold directly or indirectly, purchase or create a purchase order or
directive to purchase any auction rate securities or similar financial instruments regardless of
whether such securities are to be held by Borrower or through one or more brokerage accounts.

7.12 Maintenance of Subsidiaries. Except as set forth in Section 6.10 hereof, Borrower shall not,
and shall not permit or cause any Subsidiary to, (i) sell, dispose of, convey, or allow a Lien to
arise on any of its assets, including Intellectual Property (as defined in Exhibit A) owned by such
Subsidiary (and for this purpose, the definition of “Intellectual Property” shall be deemed to
refer to such Subsidiary) except for non-exclusive licenses entered into in the ordinary course of
business; (ii) divest or “spin-off” any Subsidiary except where as a result of such transaction
Borrower and/or Borrower’s shareholders or affiliates retain or obtain majority ownership of such
Subsidiary; (iii) merge or consolidate any Subsidiary with or into another entity (unless as a
result of such merger Borrower and/or Borrower’s shareholders or affiliates retain or obtain
majority ownership of the surviving entity); (iv) permit a Change of Control (as defined below) of
any Subsidiary; (v) make a pledge of, any capital stock of any Subsidiary in favor of any person
other than Lender; or (vi) materially change the corporate structure and business operations of the
Borrower and its Subsidiaries taken as a whole. For the purposes of this Section 7.12, a “Change
of Control” shall mean, any transaction or series of related transactions whereby the Borrower
and/or Borrower’s shareholders or affiliates of Borrower holding in excess of 50% of the
outstanding voting capital stock of any Subsidiary immediately prior to such transaction or
transactions, shall own less than 50% of the outstanding voting or capital stock of such Subsidiary
immediately following such transaction or transactions.

8. Events of Default

Any one or more of the following shall constitute an Event of Default by Borrower hereunder:

8.1 Payment. Borrower fails to pay when due and payable in accordance with the Loan Documents any
portion of the Obligations, or cancels an ACH payment or transfer Lender has initiated in
conformity with the terms hereof provided, however, that an Event of Default shall not occur on
account of a failure to pay due solely to an administrative or operational error if Borrower had
the funds to make the payment when due and makes the payment the business day following Borrower’s
knowledge of such failure to pay.

8.2 Certain Covenant Defaults. Borrower fails to perform any obligation under Section 6.5 or 6.6,
or violates any of the covenants contained in Section 7.

8.3 Other Covenant Defaults. Borrower fails or neglects to perform, keep, or observe any other
term, provision, condition, covenant, or agreement contained in this Agreement, in any of the other
Loan Documents, or in any other present or future agreement between Borrower and Lender and has
failed to cure such failure within 30 days after its occurrence.

8.4 Attachment. Any material portion of Borrower’s assets is attached, seized, subjected to a
government levy, lien, writ or distress warrant, or comes into the possession of any trustee or
receiver and the same is not returned, removed, waived, stayed, discharged or rescinded within 20
days.

8.5 Other Agreements. There is a default in any agreement to which Borrower is a party resulting
in a right by a third party, whether or not exercised, to accelerate the maturity of any
Indebtedness, in an amount greater than $200,000.

8.6 Judgments. One or more judgments for an aggregate of at least $200,000 is rendered against
Borrower and remains unsatisfied and unstayed for more than 30 days.

8.7 Injunction. Borrower is enjoined, restrained, or in any way prevented by court order from
continuing to conduct any material part of its business affairs, or if a judgment or other claim
becomes a Lien upon any material portion of Borrower’s assets.

8.8 Misrepresentation. Any representation, statement, or report made to Lenders by Borrower was
false or misleading when made in any material respect.

8

 

8.9 Enforceability. Agent or any Lender’s ability to enforce its rights against Borrower or any
Collateral is impaired in any material respect, or Borrower asserts that any Loan Document is not a
legal, valid and binding obligation of Borrower enforceable in accordance with its terms.

8.10 Involuntary Bankruptcy. An involuntary bankruptcy case remains undismissed or unstayed for 60
days or, if earlier, an order granting the relief sought is entered.

8.11 Voluntary Bankruptcy or Insolvency. Borrower commences a voluntary case under applicable
bankruptcy or insolvency law, consents to the entry of an order for relief in an involuntary case
under any such law, or consents or is subject to the appointment of or taking possession by a
receiver, liquidator, assignee, trustee, custodian or other similar official of Borrower or any
substantial part of its property, or makes an assignment for the benefit of creditors, or fails
generally or admits in writing to its inability to pay its debts as they become due, or takes any
corporate action in furtherance of any of the foregoing.

8.12 Merger, Sale or Change of Control. The occurrence of (i) a merger of Borrower with another
entity (whether or not the Borrower is the “surviving entity”) whereby the shareholders of Borrower
immediately prior to such merger own less than 50% of the outstanding voting securities of Borrower
immediately after such merger; (ii) the sale (in one or a series of related transactions) of all or
substantially all of Borrower’s assets; or (iii) any transaction (or series of related
transactions) other than a transaction that is a bona fide equity financing with the primary
purpose of raising capital for Borrower, whereby the shareholders of Borrower immediately prior to
such transaction(s) own less than 50% of the outstanding voting securities of Borrower immediately
after such transaction(s), and such acquirer or resulting entity (including, Borrower, if Borrower
is the resulting or surviving entity) fails to either: (a) pay off the Obligations in cash at the
closing of the acquisition, merger or sale or (b) provide an unconditional, unlimited guaranty or
reaffirmation of the Obligations in form and substance satisfactory to Lender and is of a credit
quality acceptable to Lender.

9. Lender’s Rights and Remedies

9.1 Rights and Remedies. Upon the occurrence and continuance of any Event of Default, Agent and
Lenders may, at each party’s election, without notice of election and without demand, do any one
or more of the following, all of which are authorized by Borrower: (i) accelerate and declare the
Loan and all Obligations immediately due and payable; (ii) make such payments and do such acts as
Agent or Lenders consider necessary or reasonable to protect Lenders’ security interests in the
Collateral, with such amounts becoming Obligations bearing interest at the Default Rate; (iii)
exercise any and all other rights and remedies available under the UCC or otherwise; (iv) require
Borrower to assemble the Collateral at such places as Agent may designate; (v) enter premises where
any Collateral is located, take, maintain possession of, or render unusable the Collateral or any
part of it; (vi) without notice to Borrower, set off and recoup against any portion of the
Obligations; (vii) ship, reclaim, recover, store, finish, maintain, repair, prepare for sale,
advertise for sale, and sell the Collateral, in connection with which Borrower hereby grants each
Lender a license to use without charge Borrower’s premises, labels, name, trademarks, and other
property necessary to complete, advertise, and sell any Collateral; and (viii) sell the Collateral
at one or more public or private sales.

9.2 Power of Attorney in Respect of the Collateral. Borrower hereby irrevocably appoints Agent
(which appointment is coupled with an interest) its true and lawful attorney in fact with full
power of substitution, for it and in its name to, upon and during the continuance of an Event of
Default: (i) ask, demand, collect, receive, sue for, compound and give acquittance for any and all
Collateral with full power to settle, adjust or compromise any claim, (ii) receive payment of and
endorse the name of Borrower on any items of Collateral, (iii) make all demands, consents and
waivers, or take any other action with respect to, the Collateral, (iv) file any claim or take any
other action, in any Lender’s or Borrower’s name, which Agent may reasonably deem appropriate to
protect its rights in the Collateral, or (v) otherwise act with respect to the Collateral as though
Agent were its outright owner.

9.3 Charges. If Borrower fails to pay any amounts required hereunder to be paid by Borrower to any
third party, Agent may at its option pay any part thereof and any amounts so paid including
Lenders’ Expenses incurred shall become Obligations, immediately due and payable, bearing interest
at the Default Rate, and secured by the Collateral. Any such payments by Agent shall not
constitute an agreement to make similar payments or a waiver of any Event of Default.

9.4 Remedies Cumulative. Agent’s and Lenders’ rights and remedies under the Loan Documents and all
other agreements with Borrower shall be cumulative. Agent and Lenders shall have all other rights
and remedies as provided under the UCC, by law, or in equity. No exercise by Agent or Lenders of
one right or remedy shall be deemed an election, and no waiver by Agent or Lenders of any Event of
Default shall be deemed a continuing waiver. No delay by Agent or any Lender shall constitute a
waiver, election, or acquiescence.

9.5 Application of Collateral Proceeds. Agent and Lenders will apply proceeds of sale, to the
extent actually received in cash, in the manner and order it determines in its sole discretion, and
as prescribed by applicable law.

9

 

10. Waivers; Indemnification

10.1 Waivers. Without limiting the generality of the other waivers made by Borrower herein, to the
maximum extent permitted under applicable law, Borrower hereby irrevocably waives all of the
following: (i) any right to assert against Lenders as a defense, counterclaim, set-off or
crossclaim, any defense (legal or equitable), set-off, counterclaim, crossclaim and/or other claim
(a) which Borrower may now or at any time hereafter have against any party liable to Lenders in any
way or manner, or (b) arising directly or indirectly from the present or future lack of perfection,
sufficiency, validity and/or enforceability of any Loan Document, or any
security interest; (ii) presentment, demand and notice of presentment, dishonor, notice of intent
to accelerate, protest, default, nonpayment, maturity, release, compromise, settlement, extension
or renewal of any or all accounts, documents, instruments, chattel paper and guaranties at any time
held by Lenders on which Borrower may in any way be liable and hereby ratifies and confirms
whatever Lender may do in this regard; (iii) the benefit of all marshalling, valuation, appraisal
and exemption laws; (iv) the right, if any, to require Lenders to (a) proceed against any person
liable for any of the Obligations as a condition to or before proceeding hereunder; or (b)
foreclose upon, sell or otherwise realize upon or collect or apply any other property, real or
personal, securing any of the Obligations, as a condition to, or before proceeding hereunder; (v)
any demand for possession before the commencement of any suit or action to recover possession of
Collateral; and (vi) any requirement that Lenders retain possession and not dispose of Collateral
until after trial or final judgment.

10.2 Lenders’ Liability for Collateral. Lenders shall not in any way or manner be liable or
responsible for: (i) the safekeeping of any Collateral; (ii) any loss or damage thereto occurring
or arising in any manner or fashion from any cause; (iii) any diminution in the value thereof; or
(iv) any act or default of any carrier, warehouseman, bailee, forwarding agency, or other person or
entity whomsoever. All risk of loss, damage or destruction of the Collateral shall be borne by
Borrower. Lenders will have no responsibility for taking any steps to preserve rights against any
parties respecting any Collateral. Lenders’ powers hereunder are conferred solely to protect its
interest in the Collateral and do not impose any duty to exercise any such powers. None of Lenders
or any of its officers, directors, employees, agents or counsel will be liable for any action
lawfully taken or omitted to be taken hereunder or in connection herewith (excepting gross
negligence or willful misconduct), nor under any circumstances have any liability to Borrower for
lost profits or other special, indirect, punitive, or consequential damages. Lenders retain any
documents delivered by Borrower only for their purposes and for such period as each Lender, at its
sole discretion, may determine necessary, after which time such Lender may destroy such records
without notice to or consent from Borrower.

10.3 Indemnification. Borrower shall, on an after tax basis, defend, indemnify, and hold each
Lender and each of its officers, directors, employees, counsel, partners, agents and
attorneys-in-fact (each, an “Indemnified Person”) harmless from and against any and all
liabilities, obligations, losses, damages, penalties, actions, judgments, suits, costs, charges,
expenses or disbursements (including Lenders’ Expenses and reasonable attorney’s fees) of any kind
or nature whatsoever with respect to the execution, delivery, enforcement, performance and
administration of this Agreement and any other Loan Documents, or the transactions contemplated
hereby and thereby, with respect to noncompliance with laws or regulations respecting Regulated
Substances, government secrecy or technology export, or any Lien not created by a Lender or right
of another against any Collateral, even if the Collateral is foreclosed upon or sold pursuant
hereto, and with respect to any investigation, litigation or proceeding before any agency, court or
other governmental authority relating to this Agreement or the Advances or the use of the proceeds
thereof, whether or not any Indemnified Person is a party thereto (all the foregoing, collectively,
the “Indemnified Liabilities”); provided, that Borrower shall have no obligation hereunder to any
Indemnified Person with respect to Indemnified Liabilities arising from the gross negligence or
willful misconduct of such Indemnified Person. The obligations in this Section shall survive the
Term. At the election of any Indemnified Person, Borrower shall defend such Indemnified Person
using legal counsel reasonably satisfactory to such Indemnified Person, at the sole cost and
expense of Borrower. All amounts owing under this Section shall be paid within 30 days after
written demand.

11. Notices 

All notices shall be in writing and personally delivered or sent by certified mail, postage
prepaid, return receipt requested, or by confirmed facsimile, at the respective addresses set forth
below:

	 	 	 

	If to Borrower:

	 	If to Agent:
	 
	 	 
	Kior, Inc.

	 	Lighthouse Capital Partners VI, L.P.
	Attention: Chief Financial Officer

	 	Attention: Contract Administrator
	13001 Bay Park Road

	 	 3555 Alameda de las Pulgas, Suite 200 
	Pasadena, Texas 77507

	 	Menlo Park, California 94025
	FAX: (281) 694-8799

	 	FAX: (650) 233-0114
	 
	 	 
	If to any Lender, to the address set forth on Schedule A hereto.
	 	 

12. General Provisions

10

 

12.1 Successors and Assigns. This Agreement shall bind and inure to the benefit of the parties’
respective successors and permitted assigns. Borrower may not assign any rights hereunder without
Agent’s prior written consent, which consent may be granted or withheld in Agent’s sole discretion.
Each Lender shall have the right without the consent of or notice to Borrower to sell, transfer,
negotiate, or grant participations in all or any part of any Loan Document, except for any such
sale, transfer, negotiation or grant of a participation to a competitor of Borrower or any of its
Subsidiaries.

12.2 Time of Essence. Time is of the essence for the performance of all Obligations.

12.3 Severability of Provisions. Each provision hereof shall be severable from every other
provision in determining its legal enforceability.

12.4 Entire Agreement. This Agreement and each of the other Loan Documents dated as of the date
hereof, taken together, constitute and contain the entire agreement between Borrower and Lenders
with respect to their subject matter and supersede any and all prior agreements, negotiations,
correspondence, understandings and communications between the parties, whether written or oral.
This Agreement is the result of negotiations between and has been reviewed by the Borrower and
Lenders as of the date hereof and their respective counsel; accordingly, this Agreement shall be
deemed to be the product of the parties hereto, and no ambiguity shall be construed in favor of or
against Borrower or Lender. The provision of any Loan Document may be modified, amended or waived
only by a written instrument signed by the parties thereto. Any waiver or consent with respect to
any provision of the Loan Documents shall be effective only in the specific instance and for the
specific purpose for which it was given. No notice to or demand on Borrower in any one case shall
entitle Borrower to any other or further notice or demand in similar or other circumstances.

12.5 Reliance by Lenders. All covenants, agreements, representations and warranties made herein by
Borrower shall, notwithstanding any investigation by any Lender, be deemed to be material to and to
have been relied upon by each Lender.

12.6 No Set-Offs by Borrower. All sums payable by Borrower pursuant to this Agreement or any of
the other Loan Documents shall be payable without notice or demand and shall be payable in United
States Dollars without set-off or reduction of any manner whatsoever.

12.7 Counterparts. This Agreement may be executed in any number of counterparts, each of which
shall be deemed to be an original, and all of which, when taken together, shall constitute one and
the same original instrument.

12.8 Survival. All covenants, representations and warranties made in this Agreement shall continue
in full force and effect so long as any Obligations remain outstanding.

12.9 No Original Issue Discount. Borrower and Lenders acknowledge and agree that the Warrant is
part of an investment unit within the meaning of Section 1273(c)(2) of the Internal Revenue Code,
which includes the Loan. Borrower and Lenders further agree as between them, that the fair market
value of each Warrant is $100 and that, pursuant to Treas. Reg. § 1.1273-2(h), $100 of the issue
price of the investment unit will be allocable to the Warrant and the balance shall be allocable to
the Loans. Borrower and Lenders agree to prepare their respective federal income tax returns in a
manner consistent with the foregoing and, pursuant to Treas. Reg. § 1.1273, the original issue
discount on the Loan shall be considered to be zero.

12.10 Relationship of Parties. The relationship between Borrower and each Lender is, and at all
times shall remain, solely that of a borrower and lender. No Lender is a partner or joint venturer
of Borrower; nor shall any Lender under any circumstances be deemed to be in a relationship of
confidence or trust or have a fiduciary relationship with Borrower or any of its affiliates, or to
owe any fiduciary duty to Borrower or any of its affiliates. No Lender undertakes or assumes any
responsibility or duty to Borrower or any of its affiliates to select, review, inspect, supervise,
pass judgment upon or otherwise inform any of them of any matter in connection with its or their
property, the Loans, any Collateral or the operations of Borrower or any of its affiliates.
Borrower and each of its affiliates shall rely entirely on their own judgment with respect to such
matters, and any review, inspection, supervision, exercise of judgment or supply of information
undertaken or assumed by any Lender in connection with such matters is solely for the protection of
such Lender and neither Borrower nor any affiliate is entitled to rely thereon.

12.11 Choice of Law and Venue; Jury Trial Waiver. This Agreement shall be governed by and
construed in accordance with, the internal laws of the State of California, without regard to
principles of conflicts of law. Each of Borrower and Lender hereby submits to the exclusive
jurisdiction and venue of the State and Federal courts located in the City and County of San
Francisco, State of California. Borrower and Each Lender hereby waive their respective rights to a
jury trial of any claim or cause of action based upon or arising out of any of the Loan Documents
or any of the transactions contemplated therein, including contract claims, tort claims, breach of
duty claims, and all other common law or statutory claims. Each party further waives any right to
consolidate any action in which a jury trial has been waived with any other action in which a jury
trial cannot be or has not been waived.

11

 

In Witness Whereof, the parties hereto have executed this Agreement as of the date first
above written.

	 	 	 	 	 	 	 	 	 

	Borrower:	 	Agent:	 	 
	 
	 	 	 	 	 	 	 	 
	Kior, Inc.	 	Lighthouse Capital Partners VI, L.P.	 	 
	 

	 	 	 	By:
	 	Lighthouse Management Partners VI, L.L.C.,

its general partner	 	 
	 
	 	 	 	 	 	 	 	 
	By:

	 	     /s/ Fred Cannon
 

	 	By:
	 	     ./s/ Christy Barnes
 

	 	 
	 
	 	 	 	 	 	 	 	 
	Name:

	 	     Fred Cannon
 

	 	Name:
	 	     Christy Barnes
 

	 	 
	 
	 	 	 	 	 	 	 	 
	Title:

	 	     Pres.
 

	 	Title:
	 	     Managing Director
 

	 	 
	 
	 	 	 	 	 	 	 	 
	Lenders:	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	LEADER LENDING, LLC — SERIES A	 	LEADER LENDING, LLC — SERIES B	 	 
	 
	 	 	 	 	 	 	 	 
	By:

	 	     /s/ Robert W. Molke
 

	 	By:
	 	     /s/ Robert W. Molke
 

	 	 
	 
	 	 	 	 	 	 	 	 
	Name:

	 	     Robert W. Molke
 

	 	Name:
	 	     Robert W. Molke
 

	 	 
	 
	 	 	 	 	 	 	 	 
	Title:

	 	     Managing Director
 

	 	Title:
	 	     Managing Director
 

	 	 

	 	 	 	 	 

	Lighthouse Capital Partners VI, L.P.	 	 
	By:

	 	Lighthouse Management Partners VI, L.L.C.,

its general partner	 	 
	By:
	 	 	 	 
	 

	 	 

	 	 
	 
	 	 	 	 
	Name:
	 	 	 	 
	 

	 	 

	 	 
	 
	 	 	 	 
	Title:
	 	 	 	 
	 

	 	 

	 	 

	 	 	 

	Schedule A

	 	Lenders (Name, Address and Percentage Interests)
	 
	 	 
	Exhibit A

	 	Collateral Description
	Exhibit B

	 	Form of Note
	Exhibit C

	 	Form of Preferred Stock Warrant
	Exhibit C-1

	 	Form of Tranche 2 Warrant
	Exhibit D

	 	Form of Notice of Borrowing
	Exhibit E

	 	Form of Incumbency Certificate
	Exhibit F

	 	Form of Officers Certificate
	Exhibit G

	 	ACH Authorization
	Exhibit H

	 	Form of Negative Pledge Agreement
	Exhibit I

	 	Control Agreement
	 
	 	 
	Schedule 1

	 	Disclosure Schedule

12

 

Schedule A

Lenders

	 	 	 	 	 

	Lighthouse Capital Partners VI, L.P. :

	 	 	70	%
	 
	 	 	 	 
	3555 Alameda de las Pulgas, Suite 200
	 	 	 	 
	Menlo Park, CA 94025
	 	 	 	 
	Attn: Contracts Administration
	 	 	 	 
	FAX: (650) 233-0114
	 	 	 	 
	 
	 	 	 	 
	Leader Lending, LLC — Series A :

	 	 	15	%
	 
	 	 	 	 
	311 California Street, Suite 420
	 	 	 	 
	San Francisco, CA 94104
	 	 	 	 
	Attn: Chief Financial Officer
	 	 	 	 
	FAX: (415) 956-8233
	 	 	 	 
	 
	 	 	 	 
	Leader Lending, LLC — Series B :

	 	 	15	%
	 
	 	 	 	 
	311 California Street, Suite 420
	 	 	 	 
	San Francisco, CA 94104
	 	 	 	 
	Attn: Chief Financial Officer
	 	 	 	 
	FAX: (415) 956-8233
	 	 	 	 
	 
	 	 	 	 
	Total

	 	 	100	%

13

 

Exhibit A

Collateral

This FINANCING STATEMENT and SECURITY AGREEMENT covers all of Debtor’s interests in all of the
following types or items of property, wherever located and whether now owned or hereafter acquired,
and Debtor hereby grants Secured Party a security interest therein as collateral for the payment
and performance of all present and future indebtedness, liabilities, guarantees and obligations of
Debtor to Secured Party, howsoever arising. Debtor agrees that said security interest may be
enforced by Secured Party in accordance with the terms of all security and other agreements between
Secured Party and Debtor, the California Uniform Commercial Code, or both, and that this document
shall be fully effective as a security agreement, even if there is no other security or other
agreement between Secured Party or Debtor:

All assets of the Debtor; all personal property of Debtor;

All “accounts”, “general intangibles”, “chattel paper”, “contract rights”, “documents”,
“instruments”, “deposit accounts”, “inventory”, “farm products”, “fixtures” and “equipment”, as
such terms are defined in Division 9 of the California Uniform Commercial Code in effect on the
date hereof;

All general intangibles of every kind, including without limitation, federal, state and local tax
refunds and claims of all kinds; all rights as a licensee or any kind; all customer lists,
telephone numbers, and purchase orders, and all rights to purchase, lease sell, or otherwise
acquire or deal with real or personal property and all rights relating thereto;

All returned and repossessed goods and all rights as a seller of goods; all collateral securing any
of the foregoing; all deposit accounts, special and general, whether on deposit with Secured Party
or others;

All life and other insurance policies, claims in contract, tort or otherwise, and all judgments now
or hereafter arising therefrom;

All right, title and interest of Debtor, and all of Debtor’s rights, remedies, security and liens,
in, to and in respect of all accounts and other collateral, including, without limitation, rights
of stoppage in transit, replevin, repossession and reclamation and other rights and remedies of an
unpaid vendor, lienor or secured party, and all guarantees and other contracts of suretyship with
respect to any accounts and other collateral, and all deposits and other security for any accounts
and other collateral, and all credit and other insurance;

All notes, drafts, letters of credit, contract rights, and things in action; all drawings,
specifications, blueprints and catalogs; and all raw materials, work in process, materials used or
consumed in Debtor’s business, goods, finished goods, returned goods and all other goods and
inventory of whatsoever kind or nature, any and all wrapping, packaging, advertising and shipping
materials, and all documents relating thereto, and all labels and other devices, names and marks
affixed or to be affixed thereto for purposes of selling or identifying the same or the seller or
manufacturer thereof;

All inventory, raw materials and work in progress wherever located; all present and future claims
against any supplier of any of the foregoing, including claims for defective goods or overpayments
to or undershipments by suppliers; all proceeds arising from the lease or rental of any of the
foregoing; INVENTORY RETURNED BY DEBTOR TO ITS SUPPLIERS SHALL REMAIN SUBJECT TO SECURED
PARTY’S SECURITY INTEREST; 

All equipment and fixtures, NONE OF WHICH THE DEBTOR IS AUTHORIZED TO SELL, LEASE OR OTHERWISE
DISPOSE OF WITHOUT THE WRITTEN CONSENT OF SECURED PARTY OR EXCEPT IN ACCORDANCE WITH THE TERMS OF
THE LOAN AGREEMENT, including without limitation all machinery, machine tools, motors, controls,
parts, vehicles, workstations, tools, dies, jigs, furniture, furnishings and fixtures; and all
attachments, accessories, accessions and property now or hereafter affixed to or used in connection
with any of the foregoing, and all substitutions and replacements for any of the foregoing; all
warranty and other claims against any vendor or lessor of any of the foregoing;

All investment property;

All books, records, ledger cards, computer data and programs and other property and general
intangibles at any time evidencing or relating to any or all of the foregoing; and

All cash and non-cash products and proceeds of any of the foregoing, in whatever form, including
proceeds in the form of inventory, equipment or any other form of personal property, including
proceeds of proceeds and proceeds of insurance, and all claims by Debtor against third parties for
loss or damage to, or destruction of, or otherwise relating to, any or all of the foregoing.

1

 

NOTICE — PURSUANT TO AN AGREEMENT BETWEEN DEBTOR AND SECURED PARTY, DEBTOR HAS AGREED NOT TO
FURTHER ENCUMBER THE COLLATERAL DESCRIBED HEREIN, THE FURTHER ENCUMBERING OF WHICH MAY CONSTITUTE
THE TORTIOUS INTERFERENCE WITH SECURED PARTY’S RIGHTS BY SUCH ENCUMBRANCER. IN THE EVENT THAT ANY
ENTITY IS GRANTED A SECURITY INTEREST IN DEBTOR’S ACCOUNTS, CHATTEL PAPER, GENERAL INTANGIBLES OR
OTHER ASSETS CONTRARY TO THE ABOVE, THE SECURED PARTY ASSERTS A CLAIM TO ANY PROCEEDS THEREOF
RECEIVED BY SUCH ENTITY.

Notwithstanding any of the foregoing, this Financing Statement and Security Agreement does not
cover any of Debtor’s interests in, and the Collateral shall not under any circumstance include,
and no security interest is granted in, Debtor’s Intellectual Property, including, without
limitation, any and all property of the Debtor that is subject to, listed in or otherwise described
in the Negative Pledge Agreement dated December __, 2009 between the Secured Party and the Debtor.
“Intellectual Property” means, collectively, all rights, priorities and privileges of the Debtor
relating to intellectual property, in any medium, of any kind or nature whatsoever, now or
hereafter owned or acquired or received by Debtor, or in which Debtor now holds or hereafter
acquires or receives any right or interest, whether arising under United States, multinational or
foreign laws or otherwise, and shall include, in any event, all copyrights, copyright licenses,
patents, patent licenses, trademarks, trademark licenses, trade secrets, internet domain names
(including any right related to the registration thereof), proprietary or confidential information,
mask works, sources object or other programming codes, inventions (whether or not patented or
patentable), technical information, procedures, designs, knowledge, know-how, software, data base,
data, skill, expertise, recipe, experience, process, models, drawings, materials or records.
Notwithstanding the foregoing, Intellectual Property as defined above does not include accounts,
accounts receivable, royalties, licensing fees, contract rights, proceeds, or other revenue
obtained or owed from or on account of the licensing or other exploitation of Intellectual
Property, none of which are excluded, and all of which are included as collateral in the security
interest granted by Debtor to Secured Party. Notwithstanding the foregoing, Collateral shall not
include any Eligible Equipment financed under (and as defined under) the Lighthouse Equipment Loan,
but only for so long as the Obligations under the Lighthouse Equipment Loan are outstanding.

	 	 	 	 	 	 	 	 	 

	“Debtor"	 	 	 	“Secured Party”, Agent on Behalf of the Lenders
	 
	 	 	 	 	 	 	 	 
	Kior, Inc., a Delaware corporation	 	 	 	Lighthouse Capital Partners VI, L.P.
	 

	 	 	 	 	 	By:
	 	Lighthouse Management Partners VI, L.L.C.,
	 

	 	 	 	 	 	 	 	its general partner
	By:
	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	Name:

	 	 	 	 	 	By:	 	 
	 

	 	 
	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	Title:

	 	 	 	 	 	Name:	 	 
	 

	 	 
	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	Title:	 	 
	 

	 	 	 	 	 	 	 	 

2

 

Exhibit B

[__________]

Secured Promissory Note — Tranche 1

This Secured Promissory Note (this “Note”) is made ____________, 200__, by Kior,
Inc. (“Borrower”) in favor of [Lighthouse Capital Partners VI, L.P.][Leader Entity]
(collectively with its assigns, “Lender”). Initially capitalized terms used and not otherwise
defined herein are defined in that certain Loan and Security Agreement No. 1452 between Borrower,
Lighthouse Capital Partners VI, L.P. as Agent, the other lenders party thereto and Lender dated
December __, 2009 (the “Loan Agreement”).

For Value Received, Borrower promises to pay in lawful money of the United States, to the
order of Lender, at [3555 Alameda de las Pulgas, Suite 200, Menlo Park, CA 94025][311 California
Street, Suite 420, San Francisco, CA 94104], or such other place as Lender may from time to time
designate (“Lender’s Office”), the principal sum of $___________ (the “Advance”), including
interest on the unpaid balance and all other amounts due or to become due hereunder according to
the terms hereof and of the Loan Agreement.

“Basic Rate” a per annum rate of interest equal to 12%.

“Final Payment” means 7.5% of the Advance.

“Loan Commencement Date” means August 1, 2010.

“Maturity Date” means the last day of the Repayment Period, or if earlier, the date of prepayment
under the Note.

“Payment Date” means the first day of each calendar month.

“Prepayment Fee” means (i) 3% of the outstanding principal amount being prepaid for any prepayment
made on or before December 31, 2011; (ii) 2% of the outstanding principal amount being prepaid for
any prepayment made during calendar year 2012; and (iii) 1% of the outstanding principal amount
being prepaid for any prepayment made during calendar year 2013 or thereafter.

“Repayment Period” means the period beginning on the Loan Commencement Date and continuing for 33
calendar months.

1. Repayment. Borrower shall pay principal and interest due hereunder from the Funding Date, until
this Note is paid in full, on each Payment Date pursuant to the terms of the Loan Agreement and
this Note. Prior to the Loan Commencement Date, Borrower shall pay to Lender, monthly in advance
on each Payment Date, interest calculated using the Basic Rate. Beginning on the Loan Commencement
Date and on each Payment Date thereafter during the Repayment Period, Borrower shall make equal
installments of principal and interest in advance, calculated at the Basic Rate. On the Maturity
Date, Borrower shall pay, in addition to all unpaid principal and interest outstanding hereunder,
the Final Payment.

2. Interest. Interest not paid when due will, to the maximum extent permitted under applicable
law, become part of principal, at Lender’s option, and thereafter bear like interest as principal.
All interest computation shall be based on a 360-day year and actual days elapsed prior to the Loan
Commencement Date and on a 360-day year and 30 day month on and after the Loan Commencement
Date. All Obligations not paid when due shall bear interest at the Default Rate unless
waived in writing by Lender. All amounts paid hereunder will be applied to the Obligations in
Lender’s discretion and as provided in the Loan Agreement.

3. Voluntary Prepayment. Borrower may prepay the Note if and only if Borrower pays to Lender (i)
the outstanding principal amount of this Note and any unpaid accrued interest; (ii) the Final
Payment; (iii) the Prepayment Fee, if applicable; and (iv) all other sums, if any, that shall have
become due and payable hereunder with respect to this Note.

4. Collateral. This Note is secured by the Collateral.

5. Waivers. Borrower, and all guarantors and endorsers of this Note, regardless of the time, order
or place of signing, hereby waive notice, demand, presentment, protest, and notices of every kind,
presentment for the purpose of accelerating maturity, diligence in collection, and, to the fullest
extent permitted by law, all rights to plead any statute of limitations as a defense to any action
on this Note.

6. Choice of Law; Venue. This Note shall be governed by, and construed in accordance with the
internal laws of the State of California, without regard to principles of conflicts of law. Each
of Borrower and

1

 

Lender hereby submits to the exclusive jurisdiction and venue of the State and
Federal courts located in the 
City and County of San Francisco, State of California. Borrower and Lender each hereby waive
their respective rights to a jury trial of any claim or cause of action based upon or arising out
of this Note. Each party further waives any right to consolidate any action in which a jury trial
has been waived with any other action in which a jury trial cannot be or has not been waived.

7. Miscellaneous. This Note may be modified only by a writing signed by Borrower and
Lender. Each provision hereof is severable from every other provision hereof and of the Loan
Agreement when determining its legal enforceability. Sections and subsections are titled for
convenience, and not for construction. “Hereof,” “herein,” “hereunder,” and similar words refer to
this Note in its entirety. “Or” is not necessarily exclusive. “Including” is not limiting. The
terms and conditions hereof inure to the benefit of and are binding upon the parties’ respective
permitted successors and assigns. This Note is subject to all the terms and conditions of the Loan
Agreement.

In Witness Whereof, Borrower has caused this Note to be executed by a duly authorized
officer as of the day and year first above written.

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Name:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 

	 	 

2

 

[__________]

Secured Promissory Note — Tranche 2

This Secured Promissory Note (this “Note”) is made ____________, 200__, by Kior,
Inc. (“Borrower”) in favor of Lighthouse Capital Partners VI, L.P. [Leader
Entity] (collectively with its assigns, “Lender”). Initially capitalized terms used and not
otherwise defined herein are defined in that certain Loan and Security Agreement No. 1452 between
Borrower, Lighthouse Capital Partners VI, L.P. as Agent, the other lenders party thereto and Lender
dated _______ (the “Loan Agreement”).

For Value Received, Borrower promises to pay in lawful money of the United States, to the
order of Lender, at [3555 Alameda de las Pulgas, Suite 200, Menlo Park, CA 94025][311 California
Street, Suite 420, San Francisco, CA 94104], or such other place as Lender may from time to time
designate (“Lender’s Office”), the principal sum of $___________ (the “Advance”), including
interest on the unpaid balance and all other amounts due or to become due hereunder according to
the terms hereof and of the Loan Agreement.

“Basic Rate” means (i)14% during the Interest Only Period and (ii) 12% on and after the Loan
Commencement Date

“Final Payment” means 10% of the Advance.

“Interest Only Period” means the period commencing on the date hereof and continuing until the Loan
Commencement Date.

“Loan Commencement Date” means August 1, 2010.

“Maturity Date” means the last day of the Repayment Period, or if earlier, the date of prepayment
under the Note.

“Payment Date” means the first day of each calendar month.

“Prepayment Fee” means (i) 3% of the outstanding principal amount being prepaid for any prepayment
made on or before December 31, 2011; (ii) 2% of the outstanding principal amount being prepaid for
any prepayment made during calendar year 2012; and (iii) 1% of the outstanding principal amount
being prepaid for any prepayment made during calendar year 2013 or thereafter.

“Repayment Period” means the period beginning on the Loan Commencement Date and continuing for 33
calendar months.

1. Repayment. Borrower shall pay principal and interest due hereunder from the Funding Date, until
this Note is paid in full, on each Payment Date pursuant to the terms of the Loan Agreement and
this Note. Prior to the Loan Commencement Date, Borrower shall pay to Lender, monthly in advance
on each Payment Date, interest calculated using the Basic Rate. Beginning on the Loan Commencement
Date and on each Payment Date thereafter during the Repayment Period, Borrower shall make equal
installments of principal and interest in advance, calculated at the Basic Rate. On the Maturity
Date, Borrower shall pay, in addition to all unpaid principal and interest outstanding hereunder,
the Final Payment.

2. Interest. Interest not paid when due will, to the maximum extent permitted under applicable
law, become part of principal, at Lender’s option, and thereafter bear like interest as principal.
All interest computation shall be based on a 360-day year and actual days elapsed prior to the Loan
Commencement Date and on a 360-day year and 30 day month on and after the Loan Commencement
Date. All Obligations not paid when due shall bear interest at the Default Rate unless
waived in writing by Lender. All amounts paid hereunder will be applied to the Obligations in
Lender’s discretion and as provided in the Loan Agreement.

3. Voluntary Prepayment. Borrower may prepay the Note if and only if Borrower pays to Lender (i)
the outstanding principal amount of this Note and any unpaid accrued interest; (ii) the Final
Payment; (iii) the Prepayment Fee, if applicable; and (iv) all other sums, if any, that shall have
become due and payable hereunder with respect to this Note.

4. Collateral. This Note is secured by the Collateral.

5. Waivers. Borrower, and all guarantors and endorsers of this Note, regardless of the time, order
or place of signing, hereby waive notice, demand, presentment, protest, and notices of every kind,
presentment for the purpose of accelerating maturity, diligence in collection, and, to the fullest
extent permitted by law, all rights to plead any statute of limitations as a defense to any action
on this Note.

6. Choice of Law; Venue. This Note shall be governed by, and construed in accordance with the
internal laws of the State of California, without regard to principles of conflicts of law. Each
of Borrower and Lender hereby submits to the exclusive jurisdiction and venue of the State and
Federal courts located in the

3

 

City and County of San Francisco, State of California. Borrower and
Lender each hereby waive their 
respective rights to a jury trial of any claim or cause of action based upon or arising out of
this Note. Each party further waives any right to consolidate any action in which a jury trial has
been waived with any other action in which a jury trial cannot be or has not been waived.

7. Miscellaneous. This Note may be modified only by a writing signed by Borrower and
Lender. Each provision hereof is severable from every other provision hereof and of the Loan
Agreement when determining its legal enforceability. Sections and subsections are titled for
convenience, and not for construction. “Hereof,” “herein,” “hereunder,” and similar words refer to
this Note in its entirety. “Or” is not necessarily exclusive. “Including” is not limiting. The
terms and conditions hereof inure to the benefit of and are binding upon the parties’ respective
permitted successors and assigns. This Note is subject to all the terms and conditions of the Loan
Agreement.

In Witness Whereof, Borrower has caused this Note to be executed by a duly authorized
officer as of the day and year first above written.

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Name:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 

	 	 

4

 

Exhibit c

Warrant

THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “1933
ACT”), OR ANY APPLICABLE STATE SECURITIES LAWS, AND MAY NOT BE SOLD OR TRANSFERRED UNLESS SUCH SALE
OR TRANSFER IS IN ACCORDANCE WITH THE REGISTRATION REQUIREMENTS OF SUCH ACT AND APPLICABLE LAWS OR
SOME OTHER EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF SUCH ACT AND APPLICABLE LAWS IS
AVAILABLE WITH RESPECT THERETO.

PREFERRED STOCK PURCHASE WARRANT

			
	 	 	 
	Warrant No.                                        
	 	Number of Shares: 51,414
	 
	 	Series A-1 Preferred Stock

Kior Inc.

Effective as of December 30, 2008

Void after December 30, 2016

     1. Issuance. This Preferred Stock Purchase Warrant (the “Warrant”) is issued to
Lighthouse Capital Partners VI, L.P. by Kior Inc., a Delaware corporation
(hereinafter with its successors called the “Company”).

     2. Purchase Price; Number of Shares. The registered holder of this Warrant (the “Holder”),
commencing on the date hereof, is entitled upon surrender of this Warrant with the subscription
form annexed hereto duly executed, at the principal office of the Company, to purchase from the
Company, at a price per share of $3.89 (the “Purchase Price”), 51,414 fully paid and nonassessable
shares of the Company’s Series A-1 Preferred Stock, $0.0001 par value (the “Preferred Stock”).

Until such time as this Warrant is exercised in full or expires, the Purchase Price and the
securities issuable upon exercise of this Warrant are subject to adjustment as hereinafter
provided. The person or persons in whose name or names any certificate representing shares of
Preferred Stock is issued hereunder shall be deemed to have become the holder of record of the
shares represented thereby as at the close of business on the date this Warrant is exercised with
respect to such shares, whether or not the transfer books of the Company shall be closed.

     3. Payment of Purchase Price. The Purchase Price may be paid (i) in cash or by check, (ii) by
the surrender by the Holder to the Company of any promissory notes or other obligations issued by
the Company, with all such notes and obligations so surrendered being credited against the Purchase
Price in an amount equal to the principal amount thereof plus accrued interest to the date of
surrender, or (iii) by any combination of the foregoing.

     4. Net Issue Election. The Holder may elect to receive, without the payment by the Holder of
any additional consideration, shares of Preferred Stock equal to the value of this Warrant or any
portion hereof by the surrender of this Warrant or such portion to the Company, with the net issue
election notice annexed hereto duly executed, at the principal office of the Company. Thereupon,
the Company shall issue to the Holder such number of fully paid and nonassessable shares of
Preferred Stock as is computed using the following formula:

1.

 

X=Y(A-B)

 A

	 	 	 	 	 

	where:

	 	X =
	 	the number of shares of Preferred Stock to be issued to the Holder pursuant to
this Section 4.
	 
	 	 	 	 
	 

	 	Y =
	 	the number of shares of Preferred Stock covered by this
Warrant in respect of which the net issue election is made pursuant to this
Section 4.
	 
	 	 	 	 
	 

	 	A =
	 	the Fair Market Value (defined below) of one share of
Preferred Stock, as determined at the time the net issue election is made
pursuant to this Section 4.
	 
	 	 	 	 
	 

	 	B =
	 	the Purchase Price in effect under this Warrant at the time
the net issue election is made pursuant to this Section 4.

          “Fair Market Value” of a share of Preferred Stock (or fully paid and nonassessable shares of
the Company’s common stock, $0.0001 par value (the “Common Stock”) if the Preferred Stock has been
automatically converted into Common Stock) as of the date that the net issue election is made (the
“Determination Date”) shall mean:

          (i) If the net issue election is made in connection with and contingent upon the closing of
the sale of the Company’s Common Stock to the public in a public offering pursuant to a
Registration Statement under the 1933 Act (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 Public” specified in the
final prospectus with respect to such offering multiplied by the number of shares of Common Stock
into which each share of Preferred Stock is then convertible.

          (ii) If the net issue election is not made in connection with and contingent upon a Public
Offering, then as follows:

               (a) If traded on a securities exchange or NASDAQ market or system, the fair market value of
the Common Stock shall be deemed to be the average of the closing or last reported sale prices of
the Common Stock on such exchange or market over the five day period ending five trading days prior
to the Determination Date, and the fair market value of the Preferred Stock shall be deemed to be
such fair market value of the Common Stock multiplied by the number of shares of Common Stock into
which each share of Preferred Stock is then convertible;

               (b) If otherwise traded in an over-the-counter market, the fair market value of the Common
Stock shall be deemed to be the average of the closing ask prices of the Common Stock over the five
day period ending five trading days prior to the Determination Date, and the fair market value of
the Preferred Stock shall be deemed to be such fair market value of the Common Stock multiplied by
the number of shares of Common Stock into which each share of Preferred Stock is then convertible;
and

               (c) If there is no public market for the Common Stock, then fair market value shall be
determined in good faith by the Company’s Board of Directors.

     5. Partial Exercise. This Warrant may be exercised in part, and the Holder shall be entitled
to receive a new warrant, which shall be dated as of the date of this Warrant, covering the number
of shares in respect of which this Warrant shall not have been exercised.

     6. Fractional Shares. In no event shall any fractional share of Preferred Stock be issued
upon any exercise of this Warrant. If, upon exercise of this Warrant in its entirety, the Holder
would, except as provided in

2.

 

this Section 6, be entitled to receive a fractional share of Preferred Stock, then the Company
shall issue the next higher number of full shares of Preferred Stock, issuing a full share with
respect to such fractional share.

          7. Expiration Date; Automatic Exercise. This Warrant shall expire at the earliest to occur of
(the “Expiration Date”) (i) at the close of business on December 30, 2016; (ii) two years after the
closing of the initial Public Offering; of the Company on the NASDAQ or other stock exchange in the
United States, and shall be void thereafter.

     Notwithstanding the term of this Warrant fixed pursuant to this Section 7, and provided Holder
has received advance written notice of at least twenty (20) days and has not earlier exercised this
Warrant, and provided this Warrant has not been assumed by the successor entity (or parent
thereof), upon the consummation of a Merger (as defined below), this Warrant shall automatically be
exercised pursuant to Section 4 hereof, without any action by Holder. “Merger” means: (i) a sale
of all or substantially all of the Company’s assets to an Unaffiliated Entity (as defined below),
or (ii) the merger, consolidation or acquisition of the Company with, into or by an Unaffiliated
Entity (other than a merger or consolidation for the principle purpose of changing the domicile of
the Company or a bona fide round of preferred stock equity financing), that results in the transfer
of fifty percent (50%) or more of the outstanding voting power of the Company. “Unaffiliated
Entity” means any entity that is owned or controlled by parties who own less than twenty percent
(20%) of the combined voting power of the voting securities of the Company immediately prior to
such merger, consolidation or acquisition. Notwithstanding the foregoing, in the event that any
outstanding warrants to purchase equity securities of the Company are assumed by the successor
entity of a Merger (or parent thereof), this Warrant shall also be similarly assumed. The Company
agrees to promptly give the Holder written notice of any proposed Merger and written notice of
termination of any proposed Merger. Notwithstanding anything to the contrary in this Warrant, the
Holder may rescind any exercise of its purchase rights after a notice of termination of the
proposed Merger if the exercise of this Warrant occurred after the Company notified the Holder that
the Merger was proposed or if the exercise was otherwise precipitated by such proposed Merger,
provided, however that such rescission right must be exercised within thirty (30) days of receipt
of such written notice of termination of the proposed Merger. In the event of such rescission,
this Warrant will continue to be exercisable on the same terms and conditions.

     8. Reserved Shares; Valid Issuance. The Company covenants that it will at all times from and
after the date hereof reserve and keep available such number of its authorized shares of Preferred
Stock and Common Stock free from all preemptive or similar rights therein, as will be sufficient to
permit, respectively, the exercise of this Warrant in full and the conversion into shares of Common
Stock of all shares of Preferred Stock receivable upon such exercise. The Company further
covenants that such shares as may be issued pursuant to such exercise and/or conversion will, upon
issuance, be duly and validly issued, fully paid and nonassessable and free from all taxes, liens
and charges with respect to the issuance thereof.

     9. Stock Splits and Dividends. If after the date hereof the Company shall subdivide the
Preferred Stock, by split-up or otherwise, or combine the Preferred Stock, or issue additional
shares of Preferred Stock in payment of a stock dividend on the Preferred Stock, the number of
shares of Preferred Stock issuable on the exercise of this Warrant shall forthwith be
proportionately increased in the case of a subdivision or stock dividend, or proportionately
decreased in the case of a combination, and the Purchase Price shall forthwith be proportionately
decreased in the case of a subdivision or stock dividend, or proportionately increased in the case
of a combination.

     10. Adjustments for Diluting Issuances. The other antidilution rights applicable to the
Preferred Stock and the Common Stock of the Company are set forth in the Amended and Restated
Certificate of Incorporation, as amended from time to time (the “Articles”), a true and complete
copy in its current form which is attached hereto as Exhibit A. Such rights shall not be restated,
amended or modified in any manner which affects the Holder differently than the holders of
Preferred Stock without such Holder’s prior written consent. The Company shall promptly provide
the Holder hereof with any restatement, amendment or modification to the Articles promptly after
the same has been made.

     11. Mergers and Reclassifications. If after the date hereof the Company shall enter into any
Reorganization (as hereinafter defined), then, as a condition of such Reorganization, lawful
provisions shall be

3.

 

made, and duly executed documents evidencing the same from the Company or its successor shall
be delivered to the Holder, so that the Holder shall thereafter have the right to purchase, at a
total price not to exceed that payable upon the exercise of this Warrant in full, the kind and
amount of shares of stock and other securities and property receivable upon such Reorganization by
a holder of the number of shares of Preferred Stock which might have been purchased by the Holder
immediately prior to such Reorganization, and in any such case appropriate provisions shall be made
with respect to the rights and interest of the Holder to the end that the provisions hereof
(including without limitation, provisions for the adjustment of the Purchase Price and the number
of shares issuable hereunder and the provisions relating to the net issue election) shall
thereafter be applicable in relation to any shares of stock or other securities and property
thereafter deliverable upon exercise hereof. For the purposes of this Section 11, the term
“Reorganization” shall include without limitation any reclassification, capital reorganization or
change of the Preferred Stock (other than as a result of a subdivision, combination or stock
dividend provided for in Section 9 hereof), or any consolidation of the Company with, or merger of
the Company into, another corporation or other business organization (other than a merger in which
the Company is the surviving corporation and which does not result in any reclassification or
change of the outstanding Preferred Stock), or any sale or conveyance to another corporation or
other business organization of all or substantially all of the assets of the Company.

     12. Certificate of Adjustment. Whenever the Purchase Price is adjusted, as herein provided,
the Company shall promptly deliver to the Holder a certificate of the Company’s chief financial
officer setting forth the Purchase Price after such adjustment and setting forth a brief statement
of the facts requiring such adjustment.

     13. Notices of Record Date, Etc. In the event of:

          (a) 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 or other
distribution, or any right to subscribe for, purchase, sell or otherwise acquire or dispose of any
shares of stock of any class or any other securities or property, or to receive any other right;

          (b) any reclassification of the capital stock of the Company, capital reorganization of the
Company, consolidation or merger involving the Company, or sale or conveyance of all or
substantially all of its assets; or

          (c) any voluntary or involuntary dissolution, liquidation or winding-up of the Company;

then in each such event the Company will provide or cause to be provided to the Holder a written
notice thereof. Such notice shall be provided at least twenty (20) business days prior to the date
specified in such notice on which any such action is to be taken.

     14. Representations, Warranties and Covenants. This Warrant is issued and delivered by the
Company and accepted by each Holder on the basis of the following representations, warranties and
covenants made by the Company:

          (a) The Company has all necessary authority to issue, execute and deliver this Warrant and to
perform its obligations hereunder. This Warrant has been duly authorized issued, executed and
delivered by the Company and is the valid and binding obligation of the Company, enforceable in
accordance with its terms.

          (b) The shares of Preferred Stock issuable upon the exercise of this Warrant 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.

          (c) The issuance, execution and delivery of this Warrant do not, and the issuance of the
shares of Preferred Stock upon the exercise of this Warrant in accordance with the terms hereof
will not, (i) violate or contravene the Company’s Articles or by-laws, or any law, statute,
regulation, rule, judgment or order applicable to the Company, (ii) violate, contravene or result
in a breach or default under any contract, agreement or instrument

4.

 

to which the Company is a party or by which the Company or any of its assets are bound or
(iii) require the consent or approval of or the filing of any notice or registration with any
person or entity.

          (d) As long as this Warrant is, or any shares of Preferred Stock issued upon exercise of this
Warrant or any shares of Common Stock issued upon conversion of such shares of Preferred Stock are,
issued and outstanding, the Company will provide to the Holder the financial and other information
described in that certain Loan and Security Agreement No. 1451 between the Company and Lighthouse
Capital Partners VI, L.P. dated as December 30, 2008.

          (e) So long as this Warrant has not terminated, Holder shall be entitled to receive such
financial and other information as the Holder would be entitled to receive under the Stock Purchase
Agreement applicable to the Preferred Stock if Holder were a holder of that number of shares
issuable upon full exercise of this Warrant.

          (f) As of the date hereof, the authorized capital stock of the Company consists of (i)
8,700,000 shares of Common Stock, $0.001 par value, of which 1,800,000 shares are issued and
outstanding and 51,414 shares are reserved for issuance upon the exercise of this Warrant with
respect to Common Stock and the conversion of the Preferred Stock into Common Stock if this Warrant
is exercised with respect to Preferred Stock, (ii) 3,000,000 shares of Series A Preferred Stock, of
which 3,000,000 are issued and outstanding shares, and (iii) 2,700,000 shares of Series A-1
Preferred Stock, of which 2,571,447 are issued and outstanding shares. Attached hereto as Exhibit
B is a capitalization table summarizing the capitalization of the Company. Once per calendar
quarter, the Company will provide Holder with a current capitalization table indicating changes, if
any, to the number of outstanding shares of common stock and preferred stock.

     15. Registration Rights. Concurrently with the issuance hereof, the Company shall deliver an
amendment to the Amended and Restated Investors’ Rights Agreement, dated as of June 16, 2008, among
the Company and the Investors and Key Holders party thereto (the “Investors’ Rights Agreement”),
substantially in the form attached as Exhibit C hereto, duly executed and delivered by the Company
and a majority of holder of Registrable Securities (as defined in the Investors’ Rights Agreement).

     16. Amendment. The terms of this Warrant may be amended, modified or waived only with the
written consent of the Holder.

     17. Representations and Covenants of the Holder. This Warrant has been entered into by the
Company in reliance upon the following representations and covenants of the Holder, which by its
execution hereof the Holder hereby confirms:

          (a) Investment Purpose. The right to acquire Preferred Stock or the Preferred Stock issuable
upon exercise of the Holder’s rights contained herein will be acquired for investment and not with
a view to the sale or distribution of any part thereof, and the Holder has no present intention of
selling or engaging in any public distribution of the same except pursuant to a registration or
exemption.

          (b) Accredited Investor. Holder is an “accredited investor” within the meaning of the
Securities and Exchange Rule 501 of Regulation D, as presently in effect.

          (c) Private Issue. The Holder understands (i) that the Preferred Stock issuable upon exercise
of the Holder’s rights contained herein is not registered under the 1933 Act or qualified under
applicable state securities laws on the ground that the issuance contemplated by this Warrant will
be exempt from the registration and qualifications requirements thereof, and (ii) that the
Company’s reliance on such exemption is predicated on the representations set forth in this Section
17.

          (d) Financial Risk. The Holder has such knowledge and experience in financial and business
matters as to be capable of evaluating the merits and risks of its investment and has the ability
to bear the economic risks of its investment.

5.

 

     18. Notices, Transfers, Etc.

          (a) Any notice or written communication required or permitted to be given to the Holder may be
given by certified mail or delivered to the Holder at the address most recently provided by the
Holder to the Company.

          (b) Subject to compliance with applicable federal and state securities laws, this Warrant may
be transferred by the Holder with respect to any or all of the shares purchasable hereunder. Upon
surrender of this Warrant to the Company, together with the assignment notice annexed hereto duly
executed, for transfer of this Warrant as an entirety by the Holder, the Company shall issue a new
warrant of the same denomination to the assignee. Upon surrender of this Warrant to the Company,
together with the assignment hereof properly endorsed, by the Holder for transfer with respect to a
portion of the shares of Preferred Stock purchasable hereunder, the Company shall issue a new
warrant to the assignee, in such denomination as shall be requested by the Holder hereof, and shall
issue to such Holder a new warrant covering the number of shares in respect of which this Warrant
shall not have been transferred.

     (c) In case this Warrant shall be mutilated, lost, stolen or destroyed, the Company shall
issue a new warrant of like tenor and denomination and deliver the same (i) in exchange and
substitution for and upon surrender and cancellation of any mutilated Warrant, or (ii) in lieu of
any Warrant lost, stolen or destroyed, upon receipt of an affidavit of the Holder or other evidence
reasonably satisfactory to the Company of the loss, theft or destruction of such Warrant

     19. No Impairment. The Company will not, by amendment of its Articles or through any
reclassification, capital reorganization, consolidation, merger, sale or conveyance of assets,
dissolution, liquidation, issue or sale of securities or any other voluntary action, avoid or seek
to avoid the observance of performance of any of the terms of this Warrant, but 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.

     20. Governing Law. The provisions and terms of this Warrant shall be governed by and
construed in accordance with the internal laws of the State of California without giving effect to
its principles regarding conflicts of laws.

     21. Successors and Assigns. This Warrant shall be binding upon the Company’s successors and
assigns and shall inure to the benefit of the Holder’s successors, legal representatives and
permitted assigns.

     22. Business Days. If the last or appointed day for the taking of any action required or the
expiration of any rights granted herein shall be a Saturday or Sunday or a legal holiday in
California, then such action may be taken or right may be exercised on the next succeeding day
which is not a Saturday or Sunday or such a legal holiday.

     23. Qualifying Public Offering. If the Company shall effect a firm commitment underwritten
public offering of shares of Common Stock which results in the conversion of the Preferred Stock
into Common Stock pursuant to the Company’s Articles in effect immediately prior to such offering,
then, effective upon such conversion, this Warrant shall change from the right to purchase shares
of Preferred Stock to the right to purchase shares of Common Stock, and the Holder shall thereupon
have the right to purchase, at a total price equal to that payable upon the exercise of this
Warrant in full, the number of shares of Common Stock which would have been receivable by the
Holder upon the exercise of this Warrant for shares of Preferred Stock immediately prior to such
conversion of such shares of Preferred Stock into shares of Common Stock, and in such event
appropriate provisions shall be made with respect to the rights and interest of the Holder to the
end that the provisions hereof (including, without limitation, the provisions for the adjustment of
the Purchase Price and of the number of shares purchasable upon exercise of this Warrant and the
provisions relating to the net issue election) shall thereafter be applicable to any shares of
Common Stock deliverable upon the exercise hereof.

6.

 

     24. Value. The Company and the Holder agree that the value of this Warrant on the date of
grant is $100.

	 	 	 	 	 	 	 

	 	 	Kior Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:

Name:
	 	/s/ Fred Cannon
 

Fred Cannon
	 	 
	 

	 	Title:
	 	President	 	 

7.

 

Subscription

To:                                                                       
         

Date:                                                                  
           

The undersigned hereby subscribes for _________________ shares of Preferred Stock covered by this
Warrant. The certificate(s) for such shares shall be issued in the name of the undersigned or as
otherwise indicated below:

	 	 	 

	 

Signature

	 	 
	 
	 
	 	 
	 

Name for Registration

	 	 
	 
	 
	 	 
	 

Mailing Address

	 	 

1.

 

Net Issue Election Notice

			
	 	 	 
	To:                                                                  
           
	 	Date:                                                                  
           

The undersigned hereby elects under Section 4 to surrender the right to purchase shares of
Preferred Stock pursuant to this Warrant. The certificate(s) for such shares issuable upon such
net issue election shall be issued in the name of the undersigned or as otherwise indicated below:

	 	 	 

	 

Signature

	 	 
	 
	 
	 	 
	 

Name for Registration

	 	 
	 
	 
	 	 
	 

Mailing Address

	 	 

1.

 

Assignment

For value received ___________________________________________________________ hereby sells, assigns and transfers unto

      

      

[Please print or typewrite name and address of Assignee]

      

the within Warrant, and does hereby irrevocably constitute and appoint ________________________ its
attorney to transfer the within Warrant on the books of the within named Company with full power of
substitution on the premises.

	 	 	 	 	 

	Dated:

	 	 

	 	
	 
	 
	 	 	 	 
	 	 	 
	Signature	 	 
	 
	 
	 	 	 	 
	 	 	 
	Name for Registration	 	 
	 
	 	 	 	 
	In the Presence of:	 	 
	 
	 
	 	 	 	 
	 	 	 

1.

 

Exhibit C-1

Tranche 2 Warrant

2

 

Exhibit d

Notice of Borrowing 

__________, ____

Lighthouse Capital Partners VI, L.P.

3555 Alameda de las Pulgas, Suite 200

Menlo Park, CA 94025

Ladies and Gentlemen:

     Reference is made to the Loan and Security Agreement No. 1452 dated as of December __, 2009
(as it has been and may be amended from time to time, the “Loan Agreement,” initially capitalized
terms used herein as defined therein), between Lighthouse Capital Partners VI, L.P., As Agent
and Lender and Kior, Inc. (the “Company”)

     The undersigned is the President of the Company, and hereby irrevocably requests an Advance
under the Loan Agreement, and in that connection certifies as follows:

     1. The amount of the proposed Advance is $_________. The business day of the proposed Advance
is _________.

     2. The Loan Commencement Date for this Advance shall be August 1, 2010.

     3. As of this date, no Event of Default, or event which with notice or the passage of time
would constitute an Event of Default, has occurred and is continuing, or will result from the
making of the proposed Advance, and the representations and warranties of the Company contained in
Section 5 of the Loan Agreement are true and correct in all material respects.

     4. No event that could reasonably be expected to have a material adverse effect on the ability
of Company to fulfill its obligations under the Loan Agreement has occurred since the date of the
most recent financial statements, submitted to you by the Company.

     The Company agrees to notify you promptly before the funding of the Advance if any of the
matters to which I have certified above shall not be true and correct on the Funding Date.

	 	 	 	 	 	 	 

	 	 	Very truly yours,	 	 
	 
	 	 	 	 	 	 
	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Name:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 

	 	 

1

 

Exhibit e

Incumbency Certificate

     The undersigned,                     , hereby certifies that:

1. He/She is the duly elected and acting                      of Kior, Inc., a Delaware
corporation (the “Company”).

2. That on the date hereof, each person listed below holds the office in the Company indicated
opposite his or her name and that the signature appearing thereon is the genuine signature of each
such person:

	 	 	 	 	 
	NAME	 	OFFICE	 	SIGNATURE
	Fred Cannon

	 	President & Chief Operating Officer	 	 
	 
	 	 	 	 
	 

	 	 
	 	 
	 
	 	 	 	 
	 

	 	 
	 	 

3. Attached hereto as Exhibit A is a true and correct copy of the Certificate of Incorporation of
the Company, as amended, as in effect as of the date hereof.

4. Attached hereto as Exhibit B is a true and correct copy of the Bylaws of the Company, as
amended, as in effect as of the date hereof.

5. Attached hereto as Exhibit C is a copy of the resolutions of the Board of Directors of the
Company authorizing and approving the Company’s execution, delivery and performance of a loan
facility with Lighthouse Capital Partners VI, L.P.

     IN WITNESS WHEREOF, the undersigned has executed this Incumbency Certificate on                     .

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	Name:
	 	 

	 	 
	 

	 	 	 	 	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 	 	 

     I, the President and Chief Operating Officer of the Company, do hereby certify that
is the duly qualified, elected and acting of the Company and                      that the above signature is his or her genuine signature.

     IN WITNESS WHEREOF, the undersigned has executed and delivered this Incumbency Certificate on                     .

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 	 	 
	 

	 	Name:
	 	Fred Cannon	 	 
	 

	 	Title:
	 	President and Chief Operating Officer	 	 

1

 

Exhibit f

Officer’s Certificate

     The undersigned, to induce Lenders to extend or continue financial accommodations to Kior,
Inc., a Delaware corporation (the “Borrower”) pursuant to the terms of that certain Loan and
Security Agreement dated December  , 2009 (the “Loan Agreement”), hereby certifies that on the
date hereof:

	 	1.	 	I am the duly elected and acting                      of Borrower.
	 
	 	2.	 	I am a Responsible Officer as that term is defined in the Loan Agreement.
	 
	 	3.	 	The information submitted herewith is in fact what it purports to be.
	 
	 	4.	 	The information delivered herewith is true, correct and complete.
	 
	 	5.	 	Borrower is currently able to meet its obligations as they come due.
	 
	 	6.	 	I understand that Lender is relying upon the truthfulness, accuracy and
completeness hereof in connection with the Loan Agreement.
	 
	 	7.	 	I will advise you if it comes to my attention that, as of the date hereof, the
information submitted herewith was not in fact true, correct and complete.

Capitalized terms not defined herein shall have the meaning ascribed such terms in the Loan
Agreement.

     IN WITNESS WHEREOF, the undersigned has executed this Officer’s Certificate on                     .

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	Name:
	 	 

	 	 
	 

	 	 	 	 	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 	 	 

1

 

Exhibit g

Authorization for Automatic Payment

The undersigned Kior, Inc. (“Borrower”) authorizes Lighthouse Capital Partners VI,
L.P. and any and all affiliated funds (collectively, “Lender”) and the bank / financial
institution (“Bank”) named below to initiate variable debit and/or credit entries to Borrower’s
deposit, checking or savings accounts as designated below and to cause funds transfers to an
account of Lender as payment of any and all amounts due under the Loan and Security Agreement
between Borrower and Lender dated December  , 2009 (the “Loan Agreement”).

1. Lender is hereby authorized to initiate variable debit and/or credit transactions and resulting
funds transfers in Borrower’s designated accounts with respect to amounts calculated by Lender to
be due and owing to Lender by Borrower periodically under the Loan Agreement. Borrower consents to
all such debit and/or credit transactions and resulting funds transfers and hereby authorizes
Lender to take all such actions as may be required by Bank with respect to such transactions.
Borrower acknowledges and agrees that such credit and/or debit entries may be made in amounts due
under the Loan Agreement in order to cause timely payments as required by the terms of the Loan
Agreement.

2. Borrower hereby authorizes Lender to release to Bank all information concerning Borrower that
may be necessary or desirable for Bank to investigate or recover any erroneous funds transfers that
may occur.

3. Borrower acknowledges and agrees that all such debit and/or credit transactions and funds
transfers are intended to be made through an Automated Clearing House system and in compliance with
the NACHA Rules and in compliance with Bank’s security procedures.

4. Borrower represents and warrants that the account information set forth below is accurate and
complete and that each of the account(s) set forth below is a business account maintained in
Borrower’s name and for Borrower’s account.

This Consent shall be effective as of December  , 2009 and shall remain in effect until the Loan
Agreement has been terminated. Any cancellation by Borrower of this consent shall (i) be made in
writing and (ii) delivered to Bank and Lender in such time as to afford Bank and Lender a
reasonable opportunity to act on said cancellation.

	 	 	 

	Silicon Valley Bank
 

(Name of Borrower’s Bank)

	 	 

	 	 	 	 	 	 	 

	3003 Tasman Drive
	 	Santa Clara
	 	CA
	 	95054
	 
	(Address of Bank)
	 	(City)
	 	(State)
	 	(Zip Code)

	 	 	 	 	 

	Bank Routing Number

	 	121140399
 

(between these symbols “ /:” “:/” on bottom left of check)
	 	 

Account Number:     3300709708     (checking)     (circle one)

     Copy of a voided check is attached to this form

	 	 	 	 	 	 	 

	Borrower Name:	 	Kior, Inc.	 	 
	Borrower Address:	 	13001 Bay Park Road

Pasadena, TX 77507	 	 
	 
	 	 	 	 	 	 
	Authorized by:
	 	 	 	 	 	 
	 	 	 	 	 
	 

	 	Its:	 	 	 	 
	 

	 	 	 	 	 	 

1

 

Authorization for Automatic Payment

The undersigned Kior, Inc. (“Borrower”) authorizes [Leader Lending, LLC-Series A
and Leader Lending, LLC-Series B] and any and all affiliated funds (collectively,
“Lender”) and the bank / financial institution (“Bank”) named below to initiate variable debit
and/or credit entries to Borrower’s deposit, checking or savings accounts as designated below and
to cause funds transfers to an account of Lender as payment of any and all amounts due under the
Loan and Security Agreement between Borrower and Lender dated December  , 2009 (the “Loan
Agreement”).

5. Lender is hereby authorized to initiate variable debit and/or credit transactions and resulting
funds transfers in Borrower’s designated accounts with respect to amounts calculated by Lender to
be due and owing to Lender by Borrower periodically under the Loan Agreement. Borrower consents to
all such debit and/or credit transactions and resulting funds transfers and hereby authorizes
Lender to take all such actions as may be required by Bank with respect to such transactions.
Borrower acknowledges and agrees that such credit and/or debit entries may be made in amounts due
under the Loan Agreement in order to cause timely payments as required by the terms of the Loan
Agreement.

6. Borrower hereby authorizes Lender to release to Bank all information concerning Borrower that
may be necessary or desirable for Bank to investigate or recover any erroneous funds transfers that
may occur.

7. Borrower acknowledges and agrees that all such debit and/or credit transactions and funds
transfers are intended to be made through an Automated Clearing House system and in compliance with
the NACHA Rules and in compliance with Bank’s security procedures.

8. Borrower represents and warrants that the account information set forth below is accurate and
complete and that each of the account(s) set forth below is a business account maintained in
Borrower’s name and for Borrower’s account.

This Consent shall be effective as of December  , 2009 and shall remain in effect until the Loan
Agreement has been terminated. Any cancellation by Borrower of this consent shall (i) be made in
writing and (ii) delivered to Bank and Lender in such time as to afford Bank and Lender a
reasonable opportunity to act on said cancellation.

	 	 	 

	Bank of America
 

(Name of Borrower’s Bank)

	 	 

	 	 	 	 	 	 	 

	12400 I 45 North Freeway
	 	Houston
	 	TX
	 	77060
	 
	(Address of Bank)
	 	(City)
	 	(State)
	 	(Zip Code)

	 	 	 	 	 

	Bank Routing Number

	 	111000025
 

(between these symbols “ /:” “:/” on bottom left of check)
	 	 

Account Number:     488019480275     (checking / deposit / savings)     (circle one)

     Copy of a voided check is attached to this form

	 	 	 	 	 	 	 

	Borrower Name:	 	Kior, Inc.	 	 
	Borrower Address:	 	13001 Bay Park Road

Pasadena, TX 77507	 	 
	 
	 	 	 	 	 	 
	Authorized by:
	 	 	 	 	 	 
	 	 	 	 	 
	 

	 	Its:	 	 	 	 
	 

	 	 	 	 	 	 

2

 

Exhibit h

Negative Pledge Agreement

     This Negative Pledge Agreement is made as of December  , 2009, by and between
Kior, Inc. (“Borrower”) and Lighthouse Capital Partners VI, L.P., Leader Lending, LLC
- Series A, and Leader Lending, LLC — Series B (“Lenders”).

In consideration of the Loan and Security Agreement between the parties of proximate date herewith
(the “Loan Agreement”), Borrower agrees as follows:

Except as otherwise permitted in the Loan Agreement, Borrower shall not sell, transfer, assign,
mortgage, pledge, lease, grant a security interest in, or encumber any of the following
intellectual property of the Borrower:

(a) Any and all copyright rights, copyright applications, copyright registration and like
protection in each work or authorship and derivative work thereof, whether published or unpublished
and whether or not the same also constitutes a trade secret, now or hereafter existing, created,
acquired or held (collectively, the “Copyrights”);

(b) Any and all trade secrets, and any and all intellectual property rights in computer software
and computer software products now or hereafter existing, created, acquired or held;

(c) Any and all design rights which may be available to Borrower now or hereafter existing,
created, acquired or held;

(d) All patents, patent applications and like protections, including, without limitation,
improvements, divisions, continuations, renewals, reissues, extensions and continuations-in-part of
the same, including, without limitation, the patents and patent applications (collectively, the
“Patents”);

(e) Any trademark and servicemark rights, whether registered or not, applications to register and
registrations of the same and like protections, and the entire goodwill of the business of Borrower
connected with and symbolized by such trademarks (collectively, the “Trademarks”);

(f) Any and all claims for damages by way of past, present and future infringements of any of the
rights included above, with the right, but not the obligation, to sue for an collect such damages
for said use or infringement of the intellectual property rights identified above;

(g) Any and all licenses or other rights to use any of the Copyrights, Patents or Trademarks and
all license fees and royalties arising from such use to the extent permitted by such license or
rights

(h) Any and all amendments, extensions, renewals and extensions of any of the Copyrights, Patents
or Trademarks; and

(i) Any and all proceeds and products of the foregoing, including, without limitation, all payments
under insurance or any indemnity or warranty payable in respect of any of the foregoing.

It shall be an Event of Default under the Loan Agreement if there is a breach of any term of this
Negative Pledge Agreement. Borrower agrees to properly execute all documents reasonably required
by Agent on behalf of all Lenders in order to fulfill the intent and purposes hereof.

All capitalized terms used herein but not defined herein shall have the meaning ascribed to such
term in the Loan Agreement.

	 	 	 	 	 	 	 	 	 	 	 

	Borrower:	 	 	 	Agent:	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	Kior, Inc.	 	 	 	Lighthouse Capital Partners VI, L.P.
	 	 
	 
	
By:	 	 	 	 	 	By: Lighthouse Management Partners VI, L.L.C., its general partner	 	 
	 

	 	 	 	 	 	 	 	 	 	 
	Name:
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:	 	 	 	 
	 

	 	 	 	 	 	 	 	 	 	 
	Title:
	 	 	 	 	 	Name:	 	 	 	 
	 

	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	Title:	 	 	 	 
	 

	 	 	 	 	 	 	 	 	 	 

1

 

	 	 	 	 	 	 	 	 	 

	Lenders:	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	LEADER LENDING, LLC — SERIES A	 	 	 	LEADER LENDING, LLC — SERIES B
	 
	 	 	 	 	 	 	 	 
	By:

	 	 	 	 	 	By:	 	 
	 

	 	 
	 	 	 	 	 	 
	Name:

	 	 	 	 	 	Name:	 	 
	 

	 	 
	 	 	 	 	 	 
	Title:

	 	 	 	 	 	Title:	 	 
	 

	 	 
	 	 	 	 	 	 

	 	 	 	 	 

	Lighthouse Capital Partners VI, L.P.	 	 
	 
	 	 	 	 
	By:

	 	Lighthouse Management Partners VI, L.L.C.,

its general partner	 	 
	 
	 	 	 	 
	By:
	 	 	 	 
	 

	 	 	 	 
	Name:
	 	 	 	 
	 

	 	 	 	 
	Title:
	 	 	 	 
	 

	 	 	 	 

2

 

Exhibit I

Control Agreement

[In form and substance acceptable to Agent in its reasonable discretion]

1

 

Schedule 1

Disclosure Schedule

Deposit and Securities Accounts

	 	 	 	 	 	 	 	 	 
	 	 	Account Information:	 	Contact Information for
	 	 	 	 	 	 	Account:
	Account Number

	 	Bank Name:
	 	Bank of America
	 	Contact Name:
	 	Tim Thurman
	 1

	 	Address:
	 	12400 I 45 North Freeway
	 	Phone:
	 	(888) 852-5000, ex 5640
	(ACH Account)

	 	City, State, Zip:
	 	Houston, TX 77060
	 	Fax:
	 	(800) 839-9516
	 

	 	Phone:
	 	 	 	E-mail:
	 	timothy.thurman@baml.com
	 

	 	Fax:	 	 	 	 	 	 
	 

	 	Type of Account:
	 	Checking	 	 	 	 
	 

	 	Account number:
	 	488019490275	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	Account Number	 	Bank Name Silicon
Valley Bank Address 3003 Tasman Drive	 	Contact Name:	 	Cynthia Brooks-Manson
	 2	 	City, State, Zip
Santa Clara, CA 95054 Phone:	 	Phone 512-372-6763	 	 
	 

	 	Fax:
	 	 	 	Fax 512-346-9207E-mail cbrooks@svb.com	 	 
	 	 	Type of Account
Checking Account number: 3300709708	 	 	 	 
	 

	 	Account number:	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	Account Number

	 	Bank Name:
	 	Bank of America
	 	Contact Name:
	 	Tim Thurman
	 3

	 	Address:
	 	12400 I 45 North Freeway
	 	Phone:
	 	(888) 852-5000, ex 5640
	 

	 	City, State, Zip:
	 	Houston, TX 77060
	 	Fax:
	 	(800) 839-9516
	 

	 	Phone:
	 	 	 	E-mail:
	 	timothy.thurman@baml.com
	 

	 	Fax:	 	 	 	 	 	 
	 

	 	Type of Account:
	 	Certificate of Deposit	 	 	 	 
	 

	 	Account number:
	 	0910-00121407355	 	 	 	 
	 

	 	(support for credit card)	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	Account Number

	 	Bank Name
	 	 	 	Contact Name	 	 
	 4

	 	Address
	 	 	 	Phone	 	 
	 

	 	City, State, ZipPhone:
	 	 	 	Fax	 	 
	 

	 	Fax:
	 	 	 	E-mail:	 	 
	 

	 	Type of Account:	 	 	 	 	 	 
	 

	 	Account number:	 	 	 	 	 	 

Permitted Liens

Existing Liens: 

	 	•	 	Lien of Lighthouse Capital Partners VI, L.P. securing obligations of Borrower under that
certain Loan and Security Agreement No. 1451 dated December 30, 2008.
	 
	 	•	 	Operating Leases as outlined below:

	 	 	 	 	 
	Vendor	 	Property Description	 	Dates Covered
	Great America

	 	Konica Minolta C351 Full Color Copier
	 	6/9/09-6/9/12
	Great America

	 	Konica Minolta Bizhub digital copier
(used)
	 	8/25/08-8/24/11

1

 

	 	 	 	 	 
	Vendor	 	Property Description	 	Dates Covered
	Quantum Analytics

	 	Pyrolyzer
	 	Starts at shipment, ends when sent back
	De Lage Landen

	 	Forklift
	 	36 mos. — starts upon shipment
	CPM LABFAB Inc.

	 	One Lab
	 	11/1/08-11/1/09
	CPM LABFAB Inc.

	 	Two Labs
	 	12/1/08-12/1/09
	Mobile Monitor

	 	Offices
	 	12/7/08-12/7/11
	Southern Ionics Inc.

	 	Plant Site
	 	11/1/08-10/31/11

Subsidiaries

Kior BV, a wholly owned subsidiary of Borrower organized under the laws of The Netherlands

Prior Names

Bio Catalytic Cracking, Inc.

5.6 Litigation and Administrative Proceedings

     The Borrower intends to initiate a lawsuit against George Huber (“Huber”), a prior member of
the Borrower’s scientific advisory board, based in part on a belief that Huber may have breached
the terms of his consulting agreement with Borrower.

5.16 KIOR BV

Kior BV currently holds approximately $146,000 of cash reserves. Kior BV is a party to (i) certain
consulting agreements with Non-US residents that provide consulting service to Borrower and (ii) an
intercompany agreement with Kior, Inc. KIOR BV currently employees one Non-US resident person.

Business Premises

[TO BE PROVIDED BY BORROWER — indicate street address and landlord contact information]

	 	 	 	 	 	 	 	 	 
	 	 	
Each Location Address where Lighthouse 	 	Landlord/Property Management
	 	 	Capital Partners has financed assets:	 	Information:
	Current

	 	Contact Name:
	 	Andre Ditsch
	 	Contact Name:
	 	Milton Sundbeck, President  
	Headquarters

	 	Address:
	 	13001 Bay Park Road
	 	Company Name:
	 	Southern Ionic Incorporated
	(Location 1)

	 	City, State, Zip:
	 	Pasadena, TX 77507
	 	Address:
	 	Drawer 1217
	 

	 	Phone:
	 	(281) 694-8710
	 	City, State, Zip:
	 	West Point, MS 39701
	 

	 	Fax:
	 	(281) 694-8799
	 	Phone:
	 	(662) 494-3055 x 201
	 

	 	 	 	 	 	Fax:
	 	(662) 495-2590
	 

	 	 	 	 	 	Local Contact:
	 	Craig Cantrell, Plant Manager
	 

	 	 	 	 	 	Local Address:
	 	12901 Baypark Rd.
	 

	 	 	 	 	 	City, State, Zip:
	 	Pasadena, TX 77507
	 

	 	 	 	 	 	Phone:
	 	(281) 474-4826 x 131
	 

	 	 	 	 	 	Cell:
	 	(281) 703-3439
	 

	 	 	 	 	 	Fax:
	 	(281) 474-4973
	 
	 	 	 	 	 	 	 	 
	Location

	 	Contact Name:
	 	 	 	Contact Name:	 	 
	2

	 	Company Name:
	 	Kior BV
	 	Company Name:	 	 
	 

	 	Address:
	 	Hogenbrinkerweg 15
	 	Address:	 	 
	 

	 	City, State, Zip:
	 	3871 KM Hoevelaker, The Netherlands
	 	City, State, Zip:	 	 
	 

	 	Phone:
	 	+31 33 254 04 23
	 	Phone:	 	 
	 

	 	Fax:
	 	+31 33 254 05 82
	 	Fax:	 	 

2

 

	 	 	 	 	 	 	 	 	 
	 	 	
Each Location Address where Lighthouse 	 	Landlord/Property Management
	 	 	Capital Partners has financed assets:	 	Information:
	Location

	 	Contact Name:
	 	 	 	Contact Name:	 	 
	3

	 	Company Name:
	 	 	 	Company Name:	 	 
	 

	 	Address:
	 	 	 	Address:	 	 
	 

	 	City, State, Zip:
	 	 	 	City, State, Zip:	 	 
	 

	 	Phone:
	 	 	 	Phone:	 	 
	 

	 	Fax:
	 	 	 	Fax:	 	 

3

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