[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

EXHIBIT 10.1A

EXECUTION COPY

LOAN AND SECURITY AGREEMENT

THIS LOAN AND SECURITY AGREEMENT, dated as of September 28, 2007 (as amended, restated, supplemented or otherwise modified from time to time (this “Agreement”)) is among GENERAL ELECTRIC CAPITAL CORPORATION (“GECC”), in its capacity as agent for Lenders (as defined below), together with its successors and assigns in such capacity, “Agent”), OXFORD FINANCE CORPORATION (“Oxford”), the other financial institutions who are or hereafter become parties to this Agreement as lenders (together with GECC and Oxford, collectively the “Lenders”, and each individually, a “Lender”) and CODEXIS, INC., a Delaware corporation (“Borrower”). Agent has an office at 83 Wooster Heights Road, Fifth Floor, Danbury, CT 06810 (the “Agent’s Office”). Borrower’s mailing address and chief executive office is 200 Penobscot Drive, Redwood City, CA 94063.

RECITALS

Borrower wishes to borrow funds from time to time from Lenders, and Lenders desire to make loans, advances and other extensions of credit, severally and not jointly, to Borrower from time to time pursuant to the terms and conditions of this Agreement.

AGREEMENT

Borrower, Agent and Lenders agree as follows:

1. DEFINITIONS.

As used in this Agreement, all capitalized terms shall have the definitions as provided herein. Any accounting term used but not defined herein shall be construed in accordance with generally accepted accounting principles in the United States of America, as in effect from time to time (“GAAP”) and all calculations shall be made in accordance with GAAP. The term “financial statements” shall include the accompanying notes and schedules. All other terms used but not defined herein shall have the meaning given to such terms in the Uniform Commercial Code as adopted in the State of New York, as amended and supplemented from time to time (the “UCC”).

2. LOANS AND TERMS OF PAYMENT.

2.1. Promise to Pay. Borrower promises to pay Agent, for the ratable accounts of Lenders, when due pursuant to the terms hereof, the aggregate unpaid principal amount of all loans, advances and other extensions of credit made severally by the Lenders to Borrower, together with interest on the unpaid principal amount of such loans, advances and other extensions of credit at the interest rates set forth herein.

2.2. Term Loans.

Lender as it may be amended to reflect assignments made in accordance with this Agreement or terminated or reduced in accordance with this Agreement, its “Commitment”, and the aggregate of all such commitments, the “Commitments”). Notwithstanding the foregoing, the aggregate principal amount of the Term Loans made hereunder shall not exceed $15,000,000 (the “Total Commitment”). Each Lender’s obligation to fund a Term Loan shall be limited to such Lender’s Pro Rata Share (as defined below) of such Term Loan. Subject to the terms and conditions hereof, the initial Term Loan shall be made on the Closing Date in an aggregate principal amount equal to $10,000,000 (the “Initial Term Loan”). After the Initial Term Loan, Borrower may request no more than five (5) additional Term Loans and such subsequent Term Loan must be in an amount equal to at least $1,000,000.

Bank Name: [*]

Bank Address: [*]

ABA#: [*]

Account #: [*]

Account Name: [*]

Ref: [*]

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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by such Lender to or on behalf of Borrower pursuant to this Agreement, in each case together with interest thereon as prescribed in Section 2.3(b).

2.3. Interest and Repayment.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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Notwithstanding any provision in this Agreement to the contrary, all unpaid principal and accrued interest with respect to each Term Loan and all other Obligations hereunder shall become due and payable in full on the earlier to occur of (such earlier date, the “Final Maturity Date”): (1) the Applicable Term Loan Maturity Date for the last Term Loan made hereunder or (2) the date that is 91 days before the first date on which any holders of the Series E preferred stock proposed to be issued by Borrower pursuant to Section 7.2(g) shall have any contractual right or rights set forth in Borrower’s organizational documents to redeem or demand repurchase of such preferred stock.

Bank Name: [*]

Bank Address: [*]

ABA#: [*]

Account Number: [*]

Account Name: [*]

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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Ref: [*]

2.4. Prepayments. Borrower can voluntarily prepay, upon 3 Business Days’ prior written notice to Agent, any Term Loan in full, but not in part. Upon the date of (a) any voluntary prepayment of a Term Loan in accordance with the immediately preceding sentence or (b) any mandatory prepayment of a Term Loan required under this Agreement (whether by acceleration of the Obligations pursuant to Section 8.2 or otherwise), Borrower shall pay to Agent, for the ratable benefit of the Lenders, a sum equal to (i) all outstanding principal plus any unpaid interest accrued through the date of such prepayment with respect to the such Term Loan, (ii) the Final Payment Fee (as such term is defined in Section 2.7(d)) for such Term Loan, and (iii) a prepayment premium (as yield maintenance for loss of bargain and not as a penalty) equal to: (A) 5% on such principal prepayment amount, if such prepayment is made on or before the one year anniversary of such Term Loan, (B) 4% on such principal prepayment amount, if such prepayment is made after the one year anniversary of such Term Loan but on or before the two year anniversary of such Term Loan, and (C) 2% on such principal prepayment amount, if such prepayment is made after the two year anniversary of such Term Loan but before the Applicable Term Loan Maturity Date for such Term Loan; provided, however, that Borrower shall not be obligated to pay the amounts described in clauses (A), (B) or (C) above in connection with a prepayment in full of the Term Loan and

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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the other Obligations hereunder in the event that either (i) Borrower has requested in writing that the Requisite Lenders consent to a transaction that is not permitted under Section 7.5 and the Requisite Lenders have not consented to such transaction on or prior to the Response Date (as defined below) or (ii) Borrower has requested in writing that the Requisite Lenders consent to any amendment, modification or waiver of the Maxygen License Agreement for which the consent of the Requisite Lenders is required under Section 7.11(a) and the Requisite Lenders have not consented to such amendment, modification or waiver on or prior to the Response Date. Borrower shall have no obligation upon any prepayment of any Term Loan hereunder to pay, in addition to the amounts specified in this Section 2.4, any yield maintenance with respect to unaccrued interest that would have accrued through the maturity of a Term Loan had such Term Loan not been prepaid.

2.5. Late Fees. If Agent does not receive any Scheduled Payment or other payment under any Debt Document from Borrower within 3 days after its due date, then, at Agent’s election, Borrower agrees to pay to Agent for the ratable benefit of all Lenders, a late fee equal to (a) 5% of the amount of such unpaid payment or (b) such lesser amount that, if paid, would not cause the interest and fees paid by Borrower under this Agreement to exceed the Maximum Lawful Rate (as defined below) (the “Late Fee”).

2.6. Default Rate. All Term Loans and other Obligations shall bear interest, at the option of Agent or upon the request of the Requisite Lenders (as defined below), from and after the occurrence and during the continuation of an Event of Default (as such terms are defined below), at a rate equal to the lesser of (a) 5% above the rate of interest applicable to such Obligations as set forth in Section 2.3(a) immediately prior to the occurrence of the Event of Default and (b) the Maximum Lawful Rate (the “Default Rate”). The application of the Default Rate shall not be interpreted or deemed to extend any cure period or waive any Default or Event of Default or otherwise limit the Agent’s or any Lender’s right or remedies hereunder. All interest payable at the Default Rate shall be payable on demand.

2.7. Lender Fees.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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2.8. Maximum Lawful Rate. Anything herein, any Note or any other Debt Document (as defined below) to the contrary notwithstanding, the obligations of Borrower hereunder and thereunder shall be subject to the limitation that payments of interest shall not be required, for any period for which interest is computed hereunder, to the extent (but only to the extent) that contracting for or receiving such payment by Agent and Lenders would be contrary to the provisions of any law applicable to Agent and Lenders limiting the highest rate of interest which may be lawfully contracted for, charged or received by Agent and Lenders, and in such event Borrower shall pay Agent and Lenders interest at the highest rate permitted by applicable law (“Maximum Lawful Rate”); provided, however, that if at any time thereafter the rate of interest payable hereunder or thereunder is less than the Maximum Lawful Rate, Borrower shall continue to pay interest hereunder at the Maximum Lawful Rate until such time as the total interest received by Agent and Lenders is equal to the total interest that would have been received had the interest payable hereunder been (but for the operation of this paragraph) the interest rate payable since the making of the Initial Term Loan as otherwise provided in this Agreement, any Note or any other Debt Document.

3. CREATION OF SECURITY INTEREST.

3.1. Grant of Security Interest. As security for the prompt payment and performance, whether at the stated maturity, by acceleration or otherwise, of all Term Loans and other debt, obligations and liabilities of any kind whatsoever of Borrower to Agent and Lenders under the Debt Documents (whether for principal, interest, fees, expenses, prepayment premiums, indemnities, reimbursements or other sums, and whether or not such amounts accrue after the filing of any petition in bankruptcy or after the commencement of any insolvency, reorganization or similar proceeding, and whether or not allowed in such case or proceeding), absolute or contingent, now existing or arising in the future, including but not limited to the payment and performance of any outstanding Notes, and any renewals, extensions and modifications of such Term Loans (such indebtedness under the Notes, Term Loans and other debt, obligations and liabilities in connection with the Debt Documents are collectively called the “Obligations”), Borrower does hereby grant to Agent, on behalf of itself and Lenders, a security interest in the property listed below (all hereinafter collectively called the “Collateral”):

All of Borrower’s personal property of every kind and nature (except for Intellectual Property, as defined in, and to the extent excluded pursuant to, Section 3.3) whether now owned or hereafter acquired by, or arising in favor of, Borrower, and regardless of where located, including, without limitation, all accounts, chattel paper (whether tangible or electronic), commercial tort claims, deposit accounts, documents, equipment, financial assets, fixtures, goods, instruments, investment property, inventory, letter-of-credit rights, letters of credit, securities, supporting obligations, cash, cash equivalents, any other contract rights (including, without limitation, rights under any license agreements), or rights to the payment of money, and general intangibles, and all books and records of Borrower relating thereto, and in and against all additions, attachments, accessories and

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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accessions to such property, all substitutions, replacements or exchanges therefor, all proceeds, insurance claims, products, profits and other rights to payments not otherwise included in the foregoing (with each of the foregoing terms that are defined in the UCC having the meaning set forth in the UCC).

Notwithstanding anything herein to the contrary, in no event shall the Collateral include or the security interest granted under Section 3.1 hereof attach to:

(a) any lease, license, contract or agreement to which Borrower is a party, and any of its rights or interest thereunder, if and to the extent that a security interest is prohibited by or in violation of (i) any law, rule or regulation applicable to Borrower, or (ii) a term, provision or condition of any such lease, license, contract, property right or agreement (unless such law, rule, regulation, term, provision or condition would be rendered ineffective with respect to the creation of the security interest hereunder pursuant to Sections 9-406, 9-407, 9-408 or 9-409 of the UCC (or any successor provision or provisions) of any relevant jurisdiction or any other applicable law (including the Bankruptcy Code) or principles of equity); provided, however, that the Collateral shall include (and such security interest shall attach) immediately at such time as the contractual or legal prohibition shall no longer be applicable and to the extent severable, shall attach immediately to any portion of such lease, license, contract or agreement not subject to the prohibitions specified in (i) or (ii) above; provided further that the exclusions referred to in clause (a) of this paragraph shall not include any proceeds of any such lease, license, contract or agreement;

(b) more than 65% of the outstanding capital stock of a Controlled Foreign Corporation (as defined in the Internal Revenue Code); or

(c) the equipment specifically listed on Schedule B hereto under “Existing Liens” and financed pursuant to (i) the Loan and Security Agreement, dated as of February 12, 2004, by and between Lighthouse Capital Partners V, L.P. and the Borrower and (ii) Master Security Agreement No. 5081102, dated as of October 25, 2005 by and between Oxford Finance Corporation and the Borrower, and in and against all additions, attachments, accessories, and accessions to such equipment, all substitutions, replacements or exchanges therefore, and all insurance and/or other proceeds thereof.

Borrower hereby represents and covenants that such security interest constitutes a valid, first priority security interest in the presently existing Collateral, and will constitute a valid, first priority security interest in Collateral acquired after the date hereof, in each case with respect to priority only, subject to any Permitted Liens with respect to the Collateral. Borrower hereby covenants that it shall give written notice to Agent promptly upon the acquisition by Borrower or creation in favor of Borrower of any commercial tort claim after the Closing Date.

3.2. Financing Statements. Borrower hereby authorizes Agent to file UCC financing statements with all appropriate jurisdictions to perfect Agent’s security interest (for the benefit of itself and the Lenders) granted hereby.

3.3. Grant of Security Interest in Proceeds of Intellectual Property. The Collateral shall not include any of Borrower’s intellectual property, which shall be defined as any and all copyright,

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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trademark, servicemark, patent, design right, software, trade secret and intangible rights of Borrower and any applications, registrations, claims, products, awards, judgments, amendments, renewals, extensions, improvements and insurance claims related thereto (collectively, “Intellectual Property”) now owned or hereafter acquired, or any claims for damages by way of any past, present or future infringement of any of the foregoing; provided, however, that the Collateral shall include all cash, royalty fees, other proceeds, accounts and general intangibles that consist of rights of payment to or on behalf of Borrower or proceeds from the sale, licensing or other disposition of all or any part of, or rights in, the Intellectual Property by or on behalf of Borrower (“Rights to Payment”). Notwithstanding the foregoing, to the extent it is necessary under applicable law in any bankruptcy or insolvency proceeding involving Borrower for Agent (on behalf of itself and Lenders) to have a security interest in the underlying Intellectual Property in order for Agent to have (i) a security interest in the Rights to Payment and (ii) a security interest in any payments with respect to Rights to Payment that are received after the commencement of such bankruptcy or insolvency proceeding, then the Collateral shall automatically, and effective as of the date hereof, include the Intellectual Property only to the extent necessary to permit attachment and perfection of Agent’s security interest (on behalf of itself and Lenders) in the Rights to Payment and any payments in respect thereof that are received after the commencement of any bankruptcy or insolvency proceeding. Agent hereby agrees on behalf of itself and the Lenders that, if Agent obtains a security interest in the Intellectual Property pursuant to the immediately preceding sentence, Agent will not exercise any remedies (under the UCC or otherwise) with respect to the Intellectual Property (other than remedies with respect to Rights to Payment or any other proceeds of the Intellectual Property). For the avoidance of doubt, none of the provisions of this Section 3.3 shall be construed to provide Lenders with a consent or other blocking right in connection with licenses granted by Borrower in accordance with the terms and conditions of Section 7.3.

3.4. Termination of Security Interest. Subject to Section 10.9, Agent’s lien on the Collateral (on behalf of itself and Lenders) shall continue until all of the Obligations are repaid in full in cash and all of the Commitments hereunder are terminated or fulfilled (the “Termination Date”). Upon the Termination Date, Agent shall, at Borrower’s sole cost and expense and without any recourse, representation or warranty, release its liens in the Collateral, and all rights remaining therein, if any, shall revert to Borrower.

4. CONDITIONS OF CREDIT EXTENSIONS

4.1. Conditions Precedent to Initial Term Loan. No Lender shall be obligated to make the Initial Term Loan, or to take, fulfill, or perform any other action hereunder, until the following have been delivered to the Agent (the date on which the Lenders make the Initial Term Loan after all such conditions shall have been satisfied in a manner satisfactory to Agent or waived in accordance with this Agreement, the “Closing Date”):

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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4.2. Conditions Precedent to All Term Loans. No Lender shall be obligated to make any Term Loan, including the Initial Term Loan, unless the following additional conditions have been satisfied:

As used herein, the term “Cash Burn Amount” means, with respect to Borrower and its consolidated Subsidiaries, as of any date of determination and based on the financial statements most recently delivered to Agent and the Lenders in accordance with this Agreement, the difference between:

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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minus

At such times that the Cash Burn Amount is zero or a positive number, Borrower will be deemed to be “Cashflow Positive” for purposes of this Agreement. Conversely, at any time that the Cash Burn Amount is a negative number, Borrower will be deemed to be “Cashflow Negative” for purposes of this Agreement.

5. REPRESENTATIONS AND WARRANTIES OF BORROWER.

Borrower represents, warrants and covenants to Agent and each Lender that:

5.1. Due Organization and Authorization. Borrower’s exact legal name is as set forth in the preamble of this Agreement and Borrower is, and will remain, duly organized, existing and in good standing under the laws of the State of Delaware, has its chief executive office at the location specified in the preamble, and is, and will remain, duly qualified and licensed in every jurisdiction wherever necessary to carry on its business and operations, except where the failure to be so qualified and licensed could not reasonably be expected to have a Material Adverse Effect. This Agreement and the other Debt Documents have been duly authorized, executed and delivered by Borrower and constitute legal, valid and binding agreements enforceable in accordance with their terms. The execution, delivery and performance by Borrower of each Debt Document executed or to be executed by it is in each case within Borrower’s powers.

5.2. Required Consents. Except for the filing of a Form D with respect to the issuance of the Warrants, no filing, registration, qualification with, or approval, consent or withholding of objections from, any governmental authority or instrumentality or any other entity or person is required with respect to the entry into, or performance by Borrower of, any of the Debt Documents, except any already obtained.

5.3. No Conflicts. The entry into, and performance by Borrower of, the Debt Documents will not (a) violate any of the organizational documents of Borrower, (b) violate any law, rule, regulation, order, award or judgment applicable to Borrower, or (c) result in any breach of or constitute a default under, or result in the creation of any lien, claim or encumbrance on any of Borrower’s property (except for liens in favor of Agent, on behalf of itself and Lenders) pursuant to, any indenture, mortgage, deed of trust, bank loan, credit agreement, or other Material Agreement (as defined below) to which Borrower is a party. As used herein, “Material Agreement” shall mean (i) any agreement or contract to which Borrower or any of its Subsidiaries is a party and involving the receipt or payment of amounts in the aggregate exceeding [*] per year, (ii) any agreement or contract to which Borrower or any of its Subsidiaries is a party the termination of which could reasonably be expected to have a Material Adverse Effect and (iii) each agreement relating to the Subordinated Indebtedness (as defined below). A description of all Material Agreements as of the Closing Date is set forth on Schedule B hereto.

5.4. Litigation. There are no actions, suits, proceedings or, to Borrower’s knowledge, investigations pending against or affecting Borrower before any court, federal, state, provincial, municipal or other governmental department, commission, board, bureau, agency or instrumentality, domestic or foreign, or any basis thereof, which involves the possibility of any judgment or liability that could

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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reasonably be expected to have a Material Adverse Effect, or which questions the validity of the Debt Documents, or the other documents required thereby or any action to be taken pursuant to any of the foregoing, nor does Borrower have reason to believe that any such actions, suits, proceedings or investigations are threatened. As used in this Agreement, the term “Material Adverse Effect” shall mean a material adverse effect on any of (a) the operations, business, assets, properties or condition (financial or otherwise) of Borrower, individually, or Borrower and its Subsidiaries (as defined below), collectively, but excluding [*], (b) the ability of Borrower to perform any of its obligations under any Debt Document to which it is a party, (c) the legality, validity or enforceability of any Debt Document, (d) the rights and remedies of Agent or Lenders under any Debt Document or (e) the validity, perfection or priority of any lien in favor of Agent, on behalf of itself and Lenders, on any of the Collateral.

5.5. Financial Statements. All financial statements delivered to Agent and Lenders pursuant to Section 6.3 have been prepared materially in accordance with GAAP (subject, in the case of unaudited financial statements, to the absence of footnotes and normal year-end and audit adjustments), and since the date of the most recent audited financial statement, no event has occurred which has had or could reasonably be expected to have a Material Adverse Effect. There has been no material adverse deviation from the most recent annual operating plan of Borrower delivered to Agent and Lenders in accordance with Section 6.3.

5.6. Use of Proceeds. The proceeds of the Term Loans shall be used for working capital and general corporate purposes.

5.7. Collateral. Borrower is, and will remain, the sole and lawful owner, and in possession of, the Collateral, and has the sole right and lawful authority to grant the security interest described in this Agreement. The Collateral is, and will remain, free and clear of all liens, claims and encumbrances of any kind whatsoever, except for (a) liens in favor of Agent, on behalf of itself and Lenders, to secure the Obligations, (b) liens (i) with respect to the payment of taxes, assessments or other governmental charges or (ii) of suppliers, carriers, materialmen, warehousemen, workmen or mechanics and other similar liens, in each case imposed by law and arising in the Ordinary Course of Business, and securing amounts that are not yet due or that are being contested in good faith by appropriate proceedings diligently conducted and with respect to which adequate reserves or other appropriate provisions are maintained on the books of Borrower or its Subsidiaries in accordance with GAAP and which do not involve, in the judgment of Agent, any risk of the sale, forfeiture or loss of any of the Collateral (a “Permitted Contest”), (c) zoning restrictions, easements, rights of way, encroachments or other restrictions on the use of, and other minor defects or irregularities in title with respect to, any real property of Borrower or its Subsidiaries so long as the same do not materially impair the use of such real property by Borrower or such Subsidiary, (d) purported liens evidenced by the filing of precautionary UCC financing statements relating solely to operating leases of personal property entered into in the Ordinary Course of Business, (e) liens in favor of customs and revenue authorities arising as a matter of law to secure payment of customs duties in connection with the importation of goods, (f) liens existing on the date hereof and set forth on Schedule B hereto, (g) liens securing Indebtedness (as defined below) permitted under Section 7.2(c) below, provided that (i) such liens exist prior to the acquisition of, or attach substantially simultaneous with, or within 20 days after the, acquisition, repair, improvement or construction of, such property financed by such Indebtedness and (ii) such liens do not extend to any property of Borrower or its Subsidiaries other than the property (and proceeds thereof) acquired or built, or the improvements or repairs, financed by such Indebtedness, and (h) licenses described in Section 7.3(b) below (all of such liens described in the foregoing clauses (a) through (h) are called “Permitted Liens”). “Ordinary Course of Business” means, with respect to Borrower and its Subsidiaries, the operation of the business of Borrower and its Subsidiaries consistent with Borrower’s business plan as of the Closing Date, it being understood and acknowledged by the Lenders that the business of Borrower and/or its Subsidiaries involves entering into

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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corporate collaborations in the fields of energy, chemicals, carbon management and pharmaceuticals pursuant to exclusive and non-exclusive licenses of Intellectual Property.

5.8. Compliance with Laws. Borrower is and will remain in full compliance in all material respects with all laws, statutes, ordinances, rules and regulations applicable to it including, without limitation, (a) for so long as Borrower is a private company, ensuring that no person who owns, directly, or indirectly, 20% or more of the capital stock of Borrower is or shall be (i) listed on the Specially Designated Nationals and Blocked Person List maintained by the Office of Foreign Assets Control (“OFAC”), Department of Treasury, and/or any other similar lists maintained by OFAC pursuant to any authorizing statute, Executive Order or regulation or (ii) a person designated under Section 1(b), (c) or (d) of Executive Order No. 13224 (September 23, 2001), any related enabling legislation or any other similar Executive Orders, (b) compliance with all applicable Bank Secrecy Act (“BSA”) laws, regulations and government guidance on BSA compliance and on the prevention and detection of money laundering violations, (c) meeting the minimum funding requirements of the United States Employee Retirement Income Security Act of 1974 (as amended, “ERISA”) with respect to any employee benefit plans subject to ERISA, (d) Borrower is not an “investment company” or a company “controlled” by an “investment company” within the meaning of the Investment Company Act of 1940 and (e) Borrower is not engaged principally, or as one of the important activities, in the business of extending credit for the purpose of purchasing or carrying margin stock (within the meaning of Regulations T, U and X of the Board of Governors of the Federal Reserve System (the “Federal Reserve Board”).

5.9. Intellectual Property. The Intellectual Property is and will remain free and clear of all liens, claims and encumbrances of any kind whatsoever, except for Permitted Liens described in clauses (b)(i) and (e) of Section 5.7. Borrower has not and will not enter into any other agreement or financing arrangement in which a negative pledge in Borrower’s Intellectual Property is granted to any other party except for exclusive licenses in existence as of the date hereof or entered into in compliance with the terms and conditions of Section 7.3(d). As of the Closing Date and each date a Term Loan is advanced to Borrower, Borrower does not have any interest in, or title to any Intellectual Property except as disclosed in the Perfection Certificate. Borrower owns or has rights to use all Intellectual Property material to the conduct of its business as now or heretofore conducted by it or proposed to be conducted by it, without any actual or claimed infringement upon the rights of third parties. Borrower is in full compliance in all material respects with all provisions of (a) that certain License Agreement between Maxygen, Inc. (“Maxygen”) and Borrower dated March 28, 2002 (as heretofore amended, supplemented or otherwise modified from time to time, the “Maxygen License Agreement”) and (b) that certain License and Collaboration Agreement between Maxygen and Novozymes, Inc. dated September 17, 1997, as assigned by Maxygen to Borrower, and as amended from time to time pursuant to the terms and conditions of this Agreement. Borrower has no knowledge of any material breach by Maxygen under the Maxygen License Agreement.

5.10. Solvency. Both immediately before and immediately after giving effect to each Term Loan, the transactions contemplated herein, and the payment and accrual of all transaction costs in connection with the foregoing, Borrower is and will be Solvent. As used herein, “Solvent” means, with respect to Borrower on a particular date, that on such date (a) the fair value of the property of Borrower is greater than the total amount of liabilities, including contingent liabilities (excluding the non-current portion of facility leases), of Borrower; (b) the present fair salable value of the assets of Borrower is not less than the amount that will be required to pay the probable liability of Borrower on its debts as they become absolute and matured; (c) Borrower does not intend to, and does not believe that it will, incur debts or liabilities beyond Borrower’s ability to pay as such debts and liabilities mature; (d) Borrower is not engaged in a business or transaction, and is not about to engage in a business or transaction, for which Borrower’s property would constitute an unreasonably small capital; and (e) is not “insolvent” within the

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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meaning of Section 101 (32) of the United States Bankruptcy Code (11 U.S.C. § 101, et. seq.), as amended. The amount of contingent liabilities (such as litigation, guaranties and pension plan liabilities) at any time shall be computed as the amount that, in light of all the facts and circumstances existing at the time, represents the amount that can be reasonably be expected to become an actual or matured liability.

5.11. Taxes; Pension. All tax returns, reports and statements, including information returns, required by any governmental authority to be filed by Borrower and its Subsidiaries have been filed with the appropriate governmental authority and except as set forth in Section 10 of the Perfection Certificate delivered on or prior to the Closing Date all taxes, levies, assessments and similar charges have been paid prior to the date on which any fine, penalty, interest or late charge may be added thereto for nonpayment thereof (or any such fine, penalty, interest, late charge or loss has been paid), excluding taxes, levies, assessments and similar charges or other amounts which are the subject of a Permitted Contest. Proper and accurate amounts have been withheld by Borrower from its respective employees for all periods in compliance with applicable laws and such withholdings have been timely paid to the respective governmental authorities. Borrower has paid all amounts necessary to fund all present pension, profit sharing and deferred compensation plans in accordance with their terms, and Borrower has not withdrawn from participation in, and has not permitted partial or complete termination of, or permitted the occurrence of any other event with respect to, any such plan which could reasonably be expected to result in any liability of Borrower in excess of $50,000 in the aggregate, including any liability to the Pension Benefit Guaranty Corporation or its successors or any other governmental authority.

5.12. Full Disclosure. Borrower hereby confirms that all of the information disclosed on the Perfection Certificate is true, correct and complete as of the date of this Agreement and true, correct and complete in all material respects as of the date of each Term Loan. No representation, warranty or other statement made by or on behalf of Borrower contains any untrue statement of a material fact or omits to state a material fact necessary to make the statements contained therein not misleading, it being recognized by Agent and Lenders that the projections and forecasts provided by Borrower in good faith and based upon reasonable and stated assumptions are not to be viewed as facts and that actual results during the period or periods covered by any such projections and forecasts may differ from the projected or forecasted results.

6. AFFIRMATIVE COVENANTS.

6.1. Good Standing. Borrower shall maintain its and each of its Subsidiaries’ existence and good standing in its jurisdiction of organization and maintain qualification in each jurisdiction in which the failure to so qualify could reasonably be expected to have a Material Adverse Effect. Borrower shall maintain, and shall cause each of its Subsidiaries to maintain, in full force all licenses, approvals and agreements, the loss of which could reasonably be expected to have a Material Adverse Effect. “Subsidiary” means, with respect to Borrower, any entity the management of which is, directly or indirectly controlled by, or of which an aggregate of more than 50% of the outstanding voting capital stock (or other voting equity interest) is, at the time, owned or controlled, directly or indirectly by, Borrower or one or more Subsidiaries of Borrower.

6.2. Notice to Agent. Borrower shall provide Agent with (a) notice of the occurrence of any Default or Event of Default, promptly (but within 3 Business Days) after the date any “officer” (as defined in Rule 16a-1 promulgated under the Securities Exchange Act of 1934, as amended) or a Proper Officer (each such “officer” or such Proper Officer, an “Executive Officer”) of Borrower becomes aware of the occurrence of any such event the occurrence of any such event, (b) copies of all statements, reports and notices made available generally by Borrower to its securityholders or to any holders of Subordinated Indebtedness (as defined below), all notices sent to Borrower by the holders of such Subordinated

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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Indebtedness, and all reports, registration statements and prospectuses filed with the Securities and Exchange Commission (“SEC”) (excluding notices filed by Borrower on behalf of officers and directors pursuant to Section 16 of the Securities Exchange Act of 1934) or any securities exchange or governmental authority exercising a similar function, promptly, but in any event within 5 days of delivering or receiving such information to or from such persons, (c) a report of any legal actions pending or threatened against Borrower or any Subsidiary that could reasonably be expected to result in damages or costs to Borrower or any Subsidiary of [*] or more promptly upon (but within 3 Business Days after) receipt of notice thereof, (d) within 45 days of the end of each calendar quarter, a list of any new applications or registrations that Borrower has made or filed in respect of any Intellectual Property or a change in status of any outstanding application or registration during the immediately preceding calendar quarter, and (e) copies of all material statements, reports and notices delivered to or by Borrower in connection with the Maxygen License Agreement promptly but in any event within 3 Business Days of delivering or receiving such information.

6.3. Financial Statements. If Borrower is a private company, it shall deliver to Agent and Lenders (a) unaudited consolidated and, if available, consolidating balance sheets, statements of operations and cash flow statements within 45 days of each month end, in a form acceptable to Agent and certified by Borrower’s chief executive officer or chief financial officer, (b) an updated capitalization table of Borrower in the form that Borrower uses with its existing investors within (i) 5 Business Days after the date of each funding of a Term Loan hereunder and (ii) 45 days after each quarter end and (c) beginning with the fiscal year ending December 31, 2008, its complete annual audited consolidated and, if available, consolidating financial statements prepared under GAAP and certified by an independent certified public accountant selected by Borrower and satisfactory to Agent (it being understood that any “Big Four” accounting firm shall be acceptable to Agent) within 120 days of the fiscal year end or, if sooner, at such time as Borrower’s Board of Directors receives the certified audit; provided, however, that Borrower shall deliver the certified audits for the fiscal years ending December 31, 2006 and December 31, 2007 to Agent and Lenders on or prior to the earlier of (x) the date that is 5 days after the date on which Borrower receives the respective certified audit and (y) June 30, 2008. If Borrower is a publicly held company, it shall provide to Agent and Lenders (A) quarterly unaudited consolidated and, if available, consolidating balance sheets, statements of operations and cash flow statements that have been reviewed in accordance with standards of the Public Accounting Oversight Board (United States) by a recognized firm of certified public accounts, and (B) annual audited consolidated and, if available, consolidating balance sheets, statements of operations and cash flows certified by a recognized firm of certified public accountants. The financial statements described in the foregoing clauses (A) and (B) shall be delivered within 5 Business Days after the statements are provided to Borrower in reviewed/certified form by such public accountants, and if Agent requests, Borrower shall deliver to Agent and Lenders monthly unaudited and unreviewed consolidated balance sheets, statements of operations and cash flow statements within 30 days after the end of each month. All such statements are to be materially prepared using GAAP (subject, in the case of unaudited financial statements, to the absence of footnotes and normal year-end and audit adjustments) and, if Borrower is a publicly held company, are to be materially in compliance with applicable SEC requirements. All financial statements delivered pursuant to this Section 6.3 shall be accompanied by a compliance certificate, signed by the chief financial officer of Borrower, in the form attached hereto as Exhibit D. Borrower shall deliver to Agent and Lenders (i) as soon as available and in any event not later than 30 days after the end of each fiscal year of Borrower, an annual operating plan for Borrower, on a consolidated and, if available, consolidating basis, approved by the Board of Directors of Borrower, for the current fiscal year, in form and substance satisfactory to Agent and (ii) such budgets, sales projections, or other financial information as Agent or any Lender may reasonably request from time to time generally prepared by Borrower in the Ordinary Course of Business. Lenders and Agent hereby acknowledge that until all of the information contained in the financial statements provided by Borrower pursuant to this section is fully disclosed in Borrower’s public filings

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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with the SEC, such information will remain both material and non-public; for the avoidance of doubt, forward-looking statements, including but not limited to the annual operating plan and sales projections that Borrower will provide to Lenders and Agent pursuant to this section, will be material and non-public information until Borrower has filed with the SEC financial statements reporting results for all of the time periods covered by such plans and projections. The Borrower hereby agrees that, notwithstanding any repayment of the Term Loans or termination of this Agreement, so long as Borrower is a private company Borrower shall continue to deliver to each Lender the documents required under this Section 6.3 until each of the Warrants have either expired by their terms or been exercised. The provisions of the immediately preceding sentence shall survive the termination of this Agreement.

6.4. Insurance. Borrower, at its expense, shall maintain, and shall cause each Subsidiary to maintain, insurance (including, without limitation, comprehensive general liability, hazard, and business interruption insurance) with respect to all of its properties and businesses (including, the Collateral), in such amounts and covering such risks as is carried generally in accordance with sound business practice by companies in similar businesses similarly situated and in any event with deductible amounts, insurers and policies that shall be reasonably acceptable to Agent. Borrower shall deliver to Agent within fourteen (14) days after the Closing Date certificates of insurance evidencing such coverage, together with endorsements to such policies naming Agent as a lender loss payee or additional insured, as appropriate, in form and substance satisfactory to Agent (except that Agent shall not be named as loss payee with respect to insurance covering equipment described in clause (c) of Section 3.1 hereof). Each policy shall provide that coverage may not be canceled or altered by the insurer except upon 10 days prior written notice to Agent and shall not be subject to co-insurance (except for retentions and deductibles that are customarily set forth in such policies). Borrower appoints Agent as its attorney-in-fact to make, settle and adjust all claims under and decisions with respect to Borrower’s policies of insurance, and to receive payment of and execute or endorse all documents, checks or drafts in connection with insurance payments only to the extent necessary to satisfy all Obligations hereunder. Agent shall not act as Borrower’s attorney-in-fact unless an Event of Default has occurred and is continuing. The appointment of Agent as Borrower’s attorney in fact is a power coupled with an interest and is irrevocable until all of the Obligations are indefeasibly paid in full. Proceeds of insurance shall be applied, at the option of Agent, to repair or replace the Collateral or to reduce any of the Obligations.

6.5. Taxes. Borrower shall, and shall cause each Subsidiary that is incorporated under the laws of any State of the United States or the District of Columbia to, timely file all tax reports and pay and discharge all federal taxes and material state and local taxes, assessments and governmental charges or levies imposed upon it, or its income or profits or upon its properties or any part thereof, before the same shall be in default and before the date on which penalties attach thereto except to the extent such taxes, assessments or governmental charges or levies are the subject of a Permitted Contest.

6.6. Agreement with Landlord/Bailee. Borrower shall obtain and maintain such Access Agreement(s) with respect to any real property on which (a) Borrower’s principal place of business, (b) any of Borrower’s books or records or (c) Collateral with an aggregate value in excess of $25,000 is located (other than real property owned by Borrower) as Agent may require.

6.7. Protection of Intellectual Property. Borrower shall take all necessary actions to: (a) protect, defend and maintain the validity and enforceability of its Intellectual Property to the extent material to the conduct of its business now or heretofore conducted by it or proposed to be conducted by it, (b) promptly advise Agent in writing of material infringements of its Intellectual Property of which any Executive Officer of Borrower has knowledge and, should the Intellectual Property be material to Borrower’s business and should Borrower have enforcement rights with respect to such Intellectual Property, promptly sue for infringement, misappropriation or dilution and to recover any and all damages

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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for such infringement, misappropriation or dilution, (c) not allow any Intellectual Property material to Borrower’s business to be abandoned, forfeited or dedicated to the public without Agent’s written consent, and (d) notify Agent reasonably promptly (but in any event within 3 Business Days) if it knows or has reason to know that any application or registration relating to any patent, trademark or copyright (now or hereafter existing) material to its business may become abandoned or dedicated, or if any adverse determination or development (including the institution of, or any such determination or development in, any proceeding in the United States Patent and Trademark Office, the United States Copyright Office or any court) regarding Borrower’s ownership of any Intellectual Property material to its business, its right to register the same, or to keep and maintain the same. Borrower shall remain liable under each of its Intellectual Property licenses pursuant to which it is a licensee (“Licenses”) to observe and perform all of the conditions and obligations to be observed and performed by it thereunder. None of Agent or any Lender shall have any obligation or liability under any such License by reason of or arising out of this Agreement, the granting of a lien, if any, in such License or the receipt by Agent (on behalf of itself and Lenders) of any payment relating to any such License. None of Agent or any Lender shall be required or obligated in any manner to perform or fulfill any of the obligations of Borrower under or pursuant to any License, or to make any payment, or to make any inquiry as to the nature or the sufficiency of any payment received by it or the sufficiency of any performance by any party under any License, or to present or file any claims, or to take any action to collect or enforce any performance or the payment of any amounts which may have been assigned to it or which it may be entitled at any time or times.

6.8. Special Collateral Covenants.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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6.9. Further Assurances. Borrower shall, upon request of Agent, furnish to Agent such further information, execute and deliver to Agent such documents and instruments (including, without limitation, UCC financing statements) and shall do such other acts and things as Agent may at any time reasonably request relating to the perfection or protection of the security interest created by this Agreement or for the purpose of carrying out the intent of this Agreement and the other Debt Documents.

6.10. Additional Subsidiaries. Promptly (and in any event within thirty (30) days) after the formation or acquisition of any Subsidiary of Borrower, Borrower shall cause to be executed and delivered to Agent the following: (i) by such new Subsidiary other than a Foreign Subsidiary (as hereinafter defined), a Guaranty pursuant to which such Subsidiary shall guarantee the payment and performance of all of the Obligations and pursuant to which Agent, for the benefit of itself and the Lenders, shall be granted a first priority (subject to Permitted Liens) and perfected security interest in all assets of such Subsidiary of the same types constituting “Collateral” under Section 3.1 hereof to secure the Obligations, (ii) by the Borrower or any Guarantor (as applicable) that is such Subsidiary’s direct parent company, an amendment to the Pledge Agreement delivered on the Closing Date or a new Pledge Agreement substantially in the form of the Pledge Agreement delivered on the Closing Date (or otherwise in form and substance reasonably satisfactory to Lender), as applicable, and pursuant to which either (1) all of the capital stock of such new Subsidiary (if such Subsidiary is not a Foreign Subsidiary) or (2) 65% of the capital stock of such new Subsidiary (if such Subsidiary is a Foreign Subsidiary) shall be pledged to Agent, for the benefit of the Lenders, on a first priority and perfected basis to secure the Obligations, and (iii) by the Borrower, such other related documents (including closing certificates, legal opinions and other similar documents) as Agent may reasonably request, all in form and substance reasonably satisfactory to Agent; provided, however, that this Section 6.10 shall not operate as a consent to any formation or acquisition of a Subsidiary that is not expressly permitted under this Agreement.

7. NEGATIVE COVENANTS

7.1. Liens. Borrower shall not, and shall not permit any Subsidiary to, create, incur, assume or permit to exist any lien, security interest, claim or encumbrance or grant any negative pledges on any Collateral or Intellectual Property, except Permitted Liens, and with respect to Intellectual Property, except as contemplated by Section 7.3(d).

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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7.2. Indebtedness. Borrower shall not, and shall not permit any Subsidiary to, directly or indirectly create, incur, assume, permit to exist, guarantee or otherwise become or remain directly or indirectly liable with respect to, any Indebtedness (as hereinafter defined), except for the following:

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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As used in this Agreement, the term “Indebtedness” shall mean, with respect to any person, at any date, without duplication, (1) all obligations of such person for borrowed money, (2) all obligations of such person evidenced by bonds, debentures, notes or other similar instruments, or upon which interest payments are customarily made, (3) all obligations of such person to pay the deferred purchase price of property or services, but excluding obligations to trade creditors incurred in the Ordinary Course of Business and not past due by more than 90 days, (4) all capital lease obligations of such person, (5) the principal balance outstanding under any synthetic lease, tax retention operating lease, off-balance sheet loan or similar off-balance sheet financing product, (6) all obligations of such person to purchase securities (or other property) which arise out of or in connection with the issuance or sale of the same or substantially similar securities (or property), (7) all contingent or non-contingent obligations of such person to reimburse any bank or other person in respect of amounts paid under a letter of credit or similar instrument, (8) all equity securities of such person subject to repurchase or redemption otherwise than at the sole option of such person, (9) all “earnouts” and similar payment obligations of such person, (10) all indebtedness secured by a lien on any asset of such person, whether or not such indebtedness is otherwise an obligation of such person, (11) all obligations of such person under any foreign exchange contract, currency swap agreement, interest rate swap, cap or collar agreement or other similar agreement or arrangement designed to alter the risks of that person arising from fluctuations in currency values or interest rates, in each case whether contingent or matured, and (12) all obligations or liabilities of others guaranteed by such person. Without limiting the generality of the immediately preceding sentence, “Indebtedness” shall not include (A) any obligations owing under operating leases for real property leased by Borrower or any of its Subsidiaries or (B) any landlord-financed tenant improvements that are capitalized into such operating leases.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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7.3. Dispositions. Borrower shall not, and shall not permit any Subsidiary to, convey, sell, rent, lease, sublease, mortgage, license, transfer or otherwise dispose of (collectively, “Transfer”) any of the Collateral or any Intellectual Property, except for the following (collectively, “Permitted Dispositions”): (a) sales of Inventory in the Ordinary Course of Business, (b) non-exclusive licenses for the use of Borrower’s Intellectual Property, in each case in the Ordinary Course of Business, (c) dispositions by Borrower or any of its Subsidiaries of tangible assets for cash and fair value that are no longer used or useful in the business of Borrower or such Subsidiary so long as (i) no Default or Event of Default exists at the time of such disposition or would be caused after giving effect thereto and (ii) the fair market value of all such assets disposed of does not exceed $50,000 in the aggregate during any calendar year, and (d) exclusive licenses for the use of Borrower’s Intellectual Property, so long as, with respect to each such exclusive license, (i) no Default of Event of Default exists at the time of such Transfer, (ii) the license constitutes an arms-length transaction made in the Ordinary Course of Business and the terms of which, on their face, do not provide for a sale or assignment of any Intellectual Property, (iii) the Borrower delivers no later than 10 days prior to execution of definitive documents, written notice and a brief summary as of such date of the terms of the license to Agent, (iv) the Borrower delivers to Agent copies of the final executed licensing documents in connection with the license promptly upon consummation of the license, and (v) all royalties, milestone payments or other proceeds arising from the licensing agreement are paid to a deposit account that is governed by an Account Control Agreement.

7.4. Change in Name, Location or Executive Office; Change in Business; Change in Fiscal Year. Borrower shall not, and shall not permit any Subsidiary to, (a) change its name or its state of organization, (b) relocate its chief executive office without 30 days prior written notification to Agent, (c) engage in any business other than or reasonably related or incidental to the businesses currently engaged in by Borrower or any of its Subsidiaries, or (d) change its fiscal year end. Borrower shall not, and taken together with its Subsidiaries as a whole shall not, cease to conduct business substantially in the manner conducted by Borrower or any of its Subsidiaries as of the date of this Agreement.

7.5. Mergers or Acquisitions. Borrower shall not merge or consolidate, or permit any Subsidiary to merge or consolidate, with or into any other person or entity (other than mergers of a Subsidiary into Borrower in which Borrower is the surviving entity) or acquire, or permit any Subsidiary to acquire, all or substantially all of the capital stock or property of another person or entity. Notwithstanding the foregoing, Borrower any of its Subsidiaries may acquire all or substantially all of the assets or stock of another person or entity (such person or entity, the “Target”) so long as (a) Agent and each Lender shall receive at least ten (10) Business Days’ prior written notice of such proposed acquisition, which notice shall include a reasonably detailed description of such proposed acquisition; (b) such acquisition shall only comprise a business, or those assets of a business, substantially of the type engaged in by Borrower or its Subsidiaries as of the Closing Date, or in the fields of energy, chemicals, carbon management and pharmaceuticals or natural extensions thereof or technologies related thereto; (c) such acquisition shall be consensual and shall have been approved by Target’s board of directors or similar governing body (as applicable); (d) that portion of the purchase price paid and/or payable in cash and Cash Equivalents in connection with all acquisitions during the term of this Agreement (less any cash or Cash Equivalents acquired from Target, but including all transaction costs and all Indebtedness, liabilities and contingent obligations incurred or assumed in connection therewith or otherwise reflected in a consolidated balance sheet of Borrower and Target) shall not exceed the greater of (1) $10,000,000 and (2) thirty-five percent (35%) of the net cash proceeds from all public offerings of common stock of the Borrower; (e) if at the time of and after giving effect to such acquisition Borrower is, or on a pro forma basis will become, Cash Flow Negative, Agent shall have received evidence satisfactory to Agent that Borrower has, at the time of and after giving effect to such acquisition, Balance Sheet Cash in an amount equal to or greater than the product of (i) negative eighteen times (ii) the Cash Burn Amount; (f) the business and assets acquired in such Permitted Acquisition shall be free and clear of all liens (other

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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than Permitted Liens); (g) at or prior to the closing of any permitted acquisition (other than an acquisition by a Foreign Subsidiary or by Borrower or Guarantor of a Foreign Subsidiary), Agent will be granted a first priority perfected lien (subject to Permitted Liens) in all assets acquired pursuant thereto or in the assets and stock of Target, and Borrower or Guarantor (as applicable) and Target shall have executed such documents and taken such actions as may be required by Agent in connection therewith; (h) on or prior to the date of such acquisition, Agent shall have received, in form and substance reasonably satisfactory to Agent, copies of the acquisition agreement and related agreements and instruments, and all opinions, certificates, lien search results and other documents reasonably requested by Agent; and (i) at the time of such acquisition and after giving effect thereto, no Default or Event of Default has occurred and is continuing.

7.6. Restricted Payments. Borrower shall not, and shall not permit any Subsidiary to, (a) declare or pay any dividends or make any other distribution or payment on account of or redeem, retire, defease or purchase any capital stock (other than (i) the payment of dividends to Borrower or any Guarantor, (ii) absent the occurrence and the continuance of a Default or Event of Default before and after giving effect to any such payment, the payment of dividends with respect to the Series B Preferred Stock and the Series D Preferred Stock, so long as such dividends do not exceed $500,000 in the aggregate during any calendar year, (iii) the distribution of dividends payable solely in capital stock of the Borrower, and (iv) absent the occurrence and the continuance of a Default or Event of Default before and after giving effect to any such repurchase payment, the repurchase of shares, options or warrants thereof from employees, former employees, directors, former directors, consultants, former consultants, advisors or former advisors and their permitted transferees or estates, of Borrower or any of its Subsidiaries upon their death, termination of their employment or service period or retirement, so long as such repurchase payments do not exceed $250,000 in the aggregate during any calendar year, and (iv) dividends payable exclusively in the capital stock of the Borrower), (b) make any payment in respect of management fees or consulting fees (or similar fees) to any equityholder or other affiliate of Borrower other than (i) fees for general and administrative services provided to Borrower and its Subsidiaries by Maxygen in an aggregate amount not to exceed [*] during any calendar year and (ii) royalties or other payments in connection with Intellectual Property licenses from Maxygen in an amount not to exceed the amounts calculated to be paid under the Maxygen License Agreement as may be amended pursuant to Section 7.11, (c) be a party to or bound by an agreement that restricts a Subsidiary from paying dividends or otherwise distributing property to Borrower, (d) make any payments of intercompany Indebtedness that is owing by Borrower or any Guarantor (except as provided in the subordination terms of the applicable Intercompany Note then in effect with respect to such intercompany Indebtedness) or (e) purchase or make any payment on or with respect to any Subordinated Indebtedness, except as expressly permitted by the subordination terms thereof that have been approved by Agent.

7.7. Investments. Borrower shall not, and shall not permit any Subsidiary to, directly or indirectly (a) acquire or own, or make any loan, advance or capital contribution (an “Investment”) in or to any person or entity, (b) acquire any Subsidiary (other than pursuant to the terms and conditions of Section 7.5 and upon the satisfaction of each of the conditions set forth in Section 6.10) or create any Subsidiary (unless each of the conditions set forth in Section 6.10 are satisfied), or (c) engage in any joint venture or partnership with any other person or entity, other than, with respect to each of the foregoing clauses (a), (b) and (c): (i) Investments existing on the date hereof and set forth on Schedule B to this Agreement, (ii) Investments in cash and Cash Equivalents (as defined below), (iii) Investments by way of intercompany loans to the extent permitted under Section 7.2(d), (iv) loans or advances to employees of Borrower or any of its Subsidiaries to finance travel, entertainment and relocation expenses and other ordinary business purposes in the ordinary course of business as presently conducted, provided that the aggregate outstanding principal amount of all loans and advances permitted pursuant to this clause (iv) shall not exceed $25,000 at any time, (v) capital contributions by the Borrower or any Guarantor to the

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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Borrower or any Guarantor; and (vi) capital contributions by Borrower or any Guarantor to the Foreign Subsidiaries (A) in an aggregate amount in any fiscal quarter which, when added to the aggregate amount of any loans made by Borrower or any Guarantor to the Foreign Subsidiaries in such fiscal quarter pursuant to Section 7.2(e), shall not exceed twenty percent (20%) of the Balance Sheet Cash of the Borrower as of the first day of the fiscal quarter in which such investment is made and (B) so long as no Default or Event of Default would occur both before and after giving effect to any such capital contribution. The term “Cash Equivalents” means (u) any readily-marketable securities (i) issued by, or directly, unconditionally and fully guaranteed or insured by the United States federal government or (ii) issued by any agency of the United States federal government the obligations of which are fully backed by the full faith and credit of the United States federal government, (v) any readily-marketable direct obligations issued by any other agency of the United States federal government, any state of the United States or any political subdivision of any such state or any public instrumentality thereof, in each case having a rating of at least “A-1” from S&P or at least “P-1” from Moody’s, (w) any commercial paper rated at least “A-1” by S&P or “P-1” by Moody’s and issued by any entity organized under the laws of any state of the United States, (x) any U.S. dollar-denominated time deposit, insured certificate of deposit, overnight bank deposit or bankers’ acceptance issued or accepted by (i) Agent or (ii) any commercial bank that is (A) organized under the laws of the United States, any state thereof or the District of Columbia, (B) “adequately capitalized” (as defined in the regulations of its primary federal banking regulators) and (C) has Tier 1 capital (as defined in such regulations) in excess of $250,000,000, (y) shares of any United States money market fund that (i) has substantially all of its assets invested continuously in the types of investments referred to in clause (u), (v), (w) or (x) above with maturities as set forth in the proviso below, (ii) has net assets in excess of $500,000,000 and (iii) has obtained from either S&P or Moody’s the highest rating obtainable for money market funds in the United States; provided, however, that the maturities of all obligations specified in any of clauses (u), (v), (w) and (x) above shall not exceed 365 days, and (z) in the case of Investments by any Foreign Subsidiary, Cash Equivalents shall also include (i) direct obligations of the sovereign nation (or any agency thereof) in which such Foreign Subsidiary is organized and is conducting business or where such Investment is made, or in obligations fully and unconditionally guaranteed by such sovereign nation (or any agency thereof), in each case maturing within 365 days after such date and having, at the time of the acquisition thereof, a rating equivalent to at least A-1 from S&P and at least P-1 from Moody’s, (ii) investments of the type and maturity described in clauses (u) through (y) above of foreign obligors, which Investments or obligors (or the parents of such obligors) have ratings described in such clauses or equivalent ratings from comparable foreign rating agencies, (iii) shares of money market mutual or similar funds which invest exclusively in assets otherwise satisfying the requirements of this definition (including this proviso) and (iv) other short-term investments utilized by Foreign Subsidiaries in accordance with normal investment practices for cash management in investments analogous to the foregoing investments in clauses (u) through (y).

7.8. Transactions with Affiliates. Borrower shall not, and shall not permit any Subsidiary to, directly or indirectly enter into or permit to exist any transaction with any Affiliate (as defined below) of Borrower or any Subsidiary except for transactions that are in the Ordinary Course of Business, upon fair and reasonable terms that are no more favorable to such Affiliate of Borrower or such Subsidiary than would be obtained in an arm’s length transaction. Without limiting the generality of the immediately preceding sentence, the following transactions and agreements shall be deemed to be in compliance with this Section 7.8: (1) the Maxygen License Agreement (as amended or modified from time to time in accordance with the terms and conditions of this Agreement) and (2) any agreements between the Borrower and Shell entered into from time to time after the Closing Date and relating to either (A) an equity investment by Shell in the Borrower and the grant by the Borrower of investor rights to Shell (including without limitation, one or more board of director seats and/or attendant rights) and (B) a licensing and/or joint venture arrangement related to one or more of the following fields: conversion of

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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biomass to chemicals, fuel additives, lubricants or fuels; conversion of sugars to chemicals, fuel additives, lubricants or fuels; and carbon management, including, but not limited to, conversion of carbon to biomass and sequestration of carbon to storage materials. As used herein, “Affiliate” shall mean, with respect to Borrower or any Subsidiary, (a) each person that, directly or indirectly, owns or controls 5% or more of the stock or membership interests having ordinary voting power in the election of directors or managers of Borrower or any Subsidiary, and (b) each person that controls, is controlled by or is under common control with Borrower or any Subsidiary.

7.9. Compliance. Borrower shall not, and shall not permit any Subsidiary to (a) fail to comply in all material respects with the laws and regulations described in clauses (a) through and including (d) of Section 5.8 herein, (b) use any portion of the Term Loans to purchase or carry margin stock (within the meaning of Regulation U of the Federal Reserve Board) or (c) fail to comply with or violate any other law or regulation, the failure or violation of which law or regulation described in this clause (c) could reasonably be expected to have a Material Adverse Effect, or permit any Subsidiary to do any of the foregoing.

7.10. Deposit Accounts and Securities Accounts. Other than with respect to deposit accounts used solely to fund payroll and withholding taxes, Borrower will not directly or indirectly maintain or establish any deposit account or securities account, unless Agent, Borrower and the depository institution or securities intermediary at which the account is or will be maintained enter into a deposit account control agreement or securities account control agreement, as the case may be (an “Account Control Agreement”), in form and substance satisfactory to Agent (which agreement shall provide that such depository institution or securities intermediary shall comply with all instructions of Agent without further consent of Borrower, including, without limitation, an instruction by Agent to follow a notice of exclusive control or similar notice (such notice, a “Notice of Exclusive Control”)), prior to or concurrently with the establishment of such deposit account or securities account (or in the case of any such deposit account or securities account maintained as of the date hereof, prior to or concurrently with the entering into this Agreement). Agent may give a Notice of Exclusive Control with respect to any deposit account or securities account at any time at which an Event of Default has occurred and is continuing.

7.11. Amendments to Certain Material Agreements. Borrower shall not amend, modify or waive any provision of (a) the Maxygen License Agreement (unless the net effect of such amendment, modification or waiver of the Maxygen License Agreement in the reasonable business judgment of the Borrower is not materially adverse to Borrower and its Subsidiaries taken as a whole) or (b) any document relating to any of the Subordinated Indebtedness, in each case without the prior written consent of Agent and the Requisite Lenders.

8. DEFAULT AND REMEDIES.

8.1. Events of Default. Borrower shall be in default under this Agreement and each of the other Debt Documents if (each of the following, an “Event of Default”):

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[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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8.2. Lender Remedies. Upon the occurrence of any Event of Default, Agent may, and at the written request of the Requisite Lenders shall, terminate the Commitments with respect to further Term Loans and declare any or all of the Obligations to be immediately due and payable, without demand or notice to Borrower and the accelerated Obligations shall bear interest at the Default Rate pursuant to Section 2.6, provided that, upon the occurrence of any Event of Default specified in Section 8.1(h) above, the Obligations shall be automatically accelerated. After the occurrence of an Event of Default, Agent shall have (on behalf of itself and Lenders) all of the rights and remedies of a secured party under the UCC, and under any other applicable law. Without limiting the foregoing, Agent shall have the right to, and at the written request of the Requisite Lenders shall, (a) notify any account debtor of Borrower or any obligor on any instrument which constitutes part of the Collateral to make payments to Agent (for the benefit of itself and Lenders), (b) with or without legal process, enter any premises where the Collateral may be and take possession of and remove the Collateral from the premises or store it on the premises, (c) sell the Collateral at public or private sale, in whole or in part, and have the right to bid and purchase at such sale, or (d) lease or otherwise dispose of all or part of the Collateral, applying proceeds from such disposition to the Obligations in accordance with Section 8.4. If requested by Agent, Borrower shall promptly assemble the Collateral and make it available to Agent at a place to be designated by Agent. Agent may also render any or all of the Collateral unusable at Borrower’s premises and may dispose of such Collateral on such premises without liability for rent or costs. Any notice that Agent is required to give to Borrower under the UCC of the time and place of any public sale or the time after which any private sale or other intended disposition of the Collateral is to be made shall be deemed to constitute reasonable notice if such notice is given in accordance with this Agreement at least 10 days prior to such action. Effective only upon the occurrence and during the continuance of an Event of Default, Borrower hereby irrevocably appoints Agent (and any of Agent’s designated officers or employees) as Borrower’s true and lawful attorney to: (i) take any of the actions specified above in this paragraph; (ii) endorse Borrower’s name on any checks or other forms of payment or security that may come into Agent’s possession; (iii) settle and adjust disputes and claims respecting the accounts directly with account debtors, for amounts and upon terms which Agent determines to be reasonable; and (iv) do such other and further acts and deeds in the name of Borrower that Agent may deem necessary or desirable to enforce its rights in or to any of the Collateral or to perfect or better perfect Agent’s security interest (on behalf of itself and Lenders) in any of the Collateral. The appointment of Agent as Borrower’s attorney in fact is a power coupled with an interest and is irrevocable until the Termination Date.

8.3. Additional Remedies. In addition to the remedies provided in Section 8.2 above, Borrower hereby grants to Agent (on behalf of itself and Lenders) and any transferee of Collateral, for purposes of exercising its remedies as provided herein, an irrevocable, nonexclusive license (exercisable without payment of royalty or other compensation to Borrower and subject to any exclusive licenses granted in compliance with the terms and conditions of Section 7.3(d)) to use, license or sublicense any Intellectual Property now owned or hereafter acquired by Borrower, and wherever the same may be located, and

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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including in such license access to all media in which any of the licensed items may be recorded or stored and to all computer software and programs used for the compilation or printout thereof.

8.4. Application of Proceeds. Proceeds from any Transfer of the Collateral or the Intellectual Property (other than Permitted Dispositions) and all payments made or proceeds of Collateral received by Agent during the continuance of an Event of Default may be applied in Agent’s sole discretion: (a) first, to pay all fees, costs, indemnities, reimbursements and expenses then due to Agent under the Debt Documents in its capacity as Agent under the Debt Documents, (b) second, to pay all fees, costs, indemnities, reimbursements and expenses then due to Lenders under the Debt Documents in accordance with their respective Pro Rata Shares, until paid in full, (c) third, to pay all interest on the Term Loans then due to Lenders in accordance with their respective Pro Rata Shares, until paid in full (other than interest accrued after the commencement of any proceeding referred to in Section 8.1(h) if a claim for such interest is not allowable in such proceeding), (d) fourth, to pay all principal on the Term Loans then due to Lenders in accordance with their respective Pro Rata Shares, until paid in full (e) fifth, to pay all other Obligations then due to Lenders in accordance with their respective Pro Rata Shares, until paid in full (including, without limitation, all interest accrued after the commencement of any proceeding referred to in Section 8.1(h) whether or not a claim for such interest is allowable in such proceeding), and (f) sixth, to Borrower or as otherwise required by law. Borrower shall remain fully liable for any deficiency.

9. THE AGENT.

9.1. Appointment of Agent.

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9.2. Agent’s Reliance, Etc. Neither Agent nor any of its affiliates nor any of their respective directors, officers, agents, employees or representatives shall be liable for any action taken or omitted to be taken by it or them hereunder or under any other Debt Documents, or in connection herewith or therewith, except for damages caused by its or their own gross negligence or willful misconduct as finally determined by a court of competent jurisdiction. Without limiting the generality of the foregoing, Agent: (a) may treat the payee of any Note as the holder thereof until such Note has been assigned in accordance

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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with Section 10.1; (b) may consult with legal counsel, independent public accountants and other experts, whether or not selected by it, and shall not be liable for any action taken or omitted to be taken by it in good faith in accordance with the advice of such counsel, accountants or experts; (c) shall not be responsible or otherwise incur liability for any action or omission taken in reliance upon the instructions of the Requisite Lenders, (d) makes no warranty or representation to any Lender and shall not be responsible to any Lender for any statements, warranties or representations made in or in connection with this Agreement or the other Debt Documents; (e) shall not have any duty to inspect the Collateral (including the books and records) or to ascertain or to inquire as to the performance or observance of any provision of any Debt Document, whether any condition set forth in any Debt Document is satisfied or waived, as to the financial condition of Borrower or as to the existence or continuation or possible occurrence or continuation of any Default or Event of Default and shall not be deemed to have notice or knowledge of such occurrence or continuation unless it has received a notice from Borrower or any Lender describing such Default or Event of Default clearly labeled “notice of default”; (f) shall not be responsible to any Lender for the due execution, legality, validity, enforceability, effectiveness, genuineness, sufficiency or value of, or the attachment, perfection or priority of any lien created or purported to be created under or in connection with, any Debt Document or any other instrument or document furnished pursuant hereto or thereto; and (g) shall incur no liability under or in respect of this Agreement or the other Debt Documents by acting upon any notice, consent, certificate or other instrument or writing (which may be by telecopy, telegram, cable or telex) believed by it to be genuine and signed or sent or otherwise authenticated by the proper party or parties.

9.3. GECC and Affiliates. GECC shall have the same rights and powers under this Agreement and the other Debt Documents as any other Lender and may exercise the same as though it were not Agent; and the term “Lender” or “Lenders” shall, unless otherwise expressly indicated, include GECC in its individual capacity. GECC and its affiliates may lend money to, invest in, and generally engage in any kind of business with, Borrower, any of Borrower’s Subsidiaries, any of their Affiliates and any person who may do business with or own securities of Borrower, any of Borrower’s Subsidiaries or any such Affiliate, all as if GECC were not Agent and without any duty to account therefor to Lenders. GECC and its affiliates may accept fees and other consideration from Borrower for services in connection with this Agreement or otherwise without having to account for the same to Lenders. Each Lender acknowledges the potential conflict of interest between GECC as a Lender holding disproportionate interests in the Term Loans and GECC as Agent, and expressly consents to, and waives, any claim based upon, such conflict of interest.

9.4. Lender Credit Decision. Each Lender acknowledges that it has, independently and without reliance upon Agent or any other Lender and based on the financial statements referred to in Section 6.3 and such other documents and information as it has deemed appropriate, made its own credit and financial analysis of Borrower and its own decision to enter into this Agreement. Each Lender also acknowledges that it will, independently and without reliance upon Agent or any other Lender and based on such documents and information as it shall deem appropriate at the time, continue to make its own credit decisions in taking or not taking action under this Agreement. Each Lender acknowledges the potential conflict of interest of each other Lender as a result of Lenders holding disproportionate interests in the Term Loans, and expressly consents to, and waives, any claim based upon, such conflict of interest.

9.5. Indemnification. Lenders shall and do hereby indemnify Agent (to the extent not reimbursed by Borrower and without limiting the obligations of Borrower hereunder), ratably according to their respective Pro Rata Shares from and against any and all liabilities, obligations, losses, damages, penalties, actions, judgments, suits, costs, expenses or disbursements of any kind or nature whatsoever that may be imposed on, incurred by, or asserted against Agent in any way relating to or arising out of this Agreement or any other Debt Document or any action taken or omitted to be taken by Agent in

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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connection therewith; provided that no Lender shall be liable for any portion of such liabilities, obligations, losses, damages, penalties, actions, judgments, suits, costs, expenses or disbursements resulting from Agent’s gross negligence or willful misconduct as finally determined by a court of competent jurisdiction. Without limiting the foregoing, each Lender agrees to reimburse Agent promptly upon demand for its Pro Rata Share of any out-of-pocket expenses (including reasonable counsel fees) incurred by Agent in connection with the preparation, execution, delivery, administration, modification, amendment or enforcement (whether through negotiations, legal proceedings or otherwise) of, or legal advice in respect of rights or responsibilities under, this Agreement and each other Debt Document, to the extent that Agent is not reimbursed for such expenses by Borrower. The provisions of this Section 9.5 shall survive the termination of this Agreement.

9.6. Successor Agent. Agent may resign at any time by giving not less than 30 days’ prior written notice thereof to Lenders and Borrower. Upon any such resignation, the Requisite Lenders shall have the right to appoint a successor Agent. If no successor Agent shall have been so appointed by the Requisite Lenders and shall have accepted such appointment within 30 days after the resigning Agent’s giving notice of resignation, then the resigning Agent may, on behalf of Lenders, appoint a successor Agent, which shall be a Lender, if a Lender is willing to accept such appointment, or otherwise shall be a commercial bank or financial institution or a subsidiary of a commercial bank or financial institution if such commercial bank or financial institution is organized under the laws of the United States of America or of any State thereof and has a combined capital and surplus of at least $300,000,000. If no successor Agent has been appointed pursuant to the foregoing, within 30 days after the date such notice of resignation was given by the resigning Agent, such resignation shall become effective and the Requisite Lenders shall thereafter perform all the duties of Agent hereunder until such time, if any, as the Requisite Lenders appoint a successor Agent as provided above. Upon the acceptance of any appointment as Agent hereunder by a successor Agent, such successor Agent shall succeed to and become vested with all the rights, powers, privileges and duties of the resigning Agent. Upon the earlier of the acceptance of any appointment as Agent hereunder by a successor Agent or the effective date of the resigning Agent’s resignation, the resigning Agent shall be discharged from its duties and obligations under this Agreement and the other Debt Documents, except that any indemnity rights or other rights in favor of such resigning Agent shall continue. After any resigning Agent’s resignation hereunder, the provisions of this Section 9 shall inure to its benefit as to any actions taken or omitted to be taken by it while it was acting as Agent under this Agreement and the other Debt Documents.

9.7. Setoff and Sharing of Payments. In addition to any rights now or hereafter granted under applicable law and not by way of limitation of any such rights, upon the occurrence and during the continuance of any Event of Default and subject to Section 9.8(e), each Lender is hereby authorized at any time or from time to time upon the direction of Agent, without notice to Borrower or any other person, any such notice being hereby expressly waived, to offset and to appropriate and to apply any and all balances held by it at any of its offices for the account of Borrower (regardless of whether such balances are then due to Borrower) and any other properties or assets at any time held or owing by that Lender or that holder to or for the credit or for the account of Borrower against and on account of any of the Obligations that are not paid when due. Any Lender exercising a right of setoff or otherwise receiving any payment on account of the Obligations in excess of its Pro Rata Share thereof shall purchase for cash (and the other Lenders or holders shall sell) such participations in each such other Lender’s or holder’s Pro Rata Share of the Obligations as would be necessary to cause such Lender to share the amount so offset or otherwise received with each other Lender or holder in accordance with their respective Pro Rata Shares of the Obligations. Borrower agrees, to the fullest extent permitted by law, that (a) any Lender may exercise its right to offset with respect to amounts in excess of its Pro Rata Share of the Obligations and may sell participations in such amounts so offset to other Lenders and holders and (b) any Lender so purchasing a participation in the Term Loans made or other Obligations held by other Lenders or holders

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may exercise all rights of offset, bankers’ lien, counterclaim or similar rights with respect to such participation as fully as if such Lender or holder were a direct holder of the Term Loans and the other Obligations in the amount of such participation. Notwithstanding the foregoing, if all or any portion of the offset amount or payment otherwise received is thereafter recovered from the Lender that has exercised the right of offset, the purchase of participations by that Lender shall be rescinded and the purchase price restored without interest. The term “Pro Rata Share” means, with respect to any Lender at any time, the percentage obtained by dividing (x) the Commitment of such Lender then in effect (or, if such Commitment is terminated, the aggregate outstanding principal amount of the Term Loans owing to such Lender) by (y) the Total Commitment then in effect (or, if the Total Commitment is terminated, the outstanding principal amount of the Term Loans owing to all Lenders).

9.8. Advances; Payments; Non-Funding Lenders; Information; Actions in Concert.

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10. MISCELLANEOUS.

10.1. Assignment. Subject to the terms of this Section 10.1, any Lender may make an assignment to an assignee of, or sell participations in, at any time or times, the Debt Documents, its Commitment, Term Loans or any portion thereof or interest therein, including any Lender’s rights, title, interests, remedies, powers or duties thereunder. Any assignment by a Lender shall: (i) except in the case of an assignment to a Qualified Assignee (as defined below), require the consent of each Lender (which consent shall not be unreasonably withheld, conditioned or delayed), (ii) in the case of an assignment to an entity that is not a Qualified Assignee (as defined below), require the consent of Borrower (which consent shall not be unreasonably withheld, conditioned or delayed), (iii) require the execution of an assignment agreement in form and substance reasonably satisfactory to, and acknowledged by, Agent (an “Assignment Agreement”); (iv) be conditioned on such assignee Lender representing to the assigning Lender and Agent that it is purchasing the applicable Commitment and/or Term Loans to be assigned to it for its own account, for investment purposes and not with a view to the distribution thereof; (v) be in an aggregate amount of not less than $1,000,000, unless such assignment is made to an existing Lender or an affiliate of an existing Lender or is of the assignor’s (together with its affiliates’) entire interest of the Term Loans or is made with the prior written consent of Agent; and (vi) include a payment to Agent of an assignment fee of $3,500. In the case of an assignment by a Lender under this Section 10.1, the assignee shall have, to the extent of such assignment, the same rights, benefits and obligations as all other Lenders hereunder. The assigning Lender shall be relieved of its obligations hereunder with respect to its Commitment and Term Loans, as applicable, or assigned portion thereof from and after the date of such

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assignment. Borrower hereby acknowledges and agrees that any assignment shall give rise to a direct obligation of Borrower to the assignee and that the assignee shall be considered to be a “Lender”. In the event any Lender assigns or otherwise transfers all or any part of the Commitments and Obligations, Agent shall so notify Borrower and Borrower shall, upon the request of Agent, execute new Notes in exchange for the Notes, if any, being assigned. Agent may amend Schedule A to this Agreement to reflect assignments made in accordance with this Section.

As used herein, “Qualified Assignee” means (a) any Lender and any affiliate of any Lender and (b) any commercial bank, savings and loan association or savings bank or any other entity which is an “accredited investor” (as defined in Regulation D under the Securities Act) which extends credit or buys loans as one of its businesses, including insurance companies, mutual funds, lease financing companies and commercial finance companies, in each case, which has a rating of BBB or higher from S&P and a rating of Baa2 or higher from Moody’s at the date that it becomes a Lender and in each case of clauses (a) and (b), which, through its applicable lending office, is capable of lending to Borrower without the imposition of any withholding or similar taxes; provided that no person proposed to become a Lender after the Closing Date and determined by Agent to be acting in the capacity of a vulture fund or distressed debt purchaser shall be a Qualified Assignee, and no person or Affiliate of such person proposed to become a Lender after the Closing Date and that holds any subordinated debt or stock issued by Borrower shall be a Qualified Assignee.

10.2. Notices. All notices, requests or other communications given in connection with this Agreement shall be in writing, shall be addressed to the parties at their respective addresses set forth on the signature pages hereto below such parties’ name or in the most recent Assignment Agreement executed by any Lender (unless and until a different address may be specified in a written notice to the other party delivered in accordance with this Section), and shall be deemed given (a) on the date of receipt if delivered by hand, (b) on the date of sender’s receipt of confirmation of proper transmission if sent by facsimile transmission, (c) on the next Business Day after being sent by a nationally-recognized overnight courier, and (d) on the fourth Business Day after being sent by registered or certified mail, postage prepaid. As used herein, the term “Business Day” shall mean and include any day other than Saturdays, Sundays, or other days on which commercial banks in New York, New York are required or authorized to be closed.

10.3. Correction of Debt Documents. Agent may correct patent errors and fill in all blanks in this Agreement or the Debt Documents consistent with the agreement of the parties.

10.4. Performance. Time is of the essence of this Agreement. This Agreement shall be binding, jointly and severally, upon all parties described as the “Borrower” and their respective successors and assigns, and shall inure to the benefit of Agent, Lenders, and their respective successors and assigns.

10.5. Payment of Fees and Expenses. Borrower agrees to pay or reimburse upon demand for all reasonable fees, costs and expenses incurred by Agent and Lenders in connection with (a) the investigation, preparation, negotiation, execution, administration of, or any amendment, modification, waiver or termination of, this Agreement or any other Debt Document, (b) the administration of any transaction contemplated hereby or thereby and (c) the enforcement, assertion, defense or preservation of Agent’s and Lenders’ rights and remedies under this Agreement or any other Debt Document, in each case of clauses (a) through (c), including, without limitation, reasonable attorney’s fees and expenses, reasonable fees of consultants, auditors and appraisers and UCC and other corporate search and filing fees and wire transfer fees; provided that Borrower’s reimbursement of the fees and expenses of Agent’s counsel incurred in connection with the preparation and negotiation of the Debt Documents on or before the Closing Date shall be subject to the limitations set forth in Section 2.7(a). Borrower further agrees

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that such fees, costs and expenses shall constitute Obligations. This provision shall survive the termination of this Agreement.

10.6. Indemnity. Borrower shall and does hereby indemnify and defend Agent, Lenders, and their respective successors and assigns, and their respective directors, officers, employees, consultants, attorneys, agents and affiliates (each an “Indemnitee”) from and against all liabilities, losses, damages, expenses, penalties, claims, actions and suits (including, without limitation, related attorneys’ fees) of any kind whatsoever arising, directly or indirectly, which may be imposed on, incurred by or asserted against such Indemnitee as a result of or in connection with this Agreement, the other Debt Documents or any of the transactions contemplated hereby or thereby (the “Indemnified Liabilities”); provided that Borrower shall have no obligation to any Indemnitee hereunder with respect to any Indemnified Liabilities to the extent such Indemnified Liabilities arise from the gross negligence, willful misconduct, or bad faith of that Indemnitee or arise from the material breach of the obligations of such Indemnitee hereunder by such Indemnitee, in each case as determined by the final non-appealable judgment of a court of competent jurisdiction. This provision shall survive the termination of this Agreement.

10.7. Rights Cumulative. Agent’s and Lenders’ rights and remedies under this Agreement or otherwise arising are cumulative and may be exercised singularly or concurrently. Neither the failure nor any delay on the part of Agent or any Lender to exercise any right, power or privilege under this Agreement shall operate as a waiver, nor shall any single or partial exercise of any right, power or privilege preclude any other or further exercise of that or any other right, power or privilege. NONE OF AGENT OR ANY LENDER SHALL BE DEEMED TO HAVE WAIVED ANY OF ITS RESPECTIVE RIGHTS UNDER THIS AGREEMENT OR UNDER ANY OTHER AGREEMENT, INSTRUMENT OR PAPER SIGNED BY BORROWER UNLESS SUCH WAIVER IS EXPRESSED IN WRITING AND SIGNED BY AGENT, REQUISITE LENDERS OR ALL LENDERS, AS APPLICABLE. A waiver on any one occasion shall not be construed as a bar to or waiver of any right or remedy on any future occasion.

10.8. Entire Agreement; Amendments, Waivers.

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10.9. Binding Effect. This Agreement shall continue in full force and effect until the Termination Date; provided, however, that the provisions of Sections 2.3(f), 9.5, 10.5, 10.6 and 10.13 and the other indemnities contained in the Debt Documents shall survive the Termination Date. The surrender, upon payment or otherwise, of any Note or any of the other Debt Documents evidencing any of the Obligations shall not affect the right of Agent to retain the Collateral for such other Obligations as may then exist or as it may be reasonably contemplated will exist in the future. This Agreement and the grant of the security interest in the Collateral pursuant to Section 3.1 shall automatically be reinstated if Agent or any Lender is ever required to return or restore the payment of all or any portion of the Obligations (all as though such payment had never been made).

10.10. Use of Logo. Borrower authorizes each Lender to use its name, logo and/or trademark without notice to or consent by Borrower, in connection with certain promotional materials that such Lender may disseminate to the public. The promotional materials may include, but are not limited to, brochures, video tape, internet website, press releases, advertising in newspaper and/or other periodicals, lucites, and any other materials relating the fact that such Lender has a financing relationship with Borrower and such materials may be developed, disseminated and used without Borrower’s review. Nothing herein obligates Lenders to use Borrower’s name, logo and/or trademark, in any promotional materials of Agent. Borrower shall not, and shall not permit any of its Affiliates to, issue any press release or other public disclosure (other than any document filed with any governmental authority relating to a public offering of the securities of Borrower) using the name, logo or otherwise referring to General

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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Electric Capital Corporation, GE Healthcare Financial Services, Inc. or of any of their affiliates, the Debt Documents or any transaction contemplated herein or therein without at least two (2) Business Days prior written notice to and the prior written consent of Agent unless, and only to the extent that, Borrower or such affiliate is required to do so under applicable law and then, only after consulting with Agent prior thereto.

10.11. Waiver of Jury Trial. EACH OF BORROWER, AGENT AND LENDERS UNCONDITIONALLY WAIVE ANY AND ALL RIGHT TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF THIS AGREEMENT, ANY OF THE OTHER DEBT DOCUMENTS, ANY OF THE INDEBTEDNESS SECURED HEREBY, ANY DEALINGS AMONG BORROWER, AGENT AND/OR LENDERS RELATING TO THE SUBJECT MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE RELATIONSHIP THAT IS BEING ESTABLISHED AMONG BORROWER, AGENT AND/OR LENDERS. THE SCOPE OF THIS WAIVER IS INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT. THIS WAIVER IS IRREVOCABLE. THIS WAIVER MAY NOT BE MODIFIED EITHER ORALLY OR IN WRITING. THE WAIVER ALSO SHALL APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS AGREEMENT, ANY OTHER DEBT DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY RELATED TRANSACTION. THIS AGREEMENT MAY BE FILED AS A WRITTEN CONSENT TO A TRIAL BY THE COURT.

10.12. Governing Law. THIS AGREEMENT, THE OTHER DEBT DOCUMENTS AND THE RIGHTS AND OBLIGATIONS OF THE PARTIES HEREUNDER AND THEREUNDER SHALL IN ALL RESPECTS BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH, THE INTERNAL LAWS OF THE STATE OF NEW YORK (WITHOUT REGARD TO THE CONFLICT OF LAWS PRINCIPLES OF SUCH STATE), INCLUDING ALL MATTERS OF CONSTRUCTION, VALIDITY AND PERFORMANCE, REGARDLESS OF THE LOCATION OF THE COLLATERAL. IF ANY ACTION ARISING OUT OF THIS AGREEMENT OR ANY OTHER DEBT DOCUMENT IS COMMENCED BY AGENT IN THE STATE COURTS OF THE STATE OF NEW YORK OR IN THE U.S. DISTRICT COURT FOR THE DISTRICT OF NEW YORK, BORROWER HEREBY CONSENTS TO THE JURISDICTION OF ANY SUCH COURT IN ANY SUCH ACTION AND TO THE LAYING OF VENUE IN THE STATE OF NEW YORK. ANY PROCESS IN ANY SUCH ACTION SHALL BE DULY SERVED IF MAILED BY REGISTERED MAIL, POSTAGE PREPAID, TO BORROWER AT ITS ADDRESS DESCRIBED IN SECTION 10.2, OR IF SERVED BY ANY OTHER MEANS PERMITTED BY APPLICABLE LAW.

10.13. Confidentiality. All of the financial statements and reports furnished by Borrower to Agent under Section 6.3 hereof shall be deemed confidential and shall not be disclosed by Agent and Lenders to any other persons except as provided herein. Agent and Lenders acknowledge that after the Borrower is a publicly traded company, such financial statements and reports may be material non-public information as more fully described in Section 6.3. In addition, any other information from time to time delivered to Agent and/or the Lenders by Borrower which is identified as confidential and which is not in the public domain shall be held by Agent or such Lender as confidential; provided that Agent and each Lender may make disclosure of such information (i) to its independent accountants and legal counsel (which persons shall be likewise bound by the provisions of this Section 10.13), (ii) pursuant to statutory and regulatory requirements, (iii) pursuant to any mandatory court order or subpoena or in connection with any legal process, (iv) pursuant to any written agreement hereafter made between Agent, any Lender and Borrower to which such information relates, which agreement permits such disclosure, (v) as necessary in connection with the exercise of any remedy by Agent or any Lender under the Debt

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

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Documents, (vi) consisting of general portfolio information that does not identify Borrower or any of its Subsidiaries, (vii) which was heretofore been publicly disclosed or is otherwise available to such Agent and/or Lender on a non-confidential basis from a source that is not, to its knowledge, subject to a confidentiality agreement with Borrower, (viii) in connection with any litigation to which Agent or any Lender or its affiliates is a party, or (ix) subject to an agreement containing provisions substantially the same as those set forth in this Section 10.13, to any assignee of or participant in, or prospective assignee of or participant in, any of the Obligations; provided that Agent shall use reasonable efforts to provide written notice to Borrower of any disclosures of such information made by Agent pursuant to the immediately preceding clauses (ii), (iii) or (viii) so long as Agent is not prohibited from delivering such notice pursuant to any of the matters described in such clauses.

10.14. Counterparts. This Agreement may be executed in any number of counterparts and by different parties in separate counterparts, each of which when so executed shall be deemed to be an original and all of which when taken together shall constitute one and the same agreement. Delivery of an executed signature page of this Agreement by facsimile transmission or electronic transmission shall be as effective as delivery of a manually executed counterpart hereof.

[Signature Page Follows]

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

39

IN WITNESS WHEREOF, Borrower, Agent and Lenders, intending to be legally bound hereby, have duly executed this Agreement in one or more counterparts, each of which shall be deemed to be an original, as of the day and year first aforesaid.

BORROWER:

CODEXIS, INC.

Address For Notices:

Codexis Inc.

Chief Financial Officer

200 Penobscot Drive

Redwood City, CA 94063

Attention: Mr. Robert Breuil

Phone: (650) 421-8120

Facsimile: (650) 298-5837

Codexis, Inc.

General Counsel

200 Penobscot Drive

Redwood City, CA 94063

Attention: Mr. Doug Sheehy

Phone: (650) 421-8160

Facsimile: (650) 421-8108

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

CODEXIS, INC.

LOAN & SECURITY AGREEMENT SIGNATURE PAGE

(10174066)

AGENT AND LENDER:

GENERAL ELECTRIC CAPITAL CORPORATION

Address For Notices:

General Electric Capital Corporation

c/o GE Healthcare Financial Services, Inc., LSF

83 Wooster Heights Road, Fifth Floor

Danbury, Connecticut 06810

Attention: Senior Vice President of Risk

Phone: (203) 205-5200

Facsimile: (203) 205-2192

With a copy to:

General Electric Capital Corporation

c/o GE Healthcare Financial Services, Inc.

Two Bethesda Metro Center, Suite 600

Bethesda, Maryland 20814

Attention: General Counsel

Phone: (301) 961-1640

Facsimile: (301) 664-9866

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

CODEXIS, INC.

LOAN & SECURITY AGREEMENT SIGNATURE PAGE

(10174066)

LENDER:

OXFORD FINANCE CORPORATION

Address For Notices:

Oxford Finance Corporation

133 North Fairfax Street

Alexandria, VA 22314

Attention: EVP + COO

Phone: (703) 519-4900

Facsimile: (703) 519-6010

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

CODEXIS, INC.

LOAN & SECURITY AGREEMENT SIGNATURE PAGE

(10174066)

SCHEDULE A

COMMITMENTS

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

SCHEDULE B

DISCLOSURES

[To be scheduled by Borrower]

Existing Liens

Existing Indebtedness

Existing Investments

Material Contracts

1.

2.

3.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

EXHIBIT A

FORM OF PROMISSORY NOTE

[September __, 2007]

FOR VALUE RECEIVED, CODEXIS, INC., a Delaware corporation located at the address stated below (“Borrower”), promises to pay to the order of [Lender] or any subsequent holder hereof (each, a “Lender”), the principal sum of ________ and _____/100 Dollars ($___________) or, if less, the aggregate unpaid principal amount of all Term Loans made by Lender to or on behalf of Borrower pursuant to the Agreement (as hereinafter defined). All capitalized terms, unless otherwise defined herein, shall have the respective meanings assigned to such terms in the Agreement.

This Promissory Note is issued pursuant to that certain Loan and Security Agreement, dated as of [August __, 2007], among Borrower, General Electric Capital Corporation, as agent and lender, [the other lenders signatory thereto] [, and Lender] (as amended, restated, supplemented or otherwise modified from time to time, the “Agreement”), is one of the Notes referred to therein, and is entitled to the benefit and security of the Debt Documents referred to therein, to which Agreement reference is hereby made for a statement of all of the terms and conditions under which the loans evidenced hereby were made.

The principal amount of the indebtedness evidenced hereby shall be payable in the amounts and on the dates specified in the Agreement. Interest thereon shall be paid until such principal amount is paid in full at such interest rates and at such times as are specified in the Agreement. The terms of the Agreement are hereby incorporated herein by reference.

All payments shall be applied in accordance with the Agreement. The acceptance by Lender of any payment which is less than payment in full of all amounts due and owing at such time shall not constitute a waiver of Lender’s right to receive payment in full at such time or at any prior or subsequent time. The payment of any Scheduled Payment prior to its due date shall result in a corresponding increase in the portion of the Scheduled Payment credited to the remaining unpaid principal balance.

All amounts due hereunder and under the other Debt Documents are payable in the lawful currency of the United States of America. Borrower hereby expressly authorizes Lender to insert the date value as is actually given in the blank space on the face hereof and on all related documents pertaining hereto.

This Note is secured as provided in the Agreement and the other Debt Documents. Reference is hereby made to the Agreement and the other Debt Documents for a description of the properties and assets in which a security interest has been granted, the nature and extent of the security interest, the terms and conditions upon which the security interest was granted and the rights of the holder of the Note in respect thereof.

Time is of the essence hereof. If Lender does not receive from Borrower payment in full of any Scheduled Payment or any other sum due under this Note or any other Debt Document within 3 days after its due date, Borrower agrees to pay the Late Fee in accordance with the Agreement. Such Late Fee will be immediately due and payable, and is in addition to any other costs, fees and expenses that Borrower may owe as a result of such late payment.

This Note may be voluntarily prepaid only as permitted under Section 2.4 of the Agreement. After a Default or an Event of Default, this Note shall bear interest at a rate per annum equal to the Default Rate pursuant to Section 2.6 of the Agreement.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

Borrower and all parties now or hereafter liable with respect to this Note, hereby waive presentment, demand for payment, notice of nonpayment, protest, notice of protest, notice of dishonor, and all other notices in connection herewith, as well as filing of suit (if permitted by law) and diligence in collecting this Note or enforcing any of the security hereof, and agree to pay (if permitted by law) all expenses incurred in collection, including reasonable attorneys’ fees and expenses.

THIS NOTE SHALL BE CONSTRUED IN ACCORDANCE WITH AND GOVERNED BY THE LAWS OF THE STATE OF NEW YORK.

No variation or modification of this Note, or any waiver of any of its provisions or conditions, shall be valid unless such variation or modification is made in accordance with Section 10.8 of the Agreement. Any such waiver, consent, modification or change shall be effective only in the specific instance and for the specific purpose given.

IN WITNESS WHEREOF, Borrower has duly executed this Note as of the date first above written.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

EXHIBIT B

SECRETARY’S CERTIFICATE OF AUTHORITY

[DATE]

Reference is made to the Loan and Security Agreement, dated as of [September __, 2007] (as amended, restated, supplemented or otherwise modified from time to time, the “Agreement”), among Codexis, Inc., a Delaware corporation (the “Borrower”), General Electric Capital Corporation, a Delaware corporation (“GECC”), as a lender and as agent (in such capacity, together with its successors and assigns in such capacity, “Agent”), and the other lenders signatory thereto from time to time (GECC and such other lenders, the “Lenders”). Capitalized terms used but not defined herein are used with the meanings assigned to such terms in the Agreement.

I, [_____________________________], do hereby certify that:

(i) I am the duly elected, qualified and acting [Assistant] Secretary of Borrower;

(ii) attached hereto as Exhibit A is a true, complete and correct copies of Borrower’s Certificate of Incorporation and the Bylaws, each of which is in full force and effect on and as of the date hereof;

(iii) each of the following named individuals is a duly elected or appointed, qualified and acting Proper Officer of Borrower who holds the offices set opposite such individual’s name, and such individual is authorized to sign the Debt Documents and all other notices, documents, instruments and certificates to be delivered pursuant thereto, and the signature written opposite the name and title of such officer is such officer’s genuine signature:

(iv) attached hereto as Exhibit B are true, complete and correct copies of resolutions adopted by the Board of Directors of Borrower (the “Board”) authorizing the execution, delivery and performance of the Debt Documents to which Borrower is a party, which resolutions were duly adopted by the Board on [DATE] and all such resolutions are in full force and effect on the date hereof in the form in which adopted without amendment, modification, rescission or revocation;

(iv) the foregoing authority shall remain in full force and effect, and Agent and each Lender shall be entitled to rely upon same, until written notice of the modification, rescission or revocation of same, in whole or in part, has been delivered to Agent and each Lender, but no such modification, rescission or revocation shall, in any event, be effective with respect to any documents executed or actions taken in reliance upon the foregoing authority before said written notice is delivered to Agent and each Lender; and

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

(v) no Default or Event of Default exists under the Agreement, and all representations and warranties of Borrower in the Debt Documents are true and correct in all respects on and as of the date hereof, except to the extent such representations and warranties expressly relate to an earlier date, in which case such representations and warranties were true and correct in all respects on and as of such earlier date.

[Signature page follows]

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

IN WITNESS WHEREOF, I have hereunto set my hand as of the first date written above

The undersigned does hereby certify on behalf of Borrower that he is the duly elected or appointed, qualified and acting [TITLE] of Borrower and that [NAME FROM ABOVE] is the duly elected or appointed, qualified and acting [Assistant] Secretary of Borrower, and that the signature set forth immediately above is his genuine signature.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

EXHIBIT B TO SECRETARY’S CERTIFICATE OF AUTHORITY

FORM OF RESOLUTIONS

BOARD RESOLUTIONS

________ ___, 2007

WHEREAS, Codexis, Inc., a Delaware corporation (“Borrower”) has requested that General Electric Capital Corporation, a Delaware corporation (“GECC”), as agent (in such capacity, the “Agent”) and lender, and certain other lenders (GECC and such other lenders, collectively, the “Lenders”) provide a credit facility in an original principal amount not to exceed $15,000,000 (the “Credit Facility”); and

WHEREAS, the terms of the Credit Facility are set forth in a loan and security agreement by and among Borrower, Agent, and the Lenders and certain related agreements, documents and instruments described in detail below; and

WHEREAS, the Board of Directors of Borrower (the “Directors”) deems it advisable and in the best interests of Borrower to execute, deliver and perform its obligations under those transaction documents described and referred to below.

NOW, THEREFORE, be it

RESOLVED, that the Credit Facility be, and it hereby is, approved; and further

RESOLVED, that the form of Loan and Security Agreement (the “Loan and Security Agreement”), by and among Borrower, Agent and the Lenders, as presented to the Directors, be and it hereby is, approved and the Chief Executive Officer, Chief Financial Officer, General Counsel and/or Controller of Borrower (collectively, the “Proper Officers”) be, and each of them hereby is, authorized and directed on behalf of Borrower to execute and deliver to Agent the Loan and Security Agreement, in substantially the form as presented to the Directors, with such changes as the Proper Officers may approve, such approval to be conclusively evidenced by execution and delivery thereof; and further

RESOLVED, that the form of Promissory Note (the “Note”), as presented to the Directors, be, and it hereby is, approved and the Proper Officers be, and each of them hereby is, authorized and directed on behalf of Borrower to execute and deliver to Lender one or more promissory Notes, in substantially the form as presented to the Directors, with such changes as the Proper Officers may approve, such approval to be conclusively evidenced by execution and delivery thereof; and further

RESOLVED, that the form of Pledge Agreement (the “Pledge Agreement”), by and among Borrower, Agent and the Lenders, as presented to the Directors, be and it hereby is, approved and the Proper Officers be, and each of them hereby is, authorized and directed on behalf of Borrower to execute and deliver to Agent the Pledge Agreement, in substantially the form as presented to the Directors, with such changes as the Proper Officers may approve, such approval to be conclusively evidenced by execution and delivery thereof; and further

RESOLVED, that issuance of a warrant to the Lenders substantially in the form of the Warrant as presented to the Directors (each, a “Warrant”), and the sale and issuance of preferred stock upon exercise of the Warrant as described therein, be, and hereby is, approved and the Proper Officers be, and each of them hereby is, authorized and directed on behalf of Borrower to execute and deliver to the Lenders the

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

Warrants, in substantially the form as presented to the Directors, with such changes as the Proper Officers may approve, such approval to be conclusively evidenced by execution and delivery thereof; and further

RESOLVED, that the Proper Officers be, and each of them hereby is, authorized and directed to execute and deliver any and all other agreements, certificates, security agreements, financing statements, indemnification agreements, instruments and documents (together with the Loan and Security Agreement, the Notes, and the Pledge Agreement, the “Debt Documents”) and take any and all other further action, in each case, as may be required or which they may deem appropriate, on behalf of Borrower, in connection with the Loan and Security Agreement and carrying into effect the foregoing resolutions, transactions and matters contemplated thereby; and further

RESOLVED, that Borrower is hereby authorized to perform its obligations under the Debt Documents, including, without limitation, the borrowing of any advances made under the Loan and Security Agreement and the granting of any security interest in Borrower’s assets contemplated thereby to secure Borrower’s obligations in connection therewith; and further

RESOLVED, that in addition to executing any documents approved in the preceding resolutions, the Secretary or any Assistant Secretary of Borrower may attest to such Debt Documents, the signature thereon or the corporate seal of Borrower thereon; and further

RESOLVED, that any actions taken by the Proper Officers prior to the date of these resolutions in connection with the transactions contemplated by these resolutions are hereby ratified and approved; and further

RESOLVED, that these resolutions shall be valid and binding upon Borrower.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

EXHIBIT C-1

FORM OF LANDLORD CONSENT

[Landlord]

[Address]

[________, _____]

Ladies and Gentlemen:

General Electric Capital Corporation (together with its successors and assigns, if any, “Agent”) and certain other lenders (the “Lenders”) have entered into, or is about to enter into, a Loan and Security Agreement, dated as of [September __, 2007] (as amended, restated, supplemented or otherwise modified from time to time, the “Agreement”) with Codexis, Inc., a Delaware corporation (“Borrower”), pursuant to which Borrower has granted, or will grant, to Agent, on behalf of itself and the Lenders, a security interest in certain assets of Borrower, including, without limitation, all of Borrower’s cash, cash equivalents, accounts, books and records, goods, inventory, machinery, equipment, furniture and trade fixtures (such as equipment bolted to floors), together with all addition, substitutions, replacements and improvements to, and proceeds, including, insurance proceeds, of the foregoing, but excluding building fixtures (such as plumbing, lighting and HVAC systems (collectively, the “Collateral”). Some or all of the Collateral is, or will be, located at certain premises known as [________] in the City or Town of [________, County of ____________ and State of ________] (“Premises”), and Borrower occupies the Premises pursuant to a lease, dated as of [DATE], between Borrower, as tenant, and you, [NAME], as [owner/landlord/mortgagee/realty manager] (as amended, restated, supplemented or otherwise modified from time to time, the “Lease”).

By your signature below, you hereby agree (and we shall rely on your agreement) that: (i) the Lease is in full force and effect and you are not aware of any existing defaults thereunder, (ii) the Collateral is, and shall remain, personal property regardless of the method by which it may be, or become, affixed to the Premises; (iii) you agree to use your best efforts to provide Agent with written notice of any default by Borrower under the Lease resulting in a termination of the Lease (“Default Notice”) and Agent shall have the right, but not the obligation to cure such default within 15 days following Agent’s receipt of such Default Notice, (iv) your interest in the Collateral and any proceeds thereof (including, without limitation, proceeds of any insurance therefor) shall be, and remain, subject and subordinate to the interests of Agent and you agree not to levy upon any Collateral or to assert any landlord lien, right of distraint or other claim against the Collateral for any reason; (v) Agent, and its employees and agents, shall have the right, from time to time, to enter into the Premises for the purpose of inspecting the Collateral; and (vi) Agent, and its employees and agents, shall have the right, upon any default by Borrower under the Agreement, to enter into the Premises and to remove or otherwise deal with the Collateral, including, without limitation, by way of public auction or private sale (provided that, if Agent conducts a public auction or private sale of the Collateral at the Premises, Agent shall use reasonable efforts to notify Landlord first and to hold such auction or sale in a manner that would not unduly disrupt Landlord’s or any other tenant’s use of the Premises). Agent agrees to repair or reimburse you for any physical damage actually caused to the Premises by Agent, or its employees or agents, during any such removal or inspection (other than ordinary wear and tear), provided that it is understood by the parties hereto that Agent shall not be liable for any diminution in value of the Premises caused by the removal or absence of the Collateral therefrom. You hereby acknowledge that Agent shall have no obligation to remove or dispose of the Collateral from the Premises and no action by Agent pursuant to this Consent

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

shall be deemed to be an assumption by Agent of any obligation under the Lease and, except as provided in the immediately preceding sentence, Agent shall not have any obligation to you.

You hereby acknowledge and agree that Borrower’s granting of a security interest in the Collateral in favor of Agent, on behalf of itself and the Lenders, shall not constitute a default under the Lease nor permit you to terminate the Lease or re-enter or repossess the Premises or otherwise be the basis for the exercise of any remedy available to you.

This Consent and the agreements contained herein shall be binding upon, and shall inure to the benefit of, any successors and assigns of the parties hereto (including any transferees of the Premises). This Consent shall terminate upon the indefeasible payment of Borrower’s indebtedness in full in immediately available funds and the satisfaction in full of Borrower’s performance of its obligations under the Agreement and the related documents.

This Consent and any amendments, waivers, consents or supplements hereto or in connection herewith may be executed in any number of counterparts and by different parties hereto in separate counterparts, each of which when so executed and delivered shall be deemed an original, but all such counterparts together shall constitute but one and the same instrument; signature pages may be detached from multiple separate counterparts and attached to a single counterpart so that all signature pages are physically attached to the same document. Delivery of an executed signature page of this Consent or any delivery contemplated hereby by facsimile or electronic transmission shall be as effective as delivery of a manually executed counterpart thereof.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

We appreciate your cooperation in this matter of mutual interest.

AGREED TO AND ACCEPTED BY:

___________________________, as [owner/landlord/mortgagee/realty manager]

Interest in the Premises (check applicable box)

Address:

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

EXHIBIT C-2

FORM OF BAILEE CONSENT

[Letterhead of GE Capital]

______ ____, 200__

[NAME OF BAILEE]

_________________________

_________________________

Dear Sirs:

Re: Codexis, Inc. (the “Borrower”)

Please accept this letter as notice that we have entered into or may enter into financing arrangements with the Borrower under which the Borrower has granted to us continuing security interests in substantially all personal property and assets of the Borrower and the proceeds thereof, including, without limitation, certain equipment owned by the Borrower held by you at the manufacturing facility (the “Premises”) owned by you and located at [____________](the “Personal Property”).

Please acknowledge that as a result of such arrangements, you are holding all of the Personal Property solely for our benefit and subject only to the terms of this letter and our instructions; provided, however, that until further written notice from us, you are authorized to use and/or release any and all of the Personal Property in your possession as directed by the Borrower in the ordinary course of business. The foregoing instructions shall continue in effect until we modify them in writing, which we may unilaterally do without any consent or approval from the Borrower. Upon receipt of our instructions, you agree that (a) you will release the Personal Property only to us or our designee; (b) you will cooperate with us in our efforts to assemble, sell (whether by public or private sale), take possession of, and remove all of the Personal Property located at the Premises; (c) you will permit the Personal Property to remain on the Premises for forty-five (45) days after your receipt of our instructions or at our option, to have the Personal Property removed from the Premises within a reasonable time, not to exceed forty-five (45) days after your receipt of our instructions; (d) you will not hinder our actions in enforcing our liens on the Personal Property; and (e) after receipt of our instructions, you will abide solely by our instructions with respect to the Personal Property, and not those of the Borrower.

You hereby waive and release in our favor: (a) any contractual lien, security interest, charge or interest and any other lien which you may be entitled to whether by contract, or arising at law or in equity against any Personal Property; (b) any and all rights granted under any present or future laws to levy or distrain for rent or any other charges which may be due to you against the Personal Property; and (c) any and all other claims, liens, rights of offset, deduction, counterclaim and demands of every kind which you have or may hereafter have against the Personal Property.

You agree that (i) you have not and will not commingle the Personal Property with any other property of a similar kind owned or held by you in any manner such that the Personal Property is not readily identifiable, (ii) you have not and will not issue any negotiable or non-negotiable documents or instruments relating to the Personal Property, and (iii) the Personal Property is not and will not be deemed to be fixtures.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

Notwithstanding the foregoing, all of your charges of any nature whatsoever shall continue to be charged to and paid by the Borrower and we shall not be liable for such charges.

You hereby authorize us to file at any time such financing statements naming you as the debtor/bailee, Borrower as the secured party/bailor, and us as the Borrower’s assignee, indicating as the collateral goods of the Borrower now or hereafter in your custody, control or possession and proceeds thereof, and including any other information with respect to the Borrower required under the Uniform Commercial Code for the sufficiency of such financing statement or for it to be accepted by the filing office of any applicable jurisdiction (and any amendments or continuations with respect thereto).

The arrangement as outlined herein is to continue without modification, until we have given you written notice to the contrary.

EACH OF THE PARTIES HERETO HEREBY WAIVES ITS RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF THIS LETTER.

Any notice(s) required or desired to be given hereunder shall be directed to the party to be notified at the address stated herein.

The terms and conditions contained herein are to be construed and enforced in accordance with the laws of the State of Connecticut.

This terms and conditions contained herein shall inure to the benefit of and be binding upon the parties hereto and their respective successors and permitted assigns.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

The Borrower has signed below to indicate its consent to and agreement with the foregoing arrangements, terms and conditions. By your signature below, you hereby agree to be bound by the terms and conditions of this letter.

Agreed to:

CODEXIS, INC.

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

EXHIBIT D

COMPLIANCE CERTIFICATE

[DATE]

Reference is made to the Loan and Security Agreement, dated as of [September __, 2007] (as amended, restated, supplemented or otherwise modified from time to time, the “Agreement”), among Codexis, Inc., a Delaware corporation (the “Borrower”), General Electric Capital Corporation, a Delaware corporation (“GECC”), in its capacity as agent (in such capacity, together with its successors and assigns, in such capacity, the “Agent”) and lender, and the other lenders signatory thereto (GECC and such other lenders, the “Lenders”). Capitalized terms used but not defined herein are used with the meanings assigned to such terms in the Agreement.

I, [______________________________], do hereby certify that:

(i) I am the duly elected, qualified and acting [TITLE] of Borrower;

(ii) attached hereto as Exhibit A are [the monthly financial statements]/[annual audited financial statements]/[quarterly financial statements] as required under Section 6.3 of the Agreement and that such financial statements are materially prepared in accordance with GAAP (subject, in the case of unaudited financial statements, to the absence of footnotes and normal year-end and audit adjustments) and are consistently applied from one period to the next except as explained in an accompanying letter or footnotes;

(iii) no Default or Event of Default has occurred under the Agreement which has not been previously disclosed, in writing, to Lender; and

[(iv) all representations and warranties of Borrower stated in the Debt Documents are true and correct in all material respects on and as of the date hereof, except to the extent such representations and warranties expressly relate to an earlier date, in which case such representations and warranties were true and correct in all respects on and as of such earlier date.]¹

IN WITNESS WHEREOF, I have hereunto set my hand as of the first date written above

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

EXHIBIT E

¨

2. Authorization Agreement for Pre-Arranged Payment Plan:

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

3. Agent Account Number(s): (Invoice Billing ID, 10-digit number formatted: 1234567-001)

5. Complete ALL Bank and Borrower Information:

6. Would you like to have property taxes paid via EPS on above accounts?

Check (X): YES: ¨     NO: ¨

7. Would you like to receive a complementary invoice?

Check (X): YES: ¨     NO: ¨

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions