Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio...

Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State) E-mail: upali@latech.edu Office: 311 Carson Taylor Hall ; Phone: 318-257-4941;Office Hours: MTW 8:00 - 10:00 am; ThF 9:00 - 10:00 am 1:00 - 2:00 pm.

December 19, 2014: Test 1 (Chapters 12-13)January 26 , 2015: Test 2 (Chapters 14-16)February 13, 2015: Test 3 (Chapters 17-19)March 2, 2015: Test 4 (Chapters 20-22March 3 , 2015: Make Up Exam: Chapters 12-22)

Bring Scantron Sheet 882-E

Chemistry 121(001) Winter 2015

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CHEM 121 Winter 2015

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Chapter 20 and GHW#10 Questions

Proteins and Peptides

CHEM 121 Winter 2015

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ProteinsNaturally occurring bioorganic polyamide polymers containing a sequence of various combinations of 20 amino acids. Amino acids contain the elements carbon, hydrogen, oxygen, and nitrogen and few also contain sulfurAmino acids: Polyfunctional bioorganic compunds

R = 20 different alkyl, alcohols, amines , acids and heterocyclic aminesZwitterion form

CHEM 121 Winter 2015

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Handedness/Chirality of Amino Acids

CHEM 121 Winter 2015

CHEM 121 Winter 20155

Groups of Amino Acids based on R group

• Hydrophobic (non-polar, neutral)

• Polar, neutral

• Polar Acidic

• Polar Basic

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1) Hydrophobic (non-polar, neutral) (5 amino acids)

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1) Hydrophobic (non-polar, neutral) continued..( 4 amino acids)

CHEM 121 Winter 2015

G AL VaLI PPerMiT

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2) Hydrophilic (polar, neutral) continued..( 6 amino acids).

CHEM 121 Winter 2015SeCTAsGulTy

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3) & 4) Polar amino acids (5 amino acids)

CHEM 121 Winter 2015

As Glue Hit Lady Argentina

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Abbreviationsglycine Gly Galanine Ala Avaline Val Vleucine Leu Lisoleucine Ile Imethionine Met Mphenylalanine Phe Ftryptophan Trp WProline Pro PCHEM 121 Winter 2015

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amino acid three letter code

single letter code

glycine Gly Galanine Ala Avaline Val V

leucine Leu Lisoleucine Ile I

methionine Met Mphenylalanine Phe F

tryptophan Trp Wproline Pro P

Abbreviations

serine Ser Sthreonine Thr Tcysteine Cys Ctyrosine Tyr Y

asparagine Asn Nglutamine Gln Q

aspartic acid Asp Dglutamic acid Glu E

lysine Lys Karginine Arg Rhistidine His H

Electrically Charged (negative)

Electrically Charged (positive)            

Non Polar Neutral

Non Polar

CHEM 121 Winter 2015

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1) Give name, abbreviation and types (neutral, polar, non-polar, basic and acidic).

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1) Give name, abbreviation and types (neutral, polar, non-polar, basic and acidic).

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Protein Function• Enzymes - catalyze biological reactions (alcohol dehydrogenase,

glucokinase) • Hormones - signals between cells (insulin, growth hormone) • Storage Proteins- store nutrients (ferritin storing iron in the

liver)• Transport Proteins - transport nutrients through the body

(hemoglobin transport of oxygen) • Structural Proteins- form structure of cells ( keratin, elastin,

collagen) • Protective Proteins- have specific protective function

(antibodies bind to foreign proteins)

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2) Draw the optical and L isomers for: cys.

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3) Use the following amino acids to answer the questions below:

Which amino acid is most polar? b. Which amino acid is most non-polar?

c. Which amino acid gives an acidic solution?

d. Which amino acid gives a basic solution?

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Primary protein structureProteins are polymers made up of amino acids.

Peptide bond - how the amino acids arelinked together to makea protein.

H |

H2NCCOOH

| R

+

H |

H2NCCOOH

| R’

H O | ||

H2N - C - C -

| R

H |N - C - COOH | |H R’ + H2O

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4) Draw the following:a) Dipeptide bond between ala and asp, and identify C- and N-terminal.

b) Tripeptide, ile-cys-thr, and identify N- ( left) and C-terminal(right).

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4) Continued….c) How many possible isomers are in the tripeptide formed with ile, cys and thr? Come up with a formula for linear chain with “ n” amino acids.

d) Give the IUPAC name of the tripeptide with the sequence, ile-cys-thr.

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5) Use the structure to answer the questions below:Use the structure to answer the questions below

a) Which letter arrow points the end of the peptide that is the "amine“ end-N-terminal?

b) Which letter arrow points the end of the peptide that is the "carboxyl" end, C-terminal?

c) Which letter arrow points to an amide or peptide bond?

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Four levels of protein structure1) Primary structureThe sequence of amino acids in a protein.

2) Secondary structureWay that chains of amino acids are coiled or folded

- (-helix, -sheet, random coil).

3) Tertiary structureWay -helix, -sheet, random coils fold and coil.

4) Quaternary structureWay that two or more peptide chains pack

together.

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Three levels of structure: telephone cord

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Summary of protein structure

primary secondary

tertiary quaternary

H O | ||H2N - C - C | R

H |N - C - COOH | |H R’’

H O | ||- NH - C - C - | R’

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6) Explain the differences between primary, secondary, tertiary, and quaternary protein structures by giving brief definitions of each. What types of bonding are used in each?

Primary Secondary Tertiary Quaternary

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7) Use the above structures to answer the questions below:

• a. Which two amino acids may link in a salt bridge in tertiary protein structure?

• b. Which two amino acids may link in hydrophobic interactions in tertiary protein structure?

• c. Which two amino acids may link in hydrogen bonding interactions in tertiary protein structure?

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Alpha Helix

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Alpha Helix

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Beta Pleated Sheets

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Beta Pleated Sheets

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8) Explain the difference between the alpha helix and the beta pleated sheet protein structures. What are the differences in the hydrogen bonding?

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Fibrous Proteinsa) a- Keratin b) Collagen etc..