PROTEINS

Place a square around the amino group Place a circle around the carboxyl group Use an arrow to point to the central carbon Why is there an R attached to the central carbon? How many different R groups are there?

What elements are common to amino acids and which one is only found in 2 amino acids? When 2 amino acids are joined the new molecule is called a ______________________ because a

_______________ bond forms between the 2 amino acids. Use the example below to draw

the dipeptide and be careful with the R groups. What CANNOT be forgotten?

HINT

Protein Structure 1

Protein StructureWhat are the levels of protein structure and what role do functional groups play?

Why?Proteins accomplish many cellular tasks such as facilitating chemical reactions, providing structure, and carrying information from one cell to another. How a protein chain coils up and folds determines its three-dimensional shape. Its shape will, in turn, determine how it interacts with other molecules and thus performs its function in the cell.

Model 1 – Formation of a Peptide BondAmino acid 1 Amino acid 2

Dipeptide

N C

CH2OH

C

O

OH

H

H

H

N C

R1

C

HH

H

N C

R2

C

O

OH

HH

O

N C

CH3

C

O

OH

H

H

OH2

CH3

R1 R2

CH2OH

H2O

+H

+

1. Examine the amino acids in Model 1.

a. Circle an amine group in the diagram.

b. Draw a triangle around a carboxylic acid (carboxyl) group.

2. How are the amino acids similar to one another?

3. How are the amino acids different from one another?

BuildingaProteinItallstartswiththe___________________________________,whichissimplytheorderoftheaminoacids.Howmanypeptidebondsarefoundintheexamplebelow?In__________________________structure,thechainofaminoacidsbeginstofoldand______bondsform.Secondarystructurewillproducebeta-pleatedsheetsoralphahelices.

Protein Structure 3

Model 2 – Protein Structure (Part A)Primary StructureAmino acid sequence: Ser – Tyr – Ala – Phe – Val – Cys – Tyr – Asp – Cys – Gly

Peptide structure:

H2N C C N C

H O

CH2OH

H

C N C

O

CH3H

H

C N C

O

CH2H

H

C N

O

HCH2H

OH

C C N C

H O

CH2SHCH

H

H

C N C

O

CH2H

H

C N C

O

CH2H

H

CH3 CH3

OH

C

O

N C

CH2SH

C

O

N CH2 CO2HH

CO2

H

–

Secondary Structure

C C

H

N

H

C N

H

C

O

C

H

CH2

N

H2N C C N C

H O

CH2OH

H

C N C

O

CH3H

H

C N C

O

CH2

H

C N

O

HCH2

OH

CC

H

CH

CH3 CH3

O

NH

CH CH2SH

C

O

OH

H

CH2

C

CO2–

OCH2

SH

OH

H H

Hydrogen bond

NCH2HO2C

H

9. Locate the primary structure of the polypeptide in Model 2.

a. Draw an arrow to two different peptide bonds in the diagram.

b. Circle three separate amino acids that were joined together to make the polypeptide.

Protein Structure 3

Model 2 – Protein Structure (Part A)Primary StructureAmino acid sequence: Ser – Tyr – Ala – Phe – Val – Cys – Tyr – Asp – Cys – Gly

Peptide structure:

H2N C C N C

H O

CH2OH

H

C N C

O

CH3H

H

C N C

O

CH2H

H

C N

O

HCH2H

OH

C C N C

H O

CH2SHCH

H

H

C N C

O

CH2H

H

C N C

O

CH2H

H

CH3 CH3

OH

C

O

N C

CH2SH

C

O

N CH2 CO2HH

CO2

H

–

Secondary Structure

C C

H

N

H

C N

H

C

O

C

H

CH2

N

H2N C C N C

H O

CH2OH

H

C N C

O

CH3H

H

C N C

O

CH2

H

C N

O

HCH2

OH

CC

H

CH

CH3 CH3

O

NH

CH CH2SH

C

O

OH

H

CH2

C

CO2–

OCH2

SH

OH

H H

Hydrogen bond

NCH2HO2C

H

9. Locate the primary structure of the polypeptide in Model 2.

a. Draw an arrow to two different peptide bonds in the diagram.

b. Circle three separate amino acids that were joined together to make the polypeptide.

4 POGIL™ Activities for AP* Biology

10. The first five amino acids in this polypeptide are serine, tyrosine, alanine, phenylalanine, and valine, in that order (Ser-Tyr-Ala-Phe-Val). If the amino acids were changed or rearranged (i.e., to Val-Phe-Ala-Ser-Tyr), the polypeptide would have a different name and identity. With your group, use this information to write a definition of the primary structure of a protein.

11. Locate the secondary protein structure in Model 2.

a. What types of bonds are holding the secondary structure in place?

b. What groups on the amino acids are always involved in these bonds?

12. Draw a rectangle around two different R groups on the amino acids in the secondary structure in Model 2.

13. Is there any interaction between R groups in the secondary structure in Model 2?

14. Secondary protein structure can take the form of an alpha(α)-helix or a beta(β)-pleated sheet, as illustrated below.

a. Which drawing represents an α-helix, Molecule 1 or Molecule 2? Explain your reasoning.

b. Which drawing represents a β-pleated sheet? Explain your reasoning.

Molecule 1 Molecule 2

R

R

R

R

R

Hydrogenbonds

Aminoacids

R R

R

R

RR

15. With your group, write a grammatically correct sentence that summarizes how the secondary protein structure is formed from the primary structure.

___________________________structureisalittlemorecomplexandinvolvesinteractionsbetween______groups.Usetheimagebelowtolabelthe:ionicbond,hydrogenbond,hydrophobicinteractionandthedisulfidebridge.

____________________________structureinvolvesmultiplepolypeptidechainsinteracting.Ionicandhydrogenbondscanoccuraswellasdisulfidebridgesandhydrophobicinteractions.

Protein Structure 5

Model 3 – Protein Structure (Part B)Tertiary Structure

H

CH2

CH3 CH3

CH3

CH3

CH

CH

(CH2 )4 NH3+

CH2O

CH2CO–

O

O

CH2 CH2S S

H

Quaternary Structure

Three polypeptide chains

CH2

CH3 CH3

CH3

CH2

(CH2 )4

NH3+

CH3

CH2

S

CH

CH

S CO

O–

GeneticdisorderslikeSickleCellAnemiacanresultbecause1hemoglobinmoleculeconsistsof4polypeptidechainsinquaternarystructure.Becausetheaminoacidsequencehasamutation(wrongorderofaminoacids),eachmoleculeisslightlymisshapen.Becauseofthis,theinteractionbetweenhemoglobinmoleculescausesredbloodcellstohaveasickleshape.Thecorrectfunctioningofaproteindependsofifitfoldsproperlyafterbeingassembled.EachproteinwillhaveanoptimaltemperatureandpHitwillfunctionin.IncorrecttemperaturesandpHcanalterthefolding,andinsomecasescausetheproteintobenon-functional.Iftheproteinunfolds,itissaidtobedenatured.NotallproteinsorenzymeshavethesameoptimaltemperatureorpH.

Protein Structure 5

Model 3 – Protein Structure (Part B)Tertiary Structure

H

CH2

CH3 CH3

CH3

CH3

CH

CH

(CH2 )4 NH3+

CH2O

CH2CO–

O

O

CH2 CH2S S

H

Quaternary Structure

Three polypeptide chains

CH2

CH3 CH3

CH3

CH2

(CH2 )4

NH3+

CH3

CH2

S

CH

CH

S CO

O–