Proteins Chapter 3 A. P. Biology Mr. Knowles Liberty Senior High School

Proteins are Most Common

Functions of Proteins 1.Enzymes- Metabolism 2.Structural- Collagen and Keratin 3.Cell Recognition- proteins on cellular surface. 4.Regulation of Gene Expression- Gene Repressors or Enhancers. 5.Defense- Antibodies.

An overview of protein functions Table 5.1

Two Types of Proteins 1.Fibrous Proteins- rope-like, structural proteins; form shape of cells and tissues. Ex. Collagen-the most abundant protein of vertebrates. 2.Globular Proteins- have specific shapes for their functions. Ex. Enzymes and antibodies.

1. Proteins can be Structural

2. Proteins can be Globular

X-ray crystallography: Is used to determine a protein’s three- dimensional structure. X-ray diffraction pattern Photographic film Diffracted X-rays X-ray source X-ray beam Crystal Nucleic acidProtein (a) X-ray diffraction pattern (b) 3D computer model Figure 5.24

Papain

Proteins Most diverse organic compound. Composed of amino acids- each with an amino group (NH 2 ) and a carboxylic acid group (COOH). Different chemical group(s) attached to central C- R group.

Amino Acid Polymers Amino acids –Are linked by peptide bonds OH DESMOSOMES OH CH 2 C N H C H O HOH Peptide bond OH H H HH H H H H H H H H N N N N N SH Side chains SH OO OO O H2OH2O CH 2 C C C CCC C C C C Peptide bond Amino end (N-terminus) Backbone (a) Figure 5.18 (b) Carboxyl end (C-terminus)

20 different amino acids make up proteins O O–O– H H3N+H3N+ C C O O–O– H CH 3 H3N+H3N+ C H C O O–O– C C O O–O– H H3N+H3N+ CH CH 3 CH 2 C H H3N+H3N+ CH 3 CH 2 CH C H H3N+H3N+ C CH 3 CH 2 C H3N+H3N+ H C O O–O– C H3N+H3N+ H C O O–O– NH H C O O–O– H3N+H3N+ C CH 2 H2CH2C H2NH2N C H C Nonpolar Glycine (Gly) Alanine (Ala) Valine (Val)Leucine (Leu)Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) C O O–O– Tryptophan (Trp) Proline (Pro) H3CH3C Figure 5.17 S O O–O–

Amino Acids Are the monomers of proteins. Only 20 naturally occurring amino acids. The R group gives each of the amino acids its unique property. All 20 amino acids can be grouped into 5 basic groups.

5 Groups of Amino Acids (Fig. 3.15) 1.Nonpolar- have R groups that contain CH 2 and CH 3. 2.Polar Uncharged- R groups that have O or only H. 3.Ionizable- have R groups that are acids and bases. 4.Aromatic- R groups that have organic rings.

5 Groups of Amino Acids (Fig. 3.15) 5. Special-function- amino acids that are only used for very specific functions; methionine begins protein synthesis, proline causes kinks in the protein polymer, cysteine links chains together.

The 20 Common Amino Acids (Fig. 3.15) Click below for another view!

Proteins Are polymers of amino acids. Joined by peptide bonds. Di- Tri- and Polypeptides.

Globular Proteins Are long amino acids chains folded into complex shapes. All of the internal amino acids are nonpolar. Water excludes nonpolar amino acids – hydrophobic interactions.

Globular Proteins Have Four Levels of Structure 1.Primary- the specific sequence of amino acids in the polypeptide chain. R groups have no role in the backbone, so any sequence of amino acids is possible. Therefore, 100 amino acids may be rearranged in different possible sequences.

Primary Structure: Is the unique sequence of amino acids in a polypeptide. Figure 5.20 – Amino acid subunits + H 3 N Amino end o Carboxyl end o c Gly ProThr Gly Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Val Arg Gly Ser Pro Ala Gly lle Ser Pro Phe His Glu His Ala Glu Val Phe Thr Ala Asn Asp Ser Gly Pro Arg Tyr Thr lle Ala Leu Ser Pro Tyr Ser Tyr Ser Thr Ala Val Thr Asn Pro Lys Glu Thr Lys Ser Tyr Trp Lys Ala Leu Glu Lle Asp

Globular Protein Structure 2. Secondary- folding or coiling of the chain into a pattern due to weak H bonds between amino acids. H bonds form between the main chain of amino acids. Two Kinds of Secondary Structure

Secondary Structures Alpha Helix- H bonds between one amino acid and another further down the chain. Pulls the chain into a coil. Beta Sheet- H bonds occur across two separate chains. If chains are parallel, they may form a sheet-like structure.

OC  helix  pleated sheet Amino acid subunits N C H C O C N H C O H R C N H C O H C R N H H R C O R C H N H C O H N C O R C H N H H C R C O C O C N H H R C C O N H H C R C O N H R C H C O N H H C R C O N H R C H C O N H H C R C O N H H C R N H O O C N C R C H O C H R N H O C R C H N H O C H C R N H C C N R H O C H C R N H O C R C H H C R N H C O C N H R C H C O N H C Secondary Structure: –Is the folding or coiling of the polypeptide into a repeating configuration. –Includes the  helix and the  pleated sheet. H H Figure 5.20

Alpha Helix- The First Type of Secondary Protein Structure

Beta Sheet- Another Type of Protein Secondary Structure

Show me the levels of protein structure.

Secondary Structures Some patterns of alpha helices and/or beta sheets are very common in protein structures. When secondary structures are organized into specific structures within proteins-motifs. Ex. Β- Barrel or α-turn-α motifs

Β-barrel Motif in a Cell Membrane Protein

Globular Protein Structure 3. Tertiary Structure- folding and positioning of nonpolar R groups into the interior of the protein (hydrophobic interactions). Held together by weak van der Waal’s forces. Precise fitting of R groups within the interior. A change may destabilize a protein’s shape.

Tertiary Structure: –Is the overall three-dimensional shape of a polypeptide. –Results from interactions between amino acids and R groups. CH 2 CH OHOH O C HO CH 2 NH 3 + C -O-O CH 2 O SS CH CH 3 H3CH3C H3CH3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Ionic bond CH 2 Disulfide bridge

Globular Protein Structure 4.Quaternary Structure- two or more polypepetide chains associate to form a protein. Each chain is called a subunit. Subunits are not necessarily the same. Ex. Hemoglobin = 2 α-chain subunits + 2 β-chain subunits.

Quaternary Structure: –Is the overall protein structure that results from the aggregation of two or more polypeptide subunits. Polypeptide chain Collagen  Chains  Chains Hemoglobin Iron Heme

The four levels of protein structure + H 3 N Amino end Amino acid subunits  helix

Quaternary Structure of Hemoglobin

Hemoglobin structure and sickle-cell disease Fibers of abnormal hemoglobin deform cell into sickle shape. Primary structure Secondary and tertiary structures Quaternary structure Function Red blood cell shape Hemoglobin A Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen     10  m     Primary structure Secondary and tertiary structures Quaternary structure Function Red blood cell shape Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced.  subunit Normal hemoglobin Sickle-cell hemoglobin... Figure 5.21 Exposed hydrophobic region ValThrHisLeuProGlulGluValHisLeu Thr Pro Val Glu

Is Protein Folding Important?

Normal Prion Scrapie Prion

Reverse Transcriptase of HIV

Cobra Toxin

Shape of the Protein Tertiary and Quaternary structures provide shape. These structures are maintained by H bonds and other weak forces between R groups of amino acids.

Protein Folding

Conditions that Affect Protein Shape Can disrupt H bonds by: High Temperature pH Changes (Acidic or Basic) Ion Concentration (Salt) Disrupting the 2°, 3°, 4° structure is called denaturation.

Denaturation: Is when a protein unravels and loses its native conformation. Denaturation Renaturation Denatured proteinNormal protein Figure 5.22

Enzymes: –Are a type of protein that acts as a catalyst, speeding up chemical reactions. Substrate (sucrose) Enzyme (sucrase) Glucose OH H O H2OH2O Fructose 3 Substrate is converted to products. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate binds to enzyme Products are released. Figure 5.16

Enzymes are Proteins Organic catalysts - increase the rate of chemical reactions in cells. Hold reactant molecules close together for reaction to occur- uses an active site. The active site is used to bind the reactant molecules-substrate.

Lock-and-Key Model Show me the model, Luke!

Write your predictions! Gelatin = Substrate Pineapple = Papain (Enzyme)