Essential Cell Biology

Third Edition

Chapter 4 Lecture Outlines Protein Structure and Function

Copyright Garland Science 2010

CHAPTER CONTENTS
THE SHAPE AND STRUCTURE OF PROTEINS HOW PROTEINS WORK HOW PROTEINS ARE CONTROLLED HOW PROTEINS ARE STUDIED

THE SHAPE AND STRUCTURE OF PROTEINS

The Shape of a Protein Is Specified by Its Amino Acid Sequence Proteins Fold into a Conformation of Lowest Energy Proteins Come in a Wide Variety of Complicated Shapes The Alpha Helix and the Beta Sheet Are Common Folding Patterns Helices Form Readily in Biological Structures Beta Sheets Form Rigid Structures at the Core of Many Proteins Proteins Have Several Levels of Organization Few of the Many Possible Polypeptide Chains Will Be Useful Proteins Can Be Classified into Families Large Protein Molecules Often Contain More Than One Polypeptide Chain Proteins Can Assemble into Filaments, Sheets, or Spheres Some Types of Proteins Have Elongated Fibrous Shapes Extracellular Proteins Are Often Stabilized by Covalent Cross-Linkages

Sequence Change vs Mutation Type

Why/How do mutations cause disease? 1 ATG met 4 7 10 13 16 19 GGA GCT CTA TTA ACC TAA gly ala leu leu thr stop

ATG met

GGA gly

GCC ala

CTA TTT leu phe

ACC thr

TAA stop

Missense Mutation

ATG met

GGA gly

GCC ala

CTA TGA ACC leu stop

TAA Nonsense Mutation

ATG met

GGA gly

GCT ala

CTA leu

TTA CAC CTA A leu his leu

Frameshift mutation!!! (insertion/deletion)

Genetic Code

Different reading frames

The code is redundant, some aminoacids are specified by more than one triplet

Figure 7-25 Essential Cell Biology ( Garland Science 2010)

The Shape of a Protein Is Specified by Its Amino Acid Sequence

Figure 4-1 Essential Cell Biology ( Garland Science 2010)

The Shape of a Protein Is Specified by Its Amino Acid Sequence

Side chain gives unique properties

Figure 4-2 Essential Cell Biology ( Garland Science 2010)

The Shape of a Protein Is Specified by Its Amino Acid Sequence

Figure 4-3 Essential Cell Biology ( Garland Science 2010)

The Shape of a Protein Is Specified by Its Amino Acid Sequence

noncovalent bonds shape the polypeptide chain (Peptide bond is covalent bond)

Noncovalent bonds: Electrostatic attractions

Hydrogen bond
Van der Waals atractions

Figure 4-4 Essential Cell Biology ( Garland Science 2010)

The Shape of a Protein Is Specified by Its Amino Acid Sequence

Hydrohpobic hydrophilic interactions

Nonpolar - Hydrophobic aa (phe, leu, val, trp) tend to cluster inside in folded protein (hydrophobic oil droplets coalesce to form larger one) Polar-Hydrophilic aa (arg, glu, his) tend to arrange near outside of protein to form H bond with water or other polar molecules

Figure 4-5 Essential Cell Biology ( Garland Science 2010)

THE SHAPE AND STRUCTURE OF PROTEINS

The Shape of a Protein Is Specified by Its Amino Acid Sequence Proteins Fold into a Conformation of Lowest Energy Proteins Come in a Wide Variety of Complicated Shapes The Alpha Helix and the Beta Sheet Are Common Folding Patterns Helices Form Readily in Biological Structures Beta Sheets Form Rigid Structures at the Core of Many Proteins Proteins Have Several Levels of Organization Few of the Many Possible Polypeptide Chains Will Be Useful Proteins Can Be Classified into Families Large Protein Molecules Often Contain More Than One Polypeptide Chain Proteins Can Assemble into Filaments, Sheets, or Spheres Some Types of Proteins Have Elongated Fibrous Shapes Extracellular Proteins Are Often Stabilized by Covalent Cross-Linkages

Proteins Fold into a Conformation of Lowest Energy

Protein shape is formed to minimize free energy (G) (by spontaneous or molecular chaperons in cytoplasm) if a protein denatured to destroy folding, it will regain its shape again

Each protein is folded into one stable conformation Sometimes the shape of proteins changes by modification or interaction

Modification: methylation, acetylation, phosphorylation of histones

Figure 4-7 Essential Cell Biology ( Garland Science 2010)

Proteins Fold into a Conformation of Lowest Energy The proper structure of protein is important for its function and solubility improper folded protein aggregate in cell, destroy cell (Alzheimers disease)

Mis-folded Prion protein aggregates: mad cow disease

Misfolded prion can convert the properly folded prion into misfolded
Figure 4-8 Essential Cell Biology ( Garland Science 2010)

THE SHAPE AND STRUCTURE OF PROTEINS

The Shape of a Protein Is Specified by Its Amino Acid Sequence Proteins Fold into a Conformation of Lowest Energy Proteins Come in a Wide Variety of Complicated Shapes The Alpha Helix and the Beta Sheet Are Common Folding Patterns Helices Form Readily in Biological Structures Beta Sheets Form Rigid Structures at the Core of Many Proteins Proteins Have Several Levels of Organization Few of the Many Possible Polypeptide Chains Will Be Useful Proteins Can Be Classified into Families Large Protein Molecules Often Contain More Than One Polypeptide Chain Proteins Can Assemble into Filaments, Sheets, or Spheres Some Types of Proteins Have Elongated Fibrous Shapes Extracellular Proteins Are Often Stabilized by Covalent Cross-Linkages

Proteins Come in a Wide Variety of Complicated Shapes

Different shapes different aa sequence, different interactions Globular or fibrous shape Different size 30 aa to 10000 aa

Figure 4-9 Essential Cell Biology ( Garland Science 2010)

THE SHAPE AND STRUCTURE OF PROTEINS

The Shape of a Protein Is Specified by Its Amino Acid Sequence Proteins Fold into a Conformation of Lowest Energy Proteins Come in a Wide Variety of Complicated Shapes The Alpha Helix and the Beta Sheet Are Common Folding Patterns Helices Form Readily in Biological Structures Beta Sheets Form Rigid Structures at the Core of Many Proteins Proteins Have Several Levels of Organization Few of the Many Possible Polypeptide Chains Will Be Useful Proteins Can Be Classified into Families Large Protein Molecules Often Contain More Than One Polypeptide Chain Proteins Can Assemble into Filaments, Sheets, or Spheres Some Types of Proteins Have Elongated Fibrous Shapes Extracellular Proteins Are Often Stabilized by Covalent Cross-Linkages

The Alpha Helix and the Beta Sheet Are Common Folding Patterns Two common folding pattern : alpha helix, beta sheet

These structure formed by H bonding between N-H and C=O atoms in polypeptide backbone

Figure 4-10 Essential Cell Biology ( Garland Science 2010)

- helix H-bond between every fourth aminoacid Abundant in proteins located in cell membrane (transport protein, receptor)

Figure 4-10ac Essential Cell Biology ( Garland Science 2010)

- helix

Coiled-coil structure
2 or more - helix wrap around one another

- helix crossing lipid bilayer n membrane

Rod-like strong fiber keratin, reinforce layer of skin Myosin, responsible for muscle contraction

Figure 4-12 Essential Cell Biology ( Garland Science 2010)

Beta Sheets Form Rigid Structures at the Core of Many Proteins

Beta sheets: H bond between polypeptide chain lying side by side Antiparallel

parallel

Figure 4-10df Essential Cell Biology ( Garland Science 2010)

Beta Sheets Form Rigid Structures at the Core of Many Proteins

Beta sheets produce very rigid, pleated structure

Silk: extraordinary tensile strength Antifreeze proteins prevent ice formation in cell

Figure 4-15 Essential Cell Biology ( Garland Science 2010)

THE SHAPE AND STRUCTURE OF PROTEINS

The Shape of a Protein Is Specified by Its Amino Acid Sequence Proteins Fold into a Conformation of Lowest Energy Proteins Come in a Wide Variety of Complicated Shapes The Alpha Helix and the Beta Sheet Are Common Folding Patterns Helices Form Readily in Biological Structures Beta Sheets Form Rigid Structures at the Core of Many Proteins Proteins Have Several Levels of Organization Few of the Many Possible Polypeptide Chains Will Be Useful Proteins Can Be Classified into Families Large Protein Molecules Often Contain More Than One Polypeptide Chain Proteins Can Assemble into Filaments, Sheets, or Spheres Some Types of Proteins Have Elongated Fibrous Shapes Extracellular Proteins Are Often Stabilized by Covalent Cross-Linkages

Proteins Have Several Levels of Organization Primary structure: aminoacid sequence, long polypeptide chain Secondary structure: alpha helix, beta sheet Tertiary structure: 3-dimentional structure combination of alpha helix, beta sheet Quaternary structure: protein contain more than one polypeptide chain

GFP

Figure 4-16 Essential Cell Biology ( Garland Science 2010)

RFP GFP

Change the aminoacids to improve the starch synthesis!

Proteins Have Several Levels of Organization

Proteins: long peptide chain

Parts of this long chain called protein domain, specific function

DNA binding domain

Protein-protein interaction domain

Catalytic domain Transmembrane domain

Figure 4-17 Essential Cell Biology ( Garland Science 2010)

Proteins Can Be Classified into Families Protein families: proteins share similar features and structures

Polymerases Proteases (protein cleaving enzyme, digestive function) Kinases (add P-grup to proteins) Membrane protein, transcription factors

Two members of protease Slight difference- different substrate

Figure 4-18 Essential Cell Biology ( Garland Science 2010)

THE SHAPE AND STRUCTURE OF PROTEINS

The Shape of a Protein Is Specified by Its Amino Acid Sequence Proteins Fold into a Conformation of Lowest Energy Proteins Come in a Wide Variety of Complicated Shapes The Alpha Helix and the Beta Sheet Are Common Folding Patterns Helices Form Readily in Biological Structures Beta Sheets Form Rigid Structures at the Core of Many Proteins Proteins Have Several Levels of Organization Few of the Many Possible Polypeptide Chains Will Be Useful Proteins Can Be Classified into Families Large Protein Molecules Often Contain More Than One Polypeptide Chain Proteins Can Assemble into Filaments, Sheets, or Spheres Some Types of Proteins Have Elongated Fibrous Shapes Extracellular Proteins Are Often Stabilized by Covalent Cross-Linkages

Large Protein Molecules Often Contain More Than One Polypeptide Chain

Different polypeptide bind each other with weak noncovalent bonds (subunits)

Figure 4-19 Essential Cell Biology ( Garland Science 2010)

Proteins Can Assemble into Filaments, Sheets, or Spheres

microtubule

Simian virus

Figure 4-21 Essential Cell Biology ( Garland Science 2010)

Some Types of Proteins Have Elongated Fibrous Shapes

Figure 4-25 Essential Cell Biology ( Garland Science 2010)

HOW PROTEINS WORK

All Proteins Bind to Other Molecules The Binding Sites of Antibodies Are Especially Versatile Enzymes Are Powerful and Highly Specific Catalysts Lysozyme Illustrates How an Enzyme Works Most Drugs Inhibit Enzymes Tightly Bound Small Molecules Add Extra Functions to Proteins

All Proteins Bind to Other Molecules

Figure 4-27 Essential Cell Biology ( Garland Science 2010)

Three dimentional structure

Binding Site/ active site

Figure 4-28a Essential Cell Biology ( Garland Science 2010)

Proteins interact with its ligand

Specific interaction! 1) Ligand fits into the binding site 2)Because of combination of weak non-covalent bonds hydrogen bonds electrostatic attraction van der Waals attraction hydrophobic interactions

Figure 4-28b Essential Cell Biology ( Garland Science 2010)

Enzymes Are Powerful and Highly Specific Catalysts

Enzyme: proteins having catalytic (enzymatic) activity Ligand is called substrate

Enzymes have catalytic domain/reaction site performing enzymatic reactions

Figure 4-30 Essential Cell Biology ( Garland Science 2010)

Most Drugs Inhibit Enzymes

Table 7-3 Essential Cell Biology ( Garland Science 2010)

Tightly Bound Small Molecules Add Extra Functions to Proteins Hemoglobin protein, oxygen carrying protein

Co-enzymes and co-factors bind to proteins and change their activity

Figure 4-33 Essential Cell Biology ( Garland Science 2010)

HOW PROTEINS ARE CONTROLLED

The amount of proteins are regulated by expression and protein modifications!!!!! Genes can be expressed with different efficiencies to regulate the amount of required protein

1 gene multiple RNA copies

rapid protein synthesis when required Protein modifications: Phosphorylation Ubiquitination Modifications are signals for degradation

The catalytic activity of enzyme can be regulated by protein modifications

Enzymes are not active eveytime but activated when required

Phosphate group is linked only to Tyrosine Threonin Serine amino acids

Phosphorylation addition of phosphate group to protein

Figure 4-38a Essential Cell Biology ( Garland Science 2010)

The catalytic activity of enzyme can be regulated by protein modifications

Modifications change the 3-dimentional structure

Figure 4-38b Essential Cell Biology ( Garland Science 2010)

Chromatin Remodeling

Modification of Histone Methylation Acetylation Phosphorylation Ubiquitination

Figure 5-27 Essential Cell Biology ( Garland Science 2010)

Protein modifications regulate: Activity of protein/enzyme Lifetime/amount of protein Location of proteins

Figure 4-44a Essential Cell Biology ( Garland Science 2010)

The Catalytic Activities of Enzymes Are Often Regulated by Other Molecules

Negative feedback

Positive Feedback

Substrate inhibit enzyme

Subtstrate increase the amount of active enzyme by binding to enzyme

Figure 4-34 Essential Cell Biology ( Garland Science 2010)

Proteins Have Several Levels of Organization

Proteins: long peptide chain

Parts of this long chain called protein domain, specific function

DNA binding domain

Protein-protein interaction domain

Catalytic domain Transmembrane domain

Allosteric Enzymes Have Binding Sites That Influence One Another The activity of Allosteric Enzymes regulated by other molecules

Figure 4-17 Essential Cell Biology ( Garland Science 2010)

Bio-Engineering