Chapter 4

Chapter 4 Lecture OutlinesProtein Structure and Function

EssentialCell Biology

Third Edition

Copyright © Garland Science 2010

CHAPTER CONTENTSTHE SHAPE AND STRUCTURE OF

PROTEINSHOW PROTEINS WORKHOW PROTEINS ARE CONTROLLEDHOW 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

1 4 7 10 13 16 19ATG GGA GCT CTA TTA ACC TAA met gly ala leu leu thr stop

ATG GGA GCC CTA TTT ACC TAA met gly ala leu phe thr stop

ATG GGA GCC CTA TGA ACC TAA met gly ala leu stop

ATG GGA GCT CTA TTA CAC CTA A met gly ala leu leu his leu

Sequence Change vs Mutation Type

Why/How do mutations cause disease?

Missense Mutation

Nonsense Mutation

Frameshift mutation!!!(insertion/deletion)

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

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

Different reading frames

Genetic Code


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



Side chain gives unique properties





noncovalent bonds shape the polypeptide chain

Noncovalent bonds:

Electrostatic attractions

Hydrogen bond

Van der Waals atractions

(Peptide bond is covalent bond)



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








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 conformationSometimes the shape of proteins changes by modification or interaction

Modification: methylation, acetylation, phosphorylation of histones


Proteins Fold into a Conformation of Lowest Energy

The proper structure of protein is important for its function and solubilityimproper folded protein aggregate in cell, destroy cell (Alzheimer’s disease)

Mis-folded Prion protein aggregates: mad cow disease

Misfolded prion can convert the properly folded prion into misfolded








Cross-Linkages


Proteins Come in a Wide Variety of Complicated Shapes

Different shapes different aa sequence, different interactions

Globular or fibrous shape

Different size30 aa to 10000 aa








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 4-10a–c Essential Cell Biology (© Garland Science 2010)

α- helix

H-bond between every fourth aminoacid

Abundant in proteins located in cell membrane (transport protein, receptor)


α- helix

α- helix crossing lipid bilayerİn membrane

Coiled-coil structure

2 or more α- helix wrap around one another

Rod-like strong fiberkeratin, reinforce layer of skinMyosin, responsible for muscle contraction

Figure 4-10d–f 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


Beta Sheets Form Rigid Structures at the Core of Many Proteins

Beta sheets produce very rigid, pleated structure

Silk: extraordinary tensile strengthAntifreeze proteins prevent ice formation in cell








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

RFPGFP

Change the aminoacids to improve the starch synthesis!



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


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 proteaseSlight difference- different substrate








Cross-Linkages


Large Protein Molecules Often Contain More Than One Polypeptide Chain

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


Proteins Can Assemble into Filaments, Sheets, or Spheres

Simian virus

microtubule


Some Types of Proteins Have Elongated Fibrous Shapes

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

Three dimentional structure

Binding Site/ active site

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

Proteins interact with its ligand

Specific interaction!

1) Ligand fits into the binding site2)Because of combination of weak non-covalent bonds

hydrogen bondselectrostatic attractionvan der Waals attractionhydrophobic interactions


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

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

Most Drugs Inhibit Enzymes


Tightly Bound Small Molecules Add Extra Functions to Proteins

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

Hemoglobin protein, oxygen carrying protein

HOW PROTEINS ARE CONTROLLED

Genes can be expressed with different efficiencies

to regulate the amount of required protein

1 gene multiple RNA copies

rapid protein synthesis when required

The amount of proteins are regulated by expression and protein modifications!!!!!

Protein modifications:

Phosphorylation

Ubiquitination

Modifications are signals for degradation


The catalytic activity of enzyme can be regulated by protein modifications

Phosphorylation – addition of phosphate group to protein

Phosphate group is linked only toTyrosineThreoninSerine amino acids

Enzymes are not active eveytime but activated when required

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

The catalytic activity of enzyme can be regulated by protein modifications

Modifications change the 3-dimentional structure


Modification of Histone

MethylationAcetylationPhosphorylationUbiquitination

Chromatin Remodeling


Protein modifications regulate:

Activity of protein/enzyme

Lifetime/amount of protein

Location of proteins


The Catalytic Activities of Enzymes Are Often Regulated by Other Molecules

Negative feedback Positive Feedback

Substrate inhibit enzyme Subtstrate increase the amount of active enzymeby binding to enzyme



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 AnotherThe activity of Allosteric Enzymes regulated by other molecules

Bio-Engineering

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