Chapter 4: Protein Structure and Function

Proteins execute

nearly all cell function and cell and tissue structure

Protein

a large macromolecule mainly consisting of one or more long chains of amino acid residues that assumes a small set of stable shapes and carries out function

Peptide

small amino acid chain, lacking function

Polypeptide

Large amino acid chain, lacking function

What distinguishes one protein from another?

• Primarily amino acid sequence

  • Also know as Central Dogma

  • Gene (DNA) sequence → mRNA sequence → protein sequence

• Structure

• Function

Amino Acids

• What proteins are composed of this

• Sequence of these define protein structure and function

Side Chain Rules (Polar vs. NonPolar)

Non-polar: comprised of Carbon and Hydrogen → Cannot react

Polar: Comprised of Carbon, Hydrogen, Oxygen, and Nitrogen

• Charged: Have charges on them

• Uncharged: No charges but are comprised of molecules more than just CH

Non Polar Amino Acids

• Uncharged

• Tend to cluster side chains together INSIDE cell

• Can engage in very weak reactions

• Can be slightly soluble in water and be very weakly polar

• Comprised of Carbon and Hydrogen only

Polar Amino Acids

• Charged

  • Very polar

  • Hydrophilic

  • Often found outside of proteins

  • Engaged in ionic bonds

  • Has charges on them

• Uncharged

  • Polar

  • Hydrophilic

  • Frequently engaged in H-bonds

  • No charges on them, but comprised of Carbon, Hydrogen, Oxygen, and Nitrogen

Primary Protein Structure

• Lowest structure

• Held together by peptide bonds

• Limited flexibility

• Allows the polypeptide to bend

• Looks like string with beads

  • String - Peptide bond

  • Beads - Amino acids

Peptide bond

• Formed through covalent bonding

  • 4 atoms involved held rigidly

  • 2 triangonal configurations overlap

  • alpha carbon can rotate @ these bonds; torsional rotation

• Amino acid is put together with a dipeptide through dehydration synthesis

• Amino acid can be taken from dipeptide through hydrolysis

• Linear chains form many shapes because there is full flexibility sue to peptide bonds

N-terminus of peptide bond

amino terminus

Side chain define

Amino acids that

• dictates structure of the final protein

  • Shape

  • Size

• are important in the function of the final protein

Amino acid positioning in primary structure

Based on possibilities which seem big but in reality is not numerous

Secondary Protein Structure

• H bonds form between atoms within the peptide bonds

• Common patterns:

  • alpha helix

  • beta sheet

• R groups do not have a role in secondary structure because they change everytime and secondary structure is universal

Secondary Structure: Alpha helix

• Key structure to embedded in cell membranes

• May form coil of coils

Secondary Structure: Beta Sheet

• Parallel and anti-parallel

  • Anti-parallel is the primary structure

• Side chains are above and below the plane

Domain

• Grouping of secondary structures

• Typical protein is built with one or more

  • Folded independently

  • Linked by unstructured polypeptide sequences

  • Often unstructured linker regions serve role which give our proteins flexibility in function

    • Scaffold proteins

  • Can add chemical groups

Tertiary Protein Structure

• Overall geometry

• Dependent on primary and secondary structures

• Stabilized by non-covalent bonds

  • Formed by many

  • Surface charge: determined by R groups on the protein surface

  • Can be disrupted by factor outside the cell such as pH, temperature, and solvents

• Shape vs sequence is associated with protein families

• Categorizes proteins

  • Overall globular or fibrous shape

  • Used in defining protein families

  • Measured through X-ray crystallography or NMR spectroscopy

Protein Denaturation

Lost tertiary structure, sometimes can re nature by re establishing the non covalent bonds driving most of protein tertiary structure

• Sometimes a temperature state

• Can often aggregate (misfold) and lead to disease

Chaperone or chaperonins

• Proteins that help other proteins fold correctly in the primary structure

  • Process consumes energy

  • Intermediate steps in folding to stable final conformation

Tertiary Structure Visualizations

1. Backbone model: overall organization

2. Ribbon model: shows polypeptide backbone, emphasizes folding patterns

3. Wire model: positions of all amino side chains, useful to predict amino acids

4. Space-filling model: reveals amino acids on the surface

Quaternary Protein Stucture

Large proteins typically contain 2 or more polypeptide chains subunits aggregate → functional protein

Tertiary structure is subunits for this complex

Disulfide covalent bonds stabilizes protein structure in both this and tertiary structures

Energy component of protein formation

Food → catabolic pathways (losing heat and energetically favorable) → useful forms of energy and the building blocks for biosynthesis such as amino acids → anabolic pathways (energetically unfavorable) → macromolecules such as proteins

Degradation Protein Systems

1. Proteosome

2. Lysosome

3. Proteinase

• Confined to specific cell compartments so that only specific proteins are degraded

Degradation System - Proteosome System

Nuclear and cytosolic proteins that are misfolded, no longer function, no longer needed:

1. Protein in marked with ubiquitin

2. Ubiquinated protein now sent to proteosome

   • Proteosome: multi-subunit protein complex that needs ATP

3. Protein binds to proteosome to be degraded

Degradation System Lysosomal Proteolysis

• Cell tries to fix it first, but if unsuccessful

• It goes to the Lysosome to degrade proteins from the endomembrane system (ER and Golgi) and the extracellular or cell surface

• Proteins are marked with phosphorylated sugars

Degradation System Proteinases/Proteinase Inhibitors

Degradation of secreted proteins in the extracellular matrix and/or between the cell membrane and cell wall

Controlled by relative concentration of proteases

Protein Binding

ligand (macromolecules organic or inorganic compounds) + protein are bounded by noncovalent bonds

• only if the binding site matches ligand

• physical/chemical properties result

Enzymes

Proteins that catalyze biochemical reactions using active sites by lowering activation energy by promoting catalysis through

• positioning the substrates molecules to encourage a reaction

• rearranging electrons in the substrate to create partial negative and positive charges that favor a reaction

• straining the bound substrate and forcing it toward a shape that favors reaction

Favorable reaction

Why is enzymes lowering activation energy important?

1. Need to avoid excessive heat

2. Need reaction to occur efficiently

3. Need to drive a specific reaction

How is energy use in cells reported?

2nd law of thermodynamics

• For a reaction to happen, the overall disorder (delta S) of the universe will increase

• But living cells generate order through Gibbs free energy (delta G)

  • Spontaneous - delta G decreases

  • Released - delta G greater than 0

How enzymes work

As reactants become products, energy released to system which is an exergonic reaction which causes free energy go down (favorable reaction)

• Gives less product than reactants

On the other hand, if ATP is used reaction than enzymes, energy to taken up which is an endergonic reaction which causes free energy to go up (unfavorable reaction)

• Gives more product than reactions

Enzymes also have special functions that are needed for reactions

• e.g. Lysozyme breaking bacterial cell wall of polysaccharides

Why are proteins controlled?

To conserve energy and facilitate proteins functioning teams called metabolic pathway

This happens by regulating enzymes

Mechanisms Used to Protein Function/Activity

1. Blocking the Active Site

2. Allosteric Changed

3. Phosphorylation

4. Covalent modification (r-groups)

5. Prosthetic groups

Controlling Proteins: Blocking the Active Site

Active site: the region of the enzyme that binds to the substrate

An inhibitor molecular occupies the active site

Controlling Proteins: Allosteric Changes

Changing conformation which can stimulate or inhibit activity through the binding of CTP molecule (negative feedback inhibition) or ADP (positive feedback inhibition)

Controlling Proteins: Phosphorylation

a. Direct phosphorylation of proteins:

1. Covalent bond of phosphate group

2. Phosphorylation can activate or inactivate the protein

   • Kinase: adding ATP and taking ADP and adding Phosphate group

   • Phosphatase: Giving away phosphate group

b. GTP Binding Proteins (Molecular Switches)

• Regulated by cyclic addition/loss of phosphate, proteins not phosphorylated

• GTP ←→ GDP causes allosteric changes, switching the enzyme on and off

• Involved in cell signaling

• GTP → GTP Hydrolysis → GDP off → Adding GTP Back → GTP on

c. ATP Hydrolysis provides direction for motor proteins

• Proteins can move but with little uniformity

• If allosteric change is reversible, then protein moves back and forth movement

• No energy input, conformational changes random

• Uses motor proteins that are regulated by ATP hydrolysis (ATPase)

• If allosteric change is irreversible, then protein moves in one direction only

  • ATP → ADP irreversible reaction

Controlling Proteins: Modification of R-Groups

Chemical modification regulate proteins

• Impact protein location

• Interactions of protein

• Modification target certain R-Groups

Some enzymes regulated through both mechanisms

• Regulatory binding sites by allosteric regulators on some subunits

• Other sites for covalent modification on other subunits

Controlling Proteins: Prosthetic Groups

Inorganic prosthetic groups are called cofactors

Organic prosthetic groups are called co-enzymes