chapter 11 slides 2017 - calvin university

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• Biomolecules are large, complex organic molecules that are present in all living things.

• There are FOUR major classes:1. Proteins2. Carbohydrates3. Lipids4. Nucleic acids (DNA and RNA)

• They are BIG and COMPLEX…….but still follow all of the chemical rules you’ve learned so far!

CHAPTER 11: Proteins: Structure and Function

BIOMOLECULES


PROTEIN FUNCTION IS DEPENDENT ON PROPER STRUCTURE!

• What is this molecule?

• What type of biomolecule is it?

• What is its function?

• 11.1 Amino Acids

• 11.2 Chirality and Amino Acids

• 11.3 Peptides

• 11.4 Protein Architecture

• 11.5 Enzymes


OUTLINE

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• Proteins have some of the most diverse functions of all biological molecules:

• Proteins are composed of amino acids linked together in chains, folded into complex structures

• Key concepts :


OVERVIEW OF PROTEINS

Ø Chemical properties of functional groups

Ø Effect of pH on acidic and basic groups

Ø CatalysisØ Structure

Ø TransportØ Information storage

• All amino acids consist of: 1. a central atom, the a-carbon2. an amine 3. a carboxylic acid4. a hydrogen atom5. a side chain (R group)


PARTS OF AMINO ACIDS

• The identity of an amino acid is determined by its R-groupØ There are 20 different

R-groups possible

• The amino group is basic; the carboxylic acidgroup is acidic:

Ø --NH2 + H2O à --NH3+ + OH-

Ø --COOH + H2O à --COO- + H3O+

• At neutral pH (7.0) both groups are ionized:Ø Compounds containing both a negative and a positive

charge are called zwitterionsØ The charge on amino acids changes with solution pH.


AMINO ACID STRUCTURE AND pH

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• There are 20 “common” amino acids that can be differentiated by their side chains (R-groups):

• Amino acid properties mostly depend on whether their R-groups are polar or nonpolar:Ø Nonpolar side chains are generally alkanes or

aromatics in structure.Ø Polar side chains may be divided into acidic, basic, or

neutral side chains.

• At physiological pH (~7.4):Ø the 3 basic side chains have positive chargeØ the 2 acidic side chains have negative charge


AMINO ACID SIDE CHAINS


NONPOLAR AMINO ACIDS

*Essential Amino Acid

Alkanes

Aromatics


POLAR AMINO ACIDS

Key functional group:

Carboxylic Acids

Key functional groups:

AlcoholsThiol

Amide

Key functional group:

Amines

Acidic Basic

Neutral

*Essential Amino Acid

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• About half of all the amino acids can be synthesized by our bodies.

• Essential amino acids are amino acids required in our diets:

Ø The ones we cannot synthesize ourselves


ESSENTIAL AMINO ACIDS

For each of the following amino acids check the boxes that apply to understand their classification:


AFTER CLASS EXERCISE

• Chirality is a property associated with many organic molecules:

Chiral molecules have at least one tetrahedral atom with four different atoms or groups attached

• Chiral molecules have mirror images that cannot be superimposable (think of two hands…)


DEFINING CHIRALITY

Ø Arrangement of the four atoms around the central carbon can occur in two distinct ways

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• Amino acids are chiral molecules relative to their central a-carbon atom à 4 distinct groups:

• Enantiomers are pairs of chiral molecules that are mirror images of one another:Ø Naturally occurring chiral molecules such as amino

acids are specifically found as only one enantiomer


AMINO ACID CHIRALITY

• Enantiomers are differentiated by one of two systems of naming:Ø Absolute configuration à R/S systemØ Rotation of polarized light à D/L system


ENANTOMERIC PAIRS & NOMENCLATURE

All naturally occurring amino acids are in the L- configuration

• A simplified way to indicate the structure of enantiomers is to use Fischer projections.

• For L-amino acids:1. the a-carbon is shown at the crosshair 2. the carboxylate to the top3. the amino group to the left4. the side chain down


FISCHER PROJECTIONS

Ø Indicate the chiral atom as crosshairs (+)

Ø the main carbon chain is written vertically

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• The physical & chemical properties of enantiomers in normal solutions are nearly identical:Ø Except rotation in polarized light

• In biological systems (cells), chiral molecules are differentiated by their interactions with biological molecules, which are also chiral:


PROPERTIES OF ENANTIONMERS

Ø Proteins are composed exclusively of L-amino acids, so they are chiral molecules……SHAPE MATTERS!!

These two drugs are enantiomers with dramatically different effects on human physiology.


A PAIR OF DRUG ENANTIONMERS

Thalidomide

This drug changed the pharmaceutical industry worldwide & strengthened FDA regulations in the United States

Sedative & anti-nausea medicine

Immune & vascular modulator

• Peptides are molecules formed by joining two or more amino acids together into a polymerØ A polymer is a “chain” of repeating chemical units

• Peptides may be: Ø small oligopeptides (2-15 amino acids)

Ø larger polypeptides (usually >50 amino acids)

Ø fully folded polypeptides are called proteins

• To form polymers, amino acids are joined by a special amide bond called a peptide bonds:


LINKING AMINO ACIDS TOGETHER

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• A peptide bond is an amide bond between two amino acidsØ Peptide bond

formation is a condensation reaction

Ø Peptide bond breakage is hydrolysis


PEPTIDE BOND FORMATION

• The nomenclature for small oligopeptides depends on amino acid number: Ø Two amino acids constitute a dipeptide.Ø Three amino acids constitute a tripeptide.

• The ends of the peptide chain are constant:Ø The N-terminus is always an ammonium ion (-NH3

+) Ø The C-terminus is always carboxylate ion (-COO-)


PEPTIDE STRUCTURE

• Glutathione, an important antioxidant in cells, is a tripeptide:


BIOLOGICALLY RELEVANT OLIGOPEPTIDES

• The endorphin, met-enkephalin, has 5 amino acids. It helps reduce pain following injury.

• Aspartame, commercially the artificial sweetener Nutrasweet™, is s dipeptide (Asp-Phe)

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• Polypeptides are long polymers of amino acids (>50 amino acids) that can assume complex 3D shapes during the process of folding:

• Proteins are properly folded polypeptides


OVERVIEW OF PROTEINS

Ø Additional molecules (coenzymes, metal ions) are often added to polypeptides to give them function

Proteins are not just “strings”—they have 3D shape!

1. Primary structureØ Sequence of amino acids from N-terminus to C-terminus

2. Secondary structureØ Localized regular folding stabilized by hydrogen bonds

3. Tertiary structureØ Complex irregular folding

of entire protein

4. Quaternary structureØ Association of two or

more subunits


FOUR LEVELS OF PROTEIN STRUCTURE

• The sequence of amino acids determines all other aspects of a protein’s structure and function.Ø If this sequence is altered, the protein may not function

properly.Ø Genetic diseases often involve disruption of a single

amino acid in a protein’s primary structure

• An amino acid is located in sequence by the number of its position from the N-terminus.


PRIMARY STRUCTURE OF A PROTEIN

Normal protein

Mutant protein

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• Secondary protein structure refers to the regular folding patterns in localized regions of a protein.

• The driving force for the folding of secondary structures is hydrogen bonding:Ø H-bonds in the peptide backbone of proteins are the

most important factor


SECONDARY STRUCTURE

Ø Between carbonyl oxygensand amide hydrogens

Ø Interactions between R-groups is less important in secondary structures

• There are two common secondary structures:


PATTERNS IN SECONDARY STRUCTURE

a-helix = coiled segment of polypeptide held in place by vertical hydrogen bondsbetween adjacent amino acid residues

b-pleated sheet = linear segment of polypeptide held in place by

horizontal hydrogen bondsbetween adjacent strands of

amino acids

Note placement of R-groups in each structure

R-groups point outward

R-groups alternate up & down

• Ribbon diagrams of proteins identify secondary structures with specific shapes:Ø a-helicies are indicated with twisted (red) ribbons

indicating the coiled structureØ b-pleated sheets are indicated with broad flat

arrows, pointing in the direction of the C-terminus


RIBBON DRAWING SECONDARY STRUCTURES

A protein may have any combination of secondary structures, including multiple a-helicies and b-sheets

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1. Label the partial positive and negative charges in the atoms involved in hydrogen bonding.

2. Why are there partial charges?

3. Orient the peptide structures below to show how they would form hydrogen bonds, and add dashes to show the corresponding hydrogen bonds.


PRACTICE PROBLEMS

• The tertiary structure of proteins describes the entire folding pattern of a single polypeptide:Ø It consists of complex and irregular folding patternsØ Not easily predicted from primary/secondary structure

• Tertiary structure is determined by interactions between the R-groups of amino acid residues:Ø May be interactions between amino acid residues that

are far apart in the primary sequence


TERTIARY STRUCTURE

• There are 4 main types of intermolecular forces between R-groups that provide tertiary structure:1. Dispersion forces (hydrophobic)

2. Hydrogen bonding (hydrophilic)

3. Salt bridges (ionic bond, hydrophilic)

4. Disulfide bridges (covalent bond, hydrophobic)


TYPES OF ELECTROSTATIC INTERACTIONS IN PROTEINS

Note: all four of these interactions are occurring at the same time to stabilize a protein tertiary structure

Increasing bond

strength

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General, Organic, and Biochemistry Chapter 11: Figure 11.17

Disulfide bridges are covalent bonds between two cysteines.

Hydrogen bonding occurs between polar residues when one residue contains either an N-H or an O-H bond

Salt bridges are ionic bonds between oppositely charged amino acid residues

Dispersion forces are weak interactions between non-polar (hydrophobic residues)

• Thiols (-SH) in adjacent cysteine residues react to form a disulfide bridges (-S-S-). Ø This is an example of an Redox ReactionØ “Perming hair” involves redox of the disulfide bonds in

keratin — a hair protein, giving the hair the shape of the rollers


DISULFIDE BRIDGES

• Dispersion forces are the weakest of the interactions stabilizing protein conformation, but play a critical role in early protein folding steps:Ø Because nonpolar groups only interact with other

nonpolar groups, these amino acids are only in the interior, away from the aqueous environment.


DISPERSION FORCES IN PROTEINS

Rosales, et al. Soft Matter, 2013,9, 8400-8414.

Unfolded polypeptide

Globular structure

Hydrophobic collapse

Ø An early phase in folding is “hydrophobic collapse”of non-polar amino acids into a hydrophobic sphere called a “globule”

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Indicate the type of bond that would likely form between each of the following pairs of amino acids if they were closely located in a protein.

Choose from the following: disulfide bond, salt bridge, hydrogen bonding, or dispersion forces.

1. aspartic acid and histidine à2. serine and lysine à3. leucine and valine à

4. two cysteines à5. tryptophan and isoleucine à


PRACTICE PROBLEMS

• For some proteins, tertiary structure also includes prosthetic groups:Ø Non-peptide organic molecules or metal ions (or a

combination) that are strongly bound to the proteinØ They are essential to a protein’s function


PROSTHETIC GROUPS

Example

Heme is an organic/iron (Fe2+) cofactor involved in oxygen transport by globin proteins

• Some proteins consist of more than one polypeptide chain; each is termed a subunit

• Quaternary structure is the relative arrangement and position of the subunits within the protein. Ø The subunits are stabilized by the same interactions

responsible for tertiary structure


QUATERNARY STRUCTURE

One subunit(monomer)

Natively folded hemoglobin is

a tetramer

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• Denaturation of a protein occurs by any process that disrupts its folding:Ø Denaturation disrupts secondary & tertiary structuresØ Protein unfolding is usually irreversible


PROTEIN DENATURATION

• Things that can denature proteins include:1. Heat2. pH changes (acid or base)3. Detergents (“soap”)4. Some metal ions (lead, Pb+2

and mercury, Hg+2)

• Partial denaturation of proteins alters their shape to form abnormal structures:Ø Partially denatured proteins are “sticky”Ø Collections of denatured proteins form

insoluble clusters called aggregates

• Several different neurological diseases are caused by protein misfolding:Ø Mad cow disease (CJD)Ø Alzheimer’s diseaseØ Parkinson’s diseaseØ Amylotrophic lateral sclerosis (ALS)

General, Organic, and Biochemistry Chapter 11: Unnumbered 11.11

PROTEIN MISFOLDING CAN CAUSE DISEASE

• There are several ways to categorize proteins:Ø StructureØ Function

• Categories that combine some of these features: 1. Fibrous proteins

Ø Poorly soluble, consists of long fibers or sheetsØ Primarily function is structural (extracellular matrix; cytoskeleton)

2. Globular proteinsØ Highly soluble; compact, “spherical”Ø Most enzymes fit into this category

3. Membrane proteinsØ Embedded within cell membrane


TYPES OF PROTEINS

Ø SolubilityØ Size

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• The different types of proteins & other molecules found in a cell can be detected by a method called fluorescence microscopy


TYPES OF PROTEINS

Fibrous proteins (actin) Globular proteins

(mitochondrial enzymes)

Nucleic acids (DNA)

• Enzymes are globular proteins that function as biological catalysts to increase reaction rate.

• An enzyme can increase reaction rate by >1 million (1x106) times!


HOW DO ENZYMES WORK?

Ø Enzymes work by lowering the activation energy(EA) for a reaction.

Ø Enzymes do not alter the overall change in bond energy of a reaction (∆H)

• Enzymes are typically named after the reaction they catalyze, with the suffix –ase added.

• The six classes of enzymes describe all of the types of biochemical reactions that are possible!


ENZYME CLASSIFICATIONS

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• The active site of an enzyme is where the reaction it catalyzes occurs:


THE ENZYME-SUBSTRATE COMPLEX

Ø Substrates are bound in the active site of an enzyme

Ø The shape of the substrate is complementary to the active site.

• Binding occurs through weak intermolecular forces: Ø Hydrogen bonds, dipole-dipole

interactions, and dispersion forcesØ Example: phosphatases

active site

Phosphoryl group

Hobiger & Friedrich. Front. Pharmacol., 10 February 2015

• The action of an enzyme can be thought of in three distinct steps:1. Enzyme (E) + substrate (S) binding: E + S à ES 2. Chemical reaction: ES à EP3. Release of the product from the enzyme: EP à E + P


THE ENZYME-SUBSTRATE COMPLEX

transition state

• Enzymes often require additional ions or small organic molecules to carry out their reaction:Ø Amino acid R-groups may not be sufficiently reactive

• Cofactors are generally metal ions required by the enzyme for its catalytic function:

Ø Examples include Mg2+, Zn2+, and Fe2+

Ø Especially useful as oxidants in redox reactions

• Coenzymes are small organic molecules required by enzymes for catalytic function:

Ø Examples include NAD+, FAD and coenzyme AØ These often function in redox reactions, too


COFACTORS AND COENZYMES

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• Enzyme inhibitors prevent an enzyme from performing its function. • Non-specific inhibitors affect all enzymes.

Ø Examples include pH and temperature.

• Specific inhibitors only affect one or a few enzymes:1. Competitive inhibitors

2. Noncompetitive inhibitors


ENZYME INHIBITORS

Most prescription drugs fit into these two categories

Don’t forget that enzymes are proteins!!

• Conditions that negatively affect protein folding will also impact enzyme performance:Ø pH: Most (but not all!) enzymes function best near pH 7Ø Temperature: Most enzymes work best at 37°C


pH AND TEMPERATURE DEPENDENCE

Suboptimal pH and temperature are “non-specific inhibitors” of enzyme activity

• Competitive inhibitors act by competing with substrate for the active site of the enzyme, preventing their binding, and thus formation of product:Ø The majority of synthetic drugs are

competitive inhibitors

• Noncompetitive inhibitors bind at a site other than the active site to inactivate an enzyme:Ø Alter overall enzyme shape, including

the active site “pocket”Ø Many natural inhibitors of enzymes

work by this mechanism


TWO TYPES OF SPECIFIC ENZYME INHIBITORS

chapter 11 slides 2017 - calvin university

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