Proteins

In Ch 2

Protein Function

2-44

• Regulation – act as chemical signals, e.g., non-steroidal hormones

• Enzymes– promotion and regulation of chemical reactions

• Transport– across the plasma membrane and through blood

• Contraction/movement– cell motility and muscle contraction

• Energy source– By breaking them down/catabolism

• Structural• Immune function

– e.g., antibodies

Basic Protein Structure

• Large molecules made of amino acids– 20 different amino acids (aa)

• Different aa sequences different proteins

– joined by peptide bonds (covalent bonds)

a b

Amino Acid Structure

– Amino acids=amino group (NH2) + carboxyl group (COOH) + functional group (R)

• Different A.A. = different functional group.

2-44Its amino world without chemistry

Example Amino Acids

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Linking Amino Acids: covalent bonds called peptide bonds

2-44

What kind of rxn is this?

Polypeptides v. Proteins

• <100 amino acids= polypeptide• >100 amino acids =protein

Protein Structure: 1° structure• Primary structure = amino acid sequence

– Covalent bonds– Strength?

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Protein Structure: 2° structure• Secondary structure = bent or twisted amino acid chains (beginning of

shape)• due to bonding among a.a./between adjacent a.a. (between H of amino group and O’s)

• Hydrogen Bonds….Strength?

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Alpha helixBeta pleated sheet

Protein Structure: 3° structure• Tertiary structure = distinct 3-D shape (conformation)• Due to bending and folding of a.a. chains (of the 2°

structure)– Hydrogen and other weak bonds between functional groups– Strength?

– Denatured (broken) by heat, pH

Protein Structure: 4° structure

• Quaternary structure = multiple polypeptide chains are joined• Not applicable to all proteins

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“composite molecules”

• proteins are combines with other molecules– Glycoproteins = protein + carbohydrate– Lipoproteins = protein + lipid– Others…..

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Enzyme: Chapter 4

• Main Topics– Enzymes and Activation Energy– Characteristics of Enzymes– Factors that influence enzyme activity/function– Metabolic/Biochemical pathways

4-2

Generic Reactions• Substrate(s)/reactant(s) = starting material• Product = ending material(s)/product made

example: A + B AB

• Activation Energy:

4-4

Requires activation energy

Background

• activation energy– cons– pros

Enzyme Introduction

• proteins* that:– allow chemical rxns to occur at need rates– allow chemical rxns to be regulated

• By their present, absence, or amount

– Almost all rxns (processes) in the body occur because of enzymes

*some enzymes are made of RNA, but we don’t go there

Enzymes continued

4-5

Few substrates react

Many substrates react

high low

Significance of Enzymes

• Allow chemical rxns to occur at needed rates under conditions that are compatible with life (i.e., that the human body can survive).

• Allow chemical rxns to be regulated so specific processes can occur when and where they are needed.

• Substrates fit into active sites• Enzyme-substrate complex

formed• Reaction occurs• Products leave enzyme• Enzyme is unaltered

– Enzyme is not used up/consumed

Mechanism of Enzyme Action

4-7

Enzyme Characteristics• PROTEINS• CATALYST: increase rates of chemical rxns without being altered or

“used up” (100’s-1000’s rxns/second!!!)

– lowering activation energy– few enzyme; lots of reaction

• SPECIFICITY: binds only w/ specific substrate – (reality a very narrow range of molecules, important clinically/pharmaceutically)

– due to shape of binding site/active site (CONFORMATION)– due to 3 structure—WEAK BONDS/H-BONDS– structural differences not involving active site do not effect the rxn or

specificity– isozymes different versions of enzyme (vary by 1-a few amino acids) in

different tissues that catalyze the same substrate/rxn• “leak” into blood after tissue damage, but don’t act due to wrong conditions/lack

of substrates but can be measured/detected and be diagnostic• Enzymes can be regulated—turned on/off• Often mediate reversible reactions

– not always, sometimes different enzymes are needed for the synthesis and decomposition of a substrate product pair.

• Names usually end in “ase” and based on substrate or reaction type

Factors that Influence Activity

• Concentration of substrates

– Saturation

• Concentration of enzyme

• Presence/absence of cofactor:

• Presence/absence of Coenzymes

• TEMPERATURE:

• pH:

• Chemical Activation/Deactivation of enzyme

Substrate Concentration• More substrate = more/faster reaction

• To a point saturation/saturated

• Saturation– plateaus because all enzymes are filled / “occupied” or “busy” with substrates

4-16

Enzyme Concentration• Related to encounter rate between enzyme and substrate and the

number of enzymes “available” to substrate(s)• Plateaus encountered when enzymes are saturated

– specific processes can be selectively regulated by altering the amount of enzyme available/active

substrate concentration

rea

ctio

n r

ate

low enzyme concentration

medium enzyme concentration

high enzyme concentration

saturation

saturation

saturation

Cofactors• cofactor: ion or molecule (often inorganic, e.g., mineral) that must

simultaneously bind the enzyme (at active site or elsewhere) for the substrate to bind (and react)

– E.g., Ca+2, Mg+2, Mn+2, Cu+2, Zn+2, & selenium

– No cofactor no enzyme function no reaction– Fewer cofactor less functional enzyme less reaction

4-14

Coenzymes• Coenzymes:

a. non-protein, organic molecules that deliver or “escort” molecules necessary for the rxn to enzymes

b. Or, a non-protein molecule needed for enzyme to have its functional shape

– No cofactor no enzyme function no reaction– Fewer cofactor less functional enzyme less reaction

4-14

Temperature• Every enzyme has a temperature range in which it works

– Optimal temp = works best• Typically near normal physiological values

• activity decreases with deviations both above an below optimum– progressively slows with decreases in temp– eventually denatures at high temp causing rxn to stop

4-11THIS DIAGRAM IS JUST A REPRESENTATIVE EXAMPLE!

pH• optimum pH = where enzyme works best

– (usually reflective of the pH of tissue where it functions)– Different enzymes can have different optimal pH

• deviations from optimum decrease activity• extreme deviations denature enzymes activity stops

4-11

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Examples of pH optima

Enzyme Activation & inhibition• Enzymes can be turned on (activated) and turned off

(deactivated) by a wide variety of means that usually involve changing the shape of or blocking the active siteExample:– Phosphorylation turns on– Dephosphorylation turns off

4-15

Phosphorylated: substrate can fit

substrate

Dephosphorylated:Substrate can’t fit

Enzyme Activation & inhibition cont.

• Inhibition or activation by other molecules

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substrate

CLINICAL AP--Isozymes

• dead and damaged cells (compartments containing enzymes specific to that tissue—isozymes) leak enzymes into other compartments such as plasma where they lack much activity because of the general absence of their specific substrates. measuring the amount of these “leaked” enzymes can be diagnostic.

Reaction Rates and Enzyme Turnover

• Reaction rates are related to enzyme concentration (number of enzymes)

• Enzymes do not last forever, they breakdown and need to be replaced enzyme turnover

• If new enzyme production < enzymes lost reaction rates go down

• If new enzyme production > enzymes lost reaction rates go up.

• Reaction rate = quantity broken down v. quantity synthesized

4-15

Reversible Reactions

• Some enzymatic reactions are reversible– Direction: higher concentration to lower

concentration

– e.g. carbonic anhydrase catalyzes

» H2O + CO2 H2CO3

4-17

Pathways and their behavior

• simple/linear pathways

• inhibitions effects

• branching pathways

• inhibition of branch point

• inhibition of one branch increases product of the other. could be good or bad, natural or pathologic (diseases of defiency or excess)

Metabolic Pathways•sequences of reactions

– Initial substrate intermediates final product

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End product inhibition:• End/final product inhibits the first (or earlier) enzyme• Slows or stops production of final product• Increasing end product trigger reduced production of end

product

End-Product Inhibition and branched pathways

• A product causes inhibition (of branch point).– Reduces final product– Pushes rxn down other pathway

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Inborn Errors of Metabolism• inherited genetic defects

– Dysfunctional enzyme

• Can cause: – ↑ intermediates– ↓ products – ↑ alternate products

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