PROTEIN NOTES: You are proteins and the result of protein action! Warm-Up: Match the function to the examples Copyright © 2008 Pearson Education, Inc.,

PROTEIN NOTES: You are proteins and the result of protein action!

• Warm-Up: Match the function to the examples

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Function Example

a. supportb. enzymesc. transportd. cell communications

(hormones)e. defense against

foreign substances

i. antibodiesii. insuliniii. ATP synthase,

sucrase, lactaseiv. proton pumpsv. keratin and collagen

• Dehydration: two monomers bond together; loss of a water molecule

• Polymers are disassembled to monomers by hydrolysis

The Synthesis and Breakdown of Polymers

Animation: PolymersAnimation: Polymers


Short polymer

HO 1 2 3 H HO H

Unlinked monomer

Dehydration removes a watermolecule, forming a new bond

HO

H2O

H1 2 3 4

Longer polymer

(a) Dehydration reaction in the synthesis of a polymer

HO 1 2 3 4 H

H2OHydrolysis adds a watermolecule, breaking a bond

HO HH HO1 2 3

(b) Hydrolysis of a polymer

Fig. 5-UN1

Fig. 5-17Nonpolar

Glycine(Gly or G)

Alanine(Ala or A)

Valine(Val or V)

Leucine(Leu or L)

Isoleucine(Ile or )

Methionine(Met or M)

Phenylalanine(Phe or F)

Trypotphan(Trp or W)

Proline(Pro or P)

Polar

Serine(Ser or S)

Threonine(Thr or T)

Cysteine(Cys or C)

Tyrosine(Tyr or Y)

Asparagine(Asn or N)

Glutamine(Gln or Q)

Electricallycharged

Acidic Basic

Aspartic acid(Asp or D)

Glutamic acid(Glu or E)

Lysine(Lys or K)

Arginine(Arg or R)

Histidine(His or H)

Quiz Make-Up: DUE Tomorrow

– 1 page on each of the following:

• A summary of the light reactions.

• Compare the potential energy in sugar, fat, and carbon dioxide.

• The role proton pumps and ATP synthase in photosynthesis.

Proteins:

•aka: polypeptide

•a polymer of amino acids

•linked by peptide bonds

•range in length

– a few amino acids

– more than a thousand amino acids

•each has a unique linear sequence of amino acids


Peptidebond

Amino end(N-terminus)

Peptidebond

Side chains

Backbone

Carboxyl end(C-terminus)

(a)

(b)

Building Proteins

• Build and DRAW an amino acid (skip the R group for now):

• In your team: 1 glycine, 1 serine, 1 threonine, 1 alanine

• Polymerize! and DRAW

Fig. 5-21

PrimaryStructure

SecondaryStructure

TertiaryStructure

pleated sheet

Examples ofamino acidsubunits

+H3N Amino end

helix

QuaternaryStructure

sequence of amino acidsfolding due to interactions among various side chains (R groups)

Protein Structure and Function: FORM FOLLOWs FUNCTION

• A protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape


A ribbon model of lysozyme(a) (b) A space-filling model of lysozyme

Active SiteActive Site

TertiaryStructure

folding due to interactions among various side chains (R groups)

Fig. 5-20

Antibody protein Protein from flu virus

Fig. 5-21g

Polypeptidechain

Chains

HemeIron

Chains

CollagenHemoglobin

Practice

• Polypeptide with amino acid sequence (glycine, alanine, serine) p. 72-73

Sickle-Cell Disease: A Change in Primary Structure

• A slight change in primary structure can affect a protein’s structure and ability to function

• Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin


Warm-Up:1.Draw the dipeptide2.What would cause it to fold? not fold?3.What kinds of factors might change a protein? Brainstorm factors other than genetic changes.

Fig. 5.19

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 5-22

Primarystructure

Secondaryand tertiarystructures

Quaternarystructure

Normalhemoglobin(top view)

Primarystructure

Secondaryand tertiarystructures

Quaternarystructure

Function Function

subunit

Molecules donot associatewith oneanother; eachcarries oxygen.

Red bloodcell shape

Normal red bloodcells are full ofindividualhemoglobinmoledules, eachcarrying oxygen.

10 µm

Normal hemoglobin

1 2 3 4 5 6 7

Val His Leu Thr Pro Glu Glu

Red bloodcell shape

subunit

Exposedhydrophobicregion

Sickle-cellhemoglobin

Moleculesinteract withone another andcrystallize intoa fiber; capacityto carry oxygenis greatly reduced.

Fibers of abnormalhemoglobin deformred blood cell intosickle shape.

10 µm

Sickle-cell hemoglobin

GluProThrLeuHisVal Val

1 2 3 4 5 6 7

http://www.nslc.wustl.edu/sicklecell/sicklecell.html

http://www.nslc.wustl.edu/sicklecell/sicklecell.html

Changes in the Tertiary Structure (Shape) of Proteins

Caused by:

Mutations in DNA: changes primary structure, which changes folding (i.e. the shape)

Denaturation: i.e. unfolding

•pH: adding protons to the environment changes the hydrogen bonding between R groups

•Heat: breaks R groups (weakest) bonds first

– ionic bonds

– hydrogen bonds

– hydrophobic interactions

Normal protein Denatured protein

Denaturation


Water is not all H2O.• 99.99% H20.• 0.01% OH-• 0.01% H30+

•Rarely, the hydrogen bond overcomes the polar covalent bond (i.e. the proton from 1 water leaves and joins another water)



Review of pH


Review of pH

Simplified:



pH: A meause of the [H+] vs [OH-]



pH: A meause of the [H+] vs [OH-]

Water (neutral): •[H+] = [OH-] •[H+] = 10-7

•pH=7

Acidic solution•[H+] > [OH-]•[H+] > 10-7 i.e. is 10-4

•pH< 7

Basic solution: •H+ < OH-•[H+] < 10-7 i.e. is 10-9

•pH> 7

Water (neutral): •[H+] = [OH-] •[H+] = 10-7

•pH=7

Acidic solution•[H+] > [OH-]•[H+] > 10-7 i.e. is 10-4

•pH< 7

Basic solution: •H+ < OH-•[H+] < 10-7 i.e. is 10-9

•pH> 7

• acid: a molecule that increases the H+ in a solution.

– Example: DRAW IT!

• hydrochloric acid is added to water

• hydrogen ions dissociate from chloride ions:

– HCl H+ + Cl-

• base: a molecule that reduces the H+ in a solution

– Example: Some bases reduce H+ directly by accepting H+

• Ammonia (NH3): nitrogen’s unshared electron pair attracts a hydrogen ion from the solution

• creating an ammonium in (NH4+).

– NH3 + H+ NH4+

– Example: Other bases reduce H+ indirectly by dissociating to OH-

– NaOH Na+ + OH-

• The OH- then decreases H+ by combining with H+ to form water.

– OH- + H+ H2O

Acids vs Bases

• acid: a molecule that increases the H+ in a solution.

– Example:

• DRAW IT!

– hydrochloric acid is added to water

– hydrogen ions dissociate from chloride ions:

• base: a molecule that reduces the H+ in a solution

– Example: Some bases reduce H+ directly by accepting H+

• DRAW IT!

– Ammonia (NH3): nitrogen’s unshared electron pair attracts a hydrogen ion from the solution

– creating an ammonium in (NH4+).

– Example: Other bases reduce H+ indirectly by dissociating to OH-

– NaOH Na+ + OH-

• The OH- then decreases H+ by combining with H+ to form water.

– OH- + H+ H2O

Acids vs Bases

TertiaryStructure

folding due to interactions among various side chains (R groups)

Why does pH affect proteins?



If hydrogen bonding is disrupted, the shape of the molecule will change.

If the shape changes, the function changes.

If hydrogen bonding is disrupted, the shape of the molecule will change.

If the shape changes, the function changes.

Fig. 6.15

Enzymes Drawings

Draw Explain

Begin 1 enzyme2 substrates "free"1 substrate "active"

Middle 1 enzyme1 substrate "free"1 substrate "active"1 of each product

End 1 enzyme0 substrate? product

Enzymes Drawings: Analysis

1. What happens to the amount of substrate during the reaction?

2. the amount of enzyme?

3. Why would the reaction stop?

4. What could make the reaction speed up?

Enzymes Model

1. What happens to the amount of substrate during the reaction?

2. the amount of enzyme?

3. Why would the reaction stop?

4. What could make the reaction speed up?

Drawing Graph Explanation

Notes: Enzymes and Activation Energy: WHY DO ENZYMES SPEED UP REACTIONS?

Warm-UP: 1.Match the drawings to the graphs.2.Sketch the drawings and graphs in a table.3.Explain what is happening.

1.Explain what is happening. Remember entropy (the 2nd law of thermodynamics)?2.Explain why the graph matches the drawing3.What would the graph look like if the arrow pointed the other direction? Explain.

1.Explain what is happening. Remember entropy (the 2nd law of thermodynamics)?2.Explain why the graph matches the drawing3.What would the graph look like if the arrow pointed the other direction? Explain.

Enzymes and Activation Energy

∆G < 0

Gibbs Free Energy

G = H - T S

S: entropy

G: free energy

As entropy increases, energy in the system decreases

∆G > 0


∆G < 0


Exergonic Reactions: “Spontaneous”•∆G < 0•Energy is released from the system•Example:

• glucose –> CO2

• Energy transferred to ATP

•Amount of energy of products is less than it was with the reactants

Activation energy:•An energy “hump”•All reaction (even exergonic) reactions have a barrier to starting•Examples:

1. Wood doesn’t just spontaneously combust.

2. Sugar isn’t digested on its own.



Enzymes speed up the rate of reactions by lowering activation energy.


∆G > 0



Endergonic Reactions•∆G > 0•Energy is added to the system•Example:

• CO2glucose • Energy transferred in: from light to glucose

•Amount of energy of products is more than it was with the reactants

What is the role of enzymes in the reaction?

Gibbs Free Energy• exergonic: spontaneous reactions: release of energy

• endergonic: energy is stored

(a) Gravitational motion (b) Diffusion (c) Chemical reaction

• More free energy (higher G)• Less stable• Greater work capacity

In a spontaneous change• The free energy of the system decreases (∆G < 0)• The system becomes more stable• The released free energy can be harnessed to do work

• Less free energy (lower G)• More stable• Less work capacity

PROTEIN NOTES: You are proteins and the result of protein action! Warm-Up: Match the function to the examples Copyright © 2008 Pearson Education, Inc.,

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