warm-up: the first law of thermodynamics states that matter and energy cannot be created or...

Warm-UP:The first law of thermodynamics states that matter and energy cannot be created or destroyed. In the picture, identify where the matter and energy went? (Note, the scale is lying…)

Homework:DUE Thursday: Concept 8.1 10 Key IdeasDUE Friday: Free Energy POGIL

Unit 3: Enzymes

Big Idea: Reactions are either spontaneous or require energy. Enzymes are a type of protein that controls metabolism (reactions in living organisms) by creating an enzyme substrate complex. Protein function is due to protein structure. The pH of the environment influences protein structure and in turn, protein function.

Reactions are either spontaneous or require energy.

1st Law of Thermodynamics: Conservation of Matter and Energy

• The matter and energy of the Universe is constant:

• Energy can be transferred, but it cannot be created or destroyed

1st Law of Thermodynamics: Conservation of Matter and Energy

• The matter and energy of the Universe is constant:

• Energy can be transferred, but it cannot be created or destroyed

2nd Law of Thermodynamics:

during spontaneous reactions, both enthalpy and entropy increase

• Enthalpy (∆H): energy that leaves the system as heat (exothermic)

• Entropy (∆S): matter tends towards disorder

2nd Law of Thermodynamics:

during spontaneous reactions, both enthalpy and entropy increase

• Enthalpy (∆H): energy that leaves the system as heat (exothermic)

• Entropy (∆S): matter tends towards disorder

Fig. 8-3

(a) First law of thermodynamics (b) Second law of thermodynamics

Chemicalenergy

Heat CO2

Warm-UP:The 2nd law of thermodynamics says that enthalpy (- temperature) will decrease (backwards math) and entropy (chaos) will increase! How does the picture show this?

Homework:DUE Tomorrow: Free Energy POGIL

Reactions are either spontaneous or require energy.Metabolic Pathways:• “Change” the form of energy:

potential, heat, kinetic, chemical• rearrange atoms in a series of steps

from reactants to products• rely on ATP mediated energy coupling:

the use of an exergonic metabolic pathway to drive an endergonic one

Warm-UP:Can you use the legos to model Catabolism? Anabolism? Draw what you did. Can you show how the products of one reaction can be the reactants for a new reaction?

DUE Now: Free Energy POGIL

Homework:DUE Monday: Concept 8.2 and 8.3 10 Key Ideas

https://www.khanacademy.org/test-prep/mcat/biomolecules/overview-metabolism/v/overview-of-metabolism-anabolism-and-catabolism

Reactions are either spontaneous or require energy.Metabolic Pathways:• Anabolic Reactions:

– “add” energy (endergonic) by putting e-’s farther from highly electronegative atoms

– decrease temperature (endothermic)– increase order (decrease entropy) by

building bigger molecules• Catabolic Reactions:

– “release” energy (exergonic) by transferring energy out of the system

– increase temperature (exothermic)– increase entropy by breaking down

bigger molecules into smaller ones

https://www.khanacademy.org/test-prep/mcat/biomolecules/overview-metabolism/v/atp-hydrolysis-gibbs-free-energy

Gibbs Free Energy: • calculates the likelihood for a

reaction to occur (ie spontaneous)• dependent on enthalpy and

entropy• ∆G= ∆H -T∆S• spontaneous when energy is

released:– exergonic: ∆G < 0

• not spontaneous when energy is “stored”:– endergonic: ∆G > 0

Gibbs Free Energy: • calculates the likelihood for a

reaction to occur (ie spontaneous)• dependent on enthalpy and

entropy• ∆G= ∆H -T∆S• spontaneous when energy is

released:– exergonic: ∆G < 0

• not spontaneous when energy is “stored”:– endergonic: ∆G > 0

Warm-UP: Welcome to Monday! All weekend, you ate all kinds of healthy, good for you (like proteins). What do you think your body is doing with them now? “You are what you eat” means something much more than “if you eat healthy, you will be healthy.”

Homework: Worksheet for Chapter 5: Building Biomolecules

I NEED ALL TESTS RETURNED: scantron, written, and multiple choice questions. IF you did the make-up, please mark the top.

Each pair: Build an amino acid: see p. 79

Make a dipeptide

Make a polypeptide: join some other teams

Building Proteins

Analysis:1. A polypeptide was 8 amino acids long. How many

waters were produced when it was polymerized?2. What could make one protein different than

another?3. How are the proteins we eat made into the proteins

we’re made of?4. Proteins are not just linear chains of amino acids.

Predict how they form many different shapes.

Building Proteins

Analysis:1. A polypeptide was 8 amino acids long. How many waters

were produced when it was polymerized? 72. What could make one protein different than another? Order

of amino acids, type of amino acids, bonds made between amino acids, length of polypeptide

3. How are the proteins we eat made into the proteins we’re made of? Polypeptides are disassembled (catabolism) into amino acids, then reassembled (anabolism) into the correct order for our proteins (by reading our genes)

4. Proteins are not just linear chains of amino acids. Predict how they form many different shapes. Interactions between R groups

Protein function is due to protein structure.

Amino Acid (subunit: monomer)• organic molecules with amino group and

carboxylic acid (carboxyl group)• differ in their properties due to differing side

chains (R groups)• linked by peptide bonds

Polypeptides • polymers built from the same set of 20 amino

acids• range in length from a few to more than a

thousand amino acids• Each has a unique linear sequence of amino

Protein • consists of one or more polypeptides

Protein function is due to protein structure.Amino Acid (subunit: monomer)• organic molecules with amino group and

carboxylic acid (carboxyl group)• differ in their properties due to differing side

chains (R groups)• linked by peptide bonds

Polypeptides • polymers built from the same set of 20 amino

acids• range in length from a few to more than a

thousand amino acids• Each has a unique linear sequence of amino

Amino Acid (subunit: monomer)• organic molecules with amino group and

carboxylic acid (carboxyl group)• differ in their properties due to differing

side chains (R groups)• linked by peptide bonds

Polypeptides • polymers built from the same set of 20

amino acids• range in length from a few to more than a

thousand amino acids• Each has a unique linear sequence of

amino acids

4 Levels of Protein Structure:

PRIMARY: sequence of amino acids

SECONDARY: hydrogen bonds between amino and carboxyl groups

TERTIARY: interactions between R groups

QUATERNARY: proteins are usually made of multiple polypeptide chains

Fig. 5-21f

Polypeptidebackbone

Hydrophobicinteractions

Disulfide bridge

Ionic bond

Hydrogenbond

Fig. 5-21

PrimaryStructure

SecondaryStructure

TertiaryStructure

pleated sheet

Examples ofamino acidsubunits

+H3N Amino end

QuaternaryStructure

Protein function is due to protein structure.Conformation:• “shape”• due to interactions between R

groups: tertiary structure• because it gives the protein its

structure, it therefore gives the protein its function

• can be denatured (changed shape) when R group interactions are changed (due to changes in environment)

Check out a computer for you and a partner

No Warm-UP

Go to my website. See documents tab: “Modeling Protein Structure”. Follow directions.

When finished, submit to turnitin.com. DUE by Friday 11/6

Please have out your homework: Building Biomolecules

Warm-UP: What happened to the protein paravalbumin when cooked? In other words, what happens to an egg when you cook it? When you refrigerate it, does it turn back?

Due Friday: Modeling Protein Structure

Due Friday: Sickle Cell Poster

• heat• pH• genetics (change in gene results

in change in primary structure)

Sickle Cell Disease Poster

Your poster needs to include the following:

1. Compare the PRIMARY structure of Hemoglobin A and Hemoglobin S using drawings and explanations• Molecular drawings of amino acids: 5th, 6th, 7th See

p. 79 and p.84• Dehydration reaction: Show the amino acids

forming into a polypeptide2. Compare the TERTIARY structure of Hemoglobin A and

Hemoglobin S using drawings and explanations• Describe R group interactions that are different in

each version of the polypeptide3. Explain the cellular and organismal level changes that

result.

Terms:central carbonR grouphydrophobichydrophilicpolarnon polarprimary structuretertiary structurequaternary structurered blood cell

hemoglobin Ahemoglobin Samine groupcarboxyl groupwaterdehydrationamino acidpolypeptideoxygen

4 Advanced 3 Proficient 2 Basic 1 Below Basic

Scientific Vocabulary

ALL words are used correctly

Most words are used correctly

Most words are used, some correctly

Some words are used correctly

Labeled Molecular Drawings

Drawings are detailed and help explain

Drawings help explain some things

Drawings are complete but lack detail

Drawings are incomplete

Explanations of changes from primary, to tertiary, to organism

Poster clearly explains the details of how primary structure changes can lead to organismal changes

Poster explains changes, but lacks details about the process

Poster shows changes but lacks complete explanation of how the small changes have organismal effects

Project has very little information about changes.

Warm-UP: Compare the 2 models. How does each help you understand proteins? Is there value in each?

Due Friday: Modeling Protein Structure

Due Friday: Sickle Cell Poster

Warm-UP: Enzymes are a type of protein that speed up reactions. How do you think they do this? Use the model to explain.

Due Wednesday: 10 Key Ideas Concept 8.4

Due: Sickle Cell Poster AND Modeling Protein Structure

Due Thursday: Enzyme-Substrate Model (Wed.’s Activity finished)

Enzymes are a type of protein that controls metabolism (reactions in living organisms) by creating an enzyme substrate complex.

enzymes: usually end in “ase”• a type of protein• the enzyme substrate complex: the enzyme’s

conformation “matches” a substrate: substrate specific

• are catalysts: speed up the rate of reactions• induced fit: lower activation energy (making them

“more” spontaneous) by “straining” substrate bonds

• are unchanged by reactions

substrate: • the molecule acted on• AKA the reactants• are changed into products• fit in the “active site”

example: sucrasesucrose → glucose + fructose

Homework DUE tomorrow: Experimental Design: Question, Alternative Hypothesis, Procedure (sketch is enough)

Warm-UP1. Describe the graph. How do the two rates compare?2. Explain the graph. What happened to the penny flipase in the two situations?

stamp today, then turn in Warm-UP sheet: Key Ideas 8.4

DUE: Penny Modeling Lab; in my basket

Lab: Factors that Effect Enzyme Rate

Question: How will ______________ affect the rate of an enzymatic reaction?

Hypothesis with reason:

YOUR EXPERIMENTAL DESIGN1. Investigative Question2. Alternative Hypothesis:

– What do you know about enzymes that makes you think so?

3. Procedure: sketch is enough

Materials:

Erlenmeyer flaskH2O2

peroxidase (orange tube)

H2O in a 100 mL beaker

plastic pippetepipettepipette tips

computerinterface + 2 cables (USB and power)pressure sensorpocket computer

Procedure: Determining a Baseline1. Using a clean 10 mL pipette, add to an Erlenmeyer

flask: – 5 mL of 3.0% H2O2 – 5 mL of water

2. Add 5 drops of peroxidase (enzyme suspension) to Erlenmeyer flask

3. QUICKLY place the pressure sensor on the Erlenmeyer flask. Click COLLECT to begin data collection.

4. When rubber stopper “pops” off, click STOP. Data collection has finished.

5. Move your data to EXCEL. Save your EXCEL file.6. Rinse the flask with water.7. Repeat AT LEAST 5 trials.

Homework DUE Monday: Experimental Design Draft 2

Warm-UP: Read your question and hypothesis to your teammates. Who has the best plan for an investigation?

Stamp Today: Experimental Design Draft 1

YOUR EXPERIMENTAL DESIGN (decide on one)1. Investigative Question2. Alternative Hypothesis:

– What do you know about enzymes that makes you think so?

3. Procedure: sketch is enough

Whiteboard:

Gallery Walk• Clarifying Questions:

– Do you understand their set-up?– Do you understand their question?

• Probing Questions: Press your classmates1. Do they have a valid experiment? Does their set-up

answer their investigative question?2. Will their experiment be reliable? controls?3. Enzymes? Does the experiment help us understand

factors that influence enzymes?

Homework DUE Tuesday: 10 Key Ideas: Concept 3.3. STOP when you get to “Buffers”

Warm-UP: 1. Read your ALTERNATIVE HYPOTHESIS to your

teammates. Who do you agree with? Why?2. To reject your null, you’ll need stats. To do stats,

you need TWO sets of numbers to compare. What TWO sets of numbers will you compare?

Stamp Today: Experimental Design Draft 2

UNIT 3 TEST NEXT Monday-Tuesday. See my website for the study guide which is DUE next Monday for the opportunity to do the test make-up.

Warm-UP: CAN YOU CALCULATE RATE?1. Calculate the rate of the reaction from

a. 0-30 sec for 10mL of H2O2

b. 120-150 sec for 10mL of H2O2?

2. Compare the reaction rates when there is more substrate.

Homework DUE Thursday: Enzyme Substrate Graph Comparisons

Stamp Today: Changes Due to Acids and Bases

Procedure: Calculating Statistics1. Create a line graph for Condition 1, with all 4 trials.

i. Organize data with time in Column A, Trial 1 in Column B, Trial 2 in Column C, Trial 3 in Column D, Trial 4 in Column E

ii. Drag a box around Column A through Eiii. Insert a scatter plotiv. Add a trendline for each trial. Display equation on Chart.

2. Repeat with Condition 2.3. Calculate stats using slope of each line. Choose ONE of

the two options: A or BA. Open Stats Spreadsheet (see documents tab on my website).

Add slope from each trendline to the data table. The spreadsheet will calculate mean, standard deviation, and percent confidence for you.

B. Do stats by hand using slope from each trendline. Calculate mean, standard deviation, calculated t. Compare calculated t to table t to estimate percent confidence.

Draw a Bohr model of hydrogen. Label: proton, neutron, electron.

Draw a second Bohr model of hydrogen. This time it’s a hydrogen ion. Take away the electron. What’s left?

Warm-UP

Lab Report: Enzymes DUE Monday

The pH of the environment influences protein structure and in turn, protein function.

• pH: measures changes due to more or less protons• Water normally occasionally (<1%) dissociates:

• H2O H+ + OH-• [H+] = [OH-]

• Acid: • increases the H+ concentration in a solution

[H+] > [OH-]• Acid donates H+ to water

• Example: HCl H+ + Cl-• Effect on Proteins: Causes hydrogen bonds in

R groups to make hydrogen bonds with the H+ in solution

• Base: • reduces the H+ concentration in a solution [H+]

< [OH-]• free H+ bond to the base

• Example: NH3 + H+ NH4+

• Base donates OH- to water• Example: NaOH Na+ + OH-

• Effect on Proteins: Causes hydrogen bonds in R groups to make hydrogen bonds with the OH- in solution

• H2O H+ + OH-• [H+] = [OH-]

If you add vinegar (solute) to water (solvent), the H+ concentration of the solution increases while the OH- concentration stays the same. You’ve made an acidic solution.

• H2O H+ + OH-• [H+] = [OH-]

If you add ammonia (solute) to water (solvent), the H+ concentration of the solution decreases while the OH- concentration stays the same. You’ve made a basic solution.

• H2O H+ + OH-• [H+] = [OH-]

Denaturation:• loss of a protein’s conformation due to changes

in• pH• heat• genetics

• breaking R group interactions: tertiary structure

Why does pH matter to enzymes?• Disrupts R group interactions: changing number

of possible hydrogen bonds in the environment• Changes protein conformation (tertiary shape)• Changes function of enzyme

Optimal pH: • the pH at which the enzyme’s active site best

matches the substrate• Causes highest rate of enzyme activity (ie fastest

rate of product produced)

Denaturation:• loss of a protein’s conformation due to changes

in• pH• heat• genetics

• breaking R group interactions: tertiary structure

Why does pH matter to enzymes?• Disrupts R group interactions: changing number

of possible hydrogen bonds in the environment• Changes protein conformation (tertiary shape)• Changes function of enzyme

Optimal pH: • the pH at which the enzyme’s active site best

matches the substrate• Causes highest rate of enzyme activity (ie fastest

rate of product produced)

pH• Scale is “backwards”• Neutral Solution:

• [H+] = [OH-]• pH= 7

• Acidic Solution: • [H+] > [OH-]• pH < 7

• Basic Solution: • [H+] < [OH-]• pH > 7

Whiteboard:Question:

Conclusion:• Answer your question and Reject/Fail to Reject H0• Use data• Why does this make sense? What do you know about enzymes

that explains your data? OR Why are you surprised?

What is happening to the protein that’s causing it to be denatured?

Warm-UP

Lab Report: Enzymes DUE Monday

Description PointsIntroduction• Why interesting? How will this question

contribute to science? What were you curious about

Design:• Question• Variables• Hypotheses: null & alternative• Materials• Procedure: is your experiment repeatable

with the procedure given?

1 2 3 4 5

Data: in a table 1 2

Graph: electronic; scatter plot; labeled axes; trendline

1 2 3 4 5

Analysis• Calculations: RATE of REACTION• Sources of error

Conclusion• Answer: reject or fail to reject the null• Include data to support your answer• Explanation: Why does this make sense?• What alternative explanations should you

consider that might also explain your results?

1 2 3 4 5 6 7

Professionalism: ON TIME, SHOWS EFFORT, REPORT FOLLOWS A LOGICAL ORDER

1 2 3 4 5

Total 30

Lab Enzymes Name: Lab Enzymes Name:

Description PointsIntroduction• Why interesting? How will this question

contribute to science? What were you curious about

Design:• Question• Variables• Hypotheses: null & alternative• Materials• Procedure: is your experiment repeatable

with the procedure given?

1 2 3 4 5

Data: in a table 1 2

Graph: electronic; scatter plot; labeled axes; trendline

1 2 3 4 5

Analysis• Calculations: RATE of REACTION• Sources of error

Conclusion• Answer: reject or fail to reject the null• Include data to support your answer• Explanation: Why does this make sense?• What alternative explanations should you

consider that might also explain your results?

1 2 3 4 5 6 7

Professionalism: ON TIME, SHOWS EFFORT, REPORT FOLLOWS A LOGICAL ORDER

1 2 3 4 5

Total 30

Fig. 5-21g

Polypeptidechain

Chains

HemeIron

Chains

CollagenHemoglobin

Competitive inhibitors bind to the active site of an enzyme, competing with the substrate

Noncompetitive inhibitors bind to the allosteric site of an enzyme, causing the enzyme to change shape and making the active site less effective

Examples: toxins, poisons, pesticides, pharmaceutical drugs, and antibiotics

warm-up: the first law of thermodynamics states that matter and energy cannot be created or...

form of energy

spontaneous reactions

free energy pogil slide

atp mediated energy

disorder reactions

h2oh2o reactions

metabolism reactions

nd law of thermodynamics

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