energy and the cell an introduction to metabolism ib biology

Energy and the CellAn Introduction to Metabolism

IB Biology

Metabolism

• The emergent property of life that arises from interactions between molecules within the orderly environment of a cell.

• A sum of all the chemical reactions within a cell.

What does it look like? Pretty complicated!

Energy

• The capacity to cause change or perform work.

Types of Energy

• Kinetic: The energy of motion.

• Potential: The energy of location or structure.

Types of Energy• Heat: The

transfer of thermal energy.

• Thermal: Kinetic energy associated with random movement of molecules.

Chemical Energy• The available energy that can be released

during a chemical reaction.

Metabolism consists of:

• Catabolic pathways– Degradative processes

• Breaking of polymers into monomers

– Release energy• Cellular respiration

• Anabolic pathways– Build more complex molecules

• Join monomers to form polymers

– Consume energy• Photosynthesis

Thermodynamics

• The study of energy transformations that occurs in a collection of matter.

Entropy• A measure of

disorder or randomness.

Thermodynamics

• 1st Law:– Energy can be transformed or transferred but not

created or destroyed.– Conservation of energy

• 2nd Law:– Every energy transformation or transfer increases

the entropy (disorder) of the universe.

• How can we reconcile the fact that life is orderly with the 2nd Law?

Free Energy• The portion of a system’s energy that can be

used to perform work.

• It is available for work but is spent at a cost to the universe.

Exergonic vs. Endergonic

Spontaneous Non-spontaneous

STOP for a Vocabulary Check

• “Break down” reaction:– Catabolic

– Spontaneous

– Exergonic

– Degradative process (breaking things down)

– Downhill reaction

– ∆G ‹ 0• Change if free energy is

negative

• Energy is released

• “Build up” reaction:– Anabolic

– Non-spontaneous

– Endergonic

– Synthesis process (building things up)

– Uphill reaction

– ∆G › 0• Change in free energy is

positive

• Energy is stored

What’s ATP used for?• ATP is the

spending money of the cell

• It allows for other molecules to be phosphorylated

• Phosphorylation allows for transport work, mechanical work, and chemical work

Energy coupling• Exergonic process drive an endergonic one.

Phosphorylation• ATP performs work by transferring the

inorganic phosphate to another molecule.

ATP Regeneration

Enzymes• Serve as a catalyst to speed up

the rate of reactions without being consumed by the reaction.

• They are reusable!

Activation Energy

Enzymes are Substrate Specific

What’s Up with Proteins?

• Amino Acid/peptide = the monomer of proteins

• Amino acids join by peptide bonds into a polypeptide

• A protein is more than just a chain of polypeptides– Shape is essential!!

COMPONENTS:

•Amine group (NH2)

•Carboxyl group (COOH)

•R group (different for each of 20 amino acids)

Protein (amino acid + amino acid + amino acid, etc.)

Are proteins diverse?

• A 20 letter “alphabet”

• Proteins can be 100s or 1000s of “letters” long– Imagine the

diversity!

Protein Functions• Structure – support (connective tissue, webs)

• Storage – store amino acids; egg white, milk, seeds

• Transport – hemoglobin (carries oxygen), channels (H+ through ATP synthase)

• Hormonal – regulation; insulin

• Receptor – Na+ and K+ receptors in nervous system

• Contractile – movement (actin/myosin in muscle)

• Defense – antibodies fight bacteria/viruses

• Enzymes – speed up chemical reactions

4 levels of Protein Structure

• Primary– Unique sequence of amino acids

• Secondary– Hydrogen bonds create coils and folds– Alpha helix– Beta pleated sheets

• Tertiary– Irregular contortions do to side chain (disulfide bridges)

• Quaternary – Two or more polypeptides joined together

Levels of Protein Structure

• Primary (1°)—amino acid sequence

• Secondary (2°)—folds/coils of amino acid change caused by hydrogen bonds

• Tertiary (3°)—interactions between R groups

• Quaternary (4°)—2+ polypeptides that form one functional protein

Primary Structure

Secondary Structure

Tertiary Structure

Quaternary Structure

Feedback Inhibition

Inhibition of Enzymes

Spitting in a Test Tube

• Figure of starch and the salivary amylase enzyme. Use it to create your diagram.

Enzymes control metabolism

Keep in mind, enzymes are used in catabolic (breakdown) and anabolic (synthesis) reactions.

Catabolic – breakdown large molecules into sub-units and release energy

Anabolic– build larger molecules and store energy

Enzymes bind to and alter substrates

1) Enzyme and substrate (maltose) before contact

2) Enzyme and substrate (maltose) fit like a “lock and key”. The active site of the enzyme triggers the chemical reaction.

3) Enzyme alters the substrate (in this case maltose is catabolized into glucose molecules)

Big Picture: Enzymes control metabolism

• Catabolism (break down of food for energy and building blocks)

• Anabolism (synthesis of larger molecules for structure or food storage)

Substrate – the molecule on which an enzyme acts

What gets changed?What stays the same?

Lab: Enzyme Action “Spittin’ in a test tube”

• Read the introduction to yourself.–What is starch?

– Polysaccharide made of many glucose molecules.

Lab: Enzyme Action “Spittin’ in a test tube”

• Question:– Does my saliva contain an enzyme (salivary

amylase) that can break starch into glucose?

• Hypothesis: – Answer the question (make a prediction)

• Procedure:1)Test for starch

and glucose in starch solutiona) Iodine test on

starch (10 drops of iodine in 2 ml of starch)

b) Benedicts test on starch (10 drops of Benedicts in 2 ml of starch) and place in hot water bath for 5 minutes.

Starch

* Heat for

5 minutes

2) Test for starch and glucose in saliva

a) Iodine test on saliva (10 drops of iodine in saliva)

b) Benedicts test on saliva (10 drops of Benedicts in saliva) and place in hot water bath for 5 minutes.

Saliva

* Heat for

5 minutes

3) Test for starch and glucose in “starch/saliva” mix

a) Add starch (2 ml) and saliva to two clean test tubes.

b) Swirl to mix and let them sit for 5 minutes.

c) Iodine test on starch/saliva mix (10 drops of iodine)

d) Benedicts test on starch/saliva mix (10 drops of Benedicts) and place in hot water bath for 5 minutes.

Starch+

Saliva

* Heat for

5 minutes

Data/Results:Iodine Test Benedict’s

TestWhat’s in it?

Starch only (control)

Blue No reaction Starch

Saliva only (control) No reaction No reaction No starchNo glucose

Starch + saliva (experiment)

No reaction Orange Glucose

Starch Only Turned Blue No Reaction

Data/Results:Iodine Test Benedict’s

TestWhat’s in it?

Starch only (control)

Blue No reaction Starch

Saliva only (control) No reaction No reaction No starchNo glucose

Starch + saliva (experiment)

No reaction Orange Glucose

Saliva Only No Reaction No Reaction

Data/Results:Iodine Test Benedict’s

TestWhat’s in it?

Starch only (control)

Blue No reaction Starch

Saliva only (control) No reaction No reaction No starchNo glucose

Starch + saliva (experiment)

No reaction Orange Glucose

Starch + Saliva No Reaction Turned Orange

Conclusion:1) Is starch or glucose present in your saliva?

How can you tell?

2) Is starch or glucose present in the starch solution? How can you tell?

3) Why bother to test the starch solution and the saliva by themselves for starch and glucose?

4) Does your saliva contain an enzyme that breaks starch into glucose? What evidence do you have to support your answer?

Draw a 3-step picture showing how amylase splits starch (the substrate) into glucose molecucules.

glucose glucoseglucose glucoseOH

H

STARCH

Salivary amylase:

glucose glucoseglucose glucoseOH

H

Substrate (starch) and Enzyme are separated

glucose glucoseglucose glucoseOH

H

Substrate (starch) and Enzyme bind together like a “lock and key” fit.

glucoseH

OH

glucoseglucose glucoseOH

H

Enzyme speeds up chemical reaction by breaking (catabolizing) starch into glucose.

glucoseH

OH

glucoseglucose glucoseOH

H

The enzyme is not consumed or changed in the previous chemical reaction and repeats breaking down starch into glucose.

glucoseH

OH

glucose

glucose

glucoseOH

H

OH

H

The enzyme continues to be reusable until ...

glucoseH

OH

glucoseOHglucose

H

OH

glucoseH

OH

H

All the starch is broken into glucose.

Interpreting Results and Writing Conclusions #1:Iodine Test Benedict’s Test

Starch only (control)

Blue No reaction

Saliva only (control)

No reaction No reaction

Starch + saliva (experiment)

No reaction Orange

1) What does Iodine test for?2) What does Benedict’s test for?3) What was found in starch? How do you know?4) What was found in saliva? How do you know?5) What was found in the “starch + saliva” mix? How do you know?6) Does this person have an enzyme? What’s your evidence?

Interpreting Results and Writing Conclusions #2:

Iodine Test Benedict’s Test

Starch only (control)

Blue No reaction

Saliva only (control)

No reaction Orange

Starch + saliva (experiment)

No reaction Orange

1) What was found in starch? How do you know?2) What was found in saliva? How do you know?3) What was found in the “starch + saliva” mix? How do you know?4) Does this person have an enzyme? What’s your evidence?

Interpreting Results and Writing Conclusions #3:

Iodine Test Benedict’s Test

Starch only (control)

Blue No reaction

Saliva only (control)

No reaction No reaction

Starch + saliva (experiment)

Blue Orange

1) What was found in starch? How do you know?2) What was found in saliva? How do you know?3) What was found in the “starch + saliva” mix? How do you know?4) Does this person have an enzyme? What’s your evidence?

Interpreting Results and Writing Conclusions #4:

Iodine Test Benedict’s Test

Starch only (control)

Blue No reaction

Saliva only (control)

No reaction Orange

Starch + saliva (experiment)

Blue Orange

1) What was found in starch? How do you know?2) What was found in saliva? How do you know?3) What was found in the “starch + saliva” mix? How do you know?4) Does this person have an enzyme? What’s your evidence?

What’s an enzyme?• A special protein that speeds up

chemical reactions to a biologically useful rate.

• What are the sub-units of a protein?– Amino acids

Enzymes have optimal environments