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BIOL108 Lecture Notes - Lecture 3: Cellular Respiration, Cellulose, Methionine

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mauvelouse967
12 Jun 2018
School
Macquarie University
Department
Biology
Course
BIOL108
Professor
Michael Gillings

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BIOL108
WEEK 3
LECTURE 1
- Everything requires energy – To grow and reproduce
- Energy originate from the sun
- 2% of energy are captured by plants
- Injected as food and out as heat
- Metabolism – made up of many little things to cause a reaction
- For a reaction to proceed, need a kick-start = Energy of activation
- Where cells work their magic in the enzymes
- Catalyze -> Lower the energy
- Catalyze and Enzyme is the same thing
- Enzymes are proteins
- Allow a substrate (sugar) to bind
- Lower the activation to the drive the reaction
- Enzyme has a 3D structure – Complex structure
- Catalyze converts hydrogen peroxide into water and oxygen - 40000000 times per second
- Easy to tell the function of an enzyme based on their name
TEMPERATURE
- Works best at 37 degrees Celsius
- Below or above that temperature will denature the enzyme -> when they change structure
pH
- Testing the acidic and basic of an enzyme
- Works best at optimum pH
- Suited to the environment it operates in
- More molecules and more enzyme
- Cycling matter and cycling energy through organs
- Energy used to break glucose -> ATP
- Many requires ATP
- Aerobic cellular respiration – To get ATP
CO2 + H2O – (Sun captured by photosynthesis) --> Cellulose + O2 – (Released by burning) --> CO2 + H2O
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BIOL108
LECTURE 2
AEROBIC CELLULAR RESPIRATION
- All animals and plants carry out this process
- Oxidising glucose into carbon dioxide and water with the production of ATP
- Some bacteria, fungi and protozoa -> Anaerobic
- Killed by exposure to oxygen
- Break glucose down to alcohols and organic acids = Fermentation
GLYCOLYSIS
- First stage in the breakdown of glucose
- Occurs in the cytoplasm
- Does not require oxygen
- A molecule of glucose (6 carbons) is broken down into 2 molecules of pyruvate (3 carbons each)
- Net production of 2 ATP molecules
GLYCOLYSIS/FERMENTATION
- Absence of oxygen – additional step reduces pyruvate to lactate, or alcohol and carbon dioxide
- Glycolysis plus the additional step = fermentation
- Yeasts ferment glucose to alcohol = beer and wine
- Lactic acid bacteria ferment glucose to lactic acid = yoghurt
- Muscle cells also produce lactic acid during heavy exercise; not enough oxygen can be
transported into muscle cells
- Lactate is converted back to pyruvate in the liver
MITOCHONDRIAL FUNCTION
- Transition reaction (pyruvate bound to coenzyme A): occurs in the Matrix of the mitochondrion
- Krebs cycle (completing the oxidation to CO2): occurs in the matrix
- Electron transport chain: embedded in the cristae; pumps hydrogen ions into the
intermembrane space
AFTER GLYCOLYSIS
- Glycolysis: Occurs in cytoplasm, further breakdown of pyruvate occurs in the mitochondria
- Transition reaction: Pyruvate enters mitochondria, converted to an acetyl group with liberation
of carbon dioxide
- Krebs cycle: In the mitochondrial matrix CO2, ATP, NADH and FADH2 are generated
- Electron transport system: On the mitochondrial cristae, more ATP is generated
THE TRANSITION REACTION
- Imports pyruvate into the mitochondrion
- Converting the products of glycolysis into acetyl CoA
- Enters the next stage of the process = Krebs cycle
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BIOL108
THE KREBS CYCLE
- The carbon atoms in acetyl CoA are oxidised to carbon dioxide
- ATP is generated
- Electrons and hydrogen atoms are transferred to NAD+ or FAD to generated NADH and FADH2
ELECTRON TRANSPORT SYSTEM: HYDROGEN ION PUMP
- Coenzymes NAD+ and FAD accept electrons and hydrogen atoms during the Krebs cycle
- Yield these up to the electron transport system
- As electrons move through the transport system, hydrogen ions are pumped into the inter-
membrane space: creating a concentration and electric gradient
- Oxygen is final electron acceptor
ELECTRON TRANSPORT SYSTEM: ATP PRODUCTION
- Relies on the gradient of hydrogen ion concentration between the matrix and the
intermembrane space
- ATP molecules diffuse out of the matrix by way of a channel protein
- Hydrogen ions flow from high concentration in the intermembrane space through the ATP
synthase complex
- Energy released allows synthesis of ATP from ADP
FINAL YIELD OF ATP FROM AERPBIC CELLULAR RESPIRATION
- Complete oxidation of glucose to CO2 and H2O = 686 kcal
- Energy in terminal phosphate bonds of 38 ATP = 278 kcal
- Aerobic respiration recovers 40% of the available energy; rest is lost as heat
- Glucose enters the cell, goes through glycolysis to produce pyruvate – generates 2 NADH and 2
ATP
- Pyruvate goes into the Matrix of the mitochondria, runs around the Krebs cycle – generates
more NADH, FADH and ATP
- NADH and FADH is fed into the cristae
- 38 ATP is generated from a single molecule of glucose: 9 times more energy efficient than
fermentation
WHERE FOOD GOES
- Virtually anything we eat goes through the same process
- Fats can break down in to fatty acids and glycerol molecules
- Carbohydrates breaks down into simple sugars
- Proteins breaks down into amino acids; where some are kept – cannot be synthesized
- Excess amino acids get secreted as urea
- All the food we eat gets generated into the system to produce energy
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Document Summary

Everything requires energy to grow and reproduce. Metabolism made up of many little things to cause a reaction. Co2 + h2o (sun captured by photosynthesis) --> cellulose + o2 (released by burning) --> co2 + h2o. For a reaction to proceed, need a kick-start = energy of activation. Where cells work their magic in the enzymes. Catalyze and enzyme is the same thing. Catalyze converts hydrogen peroxide into water and oxygen - 40000000 times per second. Lower the activation to the drive the reaction. Enzyme has a 3d structure complex structure. Easy to tell the function of an enzyme based on their name. Below or above that temperature will denature the enzyme -> when they change structure. Testing the acidic and basic of an enzyme. Suited to the environment it operates in ph. Cycling matter and cycling energy through organs. Aerobic cellular respiration to get atp. All animals and plants carry out this process.

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Related Questions

Enzyme Activity

1. Briefly explain the principle of spectrophotometry.

2. Which of the following statements is true about enzymes?(check all correct answers)

__ enzymes act on (are specific for) one or just a fewsubstrates

__ enzymes can be denatured (loose their tertiary/quaternarystructure and activity) by extreme conditions such as heat, high orlow pH,or presence of organic solvents

__most enzymes are DNA

__ enzymes are protein

__enzymes perform best at specific conditions of temperature, pHand salt concentration

5. Which enzymes break the following macromolecules?

Match the following with their correponding answers:

___ Nucleic acids A. proteases or proteinases such as pepsin

___ Cellulose B. none

___ Triglycerides C. lipases

___ Proteins D. amylases

___ Starch E. nucleases

6.Match the following enzymes totheir products.

Answers

___ pepsin, trypsin and other digestive proteases A.Nucleotides

___ salivary and pancreatic amylases and other enzymes B. AminoAcids

___ lipases C. Monosaccharides

___ nucleases D. fatty acids and glycerol

7. Based on experiments, what is the effect of extremeconditions of pH and temperature (boiling tube) on enzymeactivity?

8. ATP stores energy in the form of___

___ Chemical energy

___ Kinetic energy

___ Thermal energy

___ Activation energy

9. An allosteric site in anenzyme is____

__ the site where reactions occur

__ the site that binds aregulator

__ the site that binds thesubstrate

__ the site that binds the product

10. Enzymes increase the rate of reactions by making thetransition state less stable.
__ True

__ False

11. Enzymes increase the rate of reactions by placing reactingparts of the molecule in favorable positions.
__ True
__ False

12. Which of the followingis a mechanism for regulation of enzymes?

__ covalent modification

__ feedback inhibition

__ allosteric regulation

__ all of the above

13. Which of the following represents a correct order of eventsin an enzyme catalytic cycle?

1.enzyme changes shape

2.substrate binds to active site

3.substrate is converted to products

4. products are released from activesite

__ 1>2>3>4

__ 2>1>3>4

__ 3>2>1>4

__ 2>4>3>1

describe the definitions of substrate, enzyme active site and its general characteristics, and apoand

holo-enzymes.

· describe the fact that enzyme catalysis is specific in terms of the type of reaction and the exact

substrate structure.

· Explain the difference in the “lock-and-key’ model and the induced fit model of enzyme

substrate interaction.

· describe that reaction rate constant thus reaction rate is dependent on the activation energy.

· describe the relationship between the energy of the transition state and the activation energy.

· describe the relative binding affinity of a substrate and its transition state to the enzyme.

· Explain how enzymes speed up reaction rate, i.e., how do enzymes lower the activation

energy. Note: Factors other than preferential stabilization of transition state also contribute to increased

reaction rate. They include 1) enzymes placing one substrate (reactant) next to the other substrate (reactant)

so that the reaction is no longer dependent on the collision rate of the two substrates; 2) enzymes sequester the

substrate(s), minimizing solvent competition thus speeding up the reaction; 3) in enzyme complexes with each

enzyme catalyzing one step in a multi-step reaction sequence, the product of one reaction is fed to the active site

of another enzyme for the next step without the product diffusing away from the enzyme complex thereby

increasing reaction rate.

· describe the Michaelis-Menten equation relating the initial velocity to total substrate

concentration.

· describe the assumptions that went into the derivation of the Michaelis-Menten equation. ([E]

is constant, steady state assumption, etc)

· describe the relationship between Vmax and kcat and the fact that kcat is a constant for a given

enzyme and substrate at a given temperature and solution condition; whereas Vmax can differ

for a given enzyme and substrate at a given temperature and solution condition, depending

on the enzyme concentration.

· describe the definition of Kd (equilibrium dissociation constant for ES into E and S).

· describe the relationship between Kd and the affinity of substrate for the enzyme, i.e., the

higher the Kd, the weaker the binding between E and S.

· describe the relationship between Kd and Km, i.e., in general, the higher the Kd, the higher theKm.

· Use the Michaelis-Menten equation and the relationship between Vmax and kcat to do

calculations.

· describe the other names for the catalytic rate constant, kcat (i.e., the turn over number; also

called krelease) and why it is so called (kcat reports on per unit time per enzyme molecule the

number of product molecules formed/released, thus the name turnover number or krelease).

· Determine Vmax and Km using both the Michaelis-Menten plot (initial velocity versus [S]) and

the Lineweaver-Burk Plot (the double reciprocal plot), given the data of initial velocity and

[S].

· Draw the Michaelis-Menten plot AND the double reciprocal plot (Lineweaver Burk), given

the Vmax and Km values.

· describe the fact that the term kcat/Km is the best parameter for measuring the catalytic

capability (efficiency) of an enzyme.

· describe the existence of irreversible enzyme inhibition and the general mechanisms of

irreversible inhibition.

· describe the different types of reversible inhibitions, namely the competitive, uncompetitive,

and mixed inhibitions (noncompetitive inhibition is a special case in which the inhibitor

binds E and ES with equal affinity therefore α is equal to α’ – Km is not affected).

· Describe each type of inhibition in terms of inhibitor binding site (active site or other than

the active site), how the inhibitor affects vmax and Km and the quantitative relationship of

each parameter with and without the inhibitor present and their relationship with [I] and KI

or KI

’

.

· Show the characteristics of each type of inhibition on a Michaelis-Menten plot (initial

velocity versus total substrate concentration), i.e. draw the curves with and without the

competitive inhibitor.

· Show the characteristics of each type of inhibition on a double reciprocal plot (LineweaverBurk

Plot) by drawing the lines with and without the competitive inhibitor.

· Given the Michaelis-Menten or double reciprocal plot with and without the inhibitor,

determine the type of inhibitor.

· describe the fact that transition state analogs are potent inhibitors.

· Explain why transition state analogs are potent inhibitors.

· describe that not all enzymes obey Michaelis-Menten kinetics.

· describe situations when an enzyme will not obey Michaelis-Menten kinetics (when the enzyme

catalyzes reactions with multiple substrates or when the enzyme is allosteric, i.e. binding of

the substrate at one active site affects the other active site(s) for the same substrate).

· Name the four types of catalytic mechanisms. (electrostatic catalysis, general/specific acid

base catalysis, metal ion catalysis, covalent catalysis)

· Contrast acid/base catalysis to general acid/base catalysis, i.e., comment on their similarity

and difference.

· Name the eight common general acid/base pairs in proteins and write the formula of the

acid and base form for each pair (hint: consider the eight amino acids that have ionizable

side chains…)

· describe the meaning of covalent catalysis.

· describe the reaction catalyzed by chymotrypsin and the three catalytic residues in

chymotrypsin.

· Draw the interactions among the three catalytic residues (catalytic triad).

· State the catalytic role of each of the catalytic residues and how they accomplish that.

· describe the steps in the formation of the acyl-enzyme intermediate, and the substrate and

products in this first part of the chymotrypsin mechanism.

· Draw the transition state structure for the formation of the acyl-enzyme intermediate and

indicate by drawing how it is preferentially stabilized.

· describe the steps in the regeneration of chymotrypsin (deacylation), the substrates and

product of this second part of the chymotrypsin mechanism.

· Draw the transition state for deacylation and explain how it is preferentially bound to or

stabilized by the enzyme.

· Explain what general acid and base catalysis refers to and what groups act as the general acid

and base in the chymotrypsin mechanism.

· Explain what covalent catalysis refers to in the chymotrypsin mechanism.

· Explain the basis for the substrate specificity of chymotrypsin (consider the composition of

the active site – chymotrypsin specifically cleaves peptide bonds adjacent to aromatic

residues)

· Explain the term “serine protease”. Answer: these are proteases (enzymes that

hydrolyze peptide bonds) that have serine as a catalytic residue (that acts as a

nucleophile, which can attack the carbonyl carbon of the peptide bond).

· Key features of Hexokinase, enolase and lysozyme mechanisms that were discussed in class

(specific methods of catalysis utilized by these enzymes; general description of overall

catalytic transformation)

· describe the four regulatory strategies of enzyme catalysis

· describe the definition of feedback inhibition (mechanism of cellular regulation that regards an

enzyme that catalyzes the production of a given substance that then inhibits the cell when

concentration of that substance has reached an appropriate level – this balances/regulates

amount of product provided with amount needed)

· describe the most common type of covalent modification and the types of enzymes

responsible for the addition and removal of the chemical group in this covalent

modification.

· Explain the general mechanism of phosphorylation in regulating enzyme activity.

· describe the general naming scheme for active and inactive proteases.

· describe that protease inhibitors exist to inhibit protease.

· describe that enzymes are regulated through covalent and non-covalent processes.

· Noncovalent regulation

o Describe noncovalent modification in general terms. Elaborate on the relation

among enzyme activity, allostery, effector molecules (small molecules) and control

proteins.

o Concerning allosteric regulation, some enzymes have multiple active sites for the

same substrate and the binding of the substrate increases the activity of the enzyme

by stabilizing the R (more active) state over the T (relatively inactive) state. (Lecture

13: “Noncovalent Modification: Allosteric Regulators”)

ß Draw a curve for the initial reaction velocity versus substrate concentration.

ß describe and explain the specific shape of the v0 vs. [S] plot.

ß Draw on the same graph above a v0 vs. [S] curve for the enzyme in the

absence of allostery. and how th i.e., in the absence of conformational change

upon substrate binding. Comment on the shape of this curve.

ß Comment on the benefit of allosteric activation.

ß When an inhibitor is present for such an allosteric enzyme, the v0 versus [S]

plot will shift. Draw a v0 vs. [S] curve with and without the inhibitor.

ß When an activator is present for such an allosteric enzyme, the v0 versus [S]

plot will shift. Draw a v0 vs. [S] curve with and without the inhibitor.

ß When an activator is present for such an allosteric enzyme, the v0 versus.

ß describe the relationship between feedback inhibition and allosteric regulation

and the reason behind the term “feedback inhibition”.

· Covalent regulation

o describe the most common covalent modification, the enzymes that catalyze the

modification and the removal of that modification, respectively and the amino acid

residues that tend to be the site of this modification.

o Write the structure of the added group bonded to those residues and the reaction for

this covalent modification.

o Rationalize the effectiveness of phosphorylation on altering the activity of an

enzyme.

o describe the mechanism of chymotrypsinogen activation to chymotrypsin (cleavage of

zymogen by trypsin).

1.When something appears blue, it is absorbing all colors except__________.

yellow

blue

red

green

orange

2.During heavy exercise, lactic acid can build up in ourmuscles. Why? How does this resemble the metabolism of bacteria andyeast?

lactic acid is results from insufficient oxygen during sugarmetabolism; it is fermentation

lactic acid accumulates when we are dehydrated; bacteria andyeast use the same pathway

lactic acid is built up from carbon dioxide; bacteria and yeaststore energy in this way

3.Why must a cell keep a similar concentration of dissolvedsubstances with the fluid surrounding them?

to avoid dilution of potential energy

to avoid osmotic imbalance and rapid gain or loss of water

to maintain the correct amount of dehydration and hydrolysis

4.What is entropy?

the amount of energy in a system

the amount of disorganization

the amount of organization

5.Burning a log is the reverse reaction found in photosynthesis.What products would be formed in burning a log?

carbon dioxide and water

glucose and oxygen

oxygen and carbon dioxide

oxygen and water

6.The main reason that cellular respiration needs to occur stepby step instead of a single, big reaction is

cells don't store enough oxygen

too much energy would be released for the cell to harness

cells don't have many mitochondria.

cells produce the enzymes needed for cellular respiration veryslowly

7.Enzymes are catalysts because they operate to:

raise activation energy

lower activation energy

supply activation energy

supply the reactants

8.When ATP powers a reaction it becomes ADP. The ADP

can reform ATP by an exergonic reaction

is a waste product for lysosomal breakdown

can reform ATP by an endergonic reaction

can reform ATP by an oxidation reaction

can reform ATP by an equilibrium reaction

9.The energy source that drives photosynthesis is

water

glucose

carbon dioxide

oxygen

sunlight

10. What is the process by which enzymes regulate their ownactivity?

osmosis

self-propulsion

feedback inhibition

11.Coupled reactions are reactions in which a

endergonic reaction drives a spontaneous reaction

exergonic reaction drives a spontaneous reaction

endergonic reaction drives an exergonic reaction

exergonic reaction drives an endergonic reaction

12.How is water used in photosynthesis?

as a substrate for ATP synthase

as an electron donor

to combine with ADP forming ATP

as an electron acceptor

13.Why are the “Dark Reactions” of photosynthesis referred to as“Dark”?

they do not require light

they can only occur at night

they generate excess sugar and the leaves turn brown

14.What is the difference between potential and kineticenergy?

potential is stored, kinetic is being used

potential is being used, kinetic is ready to be used

potential is negative, kinetic is positive

15.The products of cellular respiration are

carbon dioxide, water, and ATP

glucose, water, and ATP

glucose, carbon dioxide, and ATP

oxygen, ATP, and water

carbon dioxide, glucose, and water

16.All of the following are correct about energy except:

The biological world gets its energy from the sun.

Chemical bonds store potential energy.

A boulder perched on a hill has kinetic energy.

Energy is defined as the ability to do work.

All forms of energy can be converted to heat.

17.What is needed for the end product of glycolysis, pyruvate,to enter the citric acid cycle?

More glucose for energy

ATP

Oxygen

Carbon dioxide

18.The enzyme that forms a transmembrane channel in mitochondriaand phosphorylates ADP

a carrier protein

ATP synthase

acetyl CoA

19.Fermentation is most common in

plants

microorganisms

animals

20.During adsorption of sunlight by photosystems, H+ ions aregenerated. Where do they come from? What are they used for?

from the breakdown of sugar; they help form water

water; they help form sugar

from carbon dioxide; they help dissolve NaCl

21.Glycolysis

does not use oxygen

uses oxygen

uses carbon dioxide

22.Photosynthesis is

not dependent on chlorophyll

a process that produces glucose and oxygen

a process that produces water and carbon dioxide

23.Breakdown of glucose generates many ATP molecules, each ofwhich can be used independently. Why is ATP ideally suited to powerbiological reactions?

ATP has many hydrogen bonds

ATP has enough energy to power one biological reaction

ATP readily dissolves in water

24.Objects that are not actively moving but have the capacity todo so are said to possess:

kinetic energy

entropy

potential energy

living energy

25.The first stage of cellular respiration, called ___________,takes place in the cytoplasm of the cell and needs no oxygen.

photorespiration

citric acid cycle

glycolysis

oxidation

26.Diffusion

requires energy

utilizes proteins to move molecules across a membrane

moves molecules against a concentration gradient

does not require energy

cannot occur without a membrane present

27.What is the name of the molecule on which an enzymeworks?

substrate

monomer

polymer

28.ATP contains

phenylalanine

two phosphate groups

three nitrate groups

three phosphate groups

29.How does chlorophyll function in photosynthesis?

by absorbing carbon dioxide

by absorbing the sun's energy

by absorbing water

30.Objects that are moving are said to possess:

living energy

potential energy

entropy

kinetic energy

31.The respiration pathway that evolved first is probably

glycolysis

aerobic respiration

citric acid cycle

32.The energy source for the process of photosynthesis is

oxygen

sunlight

carbon dioxide

chlorophyll

glucose

33.Burning wood generates heat and light. What type of reactionis this?

exergonic

kinetic energy

endergonic

potential energy

equilibrium

34.What is meant by a “coupled reaction” in terms of energy?

many poymers are built simultaneously

energy released by one reactions powers another reaction

some reactions occur in the same organelle

35.The First Law of Thermodynamics states:

energy is constantly being created by entropy events

energy can be changed from one form to another, but cannot becreated or destroyed

energy can be used and then destroyed because of entropy'sactions on it

energy can be destroyed while it is producing entropy

36.How do we dispose of the carbon derived from the glucose thatis metabolized during respiration?

by breathing out

via our urine

it is broken down in lysosomes

37.Both plant and animal cells have mitochondria because theyboth

carry on respiration

carry on photosynthesis.

require water

38.What is Activation Energy?

the energy needed to initiate a reaction

the energy that transports water into cells

potential energy

39.If you put a plant in a chamber and shine a light on it

oxygen will decrease and carbon dioxide will increase

oxygen will increase and carbon dioxide will decrease

oxygen and carbon dioxide will increase

oxygen and carbon dioxide will decrease

40.What are the inputs and the output molecules for the overallphotosynthetic process?

input sugar and oxygen; output carbon dioxide and water

input oxygen and water; output sugar and carbon dioxide

input carbon dioxide and water;output sugar and oxygen

41.What kind of reaction is photosynthesis?

endergonic

kinetic energy

exergonic

potential energy

equilibrium

42.In the process of glycolysis, glucose is cleaved into a pairof three-carbon molecules called

lactate

pyruvate

acetyl CoA

ATP

alcohol

43.Entropy is

order

disorder

complexity

Both order and disorder are correct

Both complexity and disorder are correct

44.Glycolysis takes place in the _____________ and the citricacid cycle and electron transport chain take place in the___________.

cytoplasm; endoplasmic reticulum

mitochondria, chloroplast

mitochondria; cytoplasm

cytoplasm; mitochondria

45.The organelle that carries out photosynthesis in plants isthe

mitochondria

chloroplast

ribosome

chlorophylllysosome

46.The energy to power the Calvin cycle comes from

cellular respiration

oxygen

the light reactions of photosynthesis

47.Which of the following can be broken down into intermediateproducts that enter cellular respiration?

Proteins

Lipids

Carbohydrates

All of these.

48.When cellular product levels get too high, the responsibleenzyme is inhibited. This is an example of

promotion

denaturation

equilibrium

a coenzyme

feedback inhibition

49.How is respiration the opposite of photosynthesis?

respiration breaks sugar down to carbon dioxide; photosynthesisbuilds sugar from carbon dioxide

respiration builds sugar from carbon dioxide; photosynthesisbreaks sugar down to carbon dioxide

respiration requires energy input; photosynthesis gives offexcess energy

50.The molecule that absorbs sunlight for photosynthesis is

oxygen

carbon dioxide

chlorophyll

glucose

sunlight