oxygen, carbon glucose and other dioxide, and large, polar ... · Total amount of energy in the universe is constant Energy flows from higher to lower energy forms ATP Main energy

Bio10 Lecture Notes 4: Cells and Energy SRJC

A. Carranza Page 1 7/24/2015

oxygen, carbon dioxide, and other small, nonpolar molecules; some water molecules

glucose and other large, polar, water-soluble molecules; ions (e.g.,H+, Na+, K+, Ca++, Cl–)

High

Concentration gradient across cell membrane

Low

Diffusion of lipid-soluble substances across bilayer

Passive transport of water- soluble substances through channel protein; no energy input needed

Active transport through ATPase; requires energy input from ATP

ATP

Fig. 4-20, p.71

4.) Cell Transport

Concentration Gradient

Different numbers of molecules or ions in different regions

Substances tend to move down gradient - from higher to lower concentration

Diffusion

Net movement of

molecules or ions down

a concentration gradient

Diffusion Rate Factors

Steepness of

concentration gradient

Steeper gradient,

faster diffusion

Molecular size

Smaller molecules,

faster diffusion

Temperature

Higher temperature,

faster diffusion

Electrical or pressure

gradients

Transport Proteins

Span the lipid bilayer

Interior can open to either side

Change shape when they interact with solute

Move water-soluble substances

across a membrane

Passive and Active Transport

Passive Transport

Doesn’t require energy

inputs

Solutes diffuse through a

channel inside the protein’s

interior

Net movement is down

concentration gradient

Active Transport

Requires ATP

Protein is an ATPase pump

Pumps solute against its concentration gradient



Endocytosis (vesicles in) Exocytosis (vesicles out)

Membrane Traffic

Exocytosis

Vesicle fuses with membrane, releasing substance into intracellular fluid

Endocytosis

Membrane forms vesicle, bringing substance into cell

Types of Endocytosis

Bulk-phase endocytosis

Receptor-mediated endocytosis

Phagocytosis

5.) Enzymes

Energy Laws

Energy: the capacity to do work

Total amount of energy in the universe is constant

Energy flows from higher to lower energy forms

ATP

Main energy carrier in cells

Can give up phosphate group to another molecule

Phosphorylation energizes molecules to react

The Cell’s Energy Currency

ATP couples energy inputs and outputs

ATP/ADP cycle regenerates ATP

Energy Changes

Endergonic reactions require energy

Synthesis of glucose from carbon dioxide and water during photosynthesis

Exergonic reactions release energy

Breakdown of glucose to carbon dioxide and water by aerobic respiration

energy

input ADP + Pi

energy output

ATP



Fig. 4-5, p.61

Highly spontaneous

equilibrium

highly spontaneous

Electron Transfers

Oxidation: loss of an electron

Reduction: gain of an electron

Electron transfer chains are vital to the formation of ATP during photosynthesis

and aerobic respiration

Participants in Metabolic Pathways

Reactants

Intermediates

Products

Energy carriers

Enzymes

Cofactors

Transport proteins

Reactions: Forward and Reverse

Most chemical reactions are reversible

Direction of reaction depends upon

Energy content of participants

Reactant-to-product ratio

Chemical Equilibrium

Reaction rate is the same in

both directions

Conversions continue, but

proportions of reactant and

product do not change

Usually amounts of reactant

and product are not equal

Metabolic Pathways

Biosynthetic (anabolic)

pathways

Require energy inputs

Assemble large

molecules from subunits

Photosynthesis

Degradative (catabolic) pathways

Release energy

Breakdown large molecules to subunits

Aerobic respiration

Enzymes

Catalyze (speed up) reactions

Recognize and bind specific substrates

Act repeatedly

Most are proteins



activation energy without enzyme

activation energy

with enzyme

energy released by the

reaction

products

starting

substance

allosteric

activator

allosteric binding site vacant

active site altered, substrate can bind

substrate cannot bind

enzyme active site

Allosteric activation

allosteric inhibitor

allosteric binding site vacant; active site can bind

substrate

active site altered, can’t bind substrate

Allosteric inhibition

Activation Energy

For a reaction to occur, an energy

barrier must be surmounted

Enzymes make the energy barrier

smaller

Factors Influencing Enzyme Activity

Coenzymes and cofactors

Allosteric regulators

Temperature

pH

Salt concentration

Allosteric Control

Activator or inhibitor binds to an

enzyme

Binding changes enzyme

shape

Change hides or exposes

active site

Feedback inhibition

Product shuts off enzyme

by binding to activation

site

Effect of Temperature

Small increase in

temperature increases

molecular collisions, reaction rates

High temperatures disrupt bonds ad destroy the shape of active site

Enzymes and the Environment

Most enzymes require specific activation conditions

Certain temperature or pH extremes can shut down activity



Fig. 5-4d, p.75

sunlight

Both stages of photosynthesis occur inside the chloroplast

light-dependent reactions

light-independent

reactions

CO2

sugars

NADPH, ATP

NADP+, ADP

O2 H2O

stroma

thylakoid compartment

thylakoid membrane

system

two outer

membranes

6.) Photosynthesis

Sunlight and Survival

Plants are photoautotrophs; they use sunlight and CO2 to produce sugar in the

process of photosynthesis

Many kinds of energy

Wavelengths of visible light

Visible Light

Wavelengths humans perceive as different colors

Violet (380 nm) to red (750 nm)

Longer wavelengths, lower energy

Pigments

Visible color is from wavelengths not absorbed (they reflect the color we see)

Pigments capture light energy from absorbed wavelengths

Light energy destabilizes bonds and boosts electrons to higher energy levels

Variety of Pigments

Chlorophylls ; green, yellow

Carotenoids; red, orange, yellow

Xanthophylls; yellow, brown, purple, blue

Anthocyanins, red, purple, blue

Phycobilins; red or blue-green

Light Receptors

Pigments capture light energy

Photosynthesis Equation

6 CO2 + 12 H2O + light energy C6H12O6 + 6 O2 + 6 H2O

Two Steps in Photosynthesis

Light-dependent reactions

Light-independent reactions

Light-Dependent Reactions

Cyclic pathway

ATP forms

Requires one type of

photosystem

Noncyclic pathway

ATP and NADPH form

Water is split and oxygen

released

Requires two types of

photosystems

Chloropasts

Organelle of photosynthesis in

plants and algae

Light-dependent reactions take

place in thylakoids

Light independent reactions take

place in stroma



Photosystems

Thylakoid Membrane Section

Role of Electron Transfer Chains

Adjacent to photosystems

Acceptor molecule accepts electrons from reaction center

As electrons pass along chain, energy released drives synthesis of ATP

Cyclic Electron Flow

Electrons are donated by chlorophyll a in photosystem I to an acceptor molecule

flow through electron transfer chain and back to photosystem

Electron flow drives ATP formation

No NADPH is formed

Noncyclic Electron Flow

Two-step pathway for light absorption and electron excitation

Uses type I and type II photosystems

Produces ATP and NADPH

Involves photolysis (splitting of water) and releases oxygen as a byproduct

NADPH

NADP + + H+

thylakoid compartmen

t thylakoid membrane

stroma ATP ADP + Pi

H+

H+ H

+

H+

H+

H+

H+ H

+ H+

H+ H

+

Photosystem I

sunlight

Photosystem II Light- Harvesting Complex

Fig. 5-7, p.77

H+

e–

e–

e–

e–

e–

e–

H+

e–

O

2

H2

O

cross-section through a disk-shaped fold in the thylakoid membrane

Po

ten

tia

l to

tra

ns

fer

en

erg

y (

vo

lts

)

H2O 1/2O2 + 2H+

(photosystem II)

(photosystem I)

e– e–

e– e–

second transfer

chain

NADPH first

transfer

chain



Fig. 5-8, p.78

REACTIONS PROCEED IN CHLOROPLAST’S

STROMA

Calvin-Benson

cycle

12 PGAL

glucose 1

ATP

ATP

NADPH

6 RuBP 12 PGA

6CO2

C4

cycle

stomata closed,

no CO2 uptake

oxaloacetate mesophyll

cell

bundle-sheath

cell

Calvin-Benson

cycle

CO

2

RuBP PGA

sugar

ATP Formation in the Noncyclic Pathway

Photolysis and electron transfer chains create electrical and H+ concentration

gradients across thylakoid membrane

H+ flows down gradients into stroma through ATP synthases

Flow of ions drives formation of ATP from ADP and phosphate

Light-Independent Reactions

Synthesis part of photosynthesis

Can proceed in the dark using energy stored in light reactions

Take place in stroma

Calvin-Benson cycle

Calvin-Benson Cycle

Reactants

Carbon dioxide

ATP

NADPH

Products

Glucose

ADP

NADP+

The C3 Pathway

In Calvin-Benson cycle, the first

stable intermediate is a three-

carbon PGA

Because the first intermediate has

three carbons, the pathway is called

the C3 pathway

Photorespiration in C3 Plants

On hot, dry days stomata close

Inside leaf

Oxygen levels rise

Carbon dioxide levels drop

Rubisco attaches RuBP to oxygen instead

of carbon dioxide

Only one PGAL forms instead of two

C4 Plants

Carbon dioxide is fixed twice

In mesophyll cells, carbon dioxide is

fixed to form 4-carbon oxaloacetate

Oxaloacetate is transferred to bundle-

sheath cells

Carbon dioxide is released and fixed again

in Calvin-Benson cycle



CAM (Crassulacean Acid Metabolism) Plants

Desert plants like cacti keep stomata closed during the day

Carbon is fixed twice (in same cells)

Night

Carbon dioxide is fixed by repeated turns of a type of C4 cycle

Day

Carbon dioxide is released and fixed in Calvin-Benson cycle

Summary of Photosynthesis

Linked Processes

Photosynthesis

Energy-storing pathway

Releases oxygen

Requires carbon dioxide

Aerobic Respiration

Energy-releasing pathway

Requires oxygen

Releases carbon dioxide

12H2O

sunlight

Calvin- Benson

cycle

6O2

Light Dependent

Reactions

Light Independent

Reactions

NADP+ ADP + Pi

6 RuBP 12 PGAL

P

end products (e.g., sucrose, starch, cellulose)

phosphorylated glucose

6H2O

6CO2

ATP NADPH



7.) Cellular Respiration: How Cells Release Chemical Energy

Main Types of Energy-Releasing Pathways

Anaerobic pathways

Evolved first

Don’t require oxygen

Start with glycolysis in cytoplasm

Completed in cytoplasm

Aerobic pathways

Evolved later

Require oxygen

Start with glycolysis in cytoplasm

Completed in mitochondria

ATP: Universal Energy Source

Photosynthesizers get light energy from the sun, store it as chemical energy, and

produce ATP

Animals eat plants or other animals and transform chemical energy to ATP

Making ATP

Plants make ATP during photosynthesis

Anaerobes make ATP by fermentation

Cells of most organisms make ATP by aerobic respiration of carbohydrates, fats,

and protein

Aerobic Respiration

Glycolysis; partial breakdown of glucose

Occurs in the cytoplasm

Produces 2 ATP

Krebs Cycle (citric acid cycle)

Break down of glycolysis byproducts to CO2 produces NADH and FADH

Electron Transport Chain

uses NADH and FADH from Krebs cycle to produce ATP

Summary Equation for Aerobic Respiration

C6H12O6 + 6O2 6CO2 + 6H2O + energy (ATP)

CYTOPLASM

Glycolysis

Electron

Transfer

Phosphorylatio

n

Krebs Cycle ATP

ATP

2 CO2

4 CO2

2

32

water

2 NADH

8 NADH

2 FADH2

2 NADH 2 pyruvate

e- + H+

e- +

oxygen

(2 ATP net)

glucose

Typical Energy Yield: 36 ATP

e-

e- + H+

e- + H+

ATP

H+

e- + H+

ATP 2 4



2 ATP invested

Energy-Requiring Steps of Glycolysis

glucose

PGAL PGAL

P P

ADP

P

ATP

glucose-6-phosphate

P fructose-6-phosphate

ATP

fructose1,6-bisphosphate P P

ADP

Energy-Releasing

Steps

ADP ATP

pyruvate

ADP ATP

pyruvate

H2O

P

PEP

H2O

P

PEP

P

2-phosphoglycerate

P

2-phosphoglycerate

ADP ATP

P 3-phosphoglycerate

ADP ATP

P 3-phosphoglycerate

NAD+ NADH Pi

1,3-bisphosphoglycerate P P

NAD+

NADH Pi

1,3-bisphosphoglycerate P P

PGAL P

PGAL P

EEnneerrggyy RReelleeaassiinngg SStteeppss ooff GGllyyccoollyyssiiss

The Role of Coenzymes

NAD+ and FAD accept electrons and hydrogen

Become NADH and FADH2

Deliver electrons and hydrogen to the electron transfer chains

Glycolysis Occurs in Two Stages

Energy-requiring steps

ATP energy activates glucose and its 6-carbon derivatives

Energy-releasing steps

The products of the first part are split into 3-carbon pyruvate molecules

ATP and NADH form

Glucose

A simple sugar

(C6H12O6)

Atoms held together by covalent bonds

Energy-Requiring Steps

Energy-Releasing Steps

Glycolysis: Net Energy Yield

Energy requiring steps:

2 ATP used

Energy releasing steps:

2 NADH formed

4 ATP formed

Net yield: 2 ATP + 2 NADH



acetyl-CoA

(CO2)

pyruvate

coenzyme A NAD+

NADH

CoA

Krebs Cycle CoA

NADH

FADH2

NADH

NADH

ATP ADP + phosphate group

NAD+

NAD+

NAD+ FAD

oxaloacetate citrate

Mitochondria

Organelles where the next two phases of aerobic respiration proceed (Krebs cycle

and electron transport chain)

Produces 34 more energy molecules ATP

Second Stage Reactions

Preparatory reactions

Pyruvate is oxidized into 2-carbon acetyl-CoA + CO2

NAD+ is reduced

Krebs cycle

Acetyl-CoA is oxidized to

two CO2

NAD+ and FAD are reduced

The Krebs Cycle

Overall Reactants

Acetyl-CoA

3 NAD+

FAD

ADP and Pi

Overall Products

Coenzyme A

2 CO2

3 NADH

FADH2

ATP

Results of the Second Stage

All of the carbon molecules in

pyruvate end up in CO2

Coenzymes are reduced (they pick up electrons and hydrogen)

One molecule of ATP is formed

4-carbon oxaloacetate is regenerated

Coenzyme Reductions During First Two Stages

Glycolysis 2 NADH

Preparatory reactions 2 NADH

Krebs cycle 2 FADH2 + 6 NADH

Total 2 FADH2 + 10 NADH



NADH

OUTER COMPARTMENT

INNER COMPARTMENT

Third Stage

Electron Transfer Phosphorylation

Occurs in mitochondria

Coenzymes deliver electrons to electron transfer systems

Electron transfer sets up H+ ion gradients

Flow of H+ down gradients powers ATP formation

Creating an H+ Gradient

Making ATP

Importance of Oxygen

Electron transport phosphorylation requires oxygen

Oxygen withdraws spent electrons from the electron transport system, then

combines with H+ to form water

Summary of Energy Harvest (per molecule of glucose)

ATP

ADP

+

Pi

INNER

COMPARTMENT

glucose

Glycolysis

e–

oxygen accepts “spent”

electrons

Electron Transfer phosphorylation

2 PGAL

2 pyruvate

2 NADH

2 CO2

ATP

ATP

2 FADH2

H+

2 NADH

6 NADH

2 FADH2

2 acetyl-CoA

ATP 2 Krebs Cycle

4CO2 ATP

ATP

ATP

32

ADP + Pi

H+

H+

H+

H+

H+

H+ H+

H+

2

4

Fig. 6-5 p.87

2 NAD+



C6H12O

6 ATP

ATP

NADH

2 acetaldehyde

electrons, hydrogen from NADH

2 NAD+

2

2 ADP

2 pyruvate

2

4

energy output

energy input

GLYCOLYSIS

ETHANOL FORMATION

2 ATP net

2 ethanol

2 H2O

2 CO2

Glycolysis

2 ATP formed by substrate-level phosphorylation

Krebs cycle and preparatory reactions

2 ATP formed by substrate-level phosphorylation

Electron transport phosphorylation

32 ATP formed

Anaerobic Pathways

Alcoholic Fermentation

Fermentation Pathways

Begin with glycolysis

Are anaerobic: don’t require oxygen

Yield only 2 ATP from glycolysis

Steps after glycolysis only regenerate NAD+

Alcoholic Fermentation

Lactate Fermentation

Alternative Energy Sources

Carbohydrates, fats, and proteins are digested and enter aerobic respiration

Evolution of Metabolic Pathways

Earliest organisms used anaerobic pathways

Later, noncyclic pathway of photosynthesis increased atmospheric oxygen

Aerobic respiration evolved due to selective pressure by oxygen

Anaerobic Archaeans

Use hydrogen sulfide as energy source

Aerobic Respiration

Uses products of photosynthesis

C6H12O6

ATP

ATP

NADH

2 lactate

electrons, hydrogen

from NADH

2 NAD+

2

2 ADP

2 pyruvate

2

4

energy output

energy input

GLYCOLYSIS

LACTATE

FORMATION

2 ATP net

oxygen, carbon glucose and other dioxide, and large, polar ... · Total amount of energy in the universe is constant Energy flows from higher to lower energy forms ATP Main energy

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