Biology Chapters 8-11

Energy

capacity to do work or the capacity for change

Potential Energy

stored energy as chemical bonds, concentration gradient, charge imbalance, etc.

Kinetic energy

energy of movement

Metabolism

sum total of all chemical reactions in an organism

Anabolic reactions

complex molecules are made from simple molecules; energy input is required

Catabolic reactions

complex molecules are broken down to simpler ones and energy is released

1st Law of Thermodynamics

energy is neither created nor destroyed

when energy is converted from one form to another, the total energy is the same before and after

2nd Law of Thermodynamics

when energy is converted from one form to another, some of that energy becomes unavailable to do work

Entropy

measure of the disorder in a system

Total energy

= usable energy + unusable energy

enthalpy

= free energy (G) + entropy (S)

delta G

free energy

Magnitude of delta G depends on

Delta H = total energy added or released

Delta S = change in entropy

If a chemical reaction increases entropy will the product be more or less disordered

more disordered

Disorder tends to increase because of

energy transfer

Exergonic reactions

release free energy

Exergonic reactions - complexity

catabolism (complexity decreases)

Endergonic reactions

consume free energy

Endergonic reactions - complexity

anabolism (complexity increases)

Chemical equilibrium Delta G =

0

Forward and reverse reactions are

balanced

ATP

Adenosine Triphosphate

ATP

captures and transfers free energy

releases a large amount of energy when hydrolyzed

can phosphorylate or donate phosphate groups to other molecules

is a nucleotide

hydrolysis of ATP yields free energy

Bioluminescence

endergonic reaction driven by ATP hydrolysis

Formation of ATP

endergonic

ADP + Pi to ATP

Endergonic reaction

ATp to ADP + Pi

Exergonic reaction

Catalysts

speed up rate of a reaction

Ezymes

act as a framework in which reactions can take place

Activation energy

amount of energy required to start the reaction

Transition state intermediates

Activation energy changes the reactants into unstable forms with higher free energy

Enzymes lower the energy barrier by

bringing the reactants together

Subrates

reactants

Enzyme-Substrate Complex

held together by hydrogen bonds, electrical attraction, or covalent bonds

E+S —> ES —> E+P

Ezyme Substrate Product

Lowers activation energy

1) orientation

2) physical strain

3) chemical change

Induced fit

when enzyme changes shape when they bind to the substrate

Concentration of an enzyme is lower than

concentration of a substrate

At saturation, all enzyme is bound to substrate

Maximum rate

How are enzyme activities regulated

metabolic pathways

Regulation of enzymes maintains

internal homeostasis

Enzyme activity regulators

1) inhibitors

2) irreversible inhibition

3) reversible inhibition

4) competitive inhibitors

5) noncompetitive inhibitors (allosteric)

Allosteric Enzyme

controls activity by changing shape

Active form of allosteric enzyme

can bind substrate

Inactive form of allosteric enzyme

cannot bind substrate but can bind to an inhibitor

Metabolic pathways first reaction

commitment step, then other reactions happen in sequence

Feedback inhibition

final product acts as a noncompetitive inhibitor of first enzyme which shuts down the pathway

How are enzymes affected by the environment

pH & temp

pH - ionization of functional groups

temp - lose tertiary structure and become denatured and high temperatures

Isozymes

enzyme with similar makeup which works better or worse under different conditions

Principles of governing metabolic pathways

1. complex chemical transformations occur in a series of reactions

2. each reaction is catalyzed by a specific enzyme

3. metabolic pathways are similar in all organisms

4. in eukaryotes, metabolic pathways are compartmentalized in organelles

5. each pathway is regulated by key enzymes

Burning/Metabolism of Glucose Equation

C6H12O6 +6O2 —> 6O2+6H2O+free energy

highly exergonic; drives endergonic formation of ATP

3 metabolic pathways the harvest glucose

1. glycolysis - glucose is converted to pyruvate

2. cellular respiration - AEROBIC - converts pyruvate into H2O, CO2, and ATP

3. fermentation - ANAEROBIC - converts pyruvate into lactic acid or ethanol, CO2, and ATP

How does glucose oxidation release chemical energy

1. redox reactions - 1 substance transfers electrons to another substance

2. reduction reactions - gain of 1 or more electrons by an atom, ion, or molecule

3. oxidation - loss of one or more electrons

reactants that become reduced

oxidizing agent

reactants that become oxidized

reducing agent

Coenzyme NAD+

Key electron carrier in redox reactions

2 forms of Coenzyme NAD+

1. NADH (reduced)

2. NAD+ (oxidized)

Where does glycolysis take place

Cytosol

Roles of glycolysis

1. Converts glucose into pyruvate

2. Produces a small amount of energy

Pyruvate oxidation purpose

Links glycolysis and citric acid cycle

Pyruvate oxidation where?

Mitochondrial matrix

Citric Acid Cycle inputs

Acetyl COA, water and electron carriers COA FAD, and GDP

Citric Acid Cycle outputs

CO2, reduced electron carriers and GTP

Aerobic pathways of glucose metabolism

Electron carriers that are reduced during citric acid cycle must be deoxidized to take part in the cycle again

Fermentation

Occurs if no O2 is present

Oxidative phosphorylation

Occurs if O2 is present

2 stages of oxidative phosphorylation

1. Electron transport

2. Chemiosis

Uncoupled protein

Brown fat - heat production

Energy harvested from glucose without oxygen

1. Lactic acid fermentation

2. Alcoholic fermentation

Polysaccharides

Hydrolyzed to glucose, enters glycolysis and cellular respiration

Lipids

Broken down into glycerol —> DAP and fatty acids —> acetyl COA

Proteins

Hydrolyzed to amino acids and feeds into glycolysis or the citric acid cycle

Gluconeogenesis

Glucose formed from citric acid cycle and glycolysis intermediates

Photosynthesis

Synthesis from light

Plants take in CO2, produce carbohydrates and release water and O2

2 Pathways of photosythesis

1. Light reactions - convert light energy to chemical energy as ATP and NADPH

2. Light independent reactions - use ATP and NADH plus CO2 to produce carbohydrates

Scattered photon

Photon bounces off molecule

Transmitted photon

Photon is passed through molecule

Absorbed photon

Molecule acquires energy of the photon

Absorption spectrum

Plot of wavelengths absorbed by a pigment

Action spectrum

Plot of biological activity as a function of exposure to varied wavelengths of light

Main pigments

1. Chlorophyll - in chloroplast

2. Accessory pigments:

   1. carotenoids - absorb blue and green wavelengths, appear deep yellow

   2. Phycobilins - absorbs yellow, green, orange wavelengths, appear red in color

Light energy becomes what energy

Chemical

Photosystem

Consists of multiple antenna systems and their pigments and surrounds a reaction center

2 systems of electron transport

1. noncyclic electron transport

2. Cyclic electron transport

Noncyclic electron transport

Light energy is used to oxidize water to O2, H+ and electrons

Photosystem I and Photosystem II

Z Scheme

Extracts electrons from water and transfers them to NADPH, using energy from photosystems I and II and resulting in ATP synthesis

Cyclic Electron Transport

Only makes ATP

Starts and ends in photosystem I

Phosphorylation

Light driven production of ATP

H+ is transported via electron carriers across the thylakoid membrane into the human creating an electrochemical gradient

CO2 fixation

CO2 is reduced to carbohydrates

Calvin Cycle

1. fixation of CO2

2. reduction of 3PG to G3P

3. regeneration of RuBP

G3P

Glyceraldenyde 3

Phosphate is the product of the Calvin cycle

Photorespiration

Consumes O2, releases CO2 and takes place in light

Stomata

Little holes on the surface of a leaf that opens and closes

CO2 in, O2 out

C3 plants

first product of CO2 fixation is the 3-C compound 3PG

cells in the mesophyll have abundant rubisco - enzyme in plant chloroplast

C4 plants

2 separate enzymes for CO2 fixation

1. rubisco in bundle sheath cells

2. PEP carboxylase

CAM plants

similar to C4, CO2 is initially fixed into a 4C molecule but timing differs

Life cycle of an organism is linked to what

Cell division

4 events must occur for cell division

1. reproductive signal - initiate cell division

2. replication - of DNA

3. segregation - distribution of the DNA into 2 new cells

4. cytokinesis - separation of 2 new cells

Binary fission

Prokaryote cell division

External factors are reproductive signals

Ori

Where replication starts

Ter

Where replication ends