cell functions and structure exam 2

definition of chemical reaction:

when atoms have enough energy to change bonding partners

Metabolism

All chemical reactions taking place in an organism

main 2 types of metabolism

anabolism, catabolism

anabolism definition

Pathways in which complex molecules are synthesized

thermodynamics definition:

the study of energy and its transformations

Catabolism definition

pathways in which larger molecules are broken down into smaller ones (releases energy)

Energy definition

capacity to do work of the capacity for change

potential energy

stored energy

potential energy example

potential energy in a drawn bow

kinetic energy

energy of motion is used, and work is performed

kinetic energy example

the bowstring pushes the arrow towards its target

energy can be converted from one form to another

energy can be converted from one form to another

Energy transformations occur where?

in organisms

kinetic energy is converted to…

potential energy

potential energy is converted to…

kinetic energy

chemical energy

potential energy is stored in chemical bonds

1st law of thermodynamics

energy cant be created or destroyed, only converted from one form to another

2nd law of thermodynamics

When energy is converted from one form to another, some usable energy (energy available to do work) is converted into heat that disperses into the surroundings (wasted energy)

heat

the kinetic energy of randomly moving particles

entropy (s)

A measure of the disorder, or randomness of energy, Organized, usable energy has a low entropy, Disorganized energy, such as heat, has a high entropy

The total entropy of the universe (organisms plus surroundings) always increases over time

The total entropy of the universe (organisms plus surroundings) always increases over time

Enthalpy (h)

The total potential energy of a system

Essentially equivalent to the total bond energy

Free energy (g)

The amount of energy available to do work under the conditions of a biochemical reaction

Enthalpy (H), free energy (G), entropy (S); and absolute temperature (T) are related

H = G + TS

As entropy increases, the amount of free energy decreases

As entropy increases, the amount of free energy decreases

The rearranged equation can be used to predict whether a particular chemical reaction will release energy or require an input of energy:

Δ G = Δ H − T Δ S

Δ G = what

Free energy

Δ G = G final – G starting

Δ G = G final – G starting

what kind of reaction is this? Negative Δ G = Spontaneous

exergonic reaction: energy released

What kind of reaction is this? Positive Δ G = Energy Required

endergonic reaction: energy required

Exergonic reaction..

releases energy = spontaneous “downhill” reaction from higher to lower free energy

ΔG is negative for exergonic reactions

ΔG is negative for exergonic reactions

When ΔG = 0…

there is no net movement and the reaction is balanced

Endergonic reaction…

reaction in which there is a gain of free energy

ΔG endergonic reactions…

has a positive value (the free energy of the products is greater than the free energy of the reactants)

endergonic reactions require

input of energy from environment

free energy is…

is a measure of a system’s instability, its tendency to change to a more stable state

During a spontaneous change…

free energy decreases and stability of a system increases

Activation Energy is

the energy required to get a reaction going.

Catalysts

increase the speed of a reaction.

Biological catalysts are…

enzymes (proteins)

Enzymes Lower Activation Energy in 3 Ways (way 1)

1. By orienting substrates so they can react

Enzymes Lower Activation Energy in 3 Ways (way 2)

2. By inducing strain through stretching the substrate weakening chemical bonds

Enzymes Lower Activation Energy in 3 Ways (way 3)

3. By temporarily adding charge to substrate

When substrate binds, the enzyme changes shape for catalysis it is

induced fit

Enzyme Activity Can be Regulated in Multiple Ways

1. Gene expression

2. Environmental changes: pH and temperature

3. Chemical modulation

Cyclooxyrgenase is an enzyme that makes

prostaglandins (locally made hormones that induce swelling and heat at site of an injury causing PAIN)

Enzyme Inhibition: 1. Irreversible Inhibition

Some enzyme inhibitions are irreversible

Enzyme Inhibition: 2. Reversible Inhibition

Some enzyme inhibitions are reversible. Competitors don’t bind covalently

Competitive Vs Noncompetitive Inhibition of Enzymes

look at the difference

Un-Competitive inhibitor

binds to the enzyme-substrate complex, preventing the release of products

non-competitive inhibitors

binds at a site other than the active site, changing enzyme structure so that normal substrate binding cannot occur

ATP = energy a cell can use

ATP (adenosine triphosphate)

ATP has

high potential energy and allows cells to do work.

ATP Hydrolysis Is Exergonic and Released Energy can drive Endergonic Reactions

ATP Hydrolysis Is Exergonic and Released Energy can drive Endergonic Reactions

The major process of making ATP is called

Cellular Respiration

As Eukaryotes, our major form of Cellular Respiration is

Aerobic Respiration (Requires Oxygen)

Aerobic respiration is a series of

redox (Oxidation-Reduction) reactions

Organisms convert energy from food molecules into ATP

Organisms convert energy from food molecules into ATP

Two Processes for Making ATP (process 1)

1. Cellular Respiration- can be either: • aerobic (requiring oxygen) • anaerobic (not requiring oxygen) But both use an electron transport chain to transfer energy

Two Processes for Making ATP (process 2)

2. Fermentation- • anaerobic process, Does NOT use an electron transport chain to transfer energy

4 Steps to Cellular Respiration

Step 1: Glycolysis

Step 2: Pyruvate processing

Step 3: The citric acid cycle (TCA)

Step 4: Electron transport, chemiosmosis, and oxidative phosphorylation

During the first three steps, energy is captured which is then used for producing ATP in step 4.

Cellular respiration produces ATP from molecules with high potential energy, such as glucose

C₆H₁₂O₆ + 6O₂ → 6CO_{2 +} 6H₂O + ENERGY (DeltaG = -686 kcal/mol

Where does Cellular Respiration take place?

Step 1: Glycolysis (cytoplasm)

Step 2: Pyruvate processing (mitochondrial matrix)

Step 3: The citric acid cycle (mitochondrial matrix)

Step 4: Electron transport, chemiosmosis, and oxidative phosphorylation (inner mitochondrial membrane)

End Goal of Cellular Respiration is……

ATP

90% from Oxidative Phosphorylation (step 4)

10% from substrate-level phosphorylation (steps 1, 2, 3)

The more reduced a molecule is the more energy it has

most reduced state → most oxidized state

highest free energy → lowest free energy

kinase enzyme function

addition of a phosphate group

isomerase enzyme function

rearrangement of binds within a molecule

dehydrogenase enzyme function

Oxidation of a molecule by removing a Hydrogen atom plus electron

mutase enzyme function

Shifting a chemical group from one position to another within a molecule

By the end of the TCA (Kreb’s) Cycle, each glucose molecule that is oxidized, has made:

6 CO2

10 NADH

2 FADH2

4 ATP by substrate-level phosphorylation.

Oxygen is

The most effective electron acceptor because it is highly electronegative.

Fermentation is extremely

Inefficient compared with cellular respiration

Fermentation produces

2 ATP molecules per glucose!!

Photosynthesis

the process that converts solar energy into organic chemical energy

Autotrophs

Organisms that carry out photosynthesis are (“self-feeders”): plants, algae, and cyanobacteria.

Heterotrophs:

(“other-feeders”) must consume other organisms, such as autotrophs or other heterotrophs, to obtain food: animals, fungi, and most other bacteria.

Photosynthesis: 2 parts PHOTO

Light capturing Reactions Generate chemical energy needed to run the chemical synthesis reactions of the Calvin cycle

Photosynthesis: 2 parts Synthesis

Calvin Cycle uses the energy generated in the light capturing reactions to “fix” carbon…what does “fix mean?

Visible light is

A small part continuous range of radiation called the electromagnetic spectrum

All radiation in this spectrum travels as..?

waves

wavelength =

distance from one wave peak to the next

visible spectrum (seen by humans) range

380 nm (violet) to 760 nm (red)

Light is composed of small packets, of energy called…?

photons

When Photons of light approach a molecule they can:

1. Pass through the molecule-transmitted light

2. Bounce off the molecule- reflected or scattered light

3. Be absorbed by atoms of the molecule, adding energy to the molecule- excited state

Chlorophyll does not absorb what color

green - it reflects it

chlorophyll absorbs what colors

blue and red

Red photons raise electrons

1 energy level

Higher-energy blue photons raise electrons

2 energy levels

Green photons are of an intermediate energy level and are

not easily absorbed by chlorophyll

Chlorophyll Structure Two main parts:

1) a porphyrin ring that absorbs light energy,

2) a long hydrocarbon side chain that makes molecule extremely non-polar

chlorophyll a

Main photosynthetic pigment that initiates light-dependent

reactions of photosynthesis

chlorophyll b

• Accessory pigment that also participates in photosynthesis

• Broadens the spectrum of light used for photosynthesis

carotenoids

1. Yellow and orange accessory photosynthetic pigments

2. absorb different wavelengths of light than chlorophyll

3. can absorb excessive light that would damage chlorophyll

action spectrum

action spectrum

absorption spectrum

The absorption spectrum of a pigment is a plot of its absorption of light at different wavelengths

Light-dependent reactions transform light energy to

a usable temporary chemical form:

Radiant energy from sunlight is captured and used to phosphorylate ADP, producing ATP, and reduces NADP+, forming NADPH

ATP and NADPH are short term usable forms

of ENERGY!!!

Two types of photosystems (II and I) are involved in

photosynthesis

Reaction center of photosystem II (P680) consists of

two

chlorophyll a molecules with an absorption peak of 680 nm