AP Biology Unit 3

Metabolism

Chemical reactions in a cell

Metabolic Pathway

begins with a specific molecule and ends with a product

Each step is catalyzed by a specific enzyme

Catabolic Process

Breaking down of compounds (energy is released)

Anabolic Process

Building up of complex compounds (requires energy)

Kinetic Energy

energy of motion

Potential energy

stored energy (chemical energy is a type of potential energy)

Thermodynamics

The study of energy transformations.

1st Law of Thermodynamics

Energy can be transferred and transformed but it cannot be created nor destroyed

2nd Law of thermodynamics

Every energy transformation of energy results in a loss of heat ( the universe needs to become more disordered)

Entropy

A measure of disorder (not reversible) (the more randomness the more disorder)

Free Energy

How much energy in a system is available for work.

How can cells make big macromolecules without breaking the laws of thermodynamics.

There can be some order in the body because the net order is still negative in the body due to the release of heat.

Free Energy Calculation

G=H-TS (H is the total energy) (T is the temperature) (S is the entropy)

Exergonic Reaction

Net release of free energy (the change in G is negative) (Ex. burning any type of fuel)

Endergonic Reaction

Absorbs free energy (breaks the 2nd law of thermodynamics)

ATP

Adenosine Triphosphate, the main energy source for the cells

ADP

Adenosine Di-phosphate Doesn't carry very much energy but it can regain a phosphate and be used for energy again.

Enzyme

A type of protein that speeds up a chemical reaction in a living thing

Catalyst

substance that speeds up the rate of a chemical reaction (enzyme is like a biological catalyst)

What effect does an enzyme affect on delta G

It doesn't affect delta G, but it does lower the activation energy

Substrate

The reactant on which an enzyme works.

Active Site

Where the substrate fits into the enzyme

Induced Fit model

The more modern model that involves the enzyme molding into the active site.

Enzyme Saturation

when no matter how much substrate you add the enzyme is working at the maximum velocity (Vmax)

only way to increase the Vmax at this point is to increase the enzyme concentration

Enzyme Denaturation

When an enzyme loses it's shape and no longer fits the substrate (this can happen due to a few factors like temperature and Ph)

Cofactor

A mineral that can help to bind a substrate to an enzyme

Coenzyme

A vitamin that can help to bind a substrate to an enzyme

Competetive Inhibition

Competetive inhibition occurs when a non-substrate that fits into the active site and inhibits the active site

Non-competetive inhibition

Occurs when an inhibiting substrate fits into a non active site in an enzyme

Allosteric Site

A specific receptor site on some part of an enzyme molecule remote from the active site.

Feedback Inhibition

A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.

Cellular Respiration

unleashes energy stored in sugar and other complex molecules.

Photosynthesis

Conversion of light energy from the sun into chemical energy.

Spontaneous Process

Can occur without an input of energy or without help

Non-spontaneous Process

Can only occur if energy is added to the reaction

Redox Reactions

When there is a transfer of one or more electrons from one reactant to another.

Oxidation

Gain of electrons (what gains the electrons)

Reduction

Loss of electrons (What loses the electrons)

What is the oxidizing and reducing reaction in a burning reaction

Oxygen is the oxidation agent because it gains electrons or is reduced. The fuel is the reducing agent because it loses some of its electrons

Why are C-H bonds a good energy source

They have a lot of chemical potential energy and make great reducing agents

What is the role of NADH, NAD+

Like a shuttle bus for electrons (NAD+ is an empty bus while NADH is the full bus)

Why do we need 02

Its like the janitor at the bottom of the electron transport chain to clean away the electrons

Autotroph

An organism that makes its own food from C02 (DNA, proteins, and fats)

Phototroph

Use light energy in the environment

Chemotroph

Use oxidizing inorganic substances for energy

Heterotroph

Eating gives energy like a dog or human

Glycolysis

The breakdown of glucose into two pyruvates

Hydrolysis

Breaking down complex molecules by the chemical addition of water

Dehydration reaction

A chemical reaction in which molecules combine by removing water

Phosphorylation

The metabolic process of introducing a phosphate group into an organic molecule. (like ADP to ATP) (This example is considered substrate level phosphorylation)

Krebs Cycle

produces molecules that carry energy to the second part of cellular respiration (also produces a small amount of ATP)

Chloroplast

organelle found in cells of plants and some other organisms that captures the energy from sunlight and converts it into chemical energy

Chlorophyll

A green pigment found in the chloroplasts of plants, algae, and some bacteria

Stomata

Small openings on the underside of a leaf through which oxygen and carbon dioxide can move

Thykaloid

a membrane system found within chloroplasts that contains the components for photosynthesis

Granum

stack of thylakoids

ATP Synthase

The enzyme that make ATP from ADPand inorganic phosphate.

Chemiosmosis

Oxidative phosphorylation (creating ATP at the end of the cycle)

H+ Gradient

proton motive force that drives the ATP synthase to make ATP (High in the christae) (low in the matrix of mitochondria) (High in thykaloid) (low outside of thykaloid)

1 Molecule of glucose creates how many ATP

36-38

Fermentation

Process by which cells release energy in the absence of oxygen

Photorespiration

Reaction in which rubisco attaches oxygen instead of carbon dioxide to ribulose bisphosphate

Rubisco

The most abundant protein on earth. Performs Carbon Fixation in the Calvin Cycle. (isn't as specific like most enzymes)

Carbon Fixation

the conversion of atmospheric carbon dioxide into organic molecules by autotrophic organisms.

Obligate Anaerobe

organism that cannot live in the presence of oxygen

Facultative Anaerobe

organism that can survive with or without oxygen

Where do fats and proteins enter respiration

Glycolysis (they are converted to glucose through different reactions)

Mesophyll

Spongy tissue in the interior of the leaf where most chloroplasts are found.

Where does Calvin Cyclye take place in chloroplasts

In the stroma

Stroma

fluid portion of the chloroplast; outside of the thylakoids

Electromagnetic Spectrum

All of the frequencies or wavelengths of electromagnetic radiation (gamma rays are the highest with the shortest waves while radio wavves are the lowest with the longest waves)

Why do we only see visible light

Visible light is what reflects at values that we can see

Why are plants green

the green wavelength is reflected, not absorbed by clorophyll

What are the best colors for light reactions

Theoretically black but not found in nature (red, violet, blue and orange are colors absorbed by clorophyll)

Chlorophyll A

Main pigment that can participate directly in the light reactions.

Clorophyll B

accessory pigment

Cyclic Flow

The primary acceptor can then send the electrons back to the top of the ETC so they call come down again and make more ATP

Linear Flow

primary electron acceptor sends electrons down the electron transport chain to photosystem I

Why would the body do cyclic flow

The body would do this to balance ATP and NADH shuttle buses

G3P (glyceraldehyde-3-phosphate)

The carbohydrate produced directly from the Calvin cycle.(Its important because it can be used like half a glucose and is a very good building block)

3 Phases of the Clavin Cycle

1. C02 Fixation

2. Rduction by NADPH (basically giving C02 a charge)

3. Regeneration of the C02 acceptor

Clavin Cycle

To turn C02 gas into sugar that autotrophs can use to grow

C4 plants

Doesn't have photorespiration happen very often

C3 Plants

Plants that fall prey to respiration

CAM plants

keep CO2 concentration high with C02 sponges

Problem with Rubisco

It can grab oxygen by mistake and ruin Calvin Cycle

What happens to stomata in hot days

The stomata closes and oxygen is much more likely to bind to rubsico