Biology Exam ll (Chapter 6) Flashcards

Energy in biological systems

Energy is in the form of a photon.

The ability to do work which means to move matter against opposing forces such as gravity and friction

Transforms carbon dioxide into glucose

Energy cannot be created or destroyed

ATP, an electrical/ion gradient, concentration gradient, NADH, Chemical Bonds
Water being held behind a dam
Stored energy
Due to structure or location

It has a change in free energy that is greater than 0. That means it has a delta G that is positive and therefore the reaction is endergonic.

Movement
Na+ and K+ molecules moving through a transport protein

It lowers the Vmax and has no affect on the Km.
Fits into the Allosteric site to change the shape of the enzyme
Can cause a conformation change which will affect the enzyme's ability to bind to a substrate

Prevent the substrate from binding the enzyme's active site

Increase the rate of the reaction by reducing the activation energy.
They don't change the direction of the reactions
They do not change the amount of free energy available
It lowers the energy barrier needed for reactants to achieve the transition state or lowers the energy of activation of a reaction
Typical biological catalyst
Have a high affinity or high degree of specificity for a substrate
Can be recycled over and over

Mostly proteins but some are RNA molecules possess enzymatic functions called ribozymes

This enzyme's optimal function is at about 37 degrees C, the enzymatic activity of the enzymes slows down around 40 C

It has been reduced

The amount of available energy that can be used to promote change do work

Increase the amount of substrate (Km) for the enzyme

Favors formation of reactants

Favors formation of products

1. substrates bind to enzyme; 2. enzyme and substrate reach transtition state; 3. substrates are converted to products; 4. products are released

Where the chemical reaction takes place
Where a competitive inhibitor competes to bind to

Every chemical reaction must increase the total entropy of the universe. Every chemical reaction represents a transfer of energy, which increases entropy

Energy must be spent to retain order - this spending of energy usually releases heat, which increases the entropy elsewhere

Only raises the Km
Tries to bind to the active site
Slows down the Vmax when it binds to the allosteric site

Exergonic

It has been oxidized.

Measure of disorder

∆G is negative/less than zero
Spontaneous reaction (doesn't mean it will occur rapidly)
Favor making products (going from left to right)
Releases free energy

∆G is positive/greater than zero
Not spontaneous
Absorbs free energy
Favors making reactants
When you go from reaction to products, you have to add energy by coupling it with an exergonic reaction to make the overall ∆G negative

Universal energy molecule
Monomer of nucleic acids
Adenine, Ribose, and 3 phosphate groups connected to each other in a sequence
Energy intermediate
Is exergonic
Gets coupled with endergonic reactions (phosphorylation) -- Gives net negative free energy change
Source of energy for 20% of proteins
Undergoes 10,000 cycles of hydrolysis and re-synthesis every day
Likely underestimated because there may be other types of ATP-binding sites
A noncompetitive inhibitor for enzymes
The "energy currency" and how that we get work done

The direction of chemical reactions

∆H - T∆S

Free energy

Total energy

Absolute temperature

Entropy

Heat

Are not efficient

Water and enzymes
The ∆G = -7.3 kcal/mole

ΔG = +3.3 Kcal/mole and it is an endergonic reaction

Coupled Reaction

Direct transfer of a phosphate group from ATP to a substrate (an example being glucose)
It energizes the molecule

Does not imply anything about its speed
Exergonic
Does not require inout of energy
Does require an enzyme

Speed up rate of reaction without being consumed

-ASE

Initial input of energy to start a reaction
Allows molecules to get close enough to cause bond rearrangement

Bonds are stretched/strained

1. Large amounts of heat
2. Using enzymes to lower activation energy

Measure your substrates and your products

Velocity of reaction near maximum rate

Substrate concentration at which VMax is at half of max rate
Shows how good your enzyme is

A lot of substrate

Plateau where nearly all active sites are occupied by substrates

To turn off or slow down an enzyme

Enzyme "helper"
Organic molecule
Vitamins
Carry electrons
Tightly bounded to the active site or bounded loosely

Enzyme "helper"
Inorganic molecule
Carry electrons
Tightly bounded to the active site or bounded loosely

Bind to the enzyme or participate in the reaction

Functions in muscle formation (collagen)
Deficiency causes scurvy (loss of teeth, pale skin, and sunken eyes)

"Nicotine acid"
Functions in the coenzymes NAD and NADP
Deficiency causes pellagra (skin lesions)

Tertiary and quaternary

When structure is lost due to heat
Once a certain temperature is reached, bonds maintaining the 2o, 3o, and 4o structure of the protein collapse and the protein loses function

1. pH - Measure of H+ (0-7 is acidic and 8-14 is basic)
2. Temperature (typically when temperature increases, rate of reaction will increase, but not always) (as temperature increases, the enzyme's active site may become unstable and function poorly)
3. Coenzymes/Cofactors

Each step is coordinated by a specific enzyme

1. Catabolic Pathways (Reactions)
2. Anabolic Pathways (Reactions)

Breaks down reactants
Used for recycling macromolecules
Used to obtain energy for endergonic reactions
Metabolic pathway is complex
Lots of intermediates (ATP & NADH)
Lots of energy transfer steps
Spontaneous, but does not happen without correct enzyme

Promote synthesis (builds up, not breaks down)
Endergonic reactions
Must be coupled to an exergonic reaction

Turns proteins into amino acids (catabolic pathway)

Breaks down RNA into nucleotides (catabolic pathway)

Releases
Is exergonic
The bonds are broken
When the terminal phosphate bond is broken, a molecule of inorganic phosphate (Pi) is formed which forms adenosine diphosphate, ADP + (Pi) which generates free energy

Requires
Is endergonic
Can be through substrate level phosphorylation or chemiosmosis

Finds a free floating Pi and takes it, which converts ADP to ATP

ATP Synthesis

Deals with an electrochemical gradient

Compounds formed between initial reactants & products

Study of energy transformation

When an enzyme and a substrate come together
Held by hydrogen and/or ionic bonds

The more substrate you have, the faster the reaction rate will be (until you reach saturation)

Chemicals that interfere with enzyme function
Are used to slow down/or stop an enzyme
Usually reversible in cells (when hydrogen or ionically bonded)

Site on the enzyme that isn't the active site
Where noncompetitive inhibitors bind to

Electron is removed from one molecule and added to another molecule

Removal of electrons

Addition of electrons

Oxidized (electron removed)

Reduced (electron added)

NAD is a type of nucleic acid
When NAD is reduced, NADH is formed
It's really easy to move electrons back and forth between NAD and NADH
Often coupled with reactions to give or remove energy

Energy

Bonds

3 types:
1. Gene regulation
2. Cellular regulation
3. Biochemical regulation

Turn genes on or off

Cell-signaling pathways like hormones

Feedback Inhibition- Product of pathway inhibits early steps to prevent over accumulation of product

Refers to a differences of solutes (dissolved substances) in an adjacent area

A. Substrate binding
B. Transition State (induced-fit and Ea is lowered)
C. Substrate converted to product
D. Product is released