Chapter 1 Intro to the chemistry of life

Fundamentals of Biochemistry

What molecules account for 97% of life?

C, H, O, N, P, Ca and S

Organic

Carbon containing

Functional Group

Reactive portions of molecules

What determines the biological activity of molecules

The functional group and its linkage

Polymer

A long molecule of similar or identical monomers linked by covalent bonds

Condensation reaction

We have a loss of water

Hydrolysis

A chemical reaction that breaks bonds by the addition of water.

A hydrolysis reaction is going to make

A polymer into monomers

Degradation

Reduction of a compound

What happens when DNA replicates?

The strands separate and direct the synthesis of the daughter strans

Catalyst

substance that promotes a chemical reaction without itself undergoing a change

Two classifications of cells

Eukaryotes and prokaryotes

Eukaryotes have a

Membrane-enclosed nucleus housing its DNA. THey are also multicellular and unicellular. Complex

Prokaryotes

Lack a nucleus

Viruses

Arent classified as living because they lack the ability to reproduce outside their hose cells

Nearly all prokaryotes lack a

Cellular membrane

Prokaryotes lack complexity unlike Eukaryotes

True

Taxonomy

Biological classification

Enthalpy is equivalent to

Heat

Entropy

A measure of a systems disorder tends to increase

How is the free energy change for a process determined?

Its change in both enthalpy and entropy

A spontaneous process occurs with a?

Decrease in free energy

Enzymes increase the rate at which?

A reaction approaches equilibrium

Describe an organism

There open systems that constantly exchange matter and energy with their surroundings while maintain homeostasis

Are organisms at equilibrium?

NO

Thermodynamics

The study of energy and its effects on matter

Spontaneous

Predicting whether that process can actually occur

Thermodynamics is used to

Describe a process and if it can spontaneous

What is the first law of thermodynamics

Energy is conserved

System

the part of the universe that is of interest

Energy

U

Energy can be

Neither created nor destroyed

When a system undergoes a change

Some of its energy is used to perform work

The energy change of the system is defined as the

Difference between heat absorbed by the system from the surrounding and work done by the system on the surrounding

Heat

q

Work

w

Delta

indicated change

Heat is?

Random molecular motion

Work

Force times the distance moved under its influence is associated with organized motion

Most biological processes take place at constant pressure

True

Enthalpy (H)

Heat

qp

Heat at constant pressure

Enthalpy is given in units of

Joules

A spontaneous process

Occurs without the input of additional energy from outside the system

The second law of thermodynamics states that

Entropy tends to increase

Spontaneous processes are characterized by

The conversion of order to disorder

Disorder defined by the second law of thermodynamics is

The number of ways of arranging the components of a system

There more ways of arranging a __ __system than a__ ___ system.

Disorder, ordered

Entropy (S)

Degree of randomness

kB

Boltzmann constant

What happens to a system when the temperature rises

Becomes more disordered

All processes increase the?

Entropy - the disorder of the universe

Entropy change in a process can be determined from

Measurements of heat and temperature

Can you determine the knowledge of the systems entropy change alone?

NO

Gibbs free energy (G)

G=H-TS

The change in free energy for a process if

Delta G

Spontaneous processes at constant temperature and pressure have

delta G=delta H-TdeltaS is less than 0

Processes in which Delta G is negative are

Exergonic

Processes that are not spontaneous have Positive Delta G values (deltaG is greater than 0) and are

energonic

What is the reverse of exergonic

Endergonic, vice versa

What determines whether a process can occur spontaneously in the direction written

delta G

Processes at equilibrium

The forward and reverse reactions are exactly balanced and characterized by DeltaG=0

Reversible

Processes that occur with delta G is approximately equal to 0 so the system remains at equilibrium throughout the process.

Irreversible

Process that occur with deltaG not equal to 0. The delta g is less than 0 and is favorable to occur spontaneously. The delta g is greater than 0 is said to be unfavorable

If delta H is negative and delta S is positive

The reaction is both enthalpically favored (exothermic) and entropically favored. It is spontaneous (exergonic) at all temperatures

If delta H is negative and delta S is negative

The reaction is enthalpically favored but entropically opposed. It is spontaneous only at temperatures below T=deltaH/deltaS

If delta H is positive and delta S is positive

The reaction is enthalpically opposed (endothermic) but
entropically favored. It is spontaneous only at temperatures
above T = ΔH/ΔS.

If delta H is positive and delta S is negative

The reaction is both enthalpically and entropically opposed. It is
nonspontaneous (endergonic) at all temperatures.

State functions

Free energy, energy, enthalpy and entropy

State functions depend on

Current state or properties of the system not on how the system reached that state

Why is heat and work not state functions

Interchangeable form of energy. And vary on the pathway taken

The energy of a substance increases with its

Volume

Free energy change of a chemical reaction depends on the

concentrations of both its reacting substances and its reaction products

Equilibrium constants are related to

Delta G

Only changes in free energy, enthalpy, and entropy can be measured not their absolute values

True

Partial molar free energy or chemical potential

GA. G has a line on top and indicates the quantity per mole

GA0 with a line on top is the

partial molar free energy of A in its standard state

GA = G°A + RT ln \[A\]

Relationship between the concentration and the free energy of a substance A

R

Gas constant

\[A\]

The molar concentration of A

.deltaG = delta G ° + RT ln ( \[C\] c \[D\] d /\[A\]a\[B\]b)

delta G ° is the free energy change of the reaction when its reactants and products are in standard states

A reaction at equilibrium

Has no net change the rates of the forward and reverse reactions are equal because the free energy change of the forward reaction exactly balances that of the reverse reaction

Equilibrium constant

Keq (eq denotes reactan and product concentration at equilibrium)

When reactants have alot in there equilibrium concentration, the net reaction will proceed in the

forward direction until the reactants have become products and we reached equilibrium

When products are in excess the reaction will go in reverse to achieve equilibrium

True

Le chatelier principle

Any deviation from equilibrium stimulates a process that tends to restore the system to equilibrium

Living organisms of a system achieve order by

Disordering (breaking down) the nutrients they consume. The entropy content of food is as important as its energy content

Living organisms are

Open systems

Isolated system

Cannot exchange matter or energy with their surrounding and eventually reaches equilibrium

Closed system

Exchange only energy

If its reactants are in excess, what happens to the forward reaction? Isolated systems

It will proceed faster than the reverse reaction until equilibrium is attained (delta G=0) at which the forward and reverse reactions are balanced.

Open systems, exchange?

Both matter and energy with their surrounding and reach equilibrium only after the flow of matter and energy has stopped.

Living organisms, take up nutrients and release waste products and generate work and heat are

Open systems and therefore can never be at equilibrium

What happens when an organism reaches equilibrium

Death

Living things maintain a

Non-equilibrium steady state ( all flows in the system are constant so that the system maintains homeostasis)

Even in a system that is not at equilibrium

matter and energy flow according to the laws of thermodynamics

In all living systems energy flow is

Downhill (deltaG is less than 0)

Enzymes catalyze

Biochemical reactions

Biological catalysts are referred to as

Enzymes

Enzymes accelerate biochemical reactions by

Physically interacting with the reactants and products to provide a more favorable pathway for the transformation of one to the other