Chapter two – chemistry, biochemistry, and cell physiology
Pages 22-25: energy
Chemical reactions follow the ruled of thermodynamics.
First law of thermodynamics (the law of conservation of energy) = energy can be converted
from one form to another but the total amount of energy in the universe remains constant.
Second law of thermodynamics (law of entropy) = the universe is becoming more chaotic.
Living organisms have the ability to obstruct the natural processes that lead to chemical
Energy = ability to do work
Standard SI unit for energy = joules
Energy Type Definition
Potential energy Energy that is stored
Kinetic energy Energy of movement
Radiant energy Energy released from an object and transmitted into another object by
waves or particles. Example: sun
Mechanical Combination of potential and kinetic energy that results from the
energy movement of charged particles down a charge gradient
Thermal energy Form of kinetic energy (movement of particles to increase temperature)
Chemical energy Form of potential energy that is held within the bond of chemical
Food webs transfer energy
Trophic levels = Plants capture energy from photons, with this energy they create sugars
herbivorous animals eat the plants carnivores eat herbivorous
During this cycle at each level, some potential energy in the diet is assimilated to form
The potential energy is either lost as heat or retained within the animal.
Animals also use the energy as kinetic energy (fuel locomotion).
Some of the potential energy cannot be accessed and will be released as waste products.
Energy is stored in electrochemical gradients
Molecules within a system tend to disperse or diffuse randomly with the available space
Two aspects of diffusion govern the properties of many biological processes.
1. Diffusion is certain to lead to random distribution of molecules
2. Tendency of molecules to diffuse is a source of energy that cells can use to drive
Animals can invest energy to prevent the random distribution of molecules.
1 Chemical gradient – arises when one type of molecule occurs at a higher concentration on
one side of the membrane.
Electrical gradient – arises if the distribution of charged molecules is unequal on either side
of the electrical barrier in a circuit (Electrical gradient = membrane potential)
If a molecule has a chemical and electrical gradient = electrochemical gradient
Thermal Energy is the movement of molecules
System gains thermal energy = increased movement of molecules within the system
Changes in thermal energy can either be exergonic reactions (releases energy) or
endergonic reactions (absorbs energy)
In a reaction involving products and (substrate) reactants … when the substrate has a great
amount of kinetic energy it can reach a transition state. The energy required to reach the
transition state is called the activation energy (EA).
Free energy = G ΔG = G products Gsubstrates
All chemical reactions are reversible.
Increasing temp = more molecules to reach activation energy
29 – 31 Diffusion, osmotic pressure, osmolarity
Solute in biological systems impose osmotic pressures
Semi-permeable membrane restricts the passage of certain molecules while allowing the
passage of others.
If a membrane exists, which only allows the passage of water. The water would distribute
equally on both side. However, if Na+ and Cl- ions were added to one of the side the water
molecules would travel towards the side with the solute and therefore the water molecules
would not be separated equally.
The movement of water in cells is restricted by the flexibility of the cell membrane.
The movement of water is the osmotic pressure (fourth colligative property of solutes)
The ability of solutions to induce water to cross a membrane is called osmolarity the units
for osmolarity is (osmoles/liter) OsM
The osmolarity and osmotic pressure of a solution are physical properties of a solution
If a cell is placed in a solution with greater osmolarity, then the solution is hyperosmotic
If the cell is placed in pure water then the solution is hyposmotic
If the osmolarity is the same on both sides then the solution is isosmotic
Differences in osmolarity can alter cell volume
Tonicity – the effect of a solution on cell volume
The difference in between osmolarity and tonicity
Osmolarity - change in the amount of water
Tonicity – change in the amount of solute
2 Pages 35 – 57 Biochemistry, enzymes, proteins, carbohydrates, lipids
Metabolic pathways can be:
Synthetic – anabolic
Degradative – catabolic (break apart)
Combination of both – amphibolic
Energy metabolism ATP production
Metabolism = the metabolic pathways with the cell, tissues and/or organisms
Enzymes are biological catalysts (convert substrates into products)
1. Active at very low concentrations (within a cell)
2. They increase the rate of a reaction and the enzymes are not altered
3. They don’t change the nature of the product (don’t take part in the reaction)
Enzymes such as ribosomes are made up of RNA but most enzymes are made up of proteins
Enzyme’s non protein component = cofactors
Cofactors that are covalently bonded to the enzyme = prosthetic group (can be metals,
copper, iron, magnesium, zinc, and selenium)
Organic cofactors/coenzymes – from vitamins (coenzyme A, FAD, NAD)
Enzyme Kinetics describe Enzymatic Properties
Enzymes don’t govern whether a chemical reaction can occur or not but they do accelerate
thermodynamically possible reactions
E = enzyme S = substrate ES = enzyme-substrate complex *transitional state P = product
Enzymes lower the activation energy
Enzyme reactions are reversible
Substrate binds to the active site of the enzyme in order to begin the enzymatic reaction
Once the substrate binds to the enzyme the enzyme changes the molecular structure of the
Enzymes usually bring two substrates together; the enzymes bring the destabilized
reactions into proximity
The Physiochemical Environment alters Enzyme Kinetics
Enzymatic reactions should occur at appropriate rates, should not occur at fate rates
Enzyme activity is regulated by metabolic pathways
Conditions that influence enzymatic reactions = enzyme kinetics
Change concentration of substrate or products
Equilibrium forward reactions = reverse reactions
Increasing concentration of the substrate increases the initial velocity
However eventually the increase in concentration will cease to have effect on the
velocity. If the enzyme is already occupied with another substrate it cannot undergo
a reaction with another substrate.
Michaelis – Menten Equation
V= Vmax X ([s]/([s]+km)) km = indicator of the affinity of an enzyme for a substrate
The physical environment alters enzyme kinetics
3 Changes in temperature, pH, salt concentration, hydrostatic can alter enzyme kinetics
1. Changes in weak bonds can alter 3-D structure of enzymes
2. Environmental conditions can alter the ionization state of critical amino acids within
the active sites
3. Environmental conditions can alter the ability of the enzyme to undergo structural